Merge branch 'master' into dpd_extended

.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
@@ -113,13 +118,13 @@ 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
   USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
   USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
-  USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF)
+  USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE)
 
 set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP)
 
@@ -382,7 +387,7 @@ else()
 endif()
 
 foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM
-        USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS)
+        USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL}) 
   endif()
@@ -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_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_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

@@ -131,7 +131,7 @@ if(GPU_API STREQUAL "CUDA")
   add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
   target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
   target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
-  target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
+  target_compile_definitions(gpu PRIVATE -DUSE_CUDA -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
   if(CUDPP_OPT)
     target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
     target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
@@ -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-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-PACE.cmake

@@ -0,0 +1,26 @@
+
+set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.4.9.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+set(PACELIB_MD5 "4db54962fbd6adcf8c18d46e1798ceb5" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+mark_as_advanced(PACELIB_URL)
+mark_as_advanced(PACELIB_MD5)
+
+# download library sources to build folder
+file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz SHOW_PROGRESS EXPECTED_HASH MD5=${PACELIB_MD5})
+
+# uncompress downloaded sources
+execute_process(
+  COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
+  COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
+  WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+)
+
+
+file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE)
+file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE/*.cpp)
+list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp)
+
+add_library(pace STATIC ${PACE_EVALUATOR_SOURCES})
+set_target_properties(pace PROPERTIES OUTPUT_NAME pace${LAMMPS_MACHINE})
+target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR})
+target_link_libraries(lammps PRIVATE pace)
+

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/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "10 March 2021" "2021-03-10"
+.TH LAMMPS "8 April 2021" "2021-04-08"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

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

@@ -52,6 +52,7 @@ This is the list of packages that may require additional steps.
    * :ref:`USER-MESONT <user-mesont>`
    * :ref:`USER-MOLFILE <user-molfile>`
    * :ref:`USER-NETCDF <user-netcdf>`
+   * :ref:`USER-PACE <user-pace>`
    * :ref:`USER-PLUMED <user-plumed>`
    * :ref:`USER-OMP <user-omp>`
    * :ref:`USER-QMMM <user-qmmm>`
@@ -125,7 +126,7 @@ 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 +170,24 @@ 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)
@@ -1240,6 +1248,46 @@ be built for the most part with all major versions of the C++ language.
 
 ----------
 
+.. _user-pace:
+
+USER-PACE package
+-----------------------------
+
+This package requires a library that can be downloaded and built 
+in lib/pace or somewhere else, which must be done before building 
+LAMMPS with this package. The code for the library can be found
+at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps-user-pace/>`_
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      By default the library will be downloaded from the git repository
+      and built automatically when the USER-PACE package is enabled with
+      ``-D PKG_USER-PACE=yes``.  The location for the sources may be
+      customized by setting the variable ``PACELIB_URL`` when
+      configuring with CMake (e.g. to use a local archive on machines
+      without internet access).  Since CMake checks the validity of the
+      archive with ``md5sum`` you may also need to set ``PACELIB_MD5``
+      if you provide a different library version than what is downloaded
+      automatically.
+
+
+   .. tab:: Traditional make
+
+      You can download and build the USER-PACE library
+      in one step from the ``lammps/src`` dir, using these commands, 
+      which invoke the ``lib/pace/Install.py`` script. 
+
+      .. code-block:: bash
+
+         $ make lib-pace                          # print help message
+         $ make lib-pace args="-b"                # download and build the default version in lib/pace
+
+      You should not need to edit the ``lib/pace/Makefile.lammps`` file.
+
+----------
+
 .. _user-plumed:
 
 USER-PLUMED package

doc/src/Build_package.rst

@@ -30,17 +30,17 @@ steps, as explained on the :doc:`Build extras <Build_extras>` page.
 These links take you to the extra instructions for those select
 packages:
 
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
 | :ref:`COMPRESS <compress>`           | :ref:`GPU <gpu>`               | :ref:`KIM <kim>`                   | :ref:`KOKKOS <kokkos>`       | :ref:`LATTE <latte>`           | :ref:`MESSAGE <message>`             |
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
 | :ref:`MSCG <mscg>`                   | :ref:`OPT <opt>`               | :ref:`POEMS <poems>`               | :ref:`PYTHON <python>`       | :ref:`VORONOI <voronoi>`       | :ref:`USER-ADIOS <user-adios>`       |
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
 | :ref:`USER-ATC <user-atc>`           | :ref:`USER-AWPMD <user-awpmd>` | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>` | :ref:`USER-INTEL <user-intel>` | :ref:`USER-MOLFILE <user-molfile>`   |
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
-| :ref:`USER-NETCDF <user-netcdf>` | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>`         | :ref:`USER-QMMM <user-qmmm>` | :ref:`USER-QUIP <user-quip>`   | :ref:`USER-SCAFACOS <user-scafacos>` |
+| :ref:`USER-NETCDF <user-netcdf>`     | :ref:`USER-PACE <user-pace>`   | :ref:`USER-PLUMED <user-plumed>`   | :ref:`USER-OMP <user-omp>`   | :ref:`USER-QMMM <user-qmmm>`   | :ref:`USER-QUIP <user-quip>`         |
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
-| :ref:`USER-SMD <user-smd>`       | :ref:`USER-VTK <user-vtk>`       |                                    |                              |                                |                                      |
+| :ref:`USER-SCAFACOS <user-scafacos>` | :ref:`USER-SMD <user-smd>`     | :ref:`USER-VTK <user-vtk>`         |                              |                                |                                      |
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
 
 The mechanism for including packages is simple but different for CMake
 versus make.

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_fix.rst

@@ -46,6 +46,7 @@ OPT.
    * :doc:`bond/react <fix_bond_react>`
    * :doc:`bond/swap <fix_bond_swap>`
    * :doc:`box/relax <fix_box_relax>`
+   * :doc:`charge/regulation <fix_charge_regulation>`
    * :doc:`client/md <fix_client_md>`
    * :doc:`cmap <fix_cmap>`
    * :doc:`colvars <fix_colvars>`

doc/src/Commands_pair.rst

@@ -26,6 +26,7 @@ OPT.
    * :doc:`zero <pair_zero>`
    * :doc:`hybrid (k) <pair_hybrid>`
    * :doc:`hybrid/overlay (k) <pair_hybrid>`
+   * :doc:`hybrid/scaled <pair_hybrid>`
    * :doc:`kim <pair_kim>`
    * :doc:`list <pair_list>`
    *
@@ -33,7 +34,6 @@ OPT.
    *
    *
    *
-   *
    * :doc:`adp (o) <pair_adp>`
    * :doc:`agni (o) <pair_agni>`
    * :doc:`airebo (io) <pair_airebo>`
@@ -69,6 +69,7 @@ OPT.
    * :doc:`comb3 <pair_comb>`
    * :doc:`cosine/squared <pair_cosine_squared>`
    * :doc:`coul/cut (gko) <pair_coul>`
+   * :doc:`coul/cut/global (o) <pair_coul>`
    * :doc:`coul/cut/soft (o) <pair_fep_soft>`
    * :doc:`coul/debye (gko) <pair_coul>`
    * :doc:`coul/diel (o) <pair_coul_diel>`
@@ -187,7 +188,7 @@ 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>`
@@ -215,6 +216,7 @@ OPT.
    * :doc:`oxrna2/stk <pair_oxrna2>`
    * :doc:`oxrna2/xstk <pair_oxrna2>`
    * :doc:`oxrna2/coaxstk <pair_oxrna2>`
+   * :doc:`pace <pair_pace>`
    * :doc:`peri/eps <pair_peri>`
    * :doc:`peri/lps (o) <pair_peri>`
    * :doc:`peri/pmb (o) <pair_peri>`

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

@@ -86,7 +86,33 @@ 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.
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      Change to your build folder and type:
+
+      .. code-block:: bash
+
+         cmake . --build
+
+      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
 
@@ -94,25 +120,25 @@ changed.  To do this, you should cd to the src directory and type:
          $ 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,
+      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
+         If you wish to edit/change a src file that is from a package,
-   package, you should edit the version of the file inside the package
+         you should edit the version of the file inside the package
-   sub-directory with src, then re-install the package.  The version in
+         sub-directory with src, then re-install the package.  The
-   the source directory is merely a copy and will be wiped out if you type "make
+         version in the source directory is merely a copy and will be
-   package-update".
+         wiped out if you type "make package-update".
 
-.. warning::
+.. admonition:: Git protocols
+   :class: note
 
-   The GitHub servers support both the "git://" and
+   The servers at github.com support the "git://" and "https://" access
-   "https://" access protocols for anonymous read-only access.  If you
+   protocols for anonymous, read-only access.  If you have a suitably
-   have a correspondingly configured GitHub account, you may also use
+   configured GitHub account, you may also use SSH protocol with the
-   SSH access with the URL "git@github.com:lammps/lammps.git".
+   URL "git@github.com:lammps/lammps.git".
 
-The LAMMPS GitHub project is managed by Christoph Junghans (LANL,
+The LAMMPS GitHub project is currently managed by Axel Kohlmeyer
-junghans at lanl.gov), Axel Kohlmeyer (Temple U, akohlmey at
+(Temple U, akohlmey at gmail.com) and Richard Berger (Temple U,
-gmail.com) and Richard Berger (Temple U, richard.berger at
+richard.berger at temple.edu).
-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
+* Once you have updated your local files you need to re-build LAMMPS.
-  don't use one or more packages.  If you are applying several patches
+  If you are applying several patches successively, you only need to
-  successively, you only need to type this once at the end. The purge
+  do the rebuild once at the end. How to do it depends on the build
-  command removes deprecated src files if any were removed by the patch
+  system you are using.
-  from package sub-directories.
+
+  .. tabs::
+
+     .. tab:: CMake build
+
+        Change to your build folder and type:
 
         .. code-block:: bash
 
-     $ make purge
+           cmake . --build
-     $ make package-update
 
-* Re-build LAMMPS via the "make" command.
+        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 source file that is part of a package,
+           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 folder in
+           you should edit the version of the file inside the package
-   src, and then re-install or update the package.  The version in the
+           sub-directory with src, then re-install the package.  The
-   src directory is merely a copy and will be wiped out when you type
+           version in the source directory is merely a copy and will be
-   "make package-update".
+           wiped out if you type "make package-update".

doc/src/Library_scatter.rst

@@ -76,7 +76,7 @@ It documents the following functions:
 
 -----------------------
 
-.. doxygenfunction:: lammps_create_atoms(void *handle, int n, int *id, int *type, double *x, double *v, int *image, int bexpand)
+.. doxygenfunction:: lammps_create_atoms(void *handle, int n, const int *id, const int *type, const double *x, const double *v, const int *image, int bexpand)
    :project: progguide
 
 

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>`
@@ -89,6 +90,7 @@ page gives those details.
    * :ref:`USER-MOLFILE <PKG-USER-MOLFILE>`
    * :ref:`USER-NETCDF <PKG-USER-NETCDF>`
    * :ref:`USER-OMP <PKG-USER-OMP>`
+   * :ref:`USER-PACE <PKG-USER-PACE>`
    * :ref:`USER-PHONON <PKG-USER-PHONON>`
    * :ref:`USER-PLUMED <PKG-USER-PLUMED>`
    * :ref:`USER-PTM <PKG-USER-PTM>`
@@ -584,7 +586,7 @@ MC package
 Several fixes and a pair style that have Monte Carlo (MC) or MC-like
 attributes.  These include fixes for creating, breaking, and swapping
 bonds, for performing atomic swaps, and performing grand-canonical MC
-(GCMC) in conjunction with dynamics.
+(GCMC) or similar processes in conjunction with dynamics.
 
 **Supporting info:**
 
@@ -592,8 +594,12 @@ bonds, for performing atomic swaps, and performing grand-canonical MC
 * :doc:`fix atom/swap <fix_atom_swap>`
 * :doc:`fix bond/break <fix_bond_break>`
 * :doc:`fix bond/create <fix_bond_create>`
+* :doc:`fix bond/create/angle <fix_bond_create>`
 * :doc:`fix bond/swap <fix_bond_swap>`
+* :doc:`fix charge/regulation <fix_charge_regulation>`
 * :doc:`fix gcmc <fix_gcmc>`
+* :doc:`fix tfmc <fix_tfmc>`
+* :doc:`fix widom <fix_widom>`
 * :doc:`pair_style dsmc <pair_dsmc>`
 * https://lammps.sandia.gov/movies.html#gcmc
 
@@ -843,6 +849,28 @@ 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
@@ -1326,6 +1354,46 @@ This package has :ref:`specific installation instructions <user-colvars>` on the
 
 ----------
 
+.. _PKG-USER-PACE:
+
+USER-PACE package
+-------------------
+
+**Contents:**
+
+A pair style for the Atomic Cluster Expansion potential (ACE).
+ACE is a methodology for deriving a highly accurate classical potential
+fit to a large archive of quantum mechanical (DFT) data. The USER-PACE
+package provides an efficient implementation for running simulations
+with ACE potentials.
+
+**Authors:**
+
+This package was written by Yury Lysogorskiy^1,
+Cas van der Oord^2, Anton Bochkarev^1,
+Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
+Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1.
+
+ ^1: Ruhr-University Bochum, Bochum, Germany
+
+ ^2: University of Cambridge, Cambridge, United Kingdom
+
+ ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
+
+ ^4: University of British Columbia, Vancouver, BC, Canada
+
+**Install:**
+
+This package has :ref:`specific installation instructions <user-pace>` on the :doc:`Build extras <Build_extras>` page.
+
+**Supporting info:**
+
+* src/USER-PACE: filenames -> commands
+* :doc:`pair_style pace <pair_pace>`
+* examples/USER/pace
+
+----------
+
 .. _PKG-USER-PLUMED:
 
 USER-PLUMED package
@@ -2456,6 +2524,6 @@ 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/Packages_user.rst

@@ -81,6 +81,8 @@ package:
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-OMP <PKG-USER-OMP>`                 | OpenMP-enabled styles                                           | :doc:`Speed omp <Speed_omp>`                                                  | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
+| :ref:`USER-PACE <PKG-USER-PACE>`               | Fast implementation of Atomic Cluster Expansion (ACE) potential | :doc:`pair pace <pair_pace>`                                                  | USER/pace                                            | ext     |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-PHONON <PKG-USER-PHONON>`           | phonon dynamical matrix                                         | :doc:`fix phonon <fix_phonon>`                                                | USER/phonon                                          | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-PLUMED <PKG-USER-PLUMED>`           | :ref:`PLUMED <PLUMED>` free energy library                      | :doc:`fix plumed <fix_plumed>`                                                | USER/plumed                                          | ext     |

doc/src/Python_module.rst

@@ -142,7 +142,7 @@ Style Constants
 Type Constants
 --------------
 
-.. py:data:: LMP_TYPE_SCALAR, LMP_TYLE_VECTOR, LMP_TYPE_ARRAY, LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS
+.. py:data:: LMP_TYPE_SCALAR, LMP_TYPE_VECTOR, LMP_TYPE_ARRAY, LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS
    :type: int
 
    Constants in the :py:mod:`lammps` module to select what type of data

doc/src/Python_neighbor.rst

@@ -1,6 +1,43 @@
 Neighbor list access
 ====================
 
+Access to neighbor lists is handled through a couple of wrapper classes
+that allows to treat it like either a python list or a NumPy array.  The
+access procedure is similar to that of the C-library interface: use one
+of the "find" functions to look up the index of the neighbor list in the
+global table of neighbor lists and then get access to the neighbor list
+data. The code sample below demonstrates reading the neighbor list data
+using the NumPy access method.
+
+.. code-block:: python
+
+   from lammps import lammps
+   import numpy as np
+
+   lmp = lammps()
+   lmp.commands_string("""
+   region box block -2 2 -2 2 -2 2
+   lattice fcc 1.0
+   create_box 1 box
+   create_atoms 1 box
+   mass 1 1.0
+   pair_style lj/cut 2.5
+   pair_coeff 1 1 1.0 1.0
+   run 0 post no""")
+
+   # look up the neighbor list
+   nlidx = lmp.find_pair_neighlist('lj/cut')
+   nl = lmp.numpy.get_neighlist(nlidx)
+   tags = lmp.extract_atom('id')
+   print("half neighbor list with {} entries".format(nl.size))
+   # print neighbor list contents
+   for i in range(0,nl.size):
+       idx, nlist  = nl.get(i)
+       print("\natom {} with ID {} has {} neighbors:".format(idx,tags[idx],nlist.size))
+       if nlist.size > 0:
+           for n in np.nditer(nlist):
+               print("  atom {} with ID {}".format(n,tags[n]))
+
 **Methods:**
 
 * :py:meth:`lammps.get_neighlist() <lammps.lammps.get_neighlist()>`: Get neighbor list for given index

doc/src/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/compute_pressure.rst

@@ -46,13 +46,14 @@ system volume (or area in 2d).  The second term is the virial, equal to
 -dU/dV, computed for all pairwise as well as 2-body, 3-body, 4-body,
 many-body, and long-range interactions, where :math:`r_i` and
 :math:`f_i` are the position and force vector of atom *i*, and the black
-dot indicates a dot product.  When periodic boundary conditions are
+dot indicates a dot product.  This is computed in parallel for each
-used, N' necessarily includes periodic image (ghost) atoms outside the
+sub-domain and then summed over all parallel processes. Thus N'
-central box, and the position and force vectors of ghost atoms are thus
+necessarily includes atoms from neighboring sub-domains (so-called ghost
-included in the summation.  When periodic boundary conditions are not
+atoms) and the position and force vectors of ghost atoms are thus
-used, N' = N = the number of atoms in the system.  :doc:`Fixes <fix>`
+included in the summation.  Only when running in serial and without
-that impose constraints (e.g. the :doc:`fix shake <fix_shake>` command)
+periodic boundary conditions is N' = N = the number of atoms in the
-also contribute to the virial term.
+system.  :doc:`Fixes <fix>` that impose constraints (e.g. the :doc:`fix
+shake <fix_shake>` command) may also contribute to the virial term.
 
 A symmetric pressure tensor, stored as a 6-element vector, is also
 calculated by this compute.  The 6 components of the vector are

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/dump_modify.rst

@@ -308,8 +308,8 @@ performed with dump style *xtc*\ .
 
 ----------
 
-The *format* keyword can be used to change the default numeric format
+The *format* keyword can be used to change the default numeric format output
-output by the text-based dump styles: *atom*\ , *custom*\ , *cfg*\ , and
+by the text-based dump styles: *atom*\ , *local*\ , *custom*\ , *cfg*\ , and
 *xyz* styles, and their MPIIO variants. Only the *line* or *none*
 options can be used with the *atom* and *xyz* styles.
 
@@ -362,7 +362,7 @@ settings, reverting all values to their default format.
 
    compute     1 all property/local batom1 batom2
    dump        1 all local 100 tmp.bonds index c_1[1] c_1[2]
-   dump_modify 1 format "%d %0.0f %0.0f"
+   dump_modify 1 format line "%d %0.0f %0.0f"
 
 will output the two atom IDs for atoms in each bond as integers.  If
 the dump_modify command were omitted, they would appear as

doc/src/fix.rst

@@ -189,6 +189,7 @@ accelerated styles exist.
 * :doc:`bond/react <fix_bond_react>` - apply topology changes to model reactions
 * :doc:`bond/swap <fix_bond_swap>` - Monte Carlo bond swapping
 * :doc:`box/relax <fix_box_relax>` - relax box size during energy minimization
+* :doc:`charge/regulation <fix_charge_regulation>` - Monte Carlo sampling of charge regulation
 * :doc:`client/md <fix_client_md>` - MD client for client/server simulations
 * :doc:`cmap <fix_cmap>` - enables CMAP cross-terms of the CHARMM force field
 * :doc:`colvars <fix_colvars>` - interface to the collective variables "Colvars" library

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_ave_histo.rst

@@ -138,8 +138,8 @@ vector or columns of the array had been listed one by one.  E.g. these
 .. code-block:: LAMMPS
 
    compute myCOM all com/chunk
-   fix 1 all ave/histo 100 1 100 c_myCOM[*] file tmp1.com mode vector
+   fix 1 all ave/histo 100 1 100 -10.0 10.0 100 c_myCOM[*] file tmp1.com mode vector
-   fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector
+   fix 2 all ave/histo 100 1 100 -10.0 10.0 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector
 
 If the fix ave/histo/weight command is used, exactly two values must
 be specified.  If the values are vectors, they must be the same

doc/src/fix_charge_regulation.rst

@@ -0,0 +1,276 @@
+
+.. index:: fix charge/regulation
+
+fix charge/regulation command
+=============================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+    fix ID group-ID charge/regulation cation_type anion_type keyword value(s)
+
+* ID, group-ID are documented in fix command
+* charge/regulation = style name of this fix command
+* cation_type = atom type of free cations
+* anion_type = atom type of free anions
+
+* zero or more keyword/value pairs may be appended
+
+  .. parsed-literal::
+
+     keyword = *pH*, *pKa*, *pKb*, *pIp*, *pIm*, *pKs*, *acid_type*, *base_type*, *lunit_nm*, *temp*, *tempfixid*, *nevery*, *nmc*, *xrd*, *seed*, *tag*, *group*, *onlysalt*, *pmcmoves*
+     *pH* value = pH of the solution
+     *pKa* value = acid dissociation constant
+     *pKb* value = base dissociation constant
+     *pIp* value = chemical potential of free cations
+     *pIm* value = chemical potential of free anions
+     *pKs* value = solution self-dissociation constant
+     *acid_type* = atom type of acid groups
+     *base_type*  = atom type of base groups
+     *lunit_nm* value = unit length used by LAMMPS (# in the units of nanometers)
+     *temp* value = temperature
+     *tempfixid* value = fix ID of temperature thermostat
+     *nevery* value = invoke this fix every nevery steps
+     *nmc* value = number of charge regulation MC moves to attempt every nevery steps
+     *xrd* value = cutoff distance for acid/base reaction
+     *seed* value = random # seed (positive integer)
+     *tag* value = yes or no (yes: The code assign unique tags to inserted ions; no: The tag of all inserted ions is "0")
+     *group* value = group-ID, inserted ions are assigned to group group-ID. Can be used multiple times to assign inserted ions to multiple groups.
+     *onlysalt* values = flag charge_cation charge_anion.
+        flag = yes or no (yes: the fix performs only ion insertion/deletion, no: perform acid/base dissociation and ion insertion/deletion)
+        charge_cation, charge_anion = value of cation/anion charge, must be an integer (only specify if flag = yes)
+     *pmcmoves* values = pmcA pmcB pmcI -  MC move fractions for acid ionization (pmcA), base ionization (pmcB) and free ion exchange (pmcI)
+
+Examples
+""""""""
+.. code-block:: LAMMPS
+
+    fix chareg all charge/regulation 1 2 acid_type 3 base_type 4 pKa 5 pKb 7 lb 1.0 nevery 200 nexchange 200 seed 123 tempfixid fT
+
+    fix chareg all charge/regulation 1 2 pIp 3 pIm 3 onlysalt yes 2 -1 seed 123 tag yes temp 1.0
+
+Description
+"""""""""""
+
+This fix performs Monte Carlo (MC) sampling of charge regulation and
+exchange of ions with a reservoir as discussed in :ref:`(Curk1) <Curk1>`
+and :ref:`(Curk2) <Curk2>`.  The implemented method is largely analogous
+to the grand-reaction ensemble method in :ref:`(Landsgesell)
+<Landsgesell>`.  The implementation is parallelized, compatible with
+existing LAMMPS functionalities, and applicable to any system utilizing
+discrete, ionizable groups or surface sites.
+
+Specifically, the fix implements the following three types of MC moves,
+which discretely change the charge state of individual particles and
+insert ions into the systems: :math:`\mathrm{A} \rightleftharpoons
+\mathrm{A}^-+\mathrm{X}^+`, :math:`\mathrm{B} \rightleftharpoons
+\mathrm{B}^++\mathrm{X}^-`, and :math:`\emptyset \rightleftharpoons
+Z^-\mathrm{X}^{Z^+}+Z^+\mathrm{X}^{-Z^-}`.  In the former two types of
+reactions, Monte Carlo moves alter the charge value of specific atoms
+(:math:`\mathrm{A}`, :math:`\mathrm{B}`) and simultaneously insert a
+counterion to preserve the charge neutrality of the system, modeling the
+dissociation/association process.  The last type of reaction performs
+grand canonical MC exchange of ion pairs with a (fictitious) reservoir.
+
+In our implementation "acid" refers to particles that can attain charge
+:math:`q=\{0,-1\}` and "base" to particles with :math:`q=\{0,1\}`,
+whereas the MC exchange of free ions allows any integer charge values of
+:math:`{Z^+}` and :math:`{Z^-}`.
+
+Here we provide several practical examples for modeling charge
+regulation effects in solvated systems.  An acid ionization reaction
+(:math:`\mathrm{A} \rightleftharpoons \mathrm{A}^-+\mathrm{H}^+`) can be
+defined via a single line in the input file
+
+.. code-block:: LAMMPS
+
+    fix acid_reaction all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 5.0 pIp 7.0 pIm 7.0
+
+where the fix attempts to charge :math:`\mathrm{A}` (discharge
+:math:`\mathrm{A}^-`) to :math:`\mathrm{A}^-` (:math:`\mathrm{A}`) and
+insert (delete) a proton (atom type 2). Besides, the fix implements
+self-ionization reaction of water :math:`\emptyset \rightleftharpoons
+\mathrm{H}^++\mathrm{OH}^-`.  However, this approach is highly
+inefficient at :math:`\mathrm{pH} \approx 7` when the concentration of
+both protons and hydroxyl ions is low, resulting in a relatively low
+acceptance rate of MC moves.
+
+A more efficient way is to allow salt ions to participate in ionization
+reactions, which can be easily achieved via
+
+.. code-block:: LAMMPS
+
+    fix acid_reaction all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 5.0 pIp 2.0 pIm 2.0
+
+where particles of atom type 4 and 5 are the salt cations and anions,
+both at chemical potential pI=2.0, see :ref:`(Curk1) <Curk1>` and
+:ref:`(Landsgesell) <Landsgesell>` for more details.
+
+
+ Similarly, we could have simultaneously added a base ionization reaction
+ (:math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{OH}^-`)
+
+.. code-block:: LAMMPS
+
+    fix base_reaction all charge/regulation 2 3 base_type 6 pH 7.0 pKb 6.0 pIp 7.0 pIm 7.0
+
+where the fix will attempt to charge :math:`\mathrm{B}` (discharge
+:math:`\mathrm{B}^+`) to :math:`\mathrm{B}^+` (:math:`\mathrm{B}`) and
+insert (delete) a hydroxyl ion :math:`\mathrm{OH}^-` of atom type 3.  If
+neither the acid or the base type is specified, for example,
+
+.. code-block:: LAMMPS
+
+    fix salt_reaction all charge/regulation 4 5 pIp 2.0 pIm 2.0
+
+the fix simply inserts or deletes an ion pair of a free cation (atom
+type 4) and a free anion (atom type 5) as done in a conventional
+grand-canonical MC simulation.
+
+
+The fix is compatible with LAMMPS sub-packages such as *molecule* or
+*rigid*. That said, the acid and base particles can be part of larger
+molecules or rigid bodies. Free ions that are inserted to or deleted
+from the system must be defined as single particles (no bonded
+interactions allowed) and cannot be part of larger molecules or rigid
+bodies. If *molecule* package is used, all inserted ions have a molecule
+ID equal to zero.
+
+Note that LAMMPS implicitly assumes a constant number of particles
+(degrees of freedom). Since using this fix alters the total number of
+particles during the simulation, any thermostat used by LAMMPS, such as
+NVT or Langevin, must use a dynamic calculation of system
+temperature. This can be achieved by specifying a dynamic temperature
+compute (e.g. dtemp) and using it with the desired thermostat, e.g. a
+Langevin thermostat:
+
+.. code-block:: LAMMPS
+
+    compute dtemp all temp
+    compute_modify dtemp dynamic yes
+    fix fT all langevin 1.0 1.0 1.0 123
+    fix_modify fT temp dtemp
+
+The chemical potential units (e.g. pH) are in the standard log10
+representation assuming reference concentration :math:`\rho_0 =
+\mathrm{mol}/\mathrm{l}`.  Therefore, to perform the internal unit
+conversion, the length (in nanometers) of the LAMMPS unit length must be
+specified via *lunit_nm* (default is set to the Bjerrum length in water
+at room temperature *lunit_nm* = 0.71nm). For example, in the dilute
+ideal solution limit, the concentration of free ions will be
+:math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`.
+
+The temperature used in MC acceptance probability is set by *temp*. This
+temperature should be the same as the temperature set by the molecular
+dynamics thermostat. For most purposes, it is probably best to use
+*tempfixid* keyword which dynamically sets the temperature equal to the
+chosen MD thermostat temperature, in the example above we assumed the
+thermostat fix-ID is *fT*. The inserted particles attain a random
+velocity corresponding to the specified temperature. Using *tempfixid*
+overrides any fixed temperature set by *temp*.
+
+The *xrd* keyword can be used to restrict the inserted/deleted
+counterions to a specific radial distance from an acid or base particle
+that is currently participating in a reaction. This can be used to
+simulate more realist reaction dynamics. If *xrd* = 0 or *xrd* > *L* /
+2, where *L* is the smallest box dimension, the radial restriction is
+automatically turned off and free ion can be inserted or deleted
+anywhere in the simulation box.
+
+If the *tag yes* is used, every inserted atom gets a unique tag ID,
+otherwise, the tag of every inserted atom is set to 0. *tag yes* might
+cause an integer overflow in very long simulations since the tags are
+unique to every particle and thus increase with every successful
+particle insertion.
+
+The *pmcmoves* keyword sets the relative probability of attempting the
+three types of MC moves (reactions): acid charging, base charging, and
+ion pair exchange.  The fix only attempts to perform particle charging
+MC moves if *acid_type* or *base_type* is defined. Otherwise fix only
+performs free ion insertion/deletion. For example, if *acid_type* is not
+defined, *pmcA* is automatically set to 0. The vector *pmcmoves* is
+automatically normalized, for example, if set to *pmcmoves* 0 0.33 0.33,
+the vector would be normalized to [0,0.5,0.5].
+
+The *only_salt* option can be used to perform multivalent
+grand-canonical ion-exchange moves. If *only_salt yes* is used, no
+charge exchange is performed, only ion insertion/deletion (*pmcmoves* is
+set to [0,0,1]), but ions can be multivalent. In the example above, an
+MC move would consist of three ion insertion/deletion to preserve the
+charge neutrality of the system.
+
+The *group* keyword can be used to add inserted particles to a specific
+group-ID. All inserted particles are automatically added to group *all*.
+
+
+Output
+""""""
+
+This fix computes a global vector of length 8, which can be accessed by
+various output commands. The vector values are the following global
+quantities:
+
+* 1 = cumulative MC attempts
+* 2 = cumulative MC successes
+* 3 = current # of neutral acid atoms
+* 4 = current # of -1 charged acid atoms
+* 5 = current # of neutral base atoms
+* 6 = current # of +1 charged base atoms
+* 7 = current # of free cations
+* 8 = current # of free anions
+
+
+Restrictions
+""""""""""""
+
+This fix is part of the MC package. It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package
+<Build_package>` doc page for more info.
+
+The :doc:`atom_style <atom_style>`, used must contain the charge
+property, for example, the style could be *charge* or *full*. Only
+usable for 3D simulations. Atoms specified as free ions cannot be part
+of rigid bodies or molecules and cannot have bonding interactions. The
+scheme is limited to integer charges, any atoms with non-integer charges
+will not be considered by the fix.
+
+All interaction potentials used must be continuous, otherwise the MD
+integration and the particle exchange MC moves do not correspond to the
+same equilibrium ensemble. For example, if an lj/cut pair style is used,
+the LJ potential must be shifted so that it vanishes at the cutoff. This
+can be easily achieved using the :doc:`pair_modify <pair_modify>`
+command, i.e., by using: *pair_modify shift yes*.
+
+.. note::
+
+   Region restrictions are not yet implemented.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix gcmc <fix_gcmc>`,
+:doc:`fix atom/swap <fix_atom_swap>`
+
+Default
+"""""""
+
+pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs = 14.0;
+acid_type = -1; base_type = -1; lunit_nm = 0.71; temp = 1.0; nevery =
+100; nmc = 100; xrd = 0; seed = 0; tag = no; onlysalt = no, pmcmoves =
+[1/3, 1/3, 1/3], group-ID = all
+
+----------
+
+.. _Curk1:
+
+**(Curk1)** T. Curk, J. Yuan, and E. Luijten, "Coarse-grained simulation of charge regulation using LAMMPS", preprint (2021).
+
+.. _Curk2:
+
+**(Curk2)** T. Curk and E. Luijten, "Charge-regulation effects in nanoparticle self-assembly", PRL (2021)
+
+.. _Landsgesell:
+
+**(Landsgesell)** J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Kosovan, and C. Holm, "Grand-reaction method for simulations of ionization equilibria coupled to ion partitioning", Macromolecules 53, 3007-3020 (2020).

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_wall_gran.rst

@@ -29,6 +29,7 @@ Syntax
              gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)
              xmu = static yield criterion (unitless value between 0.0 and 1.0e4)
              dampflag = 0 or 1 if tangential damping force is excluded or included
+             optional keyword = *limit_damping*, limit damping to prevent attractive interaction
 
   .. parsed-literal::
 
@@ -95,7 +96,8 @@ Specifically, delta = radius - r = overlap of particle with wall, m_eff
 = mass of particle, and the effective radius of contact = RiRj/Ri+Rj is
 set to the radius of the particle.
 
-The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu* and *dampflag*
+The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu*, *dampflag*,
+and the optional keyword *limit_damping*
 have the same meaning and units as those specified with the
 :doc:`pair_style gran/\* <pair_gran>` commands.  This means a NULL can be
 used for either *Kt* or *gamma_t* as described on that page.  If a

doc/src/fix_wall_gran_region.rst

@@ -181,7 +181,8 @@ radius - r = overlap of particle with wall, m_eff = mass of particle,
 and the effective radius of contact is just the radius of the
 particle.
 
-The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu* and *dampflag*
+The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu*, *dampflag*,
+and the optional keyword *limit_damping*
 have the same meaning and units as those specified with the
 :doc:`pair_style gran/\* <pair_gran>` commands.  This means a NULL can be
 used for either *Kt* or *gamma_t* as described on that page.  If a

doc/src/pair_coul.rst

@@ -10,6 +10,8 @@
 .. index:: pair_style coul/dsf/gpu
 .. index:: pair_style coul/dsf/kk
 .. index:: pair_style coul/dsf/omp
+.. index:: pair_style coul/cut/global
+.. index:: pair_style coul/cut/global/omp
 .. index:: pair_style coul/long
 .. index:: pair_style coul/long/omp
 .. index:: pair_style coul/long/kk
@@ -40,6 +42,11 @@ pair_style coul/dsf command
 
 Accelerator Variants: *coul/dsf/gpu*, *coul/dsf/kk*, *coul/dsf/omp*
 
+pair_style coul/cut/global command
+==================================
+
+Accelerator Variants: *coul/cut/omp*
+
 pair_style coul/long command
 ============================
 
@@ -76,8 +83,8 @@ Syntax
    pair_style coul/cut cutoff
    pair_style coul/debye kappa cutoff
    pair_style coul/dsf alpha cutoff
+   pair_style coul/cut/global cutoff
    pair_style coul/long cutoff
-   pair_style coul/long/gpu cutoff
    pair_style coul/wolf alpha cutoff
    pair_style coul/streitz cutoff keyword alpha
    pair_style tip4p/cut otype htype btype atype qdist cutoff
@@ -245,6 +252,11 @@ Streitz-Mintmire parameterization for the material being modeled.
 
 ----------
 
+Pair style *coul/cut/global* computes the same Coulombic interactions
+as style *coul/cut* except that it allows only a single global cutoff
+and thus makes it compatible for use in combination with long-range
+coulomb styles in :doc:`hybrid pair styles <pair_hybrid>`.
+
 Styles *coul/long* and *coul/msm* compute the same Coulombic
 interactions as style *coul/cut* except that an additional damping
 factor is applied so it can be used in conjunction with the

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_gran.rst

@@ -26,7 +26,7 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   pair_style style Kn Kt gamma_n gamma_t xmu dampflag
+   pair_style style Kn Kt gamma_n gamma_t xmu dampflag keyword
 
 * style = *gran/hooke* or *gran/hooke/history* or *gran/hertz/history*
 * Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
@@ -36,6 +36,13 @@ Syntax
 * xmu = static yield criterion (unitless value between 0.0 and 1.0e4)
 * dampflag = 0 or 1 if tangential damping force is excluded or included
 
+* keyword = *limit_damping*
+
+  .. parsed-literal::
+
+      *limit_damping* value = none
+         limit damping to prevent attractive interaction
+
 .. note::
 
    Versions of LAMMPS before 9Jan09 had different style names for
@@ -54,6 +61,8 @@ Examples
 
    pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 1
    pair_style gran/hooke 200000.0 70000.0 50.0 30.0 0.5 0
+   pair_style gran/hooke 200000.0 70000.0 50.0 30.0 0.5 0 limit_damping
+
 
 Description
 """""""""""
@@ -208,6 +217,12 @@ potential is used as a sub-style of :doc:`pair_style hybrid <pair_hybrid>`, then
 pair_coeff command to determine which atoms interact via a granular
 potential.
 
+If two particles are moving away from each other while in contact, there
+is a possibility that the particles could experience an effective attractive
+force due to damping. If the *limit_damping* keyword is used, this option
+will zero out the normal component of the force if there is an effective
+attractive force.
+
 ----------
 
 .. include:: accel_styles.rst

doc/src/pair_granular.rst

@@ -24,7 +24,7 @@ Examples
    pair_coeff * * hooke 1000.0 50.0 tangential linear_history 500.0 1.0 0.4 damping mass_velocity
 
    pair_style granular
-   pair_coeff * * hertz 1000.0 50.0 tangential mindlin 1000.0 1.0 0.4
+   pair_coeff * * hertz 1000.0 50.0 tangential mindlin 1000.0 1.0 0.4 limit_damping
 
    pair_style granular
    pair_coeff * * hertz/material 1e8 0.3 0.3 tangential mindlin_rescale NULL 1.0 0.4 damping tsuji
@@ -623,6 +623,14 @@ Finally, the twisting torque on each particle is given by:
 
 ----------
 
+If two particles are moving away from each other while in contact, there
+is a possibility that the particles could experience an effective attractive
+force due to damping. If the optional *limit_damping* keyword is used, this option
+will zero out the normal component of the force if there is an effective
+attractive force. This keyword cannot be used with the JKR or DMT models.
+
+----------
+
 The *granular* pair style can reproduce the behavior of the
 *pair gran/\** styles with the appropriate settings (some very
 minor differences can be expected due to corrections in
@@ -657,6 +665,12 @@ then LAMMPS will use that cutoff for the specified atom type
 combination, and automatically set pairwise cutoffs for the remaining
 atom types.
 
+If two particles are moving away from each other while in contact, there
+is a possibility that the particles could experience an effective attractive
+force due to damping. If the *limit_damping* keyword is used, this option
+will zero out the normal component of the force if there is an effective
+attractive force. This keyword cannot be used with the JKR or DMT models.
+
 ----------
 
 .. include:: accel_styles.rst

doc/src/pair_hybrid.rst

@@ -2,6 +2,7 @@
 .. index:: pair_style hybrid/kk
 .. index:: pair_style hybrid/overlay
 .. index:: pair_style hybrid/overlay/kk
+.. index:: pair_style hybrid/scaled
 
 pair_style hybrid command
 =========================
@@ -13,6 +14,9 @@ pair_style hybrid/overlay command
 
 Accelerator Variants: *hybrid/overlay/kk*
 
+pair_style hybrid/scaled command
+==================================
+
 Syntax
 """"""
 
@@ -20,8 +24,10 @@ Syntax
 
    pair_style hybrid style1 args style2 args ...
    pair_style hybrid/overlay style1 args style2 args ...
+   pair_style hybrid/scaled factor1 style1 args factor2 style 2 args ...
 
 * style1,style2 = list of one or more pair styles and their arguments
+* factor1,factor2 = scale factors for pair styles, may be a variable
 
 Examples
 """"""""
@@ -37,47 +43,73 @@ Examples
    pair_coeff * * lj/cut 1.0 1.0
    pair_coeff * * coul/long
 
+   pair_style hybrid/scaled 0.5 tersoff 0.5 sw
+   pair_coeff * * tersoff Si.tersoff Si
+   pair_coeff * * sw Si.sw Si
+
+   variable one equal ramp(1.0,0.0)
+   variable two equal 1.0-v_one
+   pair_style hybrid/scaled v_one lj/cut 2.5 v_two morse 2.5
+   pair_coeff 1 1 lj/cut 1.0 1.0 2.5
+   pair_coeff 1 1 morse 1.0 1.0 1.0 2.5
+
 Description
 """""""""""
 
-The *hybrid* and *hybrid/overlay* styles enable the use of multiple
+The *hybrid*, *hybrid/overlay*, and *hybrid/scaled* styles enable the
-pair styles in one simulation.  With the *hybrid* style, exactly one
+use of multiple pair styles in one simulation.  With the *hybrid* style,
-pair style is assigned to each pair of atom types.  With the
+exactly one pair style is assigned to each pair of atom types.  With the
-*hybrid/overlay* style, one or more pair styles can be assigned to
+*hybrid/overlay* and *hybrid/scaled* styles, one or more pair styles can
-each pair of atom types.  The assignment of pair styles to type pairs
+be assigned to each pair of atom types.  The assignment of pair styles
-is made via the :doc:`pair_coeff <pair_coeff>` command.
+to type pairs is made via the :doc:`pair_coeff <pair_coeff>` command.
+The major difference between the *hybrid/overlay* and *hybrid/scaled*
+styles is that the *hybrid/scaled* adds a scale factor for each
+sub-style contribution to forces, energies and stresses.  Because of the
+added complexity, the *hybrid/scaled* style has more overhead and thus
+may be slower than *hybrid/overlay*.
 
 Here are two examples of hybrid simulations.  The *hybrid* style could
-be used for a simulation of a metal droplet on a LJ surface.  The
+be used for a simulation of a metal droplet on a LJ surface.  The metal
-metal atoms interact with each other via an *eam* potential, the
+atoms interact with each other via an *eam* potential, the surface atoms
-surface atoms interact with each other via a *lj/cut* potential, and
+interact with each other via a *lj/cut* potential, and the metal/surface
-the metal/surface interaction is also computed via a *lj/cut*
+interaction is also computed via a *lj/cut* potential.  The
-potential.  The *hybrid/overlay* style could be used as in the second
+*hybrid/overlay* style could be used as in the second example above,
-example above, where multiple potentials are superposed in an additive
+where multiple potentials are superposed in an additive fashion to
-fashion to compute the interaction between atoms.  In this example,
+compute the interaction between atoms.  In this example, using *lj/cut*
-using *lj/cut* and *coul/long* together gives the same result as if
+and *coul/long* together gives the same result as if the
-the *lj/cut/coul/long* potential were used by itself.  In this case,
+*lj/cut/coul/long* potential were used by itself.  In this case, it
-it would be more efficient to use the single combined potential, but
+would be more efficient to use the single combined potential, but in
-in general any combination of pair potentials can be used together in
+general any combination of pair potentials can be used together in to
-to produce an interaction that is not encoded in any single pair_style
+produce an interaction that is not encoded in any single pair_style
 file, e.g. adding Coulombic forces between granular particles.
 
+If the *hybrid/scaled* style is used instead of *hybrid/overlay*\ ,
+contributions from sub-styles are weighted by their scale factors, which
+may be fractional or even negative.  Furthermore the scale factors may
+be variables that may change during a simulation.  This enables
+switching smoothly between two different pair styles or two different
+parameter sets during a run.
+
 All pair styles that will be used are listed as "sub-styles" following
-the *hybrid* or *hybrid/overlay* keyword, in any order.  Each
+the *hybrid* or *hybrid/overlay* keyword, in any order.  In case of the
-sub-style's name is followed by its usual arguments, as illustrated in
+*hybrid/scaled* pair style, each sub-style is prefixed with a scale
-the example above.  See the doc pages of individual pair styles for a
+factor.  The scale factor is either a floating point number or an equal
-listing and explanation of the appropriate arguments.
+style (or equivalent) variable.  Each sub-style's name is followed by
+its usual arguments, as illustrated in the examples above.  See the doc
+pages of the individual pair styles for a listing and explanation of the
+appropriate arguments for them.
 
 Note that an individual pair style can be used multiple times as a
-sub-style.  For efficiency this should only be done if your model
+sub-style.  For efficiency reasons this should only be done if your
-requires it.  E.g. if you have different regions of Si and C atoms and
+model requires it.  E.g. if you have different regions of Si and C atoms
-wish to use a Tersoff potential for pure Si for one set of atoms, and
+and wish to use a Tersoff potential for pure Si for one set of atoms,
-a Tersoff potential for pure C for the other set (presumably with some
+and a Tersoff potential for pure C for the other set (presumably with
-third potential for Si-C interactions), then the sub-style *tersoff*
+some third potential for Si-C interactions), then the sub-style
-could be listed twice.  But if you just want to use a Lennard-Jones or
+*tersoff* could be listed twice.  But if you just want to use a
-other pairwise potential for several different atom type pairs in your
+Lennard-Jones or other pairwise potential for several different atom
-model, then you should just list the sub-style once and use the
+type pairs in your model, then you should just list the sub-style once
-pair_coeff command to assign parameters for the different type pairs.
+and use the pair_coeff command to assign parameters for the different
+type pairs.
 
 .. note::
 
@@ -143,16 +175,16 @@ one sub-style.  Just as with a simulation using a single pair style,
 if you specify the same atom type pair in a second pair_coeff command,
 the previous assignment will be overwritten.
 
-For the *hybrid/overlay* style, each atom type pair I,J can be
+For the *hybrid/overlay* and *hybrid/scaled* styles, each atom type pair
-assigned to one or more sub-styles.  If you specify the same atom type
+I,J can be assigned to one or more sub-styles.  If you specify the same
-pair in a second pair_coeff command with a new sub-style, then the
+atom type pair in a second pair_coeff command with a new sub-style, then
-second sub-style is added to the list of potentials that will be
+the second sub-style is added to the list of potentials that will be
-calculated for two interacting atoms of those types.  If you specify
+calculated for two interacting atoms of those types.  If you specify the
-the same atom type pair in a second pair_coeff command with a
+same atom type pair in a second pair_coeff command with a sub-style that
-sub-style that has already been defined for that pair of atoms, then
+has already been defined for that pair of atoms, then the new pair
-the new pair coefficients simply override the previous ones, as in the
+coefficients simply override the previous ones, as in the normal usage
-normal usage of the pair_coeff command.  E.g. these two sets of
+of the pair_coeff command.  E.g. these two sets of commands are the
-commands are the same:
+same:
 
 .. code-block:: LAMMPS
 
@@ -166,23 +198,24 @@ commands are the same:
 
 Coefficients must be defined for each pair of atoms types via the
 :doc:`pair_coeff <pair_coeff>` command as described above, or in the
-data file or restart files read by the :doc:`read_data <read_data>` or
+data file read by the :doc:`read_data <read_data>` commands, or by
-:doc:`read_restart <read_restart>` commands, or by mixing as described
+mixing as described below.
-below.
 
-For both the *hybrid* and *hybrid/overlay* styles, every atom type
+For all of the *hybrid*, *hybrid/overlay*, and *hybrid/scaled* styles,
-pair I,J (where I <= J) must be assigned to at least one sub-style via
+every atom type pair I,J (where I <= J) must be assigned to at least one
-the :doc:`pair_coeff <pair_coeff>` command as in the examples above, or
+sub-style via the :doc:`pair_coeff <pair_coeff>` command as in the
-in the data file read by the :doc:`read_data <read_data>`, or by mixing
+examples above, or in the data file read by the :doc:`read_data
-as described below.
+<read_data>`, or by mixing as described below.  Also all sub-styles
+must be used at least once in a :doc:`pair_coeff <pair_coeff>` command.
 
 If you want there to be no interactions between a particular pair of
 atom types, you have 3 choices.  You can assign the type pair to some
 sub-style and use the :doc:`neigh_modify exclude type <neigh_modify>`
 command.  You can assign it to some sub-style and set the coefficients
-so that there is effectively no interaction (e.g. epsilon = 0.0 in a
+so that there is effectively no interaction (e.g. epsilon = 0.0 in a LJ
-LJ potential).  Or, for *hybrid* and *hybrid/overlay* simulations, you
+potential).  Or, for *hybrid*, *hybrid/overlay*, or *hybrid/scaled*
-can use this form of the pair_coeff command in your input script:
+simulations, you can use this form of the pair_coeff command in your
+input script:
 
 .. code-block:: LAMMPS
 
@@ -195,13 +228,13 @@ or this form in the "Pair Coeffs" section of the data file:
    3  none
 
 If an assignment to *none* is made in a simulation with the
-*hybrid/overlay* pair style, it wipes out all previous assignments of
+*hybrid/overlay* or *hybrid/scaled* pair style, it wipes out all
-that atom type pair to sub-styles.
+previous assignments of that pair of atom types to sub-styles.
 
 Note that you may need to use an :doc:`atom_style <atom_style>` hybrid
 command in your input script, if atoms in the simulation will need
 attributes from several atom styles, due to using multiple pair
-potentials.
+styles with different requirements.
 
 ----------
 
@@ -210,8 +243,9 @@ for applying weightings that change the strength of pairwise
 interactions between pairs of atoms that are also 1-2, 1-3, and 1-4
 neighbors in the molecular bond topology, as normally set by the
 :doc:`special_bonds <special_bonds>` command.  Different weights can be
-assigned to different pair hybrid sub-styles via the :doc:`pair_modify special <pair_modify>` command. This allows multiple force fields
+assigned to different pair hybrid sub-styles via the :doc:`pair_modify
-to be used in a model of a hybrid system, however, there is no consistent
+special <pair_modify>` command. This allows multiple force fields to be
+used in a model of a hybrid system, however, there is no consistent
 approach to determine parameters automatically for the interactions
 between the two force fields, this is only recommended when particles
 described by the different force fields do not mix.
@@ -260,7 +294,10 @@ the specific syntax, requirements and restrictions.
 ----------
 
 The potential energy contribution to the overall system due to an
-individual sub-style can be accessed and output via the :doc:`compute pair <compute_pair>` command.
+individual sub-style can be accessed and output via the :doc:`compute
+pair <compute_pair>` command.  Note that in the case of pair style
+*hybrid/scaled* this is the **unscaled** potential energy of the
+selected sub-style.
 
 ----------
 
@@ -282,28 +319,27 @@ Pair_style hybrid allows interactions between type pairs 2-2, 1-2,
 could even add a second interaction for 1-1 to be computed by another
 pair style, assuming pair_style hybrid/overlay is used.
 
-But you should not, as a general rule, attempt to exclude the
+But you should not, as a general rule, attempt to exclude the many-body
-many-body interactions for some subset of the type pairs within the
+interactions for some subset of the type pairs within the set of 1,3,4
-set of 1,3,4 interactions, e.g. exclude 1-1 or 1-3 interactions.  That
+interactions, e.g. exclude 1-1 or 1-3 interactions.  That is not
-is not conceptually well-defined for many-body interactions, since the
+conceptually well-defined for many-body interactions, since the
 potential will typically calculate energies and foces for small groups
 of atoms, e.g. 3 or 4 atoms, using the neighbor lists of the atoms to
-find the additional atoms in the group.  It is typically non-physical
+find the additional atoms in the group.
-to think of excluding an interaction between a particular pair of
-atoms when the potential computes 3-body or 4-body interactions.
 
 However, you can still use the pair_coeff none setting or the
 :doc:`neigh_modify exclude <neigh_modify>` command to exclude certain
 type pairs from the neighbor list that will be passed to a many-body
 sub-style.  This will alter the calculations made by a many-body
-potential, since it builds its list of 3-body, 4-body, etc
+potential beyond the specific pairs, since it builds its list of 3-body,
-interactions from the pair list.  You will need to think carefully as
+4-body, etc interactions from the pair lists.  You will need to think
-to whether it produces a physically meaningful result for your model.
+**carefully** as to whether excluding such pairs produces a physically
+meaningful result for your model.
 
 For example, imagine you have two atom types in your model, type 1 for
 atoms in one surface, and type 2 for atoms in the other, and you wish
 to use a Tersoff potential to compute interactions within each
-surface, but not between surfaces.  Then either of these two command
+surface, but not between the surfaces.  Then either of these two command
 sequences would implement that model:
 
 .. code-block:: LAMMPS
@@ -320,9 +356,9 @@ Either way, only neighbor lists with 1-1 or 2-2 interactions would be
 passed to the Tersoff potential, which means it would compute no
 3-body interactions containing both type 1 and 2 atoms.
 
-Here is another example, using hybrid/overlay, to use 2 many-body
+Here is another example to use 2 many-body potentials together in an
-potentials together, in an overlapping manner.  Imagine you have CNT
+overlapping manner using hybrid/overlay.  Imagine you have CNT (C atoms)
-(C atoms) on a Si surface.  You want to use Tersoff for Si/Si and Si/C
+on a Si surface.  You want to use Tersoff for Si/Si and Si/C
 interactions, and AIREBO for C/C interactions.  Si atoms are type 1; C
 atoms are type 2.  Something like this will work:
 
@@ -333,9 +369,9 @@ atoms are type 2.  Something like this will work:
    pair_coeff * * airebo CH.airebo NULL C
 
 Note that to prevent the Tersoff potential from computing C/C
-interactions, you would need to modify the SiC.tersoff file to turn
+interactions, you would need to **modify** the SiC.tersoff potential
-off C/C interaction, i.e. by setting the appropriate coefficients to
+file to turn off C/C interaction, i.e. by setting the appropriate
-0.0.
+coefficients to 0.0.
 
 ----------
 
@@ -343,18 +379,19 @@ Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
 hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
-page.
+page.  Pair style *hybrid/scaled* does (currently) not support the
+*gpu*, *omp*, *kk*, or *intel* suffix.
 
-Since the *hybrid* and *hybrid/overlay* styles delegate computation to
+Since the *hybrid*, *hybrid/overlay*, *hybrid/scaled* styles delegate
-the individual sub-styles, the suffix versions of the *hybrid* and
+computation to the individual sub-styles, the suffix versions of the
-*hybrid/overlay* styles are used to propagate the corresponding suffix
+*hybrid* and *hybrid/overlay* styles are used to propagate the
-to all sub-styles, if those versions exist. Otherwise the
+corresponding suffix to all sub-styles, if those versions
-non-accelerated version will be used.
+exist. Otherwise the non-accelerated version will be used.
 
-The individual accelerated sub-styles are part of the GPU, USER-OMP
+The individual accelerated sub-styles are part of the GPU, KOKKOS,
-and OPT packages, respectively.  They are only enabled if LAMMPS was
+USER-INTEL, USER-OMP, and OPT packages, respectively.  They are only
-built with those packages.  See the :doc:`Build package <Build_package>`
+enabled if LAMMPS was built with those packages.  See the :doc:`Build
-doc page for more info.
+package <Build_package>` doc page for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
@@ -372,28 +409,31 @@ Any pair potential settings made via the
 :doc:`pair_modify <pair_modify>` command are passed along to all
 sub-styles of the hybrid potential.
 
-For atom type pairs I,J and I != J, if the sub-style assigned to I,I
+For atom type pairs I,J and I != J, if the sub-style assigned to I,I and
-and J,J is the same, and if the sub-style allows for mixing, then the
+J,J is the same, and if the sub-style allows for mixing, then the
 coefficients for I,J can be mixed.  This means you do not have to
 specify a pair_coeff command for I,J since the I,J type pair will be
-assigned automatically to the sub-style defined for both I,I and J,J
+assigned automatically to the sub-style defined for both I,I and J,J and
-and its coefficients generated by the mixing rule used by that
+its coefficients generated by the mixing rule used by that sub-style.
-sub-style.  For the *hybrid/overlay* style, there is an additional
+For the *hybrid/overlay* and *hybrid/scaled* style, there is an
-requirement that both the I,I and J,J pairs are assigned to a single
+additional requirement that both the I,I and J,J pairs are assigned to a
-sub-style.  See the "pair_modify" command for details of mixing rules.
+single sub-style.  See the :doc:`pair_modify <pair_modify>` command for
-See the See the doc page for the sub-style to see if allows for
+details of mixing rules.  See the See the doc page for the sub-style to
-mixing.
+see if allows for mixing.
 
 The hybrid pair styles supports the :doc:`pair_modify <pair_modify>`
 shift, table, and tail options for an I,J pair interaction, if the
 associated sub-style supports it.
 
-For the hybrid pair styles, the list of sub-styles and their
+For the hybrid pair styles, the list of sub-styles and their respective
-respective settings are written to :doc:`binary restart files <restart>`, so a :doc:`pair_style <pair_style>` command does
+settings are written to :doc:`binary restart files <restart>`, so a
-not need to specified in an input script that reads a restart file.
+:doc:`pair_style <pair_style>` command does not need to specified in an
-However, the coefficient information is not stored in the restart
+input script that reads a restart file.  However, the coefficient
-file.  Thus, pair_coeff commands need to be re-specified in the
+information is not stored in the restart file.  Thus, pair_coeff
-restart input script.
+commands need to be re-specified in the restart input script.  For pair
+style *hybrid/scaled* also the names of any variables used as scale
+factors are restored, but not the variables themselves, so those may
+need to be redefined when continuing from a restart.
 
 These pair styles support the use of the *inner*\ , *middle*\ , and
 *outer* keywords of the :doc:`run_style respa <run_style>` command, if
@@ -409,6 +449,9 @@ e.g. *lj/cut/coul/long* or *buck/coul/long*\ .  You must insure that the
 short-range Coulombic cutoff used by each of these long pair styles is
 the same or else LAMMPS will generate an error.
 
+Pair style *hybrid/scaled* currently only works for non-accelerated
+pair styles and pair styles from the OPT package.
+
 Related commands
 """"""""""""""""
 

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_pace.rst

@@ -0,0 +1,114 @@
+.. index:: pair_style pace
+
+pair_style pace command
+========================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style pace ... keyword values ...
+
+* an optional keyword may be appended
+* keyword = *product* or *recursive*
+
+  .. parsed-literal::
+
+       *product* = use product algorithm for basis functions
+       *recursive* = use recursive algorithm for basis functions
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style pace
+   pair_style pace product
+   pair_coeff * * Cu-PBE-core-rep.ace Cu
+
+Description
+"""""""""""
+
+Pair style *pace* computes interactions using the Atomic Cluster
+Expansion (ACE), which is a general expansion of the atomic energy in
+multi-body basis functions. :ref:`(Drautz) <Drautz20191>`.
+The *pace* pair style
+provides an efficient implementation that
+is described in this paper :ref:`(Lysogorskiy) <Lysogorskiy20211>`.
+
+In ACE, the total energy is decomposed into a sum over
+atomic energies. The energy of atom *i* is expressed as a
+linear or non-linear function of one or more density functions.
+By projecting the
+density onto a local atomic base, the lowest order contributions
+to the energy can be expressed as a set of scalar polynomials in
+basis function contributions summed over neighbor atoms.
+
+Only a single pair_coeff command is used with the *pace* style which
+specifies an ACE coefficient file followed by N additional arguments
+specifying the mapping of ACE elements to LAMMPS atom types,
+where N is the number of LAMMPS atom types:
+
+* ACE coefficient file
+* N element names = mapping of ACE elements to atom types
+
+Only a single pair_coeff command is used with the *pace* style which
+specifies an ACE file that fully defines the potential.
+Note that unlike for other potentials, cutoffs are
+not set in the pair_style or pair_coeff command; they are specified in
+the ACE file.
+
+The pair_style *pace* command may be followed by an optional keyword
+*product* or *recursive*, which determines which of two algorithms
+is used for the calculation of basis functions and derivatives.
+The default is *recursive*.
+
+See the :doc:`pair_coeff <pair_coeff>` doc page for alternate ways
+to specify the path for the ACE coefficient file.
+
+Mixing, shift, table, tail correction, restart, rRESPA info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS with
+user-specifiable parameters as described above.  You never need to
+specify a pair_coeff command with I != J arguments for this style.
+
+This pair style does not support the :doc:`pair_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files.  Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+----------
+
+Restrictions
+""""""""""""
+
+This pair style is part of the USER-PACE package.  It is only enabled if LAMMPS
+was built with that package.
+See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair_style snap  <pair_snap>`
+
+Default
+"""""""
+
+recursive
+
+.. _Drautz20191:
+
+**(Drautz)** Drautz, Phys Rev B, 99, 014104 (2019).
+
+.. _Lysogorskiy20211:
+
+**(Lysogorskiy)** Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, TBD (2021).

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

@@ -95,10 +95,11 @@ accelerated styles exist.
 * :doc:`none <pair_none>` - turn off pairwise interactions
 * :doc:`hybrid <pair_hybrid>` - multiple styles of pairwise interactions
 * :doc:`hybrid/overlay <pair_hybrid>` - multiple styles of superposed pairwise interactions
+* :doc:`hybrid/scaled <pair_hybrid>` - multiple styles of scaled superposed pairwise interactions
 * :doc:`zero <pair_zero>` - neighbor list but no interactions
 
 * :doc:`adp <pair_adp>` - angular dependent potential (ADP) of Mishin
-* :doc:`agni <pair_agni>` - machine learned potential mapping atomic environment to forces
+* :doc:`agni <pair_agni>` - AGNI machine-learning potential
 * :doc:`airebo <pair_airebo>` - AIREBO potential of Stuart
 * :doc:`airebo/morse <pair_airebo>` - AIREBO with Morse instead of LJ
 * :doc:`atm <pair_atm>` - Axilrod-Teller-Muto potential
@@ -132,6 +133,7 @@ accelerated styles exist.
 * :doc:`comb3 <pair_comb>` - charge-optimized many-body (COMB3) potential
 * :doc:`cosine/squared <pair_cosine_squared>` - Cooke-Kremer-Deserno membrane model potential
 * :doc:`coul/cut <pair_coul>` - cutoff Coulomb potential
+* :doc:`coul/cut/global <pair_coul>` - cutoff Coulomb potential
 * :doc:`coul/cut/soft <pair_fep_soft>` - Coulomb potential with a soft core
 * :doc:`coul/debye <pair_coul>` - cutoff Coulomb potential with Debye screening
 * :doc:`coul/diel <pair_coul_diel>` - Coulomb potential with dielectric permittivity
@@ -250,7 +252,7 @@ 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
@@ -278,6 +280,7 @@ accelerated styles exist.
 * :doc:`oxrna2/hbond <pair_oxrna2>` -
 * :doc:`oxrna2/stk <pair_oxrna2>` -
 * :doc:`oxrna2/xstk <pair_oxrna2>` -
+* :doc:`pace <pair_pace>` - Atomic Cluster Expansion (ACE) machine-learning potential
 * :doc:`peri/eps <pair_peri>` - peridynamic EPS potential
 * :doc:`peri/lps <pair_peri>` - peridynamic LPS potential
 * :doc:`peri/pmb <pair_peri>` - peridynamic PMB potential
@@ -295,7 +298,7 @@ accelerated styles exist.
 * :doc:`smd/ulsph <pair_smd_ulsph>` -
 * :doc:`smtbq <pair_smtbq>` -
 * :doc:`mliap <pair_mliap>` - Multiple styles of machine-learning potential
-* :doc:`snap <pair_snap>` - SNAP quantum-accurate potential
+* :doc:`snap <pair_snap>` - SNAP machine-learning potential
 * :doc:`soft <pair_soft>` - Soft (cosine) potential
 * :doc:`sph/heatconduction <pair_sph_heatconduction>` -
 * :doc:`sph/idealgas <pair_sph_idealgas>` -

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/false_positives.txt

@@ -261,6 +261,7 @@ bitmask
 bitrate
 bitrates
 Bitzek
+Bjerrum
 Blaise
 blanchedalmond
 blocksize
@@ -268,6 +269,7 @@ blueviolet
 bn
 bni
 bo
+Bochkarev
 Bochum
 bocs
 bodyflag
@@ -343,6 +345,7 @@ Cao
 Capolungo
 Caro
 cartesian
+Cas
 CasP
 Caswell
 Cates
@@ -502,6 +505,8 @@ coulgauss
 coulombic
 Coulombic
 Coulombics
+counterion
+counterions
 Courant
 covalent
 covalently
@@ -730,6 +735,7 @@ DRUDE
 dsf
 dsmc
 dt
+dtemp
 dtgrow
 dtheta
 dtshrink
@@ -878,6 +884,7 @@ equilibrates
 equilibrating
 equilibration
 Equilibria
+equilibria
 equilization
 equipartitioning
 Ercolessi
@@ -1069,6 +1076,7 @@ fuer
 fx
 fy
 fz
+Gabor
 Gahler
 gainsboro
 Galindo
@@ -1193,6 +1201,7 @@ Halperin
 Halver
 Hamaker
 Hamel
+Hammerschmidt
 haptic
 Hara
 Harpertown
@@ -1212,6 +1221,7 @@ hbnewflag
 hbond
 hcp
 heatconduction
+Hebbeker
 Hebenstreit
 Hecht
 Heenen
@@ -1279,6 +1289,7 @@ hy
 hydrophobicity
 hydrostatic
 hydrostatically
+hydroxyl
 Hynninen
 Hyoungki
 hyperdynamics
@@ -1369,6 +1380,7 @@ ints
 inv
 invariants
 inversed
+ionizable
 ionocovalent
 iostreams
 iparam
@@ -1548,6 +1560,7 @@ Koning
 Kooser
 Korn
 Koskinen
+Kosovan
 Koster
 Kosztin
 Kp
@@ -1588,11 +1601,13 @@ lammps
 Lammps
 LAMMPS
 lammpsplot
+lammpsplugin
 Lampis
 Lamoureux
 Lanczos
 Lande
 Landron
+Landsgesell
 langevin
 Langevin
 Langston
@@ -1730,10 +1745,13 @@ lpsapi
 lrt
 lsfftw
 ltbbmalloc
+Lua
 lubricateU
 lucy
-Lua
 Luding
+Luijten
+lunit
+Lunkad
 Lussetti
 Lustig
 lval
@@ -1742,6 +1760,7 @@ lx
 ly
 Lybrand
 lyon
+Lysogorskiy
 Lyulin
 lz
 Maaravi
@@ -1800,8 +1819,10 @@ Materias
 mathbf
 mathjax
 matlab
+Matous
 matplotlib
 Matsubara
+Matteo
 Mattice
 Mattox
 Mattson
@@ -1862,6 +1883,7 @@ MEMALIGN
 membered
 memcheck
 Mendelev
+Menon
 mer
 Meremianin
 Mersenne
@@ -1985,6 +2007,7 @@ mpiio
 mpirun
 mplayer
 mps
+Mrovec
 Mryglod
 mscg
 MSCG
@@ -2019,6 +2042,7 @@ multiscale
 multisectioning
 multithreading
 Multithreading
+multivalent
 Mundy
 Murdick
 Murtola
@@ -2064,6 +2088,7 @@ Nanoletters
 nanomechanics
 nanometer
 nanometers
+nanoparticle
 nanoparticles
 Nanotube
 nanotube
@@ -2173,6 +2198,7 @@ nm
 Nm
 Nmax
 nmax
+nmc
 Nmin
 nmin
 Nmols
@@ -2307,9 +2333,11 @@ OMP
 oneAPI
 onelevel
 oneway
+onlysalt
 onn
 ons
 OO
+Oord
 opencl
 openKIM
 openmp
@@ -2330,6 +2358,7 @@ Orsi
 ortho
 orthonormal
 orthorhombic
+Ortner
 oso
 Otype
 Ouldridge
@@ -2389,6 +2418,8 @@ pbc
 pc
 pchain
 Pchain
+pcmoves
+pmcmoves
 Pdamp
 pdb
 pdf
@@ -2433,6 +2464,7 @@ phosphide
 Phs
 Physica
 physik
+pI
 Piaggi
 picocoulomb
 picocoulombs
@@ -2444,7 +2476,9 @@ pid
 piecewise
 Pieniazek
 Pieter
+pIm
 pimd
+pIp
 Piola
 Pisarev
 Pishevar
@@ -2459,6 +2493,9 @@ ploop
 PloS
 plt
 plumedfile
+pKa
+pKb
+pKs
 pmb
 Pmolrotate
 Pmoltrans
@@ -2619,6 +2656,7 @@ radians
 Rafferty
 rahman
 Rahman
+Ralf
 Raman
 ramped
 ramping
@@ -2680,6 +2718,7 @@ representable
 Reproducibility
 reproducibility
 repuls
+reqid
 rescale
 rescaled
 rescales
@@ -2725,6 +2764,7 @@ Rij
 RIj
 Rik
 Rin
+Rinaldi
 Rino
 RiRj
 Risi
@@ -2784,6 +2824,7 @@ rst
 rstyle
 Rubensson
 Rubia
+Rud
 Rudd
 Rudra
 Rudranarayan
@@ -2813,6 +2854,7 @@ Sandia
 sandybrown
 sanitizer
 Sanyal
+Sarath
 sc
 scafacos
 SCAFACOS

examples/USER/misc/charge_regulation/README

@@ -0,0 +1,36 @@
+This directory has two input scripts that illustrates how to use fix
+charge_regulation in LAMMPS to perform coarse-grained molecular dynamics
+(MD) simulations with incorporation of charge regulation effects. The
+charge regulation is implemented via Monte Carlo (MC) sampling following
+the reaction ensemble MC approach, producing a MC/MD hybrid tool for
+modeling charge regulation in solvated systems.
+
+The script `in.chreg-acid` sets up a simple weak acid electrolyte
+(pH=7,pKa=6,pI=3). Four different types of MC moves are implemented:
+acid protonation & de-protonation, and monovalent ion pair insertion and
+deletion. Note here we have grouped all free monovalent ions into a
+single type, a physically natural choice on the level of coarse-grained
+primitive electrolyte models, which increases the calculation
+performance but has no effects on thermodynamic observables. The
+variables such as pH, pKa, pI, and lb at the top of the input script can
+be adjusted to play with various simulation parameters. The cumulative
+MC attempted moves and cumulative number of accepted moves, as well as,
+current number of neutral and charged acid particles, neutral and
+charged base particles (in this example always 0), and the current
+number of free cations and anions in the system are printed in the
+output.
+
+The script `in.chreg-polymer` sets up a weak poly-electrolyte chain of
+N=80 beads. Each bead is a weak acid with pKa=5 and solution has pH=7
+and monovalent salt chemical potential pI=3. In this example, we choose
+to treat salt ions, protons, and hydroxyl ions separately, which results
+in 5 types of MC moves: acid [type 1] protonation & de-protonation (with
+protons [type 4] insertion & deletion), acid [type 1] protonation &
+de-protonation (with salt cation [type 2] insertion & deletion), water
+self-ionization (insertion and deletion of proton [type4] and hydroxyl
+ion [type 5] pair), insertion and deletion of monovalent salt pair [type
+2 and type 3] , insertion and deletion of a proton [type4] and salt
+anion [type 3].  The current number of neutral and charged acid
+particles, the current number of free salt cations and anions, and the
+current number of protons and hydroxyl ions are printed in the output.
+

examples/USER/misc/charge_regulation/data.chreg-acid

@@ -0,0 +1,235 @@
+LAMMPS data file generated by get_input.py
+
+219 atoms
+3 atom types
+-2.5000000000000000e+01 2.5000000000000000e+01 xlo xhi
+-2.5000000000000000e+01 2.5000000000000000e+01 ylo yhi
+-2.5000000000000000e+01 2.5000000000000000e+01 zlo zhi
+
+Masses
+
+1 1
+2 1 
+3 1 
+
+Atoms
+
+1 1 0 2.5983275747497636 -8.368052973860795 20.001288664343484
+2 1 -1 -18.182868728594865 -8.079792367885453 8.253737231981816
+3 1 -1 -17.437350808966414 8.120411567445771 10.747650340639332
+4 1 -1 6.502476583291578 -23.497326620756837 19.948223080086798
+5 1 -1 -22.528179279677296 -18.783433570718127 -17.964657736688018
+6 1 -1 -9.713496019164342 18.97235576760402 -19.495620818582825
+7 1 -1 -12.831976006720659 0.12265736526942561 -21.679396938423718
+8 1 -1 20.909063679212295 -2.16535062758771 0.46197866620165584
+9 1 -1 23.86211981166997 24.024928465132284 10.534067202515907
+10 1 -1 -0.5289298325031275 23.820222457999776 -2.657199543669442
+11 1 -1 9.57021229491361 11.973871502198485 3.4206509716759186
+12 1 -1 -10.201559985782705 7.557482594092384 12.07004973873643
+13 1 -1 4.898458045226889 2.0169997859717945 -20.765285372762087
+14 1 -1 -24.086606883730077 4.424991619615298 -4.204294764756856
+15 1 -1 3.6837161829600795 -4.763233144818308 -12.75873457519811
+16 1 -1 -12.217842496816345 -17.720229208905618 -13.556354139556914
+17 1 -1 -21.456229140133704 -7.423996317612119 -6.94398044071275
+18 1 -1 13.697298849253912 8.503639732052164 8.085487457359058
+19 1 -1 -5.764222710061347 11.49890485049034 -5.1113880296575935
+20 1 -1 3.9944161041544426 16.928204188257893 -14.875635895409372
+21 1 -1 4.509525276444776 16.63590711792657 -22.21846494992397
+22 1 -1 22.115374932704306 -18.97293932558108 -23.982486000144267
+23 1 -1 14.169061011408473 -16.69837647199978 13.779039228068108
+24 1 -1 17.186846147657228 8.827459489898189 23.055435051390333
+25 1 -1 2.9822901981431045 -16.83687718528342 -21.278623587083484
+26 1 -1 16.657554689423897 -1.6217275605348647 -11.315859420404218
+27 1 -1 19.215533149393543 -15.512634977936068 7.2701088767584565
+28 1 -1 -8.886744157248422 -24.09644410100167 4.013016013803799
+29 1 -1 20.99918340066754 4.4716257356730225 0.3847245765737597
+30 1 -1 1.3442294253060716 5.601341425720583 -14.918594492786674
+31 1 -1 -6.962977050326831 20.470183675946515 -16.37885865567279
+32 1 -1 -9.98531733187143 9.52233798117566 -24.979630708193724
+33 1 -1 -17.327989778292306 5.761352103841766 5.720220488689204
+34 1 -1 5.168359673466362 -23.698812306679418 2.6199762372169744
+35 1 -1 18.978042448492154 6.41188742965139 6.31975357155018
+36 1 -1 -16.38534911663758 -14.8262205163943 4.125239045887575
+37 1 -1 7.974455406459249 -18.88332583451115 11.00721254217055
+38 1 -1 13.779816416416402 1.8581999350851426 9.104219696003227
+39 1 -1 -23.90949397031401 -3.346877828308571 -10.228782973473443
+40 1 -1 21.61647622174447 8.443955423089903 -19.12066464239769
+41 1 -1 -8.823979405515548 14.461154001848172 16.061704411241706
+42 1 -1 -2.4406878944912513 12.5535360118296 20.606764200087852
+43 1 -1 -18.459404356124697 15.260951448001258 21.187332685021346
+44 1 -1 2.2354003384439878 -23.350013178190736 11.369307324043625
+45 1 -1 15.595889705552018 -6.6075680254604805 5.434256329408505
+46 1 -1 -17.528243443870238 4.109747707896265 -1.4167331089310942
+47 1 -1 2.161977144405782 -16.511059804921263 -12.186191310598671
+48 1 -1 -8.685671837367341 -7.0743613044263185 -1.1561844713769105
+49 1 -1 15.62258718398045 -6.559293763708908 20.556775995508488
+50 1 -1 -6.965207014475155 -14.348784897390543 -14.421447863144754
+51 1 -1 -12.099361509567913 -24.62785640990423 -15.839126670614329
+52 1 -1 6.673854222058246 7.83575773885061 -9.714128155619994
+53 1 -1 -17.413453800948826 12.386754276446203 -16.882300786608994
+54 1 -1 21.8966589175091 12.485943283688762 -14.553421680298634
+55 1 -1 -8.37629917390651 -24.783875012947064 7.454467809536389
+56 1 -1 14.081149297694104 -21.719204113108943 -17.447225564400064
+57 1 -1 4.681992702049627 1.9719544892622558 -7.823736613205725
+58 1 -1 4.353171917533494 15.86928389762705 24.669680272563014
+59 1 -1 23.31502072066573 -4.685724298328946 2.459643890128799
+60 1 -1 7.0470920520598455 23.016693234922386 -13.139471333592677
+61 1 -1 11.725555941181668 -15.809323171320772 -1.6292879532275037
+62 1 -1 -20.36388898925061 -12.084932320023162 -22.816700826388757
+63 1 -1 -2.492146614764735 -0.7314052253623018 -15.89959178250266
+64 1 -1 -22.45303825831233 -11.27996814407809 -9.553770912146142
+65 1 -1 24.76771926037101 20.128947543233757 10.528974830883733
+66 1 -1 11.326213670190818 -11.624187194192492 -9.687726413467862
+67 1 -1 -5.712764220166093 15.778887306376163 -0.9263244618113831
+68 1 -1 -15.073201136996362 -12.372916148178115 -5.461704510273556
+69 1 -1 -5.82976670348781 -4.57812040989473 9.0443548565365
+70 1 -1 -5.429195387856279 1.4542054472230177 -7.397291151203568
+71 1 -1 -23.385555726942343 -11.924588975396505 3.8215294321466153
+72 1 -1 -1.0694104826815725 2.999945633116507 3.67092922106918
+73 1 -1 12.134312161994352 1.9747455475585376 -14.895893366599623
+74 1 -1 21.30950120583112 18.97294626436546 -17.520867878211376
+75 1 -1 -24.356703356157063 3.594879254976714 17.172993705171677
+76 1 -1 12.634233603338409 24.373499564220822 4.561976273909789
+77 1 -1 -10.740243207970495 19.345205140729554 -3.3368424800818097
+78 1 -1 -3.027848793907552 10.604939843027267 7.493012332728249
+79 1 -1 5.000539296336658 11.770088203844622 17.227492055930185
+80 1 -1 1.1585200269400353 -24.45822157176123 -12.515688997756257
+81 1 -1 1.9163088584430596 -14.064330279670672 11.302445490552905
+82 1 -1 -20.857041355570576 21.292791787236673 17.397470691573346
+83 1 -1 -24.50473305235651 -12.741459355708756 -1.9325218065560357
+84 1 -1 2.658628688373309 -1.1131226252194608 7.491603553398086
+85 1 -1 -18.515435126408363 24.20642384141299 14.466889392835121
+86 1 -1 19.63928177206153 9.942655640416291 8.691463646789934
+87 1 -1 -7.69626451160762 11.762517043363786 -7.457263991495665
+88 1 -1 1.051431093064835 -11.460307039827766 16.90304637479744
+89 1 -1 0.9157815447227939 23.656751182559688 -6.538587603918376
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examples/USER/misc/charge_regulation/data.chreg-acid-real

@@ -0,0 +1,235 @@
+LAMMPS data file generated by get_input.py
+
+219 atoms
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+-180 180 ylo yhi
+-180 180 zlo zhi
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+159 2 1 -7.179797893 131.8852645 48.92705878
+160 2 1 166.7210737 111.3028256 122.5151765
+161 2 1 160.4061661 105.4292149 147.9164951
+162 2 1 70.35573238 -156.217711 -37.86968306
+163 2 1 37.82167168 128.9612675 113.5371453
+164 2 1 -149.4650805 40.2544478 -89.16446826
+165 2 1 23.15794976 -35.62998186 -128.5225995
+166 2 1 148.5909499 65.59167763 44.47571026
+167 2 1 38.20567747 91.06090259 167.2556933
+168 2 1 -173.8935359 124.3001041 -123.4154022
+169 2 1 -113.0780192 -112.7185827 -75.51909042
+170 2 1 -47.52814398 -162.0232543 -40.84518679
+171 2 1 164.6580923 96.26106544 -67.52475023
+172 2 1 -166.687599 -28.28821753 -80.04284273
+173 2 1 9.786487166 -133.5748603 -110.4924395
+174 2 1 73.69685916 -130.6229707 -12.1566579
+175 2 1 90.69039384 -12.53964183 -156.8650452
+176 2 1 -1.065055548 123.2458955 9.207883208
+177 2 1 175.3144942 -62.38332615 89.50309521
+178 2 1 -135.5554643 -135.3786299 -12.22599884
+179 2 1 -65.15130962 -12.87802388 -85.25728639
+180 2 1 -161.9760397 -159.2069523 72.10033228
+181 2 1 -116.5200037 9.430944126 5.8294178
+182 2 1 -28.85454266 -176.0245493 -141.7245957
+183 2 1 63.2968571 -114.4145268 -168.891953
+184 2 1 -61.61686575 -158.2947391 162.9099557
+185 2 1 51.43661765 119.3411567 4.253266919
+186 2 1 50.78017633 47.93871152 129.5527454
+187 2 1 151.0842128 -27.15258927 -161.0800505
+188 2 1 -63.76595621 -118.2333675 -55.31381078
+189 2 1 -103.5498203 -55.20725862 -73.28180307
+190 2 1 -165.1300235 72.52455317 27.04945294
+191 2 1 68.10471264 124.0704131 -0.252243467
+192 2 1 79.29794618 142.8637277 -42.01908928
+193 2 1 167.6806551 20.41616629 -147.6924841
+194 2 1 -135.8036012 64.48710622 102.1923975
+195 2 1 98.55703781 -115.0070794 78.85760695
+196 2 1 15.16187488 19.73322691 -170.7866955
+197 2 1 151.0729333 50.92372407 -173.3272023
+198 2 1 42.92899709 -139.8564977 161.7836767
+199 2 1 -123.3797296 144.2768906 93.18435951
+200 2 1 83.46684339 160.4439871 16.84583748
+201 2 1 -9.982765467 138.2373541 -55.3263136
+202 2 1 -161.6023131 -141.5797686 -64.66795638
+203 2 1 2.63144963 -54.92560391 117.5540027
+204 2 1 -70.31638318 175.5673808 -103.3383852
+205 2 1 -4.543770763 -40.50287551 98.39515078
+206 2 1 19.2926167 -2.671035153 112.1413205
+207 2 1 76.93260202 177.3949067 -126.2787212
+208 2 1 131.8183006 132.4167597 131.6586696
+209 2 1 -82.9844547 -85.47123292 92.81285561
+210 3 -1 115.4743016 -5.981969165 65.81311346
+211 3 -1 -86.91538943 171.1823129 -45.00079
+212 3 -1 174.0893311 141.4009485 159.8631805
+213 3 -1 164.8739505 64.21237704 -8.113691614
+214 3 -1 -75.49748308 40.97887837 158.0779944
+215 3 -1 45.16399203 72.25791157 159.9861897
+216 3 -1 105.7676225 -56.05853127 3.624467826
+217 3 -1 166.8523536 -151.4993186 -151.6124408
+218 3 -1 -43.30886503 46.05330597 155.3934201
+219 3 -1 -5.592027058 2.85325065 11.39381158

examples/USER/misc/charge_regulation/data.chreg-polymer

@@ -0,0 +1,264 @@
+##A Weak PE Chain of N=80
+
+160 atoms
+79 bonds
+
+5 atom types
+1 bond types
+
+-50 50 xlo xhi
+-50 50 ylo yhi
+-50 50 zlo zhi
+
+Masses
+
+1 1.0
+2 1.0
+3 1.0
+4 1.0
+5 1.0
+
+Atoms
+# atom_id molecule_id atom_type charge x y z 
+1 1 1 -1 0 0 -48.37753795169063
+2 1 1 -1 0 0 -47.255075903381254
+3 1 1 -1 0 0 -46.13261385507188
+4 1 1 -1 0 0 -45.01015180676251
+5 1 1 -1 0 0 -43.887689758453135
+6 1 1 -1 0 0 -42.76522771014376
+7 1 1 -1 0 0 -41.64276566183439
+8 1 1 -1 0 0 -40.520303613525016
+9 1 1 -1 0 0 -39.39784156521564
+10 1 1 -1 0 0 -38.27537951690627
+11 1 1 -1 0 0 -37.1529174685969
+12 1 1 -1 0 0 -36.030455420287524
+13 1 1 -1 0 0 -34.90799337197815
+14 1 1 -1 0 0 -33.78553132366878
+15 1 1 -1 0 0 -32.663069275359405
+16 1 1 -1 0 0 -31.54060722705003
+17 1 1 -1 0 0 -30.41814517874066
+18 1 1 -1 0 0 -29.295683130431286
+19 1 1 -1 0 0 -28.173221082121913
+20 1 1 -1 0 0 -27.05075903381254
+21 1 1 -1 0 0 -25.928296985503167
+22 1 1 -1 0 0 -24.805834937193794
+23 1 1 -1 0 0 -23.68337288888442
+24 1 1 -1 0 0 -22.560910840575048
+25 1 1 -1 0 0 -21.438448792265675
+26 1 1 -1 0 0 -20.3159867439563
+27 1 1 -1 0 0 -19.19352469564693
+28 1 1 -1 0 0 -18.071062647337556
+29 1 1 -1 0 0 -16.948600599028183
+30 1 1 -1 0 0 -15.82613855071881
+31 1 1 -1 0 0 -14.703676502409436
+32 1 1 -1 0 0 -13.581214454100063
+33 1 1 -1 0 0 -12.45875240579069
+34 1 1 -1 0 0 -11.336290357481317
+35 1 1 -1 0 0 -10.213828309171944
+36 1 1 -1 0 0 -9.091366260862571
+37 1 1 -1 0 0 -7.968904212553198
+38 1 1 -1 0 0 -6.846442164243825
+39 1 1 -1 0 0 -5.723980115934452
+40 1 1 -1 0 0 -4.601518067625079
+41 1 1 -1 0 0 -3.4790560193157063
+42 1 1 -1 0 0 -2.3565939710063333
+43 1 1 -1 0 0 -1.2341319226969603
+44 1 1 -1 0 0 -0.11166987438758724
+45 1 1 -1 0 0 1.0107921739217858
+46 1 1 -1 0 0 2.133254222231159
+47 1 1 -1 0 0 3.255716270540532
+48 1 1 -1 0 0 4.378178318849905
+49 1 1 -1 0 0 5.500640367159278
+50 1 1 -1 0 0 6.623102415468651
+51 1 1 -1 0 0 7.745564463778024
+52 1 1 -1 0 0 8.868026512087397
+53 1 1 -1 0 0 9.99048856039677
+54 1 1 -1 0 0 11.112950608706143
+55 1 1 -1 0 0 12.235412657015516
+56 1 1 -1 0 0 13.357874705324889
+57 1 1 -1 0 0 14.480336753634262
+58 1 1 -1 0 0 15.602798801943635
+59 1 1 -1 0 0 16.725260850253008
+60 1 1 -1 0 0 17.84772289856238
+61 1 1 -1 0 0 18.970184946871754
+62 1 1 -1 0 0 20.092646995181127
+63 1 1 -1 0 0 21.2151090434905
+64 1 1 -1 0 0 22.337571091799873
+65 1 1 -1 0 0 23.460033140109246
+66 1 1 -1 0 0 24.58249518841862
+67 1 1 -1 0 0 25.704957236727992
+68 1 1 -1 0 0 26.827419285037365
+69 1 1 -1 0 0 27.949881333346738
+70 1 1 -1 0 0 29.07234338165611
+71 1 1 -1 0 0 30.194805429965484
+72 1 1 -1 0 0 31.317267478274857
+73 1 1 -1 0 0 32.43972952658423
+74 1 1 -1 0 0 33.5621915748936
+75 1 1 -1 0 0 34.684653623202976
+76 1 1 -1 0 0 35.80711567151235
+77 1 1 -1 0 0 36.92957771982172
+78 1 1 -1 0 0 38.052039768131095
+79 1 1 -1 0 0 39.17450181644047
+80 1 1 -1 0 0 40.29696386474984
+81 0 2 1 -27.886422274724097 27.72001798427955 38.68169635811057
+82 0 2 1 29.812255760623188 17.871838747003693 -29.094648426460257
+83 0 2 1 -13.23881351410531 13.28123966828678 -24.422176415560116
+84 0 2 1 4.9465650593939685 -37.7521903558826 -15.115417767729575
+85 0 2 1 34.82527943387106 29.457664434004897 -25.565595338061254
+86 0 2 1 46.35660570786446 -7.161776614070412 -20.2471250527001
+87 0 2 1 39.20854546781531 34.96815569014278 13.893531822586723
+88 0 2 1 -7.797240698180197 0.07861219105048889 48.686453603015224
+89 0 2 1 43.92391845355516 -39.42362941705827 22.448930565867585
+90 0 2 1 -40.371744364329984 -17.743039071967246 -15.08153047835009
+91 0 2 1 -21.573165497710058 -0.5844447399891948 -45.73596994149077
+92 0 2 1 -19.882394451769102 -7.392447895357577 30.733607063808876
+93 0 2 1 -17.393031309514107 26.882975097407467 -47.64059480000892
+94 0 2 1 25.652222561671735 1.0229206994719107 -14.959030208952043
+95 0 2 1 26.075045766879313 19.902341017250052 46.70284805469666
+96 0 2 1 39.91980369168496 0.753749460187592 -26.203575929573407
+97 0 2 1 13.777613371273958 7.112171629839359 -33.5270487721399
+98 0 2 1 18.944534687271826 20.090215089875286 -34.381335468790574
+99 0 2 1 -23.801856387842435 -42.275962146864586 -8.322936238250279
+100 0 2 1 -31.386991395893826 29.83894468611787 8.937114269513422
+101 0 2 1 -41.07090001085809 49.59339931450579 6.666864232174753
+102 0 2 1 -46.58911504232167 -32.46068937927039 19.40424197066872
+103 0 2 1 -39.94659416571965 -36.28203465180086 5.841020764632312
+104 0 2 1 -26.027467090120137 -41.05522015175137 -1.1145958296128313
+105 0 2 1 37.09602855959457 23.76087951027276 45.09142423198867
+106 0 2 1 -27.78138413517528 -48.97344929918942 45.91491289356401
+107 0 2 1 4.468912883622387 -5.217782298407556 6.381420595433383
+108 0 2 1 36.758686966564525 48.425582881586166 -25.909273336802997
+109 0 2 1 -27.045102667146036 -19.713951008254117 4.339232870380627
+110 0 2 1 -5.984280016624311 -49.45311479123866 36.35727783065221
+111 0 2 1 27.833389147163018 -47.80144978082761 -47.71458334276804
+112 0 2 1 -23.628507668044364 -30.353876765128685 36.174277933133254
+113 0 2 1 -40.93360714431151 40.1336490864843 -27.035347797435495
+114 0 2 1 6.3523980881104976 -28.636485436097082 -10.671354350535445
+115 0 2 1 42.765716958607086 -32.85779663523676 -1.9682360265562124
+116 0 2 1 -33.68069757415453 16.800769050458484 -6.273374390373085
+117 0 2 1 13.909148568042937 4.921040289518388 12.111069913598996
+118 0 2 1 6.728324076730296 -48.44092815223126 -35.92436883370601
+119 0 2 1 -18.121173967321912 -15.76903395165283 2.2495451015454933
+120 0 2 1 -11.75253233489407 -45.82569982175387 -12.477142440015896
+121 0 2 1 1.9713864197144133 17.961034900064007 32.97992150691711
+122 0 2 1 -3.993384770632943 -47.63120435620297 27.75490859098018
+123 0 2 1 -0.32208279553454844 -47.30616152402566 -22.751109302380367
+124 0 2 1 -0.135777029397957 23.88599790464609 -31.87440560354473
+125 0 2 1 -6.123924906817393 -2.038519565120424 45.4809181974626
+126 0 2 1 -29.622588299895046 42.40404115712096 6.640479709229595
+127 0 2 1 -11.694512971272673 19.983258641775762 -38.152427411711145
+128 0 2 1 -20.93721440637313 39.46397829322392 -45.52708262202337
+129 0 2 1 34.13340147809369 36.14268504987945 -23.978137043267044
+130 0 2 1 -37.422309952611485 29.181841318883087 27.55677757161692
+131 0 2 1 30.11314373799594 18.721794400471353 1.5553303682670574
+132 0 2 1 -7.3563467211571805 46.84253369205935 -39.84708490437832
+133 0 2 1 -3.695927445484358 2.494403998274727 -7.634369981832755
+134 0 2 1 44.09701173592077 17.717328437831043 31.54108326477207
+135 0 2 1 48.070189931616795 10.601166369398662 -28.28574863896286
+136 0 2 1 -7.044858382811761 -42.080663380241766 -1.4369925734636553
+137 0 2 1 -12.485032488076918 23.87106169116919 6.178803347562642
+138 0 2 1 -15.613232443702309 10.103630885941392 -20.447182948810916
+139 0 2 1 28.610332347774147 37.08335835592116 -19.90280831362493
+140 0 2 1 25.853920233242505 -27.768648181803655 24.971357611943475
+141 0 2 1 9.256159541363296 -23.562096053197934 -4.722701100419371
+142 0 2 1 39.96929397877305 -11.88228547846326 -28.70638149104603
+143 0 2 1 -37.98545134633291 -23.50528193202669 -10.939982626098441
+144 0 2 1 25.40017763114089 -47.49220127581256 15.1783064865064
+145 0 2 1 28.073596076651768 3.6631266774864386 31.54355751177208
+146 0 2 1 -19.596457173068703 46.79824882013442 -12.302655772327597
+147 0 2 1 -36.46192411958321 -2.785830672302666 -25.1901381125736
+148 0 2 1 -27.377389198969894 11.295792272951147 39.32842550184691
+149 0 2 1 32.24967019136358 -20.517755791016402 31.20590722085157
+150 0 2 1 47.70698618147787 9.75462874031868 -28.267447889542563
+151 0 2 1 17.157803106328345 -27.48141290657965 7.7670687016760525
+152 0 2 1 15.089833959419678 5.342811012118396 27.35336620165029
+153 0 2 1 9.836963929211372 -11.047378229392443 -20.960811370690678
+154 0 2 1 44.66600586278604 14.949733274456321 -29.328965994323575
+155 0 2 1 -21.006260382140685 8.492712712433658 -46.31580169190271
+156 0 2 1 -29.970979487850748 -36.46250489415931 26.914372830947457
+157 0 2 1 -1.0821372755756329 -8.453379951300242 -19.95665062432509
+158 0 2 1 -24.033653425909772 -39.51330620205049 20.067656167683793
+159 0 2 1 27.747287624384626 -21.904990435351312 -10.819345241055956
+160 0 2 1 -40.86737066410612 -25.609300376714796 -21.128139356809783
+
+Bonds
+ # bond_id bond_type atom1_id atom2_id
+1 1 1 2
+2 1 2 3
+3 1 3 4
+4 1 4 5
+5 1 5 6
+6 1 6 7
+7 1 7 8
+8 1 8 9
+9 1 9 10
+10 1 10 11
+11 1 11 12
+12 1 12 13
+13 1 13 14
+14 1 14 15
+15 1 15 16
+16 1 16 17
+17 1 17 18
+18 1 18 19
+19 1 19 20
+20 1 20 21
+21 1 21 22
+22 1 22 23
+23 1 23 24
+24 1 24 25
+25 1 25 26
+26 1 26 27
+27 1 27 28
+28 1 28 29
+29 1 29 30
+30 1 30 31
+31 1 31 32
+32 1 32 33
+33 1 33 34
+34 1 34 35
+35 1 35 36
+36 1 36 37
+37 1 37 38
+38 1 38 39
+39 1 39 40
+40 1 40 41
+41 1 41 42
+42 1 42 43
+43 1 43 44
+44 1 44 45
+45 1 45 46
+46 1 46 47
+47 1 47 48
+48 1 48 49
+49 1 49 50
+50 1 50 51
+51 1 51 52
+52 1 52 53
+53 1 53 54
+54 1 54 55
+55 1 55 56
+56 1 56 57
+57 1 57 58
+58 1 58 59
+59 1 59 60
+60 1 60 61
+61 1 61 62
+62 1 62 63
+63 1 63 64
+64 1 64 65
+65 1 65 66
+66 1 66 67
+67 1 67 68
+68 1 68 69
+69 1 69 70
+70 1 70 71
+71 1 71 72
+72 1 72 73
+73 1 73 74
+74 1 74 75
+75 1 75 76
+76 1 76 77
+77 1 77 78
+78 1 78 79
+79 1 79 80

examples/USER/misc/charge_regulation/in.chreg-acid

@@ -0,0 +1,36 @@
+# Charge regulation lammps for simple weak electrolyte
+
+units           lj
+atom_style      charge
+neighbor        3.0 bin
+read_data       data.chreg-acid
+
+variable        cut_long equal 12.5
+variable        nevery equal 100
+variable        nmc equal 100
+variable        pH equal 7.0
+variable        pKa equal 6.0
+variable        pIm equal 3.0
+variable        pIp equal 3.0
+
+variable        cut_lj equal 2^(1.0/6.0)
+variable        lunit_nm equal 0.72 # in the units of nm
+velocity        all create 1.0 8008 loop geom
+
+pair_style      lj/cut/coul/long ${cut_lj} ${cut_long}
+pair_coeff      * *  1.0 1.0
+kspace_style    ewald 1.0e-3
+pair_modify     shift yes
+
+#########  VERLET INTEGRATION WITH LANGEVIN THERMOSTAT  ###########
+fix             fnve all nve
+compute         dtemp all temp
+compute_modify  dtemp dynamic yes
+fix             fT all langevin 1.0 1.0 1.0 123
+fix_modify      fT temp dtemp
+
+fix chareg      all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+thermo          100
+thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
+timestep        0.005
+run             2000

examples/USER/misc/charge_regulation/in.chreg-acid-real

@@ -0,0 +1,44 @@
+# Charge regulation lammps for simple weak electrolyte
+
+units           real
+atom_style      charge
+neighbor        10.0 bin
+read_data       data.chreg-acid-real
+
+#real units
+variable 	sigma equal 7.2	              # particle diameter 0.72 nm	    	
+variable	temperature equal 298         # temperature 298 K
+variable        kb index 0.0019872067         # kB in Kcal/mol/K
+variable 	epsilon equal ${kb}*${temperature}
+variable	tunit   equal 	2000          # time unit is 2000 fs    
+variable	timestep equal 0.005*${tunit}
+
+variable        cut_long equal 12.5*${sigma}
+variable        nevery equal 100
+variable        nmc equal 100
+variable        pH equal 7.0
+variable        pKa equal 6.0
+variable        pIm equal 3.0
+variable        pIp equal 3.0
+
+variable        cut_lj equal 2^(1.0/6.0)*${sigma}
+velocity        all create ${temperature} 8008 loop geom
+
+pair_style      lj/cut/coul/long ${cut_lj} ${cut_long}
+pair_coeff      * *  ${epsilon} ${sigma}
+kspace_style    pppm 1.0e-3
+dielectric	78
+pair_modify     shift yes
+
+#########  VERLET INTEGRATION WITH LANGEVIN THERMOSTAT  ###########
+fix             fnve all nve
+compute         dtemp all temp
+compute_modify  dtemp dynamic yes
+fix             fT all langevin $(v_temperature) $(v_temperature) $(v_tunit) 123
+fix_modify      fT temp dtemp
+
+fix chareg      all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+thermo          100
+thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
+timestep        ${timestep}
+run             2000

examples/USER/misc/charge_regulation/in.chreg-polymer

@@ -0,0 +1,33 @@
+# Charge regulation lammps for a polymer chain
+units           lj
+atom_style      full
+neighbor        3.0 bin
+read_data       data.chreg-polymer
+
+bond_style      harmonic
+bond_coeff      1 100 1.122462 # K R0
+velocity        all create 1.0 8008 loop geom
+
+pair_style      lj/cut/coul/long 1.122462 20
+pair_coeff      * *  1.0 1.0 1.122462 # charges
+kspace_style    pppm 1.0e-3
+pair_modify     shift yes
+dielectric      1.0
+
+#########  VERLET INTEGRATION WITH LANGEVIN THERMOSTAT  ###########
+fix             fnve all nve
+compute         dtemp all temp
+compute_modify  dtemp dynamic yes
+fix             fT all langevin 1.0 1.0 1.0 123
+fix_modify      fT temp dtemp
+
+fix chareg1 all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 seed 2345
+fix chareg2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 seed 2345
+fix chareg3 all charge/regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 seed 2345
+
+thermo          100
+#               print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions
+thermo_style    custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8]
+
+timestep        0.005
+run             2000

examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.1

@@ -0,0 +1,125 @@
+LAMMPS (10 Feb 2021)
+  using 1 OpenMP thread(s) per MPI task
+# Charge regulation lammps for simple weak electrolyte
+
+units           lj
+atom_style      charge
+neighbor        3.0 bin
+read_data       data.chreg-acid
+Reading data file ...
+  orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  219 atoms
+  read_data CPU = 0.003 seconds
+
+variable        cut_long equal 12.5
+variable        nevery equal 100
+variable        nmc equal 100
+variable        pH equal 7.0
+variable        pKa equal 6.0
+variable        pIm equal 3.0
+variable        pIp equal 3.0
+
+variable        cut_lj equal 2^(1.0/6.0)
+variable        lunit_nm equal 0.72 # in the units of nm
+velocity        all create 1.0 8008 loop geom
+
+pair_style      lj/cut/coul/long ${cut_lj} ${cut_long}
+pair_style      lj/cut/coul/long 1.12246204830937 ${cut_long}
+pair_style      lj/cut/coul/long 1.12246204830937 12.5
+pair_coeff      * *  1.0 1.0
+kspace_style    ewald 1.0e-3
+pair_modify     shift yes
+
+#########  VERLET INTEGRATION WITH LANGEVIN THERMOSTAT  ###########
+fix             fnve all nve
+compute         dtemp all temp
+compute_modify  dtemp dynamic yes
+fix             fT all langevin 1.0 1.0 1.0 123
+fix_modify      fT temp dtemp
+
+fix chareg      all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery 100 nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery 100 nmc 100 seed 2345 tempfixid fT
+thermo          100
+thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
+timestep        0.005
+run             2000
+Ewald initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
+  G vector (1/distance) = 0.14221027
+  estimated absolute RMS force accuracy = 0.0010128126
+  estimated relative force accuracy = 0.0010128126
+  KSpace vectors: actual max1d max3d = 257 5 665
+                  kxmax kymax kzmax  = 5 5 5
+0 atoms in group FixChargeRegulation:exclusion_group:chareg
+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 = 15.5
+  ghost atom cutoff = 15.5
+  binsize = 7.75, bins = 7 7 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.91 | 11.91 | 11.91 Mbytes
+Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] 
+       0 -0.049662059            1            0            0            1           99            0            0          109           10 
+     100 -0.053672881   0.99159291          100           71           16           84            0            0           92            8 
+     200 -0.053383027   0.90935145          200          156           26           74            0            0           85           11 
+     300 -0.040471335   0.97937429          300          240           21           79            0            0           87            8 
+     400 -0.036188123    1.0837424          400          319           14           86            0            0           92            6 
+     500 -0.057294925    1.0507526          500          407           10           90            0            0           98            8 
+     600 -0.056009748    1.0669354          600          487           15           85            0            0           92            7 
+     700 -0.069686562   0.99202496          700          567           14           86            0            0           96           10 
+     800 -0.054695624    1.0592933          800          647           25           75            0            0           82            7 
+     900 -0.058693653   0.97870458          900          728           27           73            0            0           83           10 
+    1000 -0.062352957    1.0008923         1000          805           24           76            0            0           84            8 
+    1100 -0.065011926   0.91691048         1100          886           22           78            0            0           87            9 
+    1200 -0.080463686   0.98879304         1200          963           23           77            0            0           88           11 
+    1300 -0.062146141    1.0566033         1300         1047           21           79            0            0           88            9 
+    1400 -0.046980246    1.0847512         1400         1129           17           83            0            0           94           11 
+    1500 -0.042935292    1.0075805         1500         1203           24           76            0            0           86           10 
+    1600 -0.056075891   0.94173489         1600         1277           23           77            0            0           90           13 
+    1700 -0.042279161    1.1126317         1700         1355           28           72            0            0           82           10 
+    1800 -0.036842528    1.0255327         1800         1436           24           76            0            0           83            7 
+    1900 -0.038816022   0.93883373         1900         1511           23           77            0            0           86            9 
+    2000 -0.047008287   0.98904085         2000         1592           26           74            0            0           81            7 
+Loop time of 11.6365 on 1 procs for 2000 steps with 188 atoms
+
+Performance: 74249.079 tau/day, 171.873 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.24337    | 0.24337    | 0.24337    |   0.0 |  2.09
+Kspace  | 4.6009     | 4.6009     | 4.6009     |   0.0 | 39.54
+Neigh   | 0.023451   | 0.023451   | 0.023451   |   0.0 |  0.20
+Comm    | 0.027729   | 0.027729   | 0.027729   |   0.0 |  0.24
+Output  | 0.0007813  | 0.0007813  | 0.0007813  |   0.0 |  0.01
+Modify  | 6.7345     | 6.7345     | 6.7345     |   0.0 | 57.87
+Other   |            | 0.005713   |            |       |  0.05
+
+Nlocal:        188.000 ave         188 max         188 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        597.000 ave         597 max         597 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:        2196.00 ave        2196 max        2196 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2196
+Ave neighs/atom = 11.680851
+Neighbor list builds = 2059
+Dangerous builds = 0
+Total wall time: 0:00:11

examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.4

@@ -0,0 +1,125 @@
+LAMMPS (10 Feb 2021)
+  using 1 OpenMP thread(s) per MPI task
+# Charge regulation lammps for simple weak electrolyte
+
+units           lj
+atom_style      charge
+neighbor        3.0 bin
+read_data       data.chreg-acid
+Reading data file ...
+  orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  219 atoms
+  read_data CPU = 0.003 seconds
+
+variable        cut_long equal 12.5
+variable        nevery equal 100
+variable        nmc equal 100
+variable        pH equal 7.0
+variable        pKa equal 6.0
+variable        pIm equal 3.0
+variable        pIp equal 3.0
+
+variable        cut_lj equal 2^(1.0/6.0)
+variable        lunit_nm equal 0.72 # in the units of nm
+velocity        all create 1.0 8008 loop geom
+
+pair_style      lj/cut/coul/long ${cut_lj} ${cut_long}
+pair_style      lj/cut/coul/long 1.12246204830937 ${cut_long}
+pair_style      lj/cut/coul/long 1.12246204830937 12.5
+pair_coeff      * *  1.0 1.0
+kspace_style    ewald 1.0e-3
+pair_modify     shift yes
+
+#########  VERLET INTEGRATION WITH LANGEVIN THERMOSTAT  ###########
+fix             fnve all nve
+compute         dtemp all temp
+compute_modify  dtemp dynamic yes
+fix             fT all langevin 1.0 1.0 1.0 123
+fix_modify      fT temp dtemp
+
+fix chareg      all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery 100 nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery 100 nmc 100 seed 2345 tempfixid fT
+thermo          100
+thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
+timestep        0.005
+run             2000
+Ewald initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
+  G vector (1/distance) = 0.14221027
+  estimated absolute RMS force accuracy = 0.0010128126
+  estimated relative force accuracy = 0.0010128126
+  KSpace vectors: actual max1d max3d = 257 5 665
+                  kxmax kymax kzmax  = 5 5 5
+0 atoms in group FixChargeRegulation:exclusion_group:chareg
+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 = 15.5
+  ghost atom cutoff = 15.5
+  binsize = 7.75, bins = 7 7 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.89 | 11.89 | 11.89 Mbytes
+Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] 
+       0 -0.049662059            1            0            0            1           99            0            0          109           10 
+     100  -0.06196414    1.0156327          100           72           15           85            0            0           93            8 
+     200 -0.053901683   0.95128403          200          160           24           76            0            0           87           11 
+     300 -0.043852423   0.98035058          300          246           22           78            0            0           85            7 
+     400 -0.048370798    1.0909844          400          324           16           84            0            0           91            7 
+     500 -0.042546472     1.026849          500          410           13           87            0            0           95            8 
+     600  -0.06133022   0.97805065          600          494           14           86            0            0           93            7 
+     700 -0.053815853    1.0641005          700          572           17           83            0            0           91            8 
+     800 -0.059974814    1.0192348          800          650           23           77            0            0           83            6 
+     900 -0.051808132    1.0773288          900          728           25           75            0            0           85           10 
+    1000 -0.050390995    1.0236954         1000          804           28           72            0            0           81            9 
+    1100 -0.069766444     1.030965         1100          890           25           75            0            0           85           10 
+    1200 -0.074580231    1.0490058         1200          963           21           79            0            0           88            9 
+    1300 -0.060169443   0.93456607         1300         1043           22           78            0            0           86            8 
+    1400  -0.05120764    1.0374062         1400         1127           19           81            0            0           92           11 
+    1500 -0.027644416   0.99804782         1500         1204           24           76            0            0           85            9 
+    1600 -0.038599195   0.99015524         1600         1283           22           78            0            0           90           12 
+    1700 -0.050222686    1.1444379         1700         1365           27           73            0            0           84           11 
+    1800 -0.049338003    1.1188048         1800         1449           22           78            0            0           84            6 
+    1900  -0.04533154   0.99894341         1900         1527           22           78            0            0           86            8 
+    2000 -0.058837311   0.95302017         2000         1608           26           74            0            0           81            7 
+Loop time of 3.98119 on 4 procs for 2000 steps with 188 atoms
+
+Performance: 217020.495 tau/day, 502.362 timesteps/s
+96.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.050626   | 0.061127   | 0.071318   |   3.4 |  1.54
+Kspace  | 1.1987     | 1.2504     | 1.288      |   3.1 | 31.41
+Neigh   | 0.0056982  | 0.0063858  | 0.0069821  |   0.7 |  0.16
+Comm    | 0.068302   | 0.11638    | 0.17922    |  12.8 |  2.92
+Output  | 0.00055408 | 0.00092399 | 0.0020106  |   0.0 |  0.02
+Modify  | 2.5399     | 2.5406     | 2.5417     |   0.0 | 63.81
+Other   |            | 0.005394   |            |       |  0.14
+
+Nlocal:        47.0000 ave          55 max          42 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+Nghost:        328.250 ave         335 max         317 min
+Histogram: 1 0 0 0 0 1 0 0 0 2
+Neighs:        547.000 ave         659 max         466 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 2188
+Ave neighs/atom = 11.638298
+Neighbor list builds = 2057
+Dangerous builds = 0
+Total wall time: 0:00:04

examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.1

@@ -0,0 +1,131 @@
+LAMMPS (10 Feb 2021)
+  using 1 OpenMP thread(s) per MPI task
+# Charge regulation lammps for a polymer chain
+units           lj
+atom_style      full
+neighbor        3.0 bin
+read_data       data.chreg-polymer
+Reading data file ...
+  orthogonal box = (-50.000000 -50.000000 -50.000000) to (50.000000 50.000000 50.000000)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  160 atoms
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  79 bonds
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     2 = max # of 1-3 neighbors
+     4 = max # of 1-4 neighbors
+     6 = max # of special neighbors
+  special bonds CPU = 0.001 seconds
+  read_data CPU = 0.009 seconds
+
+bond_style      harmonic
+bond_coeff      1 100 1.122462 # K R0
+velocity        all create 1.0 8008 loop geom
+
+pair_style      lj/cut/coul/long 1.122462 20
+pair_coeff      * *  1.0 1.0 1.122462 # charges
+kspace_style    pppm 1.0e-3
+pair_modify     shift yes
+dielectric      1.0
+
+#########  VERLET INTEGRATION WITH LANGEVIN THERMOSTAT  ###########
+fix             fnve all nve
+compute         dtemp all temp
+compute_modify  dtemp dynamic yes
+fix             fT all langevin 1.0 1.0 1.0 123
+fix_modify      fT temp dtemp
+
+fix chareg1 all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 seed 2345
+fix chareg2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 seed 2345
+fix chareg3 all charge/regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 seed 2345
+
+thermo          100
+#               print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions
+thermo_style    custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8]
+
+timestep        0.005
+run             2000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
+  G vector (1/distance) = 0.077106934
+  grid = 8 8 8
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00074388331
+  estimated relative force accuracy = 0.00074388331
+  using double precision FFTW3
+  3d grid and FFT values/proc = 2197 512
+0 atoms in group FixChargeRegulation:exclusion_group:chareg1
+0 atoms in group FixChargeRegulation:exclusion_group:chareg2
+0 atoms in group FixChargeRegulation:exclusion_group:chareg3
+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 = 23
+  ghost atom cutoff = 23
+  binsize = 11.5, bins = 9 9 9
+  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) = 6.962 | 6.962 | 6.962 Mbytes
+Step PotEng c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] 
+       0   0.50528297            1            0           80           80            0            0            0 
+     100   0.61185377   0.95892928           13           67           74            7            0            0 
+     200   0.54355177    1.1282424           19           61           76           15            0            0 
+     300    0.4519957    1.0764688           20           60           85           26            1            0 
+     400   0.41479389   0.99212685           24           56           92           36            0            0 
+     500   0.37382446   0.99776674           28           52           98           46            0            0 
+     600   0.34785337    1.1115081           28           52          109           57            0            0 
+     700   0.34637618    1.0332262           28           52          120           68            0            0 
+     800   0.21020932    1.1264036           29           51          125           74            0            0 
+     900   0.21246108    1.1168609           30           50          131           81            0            0 
+    1000   0.20997475    1.1201478           32           48          132           84            0            0 
+    1100    0.1984165    1.0209092           31           49          144           95            0            0 
+    1200    0.2061932   0.95880059           35           45          151          106            0            0 
+    1300   0.17220376     0.980077           36           44          156          112            0            0 
+    1400   0.15671143   0.93535342           37           43          161          118            0            0 
+    1500   0.16174665    0.9495928           36           44          168          124            0            0 
+    1600   0.11062965   0.94072924           40           40          164          124            0            0 
+    1700   0.13002563   0.95010828           38           42          167          125            0            0 
+    1800   0.14527814   0.93555342           37           43          172          129            0            0 
+    1900   0.17627465   0.96682495           32           48          176          128            0            0 
+    2000   0.16497265   0.95226954           33           47          180          133            0            0 
+Loop time of 7.45499 on 1 procs for 2000 steps with 393 atoms
+
+Performance: 115895.577 tau/day, 268.277 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.45607    | 0.45607    | 0.45607    |   0.0 |  6.12
+Bond    | 0.0062385  | 0.0062385  | 0.0062385  |   0.0 |  0.08
+Kspace  | 2.3257     | 2.3257     | 2.3257     |   0.0 | 31.20
+Neigh   | 0.067103   | 0.067103   | 0.067103   |   0.0 |  0.90
+Comm    | 0.02577    | 0.02577    | 0.02577    |   0.0 |  0.35
+Output  | 0.00087047 | 0.00087047 | 0.00087047 |   0.0 |  0.01
+Modify  | 4.5664     | 4.5664     | 4.5664     |   0.0 | 61.25
+Other   |            | 0.006848   |            |       |  0.09
+
+Nlocal:        393.000 ave         393 max         393 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        749.000 ave         749 max         749 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:        5359.00 ave        5359 max        5359 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5359
+Ave neighs/atom = 13.636132
+Ave special neighs/atom = 1.1908397
+Neighbor list builds = 1489
+Dangerous builds = 0
+Total wall time: 0:00:07

examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.4

@@ -0,0 +1,131 @@
+LAMMPS (10 Feb 2021)
+  using 1 OpenMP thread(s) per MPI task
+# Charge regulation lammps for a polymer chain
+units           lj
+atom_style      full
+neighbor        3.0 bin
+read_data       data.chreg-polymer
+Reading data file ...
+  orthogonal box = (-50.000000 -50.000000 -50.000000) to (50.000000 50.000000 50.000000)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  160 atoms
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  79 bonds
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     2 = max # of 1-3 neighbors
+     4 = max # of 1-4 neighbors
+     6 = max # of special neighbors
+  special bonds CPU = 0.001 seconds
+  read_data CPU = 0.016 seconds
+
+bond_style      harmonic
+bond_coeff      1 100 1.122462 # K R0
+velocity        all create 1.0 8008 loop geom
+
+pair_style      lj/cut/coul/long 1.122462 20
+pair_coeff      * *  1.0 1.0 1.122462 # charges
+kspace_style    pppm 1.0e-3
+pair_modify     shift yes
+dielectric      1.0
+
+#########  VERLET INTEGRATION WITH LANGEVIN THERMOSTAT  ###########
+fix             fnve all nve
+compute         dtemp all temp
+compute_modify  dtemp dynamic yes
+fix             fT all langevin 1.0 1.0 1.0 123
+fix_modify      fT temp dtemp
+
+fix chareg1 all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 seed 2345
+fix chareg2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 seed 2345
+fix chareg3 all charge/regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 seed 2345
+
+thermo          100
+#               print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions
+thermo_style    custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8]
+
+timestep        0.005
+run             2000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
+  G vector (1/distance) = 0.077106934
+  grid = 8 8 8
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00074388331
+  estimated relative force accuracy = 0.00074388331
+  using double precision FFTW3
+  3d grid and FFT values/proc = 1053 128
+0 atoms in group FixChargeRegulation:exclusion_group:chareg1
+0 atoms in group FixChargeRegulation:exclusion_group:chareg2
+0 atoms in group FixChargeRegulation:exclusion_group:chareg3
+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 = 23
+  ghost atom cutoff = 23
+  binsize = 11.5, bins = 9 9 9
+  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) = 6.878 | 6.935 | 6.992 Mbytes
+Step PotEng c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] 
+       0   0.50528297            1            0           80           80            0            0            0 
+     100   0.60223729   0.89547569           13           67           75            8            0            0 
+     200   0.65253636   0.87662399           18           62           78           16            0            0 
+     300   0.51550501    1.0542131           22           58           84           27            1            0 
+     400   0.43566766   0.94557633           26           54           90           36            0            0 
+     500   0.36269507    1.0386276           31           49           94           45            0            0 
+     600   0.32430641   0.99903033           27           53          111           58            0            0 
+     700   0.30255299   0.91225991           28           52          121           69            0            0 
+     800   0.27189951    0.9747089           28           52          127           75            0            0 
+     900   0.25495247    1.0747821           28           52          135           83            0            0 
+    1000   0.25950416   0.95256449           32           48          134           86            0            0 
+    1100   0.22561248    1.0102255           32           48          147           99            0            0 
+    1200    0.1734754   0.99475154           33           47          157          110            0            0 
+    1300   0.20081084   0.99873599           36           44          160          116            0            0 
+    1400   0.14240417   0.99442152           36           44          164          121            1            0 
+    1500   0.15314186   0.94559876           39           41          167          126            0            0 
+    1600   0.13574107    1.0484195           43           37          164          127            0            0 
+    1700   0.14477789    1.0105172           42           38          166          128            0            0 
+    1800   0.13493107    1.0349667           41           39          171          132            0            0 
+    1900   0.14849779    0.9994329           33           47          178          131            0            0 
+    2000   0.14485171   0.99739608           34           46          183          137            0            0 
+Loop time of 3.18871 on 4 procs for 2000 steps with 400 atoms
+
+Performance: 270955.695 tau/day, 627.212 timesteps/s
+94.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.086456   | 0.11738    | 0.18562    |  11.8 |  3.68
+Bond    | 0.00099182 | 0.0018544  | 0.0030079  |   1.8 |  0.06
+Kspace  | 0.77406    | 0.79354    | 0.80895    |   1.5 | 24.89
+Neigh   | 0.017894   | 0.017948   | 0.018002   |   0.0 |  0.56
+Comm    | 0.029044   | 0.07885    | 0.11432    |  11.3 |  2.47
+Output  | 0.00054932 | 0.0009656  | 0.0021319  |   0.0 |  0.03
+Modify  | 2.1676     | 2.1706     | 2.1733     |   0.2 | 68.07
+Other   |            | 0.007591   |            |       |  0.24
+
+Nlocal:        100.000 ave         110 max          89 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Nghost:        415.000 ave         418 max         411 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+Neighs:        1360.75 ave        1872 max        1018 min
+Histogram: 1 1 0 0 1 0 0 0 0 1
+
+Total # of neighbors = 5443
+Ave neighs/atom = 13.607500
+Ave special neighs/atom = 1.1700000
+Neighbor list builds = 1492
+Dangerous builds = 0
+Total wall time: 0:00:03

examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1

@@ -0,0 +1,145 @@
+LAMMPS (10 Feb 2021)
+# Charge regulation lammps for simple weak electrolyte
+
+units           real
+atom_style      charge
+neighbor        10.0 bin
+read_data       data.chreg-acid-real
+Reading data file ...
+  orthogonal box = (-180.00000 -180.00000 -180.00000) to (180.00000 180.00000 180.00000)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  219 atoms
+  read_data CPU = 0.002 seconds
+
+#real units
+variable 	sigma equal 7.2	              # particle diameter 0.72 nm
+variable	temperature equal 298         # temperature 298 K
+variable        kb index 0.0019872067         # kB in Kcal/mol/K
+variable 	epsilon equal ${kb}*${temperature}
+variable 	epsilon equal 0.0019872067*${temperature}
+variable 	epsilon equal 0.0019872067*298
+variable	tunit   equal 	2000          # time unit is 2000 fs
+variable	timestep equal 0.005*${tunit}
+variable	timestep equal 0.005*2000
+
+variable        cut_long equal 12.5*${sigma}
+variable        cut_long equal 12.5*7.2
+variable        nevery equal 100
+variable        nmc equal 100
+variable        pH equal 7.0
+variable        pKa equal 6.0
+variable        pIm equal 3.0
+variable        pIp equal 3.0
+
+variable        cut_lj equal 2^(1.0/6.0)*${sigma}
+variable        cut_lj equal 2^(1.0/6.0)*7.2
+velocity        all create ${temperature} 8008 loop geom
+velocity        all create 298 8008 loop geom
+
+pair_style      lj/cut/coul/long ${cut_lj} ${cut_long}
+pair_style      lj/cut/coul/long 8.08172674782749 ${cut_long}
+pair_style      lj/cut/coul/long 8.08172674782749 90
+pair_coeff      * *  ${epsilon} ${sigma}
+pair_coeff      * *  0.5921875966 ${sigma}
+pair_coeff      * *  0.5921875966 7.2
+kspace_style    pppm 1.0e-3
+dielectric	78
+pair_modify     shift yes
+
+#########  VERLET INTEGRATION WITH LANGEVIN THERMOSTAT  ###########
+fix             fnve all nve
+compute         dtemp all temp
+compute_modify  dtemp dynamic yes
+fix             fT all langevin $(v_temperature) $(v_temperature) $(v_tunit) 123
+fix             fT all langevin 298 $(v_temperature) $(v_tunit) 123
+fix             fT all langevin 298 298 $(v_tunit) 123
+fix             fT all langevin 298 298 2000 123
+fix_modify      fT temp dtemp
+
+fix chareg      all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc 100 seed 2345 tempfixid fT
+thermo          100
+thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
+timestep        ${timestep}
+timestep        10
+run             2000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:339)
+  G vector (1/distance) = 0.019408615
+  grid = 8 8 8
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00012527706
+  estimated relative force accuracy = 3.7726815e-07
+  using double precision KISS FFT
+  3d grid and FFT values/proc = 2197 512
+0 atoms in group FixChargeRegulation:exclusion_group:chareg
+WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../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 = 100
+  ghost atom cutoff = 100
+  binsize = 50, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.708 | 3.708 | 3.708 Mbytes
+Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] 
+       0   -6.4798431          298            0            0            1           99            0            0          109           10 
+     100   -6.9219668    306.44177          100           77           15           85            0            0           94            9 
+     200   -6.8175255    306.64254          200          164           23           77            0            0           87           10 
+     300   -5.2482381    331.67831          300          248           21           79            0            0           85            6 
+     400   -7.4531538     285.3495          400          326           17           83            0            0           89            6 
+     500   -6.9662528     286.2123          500          408           14           86            0            0           95            9 
+     600    -6.528214    291.41762          600          492           14           86            0            0           95            9 
+     700    -6.290871    271.50948          700          567           14           86            0            0           96           10 
+     800   -6.4944741    300.66261          800          650           23           77            0            0           83            6 
+     900   -8.0414672     305.6179          900          731           25           75            0            0           84            9 
+    1000   -8.5694583    298.73349         1000          810           25           75            0            0           83            8 
+    1100   -8.6677368    269.67435         1100          894           22           78            0            0           87            9 
+    1200   -8.2246183    284.14886         1200          969           22           78            0            0           88           10 
+    1300   -7.7674621    320.04838         1300         1040           23           77            0            0           85            8 
+    1400   -9.5186335    303.48091         1400         1124           18           82            0            0           93           11 
+    1500   -5.8437493    271.40712         1500         1204           25           75            0            0           83            8 
+    1600   -5.9149181    268.24708         1600         1285           23           77            0            0           90           13 
+    1700   -6.5047738    303.79732         1700         1369           27           73            0            0           84           11 
+    1800   -7.3010139    308.98213         1800         1450           22           78            0            0           83            5 
+    1900   -6.3505397    306.94357         1900         1527           22           78            0            0           86            8 
+    2000   -5.7144173    287.06184         2000         1605           27           73            0            0           80            7 
+Loop time of 1.17189 on 1 procs for 2000 steps with 187 atoms
+
+Performance: 1474.535 ns/day, 0.016 hours/ns, 1706.638 timesteps/s
+99.6% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.035807   | 0.035807   | 0.035807   |   0.0 |  3.06
+Kspace  | 0.37689    | 0.37689    | 0.37689    |   0.0 | 32.16
+Neigh   | 0.008694   | 0.008694   | 0.008694   |   0.0 |  0.74
+Comm    | 0.004793   | 0.004793   | 0.004793   |   0.0 |  0.41
+Output  | 0.000746   | 0.000746   | 0.000746   |   0.0 |  0.06
+Modify  | 0.74292    | 0.74292    | 0.74292    |   0.0 | 63.39
+Other   |            | 0.00205    |            |       |  0.17
+
+Nlocal:        187.000 ave         187 max         187 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        437.000 ave         437 max         437 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:        1500.00 ave        1500 max        1500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1500
+Ave neighs/atom = 8.0213904
+Neighbor list builds = 2080
+Dangerous builds = 0
+Total wall time: 0:00:01

examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4

@@ -0,0 +1,145 @@
+LAMMPS (10 Feb 2021)
+# Charge regulation lammps for simple weak electrolyte
+
+units           real
+atom_style      charge
+neighbor        10.0 bin
+read_data       data.chreg-acid-real
+Reading data file ...
+  orthogonal box = (-180.00000 -180.00000 -180.00000) to (180.00000 180.00000 180.00000)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  219 atoms
+  read_data CPU = 0.002 seconds
+
+#real units
+variable 	sigma equal 7.2	              # particle diameter 0.72 nm
+variable	temperature equal 298         # temperature 298 K
+variable        kb index 0.0019872067         # kB in Kcal/mol/K
+variable 	epsilon equal ${kb}*${temperature}
+variable 	epsilon equal 0.0019872067*${temperature}
+variable 	epsilon equal 0.0019872067*298
+variable	tunit   equal 	2000          # time unit is 2000 fs
+variable	timestep equal 0.005*${tunit}
+variable	timestep equal 0.005*2000
+
+variable        cut_long equal 12.5*${sigma}
+variable        cut_long equal 12.5*7.2
+variable        nevery equal 100
+variable        nmc equal 100
+variable        pH equal 7.0
+variable        pKa equal 6.0
+variable        pIm equal 3.0
+variable        pIp equal 3.0
+
+variable        cut_lj equal 2^(1.0/6.0)*${sigma}
+variable        cut_lj equal 2^(1.0/6.0)*7.2
+velocity        all create ${temperature} 8008 loop geom
+velocity        all create 298 8008 loop geom
+
+pair_style      lj/cut/coul/long ${cut_lj} ${cut_long}
+pair_style      lj/cut/coul/long 8.08172674782749 ${cut_long}
+pair_style      lj/cut/coul/long 8.08172674782749 90
+pair_coeff      * *  ${epsilon} ${sigma}
+pair_coeff      * *  0.5921875966 ${sigma}
+pair_coeff      * *  0.5921875966 7.2
+kspace_style    pppm 1.0e-3
+dielectric	78
+pair_modify     shift yes
+
+#########  VERLET INTEGRATION WITH LANGEVIN THERMOSTAT  ###########
+fix             fnve all nve
+compute         dtemp all temp
+compute_modify  dtemp dynamic yes
+fix             fT all langevin $(v_temperature) $(v_temperature) $(v_tunit) 123
+fix             fT all langevin 298 $(v_temperature) $(v_tunit) 123
+fix             fT all langevin 298 298 $(v_tunit) 123
+fix             fT all langevin 298 298 2000 123
+fix_modify      fT temp dtemp
+
+fix chareg      all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc 100 seed 2345 tempfixid fT
+thermo          100
+thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
+timestep        ${timestep}
+timestep        10
+run             2000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:339)
+  G vector (1/distance) = 0.019408615
+  grid = 8 8 8
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00012527706
+  estimated relative force accuracy = 3.7726815e-07
+  using double precision KISS FFT
+  3d grid and FFT values/proc = 1053 128
+0 atoms in group FixChargeRegulation:exclusion_group:chareg
+WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../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 = 100
+  ghost atom cutoff = 100
+  binsize = 50, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.624 | 3.624 | 3.624 Mbytes
+Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] 
+       0   -6.4798431          298            0            0            1           99            0            0          109           10 
+     100   -7.6327126    304.68909          100           73           15           85            0            0           94            9 
+     200   -6.1699041    272.19597          200          156           24           76            0            0           87           11 
+     300   -7.7876571    288.90801          300          240           20           80            0            0           87            7 
+     400   -6.3239918    274.65708          400          315           16           84            0            0           90            6 
+     500   -5.3978659    257.49208          500          398           15           85            0            0           93            8 
+     600   -5.6433949    322.52048          600          477           18           82            0            0           90            8 
+     700   -6.5351367    269.20244          700          558           18           82            0            0           91            9 
+     800   -6.2093085    315.21326          800          638           24           76            0            0           83            7 
+     900   -7.0795998    311.93228          900          719           28           72            0            0           82           10 
+    1000   -6.4668438    281.72674         1000          796           27           73            0            0           81            8 
+    1100   -6.2377994    318.48594         1100          875           25           75            0            0           84            9 
+    1200   -6.6305072     304.9091         1200          950           23           77            0            0           87           10 
+    1300   -5.9624552    286.05027         1300         1029           22           78            0            0           86            8 
+    1400   -4.4695814    261.81053         1400         1111           20           80            0            0           90           10 
+    1500   -5.6928652    293.72403         1500         1191           24           76            0            0           86           10 
+    1600   -6.8715413    290.47065         1600         1275           22           78            0            0           90           12 
+    1700   -6.5067505    292.74735         1700         1356           25           75            0            0           85           10 
+    1800   -5.3902702    307.79012         1800         1434           22           78            0            0           83            5 
+    1900   -5.1407153    318.48918         1900         1510           21           79            0            0           87            8 
+    2000   -4.9514719    281.87771         2000         1589           25           75            0            0           82            7 
+Loop time of 0.562889 on 4 procs for 2000 steps with 189 atoms
+
+Performance: 3069.876 ns/day, 0.008 hours/ns, 3553.097 timesteps/s
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.008399   | 0.010383   | 0.011765   |   1.2 |  1.84
+Kspace  | 0.17501    | 0.17543    | 0.1757     |   0.1 | 31.17
+Neigh   | 0.001833   | 0.0021325  | 0.002293   |   0.4 |  0.38
+Comm    | 0.023099   | 0.024255   | 0.026645   |   0.9 |  4.31
+Output  | 0.000465   | 0.000546   | 0.000783   |   0.0 |  0.10
+Modify  | 0.3464     | 0.34669    | 0.34698    |   0.0 | 61.59
+Other   |            | 0.003452   |            |       |  0.61
+
+Nlocal:        47.2500 ave          57 max          41 min
+Histogram: 1 1 0 1 0 0 0 0 0 1
+Nghost:        285.750 ave         303 max         263 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Neighs:        403.500 ave         548 max         324 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 1614
+Ave neighs/atom = 8.5396825
+Neighbor list builds = 2081
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/USER/pace/Cu-PBE-core-rep.ace

@@ -0,0 +1 @@
+../../../potentials/Cu-PBE-core-rep.ace

examples/USER/pace/in.pace.product

@@ -0,0 +1,38 @@
+# simple test of fcc Cu with ACE product  
+
+units		metal
+atom_style	atomic
+
+neighbor	0.3 bin
+neigh_modify	 every 2 delay 10 check yes
+
+variable	a equal 3.597
+lattice		fcc $a 
+region		box block 0 4 0 4 0 4
+create_box	1 box
+create_atoms	1 box
+
+mass		1 26.98
+
+group		Al type 1
+
+pair_style 	pace product
+pair_coeff  * * Cu-PBE-core-rep.ace Cu
+
+velocity        all create 300 8728 loop geom
+timestep        0.0005
+fix		1 all nve
+
+compute  	eatom all pe/atom
+compute  	energy all reduce sum c_eatom
+variable 	delenergy equal c_energy-pe
+
+compute  	satom all stress/atom NULL
+compute  	str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable 	delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
+
+thermo 		10
+thermo_style    custom step temp epair etotal press v_delenergy v_delpress
+
+run		100
+

examples/USER/pace/in.pace.recursive

@@ -0,0 +1,38 @@
+# simple test of fcc Cu with ACE recursive 
+
+units		metal
+atom_style	atomic
+
+neighbor	0.3 bin
+neigh_modify	 every 2 delay 10 check yes
+
+variable	a equal 3.597
+lattice		fcc $a 
+region		box block 0 4 0 4 0 4
+create_box	1 box
+create_atoms	1 box
+
+mass		1 26.98
+
+group		Al type 1
+
+pair_style 	pace recursive
+pair_coeff  * * Cu-PBE-core-rep.ace Cu
+
+velocity        all create 300 8728 loop geom
+timestep        0.0005
+fix		1 all nve
+
+compute  	eatom all pe/atom
+compute  	energy all reduce sum c_eatom
+variable 	delenergy equal c_energy-pe
+
+compute  	satom all stress/atom NULL
+compute  	str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable 	delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
+
+thermo 		10
+thermo_style    custom step temp epair etotal press v_delenergy v_delpress
+
+run		100
+

examples/USER/pace/log.03Feb2021.pace.product.g++.1

@@ -0,0 +1,108 @@
+LAMMPS (24 Dec 2020)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
+  using 1 OpenMP thread(s) per MPI task
+# simple test of fcc Cu with ACE product
+
+units		metal
+atom_style	atomic
+
+neighbor	0.3 bin
+neigh_modify	 every 2 delay 10 check yes
+
+variable	a equal 3.597
+lattice		fcc $a
+lattice		fcc 3.597
+Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000
+region		box block 0 4 0 4 0 4
+create_box	1 box
+Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 256 atoms
+  create_atoms CPU = 0.000 seconds
+
+mass		1 26.98
+
+group		Al type 1
+256 atoms in group Al
+
+pair_style 	pace product
+ACE version: 2021.2.3
+Product evaluator is used
+pair_coeff  * * Cu-PBE-core-rep.ace Cu
+Loading Cu-PBE-core-rep.ace
+Total number of basis functions
+	Cu: 16 (r=1) 726 (r>1)
+Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
+
+velocity        all create 300 8728 loop geom
+timestep        0.0005
+fix		1 all nve
+
+compute  	eatom all pe/atom
+compute  	energy all reduce sum c_eatom
+variable 	delenergy equal c_energy-pe
+
+compute  	satom all stress/atom NULL
+compute  	str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable 	delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
+
+thermo 		10
+thermo_style    custom step temp epair etotal press v_delenergy v_delpress
+
+run		100
+Neighbor list info ...
+  update every 2 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.7
+  ghost atom cutoff = 7.7
+  binsize = 3.85, bins = 4 4 4
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair pace, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.036 | 4.036 | 4.036 Mbytes
+Step Temp E_pair TotEng Press v_delenergy v_delpress 
+       0          300    -945.9873    -936.0989    45359.818            0 2.1827873e-11 
+      10    280.68558   -945.35055   -936.09878    46326.919            0 2.910383e-11 
+      20    228.73618   -943.63789   -936.09844    48903.598            0 -2.910383e-11 
+      30    160.53661   -941.38948   -936.09798    52222.083            0 -2.910383e-11 
+      40    97.732944   -939.31899   -936.09758    55176.875            0 2.1827873e-11 
+      50    59.165961   -938.04759    -936.0974    56850.103            0 2.910383e-11 
+      60    53.124678   -937.84857   -936.09751    56878.948            0            0 
+      70    74.623347    -938.5575   -936.09782    55565.237            0 4.3655746e-11 
+      80     109.4762   -939.70663   -936.09815    53665.652            0 2.910383e-11 
+      90    142.02657   -940.77975   -936.09837      52001.1            0            0 
+     100    161.73598   -941.42945   -936.09842    51114.997            0 1.4551915e-11 
+Loop time of 11.4718 on 1 procs for 100 steps with 256 atoms
+
+Performance: 0.377 ns/day, 63.732 hours/ns, 8.717 timesteps/s
+99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 11.468     | 11.468     | 11.468     |   0.0 | 99.96
+Neigh   | 0.001181   | 0.001181   | 0.001181   |   0.0 |  0.01
+Comm    | 0.001207   | 0.001207   | 0.001207   |   0.0 |  0.01
+Output  | 0.000876   | 0.000876   | 0.000876   |   0.0 |  0.01
+Modify  | 0.000455   | 0.000455   | 0.000455   |   0.0 |  0.00
+Other   |            | 0.000397   |            |       |  0.00
+
+Nlocal:        256.000 ave         256 max         256 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        2201.00 ave        2201 max        2201 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:         0.00000 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:      43118.0 ave       43118 max       43118 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 43118
+Ave neighs/atom = 168.42969
+Neighbor list builds = 1
+Dangerous builds = 0
+
+Total wall time: 0:00:11

examples/USER/pace/log.03Feb2021.pace.product.g++.4

@@ -0,0 +1,108 @@
+LAMMPS (24 Dec 2020)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
+  using 1 OpenMP thread(s) per MPI task
+# simple test of fcc Cu with ACE product
+
+units		metal
+atom_style	atomic
+
+neighbor	0.3 bin
+neigh_modify	 every 2 delay 10 check yes
+
+variable	a equal 3.597
+lattice		fcc $a
+lattice		fcc 3.597
+Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000
+region		box block 0 4 0 4 0 4
+create_box	1 box
+Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 256 atoms
+  create_atoms CPU = 0.000 seconds
+
+mass		1 26.98
+
+group		Al type 1
+256 atoms in group Al
+
+pair_style 	pace product
+ACE version: 2021.2.3
+Product evaluator is used
+pair_coeff  * * Cu-PBE-core-rep.ace Cu
+Loading Cu-PBE-core-rep.ace
+Total number of basis functions
+	Cu: 16 (r=1) 726 (r>1)
+Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
+
+velocity        all create 300 8728 loop geom
+timestep        0.0005
+fix		1 all nve
+
+compute  	eatom all pe/atom
+compute  	energy all reduce sum c_eatom
+variable 	delenergy equal c_energy-pe
+
+compute  	satom all stress/atom NULL
+compute  	str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable 	delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
+
+thermo 		10
+thermo_style    custom step temp epair etotal press v_delenergy v_delpress
+
+run		100
+Neighbor list info ...
+  update every 2 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.7
+  ghost atom cutoff = 7.7
+  binsize = 3.85, bins = 4 4 4
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair pace, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.005 | 4.005 | 4.005 Mbytes
+Step Temp E_pair TotEng Press v_delenergy v_delpress 
+       0          300    -945.9873    -936.0989    45359.818            0 -1.4551915e-11 
+      10    280.68558   -945.35055   -936.09878    46326.919            0 2.910383e-11 
+      20    228.73618   -943.63789   -936.09844    48903.598            0            0 
+      30    160.53661   -941.38948   -936.09798    52222.083            0 -2.910383e-11 
+      40    97.732944   -939.31899   -936.09758    55176.875            0 2.1827873e-11 
+      50    59.165961   -938.04759    -936.0974    56850.103            0 -1.4551915e-11 
+      60    53.124678   -937.84857   -936.09751    56878.948            0 7.2759576e-12 
+      70    74.623347    -938.5575   -936.09782    55565.237            0            0 
+      80     109.4762   -939.70663   -936.09815    53665.652            0 2.1827873e-11 
+      90    142.02657   -940.77975   -936.09837      52001.1            0 -1.4551915e-11 
+     100    161.73598   -941.42945   -936.09842    51114.997            0 1.4551915e-11 
+Loop time of 3.54317 on 4 procs for 100 steps with 256 atoms
+
+Performance: 1.219 ns/day, 19.684 hours/ns, 28.223 timesteps/s
+98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.1375     | 3.3058     | 3.469      |   6.5 | 93.30
+Neigh   | 0.000284   | 0.00031975 | 0.000352   |   0.0 |  0.01
+Comm    | 0.071607   | 0.23492    | 0.40336    |  24.6 |  6.63
+Output  | 0.001189   | 0.0012315  | 0.001347   |   0.2 |  0.03
+Modify  | 0.000311   | 0.00032725 | 0.000351   |   0.0 |  0.01
+Other   |            | 0.0005298  |            |       |  0.01
+
+Nlocal:        64.0000 ave          71 max          57 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Nghost:        1373.00 ave        1380 max        1366 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Neighs:         0.00000 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:      10779.5 ave       11978 max        9604 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+
+Total # of neighbors = 43118
+Ave neighs/atom = 168.42969
+Neighbor list builds = 1
+Dangerous builds = 0
+
+Total wall time: 0:00:03

examples/USER/pace/log.03Feb2021.pace.recursive.g++.1

@@ -0,0 +1,108 @@
+LAMMPS (24 Dec 2020)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
+  using 1 OpenMP thread(s) per MPI task
+# simple test of fcc Cu with ACE recursive
+
+units		metal
+atom_style	atomic
+
+neighbor	0.3 bin
+neigh_modify	 every 2 delay 10 check yes
+
+variable	a equal 3.597
+lattice		fcc $a
+lattice		fcc 3.597
+Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000
+region		box block 0 4 0 4 0 4
+create_box	1 box
+Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 256 atoms
+  create_atoms CPU = 0.000 seconds
+
+mass		1 26.98
+
+group		Al type 1
+256 atoms in group Al
+
+pair_style 	pace recursive
+ACE version: 2021.2.3
+Recursive evaluator is used
+pair_coeff  * * Cu-PBE-core-rep.ace Cu
+Loading Cu-PBE-core-rep.ace
+Total number of basis functions
+	Cu: 16 (r=1) 726 (r>1)
+Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
+
+velocity        all create 300 8728 loop geom
+timestep        0.0005
+fix		1 all nve
+
+compute  	eatom all pe/atom
+compute  	energy all reduce sum c_eatom
+variable 	delenergy equal c_energy-pe
+
+compute  	satom all stress/atom NULL
+compute  	str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable 	delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
+
+thermo 		10
+thermo_style    custom step temp epair etotal press v_delenergy v_delpress
+
+run		100
+Neighbor list info ...
+  update every 2 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.7
+  ghost atom cutoff = 7.7
+  binsize = 3.85, bins = 4 4 4
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair pace, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.036 | 4.036 | 4.036 Mbytes
+Step Temp E_pair TotEng Press v_delenergy v_delpress 
+       0          300    -945.9873    -936.0989    45359.818            0            0 
+      10    280.68558   -945.35055   -936.09878    46326.919            0 5.8207661e-11 
+      20    228.73618   -943.63789   -936.09844    48903.598            0 1.4551915e-11 
+      30    160.53661   -941.38948   -936.09798    52222.083            0 7.2759576e-11 
+      40    97.732944   -939.31899   -936.09758    55176.875            0 -5.8207661e-11 
+      50    59.165961   -938.04759    -936.0974    56850.103            0            0 
+      60    53.124678   -937.84857   -936.09751    56878.948            0 8.7311491e-11 
+      70    74.623347    -938.5575   -936.09782    55565.237            0 -1.4551915e-11 
+      80     109.4762   -939.70663   -936.09815    53665.652            0 2.1827873e-11 
+      90    142.02657   -940.77975   -936.09837      52001.1            0 2.910383e-11 
+     100    161.73598   -941.42945   -936.09842    51114.997            0            0 
+Loop time of 9.31437 on 1 procs for 100 steps with 256 atoms
+
+Performance: 0.464 ns/day, 51.746 hours/ns, 10.736 timesteps/s
+99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 9.3103     | 9.3103     | 9.3103     |   0.0 | 99.96
+Neigh   | 0.001214   | 0.001214   | 0.001214   |   0.0 |  0.01
+Comm    | 0.001176   | 0.001176   | 0.001176   |   0.0 |  0.01
+Output  | 0.000827   | 0.000827   | 0.000827   |   0.0 |  0.01
+Modify  | 0.000479   | 0.000479   | 0.000479   |   0.0 |  0.01
+Other   |            | 0.000363   |            |       |  0.00
+
+Nlocal:        256.000 ave         256 max         256 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        2201.00 ave        2201 max        2201 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:         0.00000 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:      43118.0 ave       43118 max       43118 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 43118
+Ave neighs/atom = 168.42969
+Neighbor list builds = 1
+Dangerous builds = 0
+
+Total wall time: 0:00:09

examples/USER/pace/log.03Feb2021.pace.recursive.g++.4

@@ -0,0 +1,108 @@
+LAMMPS (24 Dec 2020)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
+  using 1 OpenMP thread(s) per MPI task
+# simple test of fcc Cu with ACE recursive
+
+units		metal
+atom_style	atomic
+
+neighbor	0.3 bin
+neigh_modify	 every 2 delay 10 check yes
+
+variable	a equal 3.597
+lattice		fcc $a
+lattice		fcc 3.597
+Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000
+region		box block 0 4 0 4 0 4
+create_box	1 box
+Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 256 atoms
+  create_atoms CPU = 0.000 seconds
+
+mass		1 26.98
+
+group		Al type 1
+256 atoms in group Al
+
+pair_style 	pace recursive
+ACE version: 2021.2.3
+Recursive evaluator is used
+pair_coeff  * * Cu-PBE-core-rep.ace Cu
+Loading Cu-PBE-core-rep.ace
+Total number of basis functions
+	Cu: 16 (r=1) 726 (r>1)
+Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
+
+velocity        all create 300 8728 loop geom
+timestep        0.0005
+fix		1 all nve
+
+compute  	eatom all pe/atom
+compute  	energy all reduce sum c_eatom
+variable 	delenergy equal c_energy-pe
+
+compute  	satom all stress/atom NULL
+compute  	str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable 	delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
+
+thermo 		10
+thermo_style    custom step temp epair etotal press v_delenergy v_delpress
+
+run		100
+Neighbor list info ...
+  update every 2 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.7
+  ghost atom cutoff = 7.7
+  binsize = 3.85, bins = 4 4 4
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair pace, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.005 | 4.005 | 4.005 Mbytes
+Step Temp E_pair TotEng Press v_delenergy v_delpress 
+       0          300    -945.9873    -936.0989    45359.818            0 -5.0931703e-11 
+      10    280.68558   -945.35055   -936.09878    46326.919            0 1.4551915e-11 
+      20    228.73618   -943.63789   -936.09844    48903.598            0            0 
+      30    160.53661   -941.38948   -936.09798    52222.083            0 -2.910383e-11 
+      40    97.732944   -939.31899   -936.09758    55176.875            0            0 
+      50    59.165961   -938.04759    -936.0974    56850.103            0 -2.910383e-11 
+      60    53.124678   -937.84857   -936.09751    56878.948            0 1.4551915e-11 
+      70    74.623347    -938.5575   -936.09782    55565.237            0 3.6379788e-11 
+      80     109.4762   -939.70663   -936.09815    53665.652            0 -7.2759576e-12 
+      90    142.02657   -940.77975   -936.09837      52001.1            0 -2.910383e-11 
+     100    161.73598   -941.42945   -936.09842    51114.997            0 7.2759576e-12 
+Loop time of 2.91339 on 4 procs for 100 steps with 256 atoms
+
+Performance: 1.483 ns/day, 16.185 hours/ns, 34.324 timesteps/s
+98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.5753     | 2.723      | 2.8656     |   6.3 | 93.46
+Neigh   | 0.000308   | 0.000365   | 0.00046    |   0.0 |  0.01
+Comm    | 0.045106   | 0.18792    | 0.33552    |  24.1 |  6.45
+Output  | 0.001213   | 0.001259   | 0.001388   |   0.2 |  0.04
+Modify  | 0.000304   | 0.00033    | 0.00037    |   0.0 |  0.01
+Other   |            | 0.0005595  |            |       |  0.02
+
+Nlocal:        64.0000 ave          71 max          57 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Nghost:        1373.00 ave        1380 max        1366 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Neighs:         0.00000 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:      10779.5 ave       11978 max        9604 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+
+Total # of neighbors = 43118
+Ave neighs/atom = 168.42969
+Neighbor list builds = 1
+Dangerous builds = 0
+
+Total wall time: 0:00:03

examples/deposit/in.deposit.molecule.rigid-nve-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/nve/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.rigid-nvt-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/nvt/small molecule temp 0.1 0.1 0.1 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.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