Merge branch 'master' into gpu-unittest

# Conflicts:
#	unittest/force-styles/test_pair_style.cpp
#	unittest/force-styles/tests/angle-cosine_periodic.yaml
#	unittest/force-styles/tests/mol-pair-born.yaml
#	unittest/force-styles/tests/mol-pair-born_coul_dsf.yaml
#	unittest/force-styles/tests/mol-pair-born_coul_long.yaml
#	unittest/force-styles/tests/mol-pair-born_coul_msm.yaml
#	unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml
#	unittest/force-styles/tests/mol-pair-born_coul_wolf.yaml
#	unittest/force-styles/tests/mol-pair-morse.yaml
#	unittest/force-styles/tests/mol-pair-morse_smooth_linear.yaml

.github/workflows/unittest-macos.yml

@@ -24,7 +24,9 @@ jobs:
       shell: bash
       working-directory: ${{github.workspace}}/build
       run: |
-        cmake -C $GITHUB_WORKSPACE/cmake/presets/most.cmake $GITHUB_WORKSPACE/cmake \
+        cmake -C $GITHUB_WORKSPACE/cmake/presets/clang.cmake \
+              -C $GITHUB_WORKSPACE/cmake/presets/most.cmake \
+                 $GITHUB_WORKSPACE/cmake \
               -DENABLE_TESTING=ON -DBUILD_SHARED_LIBS=ON -DLAMMPS_EXCEPTIONS=ON
         cmake --build . --parallel 2
 

cmake/CMakeLists.txt

@@ -22,6 +22,11 @@ set(LAMMPS_TOOLS_DIR      ${LAMMPS_DIR}/tools)
 set(LAMMPS_PYTHON_DIR     ${LAMMPS_DIR}/python)
 set(LAMMPS_POTENTIALS_DIR ${LAMMPS_DIR}/potentials)
 
+set(LAMMPS_DOWNLOADS_URL "https://download.lammps.org" CACHE STRING "Base URL for LAMMPS downloads")
+set(LAMMPS_POTENTIALS_URL "${LAMMPS_DOWNLOADS_URL}/potentials")
+set(LAMMPS_THIRDPARTY_URL "${LAMMPS_DOWNLOADS_URL}/thirdparty")
+mark_as_advanced(LAMMPS_DOWNLOADS_URL)
+
 find_package(Git)
 
 # by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed
@@ -31,7 +36,7 @@ endif()
 
 # If enabled, no need to use LD_LIBRARY_PATH / DYLD_LIBRARY_PATH when installed
 option(LAMMPS_INSTALL_RPATH "Set runtime path for shared libraries linked to LAMMPS binaries" OFF)
-if (LAMMPS_INSTALL_RPATH)
+if(LAMMPS_INSTALL_RPATH)
   set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR})
   set(CMAKE_INSTALL_RPATH_USE_LINK_PATH ON)
 endif()
@@ -113,7 +118,7 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
 
 set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
   GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS
-  QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
+  PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
   USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK
   USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
   USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
@@ -533,6 +538,18 @@ foreach(PKG_WITH_INCL CORESHELL QEQ USER-OMP USER-SDPD KOKKOS OPT USER-INTEL GPU
   endif()
 endforeach()
 
+if(PKG_PLUGIN)
+  if(BUILD_SHARED_LIBS)
+    target_compile_definitions(lammps PRIVATE -DLMP_PLUGIN)
+  else()
+    message(WARNING "Plugin loading will not work unless BUILD_SHARED_LIBS is enabled")
+  endif()
+  # link with -ldl or equivalent for plugin loading; except on Windows
+  if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+    target_link_libraries(lammps PRIVATE ${CMAKE_DL_LIBS})
+  endif()
+endif()
+
 ######################################################################
 # the windows version of LAMMPS requires a couple extra libraries
 # and the MPI library - if use - has to be linked right before those

cmake/Modules/Documentation.cmake

@@ -55,11 +55,15 @@ if(BUILD_DOC)
     COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
   )
 
+  set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.2.tar.gz" CACHE STRING "URL for MathJax tarball")
+  set(MATHJAX_MD5 "a4a6a093a89bc2ccab1452d766b98e53" CACHE STRING "MD5 checksum of MathJax tarball")
+  mark_as_advanced(MATHJAX_URL)
+
   # download mathjax distribution and unpack to folder "mathjax"
   if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/mathjax/es5)
-    file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.1.2.tar.gz"
+    file(DOWNLOAD ${MATHJAX_URL}
       "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
-      EXPECTED_MD5 a4a6a093a89bc2ccab1452d766b98e53)
+      EXPECTED_MD5 ${MATHJAX_MD5})
     execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
     file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
     execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax)

cmake/Modules/GTest.cmake

@@ -8,10 +8,12 @@ endif()
 
 include(ExternalProject)
 set(GTEST_URL "https://github.com/google/googletest/archive/release-1.10.0.tar.gz" CACHE STRING "URL for GTest tarball")
+set(GTEST_MD5 "ecd1fa65e7de707cd5c00bdac56022cd" CACHE STRING "MD5 checksum of GTest tarball")
 mark_as_advanced(GTEST_URL)
+mark_as_advanced(GTEST_MD5)
 ExternalProject_Add(googletest
-                    URL ${GTEST_URL}
+                    URL             ${GTEST_URL}
-                    URL_MD5         ecd1fa65e7de707cd5c00bdac56022cd
+                    URL_MD5         ${GTEST_MD5}
                     SOURCE_DIR      "${CMAKE_BINARY_DIR}/gtest-src"
                     BINARY_DIR      "${CMAKE_BINARY_DIR}/gtest-build"
                     CMAKE_ARGS      ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_GTEST_OPTS}

cmake/Modules/LAMMPSUtils.cmake

@@ -86,7 +86,6 @@ endfunction(GenerateBinaryHeader)
 # fetch missing potential files
 function(FetchPotentials pkgfolder potfolder)
   if (EXISTS "${pkgfolder}/potentials.txt")
-    set(LAMMPS_POTENTIALS_URL "https://download.lammps.org/potentials")
     file(STRINGS "${pkgfolder}/potentials.txt" linelist REGEX "^[^#].")
     foreach(line ${linelist})
       string(FIND ${line} " " blank)

cmake/Modules/MPI4WIN.cmake

@@ -1,16 +1,25 @@
 # Download and configure custom MPICH files for Windows
 message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
+set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
+set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball")
+set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
+set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball")
+mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
+mark_as_advanced(MPICH2_WIN32_DEVEL_URL)
+mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
+mark_as_advanced(MPICH2_WIN32_DEVEL_MD5)
+
 include(ExternalProject)
 if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
   ExternalProject_Add(mpi4win_build
-    URL https://download.lammps.org/thirdparty/mpich2-win64-devel.tar.gz
+    URL     ${MPICH2_WIN64_DEVEL_URL}
-    URL_MD5 4939fdb59d13182fd5dd65211e469f14
+    URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
     CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
     BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
 else()
   ExternalProject_Add(mpi4win_build
-    URL https://download.lammps.org/thirdparty/mpich2-win32-devel.tar.gz
+    URL     ${MPICH2_WIN32_DEVEL_URL}
-    URL_MD5 a61d153500dce44e21b755ee7257e031
+    URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
     CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
     BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
 endif()

cmake/Modules/OpenCLLoader.cmake

@@ -1,11 +1,13 @@
 message(STATUS "Downloading and building OpenCL loader library")
+set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2020.12.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
+set(OPENCL_LOADER_MD5 "011cdcbd41030be94f3fced6d763a52a" CACHE STRING "MD5 checksum of OpenCL loader tarball")
+mark_as_advanced(OPENCL_LOADER_URL)
+mark_as_advanced(OPENCL_LOADER_MD5)
 
 include(ExternalProject)
-set(OPENCL_LOADER_URL "https://download.lammps.org/thirdparty/opencl-loader-2020.12.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
-mark_as_advanced(OPENCL_LOADER_URL)
 ExternalProject_Add(opencl_loader
-                    URL ${OPENCL_LOADER_URL}
+                    URL             ${OPENCL_LOADER_URL}
-                    URL_MD5         011cdcbd41030be94f3fced6d763a52a
+                    URL_MD5         ${OPENCL_LOADER_MD5}
                     SOURCE_DIR      "${CMAKE_BINARY_DIR}/opencl_loader-src"
                     BINARY_DIR      "${CMAKE_BINARY_DIR}/opencl_loader-build"
                     CMAKE_ARGS      ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_OPENCL_LOADER_OPTS}

cmake/Modules/Packages/GPU.cmake

@@ -218,7 +218,7 @@ elseif(GPU_API STREQUAL "HIP")
 
   if(NOT DEFINED HIP_PLATFORM)
       if(NOT DEFINED ENV{HIP_PLATFORM})
-          set(HIP_PLATFORM "hcc" CACHE PATH "HIP Platform to be used during compilation")
+          set(HIP_PLATFORM "amd" CACHE PATH "HIP Platform to be used during compilation")
       else()
           set(HIP_PLATFORM $ENV{HIP_PLATFORM} CACHE PATH "HIP Platform used during compilation")
       endif()
@@ -226,7 +226,7 @@ elseif(GPU_API STREQUAL "HIP")
 
   set(ENV{HIP_PLATFORM} ${HIP_PLATFORM})
 
-  if(HIP_PLATFORM STREQUAL "hcc")
+  if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
     set(HIP_ARCH "gfx906" CACHE STRING "HIP target architecture")
   elseif(HIP_PLATFORM STREQUAL "nvcc")
     find_package(CUDA REQUIRED)
@@ -284,7 +284,7 @@ elseif(GPU_API STREQUAL "HIP")
     set(CUBIN_FILE   "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}.cubin")
     set(CUBIN_H_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h")
 
-    if(HIP_PLATFORM STREQUAL "hcc")
+    if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
         configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY)
 
         if(HIP_COMPILER STREQUAL "clang")
@@ -338,11 +338,16 @@ elseif(GPU_API STREQUAL "HIP")
 
       if(DOWNLOAD_CUB)
         message(STATUS "CUB download requested")
+        set(CUB_URL "https://github.com/NVlabs/cub/archive/1.12.0.tar.gz" CACHE STRING "URL for CUB tarball")
+        set(CUB_MD5 "1cf595beacafff104700921bac8519f3" CACHE STRING "MD5 checksum of CUB tarball")
+        mark_as_advanced(CUB_URL)
+        mark_as_advanced(CUB_MD5)
+
         include(ExternalProject)
 
         ExternalProject_Add(CUB
-          GIT_REPOSITORY https://github.com/NVlabs/cub
+          URL     ${CUB_URL}
-          TIMEOUT 5
+          URL_MD5 ${CUB_MD5}
           PREFIX "${CMAKE_CURRENT_BINARY_DIR}"
           CONFIGURE_COMMAND ""
           BUILD_COMMAND ""
@@ -354,7 +359,7 @@ elseif(GPU_API STREQUAL "HIP")
       else()
         find_package(CUB)
         if(NOT CUB_FOUND)
-          message(FATAL_ERROR "CUB library not found. Help CMake to find it by setting CUB_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
+          message(FATAL_ERROR "CUB library not found. Help CMake to find it by setting CUB_INCLUDE_DIR, or set DOWNLOAD_CUB=ON to download it")
         endif()
       endif()
 
@@ -381,6 +386,12 @@ elseif(GPU_API STREQUAL "HIP")
 
     target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_HCC__)
     target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include)
+  elseif(HIP_PLATFORM STREQUAL "amd")
+    target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_AMD__)
+    target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
+
+    target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_AMD__)
+    target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include)
   endif()
 
   target_link_libraries(lammps PRIVATE gpu)

cmake/Modules/Packages/KIM.cmake

@@ -35,9 +35,13 @@ if(DOWNLOAD_KIM)
   include(ExternalProject)
   enable_language(C)
   enable_language(Fortran)
+  set(KIM_URL "https://s3.openkim.org/kim-api/kim-api-2.2.1.txz" CACHE STRING "URL for KIM tarball")
+  set(KIM_MD5 "ae1ddda2ef7017ea07934e519d023dca" CACHE STRING "MD5 checksum of KIM tarball")
+  mark_as_advanced(KIM_URL)
+  mark_as_advanced(KIM_MD5)
   ExternalProject_Add(kim_build
-    URL https://s3.openkim.org/kim-api/kim-api-2.2.1.txz
+    URL     ${KIM_URL}
-    URL_MD5 ae1ddda2ef7017ea07934e519d023dca
+    URL_MD5 ${KIM_MD5}
     BINARY_DIR build
     CMAKE_ARGS ${CMAKE_REQUEST_PIC}
                -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}

cmake/Modules/Packages/KOKKOS.cmake

@@ -37,9 +37,13 @@ if(DOWNLOAD_KOKKOS)
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
   include(ExternalProject)
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.3.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_MD5 "08201d1c7cf5bc458ce0f5b44a629d5a" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  mark_as_advanced(KOKKOS_URL)
+  mark_as_advanced(KOKKOS_MD5)
   ExternalProject_Add(kokkos_build
-    URL https://github.com/kokkos/kokkos/archive/3.3.01.tar.gz
+    URL     ${KOKKOS_URL}
-    URL_MD5 08201d1c7cf5bc458ce0f5b44a629d5a
+    URL_MD5 ${KOKKOS_MD5}
     CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
     BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
   )

cmake/Modules/Packages/LATTE.cmake

@@ -15,10 +15,14 @@ endif()
 option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
 if(DOWNLOAD_LATTE)
   message(STATUS "LATTE download requested - we will build our own")
+  set(LATTE_URL "https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz" CACHE STRING "URL for LATTE tarball")
+  set(LATTE_MD5 "820e73a457ced178c08c71389a385de7" CACHE STRING "MD5 checksum of LATTE tarball")
+  mark_as_advanced(LATTE_URL)
+  mark_as_advanced(LATTE_MD5)
   include(ExternalProject)
   ExternalProject_Add(latte_build
-    URL https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz
+    URL     ${LATTE_URL}
-    URL_MD5 820e73a457ced178c08c71389a385de7
+    URL_MD5 ${LATTE_MD5}
     SOURCE_SUBDIR cmake
     CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib
     -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}

cmake/Modules/Packages/MSCG.cmake

@@ -7,10 +7,15 @@ else()
 endif()
 option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
 if(DOWNLOAD_MSCG)
+  set(MSCG_URL "https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz" CACHE STRING "URL for MSCG tarball")
+  set(MSCG_MD5 "8c45e269ee13f60b303edd7823866a91" CACHE STRING "MD5 checksum of MSCG tarball")
+  mark_as_advanced(MSCG_URL)
+  mark_as_advanced(MSCG_MD5)
+
   include(ExternalProject)
   ExternalProject_Add(mscg_build
-    URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz
+    URL     ${MSCG_URL}
-    URL_MD5 8c45e269ee13f60b303edd7823866a91
+    URL_MD5 ${MSCG_MD5}
     SOURCE_SUBDIR src/CMake
     CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS}
                -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}

cmake/Modules/Packages/USER-INTEL.cmake

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

cmake/Modules/Packages/USER-MOLFILE.cmake

@@ -2,8 +2,4 @@ set(MOLFILE_INCLUDE_DIR "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to
 set(MOLFILE_INCLUDE_DIRS "${MOLFILE_INCLUDE_DIR}")
 add_library(molfile INTERFACE)
 target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
-# no need to link with -ldl on windows
-if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
-  target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
-endif()
 target_link_libraries(lammps PRIVATE molfile)

cmake/Modules/Packages/USER-PLUMED.cmake

@@ -53,10 +53,16 @@ if(DOWNLOAD_PLUMED)
   elseif(PLUMED_MODE STREQUAL "RUNTIME")
     set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
   endif()
+
+  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.0/plumed-src-2.7.0.tgz" CACHE STRING "URL for PLUMED tarball")
+  set(PLUMED_MD5 "95f29dd0c067577f11972ff90dfc7d12" CACHE STRING "MD5 checksum of PLUMED tarball")
+  mark_as_advanced(PLUMED_URL)
+  mark_as_advanced(PLUMED_MD5)
+
   include(ExternalProject)
   ExternalProject_Add(plumed_build
-    URL https://github.com/plumed/plumed2/releases/download/v2.7.0/plumed-src-2.7.0.tgz
+    URL     ${PLUMED_URL}
-    URL_MD5 95f29dd0c067577f11972ff90dfc7d12
+    URL_MD5 ${PLUMED_MD5}
     BUILD_IN_SOURCE 1
     CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
                                              ${CONFIGURE_REQUEST_PIC}

cmake/Modules/Packages/USER-SCAFACOS.cmake

@@ -14,15 +14,19 @@ endif()
 option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
 if(DOWNLOAD_SCAFACOS)
   message(STATUS "ScaFaCoS download requested - we will build our own")
+  set(SCAFACOS_URL "https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz" CACHE STRING "URL for SCAFACOS tarball")
+  set(SCAFACOS_MD5 "bd46d74e3296bd8a444d731bb10c1738" CACHE STRING "MD5 checksum of SCAFACOS tarball")
+  mark_as_advanced(SCAFACOS_URL)
+  mark_as_advanced(SCAFACOS_MD5)
 
   # version 1.0.1 needs a patch to compile and linke cleanly with GCC 10 and later.
-  file(DOWNLOAD https://download.lammps.org/thirdparty/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
+  file(DOWNLOAD ${LAMMPS_THIRDPARTY_URL}/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
           EXPECTED_HASH MD5=4baa1333bb28fcce102d505e1992d032)
 
   include(ExternalProject)
   ExternalProject_Add(scafacos_build
-    URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
+    URL     ${SCAFACOS_URL}
-    URL_MD5 bd46d74e3296bd8a444d731bb10c1738
+    URL_MD5 ${SCAFACOS_MD5}
     PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
     CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
                                              --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m

cmake/Modules/Packages/USER-SMD.cmake

@@ -7,10 +7,14 @@ endif()
 option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT})
 if(DOWNLOAD_EIGEN3)
   message(STATUS "Eigen3 download requested - we will build our own")
+  set(EIGEN3_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz" CACHE STRING "URL for Eigen3 tarball")
+  set(EIGEN3_MD5 "9e30f67e8531477de4117506fe44669b" CACHE STRING "MD5 checksum of Eigen3 tarball")
+  mark_as_advanced(EIGEN3_URL)
+  mark_as_advanced(EIGEN3_MD5)
   include(ExternalProject)
   ExternalProject_Add(Eigen3_build
-    URL https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz
+    URL     ${EIGEN3_URL}
-    URL_MD5 9e30f67e8531477de4117506fe44669b
+    URL_MD5 ${EIGEN3_MD5}
     CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
   )
   ExternalProject_get_property(Eigen3_build SOURCE_DIR)

cmake/Modules/Packages/VORONOI.cmake

@@ -7,6 +7,11 @@ endif()
 option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT})
 if(DOWNLOAD_VORO)
   message(STATUS "Voro++ download requested - we will build our own")
+  set(VORO_URL "${LAMMPS_THIRDPARTY_URL}/voro++-0.4.6.tar.gz" CACHE STRING "URL for Voro++ tarball")
+  set(VORO_MD5 "2338b824c3b7b25590e18e8df5d68af9" CACHE STRING "MD5 checksum for Voro++ tarball")
+  mark_as_advanced(VORO_URL)
+  mark_as_advanced(VORO_MD5)
+
   include(ExternalProject)
 
   if(BUILD_SHARED_LIBS)
@@ -22,8 +27,8 @@ if(DOWNLOAD_VORO)
   endif()
 
   ExternalProject_Add(voro_build
-    URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
+    URL     ${VORO_URL}
-    URL_MD5 2338b824c3b7b25590e18e8df5d68af9
+    URL_MD5 ${VORO_MD5}
     PATCH_COMMAND patch -b -p0 < ${LAMMPS_LIB_SOURCE_DIR}/voronoi/voro-make.patch
     CONFIGURE_COMMAND ""
     BUILD_COMMAND make ${VORO_BUILD_OPTIONS}

cmake/Modules/YAML.cmake

@@ -2,10 +2,13 @@ message(STATUS "Downloading and building YAML library")
 
 include(ExternalProject)
 set(YAML_URL "https://pyyaml.org/download/libyaml/yaml-0.2.5.tar.gz" CACHE STRING "URL for libyaml tarball")
+set(YAML_MD5 "bb15429d8fb787e7d3f1c83ae129a999" CACHE STRING "MD5 checksum of libyaml tarball")
 mark_as_advanced(YAML_URL)
+mark_as_advanced(YAML_MD5)
+
 ExternalProject_Add(libyaml
                     URL               ${YAML_URL}
-                    URL_MD5           bb15429d8fb787e7d3f1c83ae129a999
+                    URL_MD5           ${YAML_MD5}
                     SOURCE_DIR        "${CMAKE_BINARY_DIR}/yaml-src"
                     BINARY_DIR        "${CMAKE_BINARY_DIR}/yaml-build"
                     CONFIGURE_COMMAND <SOURCE_DIR>/configure ${CONFIGURE_REQUEST_PIC}

cmake/presets/most.cmake

@@ -4,7 +4,7 @@
 
 set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
         GRANULAR KSPACE MANYBODY MC MISC MLIAP MOLECULE OPT PERI
-        POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
+        PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
         USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
         USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC USER-MESODPD
         USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION

doc/src/Build_basics.rst

@@ -1,7 +1,7 @@
 Basic build options
 ===================
 
-The following topics are covered on this page, for building both with
+The following topics are covered on this page, for building with both
 CMake and make:
 
 * :ref:`Serial vs parallel build <serial>`

doc/src/Build_extras.rst

@@ -125,7 +125,7 @@ CMake build
                                 # default is sm_50
    -D HIP_ARCH=value            # primary GPU hardware choice for GPU_API=hip
                                 # value depends on selected HIP_PLATFORM
-                                # default is 'gfx906' for HIP_PLATFORM=hcc and 'sm_50' for HIP_PLATFORM=nvcc
+                                # default is 'gfx906' for HIP_PLATFORM=amd and 'sm_50' for HIP_PLATFORM=nvcc
    -D HIP_USE_DEVICE_SORT=value # enables GPU sorting
                                 # value = yes (default) or no
    -D CUDPP_OPT=value           # use GPU binning on with CUDA (should be off for modern GPUs)
@@ -169,17 +169,24 @@ desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
 
 If you are compiling with HIP, note that before running CMake you will have to
 set appropriate environment variables. Some variables such as
-:code:`HCC_AMDGPU_TARGET` or :code:`CUDA_PATH` are necessary for :code:`hipcc`
+:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc`
 and the linker to work correctly.
 
 .. code:: bash
 
-   # AMDGPU target
+   # AMDGPU target (ROCm <= 4.0)
    export HIP_PLATFORM=hcc
    export HCC_AMDGPU_TARGET=gfx906
    cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
    make -j 4
 
+.. code:: bash
+
+   # AMDGPU target (ROCm >= 4.1)
+   export HIP_PLATFORM=amd
+   cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
+   make -j 4
+
 .. code:: bash
 
    # CUDA target (not recommended, use GPU_ARCH=cuda)

doc/src/Commands_all.rst

@@ -86,6 +86,7 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`pair_style <pair_style>`
    * :doc:`pair_write <pair_write>`
    * :doc:`partition <partition>`
+   * :doc:`plugin <plugin>`
    * :doc:`prd <prd>`
    * :doc:`print <print>`
    * :doc:`processors <processors>`

doc/src/Commands_bond.rst

@@ -126,7 +126,7 @@ OPT.
    * :doc:`quadratic (o) <dihedral_quadratic>`
    * :doc:`spherical <dihedral_spherical>`
    * :doc:`table (o) <dihedral_table>`
-   * :doc:`table/cut <dihedral_table_cut>`
+   * :doc:`table/cut <dihedral_table>`
 
 .. _improper:
 

doc/src/Commands_pair.rst

@@ -187,7 +187,7 @@ OPT.
    * :doc:`mgpt <pair_mgpt>`
    * :doc:`mie/cut (g) <pair_mie>`
    * :doc:`mliap <pair_mliap>`
-   * :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
+   * :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
    * :doc:`momb <pair_momb>`
    * :doc:`morse (gkot) <pair_morse>`
    * :doc:`morse/smooth/linear (o) <pair_morse>`

doc/src/Developer.rst

@@ -14,6 +14,7 @@ of time and requests from the LAMMPS user community.
    Developer_flow
    Developer_write
    Developer_notes
+   Developer_plugins
    Developer_unittest
    Classes
    Developer_utils

doc/src/Developer_plugins.rst

@@ -0,0 +1,258 @@
+Writing plugins
+---------------
+
+Plugins provide a mechanism to add functionality to a LAMMPS executable
+without recompiling LAMMPS.  The functionality for this and the
+:doc:`plugin command <plugin>` are implemented in the
+:ref:`PLUGIN package <PKG-PLUGIN>` which must be installed to use plugins.
+
+Plugins use the operating system's capability to load dynamic shared
+object (DSO) files in a way similar shared libraries and then reference
+specific functions in those DSOs.  Any DSO file with plugins has to include
+an initialization function with a specific name, "lammpsplugin_init", that
+has to follow specific rules described below.  When loading the DSO with
+the "plugin" command, this function is looked up and called and will then
+register the contained plugin(s) with LAMMPS.
+
+From the programmer perspective this can work because of the object
+oriented design of LAMMPS where all pair style commands are derived from
+the class Pair, all fix style commands from the class Fix and so on and
+usually only functions present in those base classes are called
+directly.  When a :doc:`pair_style` command or :doc:`fix` command is
+issued a new instance of such a derived class is created.  This is done
+by a so-called factory function which is mapped to the style name.  Thus
+when, for example, the LAMMPS processes the command ``pair_style lj/cut
+2.5``, LAMMPS will look up the factory function for creating the
+``PairLJCut`` class and then execute it.  The return value of that
+function is a ``Pair *`` pointer and the pointer will be assigned to the
+location for the currently active pair style.
+
+A DSO file with a plugin thus has to implement such a factory function
+and register it with LAMMPS so that it gets added to the map of available
+styles of the given category.  To register a plugin with LAMMPS an
+initialization function has to be present in the DSO file called
+``lammpsplugin_init`` which is called with three ``void *`` arguments:
+a pointer to the current LAMMPS instance, a pointer to the opened DSO
+handle, and a pointer to the registration function.  The registration
+function takes two arguments: a pointer to a ``lammpsplugin_t`` struct
+with information about the plugin and a pointer to the current LAMMPS
+instance.  Please see below for an example of how the registration is
+done.
+
+Members of ``lammpsplugin_t``
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. list-table::
+   :header-rows: 1
+   :widths: auto
+
+   * - Member
+     - Description
+   * - version
+     - LAMMPS Version string the plugin was compiled for
+   * - style
+     - Style of the plugin (pair, bond, fix, command, etc.)
+   * - name
+     - Name of the plugin style
+   * - info
+     - String with information about the plugin
+   * - author
+     - String with the name and email of the author
+   * - creator.v1
+     - Pointer to factory function for pair, bond, angle, dihedral, or improper styles
+   * - creator.v2
+     - Pointer to factory function for compute, fix, or region styles
+   * - creator.v3
+     - Pointer to factory function for command styles
+   * - handle
+     - Pointer to the open DSO file handle
+
+Only one of the three alternate creator entries can be used at a time
+and which of those is determined by the style of plugin. The "creator.v1"
+element is for factory functions of supported styles computing forces (i.e.
+pair, bond, angle, dihedral, or improper styles) and the function takes
+as single argument the pointer to the LAMMPS instance. The factory function
+is cast to the ``lammpsplugin_factory1`` type before assignment.  The
+"creator.v2" element is for factory functions creating an instance of
+a fix, compute, or region style and takes three arguments: a pointer to
+the LAMMPS instance, an integer with the length of the argument list and
+a ``char **`` pointer to the list of arguments. The factory function pointer
+needs to be cast to the ``lammpsplugin_factory2`` type before assignment.
+The "creator.v3" element takes the same arguments as "creator.v3" but is
+specific to creating command styles: the factory function has to instantiate
+the command style locally passing the LAMMPS pointer as argument and then
+call its "command" member function with the number and list of arguments.
+The factory function pointer needs to be cast to the
+``lammpsplugin_factory3`` type before assignment.
+
+Pair style example
+^^^^^^^^^^^^^^^^^^
+
+As an example, a hypothetical pair style plugin "morse2" implemented in
+a class ``PairMorse2`` in the files ``pair_morse2.h`` and
+``pair_morse2.cpp`` with the factory function and initialization
+function would look like this:
+
+.. code-block:: C++
+
+  #include "lammpsplugin.h"
+  #include "version.h"
+  #include "pair_morse2.h"
+
+  using namespace LAMMPS_NS;
+
+  static Pair *morse2creator(LAMMPS *lmp)
+  {
+    return new PairMorse2(lmp);
+  }
+
+  extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
+  {
+    lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
+    lammpsplugin_t plugin;
+
+    plugin.version = LAMMPS_VERSION;
+    plugin.style   = "pair";
+    plugin.name    = "morse2";
+    plugin.info    = "Morse2 variant pair style v1.0";
+    plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
+    plugin.creator.v1 = (lammpsplugin_factory1 *) &morse2creator;
+    plugin.handle  = handle;
+    (*register_plugin)(&plugin,lmp);
+  }
+
+The factory function in this example is called ``morse2creator()``.  It
+receives a pointer to the LAMMPS class as only argument and thus has to
+be assigned to the *creator.v1* member of the plugin struct and cast to the
+``lammpsplugin_factory1`` pointer type.  It returns a
+pointer to the allocated class instance derived from the ``Pair`` class.
+This function may be declared static to avoid clashes with other plugins.
+The name of the derived class, ``PairMorse2``, must be unique inside
+the entire LAMMPS executable.
+
+Fix style example
+^^^^^^^^^^^^^^^^^
+
+If the factory function would be for a fix or compute, which take three
+arguments (a pointer to the LAMMPS class, the number of arguments and the
+list of argument strings), then the pointer type is ``lammpsplugin_factory2``
+and it must be assigned to the *creator.v2* member of the plugin struct.
+Below is an example for that:
+
+.. code-block:: C++
+
+  #include "lammpsplugin.h"
+  #include "version.h"
+  #include "fix_nve2.h"
+
+  using namespace LAMMPS_NS;
+
+  static Fix *nve2creator(LAMMPS *lmp, int argc, char **argv)
+  {
+    return new FixNVE2(lmp,argc,argv);
+  }
+
+  extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
+  {
+    lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
+    lammpsplugin_t plugin;
+
+    plugin.version = LAMMPS_VERSION;
+    plugin.style   = "fix";
+    plugin.name    = "nve2";
+    plugin.info    = "NVE2 variant fix style v1.0";
+    plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
+    plugin.creator.v2 = (lammpsplugin_factory2 *) &nve2creator;
+    plugin.handle  = handle;
+    (*register_plugin)(&plugin,lmp);
+  }
+
+Command style example
+^^^^^^^^^^^^^^^^^^^^^
+For command styles there is a third variant of factory function as
+demonstrated in the following example, which also shows that the
+implementation of the plugin class may also be within the same
+file as the plugin interface code:
+
+.. code-block:: C++
+
+   #include "lammpsplugin.h"
+
+   #include "comm.h"
+   #include "error.h"
+   #include "pointers.h"
+   #include "version.h"
+
+   #include <cstring>
+
+   namespace LAMMPS_NS {
+     class Hello : protected Pointers {
+      public:
+       Hello(class LAMMPS *lmp) : Pointers(lmp) {};
+       void command(int, char **);
+     };
+   }
+
+   using namespace LAMMPS_NS;
+
+   void Hello::command(int argc, char **argv)
+   {
+      if (argc != 1) error->all(FLERR,"Illegal hello command");
+      if (comm->me == 0)
+        utils::logmesg(lmp,fmt::format("Hello, {}!\n",argv[0]));
+   }
+
+   static void hellocreator(LAMMPS *lmp, int argc, char **argv)
+   {
+     Hello hello(lmp);
+     hello.command(argc,argv);
+   }
+
+   extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
+   {
+     lammpsplugin_t plugin;
+     lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
+
+     plugin.version = LAMMPS_VERSION;
+     plugin.style   = "command";
+     plugin.name    = "hello";
+     plugin.info    = "Hello world command v1.0";
+     plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
+     plugin.creator.v3 = (lammpsplugin_factory3 *) &hellocreator;
+     plugin.handle  = handle;
+     (*register_plugin)(&plugin,lmp);
+   }
+
+Additional Details
+^^^^^^^^^^^^^^^^^^
+
+The initialization function **must** be called ``lammpsplugin_init``, it
+**must** have C bindings and it takes three void pointers as arguments.
+The first is a pointer to the LAMMPS class that calls it and it needs to
+be passed to the registration function.  The second argument is a
+pointer to the internal handle of the DSO file, this needs to be added
+to the plugin info struct, so that the DSO can be closed and unloaded
+when all its contained plugins are unloaded.  The third argument is a
+function pointer to the registration function and needs to be stored
+in a variable of ``lammpsplugin_regfunc`` type and then called with a
+pointer to the ``lammpsplugin_t`` struct and the pointer to the LAMMPS
+instance as arguments to register a single plugin.  There may be multiple
+calls to multiple plugins in the same initialization function.
+
+To register a plugin a struct of the ``lammpsplugin_t`` needs to be filled
+with relevant info: current LAMMPS version string, kind of style, name of
+style, info string, author string, pointer to factory function, and the
+DSO handle.  The registration function is called with a pointer to the address
+of this struct and the pointer of the LAMMPS class.  The registration function
+will then add the factory function of the plugin style to the respective
+style map under the provided name.  It will also make a copy of the struct
+in a list of all loaded plugins and update the reference counter for loaded
+plugins from this specific DSO file.
+
+The pair style itself (i.e. the PairMorse2 class in this example) can be
+written just like any other pair style that is included in LAMMPS.  For
+a plugin, the use of the ``PairStyle`` macro in the section encapsulated
+by ``#ifdef PAIR_CLASS`` is not needed, since the mapping of the class
+name to the style name is done by the plugin registration function with
+the information from the ``lammpsplugin_t`` struct.  It may be included
+in case the new code is intended to be later included in LAMMPS directly.

doc/src/Developer_unittest.rst

@@ -4,10 +4,10 @@ Adding tests for unit testing
 This section discusses adding or expanding tests for the unit test
 infrastructure included into the LAMMPS source code distribution.
 Unlike example inputs, unit tests focus on testing the "local" behavior
-of individual features, tend to run very fast, and should be set up to
+of individual features, tend to run fast, and should be set up to cover
-cover as much of the added code as possible.  When contributing code to
+as much of the added code as possible.  When contributing code to the
-the distribution, the LAMMPS developers will appreciate if additions
+distribution, the LAMMPS developers will appreciate if additions to the
-to the integrated unit test facility are included.
+integrated unit test facility are included.
 
 Given the complex nature of MD simulations where many operations can
 only be performed when suitable "real" simulation environment has been
@@ -50,6 +50,9 @@ available:
    * - File name:
      - Test name:
      - Description:
+   * - ``test_argutils.cpp``
+     - ArgInfo
+     - Tests for ``ArgInfo`` class used by LAMMPS
    * - ``test_fmtlib.cpp``
      - FmtLib
      - Tests for ``fmtlib::`` functions used by LAMMPS
@@ -155,23 +158,27 @@ have the desired effect:
    {
        ASSERT_EQ(lmp->update->ntimestep, 0);
 
-       if (!verbose) ::testing::internal::CaptureStdout();
+       BEGIN_HIDE_OUTPUT();
-       lmp->input->one("reset_timestep 10");
+       command("reset_timestep 10");
-       if (!verbose) ::testing::internal::GetCapturedStdout();
+       END_HIDE_OUTPUT();
        ASSERT_EQ(lmp->update->ntimestep, 10);
 
-       if (!verbose) ::testing::internal::CaptureStdout();
+       BEGIN_HIDE_OUTPUT();
-       lmp->input->one("reset_timestep 0");
+       command("reset_timestep 0");
-       if (!verbose) ::testing::internal::GetCapturedStdout();
+       END_HIDE_OUTPUT();
        ASSERT_EQ(lmp->update->ntimestep, 0);
+
+       TEST_FAILURE(".*ERROR: Timestep must be >= 0.*", command("reset_timestep -10"););
+       TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", command("reset_timestep"););
+       TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", command("reset_timestep 10 10"););
+       TEST_FAILURE(".*ERROR: Expected integer .*", command("reset_timestep xxx"););
    }
 
-Please note the use of the (global) verbose variable to control whether
+Please note the use of the ``BEGIN_HIDE_OUTPUT`` and ``END_HIDE_OUTPUT``
-the LAMMPS command will be silent by capturing the output or not.  In
+functions that will capture output from running LAMMPS.  This is normally
-the default case, verbose == false, the test output will be compact and
+discarded but by setting the verbose flag (via setting the ``TEST_ARGS``
-not mixed with LAMMPS output. However setting the verbose flag (via
+environment variable, ``TEST_ARGS=-v``) it can be printed and used to
-setting the ``TEST_ARGS`` environment variable, ``TEST_ARGS=-v``) can be
+understand why tests fail unexpectedly.
-helpful to understand why tests fail unexpectedly.
 
 Another complexity of these tests stems from the need to capture
 situations where LAMMPS will stop with an error, i.e. handle so-called
@@ -210,6 +217,12 @@ The following test programs are currently available:
    * - ``test_lattice_region.cpp``
      - LatticeRegion
      - Tests to validate the :doc:`lattice <lattice>` and :doc:`region <region>` commands
+   * - ``test_groups.cpp``
+     - GroupTest
+     - Tests to validate the :doc:`group <group>` command
+   * - ``test_variables.cpp``
+     - VariableTest
+     - Tests to validate the :doc:`variable <variable>` command
    * - ``test_kim_commands.cpp``
      - KimCommands
      - Tests for several commands from the :ref:`KIM package <PKG-KIM>`

doc/src/Developer_utils.rst

@@ -101,6 +101,9 @@ and parsing files or arguments.
 .. doxygenfunction:: split_words
    :project: progguide
 
+.. doxygenfunction:: split_lines
+   :project: progguide
+
 .. doxygenfunction:: strmatch
    :project: progguide
 

doc/src/Howto_bioFF.rst

@@ -91,6 +91,7 @@ documentation for the formula it computes.
 * :doc:`bond_style <bond_harmonic>` harmonic
 * :doc:`bond_style <bond_morse>` morse
 
+* :doc:`angle_style <angle_cosine_squared>` cosine/squared
 * :doc:`angle_style <angle_harmonic>` harmonic
 * :doc:`angle_style <angle_cosine>` cosine
 * :doc:`angle_style <angle_cosine_periodic>` cosine/periodic

doc/src/Howto_granular.rst

@@ -18,12 +18,13 @@ This compute
 
 calculates rotational kinetic energy which can be :doc:`output with thermodynamic info <Howto_output>`.
 
-Use one of these 3 pair potentials, which compute forces and torques
+Use one of these 4 pair potentials, which compute forces and torques
 between interacting pairs of particles:
 
-* :doc:`pair_style <pair_style>` gran/history
+* :doc:`pair_style gran/history <pair_gran>`
-* :doc:`pair_style <pair_style>` gran/no_history
+* :doc:`pair_style gran/no_history <pair_gran>`
-* :doc:`pair_style <pair_style>` gran/hertzian
+* :doc:`pair_style gran/hertzian <pair_gran>`
+* :doc:`pair_style granular <pair_granular>`
 
 These commands implement fix options specific to granular systems:
 
@@ -31,6 +32,7 @@ These commands implement fix options specific to granular systems:
 * :doc:`fix pour <fix_pour>`
 * :doc:`fix viscous <fix_viscous>`
 * :doc:`fix wall/gran <fix_wall_gran>`
+* :doc:`fix wall/gran/region <fix_wall_gran_region>`
 
 The fix style *freeze* zeroes both the force and torque of frozen
 atoms, and should be used for granular system instead of the fix style

doc/src/Install_git.rst

@@ -86,33 +86,59 @@ check out any other desired branch) first.
 
 Once you have updated your local files with a ``git pull`` (or ``git
 checkout``), you still need to re-build LAMMPS if any source files have
-changed.  To do this, you should cd to the src directory and type:
+changed.  How to do this depends on the build system you are using.
 
-.. code-block:: bash
+.. tabs::
 
-   $ make purge             # remove any deprecated src files
+   .. tab:: CMake build
-   $ make package-update    # sync package files with src files
-   $ make foo               # re-build for your machine (mpi, serial, etc)
 
-just as described on the :doc:`Apply patch <Install_patch>` page,
+      Change to your build folder and type:
-after a patch has been installed.
 
-.. warning::
+      .. code-block:: bash
 
-   If you wish to edit/change a src file that is from a
+         cmake . --build
-   package, you should edit the version of the file inside the package
-   sub-directory with src, then re-install the package.  The version in
-   the source directory is merely a copy and will be wiped out if you type "make
-   package-update".
 
-.. warning::
+      CMake should auto-detect whether it needs to re-run the CMake
+      configuration step and otherwise redo the build for all files
+      that have been changed or files that depend on changed files.
+      In case some build options have been changed or renamed, you
+      may have to update those by running:
 
-   The GitHub servers support both the "git://" and
+      .. code-block:: bash
-   "https://" access protocols for anonymous read-only access.  If you
-   have a correspondingly configured GitHub account, you may also use
-   SSH access with the URL "git@github.com:lammps/lammps.git".
 
-The LAMMPS GitHub project is managed by Christoph Junghans (LANL,
+         cmake .
-junghans at lanl.gov), Axel Kohlmeyer (Temple U, akohlmey at
+
-gmail.com) and Richard Berger (Temple U, richard.berger at
+      and then rebuild.
-temple.edu).
+
+   .. tab:: Traditional make
+
+      Switch to the src directory and type:
+
+      .. code-block:: bash
+
+         $ make purge             # remove any deprecated src files
+         $ make package-update    # sync package files with src files
+         $ make foo               # re-build for your machine (mpi, serial, etc)
+
+      Just as described on the :doc:`Apply patch <Install_patch>` page,
+      after a patch has been installed.
+
+      .. warning::
+
+         If you wish to edit/change a src file that is from a package,
+         you should edit the version of the file inside the package
+         sub-directory with src, then re-install the package.  The
+         version in the source directory is merely a copy and will be
+         wiped out if you type "make package-update".
+
+.. admonition:: Git protocols
+   :class: note
+
+   The servers at github.com support the "git://" and "https://" access
+   protocols for anonymous, read-only access.  If you have a suitably
+   configured GitHub account, you may also use SSH protocol with the
+   URL "git@github.com:lammps/lammps.git".
+
+The LAMMPS GitHub project is currently managed by Axel Kohlmeyer
+(Temple U, akohlmey at gmail.com) and Richard Berger (Temple U,
+richard.berger at temple.edu).

doc/src/Install_patch.rst

@@ -43,24 +43,54 @@ up to date.
 * A list of updated files print out to the screen.  The -b switch
   creates backup files of your originals (e.g. src/force.cpp.orig), so
   you can manually undo the patch if something goes wrong.
-* Type the following from the src directory, to enforce consistency
-  between the src and package directories.  This is OK to do even if you
-  don't use one or more packages.  If you are applying several patches
-  successively, you only need to type this once at the end. The purge
-  command removes deprecated src files if any were removed by the patch
-  from package sub-directories.
 
-  .. code-block:: bash
+* Once you have updated your local files you need to re-build LAMMPS.
+  If you are applying several patches successively, you only need to
+  do the rebuild once at the end. How to do it depends on the build
+  system you are using.
 
-     $ make purge
+  .. tabs::
-     $ make package-update
 
-* Re-build LAMMPS via the "make" command.
+     .. tab:: CMake build
 
-.. warning::
+        Change to your build folder and type:
 
-   If you wish to edit/change a source file that is part of a package,
+        .. code-block:: bash
-   you should edit the version of the file inside the package folder in
+
-   src, and then re-install or update the package.  The version in the
+           cmake . --build
-   src directory is merely a copy and will be wiped out when you type
+
-   "make package-update".
+        CMake should auto-detect whether it needs to re-run the CMake
+        configuration step and otherwise redo the build for all files
+        that have been changed or files that depend on changed files.
+        In case some build options have been changed or renamed, you
+        may have to update those by running:
+
+        .. code-block:: bash
+
+           cmake .
+
+        and then rebuild.
+
+     .. tab:: Traditional make
+
+        Switch to the src directory and type:
+
+        .. code-block:: bash
+
+           $ make purge             # remove any deprecated src files
+           $ make package-update    # sync package files with src files
+           $ make foo               # re-build for your machine (mpi, serial, etc)
+
+        to enforce consistency of the source between the src folder
+        and package directories.  This is OK to do even if you don't
+        use any packages. The "make purge" command removes any deprecated
+        src files if they were removed by the patch from a package
+        sub-directory.
+
+        .. warning::
+
+           If you wish to edit/change a src file that is from a package,
+           you should edit the version of the file inside the package
+           sub-directory with src, then re-install the package.  The
+           version in the source directory is merely a copy and will be
+           wiped out if you type "make package-update".

doc/src/Packages_details.rst

@@ -50,6 +50,7 @@ page gives those details.
    * :ref:`MSCG <PKG-MSCG>`
    * :ref:`OPT <PKG-OPT>`
    * :ref:`PERI <PKG-PERI>`
+   * :ref:`PLUGIN <PKG-PLUGIN>`
    * :ref:`POEMS <PKG-POEMS>`
    * :ref:`PYTHON <PKG-PYTHON>`
    * :ref:`QEQ <PKG-QEQ>`
@@ -843,6 +844,28 @@ Foster (UTSA).
 
 ----------
 
+.. _PKG-PLUGIN:
+
+PLUGIN package
+--------------
+
+**Contents:**
+
+A :doc:`plugin <plugin>` command that can load and unload several
+kind of styles in LAMMPS from shared object files at runtime without
+having to recompile and relink LAMMPS.
+
+**Authors:** Axel Kohlmeyer (Temple U)
+
+**Supporting info:**
+
+* src/PLUGIN: filenames -> commands
+* :doc:`plugin command <plugin>`
+* :doc:`Information on writing plugins <Developer_plugins>`
+* examples/plugin
+
+----------
+
 .. _PKG-POEMS:
 
 POEMS package
@@ -2456,6 +2479,6 @@ which discuss the `QuickFF <quickff_>`_ methodology.
 * :doc:`bond_style mm3 <bond_mm3>`
 * :doc:`improper_style distharm <improper_distharm>`
 * :doc:`improper_style sqdistharm <improper_sqdistharm>`
-* :doc:`pair_style mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
+* :doc:`pair_style mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
 * :doc:`pair_style lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
 * examples/USER/yaff

doc/src/Packages_standard.rst

@@ -71,6 +71,8 @@ package:
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`PERI <PKG-PERI>`           | Peridynamics models                  | :doc:`pair_style peri <pair_peri>`                 | peri                                                 | no      |
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
+| :ref:`PLUGIN <PKG-PLUGIN>`       | Plugin loader command                | :doc:`plugin <plugin>`                             | plugins                                              | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`POEMS <PKG-POEMS>`         | coupled rigid body motion            | :doc:`fix poems <fix_poems>`                       | rigid                                                | int     |
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`PYTHON <PKG-PYTHON>`       | embed Python code in an input script | :doc:`python <python>`                             | python                                               | sys     |

doc/src/angle_cosine_periodic.rst

@@ -24,20 +24,17 @@ Examples
 Description
 """""""""""
 
-The *cosine/periodic* angle style uses the following potential, which
+The *cosine/periodic* angle style uses the following potential, which may be
-is commonly used in the :doc:`DREIDING <Howto_bioFF>` force field,
+particularly used for organometallic systems where :math:`n` = 4 might be used
-particularly for organometallic systems where :math:`n` = 4 might be used
 for an octahedral complex and :math:`n` = 3 might be used for a trigonal
 center:
 
 .. math::
 
-   E = C \left[ 1 - B(-1)^n\cos\left( n\theta\right) \right]
+   E = \frac{2.0}{n^2} * C \left[ 1 - B(-1)^n\cos\left( n\theta\right) \right]
 
 where :math:`C`, :math:`B` and :math:`n` are coefficients defined for each angle type.
 
-See :ref:`(Mayo) <cosine-Mayo>` for a description of the DREIDING force field
-
 The following coefficients must be defined for each angle type via the
 :doc:`angle_coeff <angle_coeff>` command as in the example above, or in
 the data file or restart files read by the :doc:`read_data <read_data>`
@@ -47,10 +44,9 @@ or :doc:`read_restart <read_restart>` commands:
 * :math:`B` = 1 or -1
 * :math:`n` = 1, 2, 3, 4, 5 or 6 for periodicity
 
-Note that the prefactor :math:`C` is specified and not the overall force
+Note that the prefactor :math:`C` is specified as coefficient and not the overall force
-constant :math:`K = \frac{C}{n^2}`.  When :math:`B = 1`, it leads to a minimum for the
+constant :math:`K = \frac{2 C}{n^2}`.  When :math:`B = 1`, it leads to a minimum for the
-linear geometry.  When :math:`B = -1`, it leads to a maximum for the linear
+linear geometry.  When :math:`B = -1`, it leads to a maximum for the linear geometry.
-geometry.
 
 ----------
 
@@ -75,9 +71,3 @@ Default
 
 none
 
-----------
-
-.. _cosine-Mayo:
-
-**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
-(1990).

doc/src/angle_cosine_squared.rst

@@ -30,8 +30,11 @@ The *cosine/squared* angle style uses the potential
 
    E = K [\cos(\theta) - \cos(\theta_0)]^2
 
-where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
+, which is commonly used in the :doc:`DREIDING <Howto_bioFF>` force field,
-prefactor.  Note that the usual 1/2 factor is included in :math:`K`.
+where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K`
+is a prefactor.  Note that the usual 1/2 factor is included in :math:`K`.
+
+See :ref:`(Mayo) <cosine-Mayo>` for a description of the DREIDING force field.
 
 The following coefficients must be defined for each angle type via the
 :doc:`angle_coeff <angle_coeff>` command as in the example above, or in
@@ -66,3 +69,10 @@ Default
 """""""
 
 none
+
+----------
+
+.. _cosine-Mayo:
+
+**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
+(1990).

doc/src/commands_list.rst

@@ -77,6 +77,7 @@ Commands
    pair_style
    pair_write
    partition
+   plugin
    prd
    print
    processors

doc/src/dihedral_style.rst

@@ -113,7 +113,7 @@ more of (g,i,k,o,t) to indicate which accelerated styles exist.
 * :doc:`quadratic <dihedral_quadratic>` - dihedral with quadratic term in angle
 * :doc:`spherical <dihedral_spherical>` - dihedral which includes angle terms to avoid singularities
 * :doc:`table <dihedral_table>` - tabulated dihedral
-* :doc:`table/cut <dihedral_table_cut>` - tabulated dihedral with analytic cutoff
+* :doc:`table/cut <dihedral_table>` - tabulated dihedral with analytic cutoff
 
 ----------
 

doc/src/dihedral_table.rst

@@ -1,19 +1,24 @@
 .. index:: dihedral_style table
 .. index:: dihedral_style table/omp
+.. index:: dihedral_style table/cut
 
 dihedral_style table command
 ============================
 
 Accelerator Variants: *table/omp*
 
+dihedral_style table/cut command
+================================
+
 Syntax
 """"""
 
 .. code-block:: LAMMPS
 
-   dihedral_style table style Ntable
+   dihedral_style style interpolation Ntable
 
-* style = *linear* or *spline* = method of interpolation
+* style = *table* or *table/cut*
+* interpolation = *linear* or *spline* = method of interpolation
 * Ntable = size of the internal lookup table
 
 Examples
@@ -26,13 +31,21 @@ Examples
    dihedral_coeff 1 file.table DIH_TABLE1
    dihedral_coeff 2 file.table DIH_TABLE2
 
+   dihedral_style table/cut spline 400
+   dihedral_style table/cut linear 1000
+   dihedral_coeff 1 aat 1.0 177 180 file.table DIH_TABLE1
+   dihedral_coeff 2 aat 0.5 170 180 file.table DIH_TABLE2
+
 Description
 """""""""""
 
-The *table* dihedral style creates interpolation tables of length
+The *table* and *table/cut* dihedral styles create interpolation tables
-*Ntable* from dihedral potential and derivative values listed in a
+of length *Ntable* from dihedral potential and derivative values listed
-file(s) as a function of the dihedral angle "phi".  The files are read
+in a file(s) as a function of the dihedral angle "phi".  The files are
-by the :doc:`dihedral_coeff <dihedral_coeff>` command.
+read by the :doc:`dihedral_coeff <dihedral_coeff>` command.  For
+dihedral style *table/cut* additionally an analytic cutoff that is
+quadratic in the bond-angle (theta) is applied in order to regularize
+the dihedral interaction.
 
 The interpolation tables are created by fitting cubic splines to the
 file values and interpolating energy and derivative values at each of
@@ -51,16 +64,53 @@ interpolated table.  For a given dihedral angle (phi), the appropriate
 coefficients are chosen from this list, and a cubic polynomial is used
 to compute the energy and the derivative at this angle.
 
-The following coefficients must be defined for each dihedral type via
+For dihedral style *table* the following coefficients must be defined
-the :doc:`dihedral_coeff <dihedral_coeff>` command as in the example
+for each dihedral type via the :doc:`dihedral_coeff <dihedral_coeff>`
-above.
+command as in the example above.
 
 * filename
 * keyword
 
-The filename specifies a file containing tabulated energy and
+The filename specifies a file containing tabulated energy and derivative
-derivative values. The keyword specifies a section of the file.  The
+values. The keyword specifies which section of the file to read.  The
-format of this file is described below.
+format of this file is the same for both dihedral styles and described
+below.
+
+For dihedral style *table/cut* the following coefficients must be
+defined for each dihedral type via the :doc:`dihedral_coeff
+<dihedral_coeff>` command as in the example above.
+
+* style (aat)
+* cutoff prefactor
+* cutoff angle1
+* cutoff angle2
+* filename
+* keyword
+
+The cutoff dihedral style uses a tabulated dihedral interaction with a
+cutoff function:
+
+.. math::
+
+   f(\theta) & = K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\
+   f(\theta) & = K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2
+
+The cutoff specifies an prefactor to the cutoff function.  While this
+value would ordinarily equal 1 there may be situations where the value
+should change.
+
+The cutoff :math:`\theta_1` specifies the angle (in degrees) below which
+the dihedral interaction is unmodified, i.e. the cutoff function is 1.
+
+The cutoff function is applied between :math:`\theta_1` and
+:math:`\theta_2`, which is the angle at which the cutoff function drops
+to zero.  The value of zero effectively "turns off" the dihedral
+interaction.
+
+The filename specifies a file containing tabulated energy and derivative
+values. The keyword specifies which section of the file to read.  The
+format of this file is the same for both dihedral styles and described
+below.
 
 ----------
 
@@ -182,18 +232,19 @@ that matches the specified keyword.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This dihedral style writes the settings for the "dihedral_style table"
+These dihedral styles write the settings for the "dihedral_style table"
-command to :doc:`binary restart files <restart>`, so a dihedral_style
+or "dihedral_style table/cut" command to :doc:`binary restart files
-command does not need to specified in an input script that reads a
+<restart>`, so a dihedral_style command does not need to specified in an
-restart file.  However, the coefficient information is not stored in
+input script that reads a restart file.  However, the coefficient
-the restart file, since it is tabulated in the potential files.  Thus,
+information loaded from the table file(s) is not stored in the restart
+file, since it is tabulated in the potential files.  Thus, suitable
 dihedral_coeff commands do need to be specified in the restart input
-script.
+script after reading the restart file.
 
 Restrictions
 """"""""""""
 
-This dihedral style can only be used if LAMMPS was built with the
+These dihedral styles can only be used if LAMMPS was built with the
 USER-MISC package.  See the :doc:`Build package <Build_package>` doc
 page for more info.
 

doc/src/dihedral_table_cut.rst

@@ -1,229 +0,0 @@
-.. index:: dihedral_style table/cut
-
-dihedral_style table/cut command
-================================
-
-Syntax
-""""""
-
-.. code-block:: LAMMPS
-
-   dihedral_style table/cut style Ntable
-
-* style = *linear* or *spline* = method of interpolation
-* Ntable = size of the internal lookup table
-
-Examples
-""""""""
-
-.. code-block:: LAMMPS
-
-   dihedral_style table/cut spline 400
-   dihedral_style table/cut linear 1000
-   dihedral_coeff 1 aat 1.0 177 180 file.table DIH_TABLE1
-   dihedral_coeff 2 aat 0.5 170 180 file.table DIH_TABLE2
-
-Description
-"""""""""""
-
-The *table/cut* dihedral style creates interpolation tables of length
-*Ntable* from dihedral potential and derivative values listed in a
-file(s) as a function of the dihedral angle "phi".  In addition, an
-analytic cutoff that is quadratic in the bond-angle (theta) is applied
-in order to regularize the dihedral interaction.  The dihedral table
-files are read by the :doc:`dihedral_coeff <dihedral_coeff>` command.
-
-The interpolation tables are created by fitting cubic splines to the
-file values and interpolating energy and derivative values at each of
-*Ntable* dihedral angles. During a simulation, these tables are used
-to interpolate energy and force values on individual atoms as
-needed. The interpolation is done in one of 2 styles: *linear* or
-*spline*\ .
-
-For the *linear* style, the dihedral angle (phi) is used to find 2
-surrounding table values from which an energy or its derivative is
-computed by linear interpolation.
-
-For the *spline* style, cubic spline coefficients are computed and
-stored at each of the *Ntable* evenly-spaced values in the
-interpolated table.  For a given dihedral angle (phi), the appropriate
-coefficients are chosen from this list, and a cubic polynomial is used
-to compute the energy and the derivative at this angle.
-
-The following coefficients must be defined for each dihedral type via
-the :doc:`dihedral_coeff <dihedral_coeff>` command as in the example
-above.
-
-* style (aat)
-* cutoff prefactor
-* cutoff angle1
-* cutoff angle2
-* filename
-* keyword
-
-The cutoff dihedral style uses a tabulated dihedral interaction with a
-cutoff function:
-
-.. math::
-
-   f(\theta) & = K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\
-   f(\theta) & = K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2
-
-The cutoff specifies an prefactor to the cutoff function.  While this value
-would ordinarily equal 1 there may be situations where the value should change.
-
-The cutoff :math:`\theta_1` specifies the angle (in degrees) below which the dihedral
-interaction is unmodified, i.e. the cutoff function is 1.
-
-The cutoff function is applied between :math:`\theta_1` and :math:`\theta_2`, which is
-the angle at which the cutoff function drops to zero.  The value of zero effectively
-"turns off" the dihedral interaction.
-
-The filename specifies a file containing tabulated energy and
-derivative values. The keyword specifies a section of the file.  The
-format of this file is described below.
-
-----------
-
-The format of a tabulated file is as follows (without the
-parenthesized comments).  It can begin with one or more comment
-or blank lines.
-
-.. parsed-literal::
-
-   # Table of the potential and its negative derivative
-
-   DIH_TABLE1                   (keyword is the first text on line)
-   N 30 DEGREES                 (N, NOF, DEGREES, RADIANS, CHECKU/F)
-                                (blank line)
-   1 -168.0 -1.40351172223 0.0423346818422
-   2 -156.0 -1.70447981034 0.00811786522531
-   3 -144.0 -1.62956100432 -0.0184129719987
-   ...
-   30 180.0 -0.707106781187 0.0719306095245
-
-   # Example 2: table of the potential. Forces omitted
-
-   DIH_TABLE2
-   N 30 NOF CHECKU testU.dat CHECKF testF.dat
-
-   1 -168.0 -1.40351172223
-   2 -156.0 -1.70447981034
-   3 -144.0 -1.62956100432
-   ...
-   30 180.0 -0.707106781187
-
-A section begins with a non-blank line whose first character is not a
-"#"; blank lines or lines starting with "#" can be used as comments
-between sections. The first line begins with a keyword which
-identifies the section. The line can contain additional text, but the
-initial text must match the argument specified in the
-:doc:`dihedral_coeff <dihedral_coeff>` command. The next line lists (in
-any order) one or more parameters for the table. Each parameter is a
-keyword followed by one or more numeric values.
-
-Following a blank line, the next N lines list the tabulated values. On
-each line, the first value is the index from 1 to N, the second value is
-the angle value, the third value is the energy (in energy units), and
-the fourth is -dE/d(phi) also in energy units). The third term is the
-energy of the 4-atom configuration for the specified angle.  The fourth
-term (when present) is the negative derivative of the energy with
-respect to the angle (in degrees, or radians depending on whether the
-user selected DEGREES or RADIANS).  Thus the units of the last term
-are still energy, not force. The dihedral angle values must increase
-from one line to the next.
-
-Dihedral table splines are cyclic.  There is no discontinuity at 180
-degrees (or at any other angle).  Although in the examples above, the
-angles range from -180 to 180 degrees, in general, the first angle in
-the list can have any value (positive, zero, or negative).  However
-the *range* of angles represented in the table must be *strictly* less
-than 360 degrees (2pi radians) to avoid angle overlap.  (You may not
-supply entries in the table for both 180 and -180, for example.)  If
-the user's table covers only a narrow range of dihedral angles,
-strange numerical behavior can occur in the large remaining gap.
-
-**Parameters:**
-
-The parameter "N" is required and its value is the number of table
-entries that follow. Note that this may be different than the N
-specified in the :doc:`dihedral_style table <dihedral_style>` command.
-Let *Ntable* is the number of table entries requested dihedral_style
-command, and let *Nfile* be the parameter following "N" in the
-tabulated file ("30" in the sparse example above).  What LAMMPS does
-is a preliminary interpolation by creating splines using the *Nfile*
-tabulated values as nodal points.  It uses these to interpolate as
-needed to generate energy and derivative values at *Ntable* different
-points (which are evenly spaced over a 360 degree range, even if the
-angles in the file are not).  The resulting tables of length *Ntable*
-are then used as described above, when computing energy and force for
-individual dihedral angles and their atoms.  This means that if you
-want the interpolation tables of length *Ntable* to match exactly what
-is in the tabulated file (with effectively nopreliminary
-interpolation), you should set *Ntable* = *Nfile*\ .  To insure the
-nodal points in the user's file are aligned with the interpolated
-table entries, the angles in the table should be integer multiples of
-360/\ *Ntable* degrees, or 2\*PI/\ *Ntable* radians (depending on your
-choice of angle units).
-
-The optional "NOF" keyword allows the user to omit the forces
-(negative energy derivatives) from the table file (normally located in
-the fourth column).  In their place, forces will be calculated
-automatically by differentiating the potential energy function
-indicated by the third column of the table (using either linear or
-spline interpolation).
-
-The optional "DEGREES" keyword allows the user to specify angles in
-degrees instead of radians (default).
-
-The optional "RADIANS" keyword allows the user to specify angles in
-radians instead of degrees.  (Note: This changes the way the forces
-are scaled in the fourth column of the data file.)
-
-The optional "CHECKU" keyword is followed by a filename.  This allows
-the user to save all of the *Ntable* different entries in the
-interpolated energy table to a file to make sure that the interpolated
-function agrees with the user's expectations.  (Note: You can
-temporarily increase the *Ntable* parameter to a high value for this
-purpose.  "\ *Ntable*\ " is explained above.)
-
-The optional "CHECKF" keyword is analogous to the "CHECKU" keyword.
-It is followed by a filename, and it allows the user to check the
-interpolated force table.  This option is available even if the user
-selected the "NOF" option.
-
-Note that one file can contain many sections, each with a tabulated
-potential. LAMMPS reads the file section by section until it finds one
-that matches the specified keyword.
-
-Restart, fix_modify, output, run start/stop, minimize info
-"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-
-This dihedral style writes the settings for the "dihedral_style table/cut"
-command to :doc:`binary restart files <restart>`, so a dihedral_style
-command does not need to specified in an input script that reads a
-restart file.  However, the coefficient information is not stored in
-the restart file, since it is tabulated in the potential files.  Thus,
-dihedral_coeff commands do need to be specified in the restart input
-script.
-
-Restrictions
-""""""""""""
-
-This dihedral style can only be used if LAMMPS was built with the
-USER-MISC package.  See the :doc:`Build package <Build_package>` doc
-page for more info.
-
-Related commands
-""""""""""""""""
-
-:doc:`dihedral_coeff <dihedral_coeff>`, :doc:`dihedral_style table <dihedral_table>`
-
-Default
-"""""""
-
-none
-
-.. _dihedralcut-Salerno:
-
-**(Salerno)** Salerno, Bernstein, J Chem Theory Comput, --, ---- (2018).

doc/src/dump.rst

@@ -349,7 +349,7 @@ the box size stored with the snapshot.
 
 The *xtc* style writes XTC files, a compressed trajectory format used
 by the GROMACS molecular dynamics package, and described
-`here <http://manual.gromacs.org/current/online/xtc.html>`_.
+`here <https://manual.gromacs.org/current/reference-manual/file-formats.html#xtc>`_.
 The precision used in XTC files can be adjusted via the
 :doc:`dump_modify <dump_modify>` command.  The default value of 1000
 means that coordinates are stored to 1/1000 nanometer accuracy.  XTC

doc/src/fix_ave_chunk.rst

@@ -307,7 +307,9 @@ atoms in the chunk.  The averaged output value for the chunk on the
 average over atoms across the entire *Nfreq* timescale.  For the
 *density/number* and *density/mass* values, the volume (bin volume or
 system volume) used in the final normalization will be the volume at
-the final *Nfreq* timestep.
+the final *Nfreq* timestep. For the *temp* values, degrees of freedom and
+kinetic energy are summed separately across the entire *Nfreq* timescale, and
+the output value is calculated by dividing those two sums.
 
 If the *norm* setting is *sample*\ , the chunk value is summed over
 atoms for each sample, as is the count, and an "average sample value"

doc/src/fix_cmap.rst

@@ -127,6 +127,11 @@ the :doc:`run <run>` command.
 The forces due to this fix are imposed during an energy minimization,
 invoked by the :doc:`minimize <minimize>` command.
 
+The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA
+<run_style>` integrator the fix is adding its forces. Default is the
+outermost level.
+
 .. note::
 
    If you want the potential energy associated with the CMAP terms

doc/src/fix_halt.rst

@@ -115,6 +115,18 @@ The version with "bondmax" will just run somewhat faster, due to less
 overhead in computing bond lengths and not storing them in a separate
 compute.
 
+A variable can be used to implement a large variety of conditions,
+including to stop when a specific file exists.  Example:
+
+.. code-block:: LAMMPS
+
+   variable exit equal is_file(EXIT)
+   fix 10 all halt 100 v_exit != 0 error soft
+
+Will stop the current run command when a file ``EXIT`` is created
+in the current working directory.  The condition can be cleared
+by removing the file through the :doc:`shell <shell>` command.
+
 The choice of operators listed above are the usual comparison
 operators.  The XOR operation (exclusive or) is also included as "\|\^".
 In this context, XOR means that if either the attribute or avalue is

doc/src/fix_rigid_meso.rst

@@ -48,8 +48,8 @@ Examples
    fix 1 ellipsoid rigid/meso single
    fix 1 rods      rigid/meso molecule
    fix 1 spheres   rigid/meso single force 1 off off on
-   fix 1 particles rigid/meso molecule force 1\*5 off off off force 6\*10 off off on
+   fix 1 particles rigid/meso molecule force 1*5 off off off force 6*10 off off on
-   fix 2 spheres   rigid/meso group 3 sphere1 sphere2 sphere3 torque \* off off off
+   fix 2 spheres   rigid/meso group 3 sphere1 sphere2 sphere3 torque * off off off
 
 Description
 """""""""""

doc/src/group.rst

@@ -120,12 +120,12 @@ specified atom types, atom IDs, or molecule IDs into the group.  These
 The first format is a list of values (types or IDs).  For example, the
 second command in the examples above puts all atoms of type 3 or 4 into
 the group named *water*\ .  Each entry in the list can be a
-colon-separated sequence A:B or A:B:C, as in two of the examples
+colon-separated sequence ``A:B`` or ``A:B:C``, as in two of the examples
 above.  A "sequence" generates a sequence of values (types or IDs),
-with an optional increment.  The first example with 500:1000 has the
+with an optional increment.  The first example with ``500:1000`` has the
 default increment of 1 and would add all atom IDs from 500 to 1000
 (inclusive) to the group sub, along with 10,25,50 since they also
-appear in the list of values.  The second example with 100:10000:10
+appear in the list of values.  The second example with ``100:10000:10``
 uses an increment of 10 and would thus would add atoms IDs
 100,110,120, ... 9990,10000 to the group sub.
 
@@ -269,7 +269,7 @@ group and running further.
 .. code-block:: LAMMPS
 
    variable        nsteps equal 5000
-   variable        rad equal 18-(step/v_nsteps)\*(18-5)
+   variable        rad equal 18-(step/v_nsteps)*(18-5)
    region          ss sphere 20 20 0 v_rad
    group           mobile dynamic all region ss
    fix             1 mobile nve

doc/src/kim_commands.rst

@@ -1205,7 +1205,7 @@ coordinates of atoms in the unit cell of the cubic crystal.  In the case of,
 e.g. a conventional fcc unit cell, the "source-value" key in the map associated
 with this key should be assigned the following value:
 
-.. code-block:: LAMMPS
+.. code-block:: text
 
    [[0.0, 0.0, 0.0],
     [0.5, 0.5, 0.0],

doc/src/pair_dpd.rst

@@ -150,7 +150,7 @@ shifted to be 0.0 at the cutoff distance Rc.
 The :doc:`pair_modify <pair_modify>` table option is not relevant
 for these pair styles.
 
-These pair style do not support the :doc:`pair_modify <pair_modify>`
+These pair styles do not support the :doc:`pair_modify <pair_modify>`
 tail option for adding long-range tail corrections to energy and
 pressure.
 

doc/src/pair_fep_soft.rst

@@ -363,7 +363,7 @@ Mixing, shift, table, tail correction, restart, rRESPA info
 
 The different versions of the *lj/cut/soft* pair styles support mixing.  For
 atom type pairs I,J and I != J, the :math:`\epsilon` and :math:`\sigma`
-coefficients and cutoff distance for these pair style can be mixed.  The default
+coefficients and cutoff distance for these pair styles can be mixed.  The default
 mix value is *geometric* for 12-6 styles.
 
 The mixing rule for epsilon and sigma for *lj/class2/soft* 9-6 potentials is to

doc/src/pair_gayberne.rst

@@ -188,7 +188,7 @@ Restrictions
 The *gayberne* style is part of the ASPHERE package.  It is only
 enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
 
-These pair style require that atoms store torque and a quaternion to
+These pair styles require that atoms store torque and a quaternion to
 represent their orientation, as defined by the
 :doc:`atom_style <atom_style>`.  It also require they store a per-type
 :doc:`shape <set>`.  The particles cannot store a per-particle

doc/src/pair_lj_switch3_coulgauss_long.rst

@@ -1,8 +1,12 @@
 .. index:: pair_style lj/switch3/coulgauss/long
+.. index:: pair_style mm3/switch3/coulgauss/long
 
 pair_style lj/switch3/coulgauss/long command
 ============================================
 
+pair_style mm3/switch3/coulgauss/long command
+=============================================
+
 Syntax
 """"""
 
@@ -10,7 +14,7 @@ Syntax
 
    pair_style style args
 
-* style = *lj/switch3/coulgauss/long*
+* style = *lj/switch3/coulgauss/long* or *mm3/switch3/coulgauss/long*
 * args = list of arguments for a particular style
 
 .. parsed-literal::
@@ -20,6 +24,11 @@ Syntax
        cutoff2 = global cutoff for Coulombic (optional) (distance units)
        width  = width parameter of the smoothing function (distance units)
 
+     *mm3/switch3/coulgauss/long* args = cutoff (cutoff2) width
+       cutoff  = global cutoff for MM3 (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+       width  = width parameter of the smoothing function (distance units)
+
 Examples
 """"""""
 
@@ -31,6 +40,12 @@ Examples
    pair_style lj/switch3/coulgauss/long   12.0 10.0 3.0
    pair_coeff 1  0.2 2.5 1.2
 
+   pair_style mm3/switch3/coulgauss/long    12.0 3.0
+   pair_coeff 1  0.2 2.5 1.2
+
+   pair_style mm3/switch3/coulgauss/long   12.0 10.0 3.0
+   pair_coeff 1  0.2 2.5 1.2
+
 Description
 """""""""""
 
@@ -41,8 +56,17 @@ vdW potential
 
    E = 4\epsilon \left[ \left(\frac{\sigma}{r}\right)^{12}-\left(\frac{\sigma}{r}\right)^{6} \right]
 
-, which goes smoothly to zero at the cutoff r_c as defined
+The *mm3/switch3/coulgauss/long* style evaluates the MM3
-by the switching function
+vdW potential :ref:`(Allinger) <mm3-allinger1989>`
+
+.. math::
+
+   E & = \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\
+   r_{v,ij} & =  r_{v,i} + r_{v,j} \\
+   \epsilon_{ij} & = \sqrt{\epsilon_i \epsilon_j}
+
+Both potentials go smoothly to zero at the cutoff r_c as defined by the
+switching function
 
 .. math::
 
@@ -85,14 +109,35 @@ commands:
 Mixing, shift, table, tail correction, restart, rRESPA info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of the lj/long pair styles can be mixed.
+The default mix value is *geometric*\ .  See the "pair_modify" command
+for details.
+
 Shifting the potential energy is not necessary because the switching
 function ensures that the potential is zero at the cut-off.
 
+These pair styles support the :doc:`pair_modify <pair_modify>` table and
+options since they can tabulate the short-range portion of the
+long-range Coulombic interactions.
+
+Thes pair styles do not support the :doc:`pair_modify <pair_modify>`
+tail option for adding a long-range tail correction to the
+Lennard-Jones portion of the energy and pressure.
+
+These pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+These pair styles can only be used via the *pair* keyword of the
+:doc:`run_style respa <run_style>` command.  They do not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
 Restrictions
 """"""""""""
 
-These styles are part of the USER-YAFF package.  They are only
+These styles are part of the USER-YAFF package.  They are only enabled
-enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+if LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` doc page for more info.
 
 Related commands
 """"""""""""""""

doc/src/pair_mm3_switch3_coulgauss_long.rst

@@ -1,109 +0,0 @@
-.. index:: pair_style mm3/switch3/coulgauss/long
-
-pair_style mm3/switch3/coulgauss/long command
-=============================================
-
-Syntax
-""""""
-
-.. code-block:: LAMMPS
-
-   pair_style style args
-
-* style = *mm3/switch3/coulgauss/long*
-* args = list of arguments for a particular style
-
-.. parsed-literal::
-
-     *mm3/switch3/coulgauss/long* args = cutoff (cutoff2) width
-       cutoff  = global cutoff for MM3 (and Coulombic if only 1 arg) (distance units)
-       cutoff2 = global cutoff for Coulombic (optional) (distance units)
-       width  = width parameter of the smoothing function (distance units)
-
-Examples
-""""""""
-
-.. code-block:: LAMMPS
-
-   pair_style mm3/switch3/coulgauss/long    12.0 3.0
-   pair_coeff 1  0.2 2.5 1.2
-
-   pair_style mm3/switch3/coulgauss/long   12.0 10.0 3.0
-   pair_coeff 1  0.2 2.5 1.2
-
-Description
-"""""""""""
-
-The *mm3/switch3/coulgauss/long* style evaluates the MM3
-vdW potential :ref:`(Allinger) <mm3-allinger1989>`
-
-.. math::
-
-   E & = \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\
-   r_{v,ij} & =  r_{v,i} + r_{v,j} \\
-   \epsilon_{ij} & = \sqrt{\epsilon_i \epsilon_j}
-
-, which goes smoothly to zero at the cutoff r_c as defined
-by the switching function
-
-.. math::
-
-   S_3(r) = \left\lbrace \begin{array}{ll}
-                       1 & \quad\mathrm{if}\quad r < r_\mathrm{c} - w \\
-                       3x^2 - 2x^3 & \quad\mathrm{if}\quad r < r_\mathrm{c} \quad\mathrm{with\quad} x=\frac{r_\mathrm{c} - r}{w} \\
-                       0 & \quad\mathrm{if}\quad r >= r_\mathrm{c}
-                   \end{array} \right.
-
-where w is the width defined in the arguments. This potential
-is combined with Coulomb interaction between Gaussian charge densities:
-
-.. math::
-
-   E = \frac{q_i q_j \mathrm{erf}\left( r/\sqrt{\gamma_1^2+\gamma_2^2} \right) }{\epsilon r_{ij}}
-
-where :math:`q_i` and :math:`q_j` are the charges on the 2 atoms,
-epsilon is the dielectric constant which can be set by the
-:doc:`dielectric <dielectric>` command, ::math:`\gamma_i` and
-:math:`\gamma_j` are the widths of the Gaussian charge distribution and
-erf() is the error-function.  This style has to be used in conjunction
-with the :doc:`kspace_style <kspace_style>` command
-
-If one cutoff is specified it is used for both the vdW and Coulomb
-terms.  If two cutoffs are specified, the first is used as the cutoff
-for the vdW terms, and the second is the cutoff for the Coulombic term.
-
-The following coefficients must be defined for each pair of atoms
-types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
-above, or in the data file or restart files read by the
-:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
-commands:
-
-* :math:`\epsilon` (energy)
-* :math:`r_v` (distance)
-* :math:`\gamma` (distance)
-
-----------
-
-Mixing, shift, table, tail correction, restart, rRESPA info
-"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-
-Mixing rules are fixed for this style as defined above.
-
-Shifting the potential energy is not necessary because the switching
-function ensures that the potential is zero at the cut-off.
-
-Restrictions
-""""""""""""
-
-These styles are part of the USER-YAFF package.  They are only
-enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-Related commands
-""""""""""""""""
-
-:doc:`pair_coeff <pair_coeff>`
-
-Default
-"""""""
-
-none

doc/src/pair_polymorphic.rst

@@ -319,7 +319,7 @@ This pair style is part of the MANYBODY 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 pair potential requires the :doc:`newtion <newton>` setting to be
+This pair potential requires the :doc:`newton <newton>` setting to be
 "on" for pair interactions.
 
 The potential files provided with LAMMPS (see the potentials directory)

doc/src/pair_style.rst

@@ -250,7 +250,7 @@ accelerated styles exist.
 * :doc:`mgpt <pair_mgpt>` - simplified model generalized pseudopotential theory (MGPT) potential
 * :doc:`mesont/tpm <pair_mesont_tpm>` - nanotubes mesoscopic force field
 * :doc:`mie/cut <pair_mie>` - Mie potential
-* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>` - smoothed MM3 vdW potential with Gaussian electrostatics
+* :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>` - smoothed MM3 vdW potential with Gaussian electrostatics
 * :doc:`momb <pair_momb>` - Many-Body Metal-Organic (MOMB) force field
 * :doc:`morse <pair_morse>` - Morse potential
 * :doc:`morse/smooth/linear <pair_morse>` - linear smoothed Morse potential

doc/src/pair_vashishta.rst

@@ -217,7 +217,7 @@ This pair style can only be used via the *pair* keyword of the
 Restrictions
 """"""""""""
 
-These pair style are part of the MANYBODY package.  They is only
+These pair styles are part of the MANYBODY package.  They are only
 enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
 
 These pair styles requires the :doc:`newton <newton>` setting to be "on"

doc/src/plugin.rst

@@ -0,0 +1,90 @@
+.. index:: plugin
+
+plugin command
+==============
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   plugin command args
+
+* command = *load* or *unload* or *list* or *clear*
+* args = list of arguments for a particular plugin command
+
+  .. parsed-literal::
+
+     *load* file = load plugin(s) from shared object in *file*
+     *unload* style name = unload plugin *name* of style *style*
+         *style* = *pair* or *bond* or *angle* or *dihedral* or *improper* or *compute* or *fix* or *region* or *command*
+     *list* = print a list of currently loaded plugins
+     *clear* = unload all currently loaded plugins
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   plugin load morse2plugin.so
+   plugin unload pair morse2/omp
+   plugin unload command hello
+   plugin list
+   plugin clear
+
+Description
+"""""""""""
+
+The plugin command allows to load (and unload) additional styles and
+commands into a LAMMPS binary from so-called dynamic shared object (DSO)
+files.  This enables to add new functionality to an existing LAMMPS
+binary without having to recompile and link the entire executable.
+
+The *load* command will load and initialize all plugins contained in the
+plugin DSO with the given filename.  A message with information the
+plugin style and name and more will be printed.  Individual DSO files
+may contain multiple plugins.  More details about how to write and
+compile the plugin DSO is given in programmer's guide part of the manual
+under :doc:`Developer_plugins`.
+
+The *unload* command will remove the given style or the given name from
+the list of available styles.  If the plugin style is currently in use,
+that style instance will be deleted.
+
+The *list* command will print a list of the loaded plugins and their
+styles and names.
+
+The *clear* command will unload all currently loaded plugins.
+
+
+Restrictions
+""""""""""""
+
+The *plugin* command is part of the PLUGIN package.  It is
+only enabled if LAMMPS was built with that package.
+See the :doc:`Build package <Build_package>` doc page for
+more info. Plugins are not available on Windows.
+
+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
+to work when the plugin was compiled with a different MPI library
+or different compilation settings or a different LAMMPS version.
+There are no checks, so if there is a mismatch the plugin object
+will either not load or data corruption and crashes may happen.
+
+
+Related commands
+""""""""""""""""
+
+none
+
+
+Default
+"""""""
+
+none

doc/src/rerun.rst

@@ -15,7 +15,7 @@ Syntax
 
   .. parsed-literal::
 
-     keyword = *first* or *last* or *every* or *skip* or *start* or *stop* or *dump*
+     keyword = *first* or *last* or *every* or *skip* or *start* or *stop* or *post* or *dump*
       *first* args = Nfirst
         Nfirst = dump timestep to start on
       *last* args = Nlast
@@ -28,6 +28,7 @@ Syntax
         Nstart = timestep on which pseudo run will start
       *stop* args = Nstop
         Nstop = timestep to which pseudo run will end
+      *post* value = *yes* or *no*
       *dump* args = same as :doc:`read_dump <read_dump>` command starting with its field arguments
 
 Examples
@@ -154,6 +155,10 @@ Also note that an error will occur if you read a snapshot from the
 dump file with a timestep value larger than the *stop* setting you
 have specified.
 
+The *post* keyword can be used to minimize the output to the screen that
+happens after a *rerun* command, similar to the post keyword of the
+:doc:`run command <run>`. It is set to *no* by default.
+
 The *dump* keyword is required and must be the last keyword specified.
 Its arguments are passed internally to the :doc:`read_dump <read_dump>`
 command.  The first argument following the *dump* keyword should be
@@ -226,4 +231,4 @@ Default
 
 The option defaults are first = 0, last = a huge value (effectively
 infinity), start = same as first, stop = same as last, every = 0, skip
-= 1;
+= 1, post = no;

doc/src/units.rst

@@ -87,7 +87,7 @@ energy is a derived unit (in SI units you equivalently have the relation
 * charge = reduced LJ charge, where :math:`q^* = q \frac{1}{\sqrt{4 \pi \varepsilon_0 \sigma \epsilon}}`
 * dipole = reduced LJ dipole, moment where :math:`\mu^* = \mu \frac{1}{\sqrt{4 \pi \varepsilon_0 \sigma^3 \epsilon}}`
 * electric field = force/charge, where :math:`E^* = E \frac{\sqrt{4 \pi \varepsilon_0 \sigma \epsilon} \sigma}{\epsilon}`
-* density = mass/volume, where :math:`\rho^* = \rho \sigma^{dim}`
+* density = mass/volume, where :math:`\rho^* = \rho \frac{\sigma^{dim}}{m}`
 
 Note that for LJ units, the default mode of thermodynamic output via
 the :doc:`thermo_style <thermo_style>` command is to normalize all

doc/src/variable.rst

@@ -65,8 +65,8 @@ Syntax
                            bound(group,dir,region), gyration(group,region), ke(group,reigon),
                            angmom(group,dim,region), torque(group,dim,region),
                            inertia(group,dimdim,region), omega(group,dim,region)
-         special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x)
+         special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name)
-         feature functions = is_active(category,feature,exact), is_defined(category,id,exact)
+         feature functions = is_available(category,feature), is_active(category,feature), is_defined(category,id)
          atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
          atom vector = id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q
          compute references = c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i]
@@ -429,7 +429,7 @@ argument.  For *equal*\ -style variables the formula computes a scalar
 quantity, which becomes the value of the variable whenever it is
 evaluated.  For *vector*\ -style variables the formula must compute a
 vector of quantities, which becomes the value of the variable whenever
-it is evaluated.  The calculated vector can be on length one, but it
+it is evaluated.  The calculated vector can be of length one, but it
 cannot be a simple scalar value like that produced by an equal-style
 compute.  I.e. the formula for a vector-style variable must have at
 least one quantity in it that refers to a global vector produced by a
@@ -821,6 +821,10 @@ Special Functions
 Special functions take specific kinds of arguments, meaning their
 arguments cannot be formulas themselves.
 
+The is_file(x) function is a test whether 'x' is a (readable) file
+and returns 1 in this case, otherwise it returns 0.  For that 'x'
+is taken as a literal string and must not have any blanks in it.
+
 The sum(x), min(x), max(x), ave(x), trap(x), and slope(x) functions
 each take 1 argument which is of the form "c_ID" or "c_ID[N]" or
 "f_ID" or "f_ID[N]" or "v_name".  The first two are computes and the

doc/utils/sphinx-config/LAMMPSLexer.py

@@ -40,7 +40,7 @@ class LAMMPSLexer(RegexLexer):
             (r'compute\s+', Keyword, 'compute'),
             (r'dump\s+', Keyword, 'dump'),
             (r'region\s+', Keyword, 'region'),
-            (r'variable\s+', Keyword, 'variable'),
+            (r'^\s*variable\s+', Keyword, 'variable_cmd'),
             (r'group\s+', Keyword, 'group'),
             (r'change_box\s+', Keyword, 'change_box'),
             (r'uncompute\s+', Keyword, 'uncompute'),
@@ -51,6 +51,7 @@ class LAMMPSLexer(RegexLexer):
             (r'#.*?\n', Comment),
             ('"', String, 'string'),
             ('\'', String, 'single_quote_string'),
+            (r'[0-9]+:[0-9]+(:[0-9]+)?', Number),
             (r'[0-9]+(\.[0-9]+)?([eE]\-?[0-9]+)?', Number),
             ('\$?\(', Name.Variable, 'expression'),
             ('\$\{', Name.Variable, 'variable'),
@@ -58,6 +59,7 @@ class LAMMPSLexer(RegexLexer):
             (r'\$[\w_]+', Name.Variable),
             (r'\s+', Whitespace),
             (r'[\+\-\*\^\|\/\!%&=<>]', Operator),
+            (r'[\~\.\w_:,@\-\/\\0-9]+', Text),
         ],
         'keywords' : [
             (words(LAMMPS_COMMANDS, suffix=r'\b', prefix=r'^'), Keyword)
@@ -99,7 +101,7 @@ class LAMMPSLexer(RegexLexer):
             (r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
             default('#pop')
         ],
-        'variable' : [
+        'variable_cmd' : [
             (r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
             default('#pop')
         ],

doc/utils/sphinx-config/false_positives.txt

@@ -1588,6 +1588,7 @@ lammps
 Lammps
 LAMMPS
 lammpsplot
+lammpsplugin
 Lampis
 Lamoureux
 Lanczos

examples/deposit/in.deposit.molecule.rigid-small

@@ -0,0 +1,56 @@
+# sample surface deposition script for molecules
+
+units		lj
+atom_style      bond
+boundary        p p f
+
+lattice		fcc 1.0
+region          box block 0 5 0 5 0 10
+create_box      3 box bond/types 1 extra/bond/per/atom 1
+
+region		substrate block INF INF INF INF INF 3
+create_atoms	1 region substrate
+
+pair_style	lj/cut 2.5
+pair_coeff	* * 1.0 1.0
+pair_coeff	1 2 1.0 1.0 5.0
+mass		* 1.0
+
+bond_style	harmonic
+bond_coeff      1 5.0 1.0
+
+neigh_modify	delay 0
+
+molecule        dimer molecule.dimer
+region          slab block 0 5 0 5 8 9
+
+group		addatoms empty
+region          mobile block 0 5 0 5 2 INF
+group		mobile region mobile
+
+compute	add addatoms temp
+compute_modify	add dynamic/dof yes extra/dof 0
+
+fix		1 addatoms rigid/small molecule mol dimer
+fix		2 mobile langevin 0.1 0.1 0.1 587283
+fix		3 mobile nve
+
+fix		4 addatoms deposit 100 0 100 12345 region slab near 1.0 &
+                mol dimer vz -1.0 -1.0 rigid 1
+fix		5 addatoms wall/reflect zhi EDGE
+
+thermo_style	custom step atoms temp epair etotal press
+thermo          100
+thermo_modify	temp add lost/bond ignore lost warn
+
+#dump		1 all atom 50 dump.deposit.atom
+
+#dump		2 all image 50 image.*.jpg type type &
+#		axes yes 0.8 0.02 view 80 -30
+#dump_modify	2 pad 5
+
+#dump		3 all movie 50 tmp.mpg type type &
+#		axes yes 0.8 0.02 view 80 -30
+#dump_modify	3 pad 5
+
+run             10000

examples/deposit/in.deposit.molecule.shake

@@ -21,11 +21,11 @@ bond_coeff      1 5.0 1.0
 
 neigh_modify	delay 0
 
-group		addatoms type 2
+group		addatoms empty
 region          mobile block 0 5 0 5 2 INF
 group		mobile region mobile
 
-compute		add addatoms temp
+compute	add addatoms temp
 compute_modify	add dynamic/dof yes extra/dof 0
 
 fix		1 addatoms nve

examples/deposit/log.10Mar21.deposit.molecule.rigid-small.g++.1

@@ -0,0 +1,218 @@
+LAMMPS (10 Mar 2021)
+  using 1 OpenMP thread(s) per MPI task
+# sample surface deposition script for molecules
+
+units		lj
+atom_style      bond
+boundary        p p f
+
+lattice		fcc 1.0
+Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
+region          box block 0 5 0 5 0 10
+create_box      3 box bond/types 1 extra/bond/per/atom 1
+Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011)
+  1 by 1 by 1 MPI processor grid
+
+region		substrate block INF INF INF INF INF 3
+create_atoms	1 region substrate
+Created 350 atoms
+  create_atoms CPU = 0.001 seconds
+
+pair_style	lj/cut 2.5
+pair_coeff	* * 1.0 1.0
+pair_coeff	1 2 1.0 1.0 5.0
+mass		* 1.0
+
+bond_style	harmonic
+bond_coeff      1 5.0 1.0
+
+neigh_modify	delay 0
+
+molecule        dimer molecule.dimer
+Read molecule template dimer:
+  1 molecules
+  2 atoms with max type 3
+  1 bonds with max type 1
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+region          slab block 0 5 0 5 8 9
+
+group		addatoms empty
+0 atoms in group addatoms
+region          mobile block 0 5 0 5 2 INF
+group		mobile region mobile
+150 atoms in group mobile
+
+compute	add addatoms temp
+compute_modify	add dynamic/dof yes extra/dof 0
+
+fix		1 addatoms rigid/small molecule mol dimer
+  create bodies CPU = 0.000 seconds
+  0 rigid bodies with 0 atoms
+  1.0000000 = max distance from body owner to body atom
+fix		2 mobile langevin 0.1 0.1 0.1 587283
+fix		3 mobile nve
+
+fix		4 addatoms deposit 100 0 100 12345 region slab near 1.0                 mol dimer vz -1.0 -1.0 rigid 1
+fix		5 addatoms wall/reflect zhi EDGE
+
+thermo_style	custom step atoms temp epair etotal press
+thermo          100
+thermo_modify	temp add lost/bond ignore lost warn
+WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468)
+
+#dump		1 all atom 50 dump.deposit.atom
+
+#dump		2 all image 50 image.*.jpg type type #		axes yes 0.8 0.02 view 80 -30
+#dump_modify	2 pad 5
+
+#dump		3 all movie 50 tmp.mpg type type #		axes yes 0.8 0.02 view 80 -30
+#dump_modify	3 pad 5
+
+run             10000
+WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.3
+  ghost atom cutoff = 5.3
+  binsize = 2.65, bins = 3 3 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.929 | 5.929 | 5.929 Mbytes
+Step Atoms Temp E_pair TotEng Press 
+       0      350            0   -6.9215833   -6.9215833   -1.0052629 
+     100      352    1.0079368   -6.8875167   -6.8803581  -0.73353914 
+     200      354    1.0081552   -6.8594643   -6.8452248  -0.70421276 
+     300      356    1.0085803   -6.8171524   -6.7959042   -0.6917826 
+     400      358    1.0099188   -6.7852701   -6.7570601  -0.70371699 
+     500      360    1.0140221   -6.7493429   -6.7141338  -0.68415307 
+     600      362     1.026148   -6.7105231   -6.6680032  -0.68314418 
+     700      364    1.0683344   -6.6725162    -6.621154  -0.65747369 
+     800      366    1.0958952   -6.6412275   -6.5813425  -0.68789614 
+     900      368    1.1250033   -6.6101882    -6.541404  -0.66674346 
+    1000      370    1.2326373   -6.5993719   -6.5160856   -0.6968868 
+    1100      372    1.1397426   -6.5912861   -6.5070309  -0.63330356 
+    1200      374    1.0514292   -6.5905747   -6.5062354  -0.71020362 
+    1300      376     1.003296   -6.5747765   -6.4880555  -0.65459732 
+    1400      378   0.82999289   -6.5681797   -6.4913285  -0.60438126 
+    1500      380   0.90239175    -6.575298   -6.4862461  -0.66528725 
+    1600      382   0.86399799   -6.5692206   -6.4787496  -0.65027781 
+    1700      384   0.64747231   -6.5644237   -6.4927634   -0.6304614 
+    1800      386   0.74288971   -6.5515735   -6.4649672  -0.67772325 
+    1900      388    0.7257202   -6.5565091   -6.4676644  -0.66173549 
+    2000      390   0.73381036   -6.5631515   -6.4690733  -0.64685916 
+    2100      392   0.76476562   -6.5574124   -6.4549885  -0.68866192 
+    2200      394   0.65932468   -6.5511557    -6.459118  -0.71728829 
+    2300      396   0.70269509   -6.5728146   -6.4707819  -0.64362081 
+    2400      398   0.60528919   -6.5845991   -6.4933494  -0.63956327 
+    2500      400   0.51025744   -6.5812452   -6.5015175  -0.68706961 
+    2600      402    0.5245131   -6.6003894   -6.5155801  -0.68972215 
+    2700      404   0.46330251   -6.5659175   -6.4885092  -0.72870942 
+    2800      406   0.48039778   -6.5715192    -6.488692    -0.753758 
+    2900      408   0.53698616   -6.5813154   -6.4858951  -0.67117541 
+    3000      410   0.50231419   -6.5886963   -6.4968096  -0.71905351 
+    3100      412   0.49420225    -6.596733   -6.5037702  -0.65947518 
+    3200      414   0.42703699   -6.5879338   -6.5054146  -0.80033546 
+    3300      416   0.44306009    -6.580249   -6.4923825  -0.76503083 
+    3400      418   0.55620672   -6.5923388   -6.4792346  -0.69367877 
+    3500      420   0.39815033   -6.5911154   -6.5081674  -0.65569211 
+    3600      422   0.44197847   -6.6026382   -6.5083774  -0.73299102 
+    3700      424   0.45049389   -6.6060616   -6.5077817   -0.7552914 
+    3800      426   0.43047295   -6.6079275     -6.51193  -0.71501328 
+    3900      428   0.43779129   -6.6099306   -6.5102001  -0.71539515 
+    4000      430   0.41113503   -6.6123009   -6.5166881  -0.74177096 
+    4100      432   0.32800011   -6.5983566   -6.5205325  -0.71688103 
+    4200      434   0.39168203   -6.6110342   -6.5162724  -0.78927697 
+    4300      436   0.48151013   -6.6183315   -6.4996106  -0.70523035 
+    4400      438   0.45391027   -6.6331732   -6.5191775   -0.7270855 
+    4500      440     0.349126   -6.6091657   -6.5199006  -0.76974115 
+    4600      442   0.43375023   -6.6219188   -6.5090653  -0.74576212 
+    4700      444   0.40071749   -6.6184164   -6.5123707  -0.71919052 
+    4800      446     0.414292   -6.6298132   -6.5183445  -0.76237313 
+    4900      448   0.44210681   -6.6364174   -6.5155288  -0.78753121 
+    5000      450   0.36101771   -6.6232703   -6.5229876  -0.73927083 
+    5100      452   0.41481171   -6.6442404   -6.5272305  -0.76316209 
+    5200      454   0.40283527   -6.6512252   -6.5358759  -0.79645689 
+    5300      456    0.3642061   -6.6530346   -6.5472072  -0.77458364 
+    5400      458   0.38449826   -6.6514864   -6.5381518  -0.73083784 
+    5500      460   0.42559408   -6.6769326   -6.5497169  -0.78932279 
+    5600      462   0.38905756   -6.6698705   -6.5519743  -0.77118812 
+    5700      464   0.38354955   -6.6706904   -6.5528977  -0.75067129 
+    5800      466   0.36760943   -6.6942519   -6.5798669    -0.685487 
+    5900      468   0.30783118   -6.6838159   -6.5867965  -0.79233808 
+    6000      470   0.33145368   -6.6733504   -6.5675673  -0.84390449 
+    6100      472   0.39252324   -6.6912189   -6.5643973  -0.83342022 
+    6200      474   0.32342144   -6.6906083   -6.5848481  -0.71262158 
+    6300      476   0.34445238   -6.7008453   -6.5868721  -0.76650756 
+    6400      478   0.38152782   -6.7017838   -6.5740758  -0.77113022 
+    6500      480   0.37540166   -6.7119996   -6.5849105  -0.79907635 
+    6600      482    0.3579419   -6.7034721   -6.5809401   -0.8141269 
+    6700      484   0.33538235   -6.6916682    -6.575601  -0.83265486 
+    6800      486   0.34081871   -6.6931924    -6.573976  -0.80582583 
+    6900      488    0.3555283   -6.6939997   -6.5683263  -0.74771423 
+    7000      490    0.3543769   -6.7093364   -6.5827732  -0.77643516 
+    7100      492   0.31263107    -6.698361   -6.5855723  -0.73108333 
+    7200      494      0.32107   -6.6959056   -6.5789166   -0.7575478 
+    7300      496   0.32908165   -6.7137605    -6.592677  -0.86538023 
+    7400      498   0.32539571   -6.7030353   -6.5821554  -0.79337428 
+    7500      500   0.33902577   -6.7078178   -6.5806832  -0.85408988 
+    7600      502   0.35530921    -6.707507   -6.5730274  -0.79914613 
+    7700      504   0.32391812   -6.6978823   -6.5741635  -0.78603595 
+    7800      506   0.36390015   -6.7151325   -6.5748943  -0.83164222 
+    7900      508    0.3372561   -6.7086718   -6.5775535   -0.7949992 
+    8000      510   0.36612946   -6.7225238   -6.5789437  -0.80322866 
+    8100      512   0.34622305   -6.7229825   -6.5860486  -0.70478659 
+    8200      514    0.3212233   -6.7202524   -6.5921381  -0.91836713 
+    8300      516    0.3402461    -6.721488   -6.5846642  -0.88273592 
+    8400      518   0.34070258   -6.7268378   -6.5887152  -0.76057264 
+    8500      520   0.36267747    -6.744602   -6.5963924  -0.81051317 
+    8600      522    0.3439948   -6.7376267    -6.595943  -0.84600203 
+    8700      524   0.30960289   -6.7276471   -6.5991382  -0.90965986 
+    8800      526   0.28868972   -6.7159628    -6.595218    -0.876093 
+    8900      528   0.31020216   -6.7162903   -6.5855707  -0.83193125 
+    9000      530   0.31836275   -6.7171479   -6.5819939  -0.82093897 
+    9100      532   0.32543293    -6.724167   -6.5850016   -0.7690143 
+    9200      534   0.32644265   -6.7139575   -6.5733549  -0.86903096 
+    9300      536   0.33050759   -6.7254715   -6.5821077  -0.94504522 
+    9400      538   0.30372582   -6.7139931   -6.5813247  -0.91128612 
+    9500      540   0.32943659   -6.7206223   -6.5757312  -0.87818439 
+    9600      542   0.30911968    -6.708091   -6.5712114  -0.79092372 
+    9700      544   0.33909826   -6.7222948   -6.5711342  -0.80266151 
+    9800      546   0.29015141   -6.7086869   -6.5784908  -0.87763769 
+    9900      548   0.33838474   -6.7384955   -6.5856667  -0.85630604 
+   10000      550   0.30213198   -6.7338924   -6.5965597  -0.75738882 
+Loop time of 17.2852 on 1 procs for 10000 steps with 550 atoms
+
+Performance: 249924.414 tau/day, 578.529 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 9.637      | 9.637      | 9.637      |   0.0 | 55.75
+Bond    | 0.025444   | 0.025444   | 0.025444   |   0.0 |  0.15
+Neigh   | 4.6852     | 4.6852     | 4.6852     |   0.0 | 27.11
+Comm    | 0.65556    | 0.65556    | 0.65556    |   0.0 |  3.79
+Output  | 0.0099883  | 0.0099883  | 0.0099883  |   0.0 |  0.06
+Modify  | 2.1895     | 2.1895     | 2.1895     |   0.0 | 12.67
+Other   |            | 0.08248    |            |       |  0.48
+
+Nlocal:        550.000 ave         550 max         550 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        2367.00 ave        2367 max        2367 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:        36781.0 ave       36781 max       36781 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 36781
+Ave neighs/atom = 66.874545
+Ave special neighs/atom = 0.36363636
+Neighbor list builds = 840
+Dangerous builds = 0
+Total wall time: 0:00:17

examples/deposit/log.10Mar21.deposit.molecule.rigid-small.g++.4

@@ -0,0 +1,218 @@
+LAMMPS (10 Mar 2021)
+  using 1 OpenMP thread(s) per MPI task
+# sample surface deposition script for molecules
+
+units		lj
+atom_style      bond
+boundary        p p f
+
+lattice		fcc 1.0
+Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
+region          box block 0 5 0 5 0 10
+create_box      3 box bond/types 1 extra/bond/per/atom 1
+Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011)
+  1 by 1 by 4 MPI processor grid
+
+region		substrate block INF INF INF INF INF 3
+create_atoms	1 region substrate
+Created 350 atoms
+  create_atoms CPU = 0.139 seconds
+
+pair_style	lj/cut 2.5
+pair_coeff	* * 1.0 1.0
+pair_coeff	1 2 1.0 1.0 5.0
+mass		* 1.0
+
+bond_style	harmonic
+bond_coeff      1 5.0 1.0
+
+neigh_modify	delay 0
+
+molecule        dimer molecule.dimer
+Read molecule template dimer:
+  1 molecules
+  2 atoms with max type 3
+  1 bonds with max type 1
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+region          slab block 0 5 0 5 8 9
+
+group		addatoms empty
+0 atoms in group addatoms
+region          mobile block 0 5 0 5 2 INF
+group		mobile region mobile
+150 atoms in group mobile
+
+compute	add addatoms temp
+compute_modify	add dynamic/dof yes extra/dof 0
+
+fix		1 addatoms rigid/small molecule mol dimer
+  create bodies CPU = 0.006 seconds
+  0 rigid bodies with 0 atoms
+  1.0000000 = max distance from body owner to body atom
+fix		2 mobile langevin 0.1 0.1 0.1 587283
+fix		3 mobile nve
+
+fix		4 addatoms deposit 100 0 100 12345 region slab near 1.0                 mol dimer vz -1.0 -1.0 rigid 1
+fix		5 addatoms wall/reflect zhi EDGE
+
+thermo_style	custom step atoms temp epair etotal press
+thermo          100
+thermo_modify	temp add lost/bond ignore lost warn
+WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468)
+
+#dump		1 all atom 50 dump.deposit.atom
+
+#dump		2 all image 50 image.*.jpg type type #		axes yes 0.8 0.02 view 80 -30
+#dump_modify	2 pad 5
+
+#dump		3 all movie 50 tmp.mpg type type #		axes yes 0.8 0.02 view 80 -30
+#dump_modify	3 pad 5
+
+run             10000
+WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.3
+  ghost atom cutoff = 5.3
+  binsize = 2.65, bins = 3 3 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.255 | 5.852 | 6.302 Mbytes
+Step Atoms Temp E_pair TotEng Press 
+       0      350            0   -6.9215833   -6.9215833   -1.0052629 
+     100      352    1.0079368   -6.8946578   -6.8874992  -0.73775337 
+     200      354    1.0081552   -6.8645575    -6.850318  -0.69629729 
+     300      356    1.0085803    -6.821677   -6.8004288  -0.69532657 
+     400      358    1.0099188   -6.7837923   -6.7555822  -0.68879568 
+     500      360    1.0140221   -6.7446709   -6.7094618  -0.72991641 
+     600      362     1.026146   -6.7129201   -6.6704003  -0.67063836 
+     700      364    1.0683193   -6.6776523   -6.6262908  -0.65572472 
+     800      366    1.0958893   -6.6402029   -6.5803182  -0.66307281 
+     900      368    1.1231768   -6.6050912   -6.5364187  -0.64076928 
+    1000      370    1.1976283   -6.5942507   -6.5133299  -0.69249019 
+    1100      372    1.0506263   -6.5772313    -6.499564  -0.63072939 
+    1200      374   0.93724351   -6.5732957   -6.4981157  -0.64963897 
+    1300      376   0.93899686   -6.5578406   -6.4766773  -0.65096289 
+    1400      378    0.8704974   -6.5468498   -6.4662482  -0.67613931 
+    1500      380   0.84490693   -6.5401094   -6.4567304  -0.64385968 
+    1600      382    0.9243154   -6.5611604   -6.4643734  -0.62096869 
+    1700      384   0.67202953   -6.5590557   -6.4846775  -0.67807465 
+    1800      386    0.8712464   -6.5654953   -6.4639251  -0.65860236 
+    1900      388   0.70011668   -6.5808612    -6.495151  -0.65146463 
+    2000      390   0.64019295   -6.5652168   -6.4831408  -0.70291888 
+    2100      392   0.67578277   -6.5596196    -6.469113  -0.63315981 
+    2200      394   0.60785287    -6.558941   -6.4740885   -0.7133822 
+    2300      396    0.8155086   -6.5756022   -6.4571887  -0.69176417 
+    2400      398   0.69028748   -6.5875474    -6.483484  -0.63743938 
+    2500      400    0.5013913   -6.5871851   -6.5088427  -0.65872179 
+    2600      402   0.51268385   -6.5782356    -6.495339  -0.74289067 
+    2700      404   0.57745388   -6.5815718   -6.4850912  -0.67922914 
+    2800      406   0.47317895   -6.5974978   -6.5159152  -0.64657562 
+    2900      408   0.50593124   -6.6019054   -6.5120034  -0.64211427 
+    3000      410   0.44423233   -6.5956684   -6.5144064  -0.66526127 
+    3100      412   0.40808865   -6.5949863   -6.5182221  -0.62722445 
+    3200      414   0.40692632   -6.5866689   -6.5080358  -0.76440608 
+    3300      416   0.43908529   -6.5851721   -6.4980939  -0.69345883 
+    3400      418   0.53825907   -6.5880076    -6.478553  -0.69726204 
+    3500      420   0.46363057   -6.6135193   -6.5169296  -0.58015901 
+    3600      422   0.39262699    -6.621857   -6.5381213  -0.74921264 
+    3700      424   0.42679205   -6.6146579   -6.5215488  -0.69040431 
+    3800      426   0.38997492   -6.6139725   -6.5270063  -0.78237667 
+    3900      428    0.5222531   -6.6403886   -6.5214174  -0.78298122 
+    4000      430   0.47841128   -6.6502681   -6.5390097  -0.68125967 
+    4100      432   0.44609186   -6.6610827   -6.5552392  -0.81157037 
+    4200      434    0.4591431   -6.6858064   -6.5747234  -0.79000753 
+    4300      436   0.40690573   -6.6800195    -6.579693   -0.6781696 
+    4400      438   0.43023944   -6.6849804   -6.5769294   -0.7620548 
+    4500      440   0.40889421   -6.6783124   -6.5737656   -0.8577593 
+    4600      442   0.41452051   -6.6968565   -6.5890061  -0.70427746 
+    4700      444   0.36740394   -6.6920933   -6.5948636  -0.69303162 
+    4800      446   0.40112316   -6.6869413   -6.5790158  -0.84792822 
+    4900      448   0.42437165   -6.6789835   -6.5629444  -0.82278531 
+    5000      450   0.41822898   -6.6770254   -6.5608507  -0.72224472 
+    5100      452   0.38445688   -6.6738997   -6.5654522   -0.7022418 
+    5200      454   0.39998238   -6.6670536   -6.5525212  -0.73639959 
+    5300      456   0.39471029   -6.6728592   -6.5581681  -0.70419927 
+    5400      458   0.35817807   -6.6702423   -6.5646658  -0.81657219 
+    5500      460   0.37151428   -6.6690855    -6.558035  -0.78076653 
+    5600      462   0.32642513   -6.6622352   -6.5633185  -0.69118644 
+    5700      464   0.43665879   -6.6811227   -6.5470195  -0.77500043 
+    5800      466   0.40704721   -6.6858874   -6.5592311  -0.72683597 
+    5900      468    0.3861903   -6.6896953   -6.5679794  -0.78001958 
+    6000      470   0.34073346   -6.6833717    -6.574627  -0.78170837 
+    6100      472   0.39953874   -6.7083668   -6.5792785  -0.81791744 
+    6200      474   0.36685189   -6.7114648   -6.5915027  -0.80545451 
+    6300      476   0.35851799   -6.7261023    -6.607475  -0.77350495 
+    6400      478   0.41771823   -6.7427425   -6.6029205  -0.85319003 
+    6500      480   0.36519478    -6.732662   -6.6090284  -0.78712805 
+    6600      482   0.30669571   -6.7269784   -6.6219892  -0.76698134 
+    6700      484    0.3384344   -6.7261448   -6.6090213  -0.79935239 
+    6800      486   0.36420902   -6.7320259   -6.6046277  -0.84650552 
+    6900      488   0.40181215   -6.7490619   -6.6070279  -0.75753238 
+    7000      490   0.30536068   -6.7398924   -6.6308351  -0.73210162 
+    7100      492   0.28813004   -6.7257287   -6.6217794  -0.92178435 
+    7200      494   0.30956277   -6.7342688   -6.6214727  -0.77532949 
+    7300      496   0.36625115   -6.7528159   -6.6180561  -0.76247835 
+    7400      498   0.30935271   -6.7401433   -6.6252231  -0.82809158 
+    7500      500   0.33222282   -6.7410421   -6.6164585  -0.81948236 
+    7600      502   0.33318693   -6.7488106    -6.622704  -0.82395904 
+    7700      504   0.34570598   -6.7547394   -6.6226989  -0.85644369 
+    7800      506   0.34587242   -6.7446006   -6.6113099  -0.82476511 
+    7900      508    0.2969166   -6.7305429   -6.6151078   -0.8210214 
+    8000      510   0.32355758   -6.7437629   -6.6168776  -0.81719054 
+    8100      512   0.33784479   -6.7545537   -6.6209335  -0.78082067 
+    8200      514   0.32351289   -6.7525032   -6.6234757  -0.87093587 
+    8300      516   0.31900134   -6.7550972   -6.6268166  -0.79928704 
+    8400      518    0.3338521   -6.7588757   -6.6235302  -0.81699503 
+    8500      520   0.33115184   -6.7614854   -6.6261589  -0.79958489 
+    8600      522   0.29478929   -6.7490188   -6.6276018  -0.81954456 
+    8700      524     0.267993   -6.7467764   -6.6355389  -0.76642994 
+    8800      526   0.28792085   -6.7527118   -6.6322887  -0.86911619 
+    8900      528   0.32430992     -6.75901   -6.6223453  -0.87087898 
+    9000      530   0.33151321   -6.7534845   -6.6127478  -0.79309499 
+    9100      532   0.32760982   -6.7599992   -6.6199028   -0.7506309 
+    9200      534   0.32579101   -6.7671489   -6.6268269  -0.94238755 
+    9300      536   0.35144354   -6.7782581    -6.625813  -0.77952234 
+    9400      538   0.33689976   -6.7804455   -6.6332867  -0.75768501 
+    9500      540    0.3052486   -6.7745436   -6.6402908  -0.89621525 
+    9600      542   0.30617581   -6.7648172   -6.6292412  -0.90623541 
+    9700      544   0.30097715   -6.7714379   -6.6372707  -0.85534149 
+    9800      546   0.31297479   -6.7814978   -6.6410604  -0.88651064 
+    9900      548   0.31832347    -6.790661   -6.6468926       -1.006 
+   10000      550   0.29239559   -6.7823137   -6.6494066   -1.0337518 
+Loop time of 34.7661 on 4 procs for 10000 steps with 550 atoms
+
+Performance: 124259.065 tau/day, 287.637 timesteps/s
+73.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0076709  | 3.1286     | 9.1834     | 211.7 |  9.00
+Bond    | 0.0040276  | 0.010416   | 0.022169   |   7.0 |  0.03
+Neigh   | 0.052413   | 1.5948     | 4.885      | 155.3 |  4.59
+Comm    | 4.9736     | 12.242     | 20.073     | 166.2 | 35.21
+Output  | 0.053549   | 0.10104    | 0.21642    |  21.0 |  0.29
+Modify  | 13.435     | 16.191     | 23.851     | 110.0 | 46.57
+Other   |            | 1.499      |            |       |  4.31
+
+Nlocal:        137.500 ave         299 max           2 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Nghost:        1898.75 ave        2679 max         524 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Neighs:        9204.00 ave       23014 max           0 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 36816
+Ave neighs/atom = 66.938182
+Ave special neighs/atom = 0.36363636
+Neighbor list builds = 832
+Dangerous builds = 0
+Total wall time: 0:00:34

examples/gcmc/in.gcmc.co2

@@ -1,4 +1,4 @@
-# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
+# GCMC for CO2 molecular fluid, rigid/small dynamics
 # Rigid CO2 TraPPE model
 # [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
 # mixtures containing alkanes, carbon dioxide and
@@ -7,7 +7,7 @@
 # variables available on command line
 
 variable        mu index -8.1
-variable	disp index 0.5
+variable        disp index 0.5
 variable        temp index 338.0
 variable        lbox index 10.0
 variable        spacing index 5.0
@@ -17,7 +17,7 @@ variable        spacing index 5.0
 units           real
 atom_style      full
 boundary        p p p
-pair_style      lj/cut/coul/long  14 
+pair_style      lj/cut/coul/long  14
 pair_modify     mix arithmetic tail yes
 kspace_style    ewald 0.0001
 bond_style      harmonic
@@ -25,7 +25,7 @@ angle_style     harmonic
 
 # box, start molecules on simple cubic lattice
 
-lattice 	sc ${spacing}
+lattice         sc ${spacing}
 region          box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
 create_box      2 box                       &
                 bond/types 1                &
@@ -34,56 +34,56 @@ create_box      2 box                       &
                 extra/angle/per/atom 1      &
                 extra/special/per/atom 2
 molecule        co2mol CO2.txt
-create_atoms   	0 box mol co2mol 464563 units box
+create_atoms    0 box mol co2mol 464563 units box
-                        
+
-# rigid CO2 TraPPE model 
+# rigid CO2 TraPPE model
 
 pair_coeff      1   1  0.053649   2.8
-pair_coeff      2   2  0.156973   3.05 
+pair_coeff      2   2  0.156973   3.05
-bond_coeff      1       0       1.16   
+bond_coeff      1       0       1.16
-angle_coeff     1       0       180 
+angle_coeff     1       0       180
 
 # masses
 
-mass 1 12.0107 
+mass 1 12.0107
-mass 2 15.9994 
+mass 2 15.9994
 
 # MD settings
 
 group           co2 type 1 2
 neighbor        2.0 bin
 neigh_modify    every 1 delay 10 check yes
-velocity       	all create ${temp} 54654
+velocity        all create ${temp} 54654
 timestep        1.0
 
-# rigid constraints with thermostat 
+# rigid constraints with thermostat
 
-fix             myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
+fix             myrigid co2 rigid/small molecule mol co2mol
 
 # dynamically update  fix rigid/nvt/small temperature ndof
-fix_modify	myrigidnvt dynamic/dof yes
+fix_modify      myrigid dynamic/dof yes
 
 # gcmc
 
 variable        tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
 fix             mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &
-                co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
+                co2mol tfac_insert ${tfac} group co2 rigid myrigid
 
 # atom counts
 
-variable 	carbon atom "type==1"
+variable        carbon atom "type==1"
 variable        oxygen atom "type==2"
-group 		carbon dynamic co2 var carbon
+group           carbon dynamic co2 var carbon
-group 	        oxygen dynamic co2 var oxygen
+group           oxygen dynamic co2 var oxygen
 variable        nC equal count(carbon)
 variable        nO equal count(oxygen)
 
 # output
 
-variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
+variable        tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
-variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
+variable        iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
-variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
+variable        dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
-variable	racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
+variable        racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
 
 # dynamically update default temperature ndof
 compute_modify  thermo_temp dynamic/dof yes

examples/gcmc/log.27Nov18.gcmc.co2.g++.1

@@ -1,196 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
-# Rigid CO2 TraPPE model
-# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
-# mixtures containing alkanes, carbon dioxide and
-# nitrogen AIChE J., 47,1676-1682 (2001)].
-
-# variables available on command line
-
-variable        mu index -8.1
-variable	disp index 0.5
-variable        temp index 338.0
-variable        lbox index 10.0
-variable        spacing index 5.0
-
-# global model settings
-
-units           real
-atom_style      full
-boundary        p p p
-pair_style      lj/cut/coul/long  14
-pair_modify     mix arithmetic tail yes
-kspace_style    ewald 0.0001
-bond_style      harmonic
-angle_style     harmonic
-
-# box, start molecules on simple cubic lattice
-
-lattice 	sc ${spacing}
-lattice 	sc 5.0
-Lattice spacing in x,y,z = 5 5 5
-region          box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
-region          box block 0 10.0 0 ${lbox} 0 ${lbox} units box
-region          box block 0 10.0 0 10.0 0 ${lbox} units box
-region          box block 0 10.0 0 10.0 0 10.0 units box
-create_box      2 box                                       bond/types 1                                angle/types 1                               extra/bond/per/atom 2                       extra/angle/per/atom 1                      extra/special/per/atom 2
-Created orthogonal box = (0 0 0) to (10 10 10)
-  1 by 1 by 1 MPI processor grid
-molecule        co2mol CO2.txt
-Read molecule co2mol:
-  3 atoms with max type 2
-  2 bonds with max type 1
-  1 angles with max type 1
-  0 dihedrals with max type 0
-  0 impropers with max type 0
-create_atoms   	0 box mol co2mol 464563 units box
-Created 24 atoms
-  Time spent = 0.00134993 secs
-
-# rigid CO2 TraPPE model
-
-pair_coeff      1   1  0.053649   2.8
-pair_coeff      2   2  0.156973   3.05
-bond_coeff      1       0       1.16
-angle_coeff     1       0       180
-
-# masses
-
-mass 1 12.0107
-mass 2 15.9994
-
-# MD settings
-
-group           co2 type 1 2
-24 atoms in group co2
-neighbor        2.0 bin
-neigh_modify    every 1 delay 10 check yes
-velocity       	all create ${temp} 54654
-velocity       	all create 338.0 54654
-timestep        1.0
-
-# rigid constraints with thermostat
-
-fix             myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
-fix             myrigidnvt co2 rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
-fix             myrigidnvt co2 rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol
-8 rigid bodies with 24 atoms
-  1.16 = max distance from body owner to body atom
-
-# dynamically update  fix rigid/nvt/small temperature ndof
-fix_modify	myrigidnvt dynamic/dof yes
-
-# gcmc
-
-variable        tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
-fix             mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
-fix             mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
-fix             mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
-fix             mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
-fix             mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
-
-# atom counts
-
-variable 	carbon atom "type==1"
-variable        oxygen atom "type==2"
-group 		carbon dynamic co2 var carbon
-dynamic group carbon defined
-group 	        oxygen dynamic co2 var oxygen
-dynamic group oxygen defined
-variable        nC equal count(carbon)
-variable        nO equal count(oxygen)
-
-# output
-
-variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
-variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
-variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
-variable	racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
-
-# dynamically update default temperature ndof
-compute_modify  thermo_temp dynamic/dof yes
-
-thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
-thermo          1000
-
-# run
-
-run             20000
-Ewald initialization ...
-  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
-  G vector (1/distance) = 0.164636
-  estimated absolute RMS force accuracy = 0.0332064
-  estimated relative force accuracy = 0.0001
-  KSpace vectors: actual max1d max3d = 16 2 62
-                  kxmax kymax kzmax  = 2 2 2
-WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:487)
-0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
-0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
-WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:471)
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 16
-  ghost atom cutoff = 16
-  binsize = 8, bins = 2 2 2
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/cut/coul/long, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 15.62 | 15.62 | 15.62 Mbytes
-Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO 
-       0    364.27579    4238.8631   -9.6809388    13.391989    0.5846359       24            0            0            0            0            8           16 
-    1000     267.9799   -73.919548   -3.6735999    5.8578459   0.36539744       15   0.23663972    0.2494423            0            0            5           10 
-    2000    409.06596   -98.033864   -6.7570039    10.974131   0.43847693       18   0.29379544   0.29816284            0            0            6           12 
-    3000     279.3225   -836.47758   -26.434976    15.819539   0.87695385       36   0.23798567   0.24203908            0            0           12           24 
-    4000     333.6181    606.63478    -30.35312    18.894592   0.87695385       36   0.19121778   0.19481508            0            0           12           24 
-    5000    405.98741   -103.97582   -14.180277    16.942399   0.65771539       27   0.15272841   0.15982952            0            0            9           18 
-    6000     283.5835   -240.01076   -6.7198093     7.607777   0.43847693       18    0.1606796   0.16536735            0            0            6           12 
-    7000    142.00717    154.95914  -0.74192319   0.98769159   0.14615898        6   0.19501993   0.20103405            0            0            2            4 
-    8000    376.67702   -118.12474   -10.774631    13.847899    0.5846359       24   0.20133396   0.20468352            0            0            8           16 
-    9000    305.43166   -1095.8633   -10.388279    9.7112935   0.51155641       21   0.19445239   0.19869334            0            0            7           14 
-   10000    244.08225   -179.31274   -12.974988    8.9732748    0.5846359       24   0.19098971   0.19586397            0            0            8           16 
-   11000    305.03389   -568.94714   -21.745425    14.244887   0.73079488       30   0.18517522   0.18978828            0            0           10           20 
-   12000    318.29735    767.76579   -37.184231    21.189508    1.0231128       42   0.17256426   0.17580267            0            0           14           28 
-   13000    411.21707    433.01125   -4.5149215    8.9889065   0.36539744       15   0.16329385   0.16767604            0            0            5           10 
-   14000    304.29535    148.28607   -2.3505844    6.6516754   0.36539744       15   0.17435868   0.17897674            0            0            5           10 
-   15000    338.00555    2384.1424   -21.438264    17.463859   0.80387436       33   0.17237066   0.17634112            0            0           11           22 
-   16000    613.56062    610.93867 -0.057364228    1.2192718  0.073079488        3   0.17128158    0.1758886            0            0            1            2 
-   17000    432.63323   -980.52384    -15.79844    18.054365   0.65771539       27   0.17145651   0.17504846            0            0            9           18 
-   18000    181.74572   -352.81765   -1.8617959    2.1669979   0.21923846        9   0.17292463   0.17654774            0            0            3            6 
-   19000    208.55292   -248.38735   -4.2287767    4.5588154   0.36539744       15   0.18168324   0.18454331            0            0            5           10 
-   20000    304.73317    -649.9896   -16.532405    12.716924   0.65771539       27   0.18085983   0.18345574            0            0            9           18 
-Loop time of 21.0434 on 1 procs for 20000 steps with 27 atoms
-
-Performance: 82.116 ns/day, 0.292 hours/ns, 950.415 timesteps/s
-98.5% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 2.2373     | 2.2373     | 2.2373     |   0.0 | 10.63
-Bond    | 0.022895   | 0.022895   | 0.022895   |   0.0 |  0.11
-Kspace  | 0.16756    | 0.16756    | 0.16756    |   0.0 |  0.80
-Neigh   | 0.11436    | 0.11436    | 0.11436    |   0.0 |  0.54
-Comm    | 0.26988    | 0.26988    | 0.26988    |   0.0 |  1.28
-Output  | 0.0014684  | 0.0014684  | 0.0014684  |   0.0 |  0.01
-Modify  | 18.193     | 18.193     | 18.193     |   0.0 | 86.45
-Other   |            | 0.03692    |            |       |  0.18
-
-Nlocal:    27 ave 27 max 27 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    2081 ave 2081 max 2081 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    6264 ave 6264 max 6264 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 6264
-Ave neighs/atom = 232
-Ave special neighs/atom = 2
-Neighbor list builds = 20177
-Dangerous builds = 0
-
-Total wall time: 0:00:21

examples/gcmc/log.31Mar21.gcmc.co2.g++.1

@@ -0,0 +1,196 @@
+LAMMPS (10 Mar 2021)
+  using 1 OpenMP thread(s) per MPI task
+# GCMC for CO2 molecular fluid, rigid/small dynamics
+# Rigid CO2 TraPPE model
+# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
+# mixtures containing alkanes, carbon dioxide and
+# nitrogen AIChE J., 47,1676-1682 (2001)].
+
+# variables available on command line
+
+variable        mu index -8.1
+variable        disp index 0.5
+variable        temp index 338.0
+variable        lbox index 10.0
+variable        spacing index 5.0
+
+# global model settings
+
+units           real
+atom_style      full
+boundary        p p p
+pair_style      lj/cut/coul/long  14
+pair_modify     mix arithmetic tail yes
+kspace_style    ewald 0.0001
+bond_style      harmonic
+angle_style     harmonic
+
+# box, start molecules on simple cubic lattice
+
+lattice         sc ${spacing}
+lattice         sc 5.0
+Lattice spacing in x,y,z = 5.0000000 5.0000000 5.0000000
+region          box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
+region          box block 0 10.0 0 ${lbox} 0 ${lbox} units box
+region          box block 0 10.0 0 10.0 0 ${lbox} units box
+region          box block 0 10.0 0 10.0 0 10.0 units box
+create_box      2 box                                       bond/types 1                                angle/types 1                               extra/bond/per/atom 2                       extra/angle/per/atom 1                      extra/special/per/atom 2
+Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (10.000000 10.000000 10.000000)
+  1 by 1 by 1 MPI processor grid
+molecule        co2mol CO2.txt
+Read molecule template co2mol:
+  1 molecules
+  3 atoms with max type 2
+  2 bonds with max type 1
+  1 angles with max type 1
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+create_atoms    0 box mol co2mol 464563 units box
+Created 24 atoms
+  create_atoms CPU = 0.002 seconds
+
+# rigid CO2 TraPPE model
+
+pair_coeff      1   1  0.053649   2.8
+pair_coeff      2   2  0.156973   3.05
+bond_coeff      1       0       1.16
+angle_coeff     1       0       180
+
+# masses
+
+mass 1 12.0107
+mass 2 15.9994
+
+# MD settings
+
+group           co2 type 1 2
+24 atoms in group co2
+neighbor        2.0 bin
+neigh_modify    every 1 delay 10 check yes
+velocity        all create ${temp} 54654
+velocity        all create 338.0 54654
+timestep        1.0
+
+# rigid constraints with thermostat
+
+fix             myrigid co2 rigid/small molecule mol co2mol
+  create bodies CPU = 0.000 seconds
+  8 rigid bodies with 24 atoms
+  1.1600000 = max distance from body owner to body atom
+
+# dynamically update  fix rigid/nvt/small temperature ndof
+fix_modify      myrigid dynamic/dof yes
+
+# gcmc
+
+variable        tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
+fix             mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigid
+fix             mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigid
+fix             mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigid
+fix             mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigid
+fix             mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 co2mol tfac_insert 1.66666666666667 group co2 rigid myrigid
+
+# atom counts
+
+variable        carbon atom "type==1"
+variable        oxygen atom "type==2"
+group           carbon dynamic co2 var carbon
+dynamic group carbon defined
+group           oxygen dynamic co2 var oxygen
+dynamic group oxygen defined
+variable        nC equal count(carbon)
+variable        nO equal count(oxygen)
+
+# output
+
+variable        tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
+variable        iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
+variable        dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
+variable        racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
+
+# dynamically update default temperature ndof
+compute_modify  thermo_temp dynamic/dof yes
+
+thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
+thermo          1000
+
+# run
+
+run             20000
+Ewald initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
+  G vector (1/distance) = 0.16463644
+  estimated absolute RMS force accuracy = 0.033206372
+  estimated relative force accuracy = 0.0001
+  KSpace vectors: actual max1d max3d = 16 2 62
+                  kxmax kymax kzmax  = 2 2 2
+WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:482)
+0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
+0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
+WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 16
+  ghost atom cutoff = 16
+  binsize = 8, bins = 2 2 2
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 15.62 | 15.62 | 15.62 Mbytes
+Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO 
+       0    364.27579    4238.8631   -9.6809388    13.391989    0.5846359       24            0            0            0            0            8           16 
+    1000    261.50949   -204.60974   -9.6459249    8.3147747   0.51155641       21  0.096366192  0.097590121            0            0            7           14 
+    2000    479.39697    231.28436   -7.0089345     10.47927   0.36539744       15  0.085531005  0.085453295            0            0            5           10 
+    3000    318.31766   -433.17133   -7.3680951    8.5396005   0.43847693       18  0.078556687  0.080101462            0            0            6           12 
+    4000    357.40776      -186.78   -16.453111    14.915105   0.65771539       27  0.082003877   0.08249082            0            0            9           18 
+    5000    399.94731    1524.2909   -16.624678    18.677282   0.73079488       30  0.071285101  0.072731705            0            0           10           20 
+    6000    354.71736    60.134827   -18.988979    16.565073   0.73079488       30  0.071615663  0.071713414            0            0           10           20 
+    7000    483.32057    966.32174   -5.7393251    10.565037   0.36539744       15  0.087027775  0.089855826            0            0            5           10 
+    8000    547.68562    494.96891    -4.125626     11.97201   0.36539744       15   0.11738082   0.11937373            0            0            5           10 
+    9000    433.76488    390.91467  -0.85312985    5.1718828   0.21923846        9   0.13265238   0.13513212            0            0            3            6 
+   10000    330.01685   -862.07457   -26.494645    18.690633   0.87695385       36   0.13775034   0.13905403            0            0           12           24 
+   11000    334.26318   -578.48274   -13.236965    12.288625    0.5846359       24   0.13713936   0.13960485            0            0            8           16 
+   12000    243.68657   -1244.7156   -25.757644    12.590645   0.80387436       33    0.1339588   0.13588739            0            0           11           22 
+   13000    307.66758   -429.66928   -17.864639    14.367878   0.73079488       30   0.12604721    0.1278094            0            0           10           20 
+   14000    330.91434    495.97112   -15.374248    13.809499   0.65771539       27   0.12011756   0.12145865            0            0            9           18 
+   15000    564.87966    982.72332   -14.810525    26.379517   0.73079488       30   0.12164324   0.12343521            0            0           10           20 
+   16000    342.63867   -54.776299   -2.2580523    5.7875978   0.29231795       12   0.13535812   0.13790758            0            0            4            8 
+   17000    461.07005   -2.4317694    -1.145154    3.2068452   0.14615898        6    0.1444739   0.14730804            0            0            2            4 
+   18000    197.21207   -40.124433   -7.0857418    5.2906654   0.43847693       18   0.14403997   0.14574329            0            0            6           12 
+   19000    393.36395   -420.49802   -11.172739    14.461366    0.5846359       24   0.15005606   0.15142063            0            0            8           16 
+   20000    356.48539    56.071962   -1.7861789    4.2504609   0.21923846        9   0.15422732   0.15627984            0            0            3            6 
+Loop time of 19.5982 on 1 procs for 20000 steps with 9 atoms
+
+Performance: 88.171 ns/day, 0.272 hours/ns, 1020.502 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    | 2.3404     | 2.3404     | 2.3404     |   0.0 | 11.94
+Bond    | 0.033919   | 0.033919   | 0.033919   |   0.0 |  0.17
+Kspace  | 0.19974    | 0.19974    | 0.19974    |   0.0 |  1.02
+Neigh   | 0.11478    | 0.11478    | 0.11478    |   0.0 |  0.59
+Comm    | 0.22538    | 0.22538    | 0.22538    |   0.0 |  1.15
+Output  | 0.00096536 | 0.00096536 | 0.00096536 |   0.0 |  0.00
+Modify  | 16.627     | 16.627     | 16.627     |   0.0 | 84.84
+Other   |            | 0.05594    |            |       |  0.29
+
+Nlocal:        9.00000 ave           9 max           9 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        703.000 ave         703 max         703 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:        719.000 ave         719 max         719 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 719
+Ave neighs/atom = 79.888889
+Ave special neighs/atom = 2.0000000
+Neighbor list builds = 20196
+Dangerous builds = 0
+
+Total wall time: 0:00:19

examples/plugins/.gitignore

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

examples/plugins/CMakeLists.txt

@@ -0,0 +1,68 @@
+##########################################
+# CMake build system for plugin examples.
+# The is meant to be used as a template for plugins that are
+# distributed independent from the LAMMPS package.
+##########################################
+
+cmake_minimum_required(VERSION 3.10)
+
+# enforce out-of-source build
+if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
+  message(FATAL_ERROR "In-source builds are not allowed. You must create and use a build directory. "
+    "Please remove CMakeCache.txt and CMakeFiles first.")
+endif()
+
+project(plugins VERSION 1.0 LANGUAGES CXX)
+
+# NOTE: the next line should be commented out when used outside of the LAMMPS package
+get_filename_component(LAMMPS_SOURCE_DIR ${PROJECT_SOURCE_DIR}/../../src ABSOLUTE)
+set(LAMMPS_HEADER_DIR ${LAMMPS_SOURCE_DIR} CACHE PATH "Location of LAMMPS headers")
+if(NOT LAMMPS_HEADER_DIR)
+  message(FATAL_ERROR "Must set LAMMPS_HEADER_DIR")
+endif()
+
+# by default, install into $HOME/.local (not /usr/local),
+# so that no root access (and sudo) is needed
+if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+  set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
+endif()
+
+# C++11 is required
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+# bail out on windows
+if(CMAKE_SYSTEM_NAME STREQUAL Windows)
+  message(FATAL_ERROR "LAMMPS plugins are currently not supported on Windows")
+endif()
+
+set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR})
+include(CheckIncludeFileCXX)
+include(LAMMPSInterfaceCXX)
+
+##########################
+# building the plugins
+
+add_library(morse2plugin MODULE morse2plugin.cpp pair_morse2.cpp pair_morse2_omp.cpp)
+target_include_directories(morse2plugin PRIVATE "${LAMMPS_HEADER_DIR}/USER-OMP")
+target_link_libraries(morse2plugin PRIVATE lammps)
+
+add_library(nve2plugin MODULE nve2plugin.cpp fix_nve2.cpp)
+target_link_libraries(nve2plugin PRIVATE lammps)
+
+add_library(helloplugin MODULE helloplugin.cpp)
+target_link_libraries(helloplugin PRIVATE lammps)
+
+add_library(zero2plugin MODULE zero2plugin.cpp pair_zero2.cpp bond_zero2.cpp
+                               angle_zero2.cpp dihedral_zero2.cpp improper_zero2.cpp)
+target_link_libraries(zero2plugin PRIVATE lammps)
+
+set_target_properties(morse2plugin nve2plugin helloplugin zero2plugin PROPERTIES
+                      PREFIX ""
+                      LINK_FLAGS "-rdynamic")
+
+# MacOS seems to need this
+if(CMAKE_SYSTEM_NAME STREQUAL Darwin)
+  set_target_properties(morse2plugin nve2plugin helloplugin zero2plugin PROPERTIES
+                        LINK_FLAGS "-Wl,-undefined,dynamic_lookup")
+endif()

examples/plugins/LAMMPSInterfaceCXX.cmake

@@ -0,0 +1,86 @@
+# Cmake script code to define the LAMMPS C++ interface
+# settings required for building LAMMPS plugins
+
+################################################################################
+# helper function
+function(validate_option name values)
+  string(TOLOWER ${${name}} needle_lower)
+  string(TOUPPER ${${name}} needle_upper)
+  list(FIND ${values} ${needle_lower} IDX_LOWER)
+  list(FIND ${values} ${needle_upper} IDX_UPPER)
+  if(${IDX_LOWER} LESS 0 AND ${IDX_UPPER} LESS 0)
+    list_to_bulletpoints(POSSIBLE_VALUE_LIST ${${values}})
+    message(FATAL_ERROR "\n########################################################################\n"
+      "Invalid value '${${name}}' for option ${name}\n"
+      "\n"
+      "Possible values are:\n"
+      "${POSSIBLE_VALUE_LIST}"
+      "########################################################################")
+  endif()
+endfunction(validate_option)
+
+#################################################################################
+# LAMMPS C++ interface. We only need the header related parts.
+add_library(lammps INTERFACE)
+target_include_directories(lammps INTERFACE ${LAMMPS_HEADER_DIR})
+
+################################################################################
+# MPI configuration
+if(NOT CMAKE_CROSSCOMPILING)
+  set(MPI_CXX_SKIP_MPICXX TRUE)
+  find_package(MPI QUIET)
+  option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
+else()
+  option(BUILD_MPI "Build MPI version" OFF)
+endif()
+
+if(BUILD_MPI)
+  find_package(MPI REQUIRED)
+  option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
+  if(LAMMPS_LONGLONG_TO_LONG)
+    target_compile_definitions(lammps INTERFACE -DLAMMPS_LONGLONG_TO_LONG)
+  endif()
+  target_link_libraries(lammps INTERFACE MPI::MPI_CXX)
+else()
+  target_include_directories(lammps INTERFACE "${LAMMPS_SOURCE_DIR}/STUBS")
+endif()
+
+set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
+set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
+set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
+validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
+string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
+target_compile_definitions(lammps INTERFACE -DLAMMPS_${LAMMPS_SIZES})
+
+################################################################################
+# detect if we may enable OpenMP support by default
+set(BUILD_OMP_DEFAULT OFF)
+find_package(OpenMP QUIET)
+if(OpenMP_FOUND)
+  check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
+  if(HAVE_OMP_H_INCLUDE)
+    set(BUILD_OMP_DEFAULT ON)
+  endif()
+endif()
+
+option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT})
+
+if(BUILD_OMP)
+  find_package(OpenMP REQUIRED)
+  check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
+  if(NOT HAVE_OMP_H_INCLUDE)
+    message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
+  endif()
+
+  if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
+      (CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR
+      ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
+      ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
+    # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
+    # Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.
+    target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=4)
+  else()
+    target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=3)
+  endif()
+  target_link_libraries(lammps INTERFACE OpenMP::OpenMP_CXX)
+endif()

examples/plugins/Makefile

@@ -0,0 +1,6 @@
+CXX=mpicxx
+CXXFLAGS=-I../../src -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP -fopenmp
+LD=$(CXX) -shared -rdynamic -fopenmp
+DSOEXT=.so
+
+include Makefile.common

examples/plugins/Makefile.common

@@ -0,0 +1,36 @@
+default: morse2plugin$(DSOEXT) nve2plugin$(DSOEXT) helloplugin$(DSOEXT) zero2plugin$(DSOEXT)
+
+helloplugin$(DSOEXT): helloplugin.o
+	$(LD) -o $@ $^
+
+morse2plugin$(DSOEXT): morse2plugin.o pair_morse2.o pair_morse2_omp.o
+	$(LD) -o $@ $^
+
+nve2plugin$(DSOEXT): nve2plugin.o fix_nve2.o
+	$(LD) -o $@ $^
+
+zero2plugin$(DSOEXT): zero2plugin.o pair_zero2.o bond_zero2.o angle_zero2.o dihedral_zero2.o improper_zero2.o
+	$(LD) -o $@ $^
+
+.cpp.o:
+	$(CXX) -o $@ $(CXXFLAGS) -c $<
+
+helloplugin.o: helloplugin.cpp
+
+pair_morse2.o: pair_morse2.cpp pair_morse2.h
+pair_morse2_omp.o: pair_morse2_omp.cpp pair_morse2_omp.h pair_morse2.h
+morse2plugin.o: morse2plugin.cpp pair_morse2.h pair_morse2_omp.h
+
+fix_nve2.o: fix_nve2.cpp fix_nve2.h
+nve2plugin.o: nve2plugin.cpp fix_nve2.h
+
+pair_zero2.o: pair_zero2.cpp pair_zero2.h
+bond_zero2.o: bond_zero2.cpp bond_zero2.h
+angle_zero2.o: angle_zero2.cpp angle_zero2.h
+dihedral_zero2.o: dihedral_zero2.cpp dihedral_zero2.h
+improper_zero2.o: improper_zero2.cpp improper_zero2.h
+zero2plugin.o: zero2plugin.cpp pair_zero2.h bond_zero2.h angle_zero2.h dihedral_zero2.h
+
+clean:
+	rm -rf *~ *.so *.dylib *.o log.lammps CMakeCache.txt CMakeFiles
+

examples/plugins/Makefile.macos

@@ -0,0 +1,6 @@
+CXX=mpicxx
+CXXFLAGS=-I../../src -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP
+LD=$(CXX) -bundle -rdynamic -Wl,-undefined,dynamic_lookup
+DSOEXT=.dylib
+
+include Makefile.common

examples/plugins/Makefile.serial

@@ -0,0 +1,6 @@
+CXX=g++
+CXXFLAGS=-I../../src -I../../src/STUBS -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP -fopenmp
+LD=$(CXX) -shared -rdynamic -fopenmp
+DSOEXT=.so
+
+include Makefile.common

examples/plugins/angle_zero2.cpp

@@ -0,0 +1,152 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://lammps.sandia.gov/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Carsten Svaneborg (SDU)
+------------------------------------------------------------------------- */
+
+#include "angle_zero2.h"
+
+#include "atom.h"
+#include "comm.h"
+#include "math_const.h"
+#include "memory.h"
+#include "error.h"
+
+#include <cstring>
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+
+/* ---------------------------------------------------------------------- */
+
+AngleZero2::AngleZero2(LAMMPS *lmp) : Angle(lmp), coeffflag(1) {}
+
+/* ---------------------------------------------------------------------- */
+
+AngleZero2::~AngleZero2()
+{
+  if (allocated && !copymode) {
+    memory->destroy(setflag);
+    memory->destroy(theta0);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AngleZero2::compute(int eflag, int vflag)
+{
+  ev_init(eflag,vflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AngleZero2::settings(int narg, char **arg)
+{
+  if ((narg != 0) && (narg != 1))
+    error->all(FLERR,"Illegal angle_style command");
+
+  if (narg == 1) {
+    if (strcmp("nocoeff",arg[0]) == 0) coeffflag=0;
+    else error->all(FLERR,"Illegal angle_style command");
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AngleZero2::allocate()
+{
+  allocated = 1;
+  int n = atom->nangletypes;
+
+  memory->create(theta0,n+1,"angle:theta0");
+  memory->create(setflag,n+1,"angle:setflag");
+  for (int i = 1; i <= n; i++) setflag[i] = 0;
+}
+
+/* ----------------------------------------------------------------------
+   set coeffs for one or more types
+------------------------------------------------------------------------- */
+
+void AngleZero2::coeff(int narg, char **arg)
+{
+  if ((narg < 1) || (coeffflag && narg > 2))
+    error->all(FLERR,"Incorrect args for angle coefficients");
+
+  if (!allocated) allocate();
+
+  int ilo,ihi;
+  utils::bounds(FLERR,arg[0],1,atom->nangletypes,ilo,ihi,error);
+
+  double theta0_one = 0.0;
+  if (coeffflag && (narg == 2))
+    theta0_one = utils::numeric(FLERR,arg[1],false,lmp);
+
+  // convert theta0 from degrees to radians
+
+  int count = 0;
+  for (int i = ilo; i <= ihi; i++) {
+    setflag[i] = 1;
+    theta0[i] = theta0_one/180.0 * MY_PI;
+    count++;
+  }
+
+  if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients");
+}
+
+/* ---------------------------------------------------------------------- */
+
+double AngleZero2::equilibrium_angle(int i)
+{
+  return theta0[i];
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes out coeffs to restart file
+------------------------------------------------------------------------- */
+
+void AngleZero2::write_restart(FILE *fp) {
+  fwrite(&theta0[1],sizeof(double),atom->nangletypes,fp);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads coeffs from restart file, bcasts them
+------------------------------------------------------------------------- */
+
+void AngleZero2::read_restart(FILE *fp)
+{
+  allocate();
+
+  if (comm->me == 0) {
+    utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
+  }
+  MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);
+
+  for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
+}
+/* ----------------------------------------------------------------------
+   proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void AngleZero2::write_data(FILE *fp)
+{
+  for (int i = 1; i <= atom->nangletypes; i++)
+    fprintf(fp,"%d %g\n",i,theta0[i]/MY_PI*180.0);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double AngleZero2::single(int /*type*/, int /*i1*/, int /*i2*/, int /*i3*/)
+{
+  return 0.0;
+}

examples/plugins/angle_zero2.h

@@ -0,0 +1,57 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_ANGLE_ZERO2_H
+#define LMP_ANGLE_ZERO2_H
+
+#include "angle.h"
+
+namespace LAMMPS_NS {
+
+class AngleZero2 : public Angle {
+ public:
+  AngleZero2(class LAMMPS *);
+  virtual ~AngleZero2();
+  virtual void compute(int, int);
+  virtual void coeff(int, char **);
+  virtual void settings(int, char **);
+
+  double equilibrium_angle(int);
+  void write_restart(FILE *);
+  void read_restart(FILE *);
+  void write_data(FILE *);
+
+  double single(int, int, int, int);
+
+ protected:
+  double *theta0;
+  int coeffflag;
+
+  void allocate();
+};
+
+}
+
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+UNDOCUMENTED
+
+E: Incorrect args for angle coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+*/

examples/plugins/bond_zero2.cpp

@@ -0,0 +1,161 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://lammps.sandia.gov/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Carsten Svaneborg (SDU)
+------------------------------------------------------------------------- */
+
+#include "bond_zero2.h"
+
+#include "atom.h"
+#include "comm.h"
+#include "error.h"
+#include "memory.h"
+
+#include <cstring>
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+BondZero2::BondZero2(LAMMPS *lmp) : Bond(lmp), coeffflag(1) {}
+
+/* ---------------------------------------------------------------------- */
+
+BondZero2::~BondZero2()
+{
+  if (allocated && !copymode) {
+    memory->destroy(setflag);
+    memory->destroy(r0);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void BondZero2::compute(int eflag, int vflag)
+{
+  ev_init(eflag,vflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void BondZero2::settings(int narg, char **arg)
+{
+  if ((narg != 0) && (narg != 1))
+    error->all(FLERR,"Illegal bond_style command");
+
+  if (narg == 1) {
+    if (strcmp("nocoeff",arg[0]) == 0) coeffflag=0;
+    else error->all(FLERR,"Illegal bond_style command");
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void BondZero2::allocate()
+{
+  allocated = 1;
+  int n = atom->nbondtypes;
+
+  memory->create(r0,n+1,"bond:r0");
+  memory->create(setflag,n+1,"bond:setflag");
+  for (int i = 1; i <= n; i++) setflag[i] = 0;
+}
+
+/* ----------------------------------------------------------------------
+   set coeffs for one or more types
+------------------------------------------------------------------------- */
+
+void BondZero2::coeff(int narg, char **arg)
+{
+  if ((narg < 1) || (coeffflag && narg > 2))
+    error->all(FLERR,"Incorrect args for bond coefficients");
+
+  if (!allocated) allocate();
+
+  int ilo,ihi;
+  utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error);
+
+  double r0_one = 0.0;
+  if (coeffflag && (narg == 2))
+    r0_one = utils::numeric(FLERR,arg[1],false,lmp);
+
+  int count = 0;
+  for (int i = ilo; i <= ihi; i++) {
+    setflag[i] = 1;
+    r0[i] = r0_one;
+    count++;
+  }
+
+  if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients");
+}
+
+/* ----------------------------------------------------------------------
+   return an equilbrium bond length
+------------------------------------------------------------------------- */
+
+double BondZero2::equilibrium_distance(int i)
+{
+  return r0[i];
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes out coeffs to restart file
+------------------------------------------------------------------------- */
+
+void BondZero2::write_restart(FILE *fp) {
+  fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads coeffs from restart file, bcasts them
+------------------------------------------------------------------------- */
+
+void BondZero2::read_restart(FILE *fp)
+{
+  allocate();
+
+  if (comm->me == 0) {
+    utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
+  }
+  MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
+
+  for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void BondZero2::write_data(FILE *fp)
+{
+  for (int i = 1; i <= atom->nbondtypes; i++)
+    fprintf(fp,"%d %g\n",i,r0[i]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double BondZero2::single(int /*type*/, double /*rsq*/, int /*i*/, int /*j*/,
+                        double & /*fforce*/)
+{
+  return 0.0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *BondZero2::extract(const char *str, int &dim)
+{
+  dim = 1;
+  if (strcmp(str,"r0")==0) return (void*) r0;
+  return nullptr;
+}

examples/plugins/bond_zero2.h

@@ -0,0 +1,58 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_BOND_ZERO2_H
+#define LMP_BOND_ZERO2_H
+
+#include "bond.h"
+
+namespace LAMMPS_NS {
+
+class BondZero2 : public Bond {
+ public:
+  BondZero2(class LAMMPS *);
+  virtual ~BondZero2();
+  virtual void compute(int, int);
+  virtual void settings(int, char **);
+
+  void coeff(int, char **);
+  double equilibrium_distance(int);
+  void write_restart(FILE *);
+  void read_restart(FILE *);
+  void write_data(FILE *);
+
+  double single(int, double, int, int, double &);
+  virtual void *extract(const char *, int &);
+
+ protected:
+  double *r0;
+  int coeffflag;
+
+  virtual void allocate();
+};
+
+}
+
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+UNDOCUMENTED
+
+E: Incorrect args for bond coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+*/

examples/plugins/dihedral_zero2.cpp

@@ -0,0 +1,121 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://lammps.sandia.gov/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Carsten Svaneborg (SDU)
+------------------------------------------------------------------------- */
+
+#include "dihedral_zero2.h"
+
+#include "atom.h"
+#include "error.h"
+#include "memory.h"
+
+#include <cstring>
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+DihedralZero2::DihedralZero2(LAMMPS *lmp) : Dihedral(lmp), coeffflag(1)
+{
+  writedata = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+DihedralZero2::~DihedralZero2()
+{
+  if (allocated && !copymode) {
+    memory->destroy(setflag);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DihedralZero2::compute(int eflag, int vflag)
+{
+  ev_init(eflag,vflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DihedralZero2::settings(int narg, char **arg)
+{
+  if ((narg != 0) && (narg != 1))
+    error->all(FLERR,"Illegal dihedral_style command");
+
+  if (narg == 1) {
+    if (strcmp("nocoeff",arg[0]) == 0) coeffflag=0;
+    else error->all(FLERR,"Illegal dihedral_style command");
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DihedralZero2::allocate()
+{
+  allocated = 1;
+  int n = atom->ndihedraltypes;
+
+  memory->create(setflag,n+1,"dihedral:setflag");
+  for (int i = 1; i <= n; i++) setflag[i] = 0;
+}
+
+/* ----------------------------------------------------------------------
+   set coeffs for one or more types
+------------------------------------------------------------------------- */
+
+void DihedralZero2::coeff(int narg, char **arg)
+{
+  if ((narg < 1) || (coeffflag && narg > 1))
+    error->all(FLERR,"Incorrect args for dihedral coefficients");
+
+  if (!allocated) allocate();
+
+  int ilo,ihi;
+  utils::bounds(FLERR,arg[0],1,atom->ndihedraltypes,ilo,ihi,error);
+
+  int count = 0;
+  for (int i = ilo; i <= ihi; i++) {
+    setflag[i] = 1;
+    count++;
+  }
+
+  if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients");
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes out coeffs to restart file
+------------------------------------------------------------------------- */
+
+void DihedralZero2::write_restart(FILE * /*fp*/) {}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads coeffs from restart file, bcasts them
+------------------------------------------------------------------------- */
+
+void DihedralZero2::read_restart(FILE * /*fp*/)
+{
+  allocate();
+  for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void DihedralZero2::write_data(FILE *fp) {
+  for (int i = 1; i <= atom->ndihedraltypes; i++)
+    fprintf(fp,"%d\n",i);
+}

examples/plugins/dihedral_zero2.h

@@ -0,0 +1,57 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+
+   Identical to dihedral harmonic, except if all k's are zero the
+   force loop is skipped.
+
+------------------------------------------------------------------------- */
+
+#ifndef LMP_DIHEDRAL_ZERO2_H
+#define LMP_DIHEDRAL_ZERO2_H
+
+#include "dihedral.h"
+
+namespace LAMMPS_NS {
+
+class DihedralZero2 : public Dihedral {
+ public:
+  DihedralZero2(class LAMMPS *);
+  virtual ~DihedralZero2();
+  virtual void compute(int, int);
+  virtual void coeff(int, char **);
+  virtual void settings(int, char **);
+
+  void write_restart(FILE *);
+  void read_restart(FILE *);
+  void write_data(FILE *);
+
+ protected:
+  int coeffflag;
+
+  virtual void allocate();
+};
+
+}
+
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+UNDOCUMENTED
+
+E: Incorrect args for dihedral coefficients
+
+UNDOCUMENTED
+
+*/

examples/plugins/fix_nve2.cpp

@@ -0,0 +1,171 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://lammps.sandia.gov/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "fix_nve2.h"
+#include <cstring>
+#include "atom.h"
+#include "force.h"
+#include "update.h"
+#include "respa.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+/* ---------------------------------------------------------------------- */
+
+FixNVE2::FixNVE2(LAMMPS *lmp, int narg, char **arg) :
+  Fix(lmp, narg, arg)
+{
+  if (strcmp(style,"nve/sphere") != 0 && narg < 3)
+    error->all(FLERR,"Illegal fix nve command");
+
+  dynamic_group_allow = 1;
+  time_integrate = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixNVE2::setmask()
+{
+  int mask = 0;
+  mask |= INITIAL_INTEGRATE;
+  mask |= FINAL_INTEGRATE;
+  mask |= INITIAL_INTEGRATE_RESPA;
+  mask |= FINAL_INTEGRATE_RESPA;
+  return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNVE2::init()
+{
+  dtv = update->dt;
+  dtf = 0.5 * update->dt * force->ftm2v;
+
+  if (strstr(update->integrate_style,"respa"))
+    step_respa = ((Respa *) update->integrate)->step;
+}
+
+/* ----------------------------------------------------------------------
+   allow for both per-type and per-atom mass
+------------------------------------------------------------------------- */
+
+void FixNVE2::initial_integrate(int /*vflag*/)
+{
+  double dtfm;
+
+  // update v and x of atoms in group
+
+  double **x = atom->x;
+  double **v = atom->v;
+  double **f = atom->f;
+  double *rmass = atom->rmass;
+  double *mass = atom->mass;
+  int *type = atom->type;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+  if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+  if (rmass) {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit) {
+        dtfm = dtf / rmass[i];
+        v[i][0] += dtfm * f[i][0];
+        v[i][1] += dtfm * f[i][1];
+        v[i][2] += dtfm * f[i][2];
+        x[i][0] += dtv * v[i][0];
+        x[i][1] += dtv * v[i][1];
+        x[i][2] += dtv * v[i][2];
+      }
+
+  } else {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit) {
+        dtfm = dtf / mass[type[i]];
+        v[i][0] += dtfm * f[i][0];
+        v[i][1] += dtfm * f[i][1];
+        v[i][2] += dtfm * f[i][2];
+        x[i][0] += dtv * v[i][0];
+        x[i][1] += dtv * v[i][1];
+        x[i][2] += dtv * v[i][2];
+      }
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNVE2::final_integrate()
+{
+  double dtfm;
+
+  // update v of atoms in group
+
+  double **v = atom->v;
+  double **f = atom->f;
+  double *rmass = atom->rmass;
+  double *mass = atom->mass;
+  int *type = atom->type;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+  if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+  if (rmass) {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit) {
+        dtfm = dtf / rmass[i];
+        v[i][0] += dtfm * f[i][0];
+        v[i][1] += dtfm * f[i][1];
+        v[i][2] += dtfm * f[i][2];
+      }
+
+  } else {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit) {
+        dtfm = dtf / mass[type[i]];
+        v[i][0] += dtfm * f[i][0];
+        v[i][1] += dtfm * f[i][1];
+        v[i][2] += dtfm * f[i][2];
+      }
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNVE2::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
+{
+  dtv = step_respa[ilevel];
+  dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
+
+  // innermost level - NVE update of v and x
+  // all other levels - NVE update of v
+
+  if (ilevel == 0) initial_integrate(vflag);
+  else final_integrate();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNVE2::final_integrate_respa(int ilevel, int /*iloop*/)
+{
+  dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
+  final_integrate();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNVE2::reset_dt()
+{
+  dtv = update->dt;
+  dtf = 0.5 * update->dt * force->ftm2v;
+}

examples/plugins/fix_nve2.h

@@ -0,0 +1,58 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(nve2,FixNVE2)
+
+#else
+
+#ifndef LMP_FIX_NVE2_H
+#define LMP_FIX_NVE2_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixNVE2 : public Fix {
+ public:
+  FixNVE2(class LAMMPS *, int, char **);
+  virtual ~FixNVE2() {}
+  int setmask();
+  virtual void init();
+  virtual void initial_integrate(int);
+  virtual void final_integrate();
+  virtual void initial_integrate_respa(int, int, int);
+  virtual void final_integrate_respa(int, int);
+  virtual void reset_dt();
+
+ protected:
+  double dtv,dtf;
+  double *step_respa;
+  int mass_require;
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+*/

examples/plugins/helloplugin.cpp

@@ -0,0 +1,47 @@
+
+#include "lammpsplugin.h"
+
+#include "comm.h"
+#include "error.h"
+#include "pointers.h"
+#include "version.h"
+
+#include <cstring>
+
+namespace LAMMPS_NS {
+  class Hello : protected Pointers {
+    public:
+      Hello(class LAMMPS *lmp) : Pointers(lmp) {};
+      void command(int, char **);
+  };
+}
+
+using namespace LAMMPS_NS;
+
+void Hello::command(int argc, char **argv)
+{
+   if (argc != 1) error->all(FLERR,"Illegal hello command");
+   if (comm->me == 0)
+     utils::logmesg(lmp,fmt::format("Hello, {}!\n",argv[0]));
+}
+
+static void hellocreator(LAMMPS *lmp, int argc, char **argv)
+{
+    Hello hello(lmp);
+    hello.command(argc,argv);
+}
+
+extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
+{
+  lammpsplugin_t plugin;
+  lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
+
+  plugin.version = LAMMPS_VERSION;
+  plugin.style   = "command";
+  plugin.name    = "hello";
+  plugin.info    = "Hello world command v1.0";
+  plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
+  plugin.creator.v3 = (lammpsplugin_factory3 *) &hellocreator;
+  plugin.handle  = handle;
+  (*register_plugin)(&plugin,lmp);
+}

examples/plugins/improper_zero2.cpp

@@ -0,0 +1,122 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://lammps.sandia.gov/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Carsten Svaneborg (SDU)
+------------------------------------------------------------------------- */
+
+#include "improper_zero2.h"
+
+#include "atom.h"
+#include "error.h"
+#include "memory.h"
+
+#include <cstring>
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+ImproperZero2::ImproperZero2(LAMMPS *lmp) : Improper(lmp), coeffflag(1)
+{
+  writedata = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ImproperZero2::~ImproperZero2()
+{
+  if (allocated && !copymode) {
+    memory->destroy(setflag);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ImproperZero2::compute(int eflag, int vflag)
+{
+  ev_init(eflag,vflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ImproperZero2::settings(int narg, char **arg)
+{
+  if ((narg != 0) && (narg != 1))
+    error->all(FLERR,"Illegal improper_style command");
+
+  if (narg == 1) {
+    if (strcmp("nocoeff",arg[0]) == 0) coeffflag=0;
+    else error->all(FLERR,"Illegal improper_style command");
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ImproperZero2::allocate()
+{
+  allocated = 1;
+  int n = atom->nimpropertypes;
+
+  memory->create(setflag,n+1,"improper:setflag");
+  for (int i = 1; i <= n; i++) setflag[i] = 0;
+}
+
+/* ----------------------------------------------------------------------
+   set coeffs for one or more types
+------------------------------------------------------------------------- */
+
+void ImproperZero2::coeff(int narg, char **arg)
+{
+  if ((narg < 1) || (coeffflag && narg > 1))
+    error->all(FLERR,"Incorrect args for improper coefficients");
+
+  if (!allocated) allocate();
+
+  int ilo,ihi;
+  utils::bounds(FLERR,arg[0],1,atom->nimpropertypes,ilo,ihi,error);
+
+  int count = 0;
+  for (int i = ilo; i <= ihi; i++) {
+    setflag[i] = 1;
+    count++;
+  }
+
+  if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients");
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes out coeffs to restart file
+------------------------------------------------------------------------- */
+
+void ImproperZero2::write_restart(FILE * /*fp*/) {}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads coeffs from restart file, bcasts them
+------------------------------------------------------------------------- */
+
+void ImproperZero2::read_restart(FILE * /*fp*/)
+{
+  allocate();
+  for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void ImproperZero2::write_data(FILE *fp) {
+  for (int i = 1; i <= atom->nimpropertypes; i++)
+    fprintf(fp,"%d\n",i);
+}
+

examples/plugins/improper_zero2.h

@@ -0,0 +1,53 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_IMPROPER_ZERO2_H
+#define LMP_IMPROPER_ZERO2_H
+
+#include "improper.h"
+
+namespace LAMMPS_NS {
+
+class ImproperZero2 : public Improper {
+ public:
+  ImproperZero2(class LAMMPS *);
+  virtual ~ImproperZero2();
+  virtual void compute(int, int);
+  virtual void coeff(int, char **);
+  virtual void settings(int, char **);
+
+  void write_restart(FILE *);
+  void read_restart(FILE *);
+  void write_data(FILE *);
+
+ protected:
+  int coeffflag;
+
+  virtual void allocate();
+};
+
+}
+
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+UNDOCUMENTED
+
+E: Incorrect args for improper coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+*/

examples/plugins/morse2plugin.cpp

@@ -0,0 +1,43 @@
+
+#include "lammpsplugin.h"
+
+#include "version.h"
+
+#include <cstring>
+
+#include "pair_morse2.h"
+#include "pair_morse2_omp.h"
+
+using namespace LAMMPS_NS;
+
+static Pair *morse2creator(LAMMPS *lmp)
+{
+    return new PairMorse2(lmp);
+}
+
+static Pair *morse2ompcreator(LAMMPS *lmp)
+{
+    return new PairMorse2OMP(lmp);
+}
+
+extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
+{
+  lammpsplugin_t plugin;
+  lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
+
+  // register plain morse2 pair style
+  plugin.version = LAMMPS_VERSION;
+  plugin.style   = "pair";
+  plugin.name    = "morse2";
+  plugin.info    = "Morse2 variant pair style v1.0";
+  plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
+  plugin.creator.v1 = (lammpsplugin_factory1 *) &morse2creator;
+  plugin.handle  = handle;
+  (*register_plugin)(&plugin,lmp);
+
+  // also register morse2/omp pair style. only need to update changed fields
+  plugin.name    = "morse2/omp";
+  plugin.info    = "Morse2 variant pair style for OpenMP v1.0";
+  plugin.creator.v1 = (lammpsplugin_factory1 *) &morse2ompcreator;
+  (*register_plugin)(&plugin,lmp);
+}

examples/plugins/nve2plugin.cpp

@@ -0,0 +1,30 @@
+
+#include "lammpsplugin.h"
+
+#include "version.h"
+
+#include <cstring>
+
+#include "fix_nve2.h"
+
+using namespace LAMMPS_NS;
+
+static Fix *nve2creator(LAMMPS *lmp, int argc, char **argv)
+{
+    return new FixNVE2(lmp, argc, argv);
+}
+
+extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
+{
+  lammpsplugin_t plugin;
+  lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
+
+  plugin.version = LAMMPS_VERSION;
+  plugin.style   = "fix";
+  plugin.name    = "nve2";
+  plugin.info    = "NVE2 variant fix style v1.0";
+  plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
+  plugin.creator.v2 = (lammpsplugin_factory2 *) &nve2creator;
+  plugin.handle  = handle;
+  (*register_plugin)(&plugin,lmp);
+}

examples/plugins/pair_morse2.cpp

@@ -0,0 +1,359 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://lammps.sandia.gov/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "pair_morse2.h"
+
+#include <cmath>
+#include <cstring>
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "neigh_list.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+PairMorse2::PairMorse2(LAMMPS *lmp) : Pair(lmp)
+{
+  writedata = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairMorse2::~PairMorse2()
+{
+  if (allocated) {
+    memory->destroy(setflag);
+    memory->destroy(cutsq);
+
+    memory->destroy(cut);
+    memory->destroy(d0);
+    memory->destroy(alpha);
+    memory->destroy(r0);
+    memory->destroy(morse1);
+    memory->destroy(offset);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairMorse2::compute(int eflag, int vflag)
+{
+  int i,j,ii,jj,inum,jnum,itype,jtype;
+  double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
+  double rsq,r,dr,dexp,factor_lj;
+  int *ilist,*jlist,*numneigh,**firstneigh;
+
+  evdwl = 0.0;
+  ev_init(eflag,vflag);
+
+  double **x = atom->x;
+  double **f = atom->f;
+  int *type = atom->type;
+  int nlocal = atom->nlocal;
+  double *special_lj = force->special_lj;
+  int newton_pair = force->newton_pair;
+
+  inum = list->inum;
+  ilist = list->ilist;
+  numneigh = list->numneigh;
+  firstneigh = list->firstneigh;
+
+  // loop over neighbors of my atoms
+
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+    itype = type[i];
+    jlist = firstneigh[i];
+    jnum = numneigh[i];
+
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+      factor_lj = special_lj[sbmask(j)];
+      j &= NEIGHMASK;
+
+      delx = xtmp - x[j][0];
+      dely = ytmp - x[j][1];
+      delz = ztmp - x[j][2];
+      rsq = delx*delx + dely*dely + delz*delz;
+      jtype = type[j];
+
+      if (rsq < cutsq[itype][jtype]) {
+        r = sqrt(rsq);
+        dr = r - r0[itype][jtype];
+        dexp = exp(-alpha[itype][jtype] * dr);
+        fpair = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r;
+
+        f[i][0] += delx*fpair;
+        f[i][1] += dely*fpair;
+        f[i][2] += delz*fpair;
+        if (newton_pair || j < nlocal) {
+          f[j][0] -= delx*fpair;
+          f[j][1] -= dely*fpair;
+          f[j][2] -= delz*fpair;
+        }
+
+        if (eflag) {
+          evdwl = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) -
+            offset[itype][jtype];
+          evdwl *= factor_lj;
+        }
+
+        if (evflag) ev_tally(i,j,nlocal,newton_pair,
+                             evdwl,0.0,fpair,delx,dely,delz);
+      }
+    }
+  }
+
+  if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ----------------------------------------------------------------------
+   allocate all arrays
+------------------------------------------------------------------------- */
+
+void PairMorse2::allocate()
+{
+  allocated = 1;
+  int n = atom->ntypes;
+
+  memory->create(setflag,n+1,n+1,"pair:setflag");
+  for (int i = 1; i <= n; i++)
+    for (int j = i; j <= n; j++)
+      setflag[i][j] = 0;
+
+  memory->create(cutsq,n+1,n+1,"pair:cutsq");
+
+  memory->create(cut,n+1,n+1,"pair:cut");
+  memory->create(d0,n+1,n+1,"pair:d0");
+  memory->create(alpha,n+1,n+1,"pair:alpha");
+  memory->create(r0,n+1,n+1,"pair:r0");
+  memory->create(morse1,n+1,n+1,"pair:morse1");
+  memory->create(offset,n+1,n+1,"pair:offset");
+}
+
+/* ----------------------------------------------------------------------
+   global settings
+------------------------------------------------------------------------- */
+
+void PairMorse2::settings(int narg, char **arg)
+{
+  if (narg != 1) error->all(FLERR,"Illegal pair_style command");
+
+  cut_global = utils::numeric(FLERR,arg[0],false,lmp);
+
+  // reset cutoffs that have been explicitly set
+
+  if (allocated) {
+    int i,j;
+    for (i = 1; i <= atom->ntypes; i++)
+      for (j = i; j <= atom->ntypes; j++)
+        if (setflag[i][j]) cut[i][j] = cut_global;
+  }
+}
+
+/* ----------------------------------------------------------------------
+   set coeffs for one or more type pairs
+------------------------------------------------------------------------- */
+
+void PairMorse2::coeff(int narg, char **arg)
+{
+  if (narg < 5 || narg > 6)
+    error->all(FLERR,"Incorrect args for pair coefficients");
+  if (!allocated) allocate();
+
+  int ilo,ihi,jlo,jhi;
+  utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
+  utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
+
+  double d0_one = utils::numeric(FLERR,arg[2],false,lmp);
+  double alpha_one = utils::numeric(FLERR,arg[3],false,lmp);
+  double r0_one = utils::numeric(FLERR,arg[4],false,lmp);
+
+  double cut_one = cut_global;
+  if (narg == 6) cut_one = utils::numeric(FLERR,arg[5],false,lmp);
+
+  int count = 0;
+  for (int i = ilo; i <= ihi; i++) {
+    for (int j = MAX(jlo,i); j <= jhi; j++) {
+      d0[i][j] = d0_one;
+      alpha[i][j] = alpha_one;
+      r0[i][j] = r0_one;
+      cut[i][j] = cut_one;
+      setflag[i][j] = 1;
+      count++;
+    }
+  }
+
+  if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
+}
+
+
+/* ----------------------------------------------------------------------
+   init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+double PairMorse2::init_one(int i, int j)
+{
+  if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+
+  morse1[i][j] = 2.0*d0[i][j]*alpha[i][j];
+
+  if (offset_flag) {
+    double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]);
+    offset[i][j] = d0[i][j] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr));
+  } else offset[i][j] = 0.0;
+
+  d0[j][i] = d0[i][j];
+  alpha[j][i] = alpha[i][j];
+  r0[j][i] = r0[i][j];
+  morse1[j][i] = morse1[i][j];
+  offset[j][i] = offset[i][j];
+
+  return cut[i][j];
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairMorse2::write_restart(FILE *fp)
+{
+  write_restart_settings(fp);
+
+  int i,j;
+  for (i = 1; i <= atom->ntypes; i++)
+    for (j = i; j <= atom->ntypes; j++) {
+      fwrite(&setflag[i][j],sizeof(int),1,fp);
+      if (setflag[i][j]) {
+        fwrite(&d0[i][j],sizeof(double),1,fp);
+        fwrite(&alpha[i][j],sizeof(double),1,fp);
+        fwrite(&r0[i][j],sizeof(double),1,fp);
+        fwrite(&cut[i][j],sizeof(double),1,fp);
+      }
+    }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairMorse2::read_restart(FILE *fp)
+{
+  read_restart_settings(fp);
+
+  allocate();
+
+  int i,j;
+  int me = comm->me;
+  for (i = 1; i <= atom->ntypes; i++)
+    for (j = i; j <= atom->ntypes; j++) {
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error);
+      MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
+      if (setflag[i][j]) {
+        if (me == 0) {
+          utils::sfread(FLERR,&d0[i][j],sizeof(double),1,fp,nullptr,error);
+          utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,nullptr,error);
+          utils::sfread(FLERR,&r0[i][j],sizeof(double),1,fp,nullptr,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error);
+        }
+        MPI_Bcast(&d0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+      }
+    }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairMorse2::write_restart_settings(FILE *fp)
+{
+  fwrite(&cut_global,sizeof(double),1,fp);
+  fwrite(&offset_flag,sizeof(int),1,fp);
+  fwrite(&mix_flag,sizeof(int),1,fp);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairMorse2::read_restart_settings(FILE *fp)
+{
+  if (comm->me == 0) {
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,nullptr,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error);
+  }
+  MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
+  MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
+  MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void PairMorse2::write_data(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    fprintf(fp,"%d %g %g %g\n",i,d0[i][i],alpha[i][i],r0[i][i]);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes all pairs to data file
+------------------------------------------------------------------------- */
+
+void PairMorse2::write_data_all(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    for (int j = i; j <= atom->ntypes; j++)
+      fprintf(fp,"%d %d %g %g %g %g\n",
+              i,j,d0[i][j],alpha[i][j],r0[i][j],cut[i][j]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairMorse2::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+                         double /*factor_coul*/, double factor_lj,
+                         double &fforce)
+{
+  double r,dr,dexp,phi;
+
+  r = sqrt(rsq);
+  dr = r - r0[itype][jtype];
+  dexp = exp(-alpha[itype][jtype] * dr);
+  fforce = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r;
+
+  phi = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) - offset[itype][jtype];
+  return factor_lj*phi;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *PairMorse2::extract(const char *str, int &dim)
+{
+  dim = 2;
+  if (strcmp(str,"d0") == 0) return (void *) d0;
+  if (strcmp(str,"r0") == 0) return (void *) r0;
+  if (strcmp(str,"alpha") == 0) return (void *) alpha;
+  return nullptr;
+}

examples/plugins/pair_morse2.h

@@ -0,0 +1,70 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_PAIR_MORSE2_H
+#define LMP_PAIR_MORSE2_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairMorse2 : public Pair {
+ public:
+  PairMorse2(class LAMMPS *);
+  virtual ~PairMorse2();
+  virtual void compute(int, int);
+
+  void settings(int, char **);
+  void coeff(int, char **);
+  double init_one(int, int);
+  void write_restart(FILE *);
+  void read_restart(FILE *);
+  void write_restart_settings(FILE *);
+  void read_restart_settings(FILE *);
+  void write_data(FILE *);
+  void write_data_all(FILE *);
+  double single(int, int, int, int, double, double, double, double &);
+  void *extract(const char *, int &);
+
+ protected:
+  double cut_global;
+  double **cut;
+  double **d0,**alpha,**r0;
+  double **morse1;
+  double **offset;
+
+  virtual void allocate();
+};
+
+}
+
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+E: All pair coeffs are not set
+
+All pair coefficients must be set in the data file or by the
+pair_coeff command before running a simulation.
+
+*/

examples/plugins/pair_morse2_omp.cpp

@@ -0,0 +1,160 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://lammps.sandia.gov/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   This software is distributed under the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Axel Kohlmeyer (Temple U)
+------------------------------------------------------------------------- */
+
+#include "pair_morse2_omp.h"
+
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "neigh_list.h"
+#include "suffix.h"
+
+#include <cmath>
+
+#include "omp_compat.h"
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+PairMorse2OMP::PairMorse2OMP(LAMMPS *lmp) :
+  PairMorse2(lmp), ThrOMP(lmp, THR_PAIR)
+{
+  suffix_flag |= Suffix::OMP;
+  respa_enable = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairMorse2OMP::compute(int eflag, int vflag)
+{
+  ev_init(eflag,vflag);
+
+  const int nall = atom->nlocal + atom->nghost;
+  const int nthreads = comm->nthreads;
+  const int inum = list->inum;
+
+#if defined(_OPENMP)
+#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag,vflag)
+#endif
+  {
+    int ifrom, ito, tid;
+
+    loop_setup_thr(ifrom, ito, tid, inum, nthreads);
+    ThrData *thr = fix->get_thr(tid);
+    thr->timer(Timer::START);
+    ev_setup_thr(eflag, vflag, nall, eatom, vatom, nullptr, thr);
+
+    if (evflag) {
+      if (eflag) {
+        if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
+        else eval<1,1,0>(ifrom, ito, thr);
+      } else {
+        if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
+        else eval<1,0,0>(ifrom, ito, thr);
+      }
+    } else {
+      if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
+      else eval<0,0,0>(ifrom, ito, thr);
+    }
+
+    thr->timer(Timer::PAIR);
+    reduce_thr(this, eflag, vflag, thr);
+  } // end of omp parallel region
+}
+
+template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
+void PairMorse2OMP::eval(int iifrom, int iito, ThrData * const thr)
+{
+  int i,j,ii,jj,jnum,itype,jtype;
+  double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
+  double rsq,r,dr,dexp,factor_lj;
+  int *ilist,*jlist,*numneigh,**firstneigh;
+
+  evdwl = 0.0;
+
+  const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
+  dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
+  const int * _noalias const type = atom->type;
+  const int nlocal = atom->nlocal;
+  const double * _noalias const special_lj = force->special_lj;
+  double fxtmp,fytmp,fztmp;
+
+  ilist = list->ilist;
+  numneigh = list->numneigh;
+  firstneigh = list->firstneigh;
+
+  // loop over neighbors of my atoms
+
+  for (ii = iifrom; ii < iito; ++ii) {
+
+    i = ilist[ii];
+    xtmp = x[i].x;
+    ytmp = x[i].y;
+    ztmp = x[i].z;
+    itype = type[i];
+    jlist = firstneigh[i];
+    jnum = numneigh[i];
+    fxtmp=fytmp=fztmp=0.0;
+
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+      factor_lj = special_lj[sbmask(j)];
+      j &= NEIGHMASK;
+
+      delx = xtmp - x[j].x;
+      dely = ytmp - x[j].y;
+      delz = ztmp - x[j].z;
+      rsq = delx*delx + dely*dely + delz*delz;
+      jtype = type[j];
+
+      if (rsq < cutsq[itype][jtype]) {
+        r = sqrt(rsq);
+        dr = r - r0[itype][jtype];
+        dexp = exp(-alpha[itype][jtype] * dr);
+        fpair = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r;
+
+        fxtmp += delx*fpair;
+        fytmp += dely*fpair;
+        fztmp += delz*fpair;
+        if (NEWTON_PAIR || j < nlocal) {
+          f[j].x -= delx*fpair;
+          f[j].y -= dely*fpair;
+          f[j].z -= delz*fpair;
+        }
+
+        if (EFLAG) {
+          evdwl = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) -
+            offset[itype][jtype];
+          evdwl *= factor_lj;
+        }
+
+        if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
+                                 evdwl,0.0,fpair,delx,dely,delz,thr);
+      }
+    }
+    f[i].x += fxtmp;
+    f[i].y += fytmp;
+    f[i].z += fztmp;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairMorse2OMP::memory_usage()
+{
+  double bytes = memory_usage_thr();
+  bytes += PairMorse2::memory_usage();
+
+  return bytes;
+}

examples/plugins/pair_morse2_omp.h

@@ -0,0 +1,41 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Axel Kohlmeyer (Temple U)
+------------------------------------------------------------------------- */
+
+#ifndef LMP_PAIR_MORSE2_OMP_H
+#define LMP_PAIR_MORSE2_OMP_H
+
+#include "pair_morse2.h"
+#include "thr_omp.h"
+
+namespace LAMMPS_NS {
+
+class PairMorse2OMP : public PairMorse2, public ThrOMP {
+
+ public:
+  PairMorse2OMP(class LAMMPS *);
+
+  virtual void compute(int, int);
+  virtual double memory_usage();
+
+ private:
+  template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
+  void eval(int ifrom, int ito, ThrData * const thr);
+};
+
+}
+
+#endif

examples/plugins/pair_zero2.cpp

@@ -0,0 +1,247 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://lammps.sandia.gov/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Carsten Svaneborg (SDU)
+------------------------------------------------------------------------- */
+
+#include "pair_zero2.h"
+
+#include "atom.h"
+#include "comm.h"
+#include "memory.h"
+#include "error.h"
+
+#include <cstring>
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+PairZero2::PairZero2(LAMMPS *lmp) : Pair(lmp) {
+  coeffflag=1;
+  writedata=1;
+  single_enable=1;
+  respa_enable=1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairZero2::~PairZero2()
+{
+  if (allocated) {
+    memory->destroy(setflag);
+    memory->destroy(cutsq);
+    memory->destroy(cut);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairZero2::compute(int eflag, int vflag)
+{
+ ev_init(eflag,vflag);
+ if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairZero2::compute_outer(int eflag, int vflag)
+{
+ ev_init(eflag,vflag);
+}
+
+/* ----------------------------------------------------------------------
+   allocate all arrays
+------------------------------------------------------------------------- */
+
+void PairZero2::allocate()
+{
+  allocated = 1;
+  int n = atom->ntypes;
+
+  memory->create(setflag,n+1,n+1,"pair:setflag");
+  for (int i = 1; i <= n; i++)
+    for (int j = i; j <= n; j++)
+      setflag[i][j] = 0;
+
+  memory->create(cutsq,n+1,n+1,"pair:cutsq");
+  memory->create(cut,n+1,n+1,"pair:cut");
+}
+
+/* ----------------------------------------------------------------------
+   global settings
+------------------------------------------------------------------------- */
+
+void PairZero2::settings(int narg, char **arg)
+{
+  if ((narg != 1) && (narg != 2))
+    error->all(FLERR,"Illegal pair_style command");
+
+  cut_global = utils::numeric(FLERR,arg[0],false,lmp);
+  if (narg == 2) {
+    if (strcmp("nocoeff",arg[1]) == 0) coeffflag=0;
+    else error->all(FLERR,"Illegal pair_style command");
+  }
+
+  // reset cutoffs that have been explicitly set
+
+  if (allocated) {
+    int i,j;
+    for (i = 1; i <= atom->ntypes; i++)
+      for (j = i+1; j <= atom->ntypes; j++)
+        cut[i][j] = cut_global;
+  }
+}
+
+/* ----------------------------------------------------------------------
+   set coeffs for one or more type pairs
+------------------------------------------------------------------------- */
+
+void PairZero2::coeff(int narg, char **arg)
+{
+  if ((narg < 2) || (coeffflag && narg > 3))
+    error->all(FLERR,"Incorrect args for pair coefficients");
+
+  if (!allocated) allocate();
+
+  int ilo,ihi,jlo,jhi;
+  utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
+  utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
+
+  double cut_one = cut_global;
+  if (coeffflag && (narg == 3)) cut_one = utils::numeric(FLERR,arg[2],false,lmp);
+
+  int count = 0;
+  for (int i = ilo; i <= ihi; i++) {
+    for (int j = MAX(jlo,i); j <= jhi; j++) {
+      cut[i][j] = cut_one;
+      setflag[i][j] = 1;
+      count++;
+    }
+  }
+
+  if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+   init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+double PairZero2::init_one(int i, int j)
+{
+  if (setflag[i][j] == 0) {
+    cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
+  }
+
+  return cut[i][j];
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairZero2::write_restart(FILE *fp)
+{
+  write_restart_settings(fp);
+
+  int i,j;
+  for (i = 1; i <= atom->ntypes; i++)
+    for (j = i; j <= atom->ntypes; j++) {
+      fwrite(&setflag[i][j],sizeof(int),1,fp);
+      if (setflag[i][j]) {
+        fwrite(&cut[i][j],sizeof(double),1,fp);
+      }
+    }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairZero2::read_restart(FILE *fp)
+{
+  read_restart_settings(fp);
+  allocate();
+
+  int i,j;
+  int me = comm->me;
+  for (i = 1; i <= atom->ntypes; i++)
+    for (j = i; j <= atom->ntypes; j++) {
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error);
+      MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
+      if (setflag[i][j]) {
+        if (me == 0) {
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error);
+        }
+        MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+      }
+    }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairZero2::write_restart_settings(FILE *fp)
+{
+  fwrite(&cut_global,sizeof(double),1,fp);
+  fwrite(&coeffflag,sizeof(int),1,fp);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairZero2::read_restart_settings(FILE *fp)
+{
+  int me = comm->me;
+  if (me == 0) {
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error);
+    utils::sfread(FLERR,&coeffflag,sizeof(int),1,fp,nullptr,error);
+  }
+  MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
+  MPI_Bcast(&coeffflag,1,MPI_INT,0,world);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void PairZero2::write_data(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    fprintf(fp,"%d\n",i);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes all pairs to data file
+------------------------------------------------------------------------- */
+
+void PairZero2::write_data_all(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    for (int j = i; j <= atom->ntypes; j++)
+      fprintf(fp,"%d %d %g\n",i,j,cut[i][j]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairZero2::single(int /*i*/, int /*j*/, int /* itype */, int /* jtype */,
+                        double /* rsq */, double /*factor_coul*/,
+                        double /* factor_lj */, double &fforce)
+{
+  fforce = 0.0;
+  return 0.0;
+}
+

examples/plugins/pair_zero2.h

@@ -0,0 +1,77 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+
+   Pair zero is a dummy pair interaction useful for requiring a
+   force cutoff distance in the absence of pair-interactions or
+   with hybrid/overlay if a larger force cutoff distance is required.
+
+   This can be used in conjunction with bond/create to create bonds
+   that are longer than the cutoff of a given force field, or to
+   calculate radial distribution functions for models without
+   pair interactions.
+
+------------------------------------------------------------------------- */
+
+#ifndef LMP_PAIR_ZERO2_H
+#define LMP_PAIR_ZERO2_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairZero2 : public Pair {
+ public:
+  PairZero2(class LAMMPS *);
+  virtual ~PairZero2();
+  virtual void compute(int, int);
+  virtual void compute_outer(int, int);
+  void settings(int, char **);
+  void coeff(int, char **);
+  double init_one(int, int);
+  void write_restart(FILE *);
+  void read_restart(FILE *);
+  void write_restart_settings(FILE *);
+  void read_restart_settings(FILE *);
+  void write_data(FILE *);
+  void write_data_all(FILE *);
+  double single(int, int, int, int, double, double, double, double &);
+
+ protected:
+  double cut_global;
+  double **cut;
+  int coeffflag;
+
+  virtual void allocate();
+};
+
+}
+
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+U: Pair cutoff < Respa interior cutoff
+
+One or more pairwise cutoffs are too short to use with the specified
+rRESPA cutoffs.
+
+*/

examples/plugins/zero2plugin.cpp

@@ -0,0 +1,78 @@
+
+#include "lammpsplugin.h"
+#include "version.h"
+
+#include <cstring>
+
+#include "pair_zero2.h"
+#include "bond_zero2.h"
+#include "angle_zero2.h"
+#include "dihedral_zero2.h"
+#include "improper_zero2.h"
+
+using namespace LAMMPS_NS;
+
+static Pair *pairzerocreator(LAMMPS *lmp)
+{
+    return new PairZero2(lmp);
+}
+
+static Bond *bondzerocreator(LAMMPS *lmp)
+{
+    return new BondZero2(lmp);
+}
+
+static Angle *anglezerocreator(LAMMPS *lmp)
+{
+    return new AngleZero2(lmp);
+}
+
+static Dihedral *dihedralzerocreator(LAMMPS *lmp)
+{
+    return new DihedralZero2(lmp);
+}
+
+static Improper *improperzerocreator(LAMMPS *lmp)
+{
+    return new ImproperZero2(lmp);
+}
+
+extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
+{
+  lammpsplugin_t plugin;
+  lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
+
+  // register zero2 pair style
+  plugin.version = LAMMPS_VERSION;
+  plugin.style   = "pair";
+  plugin.name    = "zero2";
+  plugin.info    = "Zero2 variant pair style v1.0";
+  plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
+  plugin.creator.v1 = (lammpsplugin_factory1 *) &pairzerocreator;
+  plugin.handle  = handle;
+  (*register_plugin)(&plugin,lmp);
+
+  // register zero2 bond style
+  plugin.style   = "bond";
+  plugin.info    = "Zero2 variant bond style v1.0";
+  plugin.creator.v1 = (lammpsplugin_factory1 *) &bondzerocreator;
+  (*register_plugin)(&plugin,lmp);
+
+  // register zero2 angle style
+  plugin.style   = "angle";
+  plugin.info    = "Zero2 variant angle style v1.0";
+  plugin.creator.v1 = (lammpsplugin_factory1 *) &anglezerocreator;
+  (*register_plugin)(&plugin,lmp);
+
+  // register zero2 dihedral style
+  plugin.style   = "dihedral";
+  plugin.info    = "Zero2 variant dihedral style v1.0";
+  plugin.creator.v1 = (lammpsplugin_factory1 *) &dihedralzerocreator;
+  (*register_plugin)(&plugin,lmp);
+
+  // register zero2 improper style
+  plugin.style   = "improper";
+  plugin.info    = "Zero2 variant improper style v1.0";
+  plugin.creator.v1 = (lammpsplugin_factory1 *) &improperzerocreator;
+  (*register_plugin)(&plugin,lmp);
+}

lib/README

@@ -19,12 +19,12 @@ atc           atomistic-to-continuum methods, USER-ATC package
                 from Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia)
 awpmd         antisymmetrized wave packet molecular dynamics, AWPMD package
                 from Ilya Valuev (JIHT RAS)
-colvars	      collective variable module (Metadynamics, ABF and more)
+colvars       collective variable module (Metadynamics, ABF and more)
                 from Giacomo Fiorin and Jerome Henin (ICMS, Temple U)
 compress      hook to system lib for performing I/O compression, COMPRESS pkg
-	        from Axel Kohlmeyer (Temple U)
+                from Axel Kohlmeyer (Temple U)
-gpu	      general GPU routines, GPU package
+gpu           general GPU routines, GPU package
-	        from Mike Brown (ORNL)
+                from Mike Brown (ORNL)
 h5md          ch5md library for output of MD data in HDF5 format
                 from Pierre de Buyl (KU Leuven)
 kim           hooks to the KIM library, used by KIM package
@@ -32,26 +32,28 @@ kim           hooks to the KIM library, used by KIM package
 kokkos        Kokkos package for GPU and many-core acceleration
                 from Kokkos development team (Sandia)
 linalg        set of BLAS and LAPACK routines needed by USER-ATC package
-	        from Axel Kohlmeyer (Temple U)
+                from Axel Kohlmeyer (Temple U)
 message       client/server communication library via MPI, sockets, files
-	        from Steve Plimpton (Sandia)
+                from Steve Plimpton (Sandia)
 molfile       hooks to VMD molfile plugins, used by the USER-MOLFILE package
                 from Axel Kohlmeyer (Temple U) and the VMD development team
 mscg          hooks to the MSCG library, used by fix_mscg command
                 from Jacob Wagner and Greg Voth group (U Chicago)
 netcdf        hooks to a NetCDF library installed on your system
                 from Lars Pastewka (Karlsruhe Institute of Technology)
-poems	      POEMS rigid-body integration package, POEMS package
+plugin        settings to load styles into LAMMPS from plugins
+                from Axel Kohlmeyer (Temple U)
+poems         POEMS rigid-body integration package, POEMS package
                 from Rudranarayan Mukherjee (RPI)
 python        hooks to the system Python library, used by the PYTHON package
                 from the LAMMPS development team
-qmmm	      quantum mechanics/molecular mechanics coupling interface
+qmmm          quantum mechanics/molecular mechanics coupling interface
                 from Axel Kohlmeyer (Temple U)
 quip          interface to QUIP/libAtoms framework, USER-QUIP package
                 from Albert Bartok-Partay and Gabor Csanyi (U Cambridge)
 smd           hooks to Eigen library, used by USER-SMD package
                 from Georg Ganzenmueller (Ernst Mach Institute, Germany)
 voronoi       hooks to the Voro++ library, used by compute voronoi/atom command
-	        from Daniel Schwen (LANL)
+                from Daniel Schwen (LANL)
 vtk           hooks to the VTK library, used by dump custom/vtk command
                 from Richard Berger (JKU)

lib/gpu/Makefile.hip

@@ -1,6 +1,6 @@
 # /* ----------------------------------------------------------------------
 #  Generic Linux Makefile for HIP
-#     - export HIP_PLATFORM=hcc (or nvcc) before execution
+#     - export HIP_PLATFORM=amd (or nvcc) before execution
 #     - change HIP_ARCH for your GPU
 # ------------------------------------------------------------------------- */
 
@@ -42,6 +42,10 @@ ifeq (hcc,$(HIP_PLATFORM))
 	HIP_OPTS  += -ffast-math
 	# possible values: gfx803,gfx900,gfx906
 	HIP_ARCH = gfx906
+else ifeq (amd,$(HIP_PLATFORM))
+	HIP_OPTS  += -ffast-math
+	# possible values: gfx803,gfx900,gfx906
+	HIP_ARCH = gfx906
 else ifeq (nvcc,$(HIP_PLATFORM))
 	HIP_OPTS  += --use_fast_math
 	HIP_ARCH = -gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_32,code=[sm_32,compute_32] -gencode arch=compute_35,code=[sm_35,compute_35] \

lib/gpu/README

@@ -212,8 +212,8 @@ additionally requires cub (https://nvlabs.github.io/cub). Download and
 extract the cub directory to lammps/lib/gpu/ or specify an appropriate
 path in lammps/lib/gpu/Makefile.hip.
 2. In Makefile.hip it is possible to specify the target platform via
-export HIP_PLATFORM=hcc or HIP_PLATFORM=nvcc as well as the target
+export HIP_PLATFORM=amd (ROCm >= 4.1), HIP_PLATFORM=hcc (ROCm <= 4.0)
-architecture (gfx803, gfx900, gfx906 etc.)
+or HIP_PLATFORM=nvcc as well as the target architecture (gfx803, gfx900, gfx906 etc.)
 3. If your MPI implementation does not support `mpicxx --showme` command,
 it is required to specify the corresponding MPI compiler and linker flags
 in lammps/lib/gpu/Makefile.hip and in lammps/src/MAKE/OPTIONS/Makefile.hip.
@@ -278,4 +278,3 @@ and
 Brown, W.M., Masako, Y. Implementing Molecular Dynamics on Hybrid High
 Performance Computers - Three-Body Potentials. Computer Physics Communications.
 2013. 184: p. 2785–2793.
-

lib/gpu/lal_neighbor.cpp

@@ -740,6 +740,7 @@ void Neighbor::build_nbor_list(double **x, const int inum, const int host_inum,
 
   // If binning on GPU, do this now
   if (_gpu_nbor==1) {
+    mn = _max_nbors;
     const numtyp i_cell_size=static_cast<numtyp>(1.0/_cell_size);
     const int neigh_block=_block_cell_id;
     const int GX=(int)ceil((float)nall/neigh_block);