ICODE-ADC/lammps
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Merge branch 'master' into spin-kokkos

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This commit is contained in:
Axel Kohlmeyer
2021-04-16 17:08:38 -04:00
parent 99035dc680 4ed57cb757
commit 668b74bc09
959 changed files with 35662 additions and 7361 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
.github/workflows/unittest-macos.yml vendored
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@ -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

28
cmake/CMakeLists.txt
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@ -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 $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed
@ -113,13 +118,13 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS
QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF)
USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE)
set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP)
@ -264,6 +269,7 @@ endif()
set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool")
mark_as_advanced(ENABLE_IWYU)
if(ENABLE_IWYU)
set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
find_program(IWYU_EXE NAMES include-what-you-use iwyu)
find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py)
if (IWYU_EXE AND IWYU_TOOL)
@ -382,9 +388,9 @@ else()
endif()
foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM
USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS)
USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()
endforeach()
@ -533,6 +539,18 @@ 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
@ -713,7 +731,7 @@ get_target_property(DEFINES lammps COMPILE_DEFINITIONS)
include(FeatureSummary)
feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND)
message(STATUS "<<< Build configuration >>>
Operating System: ${CMAKE_SYSTEM_NAME}
Operating System: ${CMAKE_SYSTEM_NAME} ${CMAKE_LINUX_DISTRO} ${CMAKE_DISTRO_VERSION}
Build type: ${CMAKE_BUILD_TYPE}
Install path: ${CMAKE_INSTALL_PREFIX}
Generator: ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}")

8
cmake/Modules/Documentation.cmake
View File

@ -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)

6
cmake/Modules/GTest.cmake
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@ -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 ${GTEST_URL}
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}

11
cmake/Modules/LAMMPSUtils.cmake
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@ -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 ${line} " " blank)
@ -105,3 +104,13 @@ function(FetchPotentials pkgfolder potfolder)
endforeach()
endif()
endfunction(FetchPotentials)
# set CMAKE_LINUX_DISTRO and CMAKE_DISTRO_VERSION on Linux
if((CMAKE_SYSTEM_NAME STREQUAL Linux) AND (EXISTS /etc/os-release))
file(STRINGS /etc/os-release distro REGEX "^NAME=")
string(REGEX REPLACE "NAME=\"?([^\"]*)\"?" "\\1" distro "${distro}")
file(STRINGS /etc/os-release disversion REGEX "^VERSION_ID=")
string(REGEX REPLACE "VERSION_ID=\"?([^\"]*)\"?" "\\1" disversion "${disversion}")
set(CMAKE_LINUX_DISTRO ${distro})
set(CMAKE_DISTRO_VERSION ${disversion})
endif()

17
cmake/Modules/MPI4WIN.cmake
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@ -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_MD5 4939fdb59d13182fd5dd65211e469f14
URL ${MPICH2_WIN64_DEVEL_URL}
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_MD5 a61d153500dce44e21b755ee7257e031
URL ${MPICH2_WIN32_DEVEL_URL}
URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
endif()

10
cmake/Modules/OpenCLLoader.cmake
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@ -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 ${OPENCL_LOADER_URL}
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}

25
cmake/Modules/Packages/GPU.cmake
View File

@ -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
TIMEOUT 5
URL ${CUB_URL}
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)

8
cmake/Modules/Packages/KIM.cmake
View File

@ -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_MD5 ae1ddda2ef7017ea07934e519d023dca
URL ${KIM_URL}
URL_MD5 ${KIM_MD5}
BINARY_DIR build
CMAKE_ARGS ${CMAKE_REQUEST_PIC}
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}

8
cmake/Modules/Packages/KOKKOS.cmake
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@ -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_MD5 08201d1c7cf5bc458ce0f5b44a629d5a
URL ${KOKKOS_URL}
URL_MD5 ${KOKKOS_MD5}
CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
)

8
cmake/Modules/Packages/LATTE.cmake
View File

@ -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_MD5 820e73a457ced178c08c71389a385de7
URL ${LATTE_URL}
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}

9
cmake/Modules/Packages/MSCG.cmake
View File

@ -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_MD5 8c45e269ee13f60b303edd7823866a91
URL ${MSCG_URL}
URL_MD5 ${MSCG_MD5}
SOURCE_SUBDIR src/CMake
CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS}
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}

4
cmake/Modules/Packages/USER-MOLFILE.cmake
View File

@ -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)

26
cmake/Modules/Packages/USER-PACE.cmake Normal file
View File

@ -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)

11
cmake/Modules/Packages/USER-PLUMED.cmake
View File

@ -53,10 +53,17 @@ 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/v2.7.1/plumed-src-2.7.1.tgz" CACHE STRING "URL for PLUMED tarball")
set(PLUMED_MD5 "4eac6a462ec84dfe0cec96c82421b8e8" 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_MD5 95f29dd0c067577f11972ff90dfc7d12
URL ${PLUMED_URL}
URL_MD5 ${PLUMED_MD5}
BUILD_IN_SOURCE 1
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
${CONFIGURE_REQUEST_PIC}

10
cmake/Modules/Packages/USER-SCAFACOS.cmake
View File

@ -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_MD5 bd46d74e3296bd8a444d731bb10c1738
URL ${SCAFACOS_URL}
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

8
cmake/Modules/Packages/USER-SMD.cmake
View File

@ -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_MD5 9e30f67e8531477de4117506fe44669b
URL ${EIGEN3_URL}
URL_MD5 ${EIGEN3_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
)
ExternalProject_get_property(Eigen3_build SOURCE_DIR)

9
cmake/Modules/Packages/VORONOI.cmake
View File

@ -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_MD5 2338b824c3b7b25590e18e8df5d68af9
URL ${VORO_URL}
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}

13
cmake/Modules/Testing.cmake
View File

@ -16,11 +16,14 @@ if(ENABLE_TESTING)
set(MEMORYCHECK_COMMAND "${VALGRIND_BINARY}" CACHE FILEPATH "Memory Check Command")
set(MEMORYCHECK_COMMAND_OPTIONS "${VALGRIND_DEFAULT_OPTIONS}" CACHE STRING "Memory Check Command Options")
# check if a faster linker is available.
# only verified with GNU and Clang compilers and new CMake
if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
# we need to build and link a LOT of tester executables, so it is worth checking if
# a faster linker is available. requires GNU or Clang compiler, newer CMake.
# also only verified with Fedora Linux > 30 and Ubuntu <= 18.04 (Ubuntu 20.04 fails)
if((CMAKE_SYSTEM_NAME STREQUAL Linux) AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
AND ((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")))
if (((CMAKE_LINUX_DISTRO STREQUAL Ubuntu) AND (CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04))
OR ((CMAKE_LINUX_DISTRO STREQUAL Fedora) AND (CMAKE_DISTRO_VERSION VERSION_GREATER 30)))
include(CheckCXXCompilerFlag)
set(CMAKE_CUSTOM_LINKER_DEFAULT default)
check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG)

5
cmake/Modules/YAML.cmake
View File

@ -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}

2
cmake/presets/most.cmake
View File

@ -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

10
doc/graphviz/lammps-classes.dot
View File

@ -18,8 +18,8 @@ digraph lammps {
Up [shape=box label="Update" color=blue]
Un [shape=box label="Universe" color=blue]
Ti [shape=box label="Timer" color=blue]
Lt [label="Lattice"]
Rg [label="Region" color=red]
Lt [label="Lattice"]
Rb [shape=box label="RegionBlock"]
Rs [shape=box label="RegionSphere"]
Av [label="AtomVec" color=red]
@ -34,6 +34,7 @@ digraph lammps {
Du [label="Dump" color=red]
Fi [label="Fix" color=red]
Cp [label="Compute" color=red]
Cm [label="Command" color=red]
Th [label="Thermo"]
Va [label="Variable"]
Ew [shape=box label="Ewald"]
@ -71,16 +72,19 @@ digraph lammps {
Dg [shape=box label="DumpCFG"]
Ve [shape=box label="Verlet"]
Rr [shape=box label="Respa"]
Ru [shape=box label="Run"]
Se [shape=box label="Set"]
Pt [shape=box label="PPPMTIP4P"]
Vs [shape=box label="VerletSplit"]
Ro [shape=box label="RespaOMP"]
Mc [shape=box label="MinCG"]
Mf [shape=box label="MinFire"]
La -> {At Ci Co Do Er Fo Gr In Me Mo Ne Ou Ti Up Un} [penwidth=2]
Do -> {Lt Rg} [penwidth=2]
Do -> {Rg Lt} [penwidth=2]
Rg -> {Rb Rs} [style=dashed penwidth=2]
Co -> {Cb Ct} [style=dashed penwidth=2]
In -> Va [penwidth=2]
In -> {Va Cm} [penwidth=2]
Cm -> {Ru Se} [style=dashed penwidth=2]
Mo -> {Fi Cp} [penwidth=2]
Fo -> {Pa Bo An Di Im Ks} [penwidth=2]
Ks -> {Ew Pp} [style=dashed penwidth=2]

2
doc/lammps.1
View File

@ -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.

2
doc/src/Build_basics.rst
View File

@ -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>`

54
doc/src/Build_extras.rst
View File

@ -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

22
doc/src/Build_package.rst
View File

@ -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-SMD <user-smd>` | :ref:`USER-VTK <user-vtk>` | | | | |
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :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-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-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.

1
doc/src/Commands_all.rst
View File

@ -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>`

1
doc/src/Commands_fix.rst
View File

@ -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>`

6
doc/src/Commands_pair.rst
View File

@ -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>`

1
doc/src/Developer.rst
View File

@ -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

16
doc/src/Developer_org.rst
View File

@ -49,8 +49,8 @@ underscore character '_' to separate words. Outside of bundled libraries
which may have different conventions, all C and C++ header files have a
``.h`` extension, all C++ files have a ``.cpp`` extension, and C files a
``.c`` extension. A small number of C++ classes and utility functions
are implemented with only a ``.h`` file. Examples are the Pointer class
or the MathVec functions.
are implemented with only a ``.h`` file. Examples are the Pointers and
Commands classes or the MathVec functions.
Class topology
--------------
@ -144,7 +144,7 @@ implement specific commands that can be invoked before, after, or in
between runs. For these an instance of the class is created, its
command() method called and then, after completion, the class instance
deleted. Examples for this are the create_box, create_atoms, minimize,
run, or velocity command styles.
run, set, or velocity command styles.
For all those ``styles`` certain naming conventions are employed: for
the fix nve command the class is called FixNVE and the source files are
@ -175,11 +175,11 @@ follows:
- The Input class reads and processes input input strings and files,
stores variables, and invokes :doc:`commands <Commands_all>`.
- As discussed above, command style classes are directly derived from
the Pointers class. They provide input script commands that perform
one-time operations before/after/between simulations or which invoke a
simulation. They are instantiated from within the Input class,
invoked, then immediately destructed.
- Command style classes are derived from the Command class. They provide
input script commands that perform one-time operations
before/after/between simulations or which invoke a simulation. They
are usually instantiated from within the Input class, its ``command``
method invoked, and then immediately destructed.
- The Finish class is instantiated to print statistics to the screen
after a simulation is performed, by commands like run and minimize.

251
doc/src/Developer_plugins.rst Normal file
View File

@ -0,0 +1,251 @@
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, improper or command styles
* - creator.v2
- Pointer to factory function for compute, fix, or region 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. command, 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.
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`` function 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``, however 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
^^^^^^^^^^^^^^^^^^^^^
Command styles also use the first variant of factory function as
demonstrated in the following example, which also shows that the
implementation of the plugin class may be within the same source
file as the plugin interface code:
.. code-block:: C++
#include "lammpsplugin.h"
#include "comm.h"
#include "error.h"
#include "command.h"
#include "version.h"
#include <cstring>
namespace LAMMPS_NS {
class Hello : public Command {
public:
Hello(class LAMMPS *lmp) : Command(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)
{
return new Hello(lmp);
}
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 v1.1";
plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)";
plugin.creator.v1 = (lammpsplugin_factory1 *) &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.

45
doc/src/Developer_unittest.rst
View File

@ -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
cover as much of the added code as possible. When contributing code to
the distribution, the LAMMPS developers will appreciate if additions
to the integrated unit test facility are included.
of individual features, tend to run fast, and should be set up to cover
as much of the added code as possible. When contributing code to the
distribution, the LAMMPS developers will appreciate if additions to the
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();
lmp->input->one("reset_timestep 10");
if (!verbose) ::testing::internal::GetCapturedStdout();
BEGIN_HIDE_OUTPUT();
command("reset_timestep 10");
END_HIDE_OUTPUT();
ASSERT_EQ(lmp->update->ntimestep, 10);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("reset_timestep 0");
if (!verbose) ::testing::internal::GetCapturedStdout();
BEGIN_HIDE_OUTPUT();
command("reset_timestep 0");
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
the LAMMPS command will be silent by capturing the output or not. In
the default case, verbose == false, the test output will be compact and
not mixed with LAMMPS output. However setting the verbose flag (via
setting the ``TEST_ARGS`` environment variable, ``TEST_ARGS=-v``) can be
helpful to understand why tests fail unexpectedly.
Please note the use of the ``BEGIN_HIDE_OUTPUT`` and ``END_HIDE_OUTPUT``
functions that will capture output from running LAMMPS. This is normally
discarded but by setting the verbose flag (via setting the ``TEST_ARGS``
environment variable, ``TEST_ARGS=-v``) it can be printed and used 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>`

3
doc/src/Developer_utils.rst
View File

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

10
doc/src/Howto_granular.rst
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@ -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 <pair_style>` gran/no_history
* :doc:`pair_style <pair_style>` gran/hertzian
* :doc:`pair_style gran/history <pair_gran>`
* :doc:`pair_style gran/no_history <pair_gran>`
* :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

70
doc/src/Install_git.rst
View File

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

62
doc/src/Install_patch.rst
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@ -43,24 +43,54 @@ up to date.
* A list of updated files print out to the screen. The -b switch
creates backup files of your originals (e.g. src/force.cpp.orig), so
you can manually undo the patch if something goes wrong.
* Type the following from the src directory, to enforce consistency
between the src and package directories. This is OK to do even if you
don't use one or more packages. If you are applying several patches
successively, you only need to type this once at the end. The purge
command removes deprecated src files if any were removed by the patch
from package sub-directories.
.. code-block:: bash
* Once you have updated your local files you need to re-build LAMMPS.
If you are applying several patches successively, you only need to
do the rebuild once at the end. How to do it depends on the build
system you are using.
$ make purge
$ make package-update
.. tabs::
* Re-build LAMMPS via the "make" command.
.. tab:: CMake build
.. warning::
Change to your build folder and type:
If you wish to edit/change a source file that is part of a package,
you should edit the version of the file inside the package folder in
src, and then re-install or update the package. The version in the
src directory is merely a copy and will be wiped out when you type
"make package-update".
.. 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
$ make purge # remove any deprecated src files
$ make package-update # sync package files with src files
$ make foo # re-build for your machine (mpi, serial, etc)
to enforce consistency of the source between the src folder
and package directories. This is OK to do even if you don't
use any packages. The "make purge" command removes any deprecated
src files if they were removed by the patch from a package
sub-directory.
.. warning::
If you wish to edit/change a src file that is from a package,
you should edit the version of the file inside the package
sub-directory with src, then re-install the package. The
version in the source directory is merely a copy and will be
wiped out if you type "make package-update".

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2
doc/src/Library_scatter.rst
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@ -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

17
doc/src/Modify_command.rst
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@ -1,14 +1,15 @@
Input script command style
==========================
New commands can be added to LAMMPS input scripts by adding new
classes that have a "command" method. For example, the create_atoms,
read_data, velocity, and run commands are all implemented in this
fashion. When such a command is encountered in the LAMMPS input
script, LAMMPS simply creates a class with the corresponding name,
invokes the "command" method of the class, and passes it the arguments
from the input script. The command method can perform whatever
operations it wishes on LAMMPS data structures.
New commands can be added to LAMMPS input scripts by adding new classes
that are derived from the Command class and thus must have a "command"
method. For example, the create_atoms, read_data, velocity, and run
commands are all implemented in this fashion. When such a command is
encountered in the LAMMPS input script, LAMMPS simply creates a class
instance with the corresponding name, invokes the "command" method of
the class, and passes it the arguments from the input script. The
command method can perform whatever operations it wishes on LAMMPS data
structures.
The single method your new class must define is as follows:

72
doc/src/Packages_details.rst
View File

@ -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

2
doc/src/Packages_standard.rst
View File

@ -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 |

2
doc/src/Packages_user.rst
View File

@ -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 |

2
doc/src/Python_module.rst
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@ -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

37
doc/src/Python_neighbor.rst
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@ -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

6
doc/src/angle_cosine_periodic.rst
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@ -71,9 +71,3 @@ Default
none
----------
.. _cosine-Mayo:
**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).

1
doc/src/commands_list.rst
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@ -77,6 +77,7 @@ Commands
pair_style
pair_write
partition
plugin
prd
print
processors

15
doc/src/compute_pressure.rst
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@ -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
used, N' necessarily includes periodic image (ghost) atoms outside the
central box, and the position and force vectors of ghost atoms are thus
included in the summation. When periodic boundary conditions are not
used, N' = N = the number of atoms in the system. :doc:`Fixes <fix>`
that impose constraints (e.g. the :doc:`fix shake <fix_shake>` command)
also contribute to the virial term.
dot indicates a dot product. This is computed in parallel for each
sub-domain and then summed over all parallel processes. Thus N'
necessarily includes atoms from neighboring sub-domains (so-called ghost
atoms) and the position and force vectors of ghost atoms are thus
included in the summation. Only when running in serial and without
periodic boundary conditions is N' = N = the number of atoms in the
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

4
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@ -15,10 +15,10 @@ Syntax
.. code-block:: LAMMPS
dihedral_style style interp Ntable
dihedral_style style interpolation Ntable
* style = *table* or *table/cut*
* interp = *linear* or *spline* = method of interpolation
* interpolation = *linear* or *spline* = method of interpolation
* Ntable = size of the internal lookup table
Examples

2
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@ -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

8
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@ -308,9 +308,9 @@ performed with dump style *xtc*\ .
----------
The *format* keyword can be used to change the default numeric format
output by the text-based dump styles: *atom*\ , *custom*\ , *cfg*\ , and
*xyz* styles, and their MPIIO variants. Only the *line* or *none*
The *format* keyword can be used to change the default numeric format output
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.
All the specified format strings are C-style formats, e.g. as used by
@ -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

1
doc/src/fix.rst
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@ -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

4
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@ -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"

4
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@ -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 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.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 -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

276
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@ -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).

5
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@ -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

12
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@ -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

125
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@ -56,27 +56,28 @@ Examples
Description
"""""""""""
Perform the charge equilibration (QEq) method as described in :ref:`(Rappe and Goddard) <Rappe1>` and formulated in :ref:`(Nakano) <Nakano1>` (also known
as the matrix inversion method) and in :ref:`(Rick and Stuart) <Rick1>` (also
known as the extended Lagrangian method) based on the
electronegativity equilization principle.
Perform the charge equilibration (QEq) method as described in
:ref:`(Rappe and Goddard) <Rappe1>` and formulated in :ref:`(Nakano)
<Nakano1>` (also known as the matrix inversion method) and in
:ref:`(Rick and Stuart) <Rick1>` (also known as the extended Lagrangian
method) based on the electronegativity equilization principle.
These fixes can be used with any :doc:`pair style <pair_style>` in
LAMMPS, so long as per-atom charges are defined. The most typical
use-case is in conjunction with a :doc:`pair style <pair_style>` that
performs charge equilibration periodically (e.g. every timestep), such
as the ReaxFF or Streitz-Mintmire potential.
But these fixes can also be used with
potentials that normally assume per-atom charges are fixed, e.g. a
:doc:`Buckingham <pair_buck>` or :doc:`LJ/Coulombic <pair_lj>` potential.
as the ReaxFF or Streitz-Mintmire potential. But these fixes can also
be used with potentials that normally assume per-atom charges are fixed,
e.g. a :doc:`Buckingham <pair_buck>` or :doc:`LJ/Coulombic <pair_lj>`
potential.
Because the charge equilibration calculation is effectively
independent of the pair style, these fixes can also be used to perform
a one-time assignment of charges to atoms. For example, you could
define the QEq fix, perform a zero-timestep run via the :doc:`run <run>`
command without any pair style defined which would set per-atom
charges (based on the current atom configuration), then remove the fix
via the :doc:`unfix <unfix>` command before performing further dynamics.
Because the charge equilibration calculation is effectively independent
of the pair style, these fixes can also be used to perform a one-time
assignment of charges to atoms. For example, you could define the QEq
fix, perform a zero-timestep run via the :doc:`run <run>` command
without any pair style defined which would set per-atom charges (based
on the current atom configuration), then remove the fix via the
:doc:`unfix <unfix>` command before performing further dynamics.
.. note::
@ -87,11 +88,14 @@ via the :doc:`unfix <unfix>` command before performing further dynamics.
.. note::
The :doc:`fix qeq/comb <fix_qeq_comb>` command must still be used
to perform charge equilibration with the :doc:`COMB potential <pair_comb>`. The :doc:`fix qeq/reax <fix_qeq_reax>`
command can be used to perform charge equilibration with the :doc:`ReaxFF force field <pair_reaxc>`, although fix qeq/shielded yields the
same results as fix qeq/reax if *Nevery*\ , *cutoff*\ , and *tolerance*
are the same. Eventually the fix qeq/reax command will be deprecated.
The :doc:`fix qeq/comb <fix_qeq_comb>` command must still be used to
perform charge equilibration with the :doc:`COMB potential
<pair_comb>`. The :doc:`fix qeq/reax <fix_qeq_reax>` command can be
used to perform charge equilibration with the :doc:`ReaxFF force
field <pair_reaxc>`, although fix qeq/shielded yields the same
results as fix qeq/reax if *Nevery*\ , *cutoff*\ , and *tolerance*
are the same. Eventually the fix qeq/reax command will be
deprecated.
The QEq method minimizes the electrostatic energy of the system (or
equalizes the derivative of energy with respect to charge of all the
@ -134,55 +138,57 @@ usually a good number.
The *qeq/shielded* style describes partial charges on atoms also as
point charges, but uses a shielded Coulomb potential to describe the
interaction between a pair of charged particles. Interaction through
the shielded Coulomb is given by equation (13) of the :ref:`ReaxFF force field <vanDuin>` paper. The shielding accounts for charge overlap
the shielded Coulomb is given by equation (13) of the :ref:`ReaxFF force
field <vanDuin>` paper. The shielding accounts for charge overlap
between charged particles at small separation. This style is the same
as :doc:`fix qeq/reax <fix_qeq_reax>`, and can be used with :doc:`pair_style reax/c <pair_reaxc>`. Only the *chi*\ , *eta*\ , and *gamma*
parameters from the *qfile* file are used. When using the string
*reax/c* as filename, these parameters are extracted directly from
an active *reax/c* pair style. This style solves partial
charges on atoms via the matrix inversion method. A tolerance of
1.0e-6 is usually a good number.
as :doc:`fix qeq/reax <fix_qeq_reax>`, and can be used with
:doc:`pair_style reax/c <pair_reaxc>`. Only the *chi*\ , *eta*\ , and
*gamma* parameters from the *qfile* file are used. When using the string
*reax/c* as filename, these parameters are extracted directly from an
active *reax/c* pair style. This style solves partial charges on atoms
via the matrix inversion method. A tolerance of 1.0e-6 is usually a
good number.
The *qeq/slater* style describes partial charges on atoms as spherical
charge densities centered around atoms via the Slater 1\ *s* orbital, so
that the interaction between a pair of charged particles is the
product of two Slater 1\ *s* orbitals. The expression for the Slater
1\ *s* orbital is given under equation (6) of the
:ref:`Streitz-Mintmire <Streitz1>` paper. Only the *chi*\ , *eta*\ , *zeta*\ , and
*qcore* parameters from the *qfile* file are used. When using the string
that the interaction between a pair of charged particles is the product
of two Slater 1\ *s* orbitals. The expression for the Slater 1\ *s*
orbital is given under equation (6) of the :ref:`Streitz-Mintmire
<Streitz1>` paper. Only the *chi*\ , *eta*\ , *zeta*\ , and *qcore*
parameters from the *qfile* file are used. When using the string
*coul/streitz* as filename, these parameters are extracted directly from
an active *coul/streitz* pair style. This style solves
partial charges on atoms via the matrix inversion method. A tolerance
of 1.0e-6 is usually a good number. Keyword *alpha* can be used to
change the Slater type orbital exponent.
an active *coul/streitz* pair style. This style solves partial charges
on atoms via the matrix inversion method. A tolerance of 1.0e-6 is
usually a good number. Keyword *alpha* can be used to change the Slater
type orbital exponent.
The *qeq/dynamic* style describes partial charges on atoms as point
charges that interact through 1/r, but the extended Lagrangian method
is used to solve partial charges on atoms. Only the *chi* and *eta*
charges that interact through 1/r, but the extended Lagrangian method is
used to solve partial charges on atoms. Only the *chi* and *eta*
parameters from the *qfile* file are used. Note that Coulomb
catastrophe can occur if repulsion between the pair of charged
particles is too weak. A tolerance of 1.0e-3 is usually a good
number. Keyword *qdamp* can be used to change the damping factor, while
keyword *qstep* can be used to change the time step size.
catastrophe can occur if repulsion between the pair of charged particles
is too weak. A tolerance of 1.0e-3 is usually a good number. Keyword
*qdamp* can be used to change the damping factor, while keyword *qstep*
can be used to change the time step size.
The :ref:`\ *qeq/fire*\ <Shan>` style describes the same charge model and charge
solver as the *qeq/dynamic* style, but employs a FIRE minimization
algorithm to solve for equilibrium charges.
Keyword *qdamp* can be used to change the damping factor, while
keyword *qstep* can be used to change the time step size.
The :ref:`\ *qeq/fire*\ <Shan>` style describes the same charge model
and charge solver as the *qeq/dynamic* style, but employs a FIRE
minimization algorithm to solve for equilibrium charges. Keyword
*qdamp* can be used to change the damping factor, while keyword *qstep*
can be used to change the time step size.
Note that *qeq/point*\ , *qeq/shielded*\ , and *qeq/slater* describe
different charge models, whereas the matrix inversion method and the
extended Lagrangian method (\ *qeq/dynamic* and *qeq/fire*\ ) are
different solvers.
Note that *qeq/point*\ , *qeq/dynamic* and *qeq/fire* styles all describe
charges as point charges that interact through 1/r relationship, but
solve partial charges on atoms using different solvers. These three
styles should yield comparable results if
the QEq parameters and *Nevery*\ , *cutoff*\ , and *tolerance* are the
same. Style *qeq/point* is typically faster, *qeq/dynamic* scales
better on larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ .
Note that *qeq/point*\ , *qeq/dynamic* and *qeq/fire* styles all
describe charges as point charges that interact through 1/r
relationship, but solve partial charges on atoms using different
solvers. These three styles should yield comparable results if the QEq
parameters and *Nevery*\ , *cutoff*\ , and *tolerance* are the same.
Style *qeq/point* is typically faster, *qeq/dynamic* scales better on
larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ .
.. note::
@ -200,9 +206,11 @@ better on larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ .
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about these fixes is written to :doc:`binary restart files <restart>`. No global scalar or vector or per-atom
quantities are stored by these fixes for access by various :doc:`output commands <Howto_output>`. No parameter of these fixes can be used
with the *start/stop* keywords of the :doc:`run <run>` command.
No information about these fixes is written to :doc:`binary restart
files <restart>`. No global scalar or vector or per-atom quantities are
stored by these fixes for access by various :doc:`output commands
<Howto_output>`. No parameter of these fixes can be used with the
*start/stop* keywords of the :doc:`run <run>` command.
Thexe fixes are invoked during :doc:`energy minimization <minimize>`.
@ -210,7 +218,8 @@ Restrictions
""""""""""""
These fixes are part of the QEQ package. They are only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
Related commands
""""""""""""""""

4
doc/src/fix_wall_gran.rst
View File

@ -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

3
doc/src/fix_wall_gran_region.rst
View File

@ -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

14
doc/src/pair_coul.rst
View File

@ -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

2
doc/src/pair_dpd.rst
View File

@ -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.

2
doc/src/pair_fep_soft.rst
View File

@ -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

2
doc/src/pair_gayberne.rst
View File

@ -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

17
doc/src/pair_gran.rst
View File

@ -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

16
doc/src/pair_granular.rst
View File

@ -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

247
doc/src/pair_hybrid.rst
View File

@ -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
pair styles in one simulation. With the *hybrid* style, 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
each pair of atom types. The assignment of pair styles to type pairs
is made via the :doc:`pair_coeff <pair_coeff>` command.
The *hybrid*, *hybrid/overlay*, and *hybrid/scaled* styles enable the
use of multiple pair styles in one simulation. With the *hybrid* style,
exactly one pair style is assigned to each pair of atom types. With the
*hybrid/overlay* and *hybrid/scaled* styles, one or more pair styles can
be assigned to each pair of atom types. The assignment of pair styles
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
metal atoms interact with each other via an *eam* potential, the
surface atoms interact with each other via a *lj/cut* potential, and
the metal/surface interaction is also computed via a *lj/cut*
potential. The *hybrid/overlay* style could be used as in the second
example above, where multiple potentials are superposed in an additive
fashion to compute the interaction between atoms. In this example,
using *lj/cut* and *coul/long* together gives the same result as if
the *lj/cut/coul/long* potential were used by itself. In this case,
it would be more efficient to use the single combined potential, but
in general any combination of pair potentials can be used together in
to produce an interaction that is not encoded in any single pair_style
be used for a simulation of a metal droplet on a LJ surface. The metal
atoms interact with each other via an *eam* potential, the surface atoms
interact with each other via a *lj/cut* potential, and the metal/surface
interaction is also computed via a *lj/cut* potential. The
*hybrid/overlay* style could be used as in the second example above,
where multiple potentials are superposed in an additive fashion to
compute the interaction between atoms. In this example, using *lj/cut*
and *coul/long* together gives the same result as if the
*lj/cut/coul/long* potential were used by itself. In this case, it
would be more efficient to use the single combined potential, but in
general any combination of pair potentials can be used together in to
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
sub-style's name is followed by its usual arguments, as illustrated in
the example above. See the doc pages of individual pair styles for a
listing and explanation of the appropriate arguments.
the *hybrid* or *hybrid/overlay* keyword, in any order. In case of the
*hybrid/scaled* pair style, each sub-style is prefixed with a scale
factor. The scale factor is either a floating point number or an equal
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
requires it. E.g. if you have different regions of Si and C atoms and
wish to use a Tersoff potential for pure Si for one set of atoms, and
a Tersoff potential for pure C for the other set (presumably with some
third potential for Si-C interactions), then the sub-style *tersoff*
could be listed twice. But if you just want to use a Lennard-Jones or
other pairwise potential for several different atom type pairs in your
model, then you should just list the sub-style once and use the
pair_coeff command to assign parameters for the different type pairs.
sub-style. For efficiency reasons this should only be done if your
model requires it. E.g. if you have different regions of Si and C atoms
and wish to use a Tersoff potential for pure Si for one set of atoms,
and a Tersoff potential for pure C for the other set (presumably with
some third potential for Si-C interactions), then the sub-style
*tersoff* could be listed twice. But if you just want to use a
Lennard-Jones or other pairwise potential for several different atom
type pairs in your model, then you should just list the sub-style once
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
assigned to one or more sub-styles. If you specify the same atom type
pair in a second pair_coeff command with a new sub-style, then 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
the same atom type pair in a second pair_coeff command with a
sub-style that has already been defined for that pair of atoms, then
the new pair coefficients simply override the previous ones, as in the
normal usage of the pair_coeff command. E.g. these two sets of
commands are the same:
For the *hybrid/overlay* and *hybrid/scaled* styles, each atom type pair
I,J can be assigned to one or more sub-styles. If you specify the same
atom type pair in a second pair_coeff command with a new sub-style, then
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 the
same atom type pair in a second pair_coeff command with a sub-style that
has already been defined for that pair of atoms, then the new pair
coefficients simply override the previous ones, as in the normal usage
of the pair_coeff command. E.g. these two sets of commands are the
same:
.. code-block:: LAMMPS
@ -166,42 +198,43 @@ 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
:doc:`read_restart <read_restart>` commands, or by mixing as described
below.
data file read by the :doc:`read_data <read_data>` commands, or by
mixing as described below.
For both the *hybrid* and *hybrid/overlay* styles, every atom type
pair I,J (where I <= J) must be assigned to at least one sub-style via
the :doc:`pair_coeff <pair_coeff>` command as in the examples above, or
in the data file read by the :doc:`read_data <read_data>`, or by mixing
as described below.
For all of the *hybrid*, *hybrid/overlay*, and *hybrid/scaled* styles,
every atom type pair I,J (where I <= J) must be assigned to at least one
sub-style via the :doc:`pair_coeff <pair_coeff>` command as in the
examples above, or in the data file read by the :doc:`read_data
<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
LJ potential). Or, for *hybrid* and *hybrid/overlay* simulations, you
can use this form of the pair_coeff command in your input script:
so that there is effectively no interaction (e.g. epsilon = 0.0 in a LJ
potential). Or, for *hybrid*, *hybrid/overlay*, or *hybrid/scaled*
simulations, you can use this form of the pair_coeff command in your
input script:
.. code-block:: LAMMPS
pair_coeff 2 3 none
pair_coeff 2 3 none
or this form in the "Pair Coeffs" section of the data file:
.. parsed-literal::
3 none
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
that atom type pair to sub-styles.
*hybrid/overlay* or *hybrid/scaled* pair style, it wipes out all
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
to be used in a model of a hybrid system, however, there is no consistent
assigned to different pair hybrid sub-styles via the :doc:`pair_modify
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
many-body interactions for some subset of the type pairs within the
set of 1,3,4 interactions, e.g. exclude 1-1 or 1-3 interactions. That
is not conceptually well-defined for many-body interactions, since the
But you should not, as a general rule, attempt to exclude the many-body
interactions for some subset of the type pairs within the set of 1,3,4
interactions, e.g. exclude 1-1 or 1-3 interactions. That is not
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
to think of excluding an interaction between a particular pair of
atoms when the potential computes 3-body or 4-body interactions.
find the additional atoms in the group.
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
interactions from the pair list. You will need to think carefully as
to whether it produces a physically meaningful result for your model.
potential beyond the specific pairs, since it builds its list of 3-body,
4-body, etc interactions from the pair lists. You will need to think
**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
potentials together, in an overlapping manner. Imagine you have CNT
(C atoms) on a Si surface. You want to use Tersoff for Si/Si and Si/C
Here is another example to use 2 many-body potentials together in an
overlapping manner using hybrid/overlay. Imagine you have CNT (C atoms)
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
off C/C interaction, i.e. by setting the appropriate coefficients to
0.0.
interactions, you would need to **modify** the SiC.tersoff potential
file to turn off C/C interaction, i.e. by setting the appropriate
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
the individual sub-styles, the suffix versions of the *hybrid* and
*hybrid/overlay* styles are used to propagate the corresponding suffix
to all sub-styles, if those versions exist. Otherwise the
non-accelerated version will be used.
Since the *hybrid*, *hybrid/overlay*, *hybrid/scaled* styles delegate
computation to the individual sub-styles, the suffix versions of the
*hybrid* and *hybrid/overlay* styles are used to propagate the
corresponding suffix to all sub-styles, if those versions
exist. Otherwise the non-accelerated version will be used.
The individual accelerated sub-styles are part of the GPU, USER-OMP
and OPT packages, respectively. They are only enabled if LAMMPS was
built with those packages. See the :doc:`Build package <Build_package>`
doc page for more info.
The individual accelerated sub-styles are part of the GPU, KOKKOS,
USER-INTEL, USER-OMP, and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the :doc:`Build
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
and J,J is the same, and if the sub-style allows for mixing, then the
For atom type pairs I,J and I != J, if the sub-style assigned to I,I and
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
and its coefficients generated by the mixing rule used by that
sub-style. For the *hybrid/overlay* style, there is an additional
requirement that both the I,I and J,J pairs are assigned to a single
sub-style. See the "pair_modify" command for details of mixing rules.
See the See the doc page for the sub-style to see if allows for
mixing.
assigned automatically to the sub-style defined for both I,I and J,J and
its coefficients generated by the mixing rule used by that sub-style.
For the *hybrid/overlay* and *hybrid/scaled* style, there is an
additional requirement that both the I,I and J,J pairs are assigned to a
single sub-style. See the :doc:`pair_modify <pair_modify>` command for
details of mixing rules. See the See the doc page for the sub-style to
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
respective settings are written to :doc:`binary restart files <restart>`, so a :doc:`pair_style <pair_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. Thus, pair_coeff commands need to be re-specified in the
restart input script.
For the hybrid pair styles, the list of sub-styles and their respective
settings are written to :doc:`binary restart files <restart>`, so a
:doc:`pair_style <pair_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. Thus, pair_coeff
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
""""""""""""""""

55
doc/src/pair_lj_switch3_coulgauss_long.rst
View File

@ -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
by the switching function
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}
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
enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
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
""""""""""""""""

109
doc/src/pair_mm3_switch3_coulgauss_long.rst
View File

@ -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

114
doc/src/pair_pace.rst Normal file
View File

@ -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).

9
doc/src/pair_style.rst
View File

@ -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>` -

2
doc/src/pair_vashishta.rst
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@ -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"

90
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@ -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

9
doc/src/rerun.rst
View File

@ -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;

2
doc/src/units.rst
View File

@ -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

10
doc/src/variable.rst
View File

@ -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)
feature functions = is_active(category,feature,exact), is_defined(category,id,exact)
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_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

44
doc/utils/sphinx-config/false_positives.txt
View File

@ -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

36
examples/USER/misc/charge_regulation/README Normal file
View File

@ -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.

235
examples/USER/misc/charge_regulation/data.chreg-acid Normal file
View File

@ -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
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197 2 1 20.982351847235442 7.072739454450108 -24.07322254392252
198 2 1 5.962360707177609 -19.424513569281604 22.469955103109243
199 2 1 -17.13607356062674 20.038457022813326 12.94227215395123
200 2 1 11.592617137491743 22.283887092702138 2.339699650677858
201 2 1 -1.3864952037065237 19.199632510575505 -7.684210221911414
202 2 1 -22.44476570586083 -19.66385674506424 -8.981660607669522
203 2 1 0.36547911522815824 -7.628556098996082 16.326944822668068
204 2 1 -9.766164330974753 24.38435844399602 -14.352553497163
205 2 1 -0.6310792726759544 -5.625399375968325 13.665993163571486
206 2 1 2.6795300975636103 -0.37097710463575595 15.575183407667495
207 2 1 10.68508361399715 24.638181487800373 -17.538711281692827
208 2 1 18.30809729940504 18.39121662193474 18.285926328751984
209 2 1 -11.52561870836783 -11.871004571782223 12.890674390475048
210 3 -1 16.038097437687007 -0.8308290507120688 9.140710202344948
211 3 -1 -12.071581865552927 23.77532123232212 -6.250109721970887
212 3 -1 24.179073767023887 19.6390206210449 22.20321951706368
213 3 -1 22.899159789805424 8.918385700451317 -1.1269016129923664
214 3 -1 -10.48576153865241 5.691510884812594 21.955276995406933
215 3 -1 6.272776670877239 10.035821052072265 22.22030412319301
216 3 -1 14.689947575936934 -7.785907120217196 0.5033983092114553
217 3 -1 23.173937996535116 -21.041572031861037 -21.057283440516468
218 3 -1 -6.015120142466472 6.3962924962024985 21.58241945230285
219 3 -1 -0.77667042466472 0.3962848125024985 1.582473830285

235
examples/USER/misc/charge_regulation/data.chreg-acid-real Normal file
View File

@ -0,0 +1,235 @@
LAMMPS data file generated by get_input.py
219 atoms
3 atom types
-180 180 xlo xhi
-180 180 ylo yhi
-180 180 zlo zhi
Masses
1 20
2 20
3 20
Atoms
1 1 0 18.70795854 -60.24998141 144.0092784
2 1 -1 -130.9166548 -58.17450505 59.42690807
3 1 -1 -125.5489258 58.46696329 77.38308245
4 1 -1 46.8178314 -169.1807517 143.6272062
5 1 -1 -162.2028908 -135.2407217 -129.3455357
6 1 -1 -69.93717134 136.6009615 -140.3684699
7 1 -1 -92.39022725 0.88313303 -156.091658
8 1 -1 150.5452585 -15.59052452 3.326246397
9 1 -1 171.8072626 172.9794849 75.84528386
10 1 -1 -3.808294794 171.5056017 -19.13183671
11 1 -1 68.90552852 86.21187482 24.628687
12 1 -1 -73.4512319 54.41387468 86.90435812
13 1 -1 35.26889793 14.52239846 -149.5100547
14 1 -1 -173.4235696 31.85993966 -30.27092231
15 1 -1 26.52275652 -34.29527864 -91.86288894
16 1 -1 -87.96846598 -127.5856503 -97.6057498
17 1 -1 -154.4848498 -53.45277349 -49.99665917
18 1 -1 98.62055171 61.22620607 58.21550969
19 1 -1 -41.50240351 82.79211492 -36.80199381
20 1 -1 28.75979595 121.8830702 -107.1045784
21 1 -1 32.46858199 119.7785312 -159.9729476
22 1 -1 159.2306995 -136.6051631 -172.6738992
23 1 -1 102.0172393 -120.2283106 99.20908244
24 1 -1 123.7452923 63.55770833 165.9991324
25 1 -1 21.47248943 -121.2255157 -153.2060898
26 1 -1 119.9343938 -11.67643844 -81.47418783
27 1 -1 138.3518387 -111.6909718 52.34478391
28 1 -1 -63.98455793 -173.4943975 28.8937153
29 1 -1 151.1941205 32.1957053 2.770016951
30 1 -1 9.678451862 40.32965827 -107.4138803
31 1 -1 -50.13343476 147.3853225 -117.9277823
32 1 -1 -71.89428479 68.56083346 -179.8533411
33 1 -1 -124.7615264 41.48173515 41.18558752
34 1 -1 37.21218965 -170.6314486 18.86382891
35 1 -1 136.6419056 46.16558949 45.50222572
36 1 -1 -117.9745136 -106.7487877 29.70172113
37 1 -1 57.41607893 -135.959946 79.2519303
38 1 -1 99.2146782 13.37903953 65.55038181
39 1 -1 -172.1483566 -24.09752036 -73.64723741
40 1 -1 155.6386288 60.79647905 -137.6687854
41 1 -1 -63.53265172 104.1203088 115.6442718
42 1 -1 -17.57295284 90.38545929 148.3687022
43 1 -1 -132.9077114 109.8788504 152.5487953
44 1 -1 16.09488244 -168.1200949 81.85901273
45 1 -1 112.2904059 -47.57448978 39.12664557
46 1 -1 -126.2033528 29.5901835 -10.20047838
47 1 -1 15.56623544 -118.8796306 -87.74057744
48 1 -1 -62.53683723 -50.93540139 -8.324528194
49 1 -1 112.4826277 -47.2269151 148.0087872
50 1 -1 -50.1494905 -103.3112513 -103.8344246
51 1 -1 -87.11540287 -177.3205662 -114.041712
52 1 -1 48.0517504 56.41745572 -69.94172272
53 1 -1 -125.3768674 89.18463079 -121.5525657
54 1 -1 157.6559442 89.89879164 -104.7846361
55 1 -1 -60.30935405 -178.4439001 53.67216823
56 1 -1 101.3842749 -156.3782696 -125.6200241
57 1 -1 33.71034745 14.19807232 -56.33090362
58 1 -1 31.34283781 114.2588441 177.621698
59 1 -1 167.8681492 -33.73721495 17.70943601
60 1 -1 50.73906277 165.7201913 -94.6041936
61 1 -1 84.42400278 -113.8271268 -11.73087326
62 1 -1 -146.6200007 -87.0115127 -164.2802459
63 1 -1 -17.94345563 -5.266117623 -114.4770608
64 1 -1 -161.6618755 -81.21577064 -68.78715057
65 1 -1 178.3275787 144.9284223 75.80861878
66 1 -1 81.54873843 -83.6941478 -69.75163018
67 1 -1 -41.13190239 113.6079886 -6.669536125
68 1 -1 -108.5270482 -89.08499627 -39.32427247
69 1 -1 -41.97432027 -32.96246695 65.11935497
70 1 -1 -39.09020679 10.47027922 -53.26049629
71 1 -1 -168.3760012 -85.85704062 27.51501191
72 1 -1 -7.699755475 21.59960856 26.43069039
73 1 -1 87.36704757 14.21816794 -107.2504322
74 1 -1 153.4284087 136.6052131 -126.1502487
75 1 -1 -175.3682642 25.88313064 123.6455547
76 1 -1 90.96648194 175.4891969 32.84622917
77 1 -1 -77.3297511 139.285477 -24.02526586
78 1 -1 -21.80051132 76.35556687 53.9496888
79 1 -1 36.00388293 84.74463507 124.0379428
80 1 -1 8.341344194 -176.0991953 -90.11296078
81 1 -1 13.79742378 -101.263178 81.37760753
82 1 -1 -150.1706978 153.3081009 125.261789
83 1 -1 -176.434078 -91.73850736 -13.91415701
84 1 -1 19.14212656 -8.014482902 53.93954558
85 1 -1 -133.3111329 174.2862517 104.1616036
86 1 -1 141.4028288 71.58712061 62.57853826
87 1 -1 -55.41310448 84.69012271 -53.69230074
88 1 -1 7.57030387 -82.51421069 121.7019339
89 1 -1 6.593627122 170.3286085 -47.07783075
90 1 -1 167.9772199 -52.51603119 -77.32359634
91 1 -1 9.68753279 2.580696533 63.63273049
92 1 -1 -157.900078 -78.41001295 -74.97298362
93 1 -1 157.7779932 -77.61759639 83.11626672
94 1 -1 8.735687555 -51.63741526 149.2886008
95 1 -1 166.3370649 158.0395191 2.108272744
96 1 -1 -136.2080224 -0.233620925 170.1641304
97 1 -1 54.59763504 77.34086464 -34.97254442
98 1 -1 -53.93524806 -102.0122253 -46.27109402
99 1 -1 -148.8398471 -62.976886 79.28200649
100 1 -1 -134.367229 -153.7685306 -62.89913905
101 2 1 85.68701047 47.45902631 136.9309939
102 2 1 -168.7218611 -136.4862888 34.82926874
103 2 1 -85.14342147 -27.50852705 22.44064244
104 2 1 -125.9841936 -166.432033 69.22175254
105 2 1 78.40196016 32.48784706 134.5355212
106 2 1 -158.7356866 172.6075363 -168.6081077
107 2 1 -97.70696089 125.0552693 152.541151
108 2 1 47.42532862 117.2059839 -26.2001494
109 2 1 58.97843054 49.16794046 -45.70255405
110 2 1 -113.2077086 -147.4896474 -109.0593944
111 2 1 133.7818478 137.2370883 -74.12887346
112 2 1 -151.8619681 -55.72321046 39.00697883
113 2 1 -101.5491513 -113.5421107 -135.9492067
114 2 1 -105.4410412 63.66017268 62.00391546
115 2 1 -84.37716183 -35.78408568 -7.089644848
116 2 1 140.387382 -75.00992841 -159.2710691
117 2 1 157.3753205 145.1311104 -98.29723102
118 2 1 -126.8885841 157.4914592 -47.04455377
119 2 1 52.06885202 -100.2669325 38.59257737
120 2 1 -54.06789629 137.7750035 -116.8953091
121 2 1 -29.14739431 94.50860741 -51.527097
122 2 1 -145.9322739 154.5384232 112.3421798
123 2 1 -32.24342538 -22.90490626 -133.4101075
124 2 1 155.0953371 97.30799449 -13.02231424
125 2 1 -109.6079033 -42.89844953 -51.80376701
126 2 1 -150.2770445 -55.20818421 147.7312972
127 2 1 -26.96028917 151.3053234 51.82429115
128 2 1 -42.51040448 55.12547194 -10.01649745
129 2 1 -154.7332138 -166.4922488 75.56066422
130 2 1 179.3252381 50.98353603 -103.842222
131 2 1 -87.64561442 -167.4026399 -37.04977996
132 2 1 -141.7543098 32.23109989 44.99445113
133 2 1 121.3596596 -6.092779973 129.6856923
134 2 1 124.4836766 -86.35531223 85.50625099
135 2 1 140.6305506 -165.9843021 -35.3966949
136 2 1 -89.51258901 36.2123163 54.25434215
137 2 1 107.5306105 58.22419926 141.7457531
138 2 1 -51.03564423 -166.277591 119.3103596
139 2 1 106.3738063 153.673561 100.7747233
140 2 1 -105.1662471 -49.88388187 -163.5658795
141 2 1 -123.4063552 104.6405545 -157.1806703
142 2 1 30.68517662 111.7365757 -128.0988407
143 2 1 -70.66650991 -36.87088431 101.1920697
144 2 1 59.85584345 28.56015074 -148.8751279
145 2 1 76.34296857 -18.88899045 11.99663247
146 2 1 -127.898772 9.029786744 -155.2067979
147 2 1 -61.47407783 106.6906337 -32.24644961
148 2 1 -41.82882356 105.2048819 95.67134776
149 2 1 64.70518204 -125.5606981 -130.2221179
150 2 1 -95.86998176 64.01110464 -62.69889224
151 2 1 -3.893149866 -170.4938796 -173.9425756
152 2 1 -142.5571999 -115.9852755 -42.33527796
153 2 1 -170.1094774 67.22933296 -69.41406448
154 2 1 -135.7002446 -117.3853245 -77.66219554
155 2 1 97.68794466 -176.3481416 64.0577303
156 2 1 98.30084322 -179.1048324 157.6098802
157 2 1 -61.74657154 71.45180441 36.21267022
158 2 1 148.9924395 8.130617629 2.580809806
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

264
examples/USER/misc/charge_regulation/data.chreg-polymer Normal file
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@ -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

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# 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

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# 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

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# 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

125
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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

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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

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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

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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

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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

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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

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examples/USER/pace/Cu-PBE-core-rep.ace Symbolic link
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../../../potentials/Cu-PBE-core-rep.ace

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# 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

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# 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

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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

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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

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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

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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

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# 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

56
examples/deposit/in.deposit.molecule.rigid-nvt-small Normal file
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# 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

56
examples/deposit/in.deposit.molecule.rigid-small Normal file
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# 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

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