diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000000..5ace4600a1 --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,6 @@ +version: 2 +updates: + - package-ecosystem: "github-actions" + directory: "/" + schedule: + interval: "weekly" diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml index f9503e0e1f..07f7564727 100644 --- a/.github/workflows/codeql-analysis.yml +++ b/.github/workflows/codeql-analysis.yml @@ -5,12 +5,19 @@ on: push: branches: [develop] + workflow_dispatch: + jobs: analyze: name: Analyze if: ${{ github.repository == 'lammps/lammps' }} runs-on: ubuntu-latest + permissions: + security-events: write + actions: read + contents: read + strategy: fail-fast: false matrix: @@ -18,17 +25,17 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v2 + uses: actions/checkout@v3 with: fetch-depth: 2 - name: Setup Python - uses: actions/setup-python@v2 + uses: actions/setup-python@v4 with: python-version: '3.x' - name: Initialize CodeQL - uses: github/codeql-action/init@v1 + uses: github/codeql-action/init@v2 with: languages: ${{ matrix.language }} config-file: ./.github/codeql/${{ matrix.language }}.yml @@ -46,4 +53,4 @@ jobs: cmake --build . --parallel 2 - name: Perform CodeQL Analysis - uses: github/codeql-action/analyze@v1 + uses: github/codeql-action/analyze@v2 diff --git a/.github/workflows/compile-msvc.yml b/.github/workflows/compile-msvc.yml index b31c262e32..7747be7b46 100644 --- a/.github/workflows/compile-msvc.yml +++ b/.github/workflows/compile-msvc.yml @@ -5,6 +5,8 @@ on: push: branches: [develop] + workflow_dispatch: + jobs: build: name: Windows Compilation Test @@ -13,12 +15,12 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v2 + uses: actions/checkout@v3 with: fetch-depth: 2 - name: Select Python version - uses: actions/setup-python@v2 + uses: actions/setup-python@v4 with: python-version: '3.10' diff --git a/.github/workflows/unittest-macos.yml b/.github/workflows/unittest-macos.yml index a222380f60..e6e5ccfdc8 100644 --- a/.github/workflows/unittest-macos.yml +++ b/.github/workflows/unittest-macos.yml @@ -5,6 +5,8 @@ on: push: branches: [develop] + workflow_dispatch: + jobs: build: name: MacOS Unit Test @@ -15,7 +17,7 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v2 + uses: actions/checkout@v3 with: fetch-depth: 2 @@ -26,7 +28,7 @@ jobs: run: mkdir build - name: Set up ccache - uses: actions/cache@v2 + uses: actions/cache@v3 with: path: ${{ env.CCACHE_DIR }} key: macos-ccache-${{ github.sha }} diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index b0eacc9cff..42d3de00d6 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -135,9 +135,14 @@ set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions") # ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro # and prints lots of pointless warnings about "unsafe" functions if(MSVC) - add_compile_options(/Zc:__cplusplus) - add_compile_options(/wd4244) - add_compile_options(/wd4267) + if(CMAKE_CXX_COMPILER_ID STREQUAL "MSVC") + add_compile_options(/Zc:__cplusplus) + add_compile_options(/wd4244) + add_compile_options(/wd4267) + if(LAMMPS_EXCEPTIONS) + add_compile_options(/EHsc) + endif() + endif() add_compile_definitions(_CRT_SECURE_NO_WARNINGS) endif() @@ -420,23 +425,9 @@ endif() # tweak jpeg library names to avoid linker errors with MinGW cross-compilation set(JPEG_NAMES libjpeg libjpeg-62) find_package(JPEG QUIET) -if((NOT JPEG_FOUND) AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.16)) - set(LIBJPEG_URL https://sourceforge.net/projects/libjpeg-turbo/files/2.1.3/libjpeg-turbo-2.1.3.tar.gz) - set(LIBJPEG_MD5 85244dedeaf06f636a9e7ddea6d236d8) - mark_as_advanced(LIBJPEG_URL) - mark_as_advanced(LIBJPEG_MD5) - include(ExternalCMakeProject) - ExternalCmakeProject(libjpeg ${LIBJPEG_URL} ${LIBJPEG_MD5} libjpeg-turbo . CMakeLists.jpeg) - add_library(JPEG::JPEG ALIAS jpeg-static) - target_include_directories(lammps PRIVATE "${CMAKE_BINARY_DIR}/_deps/libjpeg-src") - target_include_directories(lammps PRIVATE "${CMAKE_BINARY_DIR}/_deps/libjpeg-build") - set(JPEG_FOUND TRUE) -endif() option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND}) if(WITH_JPEG) - if(NOT JPEG_FOUND) - find_package(JPEG REQUIRED) - endif() + find_package(JPEG REQUIRED) target_compile_definitions(lammps PRIVATE -DLAMMPS_JPEG) if(CMAKE_VERSION VERSION_LESS 3.12) target_include_directories(lammps PRIVATE ${JPEG_INCLUDE_DIRS}) @@ -448,43 +439,14 @@ endif() find_package(PNG QUIET) find_package(ZLIB QUIET) -if((NOT ZLIB_FOUND) AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.16)) - set(LIBZ_URL http://prdownloads.sourceforge.net/libpng/zlib-1.2.11.tar.gz) - set(LIBZ_MD5 1c9f62f0778697a09d36121ead88e08e) - mark_as_advanced(LIBZ_URL) - mark_as_advanced(LIBZ_MD5) - include(ExternalCMakeProject) - ExternalCmakeProject(libz ${LIBZ_URL} ${LIBZ_MD5} zlib . CMakeLists.zlib) - add_library(ZLIB::ZLIB ALIAS zlibstatic) - target_include_directories(lammps PRIVATE "${CMAKE_BINARY_DIR}/_deps/libz-src") - target_include_directories(lammps PRIVATE "${CMAKE_BINARY_DIR}/_deps/libz-build") - set(ZLIB_FOUND TRUE) - set(ZLIB_INCLUDE_DIR "${CMAKE_BINARY_DIR}/_deps/libz-src;${CMAKE_BINARY_DIR}/_deps/libz-build") -endif() -if((NOT PNG_FOUND) AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.16)) - set(LIBPNG_URL http://prdownloads.sourceforge.net/libpng/libpng-1.6.37.tar.gz) - set(LIBPNG_MD5 6c7519f6c75939efa0ed3053197abd54) - mark_as_advanced(LIBPNG_URL) - mark_as_advanced(LIBPNG_MD5) - include(ExternalCMakeProject) - ExternalCmakeProject(libpng ${LIBPNG_URL} ${LIBPNG_MD5} libpng . CMakeLists.png) - add_library(PNG::PNG ALIAS png_static) - target_include_directories(lammps PRIVATE "${CMAKE_BINARY_DIR}/_deps/libpng-src") - target_include_directories(lammps PRIVATE "${CMAKE_BINARY_DIR}/_deps/libpng-build") - set(PNG_FOUND TRUE) -endif() if(PNG_FOUND AND ZLIB_FOUND) option(WITH_PNG "Enable PNG support" ON) else() option(WITH_PNG "Enable PNG support" OFF) endif() if(WITH_PNG) - if(NOT PNG_FOUND) - find_package(PNG REQUIRED) - endif() - if(NOT ZLIB_FOUND) - find_package(ZLIB REQUIRED) - endif() + find_package(PNG REQUIRED) + find_package(ZLIB REQUIRED) target_link_libraries(lammps PRIVATE PNG::PNG ZLIB::ZLIB) target_compile_definitions(lammps PRIVATE -DLAMMPS_PNG) endif() @@ -826,14 +788,16 @@ if(BUILD_SHARED_LIBS) find_package(Python COMPONENTS Interpreter) endif() if(BUILD_IS_MULTI_CONFIG) - set(LIBLAMMPS_SHARED_BINARY ${CMAKE_BINARY_DIR}/$/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX}) + set(MY_BUILD_DIR ${CMAKE_BINARY_DIR}/$) else() - set(LIBLAMMPS_SHARED_BINARY ${CMAKE_BINARY_DIR}/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX}) + set(MY_BUILD_DIR ${CMAKE_BINARY_DIR}) endif() + set(LIBLAMMPS_SHARED_BINARY ${MY_BUILD_DIR}/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX}) if(Python_EXECUTABLE) add_custom_target( install-python ${CMAKE_COMMAND} -E remove_directory build - COMMAND ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps -l ${LIBLAMMPS_SHARED_BINARY} + COMMAND ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps + -l ${LIBLAMMPS_SHARED_BINARY} -w ${MY_BUILD_DIR} COMMENT "Installing LAMMPS Python module") else() add_custom_target( diff --git a/cmake/Modules/LAMMPSInterfacePlugin.cmake b/cmake/Modules/LAMMPSInterfacePlugin.cmake new file mode 100644 index 0000000000..ec7a739785 --- /dev/null +++ b/cmake/Modules/LAMMPSInterfacePlugin.cmake @@ -0,0 +1,197 @@ +# CMake script code to define LAMMPS settings required for building LAMMPS plugins + +# enforce out-of-source build +if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR}) + message(FATAL_ERROR "In-source builds are not allowed. You must create and use a build directory. " + "Please remove CMakeCache.txt and CMakeFiles first.") +endif() + +# global LAMMPS/plugin build settings +set(LAMMPS_SOURCE_DIR "" CACHE PATH "Location of LAMMPS sources folder") +if(NOT LAMMPS_SOURCE_DIR) + message(FATAL_ERROR "Must set LAMMPS_SOURCE_DIR") +endif() + +# by default, install into $HOME/.local (not /usr/local), +# so that no root access (and sudo) is needed +if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT) + set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE) +endif() + +# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro +# and prints lots of pointless warnings about "unsafe" functions +if(MSVC) + if(CMAKE_CXX_COMPILER_ID STREQUAL "MSVC") + add_compile_options(/Zc:__cplusplus) + add_compile_options(/wd4244) + add_compile_options(/wd4267) + if(LAMMPS_EXCEPTIONS) + add_compile_options(/EHsc) + endif() + endif() + add_compile_definitions(_CRT_SECURE_NO_WARNINGS) +endif() + +# C++11 is required +set(CMAKE_CXX_STANDARD 11) +set(CMAKE_CXX_STANDARD_REQUIRED ON) + +# Need -restrict with Intel compilers +if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict") +endif() +set(CMAKE_POSITION_INDEPENDENT_CODE TRUE) + +####### +# helper functions from LAMMPSUtils.cmake +function(validate_option name values) + string(TOLOWER ${${name}} needle_lower) + string(TOUPPER ${${name}} needle_upper) + list(FIND ${values} ${needle_lower} IDX_LOWER) + list(FIND ${values} ${needle_upper} IDX_UPPER) + if(${IDX_LOWER} LESS 0 AND ${IDX_UPPER} LESS 0) + list_to_bulletpoints(POSSIBLE_VALUE_LIST ${${values}}) + message(FATAL_ERROR "\n########################################################################\n" + "Invalid value '${${name}}' for option ${name}\n" + "\n" + "Possible values are:\n" + "${POSSIBLE_VALUE_LIST}" + "########################################################################") + endif() +endfunction(validate_option) + +# helper function for getting the most recently modified file or folder from a glob pattern +function(get_newest_file path variable) + file(GLOB _dirs ${path}) + set(_besttime 2000-01-01T00:00:00) + set(_bestfile "") + foreach(_dir ${_dirs}) + file(TIMESTAMP ${_dir} _newtime) + if(_newtime IS_NEWER_THAN _besttime) + set(_bestfile ${_dir}) + set(_besttime ${_newtime}) + endif() + endforeach() + if(_bestfile STREQUAL "") + message(FATAL_ERROR "Could not find valid path at: ${path}") + endif() + set(${variable} ${_bestfile} PARENT_SCOPE) +endfunction() + +################################################################################# +# LAMMPS C++ interface. We only need the header related parts except on windows. +add_library(lammps INTERFACE) +target_include_directories(lammps INTERFACE ${LAMMPS_SOURCE_DIR}) +if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING) + target_link_libraries(lammps INTERFACE ${CMAKE_BINARY_DIR}/../liblammps.dll.a) +endif() + +################################################################################ +# MPI configuration +if(NOT CMAKE_CROSSCOMPILING) + find_package(MPI QUIET) + option(BUILD_MPI "Build MPI version" ${MPI_FOUND}) +else() + option(BUILD_MPI "Build MPI version" OFF) +endif() + +if(BUILD_MPI) + # do not include the (obsolete) MPI C++ bindings which makes + # for leaner object files and avoids namespace conflicts + set(MPI_CXX_SKIP_MPICXX TRUE) + # We use a non-standard procedure to cross-compile with MPI on Windows + if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING) + # Download and configure custom MPICH files for Windows + message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows") + set(MPICH2_WIN64_DEVEL_URL "${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 ${MPICH2_WIN64_DEVEL_URL} + URL_MD5 ${MPICH2_WIN64_DEVEL_MD5} + CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" + BUILD_BYPRODUCTS /lib/libmpi.a) + else() + ExternalProject_Add(mpi4win_build + URL ${MPICH2_WIN32_DEVEL_URL} + URL_MD5 ${MPICH2_WIN32_DEVEL_MD5} + CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" + BUILD_BYPRODUCTS /lib/libmpi.a) + endif() + + ExternalProject_get_property(mpi4win_build SOURCE_DIR) + file(MAKE_DIRECTORY "${SOURCE_DIR}/include") + add_library(MPI::MPI_CXX UNKNOWN IMPORTED) + set_target_properties(MPI::MPI_CXX PROPERTIES + IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a" + INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include" + INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX") + add_dependencies(MPI::MPI_CXX mpi4win_build) + + # set variables for status reporting at the end of CMake run + set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include") + set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX") + set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a") + else() + find_package(MPI REQUIRED) + option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF) + if(LAMMPS_LONGLONG_TO_LONG) + target_compile_definitions(lammps INTERFACE -DLAMMPS_LONGLONG_TO_LONG) + endif() + endif() + target_link_libraries(lammps INTERFACE MPI::MPI_CXX) +else() + add_library(mpi_stubs INTERFACE) + target_include_directories(mpi_stubs INTERFACE $) + target_link_libraries(lammps INTERFACE mpi_stubs) +endif() + +################################################################################ +# detect if we may enable OpenMP support by default +set(BUILD_OMP_DEFAULT OFF) +find_package(OpenMP QUIET) +if(OpenMP_FOUND) + check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE) + if(HAVE_OMP_H_INCLUDE) + set(BUILD_OMP_DEFAULT ON) + endif() +endif() + +option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT}) + +if(BUILD_OMP) + find_package(OpenMP REQUIRED) + check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE) + if(NOT HAVE_OMP_H_INCLUDE) + message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support") + endif() + + if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR + (CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR + ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR + ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0))) + # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts. + # Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe. + target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=4) + else() + target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=3) + endif() + target_link_libraries(lammps INTERFACE OpenMP::OpenMP_CXX) +endif() + +################ +# integer size selection +set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)") +set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall) +set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES}) +validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES) +string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES) +target_compile_definitions(lammps INTERFACE -DLAMMPS_${LAMMPS_SIZES}) diff --git a/cmake/Modules/LAMMPSUtils.cmake b/cmake/Modules/LAMMPSUtils.cmake index 943c3d851e..9f624fc007 100644 --- a/cmake/Modules/LAMMPSUtils.cmake +++ b/cmake/Modules/LAMMPSUtils.cmake @@ -24,6 +24,24 @@ function(validate_option name values) endif() endfunction(validate_option) +# helper function for getting the most recently modified file or folder from a glob pattern +function(get_newest_file path variable) + file(GLOB _dirs ${path}) + set(_besttime 2000-01-01T00:00:00) + set(_bestfile "") + foreach(_dir ${_dirs}) + file(TIMESTAMP ${_dir} _newtime) + if(_newtime IS_NEWER_THAN _besttime) + set(_bestfile ${_dir}) + set(_besttime ${_newtime}) + endif() + endforeach() + if(_bestfile STREQUAL "") + message(FATAL_ERROR "Could not find valid path at: ${path}") + endif() + set(${variable} ${_bestfile} PARENT_SCOPE) +endfunction() + function(get_lammps_version version_header variable) file(STRINGS ${version_header} line REGEX LAMMPS_VERSION) set(MONTHS x Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec) diff --git a/cmake/Modules/Packages/COMPRESS.cmake b/cmake/Modules/Packages/COMPRESS.cmake index d9e2ccf7ad..bdcf1aa3f8 100644 --- a/cmake/Modules/Packages/COMPRESS.cmake +++ b/cmake/Modules/Packages/COMPRESS.cmake @@ -1,6 +1,4 @@ -if(NOT ZLIB_FOUND) - find_package(ZLIB REQUIRED) -endif() +find_package(ZLIB REQUIRED) target_link_libraries(lammps PRIVATE ZLIB::ZLIB) find_package(PkgConfig QUIET) diff --git a/cmake/Modules/Packages/ML-PACE.cmake b/cmake/Modules/Packages/ML-PACE.cmake index 635a9ff2f5..c553809ff1 100644 --- a/cmake/Modules/Packages/ML-PACE.cmake +++ b/cmake/Modules/Packages/ML-PACE.cmake @@ -1,6 +1,6 @@ -set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.10.25.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources") +set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.10.25.fix2.tar.gz" CACHE STRING "URL for PACE evaluator library sources") -set(PACELIB_MD5 "e0572de57039d4afedefb25707b6ceae" CACHE STRING "MD5 checksum of PACE evaluator library tarball") +set(PACELIB_MD5 "32394d799bc282bb57696c78c456e64f" CACHE STRING "MD5 checksum of PACE evaluator library tarball") mark_as_advanced(PACELIB_URL) mark_as_advanced(PACELIB_MD5) @@ -13,8 +13,8 @@ execute_process( COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz WORKING_DIRECTORY ${CMAKE_BINARY_DIR} ) +get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace) -file(GLOB lib-pace ${CMAKE_BINARY_DIR}/lammps-user-pace-*) # enforce building libyaml-cpp as static library and turn off optional features set(YAML_BUILD_SHARED_LIBS OFF) set(YAML_CPP_BUILD_CONTRIB OFF) @@ -32,5 +32,6 @@ target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR} ${YAML_CPP_ target_link_libraries(pace PRIVATE yaml-cpp-pace) - -target_link_libraries(lammps PRIVATE pace) +if(CMAKE_PROJECT_NAME STREQUAL "lammps") + target_link_libraries(lammps PRIVATE pace) +endif() diff --git a/cmake/Modules/Packages/ML-QUIP.cmake b/cmake/Modules/Packages/ML-QUIP.cmake index 4db1eb1541..56221accab 100644 --- a/cmake/Modules/Packages/ML-QUIP.cmake +++ b/cmake/Modules/Packages/ML-QUIP.cmake @@ -43,6 +43,7 @@ if(DOWNLOAD_QUIP) file(WRITE ${CMAKE_BINARY_DIR}/quip.config "${temp}") message(STATUS "QUIP download via git requested - we will build our own") + set(CMAKE_EP_GIT_REMOTE_UPDATE_STRATEGY CHECKOUT) # QUIP has no releases (except for a tag marking the end of Python 2 support). We use the current "public" branch # The LAMMPS interface wrapper has a compatibility constant that is being checked at runtime. include(ExternalProject) diff --git a/cmake/Modules/generate_lmpgitversion.cmake b/cmake/Modules/generate_lmpgitversion.cmake index f066269723..32aaf6f2c5 100644 --- a/cmake/Modules/generate_lmpgitversion.cmake +++ b/cmake/Modules/generate_lmpgitversion.cmake @@ -31,5 +31,7 @@ set(temp "${temp}const char *LAMMPS_NS::LAMMPS::git_descriptor() { return \"${te set(temp "${temp}#endif\n\n") message(STATUS "Generating lmpgitversion.h...") -file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${temp}" ) -execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h") + +string(REPLACE "\\ " " " LAMMPS_GIT_HEADER "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h") +file(WRITE "${LAMMPS_GIT_HEADER}.tmp" "${temp}" ) +execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_GIT_HEADER}.tmp" "${LAMMPS_GIT_HEADER}") diff --git a/cmake/presets/mingw-cross.cmake b/cmake/presets/mingw-cross.cmake index 4ac9eddc98..843dd5e4ad 100644 --- a/cmake/presets/mingw-cross.cmake +++ b/cmake/presets/mingw-cross.cmake @@ -47,8 +47,8 @@ set(WIN_PACKAGES MISC ML-HDNNP ML-IAP - ML-SNAP ML-RANN + ML-SNAP MOFFF MOLECULE MOLFILE @@ -57,6 +57,7 @@ set(WIN_PACKAGES ORIENT PERI PHONON + PLUGIN POEMS PTM QEQ diff --git a/cmake/presets/windows.cmake b/cmake/presets/windows.cmake index f079e6d442..5189a90bfe 100644 --- a/cmake/presets/windows.cmake +++ b/cmake/presets/windows.cmake @@ -10,7 +10,6 @@ set(WIN_PACKAGES CLASS2 COLLOID COLVARS - COMPRESS CORESHELL DIELECTRIC DIFFRACTION diff --git a/doc/Makefile b/doc/Makefile index 07b201b07e..8841ae4825 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -13,7 +13,7 @@ VENV = $(BUILDDIR)/docenv ANCHORCHECK = $(VENV)/bin/rst_anchor_check SPHINXCONFIG = $(BUILDDIR)/utils/sphinx-config MATHJAX = $(SPHINXCONFIG)/_static/mathjax -MATHJAXTAG = 3.2.1 +MATHJAXTAG = 3.2.2 PYTHON = $(word 3,$(shell type python3)) DOXYGEN = $(word 3,$(shell type doxygen)) diff --git a/doc/lammps.1 b/doc/lammps.1 index 8ce751844a..5f1c25867e 100644 --- a/doc/lammps.1 +++ b/doc/lammps.1 @@ -1,7 +1,7 @@ -.TH LAMMPS "1" "4 May 2022" "2022-5-4" +.TH LAMMPS "1" "23 June 2022" "2022-6-23" .SH NAME .B LAMMPS -\- Molecular Dynamics Simulator. Version 24 March 2022 +\- Molecular Dynamics Simulator. Version 23 June 2022 .SH SYNOPSIS .B lmp diff --git a/doc/src/Build_settings.rst b/doc/src/Build_settings.rst index bdae796bae..7e627a052f 100644 --- a/doc/src/Build_settings.rst +++ b/doc/src/Build_settings.rst @@ -297,15 +297,15 @@ requires the following settings: .. code-block:: bash -D WITH_JPEG=value # yes or no - # default = yes + # default = yes if CMake finds JPEG files, else no -D WITH_PNG=value # yes or no - # default = yes + # default = yes if CMake finds PNG and ZLIB files, else no -D WITH_FFMPEG=value # yes or no # default = yes if CMake can find ffmpeg, else no - Usually these settings are all that is needed. If those libraries - or executables are installed but CMake cannot find the graphics header, - library, or executable files, you can set these variables accordingly: + Usually these settings are all that is needed. If CMake cannot + find the graphics header, library, executable files, you can set + these variables: .. code-block:: bash @@ -317,9 +317,6 @@ requires the following settings: -D ZLIB_LIBRARY=path # path to libz.a (.so) file -D FFMPEG_EXECUTABLE=path # path to ffmpeg executable - Otherwise, CMake will attempt to download, build, and link with - jpeg, png, and zlib libraries statically from source code. - .. tab:: Traditional make .. code-block:: make diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index e4389389c8..9f1248fd0e 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -271,6 +271,7 @@ OPT. * :doc:`spin/neel ` * :doc:`srp ` * :doc:`sw (giko) ` + * :doc:`sw/angle/table ` * :doc:`sw/mod (o) ` * :doc:`table (gko) ` * :doc:`table/rx (k) ` @@ -281,6 +282,7 @@ OPT. * :doc:`tersoff/table (o) ` * :doc:`tersoff/zbl (gko) ` * :doc:`thole ` + * :doc:`threebody/table ` * :doc:`tip4p/cut (o) ` * :doc:`tip4p/long (o) ` * :doc:`tip4p/long/soft (o) ` diff --git a/doc/src/Developer_plugins.rst b/doc/src/Developer_plugins.rst index 9bf52801a7..36fdd010b3 100644 --- a/doc/src/Developer_plugins.rst +++ b/doc/src/Developer_plugins.rst @@ -276,10 +276,27 @@ Compilation of the plugin can be managed via both, CMake or traditional GNU makefiles. Some examples that can be used as a template are in the ``examples/plugins`` folder. The CMake script code has some small adjustments to allow building the plugins for running unit tests with -them. Another example that converts the KIM package into a plugin can be -found in the ``examples/kim/plugin`` folder. No changes to the sources -of the KIM package themselves are needed; only the plugin interface and -loader code needs to be added. This example only supports building with -CMake, but is probably a more typical example. To compile you need to -run CMake with -DLAMMPS_SOURCE_DIR=. Other +them. + +Another example that converts the KIM package into a plugin can be found +in the ``examples/kim/plugin`` folder. No changes to the sources of the +KIM package themselves are needed; only the plugin interface and loader +code needs to be added. This example only supports building with CMake, +but is probably a more typical example. To compile you need to run CMake +with -DLAMMPS_SOURCE_DIR=. Other configuration setting are identical to those for compiling LAMMPS. + +A second example for a plugin from a package is in the +``examples/PACKAGES/pace/plugin`` folder that will create a plugin from +the ML-PACE package. In this case the bulk of the code is in a static +external library that is being downloaded and compiled first and then +combined with the pair style wrapper and the plugin loader. This +example also contains a NSIS script that can be used to create an +Installer package for Windows (the mutual licensing terms of the +external library and LAMMPS conflict when distributing binaries, so the +ML-PACE package cannot be linked statically, but the LAMMPS headers +required to build the plugin are also available under a less restrictive +license). This will automatically set the required environment variable +and launching a (compatible) LAMMPS binary will load and register the +plugin and the ML-PACE package can then be used as it was linked into +LAMMPS. diff --git a/doc/src/Howto_structured_data.rst b/doc/src/Howto_structured_data.rst index 4ea6c28086..18a5dfd775 100644 --- a/doc/src/Howto_structured_data.rst +++ b/doc/src/Howto_structured_data.rst @@ -184,7 +184,7 @@ frame. .. code-block:: python - import re, yaml + import yaml import pandas as pd try: @@ -193,7 +193,7 @@ frame. from yaml import SafeLoader as Loader with open("ave.yaml") as f: - ave = yaml.load(docs, Loader=Loader) + ave = yaml.load(f, Loader=Loader) keys = ave['keywords'] df = {} diff --git a/doc/src/Intro_citing.rst b/doc/src/Intro_citing.rst index 9f761a7616..e10b1857f1 100644 --- a/doc/src/Intro_citing.rst +++ b/doc/src/Intro_citing.rst @@ -30,8 +30,8 @@ initial versions of LAMMPS is: `S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995). `_ -DOI for the LAMMPS code -^^^^^^^^^^^^^^^^^^^^^^^ +DOI for the LAMMPS source code +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ LAMMPS developers use the `Zenodo service at CERN `_ to create digital object identifies (DOI) for stable releases of the diff --git a/doc/src/PDF/colvars-refman-lammps.pdf b/doc/src/PDF/colvars-refman-lammps.pdf index 71eaee867a..59d12f9253 100644 Binary files a/doc/src/PDF/colvars-refman-lammps.pdf and b/doc/src/PDF/colvars-refman-lammps.pdf differ diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index e3d6f4fbf3..3196708cc9 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -676,7 +676,7 @@ advection-diffusion-reaction systems. The equations of motion of these DPD extensions are integrated through a modified velocity-Verlet (MVV) algorithm. -**Author:** Zhen Li (Division of Applied Mathematics, Brown University) +**Author:** Zhen Li (Department of Mechanical Engineering, Clemson University) **Supporting info:** diff --git a/doc/src/Speed_measure.rst b/doc/src/Speed_measure.rst index 1daf49f4c4..888e8d9790 100644 --- a/doc/src/Speed_measure.rst +++ b/doc/src/Speed_measure.rst @@ -42,5 +42,4 @@ inaccurate relative timing data, because processors have to wait when communication occurs for other processors to catch up. Thus the reported times for "Communication" or "Other" may be higher than they really are, due to load-imbalance. If this is an issue, you can -uncomment the MPI_Barrier() lines in src/timer.cpp, and re-compile -LAMMPS, to obtain synchronized timings. +use the :doc:`timer sync ` command to obtain synchronized timings. diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index ef403daa84..b57c91ffee 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -95,7 +95,7 @@ Miscellaneous tools * :ref:`LAMMPS shell ` * :ref:`LAMMPS magic patterns for file(1) ` * :ref:`Offline build tool ` - * :ref:`singularity ` + * :ref:`singularity/apptainer ` * :ref:`SWIG interface ` * :ref:`vim ` @@ -1007,14 +1007,15 @@ Ivanov, at University of Iceland (ali5 at hi.is). .. _singularity_tool: -singularity tool ----------------------------------------- +singularity/apptainer tool +-------------------------- -The singularity sub-directory contains container definitions files -that can be used to build container images for building and testing -LAMMPS on specific OS variants using the `Singularity `_ -container software. Contributions for additional variants are welcome. -For more details please see the README.md file in that folder. +The singularity sub-directory contains container definitions files that +can be used to build container images for building and testing LAMMPS on +specific OS variants using the `Apptainer `_ or +`Singularity `_ container software. Contributions for +additional variants are welcome. For more details please see the +README.md file in that folder. ---------- diff --git a/doc/src/compute_ave_sphere_atom.rst b/doc/src/compute_ave_sphere_atom.rst index db04682865..48dbf377cb 100644 --- a/doc/src/compute_ave_sphere_atom.rst +++ b/doc/src/compute_ave_sphere_atom.rst @@ -35,16 +35,24 @@ Examples Description """"""""""" -Define a computation that calculates the local density and temperature -for each atom and neighbors inside a spherical cutoff. +Define a computation that calculates the local mass density and +temperature for each atom based on its neighbors inside a spherical +cutoff. If an atom has M neighbors, then its local mass density is +calculated as the sum of its mass and its M neighbor masses, divided +by the volume of the cutoff sphere (or circle in 2d). The local +temperature of the atom is calculated as the temperature of the +collection of M+1 atoms, after subtracting the center-of-mass velocity +of the M+1 atoms from each of the M+1 atom's velocities. This is +effectively the thermal velocity of the neighborhood of the central +atom, similar to :doc:`compute temp/com `. -The optional keyword *cutoff* defines the distance cutoff -used when searching for neighbors. The default value is the cutoff -specified by the pair style. If no pair style is defined, then a cutoff -must be defined using this keyword. If the specified cutoff is larger than -that of the pair_style plus neighbor skin (or no pair style is defined), -the *comm_modify cutoff* option must also be set to match that of the -*cutoff* keyword. +The optional keyword *cutoff* defines the distance cutoff used when +searching for neighbors. The default value is the cutoff specified by +the pair style. If no pair style is defined, then a cutoff must be +defined using this keyword. If the specified cutoff is larger than +that of the pair_style plus neighbor skin (or no pair style is +defined), the *comm_modify cutoff* option must also be set to match +that of the *cutoff* keyword. The neighbor list needed to compute this quantity is constructed each time the calculation is performed (i.e. each time a snapshot of atoms @@ -55,16 +63,16 @@ too frequently. If you have a bonded system, then the settings of :doc:`special_bonds ` command can remove pairwise - interactions between atoms in the same bond, angle, or dihedral. This - is the default setting for the :doc:`special_bonds ` - command, and means those pairwise interactions do not appear in the - neighbor list. Because this fix uses the neighbor list, it also means - those pairs will not be included in the order parameter. This - difficulty can be circumvented by writing a dump file, and using the - :doc:`rerun ` command to compute the order parameter for - snapshots in the dump file. The rerun script can use a - :doc:`special_bonds ` command that includes all pairs in - the neighbor list. + interactions between atoms in the same bond, angle, or dihedral. + This is the default setting for the :doc:`special_bonds + ` command, and means those pairwise interactions do + not appear in the neighbor list. Because this compute uses the + neighbor list, it also means those pairs will not be included in + the order parameter. This difficulty can be circumvented by + writing a dump file, and using the :doc:`rerun ` command to + compute the order parameter for snapshots in the dump file. The + rerun script can use a :doc:`special_bonds ` command + that includes all pairs in the neighbor list. ---------- @@ -77,17 +85,20 @@ too frequently. Output info """"""""""" -This compute calculates a per-atom array with two columns: density and temperature. +This compute calculates a per-atom array with two columns: mass +density in density :doc:`units ` and temperature in temperature +:doc:`units `. These values can be accessed by any command that uses per-atom values -from a compute as input. See the :doc:`Howto output ` doc -page for an overview of LAMMPS output options. +from a compute as input. See the :doc:`Howto output ` +doc page for an overview of LAMMPS output options. Restrictions """""""""""" -This compute is part of the EXTRA-COMPUTE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` page for more info. +This compute is part of the EXTRA-COMPUTE package. It is only enabled +if LAMMPS was built with that package. See the :doc:`Build package +` page for more info. Related commands """""""""""""""" @@ -97,5 +108,5 @@ Related commands Default """"""" -The option defaults are *cutoff* = pair style cutoff +The option defaults are *cutoff* = pair style cutoff. diff --git a/doc/src/fix_mdi_aimd.rst b/doc/src/fix_mdi_aimd.rst index 64bc4a3d6a..9ab2a933ed 100644 --- a/doc/src/fix_mdi_aimd.rst +++ b/doc/src/fix_mdi_aimd.rst @@ -12,7 +12,6 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * mdi/aimd = style name of this fix command -* optional keyword = *plugin* Examples """""""" @@ -20,7 +19,6 @@ Examples .. code-block:: LAMMPS fix 1 all mdi/aimd - fix 1 all mdi/aimd plugin Description """"""""""" @@ -53,14 +51,6 @@ same time as LAMMPS, or as a plugin library. See the :doc:`mdi plugin Again, the examples/mdi/README file explains how to launch both driver and engine codes so that engine is used in plugin mode. -To use this fix with a plugin engine, you must specify the -*plugin* keyword as the last argument, as illustrated above. - -.. note:: - - As of April 2022, the *plugin* keyword is needed. In a future - version of the MDI library it will no longer be necessary. - ---------- This fix performs the timestepping portion of an AIMD simulation. diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst index 59efbdc5bd..30f3e550c5 100644 --- a/doc/src/kspace_style.rst +++ b/doc/src/kspace_style.rst @@ -129,8 +129,8 @@ Examples kspace_style pppm 1.0e-4 kspace_style pppm/cg 1.0e-5 1.0e-6 - kspace style msm 1.0e-4 - kspace style scafacos fmm 1.0e-4 + kspace_style msm 1.0e-4 + kspace_style scafacos fmm 1.0e-4 kspace_style none Used in input scripts: diff --git a/doc/src/pair_e3b.rst b/doc/src/pair_e3b.rst index b75fb8450c..8ae6d10b82 100644 --- a/doc/src/pair_e3b.rst +++ b/doc/src/pair_e3b.rst @@ -50,6 +50,12 @@ Examples pair_style hybrid/overlay e3b 1 lj/cut/tip4p/long 1 2 1 1 0.15 8.5 pair_coeff * * e3b preset 2011 +Used in example input script: + +.. parsed-literal:: + + examples/PACKAGES/e3b/in.e3b-tip4p2005 + Description """"""""""" @@ -68,21 +74,27 @@ The *e3b* style computes an \"explicit three-body\" (E3B) potential for water :r 0 & r>R_f\\ \end{cases} -This potential was developed as a water model that includes the three-body cooperativity of hydrogen bonding explicitly. -To use it in this way, it must be applied in conjunction with a conventional two-body water model, through *pair_style hybrid/overlay*. -The three body interactions are split into three types: A, B, and C. -Type A corresponds to anti-cooperative double hydrogen bond donor interactions. -Type B corresponds to the cooperative interaction of molecules that both donate and accept a hydrogen bond. -Type C corresponds to anti-cooperative double hydrogen bond acceptor interactions. -The three-body interactions are smoothly cutoff by the switching function s(r) between Rs and Rc3. -The two-body interactions are designed to correct for the effective many-body interactions implicitly included in the conventional two-body potential. -The two-body interactions are cut off sharply at Rc2, because K3 is typically significantly smaller than K2. -See :ref:`(Kumar 2008) ` for more details. +This potential was developed as a water model that includes the +three-body cooperativity of hydrogen bonding explicitly. To use it in +this way, it must be applied in conjunction with a conventional two-body +water model, through pair style :doc:`hybrid/overlay `. The +three body interactions are split into three types: A, B, and C. Type A +corresponds to anti-cooperative double hydrogen bond donor interactions. +Type B corresponds to the cooperative interaction of molecules that both +donate and accept a hydrogen bond. Type C corresponds to +anti-cooperative double hydrogen bond acceptor interactions. The +three-body interactions are smoothly cutoff by the switching function +s(r) between Rs and Rc3. The two-body interactions are designed to +correct for the effective many-body interactions implicitly included in +the conventional two-body potential. The two-body interactions are cut +off sharply at Rc2, because K3 is typically significantly smaller than +K2. See :ref:`(Kumar 2008) ` for more details. -Only a single *pair_coeff* command is used with the *e3b* style. -The first two arguments must be \* \*. -The oxygen atom type for the pair style is passed as the only argument to the *pair_style* command, not in the *pair_coeff* command. -The hydrogen atom type is inferred by the ordering of the atoms. +Only a single :doc:`pair_coeff ` command is used with the +*e3b* style and the first two arguments must be \* \*. The oxygen atom +type for the pair style is passed as the only argument to the +*pair_style* command, not in the *pair_coeff* command. The hydrogen +atom type is inferred from the ordering of the atoms. .. note:: @@ -90,26 +102,41 @@ The hydrogen atom type is inferred by the ordering of the atoms. Each water molecule must have consecutive IDs with the oxygen first. This pair style does not test that this criteria is met. -The *pair_coeff* command must have at least one keyword/value pair, as described above. -The *preset* keyword sets the potential parameters to the values used in :ref:`(Tainter 2011) ` or :ref:`(Tainter 2015) `. -To use the water models defined in those references, the *e3b* style should always be used in conjunction with an *lj/cut/tip4p/long* style through *pair_style hybrid/overlay*, as demonstrated in the second example above. -The *preset 2011* option should be used with the :doc:`TIP4P water model `. -The *preset 2015* option should be used with the :doc:`TIP4P/2005 water model `. -If the *preset* keyword is used, no other keyword is needed. -Changes to the preset parameters can be made by specifying the *preset* keyword followed by the specific parameter to change, like *Ea*\ . -Note that the other keywords must come after *preset* in the pair_style command. -The *e3b* style can also be used to implement any three-body potential of the same form by specifying all the keywords except *neigh*\ : *Ea*, *Eb*, *Ec*, *E2*, *K3*, *K2*, *Rc3*, *Rc2*, *Rs*, and *bondL*\ . -The keyword *bondL* specifies the intramolecular OH bond length of the water model being used. -This is needed to include H atoms that are within the cutoff even when the attached oxygen atom is not. +The *pair_coeff* command must have at least one keyword/value pair, as +described above. The *preset* keyword sets the potential parameters to +the values used in :ref:`(Tainter 2011) ` or +:ref:`(Tainter 2015) `. To use the water models defined in +those references, the *e3b* style should always be used in conjunction +with an *lj/cut/tip4p/long* style through *pair_style hybrid/overlay*, +as demonstrated in the second example above. The *preset 2011* option +should be used with the :doc:`TIP4P water model `. The +*preset 2015* option should be used with the :doc:`TIP4P/2005 water +model `. If the *preset* keyword is used, no other keyword +is needed. Changes to the preset parameters can be made by specifying +the *preset* keyword followed by the specific parameter to change, like +*Ea*\ . Note that the other keywords must come after *preset* in the +pair_style command. The *e3b* style can also be used to implement any +three-body potential of the same form by specifying all the keywords +except *neigh*\ : *Ea*, *Eb*, *Ec*, *E2*, *K3*, *K2*, *Rc3*, *Rc2*, +*Rs*, and *bondL*\ . The keyword *bondL* specifies the intramolecular +OH bond length of the water model being used. This is needed to include +H atoms that are within the cutoff even when the attached oxygen atom is +not. -This pair style allocates arrays sized according to the number of pairwise interactions within Rc3. -To do this it needs an estimate for the number of water molecules within Rc3 of an oxygen atom. -This estimate defaults to 10 and can be changed using the *neigh* keyword, which takes an integer as an argument. -If the neigh setting is too small, the simulation will fail with the error "neigh is too small". -If the neigh setting is too large, the pair style will use more memory than necessary. +This pair style allocates arrays sized according to the number of +pairwise interactions within Rc3. To do this it needs an estimate for +the number of water molecules within Rc3 of an oxygen atom. This +estimate defaults to 10 and can be changed using the *neigh* keyword, +which takes an integer as an argument. If the neigh setting is too +small, the simulation will fail with the error "neigh is too small". If +the neigh setting is too large, the pair style will use more memory than +necessary. -This pair style tallies a breakdown of the total E3B potential energy into sub-categories, which can be accessed via the :doc:`compute pair ` command as a vector of values of length 4. -The 4 values correspond to the terms in the first equation above: the E2 term, the Ea term, the Eb term, and the Ec term. +This pair style tallies a breakdown of the total E3B potential energy +into sub-categories, which can be accessed via the :doc:`compute pair +` command as a vector of values of length 4. The 4 values +correspond to the terms in the first equation above: the E2 term, the Ea +term, the Eb term, and the Ec term. See the examples/PACKAGES/e3b directory for a complete example script. diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 6b7f898127..fe63cf402e 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -350,6 +350,7 @@ accelerated styles exist. * :doc:`spin/neel ` - * :doc:`srp ` - * :doc:`sw ` - Stillinger-Weber 3-body potential +* :doc:`sw/angle/table ` - Stillinger-Weber potential with tabulated angular term * :doc:`sw/mod ` - modified Stillinger-Weber 3-body potential * :doc:`table ` - tabulated pair potential * :doc:`table/rx ` - @@ -360,6 +361,7 @@ accelerated styles exist. * :doc:`tersoff/table ` - * :doc:`tersoff/zbl ` - Tersoff/ZBL 3-body potential * :doc:`thole ` - Coulomb interactions with thole damping +* :doc:`threebody/table ` - generic tabulated three-body potential * :doc:`tip4p/cut ` - Coulomb for TIP4P water w/out LJ * :doc:`tip4p/long ` - long-range Coulomb for TIP4P water w/out LJ * :doc:`tip4p/long/soft ` - diff --git a/doc/src/pair_sw_angle_table.rst b/doc/src/pair_sw_angle_table.rst new file mode 100644 index 0000000000..ff88711d7a --- /dev/null +++ b/doc/src/pair_sw_angle_table.rst @@ -0,0 +1,311 @@ +.. index:: pair_style sw/angle/table + +pair_style sw/angle/table command +================================= + +Syntax +"""""" + +.. code-block:: LAMMPS + + pair_style style + +* style = *sw/angle/table* + + +Examples +"""""""" + +.. code-block:: LAMMPS + + pair_style sw/angle/table + pair_coeff * * spce.sw type + +Used in example input script: + +.. parsed-literal:: + + examples/PACKAGES/manybody_table/in.spce_sw + + +Description +""""""""""" + +The *sw/angle/table* style is a modification of the original +:doc:`pair_style sw `. It has been developed for coarse-grained +simulations (of water) (:ref:`Scherer1 `), but can be employed +for all kinds of systems. It computes a modified 3-body +:ref:`Stillinger-Weber ` potential for the energy E of a +system of atoms as + +.. math:: + + E & = \sum_i \sum_{j > i} \phi_2 (r_{ij}) + + \sum_i \sum_{j \neq i} \sum_{k > j} + \phi_3 (r_{ij}, r_{ik}, \theta_{ijk}) \\ + \phi_2(r_{ij}) & = A_{ij} \epsilon_{ij} \left[ B_{ij} (\frac{\sigma_{ij}}{r_{ij}})^{p_{ij}} - + (\frac{\sigma_{ij}}{r_{ij}})^{q_{ij}} \right] + \exp \left( \frac{\sigma_{ij}}{r_{ij} - a_{ij} \sigma_{ij}} \right) \\ + \phi_3(r_{ij},r_{ik},\theta_{ijk}) & = f^{\textrm{3b}}\left(\theta_{ijk}\right) + \exp \left( \frac{\gamma_{ij} \sigma_{ij}}{r_{ij} - a_{ij} \sigma_{ij}} \right) + \exp \left( \frac{\gamma_{ik} \sigma_{ik}}{r_{ik} - a_{ik} \sigma_{ik}} \right) + +where :math:`\phi_2` is a two-body term and :math:`\phi_3` is a +three-body term. The summations in the formula are over all neighbors J +and K of atom I within a cutoff distance :math:`a \sigma`. In contrast +to the original *sw* style, *sw/angle/table* allows for a flexible +three-body term :math:`f^{\textrm{3b}}\left(\theta_{ijk}\right)` which +is read in as a tabulated interaction. It can be parameterized with the +csg_fmatch app of VOTCA as available at: +https://gitlab.mpcdf.mpg.de/votca/votca. + +Only a single pair_coeff command is used with the *sw/angle/table* style +which specifies a modified Stillinger-Weber potential file with +parameters for all needed elements. These are mapped to LAMMPS atom +types by specifying N_el additional arguments after the ".sw" filename +in the pair_coeff command, where N_el is the number of LAMMPS atom +types: + +* ".sw" filename +* N_el element names = mapping of SW elements to atom types + +See the :doc:`pair_coeff ` page for alternate ways to +specify the path for the potential file. + +As an example, imagine a file SiC.sw has Stillinger-Weber values for Si +and C. If your LAMMPS simulation has 4 atoms types and you want the +first 3 to be Si, and the fourth to be C, you would use the following +pair_coeff command: + +.. code-block:: LAMMPS + + pair_coeff * * SiC.sw Si Si Si C + +The first 2 arguments must be \* \* so as to span all LAMMPS atom types. +The first three Si arguments map LAMMPS atom types 1,2,3 to the Si +element in the SW file. The final C argument maps LAMMPS atom type 4 to +the C element in the SW file. If a mapping value is specified as NULL, +the mapping is not performed. This can be used when a *sw/angle/table* +potential is used as part of the *hybrid* pair style. The NULL values +are placeholders for atom types that will be used with other potentials. + +The (modified) Stillinger-Weber files have a ".sw" suffix. Lines that +are not blank or comments (starting with #) define parameters for a +triplet of elements. The parameters in a single entry correspond to the +two-body and three-body coefficients in the formula above. Here, also +the suffix ".sw" is used though the original Stillinger-Weber file +format is supplemented with four additional lines per parameter block to +specify the tabulated three-body interaction. A single entry then +contains: + +* element 1 (the center atom in a 3-body interaction) +* element 2 +* element 3 +* :math:`\epsilon` (energy units) +* :math:`\sigma` (distance units) +* a +* :math:`\lambda` +* :math:`\gamma` +* :math:`\cos\theta_0` +* A +* B +* p +* q +* tol +* filename +* keyword +* style +* N + +The A, B, p, and q parameters are used only for two-body interactions. +The :math:`\lambda` and :math:`\cos\theta_0` parameters, only used for +three-body interactions in the original Stillinger-Weber style, are read +in but ignored in this modified pair style. The :math:`\epsilon` +parameter is only used for two-body interactions in this modified pair +style and not for the three-body terms. The :math:`\sigma` and *a* +parameters are used for both two-body and three-body +interactions. :math:`\gamma` is used only in the three-body +interactions, but is defined for pairs of atoms. The non-annotated +parameters are unitless. + +LAMMPS introduces an additional performance-optimization parameter tol +that is used for both two-body and three-body interactions. In the +Stillinger-Weber potential, the interaction energies become negligibly +small at atomic separations substantially less than the theoretical +cutoff distances. LAMMPS therefore defines a virtual cutoff distance +based on a user defined tolerance tol. The use of the virtual cutoff +distance in constructing atom neighbor lists can significantly reduce +the neighbor list sizes and therefore the computational cost. LAMMPS +provides a *tol* value for each of the three-body entries so that they +can be separately controlled. If tol = 0.0, then the standard +Stillinger-Weber cutoff is used. + +The additional parameters *filename*, *keyword*, *style*, and *N* refer +to the tabulated angular potential +:math:`f^{\textrm{3b}}\left(\theta_{ijk}\right)`. The tabulated angular +potential has to be of the format as used in the :doc:`angle_style table +` command: + +An interpolation tables of length *N* is created. The interpolation is +done in one of 2 *styles*: *linear* or *spline*. For the *linear* +style, the angle is used to find 2 surrounding table values from which +an energy or its derivative is computed by linear interpolation. For the +*spline* style, a cubic spline coefficients are computed and stored at +each of the *N* values in the table. The angle is used to find the +appropriate set of coefficients which are used to evaluate a cubic +polynomial which computes the energy or derivative. + +The *filename* specifies the file containing the tabulated energy and +derivative values of :math:`f^{\textrm{3b}}\left(\theta_{ijk}\right)`. +The *keyword* then specifies a section of the file. The format of this +file is as follows (without the parenthesized comments): + +.. parsed-literal:: + + # Angle potential for harmonic (one or more comment or blank lines) + + HAM (keyword is the first text on line) + N 181 FP 0 0 EQ 90.0 (N, FP, EQ parameters) + (blank line) + 1 0.0 200.5 2.5 (index, angle, energy, derivative) + 2 1.0 198.0 2.5 + ... + 181 180.0 0.0 0.0 + +A section begins with a non-blank line whose first character is not a +"#"; blank lines or lines starting with "#" can be used as comments +between sections. The first line begins with a keyword which identifies +the section. The next line lists (in any order) one or more parameters +for the table. Each parameter is a keyword followed by one or more +numeric values. + +The parameter "N" is required and its value is the number of table +entries that follow. Note that this may be different than the *N* +specified in the Stillinger-Weber potential file. Let Nsw = *N* in the +".sw" file, and Nfile = "N" in the tabulated angular file. What LAMMPS +does is a preliminary interpolation by creating splines using the Nfile +tabulated values as nodal points. It uses these to interpolate as +needed to generate energy and derivative values at Ntable different +points. The resulting tables of length Nsw are then used as described +above, when computing energy and force for individual angles and their +atoms. This means that if you want the interpolation tables of length +Nsw to match exactly what is in the tabulated file (with effectively no +preliminary interpolation), you should set Nsw = Nfile. + +The "FP" parameter is optional. If used, it is followed by two values +fplo and fphi, which are the second derivatives at the innermost and +outermost angle settings. These values are needed by the spline +construction routines. If not specified by the "FP" parameter, they are +estimated (less accurately) by the first two and last two derivative +values in the table. + +The "EQ" parameter is also optional. If used, it is followed by a the +equilibrium angle value, which is used, for example, by the :doc:`fix +shake ` command. If not used, the equilibrium angle is set to +180.0. + +Following a blank line, the next N lines of the angular table file list +the tabulated values. On each line, the first value is the index from 1 +to N, the second value is the angle value (in degrees), the third value +is the energy (in energy units), and the fourth is -dE/d(theta) (also in +energy units). The third term is the energy of the 3-atom configuration +for the specified angle. The last term is the derivative of the energy +with respect to the angle (in degrees, not radians). Thus the units of +the last term are still energy, not force. The angle values must +increase from one line to the next. The angle values must also begin +with 0.0 and end with 180.0, i.e. span the full range of possible +angles. + +Note that one angular potential file can contain many sections, each +with a tabulated potential. LAMMPS reads the file section by section +until it finds one that matches the specified *keyword* of appropriate +section of the ".sw" file. + +The Stillinger-Weber potential file must contain entries for all the +elements listed in the pair_coeff command. It can also contain entries +for additional elements not being used in a particular simulation; +LAMMPS ignores those entries. + +For a single-element simulation, only a single entry is required +(e.g. SiSiSi). For a two-element simulation, the file must contain 8 +entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that +specify SW parameters for all permutations of the two elements +interacting in three-body configurations. Thus for 3 elements, 27 +entries would be required, etc. + +As annotated above, the first element in the entry is the center atom in +a three-body interaction. Thus an entry for SiCC means a Si atom with 2 +C atoms as neighbors. The parameter values used for the two-body +interaction come from the entry where the second and third elements are +the same. Thus the two-body parameters for Si interacting with C, comes +from the SiCC entry. The three-body angular potential +:math:`f^{\textrm{3b}}\left(\theta_{ijk}\right)` can in principle be +specific to the three elements of the configuration. However, the user +must ensure that it makes physically sense. Note also that the function +:math:`\phi_3` contains two exponential screening factors with parameter +values from the ij pair and ik pairs. So :math:`\phi_3` for a C atom +bonded to a Si atom and a second C atom will depend on the three-body +parameters for the CSiC entry, and also on the two-body parameters for +the CCC and CSiSi entries. Since the order of the two neighbors is +arbitrary, the three-body parameters and the tabulated angular potential +for entries CSiC and CCSi should be the same. Similarly, the two-body +parameters for entries SiCC and CSiSi should also be the same. The +parameters used only for two-body interactions (A, B, p, and q) in +entries whose second and third element are different (e.g. SiCSi) are +not used for anything and can be set to 0.0 if desired. This is also +true for the parameters in :math:`\phi_3` that are taken from the ij and +ik pairs (:math:`\sigma`, *a*, :math:`\gamma`) + +Additional input files and reference data can be found at: +https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-tutorials/spce/3body_sw + +---------- + +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 as described +above from values in the potential file, but not for the tabulated +angular potential file. + +This pair style does not support the :doc:`pair_modify ` +shift, table, and tail options. + +This pair style does not write its information to :doc:`binary restart +files `, 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 ` command. It does not support the +*inner*, *middle*, *outer* keywords. + +---------- + +Restrictions +"""""""""""" + +This pair style is part of the MANYBODY package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` page for more info. + +This pair style requires the :doc:`newton ` setting to be "on" +for pair interactions. + +Related commands +"""""""""""""""" + +:doc:`pair_coeff `, :doc:`pair_style sw `, :doc:`pair_style threebody/table ` + + +---------- + +.. _Stillinger3: + +**(Stillinger)** Stillinger and Weber, Phys Rev B, 31, 5262 (1985). + +.. _Scherer1: + +**(Scherer1)** C. Scherer and D. Andrienko, Phys. Chem. Chem. Phys. 20, 22387-22394 (2018). + diff --git a/doc/src/pair_threebody_table.rst b/doc/src/pair_threebody_table.rst new file mode 100644 index 0000000000..19c90feccd --- /dev/null +++ b/doc/src/pair_threebody_table.rst @@ -0,0 +1,281 @@ +.. index:: pair_style threebody/table + +pair_style threebody/table command +================================== + +Syntax +"""""" + +.. code-block:: LAMMPS + + pair_style style + +* style = *threebody/table* + + +Examples +"""""""" + +.. code-block:: LAMMPS + + pair_style threebody/table + pair_coeff * * spce2.3b type1 type2 + + pair_style hybrid/overlay table linear 1200 threebody/table + pair_coeff 1 1 table table_CG_CG.txt VOTCA + pair_coeff * * threebody/table spce.3b type + +Used in example input scripts: + +.. parsed-literal:: + + examples/PACKAGES/manybody_table/in.spce + examples/PACKAGES/manybody_table/in.spce2 + +Description +""""""""""" + +The *threebody/table* style is a pair style for generic tabulated +three-body interactions. It has been developed for (coarse-grained) +simulations (of water) with Kernel-based machine learning (ML) +potentials (:ref:`Scherer2 `). As for many other MANYBODY +package pair styles the energy of a system is computed as a sum over +three-body terms: + +.. math:: + + E = \sum_i \sum_{j \neq i} \sum_{k > j} \phi_3 (r_{ij}, r_{ik}, \theta_{ijk}) + +The summations in the formula are over all neighbors J and K of atom I +within a cutoff distance :math:`cut`. In contrast to the +Stillinger-Weber potential, all forces are not calculated analytically, +but read in from a three-body force/energy table which can be generated +with the csg_ml app of VOTCA as available at: +https://gitlab.mpcdf.mpg.de/votca/votca. + +Only a single pair_coeff command is used with the *threebody/table* +style which specifies a threebody potential (".3b") file with parameters +for all needed elements. These are then mapped to LAMMPS atom types by +specifying N_el additional arguments after the ".3b" filename in the +pair_coeff command, where N_el is the number of LAMMPS atom types: + +* ".3b" filename +* N_el element names = mapping of threebody elements to atom types + +See the :doc:`pair_coeff ` page for alternate ways to +specify the path for the potential file. + +As an example, imagine a file SiC.3b has three-body values for Si and C. +If your LAMMPS simulation has 4 atoms types and you want the first 3 to +be Si, and the fourth to be C, you would use the following pair_coeff +command: + +.. code-block:: LAMMPS + + pair_coeff * * SiC.3b Si Si Si C + +The first 2 arguments must be \* \* so as to span all LAMMPS atom types. +The first three Si arguments map LAMMPS atom types 1,2,3 to the Si +element in the ".3b" file. The final C argument maps LAMMPS atom type 4 +to the C element in the threebody file. If a mapping value is specified +as NULL, the mapping is not performed. This can be used when a +*threebody/table* potential is used as part of the *hybrid* pair style. +The NULL values are placeholders for atom types that will be used with +other potentials. + +The three-body files have a ".3b" suffix. Lines that are not blank or +comments (starting with #) define parameters for a triplet of +elements. The parameters in a single entry specify to the (three-body) +cutoff distance and the tabulated three-body interaction. A single entry +then contains: + +* element 1 (the center atom in a 3-body interaction) +* element 2 +* element 3 +* cut (distance units) +* filename +* keyword +* style +* N + +The parameter :math:`cut` is the (three-body) cutoff distance. When set +to 0, no interaction is calculated for this element triplet. The +parameters *filename*, *keyword*, *style*, and *N* refer to the +tabulated three-body potential. + +The tabulation is done on a three-dimensional grid of the two distances +:math:`r_{ij}` and :math:`r_{ik}` as well as the angle +:math:`\theta_{ijk}` which is constructed in the following way. There +are two different cases. If element 2 and element 3 are of the same +type (e.g. SiCC), the distance :math:`r_{ij}` is varied in "N" steps +from rmin to rmax and the distance :math:`r_{ik}` is varied from +:math:`r_{ij}` to rmax. This can be done, due to the symmetry of the +triplet. If element 2 and element 3 are not of the same type +(e.g. SiCSi), there is no additional symmetry and the distance +:math:`r_{ik}` is also varied from rmin to rmax in "N" steps. The angle +:math:`\theta_{ijk}` is always varied in "2N" steps from (0.0 + +180.0/(4N)) to (180.0 - 180.0/(4N)). Therefore, the total number of +table entries is "M = N * N * (N+1)" for the symmetric (element 2 and +element 3 are of the same type) and "M = 2 * N * N * N" for the general +case (element 2 and element 3 are not of the same type). + +The forces on all three particles I, J, and K of a triplet of this type +of three-body interaction potential (:math:`\phi_3 (r_{ij}, r_{ik}, +\theta_{ijk})`) lie within the plane defined by the three inter-particle +distance vectors :math:`{\mathbf r}_{ij}`, :math:`{\mathbf r}_{ik}`, and +:math:`{\mathbf r}_{jk}`. This property is used to project the forces +onto the inter-particle distance vectors as follows + +.. math:: + + \begin{pmatrix} + {\mathbf f}_{i} \\ + {\mathbf f}_{j} \\ + {\mathbf f}_{k} \\ + \end{pmatrix} = + \begin{pmatrix} + f_{i1} & f_{i2} & 0 \\ + f_{j1} & 0 & f_{j2} \\ + 0 & f_{k1} & f_{k2} \\ + \end{pmatrix} + \begin{pmatrix} + {\mathbf r}_{ij} \\ + {\mathbf r}_{ik} \\ + {\mathbf r}_{jk} \\ + \end{pmatrix} + +and then tabulate the 6 force constants :math:`f_{i1}`, :math:`f_{i2}`, +:math:`f_{j1}`, :math:`f_{j2}`, :math:`f_{k1}`, and :math:`f_{k2}`, as +well as the energy of a triplet e. Due to symmetry reasons, the +following relations hold: :math:`f_{i1}=-f_{j1}`, +:math:`f_{i2}=-f_{k1}`, and :math:`f_{j2}=-f_{k2}`. As in this pair +style the forces are read in directly, a correct MD simulation is also +performed in the case that the triplet energies are set to e=0. + +The *filename* specifies the file containing the tabulated energy and +derivative values of :math:`\phi_3 (r_{ij}, r_{ik}, \theta_{ijk})`. The +*keyword* then specifies a section of the file. The format of this file +is as follows (without the parenthesized comments): + +.. parsed-literal:: + + # Tabulated three-body potential for spce water (one or more comment or blank lines) + + ENTRY1 (keyword is the first text on line) + N 12 rmin 2.55 rmax 3.65 (N, rmin, rmax parameters) + (blank line) + 1 2.55 2.55 3.75 -867.212 -611.273 867.212 21386.8 611.273 -21386.8 0.0 (index, r_ij, r_ik, theta, f_i1, f_i2, f_j1, f_j2, f_k1, f_k2, e) + 2 2.55 2.55 11.25 -621.539 -411.189 621.539 5035.95 411.189 -5035.95 0.0 + ... + 1872 3.65 3.65 176.25 -0.00215132 -0.00412886 0.00215137 0.00111754 0.00412895 -0.00111757 0.0 + +A section begins with a non-blank line whose first character is not a +"#"; blank lines or lines starting with "#" can be used as comments +between sections. The first line begins with a keyword which identifies +the section. The next line lists (in any order) one or more parameters +for the table. Each parameter is a keyword followed by one or more +numeric values. + +The parameter "N" is required. It should be the same than the parameter +"N" of the ".3b" file, otherwise its value is overwritten. "N" +determines the number of table entries "M" that follow: "M = N * N * +(N+1)" (symmetric triplet, e.g. SiCC) or "M = 2 * N * N * N" (asymmetric +triplet, e.g. SiCSi). Therefore "M = 12 * 12 * 13 = 1872" in the above +symmetric example. The parameters "rmin" and "rmax" are also required +and determine the minimum and maximum of the inter-particle distances +:math:`r_{ij}` and :math:`r_{ik}`. + +Following a blank line, the next M lines of the angular table file list +the tabulated values. On each line, the first value is the index from 1 +to M, the second value is the distance :math:`r_{ij}`, the third value +is the distance :math:`r_{ik}`, the fourth value is the angle +:math:`\theta_{ijk})`, the next six values are the force constants +:math:`f_{i1}`, :math:`f_{i2}`, :math:`f_{j1}`, :math:`f_{j2}`, +:math:`f_{k1}`, and :math:`f_{k2}`, and the last value is the energy e. + +Note that one three-body potential file can contain many sections, each +with a tabulated potential. LAMMPS reads the file section by section +until it finds one that matches the specified *keyword* of appropriate +section of the ".3b" file. + +At the moment, only the *style* *linear* is allowed and +implemented. After reading in the force table, it is internally stored +in LAMMPS as a lookup table. For each triplet configuration occurring in +the simulation within the cutoff distance, the next nearest tabulated +triplet configuration is looked up. No interpolation is done. This +allows for a very efficient force calculation with the stored force +constants and energies. Due to the know table structure, the lookup can +be done efficiently. It has been tested (:ref:`Scherer2 `) +that with a reasonably small bin size, the accuracy and speed is +comparable to that of a Stillinger-Weber potential with tabulated +three-body interactions (:doc:`pair_style sw/angle/table +`) while the table format of this pair style allows +for more flexible three-body interactions. + +As for the Stillinger-Weber potential, the three-body potential file +must contain entries for all the elements listed in the pair_coeff +command. It can also contain entries for additional elements not being +used in a particular simulation; LAMMPS ignores those entries. + +For a single-element simulation, only a single entry is required +(e.g. SiSiSi). For a two-element simulation, the file must contain 8 +entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that +specify threebody parameters for all permutations of the two elements +interacting in three-body configurations. Thus for 3 elements, 27 +entries would be required, etc. + +As annotated above, the first element in the entry is the center atom in +a three-body interaction. Thus an entry for SiCC means a Si atom with 2 +C atoms as neighbors. The tabulated three-body forces can in principle +be specific to the three elements of the configuration. However, the +user must ensure that it makes physically sense. E.g., the tabulated +three-body forces for the entries CSiC and CCSi should be the same +exchanging :math:`r_{ij}` with r_{ik}, :math:`f_{j1}` with +:math:`f_{k1}`, and :math:`f_{j2}` with :math:`f_{k2}`. + +Additional input files and reference data can be found at: +https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-tutorials/ml + +---------- + +Mixing, shift, table, tail correction, restart, rRESPA info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +As all interactions are tabulated, no mixing is performed. + +This pair style does not support the :doc:`pair_modify ` +shift, table, and tail options. + +This pair style does not write its information to :doc:`binary restart +files `, 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 ` command. It does not support the +*inner*, *middle*, *outer* keywords. + +---------- + +Restrictions +"""""""""""" + +This pair style is part of the MANYBODY package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` page for more info. + +This pair style requires the :doc:`newton ` setting to be "on" +for pair interactions. + +Related commands +"""""""""""""""" + +:doc:`pair_coeff `, :doc:`pair sw/angle/table ` + + +---------- + +.. _Scherer2: + +**(Scherer2)** C. Scherer, R. Scheid, D. Andrienko, and T. Bereau, J. Chem. Theor. Comp. 16, 3194-3204 (2020). + diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index 68e1efc496..853d86785e 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -56,7 +56,7 @@ Examples read_data ../run7/data.polymer.gz read_data data.protein fix mycmap crossterm CMAP read_data data.water add append offset 3 1 1 1 1 shift 0.0 0.0 50.0 - read_data data.water add merge 1 group solvent + read_data data.water add merge group solvent Description """"""""""" @@ -622,6 +622,8 @@ of analysis. - atom-ID molecule-ID atom-type x y z * - charge - atom-ID atom-type q x y z + * - dielectric + - atom-ID atom-type q x y z normx normy normz area ed em epsilon curvature * - dipole - atom-ID atom-type q x y z mux muy muz * - dpd diff --git a/doc/src/read_restart.rst b/doc/src/read_restart.rst index 4d68167560..f3065a2a5c 100644 --- a/doc/src/read_restart.rst +++ b/doc/src/read_restart.rst @@ -11,7 +11,6 @@ Syntax read_restart file flag * file = name of binary restart file to read in -* flag = remap (optional) Examples """""""" @@ -19,44 +18,40 @@ Examples .. code-block:: LAMMPS read_restart save.10000 - read_restart save.10000 remap read_restart restart.* read_restart restart.*.mpiio - read_restart poly.*.% remap Description """"""""""" Read in a previously saved system configuration from a restart file. This allows continuation of a previous run. Details about what -information is stored (and not stored) in a restart file is given -below. Basically this operation will re-create the simulation box -with all its atoms and their attributes as well as some related global -settings, at the point in time it was written to the restart file by a -previous simulation. The simulation box will be partitioned into a -regular 3d grid of rectangular bricks, one per processor, based on the -number of processors in the current simulation and the settings of the +information is stored (and not stored) in a restart file is given below. +Basically this operation will re-create the simulation box with all its +atoms and their attributes as well as some related global settings, at +the point in time it was written to the restart file by a previous +simulation. The simulation box will be partitioned into a regular 3d +grid of rectangular bricks, one per processor, based on the number of +processors in the current simulation and the settings of the :doc:`processors ` command. The partitioning can later be -changed by the :doc:`balance ` or :doc:`fix balance ` commands. - -.. note:: - - Normally, restart files are written by the - :doc:`restart ` or :doc:`write_restart ` commands - so that all atoms in the restart file are inside the simulation box. - If this is not the case, the read_restart command will print an error - that atoms were "lost" when the file is read. This error should be - reported to the LAMMPS developers so the invalid writing of the - restart file can be fixed. If you still wish to use the restart file, - the optional *remap* flag can be appended to the read_restart command. - This should avoid the error, by explicitly remapping each atom back - into the simulation box, updating image flags for the atom - appropriately. +changed by the :doc:`balance ` or :doc:`fix balance +` commands. Restart files are saved in binary format to enable exact restarts, meaning that the trajectories of a restarted run will precisely match those produced by the original run had it continued on. +The binary restart file format was not designed with backward, forward, +or cross-platform compatibility in mind, so the files are only expected +to be read correctly by the same LAMMPS executable on the same platform. +Changes to the architecture, compilation settings, or LAMMPS version can +render a restart file unreadable or it may read the data incorrectly. +If you want a more portable format, you can use the data file format as +created by the :doc:`write_data ` command. Binary restart +files can also be converted into a data file from the command line by +the LAMMPS executable that wrote them using the :ref:`-restart2data +` command line flag. + Several things can prevent exact restarts due to round-off effects, in which case the trajectories in the 2 runs will slowly diverge. These include running on a different number of processors or changing @@ -65,7 +60,8 @@ certain settings such as those set by the :doc:`newton ` or these cases. Certain fixes will not restart exactly, though they should provide -statistically similar results. These include :doc:`fix shake ` and :doc:`fix langevin `. +statistically similar results. These include :doc:`fix shake +` and :doc:`fix langevin `. Certain pair styles will not restart exactly, though they should provide statistically similar results. This is because the forces @@ -81,18 +77,19 @@ produced the restart file, it could be a LAMMPS bug, so consider :doc:`reporting it ` if you think the behavior is a bug. Because restart files are binary, they may not be portable to other -machines. In this case, you can use the :doc:`-restart command-line switch ` to convert a restart file to a data file. +machines. In this case, you can use the :doc:`-restart command-line +switch ` to convert a restart file to a data file. -Similar to how restart files are written (see the -:doc:`write_restart ` and :doc:`restart ` -commands), the restart filename can contain two wild-card characters. -If a "\*" appears in the filename, the directory is searched for all -filenames that match the pattern where "\*" is replaced with a timestep -value. The file with the largest timestep value is read in. Thus, -this effectively means, read the latest restart file. It's useful if -you want your script to continue a run from where it left off. See -the :doc:`run ` command and its "upto" option for how to specify -the run command so it does not need to be changed either. +Similar to how restart files are written (see the :doc:`write_restart +` and :doc:`restart ` commands), the restart +filename can contain two wild-card characters. If a "\*" appears in the +filename, the directory is searched for all filenames that match the +pattern where "\*" is replaced with a timestep value. The file with the +largest timestep value is read in. Thus, this effectively means, read +the latest restart file. It's useful if you want your script to +continue a run from where it left off. See the :doc:`run ` command +and its "upto" option for how to specify the run command so it does not +need to be changed either. If a "%" character appears in the restart filename, LAMMPS expects a set of multiple files to exist. The :doc:`restart ` and @@ -222,17 +219,17 @@ its calculations in a consistent manner. .. note:: - There are a handful of commands which can be used before or - between runs which may require a system initialization. Examples - include the "balance", "displace_atoms", "delete_atoms", "set" (some - options), and "velocity" (some options) commands. This is because - they can migrate atoms to new processors. Thus they will also discard - unused "state" information from fixes. You will know the discard has + There are a handful of commands which can be used before or between + runs which may require a system initialization. Examples include the + "balance", "displace_atoms", "delete_atoms", "set" (some options), + and "velocity" (some options) commands. This is because they can + migrate atoms to new processors. Thus they will also discard unused + "state" information from fixes. You will know the discard has occurred because a list of discarded fixes will be printed to the screen and log file, as explained above. This means that if you wish to retain that info in a restarted run, you must re-specify the - relevant fixes and computes (which create fixes) before those commands - are used. + relevant fixes and computes (which create fixes) before those + commands are used. Some pair styles, like the :doc:`granular pair styles `, also use a fix to store "state" information that persists from timestep to @@ -245,18 +242,19 @@ LAMMPS allows bond interactions (angle, etc) to be turned off or deleted in various ways, which can affect how their info is stored in a restart file. -If bonds (angles, etc) have been turned off by the :doc:`fix shake ` or :doc:`delete_bonds ` command, -their info will be written to a restart file as if they are turned on. -This means they will need to be turned off again in a new run after -the restart file is read. +If bonds (angles, etc) have been turned off by the :doc:`fix shake +` or :doc:`delete_bonds ` command, their info +will be written to a restart file as if they are turned on. This means +they will need to be turned off again in a new run after the restart +file is read. Bonds that are broken (e.g. by a bond-breaking potential) are written to the restart file as broken bonds with a type of 0. Thus these bonds will still be broken when the restart file is read. -Bonds that have been broken by the :doc:`fix bond/break ` command have disappeared from the -system. No information about these bonds is written to the restart -file. +Bonds that have been broken by the :doc:`fix bond/break +` command have disappeared from the system. No +information about these bonds is written to the restart file. ---------- diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 319d1b0a41..cce6e92d05 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -94,6 +94,7 @@ amu Amzallag analytical Anders +Andrienko Andzelm Ang anglegrad @@ -119,6 +120,7 @@ Antonelli api Apoorva Appl +apptainer Apu arallel arccos @@ -239,6 +241,7 @@ benchmarking Bennet Berardi Beraun +Bereau berendsen Berendsen berger @@ -560,6 +563,7 @@ Crozier Cryst Crystallogr Csanyi +csg csh cshrc CSiC @@ -873,6 +877,7 @@ Eindhoven Eisenforschung Ejtehadi El +el elaplong elastance Electroneg @@ -1081,6 +1086,7 @@ fm fmackay fmag fmass +fmatch fmm fmt fmtlib @@ -1564,6 +1570,7 @@ jpeglib jpg JPG jpl +json Jth jtranch jtype @@ -2362,7 +2369,11 @@ nopreliminary Nord norder Nordlund +noremap normals +normx +normy +normz Noskov noslip noticable @@ -2406,6 +2417,7 @@ Nstep Nsteplast Nstop nsub +Nsw Nswap nt Nt @@ -3036,6 +3048,7 @@ scalexz scaleyz Scalfi Schaik +Scheid Schilfgarde Schimansky Schiotz @@ -3213,6 +3226,7 @@ statvolt stdin stdio stdlib +stdout steelblue Stegailov Steinbach diff --git a/examples/COUPLE/fortran2/LAMMPS-wrapper.cpp b/examples/COUPLE/fortran2/LAMMPS-wrapper.cpp index 8b6a257755..eb6f421606 100644 --- a/examples/COUPLE/fortran2/LAMMPS-wrapper.cpp +++ b/examples/COUPLE/fortran2/LAMMPS-wrapper.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ /* ------------------------------------------------------------------------ - Contributing author: Karl D. Hammond - University of Tennessee, Knoxville (USA), 2012 + Contributing author: Karl D. Hammond + University of Missouri (USA), 2012 ------------------------------------------------------------------------- */ /* This is set of "wrapper" functions to assist LAMMPS.F90, which itself @@ -23,6 +23,7 @@ #include #include "LAMMPS-wrapper.h" +#define LAMMPS_LIB_MPI 1 #include #include #include @@ -56,181 +57,40 @@ void lammps_error_all (void *ptr, const char *file, int line, const char *str) int lammps_extract_compute_vectorsize (void *ptr, char *id, int style) { - class LAMMPS *lmp = (class LAMMPS *) ptr; - int icompute = lmp->modify->find_compute(id); - if ( icompute < 0 ) return 0; - class Compute *compute = lmp->modify->compute[icompute]; - - if ( style == 0 ) - { - if ( !compute->vector_flag ) - return 0; - else - return compute->size_vector; - } - else if ( style == 1 ) - { - return lammps_get_natoms (ptr); - } - else if ( style == 2 ) - { - if ( !compute->local_flag ) - return 0; - else - return compute->size_local_rows; - } - else - return 0; + int *size; + size = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_VECTOR); + if (size) return *size; + return 0; } void lammps_extract_compute_arraysize (void *ptr, char *id, int style, int *nrows, int *ncols) { - class LAMMPS *lmp = (class LAMMPS *) ptr; - int icompute = lmp->modify->find_compute(id); - if ( icompute < 0 ) - { - *nrows = 0; - *ncols = 0; - } - class Compute *compute = lmp->modify->compute[icompute]; - - if ( style == 0 ) - { - if ( !compute->array_flag ) - { - *nrows = 0; - *ncols = 0; - } - else - { - *nrows = compute->size_array_rows; - *ncols = compute->size_array_cols; - } - } - else if ( style == 1 ) - { - if ( !compute->peratom_flag ) - { - *nrows = 0; - *ncols = 0; - } - else - { - *nrows = lammps_get_natoms (ptr); - *ncols = compute->size_peratom_cols; - } - } - else if ( style == 2 ) - { - if ( !compute->local_flag ) - { - *nrows = 0; - *ncols = 0; - } - else - { - *nrows = compute->size_local_rows; - *ncols = compute->size_local_cols; - } - } - else - { - *nrows = 0; - *ncols = 0; - } - + int *tmp; + tmp = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_ROWS); + if (tmp) *nrows = *tmp; + tmp = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_COLS); + if (tmp) *ncols = *tmp; return; } int lammps_extract_fix_vectorsize (void *ptr, char *id, int style) { - class LAMMPS *lmp = (class LAMMPS *) ptr; - int ifix = lmp->modify->find_fix(id); - if ( ifix < 0 ) return 0; - class Fix *fix = lmp->modify->fix[ifix]; - - if ( style == 0 ) - { - if ( !fix->vector_flag ) - return 0; - else - return fix->size_vector; - } - else if ( style == 1 ) - { - return lammps_get_natoms (ptr); - } - else if ( style == 2 ) - { - if ( !fix->local_flag ) - return 0; - else - return fix->size_local_rows; - } - else - return 0; + int *size; + size = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_VECTOR, 0, 0); + if (size) return *size; + return 0; } void lammps_extract_fix_arraysize (void *ptr, char *id, int style, int *nrows, int *ncols) { - class LAMMPS *lmp = (class LAMMPS *) ptr; - int ifix = lmp->modify->find_fix(id); - if ( ifix < 0 ) - { - *nrows = 0; - *ncols = 0; - } - class Fix *fix = lmp->modify->fix[ifix]; - - if ( style == 0 ) - { - if ( !fix->array_flag ) - { - *nrows = 0; - *ncols = 0; - } - else - { - *nrows = fix->size_array_rows; - *ncols = fix->size_array_cols; - } - } - else if ( style == 1 ) - { - if ( !fix->peratom_flag ) - { - *nrows = 0; - *ncols = 0; - } - else - { - *nrows = lammps_get_natoms (ptr); - *ncols = fix->size_peratom_cols; - } - } - else if ( style == 2 ) - { - if ( !fix->local_flag ) - { - *nrows = 0; - *ncols = 0; - } - else - { - *nrows = fix->size_local_rows; - *ncols = fix->size_local_cols; - } - } - else - { - *nrows = 0; - *ncols = 0; - } - + int *tmp; + tmp = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_ROWS, 0, 0); + if (tmp) *nrows = *tmp; + tmp = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_COLS, 0, 0); + if (tmp) *ncols = *tmp; return; - } /* vim: set ts=3 sts=3 expandtab: */ diff --git a/examples/COUPLE/fortran2/LAMMPS-wrapper.h b/examples/COUPLE/fortran2/LAMMPS-wrapper.h index 68e03ae05a..479af91738 100644 --- a/examples/COUPLE/fortran2/LAMMPS-wrapper.h +++ b/examples/COUPLE/fortran2/LAMMPS-wrapper.h @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ /* ------------------------------------------------------------------------ - Contributing author: Karl D. Hammond - University of Tennessee, Knoxville (USA), 2012 + Contributing author: Karl D. Hammond + University of Missouri (USA), 2012 ------------------------------------------------------------------------- */ /* This is set of "wrapper" functions to assist LAMMPS.F90, which itself diff --git a/examples/COUPLE/fortran2/LAMMPS.F90 b/examples/COUPLE/fortran2/LAMMPS.F90 index 8b74a38721..251b56f48f 100644 --- a/examples/COUPLE/fortran2/LAMMPS.F90 +++ b/examples/COUPLE/fortran2/LAMMPS.F90 @@ -1292,7 +1292,7 @@ contains !! Wrapper functions local to this module {{{1 Cname = string2Cstring (name) Ccount = size(data) / natoms if ( Ccount /= 1 .and. Ccount /= 3 ) & - call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires& + call lammps_error_all (ptr, FLERR, 'lammps_scatter_atoms requires& & count to be either 1 or 3') Fdata = data Cdata = C_loc (Fdata(1)) @@ -1355,7 +1355,7 @@ contains !! Wrapper functions local to this module {{{1 Cname = string2Cstring (name) Ccount = size(data) / ndata if ( Ccount /= 1 .and. Ccount /= 3 ) & - call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires& + call lammps_error_all (ptr, FLERR, 'lammps_scatter_atoms requires& & count to be either 1 or 3') Fdata = data Cdata = C_loc (Fdata(1)) diff --git a/examples/COUPLE/fortran2/Makefile b/examples/COUPLE/fortran2/Makefile index fe66914892..f8a2126233 100644 --- a/examples/COUPLE/fortran2/Makefile +++ b/examples/COUPLE/fortran2/Makefile @@ -14,7 +14,7 @@ CXXLIB = -lstdc++ # replace with your C++ runtime libs # Flags for Fortran compiler, C++ compiler, and C preprocessor, respectively FFLAGS = -O2 -fPIC CXXFLAGS = -O2 -fPIC -CPPFLAGS = -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX -DLAMMPS_LIB_MPI +CPPFLAGS = -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX all : liblammps_fortran.a liblammps_fortran.so diff --git a/examples/COUPLE/fortran2/README b/examples/COUPLE/fortran2/README index 1710ca8ba6..0a7b862d86 100644 --- a/examples/COUPLE/fortran2/README +++ b/examples/COUPLE/fortran2/README @@ -11,9 +11,8 @@ This interface was created by Karl Hammond who you can contact with questions: Karl D. Hammond -University of Tennessee, Knoxville -karlh at ugcs.caltech.edu -karlh at utk.edu +University of Missouri +hammondkd at missouri.edu ------------------------------------- diff --git a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp index 8b6a257755..eb6f421606 100644 --- a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp +++ b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ /* ------------------------------------------------------------------------ - Contributing author: Karl D. Hammond - University of Tennessee, Knoxville (USA), 2012 + Contributing author: Karl D. Hammond + University of Missouri (USA), 2012 ------------------------------------------------------------------------- */ /* This is set of "wrapper" functions to assist LAMMPS.F90, which itself @@ -23,6 +23,7 @@ #include #include "LAMMPS-wrapper.h" +#define LAMMPS_LIB_MPI 1 #include #include #include @@ -56,181 +57,40 @@ void lammps_error_all (void *ptr, const char *file, int line, const char *str) int lammps_extract_compute_vectorsize (void *ptr, char *id, int style) { - class LAMMPS *lmp = (class LAMMPS *) ptr; - int icompute = lmp->modify->find_compute(id); - if ( icompute < 0 ) return 0; - class Compute *compute = lmp->modify->compute[icompute]; - - if ( style == 0 ) - { - if ( !compute->vector_flag ) - return 0; - else - return compute->size_vector; - } - else if ( style == 1 ) - { - return lammps_get_natoms (ptr); - } - else if ( style == 2 ) - { - if ( !compute->local_flag ) - return 0; - else - return compute->size_local_rows; - } - else - return 0; + int *size; + size = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_VECTOR); + if (size) return *size; + return 0; } void lammps_extract_compute_arraysize (void *ptr, char *id, int style, int *nrows, int *ncols) { - class LAMMPS *lmp = (class LAMMPS *) ptr; - int icompute = lmp->modify->find_compute(id); - if ( icompute < 0 ) - { - *nrows = 0; - *ncols = 0; - } - class Compute *compute = lmp->modify->compute[icompute]; - - if ( style == 0 ) - { - if ( !compute->array_flag ) - { - *nrows = 0; - *ncols = 0; - } - else - { - *nrows = compute->size_array_rows; - *ncols = compute->size_array_cols; - } - } - else if ( style == 1 ) - { - if ( !compute->peratom_flag ) - { - *nrows = 0; - *ncols = 0; - } - else - { - *nrows = lammps_get_natoms (ptr); - *ncols = compute->size_peratom_cols; - } - } - else if ( style == 2 ) - { - if ( !compute->local_flag ) - { - *nrows = 0; - *ncols = 0; - } - else - { - *nrows = compute->size_local_rows; - *ncols = compute->size_local_cols; - } - } - else - { - *nrows = 0; - *ncols = 0; - } - + int *tmp; + tmp = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_ROWS); + if (tmp) *nrows = *tmp; + tmp = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_COLS); + if (tmp) *ncols = *tmp; return; } int lammps_extract_fix_vectorsize (void *ptr, char *id, int style) { - class LAMMPS *lmp = (class LAMMPS *) ptr; - int ifix = lmp->modify->find_fix(id); - if ( ifix < 0 ) return 0; - class Fix *fix = lmp->modify->fix[ifix]; - - if ( style == 0 ) - { - if ( !fix->vector_flag ) - return 0; - else - return fix->size_vector; - } - else if ( style == 1 ) - { - return lammps_get_natoms (ptr); - } - else if ( style == 2 ) - { - if ( !fix->local_flag ) - return 0; - else - return fix->size_local_rows; - } - else - return 0; + int *size; + size = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_VECTOR, 0, 0); + if (size) return *size; + return 0; } void lammps_extract_fix_arraysize (void *ptr, char *id, int style, int *nrows, int *ncols) { - class LAMMPS *lmp = (class LAMMPS *) ptr; - int ifix = lmp->modify->find_fix(id); - if ( ifix < 0 ) - { - *nrows = 0; - *ncols = 0; - } - class Fix *fix = lmp->modify->fix[ifix]; - - if ( style == 0 ) - { - if ( !fix->array_flag ) - { - *nrows = 0; - *ncols = 0; - } - else - { - *nrows = fix->size_array_rows; - *ncols = fix->size_array_cols; - } - } - else if ( style == 1 ) - { - if ( !fix->peratom_flag ) - { - *nrows = 0; - *ncols = 0; - } - else - { - *nrows = lammps_get_natoms (ptr); - *ncols = fix->size_peratom_cols; - } - } - else if ( style == 2 ) - { - if ( !fix->local_flag ) - { - *nrows = 0; - *ncols = 0; - } - else - { - *nrows = fix->size_local_rows; - *ncols = fix->size_local_cols; - } - } - else - { - *nrows = 0; - *ncols = 0; - } - + int *tmp; + tmp = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_ROWS, 0, 0); + if (tmp) *nrows = *tmp; + tmp = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_COLS, 0, 0); + if (tmp) *ncols = *tmp; return; - } /* vim: set ts=3 sts=3 expandtab: */ diff --git a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.h b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.h index 7d94362436..553466d138 100644 --- a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.h +++ b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.h @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ /* ------------------------------------------------------------------------ - Contributing author: Karl D. Hammond - University of Tennessee, Knoxville (USA), 2012 + Contributing author: Karl D. Hammond + University of Missouri (USA), 2012 ------------------------------------------------------------------------- */ /* This is set of "wrapper" functions to assist LAMMPS.F90, which itself diff --git a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp index 5f94363346..44d7b5bca4 100644 --- a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp +++ b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp @@ -12,8 +12,7 @@ ------------------------------------------------------------------------- */ /* ------------------------------------------------------------------------ - Contributing author: Karl D. Hammond - University of Tennessee, Knoxville (USA), 2012 + Contributing author: Nir Goldman, LLNL , 2016 ------------------------------------------------------------------------- */ /* This is set of "wrapper" functions to assist LAMMPS.F90, which itself diff --git a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.h b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.h index ed79015e78..d3705179ed 100644 --- a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.h +++ b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.h @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ /* ------------------------------------------------------------------------ - Contributing author: Nir Goldman, ngoldman@llnl.gov, Oct. 19th, 2016 + Contributing author: Nir Goldman, LLNL , 2016 ------------------------------------------------------------------------- */ /* This is set of "wrapper" functions to assist LAMMPS.F90, which itself diff --git a/examples/COUPLE/fortran_dftb/LAMMPS.F90 b/examples/COUPLE/fortran_dftb/LAMMPS.F90 index 9b18bbfa5f..188fff9d60 100644 --- a/examples/COUPLE/fortran_dftb/LAMMPS.F90 +++ b/examples/COUPLE/fortran_dftb/LAMMPS.F90 @@ -12,8 +12,8 @@ !-------------------------------------------------------------------------- !! ------------------------------------------------------------------------ -! Contributing author: Karl D. Hammond -! University of Tennessee, Knoxville (USA), 2012 +! Contributing author: Karl D. Hammond +! University of Missouri (USA), 2012 !-------------------------------------------------------------------------- !! LAMMPS, a Fortran 2003 module containing an interface between Fortran diff --git a/examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/compute_born.py b/examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/compute_born.py index 0f3265faeb..88cc8dcca2 100644 --- a/examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/compute_born.py +++ b/examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/compute_born.py @@ -1,7 +1,6 @@ #!/usr/bin/env python3 # -*- coding: utf-8 -*- -import sys import numpy as np def reduce_Born(Cf): diff --git a/examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/compute_born.py b/examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/compute_born.py index 0f3265faeb..88cc8dcca2 100644 --- a/examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/compute_born.py +++ b/examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/compute_born.py @@ -1,7 +1,6 @@ #!/usr/bin/env python3 # -*- coding: utf-8 -*- -import sys import numpy as np def reduce_Born(Cf): diff --git a/examples/ELASTIC_T/BORN_MATRIX/Silicon/elastic_utils.py b/examples/ELASTIC_T/BORN_MATRIX/Silicon/elastic_utils.py index 0daf62b1b0..2307f3d413 100644 --- a/examples/ELASTIC_T/BORN_MATRIX/Silicon/elastic_utils.py +++ b/examples/ELASTIC_T/BORN_MATRIX/Silicon/elastic_utils.py @@ -1,5 +1,5 @@ import numpy as np -from lammps import lammps, LAMMPS_INT, LMP_STYLE_GLOBAL, LMP_VAR_EQUAL, LMP_VAR_ATOM +from lammps import lammps, LMP_VAR_EQUAL # method for rotating elastic constants diff --git a/examples/PACKAGES/manybody_table/1-1-1.table b/examples/PACKAGES/manybody_table/1-1-1.table new file mode 100644 index 0000000000..76d8f8a9ec --- /dev/null +++ b/examples/PACKAGES/manybody_table/1-1-1.table @@ -0,0 +1,1875 @@ +ENTRY1 +N 12 rmin 2.55 rmax 3.65 + +1 2.55 2.55 3.75 -867.212 -611.273 867.212 21386.8 611.273 -21386.8 0.0 +2 2.55 2.55 11.25 -621.539 -411.189 621.539 5035.95 411.189 -5035.95 0.0 +3 2.55 2.55 18.75 -394.167 -243.287 394.167 1722.21 243.287 -1722.21 0.0 +4 2.55 2.55 26.25 -218.789 -127.402 218.789 560.206 127.402 -560.206 0.0 +5 2.55 2.55 33.75 -104.252 -59.5774 104.252 156.639 59.5774 -156.639 0.0 +6 2.55 2.55 41.25 -41.0722 -24.6716 41.072 36.4446 24.6716 -36.4446 0.0 +7 2.55 2.55 48.75 -12.357 -8.38061 12.3571 7.1117 8.38062 -7.1117 0.0 +8 2.55 2.55 56.25 -2.29912 -1.68047 2.29907 0.91657 1.68048 -0.916568 0.0 +9 2.55 2.55 63.75 -0.0509977 0.327321 0.0509129 -0.304729 -0.327319 0.30474 0.0 +10 2.55 2.55 71.25 0.0345509 0.431792 -0.0345867 -0.382614 -0.431782 0.382616 0.0 +11 2.55 2.55 78.75 -0.00019898 0.179593 0.000319523 -0.292658 -0.179608 0.292661 0.0 +12 2.55 2.55 86.25 0.154169 0.138217 -0.154088 -0.302917 -0.138224 0.302914 0.0 +13 2.55 2.55 93.75 0.327691 0.263922 -0.327675 -0.340147 -0.263894 0.340148 0.0 +14 2.55 2.55 101.25 0.382895 0.350591 -0.382883 -0.297308 -0.350546 0.297312 0.0 +15 2.55 2.55 108.75 0.300955 0.297417 -0.300746 -0.173862 -0.297437 0.173872 0.0 +16 2.55 2.55 116.25 0.138507 0.141879 -0.138328 -0.0349372 -0.1418 0.0349415 0.0 +17 2.55 2.55 123.75 -0.0287949 -0.0286834 0.0286744 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All inputs are for the +simulation of coarse-grained SPC/E water. + +A water molecule is represented by one coarse-grained (CG) bead. + +For the two threebody/table examples the three-body (force) tables are +in the files 1-1-1.table and 1-1-2.table. These have been parametrized +with the kernel-based machine learning (ML) with the VOTCA package +(https://gitlab.mpcdf.mpg.de/votca/votca). For a example on the +parametrization, have a look at +https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/guide +and +https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/ml. + +In both cases, the parametrization is done according to a sample system, +using the three-body forces of a Stillinger-Weber potential with +tabulated angular forces (sw/angle/table) (see in.spce_sw). These then +are learned with the covariant meshing technique with the settings files +used in +https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/ml/3body/with_binning. + +The first example, in.spce uses the LAMMPS data file (data.spce) with +the starting configuration of 1000 CG water molecules, and a threebody +file (spce.3b) which loads the 1-1-1.table file. + +A hybrid/overlay pair style is used to sum a tabulated pairwise +interaction (table_CG_CG.txt) with the tabulated threebody interactions. +The tabulated pair interaction is the effectively the same as in the +what is used by the in.spce_sw input using sw/angle/table pair style. + +IMPORTANT NOTE: The threebody tables are parameterized without storing +energies (the last column of the threebody table files is zero). This +is due to a current limitation of the paramerization procedure. + +This in.spce2 example uses the data.spce2 file and the threebody input +spce2.3b. This is essentially the same simulation as in in.spce only +the atom type of the first 100 CG water molecules has been changed from +1 to 2. This is done to demonstrate how to run a simulation with +different atom types. + +For this (artificial) two-element simulation, the threebody file now +contain 8 entries for: type1 type1 type1, type1 type1 type2, type1 type2 +type1, type1 type2 type2, type2 type1 type1, type2 type1 type2, type2 +type2 type1, type2 type2 type2. Each entry has the same structure as +above. However, entries where the second and the third element are +different require a different force table (1-1-2.table) instead of +(1-1-1.table). 1-1-2.table contains exactly the force constants as +1-1-1.table. However it has to have the asymmetric structure where both +interparticle distances (r_ij and r_ik) are varied from rmin to rmax and +therefore contains "M = 2 * N * N * N" (2 * 12 * 12 * 12 = 3456) +entries. + +The third example, in.spce_sw, contains the analytical twobody interactions +and replaces the threebody term of the Stillinger-Weber potential with an +angle/table style potential which is stored in the table_CG_CG_CG.txt file. diff --git a/examples/PACKAGES/manybody_table/data.spce b/examples/PACKAGES/manybody_table/data.spce new file mode 100644 index 0000000000..a56ab1b10c --- /dev/null +++ b/examples/PACKAGES/manybody_table/data.spce @@ -0,0 +1,1015 @@ +Data File for CG Water + +1000 atoms +1 atom types + +0 31.0648 xlo xhi +0 31.0648 ylo yhi +0 31.0648 zlo zhi + +Masses + +1 18.0154 + +Atoms + +1 1 18.26 24.7 15.77 +2 1 12.63 1.42 27.01 +3 1 10.39 29.11 13.56 +4 1 26.47 16.64 7.23 +5 1 10.66 23.41 27.33 +6 1 19.08 3.2 21.63 +7 1 11.17 26.19 1.44 +8 1 4.61 4.04 25.72 +9 1 4.61 22.91 8.33 +10 1 30.61 22.71 25.18 +11 1 6.38 18.92 16.87 +12 1 17.83 12.53 11.09 +13 1 14.89 2.43 22.44 +14 1 28.36 30.9 26.38 +15 1 25.73 28.56 8.32 +16 1 19.61 20.22 4.43 +17 1 25.96 30.32 24.22 +18 1 14.51 17.35 16.41 +19 1 30.23 17.26 10.71 +20 1 22.68 23.23 2.3 +21 1 10.89 15.76 14.33 +22 1 1.46 20.46 12.48 +23 1 12.73 19.57 2.71 +24 1 1.21 12.02 9.88 +25 1 2.63 14.4 23.71 +26 1 16.91 20.37 4.73 +27 1 28.02 7.7 30.08 +28 1 21.22 22.47 19.66 +29 1 14.0 28.15 0.14 +30 1 19.62 19.73 1.11 +31 1 28.29 24.36 10.15 +32 1 14.05 1.1 17.64 +33 1 12.2 23.75 24.83 +34 1 24.56 26.02 13.57 +35 1 12.13 8.39 7.17 +36 1 20.47 22.28 25.02 +37 1 11.06 7.63 24.11 +38 1 6.52 22.64 30.46 +39 1 16.51 24.78 18.58 +40 1 30.18 20.56 29.19 +41 1 25.26 7.8 25.98 +42 1 20.37 4.16 3.88 +43 1 18.85 27.34 27.83 +44 1 17.72 29.84 12.78 +45 1 19.26 14.48 19.38 +46 1 29.73 4.46 4.96 +47 1 9.52 26.27 30.33 +48 1 6.55 9.25 20.32 +49 1 10.49 1.91 23.31 +50 1 17.63 1.17 14.48 +51 1 1.56 25.17 4.69 +52 1 9.08 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7.64 5.7 +727 1 7.44 14.1 29.85 +728 1 7.13 12.21 3.18 +729 1 16.35 14.7 4.18 +730 1 1.43 15.6 11.58 +731 1 30.27 1.93 9.17 +732 1 2.77 2.54 27.69 +733 1 11.36 27.83 16.39 +734 1 7.83 2.36 14.66 +735 1 19.3 12.28 5.63 +736 1 28.36 12.19 19.25 +737 1 10.67 7.34 13.62 +738 1 26.6 24.47 21.0 +739 1 8.55 29.42 27.3 +740 1 25.79 25.13 4.07 +741 1 28.21 8.09 22.88 +742 1 22.44 11.07 23.78 +743 1 27.76 17.89 25.74 +744 1 2.23 0.19 23.48 +745 1 10.49 12.99 20.29 +746 1 18.74 11.84 24.74 +747 1 29.46 2.69 24.54 +748 1 3.11 29.29 15.2 +749 1 21.8 19.07 20.45 +750 1 11.21 17.26 20.08 +751 1 2.59 26.55 26.79 +752 1 23.67 25.82 17.79 +753 1 23.43 27.91 15.08 +754 1 6.86 2.11 28.13 +755 1 14.38 19.97 19.61 +756 1 29.05 26.41 8.62 +757 1 3.34 9.63 6.81 +758 1 21.41 30.88 18.45 +759 1 30.35 16.75 23.77 +760 1 19.92 6.73 20.92 +761 1 26.4 1.5 11.47 +762 1 16.6 8.88 30.96 +763 1 23.25 29.76 4.34 +764 1 17.15 13.45 7.34 +765 1 14.52 14.34 23.37 +766 1 11.77 3.31 25.06 +767 1 15.52 25.25 0.94 +768 1 21.53 27.39 12.97 +769 1 11.29 10.11 17.38 +770 1 11.07 15.06 5.47 +771 1 27.61 7.39 6.07 +772 1 15.82 4.83 27.63 +773 1 17.16 20.28 12.25 +774 1 3.18 28.03 22.92 +775 1 25.53 27.61 25.22 +776 1 1.81 16.55 1.25 +777 1 3.72 16.82 7.97 +778 1 7.68 21.57 2.11 +779 1 21.85 26.93 28.36 +780 1 10.31 8.57 4.0 +781 1 11.61 9.88 14.35 +782 1 0.41 8.48 24.13 +783 1 3.8 10.63 30.74 +784 1 2.74 17.0 21.82 +785 1 28.44 22.73 28.74 +786 1 2.08 0.43 20.23 +787 1 0.25 9.36 2.02 +788 1 27.68 11.33 26.53 +789 1 27.63 4.1 14.74 +790 1 19.68 0.89 3.22 +791 1 17.12 30.74 17.17 +792 1 16.11 25.62 24.01 +793 1 20.49 9.58 13.85 +794 1 26.77 20.78 27.64 +795 1 18.77 16.87 25.93 +796 1 7.01 13.49 6.76 +797 1 18.38 16.84 18.4 +798 1 8.54 14.44 4.51 +799 1 11.51 1.42 8.98 +800 1 17.06 14.93 12.29 +801 1 6.07 0.24 15.08 +802 1 8.76 17.53 2.01 +803 1 19.63 6.58 1.71 +804 1 10.24 4.66 10.93 +805 1 4.39 20.15 30.88 +806 1 30.31 16.7 6.24 +807 1 26.0 30.16 27.34 +808 1 6.44 21.42 21.88 +809 1 22.05 29.62 11.43 +810 1 21.94 22.11 9.22 +811 1 21.82 1.59 13.13 +812 1 27.09 0.55 16.64 +813 1 8.88 3.09 17.06 +814 1 6.95 18.85 6.3 +815 1 20.13 2.53 15.07 +816 1 17.52 12.36 3.26 +817 1 18.46 7.24 13.99 +818 1 12.61 6.94 3.36 +819 1 15.55 17.46 19.11 +820 1 16.13 27.37 11.33 +821 1 2.99 14.41 9.34 +822 1 5.81 22.26 24.67 +823 1 19.82 2.53 6.19 +824 1 28.93 5.65 7.69 +825 1 17.89 22.05 15.68 +826 1 5.63 7.81 23.81 +827 1 19.09 16.3 22.05 +828 1 1.07 19.82 27.06 +829 1 14.74 8.15 28.71 +830 1 16.98 10.27 4.92 +831 1 13.39 20.01 5.47 +832 1 21.23 3.56 30.15 +833 1 29.23 18.12 28.24 +834 1 16.76 24.31 7.29 +835 1 26.12 21.8 21.5 +836 1 0.2 13.1 12.25 +837 1 1.99 3.78 30.39 +838 1 26.67 20.02 19.27 +839 1 20.63 10.01 5.91 +840 1 4.44 3.74 1.84 +841 1 21.95 6.78 0.24 +842 1 9.86 22.51 17.05 +843 1 26.17 7.64 18.91 +844 1 17.09 20.11 19.78 +845 1 10.38 9.07 9.16 +846 1 9.92 13.21 17.39 +847 1 24.26 19.17 3.05 +848 1 13.32 18.96 29.06 +849 1 27.98 20.32 7.7 +850 1 10.35 6.44 17.04 +851 1 27.27 28.95 29.77 +852 1 7.71 19.32 24.95 +853 1 23.11 17.51 14.39 +854 1 25.37 14.39 26.26 +855 1 4.73 3.99 17.92 +856 1 28.53 17.74 8.3 +857 1 28.99 9.49 7.65 +858 1 11.37 3.77 18.66 +859 1 11.01 23.57 6.0 +860 1 7.29 17.47 30.27 +861 1 18.92 10.24 0.36 +862 1 22.76 24.44 27.3 +863 1 14.27 13.05 5.04 +864 1 3.42 14.59 30.9 +865 1 9.31 22.34 24.75 +866 1 25.78 16.96 15.63 +867 1 7.18 22.01 12.25 +868 1 5.0 18.29 28.57 +869 1 23.36 20.87 22.7 +870 1 13.16 10.8 10.17 +871 1 6.42 24.78 7.47 +872 1 28.86 3.89 20.92 +873 1 4.8 3.05 13.07 +874 1 27.07 3.53 5.63 +875 1 13.11 28.33 23.92 +876 1 14.84 13.88 20.8 +877 1 15.81 7.0 16.91 +878 1 23.41 25.39 20.56 +879 1 26.08 0.43 14.19 +880 1 6.28 17.41 19.28 +881 1 2.74 4.79 19.54 +882 1 20.98 26.42 10.11 +883 1 24.18 28.48 29.18 +884 1 12.74 29.99 12.8 +885 1 27.22 16.82 18.13 +886 1 2.08 19.98 18.27 +887 1 22.0 23.67 17.16 +888 1 17.83 3.01 29.13 +889 1 9.59 26.62 13.51 +890 1 11.48 2.18 13.45 +891 1 13.57 15.29 26.47 +892 1 1.72 0.72 9.92 +893 1 2.14 30.76 17.27 +894 1 17.9 15.88 1.47 +895 1 13.47 5.84 28.76 +896 1 8.96 22.14 21.0 +897 1 12.96 24.15 0.94 +898 1 26.13 23.25 8.89 +899 1 6.01 28.65 6.08 +900 1 22.88 20.21 6.1 +901 1 30.34 20.77 10.49 +902 1 12.19 28.16 10.6 +903 1 5.8 5.33 30.84 +904 1 29.83 26.29 15.91 +905 1 18.28 0.14 5.58 +906 1 1.91 17.34 5.88 +907 1 24.05 18.42 22.53 +908 1 10.82 21.55 3.57 +909 1 11.29 26.73 5.6 +910 1 21.34 14.41 3.22 +911 1 12.61 18.99 24.17 +912 1 25.02 18.6 25.9 +913 1 29.0 21.05 13.14 +914 1 17.72 27.28 30.27 +915 1 30.56 24.81 23.12 +916 1 17.09 20.05 24.02 +917 1 7.35 6.83 21.31 +918 1 3.39 22.32 21.05 +919 1 2.28 29.8 30.23 +920 1 5.29 25.66 14.8 +921 1 26.16 30.72 21.04 +922 1 21.63 6.32 11.68 +923 1 15.45 18.06 4.65 +924 1 5.76 28.33 24.04 +925 1 15.08 29.21 16.09 +926 1 18.76 6.14 6.94 +927 1 22.31 30.25 26.46 +928 1 18.49 22.04 30.93 +929 1 11.15 16.42 9.89 +930 1 4.34 7.98 30.25 +931 1 9.29 29.92 8.58 +932 1 22.97 27.09 8.04 +933 1 20.71 16.7 15.75 +934 1 30.36 7.49 5.24 +935 1 29.56 19.54 0.83 +936 1 30.71 14.04 20.91 +937 1 19.36 4.06 27.14 +938 1 23.41 10.8 2.14 +939 1 1.51 1.32 0.44 +940 1 8.16 14.39 1.63 +941 1 20.66 6.74 4.62 +942 1 20.78 26.26 3.85 +943 1 5.11 15.12 21.64 +944 1 12.53 20.03 17.67 +945 1 28.63 18.4 12.56 +946 1 1.95 21.69 8.08 +947 1 21.53 0.93 7.84 +948 1 2.69 22.51 17.17 +949 1 19.29 22.12 6.05 +950 1 23.68 2.14 11.01 +951 1 27.14 17.8 3.72 +952 1 2.22 14.81 3.31 +953 1 23.1 6.43 14.62 +954 1 0.22 12.59 3.57 +955 1 13.21 22.86 3.67 +956 1 13.45 2.1 20.14 +957 1 12.52 17.12 0.46 +958 1 3.07 27.45 9.03 +959 1 15.33 10.95 11.78 +960 1 0.05 4.26 9.75 +961 1 23.05 16.98 24.69 +962 1 16.15 16.28 6.51 +963 1 30.05 28.87 9.61 +964 1 6.67 29.5 16.95 +965 1 21.95 14.44 14.94 +966 1 22.58 22.47 30.33 +967 1 21.34 19.29 9.9 +968 1 29.31 21.79 20.79 +969 1 5.55 2.56 30.23 +970 1 25.88 3.17 22.22 +971 1 22.38 18.32 30.08 +972 1 6.27 19.24 8.86 +973 1 0.34 24.29 1.49 +974 1 20.49 24.13 0.25 +975 1 2.94 1.41 2.74 +976 1 24.88 25.38 7.35 +977 1 28.18 14.89 14.6 +978 1 7.84 30.36 4.39 +979 1 14.54 9.59 14.4 +980 1 27.63 12.3 15.83 +981 1 11.15 14.17 27.97 +982 1 25.27 20.88 8.35 +983 1 17.06 14.76 27.78 +984 1 3.9 14.79 15.06 +985 1 13.81 3.82 17.03 +986 1 28.55 24.1 26.15 +987 1 29.28 21.79 15.76 +988 1 15.05 30.12 27.83 +989 1 15.42 3.77 6.76 +990 1 22.65 12.12 11.24 +991 1 11.29 4.96 2.18 +992 1 2.15 7.43 7.57 +993 1 30.21 10.13 26.21 +994 1 24.42 22.18 4.42 +995 1 8.68 14.72 22.08 +996 1 23.1 6.9 27.1 +997 1 18.71 27.2 21.72 +998 1 14.12 12.7 30.76 +999 1 18.81 6.5 10.98 +1000 1 26.66 15.4 4.83 diff --git a/examples/PACKAGES/manybody_table/in.spce b/examples/PACKAGES/manybody_table/in.spce new file mode 100644 index 0000000000..6c6c6f2050 --- /dev/null +++ b/examples/PACKAGES/manybody_table/in.spce @@ -0,0 +1,21 @@ +units real +atom_style atomic + +# data file with one atom type +read_data data.spce + +pair_style hybrid/overlay table linear 1200 threebody/table + +#pair coefficients +pair_coeff 1 1 table table_CG_CG.txt VOTCA +pair_coeff * * threebody/table spce.3b type + +fix 1 all nvt temp 300.0 300.0 200.0 + +velocity all create 300 432567 dist uniform loop geom mom yes +timestep 2.0 + +thermo 100 +#dump 2 all custom 100 dump.spce id type x y z fx fy fz + +run 1000 diff --git a/examples/PACKAGES/manybody_table/in.spce2 b/examples/PACKAGES/manybody_table/in.spce2 new file mode 100644 index 0000000000..c8656c105f --- /dev/null +++ b/examples/PACKAGES/manybody_table/in.spce2 @@ -0,0 +1,22 @@ +units real +atom_style atomic + +# data file with two atom types +read_data data.spce2 + +pair_style hybrid/overlay table linear 1200 threebody/table + +#pair coefficients +pair_coeff * * table table_CG_CG.txt VOTCA +pair_coeff * * threebody/table spce2.3b type1 type2 + +fix 1 all nvt temp 300.0 300.0 200.0 + +velocity all create 300 432567 dist uniform loop geom mom yes +timestep 2.0 + +thermo 100 +#dump 2 all custom 100 dump.spce2 id type x y z fx fy fz + +run 1000 + diff --git a/examples/PACKAGES/manybody_table/in.spce_sw b/examples/PACKAGES/manybody_table/in.spce_sw new file mode 100644 index 0000000000..bb0a097743 --- /dev/null +++ b/examples/PACKAGES/manybody_table/in.spce_sw @@ -0,0 +1,20 @@ +units real +atom_style atomic + +read_data data.spce + +pair_style hybrid/overlay table linear 1200 sw/angle/table + +pair_coeff 1 1 table table_CG_CG.txt VOTCA +pair_coeff * * sw/angle/table spce.sw type + +fix 1 all nvt temp 300.0 300.0 200.0 + +velocity all create 300 432567 dist uniform mom yes + +timestep 2.0 + +thermo 100 +#dump 2 all custom 10 spce_sw.dump id type x y z fx fy fz + +run 1000 diff --git a/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.1 b/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.1 new file mode 100644 index 0000000000..ec20bd3ced --- /dev/null +++ b/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.1 @@ -0,0 +1,88 @@ +LAMMPS (4 May 2022) + using 1 OpenMP thread(s) per MPI task +units real +atom_style atomic + +# data file with one atom type +read_data data.spce +Reading data file ... + orthogonal box = (0 0 0) to (31.0648 31.0648 31.0648) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1000 atoms + read_data CPU = 0.001 seconds + +pair_style hybrid/overlay table linear 1200 threebody/table + +#pair coefficients +pair_coeff 1 1 table table_CG_CG.txt VOTCA +pair_coeff * * threebody/table spce.3b type + +fix 1 all nvt temp 300.0 300.0 200.0 + +velocity all create 300 432567 dist uniform loop geom mom yes +timestep 2.0 + +thermo 100 +#dump 2 all custom 100 dump.spce id type x y z fx fy fz + +run 1000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair table, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair threebody/table, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.487 | 5.487 | 5.487 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -5377.8719 0 -4484.5232 -320.10184 + 100 296.01121 -5418.505 0 -4537.0342 -223.39972 + 200 295.27654 -5430.3033 0 -4551.0202 794.29126 + 300 302.16526 -5445.8048 0 -4546.0083 -11.568299 + 400 308.59003 -5434.7181 0 -4515.7896 1.7337645 + 500 295.346 -5436.0896 0 -4556.5996 778.73307 + 600 293.14671 -5422.6082 0 -4549.6673 -148.64256 + 700 307.63238 -5465.187 0 -4549.1103 285.18556 + 800 313.16537 -5466.4124 0 -4533.8594 489.99301 + 900 303.42954 -5506.3208 0 -4602.7595 360.05608 + 1000 299.50926 -5446.8981 0 -4555.0107 993.95615 +Loop time of 5.15787 on 1 procs for 1000 steps with 1000 atoms + +Performance: 33.502 ns/day, 0.716 hours/ns, 193.879 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.8428 | 4.8428 | 4.8428 | 0.0 | 93.89 +Neigh | 0.27527 | 0.27527 | 0.27527 | 0.0 | 5.34 +Comm | 0.020461 | 0.020461 | 0.020461 | 0.0 | 0.40 +Output | 0.00020949 | 0.00020949 | 0.00020949 | 0.0 | 0.00 +Modify | 0.01198 | 0.01198 | 0.01198 | 0.0 | 0.23 +Other | | 0.007163 | | | 0.14 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5900 ave 5900 max 5900 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 191126 ave 191126 max 191126 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 382252 ave 382252 max 382252 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 382252 +Ave neighs/atom = 382.252 +Neighbor list builds = 27 +Dangerous builds = 0 +Total wall time: 0:00:05 diff --git a/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.4 b/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.4 new file mode 100644 index 0000000000..48b37d55fe --- /dev/null +++ b/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.4 @@ -0,0 +1,88 @@ +LAMMPS (4 May 2022) + using 1 OpenMP thread(s) per MPI task +units real +atom_style atomic + +# data file with one atom type +read_data data.spce +Reading data file ... + orthogonal box = (0 0 0) to (31.0648 31.0648 31.0648) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms + read_data CPU = 0.001 seconds + +pair_style hybrid/overlay table linear 1200 threebody/table + +#pair coefficients +pair_coeff 1 1 table table_CG_CG.txt VOTCA +pair_coeff * * threebody/table spce.3b type + +fix 1 all nvt temp 300.0 300.0 200.0 + +velocity all create 300 432567 dist uniform loop geom mom yes +timestep 2.0 + +thermo 100 +#dump 2 all custom 100 dump.spce id type x y z fx fy fz + +run 1000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair table, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair threebody/table, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.87 | 3.87 | 3.87 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -5377.8719 0 -4484.5232 -320.10184 + 100 296.01121 -5418.505 0 -4537.0342 -223.39972 + 200 295.27654 -5430.3033 0 -4551.0202 794.29126 + 300 302.16526 -5445.8048 0 -4546.0083 -11.568299 + 400 308.59003 -5434.7181 0 -4515.7896 1.7337642 + 500 295.346 -5436.0896 0 -4556.5996 778.73304 + 600 293.14648 -5422.6082 0 -4549.6681 -148.67071 + 700 307.6975 -5465.3018 0 -4549.0312 287.70203 + 800 314.09436 -5467.6073 0 -4532.2879 522.73489 + 900 300.85843 -5503.7551 0 -4607.85 491.78041 + 1000 302.84638 -5468.3331 0 -4566.5083 338.05123 +Loop time of 1.60997 on 4 procs for 1000 steps with 1000 atoms + +Performance: 107.331 ns/day, 0.224 hours/ns, 621.131 timesteps/s +94.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.28 | 1.2942 | 1.3018 | 0.8 | 80.38 +Neigh | 0.069763 | 0.070222 | 0.070788 | 0.2 | 4.36 +Comm | 0.19379 | 0.20979 | 0.23226 | 3.6 | 13.03 +Output | 0.0001711 | 0.00046947 | 0.0013621 | 0.0 | 0.03 +Modify | 0.021613 | 0.030016 | 0.038718 | 4.8 | 1.86 +Other | | 0.005309 | | | 0.33 + +Nlocal: 250 ave 257 max 240 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +Nghost: 3488.75 ave 3504 max 3478 min +Histogram: 1 1 0 0 0 1 0 0 0 1 +Neighs: 47828 ave 49169 max 45782 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +FullNghs: 95656 ave 98253 max 91425 min +Histogram: 1 0 0 0 0 1 0 0 1 1 + +Total # of neighbors = 382624 +Ave neighs/atom = 382.624 +Neighbor list builds = 27 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.1 b/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.1 new file mode 100644 index 0000000000..d6432a1c07 --- /dev/null +++ b/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.1 @@ -0,0 +1,89 @@ +LAMMPS (4 May 2022) + using 1 OpenMP thread(s) per MPI task +units real +atom_style atomic + +# data file with two atom types +read_data data.spce2 +Reading data file ... + orthogonal box = (0 0 0) to (31.0648 31.0648 31.0648) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1000 atoms + read_data CPU = 0.001 seconds + +pair_style hybrid/overlay table linear 1200 threebody/table + +#pair coefficients +pair_coeff * * table table_CG_CG.txt VOTCA +pair_coeff * * threebody/table spce2.3b type1 type2 + +fix 1 all nvt temp 300.0 300.0 200.0 + +velocity all create 300 432567 dist uniform loop geom mom yes +timestep 2.0 + +thermo 100 +#dump 2 all custom 100 dump.spce2 id type x y z fx fy fz + +run 1000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair table, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair threebody/table, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.487 | 5.487 | 5.487 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -5377.8719 0 -4484.5232 -320.10184 + 100 296.01121 -5418.505 0 -4537.0342 -223.39972 + 200 295.27654 -5430.3033 0 -4551.0202 794.29126 + 300 302.16526 -5445.8048 0 -4546.0083 -11.568299 + 400 308.59003 -5434.7181 0 -4515.7896 1.7337645 + 500 295.346 -5436.0896 0 -4556.5996 778.73307 + 600 293.14671 -5422.6082 0 -4549.6673 -148.64256 + 700 307.63238 -5465.187 0 -4549.1103 285.18556 + 800 313.16537 -5466.4124 0 -4533.8594 489.99301 + 900 303.42954 -5506.3208 0 -4602.7595 360.05608 + 1000 299.50926 -5446.8981 0 -4555.0107 993.95615 +Loop time of 5.16365 on 1 procs for 1000 steps with 1000 atoms + +Performance: 33.465 ns/day, 0.717 hours/ns, 193.661 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 | 4.8443 | 4.8443 | 4.8443 | 0.0 | 93.81 +Neigh | 0.27931 | 0.27931 | 0.27931 | 0.0 | 5.41 +Comm | 0.020302 | 0.020302 | 0.020302 | 0.0 | 0.39 +Output | 0.00022712 | 0.00022712 | 0.00022712 | 0.0 | 0.00 +Modify | 0.011944 | 0.011944 | 0.011944 | 0.0 | 0.23 +Other | | 0.007616 | | | 0.15 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5900 ave 5900 max 5900 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 191126 ave 191126 max 191126 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 382252 ave 382252 max 382252 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 382252 +Ave neighs/atom = 382.252 +Neighbor list builds = 27 +Dangerous builds = 0 + +Total wall time: 0:00:05 diff --git a/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.4 b/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.4 new file mode 100644 index 0000000000..70fb163b67 --- /dev/null +++ b/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.4 @@ -0,0 +1,89 @@ +LAMMPS (4 May 2022) + using 1 OpenMP thread(s) per MPI task +units real +atom_style atomic + +# data file with two atom types +read_data data.spce2 +Reading data file ... + orthogonal box = (0 0 0) to (31.0648 31.0648 31.0648) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms + read_data CPU = 0.004 seconds + +pair_style hybrid/overlay table linear 1200 threebody/table + +#pair coefficients +pair_coeff * * table table_CG_CG.txt VOTCA +pair_coeff * * threebody/table spce2.3b type1 type2 + +fix 1 all nvt temp 300.0 300.0 200.0 + +velocity all create 300 432567 dist uniform loop geom mom yes +timestep 2.0 + +thermo 100 +#dump 2 all custom 100 dump.spce2 id type x y z fx fy fz + +run 1000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair table, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair threebody/table, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.87 | 3.87 | 3.87 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -5377.8719 0 -4484.5232 -320.10184 + 100 296.01121 -5418.505 0 -4537.0342 -223.39972 + 200 295.27654 -5430.3033 0 -4551.0202 794.29126 + 300 302.16526 -5445.8048 0 -4546.0083 -11.568299 + 400 308.59003 -5434.7181 0 -4515.7896 1.7337642 + 500 295.346 -5436.0896 0 -4556.5996 778.73304 + 600 293.14648 -5422.6082 0 -4549.6681 -148.67071 + 700 307.6975 -5465.3018 0 -4549.0312 287.70203 + 800 314.09436 -5467.6073 0 -4532.2879 522.73489 + 900 300.85843 -5503.7551 0 -4607.85 491.78041 + 1000 302.84638 -5468.3331 0 -4566.5083 338.05123 +Loop time of 1.54853 on 4 procs for 1000 steps with 1000 atoms + +Performance: 111.590 ns/day, 0.215 hours/ns, 645.773 timesteps/s +96.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.2599 | 1.2908 | 1.3259 | 2.1 | 83.36 +Neigh | 0.069097 | 0.071294 | 0.075502 | 0.9 | 4.60 +Comm | 0.12731 | 0.15884 | 0.19196 | 5.7 | 10.26 +Output | 0.00017674 | 0.0026016 | 0.0098653 | 8.2 | 0.17 +Modify | 0.0093453 | 0.011999 | 0.014575 | 2.3 | 0.77 +Other | | 0.01295 | | | 0.84 + +Nlocal: 250 ave 257 max 240 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +Nghost: 3488.75 ave 3504 max 3478 min +Histogram: 1 1 0 0 0 1 0 0 0 1 +Neighs: 47828 ave 49169 max 45782 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +FullNghs: 95656 ave 98253 max 91425 min +Histogram: 1 0 0 0 0 1 0 0 1 1 + +Total # of neighbors = 382624 +Ave neighs/atom = 382.624 +Neighbor list builds = 27 +Dangerous builds = 0 + +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/manybody_table/log.1Jun22.spce_sw.g++.1 b/examples/PACKAGES/manybody_table/log.1Jun22.spce_sw.g++.1 new file mode 100644 index 0000000000..e64d577fae --- /dev/null +++ b/examples/PACKAGES/manybody_table/log.1Jun22.spce_sw.g++.1 @@ -0,0 +1,87 @@ +LAMMPS (4 May 2022) + using 1 OpenMP thread(s) per MPI task +units real +atom_style atomic + +read_data data.spce +Reading data file ... + orthogonal box = (0 0 0) to (31.0648 31.0648 31.0648) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1000 atoms + read_data CPU = 0.001 seconds + +pair_style hybrid/overlay table linear 1200 sw/angle/table + +pair_coeff 1 1 table table_CG_CG.txt VOTCA +pair_coeff * * sw/angle/table spce.sw type + +fix 1 all nvt temp 300.0 300.0 200.0 + +velocity all create 300 432567 dist uniform mom yes + +timestep 2.0 + +thermo 100 +#dump 2 all custom 10 spce_sw.dump id type x y z fx fy fz + +run 1000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair table, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair sw/angle/table, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.487 | 5.487 | 5.487 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -4572.9581 0 -3679.6093 -402.23914 + 100 286.5642 -4508.6912 0 -3655.352 -610.63256 + 200 291.59063 -4465.6368 0 -3597.3297 -218.54913 + 300 298.40301 -4460.64 0 -3572.0468 302.96636 + 400 305.99618 -4460.1128 0 -3548.9084 -68.022415 + 500 301.94233 -4440.337 0 -3541.2043 179.36975 + 600 308.95709 -4485.8412 0 -3565.8197 -95.917517 + 700 291.69015 -4489.4465 0 -3620.843 -56.044939 + 800 294.95653 -4496.904 0 -3618.5738 563.3456 + 900 295.50533 -4478.1134 0 -3598.149 89.234288 + 1000 308.63559 -4471.1612 0 -3552.0971 906.33706 +Loop time of 5.39753 on 1 procs for 1000 steps with 1000 atoms + +Performance: 32.015 ns/day, 0.750 hours/ns, 185.270 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.0954 | 5.0954 | 5.0954 | 0.0 | 94.40 +Neigh | 0.26201 | 0.26201 | 0.26201 | 0.0 | 4.85 +Comm | 0.020497 | 0.020497 | 0.020497 | 0.0 | 0.38 +Output | 0.00021869 | 0.00021869 | 0.00021869 | 0.0 | 0.00 +Modify | 0.011849 | 0.011849 | 0.011849 | 0.0 | 0.22 +Other | | 0.007577 | | | 0.14 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5862 ave 5862 max 5862 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 191262 ave 191262 max 191262 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 382524 ave 382524 max 382524 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 382524 +Ave neighs/atom = 382.524 +Neighbor list builds = 26 +Dangerous builds = 0 +Total wall time: 0:00:05 diff --git a/examples/PACKAGES/manybody_table/log.1Jun22.spce_sw.g++.4 b/examples/PACKAGES/manybody_table/log.1Jun22.spce_sw.g++.4 new file mode 100644 index 0000000000..b439b82286 --- /dev/null +++ b/examples/PACKAGES/manybody_table/log.1Jun22.spce_sw.g++.4 @@ -0,0 +1,87 @@ +LAMMPS (4 May 2022) + using 1 OpenMP thread(s) per MPI task +units real +atom_style atomic + +read_data data.spce +Reading data file ... + orthogonal box = (0 0 0) to (31.0648 31.0648 31.0648) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms + read_data CPU = 0.001 seconds + +pair_style hybrid/overlay table linear 1200 sw/angle/table + +pair_coeff 1 1 table table_CG_CG.txt VOTCA +pair_coeff * * sw/angle/table spce.sw type + +fix 1 all nvt temp 300.0 300.0 200.0 + +velocity all create 300 432567 dist uniform mom yes + +timestep 2.0 + +thermo 100 +#dump 2 all custom 10 spce_sw.dump id type x y z fx fy fz + +run 1000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair table, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair sw/angle/table, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.87 | 3.87 | 3.87 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -4572.9581 0 -3679.6093 -402.23914 + 100 286.5642 -4508.6912 0 -3655.352 -610.63256 + 200 291.59063 -4465.6368 0 -3597.3297 -218.54913 + 300 298.40301 -4460.64 0 -3572.0468 302.96636 + 400 305.99618 -4460.1128 0 -3548.9084 -68.022415 + 500 301.94233 -4440.337 0 -3541.2043 179.36975 + 600 308.95709 -4485.8412 0 -3565.8197 -95.917517 + 700 291.69015 -4489.4465 0 -3620.843 -56.044939 + 800 294.95653 -4496.904 0 -3618.5738 563.3456 + 900 295.50533 -4478.1134 0 -3598.149 89.234292 + 1000 308.63559 -4471.1612 0 -3552.0971 906.33708 +Loop time of 1.57073 on 4 procs for 1000 steps with 1000 atoms + +Performance: 110.012 ns/day, 0.218 hours/ns, 636.646 timesteps/s +97.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.3064 | 1.3347 | 1.3706 | 2.0 | 84.97 +Neigh | 0.065344 | 0.070299 | 0.07737 | 1.7 | 4.48 +Comm | 0.117 | 0.15297 | 0.18685 | 6.5 | 9.74 +Output | 0.00016937 | 0.00055648 | 0.0017097 | 0.0 | 0.04 +Modify | 0.0073414 | 0.0079027 | 0.0085343 | 0.6 | 0.50 +Other | | 0.0043 | | | 0.27 + +Nlocal: 250 ave 254 max 247 min +Histogram: 1 1 0 0 0 1 0 0 0 1 +Nghost: 3473.25 ave 3490 max 3450 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Neighs: 47815.5 ave 48520 max 47134 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +FullNghs: 95631 ave 97203 max 94083 min +Histogram: 1 0 1 0 0 0 1 0 0 1 + +Total # of neighbors = 382524 +Ave neighs/atom = 382.524 +Neighbor list builds = 26 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/manybody_table/spce.3b b/examples/PACKAGES/manybody_table/spce.3b new file mode 100644 index 0000000000..07f9b66433 --- /dev/null +++ b/examples/PACKAGES/manybody_table/spce.3b @@ -0,0 +1,8 @@ +type +type +type +3.7 # cut in Ang +1-1-1.table +ENTRY1 +linear +12 diff --git a/examples/PACKAGES/manybody_table/spce.sw b/examples/PACKAGES/manybody_table/spce.sw new file mode 100644 index 0000000000..8b0fd70f61 --- /dev/null +++ b/examples/PACKAGES/manybody_table/spce.sw @@ -0,0 +1,18 @@ +type +type +type +1 #epsilon in kcal/mol +1 #sigma in dimensionless +3.7 # a in Ang +1.0 #lambda dimensionless +0.8 #gamma in Ang +0.0 #costheta0 dimensionless +0 #two body part A=0 +0 #two body part B=0 +0 #two body part p=0 +0 #two body part q=0 +0.0 # use the standard Stillinger-Weber cutoff +table_CG_CG_CG.txt +VOTCA +linear +1001 diff --git a/examples/PACKAGES/manybody_table/spce2.3b b/examples/PACKAGES/manybody_table/spce2.3b new file mode 100644 index 0000000000..52fcd1e5e9 --- /dev/null +++ b/examples/PACKAGES/manybody_table/spce2.3b @@ -0,0 +1,71 @@ +type1 +type1 +type1 +3.7 # cut in Ang +1-1-1.table +ENTRY1 +linear +12 +type1 +type1 +type2 +3.7 # cut in Ang +1-1-2.table +ENTRY1 +linear +12 +type1 +type2 +type1 +3.7 # cut in Ang +1-1-2.table +ENTRY1 +linear +12 +type1 +type2 +type2 +3.7 # cut in Ang +1-1-1.table +ENTRY1 +linear +12 +type2 +type1 +type1 +3.7 # cut in Ang +1-1-1.table +ENTRY1 +linear +12 +type2 +type1 +type2 +3.7 # cut in Ang +1-1-2.table +ENTRY1 +linear +12 +type2 +type2 +type1 +3.7 # cut in Ang +1-1-2.table +ENTRY1 +linear +12 +type2 +type2 +type2 +3.7 # cut in Ang +1-1-1.table +ENTRY1 +linear +12 + + + + + + + diff --git a/examples/PACKAGES/manybody_table/table_CG_CG.txt b/examples/PACKAGES/manybody_table/table_CG_CG.txt new file mode 100644 index 0000000000..f4ccdd4b4e --- /dev/null +++ b/examples/PACKAGES/manybody_table/table_CG_CG.txt @@ -0,0 +1,1203 @@ +VOTCA +N 1200 R 0.010000 12.000000 + +1 1.0000000000e-02 1.5390100510e+15 2.1517330910e+16 +2 2.0000000000e-02 1.3370836560e+15 1.8774943350e+16 +3 3.0000000000e-02 1.1616510900e+15 1.6231560530e+16 +4 4.0000000000e-02 1.0092362200e+15 1.4101892510e+16 +5 5.0000000000e-02 8.7681900090e+14 1.2251648380e+16 +6 6.0000000000e-02 7.6177563290e+14 1.0644166230e+16 +7 7.0000000000e-02 6.6182657340e+14 9.2475943770e+15 +8 8.0000000000e-02 5.7499136800e+14 8.0342602660e+15 +9 9.0000000000e-02 4.9954940840e+14 6.9801221150e+15 +10 1.0000000000e-01 4.3400583970e+14 6.0642925570e+15 +11 1.1000000000e-01 3.7706193970e+14 5.2686247630e+15 +12 1.2000000000e-01 3.2758938550e+14 4.5773528620e+15 +13 1.3000000000e-01 2.8460789650e+14 3.9767795520e+15 +14 1.4000000000e-01 2.4726581000e+14 3.4550046890e+15 +15 1.5000000000e-01 2.1482320610e+14 3.0016894950e+15 +16 1.6000000000e-01 1.8663724620e+14 2.6078516910e+15 +17 1.7000000000e-01 1.6214943590e+14 2.2656875260e+15 +18 1.8000000000e-01 1.4087455790e+14 1.9684171380e+15 +19 1.9000000000e-01 1.2239105840e+14 1.7101502250e+15 +20 2.0000000000e-01 1.0633269330e+14 1.4857693190e+15 +21 2.1000000000e-01 9.2381272170e+13 1.2908283940e+15 +22 2.2000000000e-01 8.0260352480e+13 1.1214647680e+15 +23 2.3000000000e-01 6.9729762630e+13 9.7432255940e+14 +24 2.4000000000e-01 6.0580842800e+13 8.4648620020e+14 +25 2.5000000000e-01 5.2632310450e+13 7.3542265870e+14 +26 2.6000000000e-01 4.5726668290e+13 6.3893125110e+14 +27 2.7000000000e-01 3.9727083510e+13 5.5510003510e+14 +28 2.8000000000e-01 3.4514676520e+13 4.8226792540e+14 +29 2.9000000000e-01 2.9986165360e+13 4.1899178020e+14 +30 3.0000000000e-01 2.6051819210e+13 3.6401780550e+14 +31 3.1000000000e-01 2.2633680440e+13 3.1625671190e+14 +32 3.2000000000e-01 1.9664019850e+13 2.7476213060e+14 +33 3.3000000000e-01 1.7083994700e+13 2.3871186160e+14 +34 3.4000000000e-01 1.4842482730e+13 2.0739158160e+14 +35 3.5000000000e-01 1.2895069180e+13 1.8018069090e+14 +36 3.6000000000e-01 1.1203166760e+13 1.5654001530e+14 +37 3.7000000000e-01 9.7332510350e+12 1.3600112350e+14 +38 3.8000000000e-01 8.4561961580e+12 1.1815704470e+14 +39 3.9000000000e-01 7.3466977490e+12 1.0265420510e+14 +40 4.0000000000e-01 6.3827714970e+12 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1.79640e+02 1.9143619e+00 -1.1579483e-02 +1000 1.79820e+02 1.9164432e+00 -1.1540710e-02 +1001 1.80000e+02 1.9185186e+00 -1.1513008e-02 diff --git a/examples/PACKAGES/pace/in.pace.product b/examples/PACKAGES/pace/in.pace.product index 11049ee922..1ba1fc679c 100644 --- a/examples/PACKAGES/pace/in.pace.product +++ b/examples/PACKAGES/pace/in.pace.product @@ -1,36 +1,36 @@ -# simple test of fcc Cu with ACE product +# simple test of fcc Cu with ACE product -units metal -atom_style atomic +units metal +atom_style atomic -neighbor 0.3 bin -neigh_modify every 2 delay 10 check yes +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 +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 +mass 1 26.98 -pair_style pace product +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 +fix 1 all nve -compute eatom all pe/atom -compute energy all reduce sum c_eatom -variable delenergy equal c_energy-pe +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 +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 10 thermo_style custom step temp epair etotal press v_delenergy v_delpress -run 100 +run 100 diff --git a/examples/PACKAGES/pace/in.pace.recursive b/examples/PACKAGES/pace/in.pace.recursive index 1d6d9116f0..5d299fb033 100644 --- a/examples/PACKAGES/pace/in.pace.recursive +++ b/examples/PACKAGES/pace/in.pace.recursive @@ -1,36 +1,36 @@ -# simple test of fcc Cu with ACE recursive +# simple test of fcc Cu with ACE recursive -units metal -atom_style atomic +units metal +atom_style atomic -neighbor 0.3 bin -neigh_modify every 2 delay 10 check yes +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 +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 +mass 1 26.98 -pair_style pace recursive +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 +fix 1 all nve -compute eatom all pe/atom -compute energy all reduce sum c_eatom -variable delenergy equal c_energy-pe +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 +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 10 thermo_style custom step temp epair etotal press v_delenergy v_delpress -run 100 +run 100 diff --git a/examples/PACKAGES/pace/plugin/CMakeLists.txt b/examples/PACKAGES/pace/plugin/CMakeLists.txt new file mode 100644 index 0000000000..f4068a03c9 --- /dev/null +++ b/examples/PACKAGES/pace/plugin/CMakeLists.txt @@ -0,0 +1,36 @@ +########################################## +# CMake build system for plugin examples. +# The is meant to be used as a template for plugins that are +# distributed independent from the LAMMPS package. +########################################## + +cmake_minimum_required(VERSION 3.10) + +project(paceplugin VERSION 1.0 LANGUAGES CXX) + +set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}) +include(CheckIncludeFileCXX) +include(LAMMPSInterfacePlugin) +include(ML-PACE) + +########################## +# building the plugins + +add_library(paceplugin MODULE paceplugin.cpp ${LAMMPS_SOURCE_DIR}/ML-PACE/pair_pace.cpp) +target_link_libraries(paceplugin PRIVATE pace) +target_link_libraries(paceplugin PRIVATE lammps) +target_include_directories(paceplugin PRIVATE ${LAMMPS_SOURCE_DIR}/ML-PACE) +set_target_properties(paceplugin PROPERTIES PREFIX "" SUFFIX ".so") + +# MacOS seems to need this +if(CMAKE_SYSTEM_NAME STREQUAL Darwin) + set_target_properties(paceplugin PROPERTIES LINK_FLAGS "-Wl,-undefined,dynamic_lookup") +elseif(CMAKE_SYSTEM_NAME STREQUAL "Windows") +# tell CMake to export all symbols to a .dll on Windows with special case for MinGW cross-compilers + set_target_properties(paceplugin PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE) + if(CMAKE_CROSSCOMPILING) + set_target_properties(paceplugin PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols") + endif() +else() + set_target_properties(paceplugin PROPERTIES LINK_FLAGS "-rdynamic") +endif() diff --git a/examples/PACKAGES/pace/plugin/LAMMPSInterfacePlugin.cmake b/examples/PACKAGES/pace/plugin/LAMMPSInterfacePlugin.cmake new file mode 120000 index 0000000000..2ac6d20a54 --- /dev/null +++ b/examples/PACKAGES/pace/plugin/LAMMPSInterfacePlugin.cmake @@ -0,0 +1 @@ +../../../../cmake/Modules/LAMMPSInterfacePlugin.cmake \ No newline at end of file diff --git a/examples/PACKAGES/pace/plugin/ML-PACE.cmake b/examples/PACKAGES/pace/plugin/ML-PACE.cmake new file mode 120000 index 0000000000..3990c0d334 --- /dev/null +++ b/examples/PACKAGES/pace/plugin/ML-PACE.cmake @@ -0,0 +1 @@ +../../../../cmake/Modules/Packages/ML-PACE.cmake \ No newline at end of file diff --git a/examples/PACKAGES/pace/plugin/README.txt b/examples/PACKAGES/pace/plugin/README.txt new file mode 100644 index 0000000000..85490c3f6c --- /dev/null +++ b/examples/PACKAGES/pace/plugin/README.txt @@ -0,0 +1,2 @@ +This folder contains a loader and support files to build the ML-PACE package as plugin. +For more information please see: https://docs.lammps.org/Developer_plugins.html diff --git a/examples/PACKAGES/pace/plugin/lammps-text-logo-wide.bmp b/examples/PACKAGES/pace/plugin/lammps-text-logo-wide.bmp new file mode 100644 index 0000000000..b9ec4c35f2 Binary files /dev/null and b/examples/PACKAGES/pace/plugin/lammps-text-logo-wide.bmp differ diff --git a/examples/PACKAGES/pace/plugin/lammps.ico b/examples/PACKAGES/pace/plugin/lammps.ico new file mode 100644 index 0000000000..cce156bf79 Binary files /dev/null and b/examples/PACKAGES/pace/plugin/lammps.ico differ diff --git a/examples/PACKAGES/pace/plugin/paceplugin.cpp b/examples/PACKAGES/pace/plugin/paceplugin.cpp new file mode 100644 index 0000000000..adf1c168f9 --- /dev/null +++ b/examples/PACKAGES/pace/plugin/paceplugin.cpp @@ -0,0 +1,28 @@ + +#include "lammpsplugin.h" +#include "version.h" + +#include "pair_pace.h" + +using namespace LAMMPS_NS; + +static Pair *pair_pace_creator(LAMMPS *lmp) +{ + return new PairPACE(lmp); +} + +extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) +{ + lammpsplugin_t plugin; + lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc; + + // register pace pair style + plugin.version = LAMMPS_VERSION; + plugin.style = "pair"; + plugin.name = "pace"; + plugin.info = "PACE plugin pair style v1.0"; + plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; + plugin.creator.v1 = (lammpsplugin_factory1 *) &pair_pace_creator; + plugin.handle = handle; + (*register_plugin)(&plugin, lmp); +} diff --git a/examples/PACKAGES/pace/plugin/paceplugin.nsis b/examples/PACKAGES/pace/plugin/paceplugin.nsis new file mode 100644 index 0000000000..de8d1d8478 --- /dev/null +++ b/examples/PACKAGES/pace/plugin/paceplugin.nsis @@ -0,0 +1,157 @@ +#!Nsis Installer Command Script +# +# The following external defines are recognized: +# ${VERSION} = YYYYMMDD + +!include "MUI2.nsh" +!include "FileFunc.nsh" + +!define MUI_ICON "lammps.ico" +!define MUI_UNICON "lammps.ico" +!define MUI_HEADERIMAGE +!define MUI_HEADERIMAGE_BITMAP "lammps-text-logo-wide.bmp" +!define MUI_HEADERIMAGE_RIGHT + +Unicode true +XPStyle on + +!include "LogicLib.nsh" +!addplugindir "envvar/Plugins/x86-unicode" +!include "x64.nsh" + +RequestExecutionLevel user + +!macro VerifyUserIsAdmin +UserInfo::GetAccountType +pop $0 +${If} $0 != "admin" + messageBox mb_iconstop "Administrator rights required!" + setErrorLevel 740 ;ERROR_ELEVATION_REQUIRED + quit +${EndIf} +!macroend + +!define PACEPLUGIN "LAMMPS ML-PACE Plugin ${VERSION}" +OutFile "LAMMPS-ML-PACE-plugin-${VERSION}.exe" + +Name "${PACEPLUGIN}" +InstallDir "$LOCALAPPDATA\${PACEPLUGIN}" + +ShowInstDetails show +ShowUninstDetails show +SetCompressor lzma + +!define MUI_ABORTWARNING + +!insertmacro MUI_PAGE_DIRECTORY +!insertmacro MUI_PAGE_INSTFILES + +!insertmacro MUI_UNPAGE_CONFIRM +!insertmacro MUI_UNPAGE_INSTFILES + +!insertmacro MUI_LANGUAGE "English" + +function .onInit + # Determine if LAMMPS was already installed and check whether it was in 32-bit + # or 64-bit. Then look up path to uninstaller and offer to uninstall or quit + SetRegView 32 + ReadRegDWORD $0 HKCU "Software\LAMMPS-ML-PACE" "Bits" + SetRegView LastUsed + ${If} $0 == "32" + SetRegView 32 + ${ElseIf} $0 == "64" + SetRegView 64 + ${Else} + SetRegView 64 + ${EndIf} + ClearErrors + ReadRegStr $R0 HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-ML-PACE" "UninstallString" + SetRegView LastUsed + ${If} ${Errors} + DetailPrint "LAMMPS ML-PACE plugin not (yet) installed" + ${Else} + MessageBox MB_YESNO "LAMMPS ML-PACE plugin ($0 bit) is already installed. Uninstall existing version?" /SD IDYES IDNO Quit + Pop $R1 + StrCmp $R1 2 Quit +1 + Exec $R0 + Quit: + Quit + ${EndIf} + setShellVarContext all +functionEnd + +Section "${PACEPLUGIN}" SecPaceplugin + SectionIn RO + # Write LAMMPS installation bitness marker. Always use 32-bit registry view + SetRegView 32 + IntFmt $0 "0x%08X" 64 + WriteRegDWORD HKCU "Software\LAMMPS-ML-PACE" "Bits" $0 + + # Switch to "native" registry view + SetRegView 64 + SetShellVarContext current + + SetOutPath "$INSTDIR" + File lammps.ico + File paceplugin.so + + # Register Application and its uninstaller + WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-ML-PACE" \ + "DisplayName" "${PACEPLUGIN}" + WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-ML-PACE" \ + "Publisher" "The LAMMPS and PACE Developers" + WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-ML-PACE" \ + "URLInfoAbout" "lammps.org" + WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-ML-PACE" \ + "DisplayIcon" "$INSTDIR\lammps.ico" + WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-ML-PACE" \ + "DisplayVersion" "${VERSION}" + WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-ML-PACE" \ + "InstallLocation" "$INSTDIR" + WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-ML-PACE" \ + "UninstallString" "$\"$INSTDIR\uninstall.exe$\"" + WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-ML-PACE" \ + "QuietUninstallString" "$\"$INSTDIR\uninstall.exe$\" /S" + + ${GetSize} "$INSTDIR" "/S=0K" $0 $1 $2 + IntFmt $0 "0x%08X" $0 + WriteRegDWORD HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-ML-PACE" \ + "EstimatedSize" "$0" + + # update path variables + EnVar::SetHKCU + # add to LAMMPS plugin search path + EnVar::AddValue "LAMMPS_PLUGIN_PATH" "$INSTDIR" + + WriteUninstaller "$INSTDIR\Uninstall.exe" +SectionEnd + +function un.onInit + SetShellVarContext current +functionEnd + +Section "Uninstall" + # remove LAMMPS bitness/installation indicator always in 32-bit registry view + SetRegView 32 + DeleteRegKey HKCU "Software\LAMMPS-ML-PACE" + + # unregister extension, and uninstall info + SetRegView 64 + SetShellVarContext current + # unregister installation + DeleteRegKey HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-ML-PACE" + + # update path variables + EnVar::SetHKCU + # remove entry from LAMMPS plugin search path + EnVar::DeleteValue "LAMMPS_PLUGIN_PATH" "$INSTDIR" + + Delete /REBOOTOK "$INSTDIR\paceplugin.so" + Delete /REBOOTOK "$INSTDIR\Uninstall.exe" + Delete /REBOOTOK "$INSTDIR\lammps.ico" + RMDir /REBOOTOK "$INSTDIR" +SectionEnd + +# Local Variables: +# mode: sh +# End: diff --git a/examples/amoeba/in.ubiquitin b/examples/amoeba/in.ubiquitin index ccbcdec421..a7f540cc52 100644 --- a/examples/amoeba/in.ubiquitin +++ b/examples/amoeba/in.ubiquitin @@ -52,5 +52,5 @@ dump_modify 1 sort id fix 1 all nve -thermo 10 -run 100 +thermo 1 +run 5 diff --git a/examples/amoeba/in.water_box.hippo b/examples/amoeba/in.water_box.hippo index ec1cc1cc78..03d8118eb4 100644 --- a/examples/amoeba/in.water_box.hippo +++ b/examples/amoeba/in.water_box.hippo @@ -43,5 +43,5 @@ dump_modify 1 sort id fix 1 all nve -thermo 10 -run 100 +thermo 1 +run 5 diff --git a/examples/amoeba/in.water_dimer.amoeba b/examples/amoeba/in.water_dimer.amoeba index 6e388e9951..47a2edc193 100644 --- a/examples/amoeba/in.water_dimer.amoeba +++ b/examples/amoeba/in.water_dimer.amoeba @@ -43,5 +43,5 @@ dump_modify 1 sort id fix 1 all nve -thermo 10 -run 100 +thermo 1 +run 5 diff --git a/examples/amoeba/in.water_dimer.hippo b/examples/amoeba/in.water_dimer.hippo index 15a7327d5b..21d13512e6 100644 --- a/examples/amoeba/in.water_dimer.hippo +++ b/examples/amoeba/in.water_dimer.hippo @@ -43,5 +43,5 @@ dump_modify 1 sort id fix 1 all nve -thermo 10 -run 100 +thermo 1 +run 5 diff --git a/examples/amoeba/in.water_hexamer.amoeba b/examples/amoeba/in.water_hexamer.amoeba index b96ec3974a..24211065c9 100644 --- a/examples/amoeba/in.water_hexamer.amoeba +++ b/examples/amoeba/in.water_hexamer.amoeba @@ -43,5 +43,5 @@ dump_modify 1 sort id fix 1 all nve -thermo 10 -run 100 +thermo 1 +run 5 diff --git a/examples/amoeba/in.water_hexamer.hippo b/examples/amoeba/in.water_hexamer.hippo index 6e4b40ffa5..c56c938ce8 100644 --- a/examples/amoeba/in.water_hexamer.hippo +++ b/examples/amoeba/in.water_hexamer.hippo @@ -43,5 +43,5 @@ dump_modify 1 sort id fix 1 all nve -thermo 10 -run 100 +thermo 1 +run 5 diff --git a/examples/kim/plugin/CMakeLists.txt b/examples/kim/plugin/CMakeLists.txt index f4cb5f598d..78d117469d 100644 --- a/examples/kim/plugin/CMakeLists.txt +++ b/examples/kim/plugin/CMakeLists.txt @@ -6,46 +6,11 @@ cmake_minimum_required(VERSION 3.10) -# enforce out-of-source build -if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR}) - message(FATAL_ERROR "In-source builds are not allowed. You must create and use a build directory. " - "Please remove CMakeCache.txt and CMakeFiles first.") -endif() - project(kimplugin VERSION 1.0 LANGUAGES CXX) -set(LAMMPS_SOURCE_DIR "" CACHE PATH "Location of LAMMPS sources folder") -if(NOT LAMMPS_SOURCE_DIR) - message(FATAL_ERROR "Must set LAMMPS_SOURCE_DIR") -endif() - -# by default, install into $HOME/.local (not /usr/local), -# so that no root access (and sudo) is needed -if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT) - set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE) -endif() - -# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro -# and prints lots of pointless warnings about "unsafe" functions -if(MSVC) - add_compile_options(/Zc:__cplusplus) - add_compile_options(/wd4244) - add_compile_options(/wd4267) - add_compile_definitions(_CRT_SECURE_NO_WARNINGS) -endif() - -# C++11 is required -set(CMAKE_CXX_STANDARD 11) -set(CMAKE_CXX_STANDARD_REQUIRED ON) - -# Need -restrict with Intel compilers -if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel") - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict") -endif() - set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}) include(CheckIncludeFileCXX) -include(LAMMPSInterfaceCXX) +include(LAMMPSInterfacePlugin) ########################## # building the plugins @@ -90,9 +55,9 @@ if(CMAKE_SYSTEM_NAME STREQUAL Darwin) set_target_properties(kimplugin PROPERTIES LINK_FLAGS "-Wl,-undefined,dynamic_lookup") elseif(CMAKE_SYSTEM_NAME STREQUAL "Windows") # tell CMake to export all symbols to a .dll on Windows with special case for MinGW cross-compilers - set_target_properties(kimplugin.so PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE) + set_target_properties(kimplugin PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE) if(CMAKE_CROSSCOMPILING) - set_target_properties(kimplugin PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols") + set_target_properties(kimplugin PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols") endif() else() set_target_properties(kimplugin PROPERTIES LINK_FLAGS "-rdynamic") diff --git a/examples/kim/plugin/LAMMPSInterfaceCXX.cmake b/examples/kim/plugin/LAMMPSInterfaceCXX.cmake deleted file mode 100644 index dfbd77e28a..0000000000 --- a/examples/kim/plugin/LAMMPSInterfaceCXX.cmake +++ /dev/null @@ -1,88 +0,0 @@ -# Cmake script code to define the LAMMPS C++ interface -# settings required for building LAMMPS plugins - -################################################################################ -# helper function -function(validate_option name values) - string(TOLOWER ${${name}} needle_lower) - string(TOUPPER ${${name}} needle_upper) - list(FIND ${values} ${needle_lower} IDX_LOWER) - list(FIND ${values} ${needle_upper} IDX_UPPER) - if(${IDX_LOWER} LESS 0 AND ${IDX_UPPER} LESS 0) - list_to_bulletpoints(POSSIBLE_VALUE_LIST ${${values}}) - message(FATAL_ERROR "\n########################################################################\n" - "Invalid value '${${name}}' for option ${name}\n" - "\n" - "Possible values are:\n" - "${POSSIBLE_VALUE_LIST}" - "########################################################################") - endif() -endfunction(validate_option) - -################################################################################# -# LAMMPS C++ interface. We only need the header related parts. -add_library(lammps INTERFACE) -target_include_directories(lammps INTERFACE ${LAMMPS_SOURCE_DIR}) -if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING) - target_link_libraries(lammps INTERFACE ${CMAKE_BINARY_DIR}/../liblammps.dll.a) -endif() -################################################################################ -# MPI configuration -if(NOT CMAKE_CROSSCOMPILING) - set(MPI_CXX_SKIP_MPICXX TRUE) - find_package(MPI QUIET) - option(BUILD_MPI "Build MPI version" ${MPI_FOUND}) -else() - option(BUILD_MPI "Build MPI version" OFF) -endif() - -if(BUILD_MPI) - find_package(MPI REQUIRED) - option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF) - if(LAMMPS_LONGLONG_TO_LONG) - target_compile_definitions(lammps INTERFACE -DLAMMPS_LONGLONG_TO_LONG) - endif() - target_link_libraries(lammps INTERFACE MPI::MPI_CXX) -else() - target_include_directories(lammps INTERFACE "${LAMMPS_SOURCE_DIR}/STUBS") -endif() - -set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)") -set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall) -set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES}) -validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES) -string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES) -target_compile_definitions(lammps INTERFACE -DLAMMPS_${LAMMPS_SIZES}) - -################################################################################ -# detect if we may enable OpenMP support by default -set(BUILD_OMP_DEFAULT OFF) -find_package(OpenMP QUIET) -if(OpenMP_FOUND) - check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE) - if(HAVE_OMP_H_INCLUDE) - set(BUILD_OMP_DEFAULT ON) - endif() -endif() - -option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT}) - -if(BUILD_OMP) - find_package(OpenMP REQUIRED) - check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE) - if(NOT HAVE_OMP_H_INCLUDE) - message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support") - endif() - - if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR - (CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR - ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR - ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0))) - # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts. - # Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe. - target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=4) - else() - target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=3) - endif() - target_link_libraries(lammps INTERFACE OpenMP::OpenMP_CXX) -endif() diff --git a/examples/kim/plugin/LAMMPSInterfacePlugin.cmake b/examples/kim/plugin/LAMMPSInterfacePlugin.cmake new file mode 120000 index 0000000000..2b78a6ebcc --- /dev/null +++ b/examples/kim/plugin/LAMMPSInterfacePlugin.cmake @@ -0,0 +1 @@ +../../../cmake/Modules/LAMMPSInterfacePlugin.cmake \ No newline at end of file diff --git a/examples/kim/plugin/README.txt b/examples/kim/plugin/README.txt new file mode 100644 index 0000000000..eecc6cc7b4 --- /dev/null +++ b/examples/kim/plugin/README.txt @@ -0,0 +1,2 @@ +This folder contains a loader and support files to build the KIM package as plugin. +For more information please see: https://docs.lammps.org/Developer_plugins.html diff --git a/examples/mdi/aimd_driver.py b/examples/mdi/aimd_driver.py index 2d8fe10c1a..ee493ea31e 100644 --- a/examples/mdi/aimd_driver.py +++ b/examples/mdi/aimd_driver.py @@ -26,7 +26,7 @@ # -nsteps 5 # number of timesteps, default = 5 -import sys,math,random +import sys import mdi import numpy as np from mpi4py import MPI @@ -42,10 +42,9 @@ def error(txt=None): def perform_aimd(world,mm_comm,qm_comm): me = world.Get_rank() - nprocs = world.Get_size() # receive number of atoms from the MM engine - + mdi.MDI_Send_command(" $@ + @for src in $^ ; do \ + obj=`basename $$src .cpp`.o ; \ + $(CXX) $(CXXFLAGS) -MM $(LEPTON_INCFLAGS) \ + -MT '$$(COLVARS_OBJ_DIR)'$$obj $$src >> $@ ; \ + done + +include Makefile.lepton.deps diff --git a/lib/colvars/Makefile.lepton.deps b/lib/colvars/Makefile.lepton.deps index 93c3912384..4546339de6 100644 --- a/lib/colvars/Makefile.lepton.deps +++ b/lib/colvars/Makefile.lepton.deps @@ -1,36 +1,46 @@ -lepton/src/CompiledExpression.o: lepton/src/CompiledExpression.cpp \ + +$(COLVARS_OBJ_DIR)CompiledExpression.o: lepton/src/CompiledExpression.cpp \ lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ lepton/include/lepton/windowsIncludes.h \ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \ lepton/include/lepton/Exception.h \ lepton/include/lepton/ParsedExpression.h -lepton/src/ExpressionProgram.o: lepton/src/ExpressionProgram.cpp \ +$(COLVARS_OBJ_DIR)CompiledVectorExpression.o: \ + lepton/src/CompiledVectorExpression.cpp \ + lepton/include/lepton/CompiledVectorExpression.h \ + lepton/include/lepton/ExpressionTreeNode.h \ + lepton/include/lepton/windowsIncludes.h \ + lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \ + lepton/include/lepton/Exception.h \ + lepton/include/lepton/ParsedExpression.h +$(COLVARS_OBJ_DIR)ExpressionProgram.o: lepton/src/ExpressionProgram.cpp \ lepton/include/lepton/ExpressionProgram.h \ lepton/include/lepton/ExpressionTreeNode.h \ lepton/include/lepton/windowsIncludes.h \ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \ lepton/include/lepton/Exception.h \ lepton/include/lepton/ParsedExpression.h -lepton/src/ExpressionTreeNode.o: lepton/src/ExpressionTreeNode.cpp \ +$(COLVARS_OBJ_DIR)ExpressionTreeNode.o: lepton/src/ExpressionTreeNode.cpp \ lepton/include/lepton/ExpressionTreeNode.h \ lepton/include/lepton/windowsIncludes.h \ lepton/include/lepton/Exception.h lepton/include/lepton/Operation.h \ lepton/include/lepton/CustomFunction.h lepton/include/lepton/Exception.h -lepton/src/Operation.o: lepton/src/Operation.cpp \ +$(COLVARS_OBJ_DIR)Operation.o: lepton/src/Operation.cpp \ lepton/include/lepton/Operation.h \ lepton/include/lepton/windowsIncludes.h \ lepton/include/lepton/CustomFunction.h lepton/include/lepton/Exception.h \ lepton/include/lepton/ExpressionTreeNode.h lepton/src/MSVC_erfc.h -lepton/src/ParsedExpression.o: lepton/src/ParsedExpression.cpp \ +$(COLVARS_OBJ_DIR)ParsedExpression.o: lepton/src/ParsedExpression.cpp \ lepton/include/lepton/ParsedExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ lepton/include/lepton/windowsIncludes.h \ lepton/include/lepton/CompiledExpression.h \ + lepton/include/lepton/CompiledVectorExpression.h \ lepton/include/lepton/ExpressionProgram.h \ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \ lepton/include/lepton/Exception.h -lepton/src/Parser.o: lepton/src/Parser.cpp \ +$(COLVARS_OBJ_DIR)Parser.o: lepton/src/Parser.cpp \ lepton/include/lepton/Parser.h lepton/include/lepton/windowsIncludes.h \ lepton/include/lepton/CustomFunction.h lepton/include/lepton/Exception.h \ lepton/include/lepton/ExpressionTreeNode.h \ diff --git a/lib/colvars/colvargrid.h b/lib/colvars/colvargrid.h index e0b2ec7f03..f34c5eccab 100644 --- a/lib/colvars/colvargrid.h +++ b/lib/colvars/colvargrid.h @@ -1275,7 +1275,7 @@ public: inline cvm::real log_gradient_finite_diff(const std::vector &ix0, int n = 0) { - int A0, A1, A2; + cvm::real A0, A1, A2; std::vector ix = ix0; // TODO this can be rewritten more concisely with wrap_edge() @@ -1288,7 +1288,7 @@ public: if (A0 * A1 == 0) { return 0.; // can't handle empty bins } else { - return (cvm::logn((cvm::real)A1) - cvm::logn((cvm::real)A0)) + return (cvm::logn(A1) - cvm::logn(A0)) / (widths[n] * 2.); } } else if (ix[n] > 0 && ix[n] < nx[n]-1) { // not an edge @@ -1300,7 +1300,7 @@ public: if (A0 * A1 == 0) { return 0.; // can't handle empty bins } else { - return (cvm::logn((cvm::real)A1) - cvm::logn((cvm::real)A0)) + return (cvm::logn(A1) - cvm::logn(A0)) / (widths[n] * 2.); } } else { @@ -1313,8 +1313,8 @@ public: if (A0 * A1 * A2 == 0) { return 0.; // can't handle empty bins } else { - return (-1.5 * cvm::logn((cvm::real)A0) + 2. * cvm::logn((cvm::real)A1) - - 0.5 * cvm::logn((cvm::real)A2)) * increment / widths[n]; + return (-1.5 * cvm::logn(A0) + 2. * cvm::logn(A1) + - 0.5 * cvm::logn(A2)) * increment / widths[n]; } } } @@ -1324,7 +1324,7 @@ public: inline cvm::real gradient_finite_diff(const std::vector &ix0, int n = 0) { - int A0, A1, A2; + cvm::real A0, A1, A2; std::vector ix = ix0; // FIXME this can be rewritten more concisely with wrap_edge() @@ -1337,7 +1337,7 @@ public: if (A0 * A1 == 0) { return 0.; // can't handle empty bins } else { - return cvm::real(A1 - A0) / (widths[n] * 2.); + return (A1 - A0) / (widths[n] * 2.); } } else if (ix[n] > 0 && ix[n] < nx[n]-1) { // not an edge ix[n]--; @@ -1348,7 +1348,7 @@ public: if (A0 * A1 == 0) { return 0.; // can't handle empty bins } else { - return cvm::real(A1 - A0) / (widths[n] * 2.); + return (A1 - A0) / (widths[n] * 2.); } } else { // edge: use 2nd order derivative @@ -1357,8 +1357,8 @@ public: A0 = value(ix); ix[n] += increment; A1 = value(ix); ix[n] += increment; A2 = value(ix); - return (-1.5 * cvm::real(A0) + 2. * cvm::real(A1) - - 0.5 * cvm::real(A2)) * increment / widths[n]; + return (-1.5 * A0 + 2. * A1 + - 0.5 * A2) * increment / widths[n]; } } }; diff --git a/lib/colvars/colvarproxy_tcl.cpp b/lib/colvars/colvarproxy_tcl.cpp index 33bdc9dc38..700492f0e7 100644 --- a/lib/colvars/colvarproxy_tcl.cpp +++ b/lib/colvars/colvarproxy_tcl.cpp @@ -22,9 +22,7 @@ colvarproxy_tcl::colvarproxy_tcl() { -#ifdef COLVARS_TCL tcl_interp_ = NULL; -#endif } diff --git a/lib/colvars/colvars_version.h b/lib/colvars/colvars_version.h index 2a1d449ab5..d2a48f8af7 100644 --- a/lib/colvars/colvars_version.h +++ b/lib/colvars/colvars_version.h @@ -1,3 +1,3 @@ #ifndef COLVARS_VERSION -#define COLVARS_VERSION "2022-05-09" +#define COLVARS_VERSION "2022-05-24" #endif diff --git a/lib/colvars/lepton/include/lepton/CompiledExpression.h b/lib/colvars/lepton/include/lepton/CompiledExpression.h index c7e393e93b..82d66d5c6a 100644 --- a/lib/colvars/lepton/include/lepton/CompiledExpression.h +++ b/lib/colvars/lepton/include/lepton/CompiledExpression.h @@ -9,7 +9,7 @@ * Biological Structures at Stanford, funded under the NIH Roadmap for * * Medical Research, grant U54 GM072970. See https://simtk.org. * * * - * Portions copyright (c) 2013-2019 Stanford University and the Authors. * + * Portions copyright (c) 2013-2022 Stanford University and the Authors. * * Authors: Peter Eastman * * Contributors: * * * @@ -40,7 +40,11 @@ #include #include #ifdef LEPTON_USE_JIT - #include "asmjit.h" +#if defined(__ARM__) || defined(__ARM64__) +#include "asmjit/a64.h" +#else +#include "asmjit/x86.h" +#endif #endif namespace Lepton { @@ -101,9 +105,15 @@ private: std::map dummyVariables; double (*jitCode)(); #ifdef LEPTON_USE_JIT + void findPowerGroups(std::vector >& groups, std::vector >& groupPowers, std::vector& stepGroup); void generateJitCode(); - void generateSingleArgCall(asmjit::X86Compiler& c, asmjit::X86Xmm& dest, asmjit::X86Xmm& arg, double (*function)(double)); - void generateTwoArgCall(asmjit::X86Compiler& c, asmjit::X86Xmm& dest, asmjit::X86Xmm& arg1, asmjit::X86Xmm& arg2, double (*function)(double, double)); +#if defined(__ARM__) || defined(__ARM64__) + void generateSingleArgCall(asmjit::a64::Compiler& c, asmjit::arm::Vec& dest, asmjit::arm::Vec& arg, double (*function)(double)); + void generateTwoArgCall(asmjit::a64::Compiler& c, asmjit::arm::Vec& dest, asmjit::arm::Vec& arg1, asmjit::arm::Vec& arg2, double (*function)(double, double)); +#else + void generateSingleArgCall(asmjit::x86::Compiler& c, asmjit::x86::Xmm& dest, asmjit::x86::Xmm& arg, double (*function)(double)); + void generateTwoArgCall(asmjit::x86::Compiler& c, asmjit::x86::Xmm& dest, asmjit::x86::Xmm& arg1, asmjit::x86::Xmm& arg2, double (*function)(double, double)); +#endif std::vector constants; asmjit::JitRuntime runtime; #endif diff --git a/lib/colvars/lepton/include/lepton/CompiledVectorExpression.h b/lib/colvars/lepton/include/lepton/CompiledVectorExpression.h new file mode 100644 index 0000000000..ea3586f1b0 --- /dev/null +++ b/lib/colvars/lepton/include/lepton/CompiledVectorExpression.h @@ -0,0 +1,145 @@ +#ifndef LEPTON_VECTOR_EXPRESSION_H_ +#define LEPTON_VECTOR_EXPRESSION_H_ + +/* -------------------------------------------------------------------------- * + * Lepton * + * -------------------------------------------------------------------------- * + * This is part of the Lepton expression parser originating from * + * Simbios, the NIH National Center for Physics-Based Simulation of * + * Biological Structures at Stanford, funded under the NIH Roadmap for * + * Medical Research, grant U54 GM072970. See https://simtk.org. * + * * + * Portions copyright (c) 2013-2022 Stanford University and the Authors. * + * Authors: Peter Eastman * + * Contributors: * + * * + * Permission is hereby granted, free of charge, to any person obtaining a * + * copy of this software and associated documentation files (the "Software"), * + * to deal in the Software without restriction, including without limitation * + * the rights to use, copy, modify, merge, publish, distribute, sublicense, * + * and/or sell copies of the Software, and to permit persons to whom the * + * Software is furnished to do so, subject to the following conditions: * + * * + * The above copyright notice and this permission notice shall be included in * + * all copies or substantial portions of the Software. * + * * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL * + * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, * + * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR * + * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE * + * USE OR OTHER DEALINGS IN THE SOFTWARE. * + * -------------------------------------------------------------------------- */ + +#include "ExpressionTreeNode.h" +#include "windowsIncludes.h" +#include +#include +#include +#include +#include +#include +#ifdef LEPTON_USE_JIT +#if defined(__ARM__) || defined(__ARM64__) +#include "asmjit/a64.h" +#else +#include "asmjit/x86.h" +#endif +#endif + +namespace Lepton { + +class Operation; +class ParsedExpression; + +/** + * A CompiledVectorExpression is a highly optimized representation of an expression for cases when you want to evaluate + * it many times as quickly as possible. It is similar to CompiledExpression, with the extra feature that it uses the CPU's + * vector unit (AVX on x86, NEON on ARM) to evaluate the expression for multiple sets of arguments at once. It also differs + * from CompiledExpression and ParsedExpression in using single precision rather than double precision to evaluate the expression. + * You should treat it as an opaque object; none of the internal representation is visible. + * + * A CompiledVectorExpression is created by calling createCompiledVectorExpression() on a ParsedExpression. When you create + * it, you must specify the width of the vectors on which to compute the expression. The allowed widths depend on the type of + * CPU it is running on. 4 is always allowed, and 8 is allowed on x86 processors with AVX. Call getAllowedWidths() to query + * the allowed values. + * + * WARNING: CompiledVectorExpression is NOT thread safe. You should never access a CompiledVectorExpression from two threads at + * the same time. + */ + +class LEPTON_EXPORT CompiledVectorExpression { +public: + CompiledVectorExpression(); + CompiledVectorExpression(const CompiledVectorExpression& expression); + ~CompiledVectorExpression(); + CompiledVectorExpression& operator=(const CompiledVectorExpression& expression); + /** + * Get the width of the vectors on which the expression is computed. + */ + int getWidth() const; + /** + * Get the names of all variables used by this expression. + */ + const std::set& getVariables() const; + /** + * Get a pointer to the memory location where the value of a particular variable is stored. This can be used + * to set the value of the variable before calling evaluate(). + * + * @param name the name of the variable to query + * @return a pointer to N floating point values, where N is the vector width + */ + float* getVariablePointer(const std::string& name); + /** + * You can optionally specify the memory locations from which the values of variables should be read. + * This is useful, for example, when several expressions all use the same variable. You can then set + * the value of that variable in one place, and it will be seen by all of them. The location should + * be a pointer to N floating point values, where N is the vector width. + */ + void setVariableLocations(std::map& variableLocations); + /** + * Evaluate the expression. The values of all variables should have been set before calling this. + * + * @return a pointer to N floating point values, where N is the vector width + */ + const float* evaluate() const; + /** + * Get the list of vector widths that are supported on the current processor. + */ + static const std::vector& getAllowedWidths(); +private: + friend class ParsedExpression; + CompiledVectorExpression(const ParsedExpression& expression, int width); + void compileExpression(const ExpressionTreeNode& node, std::vector >& temps, int& workspaceSize); + int findTempIndex(const ExpressionTreeNode& node, std::vector >& temps); + int width; + std::map variablePointers; + std::vector > variablesToCopy; + std::vector > arguments; + std::vector target; + std::vector operation; + std::map variableIndices; + std::set variableNames; + mutable std::vector workspace; + mutable std::vector argValues; + std::map dummyVariables; + void (*jitCode)(); +#ifdef LEPTON_USE_JIT + void findPowerGroups(std::vector >& groups, std::vector >& groupPowers, std::vector& stepGroup); + void generateJitCode(); +#if defined(__ARM__) || defined(__ARM64__) + void generateSingleArgCall(asmjit::a64::Compiler& c, asmjit::arm::Vec& dest, asmjit::arm::Vec& arg, float (*function)(float)); + void generateTwoArgCall(asmjit::a64::Compiler& c, asmjit::arm::Vec& dest, asmjit::arm::Vec& arg1, asmjit::arm::Vec& arg2, float (*function)(float, float)); +#else + void generateSingleArgCall(asmjit::x86::Compiler& c, asmjit::x86::Ymm& dest, asmjit::x86::Ymm& arg, float (*function)(float)); + void generateTwoArgCall(asmjit::x86::Compiler& c, asmjit::x86::Ymm& dest, asmjit::x86::Ymm& arg1, asmjit::x86::Ymm& arg2, float (*function)(float, float)); +#endif + std::vector constants; + asmjit::JitRuntime runtime; +#endif +}; + +} // namespace Lepton + +#endif /*LEPTON_VECTOR_EXPRESSION_H_*/ diff --git a/lib/colvars/lepton/include/lepton/ExpressionTreeNode.h b/lib/colvars/lepton/include/lepton/ExpressionTreeNode.h index bf3a9a0902..dde26103cb 100644 --- a/lib/colvars/lepton/include/lepton/ExpressionTreeNode.h +++ b/lib/colvars/lepton/include/lepton/ExpressionTreeNode.h @@ -9,7 +9,7 @@ * Biological Structures at Stanford, funded under the NIH Roadmap for * * Medical Research, grant U54 GM072970. See https://simtk.org. * * * - * Portions copyright (c) 2009 Stanford University and the Authors. * + * Portions copyright (c) 2009-2021 Stanford University and the Authors. * * Authors: Peter Eastman * * Contributors: * * * @@ -39,6 +39,7 @@ namespace Lepton { class Operation; +class ParsedExpression; /** * This class represents a node in the abstract syntax tree representation of an expression. @@ -82,11 +83,13 @@ public: */ ExpressionTreeNode(Operation* operation); ExpressionTreeNode(const ExpressionTreeNode& node); + ExpressionTreeNode(ExpressionTreeNode&& node); ExpressionTreeNode(); ~ExpressionTreeNode(); bool operator==(const ExpressionTreeNode& node) const; bool operator!=(const ExpressionTreeNode& node) const; ExpressionTreeNode& operator=(const ExpressionTreeNode& node); + ExpressionTreeNode& operator=(ExpressionTreeNode&& node); /** * Get the Operation performed by this node. */ @@ -96,8 +99,11 @@ public: */ const std::vector& getChildren() const; private: + friend class ParsedExpression; + void assignTags(std::vector& examples) const; Operation* operation; std::vector children; + mutable int tag; }; } // namespace Lepton diff --git a/lib/colvars/lepton/include/lepton/ParsedExpression.h b/lib/colvars/lepton/include/lepton/ParsedExpression.h index d88b3d5829..e2a7572c4a 100644 --- a/lib/colvars/lepton/include/lepton/ParsedExpression.h +++ b/lib/colvars/lepton/include/lepton/ParsedExpression.h @@ -9,7 +9,7 @@ * Biological Structures at Stanford, funded under the NIH Roadmap for * * Medical Research, grant U54 GM072970. See https://simtk.org. * * * - * Portions copyright (c) 2009=2013 Stanford University and the Authors. * + * Portions copyright (c) 2009-2022 Stanford University and the Authors. * * Authors: Peter Eastman * * Contributors: * * * @@ -41,6 +41,7 @@ namespace Lepton { class CompiledExpression; class ExpressionProgram; +class CompiledVectorExpression; /** * This class represents the result of parsing an expression. It provides methods for working with the @@ -102,6 +103,16 @@ public: * Create a CompiledExpression that represents the same calculation as this expression. */ CompiledExpression createCompiledExpression() const; + /** + * Create a CompiledVectorExpression that allows the expression to be evaluated efficiently + * using the CPU's vector unit. + * + * @param width the width of the vectors to evaluate it on. The allowed values + * depend on the CPU. 4 is always allowed, and 8 is allowed on + * x86 processors with AVX. Call CompiledVectorExpression::getAllowedWidths() + * to query the allowed widths on the current processor. + */ + CompiledVectorExpression createCompiledVectorExpression(int width) const; /** * Create a new ParsedExpression which is identical to this one, except that the names of some * variables have been changed. @@ -113,9 +124,10 @@ public: private: static double evaluate(const ExpressionTreeNode& node, const std::map& variables); static ExpressionTreeNode preevaluateVariables(const ExpressionTreeNode& node, const std::map& variables); - static ExpressionTreeNode precalculateConstantSubexpressions(const ExpressionTreeNode& node); - static ExpressionTreeNode substituteSimplerExpression(const ExpressionTreeNode& node); - static ExpressionTreeNode differentiate(const ExpressionTreeNode& node, const std::string& variable); + static ExpressionTreeNode precalculateConstantSubexpressions(const ExpressionTreeNode& node, std::map& nodeCache); + static ExpressionTreeNode substituteSimplerExpression(const ExpressionTreeNode& node, std::map& nodeCache); + static ExpressionTreeNode differentiate(const ExpressionTreeNode& node, const std::string& variable, std::map& nodeCache); + static bool isConstant(const ExpressionTreeNode& node); static double getConstantValue(const ExpressionTreeNode& node); static ExpressionTreeNode renameNodeVariables(const ExpressionTreeNode& node, const std::map& replacements); ExpressionTreeNode rootNode; diff --git a/lib/colvars/lepton/src/CompiledExpression.cpp b/lib/colvars/lepton/src/CompiledExpression.cpp index 1ad348b47d..d8b6e112b2 100644 --- a/lib/colvars/lepton/src/CompiledExpression.cpp +++ b/lib/colvars/lepton/src/CompiledExpression.cpp @@ -6,7 +6,7 @@ * Biological Structures at Stanford, funded under the NIH Roadmap for * * Medical Research, grant U54 GM072970. See https://simtk.org. * * * - * Portions copyright (c) 2013-2019 Stanford University and the Authors. * + * Portions copyright (c) 2013-2022 Stanford University and the Authors. * * Authors: Peter Eastman * * Contributors: * * * @@ -151,7 +151,7 @@ void CompiledExpression::setVariableLocations(map& variableLoca if (workspace.size() > 0) generateJitCode(); -#else +#endif // Make a list of all variables we will need to copy before evaluating the expression. variablesToCopy.clear(); @@ -160,13 +160,11 @@ void CompiledExpression::setVariableLocations(map& variableLoca if (pointer != variablePointers.end()) variablesToCopy.push_back(make_pair(&workspace[iter->second], pointer->second)); } -#endif } double CompiledExpression::evaluate() const { -#ifdef LEPTON_USE_JIT - return jitCode(); -#else + if (jitCode) + return jitCode(); for (int i = 0; i < variablesToCopy.size(); i++) *variablesToCopy[i].first = *variablesToCopy[i].second; @@ -183,7 +181,6 @@ double CompiledExpression::evaluate() const { } } return workspace[workspace.size()-1]; -#endif } #ifdef LEPTON_USE_JIT @@ -192,24 +189,70 @@ static double evaluateOperation(Operation* op, double* args) { return op->evaluate(args, dummyVariables); } +void CompiledExpression::findPowerGroups(vector >& groups, vector >& groupPowers, vector& stepGroup) { + // Identify every step that raises an argument to an integer power. + + vector stepPower(operation.size(), 0); + vector stepArg(operation.size(), -1); + for (int step = 0; step < operation.size(); step++) { + Operation& op = *operation[step]; + int power = 0; + if (op.getId() == Operation::SQUARE) + power = 2; + else if (op.getId() == Operation::CUBE) + power = 3; + else if (op.getId() == Operation::POWER_CONSTANT) { + double realPower = dynamic_cast(&op)->getValue(); + if (realPower == (int) realPower) + power = (int) realPower; + } + if (power != 0) { + stepPower[step] = power; + stepArg[step] = arguments[step][0]; + } + } + + // Find groups that operate on the same argument and whose powers have the same sign. + + stepGroup.resize(operation.size(), -1); + for (int i = 0; i < operation.size(); i++) { + if (stepGroup[i] != -1) + continue; + vector group, power; + for (int j = i; j < operation.size(); j++) { + if (stepArg[i] == stepArg[j] && stepPower[i]*stepPower[j] > 0) { + stepGroup[j] = groups.size(); + group.push_back(j); + power.push_back(stepPower[j]); + } + } + groups.push_back(group); + groupPowers.push_back(power); + } +} + +#if defined(__ARM__) || defined(__ARM64__) void CompiledExpression::generateJitCode() { CodeHolder code; - code.init(runtime.getCodeInfo()); - X86Compiler c(&code); - c.addFunc(FuncSignature0()); - vector workspaceVar(workspace.size()); + code.init(runtime.environment()); + a64::Compiler c(&code); + c.addFunc(FuncSignatureT()); + vector workspaceVar(workspace.size()); for (int i = 0; i < (int) workspaceVar.size(); i++) - workspaceVar[i] = c.newXmmSd(); - X86Gp argsPointer = c.newIntPtr(); - c.mov(argsPointer, imm_ptr(&argValues[0])); + workspaceVar[i] = c.newVecD(); + arm::Gp argsPointer = c.newIntPtr(); + c.mov(argsPointer, imm(&argValues[0])); + vector > groups, groupPowers; + vector stepGroup; + findPowerGroups(groups, groupPowers, stepGroup); // Load the arguments into variables. for (set::const_iterator iter = variableNames.begin(); iter != variableNames.end(); ++iter) { map::iterator index = variableIndices.find(*iter); - X86Gp variablePointer = c.newIntPtr(); - c.mov(variablePointer, imm_ptr(&getVariableReference(index->first))); - c.movsd(workspaceVar[index->second], x86::ptr(variablePointer, 0, 0)); + arm::Gp variablePointer = c.newIntPtr(); + c.mov(variablePointer, imm(&getVariableReference(index->first))); + c.ldr(workspaceVar[index->second], arm::ptr(variablePointer, 0)); } // Make a list of all constants that will be needed for evaluation. @@ -232,6 +275,12 @@ void CompiledExpression::generateJitCode() { value = 1.0; else if (op.getId() == Operation::DELTA) value = 1.0; + else if (op.getId() == Operation::POWER_CONSTANT) { + if (stepGroup[step] == -1) + value = dynamic_cast(op).getValue(); + else + value = 1.0; + } else continue; @@ -250,19 +299,63 @@ void CompiledExpression::generateJitCode() { // Load constants into variables. - vector constantVar(constants.size()); + vector constantVar(constants.size()); if (constants.size() > 0) { - X86Gp constantsPointer = c.newIntPtr(); - c.mov(constantsPointer, imm_ptr(&constants[0])); + arm::Gp constantsPointer = c.newIntPtr(); + c.mov(constantsPointer, imm(&constants[0])); for (int i = 0; i < (int) constants.size(); i++) { - constantVar[i] = c.newXmmSd(); - c.movsd(constantVar[i], x86::ptr(constantsPointer, 8*i, 0)); + constantVar[i] = c.newVecD(); + c.ldr(constantVar[i], arm::ptr(constantsPointer, 8*i)); } } // Evaluate the operations. + vector hasComputedPower(operation.size(), false); for (int step = 0; step < (int) operation.size(); step++) { + if (hasComputedPower[step]) + continue; + + // When one or more steps involve raising the same argument to multiple integer + // powers, we can compute them all together for efficiency. + + if (stepGroup[step] != -1) { + vector& group = groups[stepGroup[step]]; + vector& powers = groupPowers[stepGroup[step]]; + arm::Vec multiplier = c.newVecD(); + if (powers[0] > 0) + c.fmov(multiplier, workspaceVar[arguments[step][0]]); + else { + c.fdiv(multiplier, constantVar[operationConstantIndex[step]], workspaceVar[arguments[step][0]]); + for (int i = 0; i < powers.size(); i++) + powers[i] = -powers[i]; + } + vector hasAssigned(group.size(), false); + bool done = false; + while (!done) { + done = true; + for (int i = 0; i < group.size(); i++) { + if (powers[i]%2 == 1) { + if (!hasAssigned[i]) + c.fmov(workspaceVar[target[group[i]]], multiplier); + else + c.fmul(workspaceVar[target[group[i]]], workspaceVar[target[group[i]]], multiplier); + hasAssigned[i] = true; + } + powers[i] >>= 1; + if (powers[i] != 0) + done = false; + } + if (!done) + c.fmul(multiplier, multiplier, multiplier); + } + for (int step : group) + hasComputedPower[step] = true; + continue; + } + + // Evaluate the step. + Operation& op = *operation[step]; vector args = arguments[step]; if (args.size() == 1) { @@ -276,33 +369,28 @@ void CompiledExpression::generateJitCode() { switch (op.getId()) { case Operation::CONSTANT: - c.movsd(workspaceVar[target[step]], constantVar[operationConstantIndex[step]]); + c.fmov(workspaceVar[target[step]], constantVar[operationConstantIndex[step]]); break; case Operation::ADD: - c.movsd(workspaceVar[target[step]], workspaceVar[args[0]]); - c.addsd(workspaceVar[target[step]], workspaceVar[args[1]]); + c.fadd(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]]); break; case Operation::SUBTRACT: - c.movsd(workspaceVar[target[step]], workspaceVar[args[0]]); - c.subsd(workspaceVar[target[step]], workspaceVar[args[1]]); + c.fsub(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]]); break; case Operation::MULTIPLY: - c.movsd(workspaceVar[target[step]], workspaceVar[args[0]]); - c.mulsd(workspaceVar[target[step]], workspaceVar[args[1]]); + c.fmul(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]]); break; case Operation::DIVIDE: - c.movsd(workspaceVar[target[step]], workspaceVar[args[0]]); - c.divsd(workspaceVar[target[step]], workspaceVar[args[1]]); + c.fdiv(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]]); break; case Operation::POWER: generateTwoArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]], pow); break; case Operation::NEGATE: - c.xorps(workspaceVar[target[step]], workspaceVar[target[step]]); - c.subsd(workspaceVar[target[step]], workspaceVar[args[0]]); + c.fneg(workspaceVar[target[step]], workspaceVar[args[0]]); break; case Operation::SQRT: - c.sqrtsd(workspaceVar[target[step]], workspaceVar[args[0]]); + c.fsqrt(workspaceVar[target[step]], workspaceVar[args[0]]); break; case Operation::EXP: generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], exp); @@ -341,56 +429,63 @@ void CompiledExpression::generateJitCode() { generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], tanh); break; case Operation::STEP: - c.xorps(workspaceVar[target[step]], workspaceVar[target[step]]); - c.cmpsd(workspaceVar[target[step]], workspaceVar[args[0]], imm(18)); // Comparison mode is _CMP_LE_OQ = 18 - c.andps(workspaceVar[target[step]], constantVar[operationConstantIndex[step]]); + c.cmge(workspaceVar[target[step]], workspaceVar[args[0]], imm(0)); + c.and_(workspaceVar[target[step]], workspaceVar[target[step]], constantVar[operationConstantIndex[step]]); break; case Operation::DELTA: - c.xorps(workspaceVar[target[step]], workspaceVar[target[step]]); - c.cmpsd(workspaceVar[target[step]], workspaceVar[args[0]], imm(16)); // Comparison mode is _CMP_EQ_OS = 16 - c.andps(workspaceVar[target[step]], constantVar[operationConstantIndex[step]]); + c.cmeq(workspaceVar[target[step]], workspaceVar[args[0]], imm(0)); + c.and_(workspaceVar[target[step]], workspaceVar[target[step]], constantVar[operationConstantIndex[step]]); break; case Operation::SQUARE: - c.movsd(workspaceVar[target[step]], workspaceVar[args[0]]); - c.mulsd(workspaceVar[target[step]], workspaceVar[args[0]]); + c.fmul(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[0]]); break; case Operation::CUBE: - c.movsd(workspaceVar[target[step]], workspaceVar[args[0]]); - c.mulsd(workspaceVar[target[step]], workspaceVar[args[0]]); - c.mulsd(workspaceVar[target[step]], workspaceVar[args[0]]); + c.fmul(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[0]]); + c.fmul(workspaceVar[target[step]], workspaceVar[target[step]], workspaceVar[args[0]]); break; case Operation::RECIPROCAL: - c.movsd(workspaceVar[target[step]], constantVar[operationConstantIndex[step]]); - c.divsd(workspaceVar[target[step]], workspaceVar[args[0]]); + c.fdiv(workspaceVar[target[step]], constantVar[operationConstantIndex[step]], workspaceVar[args[0]]); break; case Operation::ADD_CONSTANT: - c.movsd(workspaceVar[target[step]], workspaceVar[args[0]]); - c.addsd(workspaceVar[target[step]], constantVar[operationConstantIndex[step]]); + c.fadd(workspaceVar[target[step]], workspaceVar[args[0]], constantVar[operationConstantIndex[step]]); break; case Operation::MULTIPLY_CONSTANT: - c.movsd(workspaceVar[target[step]], workspaceVar[args[0]]); - c.mulsd(workspaceVar[target[step]], constantVar[operationConstantIndex[step]]); + c.fmul(workspaceVar[target[step]], workspaceVar[args[0]], constantVar[operationConstantIndex[step]]); + break; + case Operation::POWER_CONSTANT: + generateTwoArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], constantVar[operationConstantIndex[step]], pow); + break; + case Operation::MIN: + c.fmin(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]]); + break; + case Operation::MAX: + c.fmax(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]]); break; case Operation::ABS: - generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], fabs); + c.fabs(workspaceVar[target[step]], workspaceVar[args[0]]); break; case Operation::FLOOR: - generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], floor); + c.frintm(workspaceVar[target[step]], workspaceVar[args[0]]); break; case Operation::CEIL: - generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], ceil); + c.frintp(workspaceVar[target[step]], workspaceVar[args[0]]); + break; + case Operation::SELECT: + c.fcmeq(workspaceVar[target[step]], workspaceVar[args[0]], imm(0)); + c.bsl(workspaceVar[target[step]], workspaceVar[args[2]], workspaceVar[args[1]]); break; default: // Just invoke evaluateOperation(). for (int i = 0; i < (int) args.size(); i++) - c.movsd(x86::ptr(argsPointer, 8*i, 0), workspaceVar[args[i]]); - X86Gp fn = c.newIntPtr(); - c.mov(fn, imm_ptr((void*) evaluateOperation)); - CCFuncCall* call = c.call(fn, FuncSignature2()); - call->setArg(0, imm_ptr(&op)); - call->setArg(1, imm_ptr(&argValues[0])); - call->setRet(0, workspaceVar[target[step]]); + c.str(workspaceVar[args[i]], arm::ptr(argsPointer, 8*i)); + arm::Gp fn = c.newIntPtr(); + c.mov(fn, imm((void*) evaluateOperation)); + InvokeNode* invoke; + c.invoke(&invoke, fn, FuncSignatureT()); + invoke->setArg(0, imm(&op)); + invoke->setArg(1, imm(&argValues[0])); + invoke->setRet(0, workspaceVar[target[step]]); } } c.ret(workspaceVar[workspace.size()-1]); @@ -399,20 +494,319 @@ void CompiledExpression::generateJitCode() { runtime.add(&jitCode, &code); } -void CompiledExpression::generateSingleArgCall(X86Compiler& c, X86Xmm& dest, X86Xmm& arg, double (*function)(double)) { - X86Gp fn = c.newIntPtr(); - c.mov(fn, imm_ptr((void*) function)); - CCFuncCall* call = c.call(fn, FuncSignature1()); - call->setArg(0, arg); - call->setRet(0, dest); +void CompiledExpression::generateSingleArgCall(a64::Compiler& c, arm::Vec& dest, arm::Vec& arg, double (*function)(double)) { + arm::Gp fn = c.newIntPtr(); + c.mov(fn, imm((void*) function)); + InvokeNode* invoke; + c.invoke(&invoke, fn, FuncSignatureT()); + invoke->setArg(0, arg); + invoke->setRet(0, dest); } -void CompiledExpression::generateTwoArgCall(X86Compiler& c, X86Xmm& dest, X86Xmm& arg1, X86Xmm& arg2, double (*function)(double, double)) { - X86Gp fn = c.newIntPtr(); - c.mov(fn, imm_ptr((void*) function)); - CCFuncCall* call = c.call(fn, FuncSignature2()); - call->setArg(0, arg1); - call->setArg(1, arg2); - call->setRet(0, dest); +void CompiledExpression::generateTwoArgCall(a64::Compiler& c, arm::Vec& dest, arm::Vec& arg1, arm::Vec& arg2, double (*function)(double, double)) { + arm::Gp fn = c.newIntPtr(); + c.mov(fn, imm((void*) function)); + InvokeNode* invoke; + c.invoke(&invoke, fn, FuncSignatureT()); + invoke->setArg(0, arg1); + invoke->setArg(1, arg2); + invoke->setRet(0, dest); +} +#else +void CompiledExpression::generateJitCode() { + const CpuInfo& cpu = CpuInfo::host(); + if (!cpu.hasFeature(CpuFeatures::X86::kAVX)) + return; + CodeHolder code; + code.init(runtime.environment()); + x86::Compiler c(&code); + FuncNode* funcNode = c.addFunc(FuncSignatureT()); + funcNode->frame().setAvxEnabled(); + vector workspaceVar(workspace.size()); + for (int i = 0; i < (int) workspaceVar.size(); i++) + workspaceVar[i] = c.newXmmSd(); + x86::Gp argsPointer = c.newIntPtr(); + c.mov(argsPointer, imm(&argValues[0])); + vector > groups, groupPowers; + vector stepGroup; + findPowerGroups(groups, groupPowers, stepGroup); + + // Load the arguments into variables. + + x86::Gp variablePointer = c.newIntPtr(); + for (set::const_iterator iter = variableNames.begin(); iter != variableNames.end(); ++iter) { + map::iterator index = variableIndices.find(*iter); + c.mov(variablePointer, imm(&getVariableReference(index->first))); + c.vmovsd(workspaceVar[index->second], x86::ptr(variablePointer, 0, 0)); + } + + // Make a list of all constants that will be needed for evaluation. + + vector operationConstantIndex(operation.size(), -1); + for (int step = 0; step < (int) operation.size(); step++) { + // Find the constant value (if any) used by this operation. + + Operation& op = *operation[step]; + double value; + if (op.getId() == Operation::CONSTANT) + value = dynamic_cast(op).getValue(); + else if (op.getId() == Operation::ADD_CONSTANT) + value = dynamic_cast(op).getValue(); + else if (op.getId() == Operation::MULTIPLY_CONSTANT) + value = dynamic_cast(op).getValue(); + else if (op.getId() == Operation::RECIPROCAL) + value = 1.0; + else if (op.getId() == Operation::STEP) + value = 1.0; + else if (op.getId() == Operation::DELTA) + value = 1.0; + else if (op.getId() == Operation::ABS) { + long long mask = 0x7FFFFFFFFFFFFFFF; + value = *reinterpret_cast(&mask); + } + else if (op.getId() == Operation::POWER_CONSTANT) { + if (stepGroup[step] == -1) + value = dynamic_cast(op).getValue(); + else + value = 1.0; + } + else + continue; + + // See if we already have a variable for this constant. + + for (int i = 0; i < (int) constants.size(); i++) + if (value == constants[i]) { + operationConstantIndex[step] = i; + break; + } + if (operationConstantIndex[step] == -1) { + operationConstantIndex[step] = constants.size(); + constants.push_back(value); + } + } + + // Load constants into variables. + + vector constantVar(constants.size()); + if (constants.size() > 0) { + x86::Gp constantsPointer = c.newIntPtr(); + c.mov(constantsPointer, imm(&constants[0])); + for (int i = 0; i < (int) constants.size(); i++) { + constantVar[i] = c.newXmmSd(); + c.vmovsd(constantVar[i], x86::ptr(constantsPointer, 8*i, 0)); + } + } + + // Evaluate the operations. + + vector hasComputedPower(operation.size(), false); + for (int step = 0; step < (int) operation.size(); step++) { + if (hasComputedPower[step]) + continue; + + // When one or more steps involve raising the same argument to multiple integer + // powers, we can compute them all together for efficiency. + + if (stepGroup[step] != -1) { + vector& group = groups[stepGroup[step]]; + vector& powers = groupPowers[stepGroup[step]]; + x86::Xmm multiplier = c.newXmmSd(); + if (powers[0] > 0) + c.vmovsd(multiplier, workspaceVar[arguments[step][0]], workspaceVar[arguments[step][0]]); + else { + c.vdivsd(multiplier, constantVar[operationConstantIndex[step]], workspaceVar[arguments[step][0]]); + for (int i = 0; i < powers.size(); i++) + powers[i] = -powers[i]; + } + vector hasAssigned(group.size(), false); + bool done = false; + while (!done) { + done = true; + for (int i = 0; i < group.size(); i++) { + if (powers[i]%2 == 1) { + if (!hasAssigned[i]) + c.vmovsd(workspaceVar[target[group[i]]], multiplier, multiplier); + else + c.vmulsd(workspaceVar[target[group[i]]], workspaceVar[target[group[i]]], multiplier); + hasAssigned[i] = true; + } + powers[i] >>= 1; + if (powers[i] != 0) + done = false; + } + if (!done) + c.vmulsd(multiplier, multiplier, multiplier); + } + for (int step : group) + hasComputedPower[step] = true; + continue; + } + + // Evaluate the step. + + Operation& op = *operation[step]; + vector args = arguments[step]; + if (args.size() == 1) { + // One or more sequential arguments. Fill out the list. + + for (int i = 1; i < op.getNumArguments(); i++) + args.push_back(args[0]+i); + } + + // Generate instructions to execute this operation. + + switch (op.getId()) { + case Operation::CONSTANT: + c.vmovsd(workspaceVar[target[step]], constantVar[operationConstantIndex[step]], constantVar[operationConstantIndex[step]]); + break; + case Operation::ADD: + c.vaddsd(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]]); + break; + case Operation::SUBTRACT: + c.vsubsd(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]]); + break; + case Operation::MULTIPLY: + c.vmulsd(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]]); + break; + case Operation::DIVIDE: + c.vdivsd(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]]); + break; + case Operation::POWER: + generateTwoArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]], pow); + break; + case Operation::NEGATE: + c.vxorps(workspaceVar[target[step]], workspaceVar[target[step]], workspaceVar[target[step]]); + c.vsubsd(workspaceVar[target[step]], workspaceVar[target[step]], workspaceVar[args[0]]); + break; + case Operation::SQRT: + c.vsqrtsd(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[0]]); + break; + case Operation::EXP: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], exp); + break; + case Operation::LOG: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], log); + break; + case Operation::SIN: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], sin); + break; + case Operation::COS: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], cos); + break; + case Operation::TAN: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], tan); + break; + case Operation::ASIN: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], asin); + break; + case Operation::ACOS: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], acos); + break; + case Operation::ATAN: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], atan); + break; + case Operation::ATAN2: + generateTwoArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]], atan2); + break; + case Operation::SINH: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], sinh); + break; + case Operation::COSH: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], cosh); + break; + case Operation::TANH: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], tanh); + break; + case Operation::STEP: + c.vxorps(workspaceVar[target[step]], workspaceVar[target[step]], workspaceVar[target[step]]); + c.vcmpsd(workspaceVar[target[step]], workspaceVar[target[step]], workspaceVar[args[0]], imm(18)); // Comparison mode is _CMP_LE_OQ = 18 + c.vandps(workspaceVar[target[step]], workspaceVar[target[step]], constantVar[operationConstantIndex[step]]); + break; + case Operation::DELTA: + c.vxorps(workspaceVar[target[step]], workspaceVar[target[step]], workspaceVar[target[step]]); + c.vcmpsd(workspaceVar[target[step]], workspaceVar[target[step]], workspaceVar[args[0]], imm(16)); // Comparison mode is _CMP_EQ_OS = 16 + c.vandps(workspaceVar[target[step]], workspaceVar[target[step]], constantVar[operationConstantIndex[step]]); + break; + case Operation::SQUARE: + c.vmulsd(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[0]]); + break; + case Operation::CUBE: + c.vmulsd(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[0]]); + c.vmulsd(workspaceVar[target[step]], workspaceVar[target[step]], workspaceVar[args[0]]); + break; + case Operation::RECIPROCAL: + c.vdivsd(workspaceVar[target[step]], constantVar[operationConstantIndex[step]], workspaceVar[args[0]]); + break; + case Operation::ADD_CONSTANT: + c.vaddsd(workspaceVar[target[step]], workspaceVar[args[0]], constantVar[operationConstantIndex[step]]); + break; + case Operation::MULTIPLY_CONSTANT: + c.vmulsd(workspaceVar[target[step]], workspaceVar[args[0]], constantVar[operationConstantIndex[step]]); + break; + case Operation::POWER_CONSTANT: + generateTwoArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], constantVar[operationConstantIndex[step]], pow); + break; + case Operation::MIN: + c.vminsd(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]]); + break; + case Operation::MAX: + c.vmaxsd(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]]); + break; + case Operation::ABS: + c.vandpd(workspaceVar[target[step]], workspaceVar[args[0]], constantVar[operationConstantIndex[step]]); + break; + case Operation::FLOOR: + c.vroundsd(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[0]], imm(1)); + break; + case Operation::CEIL: + c.vroundsd(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[0]], imm(2)); + break; + case Operation::SELECT: + { + x86::Xmm mask = c.newXmmSd(); + c.vxorps(mask, mask, mask); + c.vcmpsd(mask, mask, workspaceVar[args[0]], imm(0)); // Comparison mode is _CMP_EQ_OQ = 0 + c.vblendvps(workspaceVar[target[step]], workspaceVar[args[1]], workspaceVar[args[2]], mask); + break; + } + default: + // Just invoke evaluateOperation(). + + for (int i = 0; i < (int) args.size(); i++) + c.vmovsd(x86::ptr(argsPointer, 8*i, 0), workspaceVar[args[i]]); + x86::Gp fn = c.newIntPtr(); + c.mov(fn, imm((void*) evaluateOperation)); + InvokeNode* invoke; + c.invoke(&invoke, fn, FuncSignatureT()); + invoke->setArg(0, imm(&op)); + invoke->setArg(1, imm(&argValues[0])); + invoke->setRet(0, workspaceVar[target[step]]); + } + } + c.ret(workspaceVar[workspace.size()-1]); + c.endFunc(); + c.finalize(); + runtime.add(&jitCode, &code); +} + +void CompiledExpression::generateSingleArgCall(x86::Compiler& c, x86::Xmm& dest, x86::Xmm& arg, double (*function)(double)) { + x86::Gp fn = c.newIntPtr(); + c.mov(fn, imm((void*) function)); + InvokeNode* invoke; + c.invoke(&invoke, fn, FuncSignatureT()); + invoke->setArg(0, arg); + invoke->setRet(0, dest); +} + +void CompiledExpression::generateTwoArgCall(x86::Compiler& c, x86::Xmm& dest, x86::Xmm& arg1, x86::Xmm& arg2, double (*function)(double, double)) { + x86::Gp fn = c.newIntPtr(); + c.mov(fn, imm((void*) function)); + InvokeNode* invoke; + c.invoke(&invoke, fn, FuncSignatureT()); + invoke->setArg(0, arg1); + invoke->setArg(1, arg2); + invoke->setRet(0, dest); } #endif +#endif diff --git a/lib/colvars/lepton/src/CompiledVectorExpression.cpp b/lib/colvars/lepton/src/CompiledVectorExpression.cpp new file mode 100644 index 0000000000..7c01a986bb --- /dev/null +++ b/lib/colvars/lepton/src/CompiledVectorExpression.cpp @@ -0,0 +1,933 @@ +/* -------------------------------------------------------------------------- * + * Lepton * + * -------------------------------------------------------------------------- * + * This is part of the Lepton expression parser originating from * + * Simbios, the NIH National Center for Physics-Based Simulation of * + * Biological Structures at Stanford, funded under the NIH Roadmap for * + * Medical Research, grant U54 GM072970. See https://simtk.org. * + * * + * Portions copyright (c) 2013-2022 Stanford University and the Authors. * + * Authors: Peter Eastman * + * Contributors: * + * * + * Permission is hereby granted, free of charge, to any person obtaining a * + * copy of this software and associated documentation files (the "Software"), * + * to deal in the Software without restriction, including without limitation * + * the rights to use, copy, modify, merge, publish, distribute, sublicense, * + * and/or sell copies of the Software, and to permit persons to whom the * + * Software is furnished to do so, subject to the following conditions: * + * * + * The above copyright notice and this permission notice shall be included in * + * all copies or substantial portions of the Software. * + * * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL * + * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, * + * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR * + * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE * + * USE OR OTHER DEALINGS IN THE SOFTWARE. * + * -------------------------------------------------------------------------- */ + +#include "lepton/CompiledVectorExpression.h" +#include "lepton/Operation.h" +#include "lepton/ParsedExpression.h" +#include +#include + +using namespace Lepton; +using namespace std; +#ifdef LEPTON_USE_JIT +using namespace asmjit; +#endif + +CompiledVectorExpression::CompiledVectorExpression() : jitCode(NULL) { +} + +CompiledVectorExpression::CompiledVectorExpression(const ParsedExpression& expression, int width) : jitCode(NULL), width(width) { + const vector allowedWidths = getAllowedWidths(); + if (find(allowedWidths.begin(), allowedWidths.end(), width) == allowedWidths.end()) + throw Exception("Unsupported width for vector expression: "+to_string(width)); + ParsedExpression expr = expression.optimize(); // Just in case it wasn't already optimized. + vector > temps; + int workspaceSize = 0; + compileExpression(expr.getRootNode(), temps, workspaceSize); + workspace.resize(workspaceSize*width); + int maxArguments = 1; + for (int i = 0; i < (int) operation.size(); i++) + if (operation[i]->getNumArguments() > maxArguments) + maxArguments = operation[i]->getNumArguments(); + argValues.resize(maxArguments); +#ifdef LEPTON_USE_JIT + generateJitCode(); +#endif +} + +CompiledVectorExpression::~CompiledVectorExpression() { + for (int i = 0; i < (int) operation.size(); i++) + if (operation[i] != NULL) + delete operation[i]; +} + +CompiledVectorExpression::CompiledVectorExpression(const CompiledVectorExpression& expression) : jitCode(NULL) { + *this = expression; +} + +CompiledVectorExpression& CompiledVectorExpression::operator=(const CompiledVectorExpression& expression) { + arguments = expression.arguments; + width = expression.width; + target = expression.target; + variableIndices = expression.variableIndices; + variableNames = expression.variableNames; + workspace.resize(expression.workspace.size()); + argValues.resize(expression.argValues.size()); + operation.resize(expression.operation.size()); + for (int i = 0; i < (int) operation.size(); i++) + operation[i] = expression.operation[i]->clone(); + setVariableLocations(variablePointers); + return *this; +} + +const vector& CompiledVectorExpression::getAllowedWidths() { + static vector widths; + if (widths.size() == 0) { + widths.push_back(4); +#ifdef LEPTON_USE_JIT + const CpuInfo& cpu = CpuInfo::host(); + if (cpu.hasFeature(CpuFeatures::X86::kAVX)) + widths.push_back(8); +#endif + } + return widths; +} + +void CompiledVectorExpression::compileExpression(const ExpressionTreeNode& node, vector >& temps, int& workspaceSize) { + if (findTempIndex(node, temps) != -1) + return; // We have already processed a node identical to this one. + + // Process the child nodes. + + vector args; + for (int i = 0; i < node.getChildren().size(); i++) { + compileExpression(node.getChildren()[i], temps, workspaceSize); + args.push_back(findTempIndex(node.getChildren()[i], temps)); + } + + // Process this node. + + if (node.getOperation().getId() == Operation::VARIABLE) { + variableIndices[node.getOperation().getName()] = workspaceSize; + variableNames.insert(node.getOperation().getName()); + } + else { + int stepIndex = (int) arguments.size(); + arguments.push_back(vector()); + target.push_back(workspaceSize); + operation.push_back(node.getOperation().clone()); + if (args.size() == 0) + arguments[stepIndex].push_back(0); // The value won't actually be used. We just need something there. + else { + // If the arguments are sequential, we can just pass a pointer to the first one. + + bool sequential = true; + for (int i = 1; i < args.size(); i++) + if (args[i] != args[i - 1] + 1) + sequential = false; + if (sequential) + arguments[stepIndex].push_back(args[0]); + else + arguments[stepIndex] = args; + } + } + temps.push_back(make_pair(node, workspaceSize)); + workspaceSize++; +} + +int CompiledVectorExpression::findTempIndex(const ExpressionTreeNode& node, vector >& temps) { + for (int i = 0; i < (int) temps.size(); i++) + if (temps[i].first == node) + return i; + return -1; +} + +int CompiledVectorExpression::getWidth() const { + return width; +} + +const set& CompiledVectorExpression::getVariables() const { + return variableNames; +} + +float* CompiledVectorExpression::getVariablePointer(const string& name) { + map::iterator pointer = variablePointers.find(name); + if (pointer != variablePointers.end()) + return pointer->second; + map::iterator index = variableIndices.find(name); + if (index == variableIndices.end()) + throw Exception("getVariableReference: Unknown variable '" + name + "'"); + return &workspace[index->second*width]; +} + +void CompiledVectorExpression::setVariableLocations(map& variableLocations) { + variablePointers = variableLocations; +#ifdef LEPTON_USE_JIT + // Rebuild the JIT code. + + if (workspace.size() > 0) + generateJitCode(); +#endif + // Make a list of all variables we will need to copy before evaluating the expression. + + variablesToCopy.clear(); + for (map::const_iterator iter = variableIndices.begin(); iter != variableIndices.end(); ++iter) { + map::iterator pointer = variablePointers.find(iter->first); + if (pointer != variablePointers.end()) + variablesToCopy.push_back(make_pair(&workspace[iter->second*width], pointer->second)); + } +} + +const float* CompiledVectorExpression::evaluate() const { + if (jitCode) { + jitCode(); + return &workspace[workspace.size()-width]; + } + for (int i = 0; i < variablesToCopy.size(); i++) + for (int j = 0; j < width; j++) + variablesToCopy[i].first[j] = variablesToCopy[i].second[j]; + + // Loop over the operations and evaluate each one. + + for (int step = 0; step < operation.size(); step++) { + const vector& args = arguments[step]; + if (args.size() == 1) { + for (int j = 0; j < width; j++) { + for (int i = 0; i < operation[step]->getNumArguments(); i++) + argValues[i] = workspace[(args[0]+i)*width+j]; + workspace[target[step]*width+j] = operation[step]->evaluate(&argValues[0], dummyVariables); + } + } else { + for (int j = 0; j < width; j++) { + for (int i = 0; i < args.size(); i++) + argValues[i] = workspace[args[i]*width+j]; + workspace[target[step]*width+j] = operation[step]->evaluate(&argValues[0], dummyVariables); + } + } + } + return &workspace[workspace.size()-width]; +} + +#ifdef LEPTON_USE_JIT + +static double evaluateOperation(Operation* op, double* args) { + static map dummyVariables; + return op->evaluate(args, dummyVariables); +} + +void CompiledVectorExpression::findPowerGroups(vector >& groups, vector >& groupPowers, vector& stepGroup) { + // Identify every step that raises an argument to an integer power. + + vector stepPower(operation.size(), 0); + vector stepArg(operation.size(), -1); + for (int step = 0; step < operation.size(); step++) { + Operation& op = *operation[step]; + int power = 0; + if (op.getId() == Operation::SQUARE) + power = 2; + else if (op.getId() == Operation::CUBE) + power = 3; + else if (op.getId() == Operation::POWER_CONSTANT) { + double realPower = dynamic_cast (&op)->getValue(); + if (realPower == (int) realPower) + power = (int) realPower; + } + if (power != 0) { + stepPower[step] = power; + stepArg[step] = arguments[step][0]; + } + } + + // Find groups that operate on the same argument and whose powers have the same sign. + + stepGroup.resize(operation.size(), -1); + for (int i = 0; i < operation.size(); i++) { + if (stepGroup[i] != -1) + continue; + vector group, power; + for (int j = i; j < operation.size(); j++) { + if (stepArg[i] == stepArg[j] && stepPower[i] * stepPower[j] > 0) { + stepGroup[j] = groups.size(); + group.push_back(j); + power.push_back(stepPower[j]); + } + } + groups.push_back(group); + groupPowers.push_back(power); + } +} + +#if defined(__ARM__) || defined(__ARM64__) + +void CompiledVectorExpression::generateJitCode() { + CodeHolder code; + code.init(runtime.environment()); + a64::Compiler c(&code); + c.addFunc(FuncSignatureT()); + vector workspaceVar(workspace.size()/width); + for (int i = 0; i < (int) workspaceVar.size(); i++) + workspaceVar[i] = c.newVecQ(); + arm::Gp argsPointer = c.newIntPtr(); + c.mov(argsPointer, imm(&argValues[0])); + vector > groups, groupPowers; + vector stepGroup; + findPowerGroups(groups, groupPowers, stepGroup); + + // Load the arguments into variables. + + arm::Gp variablePointer = c.newIntPtr(); + for (set::const_iterator iter = variableNames.begin(); iter != variableNames.end(); ++iter) { + map::iterator index = variableIndices.find(*iter); + c.mov(variablePointer, imm(getVariablePointer(index->first))); + c.ldr(workspaceVar[index->second].s4(), arm::ptr(variablePointer, 0)); + } + + // Make a list of all constants that will be needed for evaluation. + + vector operationConstantIndex(operation.size(), -1); + for (int step = 0; step < (int) operation.size(); step++) { + // Find the constant value (if any) used by this operation. + + Operation& op = *operation[step]; + float value; + if (op.getId() == Operation::CONSTANT) + value = dynamic_cast (op).getValue(); + else if (op.getId() == Operation::ADD_CONSTANT) + value = dynamic_cast (op).getValue(); + else if (op.getId() == Operation::MULTIPLY_CONSTANT) + value = dynamic_cast (op).getValue(); + else if (op.getId() == Operation::RECIPROCAL) + value = 1.0; + else if (op.getId() == Operation::STEP) + value = 1.0; + else if (op.getId() == Operation::DELTA) + value = 1.0; + else if (op.getId() == Operation::POWER_CONSTANT) { + if (stepGroup[step] == -1) + value = dynamic_cast (op).getValue(); + else + value = 1.0; + } else + continue; + + // See if we already have a variable for this constant. + + for (int i = 0; i < (int) constants.size(); i++) + if (value == constants[i]) { + operationConstantIndex[step] = i; + break; + } + if (operationConstantIndex[step] == -1) { + operationConstantIndex[step] = constants.size(); + constants.push_back(value); + } + } + + // Load constants into variables. + + vector constantVar(constants.size()); + if (constants.size() > 0) { + arm::Gp constantsPointer = c.newIntPtr(); + for (int i = 0; i < (int) constants.size(); i++) { + c.mov(constantsPointer, imm(&constants[i])); + constantVar[i] = c.newVecQ(); + c.ld1r(constantVar[i].s4(), arm::ptr(constantsPointer)); + } + } + + // Evaluate the operations. + + vector hasComputedPower(operation.size(), false); + arm::Vec argReg = c.newVecS(); + arm::Vec doubleArgReg = c.newVecD(); + arm::Vec doubleResultReg = c.newVecD(); + for (int step = 0; step < (int) operation.size(); step++) { + if (hasComputedPower[step]) + continue; + + // When one or more steps involve raising the same argument to multiple integer + // powers, we can compute them all together for efficiency. + + if (stepGroup[step] != -1) { + vector& group = groups[stepGroup[step]]; + vector& powers = groupPowers[stepGroup[step]]; + arm::Vec multiplier = c.newVecQ(); + if (powers[0] > 0) + c.mov(multiplier.s4(), workspaceVar[arguments[step][0]].s4()); + else { + c.fdiv(multiplier.s4(), constantVar[operationConstantIndex[step]].s4(), workspaceVar[arguments[step][0]].s4()); + for (int i = 0; i < powers.size(); i++) + powers[i] = -powers[i]; + } + vector hasAssigned(group.size(), false); + bool done = false; + while (!done) { + done = true; + for (int i = 0; i < group.size(); i++) { + if (powers[i] % 2 == 1) { + if (!hasAssigned[i]) + c.mov(workspaceVar[target[group[i]]].s4(), multiplier.s4()); + else + c.fmul(workspaceVar[target[group[i]]].s4(), workspaceVar[target[group[i]]].s4(), multiplier.s4()); + hasAssigned[i] = true; + } + powers[i] >>= 1; + if (powers[i] != 0) + done = false; + } + if (!done) + c.fmul(multiplier.s4(), multiplier.s4(), multiplier.s4()); + } + for (int step : group) + hasComputedPower[step] = true; + continue; + } + + // Evaluate the step. + + Operation& op = *operation[step]; + vector args = arguments[step]; + if (args.size() == 1) { + // One or more sequential arguments. Fill out the list. + + for (int i = 1; i < op.getNumArguments(); i++) + args.push_back(args[0] + i); + } + + // Generate instructions to execute this operation. + + switch (op.getId()) { + case Operation::CONSTANT: + c.mov(workspaceVar[target[step]].s4(), constantVar[operationConstantIndex[step]].s4()); + break; + case Operation::ADD: + c.fadd(workspaceVar[target[step]].s4(), workspaceVar[args[0]].s4(), workspaceVar[args[1]].s4()); + break; + case Operation::SUBTRACT: + c.fsub(workspaceVar[target[step]].s4(), workspaceVar[args[0]].s4(), workspaceVar[args[1]].s4()); + break; + case Operation::MULTIPLY: + c.fmul(workspaceVar[target[step]].s4(), workspaceVar[args[0]].s4(), workspaceVar[args[1]].s4()); + break; + case Operation::DIVIDE: + c.fdiv(workspaceVar[target[step]].s4(), workspaceVar[args[0]].s4(), workspaceVar[args[1]].s4()); + break; + case Operation::POWER: + generateTwoArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]], powf); + break; + case Operation::NEGATE: + c.fneg(workspaceVar[target[step]].s4(), workspaceVar[args[0]].s4()); + break; + case Operation::SQRT: + c.fsqrt(workspaceVar[target[step]].s4(), workspaceVar[args[0]].s4()); + break; + case Operation::EXP: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], expf); + break; + case Operation::LOG: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], logf); + break; + case Operation::SIN: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], sinf); + break; + case Operation::COS: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], cosf); + break; + case Operation::TAN: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], tanf); + break; + case Operation::ASIN: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], asinf); + break; + case Operation::ACOS: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], acosf); + break; + case Operation::ATAN: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], atanf); + break; + case Operation::ATAN2: + generateTwoArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]], atan2f); + break; + case Operation::SINH: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], sinhf); + break; + case Operation::COSH: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], coshf); + break; + case Operation::TANH: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], tanhf); + break; + case Operation::STEP: + c.cmge(workspaceVar[target[step]].s4(), workspaceVar[args[0]].s4(), imm(0)); + c.and_(workspaceVar[target[step]], workspaceVar[target[step]], constantVar[operationConstantIndex[step]]); + break; + case Operation::DELTA: + c.cmeq(workspaceVar[target[step]].s4(), workspaceVar[args[0]].s4(), imm(0)); + c.and_(workspaceVar[target[step]], workspaceVar[target[step]], constantVar[operationConstantIndex[step]]); + break; + case Operation::SQUARE: + c.fmul(workspaceVar[target[step]].s4(), workspaceVar[args[0]].s4(), workspaceVar[args[0]].s4()); + break; + case Operation::CUBE: + c.fmul(workspaceVar[target[step]].s4(), workspaceVar[args[0]].s4(), workspaceVar[args[0]].s4()); + c.fmul(workspaceVar[target[step]].s4(), workspaceVar[target[step]].s4(), workspaceVar[args[0]].s4()); + break; + case Operation::RECIPROCAL: + c.fdiv(workspaceVar[target[step]].s4(), constantVar[operationConstantIndex[step]].s4(), workspaceVar[args[0]].s4()); + break; + case Operation::ADD_CONSTANT: + c.fadd(workspaceVar[target[step]].s4(), workspaceVar[args[0]].s4(), constantVar[operationConstantIndex[step]].s4()); + break; + case Operation::MULTIPLY_CONSTANT: + c.fmul(workspaceVar[target[step]].s4(), workspaceVar[args[0]].s4(), constantVar[operationConstantIndex[step]].s4()); + break; + case Operation::POWER_CONSTANT: + generateTwoArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], constantVar[operationConstantIndex[step]], powf); + break; + case Operation::MIN: + c.fmin(workspaceVar[target[step]].s4(), workspaceVar[args[0]].s4(), workspaceVar[args[1]].s4()); + break; + case Operation::MAX: + c.fmax(workspaceVar[target[step]].s4(), workspaceVar[args[0]].s4(), workspaceVar[args[1]].s4()); + break; + case Operation::ABS: + c.fabs(workspaceVar[target[step]].s4(), workspaceVar[args[0]].s4()); + break; + case Operation::FLOOR: + c.frintm(workspaceVar[target[step]].s4(), workspaceVar[args[0]].s4()); + break; + case Operation::CEIL: + c.frintp(workspaceVar[target[step]].s4(), workspaceVar[args[0]].s4()); + break; + case Operation::SELECT: + c.fcmeq(workspaceVar[target[step]].s4(), workspaceVar[args[0]].s4(), imm(0)); + c.bsl(workspaceVar[target[step]], workspaceVar[args[2]], workspaceVar[args[1]]); + break; + default: + // Just invoke evaluateOperation(). + for (int element = 0; element < width; element++) { + for (int i = 0; i < (int) args.size(); i++) { + c.ins(argReg.s(0), workspaceVar[args[i]].s(element)); + c.fcvt(doubleArgReg, argReg); + c.str(doubleArgReg, arm::ptr(argsPointer, 8*i)); + } + arm::Gp fn = c.newIntPtr(); + c.mov(fn, imm((void*) evaluateOperation)); + InvokeNode* invoke; + c.invoke(&invoke, fn, FuncSignatureT()); + invoke->setArg(0, imm(&op)); + invoke->setArg(1, imm(&argValues[0])); + invoke->setRet(0, doubleResultReg); + c.fcvt(argReg, doubleResultReg); + c.ins(workspaceVar[target[step]].s(element), argReg.s(0)); + } + } + } + arm::Gp resultPointer = c.newIntPtr(); + c.mov(resultPointer, imm(&workspace[workspace.size()-width])); + c.str(workspaceVar.back().s4(), arm::ptr(resultPointer, 0)); + c.endFunc(); + c.finalize(); + runtime.add(&jitCode, &code); +} + +void CompiledVectorExpression::generateSingleArgCall(a64::Compiler& c, arm::Vec& dest, arm::Vec& arg, float (*function)(float)) { + arm::Gp fn = c.newIntPtr(); + c.mov(fn, imm((void*) function)); + arm::Vec a = c.newVecS(); + arm::Vec d = c.newVecS(); + for (int element = 0; element < width; element++) { + c.ins(a.s(0), arg.s(element)); + InvokeNode* invoke; + c.invoke(&invoke, fn, FuncSignatureT()); + invoke->setArg(0, a); + invoke->setRet(0, d); + c.ins(dest.s(element), d.s(0)); + } +} + +void CompiledVectorExpression::generateTwoArgCall(a64::Compiler& c, arm::Vec& dest, arm::Vec& arg1, arm::Vec& arg2, float (*function)(float, float)) { + arm::Gp fn = c.newIntPtr(); + c.mov(fn, imm((void*) function)); + arm::Vec a1 = c.newVecS(); + arm::Vec a2 = c.newVecS(); + arm::Vec d = c.newVecS(); + for (int element = 0; element < width; element++) { + c.ins(a1.s(0), arg1.s(element)); + c.ins(a2.s(0), arg2.s(element)); + InvokeNode* invoke; + c.invoke(&invoke, fn, FuncSignatureT()); + invoke->setArg(0, a1); + invoke->setArg(1, a2); + invoke->setRet(0, d); + c.ins(dest.s(element), d.s(0)); + } +} +#else + +void CompiledVectorExpression::generateJitCode() { + const CpuInfo& cpu = CpuInfo::host(); + if (!cpu.hasFeature(CpuFeatures::X86::kAVX)) + return; + CodeHolder code; + code.init(runtime.environment()); + x86::Compiler c(&code); + FuncNode* funcNode = c.addFunc(FuncSignatureT()); + funcNode->frame().setAvxEnabled(); + vector workspaceVar(workspace.size()/width); + for (int i = 0; i < (int) workspaceVar.size(); i++) + workspaceVar[i] = c.newYmmPs(); + x86::Gp argsPointer = c.newIntPtr(); + c.mov(argsPointer, imm(&argValues[0])); + vector > groups, groupPowers; + vector stepGroup; + findPowerGroups(groups, groupPowers, stepGroup); + + // Load the arguments into variables. + + for (set::const_iterator iter = variableNames.begin(); iter != variableNames.end(); ++iter) { + map::iterator index = variableIndices.find(*iter); + x86::Gp variablePointer = c.newIntPtr(); + c.mov(variablePointer, imm(getVariablePointer(index->first))); + if (width == 4) + c.vmovdqu(workspaceVar[index->second].xmm(), x86::ptr(variablePointer, 0, 0)); + else + c.vmovdqu(workspaceVar[index->second], x86::ptr(variablePointer, 0, 0)); + } + + // Make a list of all constants that will be needed for evaluation. + + vector operationConstantIndex(operation.size(), -1); + for (int step = 0; step < (int) operation.size(); step++) { + // Find the constant value (if any) used by this operation. + + Operation& op = *operation[step]; + double value; + if (op.getId() == Operation::CONSTANT) + value = dynamic_cast (op).getValue(); + else if (op.getId() == Operation::ADD_CONSTANT) + value = dynamic_cast (op).getValue(); + else if (op.getId() == Operation::MULTIPLY_CONSTANT) + value = dynamic_cast (op).getValue(); + else if (op.getId() == Operation::RECIPROCAL) + value = 1.0; + else if (op.getId() == Operation::STEP) + value = 1.0; + else if (op.getId() == Operation::DELTA) + value = 1.0; + else if (op.getId() == Operation::ABS) { + int mask = 0x7FFFFFFF; + value = *reinterpret_cast(&mask); + } + else if (op.getId() == Operation::POWER_CONSTANT) { + if (stepGroup[step] == -1) + value = dynamic_cast (op).getValue(); + else + value = 1.0; + } else + continue; + + // See if we already have a variable for this constant. + + for (int i = 0; i < (int) constants.size(); i++) + if (value == constants[i]) { + operationConstantIndex[step] = i; + break; + } + if (operationConstantIndex[step] == -1) { + operationConstantIndex[step] = constants.size(); + constants.push_back(value); + } + } + + // Load constants into variables. + + vector constantVar(constants.size()); + if (constants.size() > 0) { + x86::Gp constantsPointer = c.newIntPtr(); + c.mov(constantsPointer, imm(&constants[0])); + for (int i = 0; i < (int) constants.size(); i++) { + constantVar[i] = c.newYmmPs(); + c.vbroadcastss(constantVar[i], x86::ptr(constantsPointer, 4*i, 0)); + } + } + + // Evaluate the operations. + + vector hasComputedPower(operation.size(), false); + x86::Ymm argReg = c.newYmm(); + x86::Ymm doubleArgReg = c.newYmm(); + x86::Ymm doubleResultReg = c.newYmm(); + for (int step = 0; step < (int) operation.size(); step++) { + if (hasComputedPower[step]) + continue; + + // When one or more steps involve raising the same argument to multiple integer + // powers, we can compute them all together for efficiency. + + if (stepGroup[step] != -1) { + vector& group = groups[stepGroup[step]]; + vector& powers = groupPowers[stepGroup[step]]; + x86::Ymm multiplier = c.newYmmPs(); + if (powers[0] > 0) + c.vmovdqu(multiplier, workspaceVar[arguments[step][0]]); + else { + c.vdivps(multiplier, constantVar[operationConstantIndex[step]], workspaceVar[arguments[step][0]]); + for (int i = 0; i < powers.size(); i++) + powers[i] = -powers[i]; + } + vector hasAssigned(group.size(), false); + bool done = false; + while (!done) { + done = true; + for (int i = 0; i < group.size(); i++) { + if (powers[i] % 2 == 1) { + if (!hasAssigned[i]) + c.vmovdqu(workspaceVar[target[group[i]]], multiplier); + else + c.vmulps(workspaceVar[target[group[i]]], workspaceVar[target[group[i]]], multiplier); + hasAssigned[i] = true; + } + powers[i] >>= 1; + if (powers[i] != 0) + done = false; + } + if (!done) + c.vmulps(multiplier, multiplier, multiplier); + } + for (int step : group) + hasComputedPower[step] = true; + continue; + } + + // Evaluate the step. + + Operation& op = *operation[step]; + vector args = arguments[step]; + if (args.size() == 1) { + // One or more sequential arguments. Fill out the list. + + for (int i = 1; i < op.getNumArguments(); i++) + args.push_back(args[0] + i); + } + + // Generate instructions to execute this operation. + + switch (op.getId()) { + case Operation::CONSTANT: + c.vmovdqu(workspaceVar[target[step]], constantVar[operationConstantIndex[step]]); + break; + case Operation::ADD: + c.vaddps(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]]); + break; + case Operation::SUBTRACT: + c.vsubps(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]]); + break; + case Operation::MULTIPLY: + c.vmulps(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]]); + break; + case Operation::DIVIDE: + c.vdivps(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]]); + break; + case Operation::POWER: + generateTwoArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]], powf); + break; + case Operation::NEGATE: + c.vxorps(workspaceVar[target[step]], workspaceVar[target[step]], workspaceVar[target[step]]); + c.vsubps(workspaceVar[target[step]], workspaceVar[target[step]], workspaceVar[args[0]]); + break; + case Operation::SQRT: + c.vsqrtps(workspaceVar[target[step]], workspaceVar[args[0]]); + break; + case Operation::EXP: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], expf); + break; + case Operation::LOG: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], logf); + break; + case Operation::SIN: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], sinf); + break; + case Operation::COS: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], cosf); + break; + case Operation::TAN: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], tanf); + break; + case Operation::ASIN: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], asinf); + break; + case Operation::ACOS: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], acosf); + break; + case Operation::ATAN: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], atanf); + break; + case Operation::ATAN2: + generateTwoArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]], atan2f); + break; + case Operation::SINH: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], sinhf); + break; + case Operation::COSH: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], coshf); + break; + case Operation::TANH: + generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], tanhf); + break; + case Operation::STEP: + c.vxorps(workspaceVar[target[step]], workspaceVar[target[step]], workspaceVar[target[step]]); + c.vcmpps(workspaceVar[target[step]], workspaceVar[target[step]], workspaceVar[args[0]], imm(18)); // Comparison mode is _CMP_LE_OQ = 18 + c.vandps(workspaceVar[target[step]], workspaceVar[target[step]], constantVar[operationConstantIndex[step]]); + break; + case Operation::DELTA: + c.vxorps(workspaceVar[target[step]], workspaceVar[target[step]], workspaceVar[target[step]]); + c.vcmpps(workspaceVar[target[step]], workspaceVar[target[step]], workspaceVar[args[0]], imm(16)); // Comparison mode is _CMP_EQ_OQ = 0 + c.vandps(workspaceVar[target[step]], workspaceVar[target[step]], constantVar[operationConstantIndex[step]]); + break; + case Operation::SQUARE: + c.vmulps(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[0]]); + break; + case Operation::CUBE: + c.vmulps(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[0]]); + c.vmulps(workspaceVar[target[step]], workspaceVar[target[step]], workspaceVar[args[0]]); + break; + case Operation::RECIPROCAL: + c.vdivps(workspaceVar[target[step]], constantVar[operationConstantIndex[step]], workspaceVar[args[0]]); + break; + case Operation::ADD_CONSTANT: + c.vaddps(workspaceVar[target[step]], workspaceVar[args[0]], constantVar[operationConstantIndex[step]]); + break; + case Operation::MULTIPLY_CONSTANT: + c.vmulps(workspaceVar[target[step]], workspaceVar[args[0]], constantVar[operationConstantIndex[step]]); + break; + case Operation::POWER_CONSTANT: + generateTwoArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], constantVar[operationConstantIndex[step]], powf); + break; + case Operation::MIN: + c.vminps(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]]); + break; + case Operation::MAX: + c.vmaxps(workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]]); + break; + case Operation::ABS: + c.vandps(workspaceVar[target[step]], workspaceVar[args[0]], constantVar[operationConstantIndex[step]]); + break; + case Operation::FLOOR: + c.vroundps(workspaceVar[target[step]], workspaceVar[args[0]], imm(1)); + break; + case Operation::CEIL: + c.vroundps(workspaceVar[target[step]], workspaceVar[args[0]], imm(2)); + break; + case Operation::SELECT: + { + x86::Ymm mask = c.newYmmPs(); + c.vxorps(mask, mask, mask); + c.vcmpps(mask, mask, workspaceVar[args[0]], imm(0)); // Comparison mode is _CMP_EQ_OQ = 0 + c.vblendvps(workspaceVar[target[step]], workspaceVar[args[1]], workspaceVar[args[2]], mask); + break; + } + default: + // Just invoke evaluateOperation(). + + for (int element = 0; element < width; element++) { + for (int i = 0; i < (int) args.size(); i++) { + if (element < 4) + c.vshufps(argReg, workspaceVar[args[i]], workspaceVar[args[i]], imm(element)); + else { + c.vperm2f128(argReg, workspaceVar[args[i]], workspaceVar[args[i]], imm(1)); + c.vshufps(argReg, argReg, argReg, imm(element-4)); + } + c.vcvtss2sd(doubleArgReg.xmm(), doubleArgReg.xmm(), argReg.xmm()); + c.vmovsd(x86::ptr(argsPointer, 8*i, 0), doubleArgReg.xmm()); + } + x86::Gp fn = c.newIntPtr(); + c.mov(fn, imm((void*) evaluateOperation)); + InvokeNode* invoke; + c.invoke(&invoke, fn, FuncSignatureT()); + invoke->setArg(0, imm(&op)); + invoke->setArg(1, imm(&argValues[0])); + invoke->setRet(0, doubleResultReg); + c.vcvtsd2ss(argReg.xmm(), argReg.xmm(), doubleResultReg.xmm()); + if (element > 3) + c.vperm2f128(argReg, argReg, argReg, imm(0)); + if (element != 0) + c.vshufps(argReg, argReg, argReg, imm(0)); + c.vblendps(workspaceVar[target[step]], workspaceVar[target[step]], argReg, 1<()); + invoke->setArg(0, a); + invoke->setRet(0, d); + if (element > 3) + c.vperm2f128(d, d, d, imm(0)); + if (element != 0) + c.vshufps(d, d, d, imm(0)); + c.vblendps(dest, dest, d, 1<()); + invoke->setArg(0, a1); + invoke->setArg(1, a2); + invoke->setRet(0, d); + if (element > 3) + c.vperm2f128(d, d, d, imm(0)); + if (element != 0) + c.vshufps(d, d, d, imm(0)); + c.vblendps(dest, dest, d, 1< using namespace Lepton; using namespace std; @@ -62,6 +63,11 @@ ExpressionTreeNode::ExpressionTreeNode(Operation* operation) : operation(operati ExpressionTreeNode::ExpressionTreeNode(const ExpressionTreeNode& node) : operation(node.operation == NULL ? NULL : node.operation->clone()), children(node.getChildren()) { } +ExpressionTreeNode::ExpressionTreeNode(ExpressionTreeNode&& node) : operation(node.operation), children(move(node.children)) { + node.operation = NULL; + node.children.clear(); +} + ExpressionTreeNode::ExpressionTreeNode() : operation(NULL) { } @@ -98,6 +104,16 @@ ExpressionTreeNode& ExpressionTreeNode::operator=(const ExpressionTreeNode& node return *this; } +ExpressionTreeNode& ExpressionTreeNode::operator=(ExpressionTreeNode&& node) { + if (operation != NULL) + delete operation; + operation = node.operation; + children = move(node.children); + node.operation = NULL; + node.children.clear(); + return *this; +} + const Operation& ExpressionTreeNode::getOperation() const { return *operation; } @@ -105,3 +121,33 @@ const Operation& ExpressionTreeNode::getOperation() const { const vector& ExpressionTreeNode::getChildren() const { return children; } + +void ExpressionTreeNode::assignTags(vector& examples) const { + // Assign tag values to all nodes in a tree, such that two nodes have the same + // tag if and only if they (and all their children) are equal. This is used to + // optimize other operations. + + int numTags = examples.size(); + for (const ExpressionTreeNode& child : getChildren()) + child.assignTags(examples); + if (numTags == examples.size()) { + // All the children matched existing tags, so possibly this node does too. + + for (int i = 0; i < examples.size(); i++) { + const ExpressionTreeNode& example = *examples[i]; + bool matches = (getChildren().size() == example.getChildren().size() && getOperation() == example.getOperation()); + for (int j = 0; matches && j < getChildren().size(); j++) + if (getChildren()[j].tag != example.getChildren()[j].tag) + matches = false; + if (matches) { + tag = i; + return; + } + } + } + + // This node does not match any previous node, so assign a new tag. + + tag = examples.size(); + examples.push_back(this); +} diff --git a/lib/colvars/lepton/src/Operation.cpp b/lib/colvars/lepton/src/Operation.cpp index 78741c4814..b5a958b2f7 100644 --- a/lib/colvars/lepton/src/Operation.cpp +++ b/lib/colvars/lepton/src/Operation.cpp @@ -7,7 +7,7 @@ * Biological Structures at Stanford, funded under the NIH Roadmap for * * Medical Research, grant U54 GM072970. See https://simtk.org. * * * - * Portions copyright (c) 2009-2019 Stanford University and the Authors. * + * Portions copyright (c) 2009-2021 Stanford University and the Authors. * * Authors: Peter Eastman * * Contributors: * * * @@ -37,6 +37,12 @@ using namespace Lepton; using namespace std; +static bool isZero(const ExpressionTreeNode& node) { + if (node.getOperation().getId() != Operation::CONSTANT) + return false; + return dynamic_cast(node.getOperation()).getValue() == 0.0; +} + double Operation::Erf::evaluate(double* args, const map& variables) const { return erf(args[0]); } @@ -58,35 +64,71 @@ ExpressionTreeNode Operation::Variable::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { if (function->getNumArguments() == 0) return ExpressionTreeNode(new Operation::Constant(0.0)); - ExpressionTreeNode result = ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Custom(*this, 0), children), childDerivs[0]); - for (int i = 1; i < getNumArguments(); i++) { - result = ExpressionTreeNode(new Operation::Add(), - result, - ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Custom(*this, i), children), childDerivs[i])); + ExpressionTreeNode result; + bool foundTerm = false; + for (int i = 0; i < getNumArguments(); i++) { + if (!isZero(childDerivs[i])) { + if (foundTerm) + result = ExpressionTreeNode(new Operation::Add(), + result, + ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Custom(*this, i), children), childDerivs[i])); + else { + result = ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Custom(*this, i), children), childDerivs[i]); + foundTerm = true; + } + } } - return result; + if (foundTerm) + return result; + return ExpressionTreeNode(new Operation::Constant(0.0)); } ExpressionTreeNode Operation::Add::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return childDerivs[1]; + if (isZero(childDerivs[1])) + return childDerivs[0]; return ExpressionTreeNode(new Operation::Add(), childDerivs[0], childDerivs[1]); } ExpressionTreeNode Operation::Subtract::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) { + if (isZero(childDerivs[1])) + return ExpressionTreeNode(new Operation::Constant(0.0)); + return ExpressionTreeNode(new Operation::Negate(), childDerivs[1]); + } + if (isZero(childDerivs[1])) + return childDerivs[0]; return ExpressionTreeNode(new Operation::Subtract(), childDerivs[0], childDerivs[1]); } ExpressionTreeNode Operation::Multiply::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) { + if (isZero(childDerivs[1])) + return ExpressionTreeNode(new Operation::Constant(0.0)); + return ExpressionTreeNode(new Operation::Multiply(), children[0], childDerivs[1]); + } + if (isZero(childDerivs[1])) + return ExpressionTreeNode(new Operation::Multiply(), children[1], childDerivs[0]); return ExpressionTreeNode(new Operation::Add(), ExpressionTreeNode(new Operation::Multiply(), children[0], childDerivs[1]), ExpressionTreeNode(new Operation::Multiply(), children[1], childDerivs[0])); } ExpressionTreeNode Operation::Divide::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { - return ExpressionTreeNode(new Operation::Divide(), - ExpressionTreeNode(new Operation::Subtract(), + ExpressionTreeNode subexp; + if (isZero(childDerivs[0])) { + if (isZero(childDerivs[1])) + return ExpressionTreeNode(new Operation::Constant(0.0)); + subexp = ExpressionTreeNode(new Operation::Negate(), ExpressionTreeNode(new Operation::Multiply(), children[0], childDerivs[1])); + } + else if (isZero(childDerivs[1])) + subexp = ExpressionTreeNode(new Operation::Multiply(), children[1], childDerivs[0]); + else + subexp = ExpressionTreeNode(new Operation::Subtract(), ExpressionTreeNode(new Operation::Multiply(), children[1], childDerivs[0]), - ExpressionTreeNode(new Operation::Multiply(), children[0], childDerivs[1])), - ExpressionTreeNode(new Operation::Square(), children[1])); + ExpressionTreeNode(new Operation::Multiply(), children[0], childDerivs[1])); + return ExpressionTreeNode(new Operation::Divide(), subexp, ExpressionTreeNode(new Operation::Square(), children[1])); } ExpressionTreeNode Operation::Power::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { @@ -105,10 +147,14 @@ ExpressionTreeNode Operation::Power::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return ExpressionTreeNode(new Operation::Constant(0.0)); return ExpressionTreeNode(new Operation::Negate(), childDerivs[0]); } ExpressionTreeNode Operation::Sqrt::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return ExpressionTreeNode(new Operation::Constant(0.0)); return ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::MultiplyConstant(0.5), ExpressionTreeNode(new Operation::Reciprocal(), @@ -117,24 +163,32 @@ ExpressionTreeNode Operation::Sqrt::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return ExpressionTreeNode(new Operation::Constant(0.0)); return ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Exp(), children[0]), childDerivs[0]); } ExpressionTreeNode Operation::Log::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return ExpressionTreeNode(new Operation::Constant(0.0)); return ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Reciprocal(), children[0]), childDerivs[0]); } ExpressionTreeNode Operation::Sin::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return ExpressionTreeNode(new Operation::Constant(0.0)); return ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Cos(), children[0]), childDerivs[0]); } ExpressionTreeNode Operation::Cos::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return ExpressionTreeNode(new Operation::Constant(0.0)); return ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Negate(), ExpressionTreeNode(new Operation::Sin(), children[0])), @@ -142,6 +196,8 @@ ExpressionTreeNode Operation::Cos::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return ExpressionTreeNode(new Operation::Constant(0.0)); return ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Sec(), children[0]), @@ -150,6 +206,8 @@ ExpressionTreeNode Operation::Sec::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return ExpressionTreeNode(new Operation::Constant(0.0)); return ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Negate(), ExpressionTreeNode(new Operation::Multiply(), @@ -159,6 +217,8 @@ ExpressionTreeNode Operation::Csc::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return ExpressionTreeNode(new Operation::Constant(0.0)); return ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Square(), ExpressionTreeNode(new Operation::Sec(), children[0])), @@ -166,6 +226,8 @@ ExpressionTreeNode Operation::Tan::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return ExpressionTreeNode(new Operation::Constant(0.0)); return ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Negate(), ExpressionTreeNode(new Operation::Square(), @@ -174,6 +236,8 @@ ExpressionTreeNode Operation::Cot::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return ExpressionTreeNode(new Operation::Constant(0.0)); return ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Reciprocal(), ExpressionTreeNode(new Operation::Sqrt(), @@ -184,6 +248,8 @@ ExpressionTreeNode Operation::Asin::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return ExpressionTreeNode(new Operation::Constant(0.0)); return ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Negate(), ExpressionTreeNode(new Operation::Reciprocal(), @@ -195,6 +261,8 @@ ExpressionTreeNode Operation::Acos::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return ExpressionTreeNode(new Operation::Constant(0.0)); return ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Reciprocal(), ExpressionTreeNode(new Operation::AddConstant(1.0), @@ -213,6 +281,8 @@ ExpressionTreeNode Operation::Atan2::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return ExpressionTreeNode(new Operation::Constant(0.0)); return ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Cosh(), children[0]), @@ -220,6 +290,8 @@ ExpressionTreeNode Operation::Sinh::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return ExpressionTreeNode(new Operation::Constant(0.0)); return ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Sinh(), children[0]), @@ -227,6 +299,8 @@ ExpressionTreeNode Operation::Cosh::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return ExpressionTreeNode(new Operation::Constant(0.0)); return ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Subtract(), ExpressionTreeNode(new Operation::Constant(1.0)), @@ -236,6 +310,8 @@ ExpressionTreeNode Operation::Tanh::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return ExpressionTreeNode(new Operation::Constant(0.0)); return ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Constant(2.0/sqrt(M_PI))), @@ -246,6 +322,8 @@ ExpressionTreeNode Operation::Erf::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return ExpressionTreeNode(new Operation::Constant(0.0)); return ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Constant(-2.0/sqrt(M_PI))), @@ -264,6 +342,8 @@ ExpressionTreeNode Operation::Delta::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return ExpressionTreeNode(new Operation::Constant(0.0)); return ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::MultiplyConstant(2.0), children[0]), @@ -271,6 +351,8 @@ ExpressionTreeNode Operation::Square::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return ExpressionTreeNode(new Operation::Constant(0.0)); return ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::MultiplyConstant(3.0), ExpressionTreeNode(new Operation::Square(), children[0])), @@ -278,6 +360,8 @@ ExpressionTreeNode Operation::Cube::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return ExpressionTreeNode(new Operation::Constant(0.0)); return ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Negate(), ExpressionTreeNode(new Operation::Reciprocal(), @@ -290,11 +374,15 @@ ExpressionTreeNode Operation::AddConstant::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return ExpressionTreeNode(new Operation::Constant(0.0)); return ExpressionTreeNode(new Operation::MultiplyConstant(value), childDerivs[0]); } ExpressionTreeNode Operation::PowerConstant::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return ExpressionTreeNode(new Operation::Constant(0.0)); return ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::MultiplyConstant(value), ExpressionTreeNode(new Operation::PowerConstant(value-1), @@ -305,22 +393,18 @@ ExpressionTreeNode Operation::PowerConstant::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { ExpressionTreeNode step(new Operation::Step(), ExpressionTreeNode(new Operation::Subtract(), children[0], children[1])); - return ExpressionTreeNode(new Operation::Subtract(), - ExpressionTreeNode(new Operation::Multiply(), childDerivs[1], step), - ExpressionTreeNode(new Operation::Multiply(), childDerivs[0], - ExpressionTreeNode(new Operation::AddConstant(-1), step))); + return ExpressionTreeNode(new Operation::Select(), {step, childDerivs[1], childDerivs[0]}); } ExpressionTreeNode Operation::Max::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { ExpressionTreeNode step(new Operation::Step(), ExpressionTreeNode(new Operation::Subtract(), children[0], children[1])); - return ExpressionTreeNode(new Operation::Subtract(), - ExpressionTreeNode(new Operation::Multiply(), childDerivs[0], step), - ExpressionTreeNode(new Operation::Multiply(), childDerivs[1], - ExpressionTreeNode(new Operation::AddConstant(-1), step))); + return ExpressionTreeNode(new Operation::Select(), {step, childDerivs[0], childDerivs[1]}); } ExpressionTreeNode Operation::Abs::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + if (isZero(childDerivs[0])) + return ExpressionTreeNode(new Operation::Constant(0.0)); ExpressionTreeNode step(new Operation::Step(), children[0]); return ExpressionTreeNode(new Operation::Multiply(), childDerivs[0], @@ -337,9 +421,5 @@ ExpressionTreeNode Operation::Ceil::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { - vector derivChildren; - derivChildren.push_back(children[0]); - derivChildren.push_back(childDerivs[1]); - derivChildren.push_back(childDerivs[2]); - return ExpressionTreeNode(new Operation::Select(), derivChildren); + return ExpressionTreeNode(new Operation::Select(), {children[0], childDerivs[1], childDerivs[2]}); } diff --git a/lib/colvars/lepton/src/ParsedExpression.cpp b/lib/colvars/lepton/src/ParsedExpression.cpp index fd3b091d3c..ea2cf707d6 100644 --- a/lib/colvars/lepton/src/ParsedExpression.cpp +++ b/lib/colvars/lepton/src/ParsedExpression.cpp @@ -6,7 +6,7 @@ * Biological Structures at Stanford, funded under the NIH Roadmap for * * Medical Research, grant U54 GM072970. See https://simtk.org. * * * - * Portions copyright (c) 2009 Stanford University and the Authors. * + * Portions copyright (c) 2009-2022 Stanford University and the Authors. * * Authors: Peter Eastman * * Contributors: * * * @@ -31,6 +31,7 @@ #include "lepton/ParsedExpression.h" #include "lepton/CompiledExpression.h" +#include "lepton/CompiledVectorExpression.h" #include "lepton/ExpressionProgram.h" #include "lepton/Operation.h" #include @@ -68,9 +69,16 @@ double ParsedExpression::evaluate(const ExpressionTreeNode& node, const map examples; + result.assignTags(examples); + map nodeCache; + result = precalculateConstantSubexpressions(result, nodeCache); while (true) { - ExpressionTreeNode simplified = substituteSimplerExpression(result); + examples.clear(); + result.assignTags(examples); + nodeCache.clear(); + ExpressionTreeNode simplified = substituteSimplerExpression(result, nodeCache); if (simplified == result) break; result = simplified; @@ -80,9 +88,15 @@ ParsedExpression ParsedExpression::optimize() const { ParsedExpression ParsedExpression::optimize(const map& variables) const { ExpressionTreeNode result = preevaluateVariables(getRootNode(), variables); - result = precalculateConstantSubexpressions(result); + vector examples; + result.assignTags(examples); + map nodeCache; + result = precalculateConstantSubexpressions(result, nodeCache); while (true) { - ExpressionTreeNode simplified = substituteSimplerExpression(result); + examples.clear(); + result.assignTags(examples); + nodeCache.clear(); + ExpressionTreeNode simplified = substituteSimplerExpression(result, nodeCache); if (simplified == result) break; result = simplified; @@ -104,36 +118,67 @@ ExpressionTreeNode ParsedExpression::preevaluateVariables(const ExpressionTreeNo return ExpressionTreeNode(node.getOperation().clone(), children); } -ExpressionTreeNode ParsedExpression::precalculateConstantSubexpressions(const ExpressionTreeNode& node) { +ExpressionTreeNode ParsedExpression::precalculateConstantSubexpressions(const ExpressionTreeNode& node, map& nodeCache) { + auto cached = nodeCache.find(node.tag); + if (cached != nodeCache.end()) + return cached->second; vector children(node.getChildren().size()); for (int i = 0; i < (int) children.size(); i++) - children[i] = precalculateConstantSubexpressions(node.getChildren()[i]); + children[i] = precalculateConstantSubexpressions(node.getChildren()[i], nodeCache); ExpressionTreeNode result = ExpressionTreeNode(node.getOperation().clone(), children); - if (node.getOperation().getId() == Operation::VARIABLE || node.getOperation().getId() == Operation::CUSTOM) + if (node.getOperation().getId() == Operation::VARIABLE || node.getOperation().getId() == Operation::CUSTOM) { + nodeCache[node.tag] = result; return result; + } for (int i = 0; i < (int) children.size(); i++) - if (children[i].getOperation().getId() != Operation::CONSTANT) + if (children[i].getOperation().getId() != Operation::CONSTANT) { + nodeCache[node.tag] = result; return result; - return ExpressionTreeNode(new Operation::Constant(evaluate(result, map()))); + } + result = ExpressionTreeNode(new Operation::Constant(evaluate(result, map()))); + nodeCache[node.tag] = result; + return result; } -ExpressionTreeNode ParsedExpression::substituteSimplerExpression(const ExpressionTreeNode& node) { +ExpressionTreeNode ParsedExpression::substituteSimplerExpression(const ExpressionTreeNode& node, map& nodeCache) { vector children(node.getChildren().size()); - for (int i = 0; i < (int) children.size(); i++) - children[i] = substituteSimplerExpression(node.getChildren()[i]); + for (int i = 0; i < (int) children.size(); i++) { + const ExpressionTreeNode& child = node.getChildren()[i]; + auto cached = nodeCache.find(child.tag); + if (cached == nodeCache.end()) { + children[i] = substituteSimplerExpression(child, nodeCache); + nodeCache[child.tag] = children[i]; + } + else + children[i] = cached->second; + } + + // Collect some info on constant expressions in children + bool first_const = children.size() > 0 && isConstant(children[0]); // is first child constant? + bool second_const = children.size() > 1 && isConstant(children[1]); ; // is second child constant? + double first, second; // if yes, value of first and second child + if (first_const) + first = getConstantValue(children[0]); + if (second_const) + second = getConstantValue(children[1]); + switch (node.getOperation().getId()) { case Operation::ADD: { - double first = getConstantValue(children[0]); - double second = getConstantValue(children[1]); - if (first == 0.0) // Add 0 - return children[1]; - if (second == 0.0) // Add 0 - return children[0]; - if (first == first) // Add a constant - return ExpressionTreeNode(new Operation::AddConstant(first), children[1]); - if (second == second) // Add a constant - return ExpressionTreeNode(new Operation::AddConstant(second), children[0]); + if (first_const) { + if (first == 0.0) { // Add 0 + return children[1]; + } else { // Add a constant + return ExpressionTreeNode(new Operation::AddConstant(first), children[1]); + } + } + if (second_const) { + if (second == 0.0) { // Add 0 + return children[0]; + } else { // Add a constant + return ExpressionTreeNode(new Operation::AddConstant(second), children[0]); + } + } if (children[1].getOperation().getId() == Operation::NEGATE) // a+(-b) = a-b return ExpressionTreeNode(new Operation::Subtract(), children[0], children[1].getChildren()[0]); if (children[0].getOperation().getId() == Operation::NEGATE) // (-a)+b = b-a @@ -144,34 +189,35 @@ ExpressionTreeNode ParsedExpression::substituteSimplerExpression(const Expressio { if (children[0] == children[1]) return ExpressionTreeNode(new Operation::Constant(0.0)); // Subtracting anything from itself is 0 - double first = getConstantValue(children[0]); - if (first == 0.0) // Subtract from 0 - return ExpressionTreeNode(new Operation::Negate(), children[1]); - double second = getConstantValue(children[1]); - if (second == 0.0) // Subtract 0 - return children[0]; - if (second == second) // Subtract a constant - return ExpressionTreeNode(new Operation::AddConstant(-second), children[0]); + if (first_const) { + if (first == 0.0) // Subtract from 0 + return ExpressionTreeNode(new Operation::Negate(), children[1]); + } + if (second_const) { + if (second == 0.0) { // Subtract 0 + return children[0]; + } else { // Subtract a constant + return ExpressionTreeNode(new Operation::AddConstant(-second), children[0]); + } + } if (children[1].getOperation().getId() == Operation::NEGATE) // a-(-b) = a+b return ExpressionTreeNode(new Operation::Add(), children[0], children[1].getChildren()[0]); break; } case Operation::MULTIPLY: { - double first = getConstantValue(children[0]); - double second = getConstantValue(children[1]); - if (first == 0.0 || second == 0.0) // Multiply by 0 + if ((first_const && first == 0.0) || (second_const && second == 0.0)) // Multiply by 0 return ExpressionTreeNode(new Operation::Constant(0.0)); - if (first == 1.0) // Multiply by 1 + if (first_const && first == 1.0) // Multiply by 1 return children[1]; - if (second == 1.0) // Multiply by 1 + if (second_const && second == 1.0) // Multiply by 1 return children[0]; - if (children[0].getOperation().getId() == Operation::CONSTANT) { // Multiply by a constant + if (first_const) { // Multiply by a constant if (children[1].getOperation().getId() == Operation::MULTIPLY_CONSTANT) // Combine two multiplies into a single one return ExpressionTreeNode(new Operation::MultiplyConstant(first*dynamic_cast(&children[1].getOperation())->getValue()), children[1].getChildren()[0]); return ExpressionTreeNode(new Operation::MultiplyConstant(first), children[1]); } - if (children[1].getOperation().getId() == Operation::CONSTANT) { // Multiply by a constant + if (second_const) { // Multiply by a constant if (children[0].getOperation().getId() == Operation::MULTIPLY_CONSTANT) // Combine two multiplies into a single one return ExpressionTreeNode(new Operation::MultiplyConstant(second*dynamic_cast(&children[0].getOperation())->getValue()), children[0].getChildren()[0]); return ExpressionTreeNode(new Operation::MultiplyConstant(second), children[0]); @@ -202,18 +248,16 @@ ExpressionTreeNode ParsedExpression::substituteSimplerExpression(const Expressio { if (children[0] == children[1]) return ExpressionTreeNode(new Operation::Constant(1.0)); // Dividing anything from itself is 0 - double numerator = getConstantValue(children[0]); - if (numerator == 0.0) // 0 divided by something + if (first_const && first == 0.0) // 0 divided by something return ExpressionTreeNode(new Operation::Constant(0.0)); - if (numerator == 1.0) // 1 divided by something + if (first_const && first == 1.0) // 1 divided by something return ExpressionTreeNode(new Operation::Reciprocal(), children[1]); - double denominator = getConstantValue(children[1]); - if (denominator == 1.0) // Divide by 1 + if (second_const && second == 1.0) // Divide by 1 return children[0]; - if (children[1].getOperation().getId() == Operation::CONSTANT) { + if (second_const) { if (children[0].getOperation().getId() == Operation::MULTIPLY_CONSTANT) // Combine a multiply and a divide into one multiply - return ExpressionTreeNode(new Operation::MultiplyConstant(dynamic_cast(&children[0].getOperation())->getValue()/denominator), children[0].getChildren()[0]); - return ExpressionTreeNode(new Operation::MultiplyConstant(1.0/denominator), children[0]); // Replace a divide with a multiply + return ExpressionTreeNode(new Operation::MultiplyConstant(dynamic_cast(&children[0].getOperation())->getValue()/second), children[0].getChildren()[0]); + return ExpressionTreeNode(new Operation::MultiplyConstant(1.0/second), children[0]); // Replace a divide with a multiply } if (children[0].getOperation().getId() == Operation::NEGATE && children[1].getOperation().getId() == Operation::NEGATE) // The two negations cancel return ExpressionTreeNode(new Operation::Divide(), children[0].getChildren()[0], children[1].getChildren()[0]); @@ -229,34 +273,34 @@ ExpressionTreeNode ParsedExpression::substituteSimplerExpression(const Expressio } case Operation::POWER: { - double base = getConstantValue(children[0]); - if (base == 0.0) // 0 to any power is 0 + if (first_const && first == 0.0) // 0 to any power is 0 return ExpressionTreeNode(new Operation::Constant(0.0)); - if (base == 1.0) // 1 to any power is 1 + if (first_const && first == 1.0) // 1 to any power is 1 return ExpressionTreeNode(new Operation::Constant(1.0)); - double exponent = getConstantValue(children[1]); - if (exponent == 0.0) // x^0 = 1 - return ExpressionTreeNode(new Operation::Constant(1.0)); - if (exponent == 1.0) // x^1 = x - return children[0]; - if (exponent == -1.0) // x^-1 = recip(x) - return ExpressionTreeNode(new Operation::Reciprocal(), children[0]); - if (exponent == 2.0) // x^2 = square(x) - return ExpressionTreeNode(new Operation::Square(), children[0]); - if (exponent == 3.0) // x^3 = cube(x) - return ExpressionTreeNode(new Operation::Cube(), children[0]); - if (exponent == 0.5) // x^0.5 = sqrt(x) - return ExpressionTreeNode(new Operation::Sqrt(), children[0]); - if (exponent == exponent) // Constant power - return ExpressionTreeNode(new Operation::PowerConstant(exponent), children[0]); + if (second_const) { // Constant exponent + if (second == 0.0) // x^0 = 1 + return ExpressionTreeNode(new Operation::Constant(1.0)); + if (second == 1.0) // x^1 = x + return children[0]; + if (second == -1.0) // x^-1 = recip(x) + return ExpressionTreeNode(new Operation::Reciprocal(), children[0]); + if (second == 2.0) // x^2 = square(x) + return ExpressionTreeNode(new Operation::Square(), children[0]); + if (second == 3.0) // x^3 = cube(x) + return ExpressionTreeNode(new Operation::Cube(), children[0]); + if (second == 0.5) // x^0.5 = sqrt(x) + return ExpressionTreeNode(new Operation::Sqrt(), children[0]); + // Constant power + return ExpressionTreeNode(new Operation::PowerConstant(second), children[0]); + } break; } case Operation::NEGATE: { if (children[0].getOperation().getId() == Operation::MULTIPLY_CONSTANT) // Combine a multiply and a negate into a single multiply return ExpressionTreeNode(new Operation::MultiplyConstant(-dynamic_cast(&children[0].getOperation())->getValue()), children[0].getChildren()[0]); - if (children[0].getOperation().getId() == Operation::CONSTANT) // Negate a constant - return ExpressionTreeNode(new Operation::Constant(-getConstantValue(children[0]))); + if (first_const) // Negate a constant + return ExpressionTreeNode(new Operation::Constant(-first)); if (children[0].getOperation().getId() == Operation::NEGATE) // The two negations cancel return children[0].getChildren()[0]; break; @@ -265,7 +309,7 @@ ExpressionTreeNode ParsedExpression::substituteSimplerExpression(const Expressio { if (children[0].getOperation().getId() == Operation::MULTIPLY_CONSTANT) // Combine two multiplies into a single one return ExpressionTreeNode(new Operation::MultiplyConstant(dynamic_cast(&node.getOperation())->getValue()*dynamic_cast(&children[0].getOperation())->getValue()), children[0].getChildren()[0]); - if (children[0].getOperation().getId() == Operation::CONSTANT) // Multiply two constants + if (first_const) // Multiply two constants return ExpressionTreeNode(new Operation::Constant(dynamic_cast(&node.getOperation())->getValue()*getConstantValue(children[0]))); if (children[0].getOperation().getId() == Operation::NEGATE) // Combine a multiply and a negate into a single multiply return ExpressionTreeNode(new Operation::MultiplyConstant(-dynamic_cast(&node.getOperation())->getValue()), children[0].getChildren()[0]); @@ -293,20 +337,33 @@ ExpressionTreeNode ParsedExpression::substituteSimplerExpression(const Expressio } ParsedExpression ParsedExpression::differentiate(const string& variable) const { - return differentiate(getRootNode(), variable); + vector examples; + getRootNode().assignTags(examples); + map nodeCache; + return differentiate(getRootNode(), variable, nodeCache); } -ExpressionTreeNode ParsedExpression::differentiate(const ExpressionTreeNode& node, const string& variable) { +ExpressionTreeNode ParsedExpression::differentiate(const ExpressionTreeNode& node, const string& variable, map& nodeCache) { + auto cached = nodeCache.find(node.tag); + if (cached != nodeCache.end()) + return cached->second; vector childDerivs(node.getChildren().size()); for (int i = 0; i < (int) childDerivs.size(); i++) - childDerivs[i] = differentiate(node.getChildren()[i], variable); - return node.getOperation().differentiate(node.getChildren(),childDerivs, variable); + childDerivs[i] = differentiate(node.getChildren()[i], variable, nodeCache); + ExpressionTreeNode result = node.getOperation().differentiate(node.getChildren(), childDerivs, variable); + nodeCache[node.tag] = result; + return result; +} + +bool ParsedExpression::isConstant(const ExpressionTreeNode& node) { + return (node.getOperation().getId() == Operation::CONSTANT); } double ParsedExpression::getConstantValue(const ExpressionTreeNode& node) { - if (node.getOperation().getId() == Operation::CONSTANT) - return dynamic_cast(node.getOperation()).getValue(); - return numeric_limits::quiet_NaN(); + if (node.getOperation().getId() != Operation::CONSTANT) { + throw Exception("getConstantValue called on a non-constant ExpressionNode"); + } + return dynamic_cast(node.getOperation()).getValue(); } ExpressionProgram ParsedExpression::createProgram() const { @@ -317,6 +374,10 @@ CompiledExpression ParsedExpression::createCompiledExpression() const { return CompiledExpression(*this); } +CompiledVectorExpression ParsedExpression::createCompiledVectorExpression(int width) const { + return CompiledVectorExpression(*this, width); +} + ParsedExpression ParsedExpression::renameVariables(const map& replacements) const { return ParsedExpression(renameNodeVariables(getRootNode(), replacements)); } diff --git a/lib/install_helpers.py b/lib/install_helpers.py index 7990463736..e1ebd1cde7 100644 --- a/lib/install_helpers.py +++ b/lib/install_helpers.py @@ -1,4 +1,4 @@ -import hashlib,os,subprocess,sys +import hashlib,os,subprocess # try to auto-detect the maximum number of available CPUs def get_cpus(): diff --git a/lib/latte/Install.py b/lib/latte/Install.py index 94879ff4a0..2e8f9bee8d 100644 --- a/lib/latte/Install.py +++ b/lib/latte/Install.py @@ -71,7 +71,8 @@ buildflag = args.build pathflag = args.path is not None version = args.version suffixflag = args.machine is not None -suffix = args.machine +if suffixflag: + suffix = args.machine if pathflag: lattedir = args.path @@ -132,8 +133,6 @@ os.symlink(os.path.join(lattedir, 'src', 'latte_c_bind.o'), 'filelink.o') # copy Makefile.lammps.suffix to Makefile.lammps if suffixflag or not os.path.exists("Makefile.lammps"): - if suffix is None: - suffix = 'gfortran' print("Creating Makefile.lammps") if os.path.exists("Makefile.lammps.%s" % suffix): shutil.copyfile("Makefile.lammps.%s" % suffix, 'Makefile.lammps') diff --git a/lib/pace/Install.py b/lib/pace/Install.py index c59c249657..790acd4cf4 100644 --- a/lib/pace/Install.py +++ b/lib/pace/Install.py @@ -15,7 +15,7 @@ from install_helpers import fullpath, geturl, checkmd5sum # settings thisdir = fullpath('.') -version = 'v.2021.10.25.fix' +version = 'v.2021.10.25.fix2' # known checksums for different PACE versions. used to validate the download. checksums = { \ @@ -23,7 +23,8 @@ checksums = { \ 'v.2021.4.9' : '4db54962fbd6adcf8c18d46e1798ceb5', 'v.2021.9.28' : 'f98363bb98adc7295ea63974738c2a1b', 'v.2021.10.25' : 'a2ac3315c41a1a4a5c912bcb1bc9c5cc', - 'v.2021.10.25.fix': 'e0572de57039d4afedefb25707b6ceae' + 'v.2021.10.25.fix': 'e0572de57039d4afedefb25707b6ceae', + 'v.2021.10.25.fix2': '32394d799bc282bb57696c78c456e64f' } diff --git a/python/install.py b/python/install.py index a71a601c42..591e8525dc 100644 --- a/python/install.py +++ b/python/install.py @@ -11,7 +11,7 @@ independently and used to build the wheel without installing it. """ from __future__ import print_function -import sys,os,shutil,time,glob,subprocess +import sys,os,shutil,glob,subprocess from argparse import ArgumentParser parser = ArgumentParser(prog='install.py', @@ -23,6 +23,8 @@ parser.add_argument("-l", "--lib", required=True, help="path to the compiled LAMMPS shared library") parser.add_argument("-n", "--noinstall", action="store_true", default=False, help="only build a binary wheel. Don't attempt to install it") +parser.add_argument("-w", "--wheeldir", required=False, + help="path to a directory where the created wheel will be stored") args = parser.parse_args() @@ -30,7 +32,7 @@ args = parser.parse_args() if args.package: if not os.path.exists(args.package): - print( "ERROR: LAMMPS package %s does not exist" % args.package) + print("ERROR: LAMMPS package %s does not exist" % args.package) parser.print_help() sys.exit(1) else: @@ -38,12 +40,20 @@ if args.package: if args.lib: if not os.path.exists(args.lib): - print( "ERROR: LAMMPS shared library %s does not exist" % args.lib) + print("ERROR: LAMMPS shared library %s does not exist" % args.lib) parser.print_help() sys.exit(1) else: args.lib = os.path.abspath(args.lib) +if args.wheeldir: + if not os.path.exists(args.wheeldir): + print("ERROR: directory %s to store the wheel does not exist" % args.wheeldir) + parser.print_help() + sys.exit(1) + else: + args.wheeldir = os.path.abspath(args.wheeldir) + # we need to switch to the folder of the python package olddir = os.path.abspath('.') os.chdir(os.path.dirname(args.package)) @@ -62,10 +72,10 @@ shutil.copy(args.lib,'lammps') # create a virtual environment for building the wheel shutil.rmtree('buildwheel',True) try: - txt = subprocess.check_output([sys.executable, '-m', 'virtualenv', 'buildwheel', '-p', sys.executable], stderr=subprocess.STDOUT, shell=False) + txt = subprocess.check_output([sys.executable, '-m', 'venv', 'buildwheel'], stderr=subprocess.STDOUT, shell=False) print(txt.decode('UTF-8')) except subprocess.CalledProcessError as err: - sys.exit("Failed to create a virtualenv: {0}".format(err.output.decode('UTF-8'))) + sys.exit("Failed to create a virtual environment: {0}".format(err.output.decode('UTF-8'))) # now run the commands to build the wheel. those must be in a separate script # and run in subprocess, since this will use the virtual environment and @@ -80,10 +90,18 @@ os.remove(os.path.join('lammps',os.path.basename(args.lib))) # stop here if we were asked not to install the wheel we created if args.noinstall: - exit(0) + if args.wheeldir: + for wheel in glob.glob('lammps-*.whl'): + shutil.copy(wheel, args.wheeldir) + os.remove(wheel) + exit(0) # install the wheel with pip. first try to install in the default environment. # that will be a virtual environment, if active, or the system folder. +# if in a virtual environment, we must not use the python executable +# that is running this script (configured by cmake), but use "python" +# from the regular system path. The user may have changed to the virtual +# environment *after* running cmake. # recent versions of pip will automatically drop to use the user folder # in case the system folder is not writable. @@ -93,21 +111,35 @@ if args.noinstall: # must be uninstalled manually. We must not ignore this and drop # back to install into a (forced) user folder. -print("Installing wheel") +if "VIRTUAL_ENV" in os.environ: + print("Installing wheel into virtual environment") + py_exe = 'python' +else: + print("Installing wheel into system site-packages folder") + py_exe = sys.executable + for wheel in glob.glob('lammps-*.whl'): try: - txt = subprocess.check_output([sys.executable, '-m', 'pip', 'install', '--force-reinstall', wheel], stderr=subprocess.STDOUT, shell=False) + txt = subprocess.check_output([py_exe, '-m', 'pip', 'install', '--force-reinstall', wheel], stderr=subprocess.STDOUT, shell=False) print(txt.decode('UTF-8')) + if args.wheeldir: + shutil.copy(wheel, args.wheeldir) + else: + shutil.copy(wheel, olddir) + os.remove(wheel) continue except subprocess.CalledProcessError as err: errmsg = err.output.decode('UTF-8') if errmsg.find("distutils installed"): sys.exit(errmsg + "You need to uninstall the LAMMPS python module manually first.\n") try: - print('Installing wheel into standard site-packages folder failed. Trying user folder now') + print('Installing wheel into system site-packages folder failed. Trying user folder now') txt = subprocess.check_output([sys.executable, '-m', 'pip', 'install', '--user', '--force-reinstall', wheel], stderr=subprocess.STDOUT, shell=False) print(txt.decode('UTF-8')) + if args.wheeldir: + shutil.copy(wheel, args.wheeldir) + else: + shutil.copy(wheel, olddir) + os.remove(wheel) except: sys.exit('Failed to install wheel ' + wheel) - shutil.copy(wheel, olddir) - os.remove(wheel) diff --git a/python/lammps/core.py b/python/lammps/core.py index 23002b210c..930a40a4b0 100644 --- a/python/lammps/core.py +++ b/python/lammps/core.py @@ -188,20 +188,17 @@ class lammps(object): [c_void_p,POINTER(c_double),POINTER(c_double),c_double,c_double,c_double] self.lib.lammps_reset_box.restype = None - self.lib.lammps_gather_atoms.argtypes = \ - [c_void_p,c_char_p,c_int,c_int,c_void_p] + self.lib.lammps_gather_atoms.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p] self.lib.lammps_gather_atoms.restype = None - self.lib.lammps_gather_atoms_concat.argtypes = \ - [c_void_p,c_char_p,c_int,c_int,c_void_p] + self.lib.lammps_gather_atoms_concat.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p] self.lib.lammps_gather_atoms_concat.restype = None self.lib.lammps_gather_atoms_subset.argtypes = \ [c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p] self.lib.lammps_gather_atoms_subset.restype = None - self.lib.lammps_scatter_atoms.argtypes = \ - [c_void_p,c_char_p,c_int,c_int,c_void_p] + self.lib.lammps_scatter_atoms.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p] self.lib.lammps_scatter_atoms.restype = None self.lib.lammps_scatter_atoms_subset.argtypes = \ @@ -211,20 +208,17 @@ class lammps(object): self.lib.lammps_gather_bonds.argtypes = [c_void_p,c_void_p] self.lib.lammps_gather_bonds.restype = None - self.lib.lammps_gather.argtypes = \ - [c_void_p,c_char_p,c_int,c_int,c_void_p] + self.lib.lammps_gather.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p] self.lib.lammps_gather.restype = None - self.lib.lammps_gather_concat.argtypes = \ - [c_void_p,c_char_p,c_int,c_int,c_void_p] + self.lib.lammps_gather_concat.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p] self.lib.lammps_gather_concat.restype = None self.lib.lammps_gather_subset.argtypes = \ [c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p] self.lib.lammps_gather_subset.restype = None - self.lib.lammps_scatter.argtypes = \ - [c_void_p,c_char_p,c_int,c_int,c_void_p] + self.lib.lammps_scatter.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p] self.lib.lammps_scatter.restype = None self.lib.lammps_scatter_subset.argtypes = \ @@ -244,7 +238,8 @@ class lammps(object): self.lib.lammps_neighlist_num_elements.argtypes = [c_void_p, c_int] self.lib.lammps_neighlist_num_elements.restype = c_int - self.lib.lammps_neighlist_element_neighbors.argtypes = [c_void_p, c_int, c_int, POINTER(c_int), POINTER(c_int), POINTER(POINTER(c_int))] + self.lib.lammps_neighlist_element_neighbors.argtypes = \ + [c_void_p, c_int, c_int, POINTER(c_int), POINTER(c_int), POINTER(POINTER(c_int))] self.lib.lammps_neighlist_element_neighbors.restype = None self.lib.lammps_is_running.argtypes = [c_void_p] @@ -368,11 +363,9 @@ class lammps(object): if type(cmdargs[i]) is str: cmdargs[i] = cmdargs[i].encode() cargs = (c_char_p*narg)(*cmdargs) - self.lib.lammps_open.argtypes = [c_int, c_char_p*narg, \ - MPI_Comm, c_void_p] + self.lib.lammps_open.argtypes = [c_int, c_char_p*narg, MPI_Comm, c_void_p] else: - self.lib.lammps_open.argtypes = [c_int, c_char_p, \ - MPI_Comm, c_void_p] + self.lib.lammps_open.argtypes = [c_int, c_char_p, MPI_Comm, c_void_p] self.opened = 1 comm_ptr = self.MPI._addressof(comm) @@ -390,8 +383,7 @@ class lammps(object): if type(cmdargs[i]) is str: cmdargs[i] = cmdargs[i].encode() cargs = (c_char_p*narg)(*cmdargs) - self.lib.lammps_open_no_mpi.argtypes = [c_int, c_char_p*narg, \ - c_void_p] + self.lib.lammps_open_no_mpi.argtypes = [c_int, c_char_p*narg, c_void_p] self.lmp = c_void_p(self.lib.lammps_open_no_mpi(narg,cargs,None)) else: self.lib.lammps_open_no_mpi.argtypes = [c_int, c_char_p, c_void_p] @@ -963,17 +955,14 @@ class lammps(object): return ptr elif ctype == LMP_SIZE_COLS: - if cstyle == LMP_STYLE_GLOBAL \ - or cstyle == LMP_STYLE_ATOM \ - or cstyle == LMP_STYLE_LOCAL: + if cstyle == LMP_STYLE_GLOBAL or cstyle == LMP_STYLE_ATOM or cstyle == LMP_STYLE_LOCAL: self.lib.lammps_extract_compute.restype = POINTER(c_int) with ExceptionCheck(self): ptr = self.lib.lammps_extract_compute(self.lmp,cid,cstyle,ctype) return ptr[0] elif ctype == LMP_SIZE_VECTOR or ctype == LMP_SIZE_ROWS: - if cstyle == LMP_STYLE_GLOBAL \ - or cstyle == LMP_STYLE_LOCAL: + if cstyle == LMP_STYLE_GLOBAL or cstyle == LMP_STYLE_LOCAL: self.lib.lammps_extract_compute.restype = POINTER(c_int) with ExceptionCheck(self): ptr = self.lib.lammps_extract_compute(self.lmp,cid,cstyle,ctype) diff --git a/python/lammps/numpy_wrapper.py b/python/lammps/numpy_wrapper.py index 3619728081..ce0cb35e47 100644 --- a/python/lammps/numpy_wrapper.py +++ b/python/lammps/numpy_wrapper.py @@ -165,7 +165,7 @@ class numpy_wrapper: """ value = self.lmp.extract_compute(cid, cstyle, ctype) - if cstyle in (LMP_STYLE_GLOBAL, LMP_STYLE_LOCAL): + if cstyle == LMP_STYLE_GLOBAL: if ctype == LMP_TYPE_VECTOR: nrows = self.lmp.extract_compute(cid, cstyle, LMP_SIZE_VECTOR) return self.darray(value, nrows) @@ -173,6 +173,13 @@ class numpy_wrapper: nrows = self.lmp.extract_compute(cid, cstyle, LMP_SIZE_ROWS) ncols = self.lmp.extract_compute(cid, cstyle, LMP_SIZE_COLS) return self.darray(value, nrows, ncols) + elif cstyle == LMP_STYLE_LOCAL: + nrows = self.lmp.extract_compute(cid, cstyle, LMP_SIZE_ROWS) + ncols = self.lmp.extract_compute(cid, cstyle, LMP_SIZE_COLS) + if ncols == 0: + return self.darray(value, nrows) + else: + return self.darray(value, nrows, ncols) elif cstyle == LMP_STYLE_ATOM: if ctype == LMP_TYPE_VECTOR: nlocal = self.lmp.extract_global("nlocal") diff --git a/python/makewheel.py b/python/makewheel.py index 64ecbe2464..f13ad110ce 100644 --- a/python/makewheel.py +++ b/python/makewheel.py @@ -1,14 +1,26 @@ #!/usr/bin/env python -import sys,os,shutil +import sys,os,site -# find python script to activate the virtual environment and source it +base = os.path.abspath('buildwheel') if sys.platform == 'win32': - virtenv=os.path.join('buildwheel','Scripts','activate_this.py') + bin_dir=os.path.join(base,'Scripts') else: - virtenv=os.path.join('buildwheel','bin','activate_this.py') + bin_dir=os.path.join(base,'bin') -exec(open(virtenv).read(), {'__file__': virtenv}) +# prepend bin to PATH, set venv path +os.environ["PATH"] = os.pathsep.join([bin_dir] + os.environ.get("PATH", "").split(os.pathsep)) +os.environ["VIRTUAL_ENV"] = base + +# add the virtual environments libraries to the host python import mechanism +prev_length = len(sys.path) +for lib in "__LIB_FOLDERS__".split(os.pathsep): + path = os.path.realpath(os.path.join(bin_dir, lib)) + site.addsitedir(path) +sys.path[:] = sys.path[prev_length:] + sys.path[0:prev_length] + +sys.real_prefix = sys.prefix +sys.prefix = base # update pip and install all requirements to build the wheel os.system('python -m pip install --upgrade pip') diff --git a/python/setup.py b/python/setup.py index 0097e3d596..7794119930 100644 --- a/python/setup.py +++ b/python/setup.py @@ -3,7 +3,7 @@ from setuptools import setup from setuptools.dist import Distribution from sys import version_info -import os,time,shutil +import os,time LAMMPS_PYTHON_DIR = os.path.dirname(os.path.realpath(__file__)) LAMMPS_DIR = os.path.dirname(LAMMPS_PYTHON_DIR) LAMMPS_SOURCE_DIR = os.path.join(LAMMPS_DIR, 'src') @@ -24,7 +24,7 @@ def get_lammps_version(): class BinaryDistribution(Distribution): """Wrapper to enforce creating a binary package""" - def has_ext_modules(foo): + def has_ext_modules(self): return True if version_info.major >= 3: diff --git a/src/.gitignore b/src/.gitignore index 6657256e8f..220cd621db 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -997,6 +997,8 @@ /neb.h /netcdf_units.cpp /netcdf_units.h +/pair_threebody_table.cpp +/pair_threebody_table.h /pair_adp.cpp /pair_adp.h /pair_agni.cpp @@ -1291,6 +1293,8 @@ /pair_sph_taitwater_morris.h /pair_sw.cpp /pair_sw.h +/pair_sw_angle_table.cpp +/pair_sw_angle_table.h /pair_sw_mod.cpp /pair_sw_mod.h /pair_tersoff.cpp diff --git a/src/AMOEBA/amoeba_induce.cpp b/src/AMOEBA/amoeba_induce.cpp index 884ba71edf..9398cbf593 100644 --- a/src/AMOEBA/amoeba_induce.cpp +++ b/src/AMOEBA/amoeba_induce.cpp @@ -381,6 +381,8 @@ void PairAmoeba::induce() } } + // if (comm->me == 0) printf("CG iteration count = %d\n",iter); + // terminate the calculation if dipoles failed to converge // NOTE: could make this an error diff --git a/src/AMOEBA/fix_amoeba_bitorsion.cpp b/src/AMOEBA/fix_amoeba_bitorsion.cpp index 53f36353f0..85a87b0452 100644 --- a/src/AMOEBA/fix_amoeba_bitorsion.cpp +++ b/src/AMOEBA/fix_amoeba_bitorsion.cpp @@ -91,6 +91,13 @@ FixAmoebaBiTorsion::FixAmoebaBiTorsion(LAMMPS *lmp, int narg, char **arg) : read_grid_data(arg[3]); create_splines(); + // border comm of 1st neighbors in special list + // so chkttor() can use them when central atom = ghost to check chirality + // comm_border = max # of bonds per atom + 1 for count + + comm_border = 7; + atom->add_callback(Atom::BORDER); + // perform initial allocation of atom-based arrays num_bitorsion = nullptr; @@ -1745,6 +1752,50 @@ void FixAmoebaBiTorsion::set_arrays(int i) num_bitorsion[i] = 0; } +/* ---------------------------------------------------------------------- + pack values for border communication at re-neighboring +------------------------------------------------------------------------- */ + +int FixAmoebaBiTorsion::pack_border(int n, int *list, double *buf) +{ + int i, j, k; + + int **nspecial = atom->nspecial; + tagint **special = atom->special; + + int m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = ubuf(nspecial[j][0]).d; + for (k = 0; k < nspecial[j][0]; k++) + buf[m++] = ubuf(special[j][k]).d; + } + + return m; +} + +/* ---------------------------------------------------------------------- + unpack values for border communication at re-neighboring +------------------------------------------------------------------------- */ + +int FixAmoebaBiTorsion::unpack_border(int n, int first, double *buf) +{ + int i, k, last; + + int **nspecial = atom->nspecial; + tagint **special = atom->special; + + int m = 0; + last = first + n; + for (i = first; i < last; i++) { + nspecial[i][0] = (int) ubuf(buf[m++]).i; + for (k = 0; k < nspecial[i][0]; k++) + special[i][k] = (tagint) ubuf(buf[m++]).i; + } + + return m; +} + /* ---------------------------------------------------------------------- pack values in local atom-based array for exchange with another proc ------------------------------------------------------------------------- */ diff --git a/src/AMOEBA/fix_amoeba_bitorsion.h b/src/AMOEBA/fix_amoeba_bitorsion.h index 929ecb41b3..d401f864bd 100644 --- a/src/AMOEBA/fix_amoeba_bitorsion.h +++ b/src/AMOEBA/fix_amoeba_bitorsion.h @@ -59,6 +59,8 @@ class FixAmoebaBiTorsion : public Fix { void grow_arrays(int); void copy_arrays(int, int, int); void set_arrays(int); + int pack_border(int, int *, double *) override; + int unpack_border(int, int, double *) override; int pack_exchange(int, double *); int unpack_exchange(int, double *); @@ -69,7 +71,7 @@ class FixAmoebaBiTorsion : public Fix { int eflag_caller; int ilevel_respa; int disable; - bigint nbitorsions; + bigint nbitorsions; // total count of all bitorsions in system double ebitorsion; double onefifth; diff --git a/src/AMOEBA/pair_amoeba.cpp b/src/AMOEBA/pair_amoeba.cpp index f69600c511..dcbd3ab556 100644 --- a/src/AMOEBA/pair_amoeba.cpp +++ b/src/AMOEBA/pair_amoeba.cpp @@ -1750,14 +1750,20 @@ void PairAmoeba::precond_neigh() int *ilist,*jlist,*numneigh,**firstneigh; int *neighptr; - // set cutoffs and taper coeffs - // add skin to cutoff, same as for main neighbor list + // DEBUG + + if (comm->me == 0.0) printf("Reneighbor on step %ld\n",update->ntimestep); + + // NOTE: no skin added to cutoff for this shorter neighbor list + // also note that Tinker (and thus LAMMPS) does not apply the + // distance cutoff in the CG iterations in induce.cpp, + // rather all interactions in the precond neigh list are + // used every step until the neighbor list is rebuilt, + // this means the cutoff distance is not exactly enforced, + // on a later step atoms outside may contribute, atoms inside may not choose(USOLV); - //double off = sqrt(off2); - //off2 = (off + neighbor->skin) * (off + neighbor->skin); - // atoms and neighbor list double **x = atom->x; @@ -1802,6 +1808,7 @@ void PairAmoeba::precond_neigh() } } + /* ---------------------------------------------------------------------- allocate Vdwl arrays note that n_amclass = # of classes in Tinker PRM file diff --git a/src/ATC/fix_atc.cpp b/src/ATC/fix_atc.cpp index a7c0cf5ade..356aa2596c 100644 --- a/src/ATC/fix_atc.cpp +++ b/src/ATC/fix_atc.cpp @@ -284,7 +284,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), int me = ATC::LammpsInterface::instance()->comm_rank(); string groupName(arg[1]); - int igroup = group->find(groupName.c_str()); + int igroup = group->find(groupName); int atomCount = group->count(igroup); try { diff --git a/src/COLVARS/colvarproxy_lammps.cpp b/src/COLVARS/colvarproxy_lammps.cpp index 0989460a75..eb03c14de7 100644 --- a/src/COLVARS/colvarproxy_lammps.cpp +++ b/src/COLVARS/colvarproxy_lammps.cpp @@ -117,7 +117,7 @@ void colvarproxy_lammps::init(const char *conf_file) if (_lmp->update->ntimestep != 0) { cvm::log("Setting initial step number from LAMMPS: "+ cvm::to_str(_lmp->update->ntimestep)+"\n"); - colvars->it = colvars->it_restart = + colvarmodule::it = colvarmodule::it_restart = static_cast(_lmp->update->ntimestep); } @@ -174,7 +174,7 @@ double colvarproxy_lammps::compute() } else { // Use the time step number from LAMMPS Update object if (_lmp->update->ntimestep - previous_step == 1) { - colvars->it++; + colvarmodule::it++; b_simulation_continuing = false; } else { // Cases covered by this condition: @@ -209,7 +209,7 @@ double colvarproxy_lammps::compute() if (cvm::debug()) { cvm::log(std::string(cvm::line_marker)+ - "colvarproxy_lammps, step no. "+cvm::to_str(colvars->it)+"\n"+ + "colvarproxy_lammps, step no. "+cvm::to_str(colvarmodule::it)+"\n"+ "Updating internal data.\n"); } @@ -269,7 +269,7 @@ cvm::rvector colvarproxy_lammps::position_distance(cvm::atom_pos const &pos1, double ytmp = pos2.y - pos1.y; double ztmp = pos2.z - pos1.z; _lmp->domain->minimum_image(xtmp,ytmp,ztmp); - return cvm::rvector(xtmp, ytmp, ztmp); + return {xtmp, ytmp, ztmp}; } diff --git a/src/COLVARS/fix_colvars.cpp b/src/COLVARS/fix_colvars.cpp index 02bf8d4347..a46e6318d0 100644 --- a/src/COLVARS/fix_colvars.cpp +++ b/src/COLVARS/fix_colvars.cpp @@ -135,8 +135,6 @@ static void rebuild_table_int(inthash_t *tptr) { /* free memory used by old table */ free(old_bucket); - - return; } /* @@ -166,8 +164,6 @@ void inthash_init(inthash_t *tptr, int buckets) { /* allocate memory for table */ tptr->bucket=(inthash_node_t **) calloc(tptr->size, sizeof(inthash_node_t *)); - - return; } /* @@ -847,7 +843,6 @@ void FixColvars::post_force_respa(int vflag, int ilevel, int /*iloop*/) { /* only process colvar forces on the outmost RESPA level. */ if (ilevel == nlevels_respa-1) post_force(vflag); - return; } /* ---------------------------------------------------------------------- */ @@ -939,7 +934,7 @@ void FixColvars::end_of_step() void FixColvars::write_restart(FILE *fp) { if (me == 0) { - std::string rest_text(""); + std::string rest_text; proxy->serialize_status(rest_text); // TODO call write_output_files() const char *cvm_state = rest_text.c_str(); diff --git a/src/COLVARS/ndx_group.cpp b/src/COLVARS/ndx_group.cpp index 9560c41c6a..34b3bd7dae 100644 --- a/src/COLVARS/ndx_group.cpp +++ b/src/COLVARS/ndx_group.cpp @@ -76,7 +76,7 @@ void Ndx2Group::command(int narg, char **arg) int len; bigint num; FILE *fp; - std::string name = "", next; + std::string name, next; if (narg < 1) error->all(FLERR,"Illegal ndx2group command"); if (atom->tag_enable == 0) diff --git a/src/DIELECTRIC/atom_vec_dielectric.cpp b/src/DIELECTRIC/atom_vec_dielectric.cpp index b15b233991..67bb9f7dc3 100644 --- a/src/DIELECTRIC/atom_vec_dielectric.cpp +++ b/src/DIELECTRIC/atom_vec_dielectric.cpp @@ -78,9 +78,9 @@ AtomVecDielectric::AtomVecDielectric(LAMMPS *_lmp) : AtomVec(_lmp) "mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"}; fields_create = {"q", "molecule", "num_bond", "num_angle", "num_dihedral", "num_improper", "nspecial", "mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"}; - fields_data_atom = { "id", "molecule", "type", "q", "x", "mu3", "area", "ed", "em", "epsilon", + fields_data_atom = {"id", "molecule", "type", "q", "x", "mu3", "area", "ed", "em", "epsilon", "curvature"}; - fields_data_vel = {"id v"}; + fields_data_vel = {"id", "v"}; // clang-format on setup_fields(); diff --git a/src/DIELECTRIC/pppm_dielectric.cpp b/src/DIELECTRIC/pppm_dielectric.cpp index 7f32a0a3f3..92bd89ebd9 100644 --- a/src/DIELECTRIC/pppm_dielectric.cpp +++ b/src/DIELECTRIC/pppm_dielectric.cpp @@ -58,6 +58,9 @@ PPPMDielectric::PPPMDielectric(LAMMPS *_lmp) : PPPM(_lmp) phi = nullptr; potflag = 0; + // no warnings about non-neutral systems from qsum_qsq() + warn_nonneutral = 2; + avec = dynamic_cast( atom->style_match("dielectric")); if (!avec) error->all(FLERR,"pppm/dielectric requires atom style dielectric"); } @@ -463,25 +466,3 @@ void PPPMDielectric::slabcorr() efield[i][2] += ffact * eps[i]*(dipole_all - qsum*x[i][2]); } } - -/* ---------------------------------------------------------------------- - compute qsum,qsqsum,q2 and ignore error/warning if not charge neutral - called whenever charges are changed -------------------------------------------------------------------------- */ - -void PPPMDielectric::qsum_qsq() -{ - const double * const q = atom->q; - const int nlocal = atom->nlocal; - double qsum_local(0.0), qsqsum_local(0.0); - - for (int i = 0; i < nlocal; i++) { - qsum_local += q[i]; - qsqsum_local += q[i]*q[i]; - } - - MPI_Allreduce(&qsum_local,&qsum,1,MPI_DOUBLE,MPI_SUM,world); - MPI_Allreduce(&qsqsum_local,&qsqsum,1,MPI_DOUBLE,MPI_SUM,world); - - q2 = qsqsum * force->qqrd2e; -} diff --git a/src/DIELECTRIC/pppm_dielectric.h b/src/DIELECTRIC/pppm_dielectric.h index 92a93daa90..96ebdb1524 100644 --- a/src/DIELECTRIC/pppm_dielectric.h +++ b/src/DIELECTRIC/pppm_dielectric.h @@ -34,8 +34,6 @@ class PPPMDielectric : public PPPM { double *phi; int potflag; // 1/0 if per-atom electrostatic potential phi is needed - void qsum_qsq(); - protected: void slabcorr() override; diff --git a/src/DIELECTRIC/pppm_disp_dielectric.cpp b/src/DIELECTRIC/pppm_disp_dielectric.cpp index e525ba7384..d4d84e0f62 100644 --- a/src/DIELECTRIC/pppm_disp_dielectric.cpp +++ b/src/DIELECTRIC/pppm_disp_dielectric.cpp @@ -65,6 +65,9 @@ PPPMDispDielectric::PPPMDispDielectric(LAMMPS *_lmp) : PPPMDisp(_lmp) mu_flag = 0; + // no warnings about non-neutral systems from qsum_qsq() + warn_nonneutral = 2; + efield = nullptr; phi = nullptr; potflag = 0; @@ -837,25 +840,3 @@ double PPPMDispDielectric::memory_usage() bytes += nmax * sizeof(double); return bytes; } - -/* ---------------------------------------------------------------------- - compute qsum,qsqsum,q2 and give error/warning if not charge neutral - called initially, when particle count changes, when charges are changed -------------------------------------------------------------------------- */ - -void PPPMDispDielectric::qsum_qsq() -{ - const double * const q = atom->q; - const int nlocal = atom->nlocal; - double qsum_local(0.0), qsqsum_local(0.0); - - for (int i = 0; i < nlocal; i++) { - qsum_local += q[i]; - qsqsum_local += q[i]*q[i]; - } - - MPI_Allreduce(&qsum_local,&qsum,1,MPI_DOUBLE,MPI_SUM,world); - MPI_Allreduce(&qsqsum_local,&qsqsum,1,MPI_DOUBLE,MPI_SUM,world); - - q2 = qsqsum * force->qqrd2e; -} diff --git a/src/DIELECTRIC/pppm_disp_dielectric.h b/src/DIELECTRIC/pppm_disp_dielectric.h index b89be02f92..ce20e292aa 100644 --- a/src/DIELECTRIC/pppm_disp_dielectric.h +++ b/src/DIELECTRIC/pppm_disp_dielectric.h @@ -30,8 +30,7 @@ class PPPMDispDielectric : public PPPMDisp { ~PPPMDispDielectric() override; double memory_usage() override; void compute(int, int) override; - void qsum_qsq(); - void slabcorr(int); + void slabcorr(int) override; double **efield; double *phi; diff --git a/src/DPD-MESO/fix_mvv_dpd.cpp b/src/DPD-MESO/fix_mvv_dpd.cpp index 73290535b1..d96031c9f9 100644 --- a/src/DPD-MESO/fix_mvv_dpd.cpp +++ b/src/DPD-MESO/fix_mvv_dpd.cpp @@ -17,8 +17,8 @@ modified velocity-Verlet (MVV) algorithm. Setting verlet = 0.5 recovers the standard velocity-Verlet algorithm. - Contributing author: Zhen Li (Brown University) - Email: zhen_li@brown.edu + Contributing author: Zhen Li (Clemson University) + Email: zli7@clemson.edu ------------------------------------------------------------------------- */ #include "fix_mvv_dpd.h" diff --git a/src/DPD-MESO/fix_mvv_edpd.cpp b/src/DPD-MESO/fix_mvv_edpd.cpp index 856647d792..9b31bc4c5d 100644 --- a/src/DPD-MESO/fix_mvv_edpd.cpp +++ b/src/DPD-MESO/fix_mvv_edpd.cpp @@ -17,8 +17,8 @@ v and edpd_T) using the modified velocity-Verlet (MVV) algorithm. Setting verlet = 0.5 recovers the standard velocity-Verlet algorithm. - Contributing author: Zhen Li (Brown University) - Email: zhen_li@brown.edu + Contributing author: Zhen Li (Clemson University) + Email: zli7@clemson.edu Please cite the related publication: Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. "Energy- diff --git a/src/DPD-MESO/fix_mvv_tdpd.cpp b/src/DPD-MESO/fix_mvv_tdpd.cpp index 00c6e29968..1a0dc5d520 100644 --- a/src/DPD-MESO/fix_mvv_tdpd.cpp +++ b/src/DPD-MESO/fix_mvv_tdpd.cpp @@ -17,8 +17,8 @@ v and cc) using the modified velocity-Verlet (MVV) algorithm. Setting verlet = 0.5 recovers the standard velocity-Verlet algorithm. - Contributing author: Zhen Li (Brown University) - Email: zhen_li@brown.edu + Contributing author: Zhen Li (Clemson University) + Email: zli7@clemson.edu Please cite the related publication: Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. "Transport diff --git a/src/DPD-MESO/pair_edpd.cpp b/src/DPD-MESO/pair_edpd.cpp index ddbbd05085..b05f588b7c 100644 --- a/src/DPD-MESO/pair_edpd.cpp +++ b/src/DPD-MESO/pair_edpd.cpp @@ -13,8 +13,8 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing author: Zhen Li (Brown University) - Email: zhen_li@brown.edu + Contributing author: Zhen Li (Clemson University) + Email: zli7@clemson.edu ------------------------------------------------------------------------- */ #include "pair_edpd.h" diff --git a/src/DPD-MESO/pair_mdpd.cpp b/src/DPD-MESO/pair_mdpd.cpp index 053d322f00..ec0a57be15 100644 --- a/src/DPD-MESO/pair_mdpd.cpp +++ b/src/DPD-MESO/pair_mdpd.cpp @@ -13,8 +13,8 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing author: Zhen Li (Brown University) - Email: zhen_li@brown.edu + Contributing author: Zhen Li (Clemson University) + Email: zli7@clemson.edu ------------------------------------------------------------------------- */ #include "pair_mdpd.h" diff --git a/src/DPD-MESO/pair_mdpd_rhosum.cpp b/src/DPD-MESO/pair_mdpd_rhosum.cpp index b44ca94c4e..773248a212 100644 --- a/src/DPD-MESO/pair_mdpd_rhosum.cpp +++ b/src/DPD-MESO/pair_mdpd_rhosum.cpp @@ -17,7 +17,7 @@ before the force calculation. The code uses 3D Lucy kernel, it can be modified for other kernels. - Contributing author: Zhen Li (Brown University) + Contributing author: Zhen Li (Clemson University) ------------------------------------------------------------------------- */ #include "pair_mdpd_rhosum.h" diff --git a/src/DPD-MESO/pair_tdpd.cpp b/src/DPD-MESO/pair_tdpd.cpp index 76f4b59108..39d9a151d9 100644 --- a/src/DPD-MESO/pair_tdpd.cpp +++ b/src/DPD-MESO/pair_tdpd.cpp @@ -13,8 +13,8 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing author: Zhen Li (Brown University) - Email: zhen_li@brown.edu + Contributing author: Zhen Li (Clemson University) + Email: zli7@clemson.edu ------------------------------------------------------------------------- */ #include "pair_tdpd.h" diff --git a/src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.cpp b/src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.cpp index f5ccb15eac..7a36cdfc5c 100644 --- a/src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.cpp +++ b/src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.cpp @@ -44,7 +44,7 @@ static const double sqrt_2_inv = std::sqrt(0.5); /* ---------------------------------------------------------------------- */ PairSDPDTaitwaterIsothermal::PairSDPDTaitwaterIsothermal (LAMMPS *lmp) -: Pair (lmp) { +: Pair (lmp), random(nullptr) { restartinfo = 0; single_enable =0; } @@ -61,6 +61,7 @@ PairSDPDTaitwaterIsothermal::~PairSDPDTaitwaterIsothermal () { memory->destroy (soundspeed); memory->destroy (B); } + delete random; } /* ---------------------------------------------------------------------- */ diff --git a/src/ELECTRODE/ewald_electrode.cpp b/src/ELECTRODE/ewald_electrode.cpp index d84ef317ff..4e47d955ef 100644 --- a/src/ELECTRODE/ewald_electrode.cpp +++ b/src/ELECTRODE/ewald_electrode.cpp @@ -40,7 +40,7 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -EwaldElectrode::EwaldElectrode(LAMMPS *lmp) : Ewald(lmp), ElectrodeKSpace() +EwaldElectrode::EwaldElectrode(LAMMPS *lmp) : Ewald(lmp) { eikr_step = -1; } diff --git a/src/ELECTRODE/pppm_electrode.cpp b/src/ELECTRODE/pppm_electrode.cpp index 9733c47b14..91d6acc2d5 100644 --- a/src/ELECTRODE/pppm_electrode.cpp +++ b/src/ELECTRODE/pppm_electrode.cpp @@ -65,8 +65,7 @@ enum { FORWARD_IK, FORWARD_AD, FORWARD_IK_PERATOM, FORWARD_AD_PERATOM }; /* ---------------------------------------------------------------------- */ PPPMElectrode::PPPMElectrode(LAMMPS *lmp) : - PPPM(lmp), ElectrodeKSpace(), electrolyte_density_brick(nullptr), - electrolyte_density_fft(nullptr) + PPPM(lmp), electrolyte_density_brick(nullptr), electrolyte_density_fft(nullptr) { group_group_enable = 0; electrolyte_density_brick = nullptr; diff --git a/src/EXTRA-COMPUTE/compute_ave_sphere_atom.cpp b/src/EXTRA-COMPUTE/compute_ave_sphere_atom.cpp index 07803aca20..010051029a 100644 --- a/src/EXTRA-COMPUTE/compute_ave_sphere_atom.cpp +++ b/src/EXTRA-COMPUTE/compute_ave_sphere_atom.cpp @@ -11,10 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing author: Stan Moore (SNL) +------------------------------------------------------------------------- */ + #include "compute_ave_sphere_atom.h" #include "atom.h" #include "comm.h" +#include "domain.h" #include "error.h" #include "force.h" #include "math_const.h" @@ -98,7 +103,10 @@ void ComputeAveSphereAtom::init() } cutsq = cutoff * cutoff; - sphere_vol = 4.0 / 3.0 * MY_PI * cutsq * cutoff; + if (domain->dimension == 3) + volume = 4.0 / 3.0 * MY_PI * cutsq * cutoff; + else + volume = MY_PI * cutsq; // need an occasional full neighbor list @@ -121,7 +129,7 @@ void ComputeAveSphereAtom::compute_peratom() double xtmp, ytmp, ztmp, delx, dely, delz, rsq; int *ilist, *jlist, *numneigh, **firstneigh; int count; - double vsum[3], vavg[3], vnet[3]; + double p[3], vcom[3], vnet[3]; invoked_peratom = update->ntimestep; @@ -152,12 +160,26 @@ void ComputeAveSphereAtom::compute_peratom() double **x = atom->x; double **v = atom->v; + double *mass = atom->mass; + double *rmass = atom->rmass; + int *type = atom->type; int *mask = atom->mask; + double massone_i, massone_j, totalmass; + + double adof = domain->dimension; + double mvv2e = force->mvv2e; + double mv2d = force->mv2d; + double boltz = force->boltz; for (ii = 0; ii < inum; ii++) { i = ilist[ii]; if (mask[i] & groupbit) { + if (rmass) + massone_i = rmass[i]; + else + massone_i = mass[type[i]]; + xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -167,13 +189,18 @@ void ComputeAveSphereAtom::compute_peratom() // i atom contribution count = 1; - vsum[0] = v[i][0]; - vsum[1] = v[i][1]; - vsum[2] = v[i][2]; + totalmass = massone_i; + p[0] = v[i][0] * massone_i; + p[1] = v[i][1] * massone_i; + p[2] = v[i][2] * massone_i; for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; j &= NEIGHMASK; + if (rmass) + massone_j = rmass[j]; + else + massone_j = mass[type[j]]; delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; @@ -181,42 +208,45 @@ void ComputeAveSphereAtom::compute_peratom() rsq = delx * delx + dely * dely + delz * delz; if (rsq < cutsq) { count++; - vsum[0] += v[j][0]; - vsum[1] += v[j][1]; - vsum[2] += v[j][2]; + totalmass += massone_j; + p[0] += v[j][0] * massone_j; + p[1] += v[j][1] * massone_j; + p[2] += v[j][2] * massone_j; } } - vavg[0] = vsum[0] / count; - vavg[1] = vsum[1] / count; - vavg[2] = vsum[2] / count; + vcom[0] = p[0] / totalmass; + vcom[1] = p[1] / totalmass; + vcom[2] = p[2] / totalmass; // i atom contribution - count = 1; - vnet[0] = v[i][0] - vavg[0]; - vnet[1] = v[i][1] - vavg[1]; - vnet[2] = v[i][2] - vavg[2]; - double ke_sum = vnet[0] * vnet[0] + vnet[1] * vnet[1] + vnet[2] * vnet[2]; + vnet[0] = v[i][0] - vcom[0]; + vnet[1] = v[i][1] - vcom[1]; + vnet[2] = v[i][2] - vcom[2]; + double ke_sum = massone_i * (vnet[0] * vnet[0] + vnet[1] * vnet[1] + vnet[2] * vnet[2]); for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; j &= NEIGHMASK; + if (rmass) + massone_j = rmass[j]; + else + massone_j = mass[type[j]]; delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx * delx + dely * dely + delz * delz; if (rsq < cutsq) { - count++; - vnet[0] = v[j][0] - vavg[0]; - vnet[1] = v[j][1] - vavg[1]; - vnet[2] = v[j][2] - vavg[2]; - ke_sum += vnet[0] * vnet[0] + vnet[1] * vnet[1] + vnet[2] * vnet[2]; + vnet[0] = v[j][0] - vcom[0]; + vnet[1] = v[j][1] - vcom[1]; + vnet[2] = v[j][2] - vcom[2]; + ke_sum += massone_j * (vnet[0] * vnet[0] + vnet[1] * vnet[1] + vnet[2] * vnet[2]); } } - double density = count / sphere_vol; - double temp = ke_sum / 3.0 / count; + double density = mv2d * totalmass / volume; + double temp = mvv2e * ke_sum / (adof * count * boltz); result[i][0] = density; result[i][1] = temp; } diff --git a/src/EXTRA-COMPUTE/compute_ave_sphere_atom.h b/src/EXTRA-COMPUTE/compute_ave_sphere_atom.h index ffed09bae5..76350997f9 100644 --- a/src/EXTRA-COMPUTE/compute_ave_sphere_atom.h +++ b/src/EXTRA-COMPUTE/compute_ave_sphere_atom.h @@ -37,7 +37,7 @@ class ComputeAveSphereAtom : public Compute { protected: int nmax; - double cutoff, cutsq, sphere_vol; + double cutoff, cutsq, volume; class NeighList *list; double **result; diff --git a/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp b/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp index 5a92f6c347..2dde2397db 100644 --- a/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp +++ b/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp @@ -80,21 +80,23 @@ ComputeStressCartesian::ComputeStressCartesian(LAMMPS *lmp, int narg, char **arg dir2 = 0; bin_width1 = utils::numeric(FLERR, arg[4], false, lmp); - bin_width2 = 0.0; + bin_width2 = domain->boxhi[dir2] - domain->boxlo[dir2]; nbins1 = (int) ((domain->boxhi[dir1] - domain->boxlo[dir1]) / bin_width1); nbins2 = 1; + // adjust bin width if not a perfect match - invV = (domain->boxhi[dir1] - domain->boxlo[dir1]) / nbins1; - if ((fabs(invV - bin_width1) > SMALL) && (comm->me == 0)) - utils::logmesg(lmp, "Adjusting first bin width for compute {} from {:.6f} to {:.6f}\n", style, - bin_width1, invV); - bin_width1 = invV; + double tmp_binwidth = (domain->boxhi[dir1] - domain->boxlo[dir1]) / nbins1; + if ((fabs(tmp_binwidth - bin_width1) > SMALL) && (comm->me == 0)) + utils::logmesg(lmp, "Adjusting second bin width for compute {} from {:.6f} to {:.6f}\n", style, + bin_width1, tmp_binwidth); + bin_width1 = tmp_binwidth; if (bin_width1 <= 0.0) error->all(FLERR, "Illegal compute stress/cartesian command. Bin width must be > 0"); else if (bin_width1 > domain->boxhi[dir1] - domain->boxlo[dir1]) error->all(FLERR, "Illegal compute stress/cartesian command. Bin width larger than box."); + invV = bin_width1; if (dims == 2) { if (strcmp(arg[5], "x") == 0) dir2 = 0; @@ -107,7 +109,9 @@ ComputeStressCartesian::ComputeStressCartesian(LAMMPS *lmp, int narg, char **arg bin_width2 = utils::numeric(FLERR, arg[6], false, lmp); nbins2 = (int) ((domain->boxhi[dir2] - domain->boxlo[dir2]) / bin_width2); - double tmp_binwidth = (domain->boxhi[dir2] - domain->boxlo[dir2]) / nbins2; + + // adjust bin width if not a perfect match + tmp_binwidth = (domain->boxhi[dir2] - domain->boxlo[dir2]) / nbins2; if ((fabs(tmp_binwidth - bin_width2) > SMALL) && (comm->me == 0)) utils::logmesg(lmp, "Adjusting second bin width for compute {} from {:.6f} to {:.6f}\n", style, bin_width2, tmp_binwidth); @@ -262,7 +266,7 @@ void ComputeStressCartesian::compute_array() Pair *pair = force->pair; double **cutsq = force->pair->cutsq; - double xi1, xi2, xj1, xj2; + double xi1, xi2; for (ii = 0; ii < inum; ii++) { i = ilist[ii]; @@ -301,9 +305,6 @@ void ComputeStressCartesian::compute_array() } } } - xj1 = x[j][dir1]; - xj2 = x[j][dir2]; - delx = x[j][0] - xtmp; dely = x[j][1] - ytmp; delz = x[j][2] - ztmp; @@ -314,8 +315,7 @@ void ComputeStressCartesian::compute_array() // Check if inside cut-off if (rsq >= cutsq[itype][jtype]) continue; pair->single(i, j, itype, jtype, rsq, factor_coul, factor_lj, fpair); - if (dims == 1) compute_pressure_1d(fpair, xi1, xj1, delx, dely, delz); - if (dims == 2) compute_pressure_2d(fpair, xi1, xi2, xj1, xj2, delx, dely, delz); + compute_pressure(fpair, xi1, xi2, delx, dely, delz); } } @@ -353,107 +353,8 @@ void ComputeStressCartesian::compute_array() } } -void ComputeStressCartesian::compute_pressure_1d(double fpair, double xi, double xj, double delx, - double dely, double delz) -{ - int bin_s, bin_e, bin_step, bin, bin_limit; - double xa, xb; - - if (xi < domain->boxlo[dir1]) - xi += (domain->boxhi[dir1] - domain->boxlo[dir1]); - else if (xi > domain->boxhi[dir1]) - xi -= (domain->boxhi[dir1] - domain->boxlo[dir1]); - if (xj < domain->boxlo[dir1]) - xj += (domain->boxhi[dir1] - domain->boxlo[dir1]); - else if (xj > domain->boxhi[dir1]) - xj -= (domain->boxhi[dir1] - domain->boxlo[dir1]); - - // Integrating contour from bin_s to bin_e - bin_s = ((int) lround((xi - domain->boxlo[dir1]) / bin_width1)) % nbins1; - bin_e = ((int) lround((xj - domain->boxlo[dir1]) / bin_width1)) % nbins1; - - // If not periodic in dir1 - if (domain->periodicity[dir1] == 0) { - bin_s = ((int) lround((xi - domain->boxlo[dir1]) / bin_width1)); - bin_e = ((int) lround((xj - domain->boxlo[dir1]) / bin_width1)); - - if (bin_e == nbins1) bin_e--; - if (bin_s == nbins1) bin_s--; - } - - bin_step = 1; - if (domain->periodicity[dir1] == 1) { - if (bin_e - bin_s > 0.5 * nbins1) - bin_step = -1; - else if (bin_s - bin_e > 0.5 * nbins1) - bin_step = 1; - else if (bin_s > bin_e) - bin_step = -1; - } else { - if (bin_s > bin_e) bin_step = -1; - } - if (domain->periodicity[dir1] == 1) - bin_limit = (bin_e + bin_step) % nbins1 < 0 ? (bin_e + bin_step) % nbins1 + nbins1 - : (bin_e + bin_step) % nbins1; - else - bin_limit = bin_e + bin_step; - - bin = bin_s; - // Integrate from bin_s to bin_e with step bin_step. - while (bin < bin_limit) { - - // Calculating exit and entry point (xa, xb). Checking if inside current bin. - if (bin == bin_s) { - if (domain->periodicity[dir1] == 1) - xa = fmod(xi, domain->boxhi[dir1]) + domain->boxlo[dir1]; - else - xa = xi; - } else - xa = (bin_step == 1) ? bin * bin_width1 : (bin + 1) * bin_width1; - if (bin == bin_e) { - if (domain->periodicity[dir1] == 1) - xb = fmod(xj, domain->boxhi[dir1]) + domain->boxlo[dir1]; - else - xb = xj; - } else - xb = (bin_step == 1) ? (bin + 1) * bin_width1 : bin * bin_width1; - - if (bin < 0 || bin >= nbins1) error->all(FLERR, "ERROR: Bin outside simulation."); - - if (bin_s != bin_e) { - if (dir1 == 0) { - tpcxx[bin] += (fpair * delx * delx) * (xb - xa) / delx; - tpcyy[bin] += (fpair * dely * dely) * (xb - xa) / delx; - tpczz[bin] += (fpair * delz * delz) * (xb - xa) / delx; - } else if (dir1 == 1) { - tpcxx[bin] += (fpair * delx * delx) * (xb - xa) / dely; - tpcyy[bin] += (fpair * dely * dely) * (xb - xa) / dely; - tpczz[bin] += (fpair * delz * delz) * (xb - xa) / dely; - } else if (dir1 == 2) { - tpcxx[bin] += (fpair * delx * delx) * (xb - xa) / delz; - tpcyy[bin] += (fpair * dely * dely) * (xb - xa) / delz; - tpczz[bin] += (fpair * delz * delz) * (xb - xa) / delz; - } - } - // Particle i and j in same bin. Avoiding zero divided by zero. - else { - tpcxx[bin] += fpair * delx * delx; - tpcyy[bin] += fpair * dely * dely; - tpczz[bin] += fpair * delz * delz; - } - - // Stepping bin to next bin - if (domain->periodicity[dir1] == 1) - bin = (bin + bin_step) % nbins1 < 0 ? (bin + bin_step) % nbins1 + nbins1 - : (bin + bin_step) % nbins1; - else - bin = bin + bin_step; - } -} - -void ComputeStressCartesian::compute_pressure_2d(double fpair, double xi, double yi, double /*xj*/, - double /*yj*/, double delx, double dely, - double delz) +void ComputeStressCartesian::compute_pressure(double fpair, double xi, double yi, double delx, + double dely, double delz) { int bin1, bin2, next_bin1, next_bin2; double la = 0.0, lb = 0.0, l_sum = 0.0; diff --git a/src/EXTRA-COMPUTE/compute_stress_cartesian.h b/src/EXTRA-COMPUTE/compute_stress_cartesian.h index 30ddc8e45e..d4505a1e8e 100644 --- a/src/EXTRA-COMPUTE/compute_stress_cartesian.h +++ b/src/EXTRA-COMPUTE/compute_stress_cartesian.h @@ -41,8 +41,7 @@ class ComputeStressCartesian : public Compute { double *dens, *pkxx, *pkyy, *pkzz, *pcxx, *pcyy, *pczz; double *tdens, *tpkxx, *tpkyy, *tpkzz, *tpcxx, *tpcyy, *tpczz; class NeighList *list; - void compute_pressure_1d(double, double, double, double, double, double); - void compute_pressure_2d(double, double, double, double, double, double, double, double); + void compute_pressure(double, double, double, double, double, double); }; } // namespace LAMMPS_NS diff --git a/src/EXTRA-DUMP/dump_xtc.cpp b/src/EXTRA-DUMP/dump_xtc.cpp index 3c5be6b9be..8e0bb4a0d7 100644 --- a/src/EXTRA-DUMP/dump_xtc.cpp +++ b/src/EXTRA-DUMP/dump_xtc.cpp @@ -433,10 +433,10 @@ int xdropen(XDR *xdrs, const char *filename, const char *type) return 0; } if (*type == 'w' || *type == 'W') { - type = (char *) "w+"; + type = (char *) "wb+"; lmode = XDR_ENCODE; } else { - type = (char *) "r"; + type = (char *) "rb"; lmode = XDR_DECODE; } xdrfiles[xdrid] = fopen(filename, type); diff --git a/src/EXTRA-DUMP/dump_yaml.cpp b/src/EXTRA-DUMP/dump_yaml.cpp index d4f3208ffb..be1c9768bf 100644 --- a/src/EXTRA-DUMP/dump_yaml.cpp +++ b/src/EXTRA-DUMP/dump_yaml.cpp @@ -124,6 +124,12 @@ void DumpYAML::write_data(int n, double *mybuf) } fputs("]\n", fp); } +} + +/* ---------------------------------------------------------------------- */ + +void DumpYAML::write_footer() +{ fputs("...\n", fp); } diff --git a/src/EXTRA-DUMP/dump_yaml.h b/src/EXTRA-DUMP/dump_yaml.h index bf621dcb51..60ab894de4 100644 --- a/src/EXTRA-DUMP/dump_yaml.h +++ b/src/EXTRA-DUMP/dump_yaml.h @@ -35,6 +35,7 @@ class DumpYAML : public DumpCustom { void write() override; void write_header(bigint) override; void write_data(int, double *) override; + void write_footer() override; int modify_param(int, char **) override; }; diff --git a/src/INTERLAYER/pair_ilp_tmd.cpp b/src/INTERLAYER/pair_ilp_tmd.cpp index 15e1beede7..52119cbf12 100644 --- a/src/INTERLAYER/pair_ilp_tmd.cpp +++ b/src/INTERLAYER/pair_ilp_tmd.cpp @@ -483,7 +483,7 @@ void PairILPTMD::calc_normal() } } //############################ For the edge atoms of TMD ################################ - else if (cont > 1 && cont < Nnei) { + else if (cont < Nnei) { if (strcmp(elements[itype], "Mo") == 0 || strcmp(elements[itype], "W") == 0 || strcmp(elements[itype], "S") == 0 || strcmp(elements[itype], "Se") == 0) { // derivatives of Ni[l] respect to the cont neighbors diff --git a/src/KOKKOS/compute_ave_sphere_atom_kokkos.cpp b/src/KOKKOS/compute_ave_sphere_atom_kokkos.cpp index d2cb6682a7..7873bd0d92 100644 --- a/src/KOKKOS/compute_ave_sphere_atom_kokkos.cpp +++ b/src/KOKKOS/compute_ave_sphere_atom_kokkos.cpp @@ -11,11 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing author: Stan Moore (SNL) +------------------------------------------------------------------------- */ + #include "compute_ave_sphere_atom_kokkos.h" #include "atom_kokkos.h" #include "atom_masks.h" #include "comm.h" +#include "domain.h" #include "error.h" #include "force.h" #include "memory_kokkos.h" @@ -105,11 +110,19 @@ void ComputeAveSphereAtomKokkos::compute_peratom() // compute properties for each atom in group // use full neighbor list to count atoms less than cutoff - atomKK->sync(execution_space,X_MASK|V_MASK|TYPE_MASK|MASK_MASK); + atomKK->sync(execution_space,X_MASK|V_MASK|RMASS_MASK|TYPE_MASK|MASK_MASK); x = atomKK->k_x.view(); v = atomKK->k_v.view(); + rmass = atomKK->k_rmass.view(); + mass = atomKK->k_mass.view(); + type = atomKK->k_type.view(); mask = atomKK->k_mask.view(); + adof = domain->dimension; + mvv2e = force->mvv2e; + mv2d = force->mv2d; + boltz = force->boltz; + Kokkos::deep_copy(d_result,0.0); copymode = 1; @@ -125,8 +138,13 @@ template KOKKOS_INLINE_FUNCTION void ComputeAveSphereAtomKokkos::operator()(TagComputeAveSphereAtom, const int &ii) const { + double massone_i,massone_j; + const int i = d_ilist[ii]; if (mask[i] & groupbit) { + if (rmass.data()) massone_i = rmass[i]; + else massone_i = mass[type[i]]; + const X_FLOAT xtmp = x(i,0); const X_FLOAT ytmp = x(i,1); const X_FLOAT ztmp = x(i,2); @@ -135,14 +153,17 @@ void ComputeAveSphereAtomKokkos::operator()(TagComputeAveSphereAtom, // i atom contribution int count = 1; - double vsum[3]; - vsum[0] = v(i,0); - vsum[1] = v(i,1); - vsum[2] = v(i,2); + double totalmass = massone_i; + double p[3]; + p[0] = v(i,0)*massone_i; + p[1] = v(i,1)*massone_i; + p[2] = v(i,2)*massone_i; for (int jj = 0; jj < jnum; jj++) { int j = d_neighbors(i,jj); j &= NEIGHMASK; + if (rmass.data()) massone_j = rmass[j]; + else massone_j = mass[type[j]]; const F_FLOAT delx = x(j,0) - xtmp; const F_FLOAT dely = x(j,1) - ytmp; @@ -150,44 +171,45 @@ void ComputeAveSphereAtomKokkos::operator()(TagComputeAveSphereAtom, const F_FLOAT rsq = delx*delx + dely*dely + delz*delz; if (rsq < cutsq) { count++; - vsum[0] += v(j,0); - vsum[1] += v(j,1); - vsum[2] += v(j,2); + totalmass += massone_j; + p[0] += v(j,0)*massone_j; + p[1] += v(j,1)*massone_j; + p[2] += v(j,2)*massone_j; } } - double vavg[3]; - vavg[0] = vsum[0]/count; - vavg[1] = vsum[1]/count; - vavg[2] = vsum[2]/count; + double vcom[3]; + vcom[0] = p[0]/totalmass; + vcom[1] = p[1]/totalmass; + vcom[2] = p[2]/totalmass; // i atom contribution - count = 1; double vnet[3]; - vnet[0] = v(i,0) - vavg[0]; - vnet[1] = v(i,1) - vavg[1]; - vnet[2] = v(i,2) - vavg[2]; - double ke_sum = vnet[0]*vnet[0] + vnet[1]*vnet[1] + vnet[2]*vnet[2]; + vnet[0] = v(i,0) - vcom[0]; + vnet[1] = v(i,1) - vcom[1]; + vnet[2] = v(i,2) - vcom[2]; + double ke_sum = massone_i * (vnet[0]*vnet[0] + vnet[1]*vnet[1] + vnet[2]*vnet[2]); for (int jj = 0; jj < jnum; jj++) { int j = d_neighbors(i,jj); j &= NEIGHMASK; + if (rmass.data()) massone_j = rmass[j]; + else massone_j = mass[type[j]]; const F_FLOAT delx = x(j,0) - xtmp; const F_FLOAT dely = x(j,1) - ytmp; const F_FLOAT delz = x(j,2) - ztmp; const F_FLOAT rsq = delx*delx + dely*dely + delz*delz; if (rsq < cutsq) { - count++; - vnet[0] = v(j,0) - vavg[0]; - vnet[1] = v(j,1) - vavg[1]; - vnet[2] = v(j,2) - vavg[2]; - ke_sum += vnet[0]*vnet[0] + vnet[1]*vnet[1] + vnet[2]*vnet[2]; + vnet[0] = v(j,0) - vcom[0]; + vnet[1] = v(j,1) - vcom[1]; + vnet[2] = v(j,2) - vcom[2]; + ke_sum += massone_j * (vnet[0]*vnet[0] + vnet[1]*vnet[1] + vnet[2]*vnet[2]); } } - double density = count/sphere_vol; - double temp = ke_sum/3.0/count; + double density = mv2d*totalmass/volume; + double temp = mvv2e*ke_sum/(adof*count*boltz); d_result(i,0) = density; d_result(i,1) = temp; } diff --git a/src/KOKKOS/compute_ave_sphere_atom_kokkos.h b/src/KOKKOS/compute_ave_sphere_atom_kokkos.h index 75b5ca3aba..1ddf943e7d 100644 --- a/src/KOKKOS/compute_ave_sphere_atom_kokkos.h +++ b/src/KOKKOS/compute_ave_sphere_atom_kokkos.h @@ -46,13 +46,18 @@ template class ComputeAveSphereAtomKokkos : public ComputeAve void operator()(TagComputeAveSphereAtom, const int &) const; private: - typename AT::t_x_array_randomread x; - typename AT::t_v_array_randomread v; + double adof,mvv2e,mv2d,boltz; + + typename AT::t_x_array x; + typename AT::t_v_array v; + typename ArrayTypes::t_float_1d rmass; + typename ArrayTypes::t_float_1d mass; + typename ArrayTypes::t_int_1d type; typename ArrayTypes::t_int_1d mask; typename AT::t_neighbors_2d d_neighbors; - typename AT::t_int_1d_randomread d_ilist; - typename AT::t_int_1d_randomread d_numneigh; + typename AT::t_int_1d d_ilist; + typename AT::t_int_1d d_numneigh; DAT::tdual_float_2d k_result; typename AT::t_float_2d d_result; diff --git a/src/KOKKOS/pair_pace_kokkos.cpp b/src/KOKKOS/pair_pace_kokkos.cpp index 9d78b63167..4ffc971cea 100644 --- a/src/KOKKOS/pair_pace_kokkos.cpp +++ b/src/KOKKOS/pair_pace_kokkos.cpp @@ -534,8 +534,7 @@ void PairPACEKokkos::compute(int eflag_in, int vflag_in) } copymode = 1; - int newton_pair = force->newton_pair; - if (newton_pair == false) + if (!force->newton_pair) error->all(FLERR,"PairPACEKokkos requires 'newton on'"); if (recursive) diff --git a/src/KOKKOS/pair_reaxff_kokkos.cpp b/src/KOKKOS/pair_reaxff_kokkos.cpp index 61f3bb3037..bb6ee0c1f1 100644 --- a/src/KOKKOS/pair_reaxff_kokkos.cpp +++ b/src/KOKKOS/pair_reaxff_kokkos.cpp @@ -2628,7 +2628,7 @@ int PairReaxFFKokkos::preprocess_angular(int i, int itype, int j_sta template template KOKKOS_INLINE_FUNCTION -int PairReaxFFKokkos::preprocess_torsion(int i, int /*itype*/, int itag, +int PairReaxFFKokkos::preprocess_torsion(int i, int /*itype*/, tagint itag, F_FLOAT xtmp, F_FLOAT ytmp, F_FLOAT ztmp, int j_start, int j_end, int location_torsion) const { // in reaxff_torsion_angles: j = i, k = j, i = k; @@ -2782,174 +2782,174 @@ void PairReaxFFKokkos::operator()(TagPairReaxComputeAngularPreproces F_FLOAT fitmp[3],fjtmp[3]; for (int j = 0; j < 3; j++) fitmp[j] = 0.0; - delij[0] = x(j,0) - xtmp; - delij[1] = x(j,1) - ytmp; - delij[2] = x(j,2) - ztmp; - const F_FLOAT rsqij = delij[0]*delij[0] + delij[1]*delij[1] + delij[2]*delij[2]; - rij = sqrt(rsqij); - bo_ij = d_BO(i,j_index); + delij[0] = x(j,0) - xtmp; + delij[1] = x(j,1) - ytmp; + delij[2] = x(j,2) - ztmp; + const F_FLOAT rsqij = delij[0]*delij[0] + delij[1]*delij[1] + delij[2]*delij[2]; + rij = sqrt(rsqij); + bo_ij = d_BO(i,j_index); - BOA_ij = bo_ij - thb_cut; + BOA_ij = bo_ij - thb_cut; - const int jtype = type(j); + const int jtype = type(j); - F_FLOAT CdDelta_j = 0.0; - for (int k = 0; k < 3; k++) fjtmp[k] = 0.0; + F_FLOAT CdDelta_j = 0.0; + for (int k = 0; k < 3; k++) fjtmp[k] = 0.0; - delik[0] = x(k,0) - xtmp; - delik[1] = x(k,1) - ytmp; - delik[2] = x(k,2) - ztmp; - const F_FLOAT rsqik = delik[0]*delik[0] + delik[1]*delik[1] + delik[2]*delik[2]; - const F_FLOAT rik = sqrt(rsqik); - bo_ik = d_BO(i,k_index); - BOA_ik = bo_ik - thb_cut; + delik[0] = x(k,0) - xtmp; + delik[1] = x(k,1) - ytmp; + delik[2] = x(k,2) - ztmp; + const F_FLOAT rsqik = delik[0]*delik[0] + delik[1]*delik[1] + delik[2]*delik[2]; + const F_FLOAT rik = sqrt(rsqik); + bo_ik = d_BO(i,k_index); + BOA_ik = bo_ik - thb_cut; - const int ktype = type(k); + const int ktype = type(k); - // theta and derivatives + // theta and derivatives - cos_theta = (delij[0]*delik[0]+delij[1]*delik[1]+delij[2]*delik[2])/(rij*rik); - if (cos_theta > 1.0) cos_theta = 1.0; - if (cos_theta < -1.0) cos_theta = -1.0; - theta = acos(cos_theta); + cos_theta = (delij[0]*delik[0]+delij[1]*delik[1]+delij[2]*delik[2])/(rij*rik); + if (cos_theta > 1.0) cos_theta = 1.0; + if (cos_theta < -1.0) cos_theta = -1.0; + theta = acos(cos_theta); - const F_FLOAT inv_dists = 1.0 / (rij * rik); - const F_FLOAT Cdot_inv3 = cos_theta * inv_dists * inv_dists; + const F_FLOAT inv_dists = 1.0 / (rij * rik); + const F_FLOAT Cdot_inv3 = cos_theta * inv_dists * inv_dists; - for (int t = 0; t < 3; t++) { - dcos_theta_di[t] = -(delik[t] + delij[t]) * inv_dists + Cdot_inv3 * (rsqik * delij[t] + rsqij * delik[t]); - dcos_theta_dj[t] = delik[t] * inv_dists - Cdot_inv3 * rsqik * delij[t]; - dcos_theta_dk[t] = delij[t] * inv_dists - Cdot_inv3 * rsqij * delik[t]; - } + for (int t = 0; t < 3; t++) { + dcos_theta_di[t] = -(delik[t] + delij[t]) * inv_dists + Cdot_inv3 * (rsqik * delij[t] + rsqij * delik[t]); + dcos_theta_dj[t] = delik[t] * inv_dists - Cdot_inv3 * rsqik * delij[t]; + dcos_theta_dk[t] = delij[t] * inv_dists - Cdot_inv3 * rsqij * delik[t]; + } - sin_theta = sin(theta); - if (sin_theta < 1.0e-5) sin_theta = 1.0e-5; - p_val1 = paramsthbp(jtype,itype,ktype).p_val1; + sin_theta = sin(theta); + if (sin_theta < 1.0e-5) sin_theta = 1.0e-5; + p_val1 = paramsthbp(jtype,itype,ktype).p_val1; - // ANGLE ENERGY + // ANGLE ENERGY - p_val1 = paramsthbp(jtype,itype,ktype).p_val1; - p_val2 = paramsthbp(jtype,itype,ktype).p_val2; - p_val4 = paramsthbp(jtype,itype,ktype).p_val4; - p_val7 = paramsthbp(jtype,itype,ktype).p_val7; - theta_00 = paramsthbp(jtype,itype,ktype).theta_00; + p_val1 = paramsthbp(jtype,itype,ktype).p_val1; + p_val2 = paramsthbp(jtype,itype,ktype).p_val2; + p_val4 = paramsthbp(jtype,itype,ktype).p_val4; + p_val7 = paramsthbp(jtype,itype,ktype).p_val7; + theta_00 = paramsthbp(jtype,itype,ktype).theta_00; - exp3ij = exp(-p_val3 * pow(BOA_ij, p_val4)); - f7_ij = 1.0 - exp3ij; - Cf7ij = p_val3 * p_val4 * pow(BOA_ij, p_val4 - 1.0) * exp3ij; - exp3jk = exp(-p_val3 * pow(BOA_ik, p_val4)); - f7_jk = 1.0 - exp3jk; - Cf7jk = p_val3 * p_val4 * pow(BOA_ik, p_val4 - 1.0) * exp3jk; - expval7 = exp(-p_val7 * d_Delta_boc[i]); - trm8 = 1.0 + expval6 + expval7; - f8_Dj = p_val5 - ((p_val5 - 1.0) * (2.0 + expval6) / trm8); - Cf8j = ((1.0 - p_val5) / (trm8*trm8)) * - (p_val6 * expval6 * trm8 - (2.0 + expval6) * (p_val6*expval6 - p_val7*expval7)); - theta_0 = 180.0 - theta_00 * (1.0 - exp(-p_val10 * (2.0 - SBO2))); - theta_0 = theta_0*constPI/180.0; + exp3ij = exp(-p_val3 * pow(BOA_ij, p_val4)); + f7_ij = 1.0 - exp3ij; + Cf7ij = p_val3 * p_val4 * pow(BOA_ij, p_val4 - 1.0) * exp3ij; + exp3jk = exp(-p_val3 * pow(BOA_ik, p_val4)); + f7_jk = 1.0 - exp3jk; + Cf7jk = p_val3 * p_val4 * pow(BOA_ik, p_val4 - 1.0) * exp3jk; + expval7 = exp(-p_val7 * d_Delta_boc[i]); + trm8 = 1.0 + expval6 + expval7; + f8_Dj = p_val5 - ((p_val5 - 1.0) * (2.0 + expval6) / trm8); + Cf8j = ((1.0 - p_val5) / (trm8*trm8)) * + (p_val6 * expval6 * trm8 - (2.0 + expval6) * (p_val6*expval6 - p_val7*expval7)); + theta_0 = 180.0 - theta_00 * (1.0 - exp(-p_val10 * (2.0 - SBO2))); + theta_0 = theta_0*constPI/180.0; - expval2theta = exp(-p_val2 * (theta_0-theta)*(theta_0-theta)); - if (p_val1 >= 0) - expval12theta = p_val1 * (1.0 - expval2theta); - else // To avoid linear Me-H-Me angles (6/6/06) - expval12theta = p_val1 * -expval2theta; + expval2theta = exp(-p_val2 * (theta_0-theta)*(theta_0-theta)); + if (p_val1 >= 0) + expval12theta = p_val1 * (1.0 - expval2theta); + else // To avoid linear Me-H-Me angles (6/6/06) + expval12theta = p_val1 * -expval2theta; - CEval1 = Cf7ij * f7_jk * f8_Dj * expval12theta; - CEval2 = Cf7jk * f7_ij * f8_Dj * expval12theta; - CEval3 = Cf8j * f7_ij * f7_jk * expval12theta; - CEval4 = -2.0 * p_val1 * p_val2 * f7_ij * f7_jk * f8_Dj * expval2theta * (theta_0 - theta); - Ctheta_0 = p_val10 * theta_00*constPI/180.0 * exp(-p_val10 * (2.0 - SBO2)); - CEval5 = -CEval4 * Ctheta_0 * CSBO2; - CEval6 = CEval5 * dSBO1; - CEval7 = CEval5 * dSBO2; - CEval8 = -CEval4 / sin_theta; + CEval1 = Cf7ij * f7_jk * f8_Dj * expval12theta; + CEval2 = Cf7jk * f7_ij * f8_Dj * expval12theta; + CEval3 = Cf8j * f7_ij * f7_jk * expval12theta; + CEval4 = -2.0 * p_val1 * p_val2 * f7_ij * f7_jk * f8_Dj * expval2theta * (theta_0 - theta); + Ctheta_0 = p_val10 * theta_00*constPI/180.0 * exp(-p_val10 * (2.0 - SBO2)); + CEval5 = -CEval4 * Ctheta_0 * CSBO2; + CEval6 = CEval5 * dSBO1; + CEval7 = CEval5 * dSBO2; + CEval8 = -CEval4 / sin_theta; - e_ang = f7_ij * f7_jk * f8_Dj * expval12theta; - if (eflag) ev.ereax[3] += e_ang; + e_ang = f7_ij * f7_jk * f8_Dj * expval12theta; + if (eflag) ev.ereax[3] += e_ang; - // Penalty energy + // Penalty energy - p_pen1 = paramsthbp(jtype,itype,ktype).p_pen1; + p_pen1 = paramsthbp(jtype,itype,ktype).p_pen1; - exp_pen2ij = exp(-p_pen2 * (BOA_ij - 2.0)*(BOA_ij - 2.0)); - exp_pen2jk = exp(-p_pen2 * (BOA_ik - 2.0)*(BOA_ik - 2.0)); - exp_pen3 = exp(-p_pen3 * d_Delta[i]); - exp_pen4 = exp(p_pen4 * d_Delta[i]); - trm_pen34 = 1.0 + exp_pen3 + exp_pen4; - f9_Dj = (2.0 + exp_pen3) / trm_pen34; - Cf9j = (-p_pen3 * exp_pen3 * trm_pen34 - (2.0 + exp_pen3) * - (-p_pen3 * exp_pen3 + p_pen4 * exp_pen4))/(trm_pen34*trm_pen34); + exp_pen2ij = exp(-p_pen2 * (BOA_ij - 2.0)*(BOA_ij - 2.0)); + exp_pen2jk = exp(-p_pen2 * (BOA_ik - 2.0)*(BOA_ik - 2.0)); + exp_pen3 = exp(-p_pen3 * d_Delta[i]); + exp_pen4 = exp(p_pen4 * d_Delta[i]); + trm_pen34 = 1.0 + exp_pen3 + exp_pen4; + f9_Dj = (2.0 + exp_pen3) / trm_pen34; + Cf9j = (-p_pen3 * exp_pen3 * trm_pen34 - (2.0 + exp_pen3) * + (-p_pen3 * exp_pen3 + p_pen4 * exp_pen4))/(trm_pen34*trm_pen34); - e_pen = p_pen1 * f9_Dj * exp_pen2ij * exp_pen2jk; - if (eflag) ev.ereax[4] += e_pen; + e_pen = p_pen1 * f9_Dj * exp_pen2ij * exp_pen2jk; + if (eflag) ev.ereax[4] += e_pen; - CEpen1 = e_pen * Cf9j / f9_Dj; - temp = -2.0 * p_pen2 * e_pen; - CEpen2 = temp * (BOA_ij - 2.0); - CEpen3 = temp * (BOA_ik - 2.0); + CEpen1 = e_pen * Cf9j / f9_Dj; + temp = -2.0 * p_pen2 * e_pen; + CEpen2 = temp * (BOA_ij - 2.0); + CEpen3 = temp * (BOA_ik - 2.0); - // ConjAngle energy + // ConjAngle energy - p_coa1 = paramsthbp(jtype,itype,ktype).p_coa1; - exp_coa2 = exp(p_coa2 * Delta_val); - e_coa = p_coa1 / (1. + exp_coa2) * - exp(-p_coa3 * SQR(d_total_bo[j]-BOA_ij)) * - exp(-p_coa3 * SQR(d_total_bo[k]-BOA_ik)) * - exp(-p_coa4 * SQR(BOA_ij - 1.5)) * - exp(-p_coa4 * SQR(BOA_ik - 1.5)); + p_coa1 = paramsthbp(jtype,itype,ktype).p_coa1; + exp_coa2 = exp(p_coa2 * Delta_val); + e_coa = p_coa1 / (1. + exp_coa2) * + exp(-p_coa3 * SQR(d_total_bo[j]-BOA_ij)) * + exp(-p_coa3 * SQR(d_total_bo[k]-BOA_ik)) * + exp(-p_coa4 * SQR(BOA_ij - 1.5)) * + exp(-p_coa4 * SQR(BOA_ik - 1.5)); - CEcoa1 = -2 * p_coa4 * (BOA_ij - 1.5) * e_coa; - CEcoa2 = -2 * p_coa4 * (BOA_ik - 1.5) * e_coa; - CEcoa3 = -p_coa2 * exp_coa2 * e_coa / (1 + exp_coa2); - CEcoa4 = -2 * p_coa3 * (d_total_bo[j]-BOA_ij) * e_coa; - CEcoa5 = -2 * p_coa3 * (d_total_bo[k]-BOA_ik) * e_coa; + CEcoa1 = -2 * p_coa4 * (BOA_ij - 1.5) * e_coa; + CEcoa2 = -2 * p_coa4 * (BOA_ik - 1.5) * e_coa; + CEcoa3 = -p_coa2 * exp_coa2 * e_coa / (1 + exp_coa2); + CEcoa4 = -2 * p_coa3 * (d_total_bo[j]-BOA_ij) * e_coa; + CEcoa5 = -2 * p_coa3 * (d_total_bo[k]-BOA_ik) * e_coa; - if (eflag) ev.ereax[5] += e_coa; + if (eflag) ev.ereax[5] += e_coa; - // Forces + // Forces - a_Cdbo(i,j_index) += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4)); - a_Cdbo(j,i_index) += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4)); - a_Cdbo(i,k_index) += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5)); - a_Cdbo(k,i_index) += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5)); + a_Cdbo(i,j_index) += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4)); + a_Cdbo(j,i_index) += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4)); + a_Cdbo(i,k_index) += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5)); + a_Cdbo(k,i_index) += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5)); - CdDelta_i += ((CEval3 + CEval7) + CEpen1 + CEcoa3); - CdDelta_j += CEcoa4; - a_CdDelta[k] += CEcoa5; + CdDelta_i += ((CEval3 + CEval7) + CEpen1 + CEcoa3); + CdDelta_j += CEcoa4; + a_CdDelta[k] += CEcoa5; - for (int ll = j_start; ll < j_end; ll++) { - int l = d_bo_list[ll]; - l &= NEIGHMASK; - const int l_index = ll - j_start; + for (int ll = j_start; ll < j_end; ll++) { + int l = d_bo_list[ll]; + l &= NEIGHMASK; + const int l_index = ll - j_start; - temp_bo_jt = d_BO(i,l_index); - temp = temp_bo_jt * temp_bo_jt * temp_bo_jt; - pBOjt7 = temp * temp * temp_bo_jt; + temp_bo_jt = d_BO(i,l_index); + temp = temp_bo_jt * temp_bo_jt * temp_bo_jt; + pBOjt7 = temp * temp * temp_bo_jt; - a_Cdbo(i,l_index) += (CEval6 * pBOjt7); - a_Cdbopi(i,l_index) += CEval5; - a_Cdbopi2(i,l_index) += CEval5; - } + a_Cdbo(i,l_index) += (CEval6 * pBOjt7); + a_Cdbopi(i,l_index) += CEval5; + a_Cdbopi2(i,l_index) += CEval5; + } - for (int d = 0; d < 3; d++) fi_tmp[d] = CEval8 * dcos_theta_di[d]; - for (int d = 0; d < 3; d++) fj_tmp[d] = CEval8 * dcos_theta_dj[d]; - for (int d = 0; d < 3; d++) fk_tmp[d] = CEval8 * dcos_theta_dk[d]; - for (int d = 0; d < 3; d++) fitmp[d] -= fi_tmp[d]; - for (int d = 0; d < 3; d++) fjtmp[d] -= fj_tmp[d]; - for (int d = 0; d < 3; d++) a_f(k,d) -= fk_tmp[d]; + for (int d = 0; d < 3; d++) fi_tmp[d] = CEval8 * dcos_theta_di[d]; + for (int d = 0; d < 3; d++) fj_tmp[d] = CEval8 * dcos_theta_dj[d]; + for (int d = 0; d < 3; d++) fk_tmp[d] = CEval8 * dcos_theta_dk[d]; + for (int d = 0; d < 3; d++) fitmp[d] -= fi_tmp[d]; + for (int d = 0; d < 3; d++) fjtmp[d] -= fj_tmp[d]; + for (int d = 0; d < 3; d++) a_f(k,d) -= fk_tmp[d]; - // energy/virial tally - if (EVFLAG) { - eng_tmp = e_ang + e_pen + e_coa; - //if (eflag_atom) this->template ev_tally(ev,i,j,eng_tmp,0.0,0.0,0.0,0.0); - for (int d = 0; d < 3; d++) delki[d] = -1.0 * delik[d]; - for (int d = 0; d < 3; d++) delji[d] = -1.0 * delij[d]; - if (eflag_atom) this->template e_tally(ev,i,j,eng_tmp); - if (vflag_either) this->template v_tally3(ev,i,j,k,fj_tmp,fk_tmp,delji,delki); - } + // energy/virial tally + if (EVFLAG) { + eng_tmp = e_ang + e_pen + e_coa; + //if (eflag_atom) this->template ev_tally(ev,i,j,eng_tmp,0.0,0.0,0.0,0.0); + for (int d = 0; d < 3; d++) delki[d] = -1.0 * delik[d]; + for (int d = 0; d < 3; d++) delji[d] = -1.0 * delij[d]; + if (eflag_atom) this->template e_tally(ev,i,j,eng_tmp); + if (vflag_either) this->template v_tally3(ev,i,j,k,fj_tmp,fk_tmp,delji,delki); + } - a_CdDelta[j] += CdDelta_j; - for (int d = 0; d < 3; d++) a_f(j,d) += fjtmp[d]; + a_CdDelta[j] += CdDelta_j; + for (int d = 0; d < 3; d++) a_f(j,d) += fjtmp[d]; a_CdDelta[i] += CdDelta_i; for (int d = 0; d < 3; d++) a_f(i,d) += fitmp[d]; } @@ -3019,285 +3019,284 @@ void PairReaxFFKokkos::operator()(TagPairReaxComputeTorsionPreproces const X_FLOAT ztmp = x(i,2); Delta_i = d_Delta_boc[i]; - const int jtype = type(j); - - bo_ij = d_BO(i,j_index); - - delij[0] = x(j,0) - xtmp; - delij[1] = x(j,1) - ytmp; - delij[2] = x(j,2) - ztmp; - const F_FLOAT rsqij = delij[0]*delij[0] + delij[1]*delij[1] + delij[2]*delij[2]; - const F_FLOAT rij = sqrt(rsqij); - - BOA_ij = bo_ij - thb_cut; - Delta_j = d_Delta_boc[j]; - exp_tor2_ij = exp(-p_tor2 * BOA_ij); - exp_cot2_ij = exp(-p_cot2 * SQR(BOA_ij - 1.5)); - exp_tor3_DiDj = exp(-p_tor3 * (Delta_i + Delta_j)); - exp_tor4_DiDj = exp(p_tor4 * (Delta_i + Delta_j)); - exp_tor34_inv = 1.0 / (1.0 + exp_tor3_DiDj + exp_tor4_DiDj); - f11_DiDj = (2.0 + exp_tor3_DiDj) * exp_tor34_inv; - - const int ktype = type(k); - - bo_ik = d_BO(i,k_index); - - BOA_ik = bo_ik - thb_cut; - for (int d = 0; d < 3; d ++) delik[d] = x(k,d) - x(i,d); - const F_FLOAT rsqik = delik[0]*delik[0] + delik[1]*delik[1] + delik[2]*delik[2]; - const F_FLOAT rik = sqrt(rsqik); - - cos_ijk = (delij[0]*delik[0]+delij[1]*delik[1]+delij[2]*delik[2])/(rij*rik); - if (cos_ijk > 1.0) cos_ijk = 1.0; - if (cos_ijk < -1.0) cos_ijk = -1.0; - theta_ijk = acos(cos_ijk); - - // dcos_ijk - const F_FLOAT inv_dists = 1.0 / (rij * rik); - const F_FLOAT cos_ijk_tmp = cos_ijk / ((rij*rik)*(rij*rik)); - - for (int d = 0; d < 3; d++) { - dcos_ijk_di[d] = -(delik[d] + delij[d]) * inv_dists + cos_ijk_tmp * (rsqik * delij[d] + rsqij * delik[d]); - dcos_ijk_dj[d] = delik[d] * inv_dists - cos_ijk_tmp * rsqik * delij[d]; - dcos_ijk_dk[d] = delij[d] * inv_dists - cos_ijk_tmp * rsqij * delik[d]; - } - - sin_ijk = sin(theta_ijk); - if (sin_ijk >= 0 && sin_ijk <= 1e-10) - tan_ijk_i = cos_ijk / 1e-10; - else if (sin_ijk <= 0 && sin_ijk >= -1e-10) - tan_ijk_i = -cos_ijk / 1e-10; - else tan_ijk_i = cos_ijk / sin_ijk; - - exp_tor2_ik = exp(-p_tor2 * BOA_ik); - exp_cot2_ik = exp(-p_cot2 * SQR(BOA_ik -1.5)); - - const int ltype = type(l); - - bo_jl = d_BO(j,l_index); - - for (int d = 0; d < 3; d ++) deljl[d] = x(l,d) - x(j,d); - const F_FLOAT rsqjl = deljl[0]*deljl[0] + deljl[1]*deljl[1] + deljl[2]*deljl[2]; - const F_FLOAT rjl = sqrt(rsqjl); - BOA_jl = bo_jl - thb_cut; - - cos_jil = -(delij[0]*deljl[0]+delij[1]*deljl[1]+delij[2]*deljl[2])/(rij*rjl); - if (cos_jil > 1.0) cos_jil = 1.0; - if (cos_jil < -1.0) cos_jil = -1.0; - theta_jil = acos(cos_jil); - - // dcos_jil - const F_FLOAT inv_distjl = 1.0 / (rij * rjl); - const F_FLOAT cos_jil_tmp = cos_jil / ((rij*rjl)*(rij*rjl)); - - for (int d = 0; d < 3; d++) { - dcos_jil_di[d] = deljl[d] * inv_distjl - cos_jil_tmp * rsqjl * -delij[d]; - dcos_jil_dj[d] = (-deljl[d] + delij[d]) * inv_distjl - cos_jil_tmp * (rsqjl * delij[d] + rsqij * -deljl[d]); - dcos_jil_dk[d] = -delij[d] * inv_distjl - cos_jil_tmp * rsqij * deljl[d]; - } - - sin_jil = sin(theta_jil); - if (sin_jil >= 0 && sin_jil <= 1e-10) - tan_jil_i = cos_jil / 1e-10; - else if (sin_jil <= 0 && sin_jil >= -1e-10) - tan_jil_i = -cos_jil / 1e-10; - else tan_jil_i = cos_jil / sin_jil; - - for (int d = 0; d < 3; d ++) dellk[d] = x(k,d) - x(l,d); - const F_FLOAT rsqlk = dellk[0]*dellk[0] + dellk[1]*dellk[1] + dellk[2]*dellk[2]; - const F_FLOAT rlk = sqrt(rsqlk); + const int jtype = type(j); + + bo_ij = d_BO(i,j_index); + + delij[0] = x(j,0) - xtmp; + delij[1] = x(j,1) - ytmp; + delij[2] = x(j,2) - ztmp; + const F_FLOAT rsqij = delij[0]*delij[0] + delij[1]*delij[1] + delij[2]*delij[2]; + const F_FLOAT rij = sqrt(rsqij); + + BOA_ij = bo_ij - thb_cut; + Delta_j = d_Delta_boc[j]; + exp_tor2_ij = exp(-p_tor2 * BOA_ij); + exp_cot2_ij = exp(-p_cot2 * SQR(BOA_ij - 1.5)); + exp_tor3_DiDj = exp(-p_tor3 * (Delta_i + Delta_j)); + exp_tor4_DiDj = exp(p_tor4 * (Delta_i + Delta_j)); + exp_tor34_inv = 1.0 / (1.0 + exp_tor3_DiDj + exp_tor4_DiDj); + f11_DiDj = (2.0 + exp_tor3_DiDj) * exp_tor34_inv; + + const int ktype = type(k); + + bo_ik = d_BO(i,k_index); + + BOA_ik = bo_ik - thb_cut; + for (int d = 0; d < 3; d ++) delik[d] = x(k,d) - x(i,d); + const F_FLOAT rsqik = delik[0]*delik[0] + delik[1]*delik[1] + delik[2]*delik[2]; + const F_FLOAT rik = sqrt(rsqik); + + cos_ijk = (delij[0]*delik[0]+delij[1]*delik[1]+delij[2]*delik[2])/(rij*rik); + if (cos_ijk > 1.0) cos_ijk = 1.0; + if (cos_ijk < -1.0) cos_ijk = -1.0; + theta_ijk = acos(cos_ijk); + + // dcos_ijk + const F_FLOAT inv_dists = 1.0 / (rij * rik); + const F_FLOAT cos_ijk_tmp = cos_ijk / ((rij*rik)*(rij*rik)); + + for (int d = 0; d < 3; d++) { + dcos_ijk_di[d] = -(delik[d] + delij[d]) * inv_dists + cos_ijk_tmp * (rsqik * delij[d] + rsqij * delik[d]); + dcos_ijk_dj[d] = delik[d] * inv_dists - cos_ijk_tmp * rsqik * delij[d]; + dcos_ijk_dk[d] = delij[d] * inv_dists - cos_ijk_tmp * rsqij * delik[d]; + } + + sin_ijk = sin(theta_ijk); + if (sin_ijk >= 0 && sin_ijk <= MIN_SINE) + tan_ijk_i = cos_ijk / MIN_SINE; + else if (sin_ijk <= 0 && sin_ijk >= -MIN_SINE) + tan_ijk_i = -cos_ijk / MIN_SINE; + else tan_ijk_i = cos_ijk / sin_ijk; + + exp_tor2_ik = exp(-p_tor2 * BOA_ik); + exp_cot2_ik = exp(-p_cot2 * SQR(BOA_ik -1.5)); + + const int ltype = type(l); + + bo_jl = d_BO(j,l_index); + + for (int d = 0; d < 3; d ++) deljl[d] = x(l,d) - x(j,d); + const F_FLOAT rsqjl = deljl[0]*deljl[0] + deljl[1]*deljl[1] + deljl[2]*deljl[2]; + const F_FLOAT rjl = sqrt(rsqjl); + BOA_jl = bo_jl - thb_cut; + + cos_jil = -(delij[0]*deljl[0]+delij[1]*deljl[1]+delij[2]*deljl[2])/(rij*rjl); + if (cos_jil > 1.0) cos_jil = 1.0; + if (cos_jil < -1.0) cos_jil = -1.0; + theta_jil = acos(cos_jil); + + // dcos_jil + const F_FLOAT inv_distjl = 1.0 / (rij * rjl); + const F_FLOAT cos_jil_tmp = cos_jil / ((rij*rjl)*(rij*rjl)); + + for (int d = 0; d < 3; d++) { + dcos_jil_di[d] = deljl[d] * inv_distjl - cos_jil_tmp * rsqjl * -delij[d]; + dcos_jil_dj[d] = (-deljl[d] + delij[d]) * inv_distjl - cos_jil_tmp * (rsqjl * delij[d] + rsqij * -deljl[d]); + dcos_jil_dk[d] = -delij[d] * inv_distjl - cos_jil_tmp * rsqij * deljl[d]; + } + + sin_jil = sin(theta_jil); + if (sin_jil >= 0 && sin_jil <= MIN_SINE) + tan_jil_i = cos_jil / MIN_SINE; + else if (sin_jil <= 0 && sin_jil >= -MIN_SINE) + tan_jil_i = -cos_jil / MIN_SINE; + else tan_jil_i = cos_jil / sin_jil; + + for (int d = 0; d < 3; d ++) dellk[d] = x(k,d) - x(l,d); + const F_FLOAT rsqlk = dellk[0]*dellk[0] + dellk[1]*dellk[1] + dellk[2]*dellk[2]; + const F_FLOAT rlk = sqrt(rsqlk); - F_FLOAT unnorm_cos_omega, unnorm_sin_omega, omega; - F_FLOAT htra, htrb, htrc, hthd, hthe, hnra, hnrc, hnhd, hnhe; - F_FLOAT arg, poem, tel; - F_FLOAT cross_ij_jl[3]; + // non-Kokkos ReaxFF has a separate function for computing omega, which + // limits the scope of the MIN_SINE statements below - // omega + F_FLOAT sin_ijk_rnd = sin_ijk; + F_FLOAT sin_jil_rnd = sin_jil; - F_FLOAT dot_ij_jk = -(delij[0]*delik[0]+delij[1]*delik[1]+delij[2]*delik[2]); - F_FLOAT dot_ij_lj = delij[0]*deljl[0]+delij[1]*deljl[1]+delij[2]*deljl[2]; - F_FLOAT dot_ik_jl = delik[0]*deljl[0]+delik[1]*deljl[1]+delik[2]*deljl[2]; - unnorm_cos_omega = dot_ij_jk * dot_ij_lj + rsqij * dot_ik_jl; + if (sin_ijk >= 0 && sin_ijk <= MIN_SINE) sin_ijk_rnd = MIN_SINE; + else if (sin_ijk <= 0 && sin_ijk >= -MIN_SINE) sin_ijk_rnd = -MIN_SINE; + if (sin_jil >= 0 && sin_jil <= MIN_SINE) sin_jil_rnd = MIN_SINE; + else if (sin_jil <= 0 && sin_jil >= -MIN_SINE) sin_jil_rnd = -MIN_SINE; - cross_ij_jl[0] = delij[1]*deljl[2] - delij[2]*deljl[1]; - cross_ij_jl[1] = delij[2]*deljl[0] - delij[0]*deljl[2]; - cross_ij_jl[2] = delij[0]*deljl[1] - delij[1]*deljl[0]; + F_FLOAT unnorm_cos_omega, unnorm_sin_omega, omega; + F_FLOAT htra, htrb, htrc, hthd, hthe, hnra, hnrc, hnhd, hnhe; + F_FLOAT arg, poem, tel; + F_FLOAT cross_ij_jl[3]; - unnorm_sin_omega = -rij*(delik[0]*cross_ij_jl[0]+delik[1]*cross_ij_jl[1]+delik[2]*cross_ij_jl[2]); - omega = atan2(unnorm_sin_omega, unnorm_cos_omega); + // omega - htra = rik + cos_ijk * (rjl * cos_jil - rij); - htrb = rij - rik * cos_ijk - rjl * cos_jil; - htrc = rjl + cos_jil * (rik * cos_ijk - rij); - hthd = rik * sin_ijk * (rij - rjl * cos_jil); - hthe = rjl * sin_jil * (rij - rik * cos_ijk); - hnra = rjl * sin_ijk * sin_jil; - hnrc = rik * sin_ijk * sin_jil; - hnhd = rik * rjl * cos_ijk * sin_jil; - hnhe = rik * rjl * sin_ijk * cos_jil; + F_FLOAT dot_ij_jk = -(delij[0]*delik[0]+delij[1]*delik[1]+delij[2]*delik[2]); + F_FLOAT dot_ij_lj = delij[0]*deljl[0]+delij[1]*deljl[1]+delij[2]*deljl[2]; + F_FLOAT dot_ik_jl = delik[0]*deljl[0]+delik[1]*deljl[1]+delik[2]*deljl[2]; + unnorm_cos_omega = dot_ij_jk * dot_ij_lj + rsqij * dot_ik_jl; - poem = 2.0 * rik * rjl * sin_ijk * sin_jil; - if (poem < 1e-20) poem = 1e-20; + cross_ij_jl[0] = delij[1]*deljl[2] - delij[2]*deljl[1]; + cross_ij_jl[1] = delij[2]*deljl[0] - delij[0]*deljl[2]; + cross_ij_jl[2] = delij[0]*deljl[1] - delij[1]*deljl[0]; - tel = SQR(rik) + SQR(rij) + SQR(rjl) - SQR(rlk) - - 2.0 * (rik * rij * cos_ijk - rik * rjl * cos_ijk * cos_jil + rij * rjl * cos_jil); + unnorm_sin_omega = -rij*(delik[0]*cross_ij_jl[0]+delik[1]*cross_ij_jl[1]+delik[2]*cross_ij_jl[2]); + omega = atan2(unnorm_sin_omega, unnorm_cos_omega); - F_FLOAT inv_poem = 1.0 / poem; + htra = rik + cos_ijk * (rjl * cos_jil - rij); + htrb = rij - rik * cos_ijk - rjl * cos_jil; + htrc = rjl + cos_jil * (rik * cos_ijk - rij); + hthd = rik * sin_ijk_rnd * (rij - rjl * cos_jil); + hthe = rjl * sin_jil_rnd * (rij - rik * cos_ijk); + hnra = rjl * sin_ijk_rnd * sin_jil_rnd; + hnrc = rik * sin_ijk_rnd * sin_jil_rnd; + hnhd = rik * rjl * cos_ijk * sin_jil_rnd; + hnhe = rik * rjl * sin_ijk_rnd * cos_jil; - arg = tel * inv_poem; - if (arg > 1.0) arg = 1.0; - if (arg < -1.0) arg = -1.0; + tel = SQR(rik) + SQR(rij) + SQR(rjl) - SQR(rlk) - + 2.0 * (rik * rij * cos_ijk - rik * rjl * cos_ijk * cos_jil + rij * rjl * cos_jil); - F_FLOAT sin_ijk_rnd = sin_ijk; - F_FLOAT sin_jil_rnd = sin_jil; + poem = 2.0 * rik * rjl * sin_ijk_rnd * sin_jil_rnd; + F_FLOAT inv_poem = 1.0 / poem; - if (sin_ijk >= 0 && sin_ijk <= 1e-10) sin_ijk_rnd = 1e-10; - else if (sin_ijk <= 0 && sin_ijk >= -1e-10) sin_ijk_rnd = -1e-10; - if (sin_jil >= 0 && sin_jil <= 1e-10) sin_jil_rnd = 1e-10; - else if (sin_jil <= 0 && sin_jil >= -1e-10) sin_jil_rnd = -1e-10; + arg = tel * inv_poem; + if (arg > 1.0) arg = 1.0; + if (arg < -1.0) arg = -1.0; - cos_omega = cos(omega); - cos2omega = cos(2. * omega); - cos3omega = cos(3. * omega); + cos_omega = cos(omega); + cos2omega = cos(2. * omega); + cos3omega = cos(3. * omega); - // torsion energy + // torsion energy - p_tor1 = paramsfbp(ktype,itype,jtype,ltype).p_tor1; - p_cot1 = paramsfbp(ktype,itype,jtype,ltype).p_cot1; - V1 = paramsfbp(ktype,itype,jtype,ltype).V1; - V2 = paramsfbp(ktype,itype,jtype,ltype).V2; - V3 = paramsfbp(ktype,itype,jtype,ltype).V3; - - exp_tor1 = exp(p_tor1 * SQR(2.0 - d_BO_pi(i,j_index) - f11_DiDj)); - exp_tor2_jl = exp(-p_tor2 * BOA_jl); - exp_cot2_jl = exp(-p_cot2 * SQR(BOA_jl - 1.5)); - fn10 = (1.0 - exp_tor2_ik) * (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jl); - - CV = 0.5 * (V1 * (1.0 + cos_omega) + V2 * exp_tor1 * (1.0 - cos2omega) + V3 * (1.0 + cos3omega)); - - e_tor = fn10 * sin_ijk * sin_jil * CV; - if (eflag) ev.ereax[6] += e_tor; - - dfn11 = (-p_tor3 * exp_tor3_DiDj + (p_tor3 * exp_tor3_DiDj - p_tor4 * exp_tor4_DiDj) * - (2.0 + exp_tor3_DiDj) * exp_tor34_inv) * exp_tor34_inv; - - CEtors1 = sin_ijk * sin_jil * CV; - - CEtors2 = -fn10 * 2.0 * p_tor1 * V2 * exp_tor1 * (2.0 - d_BO_pi(i,j_index) - f11_DiDj) * - (1.0 - SQR(cos_omega)) * sin_ijk * sin_jil; - CEtors3 = CEtors2 * dfn11; - - CEtors4 = CEtors1 * p_tor2 * exp_tor2_ik * (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jl); - CEtors5 = CEtors1 * p_tor2 * (1.0 - exp_tor2_ik) * exp_tor2_ij * (1.0 - exp_tor2_jl); - CEtors6 = CEtors1 * p_tor2 * (1.0 - exp_tor2_ik) * (1.0 - exp_tor2_ij) * exp_tor2_jl; - - cmn = -fn10 * CV; - CEtors7 = cmn * sin_jil * tan_ijk_i; - CEtors8 = cmn * sin_ijk * tan_jil_i; - - CEtors9 = fn10 * sin_ijk * sin_jil * - (0.5 * V1 - 2.0 * V2 * exp_tor1 * cos_omega + 1.5 * V3 * (cos2omega + 2.0 * SQR(cos_omega))); - - // 4-body conjugation energy - - fn12 = exp_cot2_ik * exp_cot2_ij * exp_cot2_jl; - e_con = p_cot1 * fn12 * (1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jil); - if (eflag) ev.ereax[7] += e_con; - - Cconj = -2.0 * fn12 * p_cot1 * p_cot2 * (1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jil); - - CEconj1 = Cconj * (BOA_ik - 1.5e0); - CEconj2 = Cconj * (BOA_ij - 1.5e0); - CEconj3 = Cconj * (BOA_jl - 1.5e0); - - CEconj4 = -p_cot1 * fn12 * (SQR(cos_omega) - 1.0) * sin_jil * tan_ijk_i; - CEconj5 = -p_cot1 * fn12 * (SQR(cos_omega) - 1.0) * sin_ijk * tan_jil_i; - CEconj6 = 2.0 * p_cot1 * fn12 * cos_omega * sin_ijk * sin_jil; - - // forces - - // contribution to bond order - - a_Cdbopi(i,j_index) += CEtors2; - - a_CdDelta[j] += CEtors3; - a_CdDelta[i] += CEtors3; - - a_Cdbo(i,k_index) += CEtors4 + CEconj1; - a_Cdbo(i,j_index) += CEtors5 + CEconj2; - a_Cdbo(j,l_index) += CEtors6 + CEconj3; // trouble - - const F_FLOAT coeff74 = CEtors7 + CEconj4; - const F_FLOAT coeff85 = CEtors8 + CEconj5; - const F_FLOAT coeff96 = CEtors9 + CEconj6; - - const F_FLOAT inv_rij = 1.0 / rij; - const F_FLOAT inv_rik = 1.0 / rik; - const F_FLOAT inv_rjl = 1.0 / rjl; - const F_FLOAT inv_sin_ijk_rnd = 1.0 / sin_ijk_rnd; - const F_FLOAT inv_sin_jil_rnd = 1.0 / sin_jil_rnd; - - #pragma unroll - for (int d = 0; d < 3; d++) { - // dcos_omega_di - F_FLOAT dcos_omega_dk = ((htra-arg*hnra) * inv_rik) * delik[d] - dellk[d]; - dcos_omega_dk += (hthd-arg*hnhd) * inv_sin_ijk_rnd * -dcos_ijk_dk[d]; - dcos_omega_dk *= 2.0 * inv_poem; - - // dcos_omega_dj - F_FLOAT dcos_omega_di = -((htra-arg*hnra) * inv_rik) * delik[d] - htrb * inv_rij * delij[d]; - dcos_omega_di += -(hthd-arg*hnhd) * inv_sin_ijk_rnd * dcos_ijk_di[d]; - dcos_omega_di += -(hthe-arg*hnhe) * inv_sin_jil_rnd * dcos_jil_di[d]; - dcos_omega_di *= 2.0 * inv_poem; - - // dcos_omega_dk - F_FLOAT dcos_omega_dj = -((htrc-arg*hnrc) * inv_rjl) * deljl[d] + htrb * inv_rij * delij[d]; - dcos_omega_dj += -(hthd-arg*hnhd) * inv_sin_ijk_rnd * dcos_ijk_dj[d]; - dcos_omega_dj += -(hthe-arg*hnhe) * inv_sin_jil_rnd * dcos_jil_dj[d]; - dcos_omega_dj *= 2.0 * inv_poem; - - // dcos_omega_dl - F_FLOAT dcos_omega_dl = ((htrc-arg*hnrc) * inv_rjl) * deljl[d] + dellk[d]; - dcos_omega_dl += (hthe-arg*hnhe) * inv_sin_jil_rnd * -dcos_jil_dk[d]; - dcos_omega_dl *= 2.0 * inv_poem; - - // dcos_theta_ijk - fi_tmp[d] = (coeff74) * dcos_ijk_di[d]; - fj_tmp[d] = (coeff74) * dcos_ijk_dj[d]; - fk_tmp[d] = (coeff74) * dcos_ijk_dk[d]; - - // dcos_theta_jil - fi_tmp[d] += (coeff85) * dcos_jil_di[d]; - fj_tmp[d] += (coeff85) * dcos_jil_dj[d]; - F_FLOAT fl_tmp = (coeff85) * dcos_jil_dk[d]; - - // dcos_omega - fi_tmp[d] += (coeff96) * dcos_omega_di; - fj_tmp[d] += (coeff96) * dcos_omega_dj; - fk_tmp[d] += (coeff96) * dcos_omega_dk; - fl_tmp += (coeff96) * dcos_omega_dl; - - // total forces - a_f(i,d) -= fi_tmp[d]; - a_f(j,d) -= fj_tmp[d]; - a_f(k,d) -= fk_tmp[d]; - a_f(l,d) -= fl_tmp; - } - - // per-atom energy/virial tally - - if (EVFLAG) { - eng_tmp = e_tor + e_con; - //if (eflag_atom) this->template ev_tally(ev,i,j,eng_tmp,0.0,0.0,0.0,0.0); - if (eflag_atom) this->template e_tally(ev,i,j,eng_tmp); - if (vflag_either) { - for (int d = 0; d < 3; d ++) delil[d] = x(l,d) - x(i,d); - for (int d = 0; d < 3; d ++) delkl[d] = x(l,d) - x(k,d); - this->template v_tally4(ev,k,i,j,l,fk_tmp,fi_tmp,fj_tmp,delkl,delil,deljl); - } - } + p_tor1 = paramsfbp(ktype,itype,jtype,ltype).p_tor1; + p_cot1 = paramsfbp(ktype,itype,jtype,ltype).p_cot1; + V1 = paramsfbp(ktype,itype,jtype,ltype).V1; + V2 = paramsfbp(ktype,itype,jtype,ltype).V2; + V3 = paramsfbp(ktype,itype,jtype,ltype).V3; + exp_tor1 = exp(p_tor1 * SQR(2.0 - d_BO_pi(i,j_index) - f11_DiDj)); + exp_tor2_jl = exp(-p_tor2 * BOA_jl); + exp_cot2_jl = exp(-p_cot2 * SQR(BOA_jl - 1.5)); + fn10 = (1.0 - exp_tor2_ik) * (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jl); + CV = 0.5 * (V1 * (1.0 + cos_omega) + V2 * exp_tor1 * (1.0 - cos2omega) + V3 * (1.0 + cos3omega)); + + e_tor = fn10 * sin_ijk * sin_jil * CV; + if (eflag) ev.ereax[6] += e_tor; + + dfn11 = (-p_tor3 * exp_tor3_DiDj + (p_tor3 * exp_tor3_DiDj - p_tor4 * exp_tor4_DiDj) * + (2.0 + exp_tor3_DiDj) * exp_tor34_inv) * exp_tor34_inv; + + CEtors1 = sin_ijk * sin_jil * CV; + + CEtors2 = -fn10 * 2.0 * p_tor1 * V2 * exp_tor1 * (2.0 - d_BO_pi(i,j_index) - f11_DiDj) * + (1.0 - SQR(cos_omega)) * sin_ijk * sin_jil; + CEtors3 = CEtors2 * dfn11; + + CEtors4 = CEtors1 * p_tor2 * exp_tor2_ik * (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jl); + CEtors5 = CEtors1 * p_tor2 * (1.0 - exp_tor2_ik) * exp_tor2_ij * (1.0 - exp_tor2_jl); + CEtors6 = CEtors1 * p_tor2 * (1.0 - exp_tor2_ik) * (1.0 - exp_tor2_ij) * exp_tor2_jl; + + cmn = -fn10 * CV; + CEtors7 = cmn * sin_jil * tan_ijk_i; + CEtors8 = cmn * sin_ijk * tan_jil_i; + + CEtors9 = fn10 * sin_ijk * sin_jil * + (0.5 * V1 - 2.0 * V2 * exp_tor1 * cos_omega + 1.5 * V3 * (cos2omega + 2.0 * SQR(cos_omega))); + + // 4-body conjugation energy + + fn12 = exp_cot2_ik * exp_cot2_ij * exp_cot2_jl; + e_con = p_cot1 * fn12 * (1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jil); + if (eflag) ev.ereax[7] += e_con; + + Cconj = -2.0 * fn12 * p_cot1 * p_cot2 * (1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jil); + + CEconj1 = Cconj * (BOA_ik - 1.5e0); + CEconj2 = Cconj * (BOA_ij - 1.5e0); + CEconj3 = Cconj * (BOA_jl - 1.5e0); + + CEconj4 = -p_cot1 * fn12 * (SQR(cos_omega) - 1.0) * sin_jil * tan_ijk_i; + CEconj5 = -p_cot1 * fn12 * (SQR(cos_omega) - 1.0) * sin_ijk * tan_jil_i; + CEconj6 = 2.0 * p_cot1 * fn12 * cos_omega * sin_ijk * sin_jil; + + // forces + + // contribution to bond order + + a_Cdbopi(i,j_index) += CEtors2; + + a_CdDelta[j] += CEtors3; + a_CdDelta[i] += CEtors3; + + a_Cdbo(i,k_index) += CEtors4 + CEconj1; + a_Cdbo(i,j_index) += CEtors5 + CEconj2; + a_Cdbo(j,l_index) += CEtors6 + CEconj3; + + const F_FLOAT coeff74 = CEtors7 + CEconj4; + const F_FLOAT coeff85 = CEtors8 + CEconj5; + const F_FLOAT coeff96 = CEtors9 + CEconj6; + + const F_FLOAT inv_rij = 1.0 / rij; + const F_FLOAT inv_rik = 1.0 / rik; + const F_FLOAT inv_rjl = 1.0 / rjl; + const F_FLOAT inv_sin_ijk_rnd = 1.0 / sin_ijk_rnd; + const F_FLOAT inv_sin_jil_rnd = 1.0 / sin_jil_rnd; + + #pragma unroll + for (int d = 0; d < 3; d++) { + // dcos_omega_di + F_FLOAT dcos_omega_dk = ((htra-arg*hnra) * inv_rik) * delik[d] - dellk[d]; + dcos_omega_dk += (hthd-arg*hnhd) * inv_sin_ijk_rnd * -dcos_ijk_dk[d]; + dcos_omega_dk *= 2.0 * inv_poem; + + // dcos_omega_dj + F_FLOAT dcos_omega_di = -((htra-arg*hnra) * inv_rik) * delik[d] - htrb * inv_rij * delij[d]; + dcos_omega_di += -(hthd-arg*hnhd) * inv_sin_ijk_rnd * dcos_ijk_di[d]; + dcos_omega_di += -(hthe-arg*hnhe) * inv_sin_jil_rnd * dcos_jil_di[d]; + dcos_omega_di *= 2.0 * inv_poem; + + // dcos_omega_dk + F_FLOAT dcos_omega_dj = -((htrc-arg*hnrc) * inv_rjl) * deljl[d] + htrb * inv_rij * delij[d]; + dcos_omega_dj += -(hthd-arg*hnhd) * inv_sin_ijk_rnd * dcos_ijk_dj[d]; + dcos_omega_dj += -(hthe-arg*hnhe) * inv_sin_jil_rnd * dcos_jil_dj[d]; + dcos_omega_dj *= 2.0 * inv_poem; + + // dcos_omega_dl + F_FLOAT dcos_omega_dl = ((htrc-arg*hnrc) * inv_rjl) * deljl[d] + dellk[d]; + dcos_omega_dl += (hthe-arg*hnhe) * inv_sin_jil_rnd * -dcos_jil_dk[d]; + dcos_omega_dl *= 2.0 * inv_poem; + + // dcos_theta_ijk + fi_tmp[d] = (coeff74) * dcos_ijk_di[d]; + fj_tmp[d] = (coeff74) * dcos_ijk_dj[d]; + fk_tmp[d] = (coeff74) * dcos_ijk_dk[d]; + + // dcos_theta_jil + fi_tmp[d] += (coeff85) * dcos_jil_di[d]; + fj_tmp[d] += (coeff85) * dcos_jil_dj[d]; + F_FLOAT fl_tmp = (coeff85) * dcos_jil_dk[d]; + + // dcos_omega + fi_tmp[d] += (coeff96) * dcos_omega_di; + fj_tmp[d] += (coeff96) * dcos_omega_dj; + fk_tmp[d] += (coeff96) * dcos_omega_dk; + fl_tmp += (coeff96) * dcos_omega_dl; + + // total forces + a_f(i,d) -= fi_tmp[d]; + a_f(j,d) -= fj_tmp[d]; + a_f(k,d) -= fk_tmp[d]; + a_f(l,d) -= fl_tmp; + } + + // per-atom energy/virial tally + + if (EVFLAG) { + eng_tmp = e_tor + e_con; + //if (eflag_atom) this->template ev_tally(ev,i,j,eng_tmp,0.0,0.0,0.0,0.0); + if (eflag_atom) this->template e_tally(ev,i,j,eng_tmp); + if (vflag_either) { + for (int d = 0; d < 3; d ++) delil[d] = x(l,d) - x(i,d); + for (int d = 0; d < 3; d ++) delkl[d] = x(l,d) - x(k,d); + this->template v_tally4(ev,k,i,j,l,fk_tmp,fi_tmp,fj_tmp,delkl,delil,deljl); + } + } } template @@ -3471,6 +3470,9 @@ void PairReaxFFKokkos::operator()(TagPairReaxUpdateBond, Kokkos::View::value>> a_Cdbopi2 = d_Cdbopi2; const int i = d_ilist[ii]; + const X_FLOAT xtmp = x(i,0); + const X_FLOAT ytmp = x(i,1); + const X_FLOAT ztmp = x(i,2); const tagint itag = tag(i); const int j_start = d_bo_first[i]; const int j_end = j_start + d_bo_num[i]; @@ -3479,6 +3481,21 @@ void PairReaxFFKokkos::operator()(TagPairReaxUpdateBond, int j = d_bo_list[jj]; j &= NEIGHMASK; const tagint jtag = tag(j); + + int flag = 0; + + if (itag > jtag) { + if ((itag+jtag) % 2 == 0) flag = 1; + } else if (itag < jtag) { + if ((itag+jtag) % 2 == 1) flag = 1; + } else { + if (x(j,2) < ztmp) flag = 1; + if (x(j,2) == ztmp && x(j,1) < ytmp) flag = 1; + if (x(j,2) == ztmp && x(j,1) == ytmp && x(j,0) < xtmp) flag = 1; + } + + if (!flag) continue; + const int j_index = jj - j_start; const F_FLOAT Cdbo_i = d_Cdbo(i,j_index); const F_FLOAT Cdbopi_i = d_Cdbopi(i,j_index); @@ -3493,18 +3510,9 @@ void PairReaxFFKokkos::operator()(TagPairReaxUpdateBond, if (k != i) continue; const int k_index = kk - k_start; - int flag = 0; - if (itag > jtag) { - if ((itag+jtag) % 2 == 0) flag = 1; - } else if (itag < jtag) { - if ((itag+jtag) % 2 == 1) flag = 1; - } - - if (flag) { - a_Cdbo(j,k_index) += Cdbo_i; - a_Cdbopi(j,k_index) += Cdbopi_i; - a_Cdbopi2(j,k_index) += Cdbopi2_i; - } + a_Cdbo(j,k_index) += Cdbo_i; + a_Cdbopi(j,k_index) += Cdbopi_i; + a_Cdbopi2(j,k_index) += Cdbopi2_i; } } } diff --git a/src/KOKKOS/pair_reaxff_kokkos.h b/src/KOKKOS/pair_reaxff_kokkos.h index 39b323a0fe..836a2de731 100644 --- a/src/KOKKOS/pair_reaxff_kokkos.h +++ b/src/KOKKOS/pair_reaxff_kokkos.h @@ -257,7 +257,7 @@ class PairReaxFFKokkos : public PairReaxFF { // Abstraction for counting and populating torsion intermediated template KOKKOS_INLINE_FUNCTION - int preprocess_torsion(int, int, int, F_FLOAT, F_FLOAT, F_FLOAT, int, int, int) const; + int preprocess_torsion(int, int, tagint, F_FLOAT, F_FLOAT, F_FLOAT, int, int, int) const; template KOKKOS_INLINE_FUNCTION diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index 10e423f2d2..b1d128db24 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -95,6 +95,7 @@ PairBOP::PairBOP(LAMMPS *lmp) : Pair(lmp) pairParameters = nullptr; tripletParameters = nullptr; bop_elements = nullptr; + bop_masses = nullptr; bop_types = 0; pairlist1 = nullptr; @@ -183,6 +184,7 @@ PairBOP::~PairBOP() if (bop_elements) for (int i = 0; i < bop_types; i++) delete[] bop_elements[i]; delete[] bop_elements; + delete[] bop_masses; } /* ---------------------------------------------------------------------- */ @@ -198,6 +200,7 @@ void PairBOP::compute(int eflag, int vflag) int newton_pair = force->newton_pair; int nlocal = atom->nlocal; + double **x = atom->x; double **f = atom->f; int *type = atom->type; tagint *tag = atom->tag; @@ -221,7 +224,15 @@ void PairBOP::compute(int eflag, int vflag) temp_ij = BOP_index[i] + jj; j = ilist[neigh_index[temp_ij]]; j_tag = tag[j]; - if (j_tag <= i_tag) continue; + if (i_tag > j_tag) { + if ((i_tag+j_tag) % 2 == 0) continue; + } else if (i_tag < j_tag) { + if ((i_tag+j_tag) % 2 == 1) continue; + } else { + if (x[j][2] < x[i][2]) continue; + if (x[j][2] == x[i][2] && x[j][1] < x[i][1]) continue; + if (x[j][2] == x[i][2] && x[j][1] == x[i][1] && x[j][0] < x[i][0]) continue; + } jtype = map[type[j]]; int param_ij = elem2param[itype][jtype]; sigB_0 = SigmaBo(ii,jj); @@ -251,7 +262,15 @@ void PairBOP::compute(int eflag, int vflag) temp_ij = BOP_index2[i] + jj; j = ilist[neigh_index2[temp_ij]]; j_tag = tag[j]; - if (j_tag <= i_tag) continue; + if (i_tag > j_tag) { + if ((i_tag+j_tag) % 2 == 0) continue; + } else if (i_tag < j_tag) { + if ((i_tag+j_tag) % 2 == 1) continue; + } else { + if (x[j][2] < x[i][2]) continue; + if (x[j][2] == x[i][2] && x[j][1] < x[i][1]) continue; + if (x[j][2] == x[i][2] && x[j][1] == x[i][1] && x[j][0] < x[i][0]) continue; + } PairList2 & p2_ij = pairlist2[temp_ij]; dpr2 = -p2_ij.dRep / p2_ij.r; ftmp1 = dpr2 * p2_ij.dis[0]; @@ -344,16 +363,16 @@ void PairBOP::settings(int narg, char **arg) void PairBOP::coeff(int narg, char **arg) { - const int n = atom->ntypes; - delete [] map; - map = new int[n+1]; + const int np1 = atom->ntypes+1; + delete[] map; + map = new int[np1]; memory->destroy(setflag); memory->destroy(cutsq); memory->destroy(cutghost); - memory->create(setflag,n+1,n+1,"BOP:setflag"); - memory->create(cutsq,n+1,n+1,"BOP:cutsq"); - memory->create(cutghost,n+1,n+1,"BOP:cutghost"); - bytes = (n+1)*(n+1) * (sizeof (int) + 2.0*sizeof (double)); + memory->create(setflag,np1,np1,"BOP:setflag"); + memory->create(cutsq,np1,np1,"BOP:cutsq"); + memory->create(cutghost,np1,np1,"BOP:cutghost"); + bytes = np1*np1*(sizeof (int) + 2.0*sizeof (double)); map_element2type(narg-3, arg+3); @@ -365,22 +384,23 @@ void PairBOP::coeff(int narg, char **arg) // and check for missing elements if (comm->me == 0) { - for (int i = 1; i <= n; i++) { + for (int i = 1; i < np1; i++) { int j; if (map[i] >= 0) { for (j = 0; j < bop_types; j++) { - if (strcmp(elements[map[i]],bop_elements[j]) == 0) { + if (strcmp(elements[map[i]], bop_elements[j]) == 0) { map[i] = j; + atom->set_mass(FLERR, i, bop_masses[j]); break; } } if (j == bop_types) error->one(FLERR,"Element {} not found in bop potential file {}", - elements[map[i]],arg[2]); + elements[map[i]], arg[2]); } } } - MPI_Bcast(map,atom->ntypes+1,MPI_INT,0,world); + MPI_Bcast(map,np1,MPI_INT,0,world); } /* ---------------------------------------------------------------------- @@ -1844,9 +1864,10 @@ void PairBOP::read_table(char *filename) PotentialFileReader *reader = nullptr; if (bop_elements) { - for (int i = 0; i < bop_types; i++) delete [] bop_elements[i]; - delete [] bop_elements; + for (int i = 0; i < bop_types; i++) delete[] bop_elements[i]; + delete[] bop_elements; } + delete[] bop_masses; if (comm->me == 0) { try { @@ -1857,10 +1878,11 @@ void PairBOP::read_table(char *filename) "elements",bop_types)); bop_elements = new char*[bop_types]; + bop_masses = new double[bop_types]; for (int i=0; i < bop_types; ++i) { ValueTokenizer values = reader->next_values(3); - values.next_int(); // element number in PTE (ignored) - values.next_double(); // element mass (ignored) + values.next_int(); // element number (ignored) + bop_masses[i] = values.next_double(); // element mass bop_elements[i] = utils::strdup(values.next_string()); } } catch (TokenizerException &e) { @@ -1873,8 +1895,12 @@ void PairBOP::read_table(char *filename) allocate(); memory->create(rcut,npairs,"BOP:rcut"); - // copy element labels to all MPI ranks for use with write_tables() - if (comm->me != 0) bop_elements = new char*[bop_types]; + // copy element labels and masses to all MPI ranks for use with + // write_tables() and to set the per-type masses + if (comm->me != 0) { + bop_elements = new char*[bop_types]; + bop_masses = new double[bop_types]; + } for (int i = 0; i < bop_types; ++i) { int n=0; if (comm->me == 0) n = strlen(bop_elements[i])+1; @@ -1882,6 +1908,7 @@ void PairBOP::read_table(char *filename) if (comm->me != 0) bop_elements[i] = new char[n]; MPI_Bcast(bop_elements[i],n,MPI_CHAR,0,world); } + MPI_Bcast(bop_masses, bop_types, MPI_DOUBLE, 0, world); if (comm->me == 0) { try { @@ -2010,7 +2037,7 @@ void PairBOP::read_table(char *filename) } } } - delete [] singletable; + delete[] singletable; singletable = new double[nr]; for (int i = 0; i < npairs; i++) { @@ -2038,7 +2065,7 @@ void PairBOP::read_table(char *filename) p.betaP = new TabularFunction(); (p.betaP)->set_values(nr, 0.0, rcut[i], singletable); } - delete [] singletable; + delete[] singletable; singletable = new double[nBOt]; for (int i = 0; i < npairs; i++) { @@ -2048,7 +2075,7 @@ void PairBOP::read_table(char *filename) p.bo = new TabularFunction(); (p.bo)->set_values(nBOt, 0.0, 1.0, singletable); } - delete [] singletable; + delete[] singletable; nbuf = 0; for (int i = 0; i < bop_types; i++) { @@ -2102,7 +2129,7 @@ void PairBOP::read_table(char *filename) (p.cphi)->set_values(nr, 0.0, rcut[i], singletable); } } - delete [] singletable; + delete[] singletable; } memory->destroy(rcut); diff --git a/src/MANYBODY/pair_bop.h b/src/MANYBODY/pair_bop.h index aa6da378ae..483675021b 100644 --- a/src/MANYBODY/pair_bop.h +++ b/src/MANYBODY/pair_bop.h @@ -109,6 +109,7 @@ class PairBOP : public Pair { int npairs; // number of element pairs int ntriples; // number of all triples char **bop_elements; // names of elements in potential file + double *bop_masses; // masses of elements in potential file double bytes; int otfly; // = 1 faster, more memory, = 0 slower, less memory diff --git a/src/MANYBODY/pair_sw.h b/src/MANYBODY/pair_sw.h index 84088926b1..8bae7e5282 100644 --- a/src/MANYBODY/pair_sw.h +++ b/src/MANYBODY/pair_sw.h @@ -55,7 +55,7 @@ class PairSW : public Pair { void settings(int, char **) override; virtual void allocate(); - void read_file(char *); + virtual void read_file(char *); virtual void setup_params(); void twobody(Param *, double, double &, int, double &); virtual void threebody(Param *, Param *, Param *, double, double, double *, double *, double *, diff --git a/src/MANYBODY/pair_sw_angle_table.cpp b/src/MANYBODY/pair_sw_angle_table.cpp new file mode 100644 index 0000000000..d66a959d52 --- /dev/null +++ b/src/MANYBODY/pair_sw_angle_table.cpp @@ -0,0 +1,753 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Christoph Scherer (MPIP Mainz) + scherer@mpip-mainz.mpg.de +------------------------------------------------------------------------- */ + +#include "pair_sw_angle_table.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "math_const.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "table_file_reader.h" +#include "potential_file_reader.h" + +#include +#include + +using namespace LAMMPS_NS; + +using MathConst::DEG2RAD; +using MathConst::MY_PI; +using MathConst::RAD2DEG; + +#define DELTA 4 + +enum { LINEAR, SPLINE }; + +static constexpr double TINY = 1.0e-10; + +/* ---------------------------------------------------------------------- */ + +PairSWAngleTable::PairSWAngleTable(LAMMPS *lmp) : PairSW(lmp), table_params(nullptr) +{ + unit_convert_flag = utils::NOCONVERT; +} + +/* ---------------------------------------------------------------------- + check if allocated, since class can be destructed when incomplete +------------------------------------------------------------------------- */ + +PairSWAngleTable::~PairSWAngleTable() +{ + if (copymode) return; + + for (int m = 0; m < nparams; m++) free_param(&table_params[m]); // free_param will call free_table + memory->destroy(params); + memory->destroy(table_params); + memory->destroy(elem3param); + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(neighshort); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairSWAngleTable::compute(int eflag, int vflag) +{ + int i,j,k,ii,jj,kk,inum,jnum,jnumm1; + int itype,jtype,ktype,ijparam,ikparam,ijkparam; + tagint itag,jtag; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; + double rsq,rsq1,rsq2; + double delr1[3],delr2[3],fj[3],fk[3]; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + ev_init(eflag,vflag); + + double **x = atom->x; + double **f = atom->f; + tagint *tag = atom->tag; + int *type = atom->type; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + double fxtmp,fytmp,fztmp; + + // loop over full neighbor list of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + itag = tag[i]; + itype = map[type[i]]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + fxtmp = fytmp = fztmp = 0.0; + + // two-body interactions, skip half of them + + jlist = firstneigh[i]; + jnum = numneigh[i]; + int numshort = 0; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + jtype = map[type[j]]; + ijparam = elem3param[itype][jtype][jtype]; + if (rsq >= params[ijparam].cutsq) { + continue; + } else { + neighshort[numshort++] = j; + if (numshort >= maxshort) { + maxshort += maxshort/2; + memory->grow(neighshort,maxshort,"pair:neighshort"); + } + } + + jtag = tag[j]; + if (itag > jtag) { + if ((itag+jtag) % 2 == 0) continue; + } else if (itag < jtag) { + if ((itag+jtag) % 2 == 1) continue; + } else { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp && x[j][1] < ytmp) continue; + if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + + twobody(¶ms[ijparam],rsq,fpair,eflag,evdwl); + + fxtmp += delx*fpair; + fytmp += dely*fpair; + fztmp += delz*fpair; + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,0.0,fpair,delx,dely,delz); + } + + jnumm1 = numshort - 1; + + for (jj = 0; jj < jnumm1; jj++) { + j = neighshort[jj]; + jtype = map[type[j]]; + ijparam = elem3param[itype][jtype][jtype]; + delr1[0] = x[j][0] - xtmp; + delr1[1] = x[j][1] - ytmp; + delr1[2] = x[j][2] - ztmp; + rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2]; + + double fjxtmp,fjytmp,fjztmp; + fjxtmp = fjytmp = fjztmp = 0.0; + + for (kk = jj+1; kk < numshort; kk++) { + k = neighshort[kk]; + ktype = map[type[k]]; + ikparam = elem3param[itype][ktype][ktype]; + ijkparam = elem3param[itype][jtype][ktype]; + + delr2[0] = x[k][0] - xtmp; + delr2[1] = x[k][1] - ytmp; + delr2[2] = x[k][2] - ztmp; + rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2]; + + threebody_table(¶ms[ijparam],¶ms[ikparam],&table_params[ijkparam], + rsq1,rsq2,delr1,delr2,fj,fk,eflag,evdwl); + + fxtmp -= fj[0] + fk[0]; + fytmp -= fj[1] + fk[1]; + fztmp -= fj[2] + fk[2]; + fjxtmp += fj[0]; + fjytmp += fj[1]; + fjztmp += fj[2]; + f[k][0] += fk[0]; + f[k][1] += fk[1]; + f[k][2] += fk[2]; + + if (evflag) ev_tally3(i,j,k,evdwl,0.0,fj,fk,delr1,delr2); + } + f[j][0] += fjxtmp; + f[j][1] += fjytmp; + f[j][2] += fjztmp; + } + f[i][0] += fxtmp; + f[i][1] += fytmp; + f[i][2] += fztmp; + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- */ + +void PairSWAngleTable::read_file(char *file) +{ + if (params) { + for (int m = 0; m < nparams; m++) free_param(&table_params[m]); // free_param will call free_table + memory->destroy(params); + memory->destroy(table_params); + memory->destroy(elem3param); + } + + nparams = maxparam = 0; + + // open file on proc 0 + + if (comm->me == 0) { + PotentialFileReader reader(lmp, file, "sw", unit_convert_flag); + char *line; + + while ((line = reader.next_line(NPARAMS_PER_LINE))) { + try { + ValueTokenizer values(line); + + std::string iname = values.next_string(); + std::string jname = values.next_string(); + std::string kname = values.next_string(); + + // ielement,jelement,kelement = 1st args + // if all 3 args are in element list, then parse this line + // else skip to next entry in file + int ielement, jelement, kelement; + + for (ielement = 0; ielement < nelements; ielement++) + if (iname == elements[ielement]) break; + if (ielement == nelements) continue; + for (jelement = 0; jelement < nelements; jelement++) + if (jname == elements[jelement]) break; + if (jelement == nelements) continue; + for (kelement = 0; kelement < nelements; kelement++) + if (kname == elements[kelement]) break; + if (kelement == nelements) continue; + + // load up parameter settings and error check their values + + if (nparams == maxparam) { + maxparam += DELTA; + params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), + "pair:params"); + table_params = (ParamTable *) memory->srealloc(table_params,maxparam*sizeof(ParamTable), + "pair:table_params"); + + // make certain all addional allocated storage is initialized + // to avoid false positives when checking with valgrind + + memset(params + nparams, 0, DELTA*sizeof(Param)); + } + + params[nparams].ielement = ielement; + params[nparams].jelement = jelement; + params[nparams].kelement = kelement; + params[nparams].epsilon = values.next_double(); + params[nparams].sigma = values.next_double(); + params[nparams].littlea = values.next_double(); + params[nparams].lambda = values.next_double(); + params[nparams].gamma = values.next_double(); + params[nparams].costheta = values.next_double(); + params[nparams].biga = values.next_double(); + params[nparams].bigb = values.next_double(); + params[nparams].powerp = values.next_double(); + params[nparams].powerq = values.next_double(); + params[nparams].tol = values.next_double(); + + // read parameters of angle table + std::string name = values.next_string(); + table_params[nparams].tablenamelength = name.length()+1; + table_params[nparams].tablename = utils::strdup(name); + + name = values.next_string(); + table_params[nparams].keywordlength = name.length()+1; + table_params[nparams].keyword = utils::strdup(name); + + name = values.next_string(); + if (name == "linear") table_params[nparams].tabstyle = LINEAR; + else if (name == "spline") table_params[nparams].tabstyle = SPLINE; + else error->all(FLERR,"Unknown table style {} of angle table file", name); + table_params[nparams].tablength = values.next_int(); + + } catch (TokenizerException &e) { + error->one(FLERR, e.what()); + } + + if (params[nparams].epsilon < 0.0 || params[nparams].sigma < 0.0 || + params[nparams].littlea < 0.0 || params[nparams].lambda < 0.0 || + params[nparams].gamma < 0.0 || params[nparams].biga < 0.0 || + params[nparams].bigb < 0.0 || params[nparams].powerp < 0.0 || + params[nparams].powerq < 0.0 || params[nparams].tol < 0.0 || + table_params[nparams].tabstyle < 0.0 || table_params[nparams].tablength < 0.0) + error->one(FLERR,"Illegal Stillinger-Weber parameter"); + + nparams++; + } + } + + MPI_Bcast(&nparams, 1, MPI_INT, 0, world); + MPI_Bcast(&maxparam, 1, MPI_INT, 0, world); + + if (comm->me != 0) { + params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), "pair:params"); + table_params = (ParamTable *) memory->srealloc(table_params,maxparam*sizeof(ParamTable), "pair:table_params"); + } + + MPI_Bcast(params, maxparam*sizeof(Param), MPI_BYTE, 0, world); + MPI_Bcast(table_params, maxparam*sizeof(ParamTable), MPI_BYTE, 0, world); + + // for each set of parameters, broadcast table name and keyword and read angle table + for (int m = 0; m < nparams; ++m){ + if (comm->me != 0) { + table_params[m].tablename = new char[table_params[m].tablenamelength]; + table_params[m].keyword = new char[table_params[m].keywordlength]; + } + MPI_Bcast(table_params[m].tablename, table_params[m].tablenamelength, MPI_CHAR, 0, world); + MPI_Bcast(table_params[m].keyword, table_params[m].keywordlength, MPI_CHAR, 0, world); + + // initialize angtable + memory->create(table_params[m].angtable,1,"table_params:angtable"); + null_table(table_params[m].angtable); + + // call read_table to read corresponding tabulated angle file (only called by process 0) + if (comm->me == 0) read_table(table_params[m].angtable,table_params[m].tablename,table_params[m].keyword); + + // broadcast read in angtable to all processes + bcast_table(table_params[m].angtable); + + // the following table manipulations are done in all processes + // error check on table parameters + if (table_params[m].angtable->ninput <= 1) error->one(FLERR,"Invalid angle table length"); + + // error check on parameter range of angle table + double alo,ahi; + alo = table_params[m].angtable->afile[0]; + ahi = table_params[m].angtable->afile[table_params[m].angtable->ninput-1]; + if (fabs(alo-0.0) > TINY || fabs(ahi-180.0) > TINY) + error->all(FLERR,"Angle table must range from 0 to 180 degrees"); + + // convert theta from degrees to radians + for (int i = 0; i < table_params[m].angtable->ninput; ++i){ + table_params[m].angtable->afile[i] *= MY_PI/180.0; + table_params[m].angtable->ffile[i] *= 180.0/MY_PI; + } + + // spline read-in table and compute a,e,f vectors within table + spline_table(table_params[m].angtable); + // compute_table needs parameter params[m].length for this specific interaction as + // read in value length from .sw file can be different from value in angle table file + compute_table(table_params[m].angtable,table_params[m].tablength); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairSWAngleTable::threebody_table(Param *paramij, Param *paramik, ParamTable *table_paramijk, + double rsq1, double rsq2, double *delr1, double *delr2, + double *fj, double *fk, int eflag, double &eng) +{ + double r1,rinvsq1,rainv1,gsrainv1,gsrainvsq1,expgsrainv1; + double r2,rinvsq2,rainv2,gsrainv2,gsrainvsq2,expgsrainv2; + double rinv12,cs,facexp; + double ftheta,facradtable,frad1table,frad2table,var; + double acosprime,gradj1,gradj2,gradk1,gradk2,fprimetheta; + + r1 = sqrt(rsq1); + rinvsq1 = 1.0/rsq1; + rainv1 = 1.0/(r1 - paramij->cut); + gsrainv1 = paramij->sigma_gamma * rainv1; + gsrainvsq1 = gsrainv1*rainv1/r1; + expgsrainv1 = exp(gsrainv1); + + r2 = sqrt(rsq2); + rinvsq2 = 1.0/rsq2; + rainv2 = 1.0/(r2 - paramik->cut); + gsrainv2 = paramik->sigma_gamma * rainv2; + gsrainvsq2 = gsrainv2*rainv2/r2; + expgsrainv2 = exp(gsrainv2); + + facexp = expgsrainv1*expgsrainv2; + + rinv12 = 1.0/(r1*r2); + cs = (delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2]) * rinv12; + + var = acos(cs); + + // look up energy (f(theta), ftheta) and force (df(theta)/dtheta, fprimetheta) at + // angle theta (var) in angle table belonging to parameter set paramijk + uf_lookup(table_paramijk, var, ftheta, fprimetheta); + + acosprime = 1.0 / (sqrt(1 - cs*cs ) ); + + facradtable = facexp*ftheta; + frad1table = facradtable*gsrainvsq1; + frad2table = facradtable*gsrainvsq2; + gradj1 = acosprime * cs * rinvsq1 * facexp * fprimetheta; + gradj2 = acosprime * rinv12 * facexp * fprimetheta; + gradk1 = acosprime * cs * rinvsq2 * facexp * fprimetheta; + gradk2 = acosprime * rinv12 * facexp * fprimetheta; + + fj[0] = delr1[0]*(frad1table+gradj1)-delr2[0]*gradj2; + fj[1] = delr1[1]*(frad1table+gradj1)-delr2[1]*gradj2; + fj[2] = delr1[2]*(frad1table+gradj1)-delr2[2]*gradj2; + + fk[0] = delr2[0]*(frad2table+gradk1)-delr1[0]*gradk2; + fk[1] = delr2[1]*(frad2table+gradk1)-delr1[1]*gradk2; + fk[2] = delr2[2]*(frad2table+gradk1)-delr1[2]*gradk2; + + if (eflag) eng = facradtable; +} + +/* ---------------------------------------------------------------------- + read table file, only called by proc 0 +------------------------------------------------------------------------- */ + +void PairSWAngleTable::read_table(Table *tb, char *file, char *keyword) +{ + TableFileReader reader(lmp, file, "angletable"); + + char *line = reader.find_section_start(keyword); + + if (!line) { error->one(FLERR, "Did not find keyword in table file"); } + + // read args on 2nd line of section + // allocate table arrays for file values + + line = reader.next_line(); + param_extract(tb, line); + memory->create(tb->afile, tb->ninput, "angle:afile"); + memory->create(tb->efile, tb->ninput, "angle:efile"); + memory->create(tb->ffile, tb->ninput, "angle:ffile"); + + // read a,e,f table values from file + + int cerror = 0; + reader.skip_line(); + for (int i = 0; i < tb->ninput; i++) { + line = reader.next_line(4); + try { + ValueTokenizer values(line); + values.next_int(); + tb->afile[i] = values.next_double(); + tb->efile[i] = values.next_double(); + tb->ffile[i] = values.next_double(); + } catch (TokenizerException &) { + ++cerror; + } + } + + // warn if data was read incompletely, e.g. columns were missing + + if (cerror) + error->warning(FLERR, "{} of {} lines in table incomplete or could not be parsed", cerror, + tb->ninput); +} + +/* ---------------------------------------------------------------------- + build spline representation of e,f over entire range of read-in table + this function sets these values in e2file,f2file +------------------------------------------------------------------------- */ + +void PairSWAngleTable::spline_table(Table *tb) +{ + memory->create(tb->e2file, tb->ninput, "angle:e2file"); + memory->create(tb->f2file, tb->ninput, "angle:f2file"); + + double ep0 = -tb->ffile[0]; + double epn = -tb->ffile[tb->ninput - 1]; + spline(tb->afile, tb->efile, tb->ninput, ep0, epn, tb->e2file); + + if (tb->fpflag == 0) { + tb->fplo = (tb->ffile[1] - tb->ffile[0]) / (tb->afile[1] - tb->afile[0]); + tb->fphi = (tb->ffile[tb->ninput - 1] - tb->ffile[tb->ninput - 2]) / + (tb->afile[tb->ninput - 1] - tb->afile[tb->ninput - 2]); + } + + double fp0 = tb->fplo; + double fpn = tb->fphi; + spline(tb->afile, tb->ffile, tb->ninput, fp0, fpn, tb->f2file); +} + +/* ---------------------------------------------------------------------- + compute a,e,f vectors from splined values +------------------------------------------------------------------------- */ + +void PairSWAngleTable::compute_table(Table *tb,int length) +{ + // delta = table spacing in angle for N-1 bins + + int tlm1 = length - 1; + tb->delta = MY_PI / tlm1; + tb->invdelta = 1.0 / tb->delta; + tb->deltasq6 = tb->delta * tb->delta / 6.0; + + // N-1 evenly spaced bins in angle from 0 to PI + // ang,e,f = value at lower edge of bin + // de,df values = delta values of e,f + // ang,e,f are N in length so de,df arrays can compute difference + + memory->create(tb->ang, length, "angle:ang"); + memory->create(tb->e, length, "angle:e"); + memory->create(tb->de, length, "angle:de"); + memory->create(tb->f, length, "angle:f"); + memory->create(tb->df, length, "angle:df"); + memory->create(tb->e2, length, "angle:e2"); + memory->create(tb->f2, length, "angle:f2"); + + double a; + for (int i = 0; i < length; i++) { + a = i * tb->delta; + tb->ang[i] = a; + tb->e[i] = splint(tb->afile, tb->efile, tb->e2file, tb->ninput, a); + tb->f[i] = splint(tb->afile, tb->ffile, tb->f2file, tb->ninput, a); + } + + for (int i = 0; i < tlm1; i++) { + tb->de[i] = tb->e[i + 1] - tb->e[i]; + tb->df[i] = tb->f[i + 1] - tb->f[i]; + } + // get final elements from linear extrapolation + tb->de[tlm1] = 2.0 * tb->de[tlm1 - 1] - tb->de[tlm1 - 2]; + tb->df[tlm1] = 2.0 * tb->df[tlm1 - 1] - tb->df[tlm1 - 2]; + + double ep0 = -tb->f[0]; + double epn = -tb->f[tlm1]; + spline(tb->ang, tb->e, length, ep0, epn, tb->e2); + spline(tb->ang, tb->f, length, tb->fplo, tb->fphi, tb->f2); +} + +/* ---------------------------------------------------------------------- + broadcast read-in table info from proc 0 to other procs + this function communicates these values in Table: + ninput,afile,efile,ffile,fpflag,fplo,fphi,theta0 +------------------------------------------------------------------------- */ + +void PairSWAngleTable::bcast_table(Table *tb) +{ + MPI_Bcast(&tb->ninput, 1, MPI_INT, 0, world); + + int me; + MPI_Comm_rank(world, &me); + if (me > 0) { + memory->create(tb->afile, tb->ninput, "angle:afile"); + memory->create(tb->efile, tb->ninput, "angle:efile"); + memory->create(tb->ffile, tb->ninput, "angle:ffile"); + } + + MPI_Bcast(tb->afile, tb->ninput, MPI_DOUBLE, 0, world); + MPI_Bcast(tb->efile, tb->ninput, MPI_DOUBLE, 0, world); + MPI_Bcast(tb->ffile, tb->ninput, MPI_DOUBLE, 0, world); + + MPI_Bcast(&tb->fpflag, 1, MPI_INT, 0, world); + if (tb->fpflag) { + MPI_Bcast(&tb->fplo, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&tb->fphi, 1, MPI_DOUBLE, 0, world); + } + MPI_Bcast(&tb->theta0, 1, MPI_DOUBLE, 0, world); +} + +/* ---------------------------------------------------------------------- */ + +void PairSWAngleTable::null_table(Table *tb) +{ + tb->afile = tb->efile = tb->ffile = nullptr; + tb->e2file = tb->f2file = nullptr; + tb->ang = tb->e = tb->de = nullptr; + tb->f = tb->df = tb->e2 = tb->f2 = nullptr; +} + +/* ---------------------------------------------------------------------- */ + +void PairSWAngleTable::free_table(Table *tb) +{ + memory->destroy(tb->afile); + memory->destroy(tb->efile); + memory->destroy(tb->ffile); + memory->destroy(tb->e2file); + memory->destroy(tb->f2file); + + memory->destroy(tb->ang); + memory->destroy(tb->e); + memory->destroy(tb->de); + memory->destroy(tb->f); + memory->destroy(tb->df); + memory->destroy(tb->e2); + memory->destroy(tb->f2); +} + +/* ---------------------------------------------------------------------- */ + +void PairSWAngleTable::free_param(ParamTable *pm) +{ + // call free_table to destroy associated angle table + free_table(pm->angtable); + // then destroy associated angle table + delete[] pm->keyword; + delete[] pm->tablename; + memory->sfree(pm->angtable); +} + +/* ---------------------------------------------------------------------- + extract attributes from parameter line in table section + format of line: N value FP fplo fphi EQ theta0 + N is required, other params are optional + + only called by read_table, only called by proc 0 +------------------------------------------------------------------------- */ + +void PairSWAngleTable::param_extract(Table *tb, char *line) +{ + tb->ninput = 0; + tb->fpflag = 0; + tb->theta0 = MY_PI; + + try { + ValueTokenizer values(line); + + while (values.has_next()) { + std::string word = values.next_string(); + + if (word == "N") { + tb->ninput = values.next_int(); + } else if (word == "FP") { + tb->fpflag = 1; + tb->fplo = values.next_double(); + tb->fphi = values.next_double(); + tb->fplo *= RAD2DEG * RAD2DEG; + tb->fphi *= RAD2DEG * RAD2DEG; + } else if (word == "EQ") { + tb->theta0 = DEG2RAD * values.next_double(); + } else { + error->one(FLERR, "Invalid keyword in angle table parameters"); + } + } + } catch (TokenizerException &e) { + error->one(FLERR, e.what()); + } + + if (tb->ninput == 0) error->one(FLERR, "Angle table parameters did not set N"); +} + +/* ---------------------------------------------------------------------- + spline and splint routines modified from Numerical Recipes +------------------------------------------------------------------------- */ + +void PairSWAngleTable::spline(double *x, double *y, int n, double yp1, double ypn, double *y2) +{ + int i, k; + double p, qn, sig, un; + double *u = new double[n]; + + if (yp1 > 0.99e300) + y2[0] = u[0] = 0.0; + else { + y2[0] = -0.5; + u[0] = (3.0 / (x[1] - x[0])) * ((y[1] - y[0]) / (x[1] - x[0]) - yp1); + } + for (i = 1; i < n - 1; i++) { + sig = (x[i] - x[i - 1]) / (x[i + 1] - x[i - 1]); + p = sig * y2[i - 1] + 2.0; + y2[i] = (sig - 1.0) / p; + u[i] = (y[i + 1] - y[i]) / (x[i + 1] - x[i]) - (y[i] - y[i - 1]) / (x[i] - x[i - 1]); + u[i] = (6.0 * u[i] / (x[i + 1] - x[i - 1]) - sig * u[i - 1]) / p; + } + if (ypn > 0.99e300) + qn = un = 0.0; + else { + qn = 0.5; + un = (3.0 / (x[n - 1] - x[n - 2])) * (ypn - (y[n - 1] - y[n - 2]) / (x[n - 1] - x[n - 2])); + } + y2[n - 1] = (un - qn * u[n - 2]) / (qn * y2[n - 2] + 1.0); + for (k = n - 2; k >= 0; k--) y2[k] = y2[k] * y2[k + 1] + u[k]; + + delete[] u; +} +/* ---------------------------------------------------------------------- */ + +double PairSWAngleTable::splint(double *xa, double *ya, double *y2a, int n, double x) +{ + int klo, khi, k; + double h, b, a, y; + + klo = 0; + khi = n - 1; + while (khi - klo > 1) { + k = (khi + klo) >> 1; + if (xa[k] > x) + khi = k; + else + klo = k; + } + h = xa[khi] - xa[klo]; + a = (xa[khi] - x) / h; + b = (x - xa[klo]) / h; + y = a * ya[klo] + b * ya[khi] + + ((a * a * a - a) * y2a[klo] + (b * b * b - b) * y2a[khi]) * (h * h) / 6.0; + return y; +} + +/* ---------------------------------------------------------------------- + calculate potential u and force f at angle x +------------------------------------------------------------------------- */ + +void PairSWAngleTable::uf_lookup(ParamTable *pm, double x, double &u, double &f) +{ + if (!std::isfinite(x)) { error->one(FLERR, "Illegal angle in angle style table"); } + + double fraction,a,b; + + // invdelta is based on tablength-1 + int itable = static_cast(x * pm->angtable->invdelta); + if (itable < 0) itable = 0; + if (itable >= pm->tablength) itable = pm->tablength - 1; + + if (pm->tabstyle == LINEAR) { + fraction = (x - pm->angtable->ang[itable]) * pm->angtable->invdelta; + u = pm->angtable->e[itable] + fraction*pm->angtable->de[itable]; + f = pm->angtable->f[itable] + fraction*pm->angtable->df[itable]; + } else if (pm->tabstyle == SPLINE) { + fraction = (x - pm->angtable->ang[itable]) * pm->angtable->invdelta; + + b = (x - pm->angtable->ang[itable]) * pm->angtable->invdelta; + a = 1.0 - b; + u = a * pm->angtable->e[itable] + b * pm->angtable->e[itable+1] + + ((a * a * a - a) * pm->angtable->e2[itable] + (b * b * b - b) * pm->angtable->e2[itable+1]) * + pm->angtable->deltasq6; + f = a * pm->angtable->f[itable] + b * pm->angtable->f[itable+1] + + ((a * a * a - a) * pm->angtable->f2[itable] + (b * b * b - b) * pm->angtable->f2[itable+1]) * + pm->angtable->deltasq6; + } +} diff --git a/src/MANYBODY/pair_sw_angle_table.h b/src/MANYBODY/pair_sw_angle_table.h new file mode 100644 index 0000000000..6257d18283 --- /dev/null +++ b/src/MANYBODY/pair_sw_angle_table.h @@ -0,0 +1,77 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(sw/angle/table,PairSWAngleTable); +// clang-format on +#else + +#ifndef LMP_PAIR_SW_ANGLE_TABLE_H +#define LMP_PAIR_SW_ANGLE_TABLE_H + +#include "pair_sw.h" + +namespace LAMMPS_NS { + +class PairSWAngleTable : public PairSW { + public: + PairSWAngleTable(class LAMMPS *); + ~PairSWAngleTable() override; + void compute(int, int) override; + + static constexpr int NPARAMS_PER_LINE = 18; + + // use struct Table as in class AngleTable + struct Table { + int ninput, fpflag; + double fplo, fphi, theta0; + double *afile, *efile, *ffile; + double *e2file, *f2file; + double delta, invdelta, deltasq6; + double *ang, *e, *de, *f, *df, *e2, *f2; + }; + + struct ParamTable { + int tablenamelength; // length of table name + char *tablename; // name of associated angular table + int keywordlength; // length of key in table + char *keyword; // key in table + int tabstyle, tablength; // length of interpolation table (not ninput) and style + Table *angtable; // angle table + }; + + protected: + ParamTable *table_params; // tabulated parameter set for an I-J-K interaction + + void read_file(char *) override; + void threebody_table(Param *, Param *, ParamTable *, double, double, double *, double *, + double *, double *, int, double &); + + void read_table(Table *, char *, char *); + void spline_table(Table *); + void compute_table(Table *, int length); + void bcast_table(Table *); + void null_table(Table *); + void free_table(Table *); + void free_param(ParamTable *); + void param_extract(Table *, char *); + void spline(double *, double *, int, double, double, double *); + double splint(double *, double *, double *, int, double); + void uf_lookup(ParamTable *, double, double &, double &); +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/MANYBODY/pair_threebody_table.cpp b/src/MANYBODY/pair_threebody_table.cpp new file mode 100644 index 0000000000..2f4bc83f5a --- /dev/null +++ b/src/MANYBODY/pair_threebody_table.cpp @@ -0,0 +1,809 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Christoph Scherer (MPIP Mainz) + scherer@mpip-mainz.mpg.de +------------------------------------------------------------------------- */ + +#include "pair_threebody_table.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "math_const.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "potential_file_reader.h" +#include "table_file_reader.h" + +#include +#include + +using namespace LAMMPS_NS; +using MathConst::MY_PI; + +#define DELTA 4 + +/* ---------------------------------------------------------------------- */ + +PairThreebodyTable::PairThreebodyTable(LAMMPS *lmp) : + Pair(lmp), params(nullptr), neighshort(nullptr) +{ + single_enable = 0; + restartinfo = 0; + one_coeff = 1; + manybody_flag = 1; + centroidstressflag = CENTROID_NOTAVAIL; + + maxshort = 10; +} + +/* ---------------------------------------------------------------------- + check if allocated, since class can be destructed when incomplete +------------------------------------------------------------------------- */ + +PairThreebodyTable::~PairThreebodyTable() +{ + if (copymode) return; + + for (int m = 0; m < nparams; m++) free_param(¶ms[m]); // free_param will call free_table + memory->sfree(params); + memory->destroy(elem3param); + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(neighshort); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairThreebodyTable::compute(int eflag, int vflag) +{ + int i, j, k, ii, jj, kk, inum, jnum, jnumm1; + int itype, jtype, ktype, ijparam, ijkparam; + tagint itag, jtag; + double xtmp, ytmp, ztmp, delx, dely, delz, evdwl; + double rsq, rsq1, rsq2; + double delr1[3], delr2[3], fi[3], fj[3], fk[3]; + int *ilist, *jlist, *numneigh, **firstneigh; + + evdwl = 0.0; + ev_init(eflag, vflag); + + double **x = atom->x; + double **f = atom->f; + tagint *tag = atom->tag; + int *type = atom->type; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + double fxtmp, fytmp, fztmp; + + // loop over full neighbor list of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + itag = tag[i]; + itype = map[type[i]]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + fxtmp = fytmp = fztmp = 0.0; + + // two-body interactions, skip half of them + + jlist = firstneigh[i]; + jnum = numneigh[i]; + int numshort = 0; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx * delx + dely * dely + delz * delz; + + jtype = map[type[j]]; + ijparam = elem3param[itype][jtype][jtype]; + if (rsq >= params[ijparam].cutsq) { + continue; + } else { + neighshort[numshort++] = j; + if (numshort >= maxshort) { + maxshort += maxshort / 2; + memory->grow(neighshort, maxshort, "pair:neighshort"); + } + } + + jtag = tag[j]; + if (itag > jtag) { + if ((itag + jtag) % 2 == 0) continue; + } else if (itag < jtag) { + if ((itag + jtag) % 2 == 1) continue; + } else { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp && x[j][1] < ytmp) continue; + if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + + //two-body interactions are not computed + } + + jnumm1 = numshort - 1; + + for (jj = 0; jj < jnumm1; jj++) { + j = neighshort[jj]; + jtype = map[type[j]]; + ijparam = elem3param[itype][jtype][jtype]; + delr1[0] = x[j][0] - xtmp; + delr1[1] = x[j][1] - ytmp; + delr1[2] = x[j][2] - ztmp; + rsq1 = delr1[0] * delr1[0] + delr1[1] * delr1[1] + delr1[2] * delr1[2]; + + double fjxtmp, fjytmp, fjztmp; + fjxtmp = fjytmp = fjztmp = 0.0; + + for (kk = jj + 1; kk < numshort; kk++) { + k = neighshort[kk]; + ktype = map[type[k]]; + ijkparam = elem3param[itype][jtype][ktype]; + + delr2[0] = x[k][0] - xtmp; + delr2[1] = x[k][1] - ytmp; + delr2[2] = x[k][2] - ztmp; + rsq2 = delr2[0] * delr2[0] + delr2[1] * delr2[1] + delr2[2] * delr2[2]; + + threebody(¶ms[ijkparam], rsq1, rsq2, delr1, delr2, fi, fj, fk, eflag, evdwl); + + fxtmp += fi[0]; + fytmp += fi[1]; + fztmp += fi[2]; + fjxtmp += fj[0]; + fjytmp += fj[1]; + fjztmp += fj[2]; + f[k][0] += fk[0]; + f[k][1] += fk[1]; + f[k][2] += fk[2]; + + if (evflag) ev_tally3(i, j, k, evdwl, 0.0, fj, fk, delr1, delr2); + } + f[j][0] += fjxtmp; + f[j][1] += fjytmp; + f[j][2] += fjztmp; + } + f[i][0] += fxtmp; + f[i][1] += fytmp; + f[i][2] += fztmp; + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- */ + +void PairThreebodyTable::allocate() +{ + allocated = 1; + int np1 = atom->ntypes + 1; + + memory->create(setflag, np1, np1, "pair:setflag"); + memory->create(cutsq, np1, np1, "pair:cutsq"); + memory->create(neighshort, maxshort, "pair:neighshort"); + map = new int[np1]; +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairThreebodyTable::settings(int narg, char ** /*arg*/) +{ + if (narg != 0) error->all(FLERR, "Illegal pair_style command"); +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairThreebodyTable::coeff(int narg, char **arg) +{ + if (!allocated) allocate(); + + map_element2type(narg - 3, arg + 3); + + // read potential file and initialize potential parameters + + if (params) { + for (int m = 0; m < nparams; m++) free_param(¶ms[m]); // free_param will call free_table + memory->sfree(params); + params = nullptr; + } + read_file(arg[2]); + setup_params(); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairThreebodyTable::init_style() +{ + if (atom->tag_enable == 0) error->all(FLERR, "Pair style threebody/table requires atom IDs"); + if (force->newton_pair == 0) + error->all(FLERR, "Pair style threebody/table requires newton pair on"); + + // need a full neighbor list + + neighbor->add_request(this, NeighConst::REQ_FULL); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairThreebodyTable::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set"); + + return cutmax; +} + +/* ---------------------------------------------------------------------- */ + +void PairThreebodyTable::read_file(char *file) +{ + params = nullptr; + nparams = maxparam = 0; + + // open file on proc 0 + + if (comm->me == 0) { + PotentialFileReader reader(lmp, file, "threebody", unit_convert_flag); + char *line; + + while ((line = reader.next_line(NPARAMS_PER_LINE))) { + try { + ValueTokenizer values(line); + + std::string iname = values.next_string(); + std::string jname = values.next_string(); + std::string kname = values.next_string(); + + // ielement,jelement,kelement = 1st args + // if all 3 args are in element list, then parse this line + // else skip to next entry in file + int ielement, jelement, kelement; + + for (ielement = 0; ielement < nelements; ielement++) + if (iname == elements[ielement]) break; + if (ielement == nelements) continue; + for (jelement = 0; jelement < nelements; jelement++) + if (jname == elements[jelement]) break; + if (jelement == nelements) continue; + for (kelement = 0; kelement < nelements; kelement++) + if (kname == elements[kelement]) break; + if (kelement == nelements) continue; + + // load up parameter settings and error check their values + + if (nparams == maxparam) { + maxparam += DELTA; + params = (Param *) memory->srealloc(params, maxparam * sizeof(Param), "pair:params"); + + // make certain all addional allocated storage is initialized + // to avoid false positives when checking with valgrind + + memset(params + nparams, 0, DELTA * sizeof(Param)); + } + + params[nparams].ielement = ielement; + params[nparams].jelement = jelement; + params[nparams].kelement = kelement; + // if jelement = kelement, symmetric is true, if not then it is false + params[nparams].symmetric = false; + if (params[nparams].jelement == params[nparams].kelement) params[nparams].symmetric = true; + // read cut off + params[nparams].cut = values.next_double(); + + // read parameters of angle table + std::string name = values.next_string(); + params[nparams].tablenamelength = name.length() + 1; + params[nparams].tablename = utils::strdup(name); + + name = values.next_string(); + params[nparams].keywordlength = name.length() + 1; + params[nparams].keyword = utils::strdup(name); + + name = values.next_string(); + if (name != "linear") error->all(FLERR, "Unknown table style {} in threebody table", name); + params[nparams].tablength = values.next_int(); + + } catch (TokenizerException &e) { + error->one(FLERR, e.what()); + } + + if (params[nparams].cut < 0.0 || params[nparams].tablength < 0.0) + error->one(FLERR, "Illegal threebody/table parameters"); + + nparams++; + } + } + + MPI_Bcast(&nparams, 1, MPI_INT, 0, world); + MPI_Bcast(&maxparam, 1, MPI_INT, 0, world); + + if (comm->me != 0) + params = (Param *) memory->srealloc(params, maxparam * sizeof(Param), "pair:params"); + MPI_Bcast(params, maxparam * sizeof(Param), MPI_BYTE, 0, world); + + // for each set of parameters, broadcast table name and keyword and read threebody table + for (int m = 0; m < nparams; ++m) { + if (comm->me != 0) { + params[m].tablename = new char[params[m].tablenamelength]; + params[m].keyword = new char[params[m].keywordlength]; + } + + MPI_Bcast(params[m].tablename, params[m].tablenamelength, MPI_CHAR, 0, world); + MPI_Bcast(params[m].keyword, params[m].keywordlength, MPI_CHAR, 0, world); + + // initialize threebodytable + memory->create(params[m].mltable, 1, "param:threebodytable"); + null_table(params[m].mltable); + + //call read_table to read corresponding tabulated threebody file (only called by process 0) + if (comm->me == 0) { + read_table(params[m].mltable, params[m].tablename, params[m].keyword, params[m].symmetric); + } + + // broadcast read in threebodytable to all processes + bcast_table(params[m].mltable, params[m].symmetric); + + // error check on table parameters + if (params[m].mltable->ninput <= 1) error->one(FLERR, "Invalid threebody table length"); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairThreebodyTable::setup_params() +{ + int i, j, k, m, n; + double rtmp; + + // set elem3param for all triplet combinations + // must be a single exact match to lines read from file + // do not allow for ACB in place of ABC + + memory->destroy(elem3param); + memory->create(elem3param, nelements, nelements, nelements, "pair:elem3param"); + + for (i = 0; i < nelements; i++) + for (j = 0; j < nelements; j++) + for (k = 0; k < nelements; k++) { + n = -1; + for (m = 0; m < nparams; m++) { + if (i == params[m].ielement && j == params[m].jelement && k == params[m].kelement) { + if (n >= 0) error->all(FLERR, "Potential file has duplicate entry"); + n = m; + } + } + if (n < 0) error->all(FLERR, "Potential file is missing an entry"); + elem3param[i][j][k] = n; + } + + // compute parameter values derived from inputs + + // set cutsq using shortcut to reduce neighbor list for accelerated + // calculations. cut must remain unchanged as it is a potential parameter + // (cut = a) + + for (m = 0; m < nparams; m++) { + rtmp = params[m].cut; + params[m].cutsq = rtmp * rtmp; + } + + // set cutmax to max of all params + + cutmax = 0.0; + for (m = 0; m < nparams; m++) { + rtmp = sqrt(params[m].cutsq); + if (rtmp > cutmax) cutmax = rtmp; + } +} + +/* ---------------------------------------------------------------------- + read table file, only called by proc 0 +------------------------------------------------------------------------- */ + +void PairThreebodyTable::read_table(Table *tb, char *file, char *keyword, bool symmetric) +{ + TableFileReader reader(lmp, file, "threebodytable"); + + char *line = reader.find_section_start(keyword); + + if (!line) { error->one(FLERR, "Did not find keyword in table file"); } + + // read args on 2nd line of section + // allocate table arrays for file values + + line = reader.next_line(); + param_extract(tb, line); + + // if it is a symmetric threebody interaction, less table entries are required + if (symmetric) { + memory->create(tb->r12file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:r12file"); + memory->create(tb->r13file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:r13file"); + memory->create(tb->thetafile, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:thetafile"); + memory->create(tb->f11file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:f11file"); + memory->create(tb->f12file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:f12file"); + memory->create(tb->f21file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:f21file"); + memory->create(tb->f22file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:f22file"); + memory->create(tb->f31file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:f31file"); + memory->create(tb->f32file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:f32file"); + memory->create(tb->efile, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:efile"); + } + // else, more (full) table entries are required + else { + memory->create(tb->r12file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:r12file"); + memory->create(tb->r13file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:r13file"); + memory->create(tb->thetafile, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:thetafile"); + memory->create(tb->f11file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:f11file"); + memory->create(tb->f12file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:f12file"); + memory->create(tb->f21file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:f21file"); + memory->create(tb->f22file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:f22file"); + memory->create(tb->f31file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:f31file"); + memory->create(tb->f32file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:f32file"); + memory->create(tb->efile, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:efile"); + } + + // read threebody table values from file + + int cerror = 0; + reader.skip_line(); + // if it is a symmetric threebody interaction, less table entries are required + if (symmetric) { + for (int i = 0; i < tb->ninput * tb->ninput * (tb->ninput + 1); i++) { + line = reader.next_line(11); + try { + ValueTokenizer values(line); + values.next_int(); + tb->r12file[i] = values.next_double(); + tb->r13file[i] = values.next_double(); + tb->thetafile[i] = values.next_double(); + tb->f11file[i] = values.next_double(); + tb->f12file[i] = values.next_double(); + tb->f21file[i] = values.next_double(); + tb->f22file[i] = values.next_double(); + tb->f31file[i] = values.next_double(); + tb->f32file[i] = values.next_double(); + tb->efile[i] = values.next_double(); + } catch (TokenizerException &) { + ++cerror; + } + } + } else { + for (int i = 0; i < 2 * tb->ninput * tb->ninput * tb->ninput; i++) { + line = reader.next_line(11); + try { + ValueTokenizer values(line); + values.next_int(); + tb->r12file[i] = values.next_double(); + tb->r13file[i] = values.next_double(); + tb->thetafile[i] = values.next_double(); + tb->f11file[i] = values.next_double(); + tb->f12file[i] = values.next_double(); + tb->f21file[i] = values.next_double(); + tb->f22file[i] = values.next_double(); + tb->f31file[i] = values.next_double(); + tb->f32file[i] = values.next_double(); + tb->efile[i] = values.next_double(); + } catch (TokenizerException &) { + ++cerror; + } + } + } + + // warn if data was read incompletely, e.g. columns were missing + + if (cerror) + error->warning(FLERR, "{} of {} lines in table incomplete or could not be parsed", cerror, + tb->ninput); +} + +/* ---------------------------------------------------------------------- + extract attributes from parameter line in table section + format of line: N value FP fplo fphi EQ theta0 + N is required, other params are optional + + only called by read_table, only called by proc 0 +------------------------------------------------------------------------- */ + +void PairThreebodyTable::param_extract(Table *tb, char *line) +{ + tb->ninput = 0; + tb->rmin = 0.0; + tb->rmax = 0.0; + + try { + ValueTokenizer values(line); + + while (values.has_next()) { + std::string word = values.next_string(); + + if (word == "N") { + tb->ninput = values.next_int(); + } else if (word == "rmin") { + tb->rmin = values.next_double(); + } else if (word == "rmax") { + tb->rmax = values.next_double(); + } else { + error->one(FLERR, "Invalid keyword {} in angle table parameters", word); + } + } + } catch (TokenizerException &e) { + error->one(FLERR, e.what()); + } + + if (tb->ninput == 0) error->one(FLERR, "threebodytable parameters did not set N"); + if (tb->rmin == 0.0) error->one(FLERR, "threebodytable parameters did not set rmin"); + if (tb->rmax == 0.0) error->one(FLERR, "threebodytable parameters did not set rmax"); +} + +/* ---------------------------------------------------------------------- + broadcast read-in table info from proc 0 to other procs + this function communicates these values in Table: + ninput,afile,efile,ffile,fpflag,fplo,fphi,theta0 +------------------------------------------------------------------------- */ + +void PairThreebodyTable::bcast_table(Table *tb, bool symmetric) +{ + MPI_Bcast(&tb->ninput, 1, MPI_INT, 0, world); + + int me; + MPI_Comm_rank(world, &me); + if (me > 0) { + // if it is a symmetric threebody interaction, less table entries are required + if (symmetric) { + memory->create(tb->r12file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:r12file"); + memory->create(tb->r13file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:r13file"); + memory->create(tb->thetafile, tb->ninput * tb->ninput * (tb->ninput + 1), + "mltable:thetafile"); + memory->create(tb->f11file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:f11file"); + memory->create(tb->f12file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:f12file"); + memory->create(tb->f21file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:f21file"); + memory->create(tb->f22file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:f22file"); + memory->create(tb->f31file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:f31file"); + memory->create(tb->f32file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:f32file"); + memory->create(tb->efile, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:efile"); + } + // else, more (full) table entries are required + else { + memory->create(tb->r12file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:r12file"); + memory->create(tb->r13file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:r13file"); + memory->create(tb->thetafile, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:thetafile"); + memory->create(tb->f11file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:f11file"); + memory->create(tb->f12file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:f12file"); + memory->create(tb->f21file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:f21file"); + memory->create(tb->f22file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:f22file"); + memory->create(tb->f31file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:f31file"); + memory->create(tb->f32file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:f32file"); + memory->create(tb->efile, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:efile"); + } + } + + // if it is a symmetric threebody interaction, less table entries are required + if (symmetric) { + MPI_Bcast(tb->r12file, tb->ninput * tb->ninput * (tb->ninput + 1), MPI_DOUBLE, 0, world); + MPI_Bcast(tb->r13file, tb->ninput * tb->ninput * (tb->ninput + 1), MPI_DOUBLE, 0, world); + MPI_Bcast(tb->thetafile, tb->ninput * tb->ninput * (tb->ninput + 1), MPI_DOUBLE, 0, world); + MPI_Bcast(tb->f11file, tb->ninput * tb->ninput * (tb->ninput + 1), MPI_DOUBLE, 0, world); + MPI_Bcast(tb->f12file, tb->ninput * tb->ninput * (tb->ninput + 1), MPI_DOUBLE, 0, world); + MPI_Bcast(tb->f21file, tb->ninput * tb->ninput * (tb->ninput + 1), MPI_DOUBLE, 0, world); + MPI_Bcast(tb->f22file, tb->ninput * tb->ninput * (tb->ninput + 1), MPI_DOUBLE, 0, world); + MPI_Bcast(tb->f31file, tb->ninput * tb->ninput * (tb->ninput + 1), MPI_DOUBLE, 0, world); + MPI_Bcast(tb->f32file, tb->ninput * tb->ninput * (tb->ninput + 1), MPI_DOUBLE, 0, world); + MPI_Bcast(tb->efile, tb->ninput * tb->ninput * (tb->ninput + 1), MPI_DOUBLE, 0, world); + } + // else, more (full) table entries are required + else { + MPI_Bcast(tb->r12file, 2 * tb->ninput * tb->ninput * tb->ninput, MPI_DOUBLE, 0, world); + MPI_Bcast(tb->r13file, 2 * tb->ninput * tb->ninput * tb->ninput, MPI_DOUBLE, 0, world); + MPI_Bcast(tb->thetafile, 2 * tb->ninput * tb->ninput * tb->ninput, MPI_DOUBLE, 0, world); + MPI_Bcast(tb->f11file, 2 * tb->ninput * tb->ninput * tb->ninput, MPI_DOUBLE, 0, world); + MPI_Bcast(tb->f12file, 2 * tb->ninput * tb->ninput * tb->ninput, MPI_DOUBLE, 0, world); + MPI_Bcast(tb->f21file, 2 * tb->ninput * tb->ninput * tb->ninput, MPI_DOUBLE, 0, world); + MPI_Bcast(tb->f22file, 2 * tb->ninput * tb->ninput * tb->ninput, MPI_DOUBLE, 0, world); + MPI_Bcast(tb->f31file, 2 * tb->ninput * tb->ninput * tb->ninput, MPI_DOUBLE, 0, world); + MPI_Bcast(tb->f32file, 2 * tb->ninput * tb->ninput * tb->ninput, MPI_DOUBLE, 0, world); + MPI_Bcast(tb->efile, 2 * tb->ninput * tb->ninput * tb->ninput, MPI_DOUBLE, 0, world); + } + + MPI_Bcast(&tb->rmin, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&tb->rmax, 1, MPI_DOUBLE, 0, world); +} + +/* ---------------------------------------------------------------------- */ + +void PairThreebodyTable::free_param(Param *pm) +{ + // call free_table to destroy associated threebodytables + free_table(pm->mltable); + // then destroy associated threebodytable + delete[] pm->tablename; + delete[] pm->keyword; + memory->sfree(pm->mltable); +} + +/* ---------------------------------------------------------------------- */ + +void PairThreebodyTable::free_table(Table *tb) +{ + memory->destroy(tb->r12file); + memory->destroy(tb->r13file); + memory->destroy(tb->thetafile); + memory->destroy(tb->f11file); + memory->destroy(tb->f12file); + memory->destroy(tb->f21file); + memory->destroy(tb->f22file); + memory->destroy(tb->f31file); + memory->destroy(tb->f32file); + memory->destroy(tb->efile); +} + +/* ---------------------------------------------------------------------- */ + +void PairThreebodyTable::null_table(Table *tb) +{ + tb->r12file = tb->r13file = tb->thetafile = nullptr; + tb->f11file = tb->f12file = nullptr; + tb->f21file = tb->f22file = nullptr; + tb->f31file = tb->f32file = nullptr; + tb->efile = nullptr; +} + +/* ---------------------------------------------------------------------- + calculate potential u and force f at angle x +------------------------------------------------------------------------- */ + +void PairThreebodyTable::uf_lookup(Param *pm, double r12, double r13, double theta, double &f11, + double &f12, double &f21, double &f22, double &f31, double &f32, + double &u) +{ + int i, itable, nr12, nr13, ntheta; + double dr, dtheta; + dr = (pm->mltable->rmax - pm->mltable->rmin) / (pm->mltable->ninput - 1); + dtheta = (180.0 - 0.0) / (pm->mltable->ninput * 2); + + //lookup scheme + + // if it is a symmetric threebody interaction, less table entries are required + if (pm->symmetric) { + nr12 = (r12 - pm->mltable->rmin + 0.5 * dr - 0.00000001) / dr; + if (r12 == (pm->mltable->rmin - 0.5 * dr)) { nr12 = 0; } + nr13 = (r13 - pm->mltable->rmin + 0.5 * dr - 0.00000001) / dr; + if (r13 == (pm->mltable->rmin - 0.5 * dr)) { nr13 = 0; } + nr13 -= nr12; + ntheta = (theta - 0.00000001) / dtheta; + if (theta == 180.0) { ntheta = 79; } + itable = 0; + for (i = 0; i < nr12; i++) { itable += (pm->mltable->ninput - i); } + itable += nr13; + itable *= (pm->mltable->ninput * 2); + itable += ntheta; + } else { + // else, more (full) table entries are required + nr12 = (r12 - pm->mltable->rmin + 0.5 * dr - 0.00000001) / dr; + if (r12 == (pm->mltable->rmin - 0.5 * dr)) { nr12 = 0; } + nr13 = (r13 - pm->mltable->rmin + 0.5 * dr - 0.00000001) / dr; + if (r13 == (pm->mltable->rmin - 0.5 * dr)) { nr13 = 0; } + ntheta = (theta - 0.00000001) / dtheta; + if (theta == 180.0) { ntheta = 79; } + itable = nr12 * (pm->mltable->ninput); + itable += nr13; + itable *= (pm->mltable->ninput * 2); + itable += ntheta; + } + + f11 = pm->mltable->f11file[itable]; + f12 = pm->mltable->f12file[itable]; + f21 = pm->mltable->f21file[itable]; + f22 = pm->mltable->f22file[itable]; + f31 = pm->mltable->f31file[itable]; + f32 = pm->mltable->f32file[itable]; + u = pm->mltable->efile[itable]; +} + +/* ---------------------------------------------------------------------- */ + +void PairThreebodyTable::threebody(Param *paramijk, double rsq1, double rsq2, double *delr1, + double *delr2, double *fi, double *fj, double *fk, int eflag, + double &eng) +{ + double r12, r13, theta, rinv, cs; + + double f11, f12, f21, f22, f31, f32, u, temp; + bool swapped; + double dr; + dr = (paramijk->mltable->rmax - paramijk->mltable->rmin) / (paramijk->mltable->ninput - 1); + + //if swap indices or not + swapped = false; + + r12 = sqrt(rsq1); + r13 = sqrt(rsq2); + rinv = 1.0 / (r12 * r13); + cs = (delr1[0] * delr2[0] + delr1[1] * delr2[1] + delr1[2] * delr2[2]) * rinv; + //compute angle between r12 and r13 in degrees + theta = acos(cs) * 180.0 / MY_PI; + + //if r12 > r13 swap them, as in lookup table always r13 > r12 do to symmetry reasons + if (r12 > r13) { + temp = r12; + r12 = r13; + r13 = temp; + swapped = true; + } + + //look up forces and energy in table belonging to parameter set paramijk + + //only do lookup and add three-body interactions if r12 and r13 are both between rmin and rmax + + if ((r12 >= (paramijk->mltable->rmin - 0.5 * dr)) && + (r13 <= (paramijk->mltable->rmax + 0.5 * dr)) && + (r13 >= (paramijk->mltable->rmin - 0.5 * dr)) && + (r13 <= (paramijk->mltable->rmax + 0.5 * dr))) { + uf_lookup(paramijk, r12, r13, theta, f11, f12, f21, f22, f31, f32, u); + } else { + f11 = f12 = f21 = f22 = f31 = f32 = u = 0.0; + } + + // if the indices have been swapped, swap them back + if (swapped) { + temp = r12; + r12 = r13; + r13 = temp; + temp = f11; + f11 = f12; + f12 = temp; + temp = f21; + f21 = f31; + f31 = temp; + temp = f22; + f22 = -f32; + f32 = -temp; + } + + fi[0] = delr1[0] * f11 + delr2[0] * f12; + fi[1] = delr1[1] * f11 + delr2[1] * f12; + fi[2] = delr1[2] * f11 + delr2[2] * f12; + + fj[0] = delr1[0] * f21 + (delr2[0] - delr1[0]) * f22; + fj[1] = delr1[1] * f21 + (delr2[1] - delr1[1]) * f22; + fj[2] = delr1[2] * f21 + (delr2[2] - delr1[2]) * f22; + + fk[0] = delr2[0] * f31 + (delr2[0] - delr1[0]) * f32; + fk[1] = delr2[1] * f31 + (delr2[1] - delr1[1]) * f32; + fk[2] = delr2[2] * f31 + (delr2[2] - delr1[2]) * f32; + + if (eflag) eng = u; +} diff --git a/src/MANYBODY/pair_threebody_table.h b/src/MANYBODY/pair_threebody_table.h new file mode 100644 index 0000000000..218bfeebd8 --- /dev/null +++ b/src/MANYBODY/pair_threebody_table.h @@ -0,0 +1,89 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(threebody/table,PairThreebodyTable); +// clang-format on +#else + +#ifndef LMP_PAIR_THREEBODY_TABLE_H +#define LMP_PAIR_THREEBODY_TABLE_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairThreebodyTable : public Pair { + public: + PairThreebodyTable(class LAMMPS *); + ~PairThreebodyTable() override; + void compute(int, int) override; + void coeff(int, char **) override; + double init_one(int, int) override; + void init_style() override; + + static constexpr int NPARAMS_PER_LINE = 8; + + // no write or read from binary restart file + + // struct for threebody/table + struct Table { + int ninput; + double rmin, rmax; + double *r12file, *r13file, *thetafile, *f11file, *f12file, *f21file, *f22file, *f31file, + *f32file, *efile; + }; + + struct Param { + double cut, cutsq; + int ielement, jelement, kelement; + bool symmetric; // whether it is a symmetric table or not + int tablenamelength; // length of table name + char *tablename; // name of associated angular table + int keywordlength; // length of key in table + char *keyword; // key in table + int tabstyle, tablength; // length of interpolation table (not ninput) and style + Table *mltable; // threebody table + }; + + protected: + double cutmax; // max cutoff for all elements + Param *params; // parameter set for an I-J-K interaction + int maxshort; // size of short neighbor list array + int *neighshort; // short neighbor list array + + void settings(int, char **) override; + virtual void allocate(); + void read_file(char *); + virtual void setup_params(); + void threebody(Param *, double, double, double *, double *, double *, double *, double *, int, + double &); + + void read_table(Table *, char *, char *, bool); + void bcast_table(Table *, bool); + void null_table(Table *); + + void free_table(Table *); + void free_param(Param *); + + void param_extract(Table *, char *); + + void uf_lookup(Param *, double, double, double, double &, double &, double &, double &, double &, + double &, double &); +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/MC/fix_widom.cpp b/src/MC/fix_widom.cpp index 0adabe5eae..0a20e7adf3 100644 --- a/src/MC/fix_widom.cpp +++ b/src/MC/fix_widom.cpp @@ -273,7 +273,7 @@ void FixWidom::init() triclinic = domain->triclinic; - ave_widom_chemical_potential = 0; + ave_widom_chemical_potential = 0.0; if (region) volume = region_volume; else volume = domain->xprd * domain->yprd * domain->zprd; diff --git a/src/ML-PACE/pair_pace.cpp b/src/ML-PACE/pair_pace.cpp index a583ebe508..87e580b8d3 100644 --- a/src/ML-PACE/pair_pace.cpp +++ b/src/ML-PACE/pair_pace.cpp @@ -146,18 +146,8 @@ void PairPACE::compute(int eflag, int vflag) // the pointer to the list of neighbors of "i" firstneigh = list->firstneigh; - if (inum != nlocal) error->all(FLERR, "inum: {} nlocal: {} are different", inum, nlocal); - - // Aidan Thompson told RD (26 July 2019) that practically always holds: - // inum = nlocal - // i = ilist(ii) < inum - // j = jlist(jj) < nall - // neighborlist contains neighbor atoms plus skin atoms, - // skin atoms can be removed by setting skin to zero but here - // they are disregarded anyway - //determine the maximum number of neighbours - int max_jnum = -1; + int max_jnum = 0; int nei = 0; for (ii = 0; ii < list->inum; ii++) { i = ilist[ii]; @@ -190,7 +180,7 @@ void PairPACE::compute(int eflag, int vflag) try { aceimpl->ace->compute_atom(i, x, type, jnum, jlist); - } catch (exception &e) { + } catch (std::exception &e) { error->one(FLERR, e.what()); } @@ -269,7 +259,7 @@ void PairPACE::settings(int narg, char **arg) recursive = false; iarg += 1; } else if (strcmp(arg[iarg], "chunksize") == 0) { - chunksize = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + chunksize = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else error->all(FLERR, "Illegal pair_style command"); @@ -325,27 +315,34 @@ void PairPACE::coeff(int narg, char **arg) const int n = atom->ntypes; for (int i = 1; i <= n; i++) { - char *elemname = elemtypes[i - 1]; - int atomic_number = AtomicNumberByName_pace(elemname); - if (atomic_number == -1) error->all(FLERR, "'{}' is not a valid element\n", elemname); - - SPECIES_TYPE mu = aceimpl->basis_set->get_species_index_by_name(elemname); - if (mu != -1) { - if (comm->me == 0) - utils::logmesg(lmp, "Mapping LAMMPS atom type #{}({}) -> ACE species type #{}\n", i, - elemname, mu); - map[i] = mu; - // set up LAMMPS atom type to ACE species mapping for ace evaluator - aceimpl->ace->element_type_mapping(i) = mu; + char *elemname = arg[2 + i]; + if (strcmp(elemname, "NULL") == 0) { + // species_type=-1 value will not reach ACE Evaluator::compute_atom, + // but if it will ,then error will be thrown there + aceimpl->ace->element_type_mapping(i) = -1; + map[i] = -1; + if (comm->me == 0) utils::logmesg(lmp, "Skipping LAMMPS atom type #{}(NULL)\n", i); } else { - error->all(FLERR, "Element {} is not supported by ACE-potential from file {}", elemname, - potential_file_name); + int atomic_number = AtomicNumberByName_pace(elemname); + if (atomic_number == -1) error->all(FLERR, "'{}' is not a valid element\n", elemname); + SPECIES_TYPE mu = aceimpl->basis_set->get_species_index_by_name(elemname); + if (mu != -1) { + if (comm->me == 0) + utils::logmesg(lmp, "Mapping LAMMPS atom type #{}({}) -> ACE species type #{}\n", i, + elemname, mu); + map[i] = mu; + // set up LAMMPS atom type to ACE species mapping for ace evaluator + aceimpl->ace->element_type_mapping(i) = mu; + } else { + error->all(FLERR, "Element {} is not supported by ACE-potential from file {}", elemname, + potential_file_name); + } } } // initialize scale factor for (int i = 1; i <= n; i++) { - for (int j = i; j <= n; j++) { scale[i][j] = 1.0; } + for (int j = i; j <= n; j++) scale[i][j] = 1.0; } aceimpl->ace->set_basis(*aceimpl->basis_set, 1); diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp index eeb30c4d64..c3959dc898 100644 --- a/src/MOLECULE/angle_table.cpp +++ b/src/MOLECULE/angle_table.cpp @@ -402,26 +402,20 @@ void AngleTable::read_table(Table *tb, char *file, char *keyword) // read a,e,f table values from file - int cerror = 0; reader.skip_line(); for (int i = 0; i < tb->ninput; i++) { - line = reader.next_line(4); + line = reader.next_line(); try { ValueTokenizer values(line); values.next_int(); tb->afile[i] = values.next_double(); tb->efile[i] = values.next_double(); tb->ffile[i] = values.next_double(); - } catch (TokenizerException &) { - ++cerror; + } catch (TokenizerException &e) { + error->one(FLERR, "Error parsing angle table '{}' line {} of {}. {}\nLine was: {}", keyword, + i + 1, tb->ninput, e.what(), line); } } - - // warn if data was read incompletely, e.g. columns were missing - - if (cerror) - error->warning(FLERR, "{} of {} lines in table incomplete or could not be parsed", cerror, - tb->ninput); } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp index e1eac7c4c2..7af08a4a08 100644 --- a/src/MOLECULE/bond_table.cpp +++ b/src/MOLECULE/bond_table.cpp @@ -325,20 +325,20 @@ void BondTable::read_table(Table *tb, char *file, char *keyword) // read r,e,f table values from file - int cerror = 0; int r0idx = -1; reader.skip_line(); for (int i = 0; i < tb->ninput; i++) { - line = reader.next_line(4); + line = reader.next_line(); try { ValueTokenizer values(line); values.next_int(); tb->rfile[i] = values.next_double(); tb->efile[i] = values.next_double(); tb->ffile[i] = values.next_double(); - } catch (TokenizerException &) { - ++cerror; + } catch (TokenizerException &e) { + error->one(FLERR, "Error parsing bond table '{}' line {} of {}. {}\nLine was: {}", keyword, + i + 1, tb->ninput, e.what(), line); } if (tb->efile[i] < emin) { @@ -373,21 +373,11 @@ void BondTable::read_table(Table *tb, char *file, char *keyword) if (f > fleft && f > fright) ferror++; } - if (ferror) { + if (ferror) error->warning(FLERR, "{} of {} force values in table are inconsistent with -dE/dr.\n" "WARNING: Should only be flagged at inflection points", ferror, tb->ninput); - } - - // warn if data was read incompletely, e.g. columns were missing - - if (cerror) { - error->warning(FLERR, - "{} of {} lines in table were incomplete or could not be" - " parsed completely", - cerror, tb->ninput); - } } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/dihedral_table.cpp b/src/MOLECULE/dihedral_table.cpp index ea0b30cbd5..1a9bc923a7 100644 --- a/src/MOLECULE/dihedral_table.cpp +++ b/src/MOLECULE/dihedral_table.cpp @@ -1020,23 +1020,24 @@ void DihedralTable::read_table(Table *tb, char *file, char *keyword) // read a,e,f table values from file for (int i = 0; i < tb->ninput; i++) { + line = reader.next_line(); try { + ValueTokenizer values(line); if (tb->f_unspecified) { - ValueTokenizer values = reader.next_values(3); values.next_int(); tb->phifile[i] = values.next_double(); tb->efile[i] = values.next_double(); } else { - ValueTokenizer values = reader.next_values(4); values.next_int(); tb->phifile[i] = values.next_double(); tb->efile[i] = values.next_double(); tb->ffile[i] = values.next_double(); } } catch (TokenizerException &e) { - error->one(FLERR, e.what()); + error->one(FLERR, "Error parsing dihedral table '{}' line {} of {}. {}\nLine was: {}", + keyword, i + 1, tb->ninput, e.what(), line); } - } //for (int i = 0; (i < tb->ninput) && fp; i++) { + } } /* ---------------------------------------------------------------------- diff --git a/src/Makefile b/src/Makefile index d752d1dce6..14249ab517 100644 --- a/src/Makefile +++ b/src/Makefile @@ -463,7 +463,7 @@ mpi-stubs: sinclude ../lib/python/Makefile.lammps install-python: @rm -rf ../python/build - @$(PYTHON) ../python/install.py -p ../python/lammps -l ../src/liblammps.so + @$(PYTHON) ../python/install.py -p ../python/lammps -l ../src/liblammps.so -w $(PWD) # Create a tarball of src dir and packages diff --git a/src/REAXFF/fix_acks2_reaxff.cpp b/src/REAXFF/fix_acks2_reaxff.cpp index bd93dec0b7..be71bc761f 100644 --- a/src/REAXFF/fix_acks2_reaxff.cpp +++ b/src/REAXFF/fix_acks2_reaxff.cpp @@ -94,8 +94,8 @@ FixACKS2ReaxFF::~FixACKS2ReaxFF() memory->destroy(s_hist_X); memory->destroy(s_hist_last); - deallocate_storage(); - deallocate_matrix(); + FixACKS2ReaxFF::deallocate_storage(); + FixACKS2ReaxFF::deallocate_matrix(); } /* ---------------------------------------------------------------------- */ diff --git a/src/REAXFF/fix_qeq_reaxff.cpp b/src/REAXFF/fix_qeq_reaxff.cpp index aeeee7b71a..48e93f682a 100644 --- a/src/REAXFF/fix_qeq_reaxff.cpp +++ b/src/REAXFF/fix_qeq_reaxff.cpp @@ -163,7 +163,7 @@ FixQEqReaxFF::~FixQEqReaxFF() memory->destroy(t_hist); FixQEqReaxFF::deallocate_storage(); - deallocate_matrix(); + FixQEqReaxFF::deallocate_matrix(); memory->destroy(shld); @@ -640,7 +640,7 @@ void FixQEqReaxFF::compute_H() int jnum; int i, j, ii, jj, flag; double dx, dy, dz, r_sqr; - const double SMALL = 0.0001; + constexpr double EPSILON = 0.0001; int *type = atom->type; tagint *tag = atom->tag; @@ -671,10 +671,10 @@ void FixQEqReaxFF::compute_H() if (j < atom->nlocal) flag = 1; else if (tag[i] < tag[j]) flag = 1; else if (tag[i] == tag[j]) { - if (dz > SMALL) flag = 1; - else if (fabs(dz) < SMALL) { - if (dy > SMALL) flag = 1; - else if (fabs(dy) < SMALL && dx > SMALL) + if (dz > EPSILON) flag = 1; + else if (fabs(dz) < EPSILON) { + if (dy > EPSILON) flag = 1; + else if (fabs(dy) < EPSILON && dx > EPSILON) flag = 1; } } diff --git a/src/REAXFF/reaxff_defs.h b/src/REAXFF/reaxff_defs.h index 45fa182728..0650c518fe 100644 --- a/src/REAXFF/reaxff_defs.h +++ b/src/REAXFF/reaxff_defs.h @@ -56,6 +56,8 @@ #define REAX_MAX_3BODY_PARAM 5 #define REAX_MAX_4BODY_PARAM 5 +#define MIN_SINE 1e-10 + namespace ReaxFF { /******************* ENUMERATORS *************************/ enum { BONDS, THREE_BODIES, HBONDS, FAR_NBRS, LIST_N }; diff --git a/src/REAXFF/reaxff_torsion_angles.cpp b/src/REAXFF/reaxff_torsion_angles.cpp index 4bf810b431..2b94bf50ae 100644 --- a/src/REAXFF/reaxff_torsion_angles.cpp +++ b/src/REAXFF/reaxff_torsion_angles.cpp @@ -31,8 +31,6 @@ #include -#define MIN_SINE 1e-10 - namespace ReaxFF { double Calculate_Omega(rvec dvec_ij, double r_ij, rvec dvec_jk, double r_jk, rvec dvec_kl, double r_kl, rvec dvec_li, double r_li, diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index deff0cfd58..dbacf2237a 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -207,7 +207,7 @@ void AtomVec::grow(int n) if (n == 0) grow_nmax(); else - nmax = n; + nmax = MAX(n,nmax); atom->nmax = nmax; if (nmax < 0 || nmax > MAXSMALLINT) error->one(FLERR, "Per-processor system is too big"); diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp index 7b3929db62..d316644e15 100644 --- a/src/create_bonds.cpp +++ b/src/create_bonds.cpp @@ -73,7 +73,6 @@ void CreateBonds::command(int narg, char **arg) iarg = 6; } else if (strcmp(arg[0], "single/bond") == 0) { style = SBOND; - if (narg < 4) error->all(FLERR, "Illegal create_bonds command"); btype = utils::inumeric(FLERR, arg[1], false, lmp); batom1 = utils::tnumeric(FLERR, arg[2], false, lmp); batom2 = utils::tnumeric(FLERR, arg[3], false, lmp); diff --git a/src/dump.cpp b/src/dump.cpp index 3569d32165..a354be4f04 100644 --- a/src/dump.cpp +++ b/src/dump.cpp @@ -517,6 +517,8 @@ void Dump::write() if (refreshflag) modify->compute[irefresh]->refresh(); + if (filewriter && fp != nullptr) write_footer(); + // if file per timestep, close file if I am filewriter if (multifile) { diff --git a/src/dump.h b/src/dump.h index a95029ada8..90866a3567 100644 --- a/src/dump.h +++ b/src/dump.h @@ -153,6 +153,8 @@ class Dump : protected Pointers { virtual void pack(tagint *) = 0; virtual int convert_string(int, double *) { return 0; } virtual void write_data(int, double *) = 0; + virtual void write_footer() {} + void pbc_allocate(); double compute_time(); diff --git a/src/fmt/core.h b/src/fmt/core.h index 8444cd9546..2fafa777ba 100644 --- a/src/fmt/core.h +++ b/src/fmt/core.h @@ -315,7 +315,9 @@ // Enable minimal optimizations for more compact code in debug mode. FMT_GCC_PRAGMA("GCC push_options") -#ifndef __OPTIMIZE__ +// LAMMPS CUSTOMIZATION: suppress warning about pragma with KOKKOS +#if !defined(__OPTIMIZE__) && !defined(LMP_KOKKOS) +// END LAMMPS CUSTOMIZATION FMT_GCC_PRAGMA("GCC optimize(\"Og\")") #endif diff --git a/src/library.cpp b/src/library.cpp index 079534d663..cdc0a812c5 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -1659,14 +1659,18 @@ lists the available options. - LMP_TYPE_ARRAY - ``double **`` - Local data array + * - LMP_STYLE_LOCAL + - LMP_SIZE_VECTOR + - ``int *`` + - Alias for using LMP_SIZE_ROWS * - LMP_STYLE_LOCAL - LMP_SIZE_ROWS - ``int *`` - - Number of local data rows + - Number of local array rows or length of vector * - LMP_STYLE_LOCAL - LMP_SIZE_COLS - ``int *`` - - Number of local data columns + - Number of local array columns, 0 if vector .. warning:: @@ -1749,6 +1753,7 @@ void *lammps_extract_compute(void *handle, const char *id, int style, int type) if (type == LMP_TYPE_SCALAR) return (void *) &compute->size_local_rows; /* for backward compatibility */ if (type == LMP_TYPE_VECTOR) return (void *) compute->vector_local; if (type == LMP_TYPE_ARRAY) return (void *) compute->array_local; + if (type == LMP_SIZE_VECTOR) return (void *) &compute->size_local_rows; /* alias for LMP_SIZE_ROWS */ if (type == LMP_SIZE_ROWS) return (void *) &compute->size_local_rows; if (type == LMP_SIZE_COLS) return (void *) &compute->size_local_cols; } diff --git a/src/pair_table.cpp b/src/pair_table.cpp index aefe9c4c4f..11bd986822 100644 --- a/src/pair_table.cpp +++ b/src/pair_table.cpp @@ -395,20 +395,18 @@ void PairTable::read_table(Table *tb, char *file, char *keyword) union_int_float_t rsq_lookup; int rerror = 0; - int cerror = 0; - reader.skip_line(); for (int i = 0; i < tb->ninput; i++) { - line = reader.next_line(4); - + line = reader.next_line(); try { ValueTokenizer values(line); values.next_int(); rfile = values.next_double(); tb->efile[i] = conversion_factor * values.next_double(); tb->ffile[i] = conversion_factor * values.next_double(); - } catch (TokenizerException &) { - ++cerror; + } catch (TokenizerException &e) { + error->one(FLERR, "Error parsing pair table '{}' line {} of {}. {}\nLine was: {}", keyword, + i + 1, tb->ninput, e.what(), line); } rnew = rfile; @@ -474,14 +472,6 @@ void PairTable::read_table(Table *tb, char *file, char *keyword) "{} of {} distance values in table {} with relative error\n" "WARNING: over {} to re-computed values", rerror, tb->ninput, EPSILONR, keyword); - - // warn if data was read incompletely, e.g. columns were missing - - if (cerror) - error->warning(FLERR, - "{} of {} lines in table {} were incomplete\n" - "WARNING: or could not be parsed completely", - cerror, tb->ninput, keyword); } /* ---------------------------------------------------------------------- diff --git a/src/platform.cpp b/src/platform.cpp index 5e396d3f63..667481b94d 100644 --- a/src/platform.cpp +++ b/src/platform.cpp @@ -195,6 +195,8 @@ std::string platform::os_info() if (build == "6002") { buf = "Windows Vista"; + } else if (build == "6003") { + buf = "Windows Server 2008"; } else if (build == "7601") { buf = "Windows 7"; } else if (build == "9200") { @@ -227,8 +229,12 @@ std::string platform::os_info() buf = "Windows 10 21H1"; } else if (build == "19044") { buf = "Windows 10 21H2"; + } else if (build == "20348") { + buf = "Windows Server 2022"; } else if (build == "22000") { buf = "Windows 11 21H2"; + } else if (build == "22621") { + buf = "Windows 11 22H2"; } else { const char *entry = "ProductName"; RegGetValue(HKEY_LOCAL_MACHINE, subkey, entry, RRF_RT_REG_SZ, nullptr, &value, diff --git a/src/read_restart.cpp b/src/read_restart.cpp index b42dcce1ca..a7fb5a828d 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -61,9 +61,10 @@ void ReadRestart::command(int narg, char **arg) // check for remap option - int remapflag = 0; + int remapflag = 1; if (narg == 2) { - if (strcmp(arg[1],"remap") == 0) remapflag = 1; + if (strcmp(arg[1],"noremap") == 0) remapflag = 0; + else if (strcmp(arg[1],"remap") == 0) remapflag = 1; // for backward compatibility else error->all(FLERR,"Illegal read_restart command"); } @@ -643,8 +644,7 @@ void ReadRestart::header() int dimension = read_int(); domain->dimension = dimension; if (domain->dimension == 2 && domain->zperiodic == 0) - error->all(FLERR, - "Cannot run 2d simulation with non-periodic Z dimension"); + error->all(FLERR, "Cannot run 2d simulation with non-periodic Z dimension"); // read nprocs from restart file, warn if different diff --git a/src/reader.cpp b/src/reader.cpp index c7b99260e7..025445ca24 100644 --- a/src/reader.cpp +++ b/src/reader.cpp @@ -28,6 +28,12 @@ Reader::Reader(LAMMPS *lmp) : Pointers(lmp) compressed = false; } +// avoid resource leak +Reader::~Reader() +{ + if (fp != nullptr) close_file(); +} + /* ---------------------------------------------------------------------- try to open given file generic version for ASCII files with optional compression or for native binary dumps diff --git a/src/reader.h b/src/reader.h index 93f9197b7a..753b6956f7 100644 --- a/src/reader.h +++ b/src/reader.h @@ -23,6 +23,7 @@ namespace LAMMPS_NS { class Reader : protected Pointers { public: Reader(class LAMMPS *); + ~Reader() override; virtual void settings(int, char **); diff --git a/src/version.h b/src/version.h index 9de4ec5d9f..4b95d1c910 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "4 May 2022" +#define LAMMPS_VERSION "23 Jun 2022" diff --git a/tools/msi2lmp/src/msi2lmp.c b/tools/msi2lmp/src/msi2lmp.c index 87cffb4e6e..3136678023 100644 --- a/tools/msi2lmp/src/msi2lmp.c +++ b/tools/msi2lmp/src/msi2lmp.c @@ -66,9 +66,9 @@ * The program is started by supplying information at the command prompt * according to the usage described below. * -* USAGE: msi2lmp3 ROOTNAME {-print #} {-class #} {-frc FRC_FILE} {-ignore} {-nocenter} {-oldstyle} +* USAGE: msi2lmp ROOTNAME {-print #} {-class #} {-frc FRC_FILE} {-ignore} {-nocenter} {-oldstyle} * -* -- msi2lmp3 is the name of the executable +* -- msi2lmp is the name of the executable * -- ROOTNAME is the base name of the .car and .mdf files * -- all opther flags are optional and can be abbreviated (e.g. -p instead of -print) * diff --git a/tools/singularity/README.md b/tools/singularity/README.md index db7aa9e3b0..4700dac6ec 100644 --- a/tools/singularity/README.md +++ b/tools/singularity/README.md @@ -1,17 +1,19 @@ -# Singularity container definitions for compiling/testing LAMMPS +# Apptainer (aka Singularity) container definitions for compiling/testing LAMMPS The *.def files in this folder can be used to build container images -for [Singularity](https://sylabs.io), suitable for compiling and testing +for [Apptainer](https://apptainer.org) (previously called +[Singularity](https://sylabs.io)), suitable for compiling and testing LAMMPS on a variety of OS variants with support for most standard packages and - for some of them - also building/spellchecking the manual -in all supported formats. This allows to test and debug LAMMPS code on +in all supported formats. This allows to test and debug LAMMPS code on different OS variants without doing a full installation on your development workstation, e.g. when bugs are reported that can only be reproduced on a specific OS or with specific (mostly older) versions of tools, compilers, or libraries. Here is a workflow for testing a compilation of LAMMPS with a locally -built CentOS 7.x singularity container. +built CentOS 7.x Singularity container. For Apptainer replace the +`singularity` command with `apptainer`. ``` cd some/work/directory diff --git a/tools/singularity/ubuntu18.04_amd_rocm.def b/tools/singularity/ubuntu18.04_amd_rocm.def index ceedfd8144..febdf1172e 100644 --- a/tools/singularity/ubuntu18.04_amd_rocm.def +++ b/tools/singularity/ubuntu18.04_amd_rocm.def @@ -3,7 +3,7 @@ From: ubuntu:18.04 %environment export PATH=/usr/lib/ccache:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64 - export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/rocm/lib:/opt/rocm-5.1.2/llvm/lib + export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/rocm/lib:/opt/rocm-5.1.3/llvm/lib %post export DEBIAN_FRONTEND=noninteractive apt-get update @@ -22,10 +22,10 @@ From: ubuntu:18.04 apt install -y cmake ########################################################################### - # ROCm 5.1.2 + # ROCm 5.1.3 ########################################################################### - wget https://repo.radeon.com/amdgpu-install/22.10.2/ubuntu/bionic/amdgpu-install_22.10.2.50102-1_all.deb - apt-get install -y ./amdgpu-install_22.10.2.50102-1_all.deb + wget https://repo.radeon.com/amdgpu-install/22.10.3/ubuntu/bionic/amdgpu-install_22.10.3.50103-1_all.deb + apt-get install -y ./amdgpu-install_22.10.3.50103-1_all.deb apt-get update apt-get install --no-install-recommends -y \ diff --git a/tools/singularity/ubuntu18.04_gpu.def b/tools/singularity/ubuntu18.04_gpu.def index 6aa37ccf84..90034285ff 100644 --- a/tools/singularity/ubuntu18.04_gpu.def +++ b/tools/singularity/ubuntu18.04_gpu.def @@ -2,11 +2,11 @@ BootStrap: docker From: ubuntu:18.04 %environment - export PATH=/usr/lib/ccache:/usr/local/cuda-11.5/bin:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64 - export CUDADIR=/usr/local/cuda-11.5 - export CUDA_PATH=/usr/local/cuda-11.5 - export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-11.5/lib64:/opt/rocm/lib:/opt/rocm-4.5.0/llvm/lib - export LIBRARY_PATH=/usr/local/cuda-11.5/lib64/stubs + export PATH=/usr/lib/ccache:/usr/local/cuda-11.7/bin:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64 + export CUDADIR=/usr/local/cuda-11.7 + export CUDA_PATH=/usr/local/cuda-11.7 + export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-11.7/lib64:/opt/rocm/lib:/opt/rocm-5.1.3/llvm/lib + export LIBRARY_PATH=/usr/local/cuda-11.7/lib64/stubs %post export DEBIAN_FRONTEND=noninteractive apt-get update @@ -27,8 +27,8 @@ From: ubuntu:18.04 ########################################################################### # ROCm 4.5 ########################################################################### - wget https://repo.radeon.com/amdgpu-install/21.40/ubuntu/focal/amdgpu-install-21.40.40500-1_all.deb - apt-get install -y ./amdgpu-install-21.40.40500-1_all.deb + wget https://repo.radeon.com/amdgpu-install/22.10.3/ubuntu/focal/amdgpu-install_22.10.3.50103-1_all.deb + apt-get install -y ./amdgpu-install_22.10.3.50103-1_all.deb apt-get update apt-get install --no-install-recommends -y \ @@ -122,11 +122,11 @@ From: ubuntu:18.04 wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-ubuntu1804.pin mv cuda-ubuntu1804.pin /etc/apt/preferences.d/cuda-repository-pin-600 - apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/7fa2af80.pub + apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub add-apt-repository "deb http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/ /" apt-get update - export CUDA_PKG_VERSION=11.5 + export CUDA_PKG_VERSION=11.7 apt-get install -y --no-install-recommends \ cuda-libraries-${CUDA_PKG_VERSION} \ diff --git a/tools/singularity/ubuntu20.04_amd_rocm.def b/tools/singularity/ubuntu20.04_amd_rocm.def index 5e351e49a8..6034014370 100644 --- a/tools/singularity/ubuntu20.04_amd_rocm.def +++ b/tools/singularity/ubuntu20.04_amd_rocm.def @@ -3,7 +3,7 @@ From: ubuntu:20.04 %environment export PATH=/usr/lib/ccache:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64 - export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/rocm/lib:/opt/rocm-5.1.2/llvm/lib + export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/rocm/lib:/opt/rocm-5.1.3/llvm/lib %post export DEBIAN_FRONTEND=noninteractive apt-get update @@ -13,10 +13,10 @@ From: ubuntu:20.04 apt-get install --no-install-recommends -y software-properties-common ########################################################################### - # ROCm 5.1.2 + # ROCm 5.1.3 ########################################################################### - wget https://repo.radeon.com/amdgpu-install/22.10.2/ubuntu/focal/amdgpu-install_22.10.2.50102-1_all.deb - apt-get install -y ./amdgpu-install_22.10.2.50102-1_all.deb + wget https://repo.radeon.com/amdgpu-install/22.10.3/ubuntu/focal/amdgpu-install_22.10.3.50103-1_all.deb + apt-get install -y ./amdgpu-install_22.10.3.50103-1_all.deb apt-get update apt-get install --no-install-recommends -y \ diff --git a/tools/singularity/ubuntu20.04_gpu.def b/tools/singularity/ubuntu20.04_gpu.def index 23bddeb14f..f7bab1ee9d 100644 --- a/tools/singularity/ubuntu20.04_gpu.def +++ b/tools/singularity/ubuntu20.04_gpu.def @@ -2,11 +2,11 @@ BootStrap: docker From: ubuntu:20.04 %environment - export PATH=/usr/lib/ccache:/usr/local/cuda-11.5/bin:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64 - export CUDADIR=/usr/local/cuda-11.5 - export CUDA_PATH=/usr/local/cuda-11.5 - export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-11.5/lib64:/opt/rocm/lib:/opt/rocm-4.5.0/llvm/lib - export LIBRARY_PATH=/usr/local/cuda-11.5/lib64/stubs + export PATH=/usr/lib/ccache:/usr/local/cuda-11.7/bin:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64 + export CUDADIR=/usr/local/cuda-11.7 + export CUDA_PATH=/usr/local/cuda-11.7 + export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-11.7/lib64:/opt/rocm/lib:/opt/rocm-5.1.3/llvm/lib + export LIBRARY_PATH=/usr/local/cuda-11.7/lib64/stubs %post export DEBIAN_FRONTEND=noninteractive apt-get update @@ -15,10 +15,10 @@ From: ubuntu:20.04 apt-get install -y --no-install-recommends curl wget libnuma-dev gnupg ca-certificates ########################################################################### - # ROCm 4.5 + # ROCm 5.1.3 ########################################################################### - wget https://repo.radeon.com/amdgpu-install/21.40/ubuntu/focal/amdgpu-install-21.40.40500-1_all.deb - apt-get install -y ./amdgpu-install-21.40.40500-1_all.deb + wget https://repo.radeon.com/amdgpu-install/22.10.3/ubuntu/focal/amdgpu-install_22.10.3.50103-1_all.deb + apt-get install -y ./amdgpu-install_22.10.3.50103-1_all.deb apt-get update apt-get install --no-install-recommends -y \ @@ -109,7 +109,7 @@ From: ubuntu:20.04 wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-ubuntu2004.pin mv cuda-ubuntu2004.pin /etc/apt/preferences.d/cuda-repository-pin-600 - apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/7fa2af80.pub + apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/3bf863cc.pub add-apt-repository "deb http://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/ /" apt-get update diff --git a/tools/valgrind/OpenMP.supp b/tools/valgrind/OpenMP.supp index e1870e668c..15531fa8ec 100644 --- a/tools/valgrind/OpenMP.supp +++ b/tools/valgrind/OpenMP.supp @@ -134,3 +134,31 @@ fun:GOMP_parallel obj:* } +{ + OpnMP_open_part1 + Memcheck:Leak + match-leak-kinds: reachable + fun:malloc + ... + fun:openaux + ... + fun:dl_open_worker_begin + ... + fun:dl_open_worker + ... + fun:_dl_open +} +{ + OpnMP_open_part2 + Memcheck:Leak + match-leak-kinds: reachable + fun:calloc + ... + fun:openaux + ... + fun:dl_open_worker_begin + ... + fun:dl_open_worker + ... + fun:_dl_open +} diff --git a/unittest/c-library/test_library_commands.cpp b/unittest/c-library/test_library_commands.cpp index f1cc51d8d9..d4e326cd36 100644 --- a/unittest/c-library/test_library_commands.cpp +++ b/unittest/c-library/test_library_commands.cpp @@ -104,7 +104,7 @@ TEST_F(LibraryCommands, from_list) TEST_F(LibraryCommands, from_string) { - std::string cmds(""); + std::string cmds; for (auto &inp : demo_input) { cmds += inp; diff --git a/unittest/force-styles/test_angle_style.cpp b/unittest/force-styles/test_angle_style.cpp index a617ec1783..82a4731492 100644 --- a/unittest/force-styles/test_angle_style.cpp +++ b/unittest/force-styles/test_angle_style.cpp @@ -32,8 +32,8 @@ #include "input.h" #include "lammps.h" #include "modify.h" -#include "universe.h" #include "platform.h" +#include "universe.h" #include #include @@ -90,7 +90,7 @@ LAMMPS *init_lammps(int argc, char **argv, const TestConfig &cfg, const bool new // utility lambdas to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; auto parse_input_script = [&](const std::string &filename) { lmp->input->file(filename.c_str()); @@ -133,7 +133,7 @@ void run_lammps(LAMMPS *lmp) { // utility lambda to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; command("fix 1 all nve"); @@ -148,7 +148,7 @@ void restart_lammps(LAMMPS *lmp, const TestConfig &cfg) { // utility lambda to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; command("clear"); @@ -175,7 +175,7 @@ void data_lammps(LAMMPS *lmp, const TestConfig &cfg) { // utility lambdas to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; auto parse_input_script = [&](const std::string &filename) { lmp->input->file(filename.c_str()); @@ -226,7 +226,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) } const int natoms = lmp->atom->natoms; - std::string block(""); + std::string block; YamlWriter writer(outfile); @@ -285,7 +285,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) // run_stress stress = lmp->force->angle->virial; block = fmt::format("{:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e}", stress[0], - stress[1], stress[2], stress[3], stress[4], stress[5]); + stress[1], stress[2], stress[3], stress[4], stress[5]); writer.emit_block("run_stress", block); block.clear(); @@ -297,10 +297,8 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) writer.emit_block("run_forces", block); cleanup_lammps(lmp, config); - return; } - TEST(AngleStyle, plain) { if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); @@ -335,7 +333,7 @@ TEST(AngleStyle, plain) double epsilon = test_config.epsilon; ErrorStats stats; - auto angle = lmp->force->angle; + auto angle = lmp->force->angle; EXPECT_FORCES("init_forces (newton on)", lmp->atom, test_config.init_forces, epsilon); EXPECT_STRESS("init_stress (newton on)", angle->virial, test_config.init_stress, epsilon); @@ -365,10 +363,11 @@ TEST(AngleStyle, plain) // skip over these tests if newton bond is forced to be on if (lmp->force->newton_bond == 0) { - angle = lmp->force->angle; + angle = lmp->force->angle; EXPECT_FORCES("init_forces (newton off)", lmp->atom, test_config.init_forces, epsilon); - EXPECT_STRESS("init_stress (newton off)", angle->virial, test_config.init_stress, 2*epsilon); + EXPECT_STRESS("init_stress (newton off)", angle->virial, test_config.init_stress, + 2 * epsilon); stats.reset(); EXPECT_FP_LE_WITH_EPS(angle->energy, test_config.init_energy, epsilon); @@ -393,7 +392,7 @@ TEST(AngleStyle, plain) restart_lammps(lmp, test_config); if (!verbose) ::testing::internal::GetCapturedStdout(); - angle = lmp->force->angle; + angle = lmp->force->angle; EXPECT_FORCES("restart_forces", lmp->atom, test_config.init_forces, epsilon); EXPECT_STRESS("restart_stress", angle->virial, test_config.init_stress, epsilon); @@ -405,7 +404,7 @@ TEST(AngleStyle, plain) data_lammps(lmp, test_config); if (!verbose) ::testing::internal::GetCapturedStdout(); - angle = lmp->force->angle; + angle = lmp->force->angle; EXPECT_FORCES("data_forces", lmp->atom, test_config.init_forces, epsilon); EXPECT_STRESS("data_stress", angle->virial, test_config.init_stress, epsilon); @@ -455,7 +454,7 @@ TEST(AngleStyle, omp) double epsilon = 5.0 * test_config.epsilon; ErrorStats stats; - auto angle = lmp->force->angle; + auto angle = lmp->force->angle; EXPECT_FORCES("init_forces (newton on)", lmp->atom, test_config.init_forces, epsilon); EXPECT_STRESS("init_stress (newton on)", angle->virial, test_config.init_stress, 10 * epsilon); @@ -488,10 +487,11 @@ TEST(AngleStyle, omp) // skip over these tests if newton bond is forced to be on if (lmp->force->newton_bond == 0) { - angle = lmp->force->angle; + angle = lmp->force->angle; EXPECT_FORCES("init_forces (newton off)", lmp->atom, test_config.init_forces, epsilon); - EXPECT_STRESS("init_stress (newton off)", angle->virial, test_config.init_stress, 10 * epsilon); + EXPECT_STRESS("init_stress (newton off)", angle->virial, test_config.init_stress, + 10 * epsilon); stats.reset(); EXPECT_FP_LE_WITH_EPS(angle->energy, test_config.init_energy, epsilon); @@ -502,7 +502,8 @@ TEST(AngleStyle, omp) if (!verbose) ::testing::internal::GetCapturedStdout(); EXPECT_FORCES("run_forces (newton off)", lmp->atom, test_config.run_forces, 10 * epsilon); - EXPECT_STRESS("run_stress (newton off)", angle->virial, test_config.run_stress, 10 * epsilon); + EXPECT_STRESS("run_stress (newton off)", angle->virial, test_config.run_stress, + 10 * epsilon); stats.reset(); id = lmp->modify->find_compute("sum"); @@ -556,7 +557,7 @@ TEST(AngleStyle, single) // utility lambda to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; // now start over diff --git a/unittest/force-styles/test_bond_style.cpp b/unittest/force-styles/test_bond_style.cpp index a851f4341f..d0d8f26b6e 100644 --- a/unittest/force-styles/test_bond_style.cpp +++ b/unittest/force-styles/test_bond_style.cpp @@ -32,8 +32,8 @@ #include "input.h" #include "lammps.h" #include "modify.h" -#include "universe.h" #include "platform.h" +#include "universe.h" #include #include @@ -90,7 +90,7 @@ LAMMPS *init_lammps(int argc, char **argv, const TestConfig &cfg, const bool new // utility lambdas to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; auto parse_input_script = [&](const std::string &filename) { lmp->input->file(filename.c_str()); @@ -133,7 +133,7 @@ void run_lammps(LAMMPS *lmp) { // utility lambda to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; command("fix 1 all nve"); @@ -148,7 +148,7 @@ void restart_lammps(LAMMPS *lmp, const TestConfig &cfg) { // utility lambda to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; command("clear"); @@ -175,7 +175,7 @@ void data_lammps(LAMMPS *lmp, const TestConfig &cfg) { // utility lambdas to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; auto parse_input_script = [&](const std::string &filename) { lmp->input->file(filename.c_str()); @@ -226,7 +226,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) } const int natoms = lmp->atom->natoms; - std::string block(""); + std::string block; YamlWriter writer(outfile); @@ -285,7 +285,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) // run_stress stress = lmp->force->bond->virial; block = fmt::format("{:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e}", stress[0], - stress[1], stress[2], stress[3], stress[4], stress[5]); + stress[1], stress[2], stress[3], stress[4], stress[5]); writer.emit_block("run_stress", block); block.clear(); @@ -297,7 +297,6 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) writer.emit_block("run_forces", block); cleanup_lammps(lmp, config); - return; } TEST(BondStyle, plain) @@ -334,7 +333,7 @@ TEST(BondStyle, plain) double epsilon = test_config.epsilon; ErrorStats stats; - auto bond = lmp->force->bond; + auto bond = lmp->force->bond; EXPECT_FORCES("init_forces (newton on)", lmp->atom, test_config.init_forces, epsilon); EXPECT_STRESS("init_stress (newton on)", bond->virial, test_config.init_stress, epsilon); @@ -364,10 +363,11 @@ TEST(BondStyle, plain) // skip over these tests if newton bond is forced to be on if (lmp->force->newton_bond == 0) { - bond = lmp->force->bond; + bond = lmp->force->bond; EXPECT_FORCES("init_forces (newton off)", lmp->atom, test_config.init_forces, epsilon); - EXPECT_STRESS("init_stress (newton off)", bond->virial, test_config.init_stress, 2 * epsilon); + EXPECT_STRESS("init_stress (newton off)", bond->virial, test_config.init_stress, + 2 * epsilon); stats.reset(); EXPECT_FP_LE_WITH_EPS(bond->energy, test_config.init_energy, epsilon); @@ -392,7 +392,7 @@ TEST(BondStyle, plain) restart_lammps(lmp, test_config); if (!verbose) ::testing::internal::GetCapturedStdout(); - bond = lmp->force->bond; + bond = lmp->force->bond; EXPECT_FORCES("restart_forces", lmp->atom, test_config.init_forces, epsilon); EXPECT_STRESS("restart_stress", bond->virial, test_config.init_stress, epsilon); @@ -405,7 +405,7 @@ TEST(BondStyle, plain) data_lammps(lmp, test_config); if (!verbose) ::testing::internal::GetCapturedStdout(); - bond = lmp->force->bond; + bond = lmp->force->bond; EXPECT_FORCES("data_forces", lmp->atom, test_config.init_forces, epsilon); EXPECT_STRESS("data_stress", bond->virial, test_config.init_stress, epsilon); @@ -456,7 +456,7 @@ TEST(BondStyle, omp) double epsilon = 5.0 * test_config.epsilon; ErrorStats stats; - auto bond = lmp->force->bond; + auto bond = lmp->force->bond; EXPECT_FORCES("init_forces (newton on)", lmp->atom, test_config.init_forces, epsilon); EXPECT_STRESS("init_stress (newton on)", bond->virial, test_config.init_stress, 10 * epsilon); @@ -489,10 +489,11 @@ TEST(BondStyle, omp) // skip over these tests if newton bond is forced to be on if (lmp->force->newton_bond == 0) { - bond = lmp->force->bond; + bond = lmp->force->bond; EXPECT_FORCES("init_forces (newton off)", lmp->atom, test_config.init_forces, epsilon); - EXPECT_STRESS("init_stress (newton off)", bond->virial, test_config.init_stress, 10 * epsilon); + EXPECT_STRESS("init_stress (newton off)", bond->virial, test_config.init_stress, + 10 * epsilon); stats.reset(); EXPECT_FP_LE_WITH_EPS(bond->energy, test_config.init_energy, epsilon); @@ -503,7 +504,8 @@ TEST(BondStyle, omp) if (!verbose) ::testing::internal::GetCapturedStdout(); EXPECT_FORCES("run_forces (newton off)", lmp->atom, test_config.run_forces, 10 * epsilon); - EXPECT_STRESS("run_stress (newton off)", bond->virial, test_config.run_stress, 10 * epsilon); + EXPECT_STRESS("run_stress (newton off)", bond->virial, test_config.run_stress, + 10 * epsilon); stats.reset(); id = lmp->modify->find_compute("sum"); @@ -557,7 +559,7 @@ TEST(BondStyle, single) // utility lambda to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; // now start over diff --git a/unittest/force-styles/test_config.h b/unittest/force-styles/test_config.h index ef4d911b60..18b4b4f0b2 100644 --- a/unittest/force-styles/test_config.h +++ b/unittest/force-styles/test_config.h @@ -15,8 +15,8 @@ #define TEST_CONFIG_H #include -#include #include +#include #include #include @@ -96,23 +96,21 @@ public: restart_vel.clear(); global_vector.clear(); } - virtual ~TestConfig(){}; + TestConfig(const TestConfig &) = delete; + TestConfig &operator=(const TestConfig &) = delete; std::string tags_line() const { - if(tags.size() > 0) { - std::stringstream line; - line << tags[0]; - for(size_t i = 1; i < tags.size(); i++) { - line << ", " << tags[i]; - } - return line.str(); - } - return "generated"; + if (tags.size() > 0) { + std::stringstream line; + line << tags[0]; + for (size_t i = 1; i < tags.size(); i++) { + line << ", " << tags[i]; + } + return line.str(); + } + return "generated"; } - -private: - TestConfig(const TestConfig &){}; }; #endif diff --git a/unittest/force-styles/test_config_reader.cpp b/unittest/force-styles/test_config_reader.cpp index d152b4fcf4..d920128862 100644 --- a/unittest/force-styles/test_config_reader.cpp +++ b/unittest/force-styles/test_config_reader.cpp @@ -29,7 +29,7 @@ using LAMMPS_NS::utils::split_words; using LAMMPS_NS::utils::trim; -TestConfigReader::TestConfigReader(TestConfig &config) : YamlReader(), config(config) +TestConfigReader::TestConfigReader(TestConfig &config) : config(config) { consumers["lammps_version"] = &TestConfigReader::lammps_version; consumers["tags"] = &TestConfigReader::tags; diff --git a/unittest/force-styles/test_config_reader.h b/unittest/force-styles/test_config_reader.h index 1f0de8df0a..23da817622 100644 --- a/unittest/force-styles/test_config_reader.h +++ b/unittest/force-styles/test_config_reader.h @@ -22,6 +22,8 @@ class TestConfigReader : public YamlReader { public: TestConfigReader(TestConfig &config); + TestConfigReader() = delete; + const TestConfigReader & operator=(TestConfig &) = delete; void skip_tests(const yaml_event_t &event); void prerequisites(const yaml_event_t &event); diff --git a/unittest/force-styles/test_dihedral_style.cpp b/unittest/force-styles/test_dihedral_style.cpp index 0156e8e021..3f3e1248e8 100644 --- a/unittest/force-styles/test_dihedral_style.cpp +++ b/unittest/force-styles/test_dihedral_style.cpp @@ -32,8 +32,8 @@ #include "input.h" #include "lammps.h" #include "modify.h" -#include "universe.h" #include "platform.h" +#include "universe.h" #include #include @@ -90,7 +90,7 @@ LAMMPS *init_lammps(int argc, char **argv, const TestConfig &cfg, const bool new // utility lambdas to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; auto parse_input_script = [&](const std::string &filename) { lmp->input->file(filename.c_str()); @@ -133,7 +133,7 @@ void run_lammps(LAMMPS *lmp) { // utility lambda to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; command("fix 1 all nve"); @@ -148,7 +148,7 @@ void restart_lammps(LAMMPS *lmp, const TestConfig &cfg) { // utility lambda to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; command("clear"); @@ -175,7 +175,7 @@ void data_lammps(LAMMPS *lmp, const TestConfig &cfg) { // utility lambdas to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; auto parse_input_script = [&](const std::string &filename) { lmp->input->file(filename.c_str()); @@ -235,7 +235,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) } const int natoms = lmp->atom->natoms; - std::string block(""); + std::string block; YamlWriter writer(outfile); @@ -288,7 +288,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) // run_stress stress = lmp->force->dihedral->virial; block = fmt::format("{:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e}", stress[0], - stress[1], stress[2], stress[3], stress[4], stress[5]); + stress[1], stress[2], stress[3], stress[4], stress[5]); writer.emit_block("run_stress", block); block.clear(); @@ -300,7 +300,6 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) writer.emit_block("run_forces", block); cleanup_lammps(lmp, config); - return; } TEST(DihedralStyle, plain) @@ -370,7 +369,8 @@ TEST(DihedralStyle, plain) dihedral = lmp->force->dihedral; EXPECT_FORCES("init_forces (newton off)", lmp->atom, test_config.init_forces, epsilon); - EXPECT_STRESS("init_stress (newton off)", dihedral->virial, test_config.init_stress, epsilon); + EXPECT_STRESS("init_stress (newton off)", dihedral->virial, test_config.init_stress, + epsilon); stats.reset(); EXPECT_FP_LE_WITH_EPS(dihedral->energy, test_config.init_energy, epsilon); @@ -462,7 +462,8 @@ TEST(DihedralStyle, omp) auto dihedral = lmp->force->dihedral; EXPECT_FORCES("init_forces (newton on)", lmp->atom, test_config.init_forces, epsilon); - EXPECT_STRESS("init_stress (newton on)", dihedral->virial, test_config.init_stress, 10 * epsilon); + EXPECT_STRESS("init_stress (newton on)", dihedral->virial, test_config.init_stress, + 10 * epsilon); stats.reset(); EXPECT_FP_LE_WITH_EPS(dihedral->energy, test_config.init_energy, epsilon); @@ -495,7 +496,8 @@ TEST(DihedralStyle, omp) dihedral = lmp->force->dihedral; EXPECT_FORCES("init_forces (newton off)", lmp->atom, test_config.init_forces, epsilon); - EXPECT_STRESS("init_stress (newton off)", dihedral->virial, test_config.init_stress, 10 * epsilon); + EXPECT_STRESS("init_stress (newton off)", dihedral->virial, test_config.init_stress, + 10 * epsilon); stats.reset(); EXPECT_FP_LE_WITH_EPS(dihedral->energy, test_config.init_energy, epsilon); @@ -506,7 +508,8 @@ TEST(DihedralStyle, omp) if (!verbose) ::testing::internal::GetCapturedStdout(); EXPECT_FORCES("run_forces (newton off)", lmp->atom, test_config.run_forces, 10 * epsilon); - EXPECT_STRESS("run_stress (newton off)", dihedral->virial, test_config.run_stress, 10 * epsilon); + EXPECT_STRESS("run_stress (newton off)", dihedral->virial, test_config.run_stress, + 10 * epsilon); stats.reset(); id = lmp->modify->find_compute("sum"); diff --git a/unittest/force-styles/test_fix_timestep.cpp b/unittest/force-styles/test_fix_timestep.cpp index fcf6be39d3..981bc46eef 100644 --- a/unittest/force-styles/test_fix_timestep.cpp +++ b/unittest/force-styles/test_fix_timestep.cpp @@ -34,10 +34,10 @@ #include "lammps.h" #include "modify.h" #include "pair.h" +#include "platform.h" #include "universe.h" #include "utils.h" #include "variable.h" -#include "platform.h" #include #include @@ -92,7 +92,7 @@ LAMMPS *init_lammps(int argc, char **argv, const TestConfig &cfg, const bool use // utility lambda to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; command("variable input_dir index " + INPUT_FOLDER); @@ -143,7 +143,7 @@ void restart_lammps(LAMMPS *lmp, const TestConfig &cfg, bool use_rmass, bool use { // utility lambda to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; command("clear"); @@ -184,7 +184,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) } const int natoms = lmp->atom->natoms; - std::string block(""); + std::string block; YamlWriter writer(outfile); // write yaml header @@ -203,8 +203,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) // run_stress, if enabled if (fix->thermo_virial) { auto stress = fix->virial; - block = fmt::format("{:23.16e} {:23.16e} {:23.16e} " - "{:23.16e} {:23.16e} {:23.16e}", + block = fmt::format("{:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e}", stress[0], stress[1], stress[2], stress[3], stress[4], stress[5]); writer.emit_block("run_stress", block); } @@ -243,7 +242,6 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) } writer.emit_block("run_vel", block); cleanup_lammps(lmp, config); - return; } TEST(FixTimestep, plain) @@ -293,7 +291,8 @@ TEST(FixTimestep, plain) } else { Fix *fix = lmp->modify->fix[ifix]; if (fix->thermo_virial) { - EXPECT_STRESS("run_stress (normal run, verlet)", fix->virial, test_config.run_stress, epsilon); + EXPECT_STRESS("run_stress (normal run, verlet)", fix->virial, test_config.run_stress, + epsilon); } stats.reset(); @@ -342,7 +341,8 @@ TEST(FixTimestep, plain) } else { Fix *fix = lmp->modify->fix[ifix]; if (fix->thermo_virial) { - EXPECT_STRESS("run_stress (restart, verlet)", fix->virial, test_config.run_stress, epsilon); + EXPECT_STRESS("run_stress (restart, verlet)", fix->virial, test_config.run_stress, + epsilon); } stats.reset(); @@ -380,7 +380,8 @@ TEST(FixTimestep, plain) } else { Fix *fix = lmp->modify->fix[ifix]; if (fix->thermo_virial) { - EXPECT_STRESS("run_stress (rmass, verlet)", fix->virial, test_config.run_stress, epsilon); + EXPECT_STRESS("run_stress (rmass, verlet)", fix->virial, test_config.run_stress, + epsilon); } stats.reset(); @@ -432,7 +433,8 @@ TEST(FixTimestep, plain) } else { Fix *fix = lmp->modify->fix[ifix]; if (fix->thermo_virial) { - EXPECT_STRESS("run_stress (normal run, respa)", fix->virial, test_config.run_stress, 1000 * epsilon); + EXPECT_STRESS("run_stress (normal run, respa)", fix->virial, test_config.run_stress, + 1000 * epsilon); } stats.reset(); @@ -469,7 +471,8 @@ TEST(FixTimestep, plain) } else { Fix *fix = lmp->modify->fix[ifix]; if (fix->thermo_virial) { - EXPECT_STRESS("run_stress (restart, respa)", fix->virial, test_config.run_stress, 1000 * epsilon); + EXPECT_STRESS("run_stress (restart, respa)", fix->virial, test_config.run_stress, + 1000 * epsilon); } stats.reset(); @@ -507,7 +510,8 @@ TEST(FixTimestep, plain) } else { Fix *fix = lmp->modify->fix[ifix]; if (fix->thermo_virial) { - EXPECT_STRESS("run_stress (rmass, respa)", fix->virial, test_config.run_stress, 1000 * epsilon); + EXPECT_STRESS("run_stress (rmass, respa)", fix->virial, test_config.run_stress, + 1000 * epsilon); } stats.reset(); @@ -587,7 +591,8 @@ TEST(FixTimestep, omp) } else { Fix *fix = lmp->modify->fix[ifix]; if (fix->thermo_virial) { - EXPECT_STRESS("run_stress (normal run, verlet)", fix->virial, test_config.run_stress, epsilon); + EXPECT_STRESS("run_stress (normal run, verlet)", fix->virial, test_config.run_stress, + epsilon); } stats.reset(); @@ -636,7 +641,8 @@ TEST(FixTimestep, omp) } else { Fix *fix = lmp->modify->fix[ifix]; if (fix->thermo_virial) { - EXPECT_STRESS("run_stress (restart, verlet)", fix->virial, test_config.run_stress, epsilon); + EXPECT_STRESS("run_stress (restart, verlet)", fix->virial, test_config.run_stress, + epsilon); } stats.reset(); @@ -674,7 +680,8 @@ TEST(FixTimestep, omp) } else { Fix *fix = lmp->modify->fix[ifix]; if (fix->thermo_virial) { - EXPECT_STRESS("run_stress (rmass, verlet)", fix->virial, test_config.run_stress, epsilon); + EXPECT_STRESS("run_stress (rmass, verlet)", fix->virial, test_config.run_stress, + epsilon); } stats.reset(); @@ -725,7 +732,8 @@ TEST(FixTimestep, omp) } else { Fix *fix = lmp->modify->fix[ifix]; if (fix->thermo_virial) { - EXPECT_STRESS("run_stress (normal run, respa)", fix->virial, test_config.run_stress, 1000 * epsilon); + EXPECT_STRESS("run_stress (normal run, respa)", fix->virial, test_config.run_stress, + 1000 * epsilon); } stats.reset(); @@ -762,7 +770,8 @@ TEST(FixTimestep, omp) } else { Fix *fix = lmp->modify->fix[ifix]; if (fix->thermo_virial) { - EXPECT_STRESS("run_stress (restart, respa)", fix->virial, test_config.run_stress, 1000 * epsilon); + EXPECT_STRESS("run_stress (restart, respa)", fix->virial, test_config.run_stress, + 1000 * epsilon); } stats.reset(); @@ -800,7 +809,8 @@ TEST(FixTimestep, omp) } else { Fix *fix = lmp->modify->fix[ifix]; if (fix->thermo_virial) { - EXPECT_STRESS("run_stress (rmass, respa)", fix->virial, test_config.run_stress, 1000 * epsilon); + EXPECT_STRESS("run_stress (rmass, respa)", fix->virial, test_config.run_stress, + 1000 * epsilon); } stats.reset(); diff --git a/unittest/force-styles/test_improper_style.cpp b/unittest/force-styles/test_improper_style.cpp index 49b7d22cad..3d2719f7d0 100644 --- a/unittest/force-styles/test_improper_style.cpp +++ b/unittest/force-styles/test_improper_style.cpp @@ -32,8 +32,8 @@ #include "input.h" #include "lammps.h" #include "modify.h" -#include "universe.h" #include "platform.h" +#include "universe.h" #include #include @@ -90,7 +90,7 @@ LAMMPS *init_lammps(int argc, char **argv, const TestConfig &cfg, const bool new // utility lambdas to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; auto parse_input_script = [&](const std::string &filename) { lmp->input->file(filename.c_str()); @@ -133,7 +133,7 @@ void run_lammps(LAMMPS *lmp) { // utility lambda to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; command("fix 1 all nve"); @@ -148,7 +148,7 @@ void restart_lammps(LAMMPS *lmp, const TestConfig &cfg) { // utility lambda to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; command("clear"); @@ -175,7 +175,7 @@ void data_lammps(LAMMPS *lmp, const TestConfig &cfg) { // utility lambdas to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; auto parse_input_script = [&](const std::string &filename) { lmp->input->file(filename.c_str()); @@ -226,7 +226,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) } const int natoms = lmp->atom->natoms; - std::string block(""); + std::string block; YamlWriter writer(outfile); @@ -279,7 +279,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) // run_stress stress = lmp->force->improper->virial; block = fmt::format("{:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e}", stress[0], - stress[1], stress[2], stress[3], stress[4], stress[5]); + stress[1], stress[2], stress[3], stress[4], stress[5]); writer.emit_block("run_stress", block); block.clear(); @@ -291,7 +291,6 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) writer.emit_block("run_forces", block); cleanup_lammps(lmp, config); - return; } TEST(ImproperStyle, plain) @@ -361,7 +360,8 @@ TEST(ImproperStyle, plain) improper = lmp->force->improper; EXPECT_FORCES("init_forces (newton off)", lmp->atom, test_config.init_forces, epsilon); - EXPECT_STRESS("init_stress (newton off)", improper->virial, test_config.init_stress, 2 * epsilon); + EXPECT_STRESS("init_stress (newton off)", improper->virial, test_config.init_stress, + 2 * epsilon); stats.reset(); EXPECT_FP_LE_WITH_EPS(improper->energy, test_config.init_energy, epsilon); @@ -453,7 +453,8 @@ TEST(ImproperStyle, omp) auto improper = lmp->force->improper; EXPECT_FORCES("init_forces (newton on)", lmp->atom, test_config.init_forces, epsilon); - EXPECT_STRESS("init_stress (newton on)", improper->virial, test_config.init_stress, 10 * epsilon); + EXPECT_STRESS("init_stress (newton on)", improper->virial, test_config.init_stress, + 10 * epsilon); stats.reset(); EXPECT_FP_LE_WITH_EPS(improper->energy, test_config.init_energy, epsilon); @@ -486,7 +487,8 @@ TEST(ImproperStyle, omp) improper = lmp->force->improper; EXPECT_FORCES("init_forces (newton off)", lmp->atom, test_config.init_forces, epsilon); - EXPECT_STRESS("init_stress (newton off)", improper->virial, test_config.init_stress, 10 * epsilon); + EXPECT_STRESS("init_stress (newton off)", improper->virial, test_config.init_stress, + 10 * epsilon); stats.reset(); EXPECT_FP_LE_WITH_EPS(improper->energy, test_config.init_energy, epsilon); @@ -497,7 +499,8 @@ TEST(ImproperStyle, omp) if (!verbose) ::testing::internal::GetCapturedStdout(); EXPECT_FORCES("run_forces (newton off)", lmp->atom, test_config.run_forces, 10 * epsilon); - EXPECT_STRESS("run_stress (newton off)", improper->virial, test_config.run_stress, 10 * epsilon); + EXPECT_STRESS("run_stress (newton off)", improper->virial, test_config.run_stress, + 10 * epsilon); stats.reset(); id = lmp->modify->find_compute("sum"); diff --git a/unittest/force-styles/test_pair_style.cpp b/unittest/force-styles/test_pair_style.cpp index 0c8dc16c77..e56a5bba1c 100644 --- a/unittest/force-styles/test_pair_style.cpp +++ b/unittest/force-styles/test_pair_style.cpp @@ -91,7 +91,7 @@ LAMMPS *init_lammps(int argc, char **argv, const TestConfig &cfg, const bool new // utility lambdas to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; auto parse_input_script = [&](const std::string &filename) { lmp->input->file(filename.c_str()); @@ -142,7 +142,7 @@ void run_lammps(LAMMPS *lmp) { // utility lambda to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; command("fix 1 all nve"); @@ -157,7 +157,7 @@ void restart_lammps(LAMMPS *lmp, const TestConfig &cfg, bool nofdotr = false, bo { // utility lambda to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; command("clear"); @@ -188,7 +188,7 @@ void data_lammps(LAMMPS *lmp, const TestConfig &cfg) { // utility lambdas to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; auto parse_input_script = [&](const std::string &filename) { lmp->input->file(filename.c_str()); @@ -239,7 +239,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) } const int natoms = lmp->atom->natoms; - std::string block(""); + std::string block; YamlWriter writer(outfile); @@ -316,7 +316,6 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) writer.emit_block("run_forces", block); cleanup_lammps(lmp, config); - return; } TEST(PairStyle, plain) @@ -1085,7 +1084,7 @@ TEST(PairStyle, single) // utility lambda to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; command("clear"); @@ -1317,7 +1316,7 @@ TEST(PairStyle, extract) // utility lambda to improve readability auto command = [&](const std::string &line) { - lmp->input->one(line.c_str()); + lmp->input->one(line); }; if (!verbose) ::testing::internal::CaptureStdout(); diff --git a/unittest/force-styles/tests/1-1-1.table b/unittest/force-styles/tests/1-1-1.table new file mode 100644 index 0000000000..76d8f8a9ec --- /dev/null +++ b/unittest/force-styles/tests/1-1-1.table @@ -0,0 +1,1875 @@ +ENTRY1 +N 12 rmin 2.55 rmax 3.65 + +1 2.55 2.55 3.75 -867.212 -611.273 867.212 21386.8 611.273 -21386.8 0.0 +2 2.55 2.55 11.25 -621.539 -411.189 621.539 5035.95 411.189 -5035.95 0.0 +3 2.55 2.55 18.75 -394.167 -243.287 394.167 1722.21 243.287 -1722.21 0.0 +4 2.55 2.55 26.25 -218.789 -127.402 218.789 560.206 127.402 -560.206 0.0 +5 2.55 2.55 33.75 -104.252 -59.5774 104.252 156.639 59.5774 -156.639 0.0 +6 2.55 2.55 41.25 -41.0722 -24.6716 41.072 36.4446 24.6716 -36.4446 0.0 +7 2.55 2.55 48.75 -12.357 -8.38061 12.3571 7.1117 8.38062 -7.1117 0.0 +8 2.55 2.55 56.25 -2.29912 -1.68047 2.29907 0.91657 1.68048 -0.916568 0.0 +9 2.55 2.55 63.75 -0.0509977 0.327321 0.0509129 -0.304729 -0.327319 0.30474 0.0 +10 2.55 2.55 71.25 0.0345509 0.431792 -0.0345867 -0.382614 -0.431782 0.382616 0.0 +11 2.55 2.55 78.75 -0.00019898 0.179593 0.000319523 -0.292658 -0.179608 0.292661 0.0 +12 2.55 2.55 86.25 0.154169 0.138217 -0.154088 -0.302917 -0.138224 0.302914 0.0 +13 2.55 2.55 93.75 0.327691 0.263922 -0.327675 -0.340147 -0.263894 0.340148 0.0 +14 2.55 2.55 101.25 0.382895 0.350591 -0.382883 -0.297308 -0.350546 0.297312 0.0 +15 2.55 2.55 108.75 0.300955 0.297417 -0.300746 -0.173862 -0.297437 0.173872 0.0 +16 2.55 2.55 116.25 0.138507 0.141879 -0.138328 -0.0349372 -0.1418 0.0349415 0.0 +17 2.55 2.55 123.75 -0.0287949 -0.0286834 0.0286744 0.065848 0.0287665 -0.0658601 0.0 +18 2.55 2.55 131.25 -0.160323 -0.164235 0.160302 0.120341 0.164191 -0.120297 0.0 +19 2.55 2.55 138.75 -0.274013 -0.280673 0.274077 0.156939 0.280642 -0.156913 0.0 +20 2.55 2.55 146.25 -0.42361 -0.430992 0.423711 0.212433 0.430824 -0.212358 0.0 +21 2.55 2.55 153.75 -0.648177 -0.651719 0.648516 0.305821 0.651726 -0.305791 0.0 +22 2.55 2.55 161.25 -0.93181 -0.926724 0.931895 0.426805 0.926702 -0.426778 0.0 +23 2.55 2.55 168.75 -1.20276 -1.18735 1.20273 0.541966 1.18745 -0.542019 0.0 +24 2.55 2.55 176.25 -1.36933 -1.34705 1.3691 0.612284 1.34703 -0.612297 0.0 +25 2.55 2.65 3.75 -784.444 -675.519 784.444 19696.9 675.519 -19696.9 0.0 +26 2.55 2.65 11.25 -542.941 -440.852 542.941 5300.59 440.852 -5300.59 0.0 +27 2.55 2.65 18.75 -325.839 -241.234 325.839 1817.37 241.234 -1817.37 0.0 +28 2.55 2.65 26.25 -169.421 -111.015 169.421 580.214 111.015 -580.214 0.0 +29 2.55 2.65 33.75 -74.994 -43.3669 74.994 155.496 43.3669 -155.496 0.0 +30 2.55 2.65 41.25 -27.0736 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138.75 0.000108536 -0.00156718 -0.000108471 0.000330074 0.00156723 -0.000330079 0.0 +3452 3.65 3.65 146.25 -0.000640149 -0.00249673 0.000640125 0.000548861 0.00249673 -0.000548895 0.0 +3453 3.65 3.65 153.75 -0.0014021 -0.00329158 0.00140212 0.000784814 0.00329161 -0.000784826 0.0 +3454 3.65 3.65 161.25 -0.00190979 -0.00380299 0.00190977 0.000966445 0.00380303 -0.000966483 0.0 +3455 3.65 3.65 168.75 -0.00211603 -0.00404799 0.00211605 0.00107292 0.004048 -0.00107292 0.0 +3456 3.65 3.65 176.25 -0.00215132 -0.00412886 0.00215137 0.00111754 0.00412895 -0.00111757 0.0 diff --git a/unittest/force-styles/tests/atomic-pair-sw_angle_table.yaml b/unittest/force-styles/tests/atomic-pair-sw_angle_table.yaml new file mode 100644 index 0000000000..7229a3cd26 --- /dev/null +++ b/unittest/force-styles/tests/atomic-pair-sw_angle_table.yaml @@ -0,0 +1,96 @@ +--- +lammps_version: 4 May 2022 +date_generated: Wed Jun 1 15:17:22 2022 +epsilon: 1e-12 +skip_tests: single +prerequisites: ! | + pair sw/angle/table + pair table +pre_commands: ! | + variable units index real + variable newton_pair delete + variable newton_pair index on + shell cp ${input_dir}/table_CG_CG_CG.txt . +post_commands: ! "" +input_file: in.metal +pair_style: hybrid/overlay table linear 1200 sw/angle/table +pair_coeff: ! | + * * table ${input_dir}/table_CG_CG.txt VOTCA + * * sw/angle/table ${input_dir}/spce.sw type type +extract: ! "" +natoms: 32 +init_vdwl: 2428.9633428241673 +init_coul: 0 +init_stress: ! |2- + 2.1799808252981104e+04 2.2098847758334741e+04 1.5227317495796946e+04 5.5915487284825185e+03 4.2330141376182507e+02 -2.1635648030093221e+03 +init_forces: ! |2 + 1 -3.5272456427265922e+02 4.7896703188444229e+02 7.6160632749768567e+01 + 2 -2.2734507500176406e+01 -1.5821645847684510e+02 1.1028261572305695e+02 + 3 -3.6932223674029137e+02 1.7315628979419187e+03 -5.2288079251214720e+02 + 4 3.1116044194470057e+01 -3.1009878149268530e+01 -6.8414290700926671e+01 + 5 1.2157567668233901e+03 1.3361425827696451e+03 -2.4428700622833938e+02 + 6 2.1498603159595226e+02 1.2379258234822432e+01 -1.8192892150594932e+02 + 7 -5.8065242995364076e+02 6.3615913954340272e+02 -5.8940661342540871e+01 + 8 -2.9330102622037936e+02 -1.4478456371145094e+02 3.4992669050834974e+02 + 9 5.4581529315399578e+01 -1.0085658890730177e+02 -4.3539166606697755e+01 + 10 -7.5328757518773557e+02 -1.9208550331031577e+03 -5.9929086772884966e+02 + 11 -6.2073979508185595e+01 -9.3172505877146349e+01 8.8201736909256510e+01 + 12 5.2022495622775352e+02 -6.4668600468680108e+02 -1.8086255931588799e+01 + 13 -1.4637585277113917e+02 -2.4193749312797078e+01 -1.3497675472534843e+02 + 14 2.2785633726795228e+02 -1.4050021950202930e+02 4.2957377860079254e+02 + 15 -4.1589593903912913e+01 5.6849936807240290e+01 -5.3315771137404397e+01 + 16 5.0207265346701280e+02 -4.3553084670415353e+02 2.2270110539464073e+02 + 17 2.7243217976852867e+02 6.7842110608020960e+02 -1.8488293016613730e+02 + 18 -1.6339467540544510e+03 -8.6208840396403559e+02 -5.2809809085219297e+02 + 19 -1.8146991394127588e+03 -1.4248970633821093e+03 1.6246778777497133e+02 + 20 5.0143947854312678e+01 3.0349353798587607e+01 -7.6753179337391444e+01 + 21 1.1359392702527382e+03 6.7780617382057903e+02 -2.1777379118829096e+01 + 22 2.6318213617558456e+01 -1.1442799194941128e+02 -4.0723882345600529e+01 + 23 1.0173532367943421e+03 1.4870722398544501e+03 -3.3061556638580618e+02 + 24 1.8951324945224176e+03 1.3655558041004167e+03 6.3746947970957035e+02 + 25 2.1139286860441129e+02 -1.4343085616543428e+02 -2.4472193090284622e+02 + 26 -6.6054117554868481e+02 -1.7214679588856484e+03 1.1872792057456782e+03 + 27 3.8554823693482177e+02 -2.4263768110018356e+02 -1.4505783275426307e+01 + 28 -1.6156920382667545e+02 3.2681073686927527e+02 4.0195534333261003e+02 + 29 1.0269877810330740e+03 1.0972018261937728e+03 -4.9239365569732279e+01 + 30 -7.7183246664884393e+01 -1.1163723935859770e+02 -5.6015149765282524e+02 + 31 2.7330076741933460e+01 -6.2134053241130312e+02 3.7926314422192496e+02 + 32 -1.8451713394504984e+03 -9.7754451225108528e+02 -6.8151426644039077e+01 +run_vdwl: 2428.764401023566 +run_coul: 0 +run_stress: ! |2- + 2.1807179009069081e+04 2.2096249577665836e+04 1.5217251424717178e+04 5.5876293741471409e+03 4.2481794037948595e+02 -2.1641073132805273e+03 +run_forces: ! |2 + 1 -3.5657232205619187e+02 4.8051759317525114e+02 7.4589821279043520e+01 + 2 -2.2890330563537752e+01 -1.5847929947391452e+02 1.1057024581491029e+02 + 3 -3.7048240284136381e+02 1.7274339155425446e+03 -5.2721183867080663e+02 + 4 3.1213113517876284e+01 -3.0972108629752253e+01 -6.8362160774369471e+01 + 5 1.2131778379678060e+03 1.3324719919494626e+03 -2.4196312117000102e+02 + 6 2.1588387878389867e+02 1.2017400433555963e+01 -1.8323099068613300e+02 + 7 -5.8298397256607473e+02 6.3858638821865122e+02 -5.9272595884065503e+01 + 8 -2.9450691866540427e+02 -1.4488601302098704e+02 3.5084177622838757e+02 + 9 5.5071730152343321e+01 -1.0126346692429934e+02 -4.3948685147789718e+01 + 10 -7.4709028759946739e+02 -1.9173399004644243e+03 -5.9495231666550546e+02 + 11 -6.1959233740417524e+01 -9.3373357444258517e+01 8.7926257027673998e+01 + 12 5.2278142223716191e+02 -6.4849088771234563e+02 -1.8113808074276363e+01 + 13 -1.4714650249643290e+02 -2.5131629765603009e+01 -1.3479374072464537e+02 + 14 2.2857040301009684e+02 -1.3768541975979431e+02 4.2806018886113947e+02 + 15 -4.1477060277693703e+01 5.7115876564426109e+01 -5.3039366059682528e+01 + 16 4.9944201304657383e+02 -4.3383072035483559e+02 2.2091297501303973e+02 + 17 2.7228851840542382e+02 6.7799738753924669e+02 -1.8446508468678948e+02 + 18 -1.6336221792482595e+03 -8.5972791234834551e+02 -5.2898505983077177e+02 + 19 -1.8135957890859013e+03 -1.4238141052528933e+03 1.6225337159545035e+02 + 20 5.0092828583367634e+01 3.0471251647078265e+01 -7.6722240263741099e+01 + 21 1.1355438484696886e+03 6.7519841904221255e+02 -2.0182855479720033e+01 + 22 2.6571960650017800e+01 -1.1420696745726380e+02 -4.0529746043707348e+01 + 23 1.0263737261398123e+03 1.4932072283307180e+03 -3.2636823427367165e+02 + 24 1.8952730712010357e+03 1.3642712022544688e+03 6.3847090965522716e+02 + 25 2.1193565520738500e+02 -1.4318069871618528e+02 -2.4487119695300959e+02 + 26 -6.5812362830257700e+02 -1.7188102078185152e+03 1.1859492616184705e+03 + 27 3.8565010020982788e+02 -2.4238978364677456e+02 -1.4837594446360082e+01 + 28 -1.6123154438363622e+02 3.2723676308792528e+02 4.0126611479067810e+02 + 29 1.0251768164068674e+03 1.0954706244344939e+03 -4.9292343676448787e+01 + 30 -7.7077129341229522e+01 -1.1123357160671468e+02 -5.6043482841374544e+02 + 31 2.5726118886179297e+01 -6.2166714125994793e+02 3.8003828834174129e+02 + 32 -1.8520137417071724e+03 -9.8551285056318022e+02 -6.9301402300522653e+01 +... diff --git a/unittest/force-styles/tests/atomic-pair-threebody_table.yaml b/unittest/force-styles/tests/atomic-pair-threebody_table.yaml new file mode 100644 index 0000000000..bb3c8c1c1b --- /dev/null +++ b/unittest/force-styles/tests/atomic-pair-threebody_table.yaml @@ -0,0 +1,97 @@ +--- +lammps_version: 4 May 2022 +date_generated: Wed Jun 1 15:28:13 2022 +epsilon: 1e-05 +skip_tests: single +prerequisites: ! | + pair threebody/table + pair table +pre_commands: ! | + variable units index real + variable newton_pair delete + variable newton_pair index on + shell cp ${input_dir}/1-1-1.table . + shell cp ${input_dir}/1-1-2.table . +post_commands: ! "" +input_file: in.metal +pair_style: hybrid/overlay table linear 1200 threebody/table +pair_coeff: ! | + * * table ${input_dir}/table_CG_CG.txt VOTCA + * * threebody/table ${input_dir}/spce2.3b type1 type2 +extract: ! "" +natoms: 32 +init_vdwl: 1491.9850663210582 +init_coul: 0 +init_stress: ! |2- + 2.1388163370760823e+04 2.1664558645983379e+04 1.4729243404366314e+04 5.6495516964437775e+03 5.1637900223635859e+02 -2.2491014848350428e+03 +init_forces: ! |2 + 1 -3.4809429741393029e+02 4.6567597414239913e+02 9.4441973687110405e+01 + 2 -1.8412192720214428e+01 -1.6122507911305391e+02 1.1798397229543718e+02 + 3 -3.6959552927057359e+02 1.7366664628134174e+03 -5.2433878744101696e+02 + 4 1.9704833162904933e+01 -2.8473480842310366e+01 -7.6632873700899410e+01 + 5 1.2286660791793993e+03 1.3189646599149826e+03 -2.5750328829062335e+02 + 6 2.3230773636573508e+02 1.3236909769358112e+01 -1.6536673989911372e+02 + 7 -5.9250555047871524e+02 6.4419772822168966e+02 -7.3421471775369668e+01 + 8 -2.7993451614515635e+02 -1.3398848087050882e+02 3.4786818228776917e+02 + 9 6.0102535250319256e+01 -8.2958743522890487e+01 -4.2554780357129808e+01 + 10 -7.7091710125156442e+02 -1.9316366702146124e+03 -5.7574889508217711e+02 + 11 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a/unittest/force-styles/tests/manybody-pair-bop.yaml +++ b/unittest/force-styles/tests/manybody-pair-bop.yaml @@ -1,7 +1,7 @@ --- -lammps_version: 8 Apr 2021 +lammps_version: 4 May 2022 tags: slow, unstable -date_generated: Wed May 5 11:50:15 2021 +date_generated: Fri May 27 17:36:36 2022 epsilon: 5e-12 prerequisites: ! | pair bop @@ -535,521 +535,521 @@ init_forces: ! |2 510 -3.4726171480710488e+00 5.2740849860611352e+00 -2.8158025166462988e+00 511 9.0442915573980152e+00 -1.4095415165544551e+00 -3.3538829159648067e+00 512 5.7753579505879529e+00 5.6893699296338545e+00 6.1188593723557538e+00 -run_vdwl: -228.0857232848286 +run_vdwl: -227.61849029256774 run_coul: 0 run_stress: ! |2- - 2.3717664948296933e+03 2.4019359900230493e+03 2.4442550920472167e+03 -1.1171763120435550e+02 5.0043476869247547e+02 6.0439649265925254e+01 + 2.3726345230237625e+03 2.4028091143998217e+03 2.4451861002359515e+03 -1.1183772133730268e+02 5.0092092646568466e+02 6.0406121385816192e+01 run_forces: ! |2 - 1 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b/unittest/force-styles/tests/manybody-pair-bop_save.yaml @@ -1,7 +1,7 @@ --- -lammps_version: 8 Apr 2021 +lammps_version: 4 May 2022 tags: slow, unstable -date_generated: Wed May 5 11:50:24 2021 +date_generated: Fri May 27 17:36:37 2022 epsilon: 2e-11 prerequisites: ! | pair bop @@ -535,521 +535,521 @@ init_forces: ! |2 510 -2.2749371215520973e+00 3.3600739184147281e+00 -2.2482793489540440e+00 511 5.5276560306465985e+00 -1.7222471161905775e+00 -2.0146673282516816e+00 512 4.5674510924053244e+00 4.8005511894034880e+00 3.9347170870249073e+00 -run_vdwl: -1148.282038612608 +run_vdwl: -1148.085978939542 run_coul: 0 run_stress: ! |2- - 4.0607716458773768e+02 4.1990275279117287e+02 4.3189008174024184e+02 -1.5062607937984635e+02 2.6526098686927287e+02 9.4584979764475761e+01 + 4.0653370543801509e+02 4.2033870846285419e+02 4.3236415621179896e+02 -1.5065757455794261e+02 2.6546325857473971e+02 9.4558303537896379e+01 run_forces: ! |2 - 1 2.2069706541796388e-01 6.8504065097219424e-01 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+1,7 @@ --- lammps_version: 17 Feb 2022 date_generated: Fri Mar 18 22:17:48 2022 -epsilon: 5e-13 +epsilon: 5e-12 skip_tests: prerequisites: ! | pair pace diff --git a/unittest/force-styles/tests/manybody-pair-pace_recursive.yaml b/unittest/force-styles/tests/manybody-pair-pace_recursive.yaml index eef7509606..6105debb67 100644 --- a/unittest/force-styles/tests/manybody-pair-pace_recursive.yaml +++ b/unittest/force-styles/tests/manybody-pair-pace_recursive.yaml @@ -1,7 +1,7 @@ --- lammps_version: 10 Mar 2021 date_generated: Wed Apr 7 19:30:07 2021 -epsilon: 5e-13 +epsilon: 5e-12 prerequisites: ! | pair pace pre_commands: ! | diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long.yaml index 2579a3bf6c..28961cd04e 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long.yaml @@ -1,7 +1,7 @@ --- lammps_version: 17 Feb 2022 date_generated: Fri Mar 18 22:17:32 2022 -epsilon: 5e-12 +epsilon: 2e-11 skip_tests: prerequisites: ! | atom full diff --git a/unittest/force-styles/tests/spce.sw b/unittest/force-styles/tests/spce.sw new file mode 100644 index 0000000000..8b0fd70f61 --- /dev/null +++ b/unittest/force-styles/tests/spce.sw @@ -0,0 +1,18 @@ +type +type +type +1 #epsilon in kcal/mol +1 #sigma in dimensionless +3.7 # a in Ang +1.0 #lambda dimensionless +0.8 #gamma in Ang +0.0 #costheta0 dimensionless +0 #two body part A=0 +0 #two body part B=0 +0 #two body part p=0 +0 #two body part q=0 +0.0 # use the standard Stillinger-Weber cutoff +table_CG_CG_CG.txt +VOTCA +linear +1001 diff --git a/unittest/force-styles/tests/spce2.3b b/unittest/force-styles/tests/spce2.3b new file mode 100644 index 0000000000..52fcd1e5e9 --- /dev/null +++ b/unittest/force-styles/tests/spce2.3b @@ -0,0 +1,71 @@ +type1 +type1 +type1 +3.7 # cut in Ang +1-1-1.table +ENTRY1 +linear +12 +type1 +type1 +type2 +3.7 # cut in Ang +1-1-2.table +ENTRY1 +linear +12 +type1 +type2 +type1 +3.7 # cut in Ang +1-1-2.table +ENTRY1 +linear +12 +type1 +type2 +type2 +3.7 # cut in Ang +1-1-1.table +ENTRY1 +linear +12 +type2 +type1 +type1 +3.7 # cut in Ang +1-1-1.table +ENTRY1 +linear +12 +type2 +type1 +type2 +3.7 # cut in Ang +1-1-2.table +ENTRY1 +linear +12 +type2 +type2 +type1 +3.7 # cut in Ang +1-1-2.table +ENTRY1 +linear +12 +type2 +type2 +type2 +3.7 # cut in Ang +1-1-1.table +ENTRY1 +linear +12 + + + + + + + diff --git a/unittest/force-styles/tests/table_CG_CG.txt b/unittest/force-styles/tests/table_CG_CG.txt new file mode 100644 index 0000000000..f4ccdd4b4e --- /dev/null +++ b/unittest/force-styles/tests/table_CG_CG.txt @@ -0,0 +1,1203 @@ +VOTCA +N 1200 R 0.010000 12.000000 + +1 1.0000000000e-02 1.5390100510e+15 2.1517330910e+16 +2 2.0000000000e-02 1.3370836560e+15 1.8774943350e+16 +3 3.0000000000e-02 1.1616510900e+15 1.6231560530e+16 +4 4.0000000000e-02 1.0092362200e+15 1.4101892510e+16 +5 5.0000000000e-02 8.7681900090e+14 1.2251648380e+16 +6 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1.9185186e+00 -1.1513008e-02 diff --git a/unittest/force-styles/yaml_writer.h b/unittest/force-styles/yaml_writer.h index 31df8eb60d..ca95a578c1 100644 --- a/unittest/force-styles/yaml_writer.h +++ b/unittest/force-styles/yaml_writer.h @@ -22,6 +22,9 @@ class YamlWriter { public: YamlWriter(const char *outfile); virtual ~YamlWriter(); + YamlWriter() = delete; + YamlWriter(const YamlWriter &) = delete; + const YamlWriter & operator=(const YamlWriter &) = delete; // emitters void emit(const std::string &key, const double value); @@ -34,10 +37,6 @@ private: FILE *fp; yaml_emitter_t emitter; yaml_event_t event; - -private: - YamlWriter(){}; - YamlWriter(const YamlWriter &){}; }; #endif diff --git a/unittest/formats/compressed_dump_test.h b/unittest/formats/compressed_dump_test.h index d9803005e5..b209097264 100644 --- a/unittest/formats/compressed_dump_test.h +++ b/unittest/formats/compressed_dump_test.h @@ -102,7 +102,7 @@ public: BEGIN_HIDE_OUTPUT(); std::string converted_file = compressed_file.substr(0, compressed_file.find_last_of('.')); std::string cmdline = - fmt::format("{} -d -c {} > {}", COMPRESS_EXECUTABLE, compressed_file, converted_file); + fmt::format("\"{}\" -d -c {} > {}", COMPRESS_EXECUTABLE, compressed_file, converted_file); system(cmdline.c_str()); END_HIDE_OUTPUT(); return converted_file; diff --git a/unittest/formats/test_dump_atom.cpp b/unittest/formats/test_dump_atom.cpp index c9e5223f19..702325f2fb 100644 --- a/unittest/formats/test_dump_atom.cpp +++ b/unittest/formats/test_dump_atom.cpp @@ -39,22 +39,23 @@ public: END_HIDE_OUTPUT(); } - std::string dump_filename(std::string ident) + std::string dump_filename(const std::string &ident) { return fmt::format("dump_{}_{}.melt", dump_style, ident); } - std::string text_dump_filename(std::string ident) + std::string text_dump_filename(const std::string &ident) { return fmt::format("dump_{}_text_{}.melt", dump_style, ident); } - std::string binary_dump_filename(std::string ident) + std::string binary_dump_filename(const std::string &ident) { return fmt::format("dump_{}_binary_{}.melt.bin", dump_style, ident); } - void generate_dump(std::string dump_file, std::string dump_modify_options, int ntimesteps) + void generate_dump(const std::string &dump_file, const std::string &dump_modify_options, + int ntimesteps) { BEGIN_HIDE_OUTPUT(); command(fmt::format("dump id all {} 1 {}", dump_style, dump_file)); @@ -81,8 +82,8 @@ public: END_HIDE_OUTPUT(); } - void generate_text_and_binary_dump(std::string text_file, std::string binary_file, - std::string dump_modify_options, int ntimesteps) + void generate_text_and_binary_dump(const std::string &text_file, const std::string &binary_file, + const std::string &dump_modify_options, int ntimesteps) { BEGIN_HIDE_OUTPUT(); command(fmt::format("dump id0 all {} 1 {}", dump_style, text_file)); @@ -97,10 +98,10 @@ public: END_HIDE_OUTPUT(); } - std::string convert_binary_to_text(std::string binary_file) + std::string convert_binary_to_text(const std::string &binary_file) { BEGIN_HIDE_OUTPUT(); - std::string cmdline = fmt::format("{} {}", BINARY2TXT_EXECUTABLE, binary_file); + std::string cmdline = fmt::format("\"{}\" {}", BINARY2TXT_EXECUTABLE, binary_file); system(cmdline.c_str()); END_HIDE_OUTPUT(); return fmt::format("{}.txt", binary_file); diff --git a/unittest/formats/test_dump_cfg.cpp b/unittest/formats/test_dump_cfg.cpp index c2ab96c5ed..e51da8331a 100644 --- a/unittest/formats/test_dump_cfg.cpp +++ b/unittest/formats/test_dump_cfg.cpp @@ -27,8 +27,8 @@ class DumpCfgTest : public MeltTest { std::string dump_style = "cfg"; public: - void generate_dump(std::string dump_file, std::string fields, std::string dump_modify_options, - int ntimesteps) + void generate_dump(const std::string &dump_file, const std::string &fields, + const std::string &dump_modify_options, int ntimesteps) { BEGIN_HIDE_OUTPUT(); command(fmt::format("dump id all {} 1 {} {}", dump_style, dump_file, fields)); diff --git a/unittest/formats/test_dump_custom.cpp b/unittest/formats/test_dump_custom.cpp index ee297b194e..72b4adcc87 100644 --- a/unittest/formats/test_dump_custom.cpp +++ b/unittest/formats/test_dump_custom.cpp @@ -37,23 +37,23 @@ public: END_HIDE_OUTPUT(); } - std::string dump_filename(std::string ident) + std::string dump_filename(const std::string &ident) { return fmt::format("dump_{}_{}.melt", dump_style, ident); } - std::string text_dump_filename(std::string ident) + std::string text_dump_filename(const std::string &ident) { return fmt::format("dump_{}_text_{}.melt", dump_style, ident); } - std::string binary_dump_filename(std::string ident) + std::string binary_dump_filename(const std::string &ident) { return fmt::format("dump_{}_binary_{}.melt.bin", dump_style, ident); } - void generate_dump(std::string dump_file, std::string fields, std::string dump_modify_options, - int ntimesteps) + void generate_dump(const std::string &dump_file, const std::string &fields, + const std::string &dump_modify_options, int ntimesteps) { BEGIN_HIDE_OUTPUT(); command(fmt::format("dump id all {} 1 {} {}", dump_style, dump_file, fields)); @@ -80,9 +80,9 @@ public: END_HIDE_OUTPUT(); } - void generate_text_and_binary_dump(std::string text_file, std::string binary_file, - std::string fields, std::string dump_modify_options, - int ntimesteps) + void generate_text_and_binary_dump(const std::string &text_file, const std::string &binary_file, + const std::string &fields, + const std::string &dump_modify_options, int ntimesteps) { BEGIN_HIDE_OUTPUT(); command(fmt::format("dump id0 all {} 1 {} {}", dump_style, text_file, fields)); @@ -97,10 +97,10 @@ public: END_HIDE_OUTPUT(); } - std::string convert_binary_to_text(std::string binary_file) + std::string convert_binary_to_text(const std::string &binary_file) { BEGIN_HIDE_OUTPUT(); - std::string cmdline = fmt::format("{} {}", BINARY2TXT_EXECUTABLE, binary_file); + std::string cmdline = fmt::format("\"{}\" {}", BINARY2TXT_EXECUTABLE, binary_file); system(cmdline.c_str()); END_HIDE_OUTPUT(); return fmt::format("{}.txt", binary_file); diff --git a/unittest/formats/test_dump_local.cpp b/unittest/formats/test_dump_local.cpp index 5471145309..c548427201 100644 --- a/unittest/formats/test_dump_local.cpp +++ b/unittest/formats/test_dump_local.cpp @@ -39,8 +39,8 @@ public: END_HIDE_OUTPUT(); } - void generate_dump(std::string dump_file, std::string dump_options, - std::string dump_modify_options, int ntimesteps) + void generate_dump(const std::string &dump_file, const std::string &dump_options, + const std::string &dump_modify_options, int ntimesteps) { BEGIN_HIDE_OUTPUT(); command(fmt::format("dump id all {} 1 {} {}", dump_style, dump_file, dump_options)); diff --git a/unittest/formats/test_file_operations.cpp b/unittest/formats/test_file_operations.cpp index fdb3e1a815..48d043b824 100644 --- a/unittest/formats/test_file_operations.cpp +++ b/unittest/formats/test_file_operations.cpp @@ -322,7 +322,7 @@ TEST_F(FileOperationsTest, write_restart) command("write_restart multi-%.restart"); command("write_restart multi2-%.restart fileper 2"); command("write_restart multi3-%.restart nfile 1"); - if (info->has_package("MPIIO")) command("write_restart test.restart.mpiio"); + if (Info::has_package("MPIIO")) command("write_restart test.restart.mpiio"); END_HIDE_OUTPUT(); ASSERT_FILE_EXISTS("noinit.restart"); @@ -334,11 +334,11 @@ TEST_F(FileOperationsTest, write_restart) ASSERT_FILE_EXISTS("multi2-0.restart"); ASSERT_FILE_EXISTS("multi3-base.restart"); ASSERT_FILE_EXISTS("multi3-0.restart"); - if (info->has_package("MPIIO")) { + if (Info::has_package("MPIIO")) { ASSERT_FILE_EXISTS("test.restart.mpiio"); } - if (!info->has_package("MPIIO")) { + if (!Info::has_package("MPIIO")) { TEST_FAILURE(".*ERROR: Writing to MPI-IO filename when MPIIO package is not inst.*", command("write_restart test.restart.mpiio");); } else { @@ -395,7 +395,7 @@ TEST_F(FileOperationsTest, write_restart) delete_file("multi3-base.restart"); delete_file("multi3-0.restart"); delete_file("triclinic.restart"); - if (info->has_package("MPIIO")) delete_file("test.restart.mpiio"); + if (Info::has_package("MPIIO")) delete_file("test.restart.mpiio"); } TEST_F(FileOperationsTest, write_data) @@ -492,7 +492,7 @@ int main(int argc, char **argv) MPI_Init(&argc, &argv); ::testing::InitGoogleMock(&argc, argv); - if (platform::mpi_vendor() == "Open MPI" && !LAMMPS_NS::Info::has_exceptions()) + if (platform::mpi_vendor() == "Open MPI" && !Info::has_exceptions()) std::cout << "Warning: using OpenMPI without exceptions. " "Death tests will be skipped\n"; diff --git a/unittest/formats/test_text_file_reader.cpp b/unittest/formats/test_text_file_reader.cpp index 4965daab5d..325166a2b4 100644 --- a/unittest/formats/test_text_file_reader.cpp +++ b/unittest/formats/test_text_file_reader.cpp @@ -111,7 +111,7 @@ TEST_F(TextFileReaderTest, usefp) delete reader; // check that we reached EOF and the destructor didn't close the file. - ASSERT_EQ(feof(fp), 1); + ASSERT_NE(feof(fp), 0); ASSERT_EQ(fclose(fp), 0); } diff --git a/unittest/python/python-capabilities.py b/unittest/python/python-capabilities.py index 4c14cac37d..3ac66ebdc6 100644 --- a/unittest/python/python-capabilities.py +++ b/unittest/python/python-capabilities.py @@ -38,6 +38,7 @@ class PythonCapabilities(unittest.TestCase): system = platform.system() osinfo = self.lmp.get_os_info() + print("System: %s LAMMPS OS Info: %s" % (system, osinfo)) self.assertEqual(osinfo.find(system),0) def test_has_gzip_support(self): diff --git a/unittest/python/python-commands.py b/unittest/python/python-commands.py index 58a0772510..cd77fa21a1 100644 --- a/unittest/python/python-commands.py +++ b/unittest/python/python-commands.py @@ -1,6 +1,8 @@ import sys,os,unittest,ctypes -from lammps import lammps, LMP_VAR_ATOM, LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, LAMMPS_DOUBLE_2D, LAMMPS_AUTODETECT +from lammps import lammps, LMP_VAR_ATOM, LMP_STYLE_GLOBAL, LMP_STYLE_LOCAL +from lammps import LMP_TYPE_VECTOR, LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS +from lammps import LAMMPS_DOUBLE_2D, LAMMPS_AUTODETECT has_manybody=False try: @@ -311,6 +313,14 @@ create_atoms 1 single & self.assertEqual(minval,1.0) self.assertEqual(maxval,2.1) + ndist1 = self.lmp.extract_compute("dist",LMP_STYLE_LOCAL,LMP_SIZE_VECTOR) + ndist2 = self.lmp.extract_compute("dist",LMP_STYLE_LOCAL,LMP_SIZE_ROWS) + ndist3 = self.lmp.extract_compute("dist",LMP_STYLE_LOCAL,LMP_SIZE_COLS) + + self.assertEqual(ndist1,21) + self.assertEqual(ndist2,21) + self.assertEqual(ndist3,0) + self.assertNotEqual(self.lmp.find_pair_neighlist("lj/cut"),-1) self.assertNotEqual(self.lmp.find_compute_neighlist("dist"),-1) self.assertEqual(self.lmp.find_compute_neighlist("xxx"),-1) diff --git a/unittest/python/python-numpy.py b/unittest/python/python-numpy.py index 010255a81e..7cbae8e48d 100644 --- a/unittest/python/python-numpy.py +++ b/unittest/python/python-numpy.py @@ -93,17 +93,39 @@ class PythonNumpy(unittest.TestCase): # TODO pass - def testExtractComputeLocalScalar(self): - # TODO - pass - def testExtractComputeLocalVector(self): - # TODO - pass + self.lmp.command("region box block 0 2 0 2 0 2") + self.lmp.command("create_box 1 box") + self.lmp.command("create_atoms 1 single 1.0 1.0 1.0") + self.lmp.command("create_atoms 1 single 1.0 1.0 1.5") + self.lmp.command("mass 1 1.0") + self.lmp.command("pair_style lj/cut 1.9") + self.lmp.command("pair_coeff 1 1 1.0 1.0") + self.lmp.command("compute r0 all pair/local dist") + self.lmp.command("run 0 post no") + values = self.lmp.numpy.extract_compute("r0", LMP_STYLE_LOCAL, LMP_TYPE_VECTOR) + self.assertEqual(values.ndim, 1) + self.assertEqual(values.size, 2) + self.assertEqual(values[0], 0.5) + self.assertEqual(values[1], 1.5) def testExtractComputeLocalArray(self): - # TODO - pass + self.lmp.command("region box block 0 2 0 2 0 2") + self.lmp.command("create_box 1 box") + self.lmp.command("create_atoms 1 single 1.0 1.0 1.0") + self.lmp.command("create_atoms 1 single 1.0 1.0 1.5") + self.lmp.command("mass 1 1.0") + self.lmp.command("pair_style lj/cut 1.9") + self.lmp.command("pair_coeff 1 1 1.0 1.0") + self.lmp.command("compute r0 all pair/local dist dx dy dz") + self.lmp.command("run 0 post no") + values = self.lmp.numpy.extract_compute("r0", LMP_STYLE_LOCAL, LMP_TYPE_ARRAY) + self.assertEqual(values.ndim, 2) + self.assertEqual(values.size, 8) + self.assertEqual(values[0,0], 0.5) + self.assertEqual(values[0,3], -0.5) + self.assertEqual(values[1,0], 1.5) + self.assertEqual(values[1,3], 1.5) def testExtractAtomDeprecated(self): self.lmp.command("units lj") diff --git a/unittest/python/test_python_package.cpp b/unittest/python/test_python_package.cpp index db7a7a41b6..377c3a7549 100644 --- a/unittest/python/test_python_package.cpp +++ b/unittest/python/test_python_package.cpp @@ -52,7 +52,7 @@ class PythonPackageTest : public LAMMPSTest { protected: void InitSystem() override { - if (!info->has_package("PYTHON")) GTEST_SKIP(); + if (!Info::has_package("PYTHON")) GTEST_SKIP(); HIDE_OUTPUT([&] { command("units real"); @@ -73,7 +73,7 @@ class FixPythonInvokeTest : public MeltTest { protected: void InitSystem() override { - if (!info->has_package("PYTHON")) GTEST_SKIP(); + if (!Info::has_package("PYTHON")) GTEST_SKIP(); MeltTest::InitSystem(); } @@ -309,7 +309,7 @@ TEST_F(FixPythonInvokeTest, end_of_step) auto output = CAPTURE_OUTPUT([&] { command("run 50"); }); - fprintf(stderr,"lines: %s\n",output.c_str()); + fprintf(stderr, "lines: %s\n", output.c_str()); auto lines = utils::split_lines(output); int count = 0;