diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 4e8803fc5a..116812b649 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -13,40 +13,45 @@ lib/kim/* @ellio167 lib/mesont/* @iafoss # whole packages +src/ADIOS/* @pnorbert src/AMOEBA/* @sjplimp -src/COMPRESS/* @rbberger -src/GPU/* @ndtrung81 -src/KOKKOS/* @stanmoore1 -src/KIM/* @ellio167 -src/LATTE/* @cnegre -src/MLIAP/* @athomps -src/SNAP/* @athomps -src/SPIN/* @julient31 +src/BPM/* @jtclemm src/BROWNIAN/* @samueljmcameron src/CG-DNA/* @ohenrich src/CG-SPICA/* @yskmiyazaki src/COLVARS/* @giacomofiorin +src/COMPRESS/* @rbberger src/DIELECTRIC/* @ndtrung81 src/ELECTRODE/* @ludwig-ahrens src/FEP/* @agiliopadua -src/ML-HDNNP/* @singraber +src/GPU/* @ndtrung81 +src/GRANULAR/* @jtclemm @dsbolin src/INTEL/* @wmbrownintel +src/KIM/* @ellio167 +src/KOKKOS/* @stanmoore1 +src/LATTE/* @cnegre src/MANIFOLD/* @Pakketeretet2 -src/MDI/* @taylor-a-barnes +src/MDI/* @taylor-a-barnes @sjplimp src/MEAM/* @martok src/MESONT/* @iafoss +src/ML-HDNNP/* @singraber +src/ML-IAP/* @athomps +src/ML-PACE/* @yury-lysogorskiy +src/ML-POD/* @exapde @rohskopf src/MOFFF/* @hheenen src/MOLFILE/* @akohlmey src/NETCDF/* @pastewka -src/ML-PACE/* @yury-lysogorskiy -src/PLUMED/* @gtribello -src/PHONON/* @lingtikong -src/PTM/* @pmla src/OPENMP/* @akohlmey +src/PHONON/* @lingtikong +src/PLUGIN/* @akohlmey +src/PLUMED/* @gtribello +src/PTM/* @pmla src/QMMM/* @akohlmey -src/REAXFF/* @hasanmetin @stanmoore1 src/REACTION/* @jrgissing +src/REAXFF/* @hasanmetin @stanmoore1 src/SCAFACOS/* @rhalver +src/SNAP/* @athomps +src/SPIN/* @julient31 src/TALLY/* @akohlmey src/UEF/* @danicholson src/VTK/* @rbberger @@ -59,6 +64,8 @@ src/MANYBODY/pair_atm.* @sergeylishchuk src/REPLICA/*_grem.* @dstelter92 src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel src/MISC/*_tracker.* @jtclemm +src/MC/fix_gcmc.* @athomps +src/MC/fix_sgcmc.* @athomps # core LAMMPS classes src/lammps.* @sjplimp @@ -120,27 +127,32 @@ src/dump_movie.* @akohlmey src/exceptions.h @rbberger src/fix_nh.* @athomps src/info.* @akohlmey @rbberger -src/timer.* @akohlmey src/min* @sjplimp @stanmoore1 +src/platform.* @akohlmey +src/timer.* @akohlmey src/utils.* @akohlmey @rbberger src/verlet.* @sjplimp @stanmoore1 src/math_eigen_impl.h @jewettaij # tools -tools/msi2lmp/* @akohlmey +tools/coding_standard/* @akohlmey @rbberger tools/emacs/* @HaoZeke -tools/singularity/* @akohlmey @rbberger -tools/coding_standard/* @rbberger -tools/valgrind/* @akohlmey -tools/swig/* @akohlmey +tools/lammps-shell/* @akohlmey +tools/msi2lmp/* @akohlmey tools/offline/* @rbberger +tools/singularity/* @akohlmey @rbberger +tools/swig/* @akohlmey +tools/valgrind/* @akohlmey tools/vim/* @hammondkd # tests -unittest/* @akohlmey @rbberger +unittest/* @akohlmey # cmake cmake/* @junghans @rbberger +cmake/Modules/LAMMPSInterfacePlugin.cmake @akohlmey +cmake/Modules/MPI4WIN.cmake @akohlmey +cmake/Modules/OpenCLLoader.cmake @akohlmey cmake/Modules/Packages/COLVARS.cmake @junghans @rbberger @giacomofiorin cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167 cmake/presets/*.cmake @akohlmey @@ -149,13 +161,12 @@ cmake/presets/*.cmake @akohlmey python/* @rbberger # fortran -fortran/* @akohlmey +fortran/* @akohlmey @hammondkd # docs -doc/utils/*/* @rbberger -doc/Makefile @rbberger -doc/README @rbberger +doc/* @akohlmey examples/plugin/* @akohlmey +examples/PACKAGES/pace/plugin/* @akohlmey # for releases src/version.h @sjplimp diff --git a/.github/ISSUE_TEMPLATE/help_request.md b/.github/ISSUE_TEMPLATE/help_request.md index 5e5b3ebffd..bde37650b2 100644 --- a/.github/ISSUE_TEMPLATE/help_request.md +++ b/.github/ISSUE_TEMPLATE/help_request.md @@ -1,6 +1,6 @@ --- name: Request for Help -about: "Don't post help requests here, email the lammps-users mailing list" +about: "Don't post help requests here, post in the LAMMPS forum" title: "" labels: invalid assignees: '' @@ -8,8 +8,9 @@ assignees: '' --- Please **do not** post requests for help (e.g. with installing or using LAMMPS) here. -Instead send an e-mail to the lammps-users mailing list. +Instead, you can post to the LAMMPS category in the Materials Science Community +Discourse forum at: https://matsci.org/lammps/ This issue tracker is for tracking LAMMPS development related issues only. -Thanks for your cooperation. +Thank you in advance for your cooperation. diff --git a/.github/workflows/compile-msvc.yml b/.github/workflows/compile-msvc.yml index 3ec5fc4cb0..5080466728 100644 --- a/.github/workflows/compile-msvc.yml +++ b/.github/workflows/compile-msvc.yml @@ -26,15 +26,19 @@ jobs: - name: Select Python version uses: actions/setup-python@v4 with: - python-version: '3.10' + python-version: '3.11' - name: Building LAMMPS via CMake shell: bash run: | python3 -m pip install numpy python3 -m pip install pyyaml + nuget install MSMPIsdk + nuget install MSMPIDIST cmake -C cmake/presets/windows.cmake \ -D PKG_PYTHON=on \ + -D WITH_PNG=off \ + -D WITH_JPEG=off \ -S cmake -B build \ -D BUILD_SHARED_LIBS=on \ -D LAMMPS_EXCEPTIONS=on \ @@ -50,4 +54,4 @@ jobs: - name: Run Unit Tests working-directory: build shell: bash - run: ctest -V -C Release + run: ctest -V -C Release -E FixTimestep:python_move_nve diff --git a/README b/README index bb0f335848..c25506e2c0 100644 --- a/README +++ b/README @@ -16,8 +16,8 @@ National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL) version 2. -The primary author of the code is Steve Plimpton, who can be emailed -at sjplimp@sandia.gov. The LAMMPS WWW Site at www.lammps.org has +The code is maintained by the LAMMPS development team who can be emailed +at developers@lammps.org. The LAMMPS WWW Site at www.lammps.org has more information about the code and its uses. The LAMMPS distribution includes the following files and directories: diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 0aa86efcfb..6666636a09 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -7,6 +7,10 @@ cmake_minimum_required(VERSION 3.10) if(POLICY CMP0074) cmake_policy(SET CMP0074 NEW) endif() +# set policy to silence warnings about ignoring ${CMAKE_REQUIRED_LIBRARIES} but use it +if(POLICY CMP0075) + cmake_policy(SET CMP0075 NEW) +endif() # set policy to silence warnings about missing executable permissions in # pythonx.y-config when cross-compiling. review occasionally if it may be set to NEW if(POLICY CMP0109) @@ -262,6 +266,7 @@ set(STANDARD_PACKAGES ML-QUIP ML-RANN ML-SNAP + ML-POD MOFFF MOLECULE MOLFILE @@ -312,6 +317,15 @@ if(PKG_ADIOS) # script that defines the MPI::MPI_C target enable_language(C) find_package(ADIOS2 REQUIRED) + if(BUILD_MPI) + if(NOT ADIOS2_HAVE_MPI) + message(FATAL_ERROR "ADIOS2 must be built with MPI support when LAMMPS has MPI enabled") + endif() + else() + if(ADIOS2_HAVE_MPI) + message(FATAL_ERROR "ADIOS2 must be built without MPI support when LAMMPS has MPI disabled") + endif() + endif() target_link_libraries(lammps PRIVATE adios2::adios2) endif() @@ -385,9 +399,9 @@ pkg_depends(EXTRA-MOLECULE MOLECULE) # 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) +find_package(OpenMP COMPONENTS CXX QUIET) +if(OpenMP_CXX_FOUND) + check_omp_h_include() if(HAVE_OMP_H_INCLUDE) set(BUILD_OMP_DEFAULT ON) endif() @@ -396,8 +410,8 @@ 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) + find_package(OpenMP COMPONENTS CXX REQUIRED) + check_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() @@ -419,7 +433,7 @@ if(BUILD_OMP) target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX) endif() -if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE OR PKG_ELECTRODE) +if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_LATTE OR PKG_ELECTRODE) enable_language(C) if (NOT USE_INTERNAL_LINALG) find_package(LAPACK) @@ -625,7 +639,7 @@ foreach(PKG_LIB POEMS ATC AWPMD H5MD MESONT) endif() endforeach() -if(PKG_ELECTRODE) +if(PKG_ELECTRODE OR PKG_ML-POD) target_link_libraries(lammps PRIVATE ${LAPACK_LIBRARIES}) endif() @@ -654,7 +668,7 @@ endif() # packages which selectively include variants based on enabled styles # e.g. accelerator packages ###################################################################### -foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU) +foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU) if(PKG_${PKG_WITH_INCL}) include(Packages/${PKG_WITH_INCL}) endif() @@ -727,18 +741,17 @@ list(FIND LANGUAGES "Fortran" _index) if(_index GREATER -1) target_link_libraries(lammps PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES}) endif() -set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h compute.h dihedral.h domain.h error.h fix.h force.h group.h improper.h - input.h info.h kspace.h lammps.h lattice.h library.h lmppython.h lmptype.h memory.h modify.h neighbor.h neigh_list.h output.h - pair.h pointers.h region.h timer.h universe.h update.h utils.h variable.h) -if(LAMMPS_EXCEPTIONS) - list(APPEND LAMMPS_CXX_HEADERS exceptions.h) -endif() +set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h command.h compute.h dihedral.h domain.h + error.h exceptions.h fix.h force.h group.h improper.h input.h info.h kspace.h lammps.h lattice.h + library.h lmppython.h lmptype.h memory.h modify.h neighbor.h neigh_list.h output.h pair.h + platform.h pointers.h region.h timer.h universe.h update.h utils.h variable.h) +set(LAMMPS_FMT_HEADERS core.h format.h) set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE}) set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION}) set_target_properties(lammps PROPERTIES PREFIX "lib") target_include_directories(lammps PUBLIC $) -file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps) +file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt) foreach(_HEADER ${LAMMPS_CXX_HEADERS}) add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/${_HEADER}) add_custom_target(${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER}) @@ -747,6 +760,14 @@ foreach(_HEADER ${LAMMPS_CXX_HEADERS}) install(FILES ${LAMMPS_SOURCE_DIR}/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps) endif() endforeach() +foreach(_HEADER ${LAMMPS_FMT_HEADERS}) + add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER}) + add_custom_target(fmt_${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt/${_HEADER}) + add_dependencies(lammps fmt_${_HEADER}) + if(BUILD_SHARED_LIBS) + install(FILES ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps/fmt) + endif() +endforeach() target_include_directories(lammps INTERFACE $) add_library(LAMMPS::lammps ALIAS lammps) get_target_property(LAMMPS_DEFINES lammps INTERFACE_COMPILE_DEFINITIONS) @@ -969,9 +990,6 @@ if(PKG_GPU) endif() message(STATUS "GPU precision: ${GPU_PREC}") endif() -if(PKG_KOKKOS) - message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}") -endif() if(PKG_KSPACE) message(STATUS "<<< FFT settings >>> -- Primary FFT lib: ${FFT}") diff --git a/cmake/Modules/FindClangFormat.cmake b/cmake/Modules/FindClangFormat.cmake index 48393f0614..80c3b0d0ae 100644 --- a/cmake/Modules/FindClangFormat.cmake +++ b/cmake/Modules/FindClangFormat.cmake @@ -1,5 +1,10 @@ # Find clang-format find_program(ClangFormat_EXECUTABLE NAMES clang-format + clang-format-15.0 + clang-format-14.0 + clang-format-13.0 + clang-format-12.0 + clang-format-11.0 clang-format-10.0 clang-format-9.0 clang-format-8.0 @@ -14,19 +19,27 @@ if(ClangFormat_EXECUTABLE) OUTPUT_VARIABLE clang_format_version ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE) - - if(clang_format_version MATCHES "^clang-format version .*") - # Arch Linux + if(clang_format_version MATCHES "^(Ubuntu |)clang-format version .*") + # Arch Linux output: # clang-format version 10.0.0 - - # Ubuntu 18.04 LTS Output + # + # Ubuntu 18.04 LTS output: # clang-format version 6.0.0-1ubuntu2 (tags/RELEASE_600/final) - string(REGEX REPLACE "clang-format version ([0-9.]+).*" - "\\1" + # + # Ubuntu 20.04 LTS output: + # clang-format version 10.0.0-4ubuntu1 + # + # Ubuntu 22.04 LTS output: + # Ubuntu clang-format version 14.0.0-1ubuntu1 + # + # Fedora 36 output: + # clang-format version 14.0.5 (Fedora 14.0.5-1.fc36) + string(REGEX REPLACE "^(Ubuntu |)clang-format version ([0-9.]+).*" + "\\2" ClangFormat_VERSION "${clang_format_version}") elseif(clang_format_version MATCHES ".*LLVM version .*") - # CentOS 7 Output + # CentOS 7 output: # LLVM (http://llvm.org/): # LLVM version 3.4.2 # Optimized build. diff --git a/cmake/Modules/FindCythonize.cmake b/cmake/Modules/FindCythonize.cmake index 2a4cc753e8..97f0304279 100644 --- a/cmake/Modules/FindCythonize.cmake +++ b/cmake/Modules/FindCythonize.cmake @@ -22,7 +22,7 @@ endif() if(Python_EXECUTABLE) get_filename_component(_python_path ${Python_EXECUTABLE} PATH) find_program(Cythonize_EXECUTABLE - NAMES cythonize3 cythonize cythonize.bat + NAMES cythonize-${Python_VERSION_MAJOR}.${Python_VERSION_MINOR} cythonize3 cythonize cythonize.bat HINTS ${_python_path}) endif() diff --git a/cmake/Modules/FindZMQ.cmake b/cmake/Modules/FindZMQ.cmake deleted file mode 100644 index 7d612c2eb3..0000000000 --- a/cmake/Modules/FindZMQ.cmake +++ /dev/null @@ -1,19 +0,0 @@ -find_path(ZMQ_INCLUDE_DIR zmq.h) -find_library(ZMQ_LIBRARY NAMES zmq) - -include(FindPackageHandleStandardArgs) -find_package_handle_standard_args(ZMQ DEFAULT_MSG ZMQ_LIBRARY ZMQ_INCLUDE_DIR) - -# Copy the results to the output variables and target. -if(ZMQ_FOUND) - set(ZMQ_LIBRARIES ${ZMQ_LIBRARY}) - set(ZMQ_INCLUDE_DIRS ${ZMQ_INCLUDE_DIR}) - - if(NOT TARGET ZMQ::ZMQ) - add_library(ZMQ::ZMQ UNKNOWN IMPORTED) - set_target_properties(ZMQ::ZMQ PROPERTIES - IMPORTED_LINK_INTERFACE_LANGUAGES "C" - IMPORTED_LOCATION "${ZMQ_LIBRARY}" - INTERFACE_INCLUDE_DIRECTORIES "${ZMQ_INCLUDE_DIR}") - endif() -endif() diff --git a/cmake/Modules/LAMMPSInterfacePlugin.cmake b/cmake/Modules/LAMMPSInterfacePlugin.cmake index 95bb707e86..e20ae5f5cb 100644 --- a/cmake/Modules/LAMMPSInterfacePlugin.cmake +++ b/cmake/Modules/LAMMPSInterfacePlugin.cmake @@ -112,45 +112,76 @@ if(BUILD_MPI) set(MPI_CXX_SKIP_MPICXX TRUE) # We use a non-standard procedure to cross-compile with MPI on Windows if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING) - # Download and configure custom MPICH files for Windows - message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows") - set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball") - set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball") - set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball") - set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball") - mark_as_advanced(MPICH2_WIN64_DEVEL_URL) - mark_as_advanced(MPICH2_WIN32_DEVEL_URL) - mark_as_advanced(MPICH2_WIN64_DEVEL_MD5) - mark_as_advanced(MPICH2_WIN32_DEVEL_MD5) + # Download and configure MinGW compatible MPICH development files for Windows + option(USE_MSMPI "Use Microsoft's MS-MPI SDK instead of MPICH2-1.4.1" OFF) + if(USE_MSMPI) + message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation") + set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball") + set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball") + mark_as_advanced(MPICH2_WIN64_DEVEL_URL) + mark_as_advanced(MPICH2_WIN64_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) + include(ExternalProject) + if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64") + ExternalProject_Add(mpi4win_build + URL ${MPICH2_WIN64_DEVEL_URL} + URL_MD5 ${MPICH2_WIN64_DEVEL_MD5} + CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" + BUILD_BYPRODUCTS /lib/libmsmpi.a) + else() + message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI") + endif() + + ExternalProject_get_property(mpi4win_build SOURCE_DIR) + file(MAKE_DIRECTORY "${SOURCE_DIR}/include") + add_library(MPI::MPI_CXX UNKNOWN IMPORTED) + set_target_properties(MPI::MPI_CXX PROPERTIES + IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a" + INTERFACE_INCLUDE_DIRECTORIES "${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/libmsmpi.a") else() - ExternalProject_Add(mpi4win_build - URL ${MPICH2_WIN32_DEVEL_URL} - URL_MD5 ${MPICH2_WIN32_DEVEL_MD5} - CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" - BUILD_BYPRODUCTS /lib/libmpi.a) + # Download and configure custom MPICH files for Windows + message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows") + set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball") + set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball") + mark_as_advanced(MPICH2_WIN64_DEVEL_URL) + mark_as_advanced(MPICH2_WIN64_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") 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) diff --git a/cmake/Modules/LAMMPSUtils.cmake b/cmake/Modules/LAMMPSUtils.cmake index 9b75209e16..561f2168e2 100644 --- a/cmake/Modules/LAMMPSUtils.cmake +++ b/cmake/Modules/LAMMPSUtils.cmake @@ -24,6 +24,21 @@ function(validate_option name values) endif() endfunction(validate_option) +# helper function to check for usable omp.h header +function(check_omp_h_include) + find_package(OpenMP COMPONENTS CXX QUIET) + if(OpenMP_CXX_FOUND) + set(CMAKE_REQUIRED_FLAGS ${OpenMP_CXX_FLAGS}) + set(CMAKE_REQUIRED_INCLUDES ${OpenMP_CXX_INCLUDE_DIRS}) + set(CMAKE_REQUIRED_LINK_OPTIONS ${OpenMP_CXX_FLAGS}) + set(CMAKE_REQUIRED_LIBRARIES ${OpenMP_CXX_LIBRARIES}) + check_include_file_cxx(omp.h _have_omp_h) + else() + set(_have_omp_h FALSE) + endif() + set(HAVE_OMP_H_INCLUDE ${_have_omp_h} PARENT_SCOPE) +endfunction() + # helper function for getting the most recently modified file or folder from a glob pattern function(get_newest_file path variable) file(GLOB _dirs ${path}) diff --git a/cmake/Modules/MPI4WIN.cmake b/cmake/Modules/MPI4WIN.cmake index aa0c9e1833..02db6d4744 100644 --- a/cmake/Modules/MPI4WIN.cmake +++ b/cmake/Modules/MPI4WIN.cmake @@ -1,39 +1,74 @@ -# Download and configure custom MPICH files for Windows -message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows") -set(MPICH2_WIN64_DEVEL_URL "${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) +# Download and configure MinGW compatible MPICH development files for Windows +option(USE_MSMPI "Use Microsoft's MS-MPI SDK instead of MPICH2-1.4.1" OFF) -include(ExternalProject) -if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64") - ExternalProject_Add(mpi4win_build - URL ${MPICH2_WIN64_DEVEL_URL} - URL_MD5 ${MPICH2_WIN64_DEVEL_MD5} - CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" - BUILD_BYPRODUCTS /lib/libmpi.a) +if(USE_MSMPI) + message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation") + set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball") + set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball") + mark_as_advanced(MPICH2_WIN64_DEVEL_URL) + mark_as_advanced(MPICH2_WIN64_DEVEL_MD5) + + include(ExternalProject) + if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64") + ExternalProject_Add(mpi4win_build + URL ${MPICH2_WIN64_DEVEL_URL} + URL_MD5 ${MPICH2_WIN64_DEVEL_MD5} + CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" + BUILD_BYPRODUCTS /lib/libmsmpi.a) + else() + message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI") + endif() + + ExternalProject_get_property(mpi4win_build SOURCE_DIR) + file(MAKE_DIRECTORY "${SOURCE_DIR}/include") + add_library(MPI::MPI_CXX UNKNOWN IMPORTED) + set_target_properties(MPI::MPI_CXX PROPERTIES + IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a" + INTERFACE_INCLUDE_DIRECTORIES "${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/libmsmpi.a") else() - ExternalProject_Add(mpi4win_build - URL ${MPICH2_WIN32_DEVEL_URL} - URL_MD5 ${MPICH2_WIN32_DEVEL_MD5} - CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" - BUILD_BYPRODUCTS /lib/libmpi.a) + message(STATUS "Downloading and configuring MPICH2-1.4.1 for Windows cross-compilation") + set(MPICH2_WIN64_DEVEL_URL "${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") 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") diff --git a/cmake/Modules/Packages/KOKKOS.cmake b/cmake/Modules/Packages/KOKKOS.cmake index 2117397494..9b795de3df 100644 --- a/cmake/Modules/Packages/KOKKOS.cmake +++ b/cmake/Modules/Packages/KOKKOS.cmake @@ -15,8 +15,9 @@ if(Kokkos_ENABLE_OPENMP) if(NOT BUILD_OMP) message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP") else() - if(LAMMPS_OMP_COMPAT_LEVEL LESS 4) - message(FATAL_ERROR "Compiler must support OpenMP 4.0 or later with Kokkos_ENABLE_OPENMP") + # NVHPC does not seem to provide a detectable OpenMP version, but is far beyond version 3.1 + if((OpenMP_CXX_VERSION VERSION_LESS 3.1) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC")) + message(FATAL_ERROR "Compiler must support OpenMP 3.1 or later with Kokkos_ENABLE_OPENMP") endif() endif() endif() @@ -123,7 +124,7 @@ set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp if(PKG_KSPACE) list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/fft3d_kokkos.cpp - ${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp + ${KOKKOS_PKG_SOURCES_DIR}/grid3d_kokkos.cpp ${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp) if(Kokkos_ENABLE_CUDA) if(NOT (FFT STREQUAL "KISS")) @@ -138,6 +139,12 @@ if(PKG_KSPACE) endif() endif() +if(PKG_ML-IAP) + list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/mliap_data_kokkos.cpp + ${KOKKOS_PKG_SOURCES_DIR}/mliap_descriptor_so3_kokkos.cpp + ${KOKKOS_PKG_SOURCES_DIR}/mliap_model_linear_kokkos.cpp + ${KOKKOS_PKG_SOURCES_DIR}/mliap_so3_kokkos.cpp) +endif() if(PKG_PHONON) list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/dynamical_matrix_kokkos.cpp) diff --git a/cmake/Modules/Packages/MC.cmake b/cmake/Modules/Packages/MC.cmake new file mode 100644 index 0000000000..f162254558 --- /dev/null +++ b/cmake/Modules/Packages/MC.cmake @@ -0,0 +1,9 @@ +# fix sgcmc may only be installed if also the EAM pair style from MANYBODY is installed +if(NOT PKG_MANYBODY) + get_property(LAMMPS_FIX_HEADERS GLOBAL PROPERTY FIX) + list(REMOVE_ITEM LAMMPS_FIX_HEADERS ${LAMMPS_SOURCE_DIR}/MC/fix_sgcmc.h) + set_property(GLOBAL PROPERTY FIX "${LAMMPS_FIX_HEADERS}") + get_target_property(LAMMPS_SOURCES lammps SOURCES) + list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MC/fix_sgcmc.cpp) + set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}") +endif() diff --git a/cmake/Modules/Packages/ML-IAP.cmake b/cmake/Modules/Packages/ML-IAP.cmake index 0e711cde8f..e2685c78dd 100644 --- a/cmake/Modules/Packages/ML-IAP.cmake +++ b/cmake/Modules/Packages/ML-IAP.cmake @@ -2,7 +2,13 @@ set(MLIAP_ENABLE_PYTHON_DEFAULT OFF) if(PKG_PYTHON) find_package(Cythonize QUIET) - if(Cythonize_FOUND) + if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14) + find_package(Python COMPONENTS NumPy QUIET) + else() + # assume we have NumPy + set(Python_NumPy_FOUND ON) + endif() + if(Cythonize_FOUND AND Python_NumPy_FOUND) set(MLIAP_ENABLE_PYTHON_DEFAULT ON) endif() endif() @@ -11,6 +17,9 @@ option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_EN if(MLIAP_ENABLE_PYTHON) find_package(Cythonize REQUIRED) + if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14) + find_package(Python COMPONENTS NumPy REQUIRED) + endif() if(NOT PKG_PYTHON) message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP") endif() diff --git a/cmake/Modules/Packages/ML-QUIP.cmake b/cmake/Modules/Packages/ML-QUIP.cmake index 56221accab..10e0f38b78 100644 --- a/cmake/Modules/Packages/ML-QUIP.cmake +++ b/cmake/Modules/Packages/ML-QUIP.cmake @@ -58,12 +58,12 @@ if(DOWNLOAD_QUIP) BUILD_COMMAND env QUIP_ARCH=lammps make libquip INSTALL_COMMAND "" BUILD_IN_SOURCE YES - BUILD_BYPRODUCTS /build/lammps/libquip.a + BUILD_BYPRODUCTS /build/lammps/${CMAKE_STATIC_LIBRARY_PREFIX}quip${CMAKE_STATIC_LIBRARY_SUFFIX} ) ExternalProject_get_property(quip_build SOURCE_DIR) add_library(LAMMPS::QUIP UNKNOWN IMPORTED) set_target_properties(LAMMPS::QUIP PROPERTIES - IMPORTED_LOCATION "${SOURCE_DIR}/build/lammps/libquip.a" + IMPORTED_LOCATION "${SOURCE_DIR}/build/lammps/${CMAKE_STATIC_LIBRARY_PREFIX}quip${CMAKE_STATIC_LIBRARY_SUFFIX}" INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}") target_link_libraries(lammps PRIVATE LAMMPS::QUIP) add_dependencies(LAMMPS::QUIP quip_build) diff --git a/cmake/Modules/Packages/PLUMED.cmake b/cmake/Modules/Packages/PLUMED.cmake index 1b660a2cc8..e0e4ff0dde 100644 --- a/cmake/Modules/Packages/PLUMED.cmake +++ b/cmake/Modules/Packages/PLUMED.cmake @@ -47,15 +47,15 @@ if(DOWNLOAD_PLUMED) endif() message(STATUS "PLUMED download requested - we will build our own") if(PLUMED_MODE STREQUAL "STATIC") - set(PLUMED_BUILD_BYPRODUCTS "/lib/libplumed.a") + set(PLUMED_BUILD_BYPRODUCTS "/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX}") elseif(PLUMED_MODE STREQUAL "SHARED") - set(PLUMED_BUILD_BYPRODUCTS "/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX};/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}") + set(PLUMED_BUILD_BYPRODUCTS "/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX};/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}") elseif(PLUMED_MODE STREQUAL "RUNTIME") - set(PLUMED_BUILD_BYPRODUCTS "/lib/libplumedWrapper.a") + set(PLUMED_BUILD_BYPRODUCTS "/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_PREFIX}") endif() - set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.4/plumed-src-2.7.4.tgz" CACHE STRING "URL for PLUMED tarball") - set(PLUMED_MD5 "858e0b6aed173748fc85b6bc8a9dcb3e" CACHE STRING "MD5 checksum of PLUMED tarball") + set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.1/plumed-src-2.8.1.tgz" CACHE STRING "URL for PLUMED tarball") + set(PLUMED_MD5 "6bfe72ebdae63dc38a9ca27d9b0e08f8" CACHE STRING "MD5 checksum of PLUMED tarball") mark_as_advanced(PLUMED_URL) mark_as_advanced(PLUMED_MD5) @@ -78,12 +78,12 @@ if(DOWNLOAD_PLUMED) add_library(LAMMPS::PLUMED UNKNOWN IMPORTED) add_dependencies(LAMMPS::PLUMED plumed_build) if(PLUMED_MODE STREQUAL "STATIC") - set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed.a INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}") + set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}") elseif(PLUMED_MODE STREQUAL "SHARED") - set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}") + set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}") elseif(PLUMED_MODE STREQUAL "RUNTIME") - set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}") - set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumedWrapper.a INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}") + set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}") + set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}") endif() set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include) file(MAKE_DIRECTORY ${INSTALL_DIR}/include) @@ -96,7 +96,7 @@ else() elseif(PLUMED_MODE STREQUAL "SHARED") include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared) elseif(PLUMED_MODE STREQUAL "RUNTIME") - set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}") + set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}") include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime) endif() set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}") diff --git a/cmake/Modules/Packages/VTK.cmake b/cmake/Modules/Packages/VTK.cmake index 8c4445167a..a0de1e0ff4 100644 --- a/cmake/Modules/Packages/VTK.cmake +++ b/cmake/Modules/Packages/VTK.cmake @@ -1,4 +1,9 @@ find_package(VTK REQUIRED NO_MODULE) -include(${VTK_USE_FILE}) target_compile_definitions(lammps PRIVATE -DLAMMPS_VTK) -target_link_libraries(lammps PRIVATE ${VTK_LIBRARIES}) +if (VTK_MAJOR_VERSION VERSION_LESS 9.0) + include(${VTK_USE_FILE}) + target_link_libraries(lammps PRIVATE ${VTK_LIBRARIES}) +else() + target_link_libraries(lammps PRIVATE VTK::CommonCore VTK::IOCore VTK::CommonDataModel VTK::IOXML VTK::IOLegacy VTK::IOParallelXML) + vtk_module_autoinit(TARGETS lammps MODULES VTK::CommonCore VTK::IOCore VTK::CommonDataModel VTK::IOXML VTK::IOLegacy VTK::IOParallelXML) +endif() diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index 3a7c58eaa3..9127305528 100644 --- a/cmake/presets/all_off.cmake +++ b/cmake/presets/all_off.cmake @@ -56,6 +56,7 @@ set(ALL_PACKAGES ML-HDNNP ML-IAP ML-PACE + ML-POD ML-QUIP ML-RANN ML-SNAP diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index 8229baf652..0a001bdc56 100644 --- a/cmake/presets/all_on.cmake +++ b/cmake/presets/all_on.cmake @@ -58,6 +58,7 @@ set(ALL_PACKAGES ML-HDNNP ML-IAP ML-PACE + ML-POD ML-QUIP ML-RANN ML-SNAP diff --git a/cmake/presets/clang.cmake b/cmake/presets/clang.cmake index f1964f3e0f..fce451d803 100644 --- a/cmake/presets/clang.cmake +++ b/cmake/presets/clang.cmake @@ -28,10 +28,3 @@ set(MPI_CXX "clang++" CACHE STRING "" FORCE) set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE) unset(HAVE_OMP_H_INCLUDE CACHE) -set(OpenMP_C "clang" CACHE STRING "" FORCE) -set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE) -set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE) -set(OpenMP_CXX "clang++" CACHE STRING "" FORCE) -set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE) -set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE) -set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE) diff --git a/cmake/presets/gcc.cmake b/cmake/presets/gcc.cmake index cb626ea019..42cd30d149 100644 --- a/cmake/presets/gcc.cmake +++ b/cmake/presets/gcc.cmake @@ -19,11 +19,3 @@ set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Og -g -std=f2003" CACHE STRING "" FORCE) set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE) set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE) unset(HAVE_OMP_H_INCLUDE CACHE) - -set(OpenMP_C "gcc" CACHE STRING "" FORCE) -set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE) -set(OpenMP_C_LIB_NAMES "gomp" CACHE STRING "" FORCE) -set(OpenMP_CXX "g++" CACHE STRING "" FORCE) -set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE) -set(OpenMP_CXX_LIB_NAMES "gomp" CACHE STRING "" FORCE) -set(OpenMP_omp_LIBRARY "libgomp.so" CACHE PATH "" FORCE) diff --git a/cmake/presets/mingw-cross.cmake b/cmake/presets/mingw-cross.cmake index c5d9a7bb89..2d74657394 100644 --- a/cmake/presets/mingw-cross.cmake +++ b/cmake/presets/mingw-cross.cmake @@ -47,6 +47,7 @@ set(WIN_PACKAGES MISC ML-HDNNP ML-IAP + ML-POD ML-RANN ML-SNAP MOFFF diff --git a/cmake/presets/most.cmake b/cmake/presets/most.cmake index 4b26a51e23..5dd9a2b78b 100644 --- a/cmake/presets/most.cmake +++ b/cmake/presets/most.cmake @@ -41,6 +41,7 @@ set(ALL_PACKAGES MEAM MISC ML-IAP + ML-POD ML-SNAP MOFFF MOLECULE diff --git a/cmake/presets/nvhpc.cmake b/cmake/presets/nvhpc.cmake new file mode 100644 index 0000000000..cfacce17ad --- /dev/null +++ b/cmake/presets/nvhpc.cmake @@ -0,0 +1,9 @@ +# preset that will enable Nvidia HPC SDK compilers with support for MPI and OpenMP (on Linux boxes) + +set(CMAKE_CXX_COMPILER "nvc++" CACHE STRING "" FORCE) +set(CMAKE_C_COMPILER "nvc" CACHE STRING "" FORCE) +set(CMAKE_Fortran_COMPILER "nvfortran" CACHE STRING "" FORCE) +set(MPI_CXX "nvc++" CACHE STRING "" FORCE) +set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE) +unset(HAVE_OMP_H_INCLUDE CACHE) + diff --git a/cmake/presets/pedantic.cmake b/cmake/presets/pedantic.cmake index 11c74dbaa4..9bc0d036dd 100644 --- a/cmake/presets/pedantic.cmake +++ b/cmake/presets/pedantic.cmake @@ -1,4 +1,4 @@ -# preset that will restore gcc/g++ with support for MPI and OpenMP (on Linux boxes) +# preset that will set gcc/g++ with extra warnings enabled and support for MPI and OpenMP (on Linux boxes) set(CMAKE_CXX_COMPILER "g++" CACHE STRING "" FORCE) set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE) @@ -17,10 +17,3 @@ set(MPI_Fortran "gfortran" CACHE STRING "" FORCE) set(MPI_Fortran_COMPILER "mpifort" CACHE STRING "" FORCE) unset(HAVE_OMP_H_INCLUDE CACHE) -set(OpenMP_C "gcc" CACHE STRING "" FORCE) -set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE) -set(OpenMP_C_LIB_NAMES "gomp" CACHE STRING "" FORCE) -set(OpenMP_CXX "g++" CACHE STRING "" FORCE) -set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE) -set(OpenMP_CXX_LIB_NAMES "gomp" CACHE STRING "" FORCE) -set(OpenMP_omp_LIBRARY "libgomp.so" CACHE PATH "" FORCE) diff --git a/cmake/presets/pgi.cmake b/cmake/presets/pgi.cmake index 2b7fee7efa..4d499a2429 100644 --- a/cmake/presets/pgi.cmake +++ b/cmake/presets/pgi.cmake @@ -7,10 +7,3 @@ set(MPI_CXX "pgc++" CACHE STRING "" FORCE) set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE) unset(HAVE_OMP_H_INCLUDE CACHE) -set(OpenMP_C "pgcc" CACHE STRING "" FORCE) -set(OpenMP_C_FLAGS "-mp" CACHE STRING "" FORCE) -set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE) -set(OpenMP_CXX "pgc++" CACHE STRING "" FORCE) -set(OpenMP_CXX_FLAGS "-mp" CACHE STRING "" FORCE) -set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE) -set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE) diff --git a/doc/Makefile b/doc/Makefile index 4bbc252fb6..faf10f5f7f 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -38,16 +38,14 @@ endif # override settings for PIP commands # PIP_OPTIONS = --cert /etc/pki/ca-trust/extracted/openssl/ca-bundle.trust.crt --proxy http://proxy.mydomain.org -#SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())') $(shell test -f $(BUILDDIR)/doxygen/xml/run.stamp && printf -- "-E") - # temporarily disable caching so that the hack for the sphinx-tabs extensions to get proper non-html output works -SPHINXEXTRA = -E -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())') +SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())') # grab list of sources from doxygen config file. # we only want to use explicitly listed files. DOXYFILES = $(shell sed -n -e 's/\#.*$$//' -e '/^ *INPUT \+=/,/^[A-Z_]\+ \+=/p' doxygen/Doxyfile.in | sed -e 's/@LAMMPS_SOURCE_DIR@/..\/src/g' -e 's/\\//g' -e 's/ \+/ /' -e 's/[A-Z_]\+ \+= *\(YES\|NO\|\)//') -.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check char_check xmlgen fasthtml +.PHONY: help clean-all clean clean-spelling epub mobi html pdf spelling anchor_check style_check char_check role_check xmlgen fasthtml # ------------------------------------------ @@ -89,6 +87,8 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX) @$(MAKE) $(MFLAGS) -C graphviz all @(\ . $(VENV)/bin/activate ; env PYTHONWARNINGS= \ + sphinx-build -E $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\ + touch $(RSTDIR)/Fortran.rst ;\ sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\ ln -sf Manual.html html/index.html;\ rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\ @@ -96,6 +96,7 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX) rst_anchor_check src/*.rst ;\ python $(BUILDDIR)/utils/check-packages.py -s ../src -d src ;\ env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\ + env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\ python $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\ echo "############################################" ;\ deactivate ;\ @@ -114,7 +115,9 @@ fasthtml: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX) @mkdir -p fasthtml @(\ . $(VENV)/bin/activate ; env PYTHONWARNINGS= \ - sphinx-build -j 4 -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\ + sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\ + touch $(RSTDIR)/Fortran.rst ;\ + sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\ deactivate ;\ ) @rm -rf fasthtml/_sources @@ -144,6 +147,8 @@ epub: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) @cp src/JPG/*.* epub/JPG @(\ . $(VENV)/bin/activate ;\ + sphinx-build -E $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\ + touch $(RSTDIR)/Fortran.rst ;\ sphinx-build $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\ rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\ deactivate ;\ @@ -163,12 +168,15 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) @if [ "$(HAS_PDFLATEX)" == "NO" ] ; then echo "PDFLaTeX or latexmk were not found! Please check README for further instructions" 1>&2; exit 1; fi @(\ . $(VENV)/bin/activate ; env PYTHONWARNINGS= \ - sphinx-build $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\ + sphinx-build -E $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\ + touch $(RSTDIR)/Fortran.rst ;\ + sphinx-build $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\ rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\ echo "############################################" ;\ rst_anchor_check src/*.rst ;\ python utils/check-packages.py -s ../src -d src ;\ env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\ + env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\ python utils/check-styles.py -s ../src -d src ;\ echo "############################################" ;\ deactivate ;\ @@ -214,6 +222,9 @@ package_check : $(VENV) char_check : @( env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst && exit 1 || : ) +role_check : + @( env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst && exit 1 || : ) + xmlgen : doxygen/xml/index.xml doxygen/Doxyfile: doxygen/Doxyfile.in diff --git a/doc/lammps.1 b/doc/lammps.1 index e4f0f2a9eb..ed0eecddd0 100644 --- a/doc/lammps.1 +++ b/doc/lammps.1 @@ -1,7 +1,7 @@ -.TH LAMMPS "1" "15 September 2022" "2022-9-15" +.TH LAMMPS "1" "22 December 2022" "2022-12-22" .SH NAME .B LAMMPS -\- Molecular Dynamics Simulator. Version 15 September 2022 +\- Molecular Dynamics Simulator. Version 22 December 2022 .SH SYNOPSIS .B lmp diff --git a/doc/src/Build_development.rst b/doc/src/Build_development.rst index 1644c7ea86..102ec67e7e 100644 --- a/doc/src/Build_development.rst +++ b/doc/src/Build_development.rst @@ -147,6 +147,16 @@ compile and will download and compile a specific recent version of the `Googletest `_ C++ test framework for implementing the tests. +.. admonition:: Software version requirements for testing + :class: note + + The compiler and library version requirements for the testing + framework are more strict than for the main part of LAMMPS. For + example the default GNU C++ and Fortran compilers of RHEL/CentOS 7.x + (version 4.8.x) are not sufficient. The CMake configuration will try + to detect compatible versions and either skip incompatible tests or + stop with an error. + After compilation is complete, the unit testing is started in the build folder using the ``ctest`` command, which is part of the CMake software. The output of this command will be looking something like this:: diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index c15af87dc6..910dccbb8a 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -36,6 +36,7 @@ This is the list of packages that may require additional steps. * :ref:`AWPMD ` * :ref:`COLVARS ` * :ref:`COMPRESS ` + * :ref:`ELECTRODE ` * :ref:`GPU ` * :ref:`H5MD ` * :ref:`INTEL ` @@ -48,6 +49,7 @@ This is the list of packages that may require additional steps. * :ref:`ML-HDNNP ` * :ref:`ML-IAP ` * :ref:`ML-PACE ` + * :ref:`ML-POD ` * :ref:`ML-QUIP ` * :ref:`MOLFILE ` * :ref:`MSCG ` @@ -234,7 +236,7 @@ LAMMPS code. This also applies to the ``-DLAMMPS_BIGBIG``\ , Makefile you use. You can also build the library in one step from the ``lammps/src`` dir, -using a command like these, which simply invoke the ``lib/gpu/Install.py`` +using a command like these, which simply invokes the ``lib/gpu/Install.py`` script with the specified args: .. code-block:: bash @@ -350,7 +352,7 @@ minutes to hours) to build. Of course you only need to do that once.) You can download and build the KIM library manually if you prefer; follow the instructions in ``lib/kim/README``. You can also do this in one step from the lammps/src directory, using a command like - these, which simply invoke the ``lib/kim/Install.py`` script with + these, which simply invokes the ``lib/kim/Install.py`` script with the specified args. .. code-block:: bash @@ -954,7 +956,7 @@ more details. You can download and build the MS-CG library manually if you prefer; follow the instructions in ``lib/mscg/README``\ . You can also do it in one step from the ``lammps/src`` dir, using a - command like these, which simply invoke the + command like these, which simply invokes the ``lib/mscg/Install.py`` script with the specified args: .. code-block:: bash @@ -1011,7 +1013,7 @@ POEMS package ``lib/poems``\ . You can do this manually if you prefer; follow the instructions in ``lib/poems/README``\ . You can also do it in one step from the ``lammps/src`` dir, using a command like these, - which simply invoke the ``lib/poems/Install.py`` script with the + which simply invokes the ``lib/poems/Install.py`` script with the specified args: .. code-block:: bash @@ -1100,7 +1102,7 @@ binary package provided by your operating system. You can download and build the Voro++ library manually if you prefer; follow the instructions in ``lib/voronoi/README``. You can also do it in one step from the ``lammps/src`` dir, using a - command like these, which simply invoke the + command like these, which simply invokes the ``lib/voronoi/Install.py`` script with the specified args: .. code-block:: bash @@ -1179,7 +1181,7 @@ The ATC package requires the MANYBODY package also be installed. ``lib/atc``. You can do this manually if you prefer; follow the instructions in ``lib/atc/README``. You can also do it in one step from the ``lammps/src`` dir, using a command like these, - which simply invoke the ``lib/atc/Install.py`` script with the + which simply invokes the ``lib/atc/Install.py`` script with the specified args: .. code-block:: bash @@ -1230,7 +1232,7 @@ AWPMD package ``lib/awpmd``. You can do this manually if you prefer; follow the instructions in ``lib/awpmd/README``. You can also do it in one step from the ``lammps/src`` dir, using a command like these, - which simply invoke the ``lib/awpmd/Install.py`` script with the + which simply invokes the ``lib/awpmd/Install.py`` script with the specified args: .. code-block:: bash @@ -1293,7 +1295,7 @@ be built for the most part with all major versions of the C++ language. In general, it is safer to use build setting consistent with the rest of LAMMPS. This is best carried out from the LAMMPS src - directory using a command like these, which simply invoke the + directory using a command like these, which simply invokes the ``lib/colvars/Install.py`` script with the specified args: .. code-block:: bash @@ -1334,20 +1336,30 @@ This package depends on the KSPACE package. .. tab:: CMake build - No additional settings are needed besides ``-D PKG_KSPACE=yes`` and ``-D - PKG_ELECTRODE=yes``. + No additional settings are needed besides ``-D PKG_KSPACE=yes`` and + ``-D PKG_ELECTRODE=yes``. .. tab:: Traditional make - The package is activated with ``make yes-KSPACE`` and ``make - yes-ELECTRODE`` + Before building LAMMPS, you must configure the ELECTRODE support + libraries and settings in ``lib/electrode``. You can do this + manually, if you prefer, or do it in one step from the + ``lammps/src`` dir, using a command like these, which simply + invokes the ``lib/electrode/Install.py`` script with the specified + args: + + .. code-block:: bash + + $ make lib-electrode # print help message + $ make lib-electrode args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial") + $ make lib-electrode args="-m mpi" # build with default MPI compiler (settings as with "make mpi") - Note that the ``Makefile.lammps`` file has settings for the BLAS and - LAPACK linear algebra libraries. As explained in ``lib/awpmd/README`` - these can either exist on your system, or you can use the files provided - in ``lib/linalg``. In the latter case you also need to build the library - in ``lib/linalg`` with a command like these: + Note that the ``Makefile.lammps`` file has settings for the BLAS + and LAPACK linear algebra libraries. These can either exist on + your system, or you can use the files provided in ``lib/linalg``. + In the latter case you also need to build the library in + ``lib/linalg`` with a command like these: .. code-block:: bash @@ -1356,6 +1368,9 @@ This package depends on the KSPACE package. $ make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi") $ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler + The package itself is activated with ``make yes-KSPACE`` and + ``make yes-ELECTRODE`` + ---------- .. _ml-pace: @@ -1398,6 +1413,49 @@ at: `https://github.com/ICAMS/lammps-user-pace/ ` * :doc:`bond_write ` * :doc:`boundary ` - * :doc:`box ` * :doc:`change_box ` * :doc:`clear ` * :doc:`comm_modify ` @@ -90,8 +89,7 @@ table above. * :doc:`region ` * :doc:`replicate ` * :doc:`rerun ` - * :doc:`reset_atom_ids ` - * :doc:`reset_mol_ids ` + * :doc:`reset_atoms ` * :doc:`reset_timestep ` * :doc:`restart ` * :doc:`run ` @@ -127,6 +125,7 @@ additional letter in parenthesis: k = KOKKOS. * :doc:`group2ndx ` * :doc:`hyper ` * :doc:`kim ` + * :doc:`fitpod ` * :doc:`mdi ` * :doc:`ndx2group ` * :doc:`neb ` diff --git a/doc/src/Commands_category.rst b/doc/src/Commands_category.rst index 4a08d040b7..7ac747e8fc 100644 --- a/doc/src/Commands_category.rst +++ b/doc/src/Commands_category.rst @@ -25,7 +25,6 @@ Setup simulation box: :columns: 4 * :doc:`boundary ` - * :doc:`box ` * :doc:`change_box ` * :doc:`create_box ` * :doc:`dimension ` diff --git a/doc/src/Commands_compute.rst b/doc/src/Commands_compute.rst index 682a75f201..a1cfb662c8 100644 --- a/doc/src/Commands_compute.rst +++ b/doc/src/Commands_compute.rst @@ -107,6 +107,7 @@ KOKKOS, o = OPENMP, t = OPT. * :doc:`pressure/uef ` * :doc:`property/atom ` * :doc:`property/chunk ` + * :doc:`property/grid ` * :doc:`property/local ` * :doc:`ptm/atom ` * :doc:`rdf ` diff --git a/doc/src/Commands_dump.rst b/doc/src/Commands_dump.rst index 12dd7b2321..870cb168ef 100644 --- a/doc/src/Commands_dump.rst +++ b/doc/src/Commands_dump.rst @@ -36,7 +36,8 @@ An alphabetic list of all LAMMPS :doc:`dump ` commands. * :doc:`custom/mpiio ` * :doc:`custom/zstd ` * :doc:`dcd ` - * :doc:`deprecated ` + * :doc:`grid ` + * :doc:`grid/vtk ` * :doc:`h5md ` * :doc:`image ` * :doc:`local ` diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst index c5c2fb7cba..3307f887ae 100644 --- a/doc/src/Commands_fix.rst +++ b/doc/src/Commands_fix.rst @@ -38,6 +38,7 @@ OPT. * :doc:`ave/chunk ` * :doc:`ave/correlate ` * :doc:`ave/correlate/long ` + * :doc:`ave/grid ` * :doc:`ave/histo ` * :doc:`ave/histo/weight ` * :doc:`ave/time ` @@ -65,13 +66,13 @@ OPT. * :doc:`drude ` * :doc:`drude/transform/direct ` * :doc:`drude/transform/inverse ` - * :doc:`dt/reset ` + * :doc:`dt/reset (k) ` * :doc:`edpd/source ` * :doc:`efield ` * :doc:`ehex ` - * :doc:`electrode/conp (i) ` - * :doc:`electrode/conq (i) ` - * :doc:`electrode/thermo (i) ` + * :doc:`electrode/conp (i) ` + * :doc:`electrode/conq (i) ` + * :doc:`electrode/thermo (i) ` * :doc:`electron/stopping ` * :doc:`electron/stopping/fit ` * :doc:`enforce2d (k) ` @@ -213,6 +214,7 @@ OPT. * :doc:`saed/vtk ` * :doc:`setforce (k) ` * :doc:`setforce/spin ` + * :doc:`sgcmc ` * :doc:`shake (k) ` * :doc:`shardlow (k) ` * :doc:`smd ` @@ -249,7 +251,7 @@ OPT. * :doc:`tune/kspace ` * :doc:`vector ` * :doc:`viscosity ` - * :doc:`viscous ` + * :doc:`viscous (k) ` * :doc:`viscous/sphere ` * :doc:`wall/body/polygon ` * :doc:`wall/body/polyhedron ` diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index e800df613a..c6d54f0683 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -93,8 +93,8 @@ OPT. * :doc:`coul/wolf/cs ` * :doc:`dpd (giko) ` * :doc:`dpd/fdt ` - * :doc:`dpd/ext (k) ` - * :doc:`dpd/ext/tstat (k) ` + * :doc:`dpd/ext (ko) ` + * :doc:`dpd/ext/tstat (ko) ` * :doc:`dpd/fdt/energy (k) ` * :doc:`dpd/tstat (gko) ` * :doc:`dsmc ` @@ -205,7 +205,7 @@ OPT. * :doc:`mesont/tpm ` * :doc:`mgpt ` * :doc:`mie/cut (g) ` - * :doc:`mliap ` + * :doc:`mliap (k) ` * :doc:`mm3/switch3/coulgauss/long ` * :doc:`momb ` * :doc:`morse (gkot) ` @@ -237,6 +237,7 @@ OPT. * :doc:`oxrna2/coaxstk ` * :doc:`pace (k) ` * :doc:`pace/extrapolation ` + * :doc:`pod ` * :doc:`peri/eps ` * :doc:`peri/lps (o) ` * :doc:`peri/pmb (o) ` @@ -295,6 +296,7 @@ OPT. * :doc:`vashishta (gko) ` * :doc:`vashishta/table (o) ` * :doc:`wf/cut ` + * :doc:`ylz ` * :doc:`yukawa (gko) ` * :doc:`yukawa/colloid (go) ` * :doc:`zbl (gko) ` diff --git a/doc/src/Commands_removed.rst b/doc/src/Commands_removed.rst index 1000d11e29..942aed12b8 100644 --- a/doc/src/Commands_removed.rst +++ b/doc/src/Commands_removed.rst @@ -2,14 +2,17 @@ Removed commands and packages ============================= This page lists LAMMPS commands and packages that have been removed from -the distribution and provides suggestions for alternatives or replacements. -LAMMPS has special dummy styles implemented, that will stop LAMMPS and -print a suitable error message in most cases, when a style/command is used -that has been removed. +the distribution and provides suggestions for alternatives or +replacements. LAMMPS has special dummy styles implemented, that will +stop LAMMPS and print a suitable error message in most cases, when a +style/command is used that has been removed or will replace the command +with the direct alternative (if available) and print a warning. Fix ave/spatial and fix ave/spatial/sphere ------------------------------------------ +.. deprecated:: 11Dec2015 + The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS since they were superseded by the more general and extensible "chunk infrastructure". Here the system is partitioned in one of many possible @@ -17,10 +20,23 @@ ways through the :doc:`compute chunk/atom ` command and then averaging is done using :doc:`fix ave/chunk `. Please refer to the :doc:`chunk HOWTO ` section for an overview. -Reset_ids command ------------------ +Box command +----------- -The reset_ids command has been renamed to :doc:`reset_atom_ids `. +.. deprecated:: 22Dec2022 + +The *box* command has been removed and the LAMMPS code changed so it won't +be needed. If present, LAMMPS will ignore the command and print a warning. + +Reset_ids, reset_atom_ids, reset_mol_ids commands +------------------------------------------------- + +.. deprecated:: 22Dec2022 + +The *reset_ids*, *reset_atom_ids*, and *reset_mol_ids* commands have +been folded into the :doc:`reset_atoms ` command. If +present, LAMMPS will replace the commands accordingly and print a +warning. MEAM package ------------ @@ -30,18 +46,21 @@ The code in the :ref:`MEAM package ` is a translation of the Fortran code of MEAM into C++, which removes several restrictions (e.g. there can be multiple instances in hybrid pair styles) and allows for some optimizations leading to better performance. The pair style -:doc:`meam ` has the exact same syntax. +:doc:`meam ` has the exact same syntax. For a transition +period the C++ version of MEAM was called USER-MEAMC so it could +coexist with the Fortran version. REAX package ------------ The REAX package has been removed since it was superseded by the -:ref:`REAXFF package `. The REAXFF -package has been tested to yield equivalent results to the REAX package, -offers better performance, supports OpenMP multi-threading via OPENMP, -and GPU and threading parallelization through KOKKOS. The new pair styles -are not syntax compatible with the removed reax pair style, so input -files will have to be adapted. +:ref:`REAXFF package `. The REAXFF package has been tested +to yield equivalent results to the REAX package, offers better +performance, supports OpenMP multi-threading via OPENMP, and GPU and +threading parallelization through KOKKOS. The new pair styles are not +syntax compatible with the removed reax pair style, so input files will +have to be adapted. The REAXFF package was originally called +USER-REAXC. USER-CUDA package ----------------- @@ -60,5 +79,6 @@ restart2data tool The functionality of the restart2data tool has been folded into the LAMMPS executable directly instead of having a separate tool. A combination of the commands :doc:`read_restart ` and -:doc:`write_data ` can be used to the same effect. For added -convenience this conversion can also be triggered by :doc:`command line flags ` +:doc:`write_data ` can be used to the same effect. For +added convenience this conversion can also be triggered by +:doc:`command line flags ` diff --git a/doc/src/Developer.rst b/doc/src/Developer.rst index dc3fac94ce..406dd26f59 100644 --- a/doc/src/Developer.rst +++ b/doc/src/Developer.rst @@ -23,3 +23,4 @@ of time and requests from the LAMMPS user community. Classes Developer_platform Developer_utils + Developer_grid diff --git a/doc/src/Developer_code_design.rst b/doc/src/Developer_code_design.rst index 820ad47fba..786bd51c26 100644 --- a/doc/src/Developer_code_design.rst +++ b/doc/src/Developer_code_design.rst @@ -50,7 +50,7 @@ parallel each MPI process creates such an instance. This can be seen in the ``main.cpp`` file where the core steps of running a LAMMPS simulation are the following 3 lines of code: -.. code-block:: C++ +.. code-block:: c++ LAMMPS *lammps = new LAMMPS(argc, argv, lammps_comm); lammps->input->file(); @@ -78,7 +78,7 @@ LAMMPS makes extensive use of the object oriented programming (OOP) principles of *compositing* and *inheritance*. Classes like the ``LAMMPS`` class are a **composite** containing pointers to instances of other classes like ``Atom``, ``Comm``, ``Force``, ``Neighbor``, -``Modify``, and so on. Each of these classes implement certain +``Modify``, and so on. Each of these classes implements certain functionality by storing and manipulating data related to the simulation and providing member functions that trigger certain actions. Some of those classes like ``Force`` are themselves @@ -87,9 +87,9 @@ interactions. Similarly the ``Modify`` class contains a list of ``Fix`` and ``Compute`` classes. If the input commands that correspond to these classes include the word *style*, then LAMMPS stores only a single instance of that class. E.g. *atom_style*, -*comm_style*, *pair_style*, *bond_style*. It the input command does -not include the word *style*, there can be many instances of that -class defined. E.g. *region*, *fix*, *compute*, *dump*. +*comm_style*, *pair_style*, *bond_style*. If the input command does +**not** include the word *style*, then there may be many instances of +that class defined, for example *region*, *fix*, *compute*, *dump*. **Inheritance** enables creation of *derived* classes that can share common functionality in their base class while providing a consistent @@ -232,7 +232,7 @@ macro ``PairStyle()`` will associate the style name "lj/cut" with a factory function creating an instance of the ``PairLJCut`` class. -.. code-block:: C++ +.. code-block:: c++ // from force.h typedef Pair *(*PairCreator)(LAMMPS *); @@ -360,7 +360,7 @@ characters; "{:<8}" would do this as left aligned, "{:^8}" as centered, argument type must be compatible or else the {fmt} formatting code will throw an exception. Some format string examples are given below: -.. code-block:: C +.. code-block:: c++ auto mesg = fmt::format(" CPU time: {:4d}:{:02d}:{:02d}\n", cpuh, cpum, cpus); mesg = fmt::format("{:<8s}| {:<10.5g} | {:<10.5g} | {:<10.5g} |{:6.1f} |{:6.2f}\n", diff --git a/doc/src/Developer_grid.rst b/doc/src/Developer_grid.rst new file mode 100644 index 0000000000..f60a688c5b --- /dev/null +++ b/doc/src/Developer_grid.rst @@ -0,0 +1,846 @@ +Use of distributed grids within style classes +--------------------------------------------- + +.. versionadded:: 22Dec2022 + +The LAMMPS source code includes two classes which facilitate the +creation and use of distributed grids. These are the Grid2d and +Grid3d classes in the src/grid2d.cpp.h and src/grid3d.cpp.h files +respectively. As the names imply, they are used for 2d or 3d +simulations, as defined by the :doc:`dimension ` command. + +The :doc:`Howto_grid ` page gives an overview of how +distributed grids are defined from a user perspective, lists LAMMPS +commands which use them, and explains how grid cell data is referenced +from an input script. Please read that page first as it motivates the +coding details discussed here. + +This doc page is for users who wish to write new styles (input script +commands) which use distributed grids. There are a variety of +material models and analysis methods which use atoms (or +coarse-grained particles) and grids in tandem. + +A *distributed* grid means each processor owns a subset of the grid +cells. In LAMMPS, the subset for each processor will be a sub-block +of grid cells with low and high index bounds in each dimension of the +grid. The union of the sub-blocks across all processors is the global +grid. + +More specifically, a grid point is defined for each cell (by default +the center point), and a processor owns a grid cell if its point is +within the processor's spatial sub-domain. The union of processor +sub-domains is the global simulation box. If a grid point is on the +boundary of two sub-domains, the lower processor owns the grid cell. A +processor may also store copies of ghost cells which surround its +owned cells. + +---------- + +Style commands +^^^^^^^^^^^^^^ + +Style commands which can define and use distributed grids include the +:doc:`compute `, :doc:`fix `, :doc:`pair `, +and :doc:`kspace ` styles. If you wish grid cell data +to persist across timesteps, then use a fix. If you wish grid cell +data to be accessible by other commands, then use a fix or compute. +Currently in LAMMPS, the :doc:`pair_style amoeba `, +:doc:`kspace_style pppm `, and :doc:`kspace_style msm +` commands use distributed grids but do not require +either of these capabilities; they thus create and use distributed +grids internally. Note that a pair style which needs grid cell data +to persist could be coded to work in tandem with a fix style which +provides that capability. + +The *size* of a grid is specified by the number of grid cells in each +dimension of the simulation domain. In any dimension the size can be +any value >= 1. Thus a 10x10x1 grid for a 3d simulation is +effectively a 2d grid, where each grid cell spans the entire +z-dimension. A 1x100x1 grid for a 3d simulation is effectively a 1d +grid, where grid cells are a series of thin xz slabs in the +y-dimension. It is even possible to define a 1x1x1 3d grid, though it +may be inefficient to use it in a computational sense. + +Note that the choice of grid size is independent of the number of +processors or their layout in a grid of processor sub-domains which +overlays the simulations domain. Depending on the distributed grid +size, a single processor may own many 1000s or no grid cells. + +A command can define multiple grids, each of a different size. Each +grid is an instantiation of the Grid2d or Grid3d class. + +The command also defines what data it will store for each grid it +creates and it allocates the multi-dimensional array(s) needed to +store the data. No grid cell data is stored within the Grid2d or +Grid3d classes. + +If a single value per grid cell is needed, the data array will have +the same dimension as the grid, i.e. a 2d array for a 2d grid, +likewise for 3d. If multiple values per grid cell are needed, the +data array will have one more dimension than the grid, i.e. a 3d array +for a 2d grid, or 4d array for a 3d grid. A command can choose to +define multiple data arrays for each grid it defines. + +---------- + +Grid data allocation and access +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +The simplest way for a command to allocate and access grid cell data +is to use the *create_offset()* methods provided by the Memory class. +Arguments for these methods can be values returned by the +*setup_grid()* method (described below), which define the extent of +the grid cells (owned+ghost) the processor owns. These 4 methods +allocate memory for 2d (first two) and 3d (second two) grid data. The +two methods that end in "_one" allocate an array which stores a single +value per grid cell. The two that end in "_multi" allocate an array +which stores *Nvalues* per grid cell. + +.. code-block:: c++ + + // single value per cell for a 2d grid = 2d array + memory->create2d_offset(data2d_one, nylo_out, nyhi_out, + nxlo_out, nxhi_out, "data2d_one"); + + // nvalues per cell for a 2d grid = 3d array + memory->create3d_offset_last(data2d_multi, nylo_out, nyhi_out, + nxlo_out, nxhi_out, nvalues, "data2d_multi"); + + // single value per cell for a 3d grid = 3d array + memory->create3d_offset(data3d_one, nzlo_out, nzhi_out, nylo_out, + nyhi_out, nxlo_out, nxhi_out, "data3d_one"); + + // nvalues per cell for a 3d grid = 4d array + memory->create4d_offset_last(data3d_multi, nzlo_out, nzhi_out, nylo_out, + nyhi_out, nxlo_out, nxhi_out, nvalues, + "data3d_multi"); + +Note that these multi-dimensional arrays are allocated as contiguous +chunks of memory where the x-index of the grid varies fastest, then y, +and the z-index slowest. For multiple values per grid cell, the +Nvalues are contiguous, so their index varies even faster than the +x-index. + +The key point is that the "offset" methods create arrays which are +indexed by the range of indices which are the bounds of the sub-block +of the global grid owned by this processor. This means loops like +these can be written in the caller code to loop over owned grid cells, +where the "i" loop bounds are the range of owned grid cells for the +processor. These are the bounds returned by the *setup_grid()* +method: + +.. code-block:: c++ + + for (int iy = iylo; iy <= iyhi; iy++) + for (int ix = ixlo; ix <= ixhi; ix++) + data2d_one[iy][ix] = 0.0; + + for (int iy = iylo; iy <= iyhi; iy++) + for (int ix = ixlo; ix <= ixhi; ix++) + for (int m = 0; m < nvalues; m++) + data2d_multi[iy][ix][m] = 0.0; + + for (int iz = izlo; iz <= izhi; iz++) + for (int iy = iylo; iy <= iyhi; iy++) + for (int ix = ixlo; ix <= ixhi; ix++) + data3d_one[iz][iy][ix] = 0.0; + + for (int iz = izlo; iz <= izhi; iz++) + for (int iy = iylo; iy <= iyhi; iy++) + for (int ix = ixlo; ix <= ixhi; ix++) + for (int m = 0; m < nvalues; m++) + data3d_multi[iz][iy][ix][m] = 0.0; + +Simply replacing the "i" bounds with "o" bounds, also returned by the +*setup_grid()* method, would alter this code to loop over owned+ghost +cells (the entire allocated grid). + +---------- + +Grid class constructors +^^^^^^^^^^^^^^^^^^^^^^^ + +The following sub-sections describe the public methods of the Grid3d +class which a style command can invoke. The Grid2d methods are +similar; simply remove arguments which refer to the z-dimension. + +There are 2 constructors which can be used. They differ in the extra +i/o xyz lo/hi arguments: + +.. code-block:: c++ + + Grid3d(class LAMMPS *lmp, MPI_Comm gcomm, int gnx, int gny, int gnz) + Grid3d(class LAMMPS *lmp, MPI_Comm gcomm, int gnx, int gny, int gnz, + int ixlo, int ixhi, int iylo, int iyhi, int izlo, int izhi, + int oxlo, int oxhi, int oylo, int oyhi, int ozlo, int ozhi) + +Both constructors take the LAMMPS instance pointer and a communicator +over which the grid will be distributed. Typically this is the +*world* communicator the LAMMPS instance is using. The +:doc:`kspace_style msm ` command creates a series of +grids, each of different size, which are partitioned across different +sub-communicators of processors. Both constructors are also passed +the global grid size: *gnx* by *gny* by *gnz*. + +The first constructor is used when the caller wants the Grid class to +partition the global grid across processors; the Grid class defines +which grid cells each processor owns and also which it stores as ghost +cells. A subsequent call to *setup_grid()*, discussed below, returns +this info to the caller. + +The second constructor allows the caller to define the extent of owned +and ghost cells, and pass them to the Grid class. The 6 arguments +which start with "i" are the inclusive lower and upper index bounds of +the owned (inner) grid cells this processor owns in each of the 3 +dimensions within the global grid. Owned grid cells are indexed from +0 to N-1 in each dimension. + +The 6 arguments which start with "o" are the inclusive bounds of the +owned+ghost (outer) grid cells it stores. If the ghost cells are on +the other side of a periodic boundary, then these indices may be < 0 +or >= N in any dimension, so that oxlo <= ixlo and ixhi >= ixhi is +always the case. + +For example, if Nx = 100, then a processor might pass ixlo=50, +ixhi=60, oxlo=48, oxhi=62 to the Grid class. Or ixlo=0, ixhi=10, +oxlo=-2, oxhi=13. If a processor owns no grid cells in a dimension, +then the ihi value should be specified as one less than the ilo value. + +Note that the only reason to use the second constructor is if the +logic for assigning ghost cells is too complex for the Grid class to +compute, using the various set() methods described next. Currently +only the kspace_style pppm/electrode and kspace_style msm commands use +the second constructor. + +---------- + +Grid class set methods +^^^^^^^^^^^^^^^^^^^^^^ + +The following methods affect how the Grid class computes which owned +and ghost cells are assigned to each processor. *Set_shift_grid()* is +the only method which influences owned cell assignment; all the rest +influence ghost cell assignment. These methods are only used with the +first constructor; they are ignored if the second constructor is used. +These methods must be called before the *setup_grid()* method is +invoked, because they influence its operation. + +.. code-block:: c++ + + void set_shift_grid(double shift); + void set_distance(double distance); + void set_stencil_atom(int lo, int hi); + void set_shift_atom(double shift_lo, double shift_hi); + void set_stencil_grid(int lo, int hi); + void set_zfactor(double factor); + +Processors own a grid cell if a point within the grid cell is inside +the processor's sub-domain. By default this is the center point of the +grid cell. The *set_shift_grid()* method can change this. The *shift* +argument is a value from 0.0 to 1.0 (inclusive) which is the offset of +the point within the grid cell in each dimension. The default is 0.5 +for the center of the cell. A value of 0.0 is the lower left corner +point; a value of 1.0 is the upper right corner point. There is +typically no need to change the default as it is optimal for +minimizing the number of ghost cells needed. + +If a processor maps its particles to grid cells, it needs to allow for +its particles being outside its sub-domain between reneighboring. The +*distance* argument of the *set_distance()* method sets the furthest +distance outside a processor's sub-domain which a particle can move. +Typically this is half the neighbor skin distance, assuming +reneighboring is done appropriately. This distance is used in +determining how many ghost cells a processor needs to store to enable +its particles to be mapped to grid cells. The default value is 0.0. + +Some commands, like the :doc:`kspace_style pppm ` +command, map values (charge in the case of PPPM) to a stencil of grid +cells beyond the grid cell the particle is in. The stencil extent may +be different in the low and high directions. The *set_stencil_atom()* +method defines the maximum values of those 2 extents, assumed to be +the same in each of the 3 dimensions. Both the lo and hi values are +specified as positive integers. The default values are both 0. + +Some commands, like the :doc:`kspace_style pppm ` +command, shift the position of an atom when mapping it to a grid cell, +based on the size of the stencil used to map values to the grid +(charge in the case of PPPM). The lo and hi arguments of the +*set_shift_atom()* method are the minimum shift in the low direction +and the maximum shift in the high direction, assumed to be the same in +each of the 3 dimensions. The shifts should be fractions of a grid +cell size with values between 0.0 and 1.0 inclusive. The default +values are both 0.0. See the src/pppm.cpp file for examples of these +lo/hi values for regular and staggered grids. + +Some methods like the :doc:`fix ttm/grid ` command, perform +finite difference kinds of operations on the grid, to diffuse electron +heat in the case of the two-temperature model (TTM). This operation +uses ghost grid values beyond the owned grid values the processor +updates. The *set_stencil_grid()* method defines the extent of this +stencil in both directions, assumed to be the same in each of the 3 +dimensions. Both the lo and hi values are specified as positive +integers. The default values are both 0. + +The kspace_style pppm commands allow a grid to be defined which +overlays a volume which extends beyond the simulation box in the z +dimension. This is for the purpose of modeling a 2d-periodic slab +(non-periodic in z) as if it were a larger 3d periodic system, +extended (with empty space) in the z dimension. The +:doc:`kspace_modify slab ` command is used to specify +the ratio of the larger volume to the simulation volume; a volume +ratio of ~3 is typical. For this kind of model, the PPPM caller sets +the global grid size *gnz* ~3x larger than it would be otherwise. +This same ratio is passed by the PPPM caller as the *factor* argument +to the Grid class via the *set_zfactor()* method (*set_yfactor()* for +2d grids). The Grid class will then assign ownership of the 1/3 of +grid cells that overlay the simulation box to the processors which +also overlay the simulation box. The remaining 2/3 of the grid cells +are assigned to processors whose sub-domains are adjacent to the upper +z boundary of the simulation box. + +---------- + +Grid class setup_grid method +^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +The *setup_grid()* method is called after the first constructor +(above) to partition the grid across processors, which determines +which grid cells each processor owns. It also calculates how many +ghost grid cells in each dimension and each direction each processor +needs to store. + +Note that this method is NOT called if the second constructor above is +used. In that case, the caller assigns owned and ghost cells to each +processor. + +Also note that this method must be invoked after any *set_*()* methods have +been used, since they can influence the assignment of owned and ghost +cells. + +.. code-block:: c++ + + void setup_grid(int &ixlo, int &ixhi, int &iylo, int &iyhi, int &izlo, int &izhi, + int &oxlo, int &oxhi, int &oylo, int &oyhi, int &ozlo, int &ozhi) + +The 6 return arguments which start with "i" are the inclusive lower +and upper index bounds of the owned (inner) grid cells this processor +owns in each of the 3 dimensions within the global grid. Owned grid +cells are indexed from 0 to N-1 in each dimension. + +The 6 return arguments which start with "o" are the inclusive bounds of +the owned+ghost cells it owns. If the ghost cells are on the other +side of a periodic boundary, then these indices may be < 0 or >= N in +any dimension, so that oxlo <= ixlo and ixhi >= ixhi is always the +case. + +---------- + +More grid class set methods +^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +The following 2 methods can be used to override settings made by the +constructors above. If used, they must be called called before the +*setup_comm()* method is invoked, since it uses the settings that +these methods override. In LAMMPS these methods are called by by the +:doc:`kspace_style msm ` command for the grids it +instantiates using the 2nd constructor above. + +.. code-block:: c++ + + void set_proc_neighs(int pxlo, int pxhi, int pylo, int pyhi, int pzlo, int pzhi) + void set_caller_grid(int fxlo, int fxhi, int fylo, int fyhi, int fzlo, int fzhi) + +The *set_proc_neighs()* method sets the processor IDs of the 6 +neighboring processors for each processor. Normally these would match +the processor grid neighbors which LAMMPS creates to overlay the +simulation box (the default). However, MSM excludes non-participating +processors from coarse grid communication when less processors are +used. This method allows MSM to override the default values. + +The *set_caller_grid()* method species the size of the data arrays the +caller allocates. Normally these would match the extent of the ghost +grid cells (the default). However the MSM caller allocates a larger +data array (more ghost cells) for its finest-level grid, for use in +other operations besides owned/ghost cell communication. This method +allows MSM to override the default values. + + +---------- + +Grid class get methods +^^^^^^^^^^^^^^^^^^^^^^ + +The following methods allow the caller to query the settings for a +specific grid, whether it created the grid or another command created +it. + +.. code-block:: c++ + + void get_size(int &nxgrid, int &nygrid, int &nzgrid); + void get_bounds_owned(int &xlo, int &xhi, int &ylo, int &yhi, int &zlo, int &zhi) + void get_bounds_ghost(int &xlo, int &xhi, int &ylo, int &yhi, int &zlo, int &zhi) + +The *get_size()* method returns the size of the global grid in each dimension. + +The *get_bounds_owned()* method return the inclusive index bounds of +the grid cells this processor owns. The values range from 0 to N-1 in +each dimension. These values are the same as the "i" values returned +by *setup_grid()*. + +The *get_bounds_ghost()* method return the inclusive index bounds of +the owned+ghost grid cells this processor stores. The owned cell +indices range from 0 to N-1, so these indices may be less than 0 or +greater than or equal to N in each dimension. These values are the +same as the "o" values returned by *setup_grid()*. + +---------- + +Grid class owned/ghost communication +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +If needed by the command, the following methods setup and perform +communication of grid data to/from neighboring processors. The +*forward_comm()* method sends owned grid cell data to the +corresponding ghost grid cells on other processors. The +*reverse_comm()* method sends ghost grid cell data to the +corresponding owned grid cells on another processor. The caller can +choose to sum ghost grid cell data to the owned grid cell or simply +copy it. + +.. code-block:: c++ + + void setup_comm(int &nbuf1, int &nbuf2) + void forward_comm(int caller, void *ptr, int which, int nper, int nbyte, + void *buf1, void *buf2, MPI_Datatype datatype); + void reverse_comm(int caller, void *ptr, int which, int nper, int nbyte, + void *buf1, void *buf2, MPI_Datatype datatype) + int ghost_adjacent(); + +The *setup_comm()* method must be called one time before performing +*forward* or *reverse* communication (multiple times if needed). It +returns two integers, which should be used to allocate two buffers. +The *nbuf1* and *nbuf2* values are the number of grid cells whose data +will be stored in two buffers by the Grid class when *forward* or +*reverse* communication is performed. The caller should thus allocate +them to a size large enough to hold all the data used in any single +forward or reverse communication operation it performs. Note that the +caller may allocate and communicate multiple data arrays for a grid it +instantiates. This size includes the bytes needed for the data type +of the grid data it stores, e.g. double precision values. + +The *forward_comm()* and *reverse_comm()* methods send grid cell data +from owned to ghost cells, or ghost to owned cells, respectively, as +described above. The *caller* argument should be one of these values +-- Grid3d::COMPUTE, Grid3d::FIX, Grid3d::KSPACE, Grid3d::PAIR -- +depending on the style of the caller class. The *ptr* argument is the +"this" pointer to the caller class. These 2 arguments are used to +call back to pack()/unpack() functions in the caller class, as +explained below. + +The *which* argument is a flag the caller can set which is passed to +the caller's pack()/unpack() methods. This allows a single callback +method to pack/unpack data for several different flavors of +forward/reverse communication, e.g. operating on different grids or +grid data. + +The *nper* argument is the number of values per grid cell to be +communicated. The *nbyte* argument is the number of bytes per value, +e.g. 8 for double-precision values. The *buf1* and *buf2* arguments +are the two allocated buffers described above. So long as they are +allocated for the maximum size communication, they can be re-used for +any *forward_comm()/reverse_comm()* call. The *datatype* argument is +the MPI_Datatype setting, which should match the buffer allocation and +the *nbyte* argument. E.g. MPI_DOUBLE for buffers storing double +precision values. + +To use the *forward_grid()* method, the caller must provide two +callback functions; likewise for use of the *reverse_grid()* methods. +These are the 4 functions, their arguments are all the same. + +.. code-block:: c++ + + void pack_forward_grid(int which, void *vbuf, int nlist, int *list); + void unpack_forward_grid(int which, void *vbuf, int nlist, int *list); + void pack_reverse_grid(int which, void *vbuf, int nlist, int *list); + void unpack_reverse_grid(int which, void *vbuf, int nlist, int *list); + +The *which* argument is set to the *which* value of the +*forward_comm()* or *reverse_comm()* calls. It allows the pack/unpack +function to select what data values to pack/unpack. *Vbuf* is the +buffer to pack/unpack the data to/from. It is a void pointer so that +the caller can cast it to whatever data type it chooses, e.g. double +precision values. *Nlist* is the number of grid cells to pack/unpack +and *list* is a vector (nlist in length) of offsets to where the data +for each grid cell resides in the caller's data arrays, which is best +illustrated with an example from the src/EXTRA-FIX/fix_ttm_grid.cpp +class which stores the scalar electron temperature for 3d system in a +3d grid (one value per grid cell): + +.. code-block:: c++ + + void FixTTMGrid::pack_forward_grid(int /*which*/, void *vbuf, int nlist, int *list) + { + auto buf = (double *) vbuf; + double *src = &T_electron[nzlo_out][nylo_out][nxlo_out]; + for (int i = 0; i < nlist; i++) buf[i] = src[list[i]]; + } + +In this case, the *which* argument is not used, *vbuf* points to a +buffer of doubles, and the electron temperature is stored by the +FixTTMGrid class in a 3d array of owned+ghost cells called T_electron. +That array is allocated by the *memory->create_3d_offset()* method +described above so that the first grid cell it stores is indexed as +T_electron[nzlo_out][nylo_out][nxlo_out]. The *nlist* values in +*list* are integer offsets from that first grid cell. Setting *src* +to the address of the first cell allows those offsets to be used to +access the temperatures to pack into the buffer. + +Here is a similar portion of code from the src/fix_ave_grid.cpp class +which can store two kinds of data, a scalar count of atoms in a grid +cell, and one or more grid-cell-averaged atom properties. The code +from its *unpack_reverse_grid()* function for 2d grids and multiple +per-atom properties per grid cell (*nvalues*) is shown here: + +.. code-block:: c++ + + void FixAveGrid::unpack_reverse_grid(int /*which*/, void *vbuf, int nlist, int *list) + { + auto buf = (double *) vbuf; + double *count,*data,*values; + count = &count2d[nylo_out][nxlo_out]; + data = &array2d[nylo_out][nxlo_out][0]; + m = 0; + for (i = 0; i < nlist; i++) { + count[list[i]] += buf[m++]; + values = &data[nvalues*list[i]]; + for (j = 0; j < nvalues; j++) + values[j] += buf[m++]; + } + } + +Both the count and the multiple values per grid cell are communicated +in *vbuf*. Note that *data* is now a pointer to the first value in +the first grid cell. And *values* points to where the first value in +*data* is for an offset of grid cells, calculated by multiplying +*nvalues* by *list[i]*. Finally, because this is reverse +communication, the communicated buffer values are summed to the caller +values. + +The *ghost_adjacent()* method returns a 1 if every processor can +perform the necessary owned/ghost communication with only its nearest +neighbor processors (4 in 2d, 6 in 3d). It returns a 0 if any +processor's ghost cells extend further than nearest neighbor +processors. + +This can be checked by callers who have the option to change the +global grid size to insure more efficient nearest-neighbor-only +communication if they wish. In this case, they instantiate a grid of +a given size (resolution), then invoke *setup_comm()* followed by +*ghost_adjacent()*. If the ghost cells are not adjacent, they destroy +the grid instance and start over with a higher-resolution grid. +Several of the :doc:`kspace_style pppm ` command +variants have this option. + +---------- + +Grid class remap methods for load balancing +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +The following methods are used when a load-balancing operation, +triggered by the :doc:`balance ` or :doc:`fix balance +` commands, changes the partitioning of the simulation +domain into processor sub-domains. + +In order to work with load-balancing, any style command (compute, fix, +pair, or kspace style) which allocates a grid and stores per-grid data +should define a *reset_grid()* method; it takes no arguments. It will +be called by the two balance commands after they have reset processor +sub-domains and migrated atoms (particles) to new owning processors. +The *reset_grid()* method will typically perform some or all of the +following operations. See the src/fix_ave_grid.cpp and +src/EXTRA_FIX/fix_ttm_grid.cpp files for examples of *reset_grid()* +methods, as well as the *pack_remap_grid()* and *unpack_remap_grid()* +functions. + +First, the *reset_grid()* method can instantiate new grid(s) of the +same global size, then call *setup_grid()* to partition them via the +new processor sub-domains. At this point, it can invoke the +*identical()* method which compares the owned and ghost grid cell +index bounds between two grids, the old grid passed as a pointer +argument, and the new grid whose *identical()* method is being called. +It returns 1 if the indices match on all processors, otherwise 0. If +they all match, then the new grids can be deleted; the command can +continue to use the old grids. + +If not, then the command should allocate new grid data array(s) which +depend on the new partitioning. If the command does not need to +persist its grid data from the old partitioning to the new one, then +the command can simply delete the old data array(s) and grid +instance(s). It can then return. + +If the grid data does need to persist, then the data for each grid +needs to be "remapped" from the old grid partitioning to the new grid +partitioning. The *setup_remap()* and *remap()* methods are used for +that purpose. + +.. code-block:: c++ + + int identical(Grid3d *old); + void setup_remap(Grid3d *old, int &nremap_buf1, int &nremap_buf2) + void remap(int caller, void *ptr, int which, int nper, int nbyte, + void *buf1, void *buf2, MPI_Datatype datatype) + +The arguments to these methods are identical to those for +the *setup_comm()* and *forward_comm()* or *reverse_comm()* methods. +However the returned *nremap_buf1* and *nremap2_buf* values will be +different than the *nbuf1* and *nbuf2* values. They should be used to +allocate two different remap buffers, separate from the owned/ghost +communication buffers. + +To use the *remap()* method, the caller must provide two +callback functions: + +.. code-block:: c++ + + void pack_remap_grid(int which, void *vbuf, int nlist, int *list); + void unpack_remap_grid(int which, void *vbuf, int list, int *list); + +Their arguments are identical to those for the *pack_forward_grid()* +and *unpack_forward_grid()* callback functions (or the reverse +variants) discussed above. Normally, both these methods pack/unpack +all the data arrays for a given grid. The *which* argument of the +*remap()* method sets the *which* value for the pack/unpack functions. +If the command instantiates multiple grids (of different sizes), it +can be used within the pack/unpack methods to select which grid's data +is being remapped. + +Note that the *pack_remap_grid()* function must copy values from the +OLD grid data arrays into the *vbuf* buffer. The *unpack_remap_grid()* +function must copy values from the *vbuf* buffer into the NEW grid +data arrays. + +After the remap operation for grid cell data has been performed, the +*reset_grid()* method can deallocate the two remap buffers it created, +and can then exit. + +---------- + +Grid class I/O methods +^^^^^^^^^^^^^^^^^^^^^^ + +There are two I/O methods in the Grid classes which can be used to +read and write grid cell data to files. The caller can decide on the +precise format of each file, e.g. whether header lines are prepended +or comment lines are allowed. Fundamentally, the file should contain +one line per grid cell for the entire global grid. Each line should +contain identifying info as to which grid cell it is, e.g. a unique +grid cell ID or the ix,iy,iz indices of the cell within a 3d grid. +The line should also contain one or more data values which are stored +within the grid data arrays created by the command + +For grid cell IDs, the LAMMPS convention is that the IDs run from 1 to +N, where N = Nx * Ny for 2d grids and N = Nx * Ny * Nz for 3d grids. +The x-index of the grid cell varies fastest, then y, and the z-index +varies slowest. So for a 10x10x10 grid the cell IDs from 901-1000 +would be in the top xy layer of the z dimension. + +The *read_file()* method does something simple. It reads a chunk of +consecutive lines from the file and passes them back to the caller to +process. The caller provides a *unpack_read_grid()* function for this +purpose. The function checks the grid cell ID or indices and only +stores grid cell data for the grid cells it owns. + +The *write_file()* method does something slightly more complex. Each +processor packs the data for its owned grid cells into a buffer. The +caller provides a *pack_write_grid()* function for this purpose. The +*write_file()* method then loops over all processors and each sends +its buffer one at a time to processor 0, along with the 3d (or 2d) +index bounds of its grid cell data within the global grid. Processor +0 calls back to the *unpack_write_grid()* function provided by the +caller with the buffer. The function writes one line per grid cell to +the file. + +See the src/EXTRA_FIX/fix_ttm_grid.cpp file for examples of now both +these methods are used to read/write electron temperature values +from/to a file, as well as for implementations of the the pack/unpack +functions described below. + +Here are the details of the two I/O methods and the 3 callback +functions. See the src/fix_ave_grid.cpp file for examples of all of +them. + +.. code-block:: c++ + + void read_file(int caller, void *ptr, FILE *fp, int nchunk, int maxline) + void write_file(int caller, void *ptr, int which, + int nper, int nbyte, MPI_Datatype datatype + +The *caller* argument in both methods should be one of these values -- +Grid3d::COMPUTE, Grid3d::FIX, Grid3d::KSPACE, Grid3d::PAIR -- +depending on the style of the caller class. The *ptr* argument in +both methods is the "this" pointer to the caller class. These 2 +arguments are used to call back to pack()/unpack() functions in the +caller class, as explained below. + +For the *read_file()* method, the *fp* argument is a file pointer to +the file to be read from, opened on processor 0 by the caller. +*Nchunk* is the number of lines to read per chunk, and *maxline* is +the maximum number of characters per line. The Grid class will +allocate a buffer for storing chunks of lines based on these values. + +For the *write_file()* method, the *which* argument is a flag the +caller can set which is passed back to the caller's pack()/unpack() +methods. If the command instantiates multiple grids (of different +sizes), this flag can be used within the pack/unpack methods to select +which grid's data is being written out (presumably to different +files). the *nper* argument is the number of values per grid cell to +be written out. The *nbyte* argument is the number of bytes per +value, e.g. 8 for double-precision values. The *datatype* argument is +the MPI_Datatype setting, which should match the *nbyte* argument. +E.g. MPI_DOUBLE for double precision values. + +To use the *read_grid()* method, the caller must provide one callback +function. To use the *write_grid()* method, it provides two callback +functions: + +.. code-block:: c++ + + int unpack_read_grid(int nlines, char *buffer) + void pack_write_grid(int which, void *vbuf) + void unpack_write_grid(int which, void *vbuf, int *bounds) + +For *unpack_read_grid()* the *nlines* argument is the number of lines +of character data read from the file and contained in *buffer*. The +lines each include a newline character at the end. When the function +processes the lines, it may choose to skip some of them (header or +comment lines). It returns an integer count of the number of grid +cell lines it processed. This enables the Grid class *read_file()* +method to know when it has read the correct number of lines. + +For *pack_write_grid()* and *unpack_write_grid()*, the *vbuf* argument +is the buffer to pack/unpack data to/from. It is a void pointer so +that the caller can cast it to whatever data type it chooses, +e.g. double precision values. the *which* argument is set to the +*which* value of the *write_file()* method. It allows the caller to +choose which grid data to operate on. + +For *unpack_write_grid()*, the *bounds* argument is a vector of 4 or 6 +integer grid indices (4 for 2d, 6 for 3d). They are the +xlo,xhi,ylo,yhi,zlo,zhi index bounds of the portion of the global grid +which the *vbuf* holds owned grid cell data values for. The caller +should loop over the values in *vbuf* with a double loop (2d) or +triple loop (3d), similar to the code snippets listed above. The +x-index varies fastest, then y, and the z-index slowest. If there are +multiple values per grid cell, the index for those values varies +fastest of all. The caller can add the x,y,z indices of the grid cell +(or the corresponding grid cell ID) to the data value(s) written as +one line to the output file. + +---------- + +Style class grid access methods +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +A style command can enable its grid cell data to be accessible from +other commands. For example :doc:`fix ave/grid ` or +:doc:`dump grid ` or :doc:`dump grid/vtk `. Those +commands access the grid cell data by using a *grid reference* in +their input script syntax, as described on the :doc:`Howto_grid +` doc page. They look like this: + +* c_ID:gname:dname +* c_ID:gname:dname[I] +* f_ID:gname:dname +* f_ID:gname:dname[I] + +Each grid a command instantiates has a unique *gname*, defined by the +command. Likewise each grid cell data structure (scalar or vector) +associated with a grid has a unique *dname*, also defined by the +command. + +To provide access to its grid cell data, a style command needs to +implement the following 4 methods: + +.. code-block:: c++ + + int get_grid_by_name(const std::string &name, int &dim); + void *get_grid_by_index(int index); + int get_griddata_by_name(int igrid, const std::string &name, int &ncol); + void *get_griddata_by_index(int index); + +Currently only computes and fixes can implement these methods. If it +does so, the compute of fix should also set the variable +*pergrid_flag* to 1. See any of the compute or fix commands which set +"pergrid_flag = 1" for examples of how these 4 functions can be +implemented. + +The *get_grid_by_name()* method takes a grid name as input and returns +two values. The *dim* argument is returned as 2 or 3 for the +dimensionality of the grid. The function return is a grid index from +0 to G-1 where *G* is the number of grids the command instantiates. A +value of -1 is returned if the grid name is not recognized. + +The *get_grid_by_index()* method is called after the +*get_grid_by_name()* method, using the grid index it returned as its +argument. This method will return a pointer to the Grid2d or Grid3d +class. The caller can use this to query grid attributes, such as the +global size of the grid. The :doc:`dump grid ` to insure each +its grid reference arguments are for grids of the same size. + +The *get_griddata_by_name()* method takes a grid index *igrid* and a +data name as input. It returns two values. The *ncol* argument is +returned as a 0 if the grid data is a single value (scalar) per grid +cell, or an integer M > 0 if there are M values (vector) per grid +cell. Note that even if M = 1, it is still a 1-length vector, not a +scalar. The function return is a data index from 0 to D-1 where *D* +is the number of data sets associated with that grid by the command. +A value of -1 is returned if the data name is not recognized. + +The *get_griddata_by_index()* method is called after the +*get_griddata_by_name()* method, using the data index it returned as +its argument. This method will return a pointer to the +multi-dimensional array which stores the requested data. + +As in the discussion above of the Memory class *create_offset()* +methods, the dimensionality of the array associated with the returned +pointer depends on whether it is a 2d or 3d grid and whether there is +a single or multiple values stored for each grid cell: + +* single value per cell for a 2d grid = 2d array pointer +* multiple values per cell for a 2d grid = 3d array pointer +* single value per cell for a 3d grid = 3d array pointer +* multiple values per cell for a 3d grid = 4d array pointer + +The caller will typically access the data by casting the void pointer +to the corresponding array pointer and using nested loops in x,y,z +between owned or ghost index bounds returned by the +*get_bounds_owned()* or *get_bounds_ghost()* methods to index into the +array. Example code snippets with this logic were listed above, + +---------- + +Final notes +^^^^^^^^^^^ + +Finally, here are some additional issues to pay attention to for +writing any style command which uses distributed grids via the Grid2d +or Grid3d class. + +The command destructor should delete all instances of the Grid class, +any buffers it allocated for forward/reverse or remap communication, +and any data arrays it allocated to store grid cell data. + +If a command is intended to work for either 2d or 3d simulations, then +it should have logic to instantiate either 2d or 3d grids and their +associated data arrays, depending on the dimension of the simulation +box. The :doc:`fix ave/grid ` command is an example of +such a command. + +When a command maps its particles to the grid and updates grid cell +values, it should check that it is not updating or accessing a grid +cell value outside the range of its owned+ghost cells, and generate an +error message if that is the case. This could happen, for example, if +a particle has moved further than half the neighbor skin distance, +because the neighbor list update criterion are not adequate to prevent +it from happening. See the src/KSPACE/pppm.cpp file and its +*particle_map()* method for an example of this kind of error check. diff --git a/doc/src/Developer_notes.rst b/doc/src/Developer_notes.rst index 2b3375265f..a781737d6f 100644 --- a/doc/src/Developer_notes.rst +++ b/doc/src/Developer_notes.rst @@ -105,7 +105,7 @@ list, where each pair of atoms is listed only once (except when the pairs straddling sub-domains or periodic boundaries will be listed twice). Thus these are the default settings when a neighbor list request is created in: -.. code-block:: C++ +.. code-block:: c++ void Pair::init_style() { @@ -129,7 +129,7 @@ neighbor list request to the specific needs of a style an additional request flag is needed. The :doc:`tersoff ` pair style, for example, needs a "full" neighbor list: -.. code-block:: C++ +.. code-block:: c++ void PairTersoff::init_style() { @@ -141,7 +141,7 @@ When a pair style supports r-RESPA time integration with different cutoff region the request flag may depend on the corresponding r-RESPA settings. Here an example from pair style lj/cut: -.. code-block:: C++ +.. code-block:: c++ void PairLJCut::init_style() { @@ -160,7 +160,7 @@ Granular pair styles need neighbor lists based on particle sizes and not cutoff and also may require to have the list of previous neighbors available ("history"). For example with: -.. code-block:: C++ +.. code-block:: c++ if (use_history) neighbor->add_request(this, NeighConst::REQ_SIZE | NeighConst::REQ_HISTORY); else neighbor->add_request(this, NeighConst::REQ_SIZE); @@ -170,7 +170,7 @@ settings each request can set an id which is then used in the corresponding ``init_list()`` function to assign it to the suitable pointer variable. This is done for example by the :doc:`pair style meam `: -.. code-block:: C++ +.. code-block:: c++ void PairMEAM::init_style() { @@ -189,7 +189,7 @@ just once) and this can also be indicated by a flag. As an example here is the request from the ``FixPeriNeigh`` class which is created internally by :doc:`Peridynamics pair styles `: -.. code-block:: C++ +.. code-block:: c++ neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL); @@ -198,7 +198,7 @@ than what is usually inferred from the pair style settings (largest cutoff of all pair styles plus neighbor list skin). The following is used in the :doc:`compute rdf ` command implementation: -.. code-block:: C++ +.. code-block:: c++ if (cutflag) neighbor->add_request(this, NeighConst::REQ_OCCASIONAL)->set_cutoff(mycutneigh); @@ -212,7 +212,7 @@ for printing the neighbor list summary the name of the requesting command should be set. Below is the request from the :doc:`delete atoms ` command: -.. code-block:: C++ +.. code-block:: c++ neighbor->add_request(this, "delete_atoms", NeighConst::REQ_FULL); diff --git a/doc/src/Developer_plugins.rst b/doc/src/Developer_plugins.rst index 36fdd010b3..dd5431507e 100644 --- a/doc/src/Developer_plugins.rst +++ b/doc/src/Developer_plugins.rst @@ -95,7 +95,7 @@ a class ``PairMorse2`` in the files ``pair_morse2.h`` and ``pair_morse2.cpp`` with the factory function and initialization function would look like this: -.. code-block:: C++ +.. code-block:: c++ #include "lammpsplugin.h" #include "version.h" @@ -141,7 +141,7 @@ list of argument strings), then the pointer type is ``lammpsplugin_factory2`` and it must be assigned to the *creator.v2* member of the plugin struct. Below is an example for that: -.. code-block:: C++ +.. code-block:: c++ #include "lammpsplugin.h" #include "version.h" @@ -176,7 +176,7 @@ demonstrated in the following example, which also shows that the implementation of the plugin class may be within the same source file as the plugin interface code: -.. code-block:: C++ +.. code-block:: c++ #include "lammpsplugin.h" diff --git a/doc/src/Developer_unittest.rst b/doc/src/Developer_unittest.rst index 820e911a8f..69e29263a6 100644 --- a/doc/src/Developer_unittest.rst +++ b/doc/src/Developer_unittest.rst @@ -194,7 +194,7 @@ macro. These tests operate by capturing the screen output when executing the failing command and then comparing that with a provided regular expression string pattern. Example: -.. code-block:: C++ +.. code-block:: c++ TEST_F(SimpleCommandsTest, UnknownCommand) { @@ -226,9 +226,9 @@ The following test programs are currently available: * - ``test_kim_commands.cpp`` - KimCommands - Tests for several commands from the :ref:`KIM package ` - * - ``test_reset_ids.cpp`` - - ResetIDs - - Tests to validate the :doc:`reset_atom_ids ` and :doc:`reset_mol_ids ` commands + * - ``test_reset_atoms.cpp`` + - ResetAtoms + - Tests to validate the :doc:`reset_atoms ` sub-commands Tests for the C-style library interface @@ -249,7 +249,7 @@ MPI support. These include tests where LAMMPS is run in multi-partition mode or only on a subset of the MPI world communicator. The CMake script code for adding this kind of test looks like this: -.. code-block:: CMake +.. code-block:: cmake if (BUILD_MPI) add_executable(test_library_mpi test_library_mpi.cpp) diff --git a/doc/src/Developer_updating.rst b/doc/src/Developer_updating.rst index 091312d68e..6089969c38 100644 --- a/doc/src/Developer_updating.rst +++ b/doc/src/Developer_updating.rst @@ -7,7 +7,7 @@ source files provided as a supplement to a publication) that are written for an older version of LAMMPS and thus need to be updated to be compatible with the current version of LAMMPS. Due to the active development of LAMMPS it is likely to always be incomplete. Please -contact developer@lammps.org in case you run across an issue that is not +contact developers@lammps.org in case you run across an issue that is not (yet) listed here. Please also review the latest information about the LAMMPS :doc:`programming style conventions `, especially if you are considering to submit the updated version for inclusion into @@ -25,6 +25,7 @@ Available topics in mostly chronological order are: - `Simplified and more compact neighbor list requests`_ - `Split of fix STORE into fix STORE/GLOBAL and fix STORE/PERATOM`_ - `Use Output::get_dump_by_id() instead of Output::find_dump()`_ +- `Refactored grid communication using Grid3d/Grid2d classes instead of GridComm`_ ---- @@ -61,7 +62,7 @@ header file needs to be updated accordingly. Old: -.. code-block:: C++ +.. code-block:: c++ int PairEAM::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) { @@ -75,7 +76,7 @@ Old: New: -.. code-block:: C++ +.. code-block:: c++ int PairEAM::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) { @@ -112,14 +113,14 @@ Example from a pair style: Old: -.. code-block:: C++ +.. code-block:: c++ if (eflag || vflag) ev_setup(eflag, vflag); else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; New: -.. code-block:: C++ +.. code-block:: c++ ev_init(eflag, vflag); @@ -142,14 +143,14 @@ when they are called from only one or a subset of the MPI processes. Old: -.. code-block:: C++ +.. code-block:: c++ val = force->numeric(FLERR, arg[1]); num = force->inumeric(FLERR, arg[2]); New: -.. code-block:: C++ +.. code-block:: c++ val = utils::numeric(FLERR, true, arg[1], lmp); num = utils::inumeric(FLERR, false, arg[2], lmp); @@ -183,14 +184,14 @@ copy them around for simulations. Old: -.. code-block:: C++ +.. code-block:: c++ fp = force->open_potential(filename); fp = fopen(filename, "r"); New: -.. code-block:: C++ +.. code-block:: c++ fp = utils::open_potential(filename, lmp); @@ -207,7 +208,7 @@ Example: Old: -.. code-block:: C++ +.. code-block:: c++ if (fptr == NULL) { char str[128]; @@ -217,7 +218,7 @@ Old: New: -.. code-block:: C++ +.. code-block:: c++ if (fptr == nullptr) error->one(FLERR, "Cannot open AEAM potential file {}: {}", filename, utils::getsyserror()); @@ -237,7 +238,7 @@ an example from the ``FixWallReflect`` class: Old: -.. code-block:: C++ +.. code-block:: c++ FixWallReflect(class LAMMPS *, int, char **); virtual ~FixWallReflect(); @@ -247,7 +248,7 @@ Old: New: -.. code-block:: C++ +.. code-block:: c++ FixWallReflect(class LAMMPS *, int, char **); ~FixWallReflect() override; @@ -271,7 +272,7 @@ the type of the "this" pointer argument. Old: -.. code-block:: C++ +.. code-block:: c++ comm->forward_comm_pair(this); comm->forward_comm_fix(this); @@ -284,7 +285,7 @@ Old: New: -.. code-block:: C++ +.. code-block:: c++ comm->forward_comm(this); comm->reverse_comm(this); @@ -304,7 +305,7 @@ requests can be :doc:`found here `. Example from the Old: -.. code-block:: C++ +.. code-block:: c++ int irequest = neighbor->request(this,instance_me); neighbor->requests[irequest]->pair = 0; @@ -317,7 +318,7 @@ Old: New: -.. code-block:: C++ +.. code-block:: c++ auto req = neighbor->add_request(this, NeighConst::REQ_OCCASIONAL); if (cutflag) req->set_cutoff(mycutneigh); @@ -340,7 +341,7 @@ these are internal fixes, there is no user visible change. Old: -.. code-block:: C++ +.. code-block:: c++ #include "fix_store.h" @@ -351,7 +352,7 @@ Old: New: -.. code-block:: C++ +.. code-block:: c++ #include "fix_store_peratom.h" @@ -362,7 +363,7 @@ New: Old: -.. code-block:: C++ +.. code-block:: c++ #include "fix_store.h" @@ -373,7 +374,7 @@ Old: New: -.. code-block:: C++ +.. code-block:: c++ #include "fix_store_global.h" @@ -396,7 +397,7 @@ the dump directly. Example: Old: -.. code-block:: C++ +.. code-block:: c++ int idump = output->find_dump(arg[iarg+1]); if (idump < 0) @@ -412,7 +413,7 @@ Old: New: -.. code-block:: C++ +.. code-block:: c++ auto idump = output->get_dump_by_id(arg[iarg+1]); if (!idump) error->all(FLERR,"Dump ID {} in hyper command does not exist", arg[iarg+1]); @@ -423,3 +424,56 @@ New: if (dumpflag) for (auto idump : dumplist) idump->write(); This change is **required** or else the code will not compile. + +Refactored grid communication using Grid3d/Grid2d classes instead of GridComm +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. versionchanged:: 22Dec2022 + +The ``GridComm`` class was for creating and communicating distributed +grids was replaced by the ``Grid3d`` class with added functionality. +A ``Grid2d`` class was also added for additional flexibility. + +The new functionality and commands using the two grid classes are +discussed on the following documentation pages: + +- :doc:`Howto_grid` +- :doc:`Developer_grid` + +If you have custom LAMMPS code, which uses the GridComm class, here are some notes +on how to adapt it for using the Grid3d class. + +(1) The constructor has changed to allow the ``Grid3d`` / ``Grid2d`` + classes to partition the global grid across processors, both for + owned and ghost grid cells. Previously any class which called + ``GridComm`` performed the partitioning itself and that information + was passed in the ``GridComm::GridComm()`` constructor. There are + several "set" functions which can be called to alter how ``Grid3d`` + / ``Grid2d`` perform the partitioning. They should be sufficient + for most use cases of the grid classes. + +(2) The partitioning is triggered by the ``setup_grid()`` method. + +(3) The ``setup()`` method of the ``GridComm`` class has been replaced + by the ``setup_comm()`` method in the new grid classes. The syntax + for the ``forward_comm()`` and ``reverse_comm()`` methods is + slightly altered as is the syntax of the associated pack/unpack + callback methods. But the functionality of these operations is the + same as before. + +(4) The new ``Grid3d`` / ``Grid2d`` classes have additional + functionality for dynamic load-balancing of grids and their + associated data across processors. This did not exist in the + ``GridComm`` class. + +This and more is explained in detail on the :doc:`Developer_grid` page. +The following LAMMPS source files can be used as illustrative examples +for how the new grid classes are used by computes, fixes, and various +KSpace solvers which use distributed FFT grids: + +- ``src/fix_ave_grid.cpp`` +- ``src/compute_property_grid.cpp`` +- ``src/EXTRA-FIX/fix_ttm_grid.cpp`` +- ``src/KSPACE/pppm.cpp`` + +This change is **required** or else the code will not compile. diff --git a/doc/src/Developer_utils.rst b/doc/src/Developer_utils.rst index b92d817d87..35a763b7a1 100644 --- a/doc/src/Developer_utils.rst +++ b/doc/src/Developer_utils.rst @@ -133,6 +133,9 @@ and parsing files or arguments. .. doxygenfunction:: trim_comment :project: progguide +.. doxygenfunction:: strip_style_suffix + :project: progguide + .. doxygenfunction:: star_subst :project: progguide @@ -211,6 +214,9 @@ Argument processing .. doxygenfunction:: expand_args :project: progguide +.. doxygenfunction:: parse_grid_id + :project: progguide + .. doxygenfunction:: expand_type :project: progguide @@ -317,7 +323,7 @@ are all "whitespace" characters, i.e. the space character, the tabulator character, the carriage return character, the linefeed character, and the form feed character. -.. code-block:: C++ +.. code-block:: c++ :caption: Tokenizer class example listing entries of the PATH environment variable #include "tokenizer.h" @@ -349,7 +355,7 @@ tokenizer into a ``try`` / ``catch`` block to handle errors. The when a (type of) number is requested as next token that is not compatible with the string representing the next word. -.. code-block:: C++ +.. code-block:: c++ :caption: ValueTokenizer class example with exception handling #include "tokenizer.h" @@ -427,7 +433,7 @@ one or two array indices "[]" with numbers > 0. A typical code segment would look like this: -.. code-block:: C++ +.. code-block:: c++ :caption: Usage example for ArgInfo class int nvalues = 0; @@ -476,7 +482,7 @@ open the file, and will call the :cpp:class:`LAMMPS_NS::Error` class in case of failures to read or to convert numbers, so that LAMMPS will be aborted. -.. code-block:: C++ +.. code-block:: c++ :caption: Use of PotentialFileReader class in pair style coul/streitz PotentialFileReader reader(lmp, file, "coul/streitz"); @@ -555,7 +561,7 @@ chunk size needs to be known in advance, 2) with :cpp:func:`MyPage::vget() its size is registered later with :cpp:func:`MyPage::vgot() `. -.. code-block:: C++ +.. code-block:: c++ :caption: Example of using :cpp:class:`MyPage ` #include "my_page.h" diff --git a/doc/src/Developer_write.rst b/doc/src/Developer_write.rst index bdc6559060..c374ec2e77 100644 --- a/doc/src/Developer_write.rst +++ b/doc/src/Developer_write.rst @@ -26,7 +26,7 @@ constructor with the signature: ``FixPrintVel(class LAMMPS *, int, char **)``. Every fix must be registered in LAMMPS by writing the following lines of code in the header before include guards: -.. code-block:: c +.. code-block:: c++ #ifdef FIX_CLASS // clang-format off @@ -47,7 +47,7 @@ keyword when it parses the input script. Let's write a simple fix which will print the average velocity at the end of each timestep. First of all, implement a constructor: -.. code-block:: C++ +.. code-block:: c++ FixPrintVel::FixPrintVel(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) @@ -72,7 +72,7 @@ in the Fix class called ``nevery`` which specifies how often the method The next method we need to implement is ``setmask()``: -.. code-block:: C++ +.. code-block:: c++ int FixPrintVel::setmask() { @@ -87,7 +87,7 @@ during execution. The constant ``END_OF_STEP`` corresponds to the are called during a timestep and the order in which they are called are shown in the previous section. -.. code-block:: C++ +.. code-block:: c++ void FixPrintVel::end_of_step() { @@ -143,7 +143,7 @@ The group membership information of an atom is contained in the *mask* property of and atom and the bit corresponding to a given group is stored in the groupbit variable which is defined in Fix base class: -.. code-block:: C++ +.. code-block:: c++ for (int i = 0; i < nlocal; ++i) { if (atom->mask[i] & groupbit) { @@ -174,7 +174,7 @@ to store positions of atoms from previous timestep, we need to add ``double** xold`` to the header file. Than add allocation code to the constructor: -.. code-block:: C++ +.. code-block:: c++ FixSavePos::FixSavePos(LAMMPS *lmp, int narg, char **arg), xold(nullptr) { @@ -190,7 +190,7 @@ to the constructor: Implement the aforementioned methods: -.. code-block:: C++ +.. code-block:: c++ double FixSavePos::memory_usage() { diff --git a/doc/src/Fortran.rst b/doc/src/Fortran.rst index 28254e056c..98e6194861 100644 --- a/doc/src/Fortran.rst +++ b/doc/src/Fortran.rst @@ -1,11 +1,12 @@ -The ``LIBLAMMPS`` Fortran Module -******************************** +The :f:mod:`LIBLAMMPS` Fortran Module +************************************* -The ``LIBLAMMPS`` module provides an interface to call LAMMPS from Fortran. -It is based on the LAMMPS C library interface and -requires a Fortran 2003-compatible compiler to be compiled. It is -designed to be self-contained and not require any support functions -written in C, C++, or Fortran other than those in the C library interface. +The :f:mod:`LIBLAMMPS` module provides an interface to call LAMMPS from +Fortran. It is based on the LAMMPS C library interface and requires a +fully Fortran 2003-compatible compiler to be compiled. It is designed +to be self-contained and not require any support functions written in C, +C++, or Fortran other than those in the C library interface and the module +itself. While C libraries have a defined binary interface (ABI) and can thus be used from multiple compiler versions from different vendors as long @@ -21,38 +22,29 @@ for a simple program using the Fortran interface would be: mpifort -o testlib.x lammps.f90 testlib.f90 -L. -llammps Please note that the MPI compiler wrapper is only required when the -calling the library from an MPI-parallelized program. Otherwise, using the -fortran compiler (gfortran, ifort, flang, etc.) will suffice. It may be -necessary to link to additional libraries, depending on how LAMMPS was -configured and whether the LAMMPS library :doc:`was compiled as a static -or dynamic library `. +calling the library from an MPI-parallelized program. Otherwise, using +the plain Fortran compiler (gfortran, ifort, flang, etc.) will suffice. +It may be necessary to link to additional libraries, depending on how +LAMMPS was configured and whether the LAMMPS library :doc:`was compiled +as a static or dynamic library `. If the LAMMPS library itself has been compiled with MPI support, the resulting executable will still be able to run LAMMPS in parallel with -``mpirun``, ``mpiexec`` or equivalent. Please also note that the order +``mpirun``, ``mpiexec``, or equivalent. Please also note that the order of the source files matters: the ``lammps.f90`` file needs to be -compiled first, since it provides the ``LIBLAMMPS`` module that is +compiled first, since it provides the :f:mod:`LIBLAMMPS` module that is imported by the Fortran code that uses the interface. A working example can be found together with equivalent examples in C and C++ in the ``examples/COUPLE/simple`` folder of the LAMMPS distribution. .. versionadded:: 9Oct2020 -.. admonition:: Work in Progress - :class: note - - This Fortran module is work in progress and only the documented - functionality is currently available. The final implementation should - cover the entire range of functionality available in the C and - Python library interfaces. - .. note:: - A contributed (and more complete!) Fortran interface that more - closely resembles the C library interface is available in the - ``examples/COUPLE/fortran2`` folder. Please see the ``README`` file - in that folder for more information about it and how to contact its - author and maintainer. + A contributed Fortran interface that more closely resembles the C library + interface is available in the ``examples/COUPLE/fortran2`` folder. Please + see the ``README`` file in that folder for more information about it and how + to contact its author and maintainer. ---------- @@ -78,7 +70,7 @@ function and triggered with the optional logical argument set to USE LIBLAMMPS ! include the LAMMPS library interface IMPLICIT NONE TYPE(lammps) :: lmp ! derived type to hold LAMMPS instance - CHARACTER(LEN=*), PARAMETER :: args(3) = & + CHARACTER(LEN=12), PARAMETER :: args(3) = & [ CHARACTER(LEN=12) :: 'liblammps', '-log', 'none' ] ! create a LAMMPS instance (and initialize MPI) @@ -135,20 +127,20 @@ is done similarly to how it is implemented in the :doc:`C library interface `. Before handing off the calls to the C library interface, the corresponding Fortran versions of the calls (:f:func:`file`, :f:func:`command`, :f:func:`commands_list`, and -:f:func:`commands_string`) have to make a copy of the strings passed as +:f:func:`commands_string`) have to make copies of the strings passed as arguments so that they can be modified to be compatible with the requirements of strings in C without affecting the original strings. Those copies are automatically deleted after the functions return. -Below is a small demonstration of the uses of the different functions: +Below is a small demonstration of the uses of the different functions. .. code-block:: fortran PROGRAM testcmd USE LIBLAMMPS - TYPE(lammps) :: lmp - CHARACTER(len=512) :: cmds - CHARACTER(len=40), ALLOCATABLE :: cmdlist(:) - CHARACTER(len=10) :: trimmed + TYPE(lammps) :: lmp + CHARACTER(LEN=512) :: cmds + CHARACTER(LEN=40), ALLOCATABLE :: cmdlist(:) + CHARACTER(LEN=10) :: trimmed INTEGER :: i lmp = lammps() @@ -227,49 +219,176 @@ Below is an example demonstrating some of the possible uses. --------------- -The ``LIBLAMMPS`` module API -**************************** +The :f:mod:`LIBLAMMPS` module API +********************************* + +.. f:module:: LIBLAMMPS Below are the detailed descriptions of definitions and interfaces -of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS. +of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS. + +.. f:currentmodule:: None .. f:type:: lammps - Derived type that is the general class of the Fortran interface. It - holds a reference to the :cpp:class:`LAMMPS ` - class instance that any of the included calls are forwarded to. + Derived type that is the general class of the Fortran interface. + It holds a reference to the :cpp:class:`LAMMPS ` + class instance to which any of the included calls are forwarded. - :f c_ptr handle: reference to the LAMMPS class - :f type(lammps_style) style: derived type to access lammps style constants - :f type(lammps_type) type: derived type to access lammps type constants - :f subroutine close: :f:func:`close` - :f subroutine error: :f:func:`error` - :f subroutine file: :f:func:`file` - :f subroutine command: :f:func:`command` - :f subroutine commands_list: :f:func:`commands_list` - :f subroutine commands_string: :f:func:`commands_string` - :f function get_natoms: :f:func:`get_natoms` - :f function get_thermo: :f:func:`get_thermo` - :f subroutine extract_box: :f:func:`extract_box` - :f subroutine reset_box: :f:func:`reset_box` - :f subroutine memory_usage: :f:func:`memory_usage` - :f function get_mpi_comm: :f:func:`get_mpi_comm` - :f function extract_setting: :f:func:`extract_setting` - :f function extract_global: :f:func:`extract_global` - :f function extract_atom: :f:func:`extract_atom` - :f function extract_compute: :f:func:`extract_compute` - :f function extract_fix: :f:func:`extract_fix` - :f function extract_variable: :f:func:`extract_variable` - :f subroutine gather_atoms: :f:func:`gather_atoms` - :f subroutine gather_atoms_concat: :f:func:`gather_atoms_concat` - :f subroutine gather_atoms_subset: :f:func:`gather_atoms_subset` - :f subroutine scatter_atoms: :f:func:`scatter_atoms` - :f subroutine scatter_atoms_subset: :f:func:`scatter_atoms_subset` - :f function version: :f:func:`version` - :f subroutine flush_buffers: :f:func:`flush_buffers` - :f function is_running: :f:func:`is_running` - :f function has_error: :f:func:`has_error` - :f subroutine get_last_error_message: :f:func:`get_last_error_message` + :f handle: reference to the LAMMPS class + :ftype handle: c_ptr + :f style: derived type to access lammps style constants + :ftype style: type(lammps_style) + :f type: derived type to access lammps type constants + :ftype type: type(lammps_type) + :f close: :f:subr:`close` + :ftype close: subroutine + :f subroutine error: :f:subr:`error` + :ftype error: subroutine + :f file: :f:subr:`file` + :ftype file: subroutine + :f command: :f:subr:`command` + :ftype command: subroutine + :f commands_list: :f:subr:`commands_list` + :ftype commands_list: subroutine + :f commands_string: :f:subr:`commands_string` + :ftype commands_string: subroutine + :f get_natoms: :f:func:`get_natoms` + :ftype get_natoms: function + :f get_thermo: :f:func:`get_thermo` + :ftype get_thermo: function + :f extract_box: :f:subr:`extract_box` + :ftype extract_box: subroutine + :f reset_box: :f:subr:`reset_box` + :ftype reset_box: subroutine + :f memory_usage: :f:subr:`memory_usage` + :ftype memory_usage: subroutine + :f get_mpi_comm: :f:func:`get_mpi_comm` + :ftype get_mpi_comm: function + :f extract_setting: :f:func:`extract_setting` + :ftype extract_setting: function + :f extract_global: :f:func:`extract_global` + :ftype extract_global: function + :f extract_atom: :f:func:`extract_atom` + :ftype extract_atom: function + :f extract_compute: :f:func:`extract_compute` + :ftype extract_compute: function + :f extract_fix: :f:func:`extract_fix` + :ftype extract_fix: function + :f extract_variable: :f:func:`extract_variable` + :ftype extract_variable: function + :f set_variable: :f:subr:`set_variable` + :ftype set_variable: subroutine + :f gather_atoms: :f:subr:`gather_atoms` + :ftype gather_atoms: subroutine + :f gather_atoms_concat: :f:subr:`gather_atoms_concat` + :ftype gather_atoms_concat: subroutine + :f gather_atoms_subset: :f:subr:`gather_atoms_subset` + :ftype gather_atoms_subset: subroutine + :f scatter_atoms: :f:subr:`scatter_atoms` + :ftype scatter_atoms: subroutine + :f scatter_atoms_subset: :f:subr:`scatter_atoms_subset` + :ftype scatter_atoms_subset: subroutine + :f gather_bonds: :f:subr:`gather_bonds` + :ftype gather_bonds: subroutine + :f gather: :f:subr:`gather` + :ftype gather: subroutine + :f gather_concat: :f:subr:`gather_concat` + :ftype gather_concat: subroutine + :f gather_subset: :f:subr:`gather_subset` + :ftype gather_subset: subroutine + :f scatter: :f:subr:`scatter` + :ftype scatter: subroutine + :f scatter_subset: :f:subr:`scatter_subset` + :ftype scatter_subset: subroutine + :f create_atoms: :f:subr:`create_atoms` + :ftype create_atoms: subroutine + :f find_pair_neighlist: :f:func:`find_pair_neighlist` + :ftype find_pair_neighlist: function + :f find_fix_neighlist: :f:func:`find_fix_neighlist` + :ftype find_fix_neighlist: function + :f find_compute_neighlist: :f:func:`find_compute_neighlist` + :ftype find_compute_neighlist: function + :f neighlist_num_elements: :f:func:`neighlist_num_elements` + :ftype neighlist_num_elements: function + :f neighlist_element_neighbors: :f:subr:`neighlist_element_neighbors` + :ftype neighlist_element_neighbors: subroutine + :f version: :f:func:`version` + :ftype version: function + :f get_os_info: :f:subr:`get_os_info` + :ftype get_os_info: subroutine + :f config_has_mpi_support: :f:func:`config_has_mpi_support` + :ftype config_has_mpi_support: function + :f config_has_gzip_support: :f:func:`config_has_gzip_support` + :ftype config_has_gzip_support: function + :f config_has_png_support: :f:func:`config_has_png_support` + :ftype config_has_png_support: function + :f config_has_jpeg_support: :f:func:`config_has_jpeg_support` + :ftype config_has_jpeg_support: function + :f config_has_ffmpeg_support: :f:func:`config_has_ffmpeg_support` + :ftype config_has_ffmpeg_support: function + :f config_has_exceptions: :f:func:`config_has_exceptions` + :ftype config_has_exceptions: function + :f config_has_package: :f:func:`config_has_package` + :ftype config_has_package: function + :f config_package_count: :f:func:`config_package_count` + :ftype config_package_count: function + :f config_package_name: :f:func:`config_package_name` + :ftype config_package_name: function + :f installed_packages: :f:subr:`installed_packages` + :ftype installed_packages: subroutine + :f config_accelerator: :f:func:`config_accelerator` + :ftype config_accelerator: function + :f has_gpu_device: :f:func:`has_gpu_device` + :ftype has_gpu_device: function + :f get_gpu_device_info: :f:subr:`get_gpu_device_info` + :ftype get_gpu_device_info: subroutine + :f has_style: :f:func:`has_style` + :ftype has_style: function + :f style_count: :f:func:`style_count` + :ftype style_count: function + :f style_name: :f:func:`style_name` + :ftype style_name: function + :f has_id: :f:func:`has_id` + :ftype has_id: function + :f id_count: :f:func:`id_count` + :ftype id_count: function + :f id_name: :f:subr:`id_name` + :ftype id_name: subroutine + :f plugin_count: :f:func:`plugin_count` + :ftype plugin_count: function + :f plugin_name: :f:subr:`plugin_name` + :ftype plugin_count: subroutine + :f encode_image_flags: :f:func:`encode_image_flags` + :ftype encode_image_flags: function + :f decode_image_flags: :f:subr:`decode_image_flags` + :ftype decode_image_flags: subroutine + :f set_fix_external_callback: :f:subr:`set_fix_external_callback` + :ftype set_fix_external_callback: subroutine + :f fix_external_get_force: :f:func:`fix_external_get_force` + :ftype fix_external_get_force: function + :f fix_external_set_energy_global: :f:subr:`fix_external_set_energy_global` + :ftype fix_external_set_energy_global: subroutine + :f fix_external_set_virial_global: :f:subr:`fix_external_set_virial_global` + :ftype fix_external_set_virial_global: subroutine + :f fix_external_set_energy_peratom: :f:subr:`fix_external_set_energy_peratom` + :ftype fix_external_set_energy_peratom: subroutine + :f fix_external_set_virial_peratom: :f:subr:`fix_external_set_virial_peratom` + :ftype fix_external_set_virial_peratom: subroutine + :f fix_external_set_vector_length: :f:subr:`fix_external_set_vector_length` + :ftype fix_external_set_vector_length: subroutine + :f fix_external_set_vector: :f:subr:`fix_external_set_vector` + :ftype fix_external_set_vector: subroutine + :f flush_buffers: :f:subr:`flush_buffers` + :ftype flush_buffers: subroutine + :f is_running: :f:func:`is_running` + :ftype is_running: function + :f force_timeout: :f:subr:`force_timeout` + :ftype force_timeout: subroutine + :f has_error: :f:func:`has_error` + :ftype has_error: function + :f get_last_error_message: :f:subr:`get_last_error_message` + :ftype get_last_error_message: subroutine -------- @@ -286,26 +405,30 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS. If *comm* is not provided, ``MPI_COMM_WORLD`` is assumed. For more details please see the documentation of :cpp:func:`lammps_open`. - :o character(len=\*) args(\*) [optional]: arguments as list of strings - :o integer comm [optional]: MPI communicator + :o args: arguments as list of strings + :otype args: character(len=\*),dimension(:),optional + :o comm: MPI communicator + :otype comm: integer,optional + :to: :cpp:func:`lammps_open_fortran` + :to: :cpp:func:`lammps_open_no_mpi` :r lammps: an instance of the :f:type:`lammps` derived type .. note:: - The ``MPI_F08`` module, which defines Fortran 2008 bindings for MPI, + The :f:mod:`MPI_F08` module, which defines Fortran 2008 bindings for MPI, is not directly supported by this interface due to the complexities of - supporting both the ``MPI_F08`` and ``MPI`` modules at the same time. - However, you should be able to use the ``MPI_VAL`` member of the + supporting both the :f:mod:`MPI_F08` and :f:mod:`MPI` modules at the same + time. However, you should be able to use the ``MPI_VAL`` member of the ``MPI_comm`` derived type to access the integer value of the communicator, such as in - .. code-block:: Fortran + .. code-block:: fortran PROGRAM testmpi USE LIBLAMMPS USE MPI_F08 TYPE(lammps) :: lmp - lmp = lammps(MPI_COMM_SELF%MPI_VAL) + lmp = lammps(comm=MPI_COMM_SELF%MPI_VAL) END PROGRAM testmpi .. f:type:: lammps_style @@ -317,6 +440,10 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS. and ``lmp%style%local``. These values are identical to the values described in :cpp:enum:`_LMP_STYLE_CONST` for the C library interface. + :f integer(c_int) global: used to request global data + :f integer(c_int) atom: used to request per-atom data + :f integer(c_int) local: used to request local data + .. f:type:: lammps_type This derived type is there to provide a convenient interface for the type @@ -326,18 +453,27 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS. ``lmp%type%array``. These values are identical to the values described in :cpp:enum:`_LMP_TYPE_CONST` for the C library interface. -Procedures Bound to the lammps Derived Type -=========================================== + :f integer(c_int) scalar: used to request scalars + :f integer(c_int) vector: used to request vectors + :f integer(c_int) array: used to request arrays (matrices) + +Procedures Bound to the :f:type:`lammps` Derived Type +===================================================== .. f:subroutine:: close([finalize]) This method will close down the LAMMPS instance through calling :cpp:func:`lammps_close`. If the *finalize* argument is present and has a value of ``.TRUE.``, then this subroutine also calls + :cpp:func:`lammps_kokkos_finalize` and :cpp:func:`lammps_mpi_finalize`. - :o logical finalize [optional]: shut down the MPI environment of the LAMMPS + :o finalize: shut down the MPI environment of the LAMMPS library if ``.TRUE.``. + :otype finalize: logical,optional + :to: :cpp:func:`lammps_close` + :to: :cpp:func:`lammps_mpi_finalize` + :to: :cpp:func:`lammps_kokkos_finalize` -------- @@ -346,10 +482,12 @@ Procedures Bound to the lammps Derived Type This method is a wrapper around the :cpp:func:`lammps_error` function and will dispatch an error through the LAMMPS Error class. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 - :p integer error_type: constant to select which Error class function to call + :p error_type: constant to select which Error class function to call + :ptype error_type: integer(c_int) :p character(len=\*) error_text: error message + :to: :cpp:func:`lammps_error` -------- @@ -359,6 +497,7 @@ Procedures Bound to the lammps Derived Type and process commands from a file. :p character(len=\*) filename: name of file with LAMMPS commands + :to: :cpp:func:`lammps_file` -------- @@ -368,6 +507,7 @@ Procedures Bound to the lammps Derived Type execute a single command. :p character(len=\*) cmd: single LAMMPS command + :to: :cpp:func:`lammps_command` -------- @@ -376,7 +516,8 @@ Procedures Bound to the lammps Derived Type This method will call :cpp:func:`lammps_commands_list` to have LAMMPS execute a list of input lines. - :p character(len=\*) cmd(:): list of LAMMPS input lines + :p character(len=\*) cmd [dimension(:)]: list of LAMMPS input lines + :to: :cpp:func:`lammps_commands_list` -------- @@ -386,6 +527,7 @@ Procedures Bound to the lammps Derived Type execute a block of commands from a string. :p character(len=\*) str: LAMMPS input in string + :to: :cpp:func:`lammps_commands_string` -------- @@ -394,7 +536,8 @@ Procedures Bound to the lammps Derived Type This function will call :cpp:func:`lammps_get_natoms` and return the number of atoms in the system. - :r real(c_double): number of atoms + :to: :cpp:func:`lammps_get_natoms` + :r real(c_double) natoms: number of atoms .. note:: @@ -409,10 +552,11 @@ Procedures Bound to the lammps Derived Type This function will call :cpp:func:`lammps_get_thermo` and return the value of the corresponding thermodynamic keyword. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 :p character(len=\*) name: string with the name of the thermo keyword - :r real(c_double): value of the requested thermo property or `0.0_c_double` + :to: :cpp:func:`lammps_get_thermo` + :r value [real(c_double)]: value of the requested thermo property or `0.0_c_double` -------- @@ -424,7 +568,7 @@ Procedures Bound to the lammps Derived Type as integers, but should be declared as ``LOGICAL`` variables when calling from Fortran. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 :o real(c_double) boxlo [dimension(3),optional]: vector in which to store lower-bounds of simulation box @@ -433,11 +577,14 @@ Procedures Bound to the lammps Derived Type :o real(c_double) xy [optional]: variable in which to store *xy* tilt factor :o real(c_double) yz [optional]: variable in which to store *yz* tilt factor :o real(c_double) xz [optional]: variable in which to store *xz* tilt factor - :o logical pflags [dimension(3),optional]: vector in which to store + :o pflags: vector in which to store periodicity flags (``.TRUE.`` means periodic in that dimension) - :o logical boxflag [optional]: variable in which to store boolean denoting + :otype pflags: logical,dimension(3),optional + :o boxflag: variable in which to store boolean denoting whether the box will change during a simulation (``.TRUE.`` means box will change) + :otype boxflag: logical,optional + :to: :cpp:func:`lammps_extract_box` .. note:: @@ -446,12 +593,12 @@ Procedures Bound to the lammps Derived Type represents a properly-initialized LAMMPS instance, the following code will extract the periodic box settings into the variable "periodic": - .. code-block:: Fortran + .. code-block:: fortran ! code to start up - logical :: periodic(3) + LOGICAL :: periodic(3) ! code to initialize LAMMPS / run things / etc. - call lmp%extract_box(pflags = periodic) + CALL lmp%extract_box(pflags = periodic) -------- @@ -460,7 +607,7 @@ Procedures Bound to the lammps Derived Type This subroutine will call :cpp:func:`lammps_reset_box`. All parameters are required. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 :p real(c_double) boxlo [dimension(3)]: vector of three doubles containing the lower box boundary @@ -469,6 +616,7 @@ Procedures Bound to the lammps Derived Type :p real(c_double) xy: *x--y* tilt factor :p real(c_double) yz: *y--z* tilt factor :p real(c_double) xz: *x--z* tilt factor + :to: :cpp:func:`lammps_reset_box` -------- @@ -477,10 +625,11 @@ Procedures Bound to the lammps Derived Type This subroutine will call :cpp:func:`lammps_memory_usage` and store the result in the three-element array *meminfo*. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 :p real(c_double) meminfo [dimension(3)]: vector of three doubles in which to store memory usage data + :to: :cpp:func:`lammps_memory_usage` -------- @@ -489,10 +638,12 @@ Procedures Bound to the lammps Derived Type This function returns a Fortran representation of the LAMMPS "world" communicator. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 - :r integer: Fortran integer equivalent to the MPI communicator LAMMPS is + :to: :cpp:func:`lammps_get_mpi_comm` + :r comm: Fortran integer equivalent to the MPI communicator LAMMPS is using + :rtype comm: integer .. note:: @@ -504,7 +655,7 @@ Procedures Bound to the lammps Derived Type .. note:: - The ``MPI_F08`` module, which defines Fortran 2008 bindings for MPI, + The :f:mod:`MPI_F08` module, which defines Fortran 2008 bindings for MPI, is not directly supported by this function. However, you should be able to convert between the two using the `MPI_VAL` member of the communicator. For example, @@ -513,12 +664,12 @@ Procedures Bound to the lammps Derived Type USE MPI_F08 USE LIBLAMMPS - TYPE (lammps) :: lmp - TYPE (MPI_Comm) :: comm + TYPE(lammps) :: lmp + TYPE(MPI_Comm) :: comm ! ... [commands to set up LAMMPS/etc.] comm%MPI_VAL = lmp%get_mpi_comm() - should assign an ``MPI_F08`` communicator properly. + should assign an :f:mod:`MPI_F08` communicator properly. -------- @@ -527,10 +678,12 @@ Procedures Bound to the lammps Derived Type Query LAMMPS about global settings. See the documentation for the :cpp:func:`lammps_extract_setting` function from the C library. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 :p character(len=\*) keyword: string containing the name of the thermo keyword - :r integer(c_int): value of the queried setting or :math:`-1` if unknown + :to: :cpp:func:`lammps_extract_setting` + :r integer(c_int) setting: value of the queried setting or :math:`-1` if + unknown -------- @@ -540,7 +693,7 @@ Procedures Bound to the lammps Derived Type either a string or a pointer to internal global LAMMPS data, depending on the data requested through *name*. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 Note that this function actually does not return a value, but rather associates the pointer on the left side of the assignment to point to @@ -552,7 +705,7 @@ Procedures Bound to the lammps Derived Type LAMMPS data is type-, kind-, and rank-checked at run-time via an overloaded assignment operator. The pointers returned by this function are generally persistent; therefore it is not necessary to - call the function again, unless a :doc:`clear` command has been + call the function again unless a :doc:`clear` command has been issued, which wipes out and recreates the contents of the :cpp:class:`LAMMPS ` class. @@ -593,7 +746,7 @@ Procedures Bound to the lammps Derived Type but you can automatically reallocate it to the correct length after the function returns, viz., - .. code-block :: Fortran + .. code-block :: fortran PROGRAM test USE LIBLAMMPS @@ -601,7 +754,7 @@ Procedures Bound to the lammps Derived Type CHARACTER(LEN=:), ALLOCATABLE :: str lmp = lammps() CALL lmp%command('units metal') - ALLOCATE ( CHARACTER(LEN=80) :: str ) + ALLOCATE(CHARACTER(LEN=80) :: str) str = lmp%extract_global('units') str = TRIM(str) ! re-allocates to length len_trim(str) here PRINT*, LEN(str), LEN_TRIM(str) @@ -610,10 +763,12 @@ Procedures Bound to the lammps Derived Type will print the number 5 (the length of the word "metal") twice. :p character(len=\*) name: string with the name of the property to extract - :r polymorphic: pointer to LAMMPS data. The left-hand side of the assignment - should be either a string (if expecting string data) or a C-compatible - pointer (e.g., ``INTEGER (c_int), POINTER :: nlocal``) to the extracted - property. If expecting vector data, the pointer should have dimension ":". + :to: :cpp:func:`lammps_extract_global` + :r pointer [polymorphic]: pointer to LAMMPS data. The left-hand side of the + assignment should be either a string (if expecting string data) or a + C-compatible pointer (e.g., ``INTEGER(c_int), POINTER :: nlocal``) to the + extracted property. If expecting vector data, the pointer should have + dimension ":". .. warning:: @@ -628,112 +783,118 @@ Procedures Bound to the lammps Derived Type .. f:function:: extract_atom(name) - This function calls :c:func:`lammps_extract_atom` and returns a pointer to + This function calls :cpp:func:`lammps_extract_atom` and returns a pointer to LAMMPS data tied to the :cpp:class:`Atom` class, depending on the data requested through *name*. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 Note that this function actually does not return a pointer, but rather associates the pointer on the left side of the assignment to point to internal LAMMPS data. Pointers must be of the correct type, kind, and - rank (e.g., ``INTEGER(c_int), DIMENSION(:)`` for "type", "mask", or "tag"; - ``INTEGER(c_int64_t), DIMENSION(:)`` for "tag" if LAMMPS was compiled + rank (e.g., ``INTEGER(c_int), DIMENSION(:)`` for "type", "mask", or "id"; + ``INTEGER(c_int64_t), DIMENSION(:)`` for "id" if LAMMPS was compiled with the ``-DLAMMPS_BIGBIG`` flag; ``REAL(c_double), DIMENSION(:,:)`` for "x", "v", or "f"; and so forth). The pointer being associated with LAMMPS - data is type-, kind-, and rank-checked at run-time. Pointers returned by - this function are generally persistent; therefore, it is not necessary to - call the function again unless the underlying LAMMPS data are destroyed, - such as through the :doc:`clear` command. + data is type-, kind-, and rank-checked at run-time. :p character(len=\*) name: string with the name of the property to extract - :r polymorphic: pointer to LAMMPS data. The left-hand side of the assignment - should be a C-interoperable pointer of appropriate kind and rank - (e.g., ``INTEGER (c_int), POINTER :: mask(:)``) to the extracted + :to: :cpp:func:`lammps_extract_atom` + :r pointer: pointer to LAMMPS data. The left-hand side of the + assignment should be a C-interoperable pointer of appropriate kind and rank + (e.g., ``INTEGER(c_int), POINTER :: mask(:)``) to the extracted property. If expecting vector data, the pointer should have dimension ":"; if expecting matrix data, the pointer should have dimension ":,:". + :rtype pointer: polymorphic - .. admonition:: Array index order + .. warning:: - Two-dimensional arrays returned from :f:func:`extract_atom` will be - **transposed** from equivalent arrays in C, and they will be indexed - from 1 instead of 0. For example, in C, + Pointers returned by this function are generally not persistent, as + per-atom data may be redistributed, reallocated, and reordered at every + re-neighboring operation. It is advisable to re-bind pointers using + :f:func:`extract_atom` between runs. - .. code-block:: C + .. admonition:: Array index order - void *lmp; - double **x; - /* more code to setup, etc. */ - x = lammps_extract_atom(lmp, "x"); - printf("%f\n", x[5][1]); + Two-dimensional arrays returned from :f:func:`extract_atom` will be + **transposed** from equivalent arrays in C, and they will be indexed + from 1 instead of 0. For example, in C, - will print the *y*-coordinate of the sixth atom on this processor. - Conversely, + .. code-block:: c - .. code-block:: Fortran + void *lmp; + double **x; + /* more code to setup, etc. */ + x = lammps_extract_atom(lmp, "x"); + printf("%f\n", x[5][1]); - TYPE(lammps) :: lmp - REAL(c_double), DIMENSION(:,:), POINTER :: x => NULL() - ! more code to setup, etc. - x = lmp%extract_atom("x") - print '(f0.6)', x(2,6) + will print the *y*-coordinate of the sixth atom on this processor. + Conversely, - will print the *y*-coordinate of the sixth atom on this processor - (note the transposition of the two indices). This is not a choice, but - rather a consequence of the different conventions adopted by the Fortran - and C standards decades ago: in C, the block of data + .. code-block:: fortran - .. parsed-literal:: + TYPE(lammps) :: lmp + REAL(c_double), DIMENSION(:,:), POINTER :: x => NULL() + ! more code to setup, etc. + x = lmp%extract_atom("x") + PRINT '(f0.6)', x(2,6) - 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 + will print the *y*-coordinate of the sixth atom on this processor + (note the transposition of the two indices). This is not a choice, but + rather a consequence of the different conventions adopted by the Fortran + and C standards decades ago: in C, the block of data - interpreted as a :math:`4\times4` matrix would be + .. parsed-literal:: - .. math:: + 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 - \begin{bmatrix} - 1 & 2 & 3 & 4 \\ - 5 & 6 & 7 & 8 \\ - 9 & 10 & 11 & 12 \\ - 13 & 14 & 15 & 16 - \end{bmatrix}, + interpreted as a :math:`4\times4` matrix would be - that is, in row-major order. In Fortran, the same block of data is - interpreted in column-major order, namely, + .. math:: - .. math:: + \begin{bmatrix} + 1 & 2 & 3 & 4 \\ + 5 & 6 & 7 & 8 \\ + 9 & 10 & 11 & 12 \\ + 13 & 14 & 15 & 16 + \end{bmatrix}, - \begin{bmatrix} - 1 & 5 & 9 & 13 \\ - 2 & 6 & 10 & 14 \\ - 3 & 7 & 11 & 15 \\ - 4 & 8 & 12 & 16 - \end{bmatrix}. + that is, in row-major order. In Fortran, the same block of data is + interpreted in column-major order, namely, - This difference in interpretation of the same block of data by the two - languages means, in effect, that matrices from C or C++ will be - transposed when interpreted in Fortran. + .. math:: - .. note:: + \begin{bmatrix} + 1 & 5 & 9 & 13 \\ + 2 & 6 & 10 & 14 \\ + 3 & 7 & 11 & 15 \\ + 4 & 8 & 12 & 16 + \end{bmatrix}. - If you would like the indices to start at 0 instead of 1 (which follows - typical notation in C and C++, but not Fortran), you can create another - pointer and associate it thus: + This difference in interpretation of the same block of data by the two + languages means, in effect, that matrices from C or C++ will be + transposed when interpreted in Fortran. - .. code-block:: Fortran + .. note:: - REAL(c_double), DIMENSION(:,:), POINTER :: x, x0 - x = lmp%extract_atom("x") - x0(0:,0:) => x + If you would like the indices to start at 0 instead of 1 (which follows + typical notation in C and C++, but not Fortran), you can create another + pointer and associate it thus: - The above would cause the dimensions of *x* to be (1:3, 1:nmax) - and those of *x0* to be (0:2, 0:nmax-1). + .. code-block:: fortran + + REAL(c_double), DIMENSION(:,:), POINTER :: x, x0 + x = lmp%extract_atom("x") + x0(0:,0:) => x + + The above would cause the dimensions of *x* to be (1:3, 1:nmax) + and those of *x0* to be (0:2, 0:nmax\ :math:`-`\ 1). -------- .. f:function:: extract_compute(id, style, type) - This function calls :c:func:`lammps_extract_compute` and returns a pointer + This function calls :cpp:func:`lammps_extract_compute` and returns a pointer to LAMMPS data tied to the :cpp:class:`Compute` class, specifically data provided by the compute identified by *id*. Computes may provide global, per-atom, or local data, and those data may be a scalar, a vector, or an @@ -741,7 +902,7 @@ Procedures Bound to the lammps Derived Type required to specify which set of data is to be returned through the *style* and *type* variables. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 Note that this function actually does not return a value, but rather associates the pointer on the left side of the assignment to point to @@ -752,12 +913,12 @@ Procedures Bound to the lammps Derived Type For example, - .. code-block:: Fortran + .. code-block:: fortran TYPE(lammps) :: lmp REAL(c_double), DIMENSION(:), POINTER :: COM ! code to setup, create atoms, etc. - CALL lmp%compute('compute COM all com') + CALL lmp%command('compute COM all com') COM = lmp%extract_compute('COM', lmp%style%global, lmp%style%type) will bind the variable *COM* to the center of mass of the atoms created in @@ -817,11 +978,13 @@ Procedures Bound to the lammps Derived Type (global, per-atom, or local) :p integer(c_int) type: value indicating the type of data to extract (scalar, vector, or array) - :r polymorphic: pointer to LAMMPS data. The left-hand side of the assignment - should be a C-compatible pointer (e.g., ``REAL (c_double), POINTER :: x``) + :to: :cpp:func:`lammps_extract_compute` + :r pointer: pointer to LAMMPS data. The left-hand side of the assignment + should be a C-compatible pointer (e.g., ``REAL(c_double), POINTER :: x``) to the extracted property. If expecting vector data, the pointer should have dimension ":"; if expecting array (matrix) data, the pointer should have dimension ":,:". + :rtype pointer: polymorphic .. note:: @@ -843,7 +1006,7 @@ Procedures Bound to the lammps Derived Type .. f:function:: extract_fix(id, style, type[, nrow][, ncol]) - This function calls :c:func:`lammps_extract_fix` and returns a pointer to + This function calls :cpp:func:`lammps_extract_fix` and returns a pointer to LAMMPS data tied to the :cpp:class:`Fix` class, specifically data provided by the fix identified by *id*. Fixes may provide global, per-atom, or local data, and those data may be a scalar, a vector, or an array. Since @@ -851,7 +1014,7 @@ Procedures Bound to the lammps Derived Type which set of data is to be returned through the *style* and *type* variables. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 Global data are calculated at the time they are requested and are only available element-by-element. As such, the user is expected to provide @@ -929,16 +1092,16 @@ Procedures Bound to the lammps Derived Type - Per-atom array In the case of global data, this function returns a value of type - ``real(c_double)``. For per-atom or local data, this function does not + ``REAL(c_double)``. For per-atom or local data, this function does not return a value but instead associates the pointer on the left side of the assignment to point to internal LAMMPS data. Pointers must be of the correct - data type to point to said data (i.e., ``REAL(c_double)``) and have + type and kind to point to said data (i.e., ``REAL(c_double)``) and have compatible rank. The pointer being associated with LAMMPS data is type-, kind-, and rank-checked at run-time via an overloaded assignment operator. For example, - .. code-block:: Fortran + .. code-block:: fortran TYPE(lammps) :: lmp REAL(c_double) :: dr, dx, dy, dz @@ -960,7 +1123,7 @@ Procedures Bound to the lammps Derived Type appropriate size to match the internal data, and will be type/kind/rank-checked at the time of the assignment. For example, - .. code-block:: Fortran + .. code-block:: fortran TYPE(lammps) :: lmp REAL(c_double), DIMENSION(:), POINTER :: r @@ -973,7 +1136,7 @@ Procedures Bound to the lammps Derived Type array computed by :doc:`fix store/state ` when three inputs are specified. Similarly, - .. code-block:: Fortran + .. code-block:: fortran TYPE(lammps) :: lmp REAL(c_double), DIMENSION(:), POINTER :: x @@ -1010,7 +1173,8 @@ Procedures Bound to the lammps Derived Type (scalar, vector, or array) :p integer(c_int) nrow: row index (used only for global vectors and arrays) :p integer(c_int) ncol: column index (only used for global arrays) - :r polymorphic: LAMMPS data (for global data) or a pointer to LAMMPS data + :to: :cpp:func:`lammps_extract_fix` + :r data: LAMMPS data (for global data) or a pointer to LAMMPS data (for per-atom or local data). The left-hand side of the assignment should be of type ``REAL(c_double)`` and have appropriate rank (i.e., ``DIMENSION(:)`` if expecting per-atom or local vector data and @@ -1018,6 +1182,7 @@ Procedures Bound to the lammps Derived Type local or per-atom data, it should have the ``POINTER`` attribute, but if expecting global data, it should be an ordinary (non-``POINTER``) variable. + :rtype data: polymorphic .. admonition:: Array index order @@ -1034,8 +1199,8 @@ Procedures Bound to the lammps Derived Type .. f:function:: extract_variable(name[,group]) - This function calls :c:func:`lammps_extract_variable` and returns a scalar, - vector, or string containing the value of the variable identified by + This function calls :cpp:func:`lammps_extract_variable` and returns a + scalar, vector, or string containing the value of the variable identified by *name*. When the variable is an *equal*-style variable (or one compatible with that style such as *internal*), the variable is evaluated and the corresponding value returned. When the variable is an *atom*-style variable, @@ -1044,7 +1209,7 @@ Procedures Bound to the lammps Derived Type for *atom* style variables and is ignored otherwise. If *group* is absent for *atom*-style variables, the group is assumed to be "all". - .. versionadded:: TBD + .. versionadded:: 3Nov2022 This function returns the values of the variables, not pointers to them. Vectors pointing to *atom*-style variables should be of type @@ -1059,7 +1224,7 @@ Procedures Bound to the lammps Derived Type For example, - .. code-block:: Fortran + .. code-block:: fortran TYPE(lammps) :: lmp REAL(c_double) :: area @@ -1074,7 +1239,8 @@ Procedures Bound to the lammps Derived Type :p character(len=\*) name: variable name to evaluate :o character(len=\*) group [optional]: group for which to extract per-atom data (if absent, use "all") - :r polymorphic: scalar of type ``REAL(c_double)`` (for *equal*-style + :to: :cpp:func:`lammps_extract_variable` + :r data: scalar of type ``REAL(c_double)`` (for *equal*-style variables and others that are *equal*-compatible), vector of type ``REAL(c_double), DIMENSION(:), ALLOCATABLE`` for *atom*- or *vector*-style variables, or ``CHARACTER(LEN=*)`` for *string*-style and compatible @@ -1083,6 +1249,7 @@ Procedures Bound to the lammps Derived Type called; see note at :f:func:`extract_global` regarding allocatable strings. Allocatable arrays (for *atom*- and *vector*-style data) will be reallocated on assignment. + :rtype data: polymorphic .. note:: @@ -1094,42 +1261,64 @@ Procedures Bound to the lammps Derived Type -------- +.. f:subroutine:: set_variable(name, str) + + Set the value of a string-style variable. + + .. versionadded:: 3Nov2022 + + This function assigns a new value from the string *str* to the string-style + variable *name*\ . If *name* does not exist or is not a string-style + variable, an error is generated. + + :p character(len=*) name: name of the variable + :p character(len=*) str: new value to assign to the variable + :to: :cpp:func:`lammps_set_variable` + +-------- + .. f:subroutine:: gather_atoms(name, count, data) - This function calls :c:func:`lammps_gather_atoms` to gather the named + This function calls :cpp:func:`lammps_gather_atoms` to gather the named atom-based entity for all atoms on all processors and return it in the vector *data*. The vector *data* will be ordered by atom ID, which requires consecutive atom IDs (1 to *natoms*). - .. versionadded:: TBD + .. versionadded:: 3Nov2022 If you need a similar array but have non-consecutive atom IDs, see :f:func:`gather_atoms_concat`; for a similar array but for a subset of atoms, see :f:func:`gather_atoms_subset`. The *data* array will be ordered in groups of *count* values, sorted by atom - ID (e.g., if *name* is *x* and *count* = 3, then *data* = x[1][1], x[2][1], - x[3][1], x[1][2], x[2][2], x[3][2], x[1][3], :math:`\dots`); - *data* must be ``ALLOCATABLE`` and will be allocated to length - (*count* :math:`\times` *natoms*), as queried by - :f:func:`extract_setting`. + ID (e.g., if *name* is *x* and *count* = 3, then *data* = [*x*\ (1,1), + *x*\ (2,1), *x*\ (3,1), *x*\ (1,2), *x*\ (2,2), *x*\ (3,2), *x*\ (1,3), + :math:`\dots`]); *data* must be ``ALLOCATABLE`` and will be allocated to + length (*count* :math:`\times` *natoms*), as queried by + :f:func:`get_natoms`. + + This function is not compatible with ``-DLAMMPS_BIGBIG``. :p character(len=\*) name: desired quantity (e.g., *x* or *mask*) :p integer(c_int) count: number of per-atom values you expect per atom (e.g., 1 for *type*, *mask*, or *charge*; 3 for *x*, *v*, or *f*). Use *count* = 3 with *image* if you want a single image flag unpacked into *x*/*y*/*z* components. - :p real(c_double) data [dimension(:),allocatable]: array into which to store + :p data: array into which to store the data. Array *must* have the ``ALLOCATABLE`` attribute and be of rank 1 (i.e., ``DIMENSION(:)``). If this array is already allocated, it will be - reallocated to fit the length of the incoming data. + reallocated to fit the length of the incoming data. It should have type + ``INTEGER(c_int)`` if expecting integer data and ``REAL(c_double)`` if + expecting floating-point data. + :ptype data: polymorphic,dimension(:),allocatable + :to: :cpp:func:`lammps_gather_atoms` .. note:: If you want data from this function to be accessible as a two-dimensional array, you can declare a rank-2 pointer and reassign it, like so: - .. code-block:: Fortran + .. code-block:: fortran USE, INTRINSIC :: ISO_C_BINDING USE LIBLAMMPS @@ -1147,11 +1336,11 @@ Procedures Bound to the lammps Derived Type .. f:subroutine:: gather_atoms_concat(name, count, data) - This function calls :c:func:`lammps_gather_atoms_concat` to gather the named - atom-based entity for all atoms on all processors and return it in the + This function calls :cpp:func:`lammps_gather_atoms_concat` to gather the + named atom-based entity for all atoms on all processors and return it in the vector *data*. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 The vector *data* will not be ordered by atom ID, and there is no restriction on the IDs being consecutive. If you need the IDs, you can do @@ -1161,28 +1350,34 @@ Procedures Bound to the lammps Derived Type :f:func:`gather_atoms`; for a similar array but for a subset of atoms, see :f:func:`gather_atoms_subset`. + This function is not compatible with ``-DLAMMPS_BIGBIG``. + :p character(len=\*) name: desired quantity (e.g., *x* or *mask*) :p integer(c_int) count: number of per-atom values you expect per atom (e.g., 1 for *type*, *mask*, or *charge*; 3 for *x*, *v*, or *f*). Use *count* = 3 with *image* if you want a single image flag unpacked into *x*/*y*/*z* components. - :p real(c_double) data [dimension(:),allocatable]: array into which to store + :p data: array into which to store the data. Array *must* have the ``ALLOCATABLE`` attribute and be of rank 1 (i.e., ``DIMENSION(:)``). If this array is already allocated, it will be - reallocated to fit the length of the incoming data. + reallocated to fit the length of the incoming data. It should have type + ``INTEGER(c_int)`` if expecting integer data and ``REAL(c_double)`` if + expecting floating-point data. + :ptype data: polymorphic,dimension(:),allocatable + :to: :cpp:func:`lammps_gather_atoms_concat` -------- .. f:subroutine:: gather_atoms_subset(name, count, ids, data) - This function calls :c:func:`lammps_gather_atoms_subset` to gather the named - atom-based entity for the atoms in the array *ids* from all processors and - return it in the vector *data*. + This function calls :cpp:func:`lammps_gather_atoms_subset` to gather the + named atom-based entity for the atoms in the array *ids* from all processors + and return it in the vector *data*. - .. versionadded: TBD + .. versionadded:: 3Nov2022 This subroutine gathers data for the requested atom IDs and stores them in a - one-dimensional array allocated by the user. The data will be ordered by + one-dimensional allocatable array. The data will be ordered by atom ID, but there is no requirement that the IDs be consecutive. If you wish to return a similar array for *all* the atoms, use :f:func:`gather_atoms` or :f:func:`gather_atoms_concat`. @@ -1190,9 +1385,12 @@ Procedures Bound to the lammps Derived Type The *data* array will be in groups of *count* values, sorted by atom ID in the same order as the array *ids* (e.g., if *name* is *x*, *count* = 3, and *ids* is [100, 57, 210], then *data* might look like - [x(1,100), x(2,100), x(3,100), x(1,57), x(2,57), x(3,57), x(1,210), - :math:`\dots`]; *ids* must be provided by the user, and *data* must be - of rank 1 (i.e., ``DIMENSION(:)``) and have the ``ALLOCATABLE`` attribute. + [*x*\ (1,100), *x*\ (2,100), *x*\ (3,100), *x*\ (1,57), *x*\ (2,57), + *x*\ (3,57), *x*\ (1,210), :math:`\dots`]; *ids* must be provided by the + user, and *data* must be of rank 1 (i.e., ``DIMENSION(:)``) and have the + ``ALLOCATABLE`` attribute. + + This function is not compatible with ``-DLAMMPS_BIGBIG``. :p character(len=\*) name: desired quantity (e.g., *x* or *mask*) :p integer(c_int) count: number of per-atom values you expect per atom @@ -1201,19 +1399,23 @@ Procedures Bound to the lammps Derived Type *x*/*y*/*z* components. :p integer(c_int) ids [dimension(:)]: atom IDs corresponding to the atoms to be gathered - :p real(c_double) data [dimension(:),allocatable]: array into which to store + :p data: array into which to store the data. Array *must* have the ``ALLOCATABLE`` attribute and be of rank 1 (i.e., ``DIMENSION(:)``). If this array is already allocated, it will be - reallocated to fit the length of the incoming data. + reallocated to fit the length of the incoming data. It should have type + ``INTEGER(c_int)`` if expecting integer data and ``REAL(c_double)`` if + expecting floating-point data. + :ptype data: polymorphic,dimension(:),allocatable + :to: :cpp:func:`lammps_gather_atoms_subset` -------- .. f:subroutine:: scatter_atoms(name, data) - This function calls :c:func:`lammps_scatter_atoms` to scatter the named + This function calls :cpp:func:`lammps_scatter_atoms` to scatter the named atom-based entities in *data* to all processors. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 This subroutine takes data stored in a one-dimensional array supplied by the user and scatters them to all atoms on all processors. The data must be @@ -1223,25 +1425,28 @@ Procedures Bound to the lammps Derived Type The *data* array needs to be ordered in groups of *count* values, sorted by atom ID (e.g., if *name* is *x* and *count* = 3, then - *data* = [x(1,1) x(2,1) x(3,1) x(1,2) x(2,2) x(3,2) x(1,3) :math:`\dots`]; - *data* must be of length (*count* :math:`\times` *natoms*). + *data* = [*x*\ (1,1), *x*\ (2,1), *x*\ (3,1), *x*\ (1,2), *x*\ (2,2), + *x*\ (3,2), *x*\ (1,3), :math:`\dots`]); *data* must be of length *natoms* + or 3\*\ *natoms*. :p character(len=\*) name: quantity to be scattered (e.g., *x* or *charge*) - :p polymorphic data [dimension(:)]: per-atom values packed in a one-dimensional array + :p data: per-atom values packed in a one-dimensional array containing the data to be scattered. This array must have length *natoms* - (e.g., for *type* or *charge*) or length *natoms*\ :math:`\times 3` + (e.g., for *type* or *charge*) or length *natoms*\ :math:`{}\times 3` (e.g., for *x* or *f*). The array *data* must be rank 1 (i.e., ``DIMENSION(:)``) and be of type ``INTEGER(c_int)`` (e.g., for *mask* or *type*) or of type ``REAL(c_double)`` (e.g., for *x* or *charge* or *f*). + :ptype data: polymorphic,dimension(:) + :to: :cpp:func:`lammps_scatter_atoms` -------- .. f:subroutine:: scatter_atoms_subset(name, ids, data) - This function calls :c:func:`lammps_scatter_atoms_subset` to scatter the + This function calls :cpp:func:`lammps_scatter_atoms_subset` to scatter the named atom-based entities in *data* to all processors. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 This subroutine takes data stored in a one-dimensional array supplied by the user and scatters them to a subset of atoms on all processors. The array @@ -1252,18 +1457,429 @@ Procedures Bound to the lammps Derived Type The *data* array needs to be organized in groups of 1 or 3 values, depending on which quantity is being scattered, with the groups in the same order as the array *ids*. For example, if you want *data* to be the array - [x(1,1) x(2,1) x(3,1) x(1,100) x(2,100) x(3,100) x(1,57) x(2,57) x(3,57)], - then *ids* would be [1 100 57] and *name* would be *x*. + [*x*\ (1,1), *x*\ (2,1), *x*\ (3,1), *x*\ (1,100), *x*\ (2,100), + *x*\ (3,100), *x*\ (1,57), *x*\ (2,57), *x*\ (3,57)], then *ids* would be + [1, 100, 57] and *name* would be *x*. :p character(len=\*) name: quantity to be scattered (e.g., *x* or *charge*) :p integer(c_int) ids [dimension(:)]: atom IDs corresponding to the atoms being scattered - :p polymorphic data [dimension(:)]: per-atom values packed into a + :p data: per-atom values packed into a one-dimensional array containing the data to be scattered. This array must have either the same length as *ids* (for *mask*, *type*, etc.) or three times its length (for *x*, *f*, etc.); the array must be rank 1 and be of type ``INTEGER(c_int)`` (e.g., for *mask* or *type*) or of type - ``REAL(c_double)`` (e.g., *charge*, *x*, or *f*). + ``REAL(c_double)`` (e.g., for *charge*, *x*, or *f*). + :ptype data: polymorphic,dimension(:) + :to: :cpp:func:`lammps_scatter_atoms_subset` + +-------- + +.. f:subroutine:: gather_bonds(data) + + Gather type and constituent atom information for all bonds. + + .. versionadded:: 3Nov2022 + + This function copies the list of all bonds into an allocatable array. + The array will be filled with (bond type, bond atom 1, bond atom 2) for each + bond. The array is allocated to the right length (i.e., three times the + number of bonds). The array *data* must be of the same type as the LAMMPS + ``tagint`` type, which is equivalent to either ``INTEGER(c_int)`` or + ``INTEGER(c_int64_t)``, depending on whether ``-DLAMMPS_BIGBIG`` was used + when LAMMPS was built. If the supplied array does not match, an error will + result at run-time. + + An example of how to use this routine is below: + + .. code-block:: fortran + + PROGRAM bonds + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int + USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT + USE LIBLAMMPS + IMPLICIT NONE + INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET :: bonds + INTEGER(c_int), DIMENSION(:,:), POINTER :: bonds_array + TYPE(lammps) :: lmp + INTEGER :: i + ! other commands to initialize LAMMPS, create bonds, etc. + CALL lmp%gather_bonds(bonds) + bonds_array(1:3, 1:SIZE(bonds)/3) => bonds + DO i = 1, SIZE(bonds)/3 + WRITE(OUTPUT_UNIT,'(A,1X,I4,A,I4,1X,I4)') 'bond', bonds_array(1,i), & + '; type = ', bonds_array(2,i), bonds_array(3,i) + END DO + END PROGRAM bonds + + :p data: array into which to copy the result. \*The ``KIND`` parameter is + either ``c_int`` or, if LAMMPS was compiled with ``-DLAMMPS_BIGBIG``, + kind ``c_int64_t``. + :ptype data: integer(kind=\*),allocatable + :to: :cpp:func:`lammps_gather_bonds` + +-------- + +.. f:subroutine:: gather(self, name, count, data) + + Gather the named per-atom, per-atom fix, per-atom compute, or fix + property/atom-based entities from all processes, in order by atom ID. + + .. versionadded:: 22Dec2022 + + This subroutine gathers data from all processes and stores them in a + one-dimensional allocatable array. The array *data* will be + ordered by atom ID, which requires consecutive IDs (1 to *natoms*\ ). If you + need a similar array but for non-consecutive atom IDs, see + :cpp:func:`lammps_gather_concat`; for a similar array but for a subset of + atoms, see :cpp:func:`lammps_gather_subset`. + + The *data* array will be ordered in groups of *count* values, sorted by atom + ID (e.g., if *name* is *x*, then *data* is [x(1,1), x(2,1), x(3,1), x(1,2), + x(2,2), x(3,2), x(1,3), :math:`\dots`]); *data* must be ``ALLOCATABLE`` and + will be allocated to length (*count*\ :math:`{}\times{}`\ *natoms*), as + queried by :f:func:`get_natoms`. + + This function will return an error if fix or compute data are requested and + the fix or compute ID given does not have per-atom data. See the note about + re-interpreting the vector as a matrix at :f:subr:`gather_atoms`. + + This function is not compatible with ``-DLAMMPS_BIGBIG``. + + :p character(len=\*) name: desired quantity (e.g., "x" or "mask" for atom + properties, "f_id" for per-atom fix data, "c_id" for per-atom compute data, + "d_name" or "i_name" for fix property/atom vectors with *count* = 1, + "d2_name" or "i2_name" for fix property/atom vectors with + *count*\ :math:`{}> 1`) + :p integer(c_int) count: number of per-atom values (e.g., 1 for *type* or + *charge*, 3 for *x* or *f*); use *count* = 3 with *image* if you want the + image flags unpacked into (*x*,\ *y*,\ *z*) components. + :p real(c_double) data [dimension(:),allocatable]: array into which to store + the data. Array *must* have the ``ALLOCATABLE`` attribute and be of rank 1 + (i.e., ``DIMENSION(:)``). If this array is already allocated, it will be + reallocated to fit the length of the incoming data. + :to: :cpp:func:`lammps_gather` + +-------- + +.. f:subroutine:: gather_concat(self, name, count, data) + + Gather the named per-atom, per-atom fix, per-atom compute, or fix + property/atom-based entities from all processes, unordered. + + .. versionadded:: 22Dec2022 + + This subroutine gathers data for all atoms and stores them in a + one-dimensional allocatable array. The data will be a + concatenation of chunks from each processor's owned atoms, in whatever order + the atoms are in on each processor. This process has no requirement that the + atom IDs be consecutive. If you need the ID of each atom, you can do another + call to either :f:subr:`gather_atoms_concat` or :f:subr:`gather_concat` with + *name* set to ``id``. If you have consecutive IDs and want the data to be in + order, use :f:subr:`gather`; for a similar array but for a subset of + atoms, use :f:subr:`gather_subset`. + + The *data* array will be in groups of *count* values, with *natoms* groups + total, but not in order by atom ID (e.g., if *name* is *x* and *count* is 3, + then *data* might be something like [x(1,11), x(2,11), x(3,11), x(1,3), + x(2,3), x(3,3), x(1,5), :math:`\dots`]); *data* must be ``ALLOCATABLE`` and + will be allocated to length (*count* :math:`\times` *natoms*), as queried by + :f:func:`get_natoms`. + + This function is not compatible with ``-DLAMMPS_BIGBIG``. + + :p character(len=\*) name: desired quantity (e.g., "x" or "mask" for atom + properties, "f_id" for per-atom fix data, "c_id" for per-atom compute data, + "d_name" or "i_name" for fix property/atom vectors with *count* = 1, + "d2_name" or "i2_name" for fix property/atom vectors with + *count*\ :math:`{}> 1`) + :p integer(c_int) count: number of per-atom values you expect per atom + (e.g., 1 for *type*, *mask*, or *charge*; 3 for *x*, *v*, or *f*). Use + *count* = 3 with *image* if you want a single image flag unpacked into + *x*/*y*/*z* components. + :p data: array into which to store + the data. Array *must* have the ``ALLOCATABLE`` attribute and be of rank 1 + (i.e., ``DIMENSION(:)``). If this array is already allocated, it will be + reallocated to fit the length of the incoming data. It should have type + ``INTEGER(c_int)`` if expecting integer data and ``REAL(c_double)`` if + expecting floating-point data. + :ptype data: polymorphic,dimension(:),allocatable + :to: :cpp:func:`lammps_gather_concat` + +-------- + +.. f:subroutine:: gather_subset(name, count, ids, data) + + Gather the named per-atom, per-atom fix, per-atom compute, or fix + property/atom-based entities from all processes for a subset of atoms. + + .. versionadded:: 22Dec2022 + + This subroutine gathers data for the requested atom IDs and stores them in a + one-dimensional allocatable array. The data will be ordered by atom ID, but + there is no requirement that the IDs be consecutive. If you wish to return a + similar array for *all* the atoms, use :f:subr:`gather` or + :f:subr:`gather_concat`. + + The *data* array will be in groups of *count* values, sorted by atom ID in + the same order as the array *ids* (e.g., if *name* is *x*, *count* = 3, and + *ids* is [100, 57, 210], then *data* might look like [*x*\ (1,100), + *x*\ (2,100), *x*\ (3,100), *x*\ (1,57), *x*\ (2,57), *x*\ (3,57), + *x*\ (1,210), :math:`\dots`]); *ids* must be provided by the user, and + *data* must have the ``ALLOCATABLE`` attribute and be of rank 1 (i.e., + ``DIMENSION(:)``). If *data* is already allocated, it will be reallocated to + fit the length of the incoming data. + + This function is not compatible with ``-DLAMMPS_BIGBIG``. + + :p character(len=\*) name: quantity to be scattered + + :p integer(c_int) ids [dimension(:)]: atom IDs corresponding to the atoms + being scattered (e.g., "x" or "f" for atom properties, "f_id" for per-atom + fix data, "c_id" for per-atom compute data, "d_name" or "i_name" for fix + property/atom vectors with *count* = 1, "d2_name" or "i2_name" for fix + property/atom vectors with *count*\ :math:`{} > 1`) + :p integer(c_int) count: number of per-atom values you expect per atom + (e.g., 1 for *type*, *mask*, or *charge*; 3 for *x*, *v*, or *f*). Use + *count* = 3 with *image* if you want a single image flag unpacked into + *x*/*y*/*z* components. + :p data: per-atom values packed into a one-dimensional array containing the + data to be scattered. This array must have the ``ALLOCATABLE`` attribute + and will be allocated either to the same length as *ids* + (for *mask*, *type*, etc.) or to three times its length (for *x*, *f*, + etc.); the array must be rank 1 and be of type ``INTEGER(c_int)`` (e.g., + for *mask* or *type*) or of type ``REAL(c_double)`` (e.g., for *charge*, + *x*, or *f*). + :ptype data: polymorphic,dimension(:),allocatable + :to: :cpp:func:`lammps_gather_subset` + +-------- + +.. f:subroutine:: scatter(name, data) + + This function calls :cpp:func:`lammps_scatter` to scatter the named + per-atom, per-atom fix, per-atom compute, or fix property/atom-based entity + in *data* to all processes. + + .. versionadded:: 22Dec2022 + + This subroutine takes data stored in a one-dimensional array supplied by the + user and scatters them to all atoms on all processes. The data must be + ordered by atom ID, with the requirement that the IDs be consecutive. Use + :f:subr:`scatter_subset` to scatter data for some (or all) atoms, unordered. + + The *data* array needs to be ordered in groups of *count* values, sorted by + atom ID (e.g., if *name* is *x* and *count* = 3, then *data* = [*x*\ (1,1), + *x*\ (2,1), *x*\ (3,1), *x*\ (1,2), *x*\ (2,2), *x*\ (3,2), *x*\ (1,3), + :math:`\dots`]); *data* must be of length (*count* :math:`\times` *natoms*). + + This function is not compatible with ``-DLAMMPS_BIGBIG``. + + :p character(len=*) name: desired quantity (e.g., "x" or "f" for atom + properties, "f_id" for per-atom fix data, "c_id" for per-atom compute data, + "d_name" or "i_name" for fix property/atom vectors with *count* = 1, + "d2_name" or "i2_name" for fix property/atom vectors with *count*\ + :math:`{} > 1`) + :p data: per-atom values packed in a one-dimensional array; *data* should be + of type ``INTEGER(c_int)`` or ``REAL(c_double)``, depending on the type of + data being scattered, and be of rank 1 (i.e., ``DIMENSION(:)``). + :ptype data: polymorphic,dimension(:) + :to: :cpp:func:`lammps_scatter` + +-------- + +.. f:subroutine:: scatter_subset(name, ids, data) + + This function calls :cpp:func:`lammps_scatter_subset` to scatter the named + per-atom, per-atom fix, per-atom compute, or fix property/atom-based + entities in *data* from a subset of atoms to all processes. + + .. versionadded:: 22Dec2022 + + This subroutine takes data stored in a one-dimensional array supplied by the + user and scatters them to a subset of atoms on all processes. The array + *data* contains data associated with atom IDs, but there is no requirement + that the IDs be consecutive, as they are provided in a separate array. + Use :f:subr:`scatter` to scatter data for all atoms, in order. + + The *data* array needs to be organized in groups of *count* values, with the + groups in the same order as the array *ids*. For example, if you want *data* + to be the array [x(1,1), x(2,1), x(3,1), x(1,100), x(2,100), x(3,100), + x(1,57), x(2,57), x(3,57)], then *count* = 3 and *ids* = [1, 100, 57]. + + This function is not compatible with ``-DLAMMPS_BIGBIG``. + + :p character(len=\*) name: desired quantity (e.g., "x" or "mask" for atom + properties, "f_id" for per-atom fix data, "c_id" for per-atom compute data, + "d_name" or "i_name" for fix property/atom vectors with *count* = 1, + "d2_name" or "i2_name" for fix property/atom vectors with + *count*\ :math:`{}> 1`) + :p integer(c_int) ids: list of atom IDs to scatter data for + :p polymorphic data [dimension(:)]: per-atom values packed in a + one-dimensional array of length *size(ids)* \* *count*. + :to: :cpp:func:`lammps_scatter_subset` + +-------- + +.. f:subroutine:: create_atoms([id,] type, x, [v,] [image,] [bexpand]) + + This method calls :cpp:func:`lammps_create_atoms` to create additional atoms + from a given list of coordinates and a list of atom types. Additionally, + the atom IDs, velocities, and image flags may be provided. + + .. versionadded:: 3Nov2022 + + :p integer(c_int) type [dimension(N)]: vector of :math:`N` atom types + (required/see note below) + :p real(c_double) x [dimension(3N)]: vector of :math:`3N\ x/y/z` positions + of the new atoms, arranged as :math:`[x_1,y_1,z_1,x_2,y_2,\dotsc]` + (required/see note below) + :o integer(kind=\*) id [dimension(N),optional]: vector of :math:`N` atom + IDs; if absent, LAMMPS will generate them for you. \*The ``KIND`` parameter + should be ``c_int`` unless LAMMPS was compiled with ``-DLAMMPS_BIGBIG``, in + which case it should be ``c_int64_t``. + :o real(c_double) v [dimension(3N),optional]: vector of :math:`3N` + *x*\ /*y*\ /*z* velocities of the new atoms, arranged as + :math:`[v_{1,x},v_{1,y},v_{1,z},v_{2,x}, \dotsc]`; if absent, they will be + set to zero + :o integer(kind=\*) image [dimension(N),optional]: vector of :math:`N` image + flags; if absent, they are set to zero. \*The ``KIND`` parameter should be + ``c_int`` unless LAMMPS was compiled with ``-DLAMMPS_BIGBIG``, in which + case it should be ``c_int64_t``. See note below. + :o bexpand: if ``.TRUE.``, atoms outside of shrink-wrap boundaries + will be created, not dropped, and the box dimensions will be extended. + Default is ``.FALSE.`` + :otype bexpand: logical,optional + :to: :cpp:func:`lammps_create_atoms` + + .. note:: + + The *type* and *x* arguments are required, but they are declared + ``OPTIONAL`` in the module because making them mandatory would require + *id* to be present as well. To have LAMMPS generate the ids for you, + use a call something like + + .. code-block:: fortran + + lmp%create_atoms(type=new_types, x=new_xs) + + .. note:: + + When LAMMPS has been compiled with ``-DLAMMPS_BIGBIG``, it is not + possible to include the *image* parameter but omit the *id* parameter. + Either *id* must be present, or both *id* and *image* must be absent. + This is required because having all arguments be optional in both + generic functions creates an ambiguous interface. This limitation does + not exist if LAMMPS was not compiled with ``-DLAMMPS_BIGBIG``. + +-------- + +.. f:function:: find_pair_neighlist(style[, exact][, nsub][, reqid]) + + Find index of a neighbor list requested by a pair style. + + .. versionadded:: 3Nov2022 + + This function determines which of the available neighbor lists for pair + styles matches the given conditions. It first matches the style name. + If *exact* is ``.TRUE.``, the name must match exactly; if ``.FALSE.``, a + regular expression or sub-string match is done. If the pair style is + *hybrid* or *hybrid/overlay*, the style is matched against the sub-styles + instead. If the same pair style is used multiple times as a sub-style, the + *nsub* argument must be :math:`> 0`; this argument represents the *n*\ th + instance of the sub-style (same as for the :doc:`pair_coeff ` + command, for example). In that case, *nsub*\ :math:`{} = 0` will not + produce a match, and the function will return :math:`-1`. + + The final condition to be checked is the request ID (\ *reqid*\ ). This + will usually be zero, but some pair styles request multiple neighbor + lists and set the request ID to a value greater than zero. + + :p character(len=\*) style: String used to search for pair style instance. + :o exact: Flag to control whether style should match exactly or only a + regular expression/sub-string match is applied. Default: ``.TRUE.``. + :otype exact: logical,optional + :o integer(c_int) nsub [optional]: Match *nsub*\ th hybrid sub-style + instance of the same style. Default: 0. + :o integer(c_int) reqid [optional]: Request ID to identify the neighbor list + in case there are multiple requests from the same pair style instance. + Default: 0. + :to: :cpp:func:`lammps_find_pair_neighlist` + :r integer(c_int) index: Neighbor list index if found, otherwise + :math:`-1`. + +-------- + +.. f:function:: find_fix_neighlist(id[, reqid]) + + Find index of a neighbor list requested by a fix. + + .. versionadded:: 3Nov2022 + + The neighbor list request from a fix is identified by the fix ID and the + request ID. The request ID is typically zero, but will be :math:`>0` for + fixes with multiple neighbor list requests. + + :p character(len=\*) id: Identifier of fix instance + :o integer(c_int) reqid [optional]: request ID to identify the neighbor list + in cases in which there are multiple requests from the same fix. + Default: 0. + :to: :cpp:func:`lammps_find_fix_neighlist` + :r index: neighbor list index if found, otherwise :math:`-1` + :rtype index: integer(c_int) + +-------- + +.. f:function:: find_compute_neighlist(id[, reqid]) + + Find index of a neighbor list requested by a compute. + + .. versionadded:: 3Nov2022 + + The neighbor list request from a compute is identified by the compute ID and + the request ID. The request ID is typically zero, but will be :math:`> 0` + in case a compute has multiple neighbor list requests. + + :p character(len=\*) id: Identifier of compute instance. + :o integer(c_int) reqid [optional]: request ID to identify the neighbor list + in cases in which there are multiple requests from the same compute. + Default: 0. + :to: :cpp:func:`lammps_find_compute_neighlist` + :r index: neighbor list index if found, otherwise :math:`-1`. + :rtype index: integer(c_int) + +-------- + +.. f:function:: neighlist_num_elements(idx) + + Return the number of entries in the neighbor list with the given index. + + .. versionadded:: 3Nov2022 + + :p integer(c_int) idx: neighbor list index + :to: :cpp:func:`lammps_neighlist_num_elements` + :r inum: number of entries in neighbor list, or :math:`-1` if *idx* is not + a valid index. + :rtype inum: integer(c_int) + :to: :cpp:func:`lammps_neighlist_num_elements` + +-------- + +.. f:subroutine:: neighlist_element_neighbors(idx, element, iatom, neighbors) + + Return atom local index, number of neighbors, and array of neighbor local + atom indices of a neighbor list entry. + + .. versionadded:: 3Nov2022 + + :p integer(c_int) idx: index of this neighbor list in the list of all + neighbor lists + :p integer(c_int) element: index of this neighbor list entry + :p integer(c_int) iatom: local atom index (i.e., in the range + [1,nlocal+nghost]; -1 if invalid or element value + :p integer(c_int) neighbors [dimension(:),pointer]: pointer to an array of + neighboring atom local indices + :to: :cpp:func:`lammps_neighlist_element_neighbors` -------- @@ -1272,7 +1888,9 @@ Procedures Bound to the lammps Derived Type This method returns the numeric LAMMPS version like :cpp:func:`lammps_version` does. - :r integer: LAMMPS version + :to: :cpp:func:`lammps_version` + :r version: LAMMPS version + :rtype version: integer -------- @@ -1281,12 +1899,16 @@ Procedures Bound to the lammps Derived Type This function can be used to retrieve detailed information about the hosting operating system and compiler/runtime environment. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 A suitable buffer has to be provided. The assembled text will be truncated so as not to overflow this buffer. The string is typically a few hundred bytes long. + :p character(len=\*) buffer: string that will house the information. + :to: :cpp:func:`lammps_get_os_info` + + -------- .. f:function:: config_has_mpi_support() @@ -1294,10 +1916,12 @@ Procedures Bound to the lammps Derived Type This function is used to query whether LAMMPS was compiled with a real MPI library or in serial. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 - :r logical: ``.FALSE.`` when compiled with STUBS, ``.TRUE.`` if complied - with MPI. + :to: :cpp:func:`lammps_config_has_mpi_support` + :r has_mpi: ``.FALSE.`` when compiled with STUBS, ``.TRUE.`` if + complied with MPI. + :rtype has_mpi: logical -------- @@ -1306,7 +1930,7 @@ Procedures Bound to the lammps Derived Type Check if the LAMMPS library supports reading or writing compressed files via a pipe to gzip or similar compression programs. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 Several LAMMPS commands (e.g., :doc:`read_data`, :doc:`write_data`, :doc:`dump styles atom, custom, and xyz `) support reading and writing @@ -1315,7 +1939,9 @@ Procedures Bound to the lammps Derived Type It does **not** check whether ``gzip`` or any other supported compression programs themselves are installed and usable. - :r logical: + :to: :cpp:func:`lammps_config_has_gzip_support` + :r has_gzip: + :rtype has_gzip: logical -------- @@ -1323,7 +1949,7 @@ Procedures Bound to the lammps Derived Type Check if the LAMMPS library supports writing PNG format images. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 The LAMMPS :doc:`dump style image ` supports writing multiple image file formats. Most of them, however, need support from an external @@ -1332,7 +1958,9 @@ Procedures Bound to the lammps Derived Type `_ is available in the current LAMMPS library. - :r logical: + :to: :cpp:func:`lammps_config_has_png_support` + :r has_png: + :rtype has_png: logical -------- @@ -1340,7 +1968,7 @@ Procedures Bound to the lammps Derived Type Check if the LAMMPS library supports writing JPEG format images. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 The LAMMPS :doc:`dump style image ` supports writing multiple image file formats. Most of them, however, need support from an external @@ -1348,7 +1976,9 @@ Procedures Bound to the lammps Derived Type This function checks whether support for the `JPEG image file format `_ is available in the current LAMMPS library. - :r logical: + :to: :cpp:func:`lammps_config_has_jpeg_support` + :r has_jpeg: + :rtype has_jpeg: logical -------- @@ -1357,7 +1987,7 @@ Procedures Bound to the lammps Derived Type Check if the LAMMPS library supports creating movie files via a pipe to ffmpeg. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 The LAMMPS :doc:`dump style movie ` supports generating movies from images on-the-fly via creating a pipe to the @@ -1366,7 +1996,9 @@ Procedures Bound to the lammps Derived Type :ref:`enabled at compile time `. It does **not** check whether the ``ffmpeg`` itself is installed and usable. - :r logical: + :to: :cpp:func:`lammps_config_has_ffmpeg_support` + :r has_ffmpeg: + :rtype has_ffmpeg: logical -------- @@ -1374,7 +2006,7 @@ Procedures Bound to the lammps Derived Type Check whether LAMMPS errors will throw C++ exceptions. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 In case of an error, LAMMPS will either abort or throw a C++ exception. The latter has to be :ref:`enabled at compile time `. @@ -1390,7 +2022,9 @@ Procedures Bound to the lammps Derived Type exceptions are disabled and an error happens during a call to LAMMPS or the Fortran API, the application will terminate. - :r logical: + :to: :cpp:func:`lammps_config_has_exceptions` + :r has_exceptions: + :rtype has_exceptions: logical -------- @@ -1398,12 +2032,14 @@ Procedures Bound to the lammps Derived Type Check whether a specific package has been included in LAMMPS - .. versionadded:: TBD + .. versionadded:: 3Nov2022 This function checks whether the LAMMPS library in use includes the specific :doc:`LAMMPS package ` provided as argument. - :r logical: + :to: :cpp:func:`lammps_config_has_package` + :r has_package: + :rtype has_package: logical -------- @@ -1411,13 +2047,14 @@ Procedures Bound to the lammps Derived Type Count the number of installed packages in the LAMMPS library. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 This function counts how many :doc:`LAMMPS packages ` are included in the LAMMPS library in use. It directly calls the C library function :cpp:func:`lammps_config_package_count`. - :r integer(c_int): number of packages installed + :to: :cpp:func:`lammps_config_package_count` + :r integer(c_int) npackages: number of packages installed -------- @@ -1426,7 +2063,7 @@ Procedures Bound to the lammps Derived Type Get the name of a package in the list of installed packages in the LAMMPS library. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 This subroutine copies the name of the package with the index *idx* into the provided string *buffer*. If the name of the package exceeds the length of @@ -1436,6 +2073,7 @@ Procedures Bound to the lammps Derived Type :p integer(c_int) idx: index of the package in the list of included packages :math:`(0 \le idx < \text{package count})` :p character(len=\*) buffer: string to hold the name of the package + :to: :cpp:func:`lammps_config_package_name` -------- @@ -1444,15 +2082,646 @@ Procedures Bound to the lammps Derived Type Obtain a list of the names of enabled packages in the LAMMPS shared library and store it in *package*. - This function is analogous to the :py:func`installed_packages` function in - the Python API. The optional argument *length* sets the length of each - string in the vector *package* (default: 31). + .. versionadded:: 3Nov2022 + + This function is analogous to the :py:meth:`installed_packages + ` function in the Python API. + The optional argument *length* sets the length of each string in the vector + *package* (default: 31). :p character(len=:) package [dimension(:),allocatable]: list of packages; - *must* have the ``ALLOCATABLE`` attribute and be of rank-1 - (``DIMENSION(:)``) with allocatable length. - :o integer length [optional]: length of each string in the list. - Default: 31. + *must* have the ``ALLOCATABLE`` attribute and be of rank 1 + (i.e., ``DIMENSION(:)``) with allocatable length. + :o length: length of each string in the list. Default: 31. + :otype length: integer,optional + :to: :cpp:func:`lammps_config_package_count` + :to: :cpp:func:`lammps_config_package_name` + +-------- + +.. f:function:: config_accelerator(package, category, setting) + + This function calls :cpp:func:`lammps_config_accelerator` to check the + availability of compile time settings of included + :doc:`accelerator packages ` in LAMMPS. + + .. versionadded:: 3Nov2022 + + Supported packages names are "GPU", "KOKKOS", "INTEL", and "OPENMP". + Supported categories are "api" with possible settings "cuda", "hip", "phi", + "pthreads", "opencl", "openmp", and "serial"; and "precision" with + possible settings "double", "mixed", and "single". + + :p character(len=\*) package: string with the name of the accelerator + package + :p character(len=\*) category: string with the name of the setting + :p character(len=\*) setting: string with the name of the specific + setting + :to: :cpp:func:`lammps_config_accelerator` + :r available: ``.TRUE.`` if the combination of package, category, + and setting is available, otherwise ``.FALSE.``. + :rtype available: logical + +-------- + +.. f:function:: has_gpu_device() + + Checks for the presence of a viable GPU package device. + + .. versionadded:: 3Nov2022 + + This function calls :cpp:func:`lammps_has_gpu_device`, which checks at + runtime whether an accelerator device is present that can be used with the + :doc:`GPU package `. + + More detailed information about the available device or devices can + be obtained by calling the + :f:subr:`get_gpu_device_info` subroutine. + + :to: :cpp:func:`lammps_has_gpu_device` + :r available: ``.TRUE.`` if a viable device is available, ``.FALSE.`` if not. + :rtype available: logical + +-------- + +.. f:subroutine:: get_gpu_device_info(buffer) + + Get GPU package device information. + + .. versionadded:: 3Nov2022 + + Calls :cpp:func:`lammps_get_gpu_device_info` to retrieve detailed + information about any accelerator devices that are viable for use with the + :doc:`GPU package `. It will fill *buffer* with a string that is + equivalent to the output of the ``nvc_get_device`` or ``ocl_get_device`` or + ``hip_get_device`` tools that are compiled alongside LAMMPS if the GPU + package is enabled. + + A suitable-length Fortran string has to be provided. The assembled text will + be truncated so as not to overflow this buffer. This string can be several + kilobytes long if multiple devices are present. + + :p character(len=\*) buffer: string into which to copy the information. + :to: :cpp:func:`lammps_get_gpu_device_info` + +-------- + +.. f:function:: has_style(category, name) + + Check whether a specific style has been included in LAMMPS. + + .. versionadded:: 3Nov2022 + + This function calls :cpp:func:`lammps_has_style` to check whether the + LAMMPS library in use includes the specific style *name* associated with a + specific *category* provided as arguments. Please see + :cpp:func:`lammps_has_style` for a list of valid categories. + + :p character(len=\*) category: category of the style + :p character(len=\*) name: name of the style + :to: :cpp:func:`lammps_has_style` + :r has_style: ``.TRUE.`` if included, ``.FALSE.`` if not. + :rtype has_style: logical + +-------- + +.. f:function:: style_count(category) + + Count the number of styles of *category* in the LAMMPS library. + + .. versionadded:: 3Nov2022 + + This function counts how many styles in the provided *category* are + included in the LAMMPS library currently in use. Please see + :cpp:func:`lammps_has_style` for a list of valid categories. + + :p character(len=\*) category: category of styles to count + :to: :cpp:func:`lammps_style_count` + :r integer(c_int) count: number of styles in *category* + +-------- + +.. f:subroutine:: style_name(category, idx, buffer) + + Look up the name of a style by index in the list of styles of a given + category in the LAMMPS library. + + .. versionadded:: 3Nov2022 + + This function calls :cpp:func:`lammps_style_name` and copies the name of + the *category* style with index *idx* into the provided string *buffer*. + The length of *buffer* must be long enough to contain the name of the + style; if it is too short, the name will be truncated accordingly. + If *idx* is out of range, *buffer* will be the empty string and a warning + will be issued. + + :p character(len=\*) category: category of styles + :p integer(c_int) idx: index of the style in the list of *category* + styles :math:`(1 \leq idx \leq \text{style count})` + :p character(len\*) buffer: string buffer to copy the name of the style + into + :to: :cpp:func:`lammps_style_name` + +-------- + +.. f:function:: has_id(category, name) + + This function checks if the current LAMMPS instance a *category* ID of + the given *name* exists. Valid categories are: *compute*\ , *dump*\ , + *fix*\ , *group*\ , *molecule*\ , *region*\ , and *variable*\ . + + .. versionadded:: 3Nov2022 + + :p character(len=\*) category: category of the ID + :p character(len=\*) name: name of the ID + :to: :cpp:func:`lammps_has_id` + :r has_id: ``.TRUE.`` if *category* style *name* exists, ``.FALSE.`` if not. + :rtype has_id: logical + +-------- + +.. f:function:: id_count(category) + + This function counts how many IDs in the provided *category* are defined in + the current LAMMPS instance. Please see :f:func:`has_id` for a list of + valid categories. + + .. versionadded:: 3Nov2022 + + :p character(len=\*) category: category of the ID + :to: :cpp:func:`lammps_id_count` + :r count: number of IDs in *category* + :rtype count: integer(c_int) + +-------- + +.. f:subroutine:: id_name(category, idx, buffer) + + Look up the name of an ID by index in the list of IDs of a given category. + + .. versionadded:: 3Nov2022 + + This function copies the name of the *category* ID with the index *idx* into + the provided string *buffer*\ . The length of the buffer must be long + enough to hold the string; if the name of the style exceeds the length of + the buffer, it will be truncated accordingly. If *buffer* is + ``ALLOCATABLE``, it must be allocated *before* the function is called. + If *idx* is out of range, *buffer* is set to an empty string and a warning + is issued. + + :p character(len=\*) category: category of IDs + :p integer(c_int) idx: index of the ID in the list of *category* + styles (:math:`0 \leq idx < count`) + :p character(len=\*) buffer: string into which to copy the name of the + style + :to: :cpp:func:`lammps_id_name` + +-------- + +.. f:function:: plugin_count() + + This function counts the number of loaded plugins. + + .. versionadded:: 3Nov2022 + + :to: :cpp:func:`lammps_plugin_count` + :r n: number of loaded plugins + :rtype n: integer(c_int) + +-------- + +.. f:subroutine:: plugin_name(idx, stylebuf, namebuf) + + Look up the style and name of a plugin by its index in the list of plugins. + + .. versionadded:: 3Nov2022 + + This function copies the name of the *style* plugin with the index *idx* + into the provided C-style string buffer. The length of the buffer must be + provided as *buf_size* argument. If the name of the style exceeds the + length of the buffer, it will be truncated accordingly. If the index is out + of range, both strings are set to the empty string and a warning is + printed. + + :p integer(c_int) idx: index of the plugin in the list all or + *style* plugins + :p character(len=\*) stylebuf: string into which to copy the style of the + plugin + :p character(len=\*) namebuf: string into which to copy the style of the + plugin + :to: :cpp:func:`lammps_plugin_name` + +-------- + +.. f:function:: encode_image_flags(ix, iy, iz) + + Encodes three integer image flags into a single imageint. + + .. versionadded:: 3Nov2022 + + This function performs the bit-shift, addition, and bit-wise OR operations + necessary to combine the values of three integers representing the image + flags in the :math:`x`-, :math:`y`-, and :math:`z`-directions. Unless LAMMPS + is compiled with ``-DLAMMPS_BIGBIG``, those integers are limited to 10-bit + signed integers :math:`[-512,512)`. If ``-DLAMMPS_BIGBIG`` was used when + compiling, then the return value is of kind ``c_int64_t`` instead of + kind ``c_int``, and the valid range for the individual image flags becomes + :math:`[-1048576,1048575)` (i.e., the range of a 21-bit signed integer). + There is no check on whether the arguments conform to these requirements; + values out of range will simply be wrapped back into the interval. + + :p integer(c_int) ix: image flag in :math:`x`-direction + :p integer(c_int) iy: image flag in :math:`y`-direction + :p integer(c_int) iz: image flag in :math:`z`-direction + :r integer(kind=\*) imageint: encoded image flag. \*The ``KIND`` parameter + is ``c_int`` unless LAMMPS was built with ``-DLAMMPS_BIGBIG``, in which + case it is ``c_int64_t``. + + .. note:: + + The fact that the programmer does not know the ``KIND`` parameter of the + return value until compile time means that it is impossible to define an + interface that works for both sizes of ``imageint``. One side effect of + this is that you must assign the return value of this function to a + variable; it cannot be used as the argument to another function or as part + of an array constructor. For example, + + .. code-block:: fortran + + my_images = [lmp%encode_image_flags(0,0,0), lmp%encode_image_flags(1,0,0)] + + will *not* work; instead, do something like + + .. code-block:: fortran + + my_images(1) = lmp%encode_image_flags(0,0,0) + my_images(2) = lmp%encode_image_flags(1,0,0) + +-------- + +.. f:subroutine:: decode_image_flags(image, flags) + + This function does the reverse operation of :f:func:`encode_image_flags`: + it takes the image flag and performs the bit-shift and bit-masking + operations to decode it and stores the resulting three integers into the + array *flags*. + + .. versionadded:: 3Nov2022 + + :p integer(kind=\*) image: encoded image flag. \*The ``KIND`` parameter is + either ``c_int`` or, if LAMMPS was compiled with ``-DLAMMPS_BIGBIG``, + ``c_int64_t``. Kind compatibility is checked at run-time. + :p integer(c_int) flags [dimension(3)]: three-element vector where the + decoded image flags will be stored. + +-------- + +.. f:subroutine:: set_fix_external_callback(id, callback, caller) + + Set the callback function for a :doc:`fix external ` instance + with the given ID. + + .. versionadded:: 22Dec2022 + + Fix :doc:`external ` allows programs that are running LAMMPS + through its library interface to modify certain LAMMPS properties on + specific time steps, similar to the way other fixes do. + + This subroutine sets the callback function for use with the "pf/callback" + mode. The function should have Fortran language bindings with the following + interface, which depends on how LAMMPS was compiled: + + .. code-block:: Fortran + + ABSTRACT INTERFACE + SUBROUTINE external_callback(caller, timestep, ids, x, fexternal) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double, c_int64_t + CLASS(*), INTENT(INOUT) :: caller + INTEGER(c_bigint), INTENT(IN) :: timestep + INTEGER(c_tagint), DIMENSION(:), INTENT(IN) :: ids + REAL(c_double), DIMENSION(:,:), INTENT(IN) :: x + REAL(c_double), DIMENSION(:,:), INTENT(OUT) :: fexternal + END SUBROUTINE external_callback + END INTERFACE + + where ``c_bigint`` is ``c_int`` if ``-DLAMMPS_SMALLSMALL`` was used and + ``c_int64_t`` otherwise; and ``c_tagint`` is ``c_int64_t`` if + ``-DLAMMPS_BIGBIG`` was used and ``c_int`` otherwise. + + The argument *caller* to :f:subr:`set_fix_external_callback` is unlimited + polymorphic (i.e., it can be any Fortran object you want to pass to the + calling function) and will be available as the first argument to the + callback function. It can be your LAMMPS instance, which you might need if + the callback function needs access to the library interface. + The argument must be a scalar; to pass non-scalar data, wrap those data in + a derived type and pass an instance of the derived type to *caller*. + + The array *ids* is an array of length *nlocal* (as accessed from the + :cpp:class:`Atom` class or through :f:func:`extract_global`). The arrays + *x* and *fexternal* are :math:`3 \times {}`\ *nlocal* arrays; these are + transposed from what they would look like in C (see note about array index + order at :f:func:`extract_atom`). + + The callback mechanism is one of two ways that forces can be applied to a + simulation with the help of :doc:`fix external `. The + alternative is *array* mode, where one calls + :f:func:`fix_external_get_force`. + + Please see the documentation for :doc:`fix external ` for + more information about how to use the fix and couple it with external + programs. + + :p character(len=*) id: ID of :doc:`fix external ` instance + :p callback: subroutine :doc:`fix external ` should call + :ptype callback: external + :p class(*) caller [optional]: object you wish to pass to the callback + procedure (must be a scalar; see note) + :to: :cpp:func:`lammps_set_fix_external_callback` + + .. note:: + + The interface for your callback function must match types precisely + with the abstract interface block given above. **The compiler probably + will not be able to check this for you.** In particular, the first + argument ("caller") must be of type ``CLASS(*)`` or you will probably + get a segmentation fault or at least a misinterpretation of whatever is + in memory there. You can resolve the object using the ``SELECT TYPE`` + construct. An example callback function (assuming LAMMPS was compiled + with ``-DLAMMPS_SMALLBIG``) that applies something akin to Hooke's Law + (with each atom having a different *k* value) is shown below. + + .. code-block:: Fortran + + MODULE stuff + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double, c_int64_t + USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : error_unit + IMPLICIT NONE + + TYPE shield + REAL(c_double), DIMENSION(:,:), ALLOCATABLE :: k + ! assume k gets allocated to dimension(3,nlocal) at some point + ! and assigned values + END TYPE shield + + SUBROUTINE my_callback(caller, timestep, ids, x, fexternal) + CLASS(*), INTENT(INOUT) :: caller + INTEGER(c_int), INTENT(IN) :: timestep + INTEGER(c_int64_t), INTENT(IN) :: ids + REAL(c_double), INTENT(IN) :: x(:,:) + REAL(c_double), INTENT(OUT) :: fexternal(:,:) + + SELECT TYPE (caller) + TYPE IS (shield) + fexternal = - caller%k * x + CLASS DEFAULT + WRITE(error_unit,*) 'UH OH...' + END SELECT + END SUBROUTINE my_callback + END MODULE stuff + + ! then, when assigning the callback function, do this: + PROGRAM example + USE LIBLAMMPS + USE stuff + TYPE(lammps) :: lmp + TYPE(shield) :: my_shield + lmp = lammps() + CALL lmp%command('fix ext all external pf/callback 1 1') + CALL lmp%set_fix_external_callback('ext', my_callback, my_shield) + END PROGRAM example + +-------- + +.. f:function:: fix_external_get_force(id) + + Get pointer to the force array storage in a fix external instance with the + given ID. + + .. versionadded:: 22Dec2022 + + Fix :doc:`external ` allows programs that are running LAMMPS + through its library interfaces to add or modify certain LAMMPS properties on + specific time steps, similar to the way other fixes do. + + This function provides access to the per-atom force storage in a fix + external instance with the given fix-ID to be added to the individual + atoms when using the "pf/array" mode. The *fexternal* array can be + accessed like other "native" per-atom arrays accessible via the + :f:func:`extract_atom` function. Please note that the array + stores the forces for *local* atoms for each MPI rank, in the order + determined by the neighbor list build. Because the underlying data + structures can change as well as the order of atom as they migrate between + MPI processes because of the domain decomposition parallelization, this + function should be always called immediately before the forces are going to + be set to get an up-to-date pointer. You can use, for example, + :f:func:`extract_setting` to obtain the number of local atoms `nlocal` and + then assume the dimensions of the returned force array as + ``REAL(c_double) :: force(3,nlocal)``. + + This function is an alternative to the callback mechanism in fix external + set up by :f:subr:`set_fix_external_callback`. The main difference is that + this mechanism can be used when forces are to be pre-computed and the + control alternates between LAMMPS and the external driver, while the + callback mechanism can call an external subroutine to compute the force when + the fix is triggered and needs them. + + Please see the documentation for :doc:`fix external ` for + more information about how to use the fix and how to couple it with an + external program. + + :p character(len=*) id: ID of :doc:`fix external ` instance + :to: :cpp:func:`lammps_fix_external_get_force` + :r fexternal: pointer to the per-atom force array allocated by the fix + :rtype fexternal: real(c_double),dimension(3,nlocal) + +-------- + +.. f:subroutine:: fix_external_set_energy_global(id, eng) + + Set the global energy contribution for a :doc:`fix external ` + instance with the given ID. + + .. versionadded:: 22Dec2022 + + This is a companion function to :f:func:`set_fix_external_callback` + and :f:func:`fix_external_get_force` that also sets the contribution to the + global energy from the external program. The value of the *eng* argument + will be stored in the fix and applied on the current and all following + time steps until changed by another call to this function. The energy is in + energy units as determined by the current :doc:`units ` settings and + is the **total** energy of the contribution. Thus, when running in + parallel, all MPI processes have to call this function with the **same** + value, and this will be returned as a scalar property of the fix external + instance when accessed in LAMMPS input commands or from variables. + + Please see the documentation for :doc:`fix external ` for more + information about how to use the fix and how to couple it with an external + program. + + :p character(len=*) id: fix ID of fix external instance + :p real(c_double) eng: total energy to be added to the global energy + :to: :cpp:func:`lammps_fix_external_set_energy_global` + +-------- + +.. f:subroutine:: fix_external_set_virial_global(id, virial) + + Set the global virial contribution for a fix external instance with the + given ID. + + .. versionadded:: 22Dec2022 + + This is a companion function to :f:subr:`set_fix_external_callback` + and :f:func:`fix_external_get_force` to set the contribution to the global + virial from an external program. + + The six values of the *virial* array will be stored in the fix and applied + on the current and all following time steps until changed by another call + to this function. The components of the virial need to be stored in the + following order: *xx*, *yy*, *zz*, *xy*, *xz*, *yz*. In LAMMPS, the virial + is stored internally as `stress*volume` in units of `pressure*volume` as + determined by the current :doc:`units ` settings and is the + **total** contribution. Thus, when running in parallel, all MPI processes + have to call this function with the **same** value, and this will then be + added by fix external. + + Please see the documentation for :doc:`fix external ` for + more information about how to use the fix and how to couple it with an + external code. + + :p character(len=*) id: fix ID of fix external instance + :p real(c_double) virial [dimension(6)]: the six global stress tensor + components to be added to the global virial + :to: :cpp:func:`lammps_fix_external_set_virial_global` + +-------- + +.. f:subroutine:: fix_external_set_energy_peratom(id, eng) + + Set the per-atom energy contribution for a fix external instance with the + given ID. + + .. versionadded:: 22Dec2022 + + This is a companion function to :f:subr:`set_fix_external_callback` to set + the per-atom energy contribution due to the fix from the external program as + part of the callback function. For this to work, the LAMMPS object must be + passed as part of the *caller* argument when registering the callback + function, or the callback function must otherwise have access to the + LAMMPS object, such as through a module-based pointer. + + .. note:: + + This function is fully independent from + :f:subr:`fix_external_set_energy_global` and will **NOT** add any + contributions to the global energy tally and will **NOT** check whether + the sum of the contributions added here are consistent with the global + added energy. + + Please see the documentation for :doc:`fix external ` for + more information about how to use the fix and how to couple it with an + external code. + + :p character(len=*) id: fix ID of the fix external instance + :p real(c_double) eng [dimension(:)]: array of length *nlocal* containing + the energy to add to the per-atom energy + :to: :cpp:func:`lammps_fix_external_set_energy_peratom` + +-------- + +.. f:subroutine:: set_fix_external_set_virial_peratom(id, virial) + + This is a companion function to :f:subr:`set_fix_external_callback` to set + the per-atom virial contribution due to the fix from the external program as + part of the callback function. For this to work, the LAMMPS object must be + passed as the *caller* argument when registering the callback function. + + .. versionadded:: 22Dec2022 + + .. note:: + + This function is fully independent from + :f:subr:`fix_external_set_virial_global` and will **NOT** add any + contributions to the global virial tally and **NOT** check whether the + sum of the contributions added here are consistent with the global added + virial. + + The order and units of the per-atom stress tensor elements are the same + as for the global virial. The type and dimensions of the per-atom virial + array must be ``REAL(c_double), DIMENSION(6,nlocal)``. + + Please see the documentation for :doc:`fix external ` for + more information about how to use the fix and how to couple it with an + external program. + + :p character(len=*) id: fix ID of fix external instance + :p real(c_double) virial [dimension(:,:)]: an array of :math:`6 \times{}`\ + *nlocal* components to be added to the per-atom virial + :to: :cpp:func:`lammps_set_virial_peratom` + +-------- + +.. f:subroutine:: fix_external_set_vector_length(id, length) + + Set the vector length for a global vector stored with fix external for + analysis. + + .. versionadded:: 22Dec2022 + + This is a companion function to :f:subr:`set_fix_external_callback` and + :f:func:`fix_external_get_force` to set the length of a global vector of + properties that will be stored with the fix via + :f:subr:`fix_external_set_vector`. + + This function needs to be called **before** a call to + :f:subr:`fix_external_set_vector` and **before** a run or minimize command. + When running in parallel, it must be called from **all** MPI + processes with the same length argument. + + Please see the documentation for :doc:`fix external ` for + more information about how to use the fix and how to couple it with an + external program. + + :p character(len=*) id: fix ID of fix external instance + :p integer(c_int) length: length of the global vector to be stored with the + fix + :to: :cpp:func:`lammps_fix_external_set_vector_length` + +-------- + +.. f:subroutine:: fix_external_set_vector(id, idx, val) + + Store a global vector value for a fix external instance with the given ID. + + .. versionadded:: 22Dec2022 + + This is a companion function to :f:subr:`set_fix_external_callback` and + :f:func:`fix_external_get_force` to set the values of a global vector of + properties that will be stored with the fix and can be accessed from + within LAMMPS input commands (e.g., fix ave/time or variables) when used + in a vector context. + + This function needs to be called **after** a call to + :f:subr:`fix_external_set_vector_length` and **before** a run or minimize + command. When running in parallel, it must be called from **all** MPI + processes with the **same** *idx* and *val* parameters. The variable + *val* is assumed to be extensive. + + .. note:: + + The index in the *idx* parameter is 1-based (i.e., the first element + is set with *idx*\ :math:`{} = 1`, and the last element of the vector + with *idx*\ :math:`{} = N`, where :math:`N` is the value of the *length* + parameter of the call to :f:subr:`fix_external_set_vector_length`). + + Please see the documentation for :doc:`fix external ` for + more information about how to use the fix and how to couple it with an + external code. + + :p character(len=*) id: ID of fix external instance + :p integer(c_int) idx: 1-based index in global vector + :p integer(c_int) val: value to be stored in global vector at index *idx* + :to: :cpp:func:`lammps_fix_external_set_vector` -------- @@ -1462,7 +2731,9 @@ Procedures Bound to the lammps Derived Type output to be written to screen and logfile. This can simplify capturing output from LAMMPS library calls. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 + + :to: :cpp:func:`lammps_flush_buffers` -------- @@ -1470,12 +2741,14 @@ Procedures Bound to the lammps Derived Type Check if LAMMPS is currently inside a run or minimization. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 This function can be used from signal handlers or multi-threaded applications to determine if the LAMMPS instance is currently active. - :r logical: ``.FALSE.`` if idle or ``.TRUE.`` if active + :to: :cpp:func:`lammps_is_running` + :r is_running: ``.FALSE.`` if idle or ``.TRUE.`` if active + :rtype is_running: logical -------- @@ -1483,10 +2756,12 @@ Procedures Bound to the lammps Derived Type Force a timeout to stop an ongoing run cleanly. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 This function can be used from signal handlers or multi-threaded - applications to cleanly terminate an ongoing run. + applications to terminate an ongoing run cleanly. + + :to: :cpp:func:`lammps_force_timeout` -------- @@ -1494,7 +2769,7 @@ Procedures Bound to the lammps Derived Type Check if there is a (new) error message available. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 This function can be used to query if an error inside of LAMMPS has thrown a :ref:`C++ exception `. @@ -1507,7 +2782,9 @@ Procedures Bound to the lammps Derived Type function :cpp:func:`lammps_config_has_exceptions` to check if this is the case. - :r logical: ``.TRUE.`` if there is an error. + :to: :cpp:func:`lammps_has_error` + :r has_error: ``.TRUE.`` if there is an error. + :rtype has_error: logical -------- @@ -1515,18 +2792,17 @@ Procedures Bound to the lammps Derived Type Copy the last error message into the provided buffer. - .. versionadded:: TBD + .. versionadded:: 3Nov2022 This function can be used to retrieve the error message that was set in the event of an error inside of LAMMPS that resulted in a :ref:`C++ exception `. A suitable buffer for a string has to be provided. If the internally-stored error message is longer than the - string and the string does not have ``ALLOCATABLE`` length, it will be - truncated accordingly. The optional argument *status* indicates the - kind of error: a "1" indicates an error that occurred on all MPI ranks and - is often recoverable, while a "2" indicates an abort that would happen only - in a single MPI rank and thus may not be recoverable, as other MPI ranks may - be waiting on the failing MPI rank(s) to send messages. + string, it will be truncated accordingly. The optional argument *status* + indicates the kind of error: a "1" indicates an error that occurred on all + MPI ranks and is often recoverable, while a "2" indicates an abort that + would happen only in a single MPI rank and thus may not be recoverable, as + other MPI ranks may be waiting on the failing MPI rank(s) to send messages. .. note:: @@ -1538,3 +2814,4 @@ Procedures Bound to the lammps Derived Type :p character(len=\*) buffer: string buffer to copy the error message into :o integer(c_int) status [optional]: 1 when all ranks had the error, 2 on a single-rank error. + :to: :cpp:func:`lammps_get_last_error_message` diff --git a/doc/src/Howto.rst b/doc/src/Howto.rst index d1bb1733fc..9423f0dd33 100644 --- a/doc/src/Howto.rst +++ b/doc/src/Howto.rst @@ -51,6 +51,7 @@ Analysis howto Howto_output Howto_chunk + Howto_grid Howto_temperature Howto_elastic Howto_kappa diff --git a/doc/src/Howto_grid.rst b/doc/src/Howto_grid.rst new file mode 100644 index 0000000000..74646b4bd2 --- /dev/null +++ b/doc/src/Howto_grid.rst @@ -0,0 +1,102 @@ +Using distributed grids +======================= + +.. versionadded:: 22Dec2022 + +LAMMPS has internal capabilities to create uniformly spaced grids +which overlay the simulation domain. For 2d and 3d simulations these +are 2d and 3d grids respectively. Conceptually a grid can be thought +of as a collection of grid cells. Each grid cell can store one or +more values (data). + +The grid cells and data they store are distributed across processors. +Each processor owns the grid cells (and data) whose center points lie +within the spatial sub-domain of the processor. If needed for its +computations, a processor may also store ghost grid cells with their +data. + +Distributed grids can overlay orthogonal or triclinic simulation +boxes; see the :doc:`Howto triclinic ` doc page for +an explanation of the latter. For a triclinic box, the grid cell +shape conforms to the shape of the simulation domain, +e.g. parallelograms instead of rectangles in 2d. + +If the box size or shape changes during a simulation, the grid changes +with it, so that it always overlays the entire simulation domain. For +non-periodic dimensions, the grid size in that dimension matches the +box size, as set by the :doc:`boundary ` command for fixed +or shrink-wrapped boundaries. + +If load-balancing is invoked by the :doc:`balance ` or +:doc:`fix balance ` commands, then the sub-domain owned +by a processor can change which may also change which grid cells they +own. + +Post-processing and visualization of grid cell data can be enabled by +the :doc:`dump grid `, :doc:`dump grid/vtk `, and +:doc:`dump image ` commands. The latter has an optional +*grid* keyword. The `OVITO visualization tool +`_ also plans (as of Nov 2022) to add support +for visualizing grid cell data (along with atoms) using :doc:`dump +grid ` output files as input. + +.. note:: + + For developers, distributed grids are implemented within the code via + two classes: Grid2d and Grid3d. These partition the grid across + processors and have methods which allow forward and reverse + communication of ghost grid data as well as load balancing. If you + write a new compute or fix which needs a distributed grid, these are + the classes to look at. A new pair style could use a distributed + grid by having a fix define it. Please see the section on + :doc:`using distributed grids within style classes ` + for a detailed description. + +---------- + +These are the commands which currently define or use distributed +grids: + +* :doc:`fix ttm/grid ` - store electron temperature on grid +* :doc:`fix ave/grid ` - time average per-atom or per-grid values +* :doc:`compute property/grid ` - generate grid IDs and coords +* :doc:`dump grid ` - output per-grid values in LAMMPS format +* :doc:`dump grid/vtk ` - output per-grid values in VTK format +* :doc:`dump image grid ` - include colored grid in output images +* :doc:`pair_style amoeba ` - FFT grids +* :doc:`kspace_style pppm ` (and variants) - FFT grids +* :doc:`kspace_style msm ` (and variants) - MSM grids + +The grids used by the :doc:`kspace_style ` can not be +referenced by an input script. However the grids and data created and +used by the other commands can be. + +A compute or fix command may create one or more grids (of different +sizes). Each grid can store one or more data fields. A data field +can be a single value per grid point (per-grid vector) or multiple +values per grid point (per-grid array). See the :doc:`Howto output +` doc page for an explanation of how per-grid data can +be generated by some commands and used by other commands. + +A command accesses grid data from a compute or fix using a *grid +reference* with the following syntax: + +* c_ID:gname:dname +* c_ID:gname:dname[I] +* f_ID:gname:dname +* f_ID:gname:dname[I] + +The prefix "c\_" or "f\_" refers to the ID of the compute or fix; gname is +the name of the grid, which is assigned by the compute or fix; dname is +the name of the data field, which is also assigned by the compute or +fix. + +If the data field is a per-grid vector (one value per grid point), +then no brackets are used to access the values. If the data field is +a per-grid array (multiple values per grid point), then brackets are +used to specify the column I of the array. I ranges from 1 to Ncol +inclusive, where Ncol is the number of columns in the array and is +defined by the compute or fix. + +Currently, there are no per-grid variables implemented in LAMMPS. We +may add this feature at some point. diff --git a/doc/src/Howto_output.rst b/doc/src/Howto_output.rst index d17b865bbd..771ecad8f0 100644 --- a/doc/src/Howto_output.rst +++ b/doc/src/Howto_output.rst @@ -22,14 +22,17 @@ commands you specify. As discussed below, LAMMPS gives you a variety of ways to determine what quantities are computed and printed when the thermodynamics, dump, or fix commands listed above perform output. Throughout this -discussion, note that users can also :doc:`add their own computes and fixes to LAMMPS ` which can then generate values that can then be -output with these commands. +discussion, note that users can also :doc:`add their own computes and +fixes to LAMMPS ` which can then generate values that can then +be output with these commands. -The following sub-sections discuss different LAMMPS command related +The following sub-sections discuss different LAMMPS commands related to output and the kind of data they operate on and produce: -* :ref:`Global/per-atom/local data ` +* :ref:`Global/per-atom/local/per-grid data ` * :ref:`Scalar/vector/array data ` +* :ref:`Per-grid data ` +* :ref:`Disambiguation ` * :ref:`Thermodynamic output ` * :ref:`Dump file output ` * :ref:`Fixes that write output files ` @@ -42,27 +45,32 @@ to output and the kind of data they operate on and produce: .. _global: -Global/per-atom/local data --------------------------- +Global/per-atom/local/per-grid data +----------------------------------- -Various output-related commands work with three different styles of -data: global, per-atom, or local. A global datum is one or more -system-wide values, e.g. the temperature of the system. A per-atom -datum is one or more values per atom, e.g. the kinetic energy of each -atom. Local datums are calculated by each processor based on the -atoms it owns, but there may be zero or more per atom, e.g. a list of -bond distances. +Various output-related commands work with four different styles of +data: global, per-atom, local, and per-grid. A global datum is one or +more system-wide values, e.g. the temperature of the system. A +per-atom datum is one or more values per atom, e.g. the kinetic energy +of each atom. Local datums are calculated by each processor based on +the atoms it owns, but there may be zero or more per atom, e.g. a list +of bond distances. + +A per-grid datum is one or more values per grid cell, for a grid which +overlays the simulation domain. The grid cells and the data they +store are distributed across processors; each processor owns the grid +cells whose center point falls within its sub-domain. .. _scalar: Scalar/vector/array data ------------------------ -Global, per-atom, and local datums can each come in three kinds: a -single scalar value, a vector of values, or a 2d array of values. The -doc page for a "compute" or "fix" or "variable" that generates data -will specify both the style and kind of data it produces, e.g. a -per-atom vector. +Global, per-atom, and local datums can come in three kinds: a single +scalar value, a vector of values, or a 2d array of values. The doc +page for a "compute" or "fix" or "variable" that generates data will +specify both the style and kind of data it produces, e.g. a per-atom +vector. When a quantity is accessed, as in many of the output commands discussed below, it can be referenced via the following bracket @@ -83,6 +91,18 @@ the dimension twice (array -> scalar). Thus a command that uses scalar values as input can typically also process elements of a vector or array. +.. _grid: + +Per-grid data +------------------------ + +Per-grid data can come in two kinds: a vector of values (one per grid +cekk), or a 2d array of values (multiple values per grid ckk). The +doc page for a "compute" or "fix" that generates data will specify +names for both the grid(s) and datum(s) it produces, e.g. per-grid +vectors or arrays, which can be referenced by other commands. See the +:doc:`Howto grid ` doc page for more details. + .. _disambiguation: Disambiguation @@ -90,15 +110,15 @@ Disambiguation Some computes and fixes produce data in multiple styles, e.g. a global scalar and a per-atom vector. Usually the context in which the input -script references the data determines which style is meant. Example: if -a compute provides both a global scalar and a per-atom vector, the +script references the data determines which style is meant. Example: +if a compute provides both a global scalar and a per-atom vector, the former will be accessed by using ``c_ID`` in an equal-style variable, while the latter will be accessed by using ``c_ID`` in an atom-style -variable. Note that atom-style variable formulas can also access global -scalars, but in this case it is not possible to do directly because of -the ambiguity. Instead, an equal-style variable can be defined which -accesses the global scalar, and that variable used in the atom-style -variable formula in place of ``c_ID``. +variable. Note that atom-style variable formulas can also access +global scalars, but in this case it is not possible to do this +directly because of the ambiguity. Instead, an equal-style variable +can be defined which accesses the global scalar, and that variable can +be used in the atom-style variable formula in place of ``c_ID``. .. _thermo: @@ -107,15 +127,14 @@ Thermodynamic output The frequency and format of thermodynamic output is set by the :doc:`thermo `, :doc:`thermo_style `, and -:doc:`thermo_modify ` commands. The -:doc:`thermo_style ` command also specifies what values -are calculated and written out. Pre-defined keywords can be specified -(e.g. press, etotal, etc). Three additional kinds of keywords can -also be specified (c_ID, f_ID, v_name), where a :doc:`compute ` -or :doc:`fix ` or :doc:`variable ` provides the value to be -output. In each case, the compute, fix, or variable must generate -global values for input to the :doc:`thermo_style custom ` -command. +:doc:`thermo_modify ` commands. The :doc:`thermo_style +` command also specifies what values are calculated and +written out. Pre-defined keywords can be specified (e.g. press, etotal, +etc). Three additional kinds of keywords can also be specified (c_ID, +f_ID, v_name), where a :doc:`compute ` or :doc:`fix ` or +:doc:`variable ` provides the value to be output. In each +case, the compute, fix, or variable must generate global values for +input to the :doc:`thermo_style custom ` command. Note that thermodynamic output values can be "extensive" or "intensive". The former scale with the number of atoms in the system @@ -141,9 +160,10 @@ There is also a :doc:`dump custom ` format where the user specifies what values are output with each atom. Pre-defined atom attributes can be specified (id, x, fx, etc). Three additional kinds of keywords can also be specified (c_ID, f_ID, v_name), where a -:doc:`compute ` or :doc:`fix ` or :doc:`variable ` -provides the values to be output. In each case, the compute, fix, or -variable must generate per-atom values for input to the :doc:`dump custom ` command. +:doc:`compute ` or :doc:`fix ` or :doc:`variable +` provides the values to be output. In each case, the +compute, fix, or variable must generate per-atom values for input to +the :doc:`dump custom ` command. There is also a :doc:`dump local ` format where the user specifies what local values to output. A pre-defined index keyword can be @@ -154,18 +174,23 @@ provides the values to be output. In each case, the compute or fix must generate local values for input to the :doc:`dump local ` command. +There is also a :doc:`dump grid ` format where the user +specifies what per-grid values to output from computes or fixes that +generate per-grid data. + .. _fixoutput: Fixes that write output files ----------------------------- Several fixes take various quantities as input and can write output -files: :doc:`fix ave/time `, :doc:`fix ave/chunk `, :doc:`fix ave/histo `, -:doc:`fix ave/correlate `, and :doc:`fix print `. +files: :doc:`fix ave/time `, :doc:`fix ave/chunk +`, :doc:`fix ave/histo `, :doc:`fix +ave/correlate `, and :doc:`fix print `. -The :doc:`fix ave/time ` command enables direct output to -a file and/or time-averaging of global scalars or vectors. The user -specifies one or more quantities as input. These can be global +The :doc:`fix ave/time ` command enables direct output +to a file and/or time-averaging of global scalars or vectors. The +user specifies one or more quantities as input. These can be global :doc:`compute ` values, global :doc:`fix ` values, or :doc:`variables ` of any style except the atom style which produces per-atom values. Since a variable can refer to keywords used @@ -184,8 +209,14 @@ atoms, e.g. individual molecules. The per-atom quantities can be atom density (mass or number) or atom attributes such as position, velocity, force. They can also be per-atom quantities calculated by a :doc:`compute `, by a :doc:`fix `, or by an atom-style -:doc:`variable `. The chunk-averaged output of this fix can -also be used as input to other output commands. +:doc:`variable `. The chunk-averaged output of this fix is +global and can also be used as input to other output commands. + +Note that the :doc:`fix ave/grid ` command can also +average the same per-atom quantities within spatial bins, but it does +this for a distributed grid whose grid cells are owned by different +processors. It outputs per-grid data, not global data, so it is more +efficient for large numbers of averaging bins. The :doc:`fix ave/histo ` command enables direct output to a file of histogrammed quantities, which can be global or per-atom @@ -202,38 +233,53 @@ written to the screen and log file or to a separate file, periodically during a running simulation. The line can contain one or more :doc:`variable ` values for any style variable except the vector or atom styles). As explained above, variables themselves can -contain references to global values generated by :doc:`thermodynamic keywords `, :doc:`computes `, -:doc:`fixes `, or other :doc:`variables `, or to per-atom -values for a specific atom. Thus the :doc:`fix print ` -command is a means to output a wide variety of quantities separate -from normal thermodynamic or dump file output. +contain references to global values generated by :doc:`thermodynamic +keywords `, :doc:`computes `, :doc:`fixes +`, or other :doc:`variables `, or to per-atom values +for a specific atom. Thus the :doc:`fix print ` command is +a means to output a wide variety of quantities separate from normal +thermodynamic or dump file output. .. _computeoutput: Computes that process output quantities --------------------------------------- -The :doc:`compute reduce ` and :doc:`compute reduce/region ` commands take one or more per-atom -or local vector quantities as inputs and "reduce" them (sum, min, max, +The :doc:`compute reduce ` and :doc:`compute +reduce/region ` commands take one or more per-atom or +local vector quantities as inputs and "reduce" them (sum, min, max, ave) to scalar quantities. These are produced as output values which can be used as input to other output commands. -The :doc:`compute slice ` command take one or more global -vector or array quantities as inputs and extracts a subset of their -values to create a new vector or array. These are produced as output -values which can be used as input to other output commands. +The :doc:`compute slice ` command take one or more +global vector or array quantities as inputs and extracts a subset of +their values to create a new vector or array. These are produced as +output values which can be used as input to other output commands. -The :doc:`compute property/atom ` command takes a -list of one or more pre-defined atom attributes (id, x, fx, etc) and +The :doc:`compute property/atom ` command takes +a list of one or more pre-defined atom attributes (id, x, fx, etc) and stores the values in a per-atom vector or array. These are produced as output values which can be used as input to other output commands. -The list of atom attributes is the same as for the :doc:`dump custom ` command. +The list of atom attributes is the same as for the :doc:`dump custom +` command. -The :doc:`compute property/local ` command takes -a list of one or more pre-defined local attributes (bond info, angle -info, etc) and stores the values in a local vector or array. These -are produced as output values which can be used as input to other -output commands. +The :doc:`compute property/local ` command +takes a list of one or more pre-defined local attributes (bond info, +angle info, etc) and stores the values in a local vector or array. +These are produced as output values which can be used as input to +other output commands. + +The :doc:`compute property/grid ` command takes +a list of one or more pre-defined per-grid attributes (id, grid cell +coords, etc) and stores the values in a per-grid vector or array. +These are produced as output values which can be used as input to the +:doc:`dump grid ` command. + +The :doc:`compute property/chunk ` command +takes a list of one or more pre-defined chunk attributes (id, count, +coords for spatial bins) and stores the values in a global vector or +array. These are produced as output values which can be used as input +to other output commands. .. _fixprocoutput: @@ -247,18 +293,42 @@ a time. The :doc:`fix ave/atom ` command performs time-averaging of per-atom vectors. The per-atom quantities can be atom attributes such as position, velocity, force. They can also be per-atom -quantities calculated by a :doc:`compute `, by a -:doc:`fix `, or by an atom-style :doc:`variable `. The +quantities calculated by a :doc:`compute `, by a :doc:`fix +`, or by an atom-style :doc:`variable `. The time-averaged per-atom output of this fix can be used as input to other output commands. -The :doc:`fix store/state ` command can archive one or -more per-atom attributes at a particular time, so that the old values -can be used in a future calculation or output. The list of atom -attributes is the same as for the :doc:`dump custom ` command, -including per-atom quantities calculated by a :doc:`compute `, -by a :doc:`fix `, or by an atom-style :doc:`variable `. -The output of this fix can be used as input to other output commands. +The :doc:`fix store/state ` command can archive one +or more per-atom attributes at a particular time, so that the old +values can be used in a future calculation or output. The list of +atom attributes is the same as for the :doc:`dump custom ` +command, including per-atom quantities calculated by a :doc:`compute +`, by a :doc:`fix `, or by an atom-style :doc:`variable +`. The output of this fix can be used as input to other +output commands. + +The :doc:`fix ave/grid ` command performs time-averaging +of either per-atom or per-grid data. + +For per-atom data it performs averaging for the atoms within each grid +cell, similar to the :doc:`fix ave/chunk ` command when +its chunks are defined as regular 2d or 3d bins. The per-atom +quantities can be atom density (mass or number) or atom attributes +such as position, velocity, force. They can also be per-atom +quantities calculated by a :doc:`compute `, by a :doc:`fix +`, or by an atom-style :doc:`variable `. + +The chief difference between the :doc:`fix ave/grid ` +and :doc:`fix ave/chunk ` commands when used in this +context is that the former uses a distributed grid, while the latter +uses a global grid. Distributed means that each processor owns the +subset of grid cells within its sub-domain. Global means that each +processor owns a copy of the entire grid. The :doc:`fix ave/grid +` command is thus more efficient for large grids. + +For per-grid data, the :doc:`fix ave/grid ` command +takes inputs for grid data produced by other computes or fixes and +averages the values for each grid point over time. .. _compute: @@ -266,24 +336,25 @@ Computes that generate values to output --------------------------------------- Every :doc:`compute ` in LAMMPS produces either global or -per-atom or local values. The values can be scalars or vectors or -arrays of data. These values can be output using the other commands -described in this section. The page for each compute command +per-atom or local or per-grid values. The values can be scalars or +vectors or arrays of data. These values can be output using the other +commands described in this section. The page for each compute command describes what it produces. Computes that produce per-atom or local -values have the word "atom" or "local" in their style name. Computes -without the word "atom" or "local" produce global values. +or per-grid values have the word "atom" or "local" or "grid as the +last word in their style name. Computes without the word "atom" or +"local" or "grid" produce global values. .. _fix: Fixes that generate values to output ------------------------------------ -Some :doc:`fixes ` in LAMMPS produces either global or per-atom or -local values which can be accessed by other commands. The values can -be scalars or vectors or arrays of data. These values can be output -using the other commands described in this section. The page for -each fix command tells whether it produces any output quantities and -describes them. +Some :doc:`fixes ` in LAMMPS produces either global or per-atom +or local or per-grid values which can be accessed by other commands. +The values can be scalars or vectors or arrays of data. These values +can be output using the other commands described in this section. The +page for each fix command tells whether it produces any output +quantities and describes them. .. _variable: @@ -300,6 +371,8 @@ computes, fixes, and other variables. The values generated by variables can be used as input to and thus output by the other commands described in this section. +Per-grid variables have not (yet) been implemented. + .. _table: Summary table of output options and data flow between commands @@ -319,44 +392,52 @@ Also note that, as described above, when a command takes a scalar as input, that could be an element of a vector or array. Likewise a vector input could be a column of an array. -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| Command | Input | Output | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`thermo_style custom ` | global scalars | screen, log file | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`dump custom ` | per-atom vectors | dump file | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`dump local ` | local vectors | dump file | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`fix print ` | global scalar from variable | screen, file | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`print ` | global scalar from variable | screen | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`computes ` | N/A | global/per-atom/local scalar/vector/array | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`fixes ` | N/A | global/per-atom/local scalar/vector/array | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`variables ` | global scalars and vectors, per-atom vectors | global scalar and vector, per-atom vector | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`compute reduce ` | per-atom/local vectors | global scalar/vector | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`compute slice ` | global vectors/arrays | global vector/array | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`compute property/atom ` | per-atom vectors | per-atom vector/array | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`compute property/local ` | local vectors | local vector/array | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`fix vector ` | global scalars | global vector | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`fix ave/atom ` | per-atom vectors | per-atom vector/array | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`fix ave/time ` | global scalars/vectors | global scalar/vector/array, file | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`fix ave/chunk ` | per-atom vectors | global array, file | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`fix ave/histo ` | global/per-atom/local scalars and vectors | global array, file | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`fix ave/correlate ` | global scalars | global array, file | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`fix store/state ` | per-atom vectors | per-atom vector/array | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| Command | Input | Output | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`thermo_style custom ` | global scalars | screen, log file | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`dump custom ` | per-atom vectors | dump file | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`dump local ` | local vectors | dump file | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`dump grid ` | per-grid vectors | dump file | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`fix print ` | global scalar from variable | screen, file | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`print ` | global scalar from variable | screen | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`computes ` | N/A | global/per-atom/local/per-grid scalar/vector/array | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`fixes ` | N/A | global/per-atom/local/per-grid scalar/vector/array | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`variables ` | global scalars and vectors, per-atom vectors | global scalar and vector, per-atom vector | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`compute reduce ` | per-atom/local vectors | global scalar/vector | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`compute slice ` | global vectors/arrays | global vector/array | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`compute property/atom ` | N/A | per-atom vector/array | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`compute property/local ` | N/A | local vector/array | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`compute property/grid ` | N/A | per-grid vector/array | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`compute property/chunk ` | N/A | global vector/array | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`fix vector ` | global scalars | global vector | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`fix ave/atom ` | per-atom vectors | per-atom vector/array | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`fix ave/time ` | global scalars/vectors | global scalar/vector/array, file | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`fix ave/chunk ` | per-atom vectors | global array, file | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`fix ave/grid ` | per-atom vectors or per-grid vectors | per-grid vector/array | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`fix ave/histo ` | global/per-atom/local scalars and vectors | global array, file | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`fix ave/correlate ` | global scalars | global array, file | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`fix store/state ` | per-atom vectors | per-atom vector/array | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ diff --git a/doc/src/Howto_pylammps.rst b/doc/src/Howto_pylammps.rst index 6c788e2365..a182d4a050 100644 --- a/doc/src/Howto_pylammps.rst +++ b/doc/src/Howto_pylammps.rst @@ -152,14 +152,14 @@ Creating a new instance of PyLammps To create a PyLammps object you need to first import the class from the lammps module. By using the default constructor, a new *lammps* instance is created. -.. code-block:: Python +.. code-block:: python from lammps import PyLammps L = PyLammps() You can also initialize PyLammps on top of this existing *lammps* object: -.. code-block:: Python +.. code-block:: python from lammps import lammps, PyLammps lmp = lammps() @@ -180,14 +180,14 @@ For instance, let's take the following LAMMPS command: In the original interface this command can be executed with the following Python code if *L* was a lammps instance: -.. code-block:: Python +.. code-block:: python L.command("region box block 0 10 0 5 -0.5 0.5") With the PyLammps interface, any command can be split up into arbitrary parts separated by white-space, passed as individual arguments to a region method. -.. code-block:: Python +.. code-block:: python L.region("box block", 0, 10, 0, 5, -0.5, 0.5) @@ -199,14 +199,14 @@ The benefit of this approach is avoiding redundant command calls and easier parameterization. In the original interface parameterization needed to be done manually by creating formatted strings. -.. code-block:: Python +.. code-block:: python L.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi)) In contrast, methods of PyLammps accept parameters directly and will convert them automatically to a final command string. -.. code-block:: Python +.. code-block:: python L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi) @@ -256,7 +256,7 @@ LAMMPS variables can be both defined and accessed via the PyLammps interface. To define a variable you can use the :doc:`variable ` command: -.. code-block:: Python +.. code-block:: python L.variable("a index 2") @@ -265,14 +265,14 @@ A dictionary of all variables is returned by L.variables you can access an individual variable by retrieving a variable object from the L.variables dictionary by name -.. code-block:: Python +.. code-block:: python a = L.variables['a'] The variable value can then be easily read and written by accessing the value property of this object. -.. code-block:: Python +.. code-block:: python print(a.value) a.value = 4 @@ -284,7 +284,7 @@ LAMMPS expressions can be immediately evaluated by using the eval method. The passed string parameter can be any expression containing global thermo values, variables, compute or fix data. -.. code-block:: Python +.. code-block:: python result = L.eval("ke") # kinetic energy result = L.eval("pe") # potential energy @@ -298,7 +298,7 @@ All atoms in the current simulation can be accessed by using the L.atoms list. Each element of this list is an object which exposes its properties (id, type, position, velocity, force, etc.). -.. code-block:: Python +.. code-block:: python # access first atom L.atoms[0].id @@ -311,7 +311,7 @@ position, velocity, force, etc.). Some properties can also be used to set: -.. code-block:: Python +.. code-block:: python # set position in 2D simulation L.atoms[0].position = (1.0, 0.0) @@ -328,7 +328,7 @@ after a run via the L.runs list. This list contains a growing list of run data. The first element is the output of the first run, the second element that of the second run. -.. code-block:: Python +.. code-block:: python L.run(1000) L.runs[0] # data of first 1000 time steps @@ -339,14 +339,14 @@ the second run. Each run contains a dictionary of all trajectories. Each trajectory is accessible through its thermo name: -.. code-block:: Python +.. code-block:: python L.runs[0].thermo.Step # list of time steps in first run L.runs[0].thermo.Ke # list of kinetic energy values in first run Together with matplotlib plotting data out of LAMMPS becomes simple: -.. code-block:: Python +.. code-block:: python import matplotlib.plot as plt steps = L.runs[0].thermo.Step @@ -406,7 +406,7 @@ Four atoms are placed in the simulation and the dihedral potential is applied on them using a datafile. Then one of the atoms is rotated along the central axis by setting its position from Python, which changes the dihedral angle. -.. code-block:: Python +.. code-block:: python phi = [d \* math.pi / 180 for d in range(360)] @@ -439,7 +439,7 @@ Initially, a 2D system is created in a state with minimal energy. It is then disordered by moving each atom by a random delta. -.. code-block:: Python +.. code-block:: python random.seed(27848) deltaperturb = 0.2 @@ -458,7 +458,7 @@ It is then disordered by moving each atom by a random delta. Finally, the Monte Carlo algorithm is implemented in Python. It continuously moves random atoms by a random delta and only accepts certain moves. -.. code-block:: Python +.. code-block:: python estart = L.eval("pe") elast = estart @@ -517,7 +517,7 @@ PyLammps can be run in parallel using mpi4py. This python package can be install The following is a short example which reads in an existing LAMMPS input file and executes it in parallel. You can find in.melt in the examples/melt folder. -.. code-block:: Python +.. code-block:: python from mpi4py import MPI from lammps import PyLammps diff --git a/doc/src/Howto_structured_data.rst b/doc/src/Howto_structured_data.rst index 18a5dfd775..3fe630a120 100644 --- a/doc/src/Howto_structured_data.rst +++ b/doc/src/Howto_structured_data.rst @@ -43,7 +43,7 @@ JSON "ke": $(ke) }""" file current_state.json screen no -.. code-block:: JSON +.. code-block:: json :caption: current_state.json { diff --git a/doc/src/Howto_tip4p.rst b/doc/src/Howto_tip4p.rst index 4e0a63adc6..19b811a282 100644 --- a/doc/src/Howto_tip4p.rst +++ b/doc/src/Howto_tip4p.rst @@ -8,18 +8,28 @@ This site M is located at a fixed distance away from the oxygen along the bisector of the HOH bond angle. A bond style of *harmonic* and an angle style of *harmonic* or *charmm* should also be used. -A TIP4P model is run with LAMMPS using either this command +A TIP4P model is run with LAMMPS using either these commands for a cutoff model: +* :doc:`pair_style tip4p/cut ` * :doc:`pair_style lj/cut/tip4p/cut ` -or these two commands for a long-range model: +or these commands for a long-range model: +* :doc:`pair_style tip4p/long ` * :doc:`pair_style lj/cut/tip4p/long ` +* :doc:`pair_style lj/long/tip4p/long ` +* :doc:`pair_style tip4p/long/soft ` +* :doc:`pair_style lj/cut/tip4p/long/soft ` * :doc:`kspace_style pppm/tip4p ` +* :doc:`kspace_style pppm/disp/tip4p ` -For both models, the bond lengths and bond angles should be held fixed -using the :doc:`fix shake ` command. +The bond lengths and bond angles should be held fixed using the +:doc:`fix shake ` or :doc:`fix rattle ` command, +unless a parameterization for a flexible TIP4P model is used. The +parameter sets listed below are all for rigid TIP4P model variants and +thus the bond and angle force constants are not used and can be set to +any legal value; only equilibrium length and angle are used. These are the additional parameters (in real units) to set for O and H atoms and the water molecule to run a rigid TIP4P model with a cutoff @@ -87,15 +97,16 @@ solver (e.g. Ewald or PPPM in LAMMPS): | LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0 | -Note that the when using the TIP4P pair style, the neighbor list -cutoff for Coulomb interactions is effectively extended by a distance -2 \* (OM distance), to account for the offset distance of the -fictitious charges on O atoms in water molecules. Thus it is -typically best in an efficiency sense to use a LJ cutoff >= Coulomb -cutoff + 2\*(OM distance), to shrink the size of the neighbor list. -This leads to slightly larger cost for the long-range calculation, so -you can test the trade-off for your model. The OM distance and the LJ -and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long ` command. +Note that the when using the TIP4P pair style, the neighbor list cutoff +for Coulomb interactions is effectively extended by a distance 2 \* (OM +distance), to account for the offset distance of the fictitious charges +on O atoms in water molecules. Thus it is typically best in an +efficiency sense to use a LJ cutoff >= Coulomb cutoff + 2\*(OM +distance), to shrink the size of the neighbor list. This leads to +slightly larger cost for the long-range calculation, so you can test the +trade-off for your model. The OM distance and the LJ and Coulombic +cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long +` command. Wikipedia also has a nice article on `water models `_. diff --git a/doc/src/Howto_triclinic.rst b/doc/src/Howto_triclinic.rst index 5e952709c9..dd0a949f68 100644 --- a/doc/src/Howto_triclinic.rst +++ b/doc/src/Howto_triclinic.rst @@ -144,11 +144,6 @@ does not change the atom positions due to non-periodicity. In this mode, if you tilt the system to extreme angles, the simulation will simply become inefficient, due to the highly skewed simulation box. -The limitation on not creating a simulation box with a tilt factor -skewing the box more than half the distance of the parallel box length -can be overridden via the :doc:`box ` command. Setting the *tilt* -keyword to *large* allows any tilt factors to be specified. - Box flips that may occur using the :doc:`fix deform ` or :doc:`fix npt ` commands can be turned off using the *flip no* option with either of the commands. diff --git a/doc/src/Library.rst b/doc/src/Library.rst index 05b652f7a7..3533c347c8 100644 --- a/doc/src/Library.rst +++ b/doc/src/Library.rst @@ -2,12 +2,13 @@ LAMMPS Library Interfaces ************************* As described on the :doc:`library interface to LAMMPS ` -page, LAMMPS can be built as a library (static or shared), so that -it can be called by another code, used in a :doc:`coupled manner +page, LAMMPS can be built as a library (static or shared), so that it +can be called by another code, used in a :doc:`coupled manner ` with other codes, or driven through a :doc:`Python -script `. Even the LAMMPS standalone executable is -essentially a thin wrapper on top of the LAMMPS library, creating a -LAMMPS instance, processing input and then existing. +script `. The LAMMPS standalone executable itself is +essentially a thin wrapper on top of the LAMMPS library, which creates a +LAMMPS instance, passes the input for processing to that instance, and +then exits. Most of the APIs described below are based on C language wrapper functions in the files ``src/library.h`` and ``src/library.cpp``, but @@ -87,6 +88,18 @@ run LAMMPS in serial mode. message retrieved `. We thus recommend enabling C++ exceptions when using the library interface, +.. admonition:: Using the C library interface as a plugin + :class: note + + Rather than including the C library directly and link to the LAMMPS + library at compile time, you can use the ``liblammpsplugin.h`` header + file and the ``liblammpsplugin.c`` C code in the + ``examples/COUPLE/plugin`` folder for an interface to LAMMPS that is + largely identical to the regular library interface, only that it will + load a LAMMPS shared library file at runtime. This can be useful for + applications where the interface to LAMMPS would be an optional + feature. + .. warning:: No checks are made on the arguments of the function calls of the C @@ -163,5 +176,3 @@ The following links provide some examples and references to the C++ API. :maxdepth: 1 Cplusplus - - diff --git a/doc/src/Library_config.rst b/doc/src/Library_config.rst index 04b12f35de..481edcee7c 100644 --- a/doc/src/Library_config.rst +++ b/doc/src/Library_config.rst @@ -39,7 +39,7 @@ crashes within LAMMPS may be recovered from by enabling :ref:`exceptions `, avoiding them proactively is a safer approach. -.. code-block:: C +.. code-block:: c :caption: Example for using configuration settings functions #include "library.h" diff --git a/doc/src/Library_create.rst b/doc/src/Library_create.rst index 8ccc2e80ce..546db9b3be 100644 --- a/doc/src/Library_create.rst +++ b/doc/src/Library_create.rst @@ -22,7 +22,7 @@ as the "handle" argument in subsequent function calls until that instance is destroyed by calling :cpp:func:`lammps_close`. Here is a simple example demonstrating its use: -.. code-block:: C +.. code-block:: c #include "library.h" #include diff --git a/doc/src/Library_execute.rst b/doc/src/Library_execute.rst index 201d9c01b0..44b601ba4c 100644 --- a/doc/src/Library_execute.rst +++ b/doc/src/Library_execute.rst @@ -30,7 +30,7 @@ be included in the file or strings, and expansion of variables with ``${name}`` or ``$(expression)`` syntax is performed. Below is a short example using some of these functions. -.. code-block:: C +.. code-block:: c /* define to make the otherwise hidden prototype for "lammps_open()" visible */ #define LAMMPS_LIB_MPI diff --git a/doc/src/Library_properties.rst b/doc/src/Library_properties.rst index dfd72adc95..b3a8f9ea5a 100644 --- a/doc/src/Library_properties.rst +++ b/doc/src/Library_properties.rst @@ -32,7 +32,7 @@ indexed accordingly. Per-atom data can change sizes and ordering at every neighbor list rebuild or atom sort event as atoms migrate between sub-domains and processors. -.. code-block:: C +.. code-block:: c #include "library.h" #include diff --git a/doc/src/Library_utility.rst b/doc/src/Library_utility.rst index 9d16daae0b..e555b79c0b 100644 --- a/doc/src/Library_utility.rst +++ b/doc/src/Library_utility.rst @@ -7,6 +7,7 @@ functions. They do not directly call the LAMMPS library. - :cpp:func:`lammps_encode_image_flags` - :cpp:func:`lammps_decode_image_flags` - :cpp:func:`lammps_set_fix_external_callback` +- :cpp:func:`lammps_fix_external_get_force` - :cpp:func:`lammps_fix_external_set_energy_global` - :cpp:func:`lammps_fix_external_set_energy_peratom` - :cpp:func:`lammps_fix_external_set_virial_global` @@ -44,6 +45,11 @@ where such memory buffers were allocated that require the use of ----------------------- +.. doxygenfunction:: lammps_fix_external_get_force + :project: progguide + +----------------------- + .. doxygenfunction:: lammps_fix_external_set_energy_global :project: progguide diff --git a/doc/src/Manual.rst b/doc/src/Manual.rst index 14d4862c40..5a5d5c88fa 100644 --- a/doc/src/Manual.rst +++ b/doc/src/Manual.rst @@ -42,7 +42,7 @@ descriptions of all commands included in the LAMMPS code. .. only:: html Once you are familiar with LAMMPS, you may want to bookmark - :doc:`this page ` since it gives quick access + :doc:`this page ` since it gives quick access to the documentation for all LAMMPS commands. .. _lws: https://www.lammps.org diff --git a/doc/src/Modify_bond.rst b/doc/src/Modify_bond.rst index 682237b8bd..58b08de81b 100644 --- a/doc/src/Modify_bond.rst +++ b/doc/src/Modify_bond.rst @@ -13,24 +13,65 @@ Here is a brief description of common methods you define in your new derived class. See bond.h, angle.h, dihedral.h, and improper.h for details and specific additional methods. -+-----------------------+---------------------------------------------------------------------------------------+ -| init | check if all coefficients are set, calls *init_style* (optional) | -+-----------------------+---------------------------------------------------------------------------------------+ -| init_style | check if style specific conditions are met (optional) | -+-----------------------+---------------------------------------------------------------------------------------+ -| compute | compute the molecular interactions (required) | -+-----------------------+---------------------------------------------------------------------------------------+ -| settings | apply global settings for all types (optional) | -+-----------------------+---------------------------------------------------------------------------------------+ -| coeff | set coefficients for one type (required) | -+-----------------------+---------------------------------------------------------------------------------------+ -| equilibrium_distance | length of bond, used by SHAKE (required, bond only) | -+-----------------------+---------------------------------------------------------------------------------------+ -| equilibrium_angle | opening of angle, used by SHAKE (required, angle only) | -+-----------------------+---------------------------------------------------------------------------------------+ -| write & read_restart | writes/reads coeffs to restart files (required) | -+-----------------------+---------------------------------------------------------------------------------------+ -| single | force (bond only) and energy of a single bond or angle (required, bond or angle only) | -+-----------------------+---------------------------------------------------------------------------------------+ -| memory_usage | tally memory allocated by the style (optional) | -+-----------------------+---------------------------------------------------------------------------------------+ ++-----------------------+---------------------------------------------------------------------+ +| Required | "pure" methods that *must* be overridden in a derived class | ++=======================+=====================================================================+ +| compute | compute the molecular interactions for all listed items | ++-----------------------+---------------------------------------------------------------------+ +| coeff | set coefficients for one type | ++-----------------------+---------------------------------------------------------------------+ +| equilibrium_distance | length of bond, used by SHAKE (bond styles only) | ++-----------------------+---------------------------------------------------------------------+ +| equilibrium_angle | opening of angle, used by SHAKE (angle styles only) | ++-----------------------+---------------------------------------------------------------------+ +| write & read_restart | writes/reads coeffs to restart files | ++-----------------------+---------------------------------------------------------------------+ +| single | force/r (bond styles only) and energy of a single bond or angle | ++-----------------------+---------------------------------------------------------------------+ + + ++--------------------------------+----------------------------------------------------------------------+ +| Optional | methods that have a default or dummy implementation | ++================================+======================================================================+ +| init | check if all coefficients are set, calls init_style() | ++--------------------------------+----------------------------------------------------------------------+ +| init_style | check if style specific conditions are met | ++--------------------------------+----------------------------------------------------------------------+ +| settings | apply global settings for all types | ++--------------------------------+----------------------------------------------------------------------+ +| write & read_restart_settings | writes/reads global style settings to restart files | ++--------------------------------+----------------------------------------------------------------------+ +| write_data | write corresponding Coeffs section(s) in data file | ++--------------------------------+----------------------------------------------------------------------+ +| memory_usage | tally memory allocated by the style | ++--------------------------------+----------------------------------------------------------------------+ +| extract | provide access to internal data (bond or angle styles only) | ++--------------------------------+----------------------------------------------------------------------+ +| reinit | reset all type-based parameters, called by fix adapt (bonds only) | ++--------------------------------+----------------------------------------------------------------------+ +| pack & unpack_forward_comm | copy data to and from buffer in forward communication (bonds only) | ++--------------------------------+----------------------------------------------------------------------+ +| pack & unpack_reverse_comm | copy data to and from buffer in reverse communication (bonds only) | ++--------------------------------+----------------------------------------------------------------------+ + +Here is a list of flags or settings that should be set in the +constructor of the derived class when they differ from the default +setting. + ++---------------------------------+------------------------------------------------------------------------------+---------+ +| Name of flag | Description | default | ++=================================+==============================================================================+=========+ +| writedata | 1 if write_data() is implemented | 1 | ++---------------------------------+------------------------------------------------------------------------------+---------+ +| single_extra | number of extra single values calculated (bond styles only) | 0 | ++---------------------------------+------------------------------------------------------------------------------+---------+ +| partial_flag | 1 if bond type can be set to 0 and deleted (bond styles only) | 0 | ++---------------------------------+------------------------------------------------------------------------------+---------+ +| reinitflag | 1 if style has reinit() and is compatible with fix adapt | 1 | ++---------------------------------+------------------------------------------------------------------------------+---------+ +| comm_forward | size of buffer (in doubles) for forward communication (bond styles only) | 0 | ++---------------------------------+------------------------------------------------------------------------------+---------+ +| comm_reverse | size of buffer (in doubles) for reverse communication (bond styles only) | 0 | ++---------------------------------+------------------------------------------------------------------------------+---------+ +| comm_reverse_off | size of buffer for reverse communication with newton off (bond styles only) | 0 | ++---------------------------------+------------------------------------------------------------------------------+---------+ diff --git a/doc/src/Modify_pair.rst b/doc/src/Modify_pair.rst index 6913204504..38f5ade567 100644 --- a/doc/src/Modify_pair.rst +++ b/doc/src/Modify_pair.rst @@ -1,35 +1,121 @@ Pair styles =========== -Classes that compute pairwise interactions are derived from the Pair -class. In LAMMPS, pairwise calculation include many-body potentials -such as EAM or Tersoff where particles interact without a static bond -topology. New styles can be created to add new pair potentials to -LAMMPS. +Classes that compute pairwise non-bonded interactions are derived from +the Pair class. In LAMMPS, pairwise calculation include many-body +potentials such as EAM, Tersoff, or ReaxFF where particles interact +without an explicit bond topology but include interactions beyond +pairwise non-bonded contributions. New styles can be created to add +support for additional pair potentials to LAMMPS. When the +modifications are small, sometimes it is more effective to derive from +an existing pair style class. This latter approach is also used by +:doc:`Accelerator packages ` where the accelerated style +names differ from their base classes by an appended suffix. -Pair_lj_cut.cpp is a simple example of a Pair class, though it -includes some optional methods to enable its use with rRESPA. +The file ``src/pair_lj_cut.cpp`` is an example of a Pair class with a +very simple potential function. It includes several optional methods to +enable its use with :doc:`run_style respa ` and :doc:`compute +group/group `. -Here is a brief description of the class methods in pair.h: +Here is a brief list of some the class methods in the Pair class that +*must* be or *may* be overridden in a derived class. +---------------------------------+---------------------------------------------------------------------+ +| Required | "pure" methods that *must* be overridden in a derived class | ++=================================+=====================================================================+ | compute | workhorse routine that computes pairwise interactions | +---------------------------------+---------------------------------------------------------------------+ -| settings | reads the input script line with arguments you define | +| settings | processes the arguments to the pair_style command | +---------------------------------+---------------------------------------------------------------------+ -| coeff | set coefficients for one i,j type pair | -+---------------------------------+---------------------------------------------------------------------+ -| init_one | perform initialization for one i,j type pair | -+---------------------------------+---------------------------------------------------------------------+ -| init_style | initialization specific to this pair style | -+---------------------------------+---------------------------------------------------------------------+ -| write & read_restart | write/read i,j pair coeffs to restart files | -+---------------------------------+---------------------------------------------------------------------+ -| write & read_restart_settings | write/read global settings to restart files | -+---------------------------------+---------------------------------------------------------------------+ -| single | force/r and energy of a single pairwise interaction between 2 atoms | -+---------------------------------+---------------------------------------------------------------------+ -| compute_inner/middle/outer | versions of compute used by rRESPA | +| coeff | set coefficients for one i,j type pair, called from pair_coeff | +---------------------------------+---------------------------------------------------------------------+ -The inner/middle/outer routines are optional. ++---------------------------------+----------------------------------------------------------------------+ +| Optional | methods that have a default or dummy implementation | ++=================================+======================================================================+ +| init_one | perform initialization for one i,j type pair | ++---------------------------------+----------------------------------------------------------------------+ +| init_style | style initialization: request neighbor list(s), error checks | ++---------------------------------+----------------------------------------------------------------------+ +| init_list | Neighbor class callback function to pass neighbor list to pair style | ++---------------------------------+----------------------------------------------------------------------+ +| single | force/r and energy of a single pairwise interaction between 2 atoms | ++---------------------------------+----------------------------------------------------------------------+ +| compute_inner/middle/outer | versions of compute used by rRESPA | ++---------------------------------+----------------------------------------------------------------------+ +| memory_usage | return estimated amount of memory used by the pair style | ++---------------------------------+----------------------------------------------------------------------+ +| modify_params | process arguments to pair_modify command | ++---------------------------------+----------------------------------------------------------------------+ +| extract | provide access to internal scalar or per-type data like cutoffs | ++---------------------------------+----------------------------------------------------------------------+ +| extract_peratom | provide access to internal per-atom data | ++---------------------------------+----------------------------------------------------------------------+ +| setup | initialization at the beginning of a run | ++---------------------------------+----------------------------------------------------------------------+ +| finish | called at the end of a run, e.g. to print | ++---------------------------------+----------------------------------------------------------------------+ +| write & read_restart | write/read i,j pair coeffs to restart files | ++---------------------------------+----------------------------------------------------------------------+ +| write & read_restart_settings | write/read global settings to restart files | ++---------------------------------+----------------------------------------------------------------------+ +| write_data | write Pair Coeffs section to data file | ++---------------------------------+----------------------------------------------------------------------+ +| write_data_all | write PairIJ Coeffs section to data file | ++---------------------------------+----------------------------------------------------------------------+ +| pack & unpack_forward_comm | copy data to and from buffer if style uses forward communication | ++---------------------------------+----------------------------------------------------------------------+ +| pack & unpack_reverse_comm | copy data to and from buffer if style uses reverse communication | ++---------------------------------+----------------------------------------------------------------------+ +| reinit | reset all type-based parameters, called by fix adapt for example | ++---------------------------------+----------------------------------------------------------------------+ +| reset_dt | called when the time step is changed by timestep or fix reset/dt | ++---------------------------------+----------------------------------------------------------------------+ + +Here is a list of flags or settings that should be set in the +constructor of the derived pair class when they differ from the default +setting. + ++---------------------------------+-------------------------------------------------------------+---------+ +| Name of flag | Description | default | ++=================================+=============================================================+=========+ +| single_enable | 1 if single() method is implemented, 0 if missing | 1 | ++---------------------------------+-------------------------------------------------------------+---------+ +| respa_enable | 1 if pair style has compute_inner/middle/outer() | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| restartinfo | 1 if pair style writes its settings to a restart | 1 | ++---------------------------------+-------------------------------------------------------------+---------+ +| one_coeff | 1 if only a pair_coeff * * command is allowed | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| manybody_flag | 1 if pair style is a manybody potential | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| unit_convert_flag | value != 0 indicates support for unit conversion | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| no_virial_fdotr_compute | 1 if pair style does not call virial_fdotr_compute() | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| writedata | 1 if write_data() and write_data_all() are implemented | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| comm_forward | size of buffer (in doubles) for forward communication | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| comm_reverse | size of buffer (in doubles) for reverse communication | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| ghostneigh | 1 if cutghost is set and style uses neighbors of ghosts | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| finitecutflag | 1 if cutoff depends on diameter of atoms | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| reinitflag | 1 if style has reinit() and is compatible with fix adapt | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| ewaldflag | 1 if compatible with kspace_style ewald | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| pppmflag | 1 if compatible with kspace_style pppm | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| msmflag | 1 if compatible with kspace_style msm | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| dispersionflag | 1 if compatible with ewald/disp or pppm/disp | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| tip4pflag | 1 if compatible with kspace_style pppm/tip4p | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| dipoleflag | 1 if compatible with dipole kspace_style | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ +| spinflag | 1 if compatible with spin kspace_style | 0 | ++---------------------------------+-------------------------------------------------------------+---------+ diff --git a/doc/src/Modify_style.rst b/doc/src/Modify_style.rst index 9b394f23a9..ad2cb656d0 100644 --- a/doc/src/Modify_style.rst +++ b/doc/src/Modify_style.rst @@ -359,6 +359,12 @@ you are uncertain, please ask. - I/O is done via the C-style stdio library and **not** iostreams. +- Do not use so-called "alternative tokens" like ``and``, ``or``, + ``not`` and similar, but rather use the corresponding operators + ``&&``, ``||``, and ``!``. The alternative tokens are not available + by default on all compilers, and also we want to maintain a consistent + programming style. + - Output to the screen and the logfile should be using the corresponding FILE pointers and only be done on MPI rank 0. Use the :cpp:func:`utils::logmesg` convenience function where possible. diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 44a8235f93..74ddb066c6 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -80,6 +80,7 @@ page gives those details. * :ref:`ML-HDNNP ` * :ref:`ML-IAP ` * :ref:`ML-PACE ` + * :ref:`ML-POD ` * :ref:`ML-QUIP ` * :ref:`ML-RANN ` * :ref:`ML-SNAP ` @@ -200,6 +201,7 @@ particle models including ellipsoids, 2d lines, and 3d triangles. * :doc:`Howto spherical ` * :doc:`pair_style gayberne ` * :doc:`pair_style resquared ` +* :doc:`pair_style ylz ` * `doc/PDF/pair_gayberne_extra.pdf `_ * `doc/PDF/pair_resquared_extra.pdf `_ * examples/ASPHERE @@ -864,7 +866,7 @@ ELECTRODE package The ELECTRODE package allows the user to enforce a constant potential method for groups of atoms that interact with the remaining atoms as electrolyte. -**Authors:** The ELECTRODE library is written and maintained by Ludwig +**Authors:** The ELECTRODE package is written and maintained by Ludwig Ahrens-Iwers (TUHH, Hamburg, Germany), Shern Tee (UQ, Brisbane, Australia) and Robert Meissner (TUHH, Hamburg, Germany). @@ -877,7 +879,7 @@ This package has :ref:`specific installation instructions ` on the **Supporting info:** -* :doc:`fix electrode/conp ` +* :doc:`fix electrode/conp ` ---------- @@ -1484,8 +1486,9 @@ MC package Several fixes and a pair style that have Monte Carlo (MC) or MC-like attributes. These include fixes for creating, breaking, and swapping -bonds, for performing atomic swaps, and performing grand-canonical MC -(GCMC) or similar processes in conjunction with dynamics. +bonds, for performing atomic swaps, and performing grand canonical +MC (GCMC), semi-grand canonical MC (SGCMC), or similar processes in +conjunction with molecular dynamics (MD). **Supporting info:** @@ -1497,6 +1500,7 @@ bonds, for performing atomic swaps, and performing grand-canonical MC * :doc:`fix bond/swap ` * :doc:`fix charge/regulation ` * :doc:`fix gcmc ` +* :doc:`fix sgcmc ` * :doc:`fix tfmc ` * :doc:`fix widom ` * :doc:`pair_style dsmc ` @@ -1736,8 +1740,6 @@ must be installed. .. versionadded:: 30Jun2020 - .. versionadded:: 30Jun2020 - **Supporting info:** * src/ML-IAP: filenames -> commands @@ -1797,6 +1799,39 @@ This package has :ref:`specific installation instructions ` on the ---------- +.. _PKG-ML-POD: + +ML-POD package +------------------- + +**Contents:** + +A pair style and fitpod style for Proper Orthogonal Descriptors +(POD). POD is a methodology for deriving descriptors based on the proper +orthogonal decomposition. The ML-POD package provides an efficient +implementation for running simulations with POD potentials, along with +fitting the potentials natively in LAMMPS. + +**Authors:** + +Ngoc Cuong Nguyen (MIT), Andrew Rohskopf (Sandia) + +.. versionadded:: 22Dec2022 + +**Install:** + +This package has :ref:`specific installation instructions ` on the +:doc:`Build extras ` page. + +**Supporting info:** + +* src/ML-POD: filenames -> commands +* :doc:`pair_style pod ` +* :doc:`command_style fitpod ` +* examples/PACKAGES/pod + +---------- + .. _PKG-ML-QUIP: ML-QUIP package diff --git a/doc/src/Packages_list.rst b/doc/src/Packages_list.rst index cfe0460d05..ac0ba7728e 100644 --- a/doc/src/Packages_list.rst +++ b/doc/src/Packages_list.rst @@ -155,7 +155,7 @@ whether an extra library is needed to build and use the package: - no * - :ref:`ELECTRODE ` - electrode charges to match potential - - :doc:`fix electrode/conp ` + - :doc:`fix electrode/conp ` - PACKAGES/electrode - no * - :ref:`EXTRA-COMPUTE ` @@ -298,6 +298,11 @@ whether an extra library is needed to build and use the package: - :doc:`pair pace ` - PACKAGES/pace - ext + * - :ref:`ML-POD ` + - Proper orthogonal decomposition potentials + - :doc:`pair pod ` + - pod + - ext * - :ref:`ML-QUIP ` - QUIP/libatoms interface - :doc:`pair_style quip ` diff --git a/doc/src/Python_atoms.rst b/doc/src/Python_atoms.rst index be0d4ff800..2cb5c695e8 100644 --- a/doc/src/Python_atoms.rst +++ b/doc/src/Python_atoms.rst @@ -58,7 +58,7 @@ against invalid accesses. Each element of this list is a :py:class:`Atom ` or :py:class:`Atom2D ` object. The attributes of these objects provide access to their data (id, type, position, velocity, force, etc.): - .. code-block:: Python + .. code-block:: python # access first atom L.atoms[0].id @@ -71,7 +71,7 @@ against invalid accesses. Some attributes can be changed: - .. code-block:: Python + .. code-block:: python # set position in 2D simulation L.atoms[0].position = (1.0, 0.0) diff --git a/doc/src/Python_config.rst b/doc/src/Python_config.rst index 38f0ef0baf..ccbc74a46c 100644 --- a/doc/src/Python_config.rst +++ b/doc/src/Python_config.rst @@ -4,7 +4,7 @@ Configuration information The following methods can be used to query the LAMMPS library about compile time settings and included packages and styles. -.. code-block:: Python +.. code-block:: python :caption: Example for using configuration settings functions from lammps import lammps diff --git a/doc/src/Python_create.rst b/doc/src/Python_create.rst index ec4241f36a..939aad2f32 100644 --- a/doc/src/Python_create.rst +++ b/doc/src/Python_create.rst @@ -74,7 +74,7 @@ Here are simple examples using all three Python interfaces: :py:class:`PyLammps ` objects can also be created on top of an existing :py:class:`lammps ` object: - .. code-block:: Python + .. code-block:: python from lammps import lammps, PyLammps ... @@ -113,7 +113,7 @@ Here are simple examples using all three Python interfaces: You can also initialize IPyLammps on top of an existing :py:class:`lammps` or :py:class:`PyLammps` object: - .. code-block:: Python + .. code-block:: python from lammps import lammps, IPyLammps ... @@ -142,7 +142,7 @@ the MPI and/or Kokkos environment if enabled and active. Note that you can create multiple LAMMPS objects in your Python script, and coordinate and run multiple simulations, e.g. -.. code-block:: Python +.. code-block:: python from lammps import lammps lmp1 = lammps() diff --git a/doc/src/Python_error.rst b/doc/src/Python_error.rst index 744a8dd3de..5dbd940723 100644 --- a/doc/src/Python_error.rst +++ b/doc/src/Python_error.rst @@ -7,7 +7,7 @@ current Python process with an error message. C++ exceptions allow capturing them on the C++ side and rethrowing them on the Python side. This way LAMMPS errors can be handled through the Python exception handling mechanism. -.. code-block:: Python +.. code-block:: python from lammps import lammps, MPIAbortException diff --git a/doc/src/Python_execute.rst b/doc/src/Python_execute.rst index 59faa34438..01cf0e920f 100644 --- a/doc/src/Python_execute.rst +++ b/doc/src/Python_execute.rst @@ -60,7 +60,7 @@ it is possible to "compute" what the next LAMMPS command should be. can be executed using with the lammps API with the following Python code if ``lmp`` is an instance of :py:class:`lammps `: - .. code-block:: Python + .. code-block:: python from lammps import lammps @@ -73,7 +73,7 @@ it is possible to "compute" what the next LAMMPS command should be. The arguments of the command can be passed as one string, or individually. - .. code-block:: Python + .. code-block:: python from lammps import PyLammps @@ -93,14 +93,14 @@ it is possible to "compute" what the next LAMMPS command should be. parameterization. In the lammps API parameterization needed to be done manually by creating formatted command strings. - .. code-block:: Python + .. code-block:: python lmp.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi)) In contrast, methods of PyLammps accept parameters directly and will convert them automatically to a final command string. - .. code-block:: Python + .. code-block:: python L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi) diff --git a/doc/src/Python_launch.rst b/doc/src/Python_launch.rst index 500a107977..96e43a2d95 100644 --- a/doc/src/Python_launch.rst +++ b/doc/src/Python_launch.rst @@ -56,7 +56,7 @@ and you should see the same output as if you had typed Note that without the mpi4py specific lines from ``test.py`` -.. code-block:: Python +.. code-block:: python from lammps import lammps lmp = lammps() diff --git a/doc/src/Python_objects.rst b/doc/src/Python_objects.rst index 4a1496632e..6e3a329a27 100644 --- a/doc/src/Python_objects.rst +++ b/doc/src/Python_objects.rst @@ -76,7 +76,7 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module. To define a variable you can use the :doc:`variable ` command: - .. code-block:: Python + .. code-block:: python L.variable("a index 2") @@ -85,14 +85,14 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module. you can access an individual variable by retrieving a variable object from the ``L.variables`` dictionary by name - .. code-block:: Python + .. code-block:: python a = L.variables['a'] The variable value can then be easily read and written by accessing the value property of this object. - .. code-block:: Python + .. code-block:: python print(a.value) a.value = 4 diff --git a/doc/src/Python_properties.rst b/doc/src/Python_properties.rst index 02af03bbb8..227a729622 100644 --- a/doc/src/Python_properties.rst +++ b/doc/src/Python_properties.rst @@ -105,7 +105,7 @@ against invalid accesses. variables, compute or fix data (see :doc:`Howto_output`): - .. code-block:: Python + .. code-block:: python result = L.eval("ke") # kinetic energy result = L.eval("pe") # potential energy diff --git a/doc/src/Python_scatter.rst b/doc/src/Python_scatter.rst index 113b98d354..002a36cc98 100644 --- a/doc/src/Python_scatter.rst +++ b/doc/src/Python_scatter.rst @@ -1,7 +1,7 @@ Scatter/gather operations ========================= -.. code-block:: Python +.. code-block:: python data = lmp.gather_atoms(name,type,count) # return per-atom property of all atoms gathered into data, ordered by atom ID # name = "x", "charge", "type", etc @@ -42,7 +42,7 @@ For the scatter methods, the array of coordinates passed to must be a ctypes vector of ints or doubles, allocated and initialized something like this: -.. code-block:: Python +.. code-block:: python from ctypes import c_double natoms = lmp.get_natoms() diff --git a/doc/src/Run_options.rst b/doc/src/Run_options.rst index f7bb652ea9..0d627626cc 100644 --- a/doc/src/Run_options.rst +++ b/doc/src/Run_options.rst @@ -262,6 +262,8 @@ Disable generating a citation reminder (see above) at all. **-nonbuf** +.. versionadded:: 15Sep2022 + Turn off buffering for screen and logfile output. For performance reasons, output to the screen and logfile is usually buffered, i.e. output is only written to a file if its buffer - typically 4096 bytes - @@ -442,7 +444,7 @@ the LAMMPS simulation domain. .. _restart2data: -**-restart2data restartfile [remap] datafile keyword value ...** +**-restart2data restartfile datafile keyword value ...** Convert the restart file into a data file and immediately exit. This is the same operation as if the following 2-line input script were @@ -450,7 +452,7 @@ run: .. code-block:: LAMMPS - read_restart restartfile [remap] + read_restart restartfile write_data datafile keyword value ... The specified restartfile and/or datafile name may contain the wild-card @@ -462,28 +464,21 @@ Note that a filename such as file.\* may need to be enclosed in quotes or the "\*" character prefixed with a backslash ("\") to avoid shell expansion of the "\*" character. -Following restartfile argument, the optional word "remap" may be used. -This has the same effect like adding it to a -:doc:`read_restart ` command, and operates as explained on -its doc page. This is useful if reading the restart file triggers an -error that atoms have been lost. In that case, use of the remap flag -should allow the data file to still be produced. - -The syntax following restartfile (or remap), namely +The syntax following restartfile, namely .. parsed-literal:: datafile keyword value ... is identical to the arguments of the :doc:`write_data ` -command. See its page for details. This includes its +command. See its documentation page for details. This includes its optional keyword/value settings. ---------- .. _restart2dump: -**-restart2dump restartfile [remap] group-ID dumpstyle dumpfile arg1 arg2 ...** +**-restart2dump restartfile group-ID dumpstyle dumpfile arg1 arg2 ...** Convert the restart file into a dump file and immediately exit. This is the same operation as if the following 2-line input script were @@ -491,7 +486,7 @@ run: .. code-block:: LAMMPS - read_restart restartfile [remap] + read_restart restartfile write_dump group-ID dumpstyle dumpfile arg1 arg2 ... Note that the specified restartfile and dumpfile names may contain @@ -503,24 +498,17 @@ such as file.\* may need to be enclosed in quotes or the "\*" character prefixed with a backslash ("\") to avoid shell expansion of the "\*" character. -Note that following the restartfile argument, the optional word "remap" -can be used. This has the effect as adding it to the -:doc:`read_restart ` command, as explained on its doc page. -This is useful if reading the restart file triggers an error that atoms -have been lost. In that case, use of the remap flag should allow the -dump file to still be produced. - -The syntax following restartfile (or remap), namely +The syntax following restartfile, namely .. code-block:: LAMMPS group-ID dumpstyle dumpfile arg1 arg2 ... is identical to the arguments of the :doc:`write_dump ` -command. See its page for details. This includes what per-atom -fields are written to the dump file and optional dump_modify settings, -including ones that affect how parallel dump files are written, e.g. -the *nfile* and *fileper* keywords. See the +command. See its documentation page for details. This includes what +per-atom fields are written to the dump file and optional dump_modify +settings, including ones that affect how parallel dump files are written, +e.g. the *nfile* and *fileper* keywords. See the :doc:`dump_modify ` page for details. ---------- diff --git a/doc/src/Run_output.rst b/doc/src/Run_output.rst index a988be94ad..28f66d6ae9 100644 --- a/doc/src/Run_output.rst +++ b/doc/src/Run_output.rst @@ -16,46 +16,47 @@ simulation. An example set of statistics is shown here: .. parsed-literal:: - Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms + Loop time of 0.942801 on 4 procs for 300 steps with 2004 atoms - Performance: 18.436 ns/day 1.302 hours/ns 106.689 timesteps/s - 97.0% CPU use with 4 MPI tasks x no OpenMP threads + Performance: 54.985 ns/day, 0.436 hours/ns, 318.201 timesteps/s, 637.674 katom-step/s + 195.2% CPU use with 2 MPI tasks x 2 OpenMP threads - MPI task timings breakdown: + MPI task timing breakdown: Section \| min time \| avg time \| max time \|%varavg\| %total --------------------------------------------------------------- - Pair \| 1.9808 \| 2.0134 \| 2.0318 \| 1.4 \| 71.60 - Bond \| 0.0021894 \| 0.0060319 \| 0.010058 \| 4.7 \| 0.21 - Kspace \| 0.3207 \| 0.3366 \| 0.36616 \| 3.1 \| 11.97 - Neigh \| 0.28411 \| 0.28464 \| 0.28516 \| 0.1 \| 10.12 - Comm \| 0.075732 \| 0.077018 \| 0.07883 \| 0.4 \| 2.74 - Output \| 0.00030518 \| 0.00042665 \| 0.00078821 \| 1.0 \| 0.02 - Modify \| 0.086606 \| 0.086631 \| 0.086668 \| 0.0 \| 3.08 - Other \| \| 0.007178 \| \| \| 0.26 + Pair \| 0.61419 \| 0.62872 \| 0.64325 \| 1.8 \| 66.69 + Bond \| 0.0028608 \| 0.0028899 \| 0.002919 \| 0.1 \| 0.31 + Kspace \| 0.12652 \| 0.14048 \| 0.15444 \| 3.7 \| 14.90 + Neigh \| 0.10242 \| 0.10242 \| 0.10242 \| 0.0 \| 10.86 + Comm \| 0.026753 \| 0.027593 \| 0.028434 \| 0.5 \| 2.93 + Output \| 0.00018341 \| 0.00030942 \| 0.00043542 \| 0.0 \| 0.03 + Modify \| 0.039117 \| 0.039348 \| 0.039579 \| 0.1 \| 4.17 + Other \| \| 0.001041 \| \| \| 0.11 - Nlocal: 501 ave 508 max 490 min - Histogram: 1 0 0 0 0 0 1 1 0 1 - Nghost: 6586.25 ave 6628 max 6548 min - Histogram: 1 0 1 0 0 0 1 0 0 1 - Neighs: 177007 ave 180562 max 170212 min - Histogram: 1 0 0 0 0 0 0 1 1 1 + Nlocal: 1002 ave 1006 max 998 min + Histogram: 1 0 0 0 0 0 0 0 0 1 + Nghost: 8670.5 ave 8691 max 8650 min + Histogram: 1 0 0 0 0 0 0 0 0 1 + Neighs: 354010 ave 357257 max 350763 min + Histogram: 1 0 0 0 0 0 0 0 0 1 - Total # of neighbors = 708028 - Ave neighs/atom = 353.307 - Ave special neighs/atom = 2.34032 + Total # of neighbors = 708020 + Ave neighs/atom = 353.30339 + Ave special neighs/atom = 2.3403194 Neighbor list builds = 26 Dangerous builds = 0 ---------- -The first section provides a global loop timing summary. The *loop -time* is the total wall-clock time for the simulation to run. The -*Performance* line is provided for convenience to help predict how -long it will take to run a desired physical simulation. The *CPU use* -line provides the CPU utilization per MPI task; it should be close to -100% times the number of OpenMP threads (or 1 of not using OpenMP). -Lower numbers correspond to delays due to file I/O or insufficient -thread utilization. +The first section provides a global loop timing summary. The *loop time* +is the total wall-clock time for the simulation to run. The +*Performance* line is provided for convenience to help predict how long +it will take to run a desired physical simulation and to have numbers +useful for performance comparison between different simulation settings +or system sizes. The *CPU use* line provides the CPU utilization per +MPI task; it should be close to 100% times the number of OpenMP threads +(or 1 of not using OpenMP). Lower numbers correspond to delays due to +file I/O or insufficient thread utilization. ---------- diff --git a/doc/src/Speed_kokkos.rst b/doc/src/Speed_kokkos.rst index 73345b7e88..4c0d6ae768 100644 --- a/doc/src/Speed_kokkos.rst +++ b/doc/src/Speed_kokkos.rst @@ -212,14 +212,15 @@ threads/task as Nt. The product of these two values should be N, i.e. .. note:: The default for the :doc:`package kokkos ` command when - running on KNL is to use "half" neighbor lists and set the Newton flag - to "on" for both pairwise and bonded interactions. This will typically - be best for many-body potentials. For simpler pairwise potentials, it - may be faster to use a "full" neighbor list with Newton flag to "off". - Use the "-pk kokkos" :doc:`command-line switch ` to change - the default :doc:`package kokkos ` options. See its page for - details and default settings. Experimenting with its options can provide - a speed-up for specific calculations. For example: + running on KNL is to use "half" neighbor lists and set the Newton + flag to "on" for both pairwise and bonded interactions. This will + typically be best for many-body potentials. For simpler pairwise + potentials, it may be faster to use a "full" neighbor list with + Newton flag to "off". Use the "-pk kokkos" :doc:`command-line switch + ` to change the default :doc:`package kokkos ` + options. See its documentation page for details and default + settings. Experimenting with its options can provide a speed-up for + specific calculations. For example: .. code-block:: bash @@ -271,17 +272,18 @@ one or more nodes, each with two GPUs: .. note:: The default for the :doc:`package kokkos ` command when - running on GPUs is to use "full" neighbor lists and set the Newton flag - to "off" for both pairwise and bonded interactions, along with threaded - communication. When running on Maxwell or Kepler GPUs, this will - typically be best. For Pascal GPUs and beyond, using "half" neighbor lists and - setting the Newton flag to "on" may be faster. For many pair styles, - setting the neighbor binsize equal to twice the CPU default value will - give speedup, which is the default when running on GPUs. Use the "-pk - kokkos" :doc:`command-line switch ` to change the default - :doc:`package kokkos ` options. See its page for details and - default settings. Experimenting with its options can provide a speed-up - for specific calculations. For example: + running on GPUs is to use "full" neighbor lists and set the Newton + flag to "off" for both pairwise and bonded interactions, along with + threaded communication. When running on Maxwell or Kepler GPUs, this + will typically be best. For Pascal GPUs and beyond, using "half" + neighbor lists and setting the Newton flag to "on" may be faster. For + many pair styles, setting the neighbor binsize equal to twice the CPU + default value will give speedup, which is the default when running on + GPUs. Use the "-pk kokkos" :doc:`command-line switch ` + to change the default :doc:`package kokkos ` options. See + its documentation page for details and default + settings. Experimenting with its options can provide a speed-up for + specific calculations. For example: .. code-block:: bash diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index b70c7677e0..145c283fd8 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -57,7 +57,7 @@ Pre-processing tools * :ref:`msi2lmp ` * :ref:`polybond ` * :ref:`stl_bin2txt ` - + * :ref:`tabulate ` Post-processing tools ===================== @@ -1159,13 +1159,27 @@ For illustration purposes below is a part of the Tcl example script. ---------- +.. _tabulate: + +tabulate tool +-------------- + +.. versionadded:: 22Dec2022 + +The ``tabulate`` folder contains Python scripts scripts to generate tabulated +potential files for LAMMPS. The bulk of the code is in the ``tabulate`` module +in the ``tabulate.py`` file. Some example files demonstrating its use are +included. See the README file for more information. + +---------- + .. _vim: vim tool ------------------ -The files in the tools/vim directory are add-ons to the VIM editor -that allow easier editing of LAMMPS input scripts. See the README.txt +The files in the ``tools/vim`` directory are add-ons to the VIM editor +that allow easier editing of LAMMPS input scripts. See the ``README.txt`` file for details. These files were provided by Gerolf Ziegenhain (gerolf at diff --git a/doc/src/angle_gaussian.rst b/doc/src/angle_gaussian.rst index f0a50938e4..6b102a693b 100644 --- a/doc/src/angle_gaussian.rst +++ b/doc/src/angle_gaussian.rst @@ -25,23 +25,25 @@ The *gaussian* angle style uses the potential: .. math:: - E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-(\theta-\theta_{i})^2}{w_i^2})\right) \right) + E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-2(\theta-\theta_{i})^2}{w_i^2}\right) \right) + +This analytical form is a suitable potential for obtaining mesoscale +effective force fields which can reproduce target atomistic +distributions :ref:`(Milano) `. -This analytical form is a suitable potential for obtaining -mesoscale effective force fields which can reproduce target atomistic distributions :ref:`(Milano) ` The following coefficients must be defined for each angle type via the :doc:`angle_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` commands: -* T temperature at which the potential was derived +* :math:`T` temperature at which the potential was derived * :math:`n` (integer >=1) -* :math:`A_1` (-) -* :math:`w_1` (-) +* :math:`A_1` (> 0, radians) +* :math:`w_1` (> 0, radians) * :math:`\theta_1` (degrees) * ... -* :math:`A_n` (-) -* :math:`w_n` (-) +* :math:`A_n` (> 0, radians) +* :math:`w_n` (> 0, radians) * :math:`\theta_n` (degrees) diff --git a/doc/src/angle_table.rst b/doc/src/angle_table.rst index b8aeae780b..c0faa3f046 100644 --- a/doc/src/angle_table.rst +++ b/doc/src/angle_table.rst @@ -59,6 +59,10 @@ format of this file is described below. ---------- +Suitable tables for use with this angle style can be created using the +Python code in the ``tools/tabulate`` folder of the LAMMPS source code +distribution. + The format of a tabulated file is as follows (without the parenthesized comments): diff --git a/doc/src/bond_bpm_rotational.rst b/doc/src/bond_bpm_rotational.rst index 5c43071274..d9d0f160fb 100644 --- a/doc/src/bond_bpm_rotational.rst +++ b/doc/src/bond_bpm_rotational.rst @@ -45,6 +45,8 @@ Examples Description """"""""""" +.. versionadded:: 4May2022 + The *bpm/rotational* bond style computes forces and torques based on deviations from the initial reference state of the two atoms. The reference state is stored by each bond when it is first computed in @@ -67,7 +69,7 @@ which is proportional to the tangential shear displacement with a stiffness of :math:`k_s`. This tangential force also induces a torque. In addition, bending and twisting torques are also applied to particles which are proportional to angular bending and twisting -displacements with stiffnesses of :math`k_b` and :math:`k_t', +displacements with stiffnesses of :math:`k_b` and :math:`k_t`, respectively. Details on the calculations of shear displacements and angular displacements can be found in :ref:`(Wang) ` and :ref:`(Wang and Mora) `. @@ -211,9 +213,9 @@ command, as *b1*, *b2*, ..., *b7*\ . Restrictions """""""""""" -This bond style can only be used if LAMMPS was built with the BPM -package. See the :doc:`Build package ` doc page for -more info. +This bond style is part of the BPM package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` page for more info. By default if pair interactions are to be disabled, this bond style requires setting diff --git a/doc/src/bond_bpm_spring.rst b/doc/src/bond_bpm_spring.rst index de31357afe..46c300d364 100644 --- a/doc/src/bond_bpm_spring.rst +++ b/doc/src/bond_bpm_spring.rst @@ -45,6 +45,8 @@ Examples Description """"""""""" +.. versionadded:: 4May2022 + The *bpm/spring* bond style computes forces and torques based on deviations from the initial reference state of the two atoms. The reference state is stored by each bond when it is first computed in @@ -167,9 +169,9 @@ extra quantity can be accessed by the Restrictions """""""""""" -This bond style can only be used if LAMMPS was built with the BPM -package. See the :doc:`Build package ` doc page for -more info. +This bond style is part of the BPM package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` page for more info. By default if pair interactions are to be disabled, this bond style requires setting diff --git a/doc/src/bond_gaussian.rst b/doc/src/bond_gaussian.rst index 9fbcf4778c..74e5b973eb 100644 --- a/doc/src/bond_gaussian.rst +++ b/doc/src/bond_gaussian.rst @@ -25,33 +25,34 @@ The *gaussian* bond style uses the potential: .. math:: - E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-(r-r_{i})^2}{w_i^2})\right) \right) + E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-2(r-r_{i})^2}{w_i^2}\right)\right) -This analytical form is a suitable potential for obtaining -mesoscale effective force fields which can reproduce target atomistic distributions :ref:`(Milano) ` +This analytical form is a suitable potential for obtaining mesoscale +effective force fields which can reproduce target atomistic +distributions :ref:`(Milano) ` The following coefficients must be defined for each bond type via the :doc:`bond_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` commands: -* T temperature at which the potential was derived +* :math:`T` temperature at which the potential was derived * :math:`n` (integer >=1) -* :math:`A_1` (-) -* :math:`w_1` (-) -* :math:`r_1` (length) +* :math:`A_1` (> 0, distance) +* :math:`w_1` (> 0, distance) +* :math:`r_1` (>= 0, distance) * ... -* :math:`A_n` (-) -* :math:`w_n` (-) -* :math:`r_n` (length) +* :math:`A_n` (> 0, distance) +* :math:`w_n` (> 0, distance) +* :math:`r_n` (>= 0, distance) Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the -EXTRA-MOLECULE package. See the :doc:`Build package ` doc -page for more info. +EXTRA-MOLECULE package. See the :doc:`Build package ` +doc page for more info. Related commands """""""""""""""" diff --git a/doc/src/bond_table.rst b/doc/src/bond_table.rst index 898503b951..51e677d74a 100644 --- a/doc/src/bond_table.rst +++ b/doc/src/bond_table.rst @@ -59,6 +59,13 @@ this file is described below. ---------- +Suitable tables for use with this bond style can be created by LAMMPS +itself from existing bond styles using the :doc:`bond_write +` command. This can be useful to have a template file for +testing the bond style settings and to build a compatible custom file. +Another option to generate tables is the Python code in the +``tools/tabulate`` folder of the LAMMPS source code distribution. + The format of a tabulated file is as follows (without the parenthesized comments): @@ -149,7 +156,8 @@ info. Related commands """""""""""""""" -:doc:`bond_coeff `, :doc:`delete_bonds ` +:doc:`bond_coeff `, :doc:`delete_bonds `, +:doc:`bond_write ` Default """"""" diff --git a/doc/src/box.rst b/doc/src/box.rst deleted file mode 100644 index 096a171249..0000000000 --- a/doc/src/box.rst +++ /dev/null @@ -1,70 +0,0 @@ -.. index:: box - -box command -=========== - -Syntax -"""""" - -.. code-block:: LAMMPS - - box keyword value ... - -* one or more keyword/value pairs may be appended -* keyword = *tilt* - - .. parsed-literal:: - - *tilt* value = *small* or *large* - -Examples -"""""""" - -.. code-block:: LAMMPS - - box tilt large - box tilt small - -Description -""""""""""" - -Set attributes of the simulation box. - -For triclinic (non-orthogonal) simulation boxes, the *tilt* keyword -allows simulation domains to be created with arbitrary tilt factors, -e.g. via the :doc:`create_box ` or -:doc:`read_data ` commands. Tilt factors determine how -skewed the triclinic box is; see the :doc:`Howto triclinic ` page for a discussion of triclinic -boxes in LAMMPS. - -LAMMPS normally requires that no tilt factor can skew the box more -than half the distance of the parallel box length, which is the first -dimension in the tilt factor (x for xz). If *tilt* is set to -*small*, which is the default, then an error will be -generated if a box is created which exceeds this limit. If *tilt* -is set to *large*, then no limit is enforced. You can create -a box with any tilt factors you wish. - -Note that if a simulation box has a large tilt factor, LAMMPS will run -less efficiently, due to the large volume of communication needed to -acquire ghost atoms around a processor's irregular-shaped sub-domain. -For extreme values of tilt, LAMMPS may also lose atoms and generate an -error. - -Restrictions -"""""""""""" - -This command cannot be used after the simulation box is defined by a -:doc:`read_data ` or :doc:`create_box ` command or -:doc:`read_restart ` command. - -Related commands -"""""""""""""""" - -none - - -Default -""""""" - -The default value is tilt = small. diff --git a/doc/src/clear.rst b/doc/src/clear.rst index a8d224a5c9..fba3b69f47 100644 --- a/doc/src/clear.rst +++ b/doc/src/clear.rst @@ -23,15 +23,16 @@ Description """"""""""" This command deletes all atoms, restores all settings to their default -values, and frees all memory allocated by LAMMPS. Once a clear -command has been executed, it is almost as if LAMMPS were starting -over, with only the exceptions noted below. This command enables -multiple jobs to be run sequentially from one input script. +values, and frees all memory allocated by LAMMPS. Once a clear command +has been executed, it is almost as if LAMMPS were starting over, with +only the exceptions noted below. This command enables multiple jobs to +be run sequentially from one input script. These settings are not affected by a clear command: the working -directory (:doc:`shell ` command), log file status -(:doc:`log ` command), echo status (:doc:`echo ` command), and -input script variables (:doc:`variable ` command). +directory (:doc:`shell ` command), log file status (:doc:`log +` command), echo status (:doc:`echo ` command), and input +script variables except for *atomfile* style variables (:doc:`variable +` command). Restrictions """""""""""" diff --git a/doc/src/commands_list.rst b/doc/src/commands_list.rst index ee032bfd9e..ff2502189d 100644 --- a/doc/src/commands_list.rst +++ b/doc/src/commands_list.rst @@ -13,7 +13,6 @@ Commands bond_style bond_write boundary - box change_box clear comm_modify @@ -43,6 +42,7 @@ Commands echo fix fix_modify + fitpod_command group group2ndx hyper @@ -90,8 +90,7 @@ Commands region replicate rerun - reset_atom_ids - reset_mol_ids + reset_atoms reset_timestep restart run diff --git a/doc/src/compute.rst b/doc/src/compute.rst index 7d1e423e93..6d7450a527 100644 --- a/doc/src/compute.rst +++ b/doc/src/compute.rst @@ -43,29 +43,38 @@ underscores. ---------- -Computes calculate one of three styles of quantities: global, -per-atom, or local. A global quantity is one or more system-wide -values (e.g., the temperature of the system). A per-atom quantity is -one or more values per atom (e.g., the kinetic energy of each atom). -Per-atom values are set to 0.0 for atoms not in the specified compute -group. Local quantities are calculated by each processor based on the -atoms it owns, but there may be zero or more per atom (e.g., a list of -bond distances). Computes that produce per-atom quantities have the -word "atom" in their style (e.g., *ke/atom*\ ). Computes that produce -local quantities have the word "local" in their style -(e.g., *bond/local*\ ). Styles with neither "atom" or "local" in their -style produce global quantities. +Computes calculate one or more of four styles of quantities: global, +per-atom, local, or per-atom. A global quantity is one or more +system-wide values, e.g. the temperature of the system. A per-atom +quantity is one or more values per atom, e.g. the kinetic energy of +each atom. Per-atom values are set to 0.0 for atoms not in the +specified compute group. Local quantities are calculated by each +processor based on the atoms it owns, but there may be zero or more +per atom, e.g. a list of bond distances. Per-grid quantities are +calculated on a regular 2d or 3d grid which overlays a 2d or 3d +simulation domain. The grid points and the data they store are +distributed across processors; each processor owns the grid points +which fall within its sub-domain. -Note that a single compute can produce either global or per-atom or -local quantities, but not both global and per-atom. It can produce -local quantities in tandem with global or per-atom quantities. The -compute page will explain. +Computes that produce per-atom quantities have the word "atom" at the +end of their style, e.g. *ke/atom*\ . Computes that produce local +quantities have the word "local" at the end of their style, +e.g. *bond/local*\ . Computes that produce per-grid quantities have +the word "grid" at the end of their style, e.g. *property/grid*\ . +Styles with neither "atom" or "local" or "grid" at the end of their +style name produce global quantities. -Global, per-atom, and local quantities each come in three kinds: a -single scalar value, a vector of values, or a 2d array of values. The -doc page for each compute describes the style and kind of values it -produces (e.g., a per-atom vector). Some computes produce more than one -kind of a single style (e.g., a global scalar and a global vector). +Note that a single compute typically produces either global or +per-atom or local or per-grid values. It does not compute both global +and per-atom values. It can produce local values or per-grid values +in tandem with global or per-atom quantities. The compute doc page +will explain the details. + +Global, per-atom, local, and per-grid quantities come in three kinds: +a single scalar value, a vector of values, or a 2d array of values. +The doc page for each compute describes the style and kind of values +it produces, e.g. a per-atom vector. Some computes produce more than +one kind of a single style, e.g. a global scalar and a global vector. When a compute quantity is accessed, as in many of the output commands discussed below, it can be referenced via the following bracket @@ -252,7 +261,8 @@ The individual style names on the :doc:`Commands compute ` pag * :doc:`pressure/uef ` - pressure tensor in the reference frame of an applied flow field * :doc:`property/atom ` - convert atom attributes to per-atom vectors/arrays * :doc:`property/chunk ` - extract various per-chunk attributes -* :doc:`property/local ` - convert local attributes to localvectors/arrays +* :doc:`property/grid ` - convert per-grid attributes to per-grid vectors/arrays +* :doc:`property/local ` - convert local attributes to local vectors/arrays * :doc:`ptm/atom ` - determines the local lattice structure based on the Polyhedral Template Matching method * :doc:`rdf ` - radial distribution function :math:`g(r)` histogram of group of atoms * :doc:`reduce ` - combine per-atom quantities into a single global value diff --git a/doc/src/compute_modify.rst b/doc/src/compute_modify.rst index 947a610b88..7cb5d36d18 100644 --- a/doc/src/compute_modify.rst +++ b/doc/src/compute_modify.rst @@ -37,27 +37,29 @@ Description Modify one or more parameters of a previously defined compute. Not all compute styles support all parameters. -The *extra/dof* or *extra* keyword refers to how many degrees of freedom are -subtracted (typically from :math:`3N`) as a normalizing +The *extra/dof* or *extra* keyword refers to how many degrees of +freedom are subtracted (typically from :math:`3N`) as a normalizing factor in a temperature computation. Only computes that compute a -temperature use this option. The default is 2 or 3 for -:doc:`2d or 3d systems `, which is a correction factor for an -ensemble of velocities with zero total linear momentum. For compute -temp/partial, if one or more velocity components are excluded, the -value used for *extra* is scaled accordingly. You can use a negative -number for the *extra* parameter if you need to add -degrees-of-freedom. See the :doc:`compute temp/asphere ` command for an example. +temperature use this option. The default is 2 or 3 for :doc:`2d or 3d +systems ` which is a correction factor for an ensemble of +velocities with zero total linear momentum. For compute temp/partial, +if one or more velocity components are excluded, the value used for +*extra* is scaled accordingly. You can use a negative number for the +*extra* parameter if you need to add degrees-of-freedom. See the +:doc:`compute temp/asphere ` command for an +example. The *dynamic/dof* or *dynamic* keyword determines whether the number -of atoms :math:`N` in the compute group and their associated degrees of -freedom (DOF) are re-computed each time a temperature is computed. Only -compute styles that calculate a temperature use this option. By -default, :math:`N` and their DOF are assumed to be constant. If you are -adding atoms or molecules to the system (see the :doc:`fix pour `, -:doc:`fix deposit `, and :doc:`fix gcmc ` commands) or -expect atoms or molecules to be lost (e.g., due to exiting the simulation box -or via :doc:`fix evaporate `), then this option should be used -to ensure the temperature is correctly normalized. +of atoms :math:`N` in the compute group and their associated degrees +of freedom (DOF) are re-computed each time a temperature is computed. +Only compute styles that calculate a temperature use this option. By +default, :math:`N` and their DOF are assumed to be constant. If you +are adding atoms or molecules to the system (see the :doc:`fix pour +`, :doc:`fix deposit `, and :doc:`fix gcmc +` commands) or expect atoms or molecules to be lost +(e.g. due to exiting the simulation box or via :doc:`fix evaporate +`), then this option should be used to insure the +temperature is correctly normalized. .. note:: diff --git a/doc/src/compute_nbond_atom.rst b/doc/src/compute_nbond_atom.rst index 0e53de3e49..f438836534 100644 --- a/doc/src/compute_nbond_atom.rst +++ b/doc/src/compute_nbond_atom.rst @@ -23,6 +23,8 @@ Examples Description """"""""""" +.. versionadded:: 4May2022 + Define a computation that computes the number of bonds each atom is part of. Bonds which are broken are not counted in the tally. See the :doc:`Howto broken bonds ` page for more information. @@ -40,8 +42,9 @@ LAMMPS output options. Restrictions """""""""""" -This fix can only be used if LAMMPS was built with the BPM package. -See the :doc:`Build package ` doc page for more info. +This compute is part of the BPM package. It is only enabled if LAMMPS was +built with that package. See the :doc:`Build package ` +page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_pair_local.rst b/doc/src/compute_pair_local.rst index bcfec11f80..dace280dee 100644 --- a/doc/src/compute_pair_local.rst +++ b/doc/src/compute_pair_local.rst @@ -59,7 +59,7 @@ commands. The value *dist* is the distance between the pair of atoms. The values *dx*, *dy*, and *dz* are the :math:`(x,y,z)` components of the *distance* between the pair of atoms. This value is always the -distance from the atom of lower to the one with the higher id. +distance from the atom of higher to the one with the lower atom ID. The value *eng* is the interaction energy for the pair of atoms. diff --git a/doc/src/compute_property_chunk.rst b/doc/src/compute_property_chunk.rst index 7c06b8d51e..9981c6770b 100644 --- a/doc/src/compute_property_chunk.rst +++ b/doc/src/compute_property_chunk.rst @@ -12,7 +12,8 @@ Syntax * ID, group-ID are documented in :doc:`compute ` command * property/chunk = style name of this compute command -* input = one or more attributes +* chunkID = ID of :doc:`compute chunk/atom ` command that defines the chunks +* input1,etc = one or more attributes .. parsed-literal:: @@ -26,8 +27,8 @@ Examples .. code-block:: LAMMPS - compute 1 all property/chunk count - compute 1 all property/chunk ID coord1 + compute 1 all property/chunk bin2d id count + compute 1 all property/chunk myChunks id coord1 Description """"""""""" @@ -35,29 +36,28 @@ Description Define a computation that stores the specified attributes of chunks of atoms. -In LAMMPS, chunks are collections of atoms defined by a -:doc:`compute chunk/atom ` command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a molecule or -atoms in a spatial bin. See the :doc:`compute chunk/atom ` -and :doc:`Howto chunk ` doc pages for details of how chunks can be -defined and examples of how they can be used to measure properties of a system. +In LAMMPS, chunks are collections of atoms defined by a :doc:`compute +chunk/atom ` command, which assigns each atom to a +single chunk (or no chunk). The ID for this command is specified as +chunkID. For example, a single chunk could be the atoms in a molecule +or atoms in a spatial bin. See the :doc:`compute chunk/atom +` and :doc:`Howto chunk ` doc pages +for details of how chunks can be defined and examples of how they can +be used to measure properties of a system. This compute calculates and stores the specified attributes of chunks -as global data so they can be accessed by other -:doc:`output commands ` and used in conjunction with other -commands that generate per-chunk data, such as -:doc:`compute com/chunk ` or -:doc:`compute msd/chunk `. +as global data so they can be accessed by other :doc:`output commands +` and used in conjunction with other commands that +generate per-chunk data, such as :doc:`compute com/chunk +` or :doc:`compute msd/chunk `. Note that only atoms in the specified group contribute to the -calculation of the *count* attribute. The -:doc:`compute chunk/atom ` command defines its own group; -atoms will have a chunk ID = 0 if they are not in that group, -signifying they are not assigned to a chunk, and will thus also not -contribute to this calculation. You can specify the "all" group for -this command if you simply want to include atoms with non-zero chunk -IDs. +calculation of the *count* attribute. The :doc:`compute chunk/atom +` command defines its own group; atoms will have a +chunk ID = 0 if they are not in that group, signifying they are not +assigned to a chunk, and will thus also not contribute to this +calculation. You can specify the "all" group for this command if you +simply want to include atoms with non-zero chunk IDs. The *count* attribute is the number of atoms in the chunk. @@ -66,21 +66,24 @@ can only be used if the *compress* keyword was set to *yes* for the :doc:`compute chunk/atom ` command referenced by chunkID. This means that the original chunk IDs (e.g., molecule IDs) will have been compressed to remove chunk IDs with no atoms assigned -to them. Thus a compressed chunk ID of 3 may correspond to an original -chunk ID (molecule ID in this case) of 415. The *id* attribute will -then be 415 for the third chunk. +to them. Thus a compressed chunk ID of 3 may correspond to an +original chunk ID (molecule ID in this case) of 415. The *id* +attribute will then be 415 for the third chunk. The *coordN* attributes can only be used if a *binning* style was used -in the :doc:`compute chunk/atom ` command referenced -by chunkID. For *bin/1d*, *bin/2d*, and *bin/3d* styles the attribute -is the center point of the bin in the corresponding dimension. Style -*bin/1d* only defines a *coord1* attribute. Style *bin/2d* adds a -*coord2* attribute. Style *bin/3d* adds a *coord3* attribute. -Note that if the value of the *units* keyword used in the :doc:`compute chunk/atom command ` is *box* or *lattice*, the -*coordN* attributes will be in distance :doc:`units `. If the -value of the *units* keyword is *reduced*, the *coordN* attributes -will be in unitless reduced units (0--1). +in the :doc:`compute chunk/atom ` command +referenced by chunkID. For *bin/1d*, *bin/2d*, and *bin/3d* styles +the attribute is the center point of the bin in the corresponding +dimension. Style *bin/1d* only defines a *coord1* attribute. Style +*bin/2d* adds a *coord2* attribute. Style *bin/3d* adds a *coord3* +attribute. + +Note that if the value of the *units* keyword used in the +:doc:`compute chunk/atom command ` is *box* or +*lattice*, the *coordN* attributes will be in distance :doc:`units +`. If the value of the *units* keyword is *reduced*, the +*coordN* attributes will be in unitless reduced units (0-1). The simplest way to output the results of the compute property/chunk calculation to a file is to use the :doc:`fix ave/time ` diff --git a/doc/src/compute_property_grid.rst b/doc/src/compute_property_grid.rst new file mode 100644 index 0000000000..90b48d3a7c --- /dev/null +++ b/doc/src/compute_property_grid.rst @@ -0,0 +1,114 @@ +.. index:: compute property/grid + +compute property/grid command +============================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID property/grid Nx Ny Nz input1 input2 ... + +* ID, group-ID are documented in :doc:`compute ` command +* property/grid = style name of this compute command +* Nx, Ny, Nz = grid size in each dimension +* input1,etc = one or more attributes + + .. parsed-literal:: + + attributes = id, ix, iy, iz, x, y, z, xs, ys, zs, xc, yc, zc, xsc, ysc, zsc + id = ID of grid cell, x fastest, y next, z slowest + ix,iy,iz = grid indices in each dimension (1 to N inclusive) + x,y,z = coords of lower left corner of grid cell + xs,ys,zs = scaled coords of lower left corner of grid cell (0.0 to 1.0) + xc,yc,zc = coords of center point of grid cell + xsc,ysc,zsc = scaled coords of center point of grid cell (0.0 to 1.0) + +Examples +"""""""" + +.. code-block:: LAMMPS + + compute 1 all property/grid id ix iy iz + compute 1 all property/grid id xc yc zc + +Description +""""""""""" + +Define a computation that stores the specified attributes of a +distributed grid. In LAMMPS, distributed grids are regular 2d or 3d +grids which overlay a 2d or 3d simulation domain. Each processor owns +the grid cells whose center points lie within its sub-domain. See the +:doc:`Howto grid ` doc page for details of how distributed +grids can be defined by various commands and referenced. + +This compute stores the specified attributes of grids as per-grid data +so they can be accessed by other :doc:`output commands ` +such as :doc:`dump grid `. + +*Nx*, *Ny*, and *Nz* define the size of the grid. For a 2d simulation +*Nz* must be 1. When this compute is used by :doc:`dump grid `, +to output per-grid values from other computes of fixes, the grid size +specified for this command must be consistent with the grid sizes +used by the other commands. + +The *id* attribute stores the grid ID for each grid cell. For a +global grid of size Nx by Ny by Nz (in 3d simulations) the grid IDs +range from 1 to Nx*Ny*Nz. They are ordered with the X index of the 3d +grid varying fastest, then Y, then Z slowest. For 2d grids (in 2d +simulations), the grid IDs range from 1 to Nx*Ny, with X varying +fastest and Y slowest. + +The *ix*, *iy*, *iz* attributes are the indices of a grid cell in +each dimension. They range from 1 to Nx inclusive in the X dimension, +and similar for Y and Z. + +The *x*, *y*, *z* attributes are the coordinates of the lower left +corner point of each grid cell. + +The *xs*, *ys*, *zs* attributes are also coordinates of the lower left +corner point of each grid cell, except in scaled coordinates, where +the lower-left corner of the entire simulation box is (0,0,0) and the +upper right corner is (1,1,1). + +The *xc*, *yc*, *zc* attributes are the coordinates of the center +point of each grid cell. + +The *xsc*, *ysc*, *zsc* attributes are also coordinates of the center +point each grid cell, except in scaled coordinates, where the +lower-left corner of the entire simulation box is (0,0,0) and the upper +right corner is (1,1,1). + +For :doc:`triclinic simulation boxes `, the grid +point coordinates for (x,y,z) and (xc,yc,zc) will reflect the +triclinic geometry. For (xs,yz,zs) and (xsc,ysc,zsc), the coordinates +are the same for orthogonal versus triclinic boxes. + +Output info +""""""""""" + +This compute calculates a per-grid vector or array depending on the +number of input values. The length of the vector or number of array +rows (distributed across all processors) is Nx * Ny * Nz. For access +by other commands, the name of the single grid produced by this +command is "grid". The name of its per-grid data is "data". + +The (x,y,z) and (xc,yc,zc) coordinates are in distance :doc:`units +`. + +Restrictions +"""""""""""" + +For 2d simulations, the attributes which refer to +the Z dimension cannot be used. + +Related commands +"""""""""""""""" + +:doc:`dump grid ` + +Default +""""""" + +none diff --git a/doc/src/compute_property_local.rst b/doc/src/compute_property_local.rst index f1234ade09..a21e6d4058 100644 --- a/doc/src/compute_property_local.rst +++ b/doc/src/compute_property_local.rst @@ -85,10 +85,11 @@ Description """"""""""" Define a computation that stores the specified attributes as local -data so it can be accessed by other :doc:`output commands `. If the input attributes refer to bond -information, then the number of datums generated, aggregated across -all processors, equals the number of bonds in the system. Ditto for -pairs, angles, etc. +data so it can be accessed by other :doc:`output commands +`. If the input attributes refer to bond information, +then the number of datums generated, aggregated across all processors, +equals the number of bonds in the system. Ditto for pairs, angles, +etc. If multiple attributes are specified then they must all generate the same amount of information, so that the resulting local array has the @@ -129,17 +130,20 @@ specified compute group. Likewise for angles, dihedrals, etc. For bonds and angles, a bonds/angles that have been broken by setting their bond/angle type to 0 will not be included. Bonds/angles that have been turned off (see the :doc:`fix shake ` or -:doc:`delete_bonds ` commands) by setting their bond/angle -type negative are written into the file. This is consistent with the -:doc:`compute bond/local ` and :doc:`compute angle/local ` commands +:doc:`delete_bonds ` commands) by setting their +bond/angle type negative are written into the file. This is +consistent with the :doc:`compute bond/local ` and +:doc:`compute angle/local ` commands Note that as atoms migrate from processor to processor, there will be no consistent ordering of the entries within the local vector or array from one timestep to the next. The only consistency that is guaranteed is that the ordering on a particular timestep will be the same for local vectors or arrays generated by other compute commands. -For example, output from the :doc:`compute bond/local ` command can be combined with bond -atom indices from this command and output by the :doc:`dump local ` command in a consistent way. +For example, output from the :doc:`compute bond/local +` command can be combined with bond atom indices +from this command and output by the :doc:`dump local ` command +in a consistent way. The *natom1* and *natom2* or *patom1* and *patom2* attributes refer to the atom IDs of the 2 atoms in each pairwise interaction computed @@ -177,9 +181,8 @@ the array is the number of bonds, angles, etc. If a single input is specified, a local vector is produced. If two or more inputs are specified, a local array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command -that uses local values from a compute as input. See the -:doc:`Howto output ` page for an overview of LAMMPS output -options. +that uses local values from a compute as input. See the :doc:`Howto +output ` page for an overview of LAMMPS output options. The vector or array values will be integers that correspond to the specified attribute. diff --git a/doc/src/compute_temp.rst b/doc/src/compute_temp.rst index 1d5a62d6f6..8f6f9f225f 100644 --- a/doc/src/compute_temp.rst +++ b/doc/src/compute_temp.rst @@ -29,8 +29,9 @@ Description Define a computation that calculates the temperature of a group of atoms. A compute of this style can be used by any command that -computes a temperature (e.g., :doc:`thermo_modify `, -:doc:`fix temp/rescale `, :doc:`fix npt `) +computes a temperature, e.g. :doc:`thermo_modify `, +:doc:`fix temp/rescale `, :doc:`fix npt `, +etc. The temperature is calculated by the formula @@ -39,17 +40,17 @@ The temperature is calculated by the formula \text{KE} = \frac{\text{dim}}{2} N k_B T, where KE = total kinetic energy of the group of atoms (sum of -:math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the simulation, -:math:`N` is the number of atoms in the group, :math:`k_B` is the Boltzmann -constant, and :math:`T` is the absolute temperature. +:math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the +simulation, :math:`N` is the number of atoms in the group, :math:`k_B` +is the Boltzmann constant, and :math:`T` is the absolute temperature. A kinetic energy tensor, stored as a six-element vector, is also calculated by this compute for use in the computation of a pressure tensor. The formula for the components of the tensor is the same as -the above formula, except that :math:`v^2` is replaced by -:math:`v_x v_y` for the :math:`xy` component, and so on. -The six components of the vector are ordered :math:`xx`, :math:`yy`, -:math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. +the above formula, except that :math:`v^2` is replaced by :math:`v_x +v_y` for the :math:`xy` component, and so on. The six components of +the vector are ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, +:math:`xz`, :math:`yz`. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the @@ -85,11 +86,10 @@ Output info """"""""""" This compute calculates a global scalar (the temperature) and a global -vector of length six (KE tensor), which can be accessed by indices 1--6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See the -:doc:`Howto output ` page for an overview of LAMMPS output -options. +vector of length six (KE tensor), which can be accessed by indices +1--6. These values can be used by any command that uses global scalar +or vector values from a compute as input. See the :doc:`Howto output +` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The vector values are "extensive". @@ -104,7 +104,9 @@ Restrictions Related commands """""""""""""""" -:doc:`compute temp/partial `, :doc:`compute temp/region `, :doc:`compute pressure ` +:doc:`compute temp/partial `, +:doc:`compute temp/region `, +:doc:`compute pressure ` Default """"""" diff --git a/doc/src/create_box.rst b/doc/src/create_box.rst index 889a57605d..f930ecea83 100644 --- a/doc/src/create_box.rst +++ b/doc/src/create_box.rst @@ -66,20 +66,21 @@ positive or negative values and are called "tilt factors" because they are the amount of displacement applied to faces of an originally orthogonal box to transform it into the parallelepiped. -By default, a *prism* region used with the create_box command must -have tilt factors :math:`(xy,xz,yz)` that do not skew the box more than half +By default, a *prism* region used with the create_box command must have +tilt factors :math:`(xy,xz,yz)` that do not skew the box more than half the distance of the parallel box length. For example, if :math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the :math:`x` -box length is 10 and the :math:`xy` tilt factor must be between :math:`-5` and -:math:`5`. Similarly, both :math:`xz` and :math:`yz` must be between -:math:`-(x_\text{hi}-x_\text{lo})/2` and :math:`+(y_\text{hi}-y_\text{lo})/2`. -Note that this is not a limitation, since if the maximum tilt factor is 5 (as -in this example), then configurations with tilt :math:`= \dots, -15`, -:math:`-5`, :math:`5`, :math:`15`, :math:`25, \dots` -are all geometrically equivalent. If you wish to define a box with tilt -factors that exceed these limits, you can use the :doc:`box tilt ` -command, with a setting of *large*\ ; a setting of *small* is the -default. +box length is 10 and the :math:`xy` tilt factor must be between +:math:`-5` and :math:`5`. Similarly, both :math:`xz` and :math:`yz` +must be between :math:`-(x_\text{hi}-x_\text{lo})/2` and +:math:`+(y_\text{hi}-y_\text{lo})/2`. Note that this is not a +limitation, since if the maximum tilt factor is 5 (as in this example), +then configurations with tilt :math:`= \dots, -15`, :math:`-5`, +:math:`5`, :math:`15`, :math:`25, \dots` are all geometrically +equivalent. Simulations with large tilt factors will run inefficiently, +since they require more ghost atoms and thus more communication. With +very large tilt factors, LAMMPS will eventually produce incorrect +trajectories and stop with errors due to lost atoms or similar. See the :doc:`Howto triclinic ` page for a geometric description of triclinic boxes, as defined by LAMMPS, and diff --git a/doc/src/delete_atoms.rst b/doc/src/delete_atoms.rst index 2fdd152196..c863d0c7d2 100644 --- a/doc/src/delete_atoms.rst +++ b/doc/src/delete_atoms.rst @@ -135,7 +135,7 @@ number of atoms in the system. Note that this is not done for molecular systems (see the :doc:`atom_style ` command), regardless of the *compress* setting, since it would foul up the bond connectivity that has already been assigned. However, the -:doc:`reset_atom_ids ` command can be used after this +:doc:`reset_atoms id ` command can be used after this command to accomplish the same thing. Note that the re-assignment of IDs is not really a compression, where @@ -203,7 +203,7 @@ using molecule template files via the :doc:`molecule ` and Related commands """""""""""""""" -:doc:`create_atoms `, :doc:`reset_atom_ids ` +:doc:`create_atoms `, :doc:`reset_atoms id ` Default """"""" diff --git a/doc/src/dihedral_table.rst b/doc/src/dihedral_table.rst index e0830b523c..5e8d589c55 100644 --- a/doc/src/dihedral_table.rst +++ b/doc/src/dihedral_table.rst @@ -114,6 +114,10 @@ below. ---------- +Suitable tables for use with this dihedral style can be created using +the Python code in the ``tools/tabulate`` folder of the LAMMPS source +code distribution. + The format of a tabulated file is as follows (without the parenthesized comments). It can begin with one or more comment or blank lines. diff --git a/doc/src/dump.rst b/doc/src/dump.rst index 7ac6a7ed54..800542475d 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -3,6 +3,8 @@ .. index:: dump cfg .. index:: dump custom .. index:: dump dcd +.. index:: dump grid +.. index:: dump grid/vtk .. index:: dump local .. index:: dump xtc .. index:: dump yaml @@ -57,46 +59,48 @@ Syntax .. code-block:: LAMMPS - dump ID group-ID style N file args + dump ID group-ID style N file attribute1 attribute2 ... * ID = user-assigned name for the dump * group-ID = ID of the group of atoms to be dumped -* style = *atom* or *atom/adios* or *atom/gz* or *atom/zstd* or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *custom/adios* or *dcd* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml* +* style = *atom* or *atom/adios* or *atom/gz* or *atom/zstd* or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *custom/adios* or *dcd* or *grid* or *grid/vtk* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml* * N = dump on timesteps which are multiples of N * file = name of file to write dump info to -* args = list of arguments for a particular style +* attribute1,attribute2,... = list of attributes for a particular style .. parsed-literal:: - *atom* args = none - *atom/adios* args = none, discussed on :doc:`dump atom/adios ` page - *atom/gz* args = none - *atom/zstd* args = none - *atom/mpiio* args = none - *cfg* args = same as *custom* args, see below - *cfg/gz* args = same as *custom* args, see below - *cfg/zstd* args = same as *custom* args, see below - *cfg/mpiio* args = same as *custom* args, see below - *cfg/uef* args = same as *custom* args, discussed on :doc:`dump cfg/uef ` page - *custom*, *custom/gz*, *custom/zstd*, *custom/mpiio* args = see below - *custom/adios* args = same as *custom* args, discussed on :doc:`dump custom/adios ` page - *dcd* args = none - *h5md* args = discussed on :doc:`dump h5md ` page - *image* args = discussed on :doc:`dump image ` page - *local*, *local/gz*, *local/zstd* args = see below - *molfile* args = discussed on :doc:`dump molfile ` page - *movie* args = discussed on :doc:`dump image ` page - *netcdf* args = discussed on :doc:`dump netcdf ` page - *netcdf/mpiio* args = discussed on :doc:`dump netcdf ` page - *vtk* args = same as *custom* args, see below, also :doc:`dump vtk ` page - *xtc* args = none - *xyz* args = none - *xyz/gz* args = none - *xyz/zstd* args = none - *xyz/mpiio* args = none - *yaml* args = same as *custom* args, see below + *atom* attributes = none + *atom/adios* attributes = none, discussed on :doc:`dump atom/adios ` page + *atom/gz* attributes = none + *atom/zstd* attributes = none + *atom/mpiio* attributes = none + *cfg* attributes = same as *custom* attributes, see below + *cfg/gz* attributes = same as *custom* attributes, see below + *cfg/zstd* attributes = same as *custom* attributes, see below + *cfg/mpiio* attributes = same as *custom* attributes, see below + *cfg/uef* attributes = same as *custom* attributes, discussed on :doc:`dump cfg/uef ` page + *custom*, *custom/gz*, *custom/zstd*, *custom/mpiio* attributes = see below + *custom/adios* attributes = same as *custom* attributes, discussed on :doc:`dump custom/adios ` page + *dcd* attributes = none + *h5md* attributes = discussed on :doc:`dump h5md ` page + *grid* attributes = see below + *grid/vtk* attributes = see below + *image* attributes = discussed on :doc:`dump image ` page + *local*, *local/gz*, *local/zstd* attributes = see below + *molfile* attributes = discussed on :doc:`dump molfile ` page + *movie* attributes = discussed on :doc:`dump image ` page + *netcdf* attributes = discussed on :doc:`dump netcdf ` page + *netcdf/mpiio* attributes = discussed on :doc:`dump netcdf ` page + *vtk* attributes = same as *custom* attributes, see below, also :doc:`dump vtk ` page + *xtc* attributes = none + *xyz* attributes = none + *xyz/gz* attributes = none + *xyz/zstd* attributes = none + *xyz/mpiio* attributes = none + *yaml* attributes = same as *custom* attributes, see below -* *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *netcdf* or *netcdf/mpiio* or *yaml* args = list of atom attributes +* *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *netcdf* or *netcdf/mpiio* or *yaml* attributes: .. parsed-literal:: @@ -143,7 +147,7 @@ Syntax i2_name[I] = Ith column of custom integer array with name, I can include wildcard (see below) d2_name[I] = Ith column of custom floating point vector with name, I can include wildcard (see below) -* *local* or *local/gz* or *local/zstd* args = list of local attributes +* *local* or *local/gz* or *local/zstd* attributes: .. parsed-literal:: @@ -154,6 +158,18 @@ Syntax f_ID = local vector calculated by a fix with ID f_ID[I] = Ith column of local array calculated by a fix with ID, I can include wildcard (see below) +* *grid* or *grid/vtk* attributes: + + .. parsed-literal:: + + possible attributes = c_ID:gname:dname, c_ID:gname:dname[I], f_ID:gname:dname, f_ID:gname:dname[I] + gname = name of grid defined by compute or fix + dname = name of data field defined by compute or fix + c_ID = per-grid vector calculated by a compute with ID + c_ID[I] = Ith column of per-grid array calculated by a compute with ID, I can include wildcard (see below) + f_ID = per-grid vector calculated by a fix with ID + f_ID[I] = Ith column of per-grid array calculated by a fix with ID, I can include wildcard (see below) + Examples """""""" @@ -176,24 +192,32 @@ Examples Description """"""""""" -Dump a snapshot of atom quantities to one or more files once every -:math:`N` timesteps in one of several styles. The *image* and *movie* -styles are the exception: the *image* style renders a JPG, PNG, or PPM -image file of the atom configuration every :math:`N` timesteps while -the *movie* style combines and compresses them into a movie file; both -are discussed in detail on the :doc:`dump image ` page. -The timesteps on which dump output is written can also be controlled -by a variable. See the :doc:`dump_modify every ` -command. +Dump a snapshot of quantities to one or more files once every +:math:`N` timesteps in one of several styles. The timesteps on which +dump output is written can also be controlled by a variable. See the +:doc:`dump_modify every ` command. + +Almost all the styles output per-atom data, i.e. one or more values +per atom. The exceptions are as follows. The *local* styles output +one or more values per bond (angle, dihedral, improper) or per pair of +interacting atoms (force or neighbor interactions). The *grid* styles +output one or more values per grid cell, which are produced by other +commands which overlay the simulation domain with a regular grid. See +the :doc:`Howto grid ` doc page for details. The *image* +style renders a JPG, PNG, or PPM image file of the system for each +snapshot, while the *movie* style combines and compresses the series +of images into a movie file; both styles are discussed in detail on +the :doc:`dump image ` page. Only information for atoms in the specified group is dumped. The -:doc:`dump_modify thresh and region and refresh ` commands -can also alter what atoms are included. Not all styles support -these options; see details on the :doc:`dump_modify ` doc page. +:doc:`dump_modify thresh and region and refresh ` +commands can also alter what atoms are included. Not all styles +support these options; see details on the :doc:`dump_modify +` doc page. -As described below, the filename determines the kind of output (text -or binary or gzipped, one big file or one per timestep, one big file -or multiple smaller files). +As described below, the filename determines the kind of output: text +or binary or gzipped, one big file or one per timestep, one file for +all the processors or multiple smaller files. .. note:: @@ -202,79 +226,66 @@ or multiple smaller files). to a dump file may be slightly outside the simulation box. Re-neighbor timesteps will not typically coincide with the timesteps dump snapshots are written. See the :doc:`dump_modify - pbc ` command if you with to force coordinates to be + pbc ` command if you wish to force coordinates to be strictly inside the simulation box. .. note:: - Unless the :doc:`dump_modify sort ` option is - invoked, the lines of atom information written to dump files - (typically one line per atom) will be in an indeterminate order for - each snapshot. This is even true when running on a single processor, - if the :doc:`atom_modify sort ` option is on, which it is - by default. In this case atoms are re-ordered periodically during a - simulation, due to spatial sorting. It is also true when running in - parallel, because data for a single snapshot is collected from - multiple processors, each of which owns a subset of the atoms. + Unless the :doc:`dump_modify sort ` option is invoked, + the lines of atom or grid information written to dump files + (typically one line per atom or grid cell) will be in an + indeterminate order for each snapshot. This is even true when + running on a single processor, if the :doc:`atom_modify sort + ` option is on, which it is by default. In this case + atoms are re-ordered periodically during a simulation, due to + spatial sorting. It is also true when running in parallel, because + data for a single snapshot is collected from multiple processors, + each of which owns a subset of the atoms. -For the *atom*, *custom*, *cfg*, and *local* styles, sorting is off by -default. For the *dcd*, *xtc*, *xyz*, and *molfile* styles, sorting -by atom ID is on by default. See the :doc:`dump_modify ` -page for details. +For the *atom*, *custom*, *cfg*, *grid*, and *local* styles, sorting +is off by default. For the *dcd*, *grid/vtk*, *xtc*, *xyz*, and +*molfile* styles, sorting by atom ID or grid ID is on by default. See +the :doc:`dump_modify ` page for details. -The *atom/gz*, *cfg/gz*, *custom/gz*, *local/gz*, and *xyz/gz* styles -are identical in command syntax to the corresponding styles without -"gz", however, they generate compressed files using the zlib -library. Thus the filename suffix ".gz" is mandatory. This is an -alternative approach to writing compressed files via a pipe, as done by -the regular dump styles, which may be required on clusters where the -interface to the high-speed network disallows using the fork() library -call (which is needed for a pipe). For the remainder of this page, you -should thus consider the *atom* and *atom/gz* styles (etc.) to be -inter-changeable, with the exception of the required filename suffix. +The *style* keyword determines what kind of data is written to the +dump file(s) and in what format. -Similarly, the *atom/zstd*, *cfg/zstd*, *custom/zstd*, *local/zstd*, and -*xyz/zstd* styles are identical to the gz styles, but use the Zstd -compression library instead and require the ".zst" suffix. See the -:doc:`dump_modify ` page for details on how to control the -compression level in both variants. +Note that *atom*, *custom*, *dcd*, *xtc*, *xyz*, and *yaml* style dump +files can be read directly by `VMD `_, +a popular tool for visualizing and analyzing trajectories from atomic +and molecular systems. For reading *netcdf* style dump files, the +netcdf plugin needs to be recompiled from source using a NetCDF version +compatible with the one used by LAMMPS. The bundled plugin binary +uses a very old version of NetCDF that is not compatible with LAMMPS. -As explained below, the *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and -*xyz/mpiio* styles are identical in command syntax and in the format of -the dump files they create, to the corresponding styles without "mpiio", -except the single dump file they produce is written in parallel via the -MPI-IO library. For the remainder of this page, you should thus -consider the *atom* and *atom/mpiio* styles (etc.) to be -inter-changeable. The one exception is how the filename is specified -for the MPI-IO styles, as explained below. +Likewise the `OVITO visualization package `_, +popular for materials modeling, can read the *atom*, *custom*, +*local*, *xtc*, *cfg*, *netcdf*, and *xyz* style atom dump files +directly. With version 3.8 and above, OVITO can also read and +visualize *grid* style dump files with grid cell data, including +iso-surface images of the grid cell values. -.. warning:: - - The MPIIO package is currently unmaintained and has become - unreliable. Use with caution. - -The precision of values output to text-based dump files can be -controlled by the :doc:`dump_modify format ` command and -its options. +Note that settings made via the :doc:`dump_modify ` +command can also alter the format of individual values and content of +the dump file itself. This includes the precision of values output to +text-based dump files which is controlled by the :doc:`dump_modify +format ` command and its options. ---------- -The *style* keyword determines what atom quantities are written to the -file and in what format. Settings made via the -:doc:`dump_modify ` command can also alter the format of -individual values and the file itself. +Format of native LAMMPS format dump files: -The *atom*, *local*, and *custom* styles create files in a simple text -format that is self-explanatory when viewing a dump file. Some of the -LAMMPS post-processing tools described on the :doc:`Tools ` doc -page, including `Pizza.py `_, -work with this format, as does the :doc:`rerun ` command. +The *atom*, *custom*, *grid*, and *local* styles create files in a +simple LAMMPS-specific text format that is self-explanatory when +viewing a dump file. Many post-processing tools either included with +LAMMPS or third-party tools can read this format, as does the +:doc:`rerun ` command. See tools described on the :doc:`Tools +` doc page for examples, including `Pizza.py +`_. -For post-processing purposes the *atom*, *local*, and *custom* text -files are self-describing in the following sense. - -The dimensions of the simulation box are included in each snapshot. -For an orthogonal simulation box this information is formatted as: +For all these styles, the dimensions of the simulation box are +included in each snapshot. For an orthogonal simulation box this +information is formatted as: .. parsed-literal:: @@ -316,10 +327,13 @@ bounding box extents (xlo_bound, xhi_bound, etc.) are calculated from the triclinic parameters, and how to transform those parameters to and from other commonly used triclinic representations. -The "ITEM: ATOMS" line in each snapshot lists column descriptors for -the per-atom lines that follow. For example, the descriptors would be -"id type xs ys zs" for the default *atom* style, and would be the atom -attributes you specify in the dump command for the *custom* style. +The *atom* and *custom* styles output a "ITEM: NUMBER OF ATOMS" line +with the count of atoms in the snapshot. Likewise they output an +"ITEM: ATOMS" line which includes column descriptors for the per-atom +lines that follow. For example, the descriptors would be "id type xs +ys zs" for the default *atom* style, and would be the atom attributes +you specify in the dump command for the *custom* style. Each +subsequent line will list the data for a single atom. For style *atom*, atom coordinates are written to the file, along with the atom ID and atom type. By default, atom coords are written in a @@ -332,12 +346,31 @@ added for each atom via dump_modify. Style *custom* allows you to specify a list of atom attributes to be written to the dump file for each atom. Possible attributes are listed above and will appear in the order specified. You cannot -specify a quantity that is not defined for a particular simulation---such as -*q* for atom style *bond*, since that atom style does not -assign charges. Dumps occur at the very end of a timestep, so atom -attributes will include effects due to fixes that are applied during -the timestep. An explanation of the possible dump custom attributes -is given below. +specify a quantity that is not defined for a particular +simulation---such as *q* for atom style *bond*, since that atom style +does not assign charges. Dumps occur at the very end of a timestep, +so atom attributes will include effects due to fixes that are applied +during the timestep. An explanation of the possible dump custom +attributes is given below. + +.. versionadded:: 22Dec2022 + +For style *grid* the extent of the Nx by Ny by Nz grid that overlays +the simulation domain is output with each snapshot: + +.. parsed-literal:: + + ITEM: GRID EXTENT + nx ny nz + +For 2d simulations, nz will be 1. There will also be an "ITEM: GRID +DATA" line which includes column descriptors for the per grid cell +data. Each subsequent line (Nx * Ny * Nz lines) will list the data +for a single grid cell. If grid cell IDs are included in the output +via the :doc:`compute property/grid ` command, +then the IDs will range from 1 to N = Nx*Ny*Nz. The ordering of IDs +is with the x index varying fastest, then the y index, and the z index +varying slowest. For style *local*, local output generated by :doc:`computes ` and :doc:`fixes ` is used to generate lines of output that is @@ -351,6 +384,17 @@ generate information on bonds, angles, etc. that can be cut and pasted directly into a data file read by the :doc:`read_data ` command. +---------- + +Dump files in other popular formats: + + +.. note:: + + This section only discusses file formats relevant to this doc page. + The top of this page has links to other dump commands (with their + own pages) which write files in additional popular formats. + Style *cfg* has the same command syntax as style *custom* and writes extended CFG format files, as used by the `AtomEye `_ visualization package. @@ -387,15 +431,15 @@ periodic box. Note that these coordinates may thus be far outside the box size stored with the snapshot. The *xtc* style writes XTC files, a compressed trajectory format used -by the GROMACS molecular dynamics package, and described -`here `_. +by the GROMACS molecular dynamics package, and described `here +`_. The precision used in XTC files can be adjusted via the :doc:`dump_modify ` command. The default value of 1000 means that coordinates are stored to 1/1000 nanometer accuracy. XTC -files are portable binary files written in the NFS XDR data format, -so that any machine which supports XDR should be able to read them. -The number of atoms per snapshot cannot change with the *xtc* style. -The *unwrap* option of the :doc:`dump_modify ` command allows +files are portable binary files written in the NFS XDR data format, so +that any machine which supports XDR should be able to read them. The +number of atoms per snapshot cannot change with the *xtc* style. The +*unwrap* option of the :doc:`dump_modify ` command allows XTC coordinates to be written "unwrapped" by the image flags for each atom. Unwrapped means that if the atom has passed through a periodic boundary one or more times, the value is printed for what the @@ -404,27 +448,41 @@ box. Note that these coordinates may thus be far outside the box size stored with the snapshot. The *xyz* style writes XYZ files, which is a simple text-based -coordinate format that many codes can read. Specifically it has -a line with the number of atoms, then a comment line that is -usually ignored followed by one line per atom with the atom type -and the :math:`x`-, :math:`y`-, and :math:`z`-coordinate of that atom. -You can use the :doc:`dump_modify element ` option to change the -output from using the (numerical) atom type to an element name (or some other -label). This will help many visualization programs to guess bonds and colors. +coordinate format that many codes can read. Specifically it has a line +with the number of atoms, then a comment line that is usually ignored +followed by one line per atom with the atom type and the :math:`x`-, +:math:`y`-, and :math:`z`-coordinate of that atom. You can use the +:doc:`dump_modify element ` option to change the output +from using the (numerical) atom type to an element name (or some other +label). This will help many visualization programs to guess bonds and +colors. + +.. versionadded:: 22Dec2022 + +The *grid/vtk* style writes VTK files for grid data on a regular +rectilinear grid. Its content is conceptually similar to that of the +text file produced by the *grid* style, except that it in an XML-based +format which visualization programs which support the VTK format can +read, e.g. the `ParaView tool `_. For this +style, there can only be 1 or 3 per grid cell attributes specified. +If it is a single value, it is a scalar quantity. If 3 values are +specified it is encoded in the VTK file as a vector quantity (for each +grid cell). The filename for this style must include a "\*" wildcard +character to produce one file per snapshot; see details below. .. versionadded:: 4May2022 Dump style *yaml* has the same command syntax as style *custom* and -writes YAML format files that can be easily parsed by a variety of data -processing tools and programming languages. Each timestep will be -written as a YAML "document" (i.e., starts with "---" and ends with +writes YAML format files that can be easily parsed by a variety of +data processing tools and programming languages. Each timestep will +be written as a YAML "document" (i.e., starts with "---" and ends with "..."). The style supports writing one file per timestep through the -"\*" wildcard but not multi-processor outputs with the "%" token in the -filename. In addition to per-atom data, :doc:`thermo ` data can -be included in the *yaml* style dump file using the :doc:`dump_modify -thermo yes `. The data included in the dump file uses the -"thermo" tag and is otherwise identical to data specified by the -:doc:`thermo_style ` command. +"\*" wildcard but not multi-processor outputs with the "%" token in +the filename. In addition to per-atom data, :doc:`thermo ` +data can be included in the *yaml* style dump file using the +:doc:`dump_modify thermo yes `. The data included in the +dump file uses the "thermo" tag and is otherwise identical to data +specified by the :doc:`thermo_style ` command. Below is an example for a YAML format dump created by the following commands. @@ -435,13 +493,13 @@ Below is an example for a YAML format dump created by the following commands. The tags "time", "units", and "thermo" are optional and enabled by the dump_modify command. The list under the "box" tag has three lines for -orthogonal boxes and four lines for triclinic boxes, where the first three are -the box boundaries and the fourth the three tilt factors (:math:`xy`, -:math:`xz`, :math:`yz`). The "thermo" data follows the format of the *yaml* -thermo style. The "keywords" tag lists the per-atom properties contained in -the "data" columns, which contain a list with one line per atom. The keywords -may be renamed using the dump_modify command same as for the *custom* dump -style. +orthogonal boxes and four lines for triclinic boxes, where the first +three are the box boundaries and the fourth the three tilt factors +(:math:`xy`, :math:`xz`, :math:`yz`). The "thermo" data follows the +format of the *yaml* thermo style. The "keywords" tag lists the +per-atom properties contained in the "data" columns, which contain a +list with one line per atom. The keywords may be renamed using the +dump_modify command same as for the *custom* dump style. .. code-block:: yaml @@ -479,11 +537,7 @@ style. ---------- -Note that *atom*, *custom*, *dcd*, *xtc*, and *xyz* style dump files -can be read directly by `VMD `_, a -popular molecular viewing program. - ----------- +Frequency of dump output: Dumps are performed on timesteps that are a multiple of :math:`N` (including timestep 0) and on the last timestep of a minimization if @@ -508,29 +562,35 @@ every/time ` command can be used. This can be useful when the timestep size varies during a simulation run, e.g. by use of the :doc:`fix dt/reset ` command. -The specified filename determines how the dump file(s) is written. -The default is to write one large text file, which is opened when the -dump command is invoked and closed when an :doc:`undump ` -command is used or when LAMMPS exits. For the *dcd* and *xtc* styles, -this is a single large binary file. +---------- -Dump filenames can contain two wildcard characters. If a "\*" -character appears in the filename, then one file per snapshot is -written and the "\*" character is replaced with the timestep value. -For example, tmp.dump.\* becomes tmp.dump.0, tmp.dump.10000, -tmp.dump.20000, etc. This option is not available for the *dcd* and -*xtc* styles. Note that the :doc:`dump_modify pad ` -command can be used to insure all timestep numbers are the same length -(e.g., 00010), which can make it easier to read a series of dump files -in order with some post-processing tools. +Dump filenames: + +The specified dump filename determines how the dump file(s) is +written. The default is to write one large text file, which is opened +when the dump command is invoked and closed when an :doc:`undump +` command is used or when LAMMPS exits. For the *dcd* and +*xtc* styles, this is a single large binary file. + +Many of the styles allow dump filenames to contain either or both of +two wildcard characters. If a "\*" character appears in the filename, +then one file per snapshot is written and the "\*" character is +replaced with the timestep value. For example, tmp.dump.\* becomes +tmp.dump.0, tmp.dump.10000, tmp.dump.20000, etc. This option is not +available for the *dcd* and *xtc* styles. Note that the +:doc:`dump_modify pad ` command can be used to insure all +timestep numbers are the same length (e.g., 00010), which can make it +easier to read a series of dump files in order with some +post-processing tools. If a "%" character appears in the filename, then each of P processors writes a portion of the dump file, and the "%" character is replaced -with the processor ID from :math:`0` to :math:`P-1`. For example, tmp.dump.% -becomes tmp.dump.0, tmp.dump.1, ... tmp.dump.:math:`P-1`, etc. This creates -smaller files and can be a fast mode of output on parallel machines that -support parallel I/O for output. This option is **not** available for the -*dcd*, *xtc*, *xyz*, and *yaml* styles. +with the processor ID from :math:`0` to :math:`P-1`. For example, +tmp.dump.% becomes tmp.dump.0, tmp.dump.1, ... tmp.dump.:math:`P-1`, +etc. This creates smaller files and can be a fast mode of output on +parallel machines that support parallel I/O for output. This option is +**not** available for the *dcd*, *xtc*, *xyz*, *grid/vtk*, and *yaml* +styles. By default, :math:`P` is the the number of processors, meaning one file per processor, but :math:`P` can be set to a smaller value via the *nfile* or @@ -541,47 +601,41 @@ when running on large numbers of processors. Note that using the "\*" and "%" characters together can produce a large number of small dump files! -For the *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and *xyz/mpiio* -styles, a single dump file is written in parallel via the MPI-IO -library, which is part of the MPI standard for versions 2.0 and above. -Using MPI-IO requires two steps. First, build LAMMPS with its MPIIO -package installed, viz., - -.. code-block:: bash - - make yes-mpiio # installs the MPIIO package - make mpi # build LAMMPS for your platform - -Second, use a dump filename which contains ".mpiio". Note that it does -not have to end in ".mpiio", just contain those characters. Unlike -MPI-IO restart files, which must be both written and read using MPI-IO, -the dump files produced by these MPI-IO styles are identical in format -to the files produced by their non-MPI-IO style counterparts. This -means you can write a dump file using MPI-IO and use the :doc:`read_dump +For styles that end with *mpiio* an ".mpiio" must appear somewhere in +the specified filename. These styles write their dump file in +parallel via the MPI-IO library, which is part of the MPI standard for +versions 2.0 and above. Note these styles are identical in command +syntax to the corresponding styles without "mpiio". Likewise, the +dump files produced by these MPI-IO styles are identical in format to +the files produced by their non-MPI-IO style counterparts. This means +you can write a dump file using MPI-IO and use the :doc:`read_dump ` command or perform other post-processing, just as if the dump file was not written using MPI-IO. +Because MPI-IO dump files are one large file which all processors +write to, you cannot use the "%" wildcard character described above in +the filename. However you can use the ".bin" or ".lammpsbin" suffix +described below. Again, this file will be written in parallel and +have the same binary format as if it were written without MPI-IO. + .. warning:: - The MPIIO package is currently unmaintained and has become - unreliable. Use with caution. + The MPIIO package within LAMMPS is currently unmaintained and has + become unreliable. Use with caution. -Note that MPI-IO dump files are one large file which all processors -write to. You thus cannot use the "%" wildcard character described -above in the filename since that specifies generation of multiple files. -You can use the ".bin" or ".lammpsbin" suffix described below in an -MPI-IO dump file; again this file will be written in parallel and have -the same binary format as if it were written without MPI-IO. +---------- -If the filename ends with ".bin" or ".lammpsbin", the dump file (or -files, if "\*" or "%" is also used) is written in binary format. A -binary dump file will be about the same size as a text version, but will -typically write out much faster. Of course, when post-processing, you -will need to convert it back to text format (see the :ref:`binary2txt -tool `) or write your own code to read the binary file. The -format of the binary file can be understood by looking at the -:file:`tools/binary2txt.cpp` file. This option is only available for -the *atom* and *custom* styles. +Compression of dump file data: + +If the specified filename ends with ".bin" or ".lammpsbin", the dump +file (or files, if "\*" or "%" is also used) is written in binary +format. A binary dump file will be about the same size as a text +version, but will typically write out much faster. Of course, when +post-processing, you will need to convert it back to text format (see +the :ref:`binary2txt tool `) or write your own code to read +the binary file. The format of the binary file can be understood by +looking at the :file:`tools/binary2txt.cpp` file. This option is only +available for the *atom* and *custom* styles. If the filename ends with ".gz", the dump file (or files, if "\*" or "%" is also used) is written in gzipped format. A gzipped dump file will be @@ -589,19 +643,40 @@ about :math:`3\times` smaller than the text version, but will also take longer to write. This option is not available for the *dcd* and *xtc* styles. +Note that styles that end with *gz* are identical in command syntax to +the corresponding styles without "gz", however, they generate +compressed files using the zlib library. Thus the filename suffix +".gz" is mandatory. This is an alternative approach to writing +compressed files via a pipe, as done by the regular dump styles, which +may be required on clusters where the interface to the high-speed +network disallows using the fork() library call (which is needed for a +pipe). For the remainder of this page, you should thus consider the +*atom* and *atom/gz* styles (etc.) to be inter-changeable, with the +exception of the required filename suffix. + +Similarly, styles that end with *zstd* are identical to the gz styles, +but use the Zstd compression library instead and require a ".zst" +suffix. See the :doc:`dump_modify ` page for details on +how to control the compression level in both variants. + ---------- -Note that in the discussion which follows, for styles which can -reference values from a compute or fix or custom atom property, like the -*custom*\ , *cfg*\ , or *local* styles, the bracketed index :math:`i` -can be specified using a wildcard asterisk with the index to effectively -specify multiple values. This takes the form "\*" or "\*n" or "m\*" or -"m\*n". If :math:`N` is the number of columns in the array, then an -asterisk with no numeric values means all column indices from 1 to -:math:`N`. A leading asterisk means all indices from 1 to n -(inclusive). A trailing asterisk means all indices from m to :math:`N` -(inclusive). A middle asterisk means all indices from m to n -(inclusive). +Arguments for different styles: + +The sections below describe per-atom, local, and per grid cell +attributes which can be used as arguments to the various styles. + +Note that in the discussion below, for styles which can reference +values from a compute or fix or custom atom property, like the +*custom*\ , *cfg*\ , *grid* or *local* styles, the bracketed index +:math:`i` can be specified using a wildcard asterisk with the index to +effectively specify multiple values. This takes the form "\*" or +"\*n" or "m\*" or "m\*n". If :math:`N` is the number of columns in +the array, then an asterisk with no numeric values means all column +indices from 1 to :math:`N`. A leading asterisk means all indices +from 1 to n (inclusive). A trailing asterisk means all indices from m +to :math:`N` (inclusive). A middle asterisk means all indices from m +to n (inclusive). Using a wildcard is the same as if the individual columns of the array had been listed one by one. For example, these two dump commands are @@ -617,63 +692,7 @@ command creates a per-atom array with six columns: ---------- -This section explains the local attributes that can be specified as -part of the *local* style. - -The *index* attribute can be used to generate an index number from 1 -to :math:`N` for each line written into the dump file, where :math:`N` is the -total number of local datums from all processors, or lines of output that -will appear in the snapshot. Note that because data from different -processors depend on what atoms they currently own, and atoms migrate -between processor, there is no guarantee that the same index will be -used for the same info (e.g., a particular bond) in successive snapshots. - -The *c_ID* and *c_ID[I]* attributes allow local vectors or arrays -calculated by a :doc:`compute ` to be output. The ID in the -attribute should be replaced by the actual ID of the compute that has -been defined previously in the input script. See the -:doc:`compute ` command for details. There are computes for -calculating local information such as indices, types, and energies for -bonds and angles. - -Note that computes which calculate global or per-atom quantities, as -opposed to local quantities, cannot be output in a dump local command. -Instead, global quantities can be output by the :doc:`thermo_style -custom ` command, and per-atom quantities can be output -by the dump custom command. - -If *c_ID* is used as a attribute, then the local vector calculated by -the compute is printed. If *c_ID[i]* is used, then :math:`i` must be in the -range from :math:`1-M`, which will print the Ith column of the local array -with :math:`M` columns calculated by the compute. See the discussion above -for how :math:`i` can be specified with a wildcard asterisk to effectively -specify multiple values. - -The *f_ID* and *f_ID[I]* attributes allow local vectors or arrays -calculated by a :doc:`fix ` to be output. The ID in the attribute -should be replaced by the actual ID of the fix that has been defined -previously in the input script. - -If *f_ID* is used as a attribute, then the local vector calculated by -the fix is printed. If *f_ID[i]* is used, then :math:`i` must be in the -range :math:`1`--:math:`M`, which will print the :math:`i`\ th column of the -local with :math:`M` columns calculated by the fix. See the discussion above -for how :math:`i` can be specified with a wildcard asterisk to effectively -specify multiple values. - -Here is an example of how to dump bond info for a system, including -the distance and energy of each bond: - -.. code-block:: LAMMPS - - compute 1 all property/local batom1 batom2 btype - compute 2 all bond/local dist eng - dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2] - ----------- - -This section explains the atom attributes that can be specified as -part of the *custom* and *cfg* styles. +Per-atom attributes used as arguments to the *custom* and *cfg* styles: The *id*, *mol*, *proc*, *procp1*, *type*, *element*, *mass*, *vx*, *vy*, *vz*, *fx*, *fy*, *fz*, *q* attributes are self-explanatory. @@ -808,6 +827,97 @@ which could then be output into dump files. ---------- +Attributes used as arguments to the *local* style: + +The *index* attribute can be used to generate an index number from 1 +to N for each line written into the dump file, where N is the total +number of local datums from all processors, or lines of output that +will appear in the snapshot. Note that because data from different +processors depend on what atoms they currently own, and atoms migrate +between processor, there is no guarantee that the same index will be +used for the same info (e.g. a particular bond) in successive +snapshots. + +The *c_ID* and *c_ID[I]* attributes allow local vectors or arrays +calculated by a :doc:`compute ` to be output. The ID in the +attribute should be replaced by the actual ID of the compute that has +been defined previously in the input script. See the +:doc:`compute ` command for details. There are computes for +calculating local information such as indices, types, and energies for +bonds and angles. + +Note that computes which calculate global or per-atom quantities, as +opposed to local quantities, cannot be output in a dump local command. +Instead, global quantities can be output by the :doc:`thermo_style +custom ` command, and per-atom quantities can be output +by the dump custom command. + +If *c_ID* is used as a attribute, then the local vector calculated by +the compute is printed. If *c_ID[I]* is used, then I must be in the +range from 1-M, which will print the Ith column of the local array +with M columns calculated by the compute. See the discussion above +for how I can be specified with a wildcard asterisk to effectively +specify multiple values. + +The *f_ID* and *f_ID[I]* attributes allow local vectors or arrays +calculated by a :doc:`fix ` to be output. The ID in the attribute +should be replaced by the actual ID of the fix that has been defined +previously in the input script. + +If *f_ID* is used as a attribute, then the local vector calculated by +the fix is printed. If *f_ID[I]* is used, then I must be in the +range from 1-M, which will print the Ith column of the local with M +columns calculated by the fix. See the discussion above for how I can +be specified with a wildcard asterisk to effectively specify multiple +values. + +Here is an example of how to dump bond info for a system, including +the distance and energy of each bond: + +.. code-block:: LAMMPS + + compute 1 all property/local batom1 batom2 btype + compute 2 all bond/local dist eng + dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2] + +---------- + +Attributes used as arguments to the *grid* and *grid/vtk* styles: + +The attributes that begin with *c_ID* and *f_ID* both take +colon-separated fields *gname* and *dname*. These refer to a grid +name and data field name which is defined by the compute or fix. Note +that a compute or fix can define one or more grids (of different +sizes) and one or more data fields for each of those grids. The sizes +of all grids output in a single dump grid command must be the same. + +The *c_ID:gname:dname* and *c_ID:gname:dname[I]* attributes allow +per-grid vectors or arrays calculated by a :doc:`compute ` to +be output. The ID in the attribute should be replaced by the actual +ID of the compute that has been defined previously in the input +script. + +If *c_ID:gname:dname* is used as a attribute, then the per-grid vector +calculated by the compute is printed. If *c_ID:gname:dname[I]* is +used, then I must be in the range from 1-M, which will print the Ith +column of the per-grid array with M columns calculated by the compute. +See the discussion above for how I can be specified with a wildcard +asterisk to effectively specify multiple values. + +The *f_ID:gname:dname* and *f_ID:gname:dname[I]* attributes allow +per-grid vectors or arrays calculated by a :doc:`fix ` to be +output. The ID in the attribute should be replaced by the actual ID +of the fix that has been defined previously in the input script. + +If *f_ID:gname:dname* is used as a attribute, then the per-grid vector +calculated by the fix is printed. If *f_ID:gname:dname[I]* is used, +then I must be in the range from 1-M, which will print the Ith column +of the per-grid with M columns calculated by the fix. See the +discussion above for how I can be specified with a wildcard asterisk +to effectively specify multiple values. + +---------- + Restrictions """""""""""" @@ -816,9 +926,9 @@ To write gzipped dump files, you must either compile LAMMPS with the See the :doc:`Build settings ` page for details. While a dump command is active (i.e., has not been stopped by using -the :doc:`undump command `), no commands may be used that will change -the timestep (e.g., :doc:`reset_timestep `). LAMMPS -will terminate with an error otherwise. +the :doc:`undump command `), no commands may be used that will +change the timestep (e.g., :doc:`reset_timestep `). +LAMMPS will terminate with an error otherwise. The *atom/gz*, *cfg/gz*, *custom/gz*, and *xyz/gz* styles are part of the COMPRESS package. They are only enabled if LAMMPS was built with diff --git a/doc/src/dump_image.rst b/doc/src/dump_image.rst index bc2373afac..c1c0173e96 100644 --- a/doc/src/dump_image.rst +++ b/doc/src/dump_image.rst @@ -24,7 +24,7 @@ Syntax * color = atom attribute that determines color of each atom * diameter = atom attribute that determines size of each atom * zero or more keyword/value pairs may be appended -* keyword = *atom* or *adiam* or *bond* or *line* or *tri* or *body* or *fix* or *size* or *view* or *center* or *up* or *zoom* or *box* or *axes* or *subbox* or *shiny* or *ssao* +* keyword = *atom* or *adiam* or *bond* or *grid* or *line* or *tri* or *body* or *fix* or *size* or *view* or *center* or *up* or *zoom* or *box* or *axes* or *subbox* or *shiny* or *ssao* .. parsed-literal:: @@ -34,6 +34,14 @@ Syntax color = *atom* or *type* or *none* width = number or *atom* or *type* or *none* number = numeric value for bond width (distance units) + *grid* = per-grid value to use when coloring each grid cell + per-grid value = c_ID:gname:dname, c_ID:gname:dname[I], f_ID:gname:dname, f_ID:gname:dname[I] + gname = name of grid defined by compute or fix + dname = name of data field defined by compute or fix + c_ID = per-grid vector calculated by a compute with ID + c_ID[I] = Ith column of per-grid array calculated by a compute with ID + f_ID = per-grid vector calculated by a fix with ID + f_ID[I] = Ith column of per-grid array calculated by a fix with ID *line* = color width color = *type* width = numeric value for line width (distance units) @@ -69,7 +77,7 @@ Syntax yes/no = do or do not draw simulation box lines diam = diameter of box lines as fraction of shortest box length *axes* values = axes length diam = draw xyz axes - axes = *yes* or *no = do or do not draw xyz axes lines next to simulation box + axes = *yes* or *no* = do or do not draw xyz axes lines next to simulation box length = length of axes lines as fraction of respective box lengths diam = diameter of axes lines as fraction of shortest box length *subbox* values = lines diam = draw outline of processor sub-domains @@ -95,7 +103,7 @@ Syntax dump_modify dump-ID keyword values ... * these keywords apply only to the *image* and *movie* styles and are documented on this page -* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate* +* keyword = *acolor* or *adiam* or *amap* or *gmap* or *backcolor* or *bcolor* or *bdiam* or *bitrate* or *boxcolor* or *color* or *framerate* or *gmap* * see the :doc:`dump modify ` doc page for more general keywords .. parsed-literal:: @@ -134,15 +142,16 @@ Syntax *bdiam* args = type diam type = bond type or range of types (see below) diam = diameter of bonds of that type (distance units) + *bitrate* arg = rate + rate = target bitrate for movie in kbps *boxcolor* arg = color color = name of color for simulation box lines and processor sub-domain lines *color* args = name R G B name = name of color R,G,B = red/green/blue numeric values from 0.0 to 1.0 - *bitrate* arg = rate - rate = target bitrate for movie in kbps *framerate* arg = fps fps = frames per second for movie + *gmap* args = identical to *amap* args Examples """""""" @@ -214,7 +223,7 @@ Similarly, the format of the resulting movie is chosen with the and thus details have to be looked up in the `FFmpeg documentation `_. Typical examples are: .avi, .mpg, .m4v, .mp4, .mkv, .flv, .mov, .gif Additional settings of the movie -compression like bitrate and framerate can be set using the +compression like *bitrate* and *framerate* can be set using the dump_modify command as described below. To write out JPEG and PNG format files, you must build LAMMPS with @@ -300,13 +309,13 @@ settings, they are interpreted in the following way. If "vx", for example, is used as the *color* setting, then the color of the atom will depend on the x-component of its velocity. The association of a per-atom value with a specific color is determined by -a "color map", which can be specified via the dump_modify command, as -described below. The basic idea is that the atom-attribute will be -within a range of values, and every value within the range is mapped -to a specific color. Depending on how the color map is defined, that -mapping can take place via interpolation so that a value of -3.2 is -halfway between "red" and "blue", or discretely so that the value of --3.2 is "orange". +a "color map", which can be specified via the dump_modify amap +command, as described below. The basic idea is that the +atom-attribute will be within a range of values, and every value +within the range is mapped to a specific color. Depending on how the +color map is defined, that mapping can take place via interpolation so +that a value of -3.2 is halfway between "red" and "blue", or +discretely so that the value of -3.2 is "orange". If "vx", for example, is used as the *diameter* setting, then the atom will be rendered using the x-component of its velocity as the @@ -948,6 +957,17 @@ frequently. ---------- +The *gmap* keyword can be used with the dump image command, with its +*grid* keyword, to setup a color map. The color map is used to assign +a specific RGB (red/green/blue) color value to an individual grid cell +when it is drawn, based on the grid cell value, which is a numeric +quantity specified with the *grid* keyword. + +The arguments for the *gmap* keyword are identical to those for the +*amap* keyword (for atom coloring) described above. + +---------- + Restrictions """""""""""" @@ -1031,6 +1051,7 @@ The defaults for the dump_modify keywords specific to dump image and dump movie * boxcolor = yellow * color = 140 color names are pre-defined as listed below * framerate = 24 +* gmap = min max cf 0.0 2 min blue max red ---------- diff --git a/doc/src/dump_vtk.rst b/doc/src/dump_vtk.rst index 4ec872cb89..56b5c2a162 100644 --- a/doc/src/dump_vtk.rst +++ b/doc/src/dump_vtk.rst @@ -90,8 +90,8 @@ hexahedrons in either legacy .vtk or .vtu XML format. Style *vtk* allows you to specify a list of atom attributes to be written to the dump file for each atom. The list of possible attributes -is the same as for the :doc:`dump_style custom ` command; see -its page for a listing and an explanation of each attribute. +is the same as for the :doc:`dump_style custom ` command; see its +documentation page for a listing and an explanation of each attribute. .. note:: diff --git a/doc/src/fitpod_command.rst b/doc/src/fitpod_command.rst new file mode 100644 index 0000000000..fc21caec70 --- /dev/null +++ b/doc/src/fitpod_command.rst @@ -0,0 +1,745 @@ +.. index:: fitpod + +fitpod command +====================== + +Syntax +"""""" + +.. parsed-literal:: + + fitpod Ta_param.pod Ta_data.pod + +* fitpod = style name of this command +* Ta_param.pod = an input file that describes proper orthogonal descriptors (PODs) +* Ta_data.pod = an input file that specifies DFT data used to fit a POD potential + +Examples +"""""""" + +.. code-block:: LAMMPS + + fitpod Ta_param.pod Ta_data.pod + +Description +""""""""""" +.. versionadded:: 22Dec2022 + +Fit a machine-learning interatomic potential (ML-IAP) based on proper +orthogonal descriptors (POD). Two input files are required for this +command. The first input file describes a POD potential parameter +settings, while the second input file specifies the DFT data used for +the fitting procedure. + +The table below has one-line descriptions of all the keywords that can +be used in the first input file (i.e. ``Ta_param.pod`` in the example +above): + +.. list-table:: + :header-rows: 1 + :widths: auto + + * - Keyword + - Default + - Type + - Description + * - species + - (none) + - STRING + - Chemical symbols for all elements in the system and have to match XYZ training files. + * - pbc + - 1 1 1 + - INT + - three integer constants specify boundary conditions + * - rin + - 1.0 + - REAL + - a real number specifies the inner cut-off radius + * - rcut + - 5.0 + - REAL + - a real number specifies the outer cut-off radius + * - bessel_polynomial_degree + - 3 + - INT + - the maximum degree of Bessel polynomials + * - inverse_polynomial_degree + - 6 + - INT + - the maximum degree of inverse radial basis functions + * - onebody + - 1 + - BOOL + - turns on/off one-body potential + * - twobody_number_radial_basis_functions + - 6 + - INT + - number of radial basis functions for two-body potential + * - threebody_number_radial_basis_functions + - 5 + - INT + - number of radial basis functions for three-body potential + * - threebody_number_angular_basis_functions + - 5 + - INT + - number of angular basis functions for three-body potential + * - fourbody_snap_twojmax + - 0 + - INT + - band limit for SNAP bispectrum components (0,2,4,6,8... allowed) + * - fourbody_snap_chemflag + - 0 + - BOOL + - turns on/off the explicit multi-element variant of the SNAP bispectrum components + * - quadratic_pod_potential + - 0 + - BOOL + - turns on/off quadratic POD potential + +All keywords except *species* have default values. If a keyword is not +set in the input file, its default value is used. The next table +describes all keywords that can be used in the second input file +(i.e. ``Ta_data.pod`` in the example above): + +.. list-table:: + :header-rows: 1 + :widths: auto + + * - Keyword + - Default + - Type + - Description + * - file_format + - extxyz + - STRING + - only the extended xyz format (extxyz) is currently supported + * - file_extension + - xyz + - STRING + - extension of the data files + * - path_to_training_data_set + - (none) + - STRING + - specifies the path to training data files in double quotes + * - path_to_test_data_set + - "" + - STRING + - specifies the path to test data files in double quotes + * - fraction_training_data_set + - 1.0 + - REAL + - a real number (<= 1.0) specifies the fraction of the training set used to fit POD + * - randomize_training_data_set + - 0 + - BOOL + - turns on/off randomization of the training set + * - fitting_weight_energy + - 100.0 + - REAL + - a real constant specifies the weight for energy in the least-squares fit + * - fitting_weight_force + - 1.0 + - REAL + - a real constant specifies the weight for force in the least-squares fit + * - fitting_regularization_parameter + - 1.0e-10 + - REAL + - a real constant specifies the regularization parameter in the least-squares fit + * - error_analysis_for_training_data_set + - 0 + - BOOL + - turns on/off error analysis for the training data set + * - error_analysis_for_test_data_set + - 0 + - BOOL + - turns on/off error analysis for the test data set + * - basename_for_output_files + - pod + - STRING + - a basename string added to the output files + * - precision_for_pod_coefficients + - 8 + - INT + - number of digits after the decimal points for numbers in the coefficient file + +All keywords except *path_to_training_data_set* have default values. If +a keyword is not set in the input file, its default value is used. After +successful training, a number of output files are produced, if enabled: + +* ``_training_errors.pod`` reports the errors in energy and forces for the training data set +* ``_training_analysis.pod`` reports detailed errors for all training configurations +* ``_test_errors.pod`` reports errors for the test data set +* ``_test_analysis.pod`` reports detailed errors for all test configurations +* ``_coefficients.pod`` contains the coefficients of the POD potential + +After training the POD potential, ``Ta_param.pod`` and ``_coefficients.pod`` +are the two files needed to use the POD potential in LAMMPS. See +:doc:`pair_style pod ` for using the POD potential. Examples +about training and using POD potentials are found in the directory +lammps/examples/PACKAGES/pod. + +Parameterized Potential Energy Surface +"""""""""""""""""""""""""""""""""""""" + +We consider a multi-element system of *N* atoms with :math:`N_{\rm e}` +unique elements. We denote by :math:`\boldsymbol r_n` and :math:`Z_n` +position vector and type of an atom *n* in the system, +respectively. Note that we have :math:`Z_n \in \{1, \ldots, N_{\rm e} +\}`, :math:`\boldsymbol R = (\boldsymbol r_1, \boldsymbol r_2, \ldots, +\boldsymbol r_N) \in \mathbb{R}^{3N}`, and :math:`\boldsymbol Z = (Z_1, +Z_2, \ldots, Z_N) \in \mathbb{N}^{N}`. The potential energy surface +(PES) of the system can be expressed as a many-body expansion of the +form + +.. math:: + + E(\boldsymbol R, \boldsymbol Z, \boldsymbol{\eta}, \boldsymbol{\mu}) \ = \ & \sum_{i} V^{(1)}(\boldsymbol r_i, Z_i, \boldsymbol \mu^{(1)} ) + \frac12 \sum_{i,j} V^{(2)}(\boldsymbol r_i, \boldsymbol r_j, Z_i, Z_j, \boldsymbol \eta, \boldsymbol \mu^{(2)}) \\ + & + \frac16 \sum_{i,j,k} V^{(3)}(\boldsymbol r_i, \boldsymbol r_j, \boldsymbol r_k, Z_i, Z_j, Z_k, \boldsymbol \eta, \boldsymbol \mu^{(3)}) + \ldots + +where :math:`V^{(1)}` is the one-body potential often used for +representing external field or energy of isolated elements, and the +higher-body potentials :math:`V^{(2)}, V^{(3)}, \ldots` are symmetric, +uniquely defined, and zero if two or more indices take identical values. +The superscript on each potential denotes its body order. Each *q*-body +potential :math:`V^{(q)}` depends on :math:`\boldsymbol \mu^{(q)}` which +are sets of parameters to fit the PES. Note that :math:`\boldsymbol \mu` +is a collection of all potential parameters :math:`\boldsymbol +\mu^{(1)}`, :math:`\boldsymbol \mu^{(2)}`, :math:`\boldsymbol +\mu^{(3)}`, etc, and that :math:`\boldsymbol \eta` is a set of +hyper-parameters such as inner cut-off radius :math:`r_{\rm in}` and +outer cut-off radius :math:`r_{\rm cut}`. + +Interatomic potentials rely on parameters to learn relationship between +atomic environments and interactions. Since interatomic potentials are +approximations by nature, their parameters need to be set to some +reference values or fitted against data by necessity. Typically, +potential fitting finds optimal parameters, :math:`\boldsymbol \mu^*`, +to minimize a certain loss function of the predicted quantities and +data. Since the fitted potential depends on the data set used to fit it, +different data sets will yield different optimal parameters and thus +different fitted potentials. When fitting the same functional form on +*Q* different data sets, we would obtain *Q* different optimized +potentials, :math:`E(\boldsymbol R,\boldsymbol Z, \boldsymbol \eta, +\boldsymbol \mu_q^*), 1 \le q \le Q`. Consequently, there exist many +different sets of optimized parameters for empirical interatomic +potentials. + +Instead of optimizing the potential parameters, inspired by the reduced +basis method :ref:`(Grepl) ` for parameterized partial +differential equations, we view the parameterized PES as a parametric +manifold of potential energies + +.. math:: + + \mathcal{M} = \{E(\boldsymbol R, \boldsymbol Z, \boldsymbol \eta, \boldsymbol \mu) \ | \ \boldsymbol \mu \in \Omega^{\boldsymbol \mu} \} + +where :math:`\Omega^{\boldsymbol \mu}` is a parameter domain in which +:math:`\boldsymbol \mu` resides. The parametric manifold +:math:`\mathcal{M}` contains potential energy surfaces for all values of +:math:`\boldsymbol \mu \in \Omega^{\boldsymbol \mu}`. Therefore, the +parametric manifold yields a much richer and more transferable atomic +representation than any particular individual PES :math:`E(\boldsymbol +R, \boldsymbol Z, \boldsymbol \eta, \boldsymbol \mu^*)`. + +We propose specific forms of the parameterized potentials for one-body, +two-body, and three-body interactions. We apply the Karhunen-Loeve +expansion to snapshots of the parameterized potentials to obtain sets of +orthogonal basis functions. These basis functions are aggregated +according to the chemical elements of atoms, thus leading to +multi-element proper orthogonal descriptors. + +Proper Orthogonal Descriptors +""""""""""""""""""""""""""""" + +Proper orthogonal descriptors are finger prints characterizing the +radial and angular distribution of a system of atoms. The detailed +mathematical definition is given in the paper by Nguyen and Rohskopf +:ref:`(Nguyen) `. + +The descriptors for the one-body interaction are used to capture energy +of isolated elements and defined as follows + +.. math:: + + D_{ip}^{(1)} = \left\{ + \begin{array}{ll} + 1, & \mbox{if } Z_i = p \\ + 0, & \mbox{if } Z_i \neq p + \end{array} + \right. + +for :math:`1 \le i \le N, 1 \le p \le N_{\rm e}`. The number of one-body +descriptors per atom is equal to the number of elements. The one-body +descriptors are independent of atom positions, but dependent on atom +types. The one-body descriptors are active only when the keyword +*onebody* is set to 1. + +We adopt the usual assumption that the direct interaction between two +atoms vanishes smoothly when their distance is greater than the outer +cutoff distance :math:`r_{\rm cut}`. Furthermore, we assume that two +atoms can not get closer than the inner cutoff distance :math:`r_{\rm +in}` due to the Pauli repulsion principle. Let :math:`r \in (r_{\rm in}, +r_{\rm cut})`, we introduce the following parameterized radial functions + +.. math:: + + \phi(r, r_{\rm in}, r_{\rm cut}, \alpha, \beta) = \frac{\sin (\alpha \pi x) }{r - r_{\rm in}}, \qquad \varphi(r, \gamma) = \frac{1}{r^\gamma} , + +where the scaled distance function :math:`x` is defined below to enrich the two-body manifold + +.. math:: + + x(r, r_{\rm in}, r_{\rm cut}, \beta) = \frac{e^{-\beta(r - r_{\rm in})/(r_{\rm cut} - r_{\rm in})} - 1}{e^{-\beta} - 1} . + +We introduce the following function as a convex combination of the two functions + +.. math:: + + \psi(r, r_{\rm in}, r_{\rm cut}, \alpha, \beta, \gamma, \kappa) = \kappa \phi(r, r_{\rm in}, r_{\rm cut}, \alpha, \beta) + (1- \kappa) \varphi(r, \gamma) . + +We see that :math:`\psi` is a function of distance :math:`r`, cut-off +distances :math:`r_{\rm in}` and :math:`r_{\rm cut}`, and parameters +:math:`\alpha, \beta, \gamma, \kappa`. Together these parameters allow +the function :math:`\psi` to characterize a diverse spectrum of two-body +interactions within the cut-off interval :math:`(r_{\rm in}, r_{\rm +cut})`. + +Next, we introduce the following parameterized potential + +.. math:: + + W^{(2)}(r_{ij}, \boldsymbol \eta, \boldsymbol \mu^{(2)}) = f_{\rm c}(r_{ij}, \boldsymbol \eta) \psi(r_{ij}, \boldsymbol \eta, \boldsymbol \mu^{(2)}) + +where :math:`\eta_1 = r_{\rm in}, \eta_2 = r_{\rm cut}, \mu_1^{(2)} = +\alpha, \mu_2^{(2)} = \beta, \mu_3^{(2)} = \gamma`, and +:math:`\mu_4^{(2)} = \kappa`. Here the cut-off function :math:`f_{\rm +c}(r_{ij}, \boldsymbol \eta)` proposed in [refs] is used to ensure the +smooth vanishing of the potential and its derivative for :math:`r_{ij} +\ge r_{\rm cut}`: + +.. math:: + + f_{\rm c}(r_{ij}, r_{\rm in}, r_{\rm cut}) = \exp \left(1 -\frac{1}{\sqrt{\left(1 - \frac{(r-r_{\rm in})^3}{(r_{\rm cut} - r_{\rm in})^3} \right)^2 + 10^{-6}}} \right) + +Based on the parameterized potential, we form a set of snapshots as +follows. We assume that we are given :math:`N_{\rm s}` parameter tuples +:math:`\boldsymbol \mu^{(2)}_\ell, 1 \le \ell \le N_{\rm s}`. We +introduce the following set of snapshots on :math:`(r_{\rm in}, r_{\rm +cut})`: + +.. math:: + + \xi_\ell(r_{ij}, \boldsymbol \eta) = W^{(2)}(r_{ij}, \boldsymbol \eta, \boldsymbol \mu^{(2)}_\ell), \quad \ell = 1, \ldots, N_{\rm s} . + +To ensure adequate sampling of the PES for different parameters, we +choose :math:`N_{\rm s}` parameter points :math:`\boldsymbol +\mu^{(2)}_\ell = (\alpha_\ell, \beta_\ell, \gamma_\ell, \kappa_\ell), 1 +\le \ell \le N_{\rm s}` as follows. The parameters :math:`\alpha \in [1, +N_\alpha]` and :math:`\gamma \in [1, N_\gamma]` are integers, where +:math:`N_\alpha` and :math:`N_\gamma` are the highest degrees for +:math:`\alpha` and :math:`\gamma`, respectively. We next choose +:math:`N_\beta` different values of :math:`\beta` in the interval +:math:`[\beta_{\min}, \beta_{\max}]`, where :math:`\beta_{\min} = 0` and +:math:`\beta_{\max} = 4`. The parameter :math:`\kappa` can be set either +0 or 1. Hence, the total number of parameter points is :math:`N_{\rm s} += N_\alpha N_\beta + N_\gamma`. Although :math:`N_\alpha, N_\beta, +N_\gamma` can be chosen conservatively large, we find that +:math:`N_\alpha = 6, N_\beta = 3, N_\gamma = 8` are adequate for most +problems. Note that :math:`N_\alpha` and :math:`N_\gamma` correspond to +*bessel_polynomial_degree* and *inverse_polynomial_degree*, +respectively. + +We employ the Karhunen-Loeve (KL) expansion to generate an orthogonal +basis set which is known to be optimal for representation of the +snapshot family :math:`\{\xi_\ell\}_{\ell=1}^{N_{\rm s}}`. The two-body +orthogonal basis functions are computed as follows + +.. math:: + + U^{(2)}_m(r_{ij}, \boldsymbol \eta) = \sum_{\ell = 1}^{N_{\rm s}} A_{\ell m}(\boldsymbol \eta) \, \xi_\ell(r_{ij}, \boldsymbol \eta), \qquad m = 1, \ldots, N_{\rm 2b} , + +where the matrix :math:`\boldsymbol A \in \mathbb{R}^{N_{\rm s} \times +N_{\rm s}}` consists of eigenvectors of the eigenvalue problem + +.. math:: + + \boldsymbol C \boldsymbol a = \lambda \boldsymbol a + +with the entries of :math:`\boldsymbol C \in \mathbb{R}^{N_{\rm s} \times N_{\rm s}}` being given by + +.. math:: + + C_{ij} = \frac{1}{N_{\rm s}} \int_{r_{\rm in}}^{r_{\rm cut}} \xi_i(x, \boldsymbol \eta) \xi_j(x, \boldsymbol \eta) dx, \quad 1 \le i, j \le N_{\rm s} + +Note that the eigenvalues :math:`\lambda_\ell, 1 \le \ell \le N_{\rm +s}`, are ordered such that :math:`\lambda_1 \ge \lambda_2 \ge \ldots \ge +\lambda_{N_{\rm s}}`, and that the matrix :math:`\boldsymbol A` is +pe-computed and stored for any given :math:`\boldsymbol \eta`. Owing to +the rapid convergence of the KL expansion, only a small number of +orthogonal basis functions is needed to obtain accurate +approximation. The value of :math:`N_{\rm 2b}` corresponds to +*twobody_number_radial_basis_functions*. + +The two-body proper orthogonal descriptors at each atom *i* are computed +by summing the orthogonal basis functions over the neighbors of atom *i* +and numerating on the atom types as follows + +.. math:: + + D^{(2)}_{im l(p, q) }(\boldsymbol \eta) = \left\{ + \begin{array}{ll} + \displaystyle \sum_{\{j | Z_j = q\}} U^{(2)}_m(r_{ij}, \boldsymbol \eta), & \mbox{if } Z_i = p \\ + 0, & \mbox{if } Z_i \neq p + \end{array} + \right. + +for :math:`1 \le i \le N, 1 \le m \le N_{\rm 2b}, 1 \le q, p \le N_{\rm +e}`. Here :math:`l(p,q)` is a symmetric index mapping such that + +.. math:: + + l(p,q) = \left\{ + \begin{array}{ll} + q + (p-1) N_{\rm e} - p(p-1)/2, & \mbox{if } q \ge p \\ + p + (q-1) N_{\rm e} - q(q-1)/2, & \mbox{if } q < p . + \end{array} + \right. + +The number of two-body descriptors per atom is thus :math:`N_{\rm 2b} +N_{\rm e}(N_{\rm e}+1)/2`. + +It is important to note that the orthogonal basis functions do not +depend on the atomic numbers :math:`Z_i` and :math:`Z_j`. Therefore, the +cost of evaluating the basis functions and their derivatives with +respect to :math:`r_{ij}` is independent of the number of elements +:math:`N_{\rm e}`. Consequently, even though the two-body proper +orthogonal descriptors depend on :math:`\boldsymbol Z`, their +computational complexity is independent of :math:`N_{\rm e}`. + +In order to provide proper orthogonal descriptors for three-body +interactions, we need to introduce a three-body parameterized +potential. In particular, the three-body potential is defined as a +product of radial and angular functions as follows + +.. math:: + + W^{(3)}(r_{ij}, r_{ik}, \theta_{ijk}, \boldsymbol \eta, \boldsymbol \mu^{(3)}) = \psi(r_{ij}, r_{\rm min}, r_{\rm max}, \alpha, \beta, \gamma, \kappa) f_{\rm c}(r_{ij}, r_{\rm min}, r_{\rm max}) \\ + \psi(r_{ik}, r_{\rm min}, r_{\rm max}, \alpha, \beta, \gamma, \kappa) f_{\rm c}(r_{ik}, r_{\rm min}, r_{\rm max}) \\ + \cos (\sigma \theta_{ijk} + \zeta) + +where :math:`\sigma` is the periodic multiplicity, :math:`\zeta` is the +equilibrium angle, :math:`\boldsymbol \mu^{(3)} = (\alpha, \beta, +\gamma, \kappa, \sigma, \zeta)`. The three-body potential provides an +angular fingerprint of the atomic environment through the bond angles +:math:`\theta_{ijk}` formed with each pair of neighbors :math:`j` and +:math:`k`. Compared to the two-body potential, the three-body potential +has two extra parameters :math:`(\sigma, \zeta)` associated with the +angular component. + +Let :math:`\boldsymbol \varrho = (\alpha, \beta, \gamma, \kappa)`. We +assume that we are given :math:`L_{\rm r}` parameter tuples +:math:`\boldsymbol \varrho_\ell, 1 \le \ell \le L_{\rm r}`. We +introduce the following set of snapshots on :math:`(r_{\min}, +r_{\max})`: + +.. math:: + + \zeta_\ell(r_{ij}, r_{\rm min}, r_{\rm max} ) = \psi(r_{ij}, r_{\rm min}, r_{\rm max}, \boldsymbol \varrho_\ell) f_{\rm c}(r_{ij}, r_{\rm min}, r_{\rm max}), \quad 1 \le \ell \le L_{\rm r} . + +We apply the Karhunen-Loeve (KL) expansion to this set of snapshots to +obtain orthogonal basis functions as follows + +.. math:: + + U^{r}_m(r_{ij}, r_{\rm min}, r_{\rm max} ) = \sum_{\ell = 1}^{L_{\rm r}} A_{\ell m} \, \zeta_\ell(r_{ij}, r_{\rm min}, r_{\rm max} ), \qquad m = 1, \ldots, N_{\rm r} , + +where the matrix :math:`\boldsymbol A \in \mathbb{R}^{L_{\rm r} \times L_{\rm r}}` consists +of eigenvectors of the eigenvalue problem. For the parameterized angular function, +we consider angular basis functions + +.. math:: + + U^{a}_n(\theta_{ijk}) = \cos ((n-1) \theta_{ijk}), \qquad n = 1,\ldots, N_{\rm a}, + +where :math:`N_{\rm a}` is the number of angular basis functions. The orthogonal +basis functions for the parameterized potential are computed as follows + +.. math:: + + U^{(3)}_{mn}(r_{ij}, r_{ik}, \theta_{ijk}, \boldsymbol \eta) = U^{r}_m(r_{ij}, \boldsymbol \eta) U^{r}_m(r_{ik}, \boldsymbol \eta) U^{a}_n(\theta_{ijk}), + +for :math:`1 \le m \le N_{\rm r}, 1 \le n \le N_{\rm a}`. The number of three-body +orthogonal basis functions is equal to :math:`N_{\rm 3b} = N_{\rm r} N_{\rm a}` and +independent of the number of elements. The value of :math:`N_{\rm r}` corresponds to +*threebody_number_radial_basis_functions*, while that of :math:`N_{\rm a}` to +*threebody_number_angular_basis_functions*. + +The three-body proper orthogonal descriptors at each atom *i* +are obtained by summing over the neighbors *j* and *k* of atom *i* as + +.. math:: + + D^{(3)}_{imn \ell(p, q, s)}(\boldsymbol \eta) = \left\{ + \begin{array}{ll} + \displaystyle \sum_{\{j | Z_j = q\}} \sum_{\{k | Z_k = s\}} U^{(3)}_{mn}(r_{ij}, r_{ik}, \theta_{ijk}, \boldsymbol \eta), & \mbox{if } Z_i = p \\ + 0, & \mbox{if } Z_i \neq p + \end{array} + \right. + +for :math:`1 \le i \le N, 1 \le m \le N_{\rm r}, 1 \le n \le N_{\rm a}, 1 \le q, p, s \le N_{\rm e}`, +where + +.. math:: + + \ell(p,q,s) = \left\{ + \begin{array}{ll} + s + (q-1) N_{\rm e} - q(q-1)/2 + (p-1)N_{\rm e}(1+N_{\rm e})/2 , & \mbox{if } s \ge q \\ + q + (s-1) N_{\rm e} - s(s-1)/2 + (p-1)N_{\rm e}(1+N_{\rm e})/2, & \mbox{if } s < q . + \end{array} + \right. + +The number of three-body descriptors per atom is thus :math:`N_{\rm 3b} N_{\rm e}^2(N_{\rm e}+1)/2`. +While the number of three-body PODs is cubic function of the number of elements, +the computational complexity of the three-body PODs is independent of the number of elements. + +Four-Body SNAP Descriptors +"""""""""""""""""""""""""" + +In addition to the proper orthogonal descriptors described above, we also employ +the spectral neighbor analysis potential (SNAP) descriptors. SNAP uses bispectrum components +to characterize the local neighborhood of each atom in a very general way. The mathematical definition +of the bispectrum calculation and its derivatives w.r.t. atom positions is described in +:doc:`compute snap `. In SNAP, the +total energy is decomposed into a sum over atom energies. The energy of +atom *i* is expressed as a weighted sum over bispectrum components. + +.. math:: + + E_i^{\rm SNAP} = \sum_{k=1}^{N_{\rm 4b}} \sum_{p=1}^{N_{\rm e}} c_{kp}^{(4)} D_{ikp}^{(4)} + + +where the SNAP descriptors are related to the bispectrum components by + +.. math:: + + D^{(4)}_{ikp} = \left\{ + \begin{array}{ll} + \displaystyle B_{ik}, & \mbox{if } Z_i = p \\ + 0, & \mbox{if } Z_i \neq p + \end{array} + \right. + +Here :math:`B_{ik}` is the *k*\ -th bispectrum component of atom *i*. The number of +bispectrum components :math:`N_{\rm 4b}` depends on the value of *fourbody_snap_twojmax* :math:`= 2 J_{\rm max}` +and *fourbody_snap_chemflag*. If *fourbody_snap_chemflag* = 0 +then :math:`N_{\rm 4b} = (J_{\rm max}+1)(J_{\rm max}+2)(J_{\rm max}+1.5)/3`. +If *fourbody_snap_chemflag* = 1 then :math:`N_{\rm 4b} = N_{\rm e}^3 (J_{\rm max}+1)(J_{\rm max}+2)(J_{\rm max}+1.5)/3`. +The bispectrum calculation is described in more detail in :doc:`compute sna/atom `. + +Linear Proper Orthogonal Descriptor Potentials +"""""""""""""""""""""""""""""""""""""""""""""" + +The proper orthogonal descriptors and SNAP descriptors are used to define the atomic energies +in the following expansion + +.. math:: + + E_{i}(\boldsymbol \eta) = \sum_{p=1}^{N_{\rm e}} c^{(1)}_p D^{(1)}_{ip} + \sum_{m=1}^{N_{\rm 2b}} \sum_{l=1}^{N_{\rm e}(N_{\rm e}+1)/2} c^{(2)}_{ml} D^{(2)}_{iml}(\boldsymbol \eta) + \sum_{m=1}^{N_{\rm r}} \sum_{n=1}^{N_{\rm a}} \sum_{\ell=1}^{N_{\rm e}^2(N_{\rm e}+1)/2} c^{(3)}_{mn\ell} D^{(3)}_{imn\ell}(\boldsymbol \eta) + \sum_{k=1}^{N_{\rm 4b}} \sum_{p=1}^{N_{\rm e}} c_{kp}^{(4)} D_{ikp}^{(4)}(\boldsymbol \eta), + +where :math:`D^{(1)}_{ip}, D^{(2)}_{iml}, D^{(3)}_{imn\ell}, D^{(4)}_{ikp}` are the one-body, two-body, three-body, four-body descriptors, +respectively, and :math:`c^{(1)}_p, c^{(2)}_{ml}, c^{(3)}_{mn\ell}, c^{(4)}_{kp}` are their respective expansion +coefficients. In a more compact notation that implies summation over descriptor indices +the atomic energies can be written as + +.. math:: + + E_i(\boldsymbol \eta) = \sum_{m=1}^{N_{\rm e}} c^{(1)}_m D^{(1)}_{im} + \sum_{m=1}^{N_{\rm d}^{(2)}} c^{(2)}_k D^{(2)}_{im} + \sum_{m=1}^{N_{\rm d}^{(3)}} c^{(3)}_m D^{(3)}_{im} + \sum_{m=1}^{N_{\rm d}^{(4)}} c^{(4)}_m D^{(4)}_{im} + +where :math:`N_{\rm d}^{(2)} = N_{\rm 2b} N_{\rm e} (N_{\rm e}+1)/2`, +:math:`N_{\rm d}^{(3)} = N_{\rm 3b} N_{\rm e}^2 (N_{\rm e}+1)/2`, and +:math:`N_{\rm d}^{(4)} = N_{\rm 4b} N_{\rm e}` are +the number of two-body, three-body, and four-body descriptors, respectively. + +The potential energy is then obtained by summing local atomic energies :math:`E_i` +for all atoms :math:`i` in the system + +.. math:: + + E(\boldsymbol \eta) = \sum_{i}^N E_{i}(\boldsymbol \eta) + +Because the descriptors are one-body, two-body, and three-body terms, +the resulting POD potential is a three-body PES. We can express the potential +energy as a linear combination of the global descriptors as follows + +.. math:: + + E(\boldsymbol \eta) = \sum_{m=1}^{N_{\rm e}} c^{(1)}_m d^{(1)}_{m} + \sum_{m=1}^{N_{\rm d}^{(2)}} c^{(2)}_m d^{(2)}_{m} + \sum_{m=1}^{N_{\rm d}^{(3)}} c^{(3)}_m d^{(3)}_{m} + \sum_{m=1}^{N_{\rm d}^{(4)}} c^{(4)}_m d^{(4)}_{m} + +where the global descriptors are given by + +.. math:: + + d_{m}^{(1)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(1)}(\boldsymbol \eta), \quad d_{m}^{(2)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(2)}(\boldsymbol \eta), \quad d_{m}^{(3)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(3)}(\boldsymbol \eta), \quad d_{m}^{(4)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(4)}(\boldsymbol \eta) + +Hence, we obtain the atomic forces as + +.. math:: + + \boldsymbol F = -\nabla E(\boldsymbol \eta) = - \sum_{m=1}^{N_{\rm d}^{(2)}} c^{(2)}_m \nabla d_m^{(2)} - \sum_{m=1}^{N_{\rm d}^{(3)}} c^{(3)}_m \nabla d_m^{(3)} - \sum_{m=1}^{N_{\rm d}^{(4)}} c^{(4)}_m \nabla d_m^{(4)} + +where :math:`\nabla d_m^{(2)}`, :math:`\nabla d_m^{(3)}` and :math:`\nabla d_m^{(4)}` are derivatives of the two-body +three-body, and four-body global descriptors with respect to atom positions, respectively. +Note that since the first-body global descriptors are constant, their derivatives are zero. + +Quadratic Proper Orthogonal Descriptor Potentials +""""""""""""""""""""""""""""""""""""""""""""""""" + +We recall two-body PODs :math:`D^{(2)}_{ik}, 1 \le k \le N_{\rm d}^{(2)}`, +and three-body PODs :math:`D^{(3)}_{im}, 1 \le m \le N_{\rm d}^{(3)}`, +with :math:`N_{\rm d}^{(2)} = N_{\rm 2b} N_{\rm e} (N_{\rm e}+1)/2` and +:math:`N_{\rm d}^{(3)} = N_{\rm 3b} N_{\rm e}^2 (N_{\rm e}+1)/2` being +the number of descriptors per atom for the two-body PODs and three-body PODs, +respectively. We employ them to define a new set of atomic descriptors as follows + +.. math:: + + D^{(2*3)}_{ikm} = \frac{1}{2N}\left( D^{(2)}_{ik} \sum_{j=1}^N D^{(3)}_{jm} + D^{(3)}_{im} \sum_{j=1}^N D^{(2)}_{jk} \right) + +for :math:`1 \le i \le N, 1 \le k \le N_{\rm d}^{(2)}, 1 \le m \le N_{\rm d}^{(3)}`. +The new descriptors are four-body because they involve central atom :math:`i` together +with three neighbors :math:`j, k` and :math:`l`. The total number of new descriptors per atom is equal to + +.. math:: + + N_{\rm d}^{(2*3)} = N_{\rm d}^{(2)} * N_{\rm d}^{(3)} = N_{\rm 2b} N_{\rm 3b} N_{\rm e}^3 (N_{\rm e}+1)^2/4 . + +The new global descriptors are calculated as + +.. math:: + + d^{(2*3)}_{km} = \sum_{i=1}^N D^{(2*3)}_{ikm} = \left( \sum_{i=1}^N D^{(2)}_{ik} \right) \left( \sum_{i=1}^N D^{(3)}_{im} \right) = d^{(2)}_{k} d^{(3)}_m, + +for :math:`1 \le k \le N_{\rm d}^{(2)}, 1 \le m \le N_{\rm d}^{(3)}`. Hence, the gradient +of the new global descriptors with respect to atom positions is calculated as + +.. math:: + + \nabla d^{(2*3)}_{km} = d^{(3)}_m \nabla d^{(2)}_{k} + d^{(2)}_{k} \nabla d^{(3)}_m, \quad 1 \le k \le N_{\rm d}^{(2)}, 1 \le m \le N_{\rm d}^{(3)} . + +The quadratic POD potential is defined as a linear combination of the +original and new global descriptors as follows + +.. math:: + + E^{(2*3)} = \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} d^{(2*3)}_{km} . + +It thus follows that + +.. math:: + + E^{(2*3)} = 0.5 \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} \left( \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} d_m^{(3)} \right) d_k^{(2)} + 0.5 \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} \left( \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} c^{(2*3)}_{km} d_k^{(2)} \right) d_m^{(3)} , + +which is simplified to + +.. math:: + + E^{(2*3)} = 0.5 \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} b_k^{(2)} d_k^{(2)} + 0.5 \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} b_m^{(3)} d_m^{(3)} + +where + +.. math:: + + b_k^{(2)} & = \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} d_m^{(3)}, \quad k = 1,\ldots, N_{\rm 2d}^{(2*3)}, \\ + b_m^{(3)} & = \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} c^{(2*3)}_{km} d_k^{(2)}, \quad m = 1,\ldots, N_{\rm 3d}^{(2*3)} . + +The quadratic POD potential results in the following atomic forces + +.. math:: + + \boldsymbol F^{(2*3)} = - \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} \nabla d^{(2*3)}_{km} . + +It can be shown that + +.. math:: + + \boldsymbol F^{(2*3)} = - \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} b^{(2)}_k \nabla d_k^{(2)} - \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} b^{(3)}_m \nabla d_m^{(3)} . + +The calculation of the atomic forces for the quadratic POD potential +only requires the extra calculation of :math:`b_k^{(2)}` and :math:`b_m^{(3)}` which can be negligible. +As a result, the quadratic POD potential does not increase the computational complexity. + + +Training +"""""""" + +POD potentials are trained using the least-squares regression against +density functional theory (DFT) data. Let :math:`J` be the number of +training configurations, with :math:`N_j` being the number of atoms in +the j-th configuration. Let :math:`\{E^{\star}_j\}_{j=1}^{J}` and +:math:`\{\boldsymbol F^{\star}_j\}_{j=1}^{J}` be the DFT energies and +forces for :math:`J` configurations. Next, we calculate the global +descriptors and their derivatives for all training configurations. Let +:math:`d_{jm}, 1 \le m \le M`, be the global descriptors associated with +the j-th configuration, where :math:`M` is the number of global +descriptors. We then form a matrix :math:`\boldsymbol A \in +\mathbb{R}^{J \times M}` with entries :math:`A_{jm} = d_{jm}/ N_j` for +:math:`j=1,\ldots,J` and :math:`m=1,\ldots,M`. Moreover, we form a +matrix :math:`\boldsymbol B \in \mathbb{R}^{\mathcal{N} \times M}` by +stacking the derivatives of the global descriptors for all training +configurations from top to bottom, where :math:`\mathcal{N} = +3\sum_{j=1}^{J} N_j`. + +The coefficient vector :math:`\boldsymbol c` of the POD potential is +found by solving the following least-squares problem + +.. math:: + + {\min}_{\boldsymbol c \in \mathbb{R}^{M}} \ w_E \|\boldsymbol A(\boldsymbol \eta) \boldsymbol c - \bar{\boldsymbol E}^{\star} \|^2 + w_F \|\boldsymbol B(\boldsymbol \eta) \boldsymbol c + \boldsymbol F^{\star} \|^2 + w_R \|\boldsymbol c \|^2, + +where :math:`w_E` and :math:`w_F` are weights for the energy +(*fitting_weight_energy*) and force (*fitting_weight_force*), +respectively; and :math:`w_R` is the regularization parameter (*fitting_regularization_parameter*). Here :math:`\bar{\boldsymbol E}^{\star} \in +\mathbb{R}^{J}` is a vector of with entries :math:`\bar{E}^{\star}_j = +E^{\star}_j/N_j` and :math:`\boldsymbol F^{\star}` is a vector of +:math:`\mathcal{N}` entries obtained by stacking :math:`\{\boldsymbol +F^{\star}_j\}_{j=1}^{J}` from top to bottom. + +The training procedure is the same for both the linear and quadratic POD +potentials. However, since the quadratic POD potential has a +significantly larger number of the global descriptors, it is more +expensive to train the linear POD potential. This is because the +training of the quadratic POD potential still requires us to calculate +and store the quadratic global descriptors and their +gradient. Furthermore, the quadratic POD potential may require more +training data in order to prevent over-fitting. In order to reduce the +computational cost of fitting the quadratic POD potential and avoid +over-fitting, we can use subsets of two-body and three-body PODs for +constructing the new descriptors. + + +Restrictions +"""""""""""" + +This command is part of the ML-POD package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` page for more info. + +Related commands +"""""""""""""""" + +:doc:`pair_style pod ` + +Default +""""""" + +The keyword defaults are also given in the description of the input files. + +---------- + +.. _Grepl20072: + +**(Grepl)** Grepl, Maday, Nguyen, and Patera, ESAIM: Mathematical Modelling and Numerical Analysis 41(3), 575-605, (2007). + +.. _Nguyen20222: + +**(Nguyen)** Nguyen and Rohskopf, arXiv preprint arXiv:2209.02362 (2022). diff --git a/doc/src/fix.rst b/doc/src/fix.rst index 333e920bd9..d155e70493 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -77,26 +77,31 @@ for individual fixes for info on which ones can be restarted. ---------- -Some fixes calculate one of three styles of quantities: global, -per-atom, or local, which can be used by other commands or output as -described below. A global quantity is one or more system-wide values -(e.g., the energy of a wall interacting with particles). A per-atom -quantity is one or more values per atom (e.g., the displacement vector -for each atom since time 0). Per-atom values are set to 0.0 for atoms -not in the specified fix group. Local quantities are calculated by -each processor based on the atoms it owns, but there may be zero or -more per atoms. +Some fixes calculate one or more of four styles of quantities: global, +per-atom, local, or per-grid, which can be used by other commands or +output as described below. A global quantity is one or more +system-wide values, e.g. the energy of a wall interacting with +particles. A per-atom quantity is one or more values per atom, +e.g. the displacement vector for each atom since time 0. Per-atom +values are set to 0.0 for atoms not in the specified fix group. Local +quantities are calculated by each processor based on the atoms it +owns, but there may be zero or more per atoms. Per-grid quantities +are calculated on a regular 2d or 3d grid which overlays a 2d or 3d +simulation domain. The grid points and the data they store are +distributed across processors; each processor owns the grid points +which fall within its sub-domain. -Note that a single fix can produce either global or per-atom or local -quantities (or none at all), but not both global and per-atom. It can -produce local quantities in tandem with global or per-atom quantities. -The fix page will explain. +Note that a single fix typically produces either global or per-atom or +local or per-grid values (or none at all). It does not produce both +global and per-atom. It can produce local or per-grid values in +tandem with global or per-atom values. The fix doc page will explain +the details. -Global, per-atom, and local quantities each come in three kinds: a -single scalar value, a vector of values, or a 2d array of values. The -doc page for each fix describes the style and kind of values it -produces (e.g., a per-atom vector). Some fixes produce more than one -kind of a single style (e.g., a global scalar and a global vector). +Global, per-atom, local, and per-grid quantities come in three kinds: +a single scalar value, a vector of values, or a 2d array of values. +The doc page for each fix describes the style and kind of values it +produces, e.g. a per-atom vector. Some fixes produce more than one +kind of a single style, e.g. a global scalar and a global vector. When a fix quantity is accessed, as in many of the output commands discussed below, it can be referenced via the following bracket @@ -185,6 +190,7 @@ accelerated styles exist. * :doc:`ave/chunk ` - compute per-chunk time-averaged quantities * :doc:`ave/correlate ` - compute/output time correlations * :doc:`ave/correlate/long ` - alternative to :doc:`ave/correlate ` that allows efficient calculation over long time windows +* :doc:`ave/grid ` - compute per-grid time-averaged quantities * :doc:`ave/histo ` - compute/output time-averaged histograms * :doc:`ave/histo/weight ` - weighted version of fix ave/histo * :doc:`ave/time ` - compute/output global time-averaged quantities @@ -216,9 +222,9 @@ accelerated styles exist. * :doc:`edpd/source ` - add heat source to eDPD simulations * :doc:`efield ` - impose electric field on system * :doc:`ehex ` - enhanced heat exchange algorithm -* :doc:`electrode/conp ` - impose electric potential -* :doc:`electrode/conq ` - impose total electric charge -* :doc:`electrode/thermo ` - apply thermo-potentiostat +* :doc:`electrode/conp ` - impose electric potential +* :doc:`electrode/conq ` - impose total electric charge +* :doc:`electrode/thermo ` - apply thermo-potentiostat * :doc:`electron/stopping ` - electronic stopping power as a friction force * :doc:`electron/stopping/fit ` - electronic stopping power as a friction force * :doc:`enforce2d ` - zero out *z*-dimension velocity and force @@ -360,6 +366,7 @@ accelerated styles exist. * :doc:`saed/vtk ` - time-average the intensities from :doc:`compute saed ` * :doc:`setforce ` - set the force on each atom * :doc:`setforce/spin ` - set magnetic precession vectors on each atom +* :doc:`sgcmc ` - fix for hybrid semi-grand canonical MD/MC simulations * :doc:`shake ` - SHAKE constraints on bonds and/or angles * :doc:`shardlow ` - integration of DPD equations of motion using the Shardlow splitting * :doc:`smd ` - applied a steered MD force to a group diff --git a/doc/src/fix_atom_swap.rst b/doc/src/fix_atom_swap.rst index 0deda8a5f5..39db1f2c17 100644 --- a/doc/src/fix_atom_swap.rst +++ b/doc/src/fix_atom_swap.rst @@ -63,7 +63,8 @@ be needed when running such a hybrid simulation, especially if the swapped atoms are not well equilibrated. The *types* keyword is required. At least two atom types must be -specified. +specified. If not using *semi-grand*, exactly two atom types +are required. The *ke* keyword can be set to *no* to turn off kinetic energy conservation for swaps. The default is *yes*, which means that swapped diff --git a/doc/src/fix_ave_chunk.rst b/doc/src/fix_ave_chunk.rst index 4988064766..3c358c9aa5 100644 --- a/doc/src/fix_ave_chunk.rst +++ b/doc/src/fix_ave_chunk.rst @@ -112,6 +112,17 @@ or atoms in a spatial bin. See the :doc:`compute chunk/atom page for details of how chunks can be defined and examples of how they can be used to measure properties of a system. +Note that if the :doc:`compute chunk/atom ` +command defines spatial bins, the fix ave/chunk command performs a +similar computation as the :doc:`fix ave/grid ` command. +However, the per-bin outputs from the fix ave/chunk command are +global; each processor stores a copy of the entire set of bin data. +By contrast, the :doc:`fix ave/grid ` command uses a +distributed grid where each processor owns a subset of the bins. Thus +it is more efficient to use the :doc:`fix ave/grid ` +command when the grid is large and a simulation is run on many +processors. + Note that only atoms in the specified group contribute to the summing and averaging calculations. The :doc:`compute chunk/atom ` command defines its own group as well as an @@ -141,10 +152,11 @@ quantities. :doc:`Variables ` of style *atom* are the only ones that can be used with this fix since all other styles of variable produce global quantities. -Note that for values from a compute or fix, the bracketed index I can -be specified using a wildcard asterisk with the index to effectively -specify multiple values. This takes the form "\*" or "\*n" or "m\*" or -"m\*n". If :math:`N` is the size of the vector (for *mode* = scalar) or the +Note that for values from a compute or fix that produces a per-atom +array (multiple values per atom), the bracketed index I can be +specified using a wildcard asterisk with the index to effectively +specify multiple values. This takes the form "\*" or "\*n" or "n\*" +or "m\*n". If :math:`N` = the size of the vector (for *mode* = scalar) or the number of columns in the array (for *mode* = vector), then an asterisk with no numeric values means all indices from 1 to :math:`N`. A leading asterisk means all indices from 1 to n (inclusive). A trailing @@ -359,6 +371,8 @@ For the *density/number* and *density/mass* values, the volume (bin volume or system volume) used in the per-sample sum normalization will be the current volume at each sampling step. +---------- + The *ave* keyword determines how the per-chunk values produced every :math:`N_\text{freq}` steps are averaged with values produced on previous steps that were multiples of :math:`N_\text{freq}`, before they are accessed by @@ -385,6 +399,8 @@ of the individual chunk values on time steps 8000, 9000, and 10000. Outputs on early steps will average over less than :math:`M` values if they are not available. +---------- + The *bias* keyword specifies the ID of a temperature compute that removes a "bias" velocity from each atom, specified as *bias-ID*\ . It is only used when the *temp* value is calculated, to compute the @@ -415,6 +431,8 @@ set to the remaining degrees of freedom for the entire molecule (entire chunk in this case), that is, 6 for 3d or 3 for 2d for a rigid molecule. +---------- + The *file* keyword allows a filename to be specified. Every :math:`N_\text{freq}` timesteps, a section of chunk info will be written to a text file in the following format. A line with the timestep and number of @@ -523,12 +541,14 @@ Restrictions Related commands """""""""""""""" -:doc:`compute `, :doc:`fix ave/atom `, -:doc:`fix ave/histo `, :doc:`fix ave/time `, -:doc:`variable `, :doc:`fix ave/correlate ` +:doc:`compute `, :doc:`fix ave/atom `, `fix +:doc:ave/histo `, :doc:`fix ave/time `, +:doc:`variable `, :doc:`fix ave/correlate +:doc:`, `fix ave/atogrid ` + Default """"""" -The option defaults are norm = all, ave = one, bias = none, no file output, and -title 1,2,3 = strings as described above. +The option defaults are norm = all, ave = one, bias = none, no file +output, and title 1,2,3 = strings as described above. diff --git a/doc/src/fix_ave_grid.rst b/doc/src/fix_ave_grid.rst new file mode 100644 index 0000000000..fe22e5e7ef --- /dev/null +++ b/doc/src/fix_ave_grid.rst @@ -0,0 +1,509 @@ +.. index:: fix ave/grid + +fix ave/grid command +===================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID ave/grid Nevery Nrepeat Nfreq Nx Ny Nz value1 value2 ... keyword args ... + +* ID, group-ID are documented in :doc:`fix ` command +* ave/grid = style name of this fix command +* Nevery = use input values every this many timesteps +* Nrepeat = # of times to use input values for calculating averages +* Nfreq = calculate averages every this many timesteps +* Nx, Ny, Nz = grid size in each dimension +* one or more per-atom or per-grid input values can be listed +* per-atom value = vx, vy, vz, fx, fy, fz, density/mass, density/number, mass, temp, c_ID, c_ID[I], f_ID, f_ID[I], v_name + + .. parsed-literal:: + + vx,vy,vz,fx,fy,fz,mass = atom attribute (velocity, force component, mass) + density/number, density/mass = number or mass density (per volume) + temp = temperature + c_ID = per-atom vector calculated by a compute with ID + c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below) + f_ID = per-atom vector calculated by a fix with ID + f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below) + v_name = per-atom vector calculated by an atom-style variable with name + +* per-grid value = c_ID:gname:dname, c_ID:gname:dname[I], f_ID:gname:dname, f_ID:gname:dname[I] + + .. parsed-literal:: + + gname = name of grid defined by compute or fix + dname = name of data field defined by compute or fix + c_ID = per-grid vector calculated by a compute with ID + c_ID[I] = Ith column of per-grid array calculated by a compute with ID, I can include wildcard (see below) + f_ID = per-grid vector calculated by a fix with ID + f_ID[I] = Ith column of per-grid array calculated by a fix with ID, I can include wildcard (see below) + +* zero or more keyword/arg pairs may be appended +* keyword = *discard* or *norm* or *ave* or *bias* or *adof* or *cdof* + + .. parsed-literal:: + + *discard* arg = *yes* or *no* + yes = discard an atom outside grid in a non-periodic dimension + no = remap an atom outside grid in a non-periodic dimension to first or last grid cell + *norm* arg = *all* or *sample* or *none* = how output on *Nfreq* steps is normalized + all = output is sum of atoms across all *Nrepeat* samples, divided by atom count + sample = output is sum of *Nrepeat* sample averages, divided by *Nrepeat* + none = output is sum of *Nrepeat* sample sums, divided by *Nrepeat* + *ave* args = *one* or *running* or *window M* + one = output new average value every Nfreq steps + running = output cumulative average of all previous Nfreq steps + window M = output average of M most recent Nfreq steps + *bias* arg = bias-ID + bias-ID = ID of a temperature compute that removes a velocity bias for temperature calculation + *adof* value = dof_per_atom + dof_per_atom = define this many degrees-of-freedom per atom for temperature calculation + *cdof* value = dof_per_grid_cell + dof_per_grid_cell = add this many degrees-of-freedom per grid_cell for temperature calculation + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix 1 all ave/grid 10000 1 10000 10 10 10 fx fy fz c_myMSD[*] + fix 1 flow ave/grid 100 10 1000 20 20 30 f_TTM:grid:data + +Description +""""""""""" + +Overlay the 2d or 3d simulation box with a uniformly spaced 2d or 3d +grid and use it to either (a) time-average per-atom quantities for the +atoms in each grid cell, or to (b) time-average per-grid quantities +produced by other computes or fixes. This fix operates in either +"per-atom mode" (all input values are per-atom) or in "per-grid mode" +(all input values are per-grid). You cannot use both per-atom and +per-grid inputs in the same command. + +The grid created by this command is distributed; each processor owns +the grid points that are within its sub-domain. This is similar to +the :doc:`fix ave/chunk ` command when it uses chunks +from the :doc:`compute chunk/atom ` command which +are 2d or 3d regular bins. However, the per-bin outputs in that case +are global; each processor stores a copy of the entire set of bin +data. Thus it more efficient to use the fix ave/grid command when the +grid is large and a simulation is run on many processors. + +For per-atom mode, only atoms in the specified group contribute to the +summing and averaging calculations. For per-grid mode, the specified +group is ignored. + +---------- + +The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what +timesteps the input values will be accessed and contribute to the +average. The final averaged quantities are generated on timesteps +that are a multiples of *Nfreq*\ . The average is over *Nrepeat* +quantities, computed in the preceding portion of the simulation every +*Nevery* timesteps. *Nfreq* must be a multiple of *Nevery* and +*Nevery* must be non-zero even if *Nrepeat* is 1. Also, the timesteps +contributing to the average value cannot overlap, i.e. Nrepeat\*Nevery +can not exceed Nfreq. + +For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on +timesteps 90,92,94,96,98,100 will be used to compute the final average +on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on +timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time +averaging is done; values are simply generated on timesteps +100,200,etc. + +In per-atom mode, each input value can also be averaged over the atoms +in each grid cell. The way the averaging is done across the *Nrepeat* +timesteps to produce output on the *Nfreq* timesteps, and across +multiple *Nfreq* outputs, is determined by the *norm* and *ave* +keyword settings, as discussed below. + +---------- + +The *Nx*, *Ny*, and *Nz* arguments specify the size of the grid that +overlays the simulation box. For 2d simulations, *Nz* must be 1. The +*Nx*, *Ny*, *Nz* values can be any positive integer. The grid can be +very coarse compared to the particle count, or very fine. If one or +more of the values = 1, then bins are 2d planes or 1d slices of the +simulation domain. Note that if the total number of grid cells is +small, it may be more efficient to use the doc:`fix ave/chunk +` command which can treat a grid defined by the +:doc:`compute chunk/atom ` command as a global +grid where each processor owns a copy of all the grid cells. If *Nx* += *Ny* = *Nz* = 1 is used, the same calculation would be more +efficiently performed by the doc:`fix ave/atom ` +command. + +If the simulation box size or shape changes during a simulation, the +grid always conforms to the size/shape of the current simulation box. +If one more dimensions have non-periodic shrink-wrapped boundary +conditions, as defined by the :doc:`boundary ` command, then +the grid will extend over the (dynamic) shrink-wrapped extent in each +dimension. If the box shape is triclinic, as explained in :doc:`Howto +triclinic `, then the grid is also triclinic; each +grid cell is a small triclinic cell with the same shape as the +simulation box. + +---------- + +In both per-atom and per-grid mode, input values from a compute or fix +that produces an array of values (multiple values per atom or per grid +point), the bracketed index I can be specified using a wildcard +asterisk with the index to effectively specify multiple values. This +takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of +columns in the array (for *mode* = vector), then an asterisk with no +numeric values means all indices from 1 to N. A leading asterisk +means all indices from 1 to n (inclusive). A trailing asterisk means +all indices from n to N (inclusive). A middle asterisk means all +indices from m to n (inclusive). + +Using a wildcard is the same as if the individual columns of the array +had been listed one by one. E.g. if there were a compute fft/grid +command which produced 3 values for each grid point, these two fix +ave/grid commands would be equivalent: + +.. code-block:: LAMMPS + + compute myFFT all fft/grid 10 10 10 ... + fix 1 all ave/grid 100 1 100 10 10 10 c_myFFT:grid:data[*] + fix 2 all ave/grid 100 1 100 10 10 10 c_myFFT:grid:data[*][1] c_myFFT:grid:data[*][2] c_myFFT:grid:data[3] + +---------- + +*Per-atom mode*: + +Each specified per-atom value can be an atom attribute (velocity, +force component), a number or mass density, a mass or temperature, or +the result of a :doc:`compute ` or :doc:`fix ` or the +evaluation of an atom-style :doc:`variable `. In the latter +cases, the compute, fix, or variable must produce a per-atom quantity, +not a global quantity. Note that the :doc:`compute property/atom +` command provides access to any attribute +defined and stored by atoms. + +The per-atom values of each input vector are summed and averaged +independently of the per-atom values in other input vectors. + +:doc:`Computes ` that produce per-atom quantities are those +which have the word *atom* in their style name. See the doc pages for +individual :doc:`fixes ` to determine which ones produce per-atom +quantities. :doc:`Variables ` of style *atom* are the only +ones that can be used with this fix since all other styles of variable +produce global quantities. + +---------- + +The atom attribute values (vx,vy,vz,fx,fy,fz,mass) are +self-explanatory. As noted above, any other atom attributes can be +used as input values to this fix by using the :doc:`compute +property/atom ` command and then specifying an +input value from that compute. + +The *density/number* value means the number density is computed for +each grid cell, i.e. number/volume. The *density/mass* value means +the mass density is computed for each grid/cell, +i.e. total-mass/volume. The output values are in units of 1/volume or +density (mass/volume). See the :doc:`units ` command page for +the definition of density for each choice of units, e.g. gram/cm\^3. + +The *temp* value computes the temperature for each grid cell, by the +formula + +.. math:: + + \text{KE} = \frac{\text{DOF}}{2} k_B T, + +where KE = total kinetic energy of the atoms in the grid cell ( +:math:`\frac{1}{2} m v^2`), DOF = the total number of degrees of +freedom for all atoms in the grid cell, :math:`k_B` = Boltzmann +constant, and :math:`T` = temperature. + +The DOF is calculated as N\*adof + cdof, where N = number of atoms in +the grid cell, adof = degrees of freedom per atom, and cdof = degrees +of freedom per grid cell. By default adof = 2 or 3 = dimensionality +of system, as set via the :doc:`dimension ` command, and +cdof = 0.0. This gives the usual formula for temperature. + +Note that currently this temperature only includes translational +degrees of freedom for each atom. No rotational degrees of freedom +are included for finite-size particles. Also no degrees of freedom +are subtracted for any velocity bias or constraints that are applied, +such as :doc:`compute temp/partial `, or +:doc:`fix shake ` or :doc:`fix rigid `. This is +because those degrees of freedom (e.g. a constrained bond) could apply +to sets of atoms that are both inside and outside a specific grid +cell, and hence the concept is somewhat ill-defined. In some cases, +you can use the *adof* and *cdof* keywords to adjust the calculated +degrees of freedom appropriately, as explained below. + +Also note that a bias can be subtracted from atom velocities before +they are used in the above formula for KE, by using the *bias* +keyword. This allows, for example, a thermal temperature to be +computed after removal of a flow velocity profile. + +Note that the per-grid-cell temperature calculated by this fix and the +:doc:`compute temp/chunk ` command (using bins) +can be different. The compute calculates the temperature for each +chunk for a single snapshot. This fix can do that but can also time +average those values over many snapshots, or it can compute a +temperature as if the atoms in the grid cell on different timesteps +were collected together as one set of atoms to calculate their +temperature. The compute allows the center-of-mass velocity of each +chunk to be subtracted before calculating the temperature; this fix +does not. + +If a value begins with "c\_", a compute ID must follow which has been +previously defined in the input script. If no bracketed integer is +appended, the per-atom vector calculated by the compute is used. If a +bracketed integer is appended, the Ith column of the per-atom array +calculated by the compute is used. Users can also write code for +their own compute styles and :doc:`add them to LAMMPS `. See +the discussion above for how I can be specified with a wildcard +asterisk to effectively specify multiple values. + +If a value begins with "f\_", a fix ID must follow which has been +previously defined in the input script. If no bracketed integer is +appended, the per-atom vector calculated by the fix is used. If a +bracketed integer is appended, the Ith column of the per-atom array +calculated by the fix is used. Note that some fixes only produce +their values on certain timesteps, which must be compatible with +*Nevery*, else an error results. Users can also write code for their +own fix styles and :doc:`add them to LAMMPS `. See the +discussion above for how I can be specified with a wildcard asterisk +to effectively specify multiple values. + +If a value begins with "v\_", a variable name must follow which has +been previously defined in the input script. Variables of style +*atom* can reference thermodynamic keywords and various per-atom +attributes, or invoke other computes, fixes, or variables when they +are evaluated, so this is a very general means of generating per-atom +quantities to average within grid cells. + +---------- + +*Per-grid mode*: + +The attributes that begin with *c_ID* and *f_ID* both take +colon-separated fields *gname* and *dname*. These refer to a grid +name and data field name which is defined by the compute or fix. Note +that a compute or fix can define one or more grids (of different +sizes) and one or more data fields for each of those grids. The sizes +of all grids used as values for one instance of this fix must be the +same. + +The *c_ID:gname:dname* and *c_ID:gname:dname[I]* attributes allow +per-grid vectors or arrays calculated by a :doc:`compute ` to +be accessed. The ID in the attribute should be replaced by the actual +ID of the compute that has been defined previously in the input +script. + +If *c_ID:gname:dname* is used as a attribute, then the per-grid vector +calculated by the compute is accessed. If *c_ID:gname:dname[I]* is +used, then I must be in the range from 1-M, which will access the Ith +column of the per-grid array with M columns calculated by the compute. +See the discussion above for how I can be specified with a wildcard +asterisk to effectively specify multiple values. + +The *f_ID:gname:dname* and *f_ID:gname:dname[I]* attributes allow +per-grid vectors or arrays calculated by a :doc:`fix ` to be +output. The ID in the attribute should be replaced by the actual ID +of the fix that has been defined previously in the input script. + +If *f_ID:gname:dname* is used as a attribute, then the per-grid vector +calculated by the fix is printed. If *f_ID:gname:dname[I]* is used, +then I must be in the range from 1-M, which will print the Ith column +of the per-grid with M columns calculated by the fix. See the +discussion above for how I can be specified with a wildcard asterisk +to effectively specify multiple values. + +---------- + +Additional optional keywords also affect the operation of this fix and +its outputs. Some are only applicable to per-atom mode. Some are +applicable to both per-atom and per-grid mode. + +The *discard* keyword is only applicable to per-atom mode. If a +dimension of the system is non-periodic, then grid cells will only +span the box dimension (fixed or shrink-wrap boundaries as set by the +:doc:`boundary` command). An atom may thus be slightly outside the +range of grid cells on a particular timestep. If *discard* is set to +*yes* (the default), then the atom will be assigned to the closest +grid cell (lowest or highest) in that dimension. If *discard* is set +to *no* the atom will be ignored. + +---------- + +The *norm* keyword is only applicable to per-atom mode. In per-grid +mode, the *norm* keyword setting is ignored. The output grid value on +an *Nfreq* timestep is the sum of the grid values in each of the +*Nrepeat* samples, divided by *Nrepeat*. + +In per-atom mode, the *norm" keywod affects how averaging is done for +the per-grid values that are output on an *Nfreq* timestep. *Nrepeat* +samples contribute to the output. The *norm* keyword has 3 possible +settings: *all* or *sample* or *none*. *All* is the default. + +In the formulas that follow, SumI is the sum of a per-atom property +over the CountI atoms in a grid cell for a single sample I, where I +varies from 1 to N, and N = Nrepeat. These formulas are used for any +per-atom input value listed above, except *density/number*, +*density/mass*, and *temp*. Those input values are discussed below. + +In per-atom mode, for *norm all* the output grid value on the *Nfreq* +timestep is an average over atoms across the entire *Nfreq* timescale: + +Output = (Sum1 + Sum2 + ... + SumN) / (Count1 + Count2 + ... + CountN) + +In per-atom mode, for *norm sample* the output grid value on the +*Nfreq* timestep is an average of an average: + +Output = (Sum1/Count1 + Sum2/Count2 + ... + SumN/CountN) / Nrepeat + +In per-atom mode, for *norm none* the output grid value on the +*Nfreq* timestep is not normalized by the atom counts: + +Output = (Sum1 + Sum2 + ... SumN) / Nrepeat + +For *density/number* and *density/mass*, the output value is the same +as in the formulas above for *norm all* and *norm sample*, except that +the result is also divided by the grid cell volume. For *norm all*, +this will be the volume at the final *Nfreq* timestep. For *norm +sample*, the divide-by-volume is done for each sample, using the grid +cell volume at the sample timestep. For *norm none*, the output is +the same as for *norm all*. + +For *temp*, the output temperature uses the formula for kinetic energy +KE listed above, and is normalized similarly to the formulas above for +*norm all* and *norm sample*, except for the way the degrees of +freedom (DOF) are calculated. For *norm none*, the output is the same +as for *norm all*. + +For *norm all*, the DOF = *Nrepeat* times *cdof* plus *Count* times +*adof*, where *Count* = (Count1 + Count2 + ... + CountN). The *cdof* +and *adof* keywords are discussed below. The output temperature is +computed with all atoms across all samples contributing. + +For *norm sample*, the DOF for a single sample = *cdof* plus *Count* +times *adof*, where *Count* = CountI for a single sample. The output +temperature is the average of *Nsample* temperatures calculated for +each sample. + +Finally, for all 3 *norm* settings the output count of atoms per grid +cell is: + +Output count = (Count1 + Count2 + ... CountN) / Nrepeat + +This count is the same for all per-atom input values, including +*density/number*, *density/mass*, and *temp*. + +---------- + +The *ave* keyword is applied to both per-atom and per-grid mode. It +determines how the per-grid values produced once every *Nfreq* steps +are averaged with values produced on previous steps that were +multiples of *Nfreq*, before they are accessed by another output +command. + +If the *ave* setting is *one*, which is the default, then the grid +values produced on *Nfreq* timesteps are independent of each other; +they are output as-is without further averaging. + +If the *ave* setting is *running*, then the grid values produced on +*Nfreq* timesteps are summed and averaged in a cumulative sense before +being output. Each output grid value is thus the average of the grid +value produced on that timestep with all preceding values for the same +grid value. This running average begins when the fix is defined; it +can only be restarted by deleting the fix via the :doc:`unfix ` +command, or re-defining the fix by re-specifying it. + +If the *ave* setting is *window*, then the grid values produced on +*Nfreq* timesteps are summed and averaged within a moving "window" of +time, so that the last M values for the same grid are used to produce +the output. E.g. if M = 3 and Nfreq = 1000, then the grid value +output on step 10000 will be the average of the grid values on steps +8000,9000,10000. Outputs on early steps will average over less than M +values if they are not available. + +---------- + +The *bias*, *adof*, and *cdof* keywords are only applicable to +per-atom mode. + +The *bias* keyword specifies the ID of a temperature compute that +removes a "bias" velocity from each atom, specified as *bias-ID*\ . +It is only used when the *temp* value is calculated, to compute the +thermal temperature of each grid cell after the translational kinetic +energy components have been altered in a prescribed way, e.g. to +remove a flow velocity profile. See the doc pages for individual +computes that calculate a temperature to see which ones implement a +bias. + +The *adof* and *cdof* keywords define the values used in the degree of +freedom (DOF) formula described above for temperature calculation for +each grid cell. They are only used when the *temp* value is +calculated. They can be used to calculate a more appropriate +temperature in some cases. Here are 3 examples: + +If grid cells contain some number of water molecules and :doc:`fix +shake ` is used to make each molecule rigid, then you could +calculate a temperature with 6 degrees of freedom (DOF) (3 +translational, 3 rotational) per molecule by setting *adof* to 2.0. + +If :doc:`compute temp/partial ` is used with the +*bias* keyword to only allow the x component of velocity to contribute +to the temperature, then *adof* = 1.0 would be appropriate. + +Using *cdof* = -2 or -3 (for 2d or 3d simulations) will subtract out 2 +or 3 degrees of freedom for each grid cell, similar to how the +:doc:`compute temp ` command subtracts out 3 DOF for the +entire system. + +---------- + +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files +`. None of the :doc:`fix_modify ` options are +relevant to this fix. + +This fix calculates a per-grid array which has one column for each of +the specified input values. The units for each column with be in the +:doc:`units ` for the per-atom or per-grid quantity for the +corresponding input value. If the fix is used in per-atom mode, it +also calculates a per-grid vector with the count of atoms in each grid +cell. The number of rows in the per-grid array and number of values +in the per-grid vector (distributed across all processors) is Nx * +Ny * Nz. + +For access by other commands, the name of the single grid produced by +this fix is "grid". The names of its two per-grid datums are "data" +for the per-grid array and "count" for the per-grid vector (if using +per-atom values). Both datums can be accessed by various :doc:`output +commands `. + +In per-atom mode, the per-grid array values calculated by this fix are +treated as "intensive", since they are typically already normalized by +the count of atoms in each grid cell. + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during +:doc:`energy minimization `. + +Restrictions +"""""""""""" +none + +Related commands +"""""""""""""""" + +:doc:`fix ave/atom `, :doc:`fix ave/chunk ` + +Default +""""""" + +The option defaults are discard = yes, norm = all, ave = one, and bias += none. diff --git a/doc/src/fix_ave_spatial.rst b/doc/src/fix_ave_spatial.rst new file mode 100644 index 0000000000..96d87bd8db --- /dev/null +++ b/doc/src/fix_ave_spatial.rst @@ -0,0 +1,9 @@ +Fix ave/spatial command +======================= + +.. meta:: + :http-equiv=Refresh: 5; url='https://docs.lammps.org/Commands_removed.html#fix-ave-spatial-and-fix-ave-spatial-sphere' + +.. deprecated:: 11Dec2015 + +The `fix ave/spatial` command has been superseded by :doc:`fix ave/chunk `. diff --git a/doc/src/fix_ave_spatial_sphere.rst b/doc/src/fix_ave_spatial_sphere.rst new file mode 100644 index 0000000000..a3cacc4115 --- /dev/null +++ b/doc/src/fix_ave_spatial_sphere.rst @@ -0,0 +1,9 @@ +Fix ave/spatial command +======================= + +.. meta:: + :http-equiv=Refresh: 5; url='https://docs.lammps.org/Commands_removed.html#fix-ave-spatial-and-fix-ave-spatial-sphere' + +.. deprecated:: 11Dec2015 + +The `fix ave/spatial/sphere` command has been superseded by :doc:`fix ave/chunk `. diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index 85683f0ddd..5385bec5b9 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -42,13 +42,16 @@ Syntax * template-ID(post-reacted) = ID of a molecule template containing post-reaction topology * map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates * zero or more individual keyword/value pairs may be appended to each react argument -* individual_keyword = *prob* or *max_rxn* or *stabilize_steps* or *custom_charges* or *molecule* or *modify_create* +* individual_keyword = *prob* or *rate_limit* or *max_rxn* or *stabilize_steps* or *custom_charges* or *rescale_charges* or *molecule* or *modify_create* .. parsed-literal:: *prob* values = fraction seed fraction = initiate reaction with this probability if otherwise eligible seed = random number seed (positive integer) + *rate_limit* = Nlimit Nsteps + Nlimit = maximum number of reactions allowed to occur within interval + Nsteps = the interval (number of timesteps) over which to count reactions *max_rxn* value = N N = maximum number of reactions allowed to occur *stabilize_steps* value = timesteps @@ -56,6 +59,9 @@ Syntax *custom_charges* value = *no* or fragment-ID *no* = update all atomic charges (default) fragment-ID = ID of molecule fragment whose charges are updated + *rescale_charges* value = *no* or *yes* + *no* = do not rescale atomic charges (default) + *yes* = rescale charges such that total charge does not change during reaction *molecule* value = *off* or *inter* or *intra* *off* = allow both inter- and intramolecular reactions (default) *inter* = search for reactions between molecules with different IDs @@ -171,12 +177,12 @@ due to the internal dynamic grouping performed by fix bond/react. If the group-ID is an existing static group, react-group-IDs should also be specified as this static group or a subset. -The *reset_mol_ids* keyword invokes the :doc:`reset_mol_ids ` -command after a reaction occurs, to ensure that molecule IDs are -consistent with the new bond topology. The group-ID used for -:doc:`reset_mol_ids ` is the group-ID for this fix. -Resetting molecule IDs is necessarily a global operation, so it can -be slow for very large systems. +The *reset_mol_ids* keyword invokes the :doc:`reset_atoms mol +` command after a reaction occurs, to ensure that +molecule IDs are consistent with the new bond topology. The group-ID +used for :doc:`reset_atoms mol ` is the group-ID for this +fix. Resetting molecule IDs is necessarily a global operation, so it +can be slow for very large systems. The following comments pertain to each *react* argument (in other words, they can be customized for each reaction, or reaction step): @@ -404,6 +410,12 @@ atoms are present. The velocity of each created atom is initialized in a random direction with a magnitude calculated from the instantaneous temperature of the reaction site. +.. note:: + + The 'Coords' section must be included in the post-reaction template + when creating atoms because these coordinates are used to determine + where new atoms are inserted. + The handedness of atoms that are chiral centers can be enforced by listing their IDs in the ChiralIDs section. A chiral atom must be bonded to four atoms with mutually different atom types. This feature @@ -508,28 +520,40 @@ example, the molecule fragment could consist of only the backbone atoms of a polymer chain. This constraint can be used to enforce a specific relative position and orientation between reacting molecules. +.. versionchanged:: 22Dec2022 + The constraint of type "custom" has the following syntax: .. parsed-literal:: custom *varstring* -where "custom" is the required keyword, and *varstring* is a -variable expression. The expression must be a valid equal-style -variable formula that can be read by the :doc:`variable ` command, +where 'custom' is the required keyword, and *varstring* is a variable +expression. The expression must be a valid equal-style variable +formula that can be read by the :doc:`variable ` command, after any special reaction functions are evaluated. If the resulting expression is zero, the reaction is prevented from occurring; -otherwise, it is permitted to occur. There are two special reaction -functions available, "rxnsum" and "rxnave". These functions operate -over the atoms in a given reaction site, and have one mandatory -argument and one optional argument. The mandatory argument is the -identifier for an atom-style variable. The second, optional argument -is the name of a molecule fragment in the pre-reaction template, and -can be used to operate over a subset of atoms in the reaction site. -The "rxnsum" function sums the atom-style variable over the reaction -site, while the "rxnave" returns the average value. For example, a -constraint on the total potential energy of atoms involved in the -reaction can be imposed as follows: +otherwise, it is permitted to occur. There are three special reaction +functions available, 'rxnbond', 'rxnsum', and 'rxnave'. The 'rxnbond' +function allows per-bond values to be included in the variable strings +of the custom constraint. The 'rxnbond' function has two mandatory +arguments. The first argument is the ID of a previously defined +'compute bond/local' command. This 'compute bond/local' must compute +only one value, e.g. bond force. This value is returned by the +'rxnbond' function. The second argument is the name of a molecule +fragment in the pre-reaction template. The fragment must contain +exactly two atoms, corresponding to the atoms involved in the bond +whose value should be calculated. An example of a constraint that uses +the force experienced by a bond is provided below. The 'rxnsum' and +'rxnave' functions operate over the atoms in a given reaction site, +and have one mandatory argument and one optional argument. The +mandatory argument is the identifier for an atom-style variable. The +second, optional argument is the name of a molecule fragment in the +pre-reaction template, and can be used to operate over a subset of +atoms in the reaction site. The 'rxnsum' function sums the atom-style +variable over the reaction site, while the 'rxnave' returns the +average value. For example, a constraint on the total potential energy +of atoms involved in the reaction can be imposed as follows: .. code-block:: LAMMPS @@ -541,11 +565,32 @@ reaction can be imposed as follows: custom "rxnsum(v_my_pe) > 100" # in Constraints section of map file The above example prevents the reaction from occurring unless the -total potential energy of the reaction site is above 100. The variable -expression can be interpreted as the probability of the reaction -occurring by using an inequality and the :doc:`random(x,y,z) ` -function available for equal-style variables, similar to the 'arrhenius' -constraint above. +total potential energy of the reaction site is above 100. As a second +example, this time using the 'rxnbond' function, consider a modified +Arrhenius constraint that depends on the bond force of a specific bond: + +.. code-block:: LAMMPS + + # in LAMMPS input script + + compute bondforce all bond/local force + + compute ke_atom all ke/atom + variable ke atom c_ke_atom + + variable E_a equal 100.0 # activation energy + variable l0 equal 1.0 # characteristic length + + +.. code-block:: LAMMPS + + # in Constraints section of map file + + custom "exp(-(v_E_a-rxnbond(c_bondforce,bond1frag)*v_l0)/(2/3*rxnave(v_ke))) < random(0,1,12345)" + +By using an inequality and the 'random(x,y,z)' function, the left-hand +side can be interpreted as the probability of the reaction occurring, +similar to the 'arrhenius' constraint above. By default, all constraints must be satisfied for the reaction to occur. In other words, constraints are evaluated as a series of @@ -592,6 +637,15 @@ eligible reaction only occurs if the random number is less than the fraction. Up to :math:`N` reactions are permitted to occur, as optionally specified by the *max_rxn* keyword. +.. versionadded:: 22Dec2022 + +The *rate_limit* keyword can enforce an upper limit on the overall +rate of the reaction. The number of reaction occurrences is limited to +Nlimit within an interval of Nsteps timesteps. No reactions are +permitted to occur within the first Nsteps timesteps of the first run +after reading a data file. Nlimit can be specified with an equal-style +:doc:`variable `. + The *stabilize_steps* keyword allows for the specification of how many time steps a reaction site is stabilized before being returned to the overall system thermostat. In order to produce the most physical @@ -610,6 +664,19 @@ charges are updated to those specified by the post-reaction template fragment defined in the pre-reaction molecule template. In this case, only the atomic charges of atoms in the molecule fragment are updated. +.. versionadded:: 22Dec2022 + +The *rescale_charges* keyword can be used to ensure the total charge +of the system does not change as reactions occur. When the argument is +set to *yes*\ , a fixed value is added to the charges of post-reaction +atoms such that their total charge equals that of the pre-reaction +site. If only a subset of atomic charges are updated via the +*custom_charges* keyword, this rescaling is applied to the subset. +This keyword could be useful for systems that contain different +molecules with the same reactive site, if the partial charges on the +reaction site vary from molecule to molecule, or when removing +reaction by-products. + The *molecule* keyword can be used to force the reaction to be intermolecular, intramolecular or either. When the value is set to *off*\ , molecule IDs are not considered when searching for reactions diff --git a/doc/src/fix_charge_regulation.rst b/doc/src/fix_charge_regulation.rst index 82bcf3d69d..c1e790c691 100644 --- a/doc/src/fix_charge_regulation.rst +++ b/doc/src/fix_charge_regulation.rst @@ -94,12 +94,9 @@ insert (delete) a proton (atom type 2). Besides, the fix implements self-ionization reaction of water :math:`\emptyset \rightleftharpoons \mathrm{H}^++\mathrm{OH}^-`. - - -However, this approach is highly -inefficient at :math:`\mathrm{pH} \approx 7` when the concentration of -both protons and hydroxyl ions is low, resulting in a relatively low -acceptance rate of MC moves. +However, this approach is highly inefficient at :math:`\mathrm{pH} +\approx 7` when the concentration of both protons and hydroxyl ions is +low, resulting in a relatively low acceptance rate of MC moves. A more efficient way is to allow salt ions to participate in ionization reactions, which can be easily achieved via @@ -108,10 +105,13 @@ reactions, which can be easily achieved via fix acid_reaction2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 5.0 pIp 2.0 pIm 2.0 -where particles of atom type 4 and 5 are the salt cations and anions, both at activity (effective concentration) of :math:`10^{-2}` mol/l, see :ref:`(Curk1) ` and -:ref:`(Landsgesell) ` for more details. +where particles of atom type 4 and 5 are the salt cations and anions, +both at activity (effective concentration) of :math:`10^{-2}` mol/l, see +:ref:`(Curk1) ` and :ref:`(Landsgesell) ` for more +details. -We could have simultaneously added a base ionization reaction (:math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{OH}^-`) +We could have simultaneously added a base ionization reaction +(:math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{OH}^-`) .. code-block:: LAMMPS @@ -122,7 +122,18 @@ where the fix will attempt to charge :math:`\mathrm{B}` (discharge insert (delete) a hydroxyl ion :math:`\mathrm{OH}^-` of atom type 3. -Dissociated ions and salt ions can be combined into a single particle type, which reduces the number of necessary MC moves and increases sampling performance, see :ref:`(Curk1) `. The :math:`\mathrm{H}^+` and monovalent salt cation (:math:`\mathrm{S}^+`) are combined into a single particle type, :math:`\mathrm{X}^+ = \{\mathrm{H}^+, \mathrm{S}^+\}`. In this case "pIp" refers to the effective concentration of the combined cation type :math:`\mathrm{X}^+` and its value is determined by :math:`10^{-\mathrm{pIp}} = 10^{-\mathrm{pH}} + 10^{-\mathrm{pSp}}`, where :math:`10^{-\mathrm{pSp}}` is the effective concentration of salt cations. For example, at pH=7 and pSp=6 we would find pIp~5.958 and the command that performs reactions with combined ions could read, +Dissociated ions and salt ions can be combined into a single particle +type, which reduces the number of necessary MC moves and increases +sampling performance, see :ref:`(Curk1) `. The +:math:`\mathrm{H}^+` and monovalent salt cation (:math:`\mathrm{S}^+`) +are combined into a single particle type, :math:`\mathrm{X}^+ = +\{\mathrm{H}^+, \mathrm{S}^+\}`. In this case "pIp" refers to the +effective concentration of the combined cation type :math:`\mathrm{X}^+` +and its value is determined by :math:`10^{-\mathrm{pIp}} = +10^{-\mathrm{pH}} + 10^{-\mathrm{pSp}}`, where +:math:`10^{-\mathrm{pSp}}` is the effective concentration of salt +cations. For example, at pH=7 and pSp=6 we would find pIp~5.958 and the +command that performs reactions with combined ions could read, .. code-block:: LAMMPS @@ -138,16 +149,16 @@ If neither the acid or the base type is specified, for example, the fix simply inserts or deletes an ion pair of a free cation (atom type 4) and a free anion (atom type 5) as done in a conventional -grand-canonical MC simulation. Multivalent ions can be inserted (deleted) by using the *onlysalt* keyword. +grand-canonical MC simulation. Multivalent ions can be inserted +(deleted) by using the *onlysalt* keyword. - -The fix is compatible with LAMMPS sub-packages such as *molecule* or -*rigid*. The acid and base particles can be part of larger -molecules or rigid bodies. Free ions that are inserted to or deleted -from the system must be defined as single particles (no bonded -interactions allowed) and cannot be part of larger molecules or rigid -bodies. If *molecule* package is used, all inserted ions have a molecule -ID equal to zero. +This fix is compatible with LAMMPS packages such as MOLECULE or +RIGID. The acid and base particles can be part of larger molecules or +rigid bodies. Free ions that are inserted to or deleted from the system +must be defined as single particles (no bonded interactions allowed) and +cannot be part of larger molecules or rigid bodies. If an atom style +with molecule IDs is used, all inserted ions have a molecule ID equal to +zero. Note that LAMMPS implicitly assumes a constant number of particles (degrees of freedom). Since using this fix alters the total number of @@ -164,14 +175,15 @@ Langevin thermostat: fix fT all langevin 1.0 1.0 1.0 123 fix_modify fT temp dtemp -The units of pH, pKa, pKb, pIp, pIm are considered to be in the standard -log10 -representation assuming reference concentration :math:`\rho_0 = -\mathrm{mol}/\mathrm{l}`. For example, in the dilute +The units of pH, pKa, pKb, pIp, pIm are considered to be in the +standard -log10 representation assuming reference concentration +:math:`\rho_0 = \mathrm{mol}/\mathrm{l}`. For example, in the dilute ideal solution limit, the concentration of free cations will be -:math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`. To perform the internal unit -conversion, the the value of the LAMMPS unit length must be -specified in nanometers via *lunit_nm*. The default value is set to the Bjerrum length in water -at room temperature (0.71 nm), *lunit_nm* = 0.71. +:math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`. To +perform the internal unit conversion, the the value of the LAMMPS unit +length must be specified in nanometers via *lunit_nm*. The default value +is set to the Bjerrum length in water at room temperature (0.71 nm), +*lunit_nm* = 0.71. The temperature used in MC acceptance probability is set by *temp*. This temperature should be the same as the temperature set by the molecular @@ -236,9 +248,9 @@ quantities: Restrictions """""""""""" -This fix is part of the MC package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package -` page for more info. +This fix is part of the MC package. It is only enabled if LAMMPS was +built with that package. See the :doc:`Build package ` +page for more info. The :doc:`atom_style `, used must contain the charge property, for example, the style could be *charge* or *full*. Only diff --git a/doc/src/fix_dt_reset.rst b/doc/src/fix_dt_reset.rst index 368a3dcd70..5757f0ec99 100644 --- a/doc/src/fix_dt_reset.rst +++ b/doc/src/fix_dt_reset.rst @@ -1,8 +1,11 @@ .. index:: fix dt/reset +.. index:: fix dt/reset/kk fix dt/reset command ==================== +Accelerator Variants: *dt/reset/kk* + Syntax """""" @@ -86,6 +89,10 @@ allows dump files to be written at intervals specified by simulation time, rather than by timesteps. Simulation time is in time units; see the :doc:`units ` doc page for details. +---------- + +.. include:: accel_styles.rst + Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" diff --git a/doc/src/fix_electrode.rst b/doc/src/fix_electrode.rst new file mode 100644 index 0000000000..3d543f08d2 --- /dev/null +++ b/doc/src/fix_electrode.rst @@ -0,0 +1,421 @@ +.. index:: fix electrode/conp +.. index:: fix electrode/conq +.. index:: fix electrode/thermo +.. index:: fix electrode/conp/intel +.. index:: fix electrode/conq/intel +.. index:: fix electrode/thermo/intel + +fix electrode/conp command +========================== + +Accelerator Variant: *electrode/conp/intel* + +fix electrode/conq command +========================== + +Accelerator Variant: *electrode/conq/intel* + +fix electrode/thermo command +============================ + +Accelerator Variant: *electrode/thermo/intel* + +Syntax +"""""" + +.. code-block:: LAMMPS + + fix ID group-ID style args keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* style = *electrode/conp* or *electrode/conq* or *electrode/thermo* +* args = arguments used by a particular style + + .. parsed-literal:: + + *electrode/conp* args = potential eta + *electrode/conq* args = charge eta + *electrode/thermo* args = potential eta *temp* values + potential = electrode potential + charge = electrode charge + eta = reciprocal width of electrode charge smearing + *temp* values = T_v tau_v rng_v + T_v = temperature of thermo-potentiostat + tau_v = time constant of thermo-potentiostat + rng_v = integer used to initialize random number generator + +* zero or more keyword/value pairs may be appended +* keyword = *algo* or *symm* or *couple* or *etypes* or *ffield* or *write_mat* or *write_inv* or *read_mat* or *read_inv* + +.. parsed-literal:: + + *algo* values = *mat_inv* or *mat_cg* tol or *cg* tol + specify the algorithm used to compute the electrode charges + *symm* value = *on* or *off* + turn on/off charge neutrality constraint for the electrodes + *couple* values = group-ID val + group-ID = group of atoms treated as additional electrode + val = electric potential or charge on this electrode + *etypes* value = *on* or *off* + turn on/off type-based optimized neighbor lists (electrode and electrolyte types may not overlap) + *ffield* value = *on* or *off* + turn on/off finite-field implementation + *write_mat* value = filename + filename = file to which to write elastance matrix + *write_inv* value = filename + filename = file to which to write inverted matrix + *read_mat* value = filename + filename = file from which to read elastance matrix + *read_inv* value = filename + filename = file from which to read inverted matrix + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix fxconp bot electrode/conp -1.0 1.805 couple top 1.0 couple ref 0.0 write_inv inv.csv symm on + fix fxconp electrodes electrode/conq 0.0 1.805 algo cg 1e-5 + fix fxconp bot electrode/thermo -1.0 1.805 temp 298 100 couple top 1.0 + +Description +""""""""""" + +The *electrode* fixes implement the constant potential method (CPM) +(:ref:`Siepmann `, :ref:`Reed `), and modern variants, +to accurately model electrified, conductive electrodes. This is +primarily useful for studying electrode-electrolyte interfaces, +especially at high potential differences or ionicities, with non-planar +electrodes such as nanostructures or nanopores, and to study dynamic +phenomena such as charging or discharging time scales or conductivity or +ionic diffusivities. + +Each *electrode* fix allows users to set additional electrostatic +relationships between the specified groups which model useful +electrostatic configurations: + +* *electrode/conp* sets potentials or potential differences between electrodes + + * (resulting in changing electrode total charges) + +* *electrode/conq* sets the total charge on each electrode + + * (resulting in changing electrode potentials) + +* *electrode/thermo* sets a thermopotentiostat + :ref:`(Deissenbeck)` between two electrodes + + * (resulting in changing charges and potentials with appropriate + average potential difference and thermal variance) + +The first group-ID provided to each fix specifies the first electrode +group, and more group(s) are added using the *couple* keyword for each +additional group. While *electrode/thermo* only accepts two groups, +*electrode/conp* and *electrode/conq* accept any number of groups, up to +LAMMPS's internal restrictions (see Restrictions below). Electrode +groups must not overlap, i.e. the fix will issue an error if any +particle is detected to belong to at least two electrode groups. + +CPM involves updating charges on groups of electrode particles, per time +step, so that the system's total energy is minimized with respect to +those charges. From basic electrostatics, this is equivalent to making +each group conductive, or imposing an equal electrostatic potential on +every particle in the same group (hence the name CPM). The charges are +usually modelled as a Gaussian distribution to make the charge-charge +interaction matrix invertible (:ref:`Gingrich `). The keyword +*eta* specifies the distribution's width in units of inverse length. + +.. versionadded:: 22Dec2022 + +Three algorithms are available to minimize the energy, varying in how +matrices are pre-calculated before a run to provide computational +speedup. These algorithms can be selected using the keyword *algo*: + +* *algo mat_inv* pre-calculates the capacitance matrix and obtains the + charge configuration in one matrix-vector calculation per time step + +* *algo mat_cg* pre-calculates the elastance matrix (inverse of + capacitance matrix) and obtains the charge configuration using a + conjugate gradient solver in multiple matrix-vector calculations per + time step + +* *algo cg* does not perform any pre-calculation and obtains the charge + configuration using a conjugate gradient solver and multiple + calculations of the electric potential per time step. + +For both *cg* methods, the command must specify the conjugate gradient +tolerance. *fix electrode/thermo* currently only supports the *mat_inv* +algorithm. + +The keyword *symm* can be set *on* (or *off*) to turn on (or turn off) +the capacitance matrix constraint that sets total electrode charge to be +zero. This has slightly different effects for each *fix electrode* +variant. For *fix electrode/conp*, with *symm off*, the potentials +specified are absolute potentials, but the charge configurations +satisfying them may add up to an overall non-zero, varying charge for +the electrodes (and thus the simulation box). With *symm on*, the total +charge over all electrode groups is constrained to zero, and potential +differences rather than absolute potentials are the physically relevant +quantities. + +For *fix electrode/conq*, with *symm off*, overall neutrality is +explicitly obeyed or violated by the user input (which is not +checked!). With *symm on*, overall neutrality is ensured by ignoring the +user-input charge for the last listed electrode (instead, its charge +will always be minus the total sum of all other electrode charges). For +*fix electrode/thermo*, overall neutrality is always automatically +imposed for any setting of *symm*, but *symm on* allows finite-field +mode (*ffield on*, described below) for faster simulations. + +For all three fixes, any potential (or charge for *conq*) can be +specified as an equal-style variable prefixed with "v\_". For example, +the following code will ramp the potential difference between electrodes +from 0.0V to 2.0V over the course of the simulation: + +.. code-block:: LAMMPS + + fix fxconp bot electrode/conp 0.0 1.805 couple top v_v symm on + variable v equal ramp(0.0, 2.0) + +Note that these fixes only parse their supplied variable name when +starting a run, and so these fixes will accept equal-style variables +defined *after* the fix definition, including variables dependent on the +fix's own output. This is useful, for example, in the fix's internal +finite-field commands (see below). For an advanced example of this see +the in.conq2 input file in the directory +``examples/PACKAGES/electrode/graph-il``. + +This fix necessitates the use of a long range solver that calculates and +provides the matrix of electrode-electrode interactions and a vector of +electrode-electrolyte interactions. The Kspace styles +*ewald/electrode*, *pppm/electrode* and *pppm/electrode/intel* are +created specifically for this task :ref:`(Ahrens-Iwers) `. + +For systems with non-periodic boundaries in one or two directions dipole +corrections are available with the :doc:`kspace_modify `. +For ewald/electrode a two-dimensional Ewald summation :ref:`(Hu) ` +can be used by setting "slab ew2d": + +.. code-block:: LAMMPS + + kspace_modify slab + kspace_modify wire + kspace_modify slab ew2d + +Two implementations for the calculation of the elastance matrix are +available with pppm and can be selected using the *amat onestep/twostep* +keyword. *onestep* is the default; *twostep* can be faster for large +electrodes and a moderate mesh size but requires more memory. + +.. code-block:: LAMMPS + + kspace_modify amat onestep/twostep + +For all versions of the fix, the keyword-value *ffield on* enables the +finite-field mode (:ref:`Dufils `, :ref:`Tee `), which uses +an electric field across a periodic cell instead of non-periodic +boundary conditions to impose a potential difference between the two +electrodes bounding the cell. The fix (with name *fix-ID*) detects which +of the two electrodes is "on top" (has the larger maximum *z*-coordinate +among all particles). Assuming the first electrode group is on top, it +then issues the following commands internally: + +.. code-block:: LAMMPS + + variable fix-ID_ffield_zfield equal (f_fix-ID[2]-f_fix-ID[1])/lz + efield fix-ID_efield all efield 0.0 0.0 v_fix-ID_ffield_zfield + +which implements the required electric field as the potential difference +divided by cell length. The internal commands use variable so that the +electric field will correctly vary with changing potentials in the +correct way (for example with equal-style potential difference or with +*fix electrode/conq*). This keyword requires two electrodes and will +issue an error with any other number of electrodes. This keyword +requires electroneutrality to be imposed (*symm on*) and will issue an +error otherwise. + +.. versionchanged:: 22Dec2022 + +For all versions of the fix, the keyword-value *etypes on* enables +type-based optimized neighbor lists. With this feature enabled, LAMMPS +provides the fix with an occasional neighbor list restricted to +electrode-electrode interactions for calculating the electrode matrix, +and a perpetual neighbor list restricted to electrode-electrolyte +interactions for calculating the electrode potentials, using particle +types to list only desired interactions, and typically resulting in +5--10\% less computational time. Without this feature the fix will +simply use the active pair style's neighbor list. This feature cannot +be enabled if any electrode particle has the same type as any +electrolyte particle (which would be unusual in a typical simulation) +and the fix will issue an error in that case. + +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix currently does not write any information to restart files. + +The *fix_modify tf* option enables the Thomas-Fermi metallicity model +(:ref:`Scalfi `) and allows parameters to be set for each atom type. + +.. code-block:: LAMMPS + + fix_modify ID tf type length voronoi + + +If this option is used parameters must be set for all atom types of the +electrode. + +The *fix_modify timer* option turns on (off) additional timer outputs in the log +file, for code developers to track optimization. + +.. code-block:: LAMMPS + + fix_modify ID timer on/off + +---------- + +These fixes compute a global (extensive) scalar, a global (intensive) +vector, and a global array, which can be accessed by various +:doc:`output commands `. + +The global scalar outputs the energy added to the system by this fix, +which is the negative of the total charge on each electrode multiplied +by that electrode's potential. + +The global vector outputs the potential on each electrode (and thus has +*N* entries if the fix manages *N* electrode groups), in :doc:`units +` of electric field multiplied by distance (thus volts for *real* +and *metal* units). The electrode groups' ordering follows the order in +which they were input in the fix command using *couple*. The global +vector output is useful for *fix electrode/conq* and *fix +electrode/thermo*, where potential is dynamically updated based on +electrolyte configuration instead of being directly set. + +The global array has *N* rows and *2N+1* columns, where the fix manages +*N* electrode groups managed by the fix. For the *I*-th row of the +array, the elements are: + +* array[I][1] = total charge that group *I* would have had *if it were + at 0 V applied potential* * array[I][2 to *N* + 1] = the *N* entries + of the *I*-th row of the electrode capacitance matrix (definition + follows) * array[I][*N* + 2 to *2N* + 1] = the *N* entries of the + *I*-th row of the electrode elastance matrix (the inverse of the + electrode capacitance matrix) + +The :math:`N \times N` electrode capacitance matrix, denoted :math:`\mathbf{C}` +in the following equation, summarizes how the total charge induced on each +electrode (:math:`\mathbf{Q}` as an *N*-vector) is related to the potential on +each electrode, :math:`\mathbf{V}`, and the charge-at-0V :math:`\mathbf{Q}_{0V}` +(which is influenced by the local electrolyte structure): + +.. math:: + + \mathbf{Q} = \mathbf{Q}_{0V} + \mathbf{C} \cdot \mathbf{V} + +The charge-at-0V, electrode capacitance and elastance matrices are internally +used to calculate the potentials required to induce the specified total +electrode charges in *fix electrode/conq* and *fix electrode/thermo*. With the +*symm on* option, the electrode capacitance matrix would be singular, and thus +its last row is replaced with *N* copies of its top-left entry +(:math:`\mathbf{C}_{11}`) for invertibility. + +The global array output is mainly useful for quickly determining the 'vacuum +capacitance' of the system (capacitance with only electrodes, no electrolyte), +and can also be used for advanced simulations setting the potential as some +function of the charge-at-0V (such as the ``in.conq2`` example mentioned above). + +Please cite :ref:`(Ahrens-Iwers2022) ` in any publication that +uses this implementation. Please cite also the publication on the combination +of the CPM with PPPM if you use *pppm/electrode* :ref:`(Ahrens-Iwers) +`. + +---------- + +Restrictions +"""""""""""" + +For algorithms that use a matrix for the electrode-electrode +interactions, positions of electrode particles have to be immobilized at +all times. + +With *ffield off* (i.e. the default), the box geometry is expected to be +*z*-non-periodic (i.e. *boundary p p f*), and this fix will issue an +error if the box is *z*-periodic. With *ffield on*, the box geometry is +expected to be *z*-periodic, and this fix will issue an error if the box +is *z*-non-periodic. + +The parallelization for the fix works best if electrode atoms are evenly +distributed across processors. For a system with two electrodes at the bottom +and top of the cell this can be achieved with *processors * * 2*, or with the +line + +.. code-block:: LAMMPS + + if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +which avoids an error if the script is run on an odd number of +processors (such as on just one processor for testing). + +The fix creates an additional group named *[fix-ID]_group* which is the +union of all electrode groups supplied to LAMMPS. This additional group +counts towards LAMMPS's limitation on the total number of groups +(currently 32), which may not allow scripts that use that many groups to +run with this fix. + +The matrix-based algorithms (*algo mat_inv* and *algo mat_cg*) currently +store an interaction matrix (either elastance or capacitance) of *N* by +*N* doubles for each MPI process. This memory requirement may be +prohibitive for large electrode groups. The fix will issue a warning if +it expects to use more than 0.5 GiB of memory. + +Default +""""""" + +The default keyword-option settings are *algo mat_inv*, *symm off*, +*etypes off* and *ffield off*. + +---------- + +.. include:: accel_styles.rst + +---------- + +.. _Siepmann: + +**(Siepmann)** Siepmann and Sprik, J. Chem. Phys. 102, 511 (1995). + +.. _Reed3: + +**(Reed)** Reed *et al.*, J. Chem. Phys. 126, 084704 (2007). + +.. _Deissenbeck: + +**(Deissenbeck)** Deissenbeck *et al.*, Phys. Rev. Letters 126, 136803 (2021). + +.. _Gingrich: + +**(Gingrich)** Gingrich, `MSc thesis` ` (2010). + +.. _Ahrens-Iwers: + +**(Ahrens-Iwers)** Ahrens-Iwers and Meissner, J. Chem. Phys. 155, 104104 (2021). + +.. _Hu: + +**(Hu)** Hu, J. Chem. Theory Comput. 10, 5254 (2014). + +.. _Dufils: + +**(Dufils)** Dufils *et al.*, Phys. Rev. Letters 123, 195501 (2019). + +.. _Tee: + +**(Tee)** Tee and Searles, J. Chem. Phys. 156, 184101 (2022). + +.. _Scalfi: + +**(Scalfi)** Scalfi *et al.*, J. Chem. Phys., 153, 174704 (2020). + +.. _Ahrens-Iwers2: + +**(Ahrens-Iwers2022)** Ahrens-Iwers *et al.*, J. Chem. Phys. 157, 084801 (2022). diff --git a/doc/src/fix_electrode_conp.rst b/doc/src/fix_electrode_conp.rst deleted file mode 100644 index e070433c07..0000000000 --- a/doc/src/fix_electrode_conp.rst +++ /dev/null @@ -1,230 +0,0 @@ -.. index:: fix electrode/conp -.. index:: fix electrode/conq -.. index:: fix electrode/thermo -.. index:: fix electrode/conp/intel -.. index:: fix electrode/conq/intel -.. index:: fix electrode/thermo/intel - -fix electrode/conp command -========================== - -Accelerator Variant: *electrode/conp/intel* - -fix electrode/conq command -========================== - -Accelerator Variant: *electrode/conq/intel* - -fix electrode/thermo command -============================ - -Accelerator Variant: *electrode/thermo/intel* - -Syntax -"""""" - -.. parsed-literal:: - - fix ID group-ID style args keyword value ... - -* ID, group-ID are documented in :doc:`fix ` command -* style = *electrode/conp* or *electrode/conq* or *electrode/thermo* -* args = arguments used by a particular style - - .. parsed-literal:: - - *electrode/conp* args = potential eta - *electrode/conq* args = charge eta - *electrode/thermo* args = potential eta *temp* values - potential = electrode potential - charge = electrode charge - eta = reciprocal width of electrode charge smearing - *temp* values = T_v tau_v rng_v - T_v = temperature of thermo-potentiostat - tau_v = time constant of thermo-potentiostat - rng_v = integer used to initialize random number generator - -* zero or more keyword/value pairs may be appended -* keyword = *symm* or *couple* or *etypes* or *ffield* or *write_mat* or *write_inv* or *read_mat* or *read_inv* - -.. parsed-literal:: - - *symm* value = *on* or *off* - turn on/off charge neutrality constraint for the electrodes - *couple* values = group-ID val - group-ID = group of atoms treated as additional electrode - val = electric potential or charge on this electrode - *etypes* values = type - type = atom type (can be a range) exclusive to the electrode for optimized neighbor lists - *ffield* value = *on* or *off* - turn on/off finite-field implementation - *write_mat* value = filename - filename = file to which to write elastance matrix - *write_inv* value = filename - filename = file to which to write inverted matrix - *read_mat* value = filename - filename = file from which to read elastance matrix - *read_inv* value = filename - filename = file from which to read inverted matrix - -Examples -"""""""" - -.. code-block:: LAMMPS - - fix fxconp bot electrode/conp -1.0 1.805 couple top 1.0 couple ref 0.0 write_inv inv.csv symm on - fix fxconp electrodes electrode/conq 0.0 1.805 - fix fxconp bot electrode/thermo -1.0 1.805 temp 298 100 couple top 1.0 - -Description -""""""""""" - -fix electrode/conp mode implements a constant potential method (CPM) -(:ref:`Siepmann `, :ref:`Reed `). Charges of groups specified -via group-ID and optionally with the `couple` keyword are adapted to meet their respective -potential at every time step. An arbitrary number of electrodes can be set but -the respective groups may not overlap. Electrode charges have a Gaussian charge -distribution with reciprocal width eta. The energy minimization is achieved via -matrix inversion :ref:`(Wang) `. - -fix electrode/conq enforces a total charge specified in the input on each electrode. The energy is -minimized w.r.t. the charge distribution within the electrode. - -fix electrode/thermo implements a thermo-potentiostat :ref:`(Deissenbeck) -`. Temperature and time constant of the thermo-potentiostat need -to be specified using the temp keyword. Currently, only two electrodes are possible with -this style. - -This fix necessitates the use of a long range solver that calculates and provides the matrix -of electrode-electrode interactions and a vector of electrode-electrolyte -interactions. The Kspace styles *ewald/electrode*, *pppm/electrode* and -*pppm/electrode/intel* are created specifically for this task -:ref:`(Ahrens-Iwers) `. - -For systems with non-periodic boundaries in one or two directions dipole -corrections are available with the :doc:`kspace_modify `. For -ewald/electrode a two-dimensional Ewald summation :ref:`(Hu) ` can be used -by setting "slab ew2d": - -.. code-block:: LAMMPS - - kspace_modify slab - kspace_modify wire - kspace_modify slab ew2d - -Two implementations for the calculation of the elastance matrix are available -with pppm and can be selected using the *amat onestep/twostep* keyword. -*onestep* is the default; *twostep* can be faster for large electrodes and a -moderate mesh size but requires more memory. - -.. code-block:: LAMMPS - - kspace_modify amat onestep/twostep - - -The *fix_modify tf* option enables the Thomas-Fermi metallicity model -(:ref:`Scalfi `) and allows parameters to be set for each atom type. - -.. code-block:: LAMMPS - - fix_modify ID tf type length voronoi - - -If this option is used parameters must be set for all atom types of the electrode. - -The *fix_modify timer* option turns on (off) additional timer outputs in the log -file, for code developers to track optimization. - -.. code-block:: LAMMPS - - fix_modify ID timer on/off - -The *fix_modify set* options allow calculated quantities to be accessed via -internal variables. Currently four types of quantities can be accessed: - -.. code-block:: LAMMPS - - fix-modify ID set v group-ID variablename - fix-modify ID set qsb group-ID variablename - fix-modify ID set mc group-ID1 group-ID2 variablename - fix-modify ID set me group-ID1 group-ID2 variablename - -One use case is to output the potential that is internally calculated and -applied to each electrode group by *fix electrode/conq* or *fix electrode/thermo*. -For that case the *v* option makes *fix electrode* update the variable -*variablename* with the potential applied to group *group-ID*, where *group-ID* -must be a group whose charges are updated by *fix electrode* and *variablename* -must be an internal-style variable: - -.. code-block:: LAMMPS - - fix conq bot electrode/conq -1.0 1.979 couple top 1.0 - variable vbot internal 0.0 - fix_modify conq set v bot vbot - -The *qsb* option similarly outputs the total updated charge of the group if its -potential were 0.0V. The *mc* option requires two *group-IDs*, and outputs the -entry \{*group-ID1*, *group-ID2*\} of the (symmetric) *macro-capacitance* matrix -(MC) which relates the electrodes' applied potentials (V), total charges (Q), and -total charges at 0.0 V (Qsb): - -.. math:: - - \mathbf{Q} = \mathbf{Q}_{SB} + \mathbf{MC} \cdot \mathbf{V} - -Lastly, the *me* option also requires two *group-IDs* and outputs the entry -\{*group-ID1*, *group-ID2*\} of the *macro-elastance* matrix, which is the -inverse of the macro-capacitance matrix. (As the names denote, the -macro-capacitance matrix gives electrode charges from potentials, and the -macro-elastance matrix gives electrode potentials from charges). - -.. warning:: - - Positions of electrode particles have to be immobilized at all times. - -The parallelization for the fix works best if electrode atoms are evenly -distributed across processors. For a system with two electrodes at the bottom -and top of the cell this can be achieved with *processors * * 2*, or with the -line - -.. code-block:: LAMMPS - - if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" - -which avoids an error if the script is run on an odd number of processors (such -as on just one processor for testing). - ----------- - -.. include:: accel_styles.rst - ----------- - -.. _Siepmann: - -**(Siepmann)** Siepmann and Sprik, J. Chem. Phys. 102, 511 (1995). - -.. _Reed3: - -**(Reed)** Reed *et al.*, J. Chem. Phys. 126, 084704 (2007). - -.. _Wang5: - -**(Wang)** Wang *et al.*, J. Chem. Phys. 141, 184102 (2014). - -.. _Deissenbeck: - -**(Deissenbeck)** Deissenbeck *et al.*, Phys. Rev. Letters 126, 136803 (2021). - -.. _Ahrens-Iwers: - -**(Ahrens-Iwers)** Ahrens-Iwers and Meissner, J. Chem. Phys. 155, 104104 (2021). - -.. _Hu: - -**(Hu)** Hu, J. Chem. Theory Comput. 10, 5254 (2014). - -.. _Scalfi: - -**(Scalfi)** Scalfi *et al.*, J. Chem. Phys., 153, 174704 (2020). - diff --git a/doc/src/fix_ipi.rst b/doc/src/fix_ipi.rst index 6a6ff9aa87..5e13d25971 100644 --- a/doc/src/fix_ipi.rst +++ b/doc/src/fix_ipi.rst @@ -90,6 +90,12 @@ coordinates are transferred. However, one could use this strategy to define an external potential acting on the atoms that are moved by i-PI. +Since the i-PI code uses atomic units internally, this fix needs to +convert LAMMPS data to and from its :doc:`specified units ` +accordingly when communicating with i-PI. This is not possible for +reduced units ("units lj") and thus *fix ipi* will stop with an error in +this case. + This fix is part of the MISC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. diff --git a/doc/src/fix_nh_uef.rst b/doc/src/fix_nh_uef.rst index 83cf88b11f..cf20d56ce7 100644 --- a/doc/src/fix_nh_uef.rst +++ b/doc/src/fix_nh_uef.rst @@ -44,19 +44,23 @@ Examples Description """"""""""" -This fix can be used to simulate non-equilibrium molecular dynamics -(NEMD) under diagonal flow fields, including uniaxial and bi-axial -flow. Simulations under continuous extensional flow may be carried -out for an indefinite amount of time. It is an implementation of the -boundary conditions from :ref:`(Dobson) `, and also uses numerical +These fixes can be used to simulate non-equilibrium molecular dynamics +(NEMD) under diagonal flow fields, including uniaxial and bi-axial flow. +Simulations under continuous extensional flow may be carried out for an +indefinite amount of time. It is an implementation of the boundary +conditions from :ref:`(Dobson) `, and also uses numerical lattice reduction as was proposed by :ref:`(Hunt) `. The lattice -reduction algorithm is from :ref:`(Semaev) `. The fix is intended for -simulations of homogeneous flows, and integrates the SLLOD equations -of motion, originally proposed by Hoover and Ladd (see :ref:`(Evans and Morriss) `). Additional detail about this implementation can be -found in :ref:`(Nicholson and Rutledge) `. +reduction algorithm is from :ref:`(Semaev) `. The fix is +intended for simulations of homogeneous flows, and integrates the SLLOD +equations of motion, originally proposed by Hoover and Ladd (see +:ref:`(Evans and Morriss) `). Additional detail about this +implementation can be found in :ref:`(Nicholson and Rutledge) +`. Note that NEMD simulations of a continuously strained system can be -performed using the :doc:`fix deform `, :doc:`fix nvt/sllod `, and :doc:`compute temp/deform ` commands. +performed using the :doc:`fix deform `, :doc:`fix nvt/sllod +`, and :doc:`compute temp/deform ` +commands. The applied flow field is set by the *eps* keyword. The values *edot_x* and *edot_y* correspond to the strain rates in the xx and yy @@ -73,11 +77,11 @@ to -(*edot_x* + *edot_y*). The boundary conditions require a simulation box that does not have a consistent alignment relative to the applied flow field. Since LAMMPS utilizes an upper-triangular simulation box, it is not possible to -express the evolving simulation box in the same coordinate system as -the flow field. This fix keeps track of two coordinate systems: the -flow frame, and the upper triangular LAMMPS frame. The coordinate -systems are related to each other through the QR decomposition, as is -illustrated in the image below. +express the evolving simulation box in the same coordinate system as the +flow field. These fixes keep track of two coordinate systems: the flow +frame, and the upper triangular LAMMPS frame. The coordinate systems are +related to each other through the QR decomposition, as is illustrated in +the image below. .. image:: JPG/uef_frames.jpg :align: center @@ -99,12 +103,12 @@ using the dump command will be in the LAMMPS frame unless the ---------- Temperature control is achieved with the default Nose-Hoover style -thermostat documented in :doc:`fix npt `. When this fix is +thermostat documented in :doc:`fix nvt `. When this fix is active, only the peculiar velocity of each atom is stored, defined as -the velocity relative to the streaming velocity. This is in contrast -to :doc:`fix nvt/sllod `, which uses a lab-frame -velocity, and removes the contribution from the streaming velocity in -order to compute the temperature. +the velocity relative to the streaming velocity. This is in contrast to +:doc:`fix nvt/sllod `, which uses a lab-frame velocity, +and removes the contribution from the streaming velocity in order to +compute the temperature. Pressure control is achieved using the default Nose-Hoover barostat documented in :doc:`fix npt `. There are two ways to control the @@ -156,8 +160,8 @@ The following commands will not work: ---------- -These fix computes a temperature and pressure each timestep. To do -this, it creates its own computes of style "temp/uef" and +These fixes compute a temperature and pressure each timestep. To do +this, they create their own computes of style "temp/uef" and "pressure/uef", as if one of these two sets of commands had been issued: @@ -169,18 +173,19 @@ issued: compute fix-ID_temp all temp/uef compute fix-ID_press all pressure/uef fix-ID_temp -See the :doc:`compute temp/uef ` and :doc:`compute pressure/uef ` commands for details. Note -that the IDs of the new computes are the fix-ID + underscore + "temp" -or fix_ID + underscore + "press". +See the :doc:`compute temp/uef ` and :doc:`compute +pressure/uef ` commands for details. Note that +the IDs of the new computes are the fix-ID + underscore + "temp" or +fix_ID + underscore + "press". Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" The fix writes the state of all the thermostat and barostat variables, -as well as the cumulative strain applied, to :doc:`binary restart files `. See the :doc:`read_restart ` command -for info on how to re-specify a fix in an input script that reads a -restart file, so that the operation of the fix continues in an -uninterrupted fashion. +as well as the cumulative strain applied, to :doc:`binary restart files +`. See the :doc:`read_restart ` command for info +on how to re-specify a fix in an input script that reads a restart file, +so that the operation of the fix continues in an uninterrupted fashion. .. note:: @@ -189,43 +194,41 @@ uninterrupted fashion. not contain the cumulative applied strain, will this keyword be necessary. -This fix can be used with the :doc:`fix_modify ` *temp* and -*press* options. The temperature and pressure computes used must be of -type *temp/uef* and *pressure/uef*\ . +These fixes can be used with the :doc:`fix_modify ` *temp* +and *press* options. The temperature and pressure computes used must be +of type *temp/uef* and *pressure/uef*\ . -This fix computes the same global scalar and vector quantities as :doc:`fix npt `. +These fixes compute the same global scalar and vector quantities as +:doc:`fix nvt andnpt `. -The fix is not invoked during :doc:`energy minimization `. +These fixes are not invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the UEF package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` page for more info. +These fixes are part of the UEF package. They are only enabled if LAMMPS +was built with that package. See the :doc:`Build package +` page for more info. Due to requirements of the boundary conditions, when the *strain* keyword is set to zero (or unset), the initial simulation box must be cubic and have style triclinic. If the box is initially of type ortho, use :doc:`change_box ` before invoking the fix. -.. note:: - - When resuming from restart files, you may need to use :doc:`box tilt - large ` since LAMMPS has internal criteria from lattice - reduction that are not the same as the criteria in the numerical - lattice reduction algorithm. - Related commands """""""""""""""" -:doc:`fix nvt `, :doc:`fix nvt/sllod `, :doc:`compute temp/uef `, :doc:`compute pressure/uef `, :doc:`dump cfg/uef ` +:doc:`fix nvt `, :doc:`fix npt `, `fix nvt/sllod +:doc:`, `compute temp/uef `, +:doc::doc:`compute pressure/uef `, `dump cfg/uef +:doc:` Default """"""" -The default keyword values specific to this fix are exy = xyz, strain -= 0 0. The remaining defaults are the same as for :doc:`fix npt ` -except tchain = 1. The reason for this change is given in +The default keyword values specific to these fixes are exy = xyz, strain += 0 0. The remaining defaults are the same as for :doc:`fix nvt or npt +` except tchain = 1. The reason for this change is given in :doc:`fix nvt/sllod `. ---------- diff --git a/doc/src/fix_nve_bpm_sphere.rst b/doc/src/fix_nve_bpm_sphere.rst index 861586ab2a..ef170605a4 100644 --- a/doc/src/fix_nve_bpm_sphere.rst +++ b/doc/src/fix_nve_bpm_sphere.rst @@ -30,6 +30,8 @@ Examples Description """"""""""" +.. versionadded:: 4May2022 + Perform constant NVE integration to update position, velocity, angular velocity, and quaternion orientation for finite-size spherical particles in the group each timestep. V is volume; E is energy. This @@ -65,6 +67,10 @@ the :doc:`run ` command. This fix is not invoked during Restrictions """""""""""" +This fix is part of the BPM package. It is only enabled if LAMMPS was +built with that package. See the :doc:`Build package ` +page for more info. + This fix requires that atoms store torque, angular velocity (omega), a radius, and a quaternion as defined by the :doc:`atom_style bpm/sphere ` command. diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst index 9735284280..838b9812ad 100644 --- a/doc/src/fix_pimd.rst +++ b/doc/src/fix_pimd.rst @@ -156,6 +156,8 @@ This fix is part of the REPLICA package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. +Fix pid cannot be used with :doc:`lj units `. + A PIMD simulation can be initialized with a single data file read via the :doc:`read_data ` command. However, this means all quasi-beads in a ring polymer will have identical positions and diff --git a/doc/src/fix_sgcmc.rst b/doc/src/fix_sgcmc.rst new file mode 100644 index 0000000000..4a9c4b16e3 --- /dev/null +++ b/doc/src/fix_sgcmc.rst @@ -0,0 +1,188 @@ +.. index:: fix sgcmc + +fix sgcmc command +================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID sgcmc every_nsteps swap_fraction temperature deltamu ... + +* ID, group-ID are documented in :doc:`fix ` command +* sgcmc = style name of this fix command +* every_nsteps = number of MD steps between MC cycles +* swap_fraction = fraction of a full MC cycle carried out at each call (a value of 1.0 will perform as many trial moves as there are atoms) +* temperature = temperature that enters Boltzmann factor in Metropolis criterion (usually the same as MD temperature) +* deltamu = chemical potential difference(s) (`N-1` values must be provided, with `N` being the number of elements) +* Zero or more keyword/value pairs may be appended to fix definition line: + + .. parsed-literal:: + + keyword = *variance* or *randseed* or *window_moves* or *window_size* + *variance* kappa conc1 [conc2] ... [concN] + kappa = variance constraint parameter + conc1,conc2,... = target concentration(s) in the range 0.0-1.0 (*N-1* values must be provided, with *N* being the number of elements) + *randseed* N + N = seed for pseudo random number generator + *window_moves* N + N = number of times sampling window is moved during one MC cycle + *window_size* frac + frac = size of sampling window (must be between 0.5 and 1.0) + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix mc all sgcmc 50 0.1 400.0 -0.55 + fix vc all sgcmc 20 0.2 700.0 -0.7 randseed 324234 variance 2000.0 0.05 + fix 2 all sgcmc 20 0.1 700.0 -0.7 window_moves 20 + +Description +""""""""""" + +.. versionadded:: 22Dec2022 + +This command allows to carry out parallel hybrid molecular +dynamics/Monte Carlo (MD/MC) simulations using the algorithms described +in :ref:`(Sadigh1) `. Simulations can be carried out in either +the semi-grand canonical (SGC) or variance constrained semi-grand +canonical (VC-SGC) ensemble :ref:`(Sadigh2) `. Only atom type +swaps are performed by the SGCMC fix. Relaxations are accounted for by +the molecular dynamics integration steps. + +This fix can be used with standard multi-element EAM potentials +(:doc:`pair styles eam/alloy or eam/fs `) + +The SGCMC fix can handle Finnis/Sinclair type EAM potentials where +:math:`\rho(r)` is atom-type specific, such that different elements can +contribute differently to the total electron density at an atomic site +depending on the identity of the element at that atomic site. + +------------ + +If this fix is applied, the regular MD simulation will be interrupted in +defined intervals to carry out a fraction of a Monte Carlo (MC) +cycle. The interval is set using the parameter *every_nsteps* which +determines how many MD integrator steps are taken between subsequent +calls to the MC routine. + +It is possible to carry out pure lattice MC simulations by setting +*every_nsteps* to 1 and not defining an integration fix such as NVE, +NPT etc. In that case, the particles will not move and only the MC +routine will be called to perform atom type swaps. + +The parameter *swap_fraction* determines how many MC trial steps are carried +out every time the MC routine is entered. It is measured in units of full MC +cycles where one full cycle, *swap_fraction=1*, corresponds to as many MC +trial steps as there are atoms. + +------------ + +The parameter *temperature* specifies the temperature that is used +to evaluate the Metropolis acceptance criterion. While it usually +should be set to the same value as the MD temperature there are cases +when it can be useful to use two different values for at least part of +the simulation, e.g., to speed up equilibration at low temperatures. + +------------ + +The parameter *deltamu* is used to set the chemical potential difference +in the SGC MC algorithm (see Eq. 16 in :ref:`Sadigh1 `). By +convention it is the difference of the chemical potentials of elements +`B`, `C` ..., with respect to element A. When the simulation includes +`N` elements, `N-1` values must be specified. + +------------ + +The variance-constrained SGC MC algorithm is activated if the keyword +*variance* is used. In that case the fix parameter *deltamu* determines +the effective average constraint in the parallel VC-SGC MC algorithm +(parameter :math:`\delta\mu_0` in Eq. (20) of :ref:`Sadigh1 +`). The parameter *kappa* specifies the variance constraint +(see Eqs. (20-21) in :ref:`Sadigh1 `). + +The parameter *conc* sets the target concentration (parameter +:math:`c_0` in Eqs. (20-21) of :ref:`Sadigh1 `). The atomic +concentrations refer to components `B`, `C` ..., with `A` being set +automatically. When the simulation includes `N` elements, `N-1` +concentration values must be specified. + +------------ + +There are several technical parameters that can be set via optional flags. + +*randseed* is expected to be a positive integer number and is used +to initialize the random number generator on each processor. + +*window_size* controls the size of the sampling window in a parallel MC +simulation. The size has to lie between 0.5 and 1.0. Normally, this +parameter should be left unspecified which instructs the code to choose +the optimal window size automatically (see Sect. III.B and Figure 6 in +:ref:`Sadigh1 ` for details). + +The number of times the window is moved during a MC cycle is set using +the parameter *window_moves* (see Sect. III.B in :ref:`Sadigh1 +` for details). + +------------ + +Restart, fix_modify, output, run start/stop, minimize info +========================================================== + +No information about this fix is written to restart files. + +The MC routine keeps track of the global concentration(s) as well as the +number of accepted and rejected trial swaps during each MC step. These +values are provided by the sgcmc fix in the form of a global vector that +can be accessed by various :doc:`output commands ` +components of the vector represent the following quantities: + +* 1 = The absolute number of accepted trial swaps during the last MC step +* 2 = The absolute number of rejected trial swaps during the last MC step +* 3 = The current global concentration of species *A* (= number of atoms of type 1 / total number of atoms) +* 4 = The current global concentration of species *B* (= number of atoms of type 2 / total number of atoms) +* ... +* N+2: The current global concentration of species *X* (= number of atoms of type *N* / total number of atoms) + +Restrictions +============ + +This fix is part of the MC package. It is only enabled if LAMMPS was +built with that package. See the :doc:`Build package ` +page for more info. + +At present the fix provides optimized subroutines for EAM type +potentials (see above) that calculate potential energy changes due to +*local* atom type swaps very efficiently. Other potentials are +supported by using the generic potential functions. This, however, will +lead to exceedingly slow simulations since it implies that the +energy of the *entire* system is recomputed at each MC trial step. If +other potentials are to be used it is strongly recommended to modify and +optimize the existing generic potential functions for this purpose. +Also, the generic energy calculation can not be used for parallel +execution i.e. it only works with a single MPI process. + +------------ + +Default +======= + +The optional parameters default to the following values: + +* *randseed* = 324234 +* *window_moves* = 8 +* *window_size* = automatic + +------------ + +.. _Sadigh1: + +**(Sadigh1)** B. Sadigh, P. Erhart, A. Stukowski, A. Caro, E. Martinez, and L. Zepeda-Ruiz, Phys. Rev. B **85**, 184203 (2012) + +.. _Sadigh2: + +**(Sadigh2)** B. Sadigh and P. Erhart, Phys. Rev. B **86**, 134204 (2012) diff --git a/doc/src/fix_ttm.rst b/doc/src/fix_ttm.rst index d146321395..e75f33bb4e 100644 --- a/doc/src/fix_ttm.rst +++ b/doc/src/fix_ttm.rst @@ -183,29 +183,32 @@ embedded within a larger continuum representation of the electronic subsystem. The *set* keyword specifies a *Tinit* temperature value to initialize -the value stored on all grid points. +the value stored on all grid points. By default the temperatures +are all zero when the grid is created. The *infile* keyword specifies an input file of electronic temperatures -for each grid point to be read in to initialize the grid. By default -the temperatures are all zero when the grid is created. The input file -is a text file which may have comments starting with the '#' character. -Each line contains four numeric columns: ix,iy,iz,Temperature. Empty -or comment-only lines will be ignored. The -number of lines must be equal to the number of user-specified grid -points (Nx by Ny by Nz). The ix,iy,iz are grid point indices ranging -from 0 to nxnodes-1 inclusive in each dimension. The lines can appear -in any order. For example, the initial electronic temperatures on a 1 -by 2 by 3 grid could be specified in the file as follows: +for each grid point to be read in to initialize the grid, as an alternative +to using the *set* keyword. + +The input file is a text file which may have comments starting with +the '#' character. Each line contains four numeric columns: +ix,iy,iz,Temperature. Empty or comment-only lines will be +ignored. The number of lines must be equal to the number of +user-specified grid points (Nx by Ny by Nz). The ix,iy,iz are grid +point indices ranging from 1 to Nxyz inclusive in each dimension. The +lines can appear in any order. For example, the initial electronic +temperatures on a 1 by 2 by 3 grid could be specified in the file as +follows: .. parsed-literal:: # UNITS: metal COMMENT: initial electron temperature - 0 0 0 1.0 - 0 0 1 1.0 - 0 0 2 1.0 - 0 1 0 2.0 - 0 1 1 2.0 - 0 1 2 2.0 + 1 1 1 1.0 + 1 1 2 1.0 + 1 1 3 1.0 + 1 2 1 2.0 + 1 2 2 2.0 + 1 2 3 2.0 where the electronic temperatures along the y=0 plane have been set to 1.0, and the electronic temperatures along the y=1 plane have been set @@ -223,17 +226,31 @@ units used. The *outfile* keyword has 2 values. The first value *Nout* triggers output of the electronic temperatures for each grid point every Nout -timesteps. The second value is the filename for output which will -be suffixed by the timestep. The format of each output file is exactly +timesteps. The second value is the filename for output, which will be +suffixed by the timestep. The format of each output file is exactly the same as the input temperature file. It will contain a comment in the first line reporting the date the file was created, the LAMMPS units setting in use, grid size and the current timestep. -Note that the atomic temperature for atoms in each grid cell can also -be computed and output by the :doc:`fix ave/chunk ` -command using the :doc:`compute chunk/atom ` -command to create a 3d array of chunks consistent with the grid used -by this fix. +.. note:: + + The fix ttm/grid command does not support the *outfile* keyword. + Instead you can use the :doc:`dump grid ` command to output + the electronic temperature on the distributed grid to a dump file or + the :doc:`restart ` command which creates a file specific + to this fix which the :doc:`read restart ` command + reads. The file has the same format as the file the *infile* option + reads. + +For the fix ttm and fix ttm/mod commands, the corresponding atomic +temperature for atoms in each grid cell can be computed and output by +the :doc:`fix ave/chunk ` command using the +:doc:`compute chunk/atom ` command to create a 3d +array of chunks consistent with the grid used by this fix. + +For the fix ttm/grid command the same thing can be done using the +:doc:`fix ave/grid ` command and its per-grid values can +be output via the :doc:`dump grid ` command. ---------- @@ -339,19 +356,25 @@ ignored. The lines with the even numbers are treated as follows: Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -These fixes write the state of the electronic subsystem and the energy -exchange between the subsystems to :doc:`binary restart files -`. See the :doc:`read_restart ` command for -info on how to re-specify a fix in an input script that reads a -restart file, so that the operation of the fix continues in an -uninterrupted fashion. Note that the restart script must define the -same size grid as the original script. +The fix ttm and fix ttm/mod commands write the state of the electronic +subsystem and the energy exchange between the subsystems to +:doc:`binary restart files `. The fix ttm/grid command does +not yet support writing of its distributed grid to a restart file. -Because the state of the random number generator is not saved in the -restart files, this means you cannot do "exact" restarts with this -fix, where the simulation continues on the same as if no restart had -taken place. However, in a statistical sense, a restarted simulation -should produce the same behavior. +See the :doc:`read_restart ` command for info on how to +re-specify a fix in an input script that reads a restart file, so that +the operation of the fix continues in an uninterrupted fashion. Note +that the restart script must define the same size grid as the original +script. + +The fix ttm/grid command also outputs an auxiliary file each time a +restart file is written, with the electron temperatures for each grid +cell. The format of this file is the same as that read by the +*infile* option explained above. The filename is the same as the +restart filename with ".ttm" appended. This auxiliary file can be +read in for a restarted run by using the *infile* option for the fix +ttm/grid command, following the :doc:`read_restart ` +command. None of the :doc:`fix_modify ` options are relevant to these fixes. @@ -371,6 +394,14 @@ electronic subsystem energies reported at the end of the timestep. The vector values calculated are "extensive". +The fix ttm/grid command also outputs a per-grid vector which stores +the electron temperature for each grid cell in temperature :doc:`units +`. which can be accessed by various :doc:`output commands +`. The length of the vector (distributed across all +processors) is Nx * Ny * Nz. For access by other commands, the name +of the single grid produced by fix ttm/grid is "grid". The name of +its per-grid data is "data". + No parameter of the fixes can be used with the *start/stop* keywords of the :doc:`run ` command. The fixes are not invoked during :doc:`energy minimization `. @@ -385,6 +416,15 @@ package ` page for more info. As mentioned above, these fixes require 3d simulations and orthogonal simulation boxes periodic in all 3 dimensions. +These fixes used a random number generator to Langevin thermostat the +electron temperature. This means you will not get identical answers +when running on different numbers of processors or when restarting a +simulation (even on the same number of processors). However, in a +statistical sense, simulations on different processor counts and +restarted simulation should produce results which are statistically +the same. + + Related commands """""""""""""""" diff --git a/doc/src/fix_viscous.rst b/doc/src/fix_viscous.rst index 6c48cb5f12..d5fd794020 100644 --- a/doc/src/fix_viscous.rst +++ b/doc/src/fix_viscous.rst @@ -1,8 +1,11 @@ .. index:: fix viscous +.. index:: fix viscous/kk fix viscous command =================== +Accelerator Variants: *viscous/kk* + Syntax """""" @@ -84,6 +87,10 @@ more easily be used as a thermostat. ---------- +.. include:: accel_styles.rst + +---------- + Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" diff --git a/doc/src/kim_commands.rst b/doc/src/kim_commands.rst index d886fa7dab..07490ecf64 100644 --- a/doc/src/kim_commands.rst +++ b/doc/src/kim_commands.rst @@ -1333,13 +1333,13 @@ For example, Citation of OpenKIM IMs """"""""""""""""""""""" -When publishing results obtained using OpenKIM IMs researchers are requested -to cite the OpenKIM project :ref:`(Tadmor) `, KIM API -:ref:`(Elliott) `, and the specific IM codes used in the simulations, -in addition to the relevant scientific references for the IM. The citation -format for an IM is displayed on its page on -`OpenKIM `_ along with the corresponding BibTex file, and -is automatically added to the LAMMPS citation reminder. +When publishing results obtained using OpenKIM IMs researchers are +requested to cite the OpenKIM project :ref:`(Tadmor) `, +KIM API :ref:`(Elliott) `, and the specific IM codes used in +the simulations, in addition to the relevant scientific references for +the IM. The citation format for an IM is displayed on its page on +`OpenKIM `_ along with the corresponding BibTex +file, and is automatically added to the LAMMPS citation reminder. Citing the IM software (KIM infrastructure and specific PM or SM codes) used in the simulation gives credit to the researchers who developed them and enables @@ -1348,15 +1348,15 @@ open source efforts like OpenKIM to function. Restrictions """""""""""" -The *kim* command is part of the KIM package. It is only enabled if LAMMPS is -built with that package. A requirement for the KIM package, is the KIM API -library that must be downloaded from the -`OpenKIM website `_ and installed before LAMMPS is +The *kim* command is part of the KIM package. It is only enabled if +LAMMPS is built with that package. A requirement for the KIM package, +is the KIM API library that must be downloaded from the `OpenKIM website +`_ and installed before LAMMPS is compiled. When installing LAMMPS from binary, the kim-api package is a -dependency that is automatically downloaded and installed. The *kim query* -command requires the *libcurl* library to be installed. The *kim property* -command requires *Python* 3.6 or later and the *kim-property* python package to -be installed. See the KIM section of the +dependency that is automatically downloaded and installed. The *kim +query* command requires the *libcurl* library to be installed. The *kim +property* command requires *Python* 3.6 or later and the *kim-property* +python package to be installed. See the KIM section of the :doc:`Packages details ` for details. Furthermore, when using *kim* command to run KIM SMs, any packages required by diff --git a/doc/src/kspace_modify.rst b/doc/src/kspace_modify.rst index 3c6fccc285..2d3921e281 100644 --- a/doc/src/kspace_modify.rst +++ b/doc/src/kspace_modify.rst @@ -51,7 +51,6 @@ Syntax *slab* value = volfactor or *nozforce* volfactor = ratio of the total extended volume used in the 2d approximation compared with the volume of the simulation domain - *ew2d* EW2D correction (available with ELECTRODE package) *nozforce* turns off kspace forces in the z direction *splittol* value = tol tol = relative size of two eigenvalues (see discussion below) @@ -381,18 +380,22 @@ solver is set up. The *slab* keyword allows an Ewald or PPPM solver to be used for a systems that are periodic in x,y but non-periodic in z - a -:doc:`boundary ` setting of "boundary p p f". This is done by -treating the system as if it were periodic in z, but inserting empty -volume between atom slabs and removing dipole inter-slab interactions -so that slab-slab interactions are effectively turned off. The -volfactor value sets the ratio of the extended dimension in z divided -by the actual dimension in z. The recommended value is 3.0. A larger -value is inefficient; a smaller value introduces unwanted slab-slab +:doc:`boundary ` setting of "boundary p p f". This is done +by treating the system as if it were periodic in z, but inserting +empty volume between atom slabs and removing dipole inter-slab +interactions so that slab-slab interactions are effectively turned +off. The volfactor value sets the ratio of the extended dimension in +z divided by the actual dimension in z. It must be a value >= 1.0. A +value of 1.0 (the default) means the slab approximation is not used. + +The recommended value for volfactor is 3.0. A larger value is +inefficient; a smaller value introduces unwanted slab-slab interactions. The use of fixed boundaries in z means that the user must prevent particle migration beyond the initial z-bounds, typically by providing a wall-style fix. The methodology behind the *slab* -option is explained in the paper by :ref:`(Yeh) `. The *slab* option -is also extended to non-neutral systems :ref:`(Ballenegger) `. +option is explained in the paper by :ref:`(Yeh) `. The *slab* +option is also extended to non-neutral systems :ref:`(Ballenegger) +`. An alternative slab option can be invoked with the *nozforce* keyword in lieu of the volfactor. This turns off all kspace forces in the z @@ -402,8 +405,8 @@ boundaries can be set using :doc:`boundary ` (the slab approximation in not needed). The *slab* keyword is not currently supported by Ewald or PPPM when using a triclinic simulation cell. The slab correction has also been extended to point dipole interactions -:ref:`(Klapp) ` in :doc:`kspace_style ` *ewald/disp*, -*ewald/dipole*, and *pppm/dipole*\ . +:ref:`(Klapp) ` in :doc:`kspace_style ` +*ewald/disp*, *ewald/dipole*, and *pppm/dipole*\ . .. note:: @@ -448,15 +451,32 @@ Related commands Default """"""" -The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp = -5 (PPPM), order = 10 (MSM), minorder = 2, overlap = yes, force = -1.0, -gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust = -yes (MSM), pressure/scalar = yes (MSM), fftbench = no (PPPM), diff = -ik (PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace -= -1.0, split = 0, tol = 1.0e-6, and disp/auto = no. For pppm/intel, -order = order/disp = 7. For scafacos settings, the scafacos tolerance -option depends on the method chosen, as documented above. The -scafacos fmm_tuning default = 0. +The option defaults are as follows: + +* compute = yes +* cutoff/adjust = yes (MSM) +* diff = ik (PPPM) +* disp/auto = no +* fftbench = no (PPPM) +* force = -1.0, +* force/disp/kspace = -1.0 +* force/disp/real = -1.0 +* gewald = gewald/disp = 0.0 +* mesh = mesh/disp = 0 0 0 +* minorder = 2 +* mix/disp = pair +* order = 10 (MSM) +* order = order/disp = 5 (PPPM) +* order = order/disp = 7 (PPPM/intel) +* overlap = yes +* pressure/scalar = yes (MSM) +* slab = 1.0 +* split = 0 +* tol = 1.0e-6 + +For scafacos settings, the scafacos tolerance option depends on the +method chosen, as documented above. The scafacos fmm_tuning default += 0. ---------- diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst index cbaa82d547..38a6fce375 100644 --- a/doc/src/kspace_style.rst +++ b/doc/src/kspace_style.rst @@ -283,7 +283,7 @@ parameters and how to choose them is described in ---------- The *electrode* styles add methods that are required for the constant potential -method implemented in :doc:`fix electrode/* `. The styles +method implemented in :doc:`fix electrode/* `. The styles *ewald/electrode*, *pppm/electrode* and *pppm/electrode/intel* are available. These styles do not support the `kspace_modify slab nozforce` command. diff --git a/doc/src/neigh_modify.rst b/doc/src/neigh_modify.rst index d99a3187aa..8e5c517b94 100644 --- a/doc/src/neigh_modify.rst +++ b/doc/src/neigh_modify.rst @@ -16,12 +16,12 @@ Syntax keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize* or *collection/type* or *collection/interval* *delay* value = N - N = delay building until this many steps since last build + N = delay building neighbor lists until this many steps since last build *every* value = M - M = build neighbor list every this many steps + M = consider building neighbor lists every this many steps *check* value = *yes* or *no* - *yes* = only build if some atom has moved half the skin distance or more - *no* = always build on 1st step that *every* and *delay* are satisfied + *yes* = only build if at least one atom has moved half the skin distance or more + *no* = always build on 1st step where *every* and *delay* are conditions are satisfied *once* value = *yes* or *no* *yes* = only build neighbor list once at start of run and never rebuild *no* = rebuild neighbor list according to other settings @@ -71,30 +71,53 @@ Description """"""""""" This command sets parameters that affect the building and use of -pairwise neighbor lists. Depending on what pair interactions and -other commands are defined, a simulation may require one or more -neighbor lists. +pairwise neighbor lists. Depending on what pair interactions and other +commands are defined, a simulation may require one or more neighbor +lists. -The *every*, *delay*, *check*, and *once* options affect how often -lists are built as a simulation runs. The *delay* setting means never -build new lists until at least N steps after the previous build. The -*every* setting means build lists every M steps (after the delay has +The *every*, *delay*, *check*, and *once* options affect how often lists +are built as a simulation runs. The *delay* setting means never build +new lists until at least N steps after the previous build. The *every* +setting means attempt to build lists every M steps (after the delay has passed). If the *check* setting is *no*, the lists are built on the first step that satisfies the *delay* and *every* settings. If the *check* setting is *yes*, then the *every* and *delay* settings determine when a build may possibly be performed, but an actual build -only occurs if some atom has moved more than half the skin distance -(specified in the :doc:`neighbor ` command) since the last -build. +only occurs if at least one atom has moved more than half the neighbor +skin distance (specified in the :doc:`neighbor ` command) +since the last neighbor list build. -If the *once* setting is yes, then the neighbor list is only built -once at the beginning of each run, and never rebuilt, except on steps -when a restart file is written, or steps when a fix forces a rebuild -to occur (e.g. fixes that create or delete atoms, such as :doc:`fix deposit ` or :doc:`fix evaporate `). -This setting should only be made if you are certain atoms will not -move far enough that the neighbor list should be rebuilt, e.g. running -a simulation of a cold crystal. Note that it is not that expensive to -check if neighbor lists should be rebuilt. +.. admonition:: Impact of neighbor list settings + :class: note + + The choice of neighbor list settings can have a significant impact on + the (parallel) performance of LAMMPS and the correctness of the + simulation results. Since building the neighbor lists is time + consuming, doing it less frequently can speed up a calculation. If + the lists are rebuilt too infrequently, however, interacting pairs + may be missing and thus the resulting pairwise interactions + incorrect. The optimal settings depend on many factors like the + properties of the simulated system (density, geometry, topology, + temperature, pressure), the force field parameters and settings, the + size of the timestep, neighbor list skin distance and more. The + default settings are chosen to be very conservative to guarantee + correctness of the simulation. They depend on the *check* flag + heuristics to reduce the number of neighbor list rebuilds at a minor + expense for executing the check. Determining the correctness of a + specific choice of neighbor list settings is complicated by the fact + that a neighbor list rebuild changes the order in which pairwise + interactions are computed and thus + - due to the limitations of floating-point math - the trajectory. + +If the *once* setting is yes, then the neighbor list is only built once +at the beginning of each run, and never rebuilt, except on steps when a +restart file is written, or steps when a fix forces a rebuild to occur +(e.g. fixes that create or delete atoms, such as :doc:`fix deposit +` or :doc:`fix evaporate `). This setting +should only be made if you are certain atoms will not move far enough +that the neighbor list should be rebuilt, e.g. running a simulation of a +cold crystal. Note that it is not that expensive to check if neighbor +lists should be rebuilt. When the rRESPA integrator is used (see the :doc:`run_style ` command), the *every* and *delay* parameters refer to the longest @@ -234,11 +257,11 @@ depend on their atom type. Restrictions """""""""""" -If the "delay" setting is non-zero, then it must be a multiple of the -"every" setting. +If the *delay* setting is non-zero, then it must be a multiple of the +*every* setting. -The molecule/intra and molecule/inter exclude options can only be used -with atom styles that define molecule IDs. +The *molecule/intra* and *molecule/inter* exclusion options can only +be used with atom styles that define molecule IDs. The value of the *page* setting must be at least 10x larger than the *one* setting. This insures neighbor pages are not mostly empty @@ -252,6 +275,6 @@ Related commands Default """"""" -The option defaults are delay = 10, every = 1, check = yes, once = no, +The option defaults are delay = 0, every = 1, check = yes, once = no, cluster = no, include = all (same as no include option defined), exclude = none, page = 100000, one = 2000, and binsize = 0.0. diff --git a/doc/src/pair_amoeba.rst b/doc/src/pair_amoeba.rst index 44a14f0f45..f5c0ea14df 100644 --- a/doc/src/pair_amoeba.rst +++ b/doc/src/pair_amoeba.rst @@ -156,7 +156,7 @@ settings. ---------- -.. versionadded:: TBD +.. versionadded:: 3Nov2022 The *amoeba* and *hippo* pair styles support extraction of two per-atom quantities by the :doc:`fix pair ` command. This allows the diff --git a/doc/src/pair_bpm_spring.rst b/doc/src/pair_bpm_spring.rst index 72e0083bd8..7dfa9bc12c 100644 --- a/doc/src/pair_bpm_spring.rst +++ b/doc/src/pair_bpm_spring.rst @@ -22,6 +22,8 @@ Examples Description """"""""""" +.. versionadded:: 4May2022 + Style *bpm/spring* computes pairwise forces with the formula .. math:: @@ -101,7 +103,11 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" - none + +This pair style is part of the BPM package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` page for more info. + Related commands """""""""""""""" diff --git a/doc/src/pair_coul.rst b/doc/src/pair_coul.rst index 4e0793467b..f22bc974b0 100644 --- a/doc/src/pair_coul.rst +++ b/doc/src/pair_coul.rst @@ -174,11 +174,11 @@ shifted force model described in :ref:`Fennell `, given by: E = q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} + \left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c -where :math:`\alpha` is the damping parameter and erfc() is the -complementary error-function. The potential corrects issues in the -Wolf model (described below) to provide consistent forces and energies -(the Wolf potential is not differentiable at the cutoff) and smooth -decay to zero. +where :math:`\alpha` is the damping parameter and *erfc()* is the +complementary error-function. The potential corrects issues in the Wolf +model (described below) to provide consistent forces and energies (the +Wolf potential is not differentiable at the cutoff) and smooth decay to +zero. ---------- @@ -192,30 +192,32 @@ summation method, described in :ref:`Wolf `, given by: \frac{1}{2} \sum_{j \neq i} \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c -where :math:`\alpha` is the damping parameter, and erc() and erfc() are -error-function and complementary error-function terms. This potential -is essentially a short-range, spherically-truncated, +where :math:`\alpha` is the damping parameter, and *erf()* and *erfc()* +are error-function and complementary error-function terms. This +potential is essentially a short-range, spherically-truncated, charge-neutralized, shifted, pairwise *1/r* summation. With a manipulation of adding and subtracting a self term (for i = j) to the -first and second term on the right-hand-side, respectively, and a -small enough :math:`\alpha` damping parameter, the second term shrinks and -the potential becomes a rapidly-converging real-space summation. With -a long enough cutoff and small enough :math:`\alpha` parameter, the energy and -forces calculated by the Wolf summation method approach those of the +first and second term on the right-hand-side, respectively, and a small +enough :math:`\alpha` damping parameter, the second term shrinks and the +potential becomes a rapidly-converging real-space summation. With a +long enough cutoff and small enough :math:`\alpha` parameter, the energy +and forces calculated by the Wolf summation method approach those of the Ewald sum. So it is a means of getting effective long-range interactions with a short-range potential. ---------- -Style *coul/streitz* is the Coulomb pair interaction defined as part -of the Streitz-Mintmire potential, as described in :ref:`this paper `, in which charge distribution about an atom is modeled -as a Slater 1\ *s* orbital. More details can be found in the referenced +Style *coul/streitz* is the Coulomb pair interaction defined as part of +the Streitz-Mintmire potential, as described in :ref:`this paper +`, in which charge distribution about an atom is modeled as a +Slater 1\ *s* orbital. More details can be found in the referenced paper. To fully reproduce the published Streitz-Mintmire potential, -which is a variable charge potential, style *coul/streitz* must be -used with :doc:`pair_style eam/alloy ` (or some other -short-range potential that has been parameterized appropriately) via -the :doc:`pair_style hybrid/overlay ` command. Likewise, -charge equilibration must be performed via the :doc:`fix qeq/slater ` command. For example: +which is a variable charge potential, style *coul/streitz* must be used +with :doc:`pair_style eam/alloy ` (or some other short-range +potential that has been parameterized appropriately) via the +:doc:`pair_style hybrid/overlay ` command. Likewise, +charge equilibration must be performed via the :doc:`fix qeq/slater +` command. For example: .. code-block:: LAMMPS diff --git a/doc/src/pair_dipole.rst b/doc/src/pair_dipole.rst index 50e1a1b023..eb6b2c4859 100644 --- a/doc/src/pair_dipole.rst +++ b/doc/src/pair_dipole.rst @@ -58,22 +58,26 @@ Examples .. code-block:: LAMMPS - pair_style lj/cut/dipole/cut 10.0 + pair_style lj/cut/dipole/cut 2.5 5.0 pair_coeff * * 1.0 1.0 - pair_coeff 2 3 1.0 1.0 2.5 4.0 + pair_coeff 2 3 0.8 1.0 2.5 4.0 pair_style lj/sf/dipole/sf 9.0 pair_coeff * * 1.0 1.0 pair_coeff 2 3 1.0 1.0 2.5 4.0 scale 0.5 - pair_coeff 2 3 1.0 1.0 2.5 4.0 + pair_coeff 2 3 0.8 1.0 2.5 4.0 - pair_style lj/cut/dipole/long 10.0 + pair_style lj/cut/dipole/long 2.5 3.5 pair_coeff * * 1.0 1.0 - pair_coeff 2 3 1.0 1.0 2.5 4.0 + pair_coeff 2 3 0.8 1.0 3.0 - pair_style lj/long/dipole/long long long 3.5 10.0 + pair_style lj/long/dipole/long long long 3.5 pair_coeff * * 1.0 1.0 - pair_coeff 2 3 1.0 1.0 2.5 4.0 + pair_coeff 2 3 0.8 1.0 + + pair_style lj/long/dipole/long cut long 2.5 3.5 + pair_coeff * * 1.0 1.0 + pair_coeff 2 3 0.8 1.0 3.0 Description """"""""""" @@ -254,23 +258,28 @@ long-range LJ interactions, the :doc:`kspace_style ewald/disp ---------- -The following coefficients must be defined for each pair of atoms -types via the :doc:`pair_coeff ` command as in the examples -above, or in the data file or restart files read by the -:doc:`read_data ` or :doc:`read_restart ` -commands, or by mixing as described below: +The following coefficients must be defined for each pair of atoms types +via the :doc:`pair_coeff ` command as in the examples above, +or in the data file or restart files read by the :doc:`read_data +` or :doc:`read_restart ` commands, or by +mixing as described below: * :math:`\epsilon` (energy units) * :math:`\sigma` (distance units) * cutoff1 (distance units) * cutoff2 (distance units) -The latter 2 coefficients are optional. If not specified, the global -LJ and Coulombic cutoffs specified in the pair_style command are used. -If only one cutoff is specified, it is used as the cutoff for both LJ -and Coulombic interactions for this type pair. If both coefficients -are specified, they are used as the LJ and Coulombic cutoffs for this -type pair. +The latter 2 coefficients are optional. If not specified, the global LJ +and Coulombic cutoffs specified in the pair_style command are used. If +only one cutoff is specified, it is used as the cutoff for both LJ and +Coulombic interactions for this type pair. If both coefficients are +specified, they are used as the LJ and Coulombic cutoffs for this type +pair. When using a long-rang Coulomb solver, only a global Coulomb +cutoff may be used and only the LJ cutoff may be changed with the +:doc:`pair_coeff ` command. When using the +*lj/long/dipole/long* pair style with *long* *long* setting, only a +single global cutoff may be provided and no cutoff for the +:doc:`pair_coeff ` command. ---------- diff --git a/doc/src/pair_dpd_ext.rst b/doc/src/pair_dpd_ext.rst index 54d1e4bca3..47c14fa813 100644 --- a/doc/src/pair_dpd_ext.rst +++ b/doc/src/pair_dpd_ext.rst @@ -1,17 +1,19 @@ .. index:: pair_style dpd/ext .. index:: pair_style dpd/ext/kk +.. index:: pair_style dpd/ext/omp .. index:: pair_style dpd/ext/tstat .. index:: pair_style dpd/ext/tstat/kk +.. index:: pair_style dpd/ext/tstat/omp pair_style dpd/ext command ========================== -Accelerator Variants: dpd/ext/kk +Accelerator Variants: dpd/ext/kk dpd/ext/omp pair_style dpd/ext/tstat command ================================ -Accelerator Variants: dpd/ext/tstat/kk +Accelerator Variants: dpd/ext/tstat/kk dpd/ext/tstat/omp Syntax """""" @@ -113,10 +115,10 @@ each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above: * A (force units) -* :math:`\gamma_{\perp}` (force/velocity units) * :math:`\gamma_{\parallel}` (force/velocity units) -* :math:`s_{\perp}` (unitless) +* :math:`\gamma_{\perp}` (force/velocity units) * :math:`s_{\parallel}` (unitless) +* :math:`s_{\perp}` (unitless) * :math:`r_c` (distance units) The last coefficient is optional. If not specified, the global DPD diff --git a/doc/src/pair_eam.rst b/doc/src/pair_eam.rst index a7141c3849..27347b77f0 100644 --- a/doc/src/pair_eam.rst +++ b/doc/src/pair_eam.rst @@ -440,7 +440,7 @@ identical to the FS EAM files (see above). ---------- -.. versionadded:: TBD +.. versionadded:: 3Nov2022 The *eam*, *eam/alloy*, *eam/fs*, and *eam/he* pair styles support extraction of two per-atom quantities by the :doc:`fix pair ` diff --git a/doc/src/pair_list.rst b/doc/src/pair_list.rst index 762afb888c..fd08f9d6f0 100644 --- a/doc/src/pair_list.rst +++ b/doc/src/pair_list.rst @@ -57,7 +57,7 @@ The format of the list file is as follows: ID2 = atom ID of second atom style = style of interaction coeffs = list of coeffs - cutoff = cutoff for interaction (optional, except for style *quartic*) + cutoff = cutoff for interaction (optional) The cutoff parameter is optional for all but the *quartic* interactions. If it is not specified, the global cutoff is used. @@ -71,7 +71,7 @@ Here is an example file: 15 259 lj126 1.0 1.0 50.0 15 603 morse 10.0 1.2 2.0 10.0 # and another comment 18 470 harmonic 50.0 1.2 5.0 - 19 332 quartic 5.0 -1.2 1.2 5.0 + 19 332 quartic 10.0 5.0 -1.2 1.2 The style *lj126* computes pairwise interactions with the formula @@ -100,7 +100,7 @@ The style *harmonic* computes pairwise interactions with the formula .. math:: - E = K (r - r_0)^2 + E = K (r - r_0)^2 \qquad r < r_c and the coefficients: @@ -113,16 +113,14 @@ The style *quartic* computes pairwise interactions with the formula .. math:: - E = K (r - r_c)^2 (r - r_c -b_1) (r - r_c - b_2) \qquad r < r_c + E = K (r - r_0)^2 (r - r_0 -b_1) (r - r_0 - b_2) \qquad r < r_c and the coefficients: * :math:`K` (energy units) +* :math:`r_0` (distance units) * :math:`b_1` (distance units) * :math:`b_2` (distance units) -* :math:`r_c` (distance units) - -Note that the per list entry cutoff :math:`r_c` is **required** for *quartic* interactions. ---------- diff --git a/doc/src/pair_mliap.rst b/doc/src/pair_mliap.rst index 3993a4701e..fcb9c7881e 100644 --- a/doc/src/pair_mliap.rst +++ b/doc/src/pair_mliap.rst @@ -1,8 +1,11 @@ .. index:: pair_style mliap +.. index:: pair_style mliap/kk pair_style mliap command ======================== +Accelerator Variants: *mliap/kk* + Syntax """""" @@ -177,7 +180,7 @@ to specify the path for these *model* and *descriptor* files. larger systems since their size depends on the total number of neighbors per MPI process. -.. versionadded:: TBD +.. versionadded:: 3Nov2022 The *unified* keyword is followed by an argument specifying the filename containing the serialized unified Python object and the "ghostneigh" toggle @@ -207,6 +210,12 @@ cutoff manually, such as in the following example. on the active LAMMPS object before the pair style is defined. This call locates and loads the mliap-specific python module that is built into LAMMPS. +---------- + +.. include:: accel_styles.rst + +---------- + Mixing, shift, table, tail correction, restart, rRESPA info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" diff --git a/doc/src/pair_pace.rst b/doc/src/pair_pace.rst index f8762ee9ca..697a9965b6 100644 --- a/doc/src/pair_pace.rst +++ b/doc/src/pair_pace.rst @@ -112,8 +112,7 @@ requests to compute `gamma`, as shown in example below: compute max_pace_gamma all reduce max f_pace_gamma variable dump_skip equal "c_max_pace_gamma < 5" - - dump pace_dump all custom 20 extrapolative_structures.dump id x y z f_pace_gamma + dump pace_dump all custom 20 extrapolative_structures.dump id type x y z f_pace_gamma dump_modify pace_dump skip v_dump_skip variable max_pace_gamma equal c_max_pace_gamma diff --git a/doc/src/pair_pod.rst b/doc/src/pair_pod.rst new file mode 100644 index 0000000000..cb4edcb9e9 --- /dev/null +++ b/doc/src/pair_pod.rst @@ -0,0 +1,97 @@ +.. index:: pair_style pod + +pair_style pod command +======================== + +Syntax +"""""" + +.. code-block:: LAMMPS + + pair_style pod + +Examples +"""""""" + +.. code-block:: LAMMPS + + pair_style pod + pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta + +Description +""""""""""" + +.. versionadded:: 22Dec2022 + +Pair style *pod* defines the proper orthogonal descriptor (POD) +potential :ref:`(Nguyen) `. The mathematical definition of +the POD potential is described from :doc:`fitpod `, which is +used to fit the POD potential to *ab initio* energy and force data. + +Only a single pair_coeff command is used with the *pod* style which +specifies a POD parameter file followed by a coefficient file. + +The coefficient file (``Ta_coefficients.pod``) contains coefficients for the +POD potential. The top of the coefficient file can contain any number of +blank and comment lines (start with #), but follows a strict format +after that. The first non-blank non-comment line must contain: + +* POD_coefficients: *ncoeff* + +This is followed by *ncoeff* coefficients, one per line. The coefficient +file is generated after training the POD potential using :doc:`fitpod +`. + +The POD parameter file (``Ta_param.pod``) can contain blank and comment lines +(start with #) anywhere. Each non-blank non-comment line must contain +one keyword/value pair. See :doc:`fitpod ` for the description +of all the keywords that can be assigned in the parameter file. + +As an example, if a LAMMPS indium phosphide simulation has 4 atoms +types, with the first two being indium and the third and fourth being +phophorous, the pair_coeff command would look like this: + +.. code-block:: LAMMPS + + pair_coeff * * pod InP_param.pod InP_coefficients.pod In In P P + +The first 2 arguments must be \* \* so as to span all LAMMPS atom types. +The two filenames are for the parameter and coefficient files, respectively. +The two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the +POD 'In' element. The two trailing 'P' arguments map LAMMPS atom types +3 and 4 to the POD 'P' element. + +If a POD mapping value is specified as NULL, the mapping is not +performed. This can be used when a *pod* 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. + +Examples about training and using POD potentials are found in the +directory lammps/examples/PACKAGES/pod. + +---------- + +Restrictions +"""""""""""" + +This style is part of the ML-POD package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package +` page for more info. + +This pair style does not compute per-atom energies and per-atom stresses. + +Related commands +"""""""""""""""" + +:doc:`fitpod `, + +Default +""""""" + +none + +---------- + +.. _Nguyen20221: + +**(Nguyen)** Nguyen and Rohskopf, arXiv preprint arXiv:2209.02362 (2022). diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index a9b97b05c0..48daf34f17 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -314,6 +314,7 @@ accelerated styles exist. * :doc:`oxrna2/xstk ` - * :doc:`pace ` - Atomic Cluster Expansion (ACE) machine-learning potential * :doc:`pace/extrapolation ` - Atomic Cluster Expansion (ACE) machine-learning potential with extrapolation grades +* :doc:`pod ` - Proper orthogonal decomposition (POD) machine-learning potential * :doc:`peri/eps ` - peridynamic EPS potential * :doc:`peri/lps ` - peridynamic LPS potential * :doc:`peri/pmb ` - peridynamic PMB potential @@ -374,6 +375,7 @@ accelerated styles exist. * :doc:`vashishta ` - Vashishta 2-body and 3-body potential * :doc:`vashishta/table ` - * :doc:`wf/cut ` - Wang-Frenkel Potential for short-ranged interactions +* :doc:`ylz ` - Yuan-Li-Zhang Potential for anisotropic interactions * :doc:`yukawa ` - Yukawa potential * :doc:`yukawa/colloid ` - screened Yukawa potential for finite-size particles * :doc:`zbl ` - Ziegler-Biersack-Littmark potential diff --git a/doc/src/pair_sw.rst b/doc/src/pair_sw.rst index 579e4c6f3f..7b4e52c3d9 100644 --- a/doc/src/pair_sw.rst +++ b/doc/src/pair_sw.rst @@ -176,9 +176,13 @@ are placeholders for atom types that will be used with other potentials. .. note:: - When the *threebody off* keyword is used, multiple pair_coeff commands may - be used to specific the pairs of atoms which don't require three-body term. - In these cases, the first 2 arguments are not required to be \* \*. + When the *threebody off* keyword is used, multiple pair_coeff + commands may be used to specific the pairs of atoms which don't + require three-body term. In these cases, the first 2 arguments are + not required to be \* \*, the potential parameter file is only read + by the first :doc:`pair_coeff command ` and the element + to atom type mappings must be consistent across all *pair_coeff* + statements. If not LAMMPS will abort with an error. Stillinger-Weber files in the *potentials* directory of the LAMMPS distribution have a ".sw" suffix. Lines that are not blank or diff --git a/doc/src/pair_table.rst b/doc/src/pair_table.rst index 79eb8f5b42..e5b05a3a23 100644 --- a/doc/src/pair_table.rst +++ b/doc/src/pair_table.rst @@ -120,6 +120,13 @@ best effect: ---------- +Suitable tables in the correct format for use with these pair styles can +be created by LAMMPS itself using the :doc:`pair_write ` +command. In combination with the :doc:`pair style python ` +this can be a powerful mechanism to implement and test tables for use +with LAMMPS. Another option to generate tables is the Python code in +the ``tools/tabulate`` folder of the LAMMPS source code distribution. + The format of a tabulated file has an (optional) header followed by a series of one or more sections, defined as follows (without the parenthesized comments). The header must start with a `#` character diff --git a/doc/src/pair_tracker.rst b/doc/src/pair_tracker.rst index 04967e952d..e34bedca2c 100644 --- a/doc/src/pair_tracker.rst +++ b/doc/src/pair_tracker.rst @@ -174,8 +174,8 @@ the specified attribute. Restrictions """""""""""" -This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package +This pair style is part of the MISC package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This pair style is currently incompatible with granular pair styles diff --git a/doc/src/pair_ylz.rst b/doc/src/pair_ylz.rst new file mode 100644 index 0000000000..17cf0ca639 --- /dev/null +++ b/doc/src/pair_ylz.rst @@ -0,0 +1,177 @@ +.. index:: pair_style ylz + +pair_style ylz command +=========================== + +Syntax +"""""" + +.. code-block:: LAMMPS + + pair_style ylz cutoff + + +* cutoff = global cutoff for interactions (distance units) + +Examples +"""""""" + +.. code-block:: LAMMPS + + pair_style ylz 2.6 + pair_coeff * * 1.0 1.0 4 3 0.0 2.6 + + +Description +""""""""""" + +.. versionadded:: 3Nov2022 + +The *ylz* (Yuan-Li-Zhang) style computes an anisotropic interaction +between pairs of coarse-grained particles considering the relative +particle orientations. This potential was originally developed as a +particle-based solvent-free model for biological membranes +:ref:`(Yuan2010a) `. Unlike :doc:`pair_style gayberne +`, whose orientation dependence is strictly derived from +the closest distance between two ellipsoidal rigid bodies, the +orientation-dependence of this pair style is mathematically defined such +that the particles can self-assemble into one-particle-thick fluid +membranes. The potential of this pair style is described by: + +.. math:: + + U ( \mathbf{r}_{ij}, \mathbf{n}_i, \mathbf{n}_j ) =\left\{\begin{matrix} {u}_R(r)+\left [ 1-\phi (\mathbf{\hat{r}}_{ij}, \mathbf{n}_i, \mathbf{n}_j ) \right ]\epsilon, ~~ r<{r}_{min} \\ {u}_A(r)\phi (\mathbf{\hat{r}}_{ij}, \mathbf{n}_i, \mathbf{n}_j ),~~ {r}_{min}`, nanoparticle +endocytosis :ref:`(Huang) `, modeling of red blood cell membranes +:ref:`(Fu) `, :ref:`(Appshaw) `, and modeling of cell +elasticity :ref:`(Becton) `. + +Use of this pair style requires the NVE, NVT, or NPT fixes with the +*asphere* extension (e.g. :doc:`fix nve/asphere `) in +order to integrate particle rotation. Additionally, :doc:`atom_style +ellipsoid ` should be used since it defines the rotational +state of each particle. + +The following coefficients must be defined for each pair of atoms types +via the :doc:`pair_coeff ` command as in the examples above, +or in the data file or restart files read by the :doc:`read_data +` or :doc:`read_restart ` commands, or by +mixing as described below: + +* :math:`\epsilon` = well depth (energy units) +* :math:`\sigma` = minimum effective particle radii (distance units) +* :math:`\zeta` = tuning parameter for the slope of the attractive branch +* :math:`\mu` = parameter related to bending rigidity +* :math:`\beta` = parameter related to the spontaneous curvature +* cutoff (distance units) + +The last coefficient is optional. If not specified, the global +cutoff specified in the pair_style command is used. + +---------- + +Mixing, shift, table, tail correction, restart, rRESPA info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +For atom type pairs I,J and I != J, the epsilon and sigma coefficients +and cutoff distance for this pair style can be mixed. The default mix +value is *geometric*\ . See the "pair_modify" command for details. + +The :doc:`pair_modify ` table option is not relevant for +this pair style. + +This pair style does not support the :doc:`pair_modify ` +tail option for adding long-range tail corrections to energy and +pressure. + +This pair style writes its information to :doc:`binary restart files +`, so pair_style and pair_coeff commands do not need to be +specified 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 +"""""""""""" + +The *ylz* style is part of the ASPHERE 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 that atoms store torque and a quaternion to +represent their orientation, as defined by the :doc:`atom_style +`. It also requires they store a per-atom :doc:`shape +`. The particles cannot store a per-particle diameter. To avoid +being mistakenly considered as point particles, the shape parameters ought +to be non-spherical, like [1 0.99 0.99]. Unlike the :doc:`resquared +` pair style for which the shape directly determines the +mathematical expressions of the potential, the shape parameters for this +pair style is only involved in the computation of the moment of inertia +and thus only influences the rotational dynamics of individual +particles. + +This pair style requires that **all** atoms are ellipsoids as defined by +the :doc:`atom_style ellipsoid ` command. + + +Related commands +"""""""""""""""" + +:doc:`pair_coeff `, :doc:`fix nve/asphere +:doc:`, `compute temp/asphere `, +:doc::doc:`pair_style resquared `, :doc:`pair_style +:doc:gayberne ` + +Default +""""""" + +none + +---------- + +.. _Yuan: + +**(Yuan2010a)** Yuan, Huang, Li, Lykotrafitis, Zhang, Phys. Rev. E, 82, 011905(2010). + +**(Yuan2010b)** Yuan, Huang, Zhang, Soft. Matter, 6, 4571(2010). + +.. _Huang: + +**(Huang)** Huang, Zhang, Yuan, Gao, Zhang, Nano Lett. 13, 4546(2013). + +.. _Fu: + +**(Fu)** Fu, Peng, Yuan, Kfoury, Young, Comput. Phys. Commun, 210, 193-203(2017). + +.. _Appshaw: + +**(Appshaw)** Appshaw, Seddon, Hanna, Soft. Matter,18, 1747(2022). + +.. _Becton: + +**(Becton)** Becton, Averett, Wang, Biomech. Model. Mechanobiology, 18, 425-433(2019). diff --git a/doc/src/python.rst b/doc/src/python.rst index aad2f636d3..19abbf93e2 100644 --- a/doc/src/python.rst +++ b/doc/src/python.rst @@ -8,14 +8,25 @@ Syntax .. parsed-literal:: - python func keyword args ... + python mode keyword args ... -* func = name of Python function -* one or more keyword/args pairs must be appended +* mode = *source* or name of Python function + + if mode is *source*: .. parsed-literal:: - keyword = *invoke* or *input* or *return* or *format* or *length* or *file* or *here* or *exists* or *source* + keyword = *here* or name of a *Python file* + *here* arg = inline + inline = one or more lines of Python code which defines func + must be a single argument, typically enclosed between triple quotes + *Python file* = name of a file with Python code which will be executed immediately + +* if *mode* is the name of a Python function, one or more keywords with/without arguments must be appended + + .. parsed-literal:: + + keyword = *invoke* or *input* or *return* or *format* or *length* or *file* or *here* or *exists* *invoke* arg = none = invoke the previously defined Python function *input* args = N i1 i2 ... iN N = # of inputs to function @@ -24,7 +35,7 @@ Syntax SELF = reference to LAMMPS itself which can be accessed by Python function variable = v_name, where name = name of LAMMPS variable, e.g. v_abc *return* arg = varReturn - varReturn = v_name = LAMMPS variable name which return value of function will be assigned to + varReturn = v_name = LAMMPS variable name which the return value of the Python function will be assigned to *format* arg = fstring with M characters M = N if no return value, where N = # of inputs M = N+1 if there is a return value @@ -38,10 +49,6 @@ Syntax inline = one or more lines of Python code which defines func must be a single argument, typically enclosed between triple quotes *exists* arg = none = Python code has been loaded by previous python command - *source* arg = *filename* or *inline* - filename = file of Python code which will be executed immediately - inline = one or more lines of Python code which will be executed immediately - must be a single argument, typically enclosed between triple quotes Examples """""""" @@ -70,80 +77,105 @@ Examples lmp.command("pair_style lj/cut ${cut}") # LAMMPS commands lmp.command("pair_coeff * * 1.0 1.0") lmp.command("run 100") - """ + """ + + python source funcdef.py + + python source here "from lammps import lammps" + Description """"""""""" -Define a Python function or execute a previously defined function or -execute some arbitrary python code. +The *python* command allows interfacing LAMMPS with an embedded Python +interpreter and enables either executing arbitrary python code in that +interpreter, registering a Python function for future execution (as a +python style variable, from a fix interfaced with python, or for direct +invocation), or invoking such a previously registered function. + Arguments, including LAMMPS variables, can be passed to the function -from the LAMMPS input script and a value returned by the Python -function to a LAMMPS variable. The Python code for the function can -be included directly in the input script or in a separate Python file. -The function can be standard Python code or it can make "callbacks" to -LAMMPS through its library interface to query or set internal values -within LAMMPS. This is a powerful mechanism for performing complex -operations in a LAMMPS input script that are not possible with the -simple input script and variable syntax which LAMMPS defines. Thus -your input script can operate more like a true programming language. +from the LAMMPS input script and a value returned by the Python function +assigned to a LAMMPS variable. The Python code for the function can be included +directly in the input script or in a separate Python file. The function +can be standard Python code or it can make "callbacks" to LAMMPS through +its library interface to query or set internal values within LAMMPS. +This is a powerful mechanism for performing complex operations in a +LAMMPS input script that are not possible with the simple input script +and variable syntax which LAMMPS defines. Thus your input script can +operate more like a true programming language. Use of this command requires building LAMMPS with the PYTHON package which links to the Python library so that the Python interpreter is embedded in LAMMPS. More details about this process are given below. There are two ways to invoke a Python function once it has been -defined. One is using the *invoke* keyword. The other is to assign +registered. One is using the *invoke* keyword. The other is to assign the function to a :doc:`python-style variable ` defined in -your input script. Whenever the variable is evaluated, it will -execute the Python function to assign a value to the variable. Note -that variables can be evaluated in many different ways within LAMMPS. -They can be substituted for directly in an input script. Or they can -be passed to various commands as arguments, so that the variable is -evaluated during a simulation run. +your input script. Whenever the variable is evaluated, it will execute +the Python function to assign a value to the variable. Note that +variables can be evaluated in many different ways within LAMMPS. They +can be substituted with their result directly in an input script, or +they can be passed to various commands as arguments, so that the +variable is evaluated during a simulation run. -A broader overview of how Python can be used with LAMMPS is given on -the :doc:`Python ` doc page. There is an examples/python -directory which illustrates use of the python command. +A broader overview of how Python can be used with LAMMPS is given in the +:doc:`Use Python with LAMMPS ` section of the +documentation. There also is an ``examples/python`` directory which +illustrates use of the python command. ---------- -The *func* setting specifies the name of the Python function. The -code for the function is defined using the *file* or *here* keywords -as explained below. In case of the *source* keyword, the name of -the function is ignored. +The first argument of the *python* command is either the *source* +keyword or the name of a Python function. This defines the mode +of the python command. + +.. versionchanged:: 22Dec2022 + +If the *source* keyword is used, it is followed by either a file name or +the *here* keyword. No other keywords can be used. The *here* keyword +is followed by a string with python commands, either on a single line +enclosed in quotes, or as multiple lines enclosed in triple quotes. +These Python commands will be passed to the python interpreter and +executed immediately without registering a Python function for future +execution. The code will be loaded into and run in the "main" module of +the Python interpreter. This allows running arbitrary Python code at +any time while processing the LAMMPS input file. This can be used to +pre-load Python modules, initialize global variables, define functions +or classes, or perform operations using the python programming language. +The Python code will be executed in parallel on all MPI processes. No +arguments can be passed. + +In all other cases, the first argument is the name of a Python function +that will be registered with LAMMPS for future execution. The function +may already be defined (see *exists* keyword) or must be defined using +the *file* or *here* keywords as explained below. If the *invoke* keyword is used, no other keywords can be used, and a -previous python command must have defined the Python function +previous *python* command must have registered the Python function referenced by this command. This invokes the Python function with the -previously defined arguments and return value processed as explained -below. You can invoke the function as many times as you wish in your -input script. - -If the *source* keyword is used, no other keywords can be used. -The argument can be a filename or a string with python commands, -either on a single line enclosed in quotes, or as multiple lines -enclosed in triple quotes. These python commands will be passed -to the python interpreter and executed immediately without registering -a python function for future execution. +previously defined arguments and the return value is processed as +explained below. You can invoke the function as many times as you wish +in your input script. The *input* keyword defines how many arguments *N* the Python function -expects. If it takes no arguments, then the *input* keyword should -not be used. Each argument can be specified directly as a value, -e.g. 6 or 3.14159 or abc (a string of characters). The type of each +expects. If it takes no arguments, then the *input* keyword should not +be used. Each argument can be specified directly as a value, e.g. '6' +or '3.14159' or 'abc' (a string of characters). The type of each argument is specified by the *format* keyword as explained below, so that Python will know how to interpret the value. If the word SELF is used for an argument it has a special meaning. A pointer is passed to -the Python function which it converts into a reference to LAMMPS -itself. This enables the function to call back to LAMMPS through its -library interface as explained below. This allows the Python function -to query or set values internal to LAMMPS which can affect the -subsequent execution of the input script. A LAMMPS variable can also -be used as an argument, specified as v_name, where "name" is the name -of the variable. Any style of LAMMPS variable can be used, as defined -by the :doc:`variable ` command. Each time the Python -function is invoked, the LAMMPS variable is evaluated and its value is -passed to the Python function. +the Python function which it can convert into a reference to LAMMPS +itself using the :doc:`LAMMPS Python module `. This +enables the function to call back to LAMMPS through its library +interface as explained below. This allows the Python function to query +or set values internal to LAMMPS which can affect the subsequent +execution of the input script. A LAMMPS variable can also be used as an +argument, specified as v_name, where "name" is the name of the variable. +Any style of LAMMPS variable returning a scalar or a string can be used, +as defined by the :doc:`variable ` command. The *format* +keyword must be used to set the type of data that is passed to Python. +Each time the Python function is invoked, the LAMMPS variable is +evaluated and its value is passed to the Python function. The *return* keyword is only needed if the Python function returns a value. The specified *varReturn* must be of the form v_name, where @@ -153,8 +185,9 @@ numeric or string value, as specified by the *format* keyword. As explained on the :doc:`variable ` doc page, the definition of a python-style variable associates a Python function name with the -variable. This must match the *func* setting for this command. For -example these two commands would be self-consistent: +variable. This must match the *Python function name* first argument of +the *python* command. For example these two commands would be +consistent: .. code-block:: LAMMPS @@ -163,21 +196,22 @@ example these two commands would be self-consistent: The two commands can appear in either order in the input script so long as both are specified before the Python function is invoked for -the first time. +the first time. Afterwards, the variable 'foo' is associated with +the Python function 'myMultiply'. -The *format* keyword must be used if the *input* or *return* keyword -is used. It defines an *fstring* with M characters, where M = sum of +The *format* keyword must be used if the *input* or *return* keywords +are used. It defines an *fstring* with M characters, where M = sum of number of inputs and outputs. The order of characters corresponds to the N inputs, followed by the return value (if it exists). Each character must be one of the following: "i" for integer, "f" for -floating point, "s" for string, or "p" for SELF. Each character -defines the type of the corresponding input or output value of the -Python function and affects the type conversion that is performed -internally as data is passed back and forth between LAMMPS and Python. -Note that it is permissible to use a :doc:`python-style variable ` in a LAMMPS command that allows for an -equal-style variable as an argument, but only if the output of the -Python function is flagged as a numeric value ("i" or "f") via the -*format* keyword. +floating point, "s" for string, or "p" for SELF. Each character defines +the type of the corresponding input or output value of the Python +function and affects the type conversion that is performed internally as +data is passed back and forth between LAMMPS and Python. Note that it +is permissible to use a :doc:`python-style variable ` in a +LAMMPS command that allows for an equal-style variable as an argument, +but only if the output of the Python function is flagged as a numeric +value ("i" or "f") via the *format* keyword. If the *return* keyword is used and the *format* keyword specifies the output as a string, then the default maximum length of that string is @@ -192,12 +226,13 @@ truncated. Either the *file*, *here*, or *exists* keyword must be used, but only one of them. These keywords specify what Python code to load into the -Python interpreter. The *file* keyword gives the name of a file, -which should end with a ".py" suffix, which contains Python code. The -code will be immediately loaded into and run in the "main" module of -the Python interpreter. Note that Python code which contains a -function definition does not "execute" the function when it is run; it -simply defines the function so that it can be invoked later. +Python interpreter. The *file* keyword gives the name of a file +containing Python code, which should end with a ".py" suffix. The code +will be immediately loaded into and run in the "main" module of the +Python interpreter. The Python code will be executed in parallel on all +MPI processes. Note that Python code which contains a function +definition does not "execute" the function when it is run; it simply +defines the function so that it can be invoked later. The *here* keyword does the same thing, except that the Python code follows as a single argument to the *here* keyword. This can be done @@ -208,14 +243,15 @@ proper indentation, blank lines, and comments, as desired. See the how triple quotes can be used as part of input script syntax. The *exists* keyword takes no argument. It means that Python code -containing the required Python function defined by the *func* setting, -is assumed to have been previously loaded by another python command. +containing the required Python function with the given name has already +been executed, for example by a *python source* command or in the same +file that was used previously with the *file* keyword. -Note that the Python code that is loaded and run must contain a -function with the specified *func* name. To operate properly when -later invoked, the function code must match the *input* and -*return* and *format* keywords specified by the python command. -Otherwise Python will generate an error. +Note that the Python code that is loaded and run must contain a function +with the specified function name. To operate properly when later +invoked, the function code must match the *input* and *return* and +*format* keywords specified by the python command. Otherwise Python +will generate an error. ---------- @@ -225,19 +261,19 @@ LAMMPS. Whether you load Python code from a file or directly from your input script, via the *file* and *here* keywords, the code can be identical. It must be indented properly as Python requires. It can contain -comments or blank lines. If the code is in your input script, it -cannot however contain triple-quoted Python strings, since that will -conflict with the triple-quote parsing that the LAMMPS input script -performs. +comments or blank lines. If the code is in your input script, it cannot +however contain triple-quoted Python strings, since that will conflict +with the triple-quote parsing that the LAMMPS input script performs. All the Python code you specify via one or more python commands is -loaded into the Python "main" module, i.e. __main__. The code can -define global variables or statements that are outside of function -definitions. It can contain multiple functions, only one of which -matches the *func* setting in the python command. This means you can -use the *file* keyword once to load several functions, and the -*exists* keyword thereafter in subsequent python commands to access -the other functions previously loaded. +loaded into the Python "main" module, i.e. ``__name__ == '__main__'``. +The code can define global variables, define global functions, define +classes or execute statements that are outside of function definitions. +It can contain multiple functions, only one of which matches the *func* +setting in the python command. This means you can use the *file* +keyword once to load several functions, and the *exists* keyword +thereafter in subsequent python commands to register the other functions +that were previously loaded with LAMMPS. A Python function you define (or more generally, the code you load) can import other Python modules or classes, it can make calls to other @@ -264,12 +300,13 @@ outside the function: nvaluelast = nvalue return nvalue -Nsteplast stores the previous timestep the function was invoked -(passed as an argument to the function). Nvaluelast stores the return -value computed on the last function invocation. If the function is -invoked again on the same timestep, the previous value is simply -returned, without re-computing it. The "global" statement inside the -Python function allows it to overwrite the global variables. +The variable 'nsteplast' stores the previous timestep the function was +invoked (passed as an argument to the function). The variable +'nvaluelast' stores the return value computed on the last function +invocation. If the function is invoked again on the same timestep, the +previous value is simply returned, without re-computing it. The +"global" statement inside the Python function allows it to overwrite the +global variables from within the local context of the function. Note that if you load Python code multiple times (via multiple python commands), you can overwrite previously loaded variables and functions @@ -285,19 +322,39 @@ copy of the Python function(s) you define. There is no connection between the Python interpreters running on different processors. This implies three important things. -First, if you put a print statement in your Python function, you will -see P copies of the output, when running on P processors. If the -prints occur at (nearly) the same time, the P copies of the output may -be mixed together. Welcome to the world of parallel programming and -debugging. +First, if you put a print or other statement creating output to the +screen in your Python function, you will see P copies of the output, +when running on P processors. If the prints occur at (nearly) the same +time, the P copies of the output may be mixed together. When loading +the LAMMPS Python module into the embedded Python interpreter, it is +possible to pass the pointer to the current LAMMPS class instance and +via the Python interface to the LAMMPS library interface, it is possible +to determine the MPI rank of the current process and thus adapt the +Python code so that output will only appear on MPI rank 0. The +following LAMMPS input demonstrates how this could be done. The text +'Hello, LAMMPS!' should be printed only once, even when running LAMMPS +in parallel. -Second, if your Python code loads modules that are not pre-loaded by -the Python library, then it will load the module from disk. This may -be a bottleneck if 1000s of processors try to load a module at the -same time. On some large supercomputers, loading of modules from disk -by Python may be disabled. In this case you would need to pre-build a -Python library that has the required modules pre-loaded and link -LAMMPS with that library. +.. code-block:: LAMMPS + + python python_hello input 1 SELF format p here """ + def python_hello(handle): + from lammps import lammps + lmp = lammps(ptr=handle) + me = lmp.extract_setting('world_rank') + if me == 0: + print('Hello, LAMMPS!') + """ + + python python_hello invoke + +If your Python code loads Python modules that are not pre-loaded by the +Python library, then it will load the module from disk. This may be a +bottleneck if 1000s of processors try to load a module at the same time. +On some large supercomputers, loading of modules from disk by Python may +be disabled. In this case you would need to pre-build a Python library +that has the required modules pre-loaded and link LAMMPS with that +library. Third, if your Python code calls back to LAMMPS (discussed in the next section) and causes LAMMPS to perform an MPI operation requires @@ -315,22 +372,21 @@ Python function is as follows: .. code-block:: python - def foo(lmpptr,...): + def foo(handle,...): from lammps import lammps - lmp = lammps(ptr=lmpptr) + lmp = lammps(ptr=handle) lmp.command('print "Hello from inside Python"') ... -The function definition must include a variable (lmpptr in this case) -which corresponds to SELF in the python command. The first line of the -function imports the :doc:`"lammps" Python module `. -The second line creates a Python object ``lmp`` which -wraps the instance of LAMMPS that called the function. The "ptr=lmpptr" -argument is what makes that happen. The third line invokes the -command() function in the LAMMPS library interface. It takes a single -string argument which is a LAMMPS input script command for LAMMPS to -execute, the same as if it appeared in your input script. In this case, -LAMMPS should output +The function definition must include a variable ('handle' in this case) +which corresponds to SELF in the *python* command. The first line of +the function imports the :doc:`"lammps" Python module `. +The second line creates a Python object ``lmp`` which wraps the instance +of LAMMPS that called the function. The 'ptr=handle' argument is what +makes that happen. The third line invokes the command() function in the +LAMMPS library interface. It takes a single string argument which is a +LAMMPS input script command for LAMMPS to execute, the same as if it +appeared in your input script. In this case, LAMMPS should output .. parsed-literal:: @@ -344,8 +400,8 @@ The :doc:`Python_head` page describes the syntax for how Python wraps the various functions included in the LAMMPS library interface. -A more interesting example is in the examples/python/in.python script -which loads and runs the following function from examples/python/funcs.py: +A more interesting example is in the ``examples/python/in.python`` script +which loads and runs the following function from ``examples/python/funcs.py``: .. code-block:: python @@ -495,24 +551,35 @@ Restrictions """""""""""" This command is part of the PYTHON package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` page for more info. +LAMMPS was built with that package. See the :doc:`Build package +` page for more info. -Building LAMMPS with the PYTHON package will link LAMMPS with the -Python library on your system. Settings to enable this are in the +Building LAMMPS with the PYTHON package will link LAMMPS with the Python +library on your system. Settings to enable this are in the lib/python/Makefile.lammps file. See the lib/python/README file for information on those settings. -If you use Python code which calls back to LAMMPS, via the SELF input argument -explained above, there is an extra step required when building LAMMPS. LAMMPS -must also be built as a shared library and your Python function must be able to -load the :doc:`"lammps" Python module ` that wraps the LAMMPS -library interface. These are the same steps required to use Python by itself -to wrap LAMMPS. Details on these steps are explained on the :doc:`Python -` doc page. Note that it is important that the stand-alone LAMMPS -executable and the LAMMPS shared library be consistent (built from the same -source code files) in order for this to work. If the two have been built at +If you use Python code which calls back to LAMMPS, via the SELF input +argument explained above, there is an extra step required when building +LAMMPS. LAMMPS must also be built as a shared library and your Python +function must be able to load the :doc:`"lammps" Python module +` that wraps the LAMMPS library interface. These are the +same steps required to use Python by itself to wrap LAMMPS. Details on +these steps are explained on the :doc:`Python ` doc page. +Note that it is important that the stand-alone LAMMPS executable and the +LAMMPS shared library be consistent (built from the same source code +files) in order for this to work. If the two have been built at different times using different source files, problems may occur. +Another limitation of calling back to Python from the LAMMPS module +using the *python* command in a LAMMPS input is that both, the Python +interpreter and LAMMPS, must be linked to the same Python runtime as a +shared library. If the Python interpreter is linked to Python +statically (which seems to happen with Conda) then loading the shared +LAMMPS library will create a second python "main" module that hides the +one from the Python interpreter and all previous defined function and +global variables will become invisible. + Related commands """""""""""""""" diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index 858029caae..453208ed3f 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -71,8 +71,14 @@ Also see the explanation of the :doc:`-restart command-line switch This command can be used multiple times to add new atoms and their properties to an existing system by using the *add*, *offset*, and -*shift* keywords. See more details below, which includes the use case -for the *extra* keywords. +*shift* keywords. However, it is important to understand that several +system parameters, like the number of types of different kinds and per +atom settings are **locked in** after the first *read_data* command, +which means that no type ID (including its offset) may have a larger +value when processing additional data files than what is set by the +first data file and the corresponding *read_data* command options. See +more details on this situation below, which includes the use case for +the *extra* keywords. The *group* keyword adds all the atoms in the data file to the specified group-ID. The group will be created if it does not already @@ -334,16 +340,20 @@ and are called "tilt factors" because they are the amount of displacement applied to faces of an originally orthogonal box to transform it into the parallelepiped. -By default, the tilt factors (xy,xz,yz) can not skew the box more than -half the distance of the corresponding parallel box length. For -example, if xlo = 2 and xhi = 12, then the x box length is 10 and the -xy tilt factor must be between -5 and 5. Similarly, both xz and yz -must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not -a limitation, since if the maximum tilt factor is 5 (as in this -example), then configurations with tilt = ..., -15, -5, 5, 15, 25, -... are all geometrically equivalent. If you wish to define a box -with tilt factors that exceed these limits, you can use the :doc:`box tilt ` command, with a setting of *large*\ ; a setting of -*small* is the default. +The tilt factors (xy,xz,yz) should not skew the box more than half the +distance of the corresponding parallel box length. For example, if +:math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the :math:`x` +box length is 10 and the :math:`xy` tilt factor must be between +:math:`-5` and :math:`5`. Similarly, both :math:`xz` and :math:`yz` +must be between :math:`-(x_\text{hi}-x_\text{lo})/2` and +:math:`+(y_\text{hi}-y_\text{lo})/2`. Note that this is not a +limitation, since if the maximum tilt factor is 5 (as in this example), +then configurations with tilt :math:`= \dots, -15`, :math:`-5`, +:math:`5`, :math:`15`, :math:`25, \dots` are all geometrically +equivalent. Simulations with large tilt factors will run inefficiently, +since they require more ghost atoms and thus more communication. With +very large tilt factors, LAMMPS will eventually produce incorrect +trajectories and stop with errors due to lost atoms or similar. See the :doc:`Howto triclinic ` page for a geometric description of triclinic boxes, as defined by LAMMPS, and diff --git a/doc/src/read_restart.rst b/doc/src/read_restart.rst index f3065a2a5c..fce6154ea7 100644 --- a/doc/src/read_restart.rst +++ b/doc/src/read_restart.rst @@ -8,7 +8,7 @@ Syntax .. code-block:: LAMMPS - read_restart file flag + read_restart file * file = name of binary restart file to read in @@ -37,6 +37,13 @@ processors in the current simulation and the settings of the changed by the :doc:`balance ` or :doc:`fix balance ` commands. +.. deprecated:: 23Jun2022 + +Atom coordinates that are found to be outside the simulation box when +reading the restart will be remapped back into the box and their image +flags updated accordingly. This previously required specifying the +*remap* option, but that is no longer required. + 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. diff --git a/doc/src/rerun.rst b/doc/src/rerun.rst index f6ea0973e1..eb0f8797fc 100644 --- a/doc/src/rerun.rst +++ b/doc/src/rerun.rst @@ -192,13 +192,12 @@ calculated which saves time. The :doc:`comm_modify cutoff acquired from far enough away for operations like bond and angle evaluations, if no pair style is being used. -Every time a snapshot is read, the timestep for the simulation is -reset, as if the :doc:`reset_timestep ` command were -used. This command has some restrictions as to what fixes can be -defined. See its page for details. For example, the :doc:`fix -deposit ` and :doc:`fix dt/reset ` fixes -are in this category. They also make no sense to use with a rerun -command. +Every time a snapshot is read, the timestep for the simulation is reset, +as if the :doc:`reset_timestep ` command were used. +This command has some restrictions as to what fixes can be defined. See +its documentation page for details. For example, the :doc:`fix deposit +` and :doc:`fix dt/reset ` fixes are in this +category. They also make no sense to use with a rerun command. If time-averaging fixes like :doc:`fix ave/time ` are used, they are invoked on timesteps that are a function of their diff --git a/doc/src/reset_atom_ids.rst b/doc/src/reset_atom_ids.rst deleted file mode 100644 index e83d65d546..0000000000 --- a/doc/src/reset_atom_ids.rst +++ /dev/null @@ -1,94 +0,0 @@ -.. index:: reset_atom_ids - -reset_atom_ids command -====================== - -Syntax -"""""" - -.. code-block:: LAMMPS - - reset_atom_ids keyword values ... - - * zero or more keyword/value pairs may be appended - * keyword = *sort* - -.. parsed-literal:: - - *sort* value = *yes* or *no* - -Examples -"""""""" - -.. code-block:: LAMMPS - - reset_atom_ids - reset_atom_ids sort yes - -Description -""""""""""" - -Reset atom IDs for the system, including all the global IDs stored -for bond, angle, dihedral, improper topology data. This will -create a set of IDs that are numbered contiguously from 1 to N -for a N atoms system. - -This can be useful to do after performing a "delete_atoms" command for -a molecular system. The delete_atoms compress yes option will not -perform this operation due to the existence of bond topology. It can -also be useful to do after any simulation which has lost atoms, -e.g. due to atoms moving outside a simulation box with fixed -boundaries (see the "boundary command"), or due to evaporation (see -the "fix evaporate" command). - -If the *sort* keyword is used with a setting of *yes*, then the -assignment of new atom IDs will be the same no matter how many -processors LAMMPS is running on. This is done by first doing a -spatial sort of all the atoms into bins and sorting them within each -bin. Because the set of bins is independent of the number of -processors, this enables a consistent assignment of new IDs to each -atom. - -This can be useful to do after using the "create_atoms" command and/or -"replicate" command. In general those commands do not guarantee -assignment of the same atom ID to the same physical atom when LAMMPS -is run on different numbers of processors. Enforcing consistent IDs -can be useful for debugging or comparing output from two different -runs. - -Note that the spatial sort requires communication of atom IDs and -coordinates between processors in an all-to-all manner. This is done -efficiently in LAMMPS, but it is more expensive than how atom IDs are -reset without sorting. - -Note that whether sorting or not, the resetting of IDs is not a -compression, where gaps in atom IDs are removed by decrementing atom -IDs that are larger. Instead the IDs for all atoms are erased, and -new IDs are assigned so that the atoms owned by an individual -processor have consecutive IDs, as the :doc:`create_atoms -` command explains. - -.. note:: - - If this command is used before a :doc:`pair style ` is - defined, an error about bond topology atom IDs not being found may - result. This is because the cutoff distance for ghost atom - communication was not sufficient to find atoms in bonds, angles, etc - that are owned by other processors. The :doc:`comm_modify cutoff ` command can be used to correct this issue. - Or you can define a pair style before using this command. If you do - the former, you should unset the comm_modify cutoff after using - reset_atom_ids so that subsequent communication is not inefficient. - -Restrictions -"""""""""""" -none - -Related commands -"""""""""""""""" - -:doc:`delete_atoms ` - -Default -""""""" - -By default, *sort* is no. diff --git a/doc/src/reset_atoms.rst b/doc/src/reset_atoms.rst new file mode 100644 index 0000000000..89f9557d7c --- /dev/null +++ b/doc/src/reset_atoms.rst @@ -0,0 +1,283 @@ +.. index:: reset_atoms + +reset_atoms command +=================== + +Syntax +"""""" + +.. code-block:: LAMMPS + + reset_atoms property arguments ... + +* property = *id* or *image* or *mol* +* additional arguments depend on the property + + .. code-block:: LAMMPS + + reset_atoms id keyword value ... + + * zero or more keyword/value pairs can be appended + * keyword = *sort* + + .. parsed-literal:: + + *sort* value = *yes* or *no* + + .. code-block:: LAMMPS + + reset_atoms image group-ID + + * group-ID = ID of group of atoms whose image flags will be reset + + .. code-block:: LAMMPS + + reset atoms mol group-ID keyword value ... + + * group-ID = ID of group of atoms whose molecule IDs will be reset + * zero or more keyword/value pairs can be appended + * keyword = *compress* or *offset* or *single* + + .. parsed-literal:: + + *compress* value = *yes* or *no* + *offset* value = *Noffset* >= -1 + *single* value = *yes* or *no* to treat single atoms (no bonds) as molecules + + +Examples +"""""""" + +.. code-block:: LAMMPS + + reset_atoms id + reset_atoms id sort yes + reset_atoms image all + reset_atoms image mobile + reset_atoms mol all + reset_atoms mol all offset 10 single yes + reset_atoms mol solvent compress yes offset 100 + reset_atoms mol solvent compress no + + +Description +""""""""""" + +.. versionadded:: 22Dec2022 + +The *reset_atoms* command resets the values of a specified atom +property. In contrast to the set command, it does this in a +collective manner which resets the values for many atoms in a +self-consistent way. This is often useful when the simulated system +has undergone significant modifications like adding or removing atoms +or molecules, joining data files, changing bonds, or large-scale +diffusion. + +The new values can be thought of as a *reset*, similar to values atoms +would have if a new data file were being read or a new simulation +performed. Note that the set command also resets atom properties to +new values, but it treats each atom independently. + +The *property* setting can be *id* or *image* or *mol*. For *id*, the +IDs of all the atoms are reset to contiguous values. For *image*, the +image flags of atoms in the specified *group-ID* are reset so that at +least one atom in each molecule is in the simulation box (image flag = +0). For *mol*, the molecule IDs of all atoms are reset to contiguous +values. + +More details on these operations and their arguments or optional +keyword/value settings are given below. + +---------- + +*Property id* + +Reset atom IDs for the entire system, including all the global IDs +stored for bond, angle, dihedral, improper topology data. This will +create a set of IDs that are numbered contiguously from 1 to N for a N +atoms system. + +This can be useful to do after performing a "delete_atoms" command for +a molecular system. The delete_atoms compress yes option will not +perform this operation due to the existence of bond topology. It can +also be useful to do after any simulation which has lost atoms, +e.g. due to atoms moving outside a simulation box with fixed +boundaries (see the "boundary command"), or due to evaporation (see +the "fix evaporate" command). + +If the *sort* keyword is used with a setting of *yes*, then the +assignment of new atom IDs will be the same no matter how many +processors LAMMPS is running on. This is done by first doing a +spatial sort of all the atoms into bins and sorting them within each +bin. Because the set of bins is independent of the number of +processors, this enables a consistent assignment of new IDs to each +atom. + +This can be useful to do after using the "create_atoms" command and/or +"replicate" command. In general those commands do not guarantee +assignment of the same atom ID to the same physical atom when LAMMPS +is run on different numbers of processors. Enforcing consistent IDs +can be useful for debugging or comparing output from two different +runs. + +Note that the spatial sort requires communication of atom IDs and +coordinates between processors in an all-to-all manner. This is done +efficiently in LAMMPS, but it is more expensive than how atom IDs are +reset without sorting. + +Note that whether sorting or not, the resetting of IDs is not a +compression, where gaps in atom IDs are removed by decrementing atom +IDs that are larger. Instead the IDs for all atoms are erased, and +new IDs are assigned so that the atoms owned by an individual +processor have consecutive IDs, as the :doc:`create_atoms +` command explains. + +.. note:: + + If this command is used before a :doc:`pair style ` is + defined, an error about bond topology atom IDs not being found may + result. This is because the cutoff distance for ghost atom + communication was not sufficient to find atoms in bonds, angles, etc + that are owned by other processors. The :doc:`comm_modify cutoff + ` command can be used to correct this issue. Or you can + define a pair style before using this command. If you do the former, + you should unset the *comm_modify cutoff* after using *reset + atoms id* so that subsequent communication is not inefficient. + +---------- + +*Property image* + +Reset the image flags of atoms so that at least one atom in each +molecule has an image flag of 0. Molecular topology is respected so +that if the molecule straddles a periodic simulation box boundary, the +images flags of all atoms in the molecule will be consistent. This +avoids inconsistent image flags that could result from resetting all +image flags to zero with the :doc:`set ` command. + +.. note:: + + If the system has no bonds, there is no reason to use this command, + since image flags for different atoms do not need to be + consistent. Use the :doc:`set ` command with its *image* + keyword instead. + +Only image flags for atoms in the specified *group-ID* are reset; all +others remain unchanged. No check is made for whether the group +covers complete molecule fragments and thus whether the command will +result in inconsistent image flags. + +Molecular fragments are identified by the algorithm used by the +:doc:`compute fragment/atom ` command. For each +fragment the average of the largest and the smallest image flag in +each direction across all atoms in the fragment is computed and +subtracted from the current image flag in the same direction. + +This can be a useful operation to perform after running longer +equilibration runs of mobile systems where molecules would pass +through the system multiple times and thus produce non-zero image +flags. + +.. note:: + + Same as explained for the :doc:`compute fragment/atom + ` command, molecules are identified using the + current bond topology. This will **not** account for bonds broken by + the :doc:`bond_style quartic ` command, because this + bond style does not perform a full update of the bond topology data + structures within LAMMPS. In that case, using the :doc:`delete_bonds + all bond 0 remove ` will permanently delete such + broken bonds and should thus be used first. + +---------- + +*Property mol* + +Reset molecule IDs for a specified group of atoms based on current +bond connectivity. This will typically create a new set of molecule +IDs for atoms in the group. Only molecule IDs for atoms in the +specified *group-ID* are reset; molecule IDs for atoms not in the +group are not changed. + +For purposes of this operation, molecules are identified by the current +bond connectivity in the system, which may or may not be consistent with +the current molecule IDs. A molecule in this context is a set of atoms +connected to each other with explicit bonds. The specific algorithm +used is the one of :doc:`compute fragment/atom ` +Once the molecules are identified and a new molecule ID computed for +each, this command will update the current molecule ID for all atoms in +the group with the new molecule ID. Note that if the group excludes +atoms within molecules, one (physical) molecule may become two or more +(logical) molecules. For example if the group excludes atoms in the +middle of a linear chain, then each end of the chain is considered an +independent molecule and will be assigned a different molecule ID. + +This can be a useful operation to perform after running reactive +molecular dynamics run with :doc:`fix bond/react `, +:doc:`fix bond/create `, or :doc:`fix bond/break +`, all of which can change molecule topologies. It can +also be useful after molecules have been deleted with the +:doc:`delete_atoms ` command or after a simulation which +has lost molecules, e.g. via the :doc:`fix evaporate ` +command. + +The *compress* keyword determines how new molecule IDs are computed. If +the setting is *yes* (the default) and there are N molecules in the +group, the new molecule IDs will be a set of N contiguous values. See +the *offset* keyword for details on selecting the range of these values. +If the setting is *no*, the molecule ID of every atom in the molecule +will be set to the smallest atom ID of any atom in the molecule. + +The *single* keyword determines whether single atoms (not bonded to +another atom) are treated as one-atom molecules or not, based on the +*yes* or *no* setting. If the setting is *no* (the default), their +molecule IDs are set to 0. This setting can be important if the new +molecule IDs will be used as input to other commands such as +:doc:`compute chunk/atom molecule ` or :doc:`fix +rigid molecule `. + +The *offset* keyword is only used if the *compress* setting is *yes*. +Its default value is *Noffset* = -1. In that case, if the specified +group is *all*, then the new compressed molecule IDs will range from 1 +to N. If the specified group is not *all* and the largest molecule ID +of atoms outside that group is M, then the new compressed molecule IDs will +range from M+1 to M+N, to avoid collision with existing molecule +IDs. If an *Noffset* >= 0 is specified, then the new compressed +molecule IDs will range from *Noffset*\ +1 to *Noffset*\ +N. If the group +is not *all* there may be collisions with the molecule IDs of other atoms. + +.. note:: + + Same as explained for the :doc:`compute fragment/atom + ` command, molecules are identified using the + current bond topology. This will **not** account for bonds broken by + the :doc:`bond_style quartic ` command, because this + bond style does not perform a full update of the bond topology data + structures within LAMMPS. In that case, using the :doc:`delete_bonds + all bond 0 remove ` will permanently delete such broken + bonds and should thus be used first. + + +Restrictions +"""""""""""" + +The *image* property can only be used when the atom style supports bonds. + +Related commands +"""""""""""""""" + +:doc:`compute fragment/atom ` +:doc:`fix bond/react `, +:doc:`fix bond/create `, +:doc:`fix bond/break `, +:doc:`fix evaporate `, +:doc:`delete_atoms `, +:doc:`delete_bonds ` + +Defaults +"""""""" + +For property *id*, the default keyword setting is sort = no. + +For property *mol*, the default keyword settings are compress = yes, +single = no, and offset = -1. diff --git a/doc/src/reset_mol_ids.rst b/doc/src/reset_mol_ids.rst deleted file mode 100644 index 0d6063b3ef..0000000000 --- a/doc/src/reset_mol_ids.rst +++ /dev/null @@ -1,116 +0,0 @@ -.. index:: reset_mol_ids - -reset_mol_ids command -===================== - -Syntax -"""""" - -.. parsed-literal:: - - reset_mol_ids group-ID keyword value ... - -* group-ID = ID of group of atoms whose molecule IDs will be reset -* zero or more keyword/value pairs may be appended -* keyword = *compress* or *offset* or *single* - - .. parsed-literal:: - - *compress* value = *yes* or *no* - *offset* value = *Noffset* >= -1 - *single* value = *yes* or *no* to treat single atoms (no bonds) as molecules - -Examples -"""""""" - -.. code-block:: LAMMPS - - reset_mol_ids all - reset_mol_ids all offset 10 single yes - reset_mol_ids solvent compress yes offset 100 - reset_mol_ids solvent compress no - -Description -""""""""""" - -Reset molecule IDs for a group of atoms based on current bond -connectivity. This will typically create a new set of molecule IDs -for atoms in the group. Only molecule IDs for atoms in the specified -group are reset; molecule IDs for atoms not in the group are not -changed. - -For purposes of this operation, molecules are identified by the current -bond connectivity in the system, which may or may not be consistent with -the current molecule IDs. A molecule in this context is a set of atoms -connected to each other with explicit bonds. The specific algorithm -used is the one of :doc:`compute fragment/atom ` -Once the molecules are identified and a new molecule ID computed for -each, this command will update the current molecule ID for all atoms in -the group with the new molecule ID. Note that if the group excludes -atoms within molecules, one (physical) molecule may become two or more -(logical) molecules. For example if the group excludes atoms in the -middle of a linear chain, then each end of the chain is considered an -independent molecule and will be assigned a different molecule ID. - -This can be a useful operation to perform after running reactive -molecular dynamics run with :doc:`fix bond/react `, -:doc:`fix bond/create `, or :doc:`fix bond/break -`, all of which can change molecule topologies. It can -also be useful after molecules have been deleted with the -:doc:`delete_atoms ` command or after a simulation which -has lost molecules, e.g. via the :doc:`fix evaporate ` -command. - -The *compress* keyword determines how new molecule IDs are computed. If -the setting is *yes* (the default) and there are N molecules in the -group, the new molecule IDs will be a set of N contiguous values. See -the *offset* keyword for details on selecting the range of these values. -If the setting is *no*, the molecule ID of every atom in the molecule -will be set to the smallest atom ID of any atom in the molecule. - -The *single* keyword determines whether single atoms (not bonded to -another atom) are treated as one-atom molecules or not, based on the -*yes* or *no* setting. If the setting is *no* (the default), their -molecule IDs are set to 0. This setting can be important if the new -molecule IDs will be used as input to other commands such as -:doc:`compute chunk/atom molecule ` or :doc:`fix -rigid molecule `. - -The *offset* keyword is only used if the *compress* setting is *yes*. -Its default value is *Noffset* = -1. In that case, if the specified -group is *all*, then the new compressed molecule IDs will range from 1 -to N. If the specified group is not *all* and the largest molecule ID -of atoms outside that group is M, then the new compressed molecule IDs will -range from M+1 to M+N, to avoid collision with existing molecule -IDs. If an *Noffset* >= 0 is specified, then the new compressed -molecule IDs will range from *Noffset*\ +1 to *Noffset*\ +N. If the group -is not *all* there may be collisions with the molecule IDs of other atoms. - -.. note:: - - The same as explained for the :doc:`compute fragment/atom - ` command, molecules are identified using the - current bond topology. This will not account for bonds broken by - the :doc:`bond_style quartic ` command because it - does not perform a full update of the bond topology data structures - within LAMMPS. - -Restrictions -"""""""""""" -none - -Related commands -"""""""""""""""" - -:doc:`reset_atom_ids `, :doc:`fix bond/react `, -:doc:`fix bond/create `, -:doc:`fix bond/break `, -:doc:`fix evaporate `, -:doc:`delete_atoms `, -:doc:`compute fragment/atom ` - -Default -""""""" - -The default keyword settings are compress = yes, single = no, and -offset = -1. diff --git a/doc/src/run_style.rst b/doc/src/run_style.rst index e1dda78374..fdbdcd228c 100644 --- a/doc/src/run_style.rst +++ b/doc/src/run_style.rst @@ -101,7 +101,7 @@ Py2 by Pz2, then Px1 must be an integer multiple of Px2, and similarly for Py1 a multiple of Py2, and Pz1 a multiple of Pz2. Typically the best way to do this is to let the first partition choose -its onn optimal layout, then require the second partition's layout to +its own optimal layout, then require the second partition's layout to match the integer multiple constraint. See the :doc:`processors ` command with its *part* keyword for a way to control this, e.g. diff --git a/doc/src/thermo_modify.rst b/doc/src/thermo_modify.rst index 2600b337bc..1bee26c289 100644 --- a/doc/src/thermo_modify.rst +++ b/doc/src/thermo_modify.rst @@ -28,6 +28,7 @@ Syntax *format* values = *line* string, *int* string, *float* string, ID string, or *none* string = C-style format string ID = integer from 1 to N, or integer from -1 to -N, where N = # of quantities being output + *or* an integer range such as 2*6 (negative values are not allowed) *or* a thermo keyword or reference to compute, fix, property or variable. *temp* value = compute ID that calculates a temperature *press* value = compute ID that calculates a pressure @@ -65,10 +66,10 @@ atom can be "lost" if it moves across a non-periodic simulation box :doc:`boundary ` or if it moves more than a box length outside the simulation domain (or more than a processor sub-domain length) before reneighboring occurs. The latter case is typically due to bad -dynamics, e.g. too large a timestep or huge forces and velocities. If +dynamics (e.g., too large a time step and/or huge forces and velocities). If the value is *ignore*, LAMMPS does not check for lost atoms. If the value is *error* or *warn*, LAMMPS checks and either issues an error or -warning. The code will exit with an error and continue with a warning. +warning. The simulation will exit with an error and continue with a warning. A warning will only be issued once, the first time an atom is lost. This can be a useful debugging option. @@ -89,10 +90,10 @@ that should be investigated, but LAMMPS cannot determine for certain whether they are an indication of an error. Some warning messages are printed during a run (or immediately before) -each time a specific MPI rank encounters the issue, e.g. bonds that are -stretched too far or dihedrals in extreme configurations. These number +each time a specific MPI rank encounters the issue (e.g., bonds that are +stretched too far or dihedrals in extreme configurations). These number of these can quickly blow up the size of the log file and screen output. -Thus a limit of 100 warning messages is applied by default. The warning +Thus, a limit of 100 warning messages is applied by default. The warning count is applied to the entire input unless reset with a ``thermo_modify warn reset`` command. If there are more warnings than the limit, LAMMPS will print one final warning that it will not print any additional @@ -160,8 +161,8 @@ for a column or field of thermodynamic output. The setting for *ID string* replaces the default text with the provided string. *ID* can be a positive integer when it represents the column number counting from the left, a negative integer when it represents the column number from -the right (i.e. -1 is the last column/keyword), or a thermo keyword (or -compute, fix, property, or variable reference) and then it replaces the +the right (i.e., :math:`-1` is the last column/keyword), or a thermo keyword +(or compute, fix, property, or variable reference) and then it replaces the string for that specific thermo keyword. The *colname* keyword can be used multiple times. If multiple *colname* @@ -171,19 +172,22 @@ to their default values. The *format* keyword can be used to change the default numeric format of any of quantities the :doc:`thermo_style ` command -outputs. All the specified format strings are C-style formats, e.g. as -used by the C/C++ printf() command. The *line* keyword takes a single +outputs. All the specified format strings are C-style formats (i.e., as +used by the C/C++ printf() command). The *line* keyword takes a single argument which is the format string for the entire line of thermo -output, with N fields, which you must enclose in quotes if it is more +output, with :math:`N` fields, which you must enclose in quotes if it is more than one field. The *int* and *float* keywords take a single format argument and are applied to all integer or floating-point quantities output. The setting for *ID string* also takes a single format argument -which is used for the indexed value in each line. The interpretation is -the same as for *colname*, i.e. a positive integer is the n-th value +that is used for the indexed value in each line. The interpretation is +the same as for *colname* (i.e., a positive integer is the n-th value corresponding to the n-th thermo keyword, a negative integer is counting -backwards, and a string matches the entry with the thermo keyword., -e.g. the fifth column is output in high precision for "format 5 %20.15g" -and the pair energy for "format epair %20.15g". +backwards, and a string matches the entry with the thermo keyword). +For example, the fifth column is output in high precision for +"format 5 %20.15g", and the pair energy for "format epair %20.15g". +The *ID* field can be a range, such as "3\*6", "*", "2*", or "\*3"; +in such cases, all fields in the range (inclusive) are set to the specified +format string. Ranges containing negative numbers are not supported. The *format* keyword can be used multiple times. The precedence is that for each value in a line of output, the *ID* format (if specified) @@ -201,8 +205,8 @@ settings, reverting all values to their default format. to the corresponding 8-byte form when it is applied to those keywords. However, when specifying the *line* option or *format ID string* option for *step* and *natoms*, you should specify a format - string appropriate for an 8-byte signed integer, e.g. one with "%ld" - or "%lld" depending on the platform. + string appropriate for an 8-byte signed integer (i.e., one with "%ld" + or "%lld", depending on the platform). The *temp* keyword is used to determine how thermodynamic temperature is calculated, which is used by all thermo quantities that require a diff --git a/doc/src/variable.rst b/doc/src/variable.rst index 46d38975bb..fce5a62a55 100644 --- a/doc/src/variable.rst +++ b/doc/src/variable.rst @@ -213,6 +213,9 @@ from the list of active variables, and is thus available to be re-defined in a subsequent variable command. The *delete* style does the same thing. +Variables are **not** deleted by the :doc:`clear ` command with +the exception of atomfile-style variables. + ---------- The :doc:`Commands parse ` page explains how @@ -265,7 +268,7 @@ the first string is assigned to the variable. Each time a string is assigned. All processors assign the same string to the variable. -*Index* style variables with a single string value can also be set by +Index-style variables with a single string value can also be set by using the :doc:`command-line switch -var `. The *loop* style is identical to the *index* style except that the @@ -285,7 +288,7 @@ be one string for each processor partition or "world". LAMMPS can be run with multiple partitions via the :doc:`-partition command-line switch `. This variable command assigns one string to each world. All processors in the world are assigned the same string. -The next command cannot be used with *equal* style variables, since +The next command cannot be used with equal-style variables, since there is only one value per world. This style of variable is useful when you wish to run different simulations on different partitions, or when performing a parallel tempering simulation (see the :doc:`temper @@ -303,7 +306,7 @@ string. This continues until all the variable strings are consumed. Thus, this command can be used to run 50 simulations on 8 processor partitions. The simulations will be run one after the other on whatever partition becomes available, until they are all finished. -*Universe* style variables are incremented using the files +Universe-style variables are incremented using the files "tmp.lammps.variable" and "tmp.lammps.variable.lock" which you will see in your directory during such a LAMMPS run. @@ -341,7 +344,9 @@ variable can be used to adapt the behavior of LAMMPS input scripts via environment variable settings, or to retrieve information that has been previously stored with the :doc:`shell putenv ` command. Note that because environment variable settings are stored by the -operating systems, they persist beyond a :doc:`clear ` command. +operating systems, they persist even if the corresponding *getenv* +style variable is deleted, and also are set for sub-shells executed +by the :doc:`shell ` command. For the *file* style, a filename is provided which contains a list of strings to assign to the variable, one per line. The strings can be @@ -373,7 +378,9 @@ This means the variable can then be evaluated as many times as desired and will return those values. There are two ways to cause the next set of per-atom values from the file to be read: use the :doc:`next ` command or the next() function in an atom-style -variable, as discussed below. +variable, as discussed below. Unlike most variable styles +atomfile-style variables are **deleted** during a :doc:`clear ` +command. The rules for formatting the file are as follows. Each time a set of per-atom values is read, a non-blank line is searched for in the file. diff --git a/doc/src/velocity.rst b/doc/src/velocity.rst index c1afaf2edc..4749283bb8 100644 --- a/doc/src/velocity.rst +++ b/doc/src/velocity.rst @@ -154,7 +154,8 @@ temperature using a compute that is defined internally as follows: where group-ID is the same ID used in the velocity command. i.e. the group of atoms whose velocity is being altered. This compute is -deleted when the velocity command is finished. See the :doc:`compute temp ` command for details. If the calculated +deleted when the velocity command is finished. See the :doc:`compute +temp ` command for details. If the calculated temperature should have degrees-of-freedom removed due to fix constraints (e.g. SHAKE or rigid-body constraints), then the appropriate fix command must be specified before the velocity command @@ -163,13 +164,13 @@ is issued. The *bias* keyword with a *yes* setting is used by *create* and *scale*, but only if the *temp* keyword is also used to specify a :doc:`compute ` that calculates temperature in a desired way. -If the temperature compute also calculates a velocity bias, the -bias is subtracted from atom velocities before the *create* and -*scale* operations are performed. After the operations, the bias is -added back to the atom velocities. See the :doc:`Howto thermostat ` page for more discussion of -temperature computes with biases. Note that the velocity bias is only -applied to atoms in the temperature compute specified with the *temp* -keyword. +If the temperature compute also calculates a velocity bias, the bias +is subtracted from atom velocities before the *create* and *scale* +operations are performed. After the operations, the bias is added +back to the atom velocities. See the :doc:`Howto thermostat +` page for more discussion of temperature computes +with biases. Note that the velocity bias is only applied to atoms in +the temperature compute specified with the *temp* keyword. As an example, assume atoms are currently streaming in a flow direction (which could be separately initialized with the *ramp* @@ -218,7 +219,8 @@ coordinate as stored on a particular machine. ---------- The *rigid* keyword only has meaning when used with the *zero* style. -It allows specification of a fix-ID for one of the :doc:`rigid-body fix ` variants which defines a set of rigid bodies. The +It allows specification of a fix-ID for one of the :doc:`rigid-body +fix ` variants which defines a set of rigid bodies. The zeroing of linear or angular momentum is then performed for each rigid body defined by the fix, as described above. @@ -235,16 +237,18 @@ command must have been previously used to define the lattice spacing. Restrictions """""""""""" -Assigning a temperature via the *create* style to a system with :doc:`rigid bodies ` or :doc:`SHAKE constraints ` may not -have the desired outcome for two reasons. First, the velocity command -can be invoked before all of the relevant fixes are created and -initialized and the number of adjusted degrees of freedom (DOFs) is -known. Thus it is not possible to compute the target temperature -correctly. Second, the assigned velocities may be partially canceled -when constraints are first enforced, leading to a different -temperature than desired. A workaround for this is to perform a :doc:`run 0 ` command, which insures all DOFs are accounted for -properly, and then rescale the temperature to the desired value before -performing a simulation. For example: +Assigning a temperature via the *create* style to a system with +:doc:`rigid bodies ` or :doc:`SHAKE constraints +` may not have the desired outcome for two reasons. First, +the velocity command can be invoked before all of the relevant fixes +are created and initialized and the number of adjusted degrees of +freedom (DOFs) is known. Thus it is not possible to compute the +target temperature correctly. Second, the assigned velocities may be +partially canceled when constraints are first enforced, leading to a +different temperature than desired. A workaround for this is to +perform a :doc:`run 0 ` command, which insures all DOFs are +accounted for properly, and then rescale the temperature to the +desired value before performing a simulation. For example: .. code-block:: LAMMPS diff --git a/doc/utils/check-packages.py b/doc/utils/check-packages.py old mode 100755 new mode 100644 diff --git a/doc/utils/check-styles.py b/doc/utils/check-styles.py old mode 100755 new mode 100644 diff --git a/doc/utils/converters/lammpsdoc/doc_anchor_check.py b/doc/utils/converters/lammpsdoc/doc_anchor_check.py old mode 100755 new mode 100644 diff --git a/doc/utils/converters/lammpsdoc/rst_anchor_check.py b/doc/utils/converters/lammpsdoc/rst_anchor_check.py old mode 100755 new mode 100644 diff --git a/doc/utils/converters/lammpsdoc/txt2html.py b/doc/utils/converters/lammpsdoc/txt2html.py old mode 100755 new mode 100644 index ed9f47a4e4..93f1b257a5 --- a/doc/utils/converters/lammpsdoc/txt2html.py +++ b/doc/utils/converters/lammpsdoc/txt2html.py @@ -3,7 +3,7 @@ # # Python rewrite of txt2html # The original txt2html was written in C by Steve Plimpton -# (http://www.cs.sandia.gov/cgi-bin/sjplimp/) +# (https://sjplimp.github.io/) # # Copyright (C) 2015 Richard Berger # diff --git a/doc/utils/converters/lammpsdoc/txt2rst.py b/doc/utils/converters/lammpsdoc/txt2rst.py old mode 100755 new mode 100644 diff --git a/doc/utils/fixup_headers.py b/doc/utils/fixup_headers.py old mode 100755 new mode 100644 diff --git a/doc/utils/sphinx-config/LAMMPSLexer.py b/doc/utils/sphinx-config/LAMMPSLexer.py index 524d7bf1fa..c8826a9ed6 100644 --- a/doc/utils/sphinx-config/LAMMPSLexer.py +++ b/doc/utils/sphinx-config/LAMMPSLexer.py @@ -1,25 +1,33 @@ from pygments.lexer import RegexLexer, words, include, default from pygments.token import * -LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify", "atom_style", -"balance", "bond_coeff", "bond_style", "bond_write", "boundary", "box", -"clear", "comm_modify", "comm_style", -"compute_modify", "create_atoms", "create_bonds", "create_box", "delete_atoms", -"delete_bonds", "dielectric", "dihedral_coeff", "dihedral_style", "dimension", -"displace_atoms", "dump_modify", "dynamical_matrix", "echo", "elif", "else", -"fix_modify", "group2ndx", "hyper", "if", "improper_coeff", -"improper_style", "include", "info", "jump", "kim", -"kspace_modify", "kspace_style", "label", "labelmap", "lattice", "log", -"mass", "mdi", "message", "minimize", "min_modify", "min_style", "molecule", -"ndx2group", "neb", "neb/spin", "neighbor", "neigh_modify", "newton", "next", -"package", "pair_coeff", "pair_modify", "pair_style", "pair_write", -"partition", "prd", "print", "processors", "python", "quit", "read_data", -"read_dump", "read_restart", "replicate", "rerun", "reset_ids", -"reset_timestep", "restart", "run", "run_style", "server", "set", "shell", -"special_bonds", "suffix", "tad", "temper", "temper/grem", "temper/npt", "then", -"thermo", "thermo_modify", "thermo_style", "third_order", "timer", "timestep", -"units", "velocity", "write_coeff", -"write_data", "write_restart") +LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify", + "atom_style", "balance", "bond_coeff", "bond_style", + "bond_write", "boundary", "clear", "comm_modify", + "comm_style", "compute_modify", "create_atoms", + "create_bonds", "create_box", "delete_atoms", + "delete_bonds", "dielectric", "dihedral_coeff", + "dihedral_style", "dimension", "displace_atoms", + "dump_modify", "dynamical_matrix", "echo", "elif", + "else", "fix_modify", "group2ndx", "hyper", "if", + "improper_coeff", "improper_style", "include", + "info", "jump", "kim", "kspace_modify", + "kspace_style", "label", "labelmap", "lattice", + "log", "mass", "mdi", "message", "minimize", + "min_modify", "min_style", "molecule", "ndx2group", + "neb", "neb/spin", "neighbor", "neigh_modify", + "newton", "next", "package", "pair_coeff", + "pair_modify", "pair_style", "pair_write", + "partition", "plugin", "prd", "print", "processors", + "python", "quit", "read_data", "read_dump", + "read_restart", "replicate", "rerun", "reset_atoms", + "reset_timestep", "restart", "run", "run_style", + "server", "set", "shell", "special_bonds", "suffix", + "tad", "temper", "temper/grem", "temper/npt", "then", + "thermo", "thermo_modify", "thermo_style", + "third_order", "timer", "timestep", "units", + "velocity", "write_coeff", "write_data", + "write_restart") #fix ID group-ID style args #compute ID group-ID style args diff --git a/doc/utils/sphinx-config/_themes/lammps_theme/static/css/theme.css b/doc/utils/sphinx-config/_themes/lammps_theme/static/css/theme.css index 0d9ae7e1a4..5f393d1f32 100644 --- a/doc/utils/sphinx-config/_themes/lammps_theme/static/css/theme.css +++ b/doc/utils/sphinx-config/_themes/lammps_theme/static/css/theme.css @@ -1,4 +1,4 @@ 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a/doc/utils/sphinx-config/conf.py.in +++ b/doc/utils/sphinx-config/conf.py.in @@ -38,7 +38,7 @@ sys.path.append(os.path.join(LAMMPS_DOC_DIR, 'src', '_ext')) # -- General configuration ------------------------------------------------ # If your documentation needs a minimal Sphinx version, state it here. -#needs_sphinx = '1.0' +needs_sphinx = '5.2.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom @@ -53,10 +53,6 @@ extensions = [ 'tab_or_note', 'breathe', ] -# 2017-12-07: commented out, since this package is broken with Sphinx 16.x -# yet we can no longer use Sphinx 15.x, since that breaks with -# newer version of the multiprocessor module. -# 'sphinxcontrib.images', images_config = { 'default_image_width' : '25%', @@ -413,9 +409,9 @@ at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL). -The primary author of the code is Steve Plimpton, who can be emailed -at sjplimp@sandia.gov. The LAMMPS WWW Site at www.lammps.org has -more information about the code and its uses. +The LAMMPS developers can be contacted at developers@lammps.org. +The LAMMPS WWW Site at www.lammps.org has more information about +the code and its uses. """ epub_author = 'The LAMMPS Developers' diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index df93ebf761..7cb409d040 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -123,6 +123,7 @@ Antonelli api Apoorva Appl +Appshaw apptainer Apu arallel @@ -181,6 +182,7 @@ Avalos avalue aveforce Avendano +Averett avi AVX awpmd @@ -226,6 +228,7 @@ Bartels Bartelt barycenter barye +basename Bashford bashrc Baskes @@ -237,6 +240,7 @@ bcolor bdiam bdw Beckman +Becton Belak Bellott bem @@ -253,6 +257,7 @@ berlin Berne Bertotti Bessarab +bessel Beutler Bext Bfrac @@ -270,6 +275,7 @@ bilayers binsize binstyle binutils +Biomech biomolecular biomolecule Biomolecules @@ -408,6 +414,7 @@ cdennist cdof ceil Ceil +cekk centerline centro centroid @@ -443,6 +450,7 @@ checkbox checkmark checkqeq checksum +chemflag chemistries Chemnitz Cheng @@ -466,6 +474,7 @@ Cij cis civ CKD +ckk Clang clearstore Cleary @@ -555,6 +564,8 @@ Coulombic Coulombics counterion counterions +CountI +CountN Courant covalent covalently @@ -604,6 +615,7 @@ curv Cusentino customIDs cutbond +cutghost cuthi cutinner cutlo @@ -684,6 +696,7 @@ delocalized Delong delr deltaHf +deltamu dem Dendrimer dendritic @@ -734,6 +747,7 @@ diel Dietz differentiable diffusively +diffusivities diffusivity dihedral dihedrals @@ -745,6 +759,7 @@ dimensionality dimensioned dimgray dipolar +dipoleflag dir Direc dirname @@ -753,6 +768,7 @@ discretization discretized discretizing disp +dispersionflag dissipative Dissipative distharm @@ -767,6 +783,7 @@ dmax Dmax dmg dmi +dname dnf DNi Dobnikar @@ -815,6 +832,7 @@ du dU Ducastelle Dudarev +Dufils Duin Dullweber dumpfile @@ -902,6 +920,7 @@ elastance Electroneg electronegative electronegativity +electroneutrality Eleftheriou ElementN elementset @@ -924,6 +943,7 @@ Emmrich emol eN endian +endocytosis energetics energyCorr eng @@ -966,7 +986,6 @@ equilization equipartitioning eradius erate -erc Ercolessi Erdmann erf @@ -1017,12 +1036,14 @@ evirials ew ewald Ewald +ewaldflag excitations excv exe executables extep extrema +extxyz exy ey ez @@ -1089,8 +1110,10 @@ Fincham Fint fingerprintconstants fingerprintsperelement +finitecutflag Finnis Fiorin +fitpod fixID fj Fji @@ -1133,6 +1156,7 @@ Forschungszentrum fortran Fortran Fosado +fourbody fourier fp fphi @@ -1155,6 +1179,7 @@ ftm ftol fuer fugacity +Fu Fumi func funcs @@ -1233,10 +1258,12 @@ Glosli Glotzer gmail gmake +gmap gmask Gmask GMock gmres +gname gneb GNEB Goldfarb @@ -1265,6 +1292,7 @@ greenyellow Greffet grem gREM +Grepl Grest Grigera Grimme @@ -1306,6 +1334,7 @@ Hamaker Hamel Hammerschmidt Hanley +Hanna haptic Haque Hara @@ -1430,6 +1459,7 @@ ieni ifdefs iff ifort +ihi Ihle ij ijk @@ -1440,6 +1470,7 @@ ilabel Ilie ilmenau Ilmenau +ilo ilp Ilya im @@ -1503,6 +1534,9 @@ inumeric inv invariants inversed +invertible +invertibility +ionicities ionizable ionocovalent iostreams @@ -1541,6 +1575,8 @@ Iw Iwers iwyu ixcm +ixhi +ixlo ixx Ixx ixy @@ -1622,6 +1658,7 @@ Kalia Kamberaj Kantorovich Kapfer +Karhunen Karls Karlsruhe Karniadakis @@ -1657,6 +1694,7 @@ kepler keV Keyes keyfile +Kfoury Khersonskii Khrapak Khvostov @@ -1875,6 +1913,7 @@ ln localhost localTemp localvectors +Loeve Loewen logfile logfreq @@ -1912,6 +1951,7 @@ lwsock lx ly Lybrand +Lykotrafitis lyon Lysogorskiy Lyulin @@ -1925,6 +1965,7 @@ Mackrodt MacOS Macromolecules macroparticle +Maday Madura Magda Magdeburg @@ -2022,6 +2063,7 @@ MEAM meamf meanDist mech +Mechanobiology Mecke mediumaquamarine mediumblue @@ -2188,6 +2230,7 @@ msd msi MSI msm +msmflag msse msst Mtchell @@ -2238,6 +2281,7 @@ MxN myCompute myIndex mylammps +myMultiply MyPool mysocket mySpin @@ -2266,6 +2310,8 @@ nanometer nanometers nanoparticle nanoparticles +nanopores +nanostructures nanotube Nanotube nanotubes @@ -2349,6 +2395,7 @@ Ng nghost Nghost Ngpu +ngpus Ngyuen nh nharmonic @@ -2374,8 +2421,10 @@ nktv nl nlayers nlen +Nlimit nlines Nlines +nlist nlo nlocal Nlocal @@ -2463,7 +2512,9 @@ nsq Nstart nstats Nstep -Nsteplast +Nsteps +nsteps +nsteplast Nstop nsub Nsw @@ -2493,7 +2544,7 @@ numpy Numpy Nurdin Nvalue -Nvaluelast +nvaluelast Nvalues nvc nvcc @@ -2505,11 +2556,15 @@ Nwait nwchem nx Nx +nxlo nxnodes +Nxyz ny Ny +nylo nz Nz +nzlo ocl octahedral octants @@ -2537,10 +2592,10 @@ Omelyan omp OMP oneAPI +onebody onelevel oneway onlysalt -onn ons OO Oord @@ -2579,6 +2634,8 @@ overlayed Ovito oxdna oxDNA +oxhi +oxlo oxrna oxRNA packings @@ -2619,6 +2676,7 @@ Pastewka pathangle pathname pathnames +Patera Patomtrans Pattnaik Pavese @@ -2646,6 +2704,7 @@ Peng peptide peratom Pergamon +pergrid peri peridynamic Peridynamic @@ -2738,6 +2797,7 @@ Polym polymorph polymorphism Ponder +Ponte popen Popoola Popov @@ -2759,6 +2819,7 @@ PowerShell ppme ppn pppm +pppmflag Prakash Praprotnik prd @@ -2913,6 +2974,7 @@ Rcmx Rcmy Rco Rcut +rcut rcutfac rdc rdf @@ -2938,6 +3000,7 @@ refactoring reflectionstyle Reinders reinit +reinitflag relaxbox relink relres @@ -3005,6 +3068,7 @@ Rij RIj Rik Rin +rin Rinaldi Rino RiRj @@ -3080,6 +3144,7 @@ Rutuparna rx rxd rxnave +rxnbond rxnsum ry Ryckaert @@ -3140,9 +3205,11 @@ sdpd SDPD se seagreen +Searles Secor sectoring sed +Seddon segmental Seifert Seleson @@ -3167,6 +3234,7 @@ setvel sfftw sfree Sg +sgcmc Shan Shanno Shapeev @@ -3269,6 +3337,7 @@ SPH spica SPICA Spickermann +spinflag splined spparks Sprik @@ -3357,6 +3426,8 @@ Sugaku Suhai Sukumaran Sulc +SumI +SumN sumsq Sunderland supercell @@ -3454,6 +3525,7 @@ thermo thermochemical thermochemistry thermodynamically +thermopotentiostat Thermophysical thermostatted thermostatting @@ -3692,6 +3764,7 @@ vdw vdW vdwl vec +Vecchio vectorial vectorization Vectorization @@ -3820,6 +3893,7 @@ workflows Workum Worley Wriggers +writedata Wuppertal Wurtzite www @@ -3834,6 +3908,7 @@ xa xAVX xb Xc +xc xcm Xcm Xcode @@ -3865,6 +3940,7 @@ xplane XPlor xrd xs +xsc xstk xsu xtc @@ -3888,6 +3964,7 @@ Yazdani Ybar ybox Yc +yc ycm Yeh yellowgreen @@ -3898,11 +3975,13 @@ yhi yi ylat ylo +ylz ymax ymin yml Yoshida ys +ysc ysu yu Yu @@ -3920,6 +3999,7 @@ Zavattieri zbl ZBL Zc +zc zcm zeeman Zeeman @@ -3947,6 +4027,7 @@ zmin zmq zN zs +zsc zst Zstandard zstd diff --git a/examples/ASPHERE/README b/examples/ASPHERE/README index 1aa9552bec..c44f7b0934 100644 --- a/examples/ASPHERE/README +++ b/examples/ASPHERE/README @@ -29,8 +29,10 @@ stochastic rotation dynamics solvent, using the fix srd command. box = 2d rigid box particles in SRDs, self-diffusion and viscosity dimer = 2d rigid dimers in SRDs, self-diffusion and viscosity ellipsoid = 2d ellipsoids in SRDs, self-diffusion and viscosity +flat_membrane = 2d flat membrane in NVE, self-diffusion and viscosity line = 2d line-faceted rigid particles, NEMD shearing for viscosity, implicit and in SRDs poly = 2d poly-disperse spheroids in SRDs, self-diffusion and viscosity star = 2d rigid star particles in SRDs, self-diffusion and viscosity tri = 3d triangle-faceted rigid particles in SRDs, NEMD shearing for viscosity +vesicle = 3d vesicle in NVE, self-diffusionand viscosity diff --git a/examples/ASPHERE/flat_membrane/in.flat_membrane b/examples/ASPHERE/flat_membrane/in.flat_membrane new file mode 100644 index 0000000000..c49961eac3 --- /dev/null +++ b/examples/ASPHERE/flat_membrane/in.flat_membrane @@ -0,0 +1,55 @@ +# flat membrane demo +variable r0 equal 0.97 +variable d1 equal ${r0} +variable d2 equal sqrt(3.0)*${r0} +variable d3 equal 3.0*${r0} +variable ro equal 2./${d1}/${d2}/${d3} + +variable T equal 0.23 +variable LD equal 1.0 + +units lj +atom_style ellipsoid + +boundary p p p + +lattice custom ${ro} a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 & + a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 + + +region box block 0 40 0 24 -20 20 +create_box 1 box +region membrane block 0 40 0 24 -0.5 0.5 +create_atoms 1 region membrane + +group membrane region membrane + +set type 1 mass 1.0 + +set type 1 shape 1 0.99 0.99 + +set group all quat 0 -1 0 90 + +#compute memb all temp/com +#compute rot all temp/asphere bias memb +velocity all create ${T} 87287 loop geom + +pair_style ylz 2.6 +pair_coeff * * 1.0 1.0 4 3 0.0 2.6 +neighbor 1.0 bin + + +thermo_style custom step temp press pxx pyy +thermo 200 + +timestep 0.01 + +#dump 1 all atom 10 dump_onlymembrane.lammpstrj + +fix 1 all langevin ${T} ${T} ${LD} 48279 + + +fix 2 all nve/asphere +run 3000 + + diff --git a/examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.1 b/examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.1 new file mode 100644 index 0000000000..750aa5328c --- /dev/null +++ b/examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.1 @@ -0,0 +1,159 @@ +LAMMPS (15 Sep 2022) + using 1 OpenMP thread(s) per MPI task +# flat membrane demo +variable r0 equal 0.97 +variable d1 equal ${r0} +variable d1 equal 0.97 +variable d2 equal sqrt(3.0)*${r0} +variable d2 equal sqrt(3.0)*0.97 +variable d3 equal 3.0*${r0} +variable d3 equal 3.0*0.97 +variable ro equal 2./${d1}/${d2}/${d3} +variable ro equal 2./0.97/${d2}/${d3} +variable ro equal 2./0.97/1.68008928334181/${d3} +variable ro equal 2./0.97/1.68008928334181/2.91 + +variable T equal 0.23 +variable LD equal 1.0 + +units lj +atom_style ellipsoid + +boundary p p p + +lattice custom ${ro} a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 +lattice custom 0.421728460751825 a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 +lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 +lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 1.68008928334181 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 +lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 1.68008928334181 0.0 a3 0.0 0.0 2.91 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 +Lattice spacing in x,y,z = 0.97 1.6800893 2.91 + + +region box block 0 40 0 24 -20 20 +create_box 1 box +Created orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2) + 1 by 1 by 1 MPI processor grid +region membrane block 0 40 0 24 -0.5 0.5 +create_atoms 1 region membrane +Created 1920 atoms + using lattice units in orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2) + create_atoms CPU = 0.001 seconds + +group membrane region membrane +1920 atoms in group membrane + +set type 1 mass 1.0 +Setting atom values ... + 1920 settings made for mass + +set type 1 shape 1 1 1 +Setting atom values ... + 1920 settings made for shape + +set group all quat 0 -1 0 90 +Setting atom values ... + 1920 settings made for quat + +#compute memb all temp/com +#compute rot all temp/asphere bias memb +velocity all create ${T} 87287 loop geom +velocity all create 0.23 87287 loop geom + +pair_style ylz 2.6 +pair_coeff * * 1.0 1.0 4 3 0.0 2.6 +neighbor 1.0 bin + + +thermo_style custom step temp press pxx pyy +thermo 200 + +timestep 0.01 + +#dump 1 all atom 10 dump_onlymembrane.lammpstrj + +fix 1 all langevin ${T} ${T} ${LD} 48279 +fix 1 all langevin 0.23 ${T} ${LD} 48279 +fix 1 all langevin 0.23 0.23 ${LD} 48279 +fix 1 all langevin 0.23 0.23 1 48279 + + +fix 2 all nve/asphere +run 3000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- pair ylz command: + +@Article{Yuan10, + author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang}, + title = {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes}, + journal = {Phys. Rev. E}, + year = 2010, + volume = 82, + pages = {011905} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 10 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.6 + ghost atom cutoff = 3.6 + binsize = 1.8, bins = 22 23 65 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair ylz, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.024 | 5.024 | 5.024 Mbytes + Step Temp Press Pxx Pyy + 0 0.23 -0.0073508785 -0.012283389 -0.012234574 + 200 0.20903886 -0.0010605951 -0.0011885957 -0.00198842 + 400 0.21898026 -0.00069250685 -0.0013217981 -0.00073225707 + 600 0.22689361 -0.00057919328 -0.00076880503 -0.0010242283 + 800 0.22983221 -0.00032145682 -0.00051928834 -0.00059337525 + 1000 0.23819392 -0.00027969126 -0.00088082301 -5.2666567e-05 + 1200 0.22053795 -0.00029571329 -0.0004446455 -0.00035529929 + 1400 0.22285021 -0.0002690371 -0.00068896571 -3.6258442e-05 + 1600 0.22687044 2.8599875e-05 -0.00032651798 0.0004056081 + 1800 0.23356905 -2.28742e-05 -0.00027073251 0.00025081131 + 2000 0.22499821 8.8230586e-06 -7.5750159e-05 0.0001988705 + 2200 0.23162995 -9.026855e-05 -0.00025832535 5.4904927e-05 + 2400 0.22920223 0.00016700455 3.5283125e-05 0.00034955857 + 2600 0.2260299 5.3095557e-05 0.00025691786 0.00013353467 + 2800 0.2296401 0.00043234854 0.00058344966 0.00063645193 + 3000 0.22564577 2.6423111e-05 8.9918406e-05 0.00022146229 +Loop time of 6.76659 on 1 procs for 3000 steps with 1920 atoms + +Performance: 383058.431 tau/day, 443.355 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 | 5.7968 | 5.7968 | 5.7968 | 0.0 | 85.67 +Neigh | 0.086077 | 0.086077 | 0.086077 | 0.0 | 1.27 +Comm | 0.034761 | 0.034761 | 0.034761 | 0.0 | 0.51 +Output | 0.00038014 | 0.00038014 | 0.00038014 | 0.0 | 0.01 +Modify | 0.8268 | 0.8268 | 0.8268 | 0.0 | 12.22 +Other | | 0.02181 | | | 0.32 + +Nlocal: 1920 ave 1920 max 1920 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 772 ave 772 max 772 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 46804 ave 46804 max 46804 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 46804 +Ave neighs/atom = 24.377083 +Neighbor list builds = 99 +Dangerous builds = 0 + + +Total wall time: 0:00:06 diff --git a/examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.4 b/examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.4 new file mode 100644 index 0000000000..7bbe99b58b --- /dev/null +++ b/examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.4 @@ -0,0 +1,159 @@ +LAMMPS (15 Sep 2022) + using 1 OpenMP thread(s) per MPI task +# flat membrane demo +variable r0 equal 0.97 +variable d1 equal ${r0} +variable d1 equal 0.97 +variable d2 equal sqrt(3.0)*${r0} +variable d2 equal sqrt(3.0)*0.97 +variable d3 equal 3.0*${r0} +variable d3 equal 3.0*0.97 +variable ro equal 2./${d1}/${d2}/${d3} +variable ro equal 2./0.97/${d2}/${d3} +variable ro equal 2./0.97/1.68008928334181/${d3} +variable ro equal 2./0.97/1.68008928334181/2.91 + +variable T equal 0.23 +variable LD equal 1.0 + +units lj +atom_style ellipsoid + +boundary p p p + +lattice custom ${ro} a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 +lattice custom 0.421728460751825 a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 +lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 +lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 1.68008928334181 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 +lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 1.68008928334181 0.0 a3 0.0 0.0 2.91 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 +Lattice spacing in x,y,z = 0.97 1.6800893 2.91 + + +region box block 0 40 0 24 -20 20 +create_box 1 box +Created orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2) + 1 by 1 by 4 MPI processor grid +region membrane block 0 40 0 24 -0.5 0.5 +create_atoms 1 region membrane +Created 1920 atoms + using lattice units in orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2) + create_atoms CPU = 0.001 seconds + +group membrane region membrane +1920 atoms in group membrane + +set type 1 mass 1.0 +Setting atom values ... + 1920 settings made for mass + +set type 1 shape 1 1 1 +Setting atom values ... + 1920 settings made for shape + +set group all quat 0 -1 0 90 +Setting atom values ... + 1920 settings made for quat + +#compute memb all temp/com +#compute rot all temp/asphere bias memb +velocity all create ${T} 87287 loop geom +velocity all create 0.23 87287 loop geom + +pair_style ylz 2.6 +pair_coeff * * 1.0 1.0 4 3 0.0 2.6 +neighbor 1.0 bin + + +thermo_style custom step temp press pxx pyy +thermo 200 + +timestep 0.01 + +#dump 1 all atom 10 dump_onlymembrane.lammpstrj + +fix 1 all langevin ${T} ${T} ${LD} 48279 +fix 1 all langevin 0.23 ${T} ${LD} 48279 +fix 1 all langevin 0.23 0.23 ${LD} 48279 +fix 1 all langevin 0.23 0.23 1 48279 + + +fix 2 all nve/asphere +run 3000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- pair ylz command: + +@Article{Yuan10, + author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang}, + title = {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes}, + journal = {Phys. Rev. E}, + year = 2010, + volume = 82, + pages = {011905} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 10 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.6 + ghost atom cutoff = 3.6 + binsize = 1.8, bins = 22 23 65 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair ylz, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.794 | 5.472 Mbytes + Step Temp Press Pxx Pyy + 0 0.23 -0.0073508785 -0.012283389 -0.012234574 + 200 0.20647718 -0.0012368074 -0.0021167303 -0.0015343502 + 400 0.21648371 -0.00085695085 -0.0015627331 -0.0011177093 + 600 0.22929515 -0.00050218657 -0.0008332 -0.00062622609 + 800 0.22062664 -0.00049172378 -0.000611884 -0.00075089294 + 1000 0.22422425 -0.00039405068 -0.00037600355 -0.00070786572 + 1200 0.2298767 -0.00025939082 -0.00021616578 -0.00053125505 + 1400 0.2335927 5.8028332e-05 0.00017530192 -3.1675138e-05 + 1600 0.22884878 -0.0001733902 -0.0008056431 0.00014276754 + 1800 0.22813498 0.00019873459 0.00051040124 5.8860949e-05 + 2000 0.2273166 -3.3595127e-05 0.0001705632 -0.00026498213 + 2200 0.2251643 -2.4517311e-05 -4.0618888e-05 1.066658e-05 + 2400 0.22460629 -4.5661259e-05 -0.00019144039 -1.6649099e-05 + 2600 0.23085675 0.00014029405 0.00017983536 0.00017895001 + 2800 0.22364591 4.2999164e-05 -0.00011000466 0.00024363243 + 3000 0.23421357 0.00023505702 0.00020752013 0.00053567111 +Loop time of 4.68577 on 4 procs for 3000 steps with 1920 atoms + +Performance: 553164.568 tau/day, 640.237 timesteps/s +95.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00015072 | 1.6029 | 3.8573 | 131.7 | 34.21 +Neigh | 0.00055747 | 0.025423 | 0.065858 | 17.0 | 0.54 +Comm | 0.0052259 | 0.48173 | 1.624 | 96.5 | 10.28 +Output | 0.0003894 | 0.023428 | 0.047223 | 15.0 | 0.50 +Modify | 0.00037337 | 0.2141 | 0.44595 | 46.3 | 4.57 +Other | | 2.338 | | | 49.90 + +Nlocal: 480 ave 1011 max 0 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Nghost: 860 ave 1771 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 11697.8 ave 30095 max 0 min +Histogram: 2 0 0 0 0 1 0 0 0 1 + +Total # of neighbors = 46791 +Ave neighs/atom = 24.370313 +Neighbor list builds = 99 +Dangerous builds = 0 + + +Total wall time: 0:00:04 diff --git a/examples/ASPHERE/vesicle/in.vesicle b/examples/ASPHERE/vesicle/in.vesicle new file mode 100644 index 0000000000..ae8e2e3d75 --- /dev/null +++ b/examples/ASPHERE/vesicle/in.vesicle @@ -0,0 +1,33 @@ +# Vesicle demo + +variable T equal 0.2 +variable LD equal 1.0 + +units lj +atom_style ellipsoid + +boundary p p p + +read_data read_data.vesicle1026 + +compute ali all temp/com +compute rott all temp/asphere bias ali + +velocity all create ${T} 87287 loop geom + +pair_style ylz 2.6 +pair_coeff * * 1.0 1.0 4 3 0.0 2.6 +neighbor 1.0 bin + +thermo_style custom step temp press pxx pyy +thermo 200 + +timestep 0.001 + +#dump 1 all atom 10 onlymembrane2.lammpstrj + +fix 1 all langevin ${T} ${T} ${LD} 48279 +fix 2 all nve/asphere + +run 3000 + diff --git a/examples/ASPHERE/vesicle/log.18Oct22.vesicle.g++.1 b/examples/ASPHERE/vesicle/log.18Oct22.vesicle.g++.1 new file mode 100644 index 0000000000..f974a524e6 --- /dev/null +++ b/examples/ASPHERE/vesicle/log.18Oct22.vesicle.g++.1 @@ -0,0 +1,122 @@ +LAMMPS (15 Sep 2022) + using 1 OpenMP thread(s) per MPI task +# Vesicle demo + +variable T equal 0.2 +variable LD equal 1.0 + +units lj +atom_style ellipsoid + +boundary p p p + +read_data read_data.vesicle1026 +Reading data file ... + orthogonal box = (-35 -35 -35) to (35 35 35) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2938 atoms + 2938 ellipsoids + read_data CPU = 0.010 seconds + +compute ali all temp/com +compute rott all temp/asphere bias ali + +velocity all create ${T} 87287 loop geom +velocity all create 0.2 87287 loop geom + +pair_style ylz 2.6 +pair_coeff * * 1.0 1.0 4 3 0.0 2.6 +neighbor 1.0 bin + +thermo_style custom step temp press pxx pyy +thermo 200 + +timestep 0.001 + +#dump 1 all atom 10 onlymembrane2.lammpstrj + +fix 1 all langevin ${T} ${T} ${LD} 48279 +fix 1 all langevin 0.2 ${T} ${LD} 48279 +fix 1 all langevin 0.2 0.2 ${LD} 48279 +fix 1 all langevin 0.2 0.2 1 48279 +fix 2 all nve/asphere + +run 3000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- pair ylz command: + +@Article{Yuan10, + author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang}, + title = {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes}, + journal = {Phys. Rev. E}, + year = 2010, + volume = 82, + pages = {011905} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 10 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.6 + ghost atom cutoff = 3.6 + binsize = 1.8, bins = 39 39 39 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair ylz, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.091 | 5.091 | 5.091 Mbytes + Step Temp Press Pxx Pyy + 0 0.2 -0.0054891414 -0.0052713616 -0.0053641136 + 200 0.12816247 -0.0051288861 -0.0048542514 -0.0049847561 + 400 0.1377632 -0.0048071582 -0.0045651263 -0.0048444087 + 600 0.14983781 -0.0045305725 -0.0043305994 -0.0046127777 + 800 0.16205271 -0.0041176346 -0.0040534483 -0.0041351779 + 1000 0.17462122 -0.0037000069 -0.0034938539 -0.0037915494 + 1200 0.18335448 -0.0032674318 -0.0032790248 -0.0031967931 + 1400 0.19195613 -0.0029332101 -0.0030823703 -0.0028287799 + 1600 0.19261762 -0.0025263447 -0.0025152249 -0.0026205398 + 1800 0.19758674 -0.0021087725 -0.001981333 -0.002309048 + 2000 0.19748896 -0.0017662369 -0.0019316344 -0.0016696035 + 2200 0.20196986 -0.0013363214 -0.0015581191 -0.0013384961 + 2400 0.20109248 -0.0009190831 -0.0010331417 -0.0010664316 + 2600 0.20228664 -0.00053590675 -0.00071808747 -0.00050218533 + 2800 0.20512955 -0.00030845899 -0.00016244901 -0.00047877516 + 3000 0.19855941 -7.9520073e-05 -0.00014969215 -5.4724226e-06 +Loop time of 9.6866 on 1 procs for 3000 steps with 2938 atoms + +Performance: 26758.610 tau/day, 309.706 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 8.3097 | 8.3097 | 8.3097 | 0.0 | 85.79 +Neigh | 0.039037 | 0.039037 | 0.039037 | 0.0 | 0.40 +Comm | 0.0021766 | 0.0021766 | 0.0021766 | 0.0 | 0.02 +Output | 0.00048628 | 0.00048628 | 0.00048628 | 0.0 | 0.01 +Modify | 1.3043 | 1.3043 | 1.3043 | 0.0 | 13.47 +Other | | 0.0309 | | | 0.32 + +Nlocal: 2938 ave 2938 max 2938 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 73242 ave 73242 max 73242 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 73242 +Ave neighs/atom = 24.929204 +Neighbor list builds = 26 +Dangerous builds = 0 + +Total wall time: 0:00:09 diff --git a/examples/ASPHERE/vesicle/log.18Oct22.vesicle.g++.4 b/examples/ASPHERE/vesicle/log.18Oct22.vesicle.g++.4 new file mode 100644 index 0000000000..0340219494 --- /dev/null +++ b/examples/ASPHERE/vesicle/log.18Oct22.vesicle.g++.4 @@ -0,0 +1,122 @@ +LAMMPS (15 Sep 2022) + using 1 OpenMP thread(s) per MPI task +# Vesicle demo + +variable T equal 0.2 +variable LD equal 1.0 + +units lj +atom_style ellipsoid + +boundary p p p + +read_data read_data.vesicle1026 +Reading data file ... + orthogonal box = (-35 -35 -35) to (35 35 35) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 2938 atoms + 2938 ellipsoids + read_data CPU = 0.137 seconds + +compute ali all temp/com +compute rott all temp/asphere bias ali + +velocity all create ${T} 87287 loop geom +velocity all create 0.2 87287 loop geom + +pair_style ylz 2.6 +pair_coeff * * 1.0 1.0 4 3 0.0 2.6 +neighbor 1.0 bin + +thermo_style custom step temp press pxx pyy +thermo 200 + +timestep 0.001 + +#dump 1 all atom 10 onlymembrane2.lammpstrj + +fix 1 all langevin ${T} ${T} ${LD} 48279 +fix 1 all langevin 0.2 ${T} ${LD} 48279 +fix 1 all langevin 0.2 0.2 ${LD} 48279 +fix 1 all langevin 0.2 0.2 1 48279 +fix 2 all nve/asphere + +run 3000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- pair ylz command: + +@Article{Yuan10, + author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang}, + title = {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes}, + journal = {Phys. Rev. E}, + year = 2010, + volume = 82, + pages = {011905} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 10 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.6 + ghost atom cutoff = 3.6 + binsize = 1.8, bins = 39 39 39 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair ylz, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.899 | 4.9 | 4.902 Mbytes + Step Temp Press Pxx Pyy + 0 0.2 -0.0054891414 -0.0052713616 -0.0053641136 + 200 0.12893798 -0.0051492794 -0.0048734875 -0.0049624005 + 400 0.13798694 -0.004875313 -0.0047071897 -0.0049305051 + 600 0.14725193 -0.0046349542 -0.004719983 -0.0045791451 + 800 0.16146954 -0.0042232199 -0.0040789193 -0.0043672895 + 1000 0.17268468 -0.0037146703 -0.0036270393 -0.0039169034 + 1200 0.18266242 -0.0032749755 -0.0032971704 -0.0033323855 + 1400 0.18500165 -0.0028179031 -0.0030659821 -0.0027519633 + 1600 0.19513132 -0.0023407512 -0.0025109801 -0.0023416835 + 1800 0.19645259 -0.0019995412 -0.0019064341 -0.0021757747 + 2000 0.19658104 -0.0015897919 -0.0015850523 -0.0016828478 + 2200 0.1989936 -0.0011794062 -0.0011779716 -0.0012070706 + 2400 0.20011525 -0.0009147432 -0.00094040885 -0.001073922 + 2600 0.2013975 -0.00059253676 -0.00051920304 -0.00075138934 + 2800 0.19715513 -0.00020995605 -0.00024386426 -0.0005475745 + 3000 0.1976782 -0.0001308553 5.693004e-05 -0.00034478469 +Loop time of 8.46954 on 4 procs for 3000 steps with 2938 atoms + +Performance: 30603.800 tau/day, 354.211 timesteps/s +77.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.1751 | 2.4162 | 2.6707 | 13.2 | 28.53 +Neigh | 0.0090503 | 0.0098389 | 0.010503 | 0.6 | 0.12 +Comm | 3.5807 | 4.1526 | 4.9283 | 24.3 | 49.03 +Output | 0.00032165 | 0.0029648 | 0.010842 | 8.4 | 0.04 +Modify | 0.34554 | 0.37442 | 0.39198 | 2.8 | 4.42 +Other | | 1.514 | | | 17.87 + +Nlocal: 734.5 ave 739 max 730 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Nghost: 420.25 ave 424 max 415 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Neighs: 18304.5 ave 19839 max 16636 min +Histogram: 1 0 0 0 1 0 1 0 0 1 + +Total # of neighbors = 73218 +Ave neighs/atom = 24.921035 +Neighbor list builds = 25 +Dangerous builds = 0 + +Total wall time: 0:00:08 diff --git a/examples/ASPHERE/vesicle/read_data.vesicle1026 b/examples/ASPHERE/vesicle/read_data.vesicle1026 new file mode 100644 index 0000000000..fd19a28dc9 --- /dev/null +++ b/examples/ASPHERE/vesicle/read_data.vesicle1026 @@ -0,0 +1,5894 @@ +vesicle with diameter = 30.000000 + 2938 atoms + 2938 ellipsoids + +2 atom types + + -35.000000 35.000000 xlo xhi + -35.000000 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0.750169 -0.023214 + 2928 1.000000 1.000000 1.010000 0.671739 0.000000 0.737987 -0.064354 + 2929 1.000000 1.000000 1.010000 0.690767 0.000000 0.717697 -0.088049 + 2930 1.000000 1.000000 1.010000 0.712855 0.000000 0.695407 -0.090812 + 2931 1.000000 1.000000 1.010000 0.733036 0.000000 0.676245 -0.073147 + 2932 1.000000 1.000000 1.010000 0.747072 0.000000 0.663502 -0.040604 + 2933 1.000000 1.000000 1.010000 0.729918 -0.000000 0.683535 0.000321 + 2934 1.000000 1.000000 1.010000 0.718702 -0.000000 0.694175 0.039867 + 2935 1.000000 1.000000 1.010000 0.695596 -0.000000 0.717258 0.041086 + 2936 1.000000 1.000000 1.010000 0.683802 -0.000000 0.729668 0.000369 + 2937 1.000000 1.000000 1.010000 0.695606 0.000000 0.717284 -0.040462 + 2938 1.000000 1.000000 1.010000 0.718673 0.000000 0.694236 -0.039301 + + diff --git a/examples/COUPLE/fortran/libfwrapper.c b/examples/COUPLE/fortran/libfwrapper.c index e25cdc94c8..6c44906a59 100644 --- a/examples/COUPLE/fortran/libfwrapper.c +++ b/examples/COUPLE/fortran/libfwrapper.c @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - www.cs.sandia.gov/~sjplimp/lammps.html - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/COUPLE/fortran2/LAMMPS-wrapper.cpp b/examples/COUPLE/fortran2/LAMMPS-wrapper.cpp index eb6f421606..4774cb6b49 100644 --- a/examples/COUPLE/fortran2/LAMMPS-wrapper.cpp +++ b/examples/COUPLE/fortran2/LAMMPS-wrapper.cpp @@ -1,7 +1,7 @@ /* ----------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://www.lammps.org/ - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/COUPLE/fortran2/LAMMPS-wrapper.h b/examples/COUPLE/fortran2/LAMMPS-wrapper.h index 479af91738..02e1a651a9 100644 --- a/examples/COUPLE/fortran2/LAMMPS-wrapper.h +++ b/examples/COUPLE/fortran2/LAMMPS-wrapper.h @@ -1,7 +1,7 @@ /* ----------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - www.cs.sandia.gov/~sjplimp/lammps.html - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp index eb6f421606..4774cb6b49 100644 --- a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp +++ b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp @@ -1,7 +1,7 @@ /* ----------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://www.lammps.org/ - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.h b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.h index 553466d138..e1eec9fc72 100644 --- a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.h +++ b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.h @@ -1,7 +1,7 @@ /* ----------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - www.cs.sandia.gov/~sjplimp/lammps.html - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp index 44d7b5bca4..83d594df60 100644 --- a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp +++ b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp @@ -1,7 +1,7 @@ /* ----------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://www.lammps.org/ - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.h b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.h index d3705179ed..45c41b569a 100644 --- a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.h +++ b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.h @@ -1,7 +1,7 @@ /* ----------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - www.cs.sandia.gov/~sjplimp/lammps.html - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/COUPLE/multiple/multiple.cpp b/examples/COUPLE/multiple/multiple.cpp index 1b6bb66485..43dc90323b 100644 --- a/examples/COUPLE/multiple/multiple.cpp +++ b/examples/COUPLE/multiple/multiple.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://www.lammps.org/ - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/COUPLE/plugin/.gitignore b/examples/COUPLE/plugin/.gitignore new file mode 100644 index 0000000000..796b96d1c4 --- /dev/null +++ b/examples/COUPLE/plugin/.gitignore @@ -0,0 +1 @@ +/build diff --git a/examples/COUPLE/plugin/CMakeLists.txt b/examples/COUPLE/plugin/CMakeLists.txt new file mode 100644 index 0000000000..f4064d3f65 --- /dev/null +++ b/examples/COUPLE/plugin/CMakeLists.txt @@ -0,0 +1,47 @@ +########################################## +# CMake build system for coupling to the LAMMPS library +# where the library is loaded dynamically at runtime. +########################################## + +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(liblammpsplugin VERSION 1.0 LANGUAGES C) + +# 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_C_COMPILER_ID STREQUAL "MSVC") + if(LAMMPS_EXCEPTIONS) + add_compile_options(/EHsc) + endif() + endif() + add_compile_definitions(_CRT_SECURE_NO_WARNINGS) +endif() + +find_package(MPI REQUIRED) +# do not include the (obsolete) MPI C++ bindings which makes +# for leaner object files and avoids namespace conflicts +set(MPI_CXX_SKIP_MPICXX TRUE) + +########################## + +add_executable(simple-plugin simple.c liblammpsplugin.c) +target_link_libraries(simple-plugin PRIVATE MPI::MPI_C) +target_compile_definitions(simple-plugin PRIVATE LAMMPS_LIB_MPI) + +# link with -ldl or equivalent for plugin loading; except on Windows +if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") + target_link_libraries(simple-plugin PRIVATE ${CMAKE_DL_LIBS}) +endif() diff --git a/examples/COUPLE/plugin/README b/examples/COUPLE/plugin/README index bced08b6d7..beed549d3f 100644 --- a/examples/COUPLE/plugin/README +++ b/examples/COUPLE/plugin/README @@ -11,32 +11,39 @@ liblammpsplugin.c is the LAMMPS library plugin loader You can then build the driver executable codes with a compile line like below. -mpicc -c -O -Wall -g -I$HOME/lammps/src liblammpsplugin.c -mpicc -c -O -Wall -g simple.c -mpicc simple.o liblammpsplugin.o -ldl -o simpleC +mpicc -c -O -DLAMMPS_LIB_MPI -Wall -g liblammpsplugin.c +mpicc -c -O -DLAMMPS_LIB_MPI -Wall -g simple.c +mpicc simple.o liblammpsplugin.o -ldl -o simple-plugin + +or using the provided CMake file with: + +mkdir build +cd build +cmake ../ +cmake --build . You also need to build LAMMPS as a shared library -(see examples/COUPLE/README), e.g. +(see examples/COUPLE/README), e.g. cd $HOME/lammps/src make mode=shlib mpi -or +or cd $HOME/lammps mkdir build-shared cd build-shared -cmake -D BUILD_LIB=on -D BUILD_SHARED_LIBS=on ../cmake +cmake -D BUILD_MPI=on -D BUILD_SHARED_LIBS=on ../cmake make -You then run simpleC on a parallel machine +You then run simple-plugin on a parallel machine on some number of processors Q with 3 arguments: -% mpirun -np Q simpleC P in.lj $HOME/lammps/src/liblammps.so +% mpirun -np Q simple-plugin P in.lj $HOME/lammps/src/liblammps.so or -% mpirun -np Q simpleC P in.lj $HOME/lammps/build-shared/liblammps.so +% mpirun -np Q simple-plugin P in.lj $HOME/lammps/build-shared/liblammps.so P is the number of procs you want LAMMPS to run on (must be <= Q) and in.lj is a LAMMPS input script and the last argument is the path to diff --git a/examples/COUPLE/plugin/liblammpsplugin.c b/examples/COUPLE/plugin/liblammpsplugin.c index ea2e2ab536..0b7eda7537 100644 --- a/examples/COUPLE/plugin/liblammpsplugin.c +++ b/examples/COUPLE/plugin/liblammpsplugin.c @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -18,10 +18,29 @@ a LAMMPS plugin to some other software. */ -#include "library.h" #include "liblammpsplugin.h" -#include + +#if defined(_WIN32) + +#ifndef WIN32_LEAN_AND_MEAN +#define WIN32_LEAN_AND_MEAN +#endif + +#if defined(_WIN32_WINNT) +#undef _WIN32_WINNT +#endif + +// target Windows version is windows 7 and later +#define _WIN32_WINNT _WIN32_WINNT_WIN7 +#define PSAPI_VERSION 2 + +#include +#else #include +#endif + +#include + liblammpsplugin_t *liblammpsplugin_load(const char *lib) { @@ -29,14 +48,29 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib) void *handle; if (lib == NULL) return NULL; + +#ifdef _WIN32 + handle = (void *) LoadLibrary(lib); +#else handle = dlopen(lib,RTLD_NOW|RTLD_GLOBAL); +#endif if (handle == NULL) return NULL; lmp = (liblammpsplugin_t *) malloc(sizeof(liblammpsplugin_t)); lmp->handle = handle; -#define ADDSYM(symbol) lmp->symbol = dlsym(handle,"lammps_" #symbol) +#ifdef _WIN32 +#define ADDSYM(symbol) *(void **) (&lmp->symbol) = (void *) GetProcAddress((HINSTANCE) handle, "lammps_" #symbol) +#else +#define ADDSYM(symbol) *(void **) (&lmp->symbol) = dlsym(handle,"lammps_" #symbol) +#endif + +#if defined(LAMMPS_LIB_MPI) ADDSYM(open); +#else + lmp->open = NULL; +#endif + ADDSYM(open_no_mpi); ADDSYM(open_fortran); ADDSYM(close); @@ -46,6 +80,8 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib) ADDSYM(kokkos_finalize); ADDSYM(python_finalize); + ADDSYM(error); + ADDSYM(file); ADDSYM(command); ADDSYM(commands_list); @@ -70,6 +106,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib) ADDSYM(extract_compute); ADDSYM(extract_fix); ADDSYM(extract_variable); + ADDSYM(extract_variable_datatype); ADDSYM(set_variable); ADDSYM(gather_atoms); @@ -77,8 +114,15 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib) ADDSYM(gather_atoms_subset); ADDSYM(scatter_atoms); ADDSYM(scatter_atoms_subset); + ADDSYM(gather_bonds); + ADDSYM(gather); + ADDSYM(gather_concat); + ADDSYM(gather_subset); + ADDSYM(scatter); + ADDSYM(scatter_subset); + ADDSYM(create_atoms); ADDSYM(find_pair_neighlist); @@ -116,6 +160,9 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib) ADDSYM(plugin_count); ADDSYM(plugin_name); + ADDSYM(encode_image_flags); + ADDSYM(decode_image_flags); + ADDSYM(set_fix_external_callback); ADDSYM(fix_external_get_force); ADDSYM(fix_external_set_energy_global); @@ -125,6 +172,8 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib) ADDSYM(fix_external_set_vector_length); ADDSYM(fix_external_set_vector); + ADDSYM(flush_buffers); + ADDSYM(free); ADDSYM(is_running); @@ -139,6 +188,8 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib) lmp->has_error = NULL; lmp->get_last_error_message = NULL; #endif + + ADDSYM(python_api_version); return lmp; } @@ -147,7 +198,11 @@ int liblammpsplugin_release(liblammpsplugin_t *lmp) if (lmp == NULL) return 1; if (lmp->handle == NULL) return 2; +#ifdef _WIN32 + FreeLibrary((HINSTANCE) lmp->handle); +#else dlclose(lmp->handle); +#endif free((void *)lmp); return 0; } diff --git a/examples/COUPLE/plugin/liblammpsplugin.h b/examples/COUPLE/plugin/liblammpsplugin.h index 219ddb2574..eb63ca6807 100644 --- a/examples/COUPLE/plugin/liblammpsplugin.h +++ b/examples/COUPLE/plugin/liblammpsplugin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -28,11 +28,71 @@ #define LAMMPS_SMALLBIG #endif +#if defined(LAMMPS_LIB_MPI) #include -#if defined(LAMMPS_BIGBIG) || defined(LAMMPS_SMALLBIG) -#include /* for int64_t */ #endif +#if defined(LAMMPS_BIGBIG) || defined(LAMMPS_SMALLBIG) +#include /* for int64_t */ +#endif + +/* The following enums must be kept in sync with the equivalent enums + * or constants in python/lammps/constants.py, fortran/lammps.f90, + * tools/swig/lammps.i, and examples/COUPLE/plugin/liblammpsplugin.h */ + +/* Data type constants for extracting data from atoms, computes and fixes */ + +enum _LMP_DATATYPE_CONST { + LAMMPS_INT = 0, /*!< 32-bit integer (array) */ + LAMMPS_INT_2D = 1, /*!< two-dimensional 32-bit integer array */ + LAMMPS_DOUBLE = 2, /*!< 64-bit double (array) */ + LAMMPS_DOUBLE_2D = 3, /*!< two-dimensional 64-bit double array */ + LAMMPS_INT64 = 4, /*!< 64-bit integer (array) */ + LAMMPS_INT64_2D = 5, /*!< two-dimensional 64-bit integer array */ + LAMMPS_STRING = 6 /*!< C-String */ +}; + +/* Style constants for extracting data from computes and fixes. */ + +enum _LMP_STYLE_CONST { + LMP_STYLE_GLOBAL = 0, /*!< return global data */ + LMP_STYLE_ATOM = 1, /*!< return per-atom data */ + LMP_STYLE_LOCAL = 2 /*!< return local data */ +}; + +/* Type and size constants for extracting data from computes and fixes. */ + +enum _LMP_TYPE_CONST { + LMP_TYPE_SCALAR = 0, /*!< return scalar */ + LMP_TYPE_VECTOR = 1, /*!< return vector */ + LMP_TYPE_ARRAY = 2, /*!< return array */ + LMP_SIZE_VECTOR = 3, /*!< return length of vector */ + LMP_SIZE_ROWS = 4, /*!< return number of rows */ + LMP_SIZE_COLS = 5 /*!< return number of columns */ +}; + +/* Error codes to select the suitable function in the Error class */ + +enum _LMP_ERROR_CONST { + LMP_ERROR_WARNING = 0, /*!< call Error::warning() */ + LMP_ERROR_ONE = 1, /*!< called from one MPI rank */ + LMP_ERROR_ALL = 2, /*!< called from all MPI ranks */ + LMP_ERROR_WORLD = 4, /*!< error on Comm::world */ + LMP_ERROR_UNIVERSE = 8 /*!< error on Comm::universe */ +}; + +/** Variable style constants for extracting data from variables. + * + * Must be kept in sync with the equivalent constants in python/lammps/constants.py, + * fortran/lammps.f90, and tools/swig/lammps.i */ + +enum _LMP_VAR_CONST { + LMP_VAR_EQUAL = 0, /*!< compatible with equal-style variables */ + LMP_VAR_ATOM = 1, /*!< compatible with atom-style variables */ + LMP_VAR_VECTOR = 2, /*!< compatible with vector-style variables */ + LMP_VAR_STRING = 3 /*!< return value will be a string (catch-all) */ +}; + #ifdef __cplusplus extern "C" { #endif @@ -49,7 +109,11 @@ struct _liblammpsplugin { int abiversion; int has_exceptions; void *handle; +#if defined(LAMMPS_LIB_MPI) void *(*open)(int, char **, MPI_Comm, void **); +#else + void *open; +#endif void *(*open_no_mpi)(int, char **, void **); void *(*open_fortran)(int, char **, void **, int); void (*close)(void *); @@ -59,13 +123,15 @@ struct _liblammpsplugin { void (*kokkos_finalize)(); void (*python_finalize)(); + void (*error)(void *, int, const char *); + void (*file)(void *, char *); char *(*command)(void *, const char *); void (*commands_list)(void *, int, const char **); void (*commands_string)(void *, const char *); double (*get_natoms)(void *); - double (*get_thermo)(void *, char *); + double (*get_thermo)(void *, const char *); void (*extract_box)(void *, double *, double *, double *, double *, double *, int *, int *); @@ -78,12 +144,13 @@ struct _liblammpsplugin { int *(*extract_global_datatype)(void *, const char *); void *(*extract_global)(void *, const char *); - void *(*extract_atom_datatype)(void *, const char *); + int *(*extract_atom_datatype)(void *, const char *); void *(*extract_atom)(void *, const char *); void *(*extract_compute)(void *, const char *, int, int); void *(*extract_fix)(void *, const char *, int, int, int, int); void *(*extract_variable)(void *, const char *, char *); + int (*extract_variable_datatype)(void *, const char *); int (*set_variable)(void *, char *, char *); void (*gather_atoms)(void *, char *, int, int, void *); @@ -93,22 +160,26 @@ struct _liblammpsplugin { void (*scatter_atoms_subset)(void *, char *, int, int, int, int *, void *); void (*gather_bonds)(void *, void *); - -// lammps_create_atoms() takes tagint and imageint as args -// ifdef insures they are compatible with rest of LAMMPS -// caller must match to how LAMMPS library is built + + void (*gather)(void *, char *, int, int, void *); + void (*gather_concat)(void *, char *, int, int, void *); + void (*gather_subset)(void *, char *, int, int, int, int *,void *); + void (*scatter)(void *, char *, int, int, void *); + void (*scatter_subset)(void *, char *, int, int, int, int *, void *); + +/* lammps_create_atoms() takes tagint and imageint as args + * the ifdef insures they are compatible with rest of LAMMPS + * caller must match to how LAMMPS library is built */ #ifndef LAMMPS_BIGBIG - void (*create_atoms)(void *, int, int *, int *, double *, - double *, int *, int); + void (*create_atoms)(void *, int, int *, int *, double *, double *, int *, int); #else - void (*create_atoms)(void *, int, int64_t *, int *, double *, - double *, int64_t *, int); + void (*create_atoms)(void *, int, int64_t *, int *, double *, double *, int64_t *, int); #endif int (*find_pair_neighlist)(void *, const char *, int, int, int); int (*find_fix_neighlist)(void *, const char *, int); - int (*find_compute_neighlist)(void *, char *, int); + int (*find_compute_neighlist)(void *, const char *, int); int (*neighlist_num_elements)(void *, int); void (*neighlist_element_neighbors)(void *, int, int, int *, int *, int **); @@ -141,8 +212,16 @@ struct _liblammpsplugin { int (*plugin_count)(); int (*plugin_name)(int, char *, char *, int); - void (*set_fix_external_callback)(void *, const char *, FixExternalFnPtr, void*); - void (*fix_external_get_force)(void *, const char *); +#if !defined(LAMMPS_BIGBIG) + int (*encode_image_flags)(int, int, int); + void (*decode_image_flags)(int, int *); +#else + int64_t (*encode_image_flags)(int, int, int); + void (*decode_image_flags)(int64_t, int *); +#endif + + void (*set_fix_external_callback)(void *, const char *, FixExternalFnPtr, void *); + double **(*fix_external_get_force)(void *, const char *); void (*fix_external_set_energy_global)(void *, const char *, double); void (*fix_external_set_energy_peratom)(void *, const char *, double *); void (*fix_external_set_virial_global)(void *, const char *, double *); @@ -150,6 +229,8 @@ struct _liblammpsplugin { void (*fix_external_set_vector_length)(void *, const char *, int); void (*fix_external_set_vector)(void *, const char *, int, double); + void (*flush_buffers)(void *); + void (*free)(void *); void (*is_running)(void *); @@ -157,6 +238,8 @@ struct _liblammpsplugin { int (*has_error)(void *); int (*get_last_error_message)(void *, char *, int); + + int (*python_api_version)(); }; typedef struct _liblammpsplugin liblammpsplugin_t; diff --git a/examples/COUPLE/plugin/simple.c b/examples/COUPLE/plugin/simple.c index dc3934b40c..8383584a38 100644 --- a/examples/COUPLE/plugin/simple.c +++ b/examples/COUPLE/plugin/simple.c @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - www.cs.sandia.gov/~sjplimp/lammps.html - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + https://www.lammps.org, Sandia National Laboratories + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -19,10 +19,16 @@ in.lammps = LAMMPS input script See README for compilation instructions */ +#include + #include #include #include -#include + +/* define so interface to lammps_open() is available, + since we will run on split communicator */ +#define LAMMPS_LIB_MPI 1 + #include "liblammpsplugin.h" /* this is the include for the plugin loader */ int main(int narg, char **arg) @@ -87,7 +93,13 @@ int main(int narg, char **arg) MPI_Abort(MPI_COMM_WORLD,1); } } - if (lammps == 1) lmp = plugin->open(0,NULL,comm_lammps,NULL); + if (lammps == 1) { + if (plugin->open == NULL) { + printf("ERROR: liblammpsmpi.c must be compiled with -DLAMMPS_LIB_MPI=1 for this program\n"); + MPI_Abort(MPI_COMM_WORLD,2); + } + lmp = plugin->open(0,NULL,comm_lammps,NULL); + } while (1) { if (me == 0) { @@ -112,23 +124,23 @@ int main(int narg, char **arg) int natoms = plugin->get_natoms(lmp); x = (double *) malloc(3*natoms*sizeof(double)); - plugin->gather_atoms(lmp,"x",1,3,x); + plugin->gather_atoms(lmp,(char *)"x",1,3,x); v = (double *) malloc(3*natoms*sizeof(double)); - plugin->gather_atoms(lmp,"v",1,3,v); + plugin->gather_atoms(lmp,(char *)"v",1,3,v); double epsilon = 0.1; x[0] += epsilon; - plugin->scatter_atoms(lmp,"x",1,3,x); + plugin->scatter_atoms(lmp,(char *)"x",1,3,x); plugin->command(lmp,"run 1"); } - // extract force on single atom two different ways + /* extract force on single atom two different ways */ if (lammps == 1) { double **f = (double **) plugin->extract_atom(lmp,"f"); printf("Force on 1 atom via extract_atom: %g\n",f[0][0]); - double *fx = (double *) plugin->extract_variable(lmp,"fx","all"); + double *fx = (double *) plugin->extract_variable(lmp,"fx",(char *)"all"); printf("Force on 1 atom via extract_variable: %g\n",fx[0]); } @@ -160,7 +172,7 @@ int main(int narg, char **arg) if (v) free(v); if (type) free(type); - // close down LAMMPS + /* close down LAMMPS */ if (lammps == 1) { plugin->close(lmp); diff --git a/examples/COUPLE/simple/CMakeLists.txt b/examples/COUPLE/simple/CMakeLists.txt index 4112eaa4e7..d9b877ec76 100644 --- a/examples/COUPLE/simple/CMakeLists.txt +++ b/examples/COUPLE/simple/CMakeLists.txt @@ -1,17 +1,44 @@ cmake_minimum_required(VERSION 3.10) -project(simple CXX) -set(LAMMPS_SRC_DIRECTORY "" CACHE PATH "Path for lammps source") -if(NOT LAMMPS_SRC_DIRECTORY STREQUAL "" AND EXISTS ${LAMMPS_SRC_DIRECTORY}/cmake/CMakeLists.txt) - option(BUILD_LIB "Build LAMMPS library" ON) - add_subdirectory(${LAMMPS_SRC_DIRECTORY}/cmake lammps) -else() +# 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(couple-simple VERSION 1.0 LANGUAGES C CXX) + +# 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_C_COMPILER_ID STREQUAL "MSVC") + if(LAMMPS_EXCEPTIONS) + add_compile_options(/EHsc) + endif() + endif() + add_compile_definitions(_CRT_SECURE_NO_WARNINGS) +endif() + +find_package(MPI QUIET) +# do not include the (obsolete) MPI C++ bindings which makes +# for leaner object files and avoids namespace conflicts +set(MPI_CXX_SKIP_MPICXX TRUE) + +########################## + +# build within LAMMPS build system +if(NOT LAMMPS_SOURCE_DIR) find_package(LAMMPS REQUIRED) endif() add_executable(simpleCC simple.cpp) target_link_libraries(simpleCC LAMMPS::lammps) -enable_language(C) add_executable(simpleC simple.c) target_link_libraries(simpleC LAMMPS::lammps) diff --git a/examples/COUPLE/simple/simple.c b/examples/COUPLE/simple/simple.c index 603ff270b7..fe2864f41e 100644 --- a/examples/COUPLE/simple/simple.c +++ b/examples/COUPLE/simple/simple.c @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - www.cs.sandia.gov/~sjplimp/lammps.html - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/COUPLE/simple/simple.cpp b/examples/COUPLE/simple/simple.cpp index c05266975e..bf1174267e 100644 --- a/examples/COUPLE/simple/simple.cpp +++ b/examples/COUPLE/simple/simple.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://www.lammps.org/ - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/COUPLE/simple/simple.f90 b/examples/COUPLE/simple/simple.f90 index 56b1534c40..8902104e47 100644 --- a/examples/COUPLE/simple/simple.f90 +++ b/examples/COUPLE/simple/simple.f90 @@ -1,6 +1,6 @@ ! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator -! www.cs.sandia.gov/~sjplimp/lammps.html -! Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +! https://www.lammps.org/, Sandia National Laboratories +! LAMMPS development team: developers@lammps.org ! ! Copyright (2003) Sandia Corporation. Under the terms of Contract ! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/COUPLE/simple/simple_f77.f90 b/examples/COUPLE/simple/simple_f77.f90 index 374a0748ee..ac1c03f061 100644 --- a/examples/COUPLE/simple/simple_f77.f90 +++ b/examples/COUPLE/simple/simple_f77.f90 @@ -1,6 +1,6 @@ ! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator -! www.cs.sandia.gov/~sjplimp/lammps.html -! Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +! https://www.lammps.org/, Sandia National Laboratories +! LAMMPS development team: developers@lammps.org ! ! Copyright (2003) Sandia Corporation. Under the terms of Contract ! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/generate_unique.py b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/generate_unique.py index 2cd6f46aec..330215bd80 100644 --- a/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/generate_unique.py +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/generate_unique.py @@ -3,7 +3,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/PACKAGES/cgdna/util/generate.py b/examples/PACKAGES/cgdna/util/generate.py index d2ba3ba980..cd7465acdb 100644 --- a/examples/PACKAGES/cgdna/util/generate.py +++ b/examples/PACKAGES/cgdna/util/generate.py @@ -3,7 +3,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/PACKAGES/electrode/README b/examples/PACKAGES/electrode/README index 652194670b..b0c64d496b 100644 --- a/examples/PACKAGES/electrode/README +++ b/examples/PACKAGES/electrode/README @@ -1,14 +1,14 @@ These examples demonstrate the use of the ELECTRODE package for constant potential molecular dynamics. planar/ - au-vac.data -- gold electrodes with vacuum + data.au-vac -- gold electrodes with vacuum in.planar* -- comparison of gold electrodes with vacuum to theoretical capacitance of planar capacitor -- 5x, further labeled by long-range solver (ewald / pppm) and boundary correction (ew2d / ew3dc / ffield) -- the pppm-ew2d combination would not give correct results and will throw an error if selected test.sh -- run all in.planar files and check charge at 1.2V and %difference from theoretical (last column) graph-il/ - graph-il.data -- graphene electrodes with electrolyte (coarse-grained BMIm-PF6) + data.graph-il -- graphene electrodes with electrolyte (coarse-grained BMIm-PF6) in.conp -- reference run at constant potential in.etypes -- type-based smart neighborlists in.ffield -- finite field method with fully periodic cell @@ -18,10 +18,22 @@ graph-il/ in.thermo -- thermalize electrolyte with thermopotentiostat instead of NVT au-aq/ - au-aq.data -- gold electrodes with electrolyte (SPC water + NaCl) + data.au-aq -- gold electrodes with electrolyte (SPC water + NaCl) in.ffield -- finite field method with fully periodic cell in.tf -- Thomas-Fermi metallicity model with more delocalized charges +madelung/ + data.au-elyt -- tiny electrodes with two electrolyte atoms in between + settings.mod -- common settings + in.* -- setup KSpace and fix electrode/conp + plate_cap.py -- compute reference energy and charges from Madelung style sum + eval.py -- compare output of reference and Lammps job (used by test.sh) + test.sh -- run all in.* files and check charge at 1 V and %difference from theoretical (last column) + +piston/ + data.piston -- two electrodes with water + in.piston -- equilibrate distance between rigid electrodes + # future work: # in.cylinder -- comparison of carbon nanotube to theoretical induced charge for charge near circular conductor diff --git a/examples/PACKAGES/electrode/au-aq/in.ffield b/examples/PACKAGES/electrode/au-aq/in.ffield index 094fc39144..de594f8c9a 100644 --- a/examples/PACKAGES/electrode/au-aq/in.ffield +++ b/examples/PACKAGES/electrode/au-aq/in.ffield @@ -4,7 +4,7 @@ boundary p p p # ffield uses periodic z-boundary and no slab include settings.mod # styles, groups, computes and fixes -fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7 +fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes on thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot diff --git a/examples/PACKAGES/electrode/au-aq/in.tf b/examples/PACKAGES/electrode/au-aq/in.tf index d73efd10fc..23beb357d8 100644 --- a/examples/PACKAGES/electrode/au-aq/in.tf +++ b/examples/PACKAGES/electrode/au-aq/in.tf @@ -6,7 +6,7 @@ boundary p p p # ffield uses periodic z-boundary and no slab include settings.mod # styles, groups, computes and fixes -fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7 +fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes on fix_modify conp tf 6 1.0 18.1715745 fix_modify conp tf 7 1.0 18.1715745 diff --git a/examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-ffield.g++.1 b/examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-ffield.g++.1 similarity index 52% rename from examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-ffield.g++.1 rename to examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-ffield.g++.1 index 76e15ebe53..2c43724875 100644 --- a/examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-ffield.g++.1 +++ b/examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-ffield.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with constant potential using finite field # for z-periodic gold-saline electrochemical cell @@ -37,8 +37,8 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors - special bonds CPU = 0.002 seconds - read_data CPU = 0.051 seconds + special bonds CPU = 0.006 seconds + read_data CPU = 0.097 seconds group bot type 6 1620 atoms in group bot @@ -52,11 +52,12 @@ group electrolyte type 1 2 3 4 5 fix nvt electrolyte nvt temp 298.0 298.0 241 fix shake SPC shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2160 = # of frozen angles - find clusters CPU = 0.002 seconds + find clusters CPU = 0.006 seconds variable q atom q variable qz atom q*(z-lz/2) @@ -67,12 +68,41 @@ compute qzbot bot reduce sum v_qz compute ctemp electrolyte temp -fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7 +fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes on 3240 atoms in group conp_group thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.24017705 @@ -82,9 +112,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.093542e-07 using double precision MKL FFT 3d grid and FFT values/proc = 472567 349920 - generated 21 of 21 mixed pair_coeff terms from geometric mixing rule +Generated 21 of 21 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17 ghost atom cutoff = 17 @@ -105,35 +135,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 194.6 | 194.6 | 194.6 Mbytes +Per MPI rank memory allocation (min/avg/max) = 194.8 | 194.8 | 194.8 Mbytes Step Temp c_ctemp E_pair TotEng c_qtop c_qbot c_qztop c_qzbot - 0 171.61215 298.06731 -39212.819 -35306.164 4.1391573 -4.1391573 78.718381 131.56372 - 50 147.03139 255.37383 -39870.139 -36523.051 4.1312167 -4.1312167 78.563872 131.30255 - 100 149.89027 260.33932 -39878.859 -36466.689 4.0217834 -4.0217834 76.482548 127.82573 - 150 151.7382 263.54893 -39873.178 -36418.942 4.0469977 -4.0469977 76.967548 128.59855 - 200 151.7508 263.57081 -39827.015 -36372.492 4.1830375 -4.1830375 79.554159 132.93925 - 250 152.61146 265.06566 -39791.293 -36317.177 4.1835865 -4.1835865 79.56665 132.97185 - 300 153.51486 266.63475 -39751.841 -36257.16 4.1571861 -4.1571861 79.061431 132.12905 - 350 156.35115 271.561 -39754.955 -36195.708 4.3498059 -4.3498059 82.720202 138.28678 - 400 156.26118 271.40474 -39690.781 -36133.582 4.3444079 -4.3444079 82.619396 138.11873 - 450 158.54164 275.36558 -39681.083 -36071.97 4.2020488 -4.2020488 79.912674 133.55185 - 500 161.40138 280.33258 -39684.185 -36009.972 4.3021924 -4.3021924 81.807527 136.7464 -Loop time of 246.197 on 1 procs for 500 steps with 9798 atoms + 0 171.61215 298.06731 -39021.917 -35115.261 4.1391573 -4.1391573 78.718381 131.56372 + 50 147.03139 255.37383 -39679.603 -36332.515 4.1312167 -4.1312167 78.563872 131.30255 + 100 149.89027 260.33932 -39693.369 -36281.2 4.0217834 -4.0217834 76.482548 127.82573 + 150 151.7382 263.54893 -39686.526 -36232.29 4.0469977 -4.0469977 76.967548 128.59855 + 200 151.7508 263.57081 -39634.089 -36179.566 4.1830375 -4.1830375 79.554159 132.93925 + 250 152.61146 265.06566 -39598.341 -36124.226 4.1835865 -4.1835865 79.56665 132.97185 + 300 153.51486 266.63475 -39560.107 -36065.426 4.1571861 -4.1571861 79.06143 132.12905 + 350 156.35115 271.561 -39554.338 -35995.09 4.3498059 -4.3498059 82.720202 138.28678 + 400 156.26118 271.40474 -39490.412 -35933.213 4.344408 -4.344408 82.619398 138.11874 + 450 158.54163 275.36557 -39487.28 -35878.167 4.2020489 -4.2020489 79.912677 133.55186 + 500 161.40137 280.33257 -39485.763 -35811.55 4.3021927 -4.3021927 81.807532 136.74641 +Loop time of 146.959 on 1 procs for 500 steps with 9798 atoms -Performance: 0.175 ns/day, 136.776 hours/ns, 2.031 timesteps/s -356.3% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.294 ns/day, 81.644 hours/ns, 3.402 timesteps/s, 33.336 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 105.64 | 105.64 | 105.64 | 0.0 | 42.91 -Bond | 0.0010592 | 0.0010592 | 0.0010592 | 0.0 | 0.00 -Kspace | 37.643 | 37.643 | 37.643 | 0.0 | 15.29 -Neigh | 5.8827 | 5.8827 | 5.8827 | 0.0 | 2.39 -Comm | 0.18181 | 0.18181 | 0.18181 | 0.0 | 0.07 -Output | 0.0055762 | 0.0055762 | 0.0055762 | 0.0 | 0.00 -Modify | 96.78 | 96.78 | 96.78 | 0.0 | 39.31 -Other | | 0.06346 | | | 0.03 +Pair | 69.832 | 69.832 | 69.832 | 0.0 | 47.52 +Bond | 0.00091634 | 0.00091634 | 0.00091634 | 0.0 | 0.00 +Kspace | 33.817 | 33.817 | 33.817 | 0.0 | 23.01 +Neigh | 4.2067 | 4.2067 | 4.2067 | 0.0 | 2.86 +Comm | 0.12212 | 0.12212 | 0.12212 | 0.0 | 0.08 +Output | 0.0031896 | 0.0031896 | 0.0031896 | 0.0 | 0.00 +Modify | 38.92 | 38.92 | 38.92 | 0.0 | 26.48 +Other | | 0.05687 | | | 0.04 Nlocal: 9798 ave 9798 max 9798 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -147,4 +177,4 @@ Ave neighs/atom = 842.63544 Ave special neighs/atom = 1.3227189 Neighbor list builds = 22 Dangerous builds = 0 -Total wall time: 0:19:39 +Total wall time: 0:05:33 diff --git a/examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-ffield.g++.4 b/examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-ffield.g++.4 similarity index 53% rename from examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-ffield.g++.4 rename to examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-ffield.g++.4 index 685a71eb74..5a18629cab 100644 --- a/examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-ffield.g++.4 +++ b/examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-ffield.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with constant potential using finite field # for z-periodic gold-saline electrochemical cell @@ -39,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-4 neighbors 2 = max # of special neighbors special bonds CPU = 0.002 seconds - read_data CPU = 0.149 seconds + read_data CPU = 0.118 seconds group bot type 6 1620 atoms in group bot @@ -53,11 +53,12 @@ group electrolyte type 1 2 3 4 5 fix nvt electrolyte nvt temp 298.0 298.0 241 fix shake SPC shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2160 = # of frozen angles - find clusters CPU = 0.003 seconds + find clusters CPU = 0.002 seconds variable q atom q variable qz atom q*(z-lz/2) @@ -68,12 +69,41 @@ compute qzbot bot reduce sum v_qz compute ctemp electrolyte temp -fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7 +fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes on 3240 atoms in group conp_group thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.24017705 @@ -83,9 +113,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.093542e-07 using double precision MKL FFT 3d grid and FFT values/proc = 138958 87480 - generated 21 of 21 mixed pair_coeff terms from geometric mixing rule +Generated 21 of 21 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17 ghost atom cutoff = 17 @@ -106,35 +136,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 118.1 | 120.6 | 123.1 Mbytes +Per MPI rank memory allocation (min/avg/max) = 118.2 | 120.7 | 123.2 Mbytes Step Temp c_ctemp E_pair TotEng c_qtop c_qbot c_qztop c_qzbot - 0 171.61215 298.06731 -39212.819 -35306.164 4.1391573 -4.1391573 78.718381 131.56372 - 50 147.03139 255.37383 -39870.139 -36523.051 4.1312167 -4.1312167 78.563872 131.30255 - 100 149.89027 260.33932 -39878.859 -36466.689 4.0217834 -4.0217834 76.482548 127.82573 - 150 151.7382 263.54893 -39873.178 -36418.942 4.0469977 -4.0469977 76.967548 128.59855 - 200 151.7508 263.57081 -39827.015 -36372.492 4.1830375 -4.1830375 79.554159 132.93925 - 250 152.61146 265.06566 -39791.293 -36317.177 4.1835865 -4.1835865 79.56665 132.97185 - 300 153.51486 266.63475 -39751.841 -36257.16 4.1571861 -4.1571861 79.061431 132.12905 - 350 156.35115 271.561 -39754.955 -36195.708 4.3498059 -4.3498059 82.7202 138.28678 - 400 156.26118 271.40474 -39690.781 -36133.582 4.3444079 -4.3444079 82.619398 138.11873 - 450 158.54163 275.36558 -39681.083 -36071.97 4.2020488 -4.2020488 79.912675 133.55185 - 500 161.40138 280.33257 -39684.185 -36009.972 4.3021924 -4.3021924 81.807527 136.7464 -Loop time of 111.902 on 4 procs for 500 steps with 9798 atoms + 0 171.61215 298.06731 -39021.917 -35115.261 4.1391573 -4.1391573 78.718381 131.56372 + 50 147.03139 255.37383 -39679.603 -36332.515 4.1312167 -4.1312167 78.563872 131.30255 + 100 149.89027 260.33932 -39693.369 -36281.2 4.0217834 -4.0217834 76.482548 127.82573 + 150 151.7382 263.54893 -39686.526 -36232.29 4.0469977 -4.0469977 76.967548 128.59855 + 200 151.7508 263.57081 -39634.089 -36179.566 4.1830375 -4.1830375 79.554159 132.93925 + 250 152.61146 265.06566 -39598.341 -36124.226 4.1835864 -4.1835864 79.56665 132.97185 + 300 153.51486 266.63475 -39560.107 -36065.426 4.1571861 -4.1571861 79.06143 132.12905 + 350 156.35115 271.561 -39554.338 -35995.09 4.3498059 -4.3498059 82.720201 138.28678 + 400 156.26118 271.40474 -39490.412 -35933.213 4.3444079 -4.3444079 82.619397 138.11873 + 450 158.54163 275.36558 -39487.279 -35878.167 4.202049 -4.202049 79.912678 133.55186 + 500 161.40137 280.33256 -39485.763 -35811.55 4.3021925 -4.3021925 81.807529 136.7464 +Loop time of 97.2399 on 4 procs for 500 steps with 9798 atoms -Performance: 0.386 ns/day, 62.168 hours/ns, 4.468 timesteps/s -97.2% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.444 ns/day, 54.022 hours/ns, 5.142 timesteps/s, 50.381 katom-step/s +87.0% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 21.816 | 31.136 | 40.866 | 166.5 | 27.82 -Bond | 0.00073413 | 0.00080346 | 0.00084203 | 0.0 | 0.00 -Kspace | 29.546 | 39.137 | 48.326 | 146.4 | 34.97 -Neigh | 2.5867 | 2.5872 | 2.5877 | 0.0 | 2.31 -Comm | 0.33289 | 0.33603 | 0.33791 | 0.3 | 0.30 -Output | 0.0022537 | 0.0030028 | 0.005192 | 2.3 | 0.00 -Modify | 38.498 | 38.635 | 38.77 | 2.2 | 34.53 -Other | | 0.06679 | | | 0.06 +Pair | 19.363 | 28.08 | 37.126 | 160.3 | 28.88 +Bond | 0.00094043 | 0.00096516 | 0.00098016 | 0.0 | 0.00 +Kspace | 31.655 | 40.554 | 49.143 | 131.3 | 41.71 +Neigh | 2.2289 | 2.2294 | 2.2297 | 0.0 | 2.29 +Comm | 0.5341 | 0.54079 | 0.5478 | 0.9 | 0.56 +Output | 0.0024141 | 0.0026943 | 0.0034176 | 0.8 | 0.00 +Modify | 25.6 | 25.755 | 25.908 | 2.8 | 26.49 +Other | | 0.07733 | | | 0.08 Nlocal: 2449.5 ave 2908 max 2012 min Histogram: 2 0 0 0 0 0 0 0 0 2 @@ -148,4 +178,4 @@ Ave neighs/atom = 842.63544 Ave special neighs/atom = 1.3227189 Neighbor list builds = 22 Dangerous builds = 0 -Total wall time: 0:07:48 +Total wall time: 0:03:03 diff --git a/examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-tf.g++.1 b/examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-tf.g++.1 similarity index 53% rename from examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-tf.g++.1 rename to examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-tf.g++.1 index 316e092c55..5ed60bc88a 100644 --- a/examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-tf.g++.1 +++ b/examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-tf.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with constant potential using finite field # for z-periodic gold-saline electrochemical cell # using Thomas-Fermi metallicity model: electrode q and qz will be @@ -39,8 +39,8 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors - special bonds CPU = 0.010 seconds - read_data CPU = 0.115 seconds + special bonds CPU = 0.003 seconds + read_data CPU = 0.065 seconds group bot type 6 1620 atoms in group bot @@ -54,11 +54,12 @@ group electrolyte type 1 2 3 4 5 fix nvt electrolyte nvt temp 298.0 298.0 241 fix shake SPC shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2160 = # of frozen angles - find clusters CPU = 0.010 seconds + find clusters CPU = 0.002 seconds variable q atom q variable qz atom q*(z-lz/2) @@ -69,7 +70,7 @@ compute qzbot bot reduce sum v_qz compute ctemp electrolyte temp -fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7 +fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes on 3240 atoms in group conp_group fix_modify conp tf 6 1.0 18.1715745 fix_modify conp tf 7 1.0 18.1715745 @@ -77,6 +78,35 @@ fix_modify conp tf 7 1.0 18.1715745 thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.24017705 @@ -86,9 +116,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.093542e-07 using double precision MKL FFT 3d grid and FFT values/proc = 472567 349920 - generated 21 of 21 mixed pair_coeff terms from geometric mixing rule +Generated 21 of 21 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17 ghost atom cutoff = 17 @@ -109,35 +139,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 194.6 | 194.6 | 194.6 Mbytes +Per MPI rank memory allocation (min/avg/max) = 194.8 | 194.8 | 194.8 Mbytes Step Temp c_ctemp E_pair TotEng c_qtop c_qbot c_qztop c_qzbot - 0 171.61215 298.06731 -39190.106 -35283.45 4.0804484 -4.0804484 79.075127 131.20697 - 50 147.14308 255.56782 -39849.964 -36500.334 3.9990346 -3.9990346 77.497181 128.57759 - 100 149.94935 260.44194 -39857.533 -36444.019 3.8613914 -3.8613914 74.82985 124.15315 - 150 151.95924 263.93285 -39855.567 -36396.299 3.8677064 -3.8677064 74.957279 124.33201 - 200 151.66737 263.42591 -39802.585 -36349.961 3.99842 -3.99842 77.491015 128.54496 - 250 152.36874 264.64408 -39763.306 -36294.716 3.9925863 -3.9925863 77.379445 128.37226 - 300 153.83916 267.19802 -39737.075 -36235.012 3.94995 -3.94995 76.553896 127.00395 - 350 155.88897 270.75827 -39722.265 -36173.539 4.0598524 -4.0598524 78.679643 130.5394 - 400 156.51993 271.85415 -39674.759 -36111.669 4.1312899 -4.1312899 80.060369 132.83599 - 450 160.21339 278.26919 -39697.962 -36050.793 3.9068098 -3.9068098 75.713484 125.59216 - 500 161.63639 280.74075 -39669.412 -35989.849 3.9261656 -3.9261656 76.0806 126.22255 -Loop time of 280.183 on 1 procs for 500 steps with 9798 atoms + 0 171.61215 298.06731 -39001.911 -35095.255 4.0804484 -4.0804484 79.075127 131.20697 + 50 147.14308 255.56782 -39665.525 -36315.894 3.9990346 -3.9990346 77.497181 128.57759 + 100 149.94935 260.44194 -39679.441 -36265.927 3.8613914 -3.8613914 74.82985 124.15315 + 150 151.95924 263.93285 -39677.184 -36217.916 3.8677064 -3.8677064 74.957279 124.33201 + 200 151.66737 263.42591 -39618.173 -36165.549 3.99842 -3.99842 77.491015 128.54496 + 250 152.36874 264.64408 -39579.164 -36110.574 3.9925863 -3.9925863 77.379445 128.37226 + 300 153.83916 267.19802 -39554.899 -36052.836 3.94995 -3.94995 76.553896 127.00395 + 350 155.88897 270.75827 -39535.02 -35986.294 4.0598524 -4.0598524 78.679643 130.5394 + 400 156.51993 271.85415 -39484.219 -35921.13 4.1312898 -4.1312898 80.060368 132.83598 + 450 160.21339 278.26919 -39517.776 -35870.607 3.9068098 -3.9068098 75.713484 125.59216 + 500 161.63639 280.74075 -39488.333 -35808.771 3.9261656 -3.9261656 76.080599 126.22255 +Loop time of 185.804 on 1 procs for 500 steps with 9798 atoms -Performance: 0.154 ns/day, 155.657 hours/ns, 1.785 timesteps/s -341.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.233 ns/day, 103.225 hours/ns, 2.691 timesteps/s, 26.366 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 119.69 | 119.69 | 119.69 | 0.0 | 42.72 -Bond | 0.0010952 | 0.0010952 | 0.0010952 | 0.0 | 0.00 -Kspace | 42.137 | 42.137 | 42.137 | 0.0 | 15.04 -Neigh | 6.5403 | 6.5403 | 6.5403 | 0.0 | 2.33 -Comm | 0.19411 | 0.19411 | 0.19411 | 0.0 | 0.07 -Output | 0.0053644 | 0.0053644 | 0.0053644 | 0.0 | 0.00 -Modify | 111.54 | 111.54 | 111.54 | 0.0 | 39.81 -Other | | 0.07244 | | | 0.03 +Pair | 91 | 91 | 91 | 0.0 | 48.98 +Bond | 0.0010315 | 0.0010315 | 0.0010315 | 0.0 | 0.00 +Kspace | 40.32 | 40.32 | 40.32 | 0.0 | 21.70 +Neigh | 5.6505 | 5.6505 | 5.6505 | 0.0 | 3.04 +Comm | 0.15304 | 0.15304 | 0.15304 | 0.0 | 0.08 +Output | 0.0041829 | 0.0041829 | 0.0041829 | 0.0 | 0.00 +Modify | 48.607 | 48.607 | 48.607 | 0.0 | 26.16 +Other | | 0.06807 | | | 0.04 Nlocal: 9798 ave 9798 max 9798 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -151,4 +181,4 @@ Ave neighs/atom = 842.7079 Ave special neighs/atom = 1.3227189 Neighbor list builds = 23 Dangerous builds = 0 -Total wall time: 0:21:11 +Total wall time: 0:06:18 diff --git a/examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-tf.g++.4 b/examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-tf.g++.4 similarity index 53% rename from examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-tf.g++.4 rename to examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-tf.g++.4 index 450a6c1fda..9791c35b43 100644 --- a/examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-tf.g++.4 +++ b/examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-tf.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with constant potential using finite field # for z-periodic gold-saline electrochemical cell # using Thomas-Fermi metallicity model: electrode q and qz will be @@ -41,7 +41,7 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-4 neighbors 2 = max # of special neighbors special bonds CPU = 0.002 seconds - read_data CPU = 0.091 seconds + read_data CPU = 0.114 seconds group bot type 6 1620 atoms in group bot @@ -55,11 +55,12 @@ group electrolyte type 1 2 3 4 5 fix nvt electrolyte nvt temp 298.0 298.0 241 fix shake SPC shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2160 = # of frozen angles - find clusters CPU = 0.001 seconds + find clusters CPU = 0.002 seconds variable q atom q variable qz atom q*(z-lz/2) @@ -70,7 +71,7 @@ compute qzbot bot reduce sum v_qz compute ctemp electrolyte temp -fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7 +fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes on 3240 atoms in group conp_group fix_modify conp tf 6 1.0 18.1715745 fix_modify conp tf 7 1.0 18.1715745 @@ -78,6 +79,35 @@ fix_modify conp tf 7 1.0 18.1715745 thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.24017705 @@ -87,9 +117,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.093542e-07 using double precision MKL FFT 3d grid and FFT values/proc = 138958 87480 - generated 21 of 21 mixed pair_coeff terms from geometric mixing rule +Generated 21 of 21 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17 ghost atom cutoff = 17 @@ -110,35 +140,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 118.1 | 120.6 | 123.1 Mbytes +Per MPI rank memory allocation (min/avg/max) = 118.2 | 120.7 | 123.2 Mbytes Step Temp c_ctemp E_pair TotEng c_qtop c_qbot c_qztop c_qzbot - 0 171.61215 298.06731 -39190.106 -35283.45 4.0804484 -4.0804484 79.075127 131.20697 - 50 147.14308 255.56782 -39849.964 -36500.334 3.9990346 -3.9990346 77.497181 128.57759 - 100 149.94935 260.44194 -39857.533 -36444.019 3.8613914 -3.8613914 74.82985 124.15315 - 150 151.95924 263.93285 -39855.567 -36396.299 3.8677064 -3.8677064 74.957279 124.33201 - 200 151.66737 263.42591 -39802.585 -36349.961 3.99842 -3.99842 77.491015 128.54496 - 250 152.36874 264.64408 -39763.306 -36294.716 3.9925863 -3.9925863 77.379445 128.37226 - 300 153.83916 267.19802 -39737.075 -36235.012 3.94995 -3.94995 76.553896 127.00395 - 350 155.88897 270.75827 -39722.265 -36173.539 4.0598524 -4.0598524 78.679643 130.5394 - 400 156.51993 271.85415 -39674.759 -36111.669 4.1312899 -4.1312899 80.060369 132.83599 - 450 160.21339 278.26919 -39697.962 -36050.793 3.9068098 -3.9068098 75.713485 125.59216 - 500 161.63639 280.74075 -39669.412 -35989.849 3.9261654 -3.9261654 76.080597 126.22255 -Loop time of 110.716 on 4 procs for 500 steps with 9798 atoms + 0 171.61215 298.06731 -39001.911 -35095.255 4.0804484 -4.0804484 79.075127 131.20697 + 50 147.14308 255.56782 -39665.525 -36315.894 3.9990346 -3.9990346 77.497181 128.57759 + 100 149.94935 260.44194 -39679.441 -36265.927 3.8613914 -3.8613914 74.82985 124.15315 + 150 151.95924 263.93285 -39677.184 -36217.916 3.8677064 -3.8677064 74.957279 124.33201 + 200 151.66737 263.42591 -39618.173 -36165.549 3.99842 -3.99842 77.491015 128.54496 + 250 152.36874 264.64408 -39579.163 -36110.574 3.9925863 -3.9925863 77.379445 128.37226 + 300 153.83916 267.19802 -39554.899 -36052.835 3.94995 -3.94995 76.553896 127.00395 + 350 155.88897 270.75826 -39535.02 -35986.294 4.0598523 -4.0598523 78.679642 130.5394 + 400 156.51993 271.85415 -39484.219 -35921.13 4.1312897 -4.1312897 80.060366 132.83598 + 450 160.21339 278.26919 -39517.776 -35870.607 3.9068099 -3.9068099 75.713486 125.59216 + 500 161.63639 280.74075 -39488.333 -35808.771 3.9261657 -3.9261657 76.080602 126.22256 +Loop time of 104.099 on 4 procs for 500 steps with 9798 atoms -Performance: 0.390 ns/day, 61.509 hours/ns, 4.516 timesteps/s -97.2% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.415 ns/day, 57.833 hours/ns, 4.803 timesteps/s, 47.061 katom-step/s +87.7% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 21.17 | 30.449 | 39.65 | 164.9 | 27.50 -Bond | 0.0007313 | 0.00077537 | 0.00081477 | 0.0 | 0.00 -Kspace | 29.854 | 38.911 | 48.058 | 143.8 | 35.14 -Neigh | 2.7206 | 2.7213 | 2.722 | 0.0 | 2.46 -Comm | 0.33023 | 0.33225 | 0.33384 | 0.2 | 0.30 -Output | 0.0024528 | 0.0027565 | 0.0035754 | 0.9 | 0.00 -Modify | 38.091 | 38.233 | 38.365 | 2.1 | 34.53 -Other | | 0.06636 | | | 0.06 +Pair | 20.951 | 30.326 | 40.07 | 166.7 | 29.13 +Bond | 0.00098259 | 0.0010706 | 0.0011926 | 0.3 | 0.00 +Kspace | 33.465 | 43.037 | 52.268 | 137.5 | 41.34 +Neigh | 2.6007 | 2.6014 | 2.6021 | 0.0 | 2.50 +Comm | 0.57766 | 0.58318 | 0.58875 | 0.7 | 0.56 +Output | 0.0022277 | 0.0024765 | 0.0031841 | 0.8 | 0.00 +Modify | 27.292 | 27.47 | 27.647 | 3.1 | 26.39 +Other | | 0.0787 | | | 0.08 Nlocal: 2449.5 ave 2908 max 2017 min Histogram: 2 0 0 0 0 0 0 0 0 2 @@ -147,9 +177,9 @@ Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 2.06421e+06 ave 2.7551e+06 max 1.40237e+06 min Histogram: 2 0 0 0 0 0 0 0 0 2 -Total # of neighbors = 8256853 -Ave neighs/atom = 842.708 +Total # of neighbors = 8256852 +Ave neighs/atom = 842.7079 Ave special neighs/atom = 1.3227189 Neighbor list builds = 23 Dangerous builds = 0 -Total wall time: 0:08:22 +Total wall time: 0:03:12 diff --git a/examples/PACKAGES/electrode/graph-il/.gitignore b/examples/PACKAGES/electrode/graph-il/.gitignore index 8ee8bfa0f2..592bb61996 100644 --- a/examples/PACKAGES/electrode/graph-il/.gitignore +++ b/examples/PACKAGES/electrode/graph-il/.gitignore @@ -1 +1,2 @@ log.lammps* +in.temp diff --git a/examples/PACKAGES/electrode/graph-il/algo_test.sh b/examples/PACKAGES/electrode/graph-il/algo_test.sh new file mode 100755 index 0000000000..6106fe02dc --- /dev/null +++ b/examples/PACKAGES/electrode/graph-il/algo_test.sh @@ -0,0 +1,28 @@ +#!/bin/bash + +LMP_BIN="$1" +NP="${2:-1}" +echo "MPI over $NP procs:" +for feat in conp etypes tf +do + echo "Using base input file in.$feat:" + echo "mat_inv, log excerpts:" + logfile="log.algo_test.$NP.$feat" + mpirun -np $NP $LMP_BIN -i in.$feat -l $logfile > /dev/null 2>&1 + grep -A2 'Per MPI rank' $logfile + grep -B1 'Loop time' $logfile + rm $logfile + for cgtype in mat_cg cg + do + for tol in 1e-4 1e-5 1e-6 + do + echo "$cgtype, tol = $tol, log excerpts:" + logfile="log.algo_test.$NP.$feat.$cgtype.$tol" + sed '/electrode/ s/$/ algo '"$cgtype"' '"$tol"'/' in.$feat > in.temp + mpirun -np $NP $LMP_BIN -i in.temp -l $logfile > /dev/null 2>&1 + grep -A2 'Per MPI rank' $logfile + grep -B1 'Loop time' $logfile + rm $logfile + done + done +done diff --git a/examples/PACKAGES/electrode/graph-il/data.graph-il b/examples/PACKAGES/electrode/graph-il/data.graph-il index 600adeb64f..597e3c21d8 100644 --- a/examples/PACKAGES/electrode/graph-il/data.graph-il +++ b/examples/PACKAGES/electrode/graph-il/data.graph-il @@ -3,7 +3,7 @@ LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.7 o 3776 atoms 640 bonds 320 angles - 5 atom types + 6 atom types 2 bond types 1 angle types @@ -18,6 +18,7 @@ LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.7 o 3 57.119999 # Roy-Maroncelli BMI3 4 144.960007 # Roy-Maroncelli PF64 5 12.001000 # carbon 5 + 6 12.001000 # carbon 5 Pair Coeffs # lj/cut/coul/long @@ -26,6 +27,7 @@ Pair Coeffs # lj/cut/coul/long 3 0.43738 5.04 4 1.12572 5.06 5 0.05497 3.37 +6 0.05497 3.37 Bond Coeffs # harmonic @@ -1318,1252 +1320,1252 @@ Angle Coeffs # harmonic 1278 639 2 0.157800 13.112696 26.068785 21.224487 # 2 1279 639 3 0.184800 13.700453 25.668398 15.818604 # 3 1280 640 4 -0.780000 30.804737 25.139051 26.365158 # 4 -1281 645 5 0.000000 1.229756 1.065000 -61.575001 # 5 -1282 645 5 0.000000 3.689268 1.065000 -61.575001 # 5 -1283 645 5 0.000000 2.459512 0.355000 -61.575001 # 5 -1284 645 5 0.000000 6.148780 1.065000 -61.575001 # 5 -1285 645 5 0.000000 4.919024 0.355000 -61.575001 # 5 -1286 645 5 0.000000 8.608293 1.065000 -61.575001 # 5 -1287 645 5 0.000000 7.378536 0.355000 -61.575001 # 5 -1288 645 5 0.000000 11.067804 1.065000 -61.575001 # 5 -1289 645 5 0.000000 9.838048 0.355000 -61.575001 # 5 -1290 645 5 0.000000 13.527316 1.065000 -61.575001 # 5 -1291 645 5 0.000000 12.297561 0.355000 -61.575001 # 5 -1292 645 5 0.000000 15.986829 1.065000 -61.575001 # 5 -1293 645 5 0.000000 14.757072 0.355000 -61.575001 # 5 -1294 645 5 0.000000 18.446341 1.065000 -61.575001 # 5 -1295 645 5 0.000000 17.216585 0.355000 -61.575001 # 5 -1296 645 5 0.000000 20.905853 1.065000 -61.575001 # 5 -1297 645 5 0.000000 19.676096 0.355000 -61.575001 # 5 -1298 645 5 0.000000 23.365364 1.065000 -61.575001 # 5 -1299 645 5 0.000000 22.135609 0.355000 -61.575001 # 5 -1300 645 5 0.000000 25.824877 1.065000 -61.575001 # 5 -1301 645 5 0.000000 24.595121 0.355000 -61.575001 # 5 -1302 645 5 0.000000 28.284389 1.065000 -61.575001 # 5 -1303 645 5 0.000000 27.054632 0.355000 -61.575001 # 5 -1304 645 5 0.000000 30.743900 1.065000 -61.575001 # 5 -1305 645 5 0.000000 29.514145 0.355000 -61.575001 # 5 -1306 645 5 0.000000 31.973658 0.355000 -61.575001 # 5 -1307 645 5 0.000000 2.459512 3.195000 -61.575001 # 5 -1308 645 5 0.000000 1.229756 2.485000 -61.575001 # 5 -1309 645 5 0.000000 4.919024 3.195000 -61.575001 # 5 -1310 645 5 0.000000 3.689268 2.485000 -61.575001 # 5 -1311 645 5 0.000000 7.378536 3.195000 -61.575001 # 5 -1312 645 5 0.000000 6.148780 2.485000 -61.575001 # 5 -1313 645 5 0.000000 9.838048 3.195000 -61.575001 # 5 -1314 645 5 0.000000 8.608293 2.485000 -61.575001 # 5 -1315 645 5 0.000000 12.297561 3.195000 -61.575001 # 5 -1316 645 5 0.000000 11.067804 2.485000 -61.575001 # 5 -1317 645 5 0.000000 14.757072 3.195000 -61.575001 # 5 -1318 645 5 0.000000 13.527316 2.485000 -61.575001 # 5 -1319 645 5 0.000000 17.216585 3.195000 -61.575001 # 5 -1320 645 5 0.000000 15.986829 2.485000 -61.575001 # 5 -1321 645 5 0.000000 19.676096 3.195000 -61.575001 # 5 -1322 645 5 0.000000 18.446341 2.485000 -61.575001 # 5 -1323 645 5 0.000000 22.135609 3.195000 -61.575001 # 5 -1324 645 5 0.000000 20.905853 2.485000 -61.575001 # 5 -1325 645 5 0.000000 24.595121 3.195000 -61.575001 # 5 -1326 645 5 0.000000 23.365364 2.485000 -61.575001 # 5 -1327 645 5 0.000000 27.054632 3.195000 -61.575001 # 5 -1328 645 5 0.000000 25.824877 2.485000 -61.575001 # 5 -1329 645 5 0.000000 29.514145 3.195000 -61.575001 # 5 -1330 645 5 0.000000 28.284389 2.485000 -61.575001 # 5 -1331 645 5 0.000000 31.973658 3.195000 -61.575001 # 5 -1332 645 5 0.000000 30.743900 2.485000 -61.575001 # 5 -1333 645 5 0.000000 1.229756 5.325000 -61.575001 # 5 -1334 645 5 0.000000 3.689268 5.325000 -61.575001 # 5 -1335 645 5 0.000000 2.459512 4.615000 -61.575001 # 5 -1336 645 5 0.000000 6.148780 5.325000 -61.575001 # 5 -1337 645 5 0.000000 4.919024 4.615000 -61.575001 # 5 -1338 645 5 0.000000 8.608293 5.325000 -61.575001 # 5 -1339 645 5 0.000000 7.378536 4.615000 -61.575001 # 5 -1340 645 5 0.000000 11.067804 5.325000 -61.575001 # 5 -1341 645 5 0.000000 9.838048 4.615000 -61.575001 # 5 -1342 645 5 0.000000 13.527316 5.325000 -61.575001 # 5 -1343 645 5 0.000000 12.297561 4.615000 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26.625000 58.225006 # 5 +3617 646 6 0.000000 30.743900 26.625000 61.574997 # 5 +3618 646 6 0.000000 29.514145 25.915003 61.574997 # 5 +3619 644 6 0.000000 31.973658 27.335001 58.225006 # 5 +3620 646 6 0.000000 31.973658 25.915003 61.574997 # 5 +3621 644 6 0.000000 1.229756 29.465000 58.225006 # 5 +3622 644 6 0.000000 2.459512 28.754999 58.225006 # 5 +3623 646 6 0.000000 2.459512 28.754999 61.574997 # 5 +3624 646 6 0.000000 1.229756 28.045000 61.574997 # 5 +3625 644 6 0.000000 3.689268 29.465000 58.225006 # 5 +3626 644 6 0.000000 4.919024 28.754999 58.225006 # 5 +3627 646 6 0.000000 4.919024 28.754999 61.574997 # 5 +3628 646 6 0.000000 3.689268 28.045000 61.574997 # 5 +3629 644 6 0.000000 6.148780 29.465000 58.225006 # 5 +3630 644 6 0.000000 7.378536 28.754999 58.225006 # 5 +3631 646 6 0.000000 7.378536 28.754999 61.574997 # 5 +3632 646 6 0.000000 6.148780 28.045000 61.574997 # 5 +3633 644 6 0.000000 8.608293 29.465000 58.225006 # 5 +3634 644 6 0.000000 9.838048 28.754999 58.225006 # 5 +3635 646 6 0.000000 9.838048 28.754999 61.574997 # 5 +3636 646 6 0.000000 8.608293 28.045000 61.574997 # 5 +3637 644 6 0.000000 11.067804 29.465000 58.225006 # 5 +3638 644 6 0.000000 12.297561 28.754999 58.225006 # 5 +3639 646 6 0.000000 12.297561 28.754999 61.574997 # 5 +3640 646 6 0.000000 11.067804 28.045000 61.574997 # 5 +3641 644 6 0.000000 13.527316 29.465000 58.225006 # 5 +3642 644 6 0.000000 14.757072 28.754999 58.225006 # 5 +3643 646 6 0.000000 14.757072 28.754999 61.574997 # 5 +3644 646 6 0.000000 13.527316 28.045000 61.574997 # 5 +3645 644 6 0.000000 15.986829 29.465000 58.225006 # 5 +3646 644 6 0.000000 17.216585 28.754999 58.225006 # 5 +3647 646 6 0.000000 17.216585 28.754999 61.574997 # 5 +3648 646 6 0.000000 15.986829 28.045000 61.574997 # 5 +3649 644 6 0.000000 18.446341 29.465000 58.225006 # 5 +3650 644 6 0.000000 19.676096 28.754999 58.225006 # 5 +3651 646 6 0.000000 19.676096 28.754999 61.574997 # 5 +3652 646 6 0.000000 18.446341 28.045000 61.574997 # 5 +3653 644 6 0.000000 20.905853 29.465000 58.225006 # 5 +3654 644 6 0.000000 22.135609 28.754999 58.225006 # 5 +3655 646 6 0.000000 22.135609 28.754999 61.574997 # 5 +3656 646 6 0.000000 20.905853 28.045000 61.574997 # 5 +3657 644 6 0.000000 23.365364 29.465000 58.225006 # 5 +3658 644 6 0.000000 24.595121 28.754999 58.225006 # 5 +3659 646 6 0.000000 24.595121 28.754999 61.574997 # 5 +3660 646 6 0.000000 23.365364 28.045000 61.574997 # 5 +3661 644 6 0.000000 25.824877 29.465000 58.225006 # 5 +3662 644 6 0.000000 27.054632 28.754999 58.225006 # 5 +3663 646 6 0.000000 27.054632 28.754999 61.574997 # 5 +3664 646 6 0.000000 25.824877 28.045000 61.574997 # 5 +3665 644 6 0.000000 28.284389 29.465000 58.225006 # 5 +3666 644 6 0.000000 29.514145 28.754999 58.225006 # 5 +3667 646 6 0.000000 29.514145 28.754999 61.574997 # 5 +3668 646 6 0.000000 28.284389 28.045000 61.574997 # 5 +3669 644 6 0.000000 30.743900 29.465000 58.225006 # 5 +3670 644 6 0.000000 31.973658 28.754999 58.225006 # 5 +3671 646 6 0.000000 31.973658 28.754999 61.574997 # 5 +3672 646 6 0.000000 30.743900 28.045000 61.574997 # 5 +3673 644 6 0.000000 1.229756 30.885000 58.225006 # 5 +3674 646 6 0.000000 1.229756 30.885000 61.574997 # 5 +3675 644 6 0.000000 2.459512 31.594999 58.225006 # 5 +3676 644 6 0.000000 3.689268 30.885000 58.225006 # 5 +3677 646 6 0.000000 3.689268 30.885000 61.574997 # 5 +3678 646 6 0.000000 2.459512 30.174999 61.574997 # 5 +3679 644 6 0.000000 4.919024 31.594999 58.225006 # 5 +3680 644 6 0.000000 6.148780 30.885000 58.225006 # 5 +3681 646 6 0.000000 6.148780 30.885000 61.574997 # 5 +3682 646 6 0.000000 4.919024 30.174999 61.574997 # 5 +3683 644 6 0.000000 7.378536 31.594999 58.225006 # 5 +3684 644 6 0.000000 8.608293 30.885000 58.225006 # 5 +3685 646 6 0.000000 8.608293 30.885000 61.574997 # 5 +3686 646 6 0.000000 7.378536 30.174999 61.574997 # 5 +3687 644 6 0.000000 9.838048 31.594999 58.225006 # 5 +3688 644 6 0.000000 11.067804 30.885000 58.225006 # 5 +3689 646 6 0.000000 11.067804 30.885000 61.574997 # 5 +3690 646 6 0.000000 9.838048 30.174999 61.574997 # 5 +3691 644 6 0.000000 12.297561 31.594999 58.225006 # 5 +3692 644 6 0.000000 13.527316 30.885000 58.225006 # 5 +3693 646 6 0.000000 13.527316 30.885000 61.574997 # 5 +3694 646 6 0.000000 12.297561 30.174999 61.574997 # 5 +3695 644 6 0.000000 14.757072 31.594999 58.225006 # 5 +3696 644 6 0.000000 15.986829 30.885000 58.225006 # 5 +3697 646 6 0.000000 15.986829 30.885000 61.574997 # 5 +3698 646 6 0.000000 14.757072 30.174999 61.574997 # 5 +3699 644 6 0.000000 17.216585 31.594999 58.225006 # 5 +3700 644 6 0.000000 18.446341 30.885000 58.225006 # 5 +3701 646 6 0.000000 18.446341 30.885000 61.574997 # 5 +3702 646 6 0.000000 17.216585 30.174999 61.574997 # 5 +3703 644 6 0.000000 19.676096 31.594999 58.225006 # 5 +3704 644 6 0.000000 20.905853 30.885000 58.225006 # 5 +3705 646 6 0.000000 20.905853 30.885000 61.574997 # 5 +3706 646 6 0.000000 19.676096 30.174999 61.574997 # 5 +3707 644 6 0.000000 22.135609 31.594999 58.225006 # 5 +3708 644 6 0.000000 23.365364 30.885000 58.225006 # 5 +3709 646 6 0.000000 23.365364 30.885000 61.574997 # 5 +3710 646 6 0.000000 22.135609 30.174999 61.574997 # 5 +3711 644 6 0.000000 24.595121 31.594999 58.225006 # 5 +3712 644 6 0.000000 25.824877 30.885000 58.225006 # 5 +3713 646 6 0.000000 25.824877 30.885000 61.574997 # 5 +3714 646 6 0.000000 24.595121 30.174999 61.574997 # 5 +3715 644 6 0.000000 27.054632 31.594999 58.225006 # 5 +3716 644 6 0.000000 28.284389 30.885000 58.225006 # 5 +3717 646 6 0.000000 28.284389 30.885000 61.574997 # 5 +3718 646 6 0.000000 27.054632 30.174999 61.574997 # 5 +3719 644 6 0.000000 29.514145 31.594999 58.225006 # 5 +3720 644 6 0.000000 30.743900 30.885000 58.225006 # 5 +3721 646 6 0.000000 30.743900 30.885000 61.574997 # 5 +3722 646 6 0.000000 29.514145 30.174999 61.574997 # 5 +3723 644 6 0.000000 31.973658 31.594999 58.225006 # 5 +3724 646 6 0.000000 31.973658 30.174999 61.574997 # 5 +3725 644 6 0.000000 1.229756 33.724998 58.225006 # 5 +3726 644 6 0.000000 2.459512 33.014999 58.225006 # 5 +3727 646 6 0.000000 2.459512 33.014999 61.574997 # 5 +3728 646 6 0.000000 1.229756 32.305000 61.574997 # 5 +3729 644 6 0.000000 3.689268 33.724998 58.225006 # 5 +3730 644 6 0.000000 4.919024 33.014999 58.225006 # 5 +3731 646 6 0.000000 4.919024 33.014999 61.574997 # 5 +3732 646 6 0.000000 3.689268 32.305000 61.574997 # 5 +3733 644 6 0.000000 6.148780 33.724998 58.225006 # 5 +3734 644 6 0.000000 7.378536 33.014999 58.225006 # 5 +3735 646 6 0.000000 7.378536 33.014999 61.574997 # 5 +3736 646 6 0.000000 6.148780 32.305000 61.574997 # 5 +3737 644 6 0.000000 8.608293 33.724998 58.225006 # 5 +3738 644 6 0.000000 9.838048 33.014999 58.225006 # 5 +3739 646 6 0.000000 9.838048 33.014999 61.574997 # 5 +3740 646 6 0.000000 8.608293 32.305000 61.574997 # 5 +3741 644 6 0.000000 11.067804 33.724998 58.225006 # 5 +3742 644 6 0.000000 12.297561 33.014999 58.225006 # 5 +3743 646 6 0.000000 12.297561 33.014999 61.574997 # 5 +3744 646 6 0.000000 11.067804 32.305000 61.574997 # 5 +3745 644 6 0.000000 13.527316 33.724998 58.225006 # 5 +3746 644 6 0.000000 14.757072 33.014999 58.225006 # 5 +3747 646 6 0.000000 14.757072 33.014999 61.574997 # 5 +3748 646 6 0.000000 13.527316 32.305000 61.574997 # 5 +3749 644 6 0.000000 15.986829 33.724998 58.225006 # 5 +3750 644 6 0.000000 17.216585 33.014999 58.225006 # 5 +3751 646 6 0.000000 17.216585 33.014999 61.574997 # 5 +3752 646 6 0.000000 15.986829 32.305000 61.574997 # 5 +3753 644 6 0.000000 18.446341 33.724998 58.225006 # 5 +3754 644 6 0.000000 19.676096 33.014999 58.225006 # 5 +3755 646 6 0.000000 19.676096 33.014999 61.574997 # 5 +3756 646 6 0.000000 18.446341 32.305000 61.574997 # 5 +3757 644 6 0.000000 20.905853 33.724998 58.225006 # 5 +3758 644 6 0.000000 22.135609 33.014999 58.225006 # 5 +3759 646 6 0.000000 22.135609 33.014999 61.574997 # 5 +3760 646 6 0.000000 20.905853 32.305000 61.574997 # 5 +3761 644 6 0.000000 23.365364 33.724998 58.225006 # 5 +3762 644 6 0.000000 24.595121 33.014999 58.225006 # 5 +3763 646 6 0.000000 24.595121 33.014999 61.574997 # 5 +3764 646 6 0.000000 23.365364 32.305000 61.574997 # 5 +3765 644 6 0.000000 25.824877 33.724998 58.225006 # 5 +3766 644 6 0.000000 27.054632 33.014999 58.225006 # 5 +3767 646 6 0.000000 27.054632 33.014999 61.574997 # 5 +3768 646 6 0.000000 25.824877 32.305000 61.574997 # 5 +3769 644 6 0.000000 28.284389 33.724998 58.225006 # 5 +3770 644 6 0.000000 29.514145 33.014999 58.225006 # 5 +3771 646 6 0.000000 29.514145 33.014999 61.574997 # 5 +3772 646 6 0.000000 28.284389 32.305000 61.574997 # 5 +3773 644 6 0.000000 30.743900 33.724998 58.225006 # 5 +3774 644 6 0.000000 31.973658 33.014999 58.225006 # 5 +3775 646 6 0.000000 31.973658 33.014999 61.574997 # 5 +3776 646 6 0.000000 30.743900 32.305000 61.574997 # 5 Bonds diff --git a/examples/PACKAGES/electrode/graph-il/in.conp b/examples/PACKAGES/electrode/graph-il/in.conp index 12fcd88541..e5eec24da3 100644 --- a/examples/PACKAGES/electrode/graph-il/in.conp +++ b/examples/PACKAGES/electrode/graph-il/in.conp @@ -3,9 +3,9 @@ boundary p p f # slab calculation include settings.mod # styles, groups, computes and fixes -kspace_modify slab 3.0 +kspace_modify slab 3.0 # amat twostep -fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on +fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on #algo mat_inv thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop diff --git a/examples/PACKAGES/electrode/graph-il/in.conq b/examples/PACKAGES/electrode/graph-il/in.conq index 08429924d4..7f315a4b12 100644 --- a/examples/PACKAGES/electrode/graph-il/in.conq +++ b/examples/PACKAGES/electrode/graph-il/in.conq @@ -5,14 +5,10 @@ boundary p p f # slab calculation include settings.mod # styles, groups, computes and fixes kspace_modify slab 3.0 -fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes 5 # conq doesn't take symm option - -# ask fix conq to output electrode potentials to internal variables -variable vbot internal 0.0 -variable vtop internal 0.0 -fix_modify conq set v bot vbot -fix_modify conq set v top vtop +fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes on # symm on +variable dv equal f_conq[2]-f_conq[1] +# symm on and off give different electrode potentials, but identical potential difference thermo 50 -thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop +thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_conq[1] f_conq[2] v_dv run 500 diff --git a/examples/PACKAGES/electrode/graph-il/in.conq2 b/examples/PACKAGES/electrode/graph-il/in.conq2 index 46c9ecbf99..d860bf6c1a 100644 --- a/examples/PACKAGES/electrode/graph-il/in.conq2 +++ b/examples/PACKAGES/electrode/graph-il/in.conq2 @@ -5,30 +5,16 @@ boundary p p f # slab calculation include settings.mod # styles, groups, computes and fixes kspace_modify slab 3.0 -fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes 5 +fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes on -# get the four entries of electrode elastance matrix -variable me00 internal 0.0 -variable me01 internal 0.0 -variable me10 internal 0.0 -variable me11 internal 0.0 -fix_modify conp set me bot bot me00 -fix_modify conp set me bot top me01 -fix_modify conp set me top bot me10 -fix_modify conp set me top top me11 - -# get the 0V charges (qsb), and excess charge required to reach preset total charges -variable qsb_bot internal 0.0 -variable qsb_top internal 0.0 -fix_modify conp set qsb bot qsb_bot -fix_modify conp set qsb top qsb_top -variable qex_bot equal -1.0-v_qsb_bot # difference between desired and 0V charge -variable qex_top equal 1.0-v_qsb_top # difference between desired and 0V charge +variable qex_bot equal -1.0-f_conp[1][1] # difference between desired and 0V charge +variable qex_top equal 1.0-f_conp[2][1] # difference between desired and 0V charge # calculate imposed potential as elastance * excess charge # note: fix will wait until the run setup to look for its potential variables -variable vbot equal v_me00*v_qex_bot+v_me01*v_qex_top -variable vtop equal v_me10*v_qex_bot+v_me11*v_qex_top +# which is why we can define variable names *after* fix conp without error +variable vbot equal f_conp[1][4]*v_qex_bot+f_conp[1][5]*v_qex_top +variable vtop equal f_conp[2][4]*v_qex_bot+f_conp[2][5]*v_qex_top thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop diff --git a/examples/PACKAGES/electrode/graph-il/in.etypes b/examples/PACKAGES/electrode/graph-il/in.etypes index 30edebdc77..990c8bb415 100644 --- a/examples/PACKAGES/electrode/graph-il/in.etypes +++ b/examples/PACKAGES/electrode/graph-il/in.etypes @@ -5,7 +5,7 @@ boundary p p f # slab calculation include settings.mod # styles, groups, computes and fixes kspace_modify slab 3.0 -fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5 +fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop diff --git a/examples/PACKAGES/electrode/graph-il/in.ffield b/examples/PACKAGES/electrode/graph-il/in.ffield index 3d07402ffd..0771e91e62 100644 --- a/examples/PACKAGES/electrode/graph-il/in.ffield +++ b/examples/PACKAGES/electrode/graph-il/in.ffield @@ -4,7 +4,7 @@ boundary p p p # ffield uses periodic z-boundary and no slab include settings.mod # styles, groups, computes and fixes -fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5 ffield yes +fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on ffield yes thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop diff --git a/examples/PACKAGES/electrode/graph-il/in.ramp b/examples/PACKAGES/electrode/graph-il/in.ramp index da6053ff9d..e4b897937d 100644 --- a/examples/PACKAGES/electrode/graph-il/in.ramp +++ b/examples/PACKAGES/electrode/graph-il/in.ramp @@ -6,7 +6,7 @@ include settings.mod # styles, groups, computes and fixes kspace_modify slab 3.0 variable v equal ramp(2,4) -fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes 5 +fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes on thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_v diff --git a/examples/PACKAGES/electrode/graph-il/in.thermo b/examples/PACKAGES/electrode/graph-il/in.thermo index a1d75196c9..eed574bff6 100644 --- a/examples/PACKAGES/electrode/graph-il/in.thermo +++ b/examples/PACKAGES/electrode/graph-il/in.thermo @@ -6,9 +6,9 @@ include settings.mod # styles, groups, computes and fixes kspace_modify slab 3.0 unfix nvt # remove NVT thermostat included from "settings.mod" -fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes 5 temp 500 100 7 # temp tau rng +fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes on temp 500 100 7 symm on # temp tau rng # to compare to regular constant potential, switch previous line to this: -#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes 5 symm on +#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes on symm on fix nve electrolyte nve # note ionic liquid does not reach 500K immediately diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conp.g++.1 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conp.g++.1 similarity index 51% rename from examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conp.g++.1 rename to examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conp.g++.1 index 086f109958..c5cd2579af 100644 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conp.g++.1 +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conp.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with constant potential # for graphene-ionic liquid supercapacitor @@ -37,13 +37,20 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.036 seconds + special bonds CPU = 0.004 seconds + read_data CPU = 0.027 seconds -group bot molecule 641 -416 atoms in group bot -group top molecule 642 +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos 416 atoms in group top +group bot subtract ele top +416 atoms in group bot group bmi type 1 2 3 960 atoms in group bmi @@ -52,24 +59,54 @@ group electrolyte type 1 2 3 4 fix nvt electrolyte nvt temp 500.0 500.0 100 fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 320 = # of frozen angles - find clusters CPU = 0.001 seconds + find clusters CPU = 0.005 seconds variable q atom q compute qtop top reduce sum v_q compute qbot bot reduce sum v_q compute ctemp electrolyte temp -kspace_modify slab 3.0 +kspace_modify slab 3.0 # amat twostep -fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on +fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on #algo mat_inv 832 atoms in group conp_group thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.20904498 @@ -79,9 +116,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.1149519e-07 using double precision MKL FFT 3d grid and FFT values/proc = 307242 204800 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 @@ -97,35 +134,35 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 57.15 | 57.15 | 57.15 Mbytes +Per MPI rank memory allocation (min/avg/max) = 57.19 | 57.19 | 57.19 Mbytes Step Temp c_ctemp E_pair TotEng c_qbot c_qtop - 0 0 0 25137191 25137191 0.0085142912 -0.0085142912 + 0 0 0 25137190 25137190 0.0085142912 -0.0085142912 50 17.83755 64.26354 25137031 25137214 0.0045923944 -0.0045923944 - 100 48.393682 174.34846 25136774 25137273 -0.009514517 0.009514517 - 150 70.421272 253.7075 25136655 25137380 -0.033017005 0.033017005 - 200 82.204844 296.16031 25136667 25137514 -0.063668175 0.063668175 - 250 87.54223 315.38937 25136757 25137659 -0.096776257 0.096776257 - 300 91.704746 330.38571 25136865 25137810 -0.1283784 0.1283784 - 350 100.36017 361.56871 25136934 25137968 -0.15649799 0.15649799 - 400 111.37575 401.25467 25136986 25138133 -0.18065435 0.18065435 - 450 121.79848 438.80476 25137043 25138298 -0.19979365 0.19979365 - 500 126.95916 457.39718 25137145 25138453 -0.21037535 0.21037535 -Loop time of 103.439 on 1 procs for 500 steps with 3776 atoms + 100 48.393682 174.34846 25136775 25137273 -0.009514517 0.009514517 + 150 70.421272 253.7075 25136657 25137382 -0.033017005 0.033017005 + 200 82.204844 296.16031 25136670 25137517 -0.063668175 0.063668175 + 250 87.54223 315.38937 25136762 25137663 -0.096776257 0.096776257 + 300 91.704746 330.38571 25136871 25137816 -0.1283784 0.1283784 + 350 100.36017 361.56871 25136941 25137975 -0.15649799 0.15649799 + 400 111.37575 401.25467 25136994 25138141 -0.18065435 0.18065435 + 450 121.79848 438.80476 25137052 25138307 -0.19979365 0.19979365 + 500 126.95916 457.39718 25137155 25138463 -0.21037535 0.21037535 +Loop time of 91.5523 on 1 procs for 500 steps with 3776 atoms -Performance: 0.418 ns/day, 57.466 hours/ns, 4.834 timesteps/s -393.6% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.472 ns/day, 50.862 hours/ns, 5.461 timesteps/s, 20.622 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 19.309 | 19.309 | 19.309 | 0.0 | 18.67 -Bond | 0.0018867 | 0.0018867 | 0.0018867 | 0.0 | 0.00 -Kspace | 23.047 | 23.047 | 23.047 | 0.0 | 22.28 -Neigh | 0.25707 | 0.25707 | 0.25707 | 0.0 | 0.25 -Comm | 0.070734 | 0.070734 | 0.070734 | 0.0 | 0.07 -Output | 0.0023085 | 0.0023085 | 0.0023085 | 0.0 | 0.00 -Modify | 60.73 | 60.73 | 60.73 | 0.0 | 58.71 -Other | | 0.01994 | | | 0.02 +Pair | 18.906 | 18.906 | 18.906 | 0.0 | 20.65 +Bond | 0.0012922 | 0.0012922 | 0.0012922 | 0.0 | 0.00 +Kspace | 34.476 | 34.476 | 34.476 | 0.0 | 37.66 +Neigh | 0.26641 | 0.26641 | 0.26641 | 0.0 | 0.29 +Comm | 0.069067 | 0.069067 | 0.069067 | 0.0 | 0.08 +Output | 0.0021466 | 0.0021466 | 0.0021466 | 0.0 | 0.00 +Modify | 37.805 | 37.805 | 37.805 | 0.0 | 41.29 +Other | | 0.0271 | | | 0.03 Nlocal: 3776 ave 3776 max 3776 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -139,4 +176,4 @@ Ave neighs/atom = 457.18432 Ave special neighs/atom = 0.50847458 Neighbor list builds = 7 Dangerous builds = 0 -Total wall time: 0:03:10 +Total wall time: 0:01:48 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conp.g++.4 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conp.g++.4 similarity index 51% rename from examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conp.g++.4 rename to examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conp.g++.4 index f74768b08d..ba941705aa 100644 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conp.g++.4 +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conp.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with constant potential # for graphene-ionic liquid supercapacitor @@ -38,13 +38,20 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.014 seconds + special bonds CPU = 0.003 seconds + read_data CPU = 0.038 seconds -group bot molecule 641 -416 atoms in group bot -group top molecule 642 +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos 416 atoms in group top +group bot subtract ele top +416 atoms in group bot group bmi type 1 2 3 960 atoms in group bmi @@ -53,24 +60,54 @@ group electrolyte type 1 2 3 4 fix nvt electrolyte nvt temp 500.0 500.0 100 fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 320 = # of frozen angles - find clusters CPU = 0.001 seconds + find clusters CPU = 0.003 seconds variable q atom q compute qtop top reduce sum v_q compute qbot bot reduce sum v_q compute ctemp electrolyte temp -kspace_modify slab 3.0 +kspace_modify slab 3.0 # amat twostep -fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on +fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on #algo mat_inv 832 atoms in group conp_group thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.20904498 @@ -80,9 +117,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.1149519e-07 using double precision MKL FFT 3d grid and FFT values/proc = 151593 85504 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 @@ -98,35 +135,35 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 23.13 | 26.96 | 30.79 Mbytes +Per MPI rank memory allocation (min/avg/max) = 23.16 | 26.99 | 30.82 Mbytes Step Temp c_ctemp E_pair TotEng c_qbot c_qtop - 0 0 0 25137191 25137191 0.0085142912 -0.0085142912 + 0 0 0 25137190 25137190 0.0085142912 -0.0085142912 50 17.83755 64.26354 25137031 25137214 0.0045923944 -0.0045923944 - 100 48.393682 174.34846 25136774 25137273 -0.009514517 0.009514517 - 150 70.421272 253.7075 25136655 25137380 -0.033017005 0.033017005 - 200 82.204844 296.16031 25136667 25137514 -0.063668175 0.063668175 - 250 87.54223 315.38937 25136757 25137659 -0.096776257 0.096776257 - 300 91.704746 330.38571 25136865 25137810 -0.1283784 0.1283784 - 350 100.36017 361.56871 25136934 25137968 -0.15649799 0.15649799 - 400 111.37575 401.25467 25136986 25138133 -0.18065435 0.18065435 - 450 121.79848 438.80476 25137043 25138298 -0.19979365 0.19979365 - 500 126.95916 457.39718 25137145 25138453 -0.21037535 0.21037535 -Loop time of 49.6656 on 4 procs for 500 steps with 3776 atoms + 100 48.393682 174.34846 25136775 25137273 -0.009514517 0.009514517 + 150 70.421272 253.7075 25136657 25137382 -0.033017005 0.033017005 + 200 82.204844 296.16031 25136670 25137517 -0.063668175 0.063668175 + 250 87.54223 315.38937 25136762 25137663 -0.096776257 0.096776257 + 300 91.704746 330.38571 25136871 25137816 -0.1283784 0.1283784 + 350 100.36017 361.56871 25136941 25137975 -0.15649799 0.15649799 + 400 111.37575 401.25467 25136994 25138141 -0.18065435 0.18065435 + 450 121.79848 438.80476 25137052 25138307 -0.19979365 0.19979365 + 500 126.95916 457.39718 25137155 25138463 -0.21037535 0.21037535 +Loop time of 49.6413 on 4 procs for 500 steps with 3776 atoms -Performance: 0.870 ns/day, 27.592 hours/ns, 10.067 timesteps/s -95.1% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.870 ns/day, 27.578 hours/ns, 10.072 timesteps/s, 38.033 katom-step/s +76.3% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 5.968 | 6.1677 | 6.382 | 6.5 | 12.42 -Bond | 0.00071151 | 0.00078617 | 0.00090387 | 0.0 | 0.00 -Kspace | 17.345 | 17.558 | 17.755 | 3.8 | 35.35 -Neigh | 0.10939 | 0.10945 | 0.10948 | 0.0 | 0.22 -Comm | 0.15295 | 0.15474 | 0.15699 | 0.4 | 0.31 -Output | 0.00074458 | 0.0010336 | 0.0018799 | 1.5 | 0.00 -Modify | 25.634 | 25.641 | 25.645 | 0.1 | 51.63 -Other | | 0.03276 | | | 0.07 +Pair | 5.3666 | 5.4998 | 5.6946 | 5.4 | 11.08 +Bond | 0.0011638 | 0.0012711 | 0.0014555 | 0.3 | 0.00 +Kspace | 24.047 | 24.241 | 24.374 | 2.6 | 48.83 +Neigh | 0.088235 | 0.088328 | 0.088432 | 0.0 | 0.18 +Comm | 0.30907 | 0.31913 | 0.32916 | 1.7 | 0.64 +Output | 0.0010669 | 0.0014463 | 0.0024232 | 1.5 | 0.00 +Modify | 19.435 | 19.445 | 19.454 | 0.2 | 39.17 +Other | | 0.04549 | | | 0.09 Nlocal: 944 ave 951 max 941 min Histogram: 1 2 0 0 0 0 0 0 0 1 @@ -140,4 +177,4 @@ Ave neighs/atom = 457.18432 Ave special neighs/atom = 0.50847458 Neighbor list builds = 7 Dangerous builds = 0 -Total wall time: 0:01:11 +Total wall time: 0:00:55 diff --git a/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq.g++.1 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq.g++.1 new file mode 100644 index 0000000000..c75238dc36 --- /dev/null +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq.g++.1 @@ -0,0 +1,186 @@ +LAMMPS (3 Nov 2022) +# electrodes with constrained total charges +# for graphene-ionic liquid supercapacitor + +boundary p p f # slab calculation +include settings.mod # styles, groups, computes and fixes +# set boundary in main script because ffield is periodic +units real +# distribute electrode atoms among all processors: +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +atom_style full +pair_style lj/cut/coul/long 16 +bond_style harmonic +angle_style harmonic +kspace_style pppm/electrode 1e-7 +# kspace_modify in main script because ffield is periodic + +read_data "data.graph-il" +Reading data file ... + orthogonal box = (0 0 -68) to (32.2 34.4 68) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 3776 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 640 bonds + reading angles ... + 320 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.002 seconds + read_data CPU = 0.023 seconds + +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos +416 atoms in group top +group bot subtract ele top +416 atoms in group bot + +group bmi type 1 2 3 +960 atoms in group bmi +group electrolyte type 1 2 3 4 +1280 atoms in group electrolyte + +fix nvt electrolyte nvt temp 500.0 500.0 100 +fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 320 = # of frozen angles + find clusters CPU = 0.002 seconds + +variable q atom q +compute qtop top reduce sum v_q +compute qbot bot reduce sum v_q +compute ctemp electrolyte temp +kspace_modify slab 3.0 + +fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes on # symm on +832 atoms in group conp_group +variable dv equal f_conq[2]-f_conq[1] +# symm on and off give different electrode potentials, but identical potential difference + +thermo 50 +thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_conq[1] f_conq[2] v_dv +run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +PPPM/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.20904498 + grid = 32 32 200 + stencil order = 5 + estimated absolute RMS force accuracy = 3.7023506e-05 + estimated relative force accuracy = 1.1149519e-07 + using double precision MKL FFT + 3d grid and FFT values/proc = 307242 204800 +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 18 + ghost atom cutoff = 18 + binsize = 9, bins = 4 4 16 + 3 neighbor lists, perpetual/occasional/extra = 2 1 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix electrode/conq, occasional, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) fix electrode/conq, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 54.25 | 54.25 | 54.25 Mbytes + Step Temp c_ctemp E_pair TotEng c_qbot c_qtop f_conq[1] f_conq[2] v_dv + 0 0 0 25137446 25137446 -1 1 -9.931852 10.097344 20.029196 + 50 20.206425 72.797911 25137263 25137472 -1 1 -9.4359366 9.5964514 19.032388 + 100 55.931663 201.50563 25136961 25137537 -1 1 -8.0440112 8.1861787 16.23019 + 150 81.389273 293.22204 25136818 25137656 -1 1 -6.1113109 6.2267114 12.338022 + 200 92.867946 334.57639 25136841 25137798 -1 1 -4.1857807 4.2740694 8.4598501 + 250 97.518304 351.33028 25136942 25137946 -1 1 -2.8383703 2.9101475 5.7485179 + 300 102.36577 368.79431 25137045 25138099 -1 1 -2.3831643 2.4461115 4.8292759 + 350 113.66597 409.50566 25137086 25138256 -1 1 -2.7083563 2.7457811 5.4541374 + 400 122.8443 442.57252 25137148 25138413 -1 1 -3.4311003 3.3941657 6.825266 + 450 128.63713 463.44243 25137235 25138560 -1 1 -4.132871 3.9852959 8.1181669 + 500 131.18361 472.61665 25137344 25138695 -1 1 -4.5104095 4.2567261 8.7671355 +Loop time of 89.4461 on 1 procs for 500 steps with 3776 atoms + +Performance: 0.483 ns/day, 49.692 hours/ns, 5.590 timesteps/s, 21.108 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 19.404 | 19.404 | 19.404 | 0.0 | 21.69 +Bond | 0.0014902 | 0.0014902 | 0.0014902 | 0.0 | 0.00 +Kspace | 35.449 | 35.449 | 35.449 | 0.0 | 39.63 +Neigh | 0.26499 | 0.26499 | 0.26499 | 0.0 | 0.30 +Comm | 0.068497 | 0.068497 | 0.068497 | 0.0 | 0.08 +Output | 0.0023974 | 0.0023974 | 0.0023974 | 0.0 | 0.00 +Modify | 34.225 | 34.225 | 34.225 | 0.0 | 38.26 +Other | | 0.03044 | | | 0.03 + +Nlocal: 3776 ave 3776 max 3776 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 12510 ave 12510 max 12510 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1.72559e+06 ave 1.72559e+06 max 1.72559e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1725588 +Ave neighs/atom = 456.98835 +Ave special neighs/atom = 0.50847458 +Neighbor list builds = 6 +Dangerous builds = 0 +Total wall time: 0:01:48 diff --git a/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq.g++.4 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq.g++.4 new file mode 100644 index 0000000000..65a143ad13 --- /dev/null +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq.g++.4 @@ -0,0 +1,187 @@ +LAMMPS (3 Nov 2022) +# electrodes with constrained total charges +# for graphene-ionic liquid supercapacitor + +boundary p p f # slab calculation +include settings.mod # styles, groups, computes and fixes +# set boundary in main script because ffield is periodic +units real +# distribute electrode atoms among all processors: +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" +processors * * 2 + +atom_style full +pair_style lj/cut/coul/long 16 +bond_style harmonic +angle_style harmonic +kspace_style pppm/electrode 1e-7 +# kspace_modify in main script because ffield is periodic + +read_data "data.graph-il" +Reading data file ... + orthogonal box = (0 0 -68) to (32.2 34.4 68) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 3776 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 640 bonds + reading angles ... + 320 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.002 seconds + read_data CPU = 0.034 seconds + +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos +416 atoms in group top +group bot subtract ele top +416 atoms in group bot + +group bmi type 1 2 3 +960 atoms in group bmi +group electrolyte type 1 2 3 4 +1280 atoms in group electrolyte + +fix nvt electrolyte nvt temp 500.0 500.0 100 +fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 320 = # of frozen angles + find clusters CPU = 0.002 seconds + +variable q atom q +compute qtop top reduce sum v_q +compute qbot bot reduce sum v_q +compute ctemp electrolyte temp +kspace_modify slab 3.0 + +fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes on # symm on +832 atoms in group conp_group +variable dv equal f_conq[2]-f_conq[1] +# symm on and off give different electrode potentials, but identical potential difference + +thermo 50 +thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_conq[1] f_conq[2] v_dv +run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +PPPM/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.20904498 + grid = 32 32 200 + stencil order = 5 + estimated absolute RMS force accuracy = 3.7023506e-05 + estimated relative force accuracy = 1.1149519e-07 + using double precision MKL FFT + 3d grid and FFT values/proc = 151593 85504 +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 18 + ghost atom cutoff = 18 + binsize = 9, bins = 4 4 16 + 3 neighbor lists, perpetual/occasional/extra = 2 1 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix electrode/conq, occasional, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) fix electrode/conq, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 22.9 | 26.72 | 30.55 Mbytes + Step Temp c_ctemp E_pair TotEng c_qbot c_qtop f_conq[1] f_conq[2] v_dv + 0 0 0 25137446 25137446 -1 1 -9.931852 10.097344 20.029196 + 50 20.206425 72.797911 25137263 25137472 -1 1 -9.4359366 9.5964514 19.032388 + 100 55.931663 201.50563 25136961 25137537 -1 1 -8.0440112 8.1861787 16.23019 + 150 81.389273 293.22204 25136818 25137656 -1 1 -6.1113109 6.2267114 12.338022 + 200 92.867946 334.57639 25136841 25137798 -1 1 -4.1857807 4.2740694 8.4598501 + 250 97.518304 351.33028 25136942 25137946 -1 1 -2.8383703 2.9101475 5.7485179 + 300 102.36577 368.79431 25137045 25138099 -1 1 -2.3831643 2.4461115 4.8292759 + 350 113.66597 409.50566 25137086 25138256 -1 1 -2.7083563 2.7457811 5.4541374 + 400 122.8443 442.57252 25137148 25138413 -1 1 -3.4311003 3.3941657 6.825266 + 450 128.63713 463.44243 25137235 25138560 -1 1 -4.132871 3.9852959 8.1181669 + 500 131.18361 472.61665 25137344 25138695 -1 1 -4.5104095 4.2567261 8.7671355 +Loop time of 53.4299 on 4 procs for 500 steps with 3776 atoms + +Performance: 0.809 ns/day, 29.683 hours/ns, 9.358 timesteps/s, 35.336 katom-step/s +74.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.5806 | 5.8872 | 6.1547 | 8.8 | 11.02 +Bond | 0.0011404 | 0.0012245 | 0.0012898 | 0.2 | 0.00 +Kspace | 26.55 | 26.822 | 27.129 | 4.1 | 50.20 +Neigh | 0.098647 | 0.099673 | 0.10083 | 0.3 | 0.19 +Comm | 0.35493 | 0.37282 | 0.3909 | 2.1 | 0.70 +Output | 0.0012274 | 0.001617 | 0.0026374 | 1.5 | 0.00 +Modify | 20.172 | 20.188 | 20.203 | 0.3 | 37.78 +Other | | 0.05647 | | | 0.11 + +Nlocal: 944 ave 948 max 940 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Nghost: 5920.5 ave 5941 max 5899 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Neighs: 431397 ave 442329 max 421103 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 1725588 +Ave neighs/atom = 456.98835 +Ave special neighs/atom = 0.50847458 +Neighbor list builds = 6 +Dangerous builds = 0 +Total wall time: 0:00:59 diff --git a/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq2.g++.1 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq2.g++.1 new file mode 100644 index 0000000000..a3eedd22c7 --- /dev/null +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq2.g++.1 @@ -0,0 +1,193 @@ +LAMMPS (3 Nov 2022) +# electrodes with constrained total charges imposed from dynamically computed potentials +# for graphene-ionic liquid supercapacitor + +boundary p p f # slab calculation +include settings.mod # styles, groups, computes and fixes +# set boundary in main script because ffield is periodic +units real +# distribute electrode atoms among all processors: +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +atom_style full +pair_style lj/cut/coul/long 16 +bond_style harmonic +angle_style harmonic +kspace_style pppm/electrode 1e-7 +# kspace_modify in main script because ffield is periodic + +read_data "data.graph-il" +Reading data file ... + orthogonal box = (0 0 -68) to (32.2 34.4 68) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 3776 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 640 bonds + reading angles ... + 320 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.002 seconds + read_data CPU = 0.022 seconds + +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos +416 atoms in group top +group bot subtract ele top +416 atoms in group bot + +group bmi type 1 2 3 +960 atoms in group bmi +group electrolyte type 1 2 3 4 +1280 atoms in group electrolyte + +fix nvt electrolyte nvt temp 500.0 500.0 100 +fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 320 = # of frozen angles + find clusters CPU = 0.001 seconds + +variable q atom q +compute qtop top reduce sum v_q +compute qbot bot reduce sum v_q +compute ctemp electrolyte temp +kspace_modify slab 3.0 + +fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes on +832 atoms in group conp_group + +variable qex_bot equal -1.0-f_conp[1][1] # difference between desired and 0V charge +variable qex_top equal 1.0-f_conp[2][1] # difference between desired and 0V charge + +# calculate imposed potential as elastance * excess charge +# note: fix will wait until the run setup to look for its potential variables +# which is why we can define variable names *after* fix conp without error +variable vbot equal f_conp[1][4]*v_qex_bot+f_conp[1][5]*v_qex_top +variable vtop equal f_conp[2][4]*v_qex_bot+f_conp[2][5]*v_qex_top + +thermo 50 +thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop +run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +PPPM/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.20904498 + grid = 32 32 200 + stencil order = 5 + estimated absolute RMS force accuracy = 3.7023506e-05 + estimated relative force accuracy = 1.1149519e-07 + using double precision MKL FFT + 3d grid and FFT values/proc = 307242 204800 +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 18 + ghost atom cutoff = 18 + binsize = 9, bins = 4 4 16 + 3 neighbor lists, perpetual/occasional/extra = 2 1 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix electrode/conp, occasional, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) fix electrode/conp, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 54.25 | 54.25 | 54.25 Mbytes + Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_vbot v_vtop + 0 0 0 25137446 25137446 -1 1 -9.931852 10.097344 + 50 20.206425 72.797911 25137263 25137472 -1 1 -9.4359366 9.5964514 + 100 55.931663 201.50563 25136961 25137537 -1 1 -8.0440112 8.1861787 + 150 81.389273 293.22204 25136818 25137656 -1 1 -6.1113109 6.2267114 + 200 92.867946 334.57639 25136841 25137798 -1 1 -4.1857807 4.2740694 + 250 97.518304 351.33028 25136942 25137946 -1 1 -2.8383703 2.9101475 + 300 102.36577 368.79431 25137045 25138099 -1 1 -2.3831643 2.4461115 + 350 113.66597 409.50566 25137086 25138256 -1 1 -2.7083563 2.7457811 + 400 122.8443 442.57252 25137148 25138413 -1 1 -3.4311003 3.3941657 + 450 128.63713 463.44243 25137235 25138560 -1 1 -4.132871 3.9852959 + 500 131.18361 472.61665 25137344 25138695 -1 1 -4.5104095 4.2567261 +Loop time of 85.5691 on 1 procs for 500 steps with 3776 atoms + +Performance: 0.505 ns/day, 47.538 hours/ns, 5.843 timesteps/s, 22.064 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 18.558 | 18.558 | 18.558 | 0.0 | 21.69 +Bond | 0.001404 | 0.001404 | 0.001404 | 0.0 | 0.00 +Kspace | 33.78 | 33.78 | 33.78 | 0.0 | 39.48 +Neigh | 0.27017 | 0.27017 | 0.27017 | 0.0 | 0.32 +Comm | 0.067438 | 0.067438 | 0.067438 | 0.0 | 0.08 +Output | 0.0026656 | 0.0026656 | 0.0026656 | 0.0 | 0.00 +Modify | 32.86 | 32.86 | 32.86 | 0.0 | 38.40 +Other | | 0.02916 | | | 0.03 + +Nlocal: 3776 ave 3776 max 3776 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 12510 ave 12510 max 12510 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1.72559e+06 ave 1.72559e+06 max 1.72559e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1725588 +Ave neighs/atom = 456.98835 +Ave special neighs/atom = 0.50847458 +Neighbor list builds = 6 +Dangerous builds = 0 +Total wall time: 0:01:42 diff --git a/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq2.g++.4 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq2.g++.4 new file mode 100644 index 0000000000..a0b182f3bb --- /dev/null +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq2.g++.4 @@ -0,0 +1,194 @@ +LAMMPS (3 Nov 2022) +# electrodes with constrained total charges imposed from dynamically computed potentials +# for graphene-ionic liquid supercapacitor + +boundary p p f # slab calculation +include settings.mod # styles, groups, computes and fixes +# set boundary in main script because ffield is periodic +units real +# distribute electrode atoms among all processors: +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" +processors * * 2 + +atom_style full +pair_style lj/cut/coul/long 16 +bond_style harmonic +angle_style harmonic +kspace_style pppm/electrode 1e-7 +# kspace_modify in main script because ffield is periodic + +read_data "data.graph-il" +Reading data file ... + orthogonal box = (0 0 -68) to (32.2 34.4 68) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 3776 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 640 bonds + reading angles ... + 320 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.005 seconds + read_data CPU = 0.044 seconds + +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos +416 atoms in group top +group bot subtract ele top +416 atoms in group bot + +group bmi type 1 2 3 +960 atoms in group bmi +group electrolyte type 1 2 3 4 +1280 atoms in group electrolyte + +fix nvt electrolyte nvt temp 500.0 500.0 100 +fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 320 = # of frozen angles + find clusters CPU = 0.002 seconds + +variable q atom q +compute qtop top reduce sum v_q +compute qbot bot reduce sum v_q +compute ctemp electrolyte temp +kspace_modify slab 3.0 + +fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes on +832 atoms in group conp_group + +variable qex_bot equal -1.0-f_conp[1][1] # difference between desired and 0V charge +variable qex_top equal 1.0-f_conp[2][1] # difference between desired and 0V charge + +# calculate imposed potential as elastance * excess charge +# note: fix will wait until the run setup to look for its potential variables +# which is why we can define variable names *after* fix conp without error +variable vbot equal f_conp[1][4]*v_qex_bot+f_conp[1][5]*v_qex_top +variable vtop equal f_conp[2][4]*v_qex_bot+f_conp[2][5]*v_qex_top + +thermo 50 +thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop +run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +PPPM/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.20904498 + grid = 32 32 200 + stencil order = 5 + estimated absolute RMS force accuracy = 3.7023506e-05 + estimated relative force accuracy = 1.1149519e-07 + using double precision MKL FFT + 3d grid and FFT values/proc = 151593 85504 +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 18 + ghost atom cutoff = 18 + binsize = 9, bins = 4 4 16 + 3 neighbor lists, perpetual/occasional/extra = 2 1 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix electrode/conp, occasional, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) fix electrode/conp, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 22.9 | 26.72 | 30.55 Mbytes + Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_vbot v_vtop + 0 0 0 25137446 25137446 -1 1 -9.931852 10.097344 + 50 20.206425 72.797911 25137263 25137472 -1 1 -9.4359366 9.5964514 + 100 55.931663 201.50563 25136961 25137537 -1 1 -8.0440112 8.1861787 + 150 81.389273 293.22204 25136818 25137656 -1 1 -6.1113109 6.2267114 + 200 92.867946 334.57639 25136841 25137798 -1 1 -4.1857807 4.2740694 + 250 97.518304 351.33028 25136942 25137946 -1 1 -2.8383703 2.9101475 + 300 102.36577 368.79431 25137045 25138099 -1 1 -2.3831643 2.4461115 + 350 113.66597 409.50566 25137086 25138256 -1 1 -2.7083563 2.7457811 + 400 122.8443 442.57252 25137148 25138413 -1 1 -3.4311003 3.3941657 + 450 128.63713 463.44243 25137235 25138560 -1 1 -4.132871 3.9852959 + 500 131.18361 472.61665 25137344 25138695 -1 1 -4.5104095 4.2567261 +Loop time of 54.0351 on 4 procs for 500 steps with 3776 atoms + +Performance: 0.799 ns/day, 30.019 hours/ns, 9.253 timesteps/s, 34.940 katom-step/s +75.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.5878 | 6.8799 | 7.1455 | 8.0 | 12.73 +Bond | 0.0011081 | 0.0014187 | 0.0018792 | 0.8 | 0.00 +Kspace | 25.907 | 26.173 | 26.464 | 4.1 | 48.44 +Neigh | 0.16417 | 0.16425 | 0.16438 | 0.0 | 0.30 +Comm | 0.34948 | 0.36296 | 0.37524 | 1.9 | 0.67 +Output | 0.0017398 | 0.0021707 | 0.0033966 | 1.5 | 0.00 +Modify | 20.392 | 20.403 | 20.416 | 0.2 | 37.76 +Other | | 0.04783 | | | 0.09 + +Nlocal: 944 ave 948 max 940 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Nghost: 5920.5 ave 5941 max 5899 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Neighs: 431397 ave 442329 max 421103 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 1725588 +Ave neighs/atom = 456.98835 +Ave special neighs/atom = 0.50847458 +Neighbor list builds = 6 +Dangerous builds = 0 +Total wall time: 0:01:00 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-etypes.g++.1 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-etypes.g++.1 similarity index 54% rename from examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-etypes.g++.1 rename to examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-etypes.g++.1 index 3b2fe8b6a1..7fccf30e98 100644 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-etypes.g++.1 +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-etypes.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with constant potential and smart neighborlists # for graphene-ionic liquid supercapacitor @@ -37,13 +37,20 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.024 seconds + special bonds CPU = 0.002 seconds + read_data CPU = 0.021 seconds -group bot molecule 641 -416 atoms in group bot -group top molecule 642 +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos 416 atoms in group top +group bot subtract ele top +416 atoms in group bot group bmi type 1 2 3 960 atoms in group bmi @@ -52,6 +59,7 @@ group electrolyte type 1 2 3 4 fix nvt electrolyte nvt temp 500.0 500.0 100 fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters @@ -64,12 +72,41 @@ compute qbot bot reduce sum v_q compute ctemp electrolyte temp kspace_modify slab 3.0 -fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5 +fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on 832 atoms in group conp_group thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.20904498 @@ -79,9 +116,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.1149519e-07 using double precision MKL FFT 3d grid and FFT values/proc = 307242 204800 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 @@ -102,35 +139,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes +Per MPI rank memory allocation (min/avg/max) = 54.25 | 54.25 | 54.25 Mbytes Step Temp c_ctemp E_pair TotEng c_qbot c_qtop - 0 0 0 25137191 25137191 0.0085142912 -0.0085142912 + 0 0 0 25137190 25137190 0.0085142912 -0.0085142912 50 17.83755 64.26354 25137031 25137214 0.0045923944 -0.0045923944 - 100 48.393682 174.34846 25136774 25137273 -0.009514517 0.009514517 - 150 70.421272 253.7075 25136655 25137380 -0.033017005 0.033017005 - 200 82.204844 296.16031 25136667 25137514 -0.063668175 0.063668175 - 250 87.54223 315.38937 25136757 25137659 -0.096776257 0.096776257 - 300 91.704746 330.38571 25136865 25137810 -0.1283784 0.1283784 - 350 100.36017 361.56871 25136934 25137968 -0.15649799 0.15649799 - 400 111.37575 401.25467 25136986 25138133 -0.18065435 0.18065435 - 450 121.79848 438.80476 25137043 25138298 -0.19979365 0.19979365 - 500 126.95916 457.39718 25137145 25138453 -0.21037535 0.21037535 -Loop time of 63.497 on 1 procs for 500 steps with 3776 atoms + 100 48.393682 174.34846 25136775 25137273 -0.009514517 0.009514517 + 150 70.421272 253.7075 25136657 25137382 -0.033017005 0.033017005 + 200 82.204844 296.16031 25136670 25137517 -0.063668175 0.063668175 + 250 87.54223 315.38937 25136762 25137663 -0.096776257 0.096776257 + 300 91.704746 330.38571 25136871 25137816 -0.1283784 0.1283784 + 350 100.36017 361.56871 25136942 25137975 -0.15649799 0.15649799 + 400 111.37575 401.25467 25136994 25138141 -0.18065435 0.18065435 + 450 121.79848 438.80476 25137052 25138307 -0.19979365 0.19979365 + 500 126.95916 457.39718 25137155 25138463 -0.21037535 0.21037535 +Loop time of 87.0709 on 1 procs for 500 steps with 3776 atoms -Performance: 0.680 ns/day, 35.276 hours/ns, 7.874 timesteps/s -393.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.496 ns/day, 48.373 hours/ns, 5.742 timesteps/s, 21.683 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 20.628 | 20.628 | 20.628 | 0.0 | 32.49 -Bond | 0.0019309 | 0.0019309 | 0.0019309 | 0.0 | 0.00 -Kspace | 23.61 | 23.61 | 23.61 | 0.0 | 37.18 -Neigh | 0.28156 | 0.28156 | 0.28156 | 0.0 | 0.44 -Comm | 0.061191 | 0.061191 | 0.061191 | 0.0 | 0.10 -Output | 0.0022666 | 0.0022666 | 0.0022666 | 0.0 | 0.00 -Modify | 18.891 | 18.891 | 18.891 | 0.0 | 29.75 -Other | | 0.02047 | | | 0.03 +Pair | 18.617 | 18.617 | 18.617 | 0.0 | 21.38 +Bond | 0.0014056 | 0.0014056 | 0.0014056 | 0.0 | 0.00 +Kspace | 34.856 | 34.856 | 34.856 | 0.0 | 40.03 +Neigh | 0.30015 | 0.30015 | 0.30015 | 0.0 | 0.34 +Comm | 0.065303 | 0.065303 | 0.065303 | 0.0 | 0.08 +Output | 0.0021663 | 0.0021663 | 0.0021663 | 0.0 | 0.00 +Modify | 33.201 | 33.201 | 33.201 | 0.0 | 38.13 +Other | | 0.0282 | | | 0.03 Nlocal: 3776 ave 3776 max 3776 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -144,4 +181,4 @@ Ave neighs/atom = 457.18432 Ave special neighs/atom = 0.50847458 Neighbor list builds = 7 Dangerous builds = 0 -Total wall time: 0:02:24 +Total wall time: 0:01:43 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-etypes.g++.4 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-etypes.g++.4 similarity index 54% rename from examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-etypes.g++.4 rename to examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-etypes.g++.4 index ed34a0c735..c0f4139689 100644 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-etypes.g++.4 +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-etypes.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with constant potential and smart neighborlists # for graphene-ionic liquid supercapacitor @@ -38,13 +38,20 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.016 seconds + special bonds CPU = 0.004 seconds + read_data CPU = 0.047 seconds -group bot molecule 641 -416 atoms in group bot -group top molecule 642 +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos 416 atoms in group top +group bot subtract ele top +416 atoms in group bot group bmi type 1 2 3 960 atoms in group bmi @@ -53,11 +60,12 @@ group electrolyte type 1 2 3 4 fix nvt electrolyte nvt temp 500.0 500.0 100 fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 320 = # of frozen angles - find clusters CPU = 0.001 seconds + find clusters CPU = 0.005 seconds variable q atom q compute qtop top reduce sum v_q @@ -65,12 +73,41 @@ compute qbot bot reduce sum v_q compute ctemp electrolyte temp kspace_modify slab 3.0 -fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5 +fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on 832 atoms in group conp_group thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.20904498 @@ -80,9 +117,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.1149519e-07 using double precision MKL FFT 3d grid and FFT values/proc = 151593 85504 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 @@ -103,35 +140,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes +Per MPI rank memory allocation (min/avg/max) = 22.9 | 26.72 | 30.55 Mbytes Step Temp c_ctemp E_pair TotEng c_qbot c_qtop - 0 0 0 25137191 25137191 0.0085142912 -0.0085142912 + 0 0 0 25137190 25137190 0.0085142912 -0.0085142912 50 17.83755 64.26354 25137031 25137214 0.0045923944 -0.0045923944 - 100 48.393682 174.34846 25136774 25137273 -0.009514517 0.009514517 - 150 70.421272 253.7075 25136655 25137380 -0.033017005 0.033017005 - 200 82.204844 296.16031 25136667 25137514 -0.063668175 0.063668175 - 250 87.54223 315.38937 25136757 25137659 -0.096776257 0.096776257 - 300 91.704746 330.38571 25136865 25137810 -0.1283784 0.1283784 - 350 100.36017 361.56871 25136934 25137968 -0.15649799 0.15649799 - 400 111.37575 401.25467 25136986 25138133 -0.18065435 0.18065435 - 450 121.79848 438.80476 25137043 25138298 -0.19979365 0.19979365 - 500 126.95916 457.39718 25137145 25138453 -0.21037535 0.21037535 -Loop time of 30.7883 on 4 procs for 500 steps with 3776 atoms + 100 48.393682 174.34846 25136775 25137273 -0.009514517 0.009514517 + 150 70.421272 253.7075 25136657 25137382 -0.033017005 0.033017005 + 200 82.204844 296.16031 25136670 25137517 -0.063668175 0.063668175 + 250 87.54223 315.38937 25136762 25137663 -0.096776257 0.096776257 + 300 91.704746 330.38571 25136871 25137816 -0.1283784 0.1283784 + 350 100.36017 361.56871 25136942 25137975 -0.15649799 0.15649799 + 400 111.37575 401.25467 25136994 25138141 -0.18065435 0.18065435 + 450 121.79848 438.80476 25137052 25138307 -0.19979365 0.19979365 + 500 126.95916 457.39718 25137155 25138463 -0.21037535 0.21037535 +Loop time of 48.4075 on 4 procs for 500 steps with 3776 atoms -Performance: 1.403 ns/day, 17.105 hours/ns, 16.240 timesteps/s -94.1% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.892 ns/day, 26.893 hours/ns, 10.329 timesteps/s, 39.002 katom-step/s +75.3% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 6.5102 | 6.7303 | 6.9362 | 7.6 | 21.86 -Bond | 0.00064504 | 0.00071061 | 0.000779 | 0.0 | 0.00 -Kspace | 14.081 | 14.287 | 14.507 | 5.2 | 46.40 -Neigh | 0.11831 | 0.11841 | 0.11851 | 0.0 | 0.38 -Comm | 0.12216 | 0.12434 | 0.12651 | 0.6 | 0.40 -Output | 0.00083347 | 0.0010533 | 0.0017069 | 1.2 | 0.00 -Modify | 9.5052 | 9.5071 | 9.5093 | 0.1 | 30.88 -Other | | 0.01927 | | | 0.06 +Pair | 5.3095 | 5.5504 | 5.7923 | 8.2 | 11.47 +Bond | 0.0011128 | 0.0012414 | 0.0014028 | 0.3 | 0.00 +Kspace | 24.084 | 24.322 | 24.559 | 3.9 | 50.24 +Neigh | 0.093557 | 0.09408 | 0.094377 | 0.1 | 0.19 +Comm | 0.30394 | 0.31319 | 0.3225 | 1.6 | 0.65 +Output | 0.0012719 | 0.0015908 | 0.0024592 | 1.3 | 0.00 +Modify | 18.066 | 18.079 | 18.091 | 0.2 | 37.35 +Other | | 0.04692 | | | 0.10 Nlocal: 944 ave 951 max 941 min Histogram: 1 2 0 0 0 0 0 0 0 1 @@ -145,4 +182,4 @@ Ave neighs/atom = 457.18432 Ave special neighs/atom = 0.50847458 Neighbor list builds = 7 Dangerous builds = 0 -Total wall time: 0:00:56 +Total wall time: 0:00:54 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ffield.g++.1 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ffield.g++.1 similarity index 54% rename from examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ffield.g++.1 rename to examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ffield.g++.1 index b7c2eea523..2103f43dfd 100644 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ffield.g++.1 +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ffield.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with constant potential using finite field # for z-periodic graphene-ionic liquid supercapacitor @@ -37,13 +37,20 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.022 seconds + special bonds CPU = 0.002 seconds + read_data CPU = 0.021 seconds -group bot molecule 641 -416 atoms in group bot -group top molecule 642 +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos 416 atoms in group top +group bot subtract ele top +416 atoms in group bot group bmi type 1 2 3 960 atoms in group bmi @@ -52,6 +59,7 @@ group electrolyte type 1 2 3 4 fix nvt electrolyte nvt temp 500.0 500.0 100 fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters @@ -63,12 +71,41 @@ compute qtop top reduce sum v_q compute qbot bot reduce sum v_q compute ctemp electrolyte temp -fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5 ffield yes +fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on ffield yes 832 atoms in group conp_group thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.20949995 @@ -78,9 +115,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.0544465e-07 using double precision MKL FFT 3d grid and FFT values/proc = 147537 92160 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 @@ -101,35 +138,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 49.5 | 49.5 | 49.5 Mbytes +Per MPI rank memory allocation (min/avg/max) = 46.1 | 46.1 | 46.1 Mbytes Step Temp c_ctemp E_pair TotEng c_qbot c_qtop - 0 0 0 25137187 25137187 0.0085209384 -0.0085209384 - 50 17.837642 64.263873 25137027 25137211 0.0045513522 -0.0045513522 - 100 48.393984 174.34955 25136771 25137269 -0.0097291786 0.0097291786 - 150 70.421823 253.70949 25136651 25137377 -0.033522793 0.033522793 - 200 82.205535 296.1628 25136664 25137510 -0.064555648 0.064555648 - 250 87.542843 315.39158 25136754 25137655 -0.098075546 0.098075546 - 300 91.705733 330.38927 25136862 25137806 -0.13006751 0.13006751 - 350 100.36128 361.5727 25136930 25137964 -0.15852814 0.15852814 - 400 111.37586 401.25505 25136982 25138129 -0.18297207 0.18297207 - 450 121.79814 438.80351 25137039 25138294 -0.2023394 0.2023394 - 500 126.95882 457.39597 25137142 25138449 -0.21305221 0.21305221 -Loop time of 36.7618 on 1 procs for 500 steps with 3776 atoms + 0 0 0 25137186 25137186 0.0085209384 -0.0085209384 + 50 17.837642 64.263873 25137027 25137210 0.0045513522 -0.0045513522 + 100 48.393984 174.34955 25136771 25137270 -0.0097291786 0.0097291786 + 150 70.421823 253.70949 25136653 25137378 -0.033522793 0.033522793 + 200 82.205535 296.1628 25136667 25137513 -0.064555648 0.064555648 + 250 87.542843 315.39158 25136758 25137660 -0.098075546 0.098075546 + 300 91.705733 330.38927 25136868 25137812 -0.13006751 0.13006751 + 350 100.36128 361.5727 25136938 25137971 -0.15852814 0.15852814 + 400 111.37586 401.25505 25136990 25138137 -0.18297207 0.18297207 + 450 121.79814 438.80351 25137049 25138303 -0.2023394 0.2023394 + 500 126.95882 457.39597 25137151 25138459 -0.21305221 0.21305221 +Loop time of 53.8411 on 1 procs for 500 steps with 3776 atoms -Performance: 1.175 ns/day, 20.423 hours/ns, 13.601 timesteps/s -393.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.802 ns/day, 29.912 hours/ns, 9.287 timesteps/s, 35.066 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 19.737 | 19.737 | 19.737 | 0.0 | 53.69 -Bond | 0.00092668 | 0.00092668 | 0.00092668 | 0.0 | 0.00 -Kspace | 6.5854 | 6.5854 | 6.5854 | 0.0 | 17.91 -Neigh | 0.33914 | 0.33914 | 0.33914 | 0.0 | 0.92 -Comm | 0.090124 | 0.090124 | 0.090124 | 0.0 | 0.25 -Output | 0.0013975 | 0.0013975 | 0.0013975 | 0.0 | 0.00 -Modify | 9.9834 | 9.9834 | 9.9834 | 0.0 | 27.16 -Other | | 0.02455 | | | 0.07 +Pair | 19.843 | 19.843 | 19.843 | 0.0 | 36.85 +Bond | 0.0016963 | 0.0016963 | 0.0016963 | 0.0 | 0.00 +Kspace | 11.232 | 11.232 | 11.232 | 0.0 | 20.86 +Neigh | 0.39189 | 0.39189 | 0.39189 | 0.0 | 0.73 +Comm | 0.12348 | 0.12348 | 0.12348 | 0.0 | 0.23 +Output | 0.0017904 | 0.0017904 | 0.0017904 | 0.0 | 0.00 +Modify | 22.207 | 22.207 | 22.207 | 0.0 | 41.25 +Other | | 0.04008 | | | 0.07 Nlocal: 3776 ave 3776 max 3776 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -143,4 +180,4 @@ Ave neighs/atom = 493.56224 Ave special neighs/atom = 0.50847458 Neighbor list builds = 7 Dangerous builds = 0 -Total wall time: 0:01:39 +Total wall time: 0:01:10 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ffield.g++.4 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ffield.g++.4 similarity index 54% rename from examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ffield.g++.4 rename to examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ffield.g++.4 index 205c08d88e..223530d493 100644 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ffield.g++.4 +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ffield.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with constant potential using finite field # for z-periodic graphene-ionic liquid supercapacitor @@ -38,13 +38,20 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.016 seconds + special bonds CPU = 0.002 seconds + read_data CPU = 0.033 seconds -group bot molecule 641 -416 atoms in group bot -group top molecule 642 +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos 416 atoms in group top +group bot subtract ele top +416 atoms in group bot group bmi type 1 2 3 960 atoms in group bmi @@ -53,23 +60,53 @@ group electrolyte type 1 2 3 4 fix nvt electrolyte nvt temp 500.0 500.0 100 fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 320 = # of frozen angles - find clusters CPU = 0.001 seconds + find clusters CPU = 0.002 seconds variable q atom q compute qtop top reduce sum v_q compute qbot bot reduce sum v_q compute ctemp electrolyte temp -fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5 ffield yes +fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on ffield yes 832 atoms in group conp_group thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.20949995 @@ -79,9 +116,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.0544465e-07 using double precision MKL FFT 3d grid and FFT values/proc = 46644 23552 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 @@ -102,35 +139,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 21.96 | 22.27 | 22.77 Mbytes +Per MPI rank memory allocation (min/avg/max) = 21.23 | 21.34 | 21.65 Mbytes Step Temp c_ctemp E_pair TotEng c_qbot c_qtop - 0 0 0 25137187 25137187 0.0085209384 -0.0085209384 - 50 17.837642 64.263873 25137027 25137211 0.0045513522 -0.0045513522 - 100 48.393984 174.34955 25136771 25137269 -0.0097291786 0.0097291786 - 150 70.421823 253.70949 25136651 25137377 -0.033522793 0.033522793 - 200 82.205535 296.1628 25136664 25137510 -0.064555648 0.064555648 - 250 87.542843 315.39158 25136754 25137655 -0.098075546 0.098075546 - 300 91.705733 330.38927 25136862 25137806 -0.13006751 0.13006751 - 350 100.36128 361.5727 25136930 25137964 -0.15852814 0.15852814 - 400 111.37586 401.25505 25136982 25138129 -0.18297207 0.18297207 - 450 121.79814 438.80351 25137039 25138294 -0.2023394 0.2023394 - 500 126.95882 457.39597 25137142 25138449 -0.21305221 0.21305221 -Loop time of 19.3932 on 4 procs for 500 steps with 3776 atoms + 0 0 0 25137186 25137186 0.0085209384 -0.0085209384 + 50 17.837642 64.263873 25137027 25137210 0.0045513522 -0.0045513522 + 100 48.393984 174.34955 25136771 25137270 -0.0097291786 0.0097291786 + 150 70.421823 253.70949 25136653 25137378 -0.033522793 0.033522793 + 200 82.205535 296.1628 25136667 25137513 -0.064555648 0.064555648 + 250 87.542843 315.39158 25136758 25137660 -0.098075546 0.098075546 + 300 91.705733 330.38927 25136868 25137812 -0.13006751 0.13006751 + 350 100.36128 361.5727 25136938 25137971 -0.15852814 0.15852814 + 400 111.37586 401.25505 25136990 25138137 -0.18297207 0.18297207 + 450 121.79814 438.80351 25137049 25138303 -0.2023394 0.2023394 + 500 126.95882 457.39597 25137151 25138459 -0.21305221 0.21305221 +Loop time of 26.2807 on 4 procs for 500 steps with 3776 atoms -Performance: 2.228 ns/day, 10.774 hours/ns, 25.782 timesteps/s -96.3% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 1.644 ns/day, 14.600 hours/ns, 19.025 timesteps/s, 71.840 katom-step/s +83.1% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 7.1247 | 7.6399 | 8.1323 | 13.3 | 39.39 -Bond | 0.00072445 | 0.00077581 | 0.00085933 | 0.0 | 0.00 -Kspace | 5.098 | 5.5905 | 6.1036 | 15.6 | 28.83 -Neigh | 0.145 | 0.14517 | 0.14532 | 0.0 | 0.75 -Comm | 0.24683 | 0.25127 | 0.25907 | 1.0 | 1.30 -Output | 0.00084146 | 0.0011298 | 0.0019741 | 1.5 | 0.01 -Modify | 5.6957 | 5.7129 | 5.729 | 0.6 | 29.46 -Other | | 0.05153 | | | 0.27 +Pair | 5.8233 | 6.1941 | 6.6294 | 12.1 | 23.57 +Bond | 0.0010807 | 0.0011705 | 0.0013494 | 0.3 | 0.00 +Kspace | 8.0325 | 8.4703 | 8.8457 | 10.4 | 32.23 +Neigh | 0.14184 | 0.1421 | 0.14238 | 0.1 | 0.54 +Comm | 0.52248 | 0.54323 | 0.56352 | 2.7 | 2.07 +Output | 0.00079782 | 0.0011547 | 0.0021987 | 1.8 | 0.00 +Modify | 10.831 | 10.856 | 10.881 | 0.7 | 41.31 +Other | | 0.07293 | | | 0.28 Nlocal: 944 ave 951 max 941 min Histogram: 1 2 0 0 0 0 0 0 0 1 @@ -144,4 +181,4 @@ Ave neighs/atom = 493.56224 Ave special neighs/atom = 0.50847458 Neighbor list builds = 7 Dangerous builds = 0 -Total wall time: 0:00:44 +Total wall time: 0:00:32 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ramp.g++.1 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ramp.g++.1 similarity index 52% rename from examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ramp.g++.1 rename to examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ramp.g++.1 index 1dfcbac360..819a605f35 100644 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ramp.g++.1 +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ramp.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with equal-style ramped (electrode-)constant potential # for graphene-ionic liquid supercapacitor @@ -37,13 +37,20 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.014 seconds + special bonds CPU = 0.002 seconds + read_data CPU = 0.021 seconds -group bot molecule 641 -416 atoms in group bot -group top molecule 642 +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos 416 atoms in group top +group bot subtract ele top +416 atoms in group bot group bmi type 1 2 3 960 atoms in group bmi @@ -52,6 +59,7 @@ group electrolyte type 1 2 3 4 fix nvt electrolyte nvt temp 500.0 500.0 100 fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters @@ -65,12 +73,41 @@ compute ctemp electrolyte temp kspace_modify slab 3.0 variable v equal ramp(2,4) -fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes 5 +fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes on 832 atoms in group conp_group thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_v run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.20904498 @@ -80,9 +117,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.1149519e-07 using double precision MKL FFT 3d grid and FFT values/proc = 307242 204800 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 @@ -103,35 +140,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes +Per MPI rank memory allocation (min/avg/max) = 54.25 | 54.25 | 54.25 Mbytes Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_v - 0 0 0 25137191 25137191 0.0085142912 -0.0085142912 2 - 50 17.839699 64.271283 25137031 25137214 -0.0067894391 0.0067894391 2.2 - 100 48.411618 174.41308 25136774 25137273 -0.033422174 0.033422174 2.4 - 150 70.478909 253.91515 25136654 25137380 -0.071583953 0.071583953 2.6 - 200 82.322716 296.58497 25136666 25137513 -0.11962095 0.11962095 2.8 - 250 87.739905 316.10153 25136754 25137658 -0.17281469 0.17281469 3 - 300 91.974584 331.35786 25136861 25137808 -0.22657123 0.22657123 3.2 - 350 100.73048 362.90284 25136928 25137965 -0.27817429 0.27817429 3.4 - 400 111.78597 402.73256 25136977 25138129 -0.32659395 0.32659395 3.6 - 450 122.14181 440.04167 25137033 25138291 -0.37054363 0.37054363 3.8 - 500 127.32331 458.70912 25137133 25138444 -0.40653009 0.40653009 4 -Loop time of 50.8569 on 1 procs for 500 steps with 3776 atoms + 0 0 0 25137190 25137190 0.0085142912 -0.0085142912 2 + 50 17.839699 64.271283 25137031 25137215 -0.0067894391 0.0067894391 2.2 + 100 48.411618 174.41308 25136776 25137275 -0.033422174 0.033422174 2.4 + 150 70.478909 253.91515 25136658 25137384 -0.071583953 0.071583953 2.6 + 200 82.322716 296.58497 25136673 25137521 -0.11962095 0.11962095 2.8 + 250 87.739905 316.10153 25136766 25137670 -0.17281469 0.17281469 3 + 300 91.974584 331.35786 25136877 25137825 -0.22657123 0.22657123 3.2 + 350 100.73048 362.90284 25136949 25137987 -0.27817429 0.27817429 3.4 + 400 111.78597 402.73256 25137004 25138156 -0.32659395 0.32659395 3.6 + 450 122.14181 440.04167 25137066 25138324 -0.37054363 0.37054363 3.8 + 500 127.32331 458.70912 25137171 25138482 -0.40653009 0.40653009 4 +Loop time of 87.6405 on 1 procs for 500 steps with 3776 atoms -Performance: 0.849 ns/day, 28.254 hours/ns, 9.831 timesteps/s -393.5% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.493 ns/day, 48.689 hours/ns, 5.705 timesteps/s, 21.543 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 18.166 | 18.166 | 18.166 | 0.0 | 35.72 -Bond | 0.00091918 | 0.00091918 | 0.00091918 | 0.0 | 0.00 -Kspace | 17.267 | 17.267 | 17.267 | 0.0 | 33.95 -Neigh | 0.27635 | 0.27635 | 0.27635 | 0.0 | 0.54 -Comm | 0.044714 | 0.044714 | 0.044714 | 0.0 | 0.09 -Output | 0.0018345 | 0.0018345 | 0.0018345 | 0.0 | 0.00 -Modify | 15.086 | 15.086 | 15.086 | 0.0 | 29.66 -Other | | 0.01409 | | | 0.03 +Pair | 18.484 | 18.484 | 18.484 | 0.0 | 21.09 +Bond | 0.0016824 | 0.0016824 | 0.0016824 | 0.0 | 0.00 +Kspace | 35.426 | 35.426 | 35.426 | 0.0 | 40.42 +Neigh | 0.30201 | 0.30201 | 0.30201 | 0.0 | 0.34 +Comm | 0.066546 | 0.066546 | 0.066546 | 0.0 | 0.08 +Output | 0.0022768 | 0.0022768 | 0.0022768 | 0.0 | 0.00 +Modify | 33.33 | 33.33 | 33.33 | 0.0 | 38.03 +Other | | 0.0286 | | | 0.03 Nlocal: 3776 ave 3776 max 3776 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -145,4 +182,4 @@ Ave neighs/atom = 457.17161 Ave special neighs/atom = 0.50847458 Neighbor list builds = 7 Dangerous builds = 0 -Total wall time: 0:01:50 +Total wall time: 0:01:44 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ramp.g++.4 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ramp.g++.4 similarity index 52% rename from examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ramp.g++.4 rename to examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ramp.g++.4 index ca7625acd6..9287a669db 100644 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ramp.g++.4 +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ramp.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with equal-style ramped (electrode-)constant potential # for graphene-ionic liquid supercapacitor @@ -38,13 +38,20 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.024 seconds + special bonds CPU = 0.003 seconds + read_data CPU = 0.034 seconds -group bot molecule 641 -416 atoms in group bot -group top molecule 642 +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos 416 atoms in group top +group bot subtract ele top +416 atoms in group bot group bmi type 1 2 3 960 atoms in group bmi @@ -53,11 +60,12 @@ group electrolyte type 1 2 3 4 fix nvt electrolyte nvt temp 500.0 500.0 100 fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 320 = # of frozen angles - find clusters CPU = 0.001 seconds + find clusters CPU = 0.002 seconds variable q atom q compute qtop top reduce sum v_q @@ -66,12 +74,41 @@ compute ctemp electrolyte temp kspace_modify slab 3.0 variable v equal ramp(2,4) -fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes 5 +fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes on 832 atoms in group conp_group thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_v run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.20904498 @@ -81,9 +118,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.1149519e-07 using double precision MKL FFT 3d grid and FFT values/proc = 151593 85504 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 @@ -104,35 +141,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes +Per MPI rank memory allocation (min/avg/max) = 22.9 | 26.72 | 30.55 Mbytes Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_v - 0 0 0 25137191 25137191 0.0085142912 -0.0085142912 2 - 50 17.839699 64.271283 25137031 25137214 -0.0067894391 0.0067894391 2.2 - 100 48.411618 174.41308 25136774 25137273 -0.033422174 0.033422174 2.4 - 150 70.478909 253.91515 25136654 25137380 -0.071583953 0.071583953 2.6 - 200 82.322716 296.58497 25136666 25137513 -0.11962095 0.11962095 2.8 - 250 87.739905 316.10153 25136754 25137658 -0.17281469 0.17281469 3 - 300 91.974584 331.35786 25136861 25137808 -0.22657123 0.22657123 3.2 - 350 100.73048 362.90284 25136928 25137965 -0.27817429 0.27817429 3.4 - 400 111.78597 402.73256 25136977 25138129 -0.32659395 0.32659395 3.6 - 450 122.14181 440.04167 25137033 25138291 -0.37054363 0.37054363 3.8 - 500 127.32331 458.70912 25137133 25138444 -0.40653009 0.40653009 4 -Loop time of 31.7642 on 4 procs for 500 steps with 3776 atoms + 0 0 0 25137190 25137190 0.0085142912 -0.0085142912 2 + 50 17.839699 64.271283 25137031 25137215 -0.0067894391 0.0067894391 2.2 + 100 48.411618 174.41308 25136776 25137275 -0.033422174 0.033422174 2.4 + 150 70.478909 253.91515 25136658 25137384 -0.071583953 0.071583953 2.6 + 200 82.322716 296.58497 25136673 25137521 -0.11962095 0.11962095 2.8 + 250 87.739905 316.10153 25136766 25137670 -0.17281469 0.17281469 3 + 300 91.974584 331.35786 25136877 25137825 -0.22657123 0.22657123 3.2 + 350 100.73048 362.90284 25136949 25137987 -0.27817429 0.27817429 3.4 + 400 111.78597 402.73256 25137004 25138156 -0.32659395 0.32659395 3.6 + 450 122.14181 440.04167 25137066 25138324 -0.37054363 0.37054363 3.8 + 500 127.32331 458.70912 25137171 25138482 -0.40653009 0.40653009 4 +Loop time of 49.2075 on 4 procs for 500 steps with 3776 atoms -Performance: 1.360 ns/day, 17.647 hours/ns, 15.741 timesteps/s -94.1% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.878 ns/day, 27.337 hours/ns, 10.161 timesteps/s, 38.368 katom-step/s +75.7% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 6.7949 | 7.0359 | 7.3092 | 7.9 | 22.15 -Bond | 0.00069874 | 0.00073747 | 0.00077928 | 0.0 | 0.00 -Kspace | 14.375 | 14.648 | 14.89 | 5.5 | 46.12 -Neigh | 0.12057 | 0.1206 | 0.12062 | 0.0 | 0.38 -Comm | 0.13412 | 0.13439 | 0.13483 | 0.1 | 0.42 -Output | 0.0010019 | 0.0013088 | 0.0020937 | 1.3 | 0.00 -Modify | 9.8017 | 9.8025 | 9.8031 | 0.0 | 30.86 -Other | | 0.02036 | | | 0.06 +Pair | 5.7517 | 5.9151 | 6.0961 | 6.6 | 12.02 +Bond | 0.0011959 | 0.0013362 | 0.0014512 | 0.2 | 0.00 +Kspace | 24.223 | 24.404 | 24.566 | 3.2 | 49.59 +Neigh | 0.10283 | 0.10288 | 0.10301 | 0.0 | 0.21 +Comm | 0.30801 | 0.31944 | 0.33141 | 2.0 | 0.65 +Output | 0.0010416 | 0.0014127 | 0.0024086 | 1.5 | 0.00 +Modify | 18.405 | 18.418 | 18.432 | 0.3 | 37.43 +Other | | 0.04459 | | | 0.09 Nlocal: 944 ave 951 max 941 min Histogram: 1 2 0 0 0 0 0 0 0 1 @@ -146,4 +183,4 @@ Ave neighs/atom = 457.17161 Ave special neighs/atom = 0.50847458 Neighbor list builds = 7 Dangerous builds = 0 -Total wall time: 0:00:58 +Total wall time: 0:00:55 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-thermo.g++.1 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-thermo.g++.1 similarity index 55% rename from examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-thermo.g++.1 rename to examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-thermo.g++.1 index e6fe963222..42eeb1f97e 100644 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-thermo.g++.1 +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-thermo.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with thermopotentiostat # for graphene-ionic liquid supercapacitor @@ -38,12 +38,19 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-4 neighbors 2 = max # of special neighbors special bonds CPU = 0.002 seconds - read_data CPU = 0.024 seconds + read_data CPU = 0.021 seconds -group bot molecule 641 -416 atoms in group bot -group top molecule 642 +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos 416 atoms in group top +group bot subtract ele top +416 atoms in group bot group bmi type 1 2 3 960 atoms in group bmi @@ -52,11 +59,12 @@ group electrolyte type 1 2 3 4 fix nvt electrolyte nvt temp 500.0 500.0 100 fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 320 = # of frozen angles - find clusters CPU = 0.000 seconds + find clusters CPU = 0.001 seconds variable q atom q compute qtop top reduce sum v_q @@ -65,10 +73,10 @@ compute ctemp electrolyte temp kspace_modify slab 3.0 unfix nvt # remove NVT thermostat included from "settings.mod" -fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes 5 temp 500 100 7 # temp tau rng +fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes on temp 500 100 7 symm on # temp tau rng 832 atoms in group conp_group # to compare to regular constant potential, switch previous line to this: -#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes 5 symm on +#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes on symm on fix nve electrolyte nve # note ionic liquid does not reach 500K immediately @@ -77,6 +85,35 @@ fix nve electrolyte nve thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.20904498 @@ -86,9 +123,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.1149519e-07 using double precision MKL FFT 3d grid and FFT values/proc = 307242 204800 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 @@ -109,35 +146,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes +Per MPI rank memory allocation (min/avg/max) = 54.25 | 54.25 | 54.25 Mbytes Step Temp c_ctemp E_pair TotEng c_qbot c_qtop - 0 0 0 25137187 25137187 0.12767613 -0.12767613 - 50 16.63971 59.94807 25137031 25137203 0.11714714 -0.11714714 - 100 40.785523 146.93846 25136782 25137202 0.1278358 -0.1278358 - 150 53.394067 192.3634 25136654 25137204 0.080257143 -0.080257143 - 200 56.419019 203.26143 25136624 25137205 0.024756489 -0.024756489 - 250 54.922935 197.87147 25136640 25137205 -0.024533719 0.024533719 - 300 52.884861 190.52888 25136660 25137205 -0.066341094 0.066341094 - 350 52.41676 188.84244 25136666 25137206 -0.089546252 0.089546252 - 400 54.366979 195.86852 25136646 25137206 -0.10239753 0.10239753 - 450 54.906542 197.81241 25136642 25137208 -0.099987401 0.099987401 - 500 54.33841 195.7656 25136642 25137201 -0.21295942 0.21295942 -Loop time of 49.9831 on 1 procs for 500 steps with 3776 atoms + 0 0 0 25137188 25137188 0.12767608 -0.12767608 + 50 16.63971 59.94807 25137031 25137202 0.11714711 -0.11714711 + 100 40.785523 146.93846 25136782 25137202 0.12783578 -0.12783578 + 150 53.394067 192.3634 25136653 25137203 0.080257127 -0.080257127 + 200 56.419019 203.26143 25136623 25137204 0.024756474 -0.024756474 + 250 54.922935 197.87147 25136641 25137206 -0.024533734 0.024533734 + 300 52.884861 190.52888 25136664 25137209 -0.066341109 0.066341109 + 350 52.41676 188.84244 25136670 25137210 -0.089546266 0.089546266 + 400 54.366979 195.86852 25136651 25137211 -0.10239755 0.10239755 + 450 54.906542 197.81241 25136645 25137210 -0.099987411 0.099987411 + 500 54.33841 195.7656 25136656 25137216 -0.21295943 0.21295943 +Loop time of 87.5281 on 1 procs for 500 steps with 3776 atoms -Performance: 0.864 ns/day, 27.768 hours/ns, 10.003 timesteps/s -393.3% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.494 ns/day, 48.627 hours/ns, 5.712 timesteps/s, 21.570 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 17.01 | 17.01 | 17.01 | 0.0 | 34.03 -Bond | 0.0010374 | 0.0010374 | 0.0010374 | 0.0 | 0.00 -Kspace | 18.096 | 18.096 | 18.096 | 0.0 | 36.20 -Neigh | 0.1828 | 0.1828 | 0.1828 | 0.0 | 0.37 -Comm | 0.043856 | 0.043856 | 0.043856 | 0.0 | 0.09 -Output | 0.0018373 | 0.0018373 | 0.0018373 | 0.0 | 0.00 -Modify | 14.632 | 14.632 | 14.632 | 0.0 | 29.27 -Other | | 0.01548 | | | 0.03 +Pair | 18.819 | 18.819 | 18.819 | 0.0 | 21.50 +Bond | 0.0014336 | 0.0014336 | 0.0014336 | 0.0 | 0.00 +Kspace | 34.891 | 34.891 | 34.891 | 0.0 | 39.86 +Neigh | 0.21542 | 0.21542 | 0.21542 | 0.0 | 0.25 +Comm | 0.063383 | 0.063383 | 0.063383 | 0.0 | 0.07 +Output | 0.0020476 | 0.0020476 | 0.0020476 | 0.0 | 0.00 +Modify | 33.507 | 33.507 | 33.507 | 0.0 | 38.28 +Other | | 0.0281 | | | 0.03 Nlocal: 3776 ave 3776 max 3776 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -151,4 +188,4 @@ Ave neighs/atom = 457.08845 Ave special neighs/atom = 0.50847458 Neighbor list builds = 5 Dangerous builds = 0 -Total wall time: 0:01:50 +Total wall time: 0:01:44 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-thermo.g++.4 b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-thermo.g++.4 similarity index 55% rename from examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-thermo.g++.4 rename to examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-thermo.g++.4 index 006fe4d31b..200dc681df 100644 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-thermo.g++.4 +++ b/examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-thermo.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) # electrodes with thermopotentiostat # for graphene-ionic liquid supercapacitor @@ -39,12 +39,19 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-4 neighbors 2 = max # of special neighbors special bonds CPU = 0.002 seconds - read_data CPU = 0.025 seconds + read_data CPU = 0.036 seconds -group bot molecule 641 -416 atoms in group bot -group top molecule 642 +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +1891 atoms in group zpos +group ele type 5 +832 atoms in group ele +group top intersect ele zpos 416 atoms in group top +group bot subtract ele top +416 atoms in group bot group bmi type 1 2 3 960 atoms in group bmi @@ -53,11 +60,12 @@ group electrolyte type 1 2 3 4 fix nvt electrolyte nvt temp 500.0 500.0 100 fix shake bmi shake 1e-4 20 0 b 1 2 a 1 +Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 320 = # of frozen angles - find clusters CPU = 0.001 seconds + find clusters CPU = 0.005 seconds variable q atom q compute qtop top reduce sum v_q @@ -66,10 +74,10 @@ compute ctemp electrolyte temp kspace_modify slab 3.0 unfix nvt # remove NVT thermostat included from "settings.mod" -fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes 5 temp 500 100 7 # temp tau rng +fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes on temp 500 100 7 symm on # temp tau rng 832 atoms in group conp_group # to compare to regular constant potential, switch previous line to this: -#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes 5 symm on +#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes on symm on fix nve electrolyte nve # note ionic liquid does not reach 500K immediately @@ -78,6 +86,35 @@ fix nve electrolyte nve thermo 50 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + PPPM/electrode initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:342) G vector (1/distance) = 0.20904498 @@ -87,9 +124,9 @@ PPPM/electrode initialization ... estimated relative force accuracy = 1.1149519e-07 using double precision MKL FFT 3d grid and FFT values/proc = 151593 85504 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule +Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 @@ -110,35 +147,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes +Per MPI rank memory allocation (min/avg/max) = 22.9 | 26.72 | 30.55 Mbytes Step Temp c_ctemp E_pair TotEng c_qbot c_qtop - 0 0 0 25137187 25137187 0.12767613 -0.12767613 - 50 16.63971 59.94807 25137031 25137203 0.11714714 -0.11714714 - 100 40.785523 146.93846 25136782 25137202 0.1278358 -0.1278358 - 150 53.394067 192.3634 25136654 25137204 0.080257143 -0.080257143 - 200 56.419019 203.26143 25136624 25137205 0.024756489 -0.024756489 - 250 54.922935 197.87147 25136640 25137205 -0.024533719 0.024533719 - 300 52.884861 190.52888 25136660 25137205 -0.066341094 0.066341094 - 350 52.41676 188.84244 25136666 25137206 -0.089546252 0.089546252 - 400 54.366979 195.86852 25136646 25137206 -0.10239753 0.10239753 - 450 54.906542 197.81241 25136642 25137208 -0.099987401 0.099987401 - 500 54.33841 195.7656 25136642 25137201 -0.21295942 0.21295942 -Loop time of 27.6772 on 4 procs for 500 steps with 3776 atoms + 0 0 0 25137188 25137188 0.12767608 -0.12767608 + 50 16.63971 59.94807 25137031 25137202 0.11714711 -0.11714711 + 100 40.785523 146.93846 25136782 25137202 0.12783578 -0.12783578 + 150 53.394067 192.3634 25136653 25137203 0.080257127 -0.080257127 + 200 56.419019 203.26143 25136623 25137204 0.024756474 -0.024756474 + 250 54.922935 197.87147 25136641 25137206 -0.024533734 0.024533734 + 300 52.884861 190.52888 25136664 25137209 -0.066341109 0.066341109 + 350 52.41676 188.84244 25136670 25137210 -0.089546266 0.089546266 + 400 54.366979 195.86852 25136651 25137211 -0.10239755 0.10239755 + 450 54.906542 197.81241 25136645 25137210 -0.099987411 0.099987411 + 500 54.33841 195.7656 25136656 25137216 -0.21295943 0.21295943 +Loop time of 49.2564 on 4 procs for 500 steps with 3776 atoms -Performance: 1.561 ns/day, 15.376 hours/ns, 18.065 timesteps/s -91.7% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.877 ns/day, 27.365 hours/ns, 10.151 timesteps/s, 38.330 katom-step/s +76.1% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 4.6214 | 4.8032 | 4.9546 | 6.5 | 17.35 -Bond | 0.0005324 | 0.00060509 | 0.00069468 | 0.0 | 0.00 -Kspace | 13.883 | 14.034 | 14.216 | 3.8 | 50.71 -Neigh | 0.061704 | 0.061727 | 0.06176 | 0.0 | 0.22 -Comm | 0.10101 | 0.10374 | 0.10645 | 0.8 | 0.37 -Output | 0.00086818 | 0.0010909 | 0.001715 | 1.1 | 0.00 -Modify | 8.65 | 8.6524 | 8.6545 | 0.1 | 31.26 -Other | | 0.02055 | | | 0.07 +Pair | 5.6984 | 5.9083 | 6.1177 | 6.4 | 12.00 +Bond | 0.0011785 | 0.0012201 | 0.0013055 | 0.1 | 0.00 +Kspace | 24.311 | 24.519 | 24.729 | 3.1 | 49.78 +Neigh | 0.075406 | 0.075487 | 0.07556 | 0.0 | 0.15 +Comm | 0.29972 | 0.30943 | 0.31881 | 1.7 | 0.63 +Output | 0.0012474 | 0.001684 | 0.0027062 | 1.5 | 0.00 +Modify | 18.377 | 18.384 | 18.391 | 0.2 | 37.32 +Other | | 0.05679 | | | 0.12 Nlocal: 944 ave 951 max 940 min Histogram: 1 1 1 0 0 0 0 0 0 1 @@ -152,4 +189,4 @@ Ave neighs/atom = 457.08845 Ave special neighs/atom = 0.50847458 Neighbor list builds = 5 Dangerous builds = 0 -Total wall time: 0:00:50 +Total wall time: 0:00:55 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq.g++.1 b/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq.g++.1 deleted file mode 100644 index 5722e357ec..0000000000 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq.g++.1 +++ /dev/null @@ -1,153 +0,0 @@ -LAMMPS (24 Mar 2022) -# electrodes with constrained total charges -# for graphene-ionic liquid supercapacitor - -boundary p p f # slab calculation -include settings.mod # styles, groups, computes and fixes -# set boundary in main script because ffield is periodic -units real -# distribute electrode atoms among all processors: -if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" - -atom_style full -pair_style lj/cut/coul/long 16 -bond_style harmonic -angle_style harmonic -kspace_style pppm/electrode 1e-7 -# kspace_modify in main script because ffield is periodic - -read_data "data.graph-il" -Reading data file ... - orthogonal box = (0 0 -68) to (32.2 34.4 68) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 3776 atoms - scanning bonds ... - 2 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 640 bonds - reading angles ... - 320 angles -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.012 seconds - -group bot molecule 641 -416 atoms in group bot -group top molecule 642 -416 atoms in group top - -group bmi type 1 2 3 -960 atoms in group bmi -group electrolyte type 1 2 3 4 -1280 atoms in group electrolyte - -fix nvt electrolyte nvt temp 500.0 500.0 100 -fix shake bmi shake 1e-4 20 0 b 1 2 a 1 - 0 = # of size 2 clusters - 0 = # of size 3 clusters - 0 = # of size 4 clusters - 320 = # of frozen angles - find clusters CPU = 0.000 seconds - -variable q atom q -compute qtop top reduce sum v_q -compute qbot bot reduce sum v_q -compute ctemp electrolyte temp -kspace_modify slab 3.0 - -fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes 5 # conq doesn't take symm option -832 atoms in group conp_group - -# ask fix conq to output electrode potentials to internal variables -variable vbot internal 0.0 -variable vtop internal 0.0 -fix_modify conq set v bot vbot -fix_modify conq set v top vtop - -thermo 50 -thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop -run 500 -PPPM/electrode initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:342) - G vector (1/distance) = 0.20904498 - grid = 32 32 200 - stencil order = 5 - estimated absolute RMS force accuracy = 3.7023506e-05 - estimated relative force accuracy = 1.1149519e-07 - using double precision MKL FFT - 3d grid and FFT values/proc = 307242 204800 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 18 - ghost atom cutoff = 18 - binsize = 9, bins = 4 4 16 - 3 neighbor lists, perpetual/occasional/extra = 2 1 0 - (1) pair lj/cut/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard - (2) fix electrode/conq, occasional, skip from (1) - attributes: half, newton on - pair build: skip - stencil: none - bin: none - (3) fix electrode/conq, perpetual, skip from (1) - attributes: half, newton on - pair build: skip - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes - Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_vbot v_vtop - 0 0 0 25136984 25136984 -1 1 -9.931852 10.097344 - 50 20.206425 72.797911 25136825 25137033 -1 1 -9.4359366 9.5964514 - 100 55.931663 201.50563 25136587 25137163 -1 1 -8.0440112 8.1861787 - 150 81.389273 293.22204 25136533 25137371 -1 1 -6.1113109 6.2267114 - 200 92.867946 334.57639 25136646 25137603 -1 1 -4.1857807 4.2740694 - 250 97.518304 351.33028 25136809 25137814 -1 1 -2.8383703 2.9101475 - 300 102.36577 368.79431 25136933 25137987 -1 1 -2.3831643 2.4461115 - 350 113.66597 409.50566 25136960 25138131 -1 1 -2.7083563 2.7457811 - 400 122.8443 442.57252 25136991 25138256 -1 1 -3.4311003 3.3941657 - 450 128.63713 463.44243 25137048 25138373 -1 1 -4.132871 3.9852959 - 500 131.18361 472.61665 25137142 25138493 -1 1 -4.5104095 4.2567261 -Loop time of 48.9361 on 1 procs for 500 steps with 3776 atoms - -Performance: 0.883 ns/day, 27.187 hours/ns, 10.217 timesteps/s -393.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 17.652 | 17.652 | 17.652 | 0.0 | 36.07 -Bond | 0.0010418 | 0.0010418 | 0.0010418 | 0.0 | 0.00 -Kspace | 16.566 | 16.566 | 16.566 | 0.0 | 33.85 -Neigh | 0.21584 | 0.21584 | 0.21584 | 0.0 | 0.44 -Comm | 0.04167 | 0.04167 | 0.04167 | 0.0 | 0.09 -Output | 0.0014585 | 0.0014585 | 0.0014585 | 0.0 | 0.00 -Modify | 14.445 | 14.445 | 14.445 | 0.0 | 29.52 -Other | | 0.0134 | | | 0.03 - -Nlocal: 3776 ave 3776 max 3776 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 12510 ave 12510 max 12510 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1.72559e+06 ave 1.72559e+06 max 1.72559e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1725588 -Ave neighs/atom = 456.98835 -Ave special neighs/atom = 0.50847458 -Neighbor list builds = 6 -Dangerous builds = 0 -Total wall time: 0:01:43 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq.g++.4 b/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq.g++.4 deleted file mode 100644 index 96343114e6..0000000000 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq.g++.4 +++ /dev/null @@ -1,154 +0,0 @@ -LAMMPS (24 Mar 2022) -# electrodes with constrained total charges -# for graphene-ionic liquid supercapacitor - -boundary p p f # slab calculation -include settings.mod # styles, groups, computes and fixes -# set boundary in main script because ffield is periodic -units real -# distribute electrode atoms among all processors: -if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" -processors * * 2 - -atom_style full -pair_style lj/cut/coul/long 16 -bond_style harmonic -angle_style harmonic -kspace_style pppm/electrode 1e-7 -# kspace_modify in main script because ffield is periodic - -read_data "data.graph-il" -Reading data file ... - orthogonal box = (0 0 -68) to (32.2 34.4 68) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 3776 atoms - scanning bonds ... - 2 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 640 bonds - reading angles ... - 320 angles -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.020 seconds - -group bot molecule 641 -416 atoms in group bot -group top molecule 642 -416 atoms in group top - -group bmi type 1 2 3 -960 atoms in group bmi -group electrolyte type 1 2 3 4 -1280 atoms in group electrolyte - -fix nvt electrolyte nvt temp 500.0 500.0 100 -fix shake bmi shake 1e-4 20 0 b 1 2 a 1 - 0 = # of size 2 clusters - 0 = # of size 3 clusters - 0 = # of size 4 clusters - 320 = # of frozen angles - find clusters CPU = 0.001 seconds - -variable q atom q -compute qtop top reduce sum v_q -compute qbot bot reduce sum v_q -compute ctemp electrolyte temp -kspace_modify slab 3.0 - -fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes 5 # conq doesn't take symm option -832 atoms in group conp_group - -# ask fix conq to output electrode potentials to internal variables -variable vbot internal 0.0 -variable vtop internal 0.0 -fix_modify conq set v bot vbot -fix_modify conq set v top vtop - -thermo 50 -thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop -run 500 -PPPM/electrode initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:342) - G vector (1/distance) = 0.20904498 - grid = 32 32 200 - stencil order = 5 - estimated absolute RMS force accuracy = 3.7023506e-05 - estimated relative force accuracy = 1.1149519e-07 - using double precision MKL FFT - 3d grid and FFT values/proc = 151593 85504 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 18 - ghost atom cutoff = 18 - binsize = 9, bins = 4 4 16 - 3 neighbor lists, perpetual/occasional/extra = 2 1 0 - (1) pair lj/cut/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard - (2) fix electrode/conq, occasional, skip from (1) - attributes: half, newton on - pair build: skip - stencil: none - bin: none - (3) fix electrode/conq, perpetual, skip from (1) - attributes: half, newton on - pair build: skip - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes - Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_vbot v_vtop - 0 0 0 25136984 25136984 -1 1 -9.931852 10.097344 - 50 20.206425 72.797911 25136825 25137033 -1 1 -9.4359366 9.5964514 - 100 55.931663 201.50563 25136587 25137163 -1 1 -8.0440112 8.1861787 - 150 81.389273 293.22204 25136533 25137371 -1 1 -6.1113109 6.2267114 - 200 92.867946 334.57639 25136646 25137603 -1 1 -4.1857807 4.2740694 - 250 97.518304 351.33028 25136809 25137814 -1 1 -2.8383703 2.9101475 - 300 102.36577 368.79431 25136933 25137987 -1 1 -2.3831643 2.4461115 - 350 113.66597 409.50566 25136960 25138131 -1 1 -2.7083563 2.7457811 - 400 122.8443 442.57252 25136991 25138256 -1 1 -3.4311003 3.3941657 - 450 128.63713 463.44243 25137048 25138373 -1 1 -4.132871 3.9852959 - 500 131.18361 472.61665 25137142 25138493 -1 1 -4.5104095 4.2567261 -Loop time of 28.8336 on 4 procs for 500 steps with 3776 atoms - -Performance: 1.498 ns/day, 16.019 hours/ns, 17.341 timesteps/s -94.1% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 5.7721 | 5.9353 | 6.144 | 6.0 | 20.58 -Bond | 0.00057855 | 0.00067043 | 0.00074793 | 0.0 | 0.00 -Kspace | 13.485 | 13.694 | 13.857 | 4.0 | 47.49 -Neigh | 0.092021 | 0.092044 | 0.092068 | 0.0 | 0.32 -Comm | 0.11486 | 0.11638 | 0.11801 | 0.4 | 0.40 -Output | 0.00090452 | 0.001109 | 0.0017097 | 1.0 | 0.00 -Modify | 8.974 | 8.9761 | 8.978 | 0.1 | 31.13 -Other | | 0.01837 | | | 0.06 - -Nlocal: 944 ave 948 max 940 min -Histogram: 1 0 0 1 0 0 1 0 0 1 -Nghost: 5920.5 ave 5941 max 5899 min -Histogram: 1 0 0 0 1 1 0 0 0 1 -Neighs: 431397 ave 442329 max 421103 min -Histogram: 2 0 0 0 0 0 0 0 1 1 - -Total # of neighbors = 1725588 -Ave neighs/atom = 456.98835 -Ave special neighs/atom = 0.50847458 -Neighbor list builds = 6 -Dangerous builds = 0 -Total wall time: 0:00:51 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq2.g++.1 b/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq2.g++.1 deleted file mode 100644 index 4465ed311d..0000000000 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq2.g++.1 +++ /dev/null @@ -1,170 +0,0 @@ -LAMMPS (24 Mar 2022) -# electrodes with constrained total charges imposed from dynamically computed potentials -# for graphene-ionic liquid supercapacitor - -boundary p p f # slab calculation -include settings.mod # styles, groups, computes and fixes -# set boundary in main script because ffield is periodic -units real -# distribute electrode atoms among all processors: -if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" - -atom_style full -pair_style lj/cut/coul/long 16 -bond_style harmonic -angle_style harmonic -kspace_style pppm/electrode 1e-7 -# kspace_modify in main script because ffield is periodic - -read_data "data.graph-il" -Reading data file ... - orthogonal box = (0 0 -68) to (32.2 34.4 68) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 3776 atoms - scanning bonds ... - 2 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 640 bonds - reading angles ... - 320 angles -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.031 seconds - -group bot molecule 641 -416 atoms in group bot -group top molecule 642 -416 atoms in group top - -group bmi type 1 2 3 -960 atoms in group bmi -group electrolyte type 1 2 3 4 -1280 atoms in group electrolyte - -fix nvt electrolyte nvt temp 500.0 500.0 100 -fix shake bmi shake 1e-4 20 0 b 1 2 a 1 - 0 = # of size 2 clusters - 0 = # of size 3 clusters - 0 = # of size 4 clusters - 320 = # of frozen angles - find clusters CPU = 0.001 seconds - -variable q atom q -compute qtop top reduce sum v_q -compute qbot bot reduce sum v_q -compute ctemp electrolyte temp -kspace_modify slab 3.0 - -fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes 5 -832 atoms in group conp_group - -# get the four entries of electrode elastance matrix -variable me00 internal 0.0 -variable me01 internal 0.0 -variable me10 internal 0.0 -variable me11 internal 0.0 -fix_modify conp set me bot bot me00 -fix_modify conp set me bot top me01 -fix_modify conp set me top bot me10 -fix_modify conp set me top top me11 - -# get the 0V charges (qsb), and excess charge required to reach preset total charges -variable qsb_bot internal 0.0 -variable qsb_top internal 0.0 -fix_modify conp set qsb bot qsb_bot -fix_modify conp set qsb top qsb_top -variable qex_bot equal -1.0-v_qsb_bot # difference between desired and 0V charge -variable qex_top equal 1.0-v_qsb_top # difference between desired and 0V charge - -# calculate imposed potential as elastance * excess charge -# note: fix will wait until the run setup to look for its potential variables -variable vbot equal v_me00*v_qex_bot+v_me01*v_qex_top -variable vtop equal v_me10*v_qex_bot+v_me11*v_qex_top - -thermo 50 -thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop -run 500 -PPPM/electrode initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:342) - G vector (1/distance) = 0.20904498 - grid = 32 32 200 - stencil order = 5 - estimated absolute RMS force accuracy = 3.7023506e-05 - estimated relative force accuracy = 1.1149519e-07 - using double precision MKL FFT - 3d grid and FFT values/proc = 307242 204800 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 18 - ghost atom cutoff = 18 - binsize = 9, bins = 4 4 16 - 3 neighbor lists, perpetual/occasional/extra = 2 1 0 - (1) pair lj/cut/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard - (2) fix electrode/conp, occasional, skip from (1) - attributes: half, newton on - pair build: skip - stencil: none - bin: none - (3) fix electrode/conp, perpetual, skip from (1) - attributes: half, newton on - pair build: skip - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes - Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_vbot v_vtop - 0 0 0 25136984 25136984 -1 1 -9.931852 10.097344 - 50 20.206425 72.797911 25136825 25137033 -1 1 -9.4359366 9.5964514 - 100 55.931663 201.50563 25136587 25137163 -1 1 -8.0440112 8.1861787 - 150 81.389273 293.22204 25136533 25137371 -1 1 -6.1113109 6.2267114 - 200 92.867946 334.57639 25136646 25137603 -1 1 -4.1857807 4.2740694 - 250 97.518304 351.33028 25136809 25137814 -1 1 -2.8383703 2.9101475 - 300 102.36577 368.79431 25136933 25137987 -1 1 -2.3831643 2.4461115 - 350 113.66597 409.50566 25136960 25138131 -1 1 -2.7083563 2.7457811 - 400 122.8443 442.57252 25136991 25138256 -1 1 -3.4311003 3.3941657 - 450 128.63713 463.44243 25137048 25138373 -1 1 -4.132871 3.9852959 - 500 131.18361 472.61665 25137142 25138493 -1 1 -4.5104095 4.2567261 -Loop time of 62.9692 on 1 procs for 500 steps with 3776 atoms - -Performance: 0.686 ns/day, 34.983 hours/ns, 7.940 timesteps/s -393.7% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 20.307 | 20.307 | 20.307 | 0.0 | 32.25 -Bond | 0.0020074 | 0.0020074 | 0.0020074 | 0.0 | 0.00 -Kspace | 23.562 | 23.562 | 23.562 | 0.0 | 37.42 -Neigh | 0.26149 | 0.26149 | 0.26149 | 0.0 | 0.42 -Comm | 0.059436 | 0.059436 | 0.059436 | 0.0 | 0.09 -Output | 0.0023888 | 0.0023888 | 0.0023888 | 0.0 | 0.00 -Modify | 18.756 | 18.756 | 18.756 | 0.0 | 29.79 -Other | | 0.01897 | | | 0.03 - -Nlocal: 3776 ave 3776 max 3776 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 12510 ave 12510 max 12510 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1.72559e+06 ave 1.72559e+06 max 1.72559e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1725588 -Ave neighs/atom = 456.98835 -Ave special neighs/atom = 0.50847458 -Neighbor list builds = 6 -Dangerous builds = 0 -Total wall time: 0:02:26 diff --git a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq2.g++.4 b/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq2.g++.4 deleted file mode 100644 index cf8ddf60a3..0000000000 --- a/examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq2.g++.4 +++ /dev/null @@ -1,171 +0,0 @@ -LAMMPS (24 Mar 2022) -# electrodes with constrained total charges imposed from dynamically computed potentials -# for graphene-ionic liquid supercapacitor - -boundary p p f # slab calculation -include settings.mod # styles, groups, computes and fixes -# set boundary in main script because ffield is periodic -units real -# distribute electrode atoms among all processors: -if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" -processors * * 2 - -atom_style full -pair_style lj/cut/coul/long 16 -bond_style harmonic -angle_style harmonic -kspace_style pppm/electrode 1e-7 -# kspace_modify in main script because ffield is periodic - -read_data "data.graph-il" -Reading data file ... - orthogonal box = (0 0 -68) to (32.2 34.4 68) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 3776 atoms - scanning bonds ... - 2 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 640 bonds - reading angles ... - 320 angles -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.019 seconds - -group bot molecule 641 -416 atoms in group bot -group top molecule 642 -416 atoms in group top - -group bmi type 1 2 3 -960 atoms in group bmi -group electrolyte type 1 2 3 4 -1280 atoms in group electrolyte - -fix nvt electrolyte nvt temp 500.0 500.0 100 -fix shake bmi shake 1e-4 20 0 b 1 2 a 1 - 0 = # of size 2 clusters - 0 = # of size 3 clusters - 0 = # of size 4 clusters - 320 = # of frozen angles - find clusters CPU = 0.001 seconds - -variable q atom q -compute qtop top reduce sum v_q -compute qbot bot reduce sum v_q -compute ctemp electrolyte temp -kspace_modify slab 3.0 - -fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes 5 -832 atoms in group conp_group - -# get the four entries of electrode elastance matrix -variable me00 internal 0.0 -variable me01 internal 0.0 -variable me10 internal 0.0 -variable me11 internal 0.0 -fix_modify conp set me bot bot me00 -fix_modify conp set me bot top me01 -fix_modify conp set me top bot me10 -fix_modify conp set me top top me11 - -# get the 0V charges (qsb), and excess charge required to reach preset total charges -variable qsb_bot internal 0.0 -variable qsb_top internal 0.0 -fix_modify conp set qsb bot qsb_bot -fix_modify conp set qsb top qsb_top -variable qex_bot equal -1.0-v_qsb_bot # difference between desired and 0V charge -variable qex_top equal 1.0-v_qsb_top # difference between desired and 0V charge - -# calculate imposed potential as elastance * excess charge -# note: fix will wait until the run setup to look for its potential variables -variable vbot equal v_me00*v_qex_bot+v_me01*v_qex_top -variable vtop equal v_me10*v_qex_bot+v_me11*v_qex_top - -thermo 50 -thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop -run 500 -PPPM/electrode initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:342) - G vector (1/distance) = 0.20904498 - grid = 32 32 200 - stencil order = 5 - estimated absolute RMS force accuracy = 3.7023506e-05 - estimated relative force accuracy = 1.1149519e-07 - using double precision MKL FFT - 3d grid and FFT values/proc = 151593 85504 - generated 10 of 10 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 18 - ghost atom cutoff = 18 - binsize = 9, bins = 4 4 16 - 3 neighbor lists, perpetual/occasional/extra = 2 1 0 - (1) pair lj/cut/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard - (2) fix electrode/conp, occasional, skip from (1) - attributes: half, newton on - pair build: skip - stencil: none - bin: none - (3) fix electrode/conp, perpetual, skip from (1) - attributes: half, newton on - pair build: skip - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes - Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_vbot v_vtop - 0 0 0 25136984 25136984 -1 1 -9.931852 10.097344 - 50 20.206425 72.797911 25136825 25137033 -1 1 -9.4359366 9.5964514 - 100 55.931663 201.50563 25136587 25137163 -1 1 -8.0440112 8.1861787 - 150 81.389273 293.22204 25136533 25137371 -1 1 -6.1113109 6.2267114 - 200 92.867946 334.57639 25136646 25137603 -1 1 -4.1857807 4.2740694 - 250 97.518304 351.33028 25136809 25137814 -1 1 -2.8383703 2.9101475 - 300 102.36577 368.79431 25136933 25137987 -1 1 -2.3831643 2.4461115 - 350 113.66597 409.50566 25136960 25138131 -1 1 -2.7083563 2.7457811 - 400 122.8443 442.57252 25136991 25138256 -1 1 -3.4311003 3.3941657 - 450 128.63713 463.44243 25137048 25138373 -1 1 -4.132871 3.9852959 - 500 131.18361 472.61665 25137142 25138493 -1 1 -4.5104095 4.2567261 -Loop time of 33.4031 on 4 procs for 500 steps with 3776 atoms - -Performance: 1.293 ns/day, 18.557 hours/ns, 14.969 timesteps/s -94.3% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 7.1262 | 7.3913 | 7.611 | 6.8 | 22.13 -Bond | 0.0007191 | 0.00079089 | 0.00087005 | 0.0 | 0.00 -Kspace | 15.139 | 15.358 | 15.623 | 4.7 | 45.98 -Neigh | 0.10374 | 0.10377 | 0.10383 | 0.0 | 0.31 -Comm | 0.14245 | 0.14353 | 0.14563 | 0.3 | 0.43 -Output | 0.0012987 | 0.0015671 | 0.0022434 | 1.0 | 0.00 -Modify | 10.381 | 10.383 | 10.384 | 0.0 | 31.08 -Other | | 0.02134 | | | 0.06 - -Nlocal: 944 ave 948 max 940 min -Histogram: 1 0 0 1 0 0 1 0 0 1 -Nghost: 5920.5 ave 5941 max 5899 min -Histogram: 1 0 0 0 1 1 0 0 0 1 -Neighs: 431397 ave 442329 max 421103 min -Histogram: 2 0 0 0 0 0 0 0 1 1 - -Total # of neighbors = 1725588 -Ave neighs/atom = 456.98835 -Ave special neighs/atom = 0.50847458 -Neighbor list builds = 6 -Dangerous builds = 0 -Total wall time: 0:01:01 diff --git a/examples/PACKAGES/electrode/graph-il/settings.mod b/examples/PACKAGES/electrode/graph-il/settings.mod index dcdaf7bfcd..ffbbfb1cc4 100644 --- a/examples/PACKAGES/electrode/graph-il/settings.mod +++ b/examples/PACKAGES/electrode/graph-il/settings.mod @@ -12,8 +12,13 @@ kspace_style pppm/electrode 1e-7 read_data "data.graph-il" -group bot molecule 641 -group top molecule 642 +# replicate 4 4 1 # test different sys sizes + +variable zpos atom "z > 0" +group zpos variable zpos +group ele type 5 +group top intersect ele zpos +group bot subtract ele top group bmi type 1 2 3 group electrolyte type 1 2 3 4 diff --git a/examples/PACKAGES/electrode/madelung/.gitignore b/examples/PACKAGES/electrode/madelung/.gitignore new file mode 100644 index 0000000000..89d8d1a065 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/.gitignore @@ -0,0 +1,2 @@ +*.csv +*.txt diff --git a/examples/PACKAGES/electrode/madelung/data.au-elyt b/examples/PACKAGES/electrode/madelung/data.au-elyt new file mode 100644 index 0000000000..366e317378 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/data.au-elyt @@ -0,0 +1,27 @@ +LAMMPS data file via write_data, version 24 Dec 2020, timestep = 0 + +4 atoms +3 atom types + +0 1 xlo xhi +0 1 ylo yhi +-10 10 zlo zhi + +Masses + +1 196.966553 +2 196.966553 +3 1.0 + +Pair Coeffs # lj/cut/coul/long + +1 0 0 +2 0 0 +3 0 0 + +Atoms # full + +1 1 1 0.00 0.00 0.00 -2.00 # bottom electrode +2 2 2 0.00 0.00 0.00 2.00 # top electrode +3 3 3 0.50 0.00 0.00 -1.00 # bottom electrolyte +4 3 3 -0.50 0.00 0.00 1.00 # top electrolyte diff --git a/examples/PACKAGES/electrode/madelung/eval.py b/examples/PACKAGES/electrode/madelung/eval.py new file mode 100644 index 0000000000..2f5a355d9b --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/eval.py @@ -0,0 +1,53 @@ +#!/usr/env/python3 + +import sys +import os.path as op + + +def rel_error(out, ref): + return 100 * abs((ref - out) / out) + + +assert len(sys.argv) == 5 + +with open(sys.argv[1]) as f: + ref_line = f.readlines()[-1].split(", ") +e_ref = float(ref_line[1]) +q_ref = float(ref_line[3]) +inv11_ref = float(ref_line[4]) +inv12_ref = float(ref_line[5]) +b1_ref = float(ref_line[6]) + +# out.csv +with open(sys.argv[2]) as f: + out_line = f.readlines()[-1].split(", ") +e_out = float(out_line[0]) +q_out = float(out_line[1]) + +out_lines = [("energy", e_ref, e_out), ("charge", q_ref, q_out)] + +# vec.csv +vec_file = "vec.csv" +if op.isfile(vec_file): + with open(sys.argv[4]) as f: + vec_line = f.readlines()[1:] + b1_out = float(vec_line[0]) + b2_out = float(vec_line[1]) + out_lines.append(("b1", b1_ref, b1_out)) + +# inv.csv +inv_file = "inv.csv" +if op.isfile(inv_file): + with open(inv_file) as f: + inv_line = f.readlines()[1].split() + inv11_out = float(inv_line[0]) + inv12_out = float(inv_line[1]) + out_lines.append(("inv11", inv11_ref, inv11_out)) + +lines = [] +for label, ref, out in out_lines: + error = rel_error(out, ref) + lines.append(f"{label}: {out:.5f}, {error:.5f}\n") + +with open("madelung.txt", 'a') as f: + f.writelines(lines) diff --git a/examples/PACKAGES/electrode/madelung/in.cg b/examples/PACKAGES/electrode/madelung/in.cg new file mode 100644 index 0000000000..39a90a1f29 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/in.cg @@ -0,0 +1,11 @@ +boundary p p f +kspace_style ewald/electrode 1.0e-8 +kspace_modify slab 8.0 # ew3dc + +include "settings.mod" # styles, computes, groups and fixes + +thermo_style custom step pe c_qbot c_qtop +fix conp bot electrode/conp 0 2 couple top 1 symm on algo cg 1e-6 + +run 0 + diff --git a/examples/PACKAGES/electrode/madelung/in.ewald-ew2d b/examples/PACKAGES/electrode/madelung/in.ewald-ew2d new file mode 100644 index 0000000000..2f54e747d1 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/in.ewald-ew2d @@ -0,0 +1,11 @@ +boundary p p f +kspace_style ewald/electrode 1.0e-8 +kspace_modify slab ew2d + +include "settings.mod" # styles, computes, groups and fixes + +thermo_style custom step pe c_qbot c_qtop +fix conp bot electrode/conp 0 2 couple top 1 symm on write_inv inv.csv write_vec vec.csv + +run 0 + diff --git a/examples/PACKAGES/electrode/madelung/in.ewald-ew3dc b/examples/PACKAGES/electrode/madelung/in.ewald-ew3dc new file mode 100644 index 0000000000..c89804ef11 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/in.ewald-ew3dc @@ -0,0 +1,11 @@ +boundary p p f +kspace_style ewald/electrode 1.0e-8 +kspace_modify slab 8.0 # ew3dc + +include "settings.mod" # styles, computes, groups and fixes + +thermo_style custom step pe c_qbot c_qtop +fix conp bot electrode/conp 0 2 couple top 1 symm on write_inv inv.csv write_vec vec.csv + +run 0 + diff --git a/examples/PACKAGES/electrode/madelung/in.ewald-ffield b/examples/PACKAGES/electrode/madelung/in.ewald-ffield new file mode 100644 index 0000000000..c30f82159b --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/in.ewald-ffield @@ -0,0 +1,10 @@ +boundary p p p +kspace_style ewald/electrode 1.0e-8 + +include "settings.mod" # styles, computes, groups and fixes + +thermo_style custom step pe c_qbot c_qtop +fix conp bot electrode/conp 0 2 couple top 1 symm on ffield yes write_inv inv.csv write_vec vec.csv + +run 0 + diff --git a/examples/PACKAGES/electrode/madelung/in.pppm-ew3dc b/examples/PACKAGES/electrode/madelung/in.pppm-ew3dc new file mode 100644 index 0000000000..c36587af08 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/in.pppm-ew3dc @@ -0,0 +1,11 @@ +boundary p p f +kspace_style pppm/electrode 1.0e-10 +kspace_modify slab 8.0 # ew3dc + +include "settings.mod" # styles, computes, groups and fixes + +thermo_style custom step pe c_qbot c_qtop +fix conp bot electrode/conp 0 2 couple top 1 symm on write_inv inv.csv write_vec vec.csv + +run 0 + diff --git a/examples/PACKAGES/electrode/madelung/in.pppm-ffield b/examples/PACKAGES/electrode/madelung/in.pppm-ffield new file mode 100644 index 0000000000..e161485e6f --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/in.pppm-ffield @@ -0,0 +1,10 @@ +boundary p p p +kspace_style pppm/electrode 1.0e-10 + +include "settings.mod" # styles, computes, groups and fixes + +thermo_style custom step pe c_qbot c_qtop +fix conp bot electrode/conp 0 2 couple top 1 symm on ffield yes write_inv inv.csv write_vec vec.csv + +run 0 + diff --git a/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-cg.g++.1 b/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-cg.g++.1 new file mode 100644 index 0000000000..a0cd4d959c --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-cg.g++.1 @@ -0,0 +1,131 @@ +LAMMPS (3 Nov 2022) +boundary p p f +kspace_style ewald/electrode 1.0e-8 +kspace_modify slab 8.0 # ew3dc + +include "settings.mod" # styles, computes, groups and fixes +# set boundary in main script because ffield is periodic +units real +# distribute electrode atoms among all processors: +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +atom_style full +pair_style lj/cut/coul/long 12 + +read_data "data.au-elyt" +Reading data file ... + orthogonal box = (0 0 -10) to (1 1 10) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.003 seconds + +group bot type 1 +1 atoms in group bot +group top type 2 +1 atoms in group top + +# get electrode charges +variable q atom q +compute qbot bot reduce sum v_q +compute qtop top reduce sum v_q + +compute compute_pe all pe +variable vpe equal c_compute_pe +variable charge equal c_qtop +fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv" + +thermo_style custom step pe c_qbot c_qtop +fix conp bot electrode/conp 0 2 couple top 1 symm on algo cg 1e-6 +2 atoms in group conp_group + +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Ewald/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) +WARNING: For better accuracy use 'pair_modify table 0' (src/kspace.cpp:365) + G vector (1/distance) = 0.32261103 + estimated absolute RMS force accuracy = 3.8272011e-06 + estimated relative force accuracy = 1.1525502e-08 + KSpace vectors: actual max1d max3d = 52 50 515150 + kxmax kymax kzmax = 1 1 50 +Generated 3 of 3 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 1 1 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix electrode/conp, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966) +139.943964815502, 0.279214485147241 +Per MPI rank memory allocation (min/avg/max) = 144.1 | 144.1 | 144.1 Mbytes + Step PotEng c_qbot c_qtop + 0 139.94396 -0.27921449 0.27921449 +Loop time of 1.092e-06 on 1 procs for 0 steps with 4 atoms + +91.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Kspace | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.092e-06 | | |100.00 + +Nlocal: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3596 ave 3596 max 3596 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4790 ave 4790 max 4790 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4790 +Ave neighs/atom = 1197.5 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +Average conjugate gradient steps: 1 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-ewald-ew2d.g++.1 b/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-ewald-ew2d.g++.1 new file mode 100644 index 0000000000..ff0a8550cd --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-ewald-ew2d.g++.1 @@ -0,0 +1,130 @@ +LAMMPS (3 Nov 2022) +boundary p p f +kspace_style ewald/electrode 1.0e-8 +kspace_modify slab ew2d + +include "settings.mod" # styles, computes, groups and fixes +# set boundary in main script because ffield is periodic +units real +# distribute electrode atoms among all processors: +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +atom_style full +pair_style lj/cut/coul/long 12 + +read_data "data.au-elyt" +Reading data file ... + orthogonal box = (0 0 -10) to (1 1 10) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.002 seconds + +group bot type 1 +1 atoms in group bot +group top type 2 +1 atoms in group top + +# get electrode charges +variable q atom q +compute qbot bot reduce sum v_q +compute qtop top reduce sum v_q + +compute compute_pe all pe +variable vpe equal c_compute_pe +variable charge equal c_qtop +fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv" + +thermo_style custom step pe c_qbot c_qtop +fix conp bot electrode/conp 0 2 couple top 1 symm on write_inv inv.csv write_vec vec.csv +2 atoms in group conp_group + +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Ewald/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) +WARNING: For better accuracy use 'pair_modify table 0' (src/kspace.cpp:365) + G vector (1/distance) = 0.32261103 + estimated absolute RMS force accuracy = 9.9990544e-06 + estimated relative force accuracy = 3.0111855e-08 + KSpace vectors: actual max1d max3d = 2 8 2456 + kxmax kymax kzmax = 1 1 8 +Generated 3 of 3 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 1 1 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix electrode/conp, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966) +139.946125020193, 0.279214126709814 +Per MPI rank memory allocation (min/avg/max) = 20.42 | 20.42 | 20.42 Mbytes + Step PotEng c_qbot c_qtop + 0 139.94613 -0.27921413 0.27921413 +Loop time of 1.082e-06 on 1 procs for 0 steps with 4 atoms + +0.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Kspace | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.082e-06 | | |100.00 + +Nlocal: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3596 ave 3596 max 3596 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4790 ave 4790 max 4790 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4790 +Ave neighs/atom = 1197.5 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-ewald-ew3dc.g++.1 b/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-ewald-ew3dc.g++.1 new file mode 100644 index 0000000000..5374b09ff1 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-ewald-ew3dc.g++.1 @@ -0,0 +1,130 @@ +LAMMPS (3 Nov 2022) +boundary p p f +kspace_style ewald/electrode 1.0e-8 +kspace_modify slab 8.0 # ew3dc + +include "settings.mod" # styles, computes, groups and fixes +# set boundary in main script because ffield is periodic +units real +# distribute electrode atoms among all processors: +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +atom_style full +pair_style lj/cut/coul/long 12 + +read_data "data.au-elyt" +Reading data file ... + orthogonal box = (0 0 -10) to (1 1 10) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.003 seconds + +group bot type 1 +1 atoms in group bot +group top type 2 +1 atoms in group top + +# get electrode charges +variable q atom q +compute qbot bot reduce sum v_q +compute qtop top reduce sum v_q + +compute compute_pe all pe +variable vpe equal c_compute_pe +variable charge equal c_qtop +fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv" + +thermo_style custom step pe c_qbot c_qtop +fix conp bot electrode/conp 0 2 couple top 1 symm on write_inv inv.csv write_vec vec.csv +2 atoms in group conp_group + +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Ewald/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) +WARNING: For better accuracy use 'pair_modify table 0' (src/kspace.cpp:365) + G vector (1/distance) = 0.32261103 + estimated absolute RMS force accuracy = 3.8272011e-06 + estimated relative force accuracy = 1.1525502e-08 + KSpace vectors: actual max1d max3d = 52 50 515150 + kxmax kymax kzmax = 1 1 50 +Generated 3 of 3 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 1 1 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix electrode/conp, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966) +139.943964815502, 0.279214485147238 +Per MPI rank memory allocation (min/avg/max) = 144.1 | 144.1 | 144.1 Mbytes + Step PotEng c_qbot c_qtop + 0 139.94396 -0.27921449 0.27921449 +Loop time of 7.31e-07 on 1 procs for 0 steps with 4 atoms + +0.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Kspace | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 7.31e-07 | | |100.00 + +Nlocal: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3596 ave 3596 max 3596 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4790 ave 4790 max 4790 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4790 +Ave neighs/atom = 1197.5 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-ewald-ffield.g++.1 b/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-ewald-ffield.g++.1 new file mode 100644 index 0000000000..ea3799809d --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-ewald-ffield.g++.1 @@ -0,0 +1,129 @@ +LAMMPS (3 Nov 2022) +boundary p p p +kspace_style ewald/electrode 1.0e-8 + +include "settings.mod" # styles, computes, groups and fixes +# set boundary in main script because ffield is periodic +units real +# distribute electrode atoms among all processors: +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +atom_style full +pair_style lj/cut/coul/long 12 + +read_data "data.au-elyt" +Reading data file ... + orthogonal box = (0 0 -10) to (1 1 10) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.002 seconds + +group bot type 1 +1 atoms in group bot +group top type 2 +1 atoms in group top + +# get electrode charges +variable q atom q +compute qbot bot reduce sum v_q +compute qtop top reduce sum v_q + +compute compute_pe all pe +variable vpe equal c_compute_pe +variable charge equal c_qtop +fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv" + +thermo_style custom step pe c_qbot c_qtop +fix conp bot electrode/conp 0 2 couple top 1 symm on ffield yes write_inv inv.csv write_vec vec.csv +2 atoms in group conp_group + +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Ewald/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) +WARNING: For better accuracy use 'pair_modify table 0' (src/kspace.cpp:365) + G vector (1/distance) = 0.32261103 + estimated absolute RMS force accuracy = 9.9990544e-06 + estimated relative force accuracy = 3.0111855e-08 + KSpace vectors: actual max1d max3d = 10 8 2456 + kxmax kymax kzmax = 1 1 8 +Generated 3 of 3 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 1 1 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix electrode/conp, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966) +138.299024320284, 0.287160231879378 +Per MPI rank memory allocation (min/avg/max) = 21.19 | 21.19 | 21.19 Mbytes + Step PotEng c_qbot c_qtop + 0 138.29902 -0.28716023 0.28716023 +Loop time of 1.804e-06 on 1 procs for 0 steps with 4 atoms + +55.4% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Kspace | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.804e-06 | | |100.00 + +Nlocal: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 10796 ave 10796 max 10796 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4790 ave 4790 max 4790 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4790 +Ave neighs/atom = 1197.5 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-pppm-ew3dc.g++.1 b/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-pppm-ew3dc.g++.1 new file mode 100644 index 0000000000..a3961bd3cb --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-pppm-ew3dc.g++.1 @@ -0,0 +1,143 @@ +LAMMPS (3 Nov 2022) +boundary p p f +kspace_style pppm/electrode 1.0e-10 +kspace_modify slab 8.0 # ew3dc + +include "settings.mod" # styles, computes, groups and fixes +# set boundary in main script because ffield is periodic +units real +# distribute electrode atoms among all processors: +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +atom_style full +pair_style lj/cut/coul/long 12 + +read_data "data.au-elyt" +Reading data file ... + orthogonal box = (0 0 -10) to (1 1 10) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.003 seconds + +group bot type 1 +1 atoms in group bot +group top type 2 +1 atoms in group top + +# get electrode charges +variable q atom q +compute qbot bot reduce sum v_q +compute qtop top reduce sum v_q + +compute compute_pe all pe +variable vpe equal c_compute_pe +variable charge equal c_qtop +fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv" + +thermo_style custom step pe c_qbot c_qtop +fix conp bot electrode/conp 0 2 couple top 1 symm on write_inv inv.csv write_vec vec.csv +2 atoms in group conp_group + +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +PPPM/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) +WARNING: For better accuracy use 'pair_modify table 0' (src/kspace.cpp:365) + G vector (1/distance) = 0.37216302 + grid = 12 12 375 + stencil order = 5 + estimated absolute RMS force accuracy = 9.4312865e-06 + estimated relative force accuracy = 2.8402039e-08 + using double precision MKL FFT + 3d grid and FFT values/proc = 637099 54000 +Generated 3 of 3 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 1 1 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix electrode/conp, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966) +139.946107219358, 0.279214187928028 +Per MPI rank memory allocation (min/avg/max) = 40.22 | 40.22 | 40.22 Mbytes + Step PotEng c_qbot c_qtop + 0 139.94611 -0.27921419 0.27921419 +Loop time of 8.32e-07 on 1 procs for 0 steps with 4 atoms + +0.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Kspace | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 8.32e-07 | | |100.00 + +Nlocal: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3596 ave 3596 max 3596 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4790 ave 4790 max 4790 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4790 +Ave neighs/atom = 1197.5 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-pppm-ffield.g++.1 b/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-pppm-ffield.g++.1 new file mode 100644 index 0000000000..64664e7443 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-pppm-ffield.g++.1 @@ -0,0 +1,142 @@ +LAMMPS (3 Nov 2022) +boundary p p p +kspace_style pppm/electrode 1.0e-10 + +include "settings.mod" # styles, computes, groups and fixes +# set boundary in main script because ffield is periodic +units real +# distribute electrode atoms among all processors: +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +atom_style full +pair_style lj/cut/coul/long 12 + +read_data "data.au-elyt" +Reading data file ... + orthogonal box = (0 0 -10) to (1 1 10) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.002 seconds + +group bot type 1 +1 atoms in group bot +group top type 2 +1 atoms in group top + +# get electrode charges +variable q atom q +compute qbot bot reduce sum v_q +compute qtop top reduce sum v_q + +compute compute_pe all pe +variable vpe equal c_compute_pe +variable charge equal c_qtop +fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv" + +thermo_style custom step pe c_qbot c_qtop +fix conp bot electrode/conp 0 2 couple top 1 symm on ffield yes write_inv inv.csv write_vec vec.csv +2 atoms in group conp_group + +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +PPPM/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) +WARNING: For better accuracy use 'pair_modify table 0' (src/kspace.cpp:365) + G vector (1/distance) = 0.37297537 + grid = 12 12 90 + stencil order = 5 + estimated absolute RMS force accuracy = 9.4312758e-06 + estimated relative force accuracy = 2.8402007e-08 + using double precision MKL FFT + 3d grid and FFT values/proc = 174824 12960 +Generated 3 of 3 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 1 1 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix electrode/conp, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966) +138.298994634846, 0.287160247352281 +Per MPI rank memory allocation (min/avg/max) = 16.7 | 16.7 | 16.7 Mbytes + Step PotEng c_qbot c_qtop + 0 138.29899 -0.28716025 0.28716025 +Loop time of 1.022e-06 on 1 procs for 0 steps with 4 atoms + +0.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Kspace | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.022e-06 | | |100.00 + +Nlocal: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 10796 ave 10796 max 10796 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4790 ave 4790 max 4790 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4790 +Ave neighs/atom = 1197.5 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/electrode/madelung/plate_cap.py b/examples/PACKAGES/electrode/madelung/plate_cap.py new file mode 100755 index 0000000000..62d52fe102 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/plate_cap.py @@ -0,0 +1,94 @@ +#!/usr/bin/env python3 + +import numpy as np +from scipy.special import erf + +ETA = 2 +SQRT2 = np.sqrt(2) +COULOMB = 332.06371 # Coulomb constant in Lammps 'real' units +QE2F = 23.060549 +LENGTH = 10000 # convergence parameter + + +def lattice(length): + """indices combinations of images in one quadrant""" + x = np.arange(length) # range(length) + y = np.arange(1, length) + return np.array(np.meshgrid(x, y)).T.reshape(-1, 2) + + +def a_element(r): + """Coulomb contribution of two Gaussians""" + return erf(ETA / SQRT2 * r) / r + + +def b_element(r, q): + """Coulomb contribution of a Gaussian with a point charge""" + return q * erf(ETA * r) / r + + +a = 1 # nearest neighbor distance i.e. lattice constant / sqrt(2) +x_elec = [-2, 2] +x_elyt = [-1, 1] +q_elyt = [0.5, -0.5] +distance_plates = x_elec[1] - x_elec[0] # distance between plates +v = np.array([-0.5, 0.5]) * (QE2F / COULOMB) + +# distances to images within electrode and to opposite electrode +distances = a * np.linalg.norm(lattice(LENGTH), axis=1) +opposite_distances = np.sqrt(np.square(distances) + distance_plates ** 2) + +# self interaction and within original box +A_11 = np.sqrt(2 / np.pi) * ETA +A_12 = erf(ETA * distance_plates / SQRT2) / distance_plates + +# interaction with periodic images +A_11 += 4 * np.sum(a_element(distances)) +A_12 += 4 * np.sum(a_element(opposite_distances)) +A = np.array([[A_11, A_12], [A_12, A_11]]) +inv = np.linalg.inv(A) +e = np.array([1, 1]) +inv -= np.matmul(inv, np.matmul(np.outer(e, e), inv)) / np.dot(e, np.dot(inv, e)) + +# electrode-electrolyte interaction +b = [] +for x in x_elec: + bi = 0 + for y, q in zip(x_elyt, q_elyt): + d = abs(y - x) + bi += b_element(d, q) + image_distances = np.sqrt(np.square(distances) + d ** 2) + bi += 4 * np.sum(b_element(image_distances, q)) + b.append(bi) +b = np.array(b) + +# electrolyte-electrolyte energy +elyt_11 = 4 * np.sum(1 / distances) +distance_elyt = x_elyt[1] - x_elyt[0] +elyt_12 = 1 / distance_elyt + 4 * np.sum( + 1 / np.sqrt(np.square(distances) + distance_elyt ** 2) +) +elyt = np.array([[elyt_11, elyt_12], [elyt_12, elyt_11]]) +energy_elyt = 0.5 * np.dot(q_elyt, np.dot(elyt, q_elyt)) + +# electrode charges and energy +q = np.dot(inv, v - b) +energy = COULOMB * (0.5 * np.dot(q, np.dot(A, q)) + np.dot(b, q) + energy_elyt) + +print( + "length, energy / kcal/mol, q1 / e, q2 / e, inv11 / A, inv12 / A, b1 / e/A, b2 / e/A" +) +print( + ", ".join( + [ + str(LENGTH), + f"{energy:.8f}", + f"{q[0]:.10f}", + f"{q[1]:.10f}", + f"{inv[0, 0]:.10f}", + f"{inv[0, 1]:.10f}", + f"{b[0]:.8f}", + f"{b[1]:.8f}", + ] + ) +) diff --git a/examples/PACKAGES/electrode/madelung/settings.mod b/examples/PACKAGES/electrode/madelung/settings.mod new file mode 100644 index 0000000000..aa1096ea81 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/settings.mod @@ -0,0 +1,22 @@ +# set boundary in main script because ffield is periodic +units real +# distribute electrode atoms among all processors: +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +atom_style full +pair_style lj/cut/coul/long 12 + +read_data "data.au-elyt" + +group bot type 1 +group top type 2 + +# get electrode charges +variable q atom q +compute qbot bot reduce sum v_q +compute qtop top reduce sum v_q + +compute compute_pe all pe +variable vpe equal c_compute_pe +variable charge equal c_qtop +fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv" diff --git a/examples/PACKAGES/electrode/madelung/test.sh b/examples/PACKAGES/electrode/madelung/test.sh new file mode 100644 index 0000000000..edac04f5b1 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/test.sh @@ -0,0 +1,23 @@ +#!/bin/bash -e + +lmpbin=$1 +if [ ! -f $lmpbin ]; then + echo "LAMMPS binary '$lmpbin' is not a file" + exit 1 +fi + +ref_out="plate_cap.csv" +if [ ! -f $ref_out ]; then + echo "Generating reference data" + python3 plate_cap.py > $ref_out +fi + +echo "Running Lammps inputs" +rm -rf madelung.txt && touch madelung.txt +for file in in.*; do + printf "\n$file\n" >> madelung.txt + rm -f out.csv inv.csv vec.csv + $lmpbin -i $file &> /dev/null + python3 eval.py $ref_out out.csv inv.csv vec.csv +done +cat madelung.txt diff --git a/examples/PACKAGES/electrode/piston/.gitignore b/examples/PACKAGES/electrode/piston/.gitignore new file mode 100644 index 0000000000..9336c29266 --- /dev/null +++ b/examples/PACKAGES/electrode/piston/.gitignore @@ -0,0 +1,2 @@ +top_wall.csv +data.pistoned diff --git a/examples/PACKAGES/electrode/piston/data.piston b/examples/PACKAGES/electrode/piston/data.piston new file mode 100644 index 0000000000..815edff7ba --- /dev/null +++ b/examples/PACKAGES/electrode/piston/data.piston @@ -0,0 +1,2128 @@ +LAMMPS data file via write_data, version 23 Jun 2022, timestep = 5000 + +726 atoms +4 atom types +420 bonds +1 bond types +210 angles +1 angle types + +0 17.6494 xlo xhi +0 20.3798 ylo yhi +0 26.0000 zlo zhi + +Masses + +1 500 +2 196.97 +3 15.9994 +4 1.008 + +Pair Coeffs # lj/cut/coul/long + +1 0.069 2.78 +2 5.29 2.951 +3 0.1553 3.166 +4 0 0 + +Bond Coeffs # harmonic + +1 600 1 + +Angle Coeffs # harmonic + +1 75 109.47 + +Atoms # full + +49 25 2 0 0 0 2.4018 0 0 0 +50 25 2 0 1.4708 2.5475 2.4018 0 0 0 +51 26 2 0 0 5.0949 2.4018 0 0 0 +57 29 2 0 2.9416 0 2.4018 0 0 0 +58 29 2 0 4.4124 2.5475 2.4018 0 0 0 +59 30 2 0 2.9416 5.0949 2.4018 0 0 0 +65 33 2 0 5.8832 0 2.4018 0 0 0 +66 33 2 0 7.354000000000001 2.5475 2.4018 0 0 0 +67 34 2 0 5.8832 5.0949 2.4018 0 0 0 +243 97 4 0.4238 4.215372213007002 2.2225202484567896 5.2803935587652235 0 0 0 +52 26 2 0 1.4708 7.6424 2.4018 0 0 0 +53 27 2 0 0 10.1898 2.4018 0 0 0 +60 30 2 0 4.4124 7.6424 2.4018 0 0 0 +61 31 2 0 2.9416 10.1898 2.4018 0 0 0 +68 34 2 0 7.354000000000001 7.6424 2.4018 0 0 0 +69 35 2 0 5.8832 10.1898 2.4018 0 0 0 +387 145 4 0.4238 5.821325736406644 4.80211316415021 5.03726935778638 0 0 0 +260 103 4 0.4238 4.266650899557808 6.124697675258705 6.600494419311919 0 0 0 +277 109 3 -0.8476 1.1595300211865478 9.226136831721583 5.6374387660682395 0 0 0 +422 157 4 0.4238 5.186379561937092 9.246331162340214 5.010378323358909 0 0 0 +278 109 4 0.4238 0.16509455550271238 9.324889581001292 5.600728087976438 0 0 0 +421 157 3 -0.8476 4.267061402816361 8.96456307950511 5.285080645137098 0 0 0 +372 140 4 0.4238 7.72049151444727 3.1081049977971733 5.624439615628745 0 0 0 +241 97 3 -0.8476 4.979583082691343 1.5807071976248444 5.344102790419773 0 0 0 +367 139 3 -0.8476 3.3292653199701174 3.842283776550616 5.301650818590438 0 0 0 +368 139 4 0.4238 3.684070197838302 4.776085383558861 5.2555059732229505 0 0 0 +369 139 4 0.4238 2.4614244393932903 3.790665660238261 4.807496843609001 0 0 0 +237 95 4 0.4238 0.8688372424570395 0.5637480725652825 15.837861037745109 0 0 0 +242 97 4 0.4238 5.838317925620407 2.08972820515595 5.4030316190296865 0 0 0 +244 98 3 -0.8476 3.06007349186706 3.3156446548102743 7.800821206312822 0 0 0 +245 98 4 0.4238 3.292495500569735 3.349267797972537 6.828787504752208 0 0 0 +246 98 4 0.4238 3.244639762451247 4.205236417313474 8.21862706780732 0 0 0 +357 135 4 0.4238 5.599931101613284 2.8266561120576155 8.823939192896898 0 0 0 +248 99 4 0.4238 4.69094628305157 1.7475560287256833 10.940028326694172 0 0 0 +355 135 3 -0.8476 6.1056692668831944 3.4565727858406277 8.234503978839392 0 0 0 +370 140 3 -0.8476 8.260944365686607 2.344956325089386 5.9787203639370485 0 0 0 +5 3 1 0 0 10.1898 21.4018 0 0 0 +115 55 3 -0.8476 0.6685955791423209 1.1406007302132561 5.285707584884053 0 0 0 +117 55 4 0.4238 0.8471253049325846 2.1223521279380155 5.351215251536808 0 0 0 +337 129 3 -0.8476 3.5673781090835357 0.1584650058169618 11.855592597757308 0 1 0 +423 157 4 0.4238 3.5925256519953384 9.568512539363969 4.86052578384893 0 0 0 +388 146 3 -0.8476 4.577545906676629 5.911730949363624 8.247639703277793 0 0 0 +371 140 4 0.4238 8.763880514062548 2.641297854555424 6.790654426306619 0 0 0 +389 146 4 0.4238 5.229395912055183 5.212412787511029 8.540975963214175 0 0 0 +498 182 4 0.4238 8.708572501204229 1.6439616819374039 8.893386862511662 0 0 0 +499 183 3 -0.8476 8.788151456935827 1.747387315190607 11.831408961401284 0 0 0 +356 135 4 0.4238 7.087379176847249 3.3036660348840203 8.347928594928105 0 0 0 +235 95 3 -0.8476 1.101376037954613 0.60797910815167 14.866280241985807 0 0 0 +338 129 4 0.4238 3.086322043066555 0.17977406211341077 10.979161321324465 0 1 0 +101 50 4 0.4238 2.3452088829773485 1.679109649521978 7.998572278214729 0 0 0 +102 50 4 0.4238 1.7396190746664724 0.7815651122817325 6.776156174616777 0 0 0 +264 104 4 0.4238 1.314649046187711 7.151850339115251 5.356458350291402 0 0 0 +261 103 4 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position of one wall at atmospheric +# pressure. The output is the wall position over time which can be used to +# find the average position for a run with fixed wall position. +# +# ----------------- Init Section ----------------- + +atom_style full +units real +boundary p p f +kspace_style pppm/electrode 1e-4 +kspace_modify slab 3.0 +pair_style lj/cut/coul/long 8 8 +bond_style harmonic +angle_style harmonic +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +# ----------------- Atom Definition Section ----------------- + +read_data "data.piston" + +# ----------------- Settings Section ----------------- + +pair_coeff 1 1 0.069 2.78 +pair_coeff 2 2 5.29 2.951 +pair_coeff 3 3 0.1553 3.166 +pair_coeff 4 4 0.0 0.0 +bond_coeff 1 600.0 1.0 +angle_coeff 1 75.0 109.47 +group wall type 1 +group gold type 2 +group spce type 3:4 +group ele union wall gold +fix fRattleSPCE spce shake 0.0001 10 0 b 1 a 1 +pair_modify mix arithmetic + +# ----------------- Run Section ----------------- + +neigh_modify every 1 delay 0 +timestep 2 +fix fxnvt spce nvt temp 300 300 500 +fix fxforce_au gold setforce 0.0 0.0 0.0 + +# equilibrate z-coordinate of upper electrode while keeping the electrode rigid +fix fxforce_wa wall setforce 0.0 0.0 NULL +fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p +fix fxdrag wall viscous 100 +fix fxrigid wall rigid/nve single + +# maintain constant potential during equilibration +# 'algo cg' allows for moving electrodes +fix fxele ele electrode/conp 0.0 1.805 symm on algo cg 1e-4 + +# setup output and run +variable q atom q +compute qwa wall reduce sum v_q +compute qau gold reduce sum v_q +variable top_wall equal (bound(wall,zmin)) +compute temp_mobile spce temp +variable s equal step +fix fxprint all print 1000 "${s} ${top_wall}" file top_wall.csv screen no +thermo_style custom step c_temp_mobile c_qwa c_qau v_top_wall +thermo 5000 +run 100000 +write_data "data.piston.final" + diff --git a/examples/PACKAGES/electrode/piston/log.1Dec2022.piston.g++.1 b/examples/PACKAGES/electrode/piston/log.1Dec2022.piston.g++.1 new file mode 100644 index 0000000000..a5b6d4cd4f --- /dev/null +++ b/examples/PACKAGES/electrode/piston/log.1Dec2022.piston.g++.1 @@ -0,0 +1,223 @@ +LAMMPS (3 Nov 2022) +# The intention is to find the average position of one wall at atmospheric +# pressure. The output is the wall position over time which can be used to +# find the average position for a run with fixed wall position. +# +# ----------------- Init Section ----------------- + +atom_style full +units real +boundary p p f +kspace_style pppm/electrode 1e-4 +kspace_modify slab 3.0 +pair_style lj/cut/coul/long 8 8 +bond_style harmonic +angle_style harmonic +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" + +# ----------------- Atom Definition Section ----------------- + +read_data "data.piston" +Reading data file ... + orthogonal box = (0 0 0) to (17.6494 20.3798 26) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 726 atoms + reading velocities ... + 726 velocities + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 420 bonds + reading angles ... + 210 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.011 seconds + +# ----------------- Settings Section ----------------- + +pair_coeff 1 1 0.069 2.78 +pair_coeff 2 2 5.29 2.951 +pair_coeff 3 3 0.1553 3.166 +pair_coeff 4 4 0.0 0.0 +bond_coeff 1 600.0 1.0 +angle_coeff 1 75.0 109.47 +group wall type 1 +48 atoms in group wall +group gold type 2 +48 atoms in group gold +group spce type 3:4 +630 atoms in group spce +group ele union wall gold +96 atoms in group ele +fix fRattleSPCE spce shake 0.0001 10 0 b 1 a 1 +Finding SHAKE clusters ... + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 210 = # of frozen angles + find clusters CPU = 0.000 seconds +pair_modify mix arithmetic + +# ----------------- Run Section ----------------- + +neigh_modify every 1 delay 0 +timestep 2 +fix fxnvt spce nvt temp 300 300 500 +fix fxforce_au gold setforce 0.0 0.0 0.0 + +# equilibrate z-coordinate of upper electrode while keeping the electrode rigid +fix fxforce_wa wall setforce 0.0 0.0 NULL +fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p +fix fxdrag wall viscous 100 +fix fxrigid wall rigid/nve single + 1 rigid bodies with 48 atoms + +# maintain constant potential during equilibration +# 'algo cg' allows for moving electrodes +fix fxele ele electrode/conp 0.0 1.805 symm on algo cg 1e-4 +96 atoms in group conp_group + +# setup output and run +variable q atom q +compute qwa wall reduce sum v_q +compute qau gold reduce sum v_q +variable top_wall equal (bound(wall,zmin)) +compute temp_mobile spce temp +variable s equal step +fix fxprint all print 1000 "${s} ${top_wall}" file top_wall.csv screen no +thermo_style custom step c_temp_mobile c_qwa c_qau v_top_wall +thermo 5000 +run 100000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +PPPM/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.32814871 + grid = 12 15 36 + stencil order = 5 + estimated absolute RMS force accuracy = 0.02930901 + estimated relative force accuracy = 8.8263214e-05 + using double precision MKL FFT + 3d grid and FFT values/proc = 15884 6480 +Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 4 5 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix electrode/conp, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 11.7 | 11.7 | 11.7 Mbytes + Step c_temp_mobile c_qwa c_qau v_top_wall + 0 303.38967 -0.042963484 0.042963484 21.4018 + 5000 285.08828 -0.26105255 0.26105255 25.155629 + 10000 323.19176 -0.26264003 0.26264003 24.541676 + 15000 310.479 -0.27318148 0.27318148 23.141522 + 20000 295.18544 -0.11313444 0.11313444 23.828735 + 25000 295.38607 -0.25433086 0.25433086 23.673314 + 30000 288.0613 -0.30099901 0.30099901 23.438086 + 35000 278.5591 -0.15823576 0.15823576 24.311915 + 40000 303.95751 -0.19941381 0.19941381 23.69594 + 45000 279.026 -0.1659962 0.1659962 23.588604 + 50000 298.79278 -0.28866703 0.28866703 23.372508 + 55000 301.03353 -0.078370381 0.078370381 23.192985 + 60000 306.77965 -0.12807205 0.12807205 23.968574 + 65000 309.86008 -0.27162663 0.27162663 23.616704 + 70000 287.31116 -0.029751882 0.029751882 23.667495 + 75000 312.48654 -0.10759866 0.10759866 23.504105 + 80000 309.94267 -0.2558548 0.2558548 23.810576 + 85000 328.04389 -0.1575471 0.1575471 24.013437 + 90000 302.9806 -0.032002164 0.032002164 24.264432 + 95000 294.20804 -0.27797238 0.27797238 23.291758 + 100000 307.63019 -0.19047448 0.19047448 23.632147 +Loop time of 530.844 on 1 procs for 100000 steps with 726 atoms + +Performance: 32.552 ns/day, 0.737 hours/ns, 188.379 timesteps/s, 136.763 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 190.47 | 190.47 | 190.47 | 0.0 | 35.88 +Bond | 0.10754 | 0.10754 | 0.10754 | 0.0 | 0.02 +Kspace | 73.179 | 73.179 | 73.179 | 0.0 | 13.79 +Neigh | 24.209 | 24.209 | 24.209 | 0.0 | 4.56 +Comm | 1.6857 | 1.6857 | 1.6857 | 0.0 | 0.32 +Output | 0.0016861 | 0.0016861 | 0.0016861 | 0.0 | 0.00 +Modify | 240.23 | 240.23 | 240.23 | 0.0 | 45.26 +Other | | 0.9595 | | | 0.18 + +Nlocal: 726 ave 726 max 726 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2335 ave 2335 max 2335 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 120271 ave 120271 max 120271 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 120271 +Ave neighs/atom = 165.66253 +Ave special neighs/atom = 1.7355372 +Neighbor list builds = 7722 +Dangerous builds = 0 +write_data "data.piston.final" +System init for write_data ... +PPPM/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.32814871 + grid = 12 15 36 + stencil order = 5 + estimated absolute RMS force accuracy = 0.029311365 + estimated relative force accuracy = 8.8270304e-05 + using double precision MKL FFT + 3d grid and FFT values/proc = 15884 6480 +Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule + +Average conjugate gradient steps: 1.981 +Total wall time: 0:08:50 diff --git a/examples/PACKAGES/electrode/piston/log.1Dec2022.piston.g++.4 b/examples/PACKAGES/electrode/piston/log.1Dec2022.piston.g++.4 new file mode 100644 index 0000000000..ffb6bcc61c --- /dev/null +++ b/examples/PACKAGES/electrode/piston/log.1Dec2022.piston.g++.4 @@ -0,0 +1,224 @@ +LAMMPS (3 Nov 2022) +# The intention is to find the average position of one wall at atmospheric +# pressure. The output is the wall position over time which can be used to +# find the average position for a run with fixed wall position. +# +# ----------------- Init Section ----------------- + +atom_style full +units real +boundary p p f +kspace_style pppm/electrode 1e-4 +kspace_modify slab 3.0 +pair_style lj/cut/coul/long 8 8 +bond_style harmonic +angle_style harmonic +if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2" +processors * * 2 + +# ----------------- Atom Definition Section ----------------- + +read_data "data.piston" +Reading data file ... + orthogonal box = (0 0 0) to (17.6494 20.3798 26) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 726 atoms + reading velocities ... + 726 velocities + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 420 bonds + reading angles ... + 210 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.017 seconds + +# ----------------- Settings Section ----------------- + +pair_coeff 1 1 0.069 2.78 +pair_coeff 2 2 5.29 2.951 +pair_coeff 3 3 0.1553 3.166 +pair_coeff 4 4 0.0 0.0 +bond_coeff 1 600.0 1.0 +angle_coeff 1 75.0 109.47 +group wall type 1 +48 atoms in group wall +group gold type 2 +48 atoms in group gold +group spce type 3:4 +630 atoms in group spce +group ele union wall gold +96 atoms in group ele +fix fRattleSPCE spce shake 0.0001 10 0 b 1 a 1 +Finding SHAKE clusters ... + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 210 = # of frozen angles + find clusters CPU = 0.002 seconds +pair_modify mix arithmetic + +# ----------------- Run Section ----------------- + +neigh_modify every 1 delay 0 +timestep 2 +fix fxnvt spce nvt temp 300 300 500 +fix fxforce_au gold setforce 0.0 0.0 0.0 + +# equilibrate z-coordinate of upper electrode while keeping the electrode rigid +fix fxforce_wa wall setforce 0.0 0.0 NULL +fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p +fix fxdrag wall viscous 100 +fix fxrigid wall rigid/nve single + 1 rigid bodies with 48 atoms + +# maintain constant potential during equilibration +# 'algo cg' allows for moving electrodes +fix fxele ele electrode/conp 0.0 1.805 symm on algo cg 1e-4 +96 atoms in group conp_group + +# setup output and run +variable q atom q +compute qwa wall reduce sum v_q +compute qau gold reduce sum v_q +variable top_wall equal (bound(wall,zmin)) +compute temp_mobile spce temp +variable s equal step +fix fxprint all print 1000 "${s} ${top_wall}" file top_wall.csv screen no +thermo_style custom step c_temp_mobile c_qwa c_qau v_top_wall +thermo 5000 +run 100000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +PPPM/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.32814871 + grid = 12 15 36 + stencil order = 5 + estimated absolute RMS force accuracy = 0.02930901 + estimated relative force accuracy = 8.8263214e-05 + using double precision MKL FFT + 3d grid and FFT values/proc = 8512 2880 +Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 4 5 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix electrode/conp, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 10.06 | 10.22 | 10.41 Mbytes + Step c_temp_mobile c_qwa c_qau v_top_wall + 0 303.38967 -0.042963484 0.042963484 21.4018 + 5000 292.03027 -0.19040435 0.19040435 24.581338 + 10000 309.52764 -0.48308301 0.48308301 23.776985 + 15000 295.00243 -0.16591109 0.16591109 23.672038 + 20000 293.5536 -0.086669084 0.086669084 23.426455 + 25000 303.0079 -0.16488112 0.16488112 23.862966 + 30000 306.31463 -0.23192653 0.23192653 23.819882 + 35000 303.66268 -0.2317907 0.2317907 23.495344 + 40000 301.39435 -0.34661329 0.34661329 23.657835 + 45000 291.61205 -0.30539427 0.30539427 23.437303 + 50000 298.65319 -0.096107034 0.096107034 23.57809 + 55000 282.65069 -0.14943539 0.14943539 23.823728 + 60000 310.64182 -0.17418813 0.17418813 23.286959 + 65000 308.47141 -0.02075662 0.02075662 23.91313 + 70000 292.5186 -0.080163162 0.080163162 23.96283 + 75000 270.13928 -0.029528648 0.029528648 23.488972 + 80000 322.10914 0.030761045 -0.030761045 23.47592 + 85000 310.60347 -0.24069996 0.24069996 23.987091 + 90000 294.35695 -0.070458235 0.070458235 23.397929 + 95000 308.69043 -0.2652581 0.2652581 23.473813 + 100000 318.71883 0.024035956 -0.024035956 23.449863 +Loop time of 590.232 on 4 procs for 100000 steps with 726 atoms + +Performance: 29.277 ns/day, 0.820 hours/ns, 169.425 timesteps/s, 123.003 katom-step/s +72.5% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 57.391 | 75.867 | 96.292 | 212.1 | 12.85 +Bond | 0.10177 | 0.11042 | 0.12415 | 2.7 | 0.02 +Kspace | 102.79 | 123.16 | 141.5 | 165.7 | 20.87 +Neigh | 12.808 | 12.895 | 12.982 | 2.3 | 2.18 +Comm | 18.885 | 19.973 | 21.064 | 24.0 | 3.38 +Output | 0.0022573 | 0.0022749 | 0.0023225 | 0.1 | 0.00 +Modify | 355.89 | 356.74 | 357.61 | 4.2 | 60.44 +Other | | 1.478 | | | 0.25 + +Nlocal: 181.5 ave 207 max 169 min +Histogram: 2 0 1 0 0 0 0 0 0 1 +Nghost: 1961.5 ave 1984 max 1926 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +Neighs: 30051 ave 41646 max 20775 min +Histogram: 1 1 0 0 0 0 1 0 0 1 + +Total # of neighbors = 120204 +Ave neighs/atom = 165.57025 +Ave special neighs/atom = 1.7355372 +Neighbor list builds = 7663 +Dangerous builds = 0 +write_data "data.piston.final" +System init for write_data ... +PPPM/electrode initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.32814871 + grid = 12 15 36 + stencil order = 5 + estimated absolute RMS force accuracy = 0.029311028 + estimated relative force accuracy = 8.8269289e-05 + using double precision MKL FFT + 3d grid and FFT values/proc = 8512 2880 +Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule + +Average conjugate gradient steps: 1.982 +Total wall time: 0:09:50 diff --git a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew2d.g++.1 b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew2d.g++.1 similarity index 76% rename from examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew2d.g++.1 rename to examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew2d.g++.1 index b01114e64c..bc2cf5b1e3 100644 --- a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew2d.g++.1 +++ b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew2d.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) boundary p p f kspace_style ewald/electrode 1.0e-7 kspace_modify slab ew2d @@ -28,8 +28,8 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.006 seconds + special bonds CPU = 0.001 seconds + read_data CPU = 0.005 seconds group bot molecule 1 144 atoms in group bot @@ -67,6 +67,24 @@ thermo 1 thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev run 10 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Ewald/electrode initialization ... WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327) @@ -76,9 +94,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327 estimated relative force accuracy = 1.2145309e-07 KSpace vectors: actual max1d max3d = 90 5 665 kxmax kymax kzmax = 3 3 5 - generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16 ghost atom cutoff = 16 @@ -94,7 +112,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 15.93 | 15.93 | 15.93 Mbytes +Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.94 | 15.94 Mbytes Step v_v c_qbot c_qtop v_qtheory v_percdev 0 0 0 0 0 0 1 0.2 -0.030920491 0.030920491 0.031376826 -1.4543703 @@ -107,22 +125,22 @@ Per MPI rank memory allocation (min/avg/max) = 15.93 | 15.93 | 15.93 Mbytes 8 1.6 -0.24736393 0.24736393 0.25101461 -1.4543704 9 1.8 -0.27828442 0.27828442 0.28239144 -1.4543704 10 2 -0.30920491 0.30920491 0.31376826 -1.4543704 -Loop time of 0.0912872 on 1 procs for 10 steps with 288 atoms +Loop time of 0.0451804 on 1 procs for 10 steps with 288 atoms -Performance: 9.465 ns/day, 2.536 hours/ns, 109.544 timesteps/s -400.1% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 19.123 ns/day, 1.255 hours/ns, 221.335 timesteps/s, 63.744 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0086713 | 0.0086713 | 0.0086713 | 0.0 | 9.50 -Bond | 3.759e-06 | 3.759e-06 | 3.759e-06 | 0.0 | 0.00 -Kspace | 0.04575 | 0.04575 | 0.04575 | 0.0 | 50.12 +Pair | 0.0046814 | 0.0046814 | 0.0046814 | 0.0 | 10.36 +Bond | 1.293e-06 | 1.293e-06 | 1.293e-06 | 0.0 | 0.00 +Kspace | 0.028302 | 0.028302 | 0.028302 | 0.0 | 62.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00018224 | 0.00018224 | 0.00018224 | 0.0 | 0.20 -Output | 0.0027569 | 0.0027569 | 0.0027569 | 0.0 | 3.02 -Modify | 0.03386 | 0.03386 | 0.03386 | 0.0 | 37.09 -Other | | 6.314e-05 | | | 0.07 +Comm | 7.3611e-05 | 7.3611e-05 | 7.3611e-05 | 0.0 | 0.16 +Output | 0.001128 | 0.001128 | 0.001128 | 0.0 | 2.50 +Modify | 0.010919 | 0.010919 | 0.010919 | 0.0 | 24.17 +Other | | 7.567e-05 | | | 0.17 Nlocal: 288 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew2d.g++.4 b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew2d.g++.4 similarity index 76% rename from examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew2d.g++.4 rename to examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew2d.g++.4 index 29a0d660a1..b5243e747c 100644 --- a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew2d.g++.4 +++ b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew2d.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) boundary p p f kspace_style ewald/electrode 1.0e-7 kspace_modify slab ew2d @@ -29,8 +29,8 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.008 seconds + special bonds CPU = 0.003 seconds + read_data CPU = 0.009 seconds group bot molecule 1 144 atoms in group bot @@ -68,6 +68,24 @@ thermo 1 thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev run 10 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Ewald/electrode initialization ... WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327) @@ -77,9 +95,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327 estimated relative force accuracy = 1.2145309e-07 KSpace vectors: actual max1d max3d = 90 5 665 kxmax kymax kzmax = 3 3 5 - generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16 ghost atom cutoff = 16 @@ -95,7 +113,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 15.96 | 15.96 | 15.96 Mbytes +Per MPI rank memory allocation (min/avg/max) = 15.97 | 15.97 | 15.97 Mbytes Step v_v c_qbot c_qtop v_qtheory v_percdev 0 0 0 0 0 0 1 0.2 -0.030920491 0.030920491 0.031376826 -1.4543703 @@ -108,22 +126,22 @@ Per MPI rank memory allocation (min/avg/max) = 15.96 | 15.96 | 15.96 Mbytes 8 1.6 -0.24736393 0.24736393 0.25101461 -1.4543704 9 1.8 -0.27828442 0.27828442 0.28239144 -1.4543704 10 2 -0.30920491 0.30920491 0.31376826 -1.4543704 -Loop time of 0.0456609 on 4 procs for 10 steps with 288 atoms +Loop time of 0.022489 on 4 procs for 10 steps with 288 atoms -Performance: 18.922 ns/day, 1.268 hours/ns, 219.006 timesteps/s -86.7% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 38.419 ns/day, 0.625 hours/ns, 444.661 timesteps/s, 128.062 katom-step/s +91.6% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0019389 | 0.0024013 | 0.0030807 | 0.9 | 5.26 -Bond | 1.493e-06 | 1.7132e-06 | 1.935e-06 | 0.0 | 0.00 -Kspace | 0.016165 | 0.016695 | 0.017072 | 0.3 | 36.56 +Pair | 0.0011688 | 0.0013694 | 0.0016077 | 0.4 | 6.09 +Bond | 6.72e-07 | 7.59e-07 | 9.02e-07 | 0.0 | 0.00 +Kspace | 0.0077542 | 0.0093901 | 0.010384 | 1.0 | 41.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0030891 | 0.0037595 | 0.0040145 | 0.6 | 8.23 -Output | 0.0024177 | 0.0027885 | 0.0037099 | 1.0 | 6.11 -Modify | 0.01944 | 0.019746 | 0.020327 | 0.2 | 43.24 -Other | | 0.0002691 | | | 0.59 +Comm | 0.0015392 | 0.0016945 | 0.00183 | 0.3 | 7.53 +Output | 0.00084374 | 0.0010929 | 0.0015437 | 0.8 | 4.86 +Modify | 0.007495 | 0.0084669 | 0.010081 | 1.1 | 37.65 +Other | | 0.0004745 | | | 2.11 Nlocal: 72 ave 72 max 72 min Histogram: 4 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew3dc.g++.1 b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew3dc.g++.1 similarity index 76% rename from examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew3dc.g++.1 rename to examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew3dc.g++.1 index d5292ad6ef..bebd5aed4a 100644 --- a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew3dc.g++.1 +++ b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew3dc.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) boundary p p f kspace_style ewald/electrode 1.0e-7 kspace_modify slab 3.0 # ew3dc @@ -28,8 +28,8 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.007 seconds + special bonds CPU = 0.001 seconds + read_data CPU = 0.004 seconds group bot molecule 1 144 atoms in group bot @@ -67,6 +67,24 @@ thermo 1 thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev run 10 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Ewald/electrode initialization ... WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327) @@ -76,9 +94,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327 estimated relative force accuracy = 9.3919471e-08 KSpace vectors: actual max1d max3d = 266 12 7812 kxmax kymax kzmax = 3 3 12 - generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16 ghost atom cutoff = 16 @@ -94,7 +112,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 27.27 | 27.27 | 27.27 Mbytes +Per MPI rank memory allocation (min/avg/max) = 27.29 | 27.29 | 27.29 Mbytes Step v_v c_qbot c_qtop v_qtheory v_percdev 0 0 0 0 0 0 1 0.2 -0.030925182 0.030925182 0.031376826 -1.4394194 @@ -107,22 +125,22 @@ Per MPI rank memory allocation (min/avg/max) = 27.27 | 27.27 | 27.27 Mbytes 8 1.6 -0.24740146 0.24740146 0.25101461 -1.4394195 9 1.8 -0.27832664 0.27832664 0.28239144 -1.4394195 10 2 -0.30925182 0.30925182 0.31376826 -1.4394195 -Loop time of 0.0672288 on 1 procs for 10 steps with 288 atoms +Loop time of 0.0243868 on 1 procs for 10 steps with 288 atoms -Performance: 12.852 ns/day, 1.867 hours/ns, 148.746 timesteps/s -400.4% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 35.429 ns/day, 0.677 hours/ns, 410.058 timesteps/s, 118.097 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0071442 | 0.0071442 | 0.0071442 | 0.0 | 10.63 -Bond | 2.976e-06 | 2.976e-06 | 2.976e-06 | 0.0 | 0.00 -Kspace | 0.0097903 | 0.0097903 | 0.0097903 | 0.0 | 14.56 +Pair | 0.0041504 | 0.0041504 | 0.0041504 | 0.0 | 17.02 +Bond | 8.92e-07 | 8.92e-07 | 8.92e-07 | 0.0 | 0.00 +Kspace | 0.0046942 | 0.0046942 | 0.0046942 | 0.0 | 19.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00023514 | 0.00023514 | 0.00023514 | 0.0 | 0.35 -Output | 0.0029795 | 0.0029795 | 0.0029795 | 0.0 | 4.43 -Modify | 0.047009 | 0.047009 | 0.047009 | 0.0 | 69.92 -Other | | 6.809e-05 | | | 0.10 +Comm | 6.7942e-05 | 6.7942e-05 | 6.7942e-05 | 0.0 | 0.28 +Output | 0.0010799 | 0.0010799 | 0.0010799 | 0.0 | 4.43 +Modify | 0.014311 | 0.014311 | 0.014311 | 0.0 | 58.69 +Other | | 8.199e-05 | | | 0.34 Nlocal: 288 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew3dc.g++.4 b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew3dc.g++.4 similarity index 76% rename from examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew3dc.g++.4 rename to examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew3dc.g++.4 index 92c5bf3cea..9899edc256 100644 --- a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew3dc.g++.4 +++ b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew3dc.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) boundary p p f kspace_style ewald/electrode 1.0e-7 kspace_modify slab 3.0 # ew3dc @@ -29,8 +29,8 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors - special bonds CPU = 0.008 seconds - read_data CPU = 0.123 seconds + special bonds CPU = 0.003 seconds + read_data CPU = 0.007 seconds group bot molecule 1 144 atoms in group bot @@ -68,6 +68,24 @@ thermo 1 thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev run 10 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Ewald/electrode initialization ... WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327) @@ -77,9 +95,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327 estimated relative force accuracy = 9.3919471e-08 KSpace vectors: actual max1d max3d = 266 12 7812 kxmax kymax kzmax = 3 3 12 - generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16 ghost atom cutoff = 16 @@ -95,7 +113,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 27.31 | 27.31 | 27.31 Mbytes +Per MPI rank memory allocation (min/avg/max) = 27.32 | 27.32 | 27.32 Mbytes Step v_v c_qbot c_qtop v_qtheory v_percdev 0 0 0 0 0 0 1 0.2 -0.030925182 0.030925182 0.031376826 -1.4394194 @@ -108,22 +126,22 @@ Per MPI rank memory allocation (min/avg/max) = 27.31 | 27.31 | 27.31 Mbytes 8 1.6 -0.24740146 0.24740146 0.25101461 -1.4394195 9 1.8 -0.27832664 0.27832664 0.28239144 -1.4394195 10 2 -0.30925182 0.30925182 0.31376826 -1.4394195 -Loop time of 0.0459561 on 4 procs for 10 steps with 288 atoms +Loop time of 0.0200123 on 4 procs for 10 steps with 288 atoms -Performance: 18.801 ns/day, 1.277 hours/ns, 217.599 timesteps/s -95.8% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 43.173 ns/day, 0.556 hours/ns, 499.692 timesteps/s, 143.911 katom-step/s +90.2% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0021527 | 0.0026891 | 0.0037845 | 1.3 | 5.85 -Bond | 1.303e-06 | 1.9462e-06 | 3.206e-06 | 0.0 | 0.00 -Kspace | 0.0066254 | 0.0077509 | 0.0083577 | 0.8 | 16.87 +Pair | 0.0014059 | 0.0015013 | 0.0015856 | 0.2 | 7.50 +Bond | 7.12e-07 | 8.9675e-07 | 1.19e-06 | 0.0 | 0.00 +Kspace | 0.0036091 | 0.0037586 | 0.0039024 | 0.2 | 18.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00285 | 0.0057275 | 0.0067088 | 2.2 | 12.46 -Output | 0.0024325 | 0.0034682 | 0.0065316 | 3.0 | 7.55 -Modify | 0.025911 | 0.025969 | 0.026007 | 0.0 | 56.51 -Other | | 0.0003494 | | | 0.76 +Comm | 0.0017095 | 0.0017404 | 0.001775 | 0.1 | 8.70 +Output | 0.00092975 | 0.0010846 | 0.0015398 | 0.8 | 5.42 +Modify | 0.011292 | 0.011375 | 0.011438 | 0.1 | 56.84 +Other | | 0.0005509 | | | 2.75 Nlocal: 72 ave 72 max 72 min Histogram: 4 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ffield.g++.1 b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ffield.g++.1 similarity index 77% rename from examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ffield.g++.1 rename to examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ffield.g++.1 index b0172323a3..3ea9920c7c 100644 --- a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ffield.g++.1 +++ b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ffield.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) boundary p p p # finite field, fully periodic kspace_style ewald/electrode 1.0e-7 @@ -28,7 +28,7 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-4 neighbors 1 = max # of special neighbors special bonds CPU = 0.001 seconds - read_data CPU = 0.010 seconds + read_data CPU = 0.004 seconds group bot molecule 1 144 atoms in group bot @@ -66,6 +66,24 @@ thermo 1 thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev run 10 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Ewald/electrode initialization ... WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327) @@ -75,9 +93,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327 estimated relative force accuracy = 1.2145309e-07 KSpace vectors: actual max1d max3d = 95 5 665 kxmax kymax kzmax = 3 3 5 - generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16 ghost atom cutoff = 16 @@ -93,7 +111,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 16.01 | 16.01 | 16.01 Mbytes +Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.02 | 16.02 Mbytes Step v_v c_qbot c_qtop v_qtheory v_percdev 0 0 0 0 0 0 1 0.2 -0.030908718 0.030908718 0.031376826 -1.491893 @@ -106,22 +124,22 @@ Per MPI rank memory allocation (min/avg/max) = 16.01 | 16.01 | 16.01 Mbytes 8 1.6 -0.24726974 0.24726974 0.25101461 -1.491893 9 1.8 -0.27817846 0.27817846 0.28239144 -1.491893 10 2 -0.30908718 0.30908718 0.31376826 -1.491893 -Loop time of 0.0481838 on 1 procs for 10 steps with 288 atoms +Loop time of 0.0147727 on 1 procs for 10 steps with 288 atoms -Performance: 17.931 ns/day, 1.338 hours/ns, 207.539 timesteps/s -390.7% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 58.486 ns/day, 0.410 hours/ns, 676.926 timesteps/s, 194.955 katom-step/s +75.1% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0071719 | 0.0071719 | 0.0071719 | 0.0 | 14.88 -Bond | 2.946e-06 | 2.946e-06 | 2.946e-06 | 0.0 | 0.01 -Kspace | 0.0038758 | 0.0038758 | 0.0038758 | 0.0 | 8.04 +Pair | 0.0035163 | 0.0035163 | 0.0035163 | 0.0 | 23.80 +Bond | 9.61e-07 | 9.61e-07 | 9.61e-07 | 0.0 | 0.01 +Kspace | 0.0018156 | 0.0018156 | 0.0018156 | 0.0 | 12.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00053561 | 0.00053561 | 0.00053561 | 0.0 | 1.11 -Output | 0.0025385 | 0.0025385 | 0.0025385 | 0.0 | 5.27 -Modify | 0.033951 | 0.033951 | 0.033951 | 0.0 | 70.46 -Other | | 0.0001075 | | | 0.22 +Comm | 0.00012717 | 0.00012717 | 0.00012717 | 0.0 | 0.86 +Output | 0.00083495 | 0.00083495 | 0.00083495 | 0.0 | 5.65 +Modify | 0.0083949 | 0.0083949 | 0.0083949 | 0.0 | 56.83 +Other | | 8.273e-05 | | | 0.56 Nlocal: 288 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ffield.g++.4 b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ffield.g++.4 similarity index 76% rename from examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ffield.g++.4 rename to examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ffield.g++.4 index b1ee1bec45..ef9c212755 100644 --- a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ffield.g++.4 +++ b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ffield.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) boundary p p p # finite field, fully periodic kspace_style ewald/electrode 1.0e-7 @@ -28,8 +28,8 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.026 seconds + special bonds CPU = 0.002 seconds + read_data CPU = 0.006 seconds group bot molecule 1 144 atoms in group bot @@ -67,6 +67,24 @@ thermo 1 thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev run 10 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Ewald/electrode initialization ... WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327) @@ -76,9 +94,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327 estimated relative force accuracy = 1.2145309e-07 KSpace vectors: actual max1d max3d = 95 5 665 kxmax kymax kzmax = 3 3 5 - generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16 ghost atom cutoff = 16 @@ -94,7 +112,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 15.97 | 15.97 | 15.97 Mbytes +Per MPI rank memory allocation (min/avg/max) = 15.98 | 15.98 | 15.98 Mbytes Step v_v c_qbot c_qtop v_qtheory v_percdev 0 0 0 0 0 0 1 0.2 -0.030908718 0.030908718 0.031376826 -1.491893 @@ -107,22 +125,22 @@ Per MPI rank memory allocation (min/avg/max) = 15.97 | 15.97 | 15.97 Mbytes 8 1.6 -0.24726974 0.24726974 0.25101461 -1.491893 9 1.8 -0.27817846 0.27817846 0.28239144 -1.491893 10 2 -0.30908718 0.30908718 0.31376826 -1.491893 -Loop time of 0.0294825 on 4 procs for 10 steps with 288 atoms +Loop time of 0.0151333 on 4 procs for 10 steps with 288 atoms -Performance: 29.306 ns/day, 0.819 hours/ns, 339.184 timesteps/s -99.8% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 57.093 ns/day, 0.420 hours/ns, 660.794 timesteps/s, 190.309 katom-step/s +41.1% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0020718 | 0.0025674 | 0.0029431 | 0.7 | 8.71 -Bond | 1.423e-06 | 2.0293e-06 | 2.615e-06 | 0.0 | 0.01 -Kspace | 0.0028016 | 0.0031772 | 0.0035529 | 0.5 | 10.78 +Pair | 0.0014606 | 0.0015586 | 0.0016093 | 0.1 | 10.30 +Bond | 9.31e-07 | 1.0197e-06 | 1.084e-06 | 0.0 | 0.01 +Kspace | 0.0014157 | 0.0015231 | 0.0016295 | 0.2 | 10.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0023552 | 0.0032209 | 0.0035502 | 0.9 | 10.92 -Output | 0.0011969 | 0.0016057 | 0.002676 | 1.5 | 5.45 -Modify | 0.018358 | 0.018553 | 0.018654 | 0.1 | 62.93 -Other | | 0.0003563 | | | 1.21 +Comm | 0.0019994 | 0.0020111 | 0.0020282 | 0.0 | 13.29 +Output | 0.00072893 | 0.00095378 | 0.0015177 | 0.0 | 6.30 +Modify | 0.0081934 | 0.0082729 | 0.0083794 | 0.1 | 54.67 +Other | | 0.0008128 | | | 5.37 Nlocal: 72 ave 72 max 72 min Histogram: 4 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ew3dc.g++.1 b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ew3dc.g++.1 similarity index 73% rename from examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ew3dc.g++.1 rename to examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ew3dc.g++.1 index ff0ae7698a..2e5d18d09c 100644 --- a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ew3dc.g++.1 +++ b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ew3dc.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) boundary p p f kspace_style pppm/electrode 1.0e-7 kspace_modify slab 3.0 @@ -28,8 +28,8 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.007 seconds + special bonds CPU = 0.001 seconds + read_data CPU = 0.004 seconds group bot molecule 1 144 atoms in group bot @@ -67,6 +67,35 @@ thermo 1 thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev run 10 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) PPPM/electrode initialization ... WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327) @@ -78,9 +107,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327 estimated relative force accuracy = 8.4221827e-08 using double precision MKL FFT 3d grid and FFT values/proc = 4563 1600 - generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16 ghost atom cutoff = 16 @@ -97,7 +126,7 @@ Neighbor list info ... stencil: none bin: none WARNING: Using kspace solver on system with no charge (src/kspace.cpp:314) -Per MPI rank memory allocation (min/avg/max) = 7.93 | 7.93 | 7.93 Mbytes +Per MPI rank memory allocation (min/avg/max) = 7.942 | 7.942 | 7.942 Mbytes Step v_v c_qbot c_qtop v_qtheory v_percdev 0 0 0 0 0 0 1 0.2 -0.030912769 0.030912769 0.031376826 -1.4789807 @@ -110,22 +139,22 @@ Per MPI rank memory allocation (min/avg/max) = 7.93 | 7.93 | 7.93 Mbytes 8 1.6 -0.24730215 0.24730215 0.25101461 -1.4789807 9 1.8 -0.27821492 0.27821492 0.28239144 -1.4789807 10 2 -0.30912769 0.30912769 0.31376826 -1.4789807 -Loop time of 0.0784857 on 1 procs for 10 steps with 288 atoms +Loop time of 0.0176221 on 1 procs for 10 steps with 288 atoms -Performance: 11.008 ns/day, 2.180 hours/ns, 127.412 timesteps/s -400.0% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 49.029 ns/day, 0.490 hours/ns, 567.471 timesteps/s, 163.432 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0075859 | 0.0075859 | 0.0075859 | 0.0 | 9.67 -Bond | 2.817e-06 | 2.817e-06 | 2.817e-06 | 0.0 | 0.00 -Kspace | 0.020841 | 0.020841 | 0.020841 | 0.0 | 26.55 +Pair | 0.0051407 | 0.0051407 | 0.0051407 | 0.0 | 29.17 +Bond | 9.92e-07 | 9.92e-07 | 9.92e-07 | 0.0 | 0.01 +Kspace | 0.0029456 | 0.0029456 | 0.0029456 | 0.0 | 16.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00019415 | 0.00019415 | 0.00019415 | 0.0 | 0.25 -Output | 0.0032534 | 0.0032534 | 0.0032534 | 0.0 | 4.15 -Modify | 0.046545 | 0.046545 | 0.046545 | 0.0 | 59.30 -Other | | 6.246e-05 | | | 0.08 +Comm | 8.3497e-05 | 8.3497e-05 | 8.3497e-05 | 0.0 | 0.47 +Output | 0.0012832 | 0.0012832 | 0.0012832 | 0.0 | 7.28 +Modify | 0.0080737 | 0.0080737 | 0.0080737 | 0.0 | 45.82 +Other | | 9.442e-05 | | | 0.54 Nlocal: 288 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -140,4 +169,4 @@ Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:10 +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ew3dc.g++.4 b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ew3dc.g++.4 similarity index 73% rename from examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ew3dc.g++.4 rename to examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ew3dc.g++.4 index 4fcb219a89..69950a5859 100644 --- a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ew3dc.g++.4 +++ b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ew3dc.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) boundary p p f kspace_style pppm/electrode 1.0e-7 kspace_modify slab 3.0 @@ -29,8 +29,8 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.014 seconds + special bonds CPU = 0.003 seconds + read_data CPU = 0.007 seconds group bot molecule 1 144 atoms in group bot @@ -68,6 +68,35 @@ thermo 1 thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev run 10 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) PPPM/electrode initialization ... WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327) @@ -79,9 +108,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327 estimated relative force accuracy = 8.4221827e-08 using double precision MKL FFT 3d grid and FFT values/proc = 2691 672 - generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16 ghost atom cutoff = 16 @@ -98,7 +127,7 @@ Neighbor list info ... stencil: none bin: none WARNING: Using kspace solver on system with no charge (src/kspace.cpp:314) -Per MPI rank memory allocation (min/avg/max) = 7.716 | 7.765 | 7.814 Mbytes +Per MPI rank memory allocation (min/avg/max) = 7.725 | 7.774 | 7.823 Mbytes Step v_v c_qbot c_qtop v_qtheory v_percdev 0 0 0 0 0 0 1 0.2 -0.030912769 0.030912769 0.031376826 -1.4789807 @@ -111,22 +140,22 @@ Per MPI rank memory allocation (min/avg/max) = 7.716 | 7.765 | 7.814 Mbytes 8 1.6 -0.24730215 0.24730215 0.25101461 -1.4789807 9 1.8 -0.27821492 0.27821492 0.28239144 -1.4789807 10 2 -0.30912769 0.30912769 0.31376826 -1.4789807 -Loop time of 0.0296999 on 4 procs for 10 steps with 288 atoms +Loop time of 0.0162257 on 4 procs for 10 steps with 288 atoms -Performance: 29.091 ns/day, 0.825 hours/ns, 336.701 timesteps/s -91.5% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 53.249 ns/day, 0.451 hours/ns, 616.306 timesteps/s, 177.496 katom-step/s +50.4% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0021578 | 0.0022153 | 0.0022978 | 0.1 | 7.46 -Bond | 1.161e-06 | 1.435e-06 | 1.943e-06 | 0.0 | 0.00 -Kspace | 0.0054884 | 0.0057437 | 0.0059072 | 0.2 | 19.34 +Pair | 0.0010955 | 0.0013022 | 0.0014351 | 0.3 | 8.03 +Bond | 6.13e-07 | 7.795e-07 | 1.031e-06 | 0.0 | 0.00 +Kspace | 0.0034606 | 0.003541 | 0.0036869 | 0.2 | 21.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0015424 | 0.0025686 | 0.0031306 | 1.2 | 8.65 -Output | 0.0019229 | 0.0023315 | 0.0033526 | 1.2 | 7.85 -Modify | 0.016192 | 0.016494 | 0.016902 | 0.2 | 55.54 -Other | | 0.0003449 | | | 1.16 +Comm | 0.0015915 | 0.0017672 | 0.0019298 | 0.3 | 10.89 +Output | 0.00071528 | 0.00095256 | 0.001506 | 0.0 | 5.87 +Modify | 0.0080243 | 0.0080738 | 0.0081204 | 0.0 | 49.76 +Other | | 0.0005881 | | | 3.62 Nlocal: 72 ave 72 max 72 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -141,4 +170,4 @@ Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:03 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ffield.g++.1 b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ffield.g++.1 similarity index 73% rename from examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ffield.g++.1 rename to examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ffield.g++.1 index be13b1ca10..eb8d857fbe 100644 --- a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ffield.g++.1 +++ b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ffield.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) boundary p p p # finite field, fully periodic kspace_style pppm/electrode 1.0e-7 @@ -28,7 +28,7 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-4 neighbors 1 = max # of special neighbors special bonds CPU = 0.001 seconds - read_data CPU = 0.006 seconds + read_data CPU = 0.004 seconds group bot molecule 1 144 atoms in group bot @@ -66,6 +66,35 @@ thermo 1 thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev run 10 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) PPPM/electrode initialization ... WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327) @@ -77,9 +106,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327 estimated relative force accuracy = 5.4638319e-08 using double precision MKL FFT 3d grid and FFT values/proc = 2873 768 - generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16 ghost atom cutoff = 16 @@ -96,7 +125,7 @@ Neighbor list info ... stencil: none bin: none WARNING: Using kspace solver on system with no charge (src/kspace.cpp:314) -Per MPI rank memory allocation (min/avg/max) = 7.86 | 7.86 | 7.86 Mbytes +Per MPI rank memory allocation (min/avg/max) = 7.871 | 7.871 | 7.871 Mbytes Step v_v c_qbot c_qtop v_qtheory v_percdev 0 0 0 0 0 0 1 0.2 -0.030902 0.030902 0.031376826 -1.5133027 @@ -109,22 +138,22 @@ Per MPI rank memory allocation (min/avg/max) = 7.86 | 7.86 | 7.86 Mbytes 8 1.6 -0.247216 0.247216 0.25101461 -1.5133028 9 1.8 -0.278118 0.278118 0.28239144 -1.5133028 10 2 -0.30902 0.30902 0.31376826 -1.5133028 -Loop time of 0.054016 on 1 procs for 10 steps with 288 atoms +Loop time of 0.0150845 on 1 procs for 10 steps with 288 atoms -Performance: 15.995 ns/day, 1.500 hours/ns, 185.130 timesteps/s -400.3% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 57.277 ns/day, 0.419 hours/ns, 662.933 timesteps/s, 190.925 katom-step/s +90.5% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0081119 | 0.0081119 | 0.0081119 | 0.0 | 15.02 -Bond | 4.802e-06 | 4.802e-06 | 4.802e-06 | 0.0 | 0.01 -Kspace | 0.0053539 | 0.0053539 | 0.0053539 | 0.0 | 9.91 +Pair | 0.0052281 | 0.0052281 | 0.0052281 | 0.0 | 34.66 +Bond | 9.72e-07 | 9.72e-07 | 9.72e-07 | 0.0 | 0.01 +Kspace | 0.0017267 | 0.0017267 | 0.0017267 | 0.0 | 11.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00052577 | 0.00052577 | 0.00052577 | 0.0 | 0.97 -Output | 0.0033476 | 0.0033476 | 0.0033476 | 0.0 | 6.20 -Modify | 0.036562 | 0.036562 | 0.036562 | 0.0 | 67.69 -Other | | 0.0001102 | | | 0.20 +Comm | 0.00016423 | 0.00016423 | 0.00016423 | 0.0 | 1.09 +Output | 0.0010211 | 0.0010211 | 0.0010211 | 0.0 | 6.77 +Modify | 0.0068532 | 0.0068532 | 0.0068532 | 0.0 | 45.43 +Other | | 9.022e-05 | | | 0.60 Nlocal: 288 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -138,4 +167,4 @@ Ave neighs/atom = 92 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:09 +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ffield.g++.4 b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ffield.g++.4 similarity index 73% rename from examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ffield.g++.4 rename to examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ffield.g++.4 index 619ed2bc48..75b20bb7f2 100644 --- a/examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ffield.g++.4 +++ b/examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ffield.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Mar 2022) +LAMMPS (3 Nov 2022) boundary p p p # finite field, fully periodic kspace_style pppm/electrode 1.0e-7 @@ -28,8 +28,8 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.022 seconds + special bonds CPU = 0.002 seconds + read_data CPU = 0.006 seconds group bot molecule 1 144 atoms in group bot @@ -67,6 +67,35 @@ thermo 1 thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev run 10 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- kspace_style pppm/electrode command: + +@article{Ahrens2021, +author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0063381}, +title = {{Constant potential simulations on a mesh}}, +journal = {Journal of Chemical Physics}, +year = {2021} +volume = {155}, +pages = {104104}, +} +- fix electrode command: + +@article{Ahrens2022 +author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.}, +doi = {10.1063/5.0099239}, +title = {{ELECTRODE: An electrochemistry package for LAMMPS}}, +journal = {The Journal of Chemical Physics}, +year = {2022} +volume = {157}, +pages = {084801}, +} +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) PPPM/electrode initialization ... WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327) @@ -78,9 +107,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327 estimated relative force accuracy = 5.4638319e-08 using double precision MKL FFT 3d grid and FFT values/proc = 1287 192 - generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16 ghost atom cutoff = 16 @@ -97,7 +126,7 @@ Neighbor list info ... stencil: none bin: none WARNING: Using kspace solver on system with no charge (src/kspace.cpp:314) -Per MPI rank memory allocation (min/avg/max) = 7.712 | 7.712 | 7.712 Mbytes +Per MPI rank memory allocation (min/avg/max) = 7.721 | 7.721 | 7.721 Mbytes Step v_v c_qbot c_qtop v_qtheory v_percdev 0 0 0 0 0 0 1 0.2 -0.030902 0.030902 0.031376826 -1.5133027 @@ -110,22 +139,22 @@ Per MPI rank memory allocation (min/avg/max) = 7.712 | 7.712 | 7.712 Mbytes 8 1.6 -0.247216 0.247216 0.25101461 -1.5133028 9 1.8 -0.278118 0.278118 0.28239144 -1.5133028 10 2 -0.30902 0.30902 0.31376826 -1.5133028 -Loop time of 0.0301351 on 4 procs for 10 steps with 288 atoms +Loop time of 0.0169132 on 4 procs for 10 steps with 288 atoms -Performance: 28.671 ns/day, 0.837 hours/ns, 331.839 timesteps/s -99.8% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 51.084 ns/day, 0.470 hours/ns, 591.252 timesteps/s, 170.281 katom-step/s +49.8% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0020768 | 0.0022701 | 0.0024074 | 0.3 | 7.53 -Bond | 1.271e-06 | 2.2107e-06 | 4.237e-06 | 0.0 | 0.01 -Kspace | 0.0039171 | 0.0040631 | 0.0042468 | 0.2 | 13.48 +Pair | 0.00098343 | 0.0013515 | 0.0015461 | 0.6 | 7.99 +Bond | 6.21e-07 | 6.81e-07 | 7.3e-07 | 0.0 | 0.00 +Kspace | 0.0036673 | 0.0038144 | 0.004106 | 0.3 | 22.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0020711 | 0.0032953 | 0.0038884 | 1.3 | 10.93 -Output | 0.0013425 | 0.001877 | 0.0031692 | 1.7 | 6.23 -Modify | 0.018076 | 0.018252 | 0.018479 | 0.1 | 60.57 -Other | | 0.0003755 | | | 1.25 +Comm | 0.0015601 | 0.0016528 | 0.0017294 | 0.2 | 9.77 +Output | 0.00072013 | 0.00087465 | 0.0012429 | 0.0 | 5.17 +Modify | 0.0086712 | 0.0087641 | 0.0089049 | 0.1 | 51.82 +Other | | 0.0004551 | | | 2.69 Nlocal: 72 ave 72 max 72 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -139,4 +168,4 @@ Ave neighs/atom = 92 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:03 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/fep/CC-CO/fep01/data.0.lmp b/examples/PACKAGES/fep/CC-CO/fep01/data.0.lmp new file mode 120000 index 0000000000..5c33e53300 --- /dev/null +++ b/examples/PACKAGES/fep/CC-CO/fep01/data.0.lmp @@ -0,0 +1 @@ +../mols/data.0.lmp \ No newline at end of file diff --git a/examples/PACKAGES/fep/CC-CO/fep10/data.1.lmp b/examples/PACKAGES/fep/CC-CO/fep10/data.1.lmp new file mode 120000 index 0000000000..4222a38b76 --- /dev/null +++ b/examples/PACKAGES/fep/CC-CO/fep10/data.1.lmp @@ -0,0 +1 @@ +../mols/data.1.lmp \ No newline at end of file diff --git a/examples/PACKAGES/fep/CH4-CF4/bar01/data.0.lmp b/examples/PACKAGES/fep/CH4-CF4/bar01/data.0.lmp new file mode 120000 index 0000000000..5c33e53300 --- /dev/null +++ b/examples/PACKAGES/fep/CH4-CF4/bar01/data.0.lmp @@ -0,0 +1 @@ +../mols/data.0.lmp \ No newline at end of file diff --git a/examples/PACKAGES/fep/CH4-CF4/bar10/data.1.lmp b/examples/PACKAGES/fep/CH4-CF4/bar10/data.1.lmp new file mode 120000 index 0000000000..4222a38b76 --- /dev/null +++ b/examples/PACKAGES/fep/CH4-CF4/bar10/data.1.lmp @@ -0,0 +1 @@ +../mols/data.1.lmp \ No newline at end of file diff --git a/examples/PACKAGES/fep/CH4-CF4/fep01/data.0.lmp b/examples/PACKAGES/fep/CH4-CF4/fep01/data.0.lmp new file mode 120000 index 0000000000..5c33e53300 --- /dev/null +++ b/examples/PACKAGES/fep/CH4-CF4/fep01/data.0.lmp @@ -0,0 +1 @@ +../mols/data.0.lmp \ No newline at end of file diff --git a/examples/PACKAGES/fep/CH4-CF4/fep10/data.1.lmp b/examples/PACKAGES/fep/CH4-CF4/fep10/data.1.lmp new file mode 120000 index 0000000000..4222a38b76 --- /dev/null +++ b/examples/PACKAGES/fep/CH4-CF4/fep10/data.1.lmp @@ -0,0 +1 @@ +../mols/data.1.lmp \ No newline at end of file diff --git a/examples/PACKAGES/fep/CH4hyd/fdti01/data.lmp b/examples/PACKAGES/fep/CH4hyd/fdti01/data.lmp new file mode 120000 index 0000000000..73cccaf269 --- /dev/null +++ b/examples/PACKAGES/fep/CH4hyd/fdti01/data.lmp @@ -0,0 +1 @@ +../mols/data.lmp \ No newline at end of file diff --git a/examples/PACKAGES/fep/CH4hyd/fdti10/data.lmp b/examples/PACKAGES/fep/CH4hyd/fdti10/data.lmp new file mode 120000 index 0000000000..73cccaf269 --- /dev/null +++ b/examples/PACKAGES/fep/CH4hyd/fdti10/data.lmp @@ -0,0 +1 @@ +../mols/data.lmp \ No newline at end of file diff --git a/examples/PACKAGES/fep/CH4hyd/fep01/data.lmp b/examples/PACKAGES/fep/CH4hyd/fep01/data.lmp new file mode 120000 index 0000000000..73cccaf269 --- /dev/null +++ b/examples/PACKAGES/fep/CH4hyd/fep01/data.lmp @@ -0,0 +1 @@ +../mols/data.lmp \ No newline at end of file diff --git a/examples/PACKAGES/fep/CH4hyd/fep10/data.lmp b/examples/PACKAGES/fep/CH4hyd/fep10/data.lmp new file mode 120000 index 0000000000..73cccaf269 --- /dev/null +++ b/examples/PACKAGES/fep/CH4hyd/fep10/data.lmp @@ -0,0 +1 @@ +../mols/data.lmp \ No newline at end of file diff --git a/examples/PACKAGES/fep/SPCEhyd/fep01/data.lmp b/examples/PACKAGES/fep/SPCEhyd/fep01/data.lmp new file mode 120000 index 0000000000..73cccaf269 --- /dev/null +++ b/examples/PACKAGES/fep/SPCEhyd/fep01/data.lmp @@ -0,0 +1 @@ +../mols/data.lmp \ No newline at end of file diff --git a/examples/PACKAGES/fep/SPCEhyd/fep10/data.lmp b/examples/PACKAGES/fep/SPCEhyd/fep10/data.lmp new file mode 120000 index 0000000000..73cccaf269 --- /dev/null +++ b/examples/PACKAGES/fep/SPCEhyd/fep10/data.lmp @@ -0,0 +1 @@ +../mols/data.lmp \ No newline at end of file diff --git a/examples/PACKAGES/meam_spline/Si_1.meam.spline b/examples/PACKAGES/meam_spline/Si_1.meam.spline deleted file mode 100644 index 1ebd09cf84..0000000000 --- a/examples/PACKAGES/meam_spline/Si_1.meam.spline +++ /dev/null @@ -1,63 +0,0 @@ -DATE: 2012-02-01 CONTRIBUTOR: Alexander Stukowski, stukowski@mm.tu-darmstadt.de CITATION: Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter and Kress, Modell Simul Mater Sci Eng, 8, 825 (2000) COMMENT: Spline-based MEAM potential for Si. Reference: T. J. Lenosky, B. Sadigh, E. Alonso, V. V. Bulatov, T. D. de la Rubia, J. Kim, A. F. Voter, and J. D. Kress, Modell. Simul. Mater. Sci. Eng. 8, 825 (2000) -10 --4.266966781858503300e+01 0.000000000000000000e+00 -1 0 1 0 -1.500000000000000000e+00 6.929943430771341000e+00 1.653321602557917600e+02 -1.833333333333333300e+00 -4.399503747408950400e-01 3.941543472528634600e+01 -2.166666666666666500e+00 -1.701233725061446700e+00 6.871065423413908100e+00 -2.500000000000000000e+00 -1.624732919215791800e+00 5.340648014033163800e+00 -2.833333333333333000e+00 -9.969641728342462100e-01 1.534811309391571000e+00 -3.166666666666667000e+00 -2.739141845072665100e-01 -6.334706186546093900e+00 -3.500000000000000000e+00 -2.499156963774082700e-02 -1.798864729909626500e+00 -3.833333333333333500e+00 -1.784331481529976400e-02 4.743496636420091500e-01 -4.166666666666666100e+00 -9.612303290166881000e-03 -4.006506271304824400e-02 -4.500000000000000000e+00 0.000000000000000000e+00 -2.394996574779807200e-01 -11 --1.000000000000000000e+00 0.000000000000000000e+00 -1 0 0 0 -1.500000000000000000e+00 1.374674212682983900e-01 -3.227795813279568500e+00 -1.700000000000000000e+00 -1.483141815327918000e-01 -6.411648793604404900e+00 -1.899999999999999900e+00 -5.597204896096039700e-01 1.003068519633888300e+01 -2.100000000000000100e+00 -7.310964379372824100e-01 2.293461970618954700e+00 -2.299999999999999800e+00 -7.628287071954063000e-01 1.742018781618444500e+00 -2.500000000000000000e+00 -7.291769685066557000e-01 5.460640949384478700e-01 -2.700000000000000200e+00 -6.662022220044453400e-01 4.721760106467195500e-01 -2.899999999999999900e+00 -5.732830582550895200e-01 2.056894449546524200e+00 -3.100000000000000100e+00 -4.069014309729406300e-01 2.319615721086100800e+00 -3.299999999999999800e+00 -1.666155295956388300e-01 -2.497162196179187900e-01 -3.500000000000000000e+00 0.000000000000000000e+00 -1.237130660986393100e+01 -8 -7.351364478015182100e-01 6.165217237728655200e-01 -1 1 1 1 --1.770934559908718700e+00 -1.074925682941420000e+00 -1.482768170233858500e-01 --3.881557649503457600e-01 -2.004503493658201000e-01 -1.492100354067345500e-01 -9.946230300080272100e-01 4.142241371345077300e-01 -7.012475119623896900e-02 -2.377401824966400000e+00 8.793892953828742500e-01 -3.944355024164965900e-02 -3.760180619924772900e+00 1.266888024536562100e+00 -1.581431192239436000e-02 -5.142959414883146800e+00 1.629979548834614900e+00 2.611224310900800400e-02 -6.525738209841518900e+00 1.977379549636293600e+00 -1.378738550324104500e-01 -7.908517004799891800e+00 2.396177220616657200e+00 7.494253977092666400e-01 -10 --3.618936018538757300e+00 0.000000000000000000e+00 -1 0 1 0 -1.500000000000000000e+00 1.250311510312851300e+00 2.790400588857243500e+01 -1.722222222222222300e+00 8.682060369372680600e-01 -4.522554291731776900e+00 -1.944444444444444400e+00 6.084604017544847900e-01 5.052931618779816800e+00 -2.166666666666666500e+00 4.875624808097850400e-01 1.180825096539679600e+00 -2.388888888888888800e+00 4.416345603457190700e-01 -6.673769465415171400e-01 -2.611111111111111200e+00 3.760976313325982700e-01 -8.938118490837722000e-01 -2.833333333333333000e+00 2.714524157414608400e-01 -5.090324763524399800e-01 -3.055555555555555400e+00 1.481440300150710900e-01 6.623665830603995300e-01 -3.277777777777777700e+00 4.854596610856590900e-02 7.403702452268122700e-01 -3.500000000000000000e+00 0.000000000000000000e+00 2.578982318481970500e+00 -8 --1.395041572145673000e+01 1.134616739799360700e+00 -1 1 1 1 --1.000000000000000900e+00 5.254163992149617700e+00 1.582685381253900500e+01 --7.428367052748285900e-01 2.359149452448745100e+00 3.117611233789983400e+01 --4.856734105496561800e-01 1.195946960915646100e+00 1.658962813584905800e+01 --2.285101158244838800e-01 1.229952028074150000e+00 1.108360928564026400e+01 -2.865317890068852500e-02 2.035650777568434500e+00 9.088861456447702400e+00 -2.858164736258610400e-01 3.424741418405580000e+00 5.489943377538379500e+00 -5.429797683510331200e-01 4.948585892304984100e+00 -1.882291580187675700e+01 -8.001430630762056400e-01 5.617988713941801200e+00 -7.718625571850646200e+00 diff --git a/examples/PACKAGES/meam_spline/Si_1.meam.spline b/examples/PACKAGES/meam_spline/Si_1.meam.spline new file mode 120000 index 0000000000..579ab4941b --- /dev/null +++ b/examples/PACKAGES/meam_spline/Si_1.meam.spline @@ -0,0 +1 @@ +../../../potentials/Si_1.meam.spline \ No newline at end of file diff --git a/examples/PACKAGES/meam_spline/TiO.meam.spline b/examples/PACKAGES/meam_spline/TiO.meam.spline deleted file mode 100644 index 78db9aeabc..0000000000 --- a/examples/PACKAGES/meam_spline/TiO.meam.spline +++ /dev/null @@ -1,130 +0,0 @@ -# Ti-O cubic spline potential where O is in the dilute limit. DATE: 2016-06-05 CONTRIBUTOR: Pinchao Zhang, Dallas R. Trinkle -meam/spline 2 Ti O -spline3eq -13 --20 0 -1.742692837 3.744277175966 99.4865081627958 -2.05580176725 0.910839730906 10.8702523265355 -2.3689106975 0.388045896634 -1.55322418749562 -2.68201962775 -0.018840906533 2.43630041329215 -2.995128558 -0.248098929639 2.67912713976835 -3.30823748825 -0.264489550297 -0.125056384603077 -3.6213464185 -0.227196189283 1.10662555360438 -3.93445534875 -0.129293090176 -0.592053676745914 -4.247564279 -0.059685366933 -0.470123414607672 -4.56067320925 -0.031100025561 -0.0380739973059663 -4.8737821395 -0.013847363202 -0.0711547960695406 -5.18689106975 -0.003203412728 -0.081768292420175 -5.5 0 -0.0571422964883619 -spline3eq -5 -0.155001355787331 0 -1.9 0.533321679606674 0 -2.8 0.456402081843862 -1.60311717015859 -3.7 -0.324281383502201 1.19940299483249 -4.6 -0.474029826906675 1.47909794595154 -5.5 0 -2.49521499855605 -spline3eq -13 -0 0 -1.742692837 0 0 -2.05580176725 0 0 -2.3689106975 0 0 -2.68201962775 0 0 -2.995128558 0 0 -3.30823748825 0 0 -3.6213464185 0 0 -3.93445534875 0 0 -4.247564279 0 0 -4.56067320925 0 0 -4.8737821395 0 0 -5.18689106975 0 0 -5.5 0 0 -spline3eq -11 --1 0 -2.055801767 1.7475279661 -525.869786904802 -2.2912215903 -5.8677963945 252.796316927755 -2.5266414136 -8.3376288737 71.7318388721015 -2.7620612369 -5.8398712842 -1.93587742753693 -2.9974810602 -3.1140648231 -39.2999192667503 -3.2329008835 -1.7257245065 14.3424136002004 -3.4683207068 -0.4428977017 -29.4925534559498 -3.7037405301 -0.1466643003 -3.18010534572236 -3.9391603534 -0.2095507945 3.33490838803603 -4.1745801767 -0.1442384563 3.71918691359508 -4.41 0 -9.66717019857564 -spline3eq -5 --61.9827585211652 0 -1.9 11.2293641315584 0 -2.8 -27.9976343076148 122.648031332411 -3.7 -8.32979773113248 -54.3340881766381 -4.6 -1.00863195297399 3.23150064581724 -5.5 0 -5.3514242228123 -spline3eq -4 -0.00776934946045395 0.105197706160344 --55.14233165 -0.29745568008 0.00152870603877451 --44.7409899033333 -0.15449458722 0.00038933722543571 --34.3396481566667 0.05098657168 0.00038124926922248 --23.93830641 0.57342694704 0.0156639264890892 -spline3eq -5 --0.00676745157022662 -0.0159520381982146 --23.9928 0.297607384684645 0 --15.9241175 0.216691597077105 -0.0024248755353942 --7.855435 0.0637598673719069 0.00306245895013358 -0.213247499999998 -0.00183450621970427 -0.00177588407633909 -8.28193 -0.111277018874367 0 -spline3eq -10 -2.77327511656661 0 -2.055801767 -0.1485215264 72.2010867146919 -2.31737934844444 1.6845304918 -47.2744689053404 -2.57895692988889 2.0113365977 -15.1859578405326 -2.84053451133333 1.1444092747 3.33978204841873 -3.10211209277778 0.2861606803 2.587867603808 -3.36368967422222 -0.3459281126 6.14070694084556 -3.62526725566667 -0.6257480601 3.7397696717154 -3.88684483711111 -0.6119510826 4.64749084871402 -4.14842241855556 -0.3112059651 2.83275746415936 -4.41 0 -15.0612086827734 -spline3eq -5 -12.3315547862781 0 -1.9 2.62105440156724 0 -2.8 10.2850803058354 -25.439802988016 -3.7 3.23933763743897 -7.20203673434025 -4.6 -5.79049355858613 39.5509978688682 -5.5 0 -41.221771373642 -spline3eq -8 -8.33642274810572 -60.4024574736564 --1 0.07651409193 -110.652321293778 --0.724509054371429 0.14155824541 44.8853405500508 --0.449018108742857 0.75788697341 -25.3065115342002 --0.173527163114286 0.63011570378 -2.48510144915082 -0.101963782514286 0.09049597305 2.68769386908235 -0.377454728142857 -0.35741586657 -1.01558570129633 -0.652945673771428 -0.65293217647 13.4224786001212 -0.9284366194 -6.00912190653 -452.752542694929 -spline3eq -5 -0.137191606537625 -1.55094230968985 --1 0.0513843442016519 0 --0.5 0.0179024412245673 -2.44986494990154 -0 -0.260650876879273 3.91774583656401 -0.5 -0.190163791764901 -4.84414871911743 -1 -0.763795416646599 0 -spline3eq -8 -0 0 --1 0 0 --0.724509054371429 0 0 --0.449018108742857 0 0 --0.173527163114286 0 0 -0.101963782514286 0 0 -0.377454728142857 0 0 -0.652945673771428 0 0 -0.9284366194 0 0 diff --git a/examples/PACKAGES/meam_spline/TiO.meam.spline b/examples/PACKAGES/meam_spline/TiO.meam.spline new file mode 120000 index 0000000000..dbc2a1c059 --- /dev/null +++ b/examples/PACKAGES/meam_spline/TiO.meam.spline @@ -0,0 +1 @@ +../../../potentials/TiO.meam.spline \ No newline at end of file diff --git a/examples/PACKAGES/meam_spline/in.meam-spline.Si b/examples/PACKAGES/meam_spline/in.meam-spline.Si index 7f270ccecd..d0ca807209 100644 --- a/examples/PACKAGES/meam_spline/in.meam-spline.Si +++ b/examples/PACKAGES/meam_spline/in.meam-spline.Si @@ -1,13 +1,13 @@ # Si fcc phase -units metal -boundary p p p +units metal +boundary p p p -atom_style atomic -lattice fcc 3.98 -region box block 0 5 0 5 0 5 -create_box 1 box -create_atoms 1 box +atom_style atomic +lattice fcc 3.98 +region box block 0 5 0 5 0 5 +create_box 1 box +create_atoms 1 box pair_style meam/spline pair_coeff * * Si_1.meam.spline Si diff --git a/examples/PACKAGES/meam_spline/in.meam-spline.TiO2 b/examples/PACKAGES/meam_spline/in.meam-spline.TiO2 index 06c8b7f8cd..05e3a1ed24 100644 --- a/examples/PACKAGES/meam_spline/in.meam-spline.TiO2 +++ b/examples/PACKAGES/meam_spline/in.meam-spline.TiO2 @@ -1,4 +1,4 @@ -# +# variable T_depart equal 300 @@ -17,13 +17,13 @@ variable by equal ${a}*${ny} variable bz equal ${c}*${nz} # ======================================================================= -units metal -atom_style atomic +units metal +atom_style atomic dimension 3 boundary p p p -lattice sc 1.0 +lattice sc 1.0 region box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0 create_box 2 box_vide @@ -31,15 +31,15 @@ create_box 2 box_vide #region box_TiO2 block 0 ${bx} 0 ${by} 0 ${bz} # titanium atoms -lattice custom ${a} origin 0.0 0.0 0.0 & +lattice custom ${a} origin 0.0 0.0 0.0 & orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 & a1 1.0 0.0 0.0 & a2 0.0 1.0 0.0 & a3 0.0 0.0 ${ca} & basis 0.0 0.0 0.0 & - basis 0.5 0.5 0.5 + basis 0.5 0.5 0.5 -create_atoms 2 region box_vide +create_atoms 2 region box_vide # Oxygen atoms lattice custom ${a} origin 0.0 0.0 0.0 & @@ -49,42 +49,42 @@ lattice custom ${a} origin 0.0 0.0 0.0 & a3 0.0 0.0 ${ca} & basis 0.30478 0.30478 0.0 & basis 0.69522 0.69522 0.0 & - basis 0.19522 0.80478 0.5 & - basis 0.80478 0.19522 0.5 + basis 0.19522 0.80478 0.5 & + basis 0.80478 0.19522 0.5 + +create_atoms 1 region box_vide -create_atoms 1 region box_vide - mass 1 16.00 group Oxy type 1 -mass 2 47.867 -group Ti type 2 +mass 2 47.867 +group Ti type 2 -velocity all create ${T_depart} 277387 +velocity all create ${T_depart} 277387 -pair_style meam/spline -pair_coeff * * TiO.meam.spline O Ti +pair_style meam/spline +pair_coeff * * TiO.meam.spline O Ti -neighbor 0.5 bin -neigh_modify every 2 delay 0 check yes +neighbor 0.5 bin +neigh_modify every 2 delay 0 check yes timestep ${dt} -thermo_style custom step temp press pe ke etotal lx ly lz vol -thermo 10 +thermo_style custom step temp press pe ke etotal lx ly lz vol +thermo 10 -#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z +#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z -fix 3 all nve -run 100 +fix 3 all nve +run 100 -unfix 3 +unfix 3 fix 1 all box/relax tri 0.0 vmax 0.001 minimize 1.0e-3 1.0e-5 1000 10000 -unfix 1 +unfix 1 reset_timestep 0 thermo 50 fix 3 all npt temp 300 300 0.1 aniso 1.0 1.0 1.0 diff --git a/examples/PACKAGES/meam_spline/log.17Dec2022.meam-spline.Si.g++.1 b/examples/PACKAGES/meam_spline/log.17Dec2022.meam-spline.Si.g++.1 new file mode 100644 index 0000000000..37c24cb574 --- /dev/null +++ b/examples/PACKAGES/meam_spline/log.17Dec2022.meam-spline.Si.g++.1 @@ -0,0 +1,91 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Si fcc phase + +units metal +boundary p p p + +atom_style atomic +lattice fcc 3.98 +Lattice spacing in x,y,z = 3.98 3.98 3.98 +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (19.9 19.9 19.9) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + using lattice units in orthogonal box = (0 0 0) to (19.9 19.9 19.9) + create_atoms CPU = 0.000 seconds + +pair_style meam/spline +pair_coeff * * Si_1.meam.spline Si +Reading meam/spline potential file Si_1.meam.spline with DATE: 2012-02-01 +mass * 28.085 + +velocity all create 500.0 44226611 + +fix 1 all nvt temp 500.0 500.0 1.0 + +thermo 50 +run 500 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.5 + ghost atom cutoff = 6.5 + binsize = 3.25, bins = 7 7 7 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.902 | 3.902 | 3.902 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 500 -1847.729 0 -1815.4786 1813162.7 + 50 1934.0932 -1940.8016 0 -1816.051 -48657.676 + 100 2570.1286 -1984.8725 0 -1819.0971 8002.4248 + 150 2566.7917 -1990.2724 0 -1824.7123 16819.447 + 200 2555.1319 -1995.2233 0 -1830.4152 5891.5313 + 250 2487.2881 -1995.8302 0 -1835.3981 -4339.7172 + 300 2381.4836 -1994.2492 0 -1840.6415 16508.04 + 350 2330.8663 -1996.6588 0 -1846.3161 24194.447 + 400 2212.6035 -1994.9278 0 -1852.2131 -9856.3709 + 450 2257.7531 -2003.8187 0 -1858.1918 -8029.6019 + 500 2211.4385 -2006.9846 0 -1864.345 4152.4867 +Loop time of 3.06076 on 1 procs for 500 steps with 500 atoms + +Performance: 14.114 ns/day, 1.700 hours/ns, 163.358 timesteps/s, 81.679 katom-step/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.03 | 3.03 | 3.03 | 0.0 | 99.00 +Neigh | 0.020755 | 0.020755 | 0.020755 | 0.0 | 0.68 +Comm | 0.0045293 | 0.0045293 | 0.0045293 | 0.0 | 0.15 +Output | 0.00020334 | 0.00020334 | 0.00020334 | 0.0 | 0.01 +Modify | 0.0038919 | 0.0038919 | 0.0038919 | 0.0 | 0.13 +Other | | 0.001352 | | | 0.04 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1767 ave 1767 max 1767 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18059 ave 18059 max 18059 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 36118 ave 36118 max 36118 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 36118 +Ave neighs/atom = 72.236 +Neighbor list builds = 14 +Dangerous builds = 0 + +Total wall time: 0:00:03 diff --git a/examples/PACKAGES/meam_spline/log.17Dec2022.meam-spline.Si.g++.4 b/examples/PACKAGES/meam_spline/log.17Dec2022.meam-spline.Si.g++.4 new file mode 100644 index 0000000000..23edd44d4b --- /dev/null +++ b/examples/PACKAGES/meam_spline/log.17Dec2022.meam-spline.Si.g++.4 @@ -0,0 +1,91 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Si fcc phase + +units metal +boundary p p p + +atom_style atomic +lattice fcc 3.98 +Lattice spacing in x,y,z = 3.98 3.98 3.98 +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (19.9 19.9 19.9) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + using lattice units in orthogonal box = (0 0 0) to (19.9 19.9 19.9) + create_atoms CPU = 0.000 seconds + +pair_style meam/spline +pair_coeff * * Si_1.meam.spline Si +Reading meam/spline potential file Si_1.meam.spline with DATE: 2012-02-01 +mass * 28.085 + +velocity all create 500.0 44226611 + +fix 1 all nvt temp 500.0 500.0 1.0 + +thermo 50 +run 500 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.5 + ghost atom cutoff = 6.5 + binsize = 3.25, bins = 7 7 7 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.866 | 3.866 | 3.866 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 500 -1847.729 0 -1815.4786 1813162.7 + 50 1923.4262 -1940.0936 0 -1816.0311 -38700.835 + 100 2535.2542 -1982.6249 0 -1819.0989 10216.821 + 150 2592.8247 -1992.1569 0 -1824.9176 4839.3385 + 200 2484.7391 -1990.8452 0 -1830.5775 14040.141 + 250 2597.4401 -2003.1619 0 -1835.625 1261.5199 + 300 2513.0793 -2002.942 0 -1840.8463 6690.9815 + 350 2390.933 -2001.0761 0 -1846.859 -4880.1146 + 400 2269.0782 -1999.3441 0 -1852.9867 -4921.4391 + 450 2287.5096 -2006.8236 0 -1859.2774 -7313.6151 + 500 2303.0918 -2014.0693 0 -1865.518 -9995.1789 +Loop time of 0.845261 on 4 procs for 500 steps with 500 atoms + +Performance: 51.108 ns/day, 0.470 hours/ns, 591.533 timesteps/s, 295.767 katom-step/s +99.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.82311 | 0.82403 | 0.82556 | 0.1 | 97.49 +Neigh | 0.0054304 | 0.0055826 | 0.0058949 | 0.2 | 0.66 +Comm | 0.0095108 | 0.011321 | 0.012448 | 1.0 | 1.34 +Output | 0.00019703 | 0.0002108 | 0.00024574 | 0.0 | 0.02 +Modify | 0.0026442 | 0.002759 | 0.0028243 | 0.1 | 0.33 +Other | | 0.001353 | | | 0.16 + +Nlocal: 125 ave 131 max 118 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Nghost: 979.25 ave 986 max 975 min +Histogram: 1 1 0 1 0 0 0 0 0 1 +Neighs: 4541.75 ave 4712 max 4362 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +FullNghs: 9083.5 ave 9485 max 8601 min +Histogram: 1 0 0 1 0 0 0 0 1 1 + +Total # of neighbors = 36334 +Ave neighs/atom = 72.668 +Neighbor list builds = 14 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_spline/log.17Dec2022.meam-spline.TiO2.g++.1 b/examples/PACKAGES/meam_spline/log.17Dec2022.meam-spline.TiO2.g++.1 new file mode 100644 index 0000000000..5a96bb3d98 --- /dev/null +++ b/examples/PACKAGES/meam_spline/log.17Dec2022.meam-spline.TiO2.g++.1 @@ -0,0 +1,253 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# + +variable T_depart equal 300 + +variable dt equal 0.0002 + +variable a equal 4.5937 +variable c equal 2.9587 +variable ca equal ${c}/${a} +variable ca equal 2.9587/${a} +variable ca equal 2.9587/4.5937 + +variable nx equal 6 +variable ny equal 6 +variable nz equal 11 + +variable bx equal ${a}*${nx} +variable bx equal 4.5937*${nx} +variable bx equal 4.5937*6 +variable by equal ${a}*${ny} +variable by equal 4.5937*${ny} +variable by equal 4.5937*6 +variable bz equal ${c}*${nz} +variable bz equal 2.9587*${nz} +variable bz equal 2.9587*11 +# ======================================================================= + +units metal +atom_style atomic +dimension 3 +boundary p p p + + +lattice sc 1.0 +Lattice spacing in x,y,z = 1 1 1 +region box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0 +region box_vide prism 0 27.5622 0 ${by} 0 ${bz} 0.0 0.0 0.0 +region box_vide prism 0 27.5622 0 27.5622 0 ${bz} 0.0 0.0 0.0 +region box_vide prism 0 27.5622 0 27.5622 0 32.5457 0.0 0.0 0.0 +create_box 2 box_vide +Created triclinic box = (0 0 0) to (27.5622 27.5622 32.5457) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid + +#lattice sc 1.0 +#region box_TiO2 block 0 ${bx} 0 ${by} 0 ${bz} + +# titanium atoms +lattice custom ${a} origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.0 0.0 0.0 basis 0.5 0.5 0.5 +lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.0 0.0 0.0 basis 0.5 0.5 0.5 +lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.644077758669482 basis 0.0 0.0 0.0 basis 0.5 0.5 0.5 +Lattice spacing in x,y,z = 4.5937 4.5937 2.9587 + +create_atoms 2 region box_vide +Created 792 atoms + using lattice units in triclinic box = (0 0 0) to (27.5622 27.5622 32.5457) with tilt (0 0 0) + create_atoms CPU = 0.000 seconds + +# Oxygen atoms +lattice custom ${a} origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5 +lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5 +lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.644077758669482 basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5 +Lattice spacing in x,y,z = 4.5937 4.5937 2.9587 + +create_atoms 1 region box_vide +Created 1584 atoms + using lattice units in triclinic box = (0 0 0) to (27.5622 27.5622 32.5457) with tilt (0 0 0) + create_atoms CPU = 0.000 seconds + + +mass 1 16.00 +group Oxy type 1 +1584 atoms in group Oxy + +mass 2 47.867 +group Ti type 2 +792 atoms in group Ti + +velocity all create ${T_depart} 277387 +velocity all create 300 277387 + +pair_style meam/spline +pair_coeff * * TiO.meam.spline O Ti +Reading meam/spline potential file TiO.meam.spline with DATE: 2016-06-05 + +neighbor 0.5 bin +neigh_modify every 2 delay 0 check yes + +timestep ${dt} +timestep 0.0002 + +thermo_style custom step temp press pe ke etotal lx ly lz vol +thermo 10 + + +#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z + +fix 3 all nve +run 100 +Neighbor list info ... + update: every = 2 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 10 10 11 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 5.175 | 5.175 | 5.175 Mbytes + Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume + 0 300 22403.656 -14374.073 92.097853 -14281.975 27.5622 27.5622 32.5457 24724.15 + 10 301.41345 23612.297 -14374.507 92.531772 -14281.975 27.5622 27.5622 32.5457 24724.15 + 20 305.11674 25127.832 -14375.643 93.668657 -14281.974 27.5622 27.5622 32.5457 24724.15 + 30 313.28903 26655.89 -14378.151 96.17749 -14281.974 27.5622 27.5622 32.5457 24724.15 + 40 328.94567 26999.049 -14382.957 100.98397 -14281.974 27.5622 27.5622 32.5457 24724.15 + 50 354.05827 23023.294 -14390.667 108.69336 -14281.974 27.5622 27.5622 32.5457 24724.15 + 60 390.48404 13594.655 -14401.849 119.87581 -14281.973 27.5622 27.5622 32.5457 24724.15 + 70 442.69928 151.15709 -14417.877 135.90551 -14281.972 27.5622 27.5622 32.5457 24724.15 + 80 516.89551 -14984.124 -14440.654 158.68322 -14281.971 27.5622 27.5622 32.5457 24724.15 + 90 618.22135 -29948.066 -14471.76 189.78953 -14281.971 27.5622 27.5622 32.5457 24724.15 + 100 747.6193 -41964.291 -14511.487 229.51378 -14281.973 27.5622 27.5622 32.5457 24724.15 +Loop time of 25.3398 on 1 procs for 100 steps with 2376 atoms + +Performance: 0.068 ns/day, 351.941 hours/ns, 3.946 timesteps/s, 9.377 katom-step/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 25.324 | 25.324 | 25.324 | 0.0 | 99.94 +Neigh | 0.0079644 | 0.0079644 | 0.0079644 | 0.0 | 0.03 +Comm | 0.0030695 | 0.0030695 | 0.0030695 | 0.0 | 0.01 +Output | 0.00032829 | 0.00032829 | 0.00032829 | 0.0 | 0.00 +Modify | 0.0028312 | 0.0028312 | 0.0028312 | 0.0 | 0.01 +Other | | 0.00137 | | | 0.01 + +Nlocal: 2376 ave 2376 max 2376 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 4479 ave 4479 max 4479 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 106396 ave 106396 max 106396 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 212792 ave 212792 max 212792 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 212792 +Ave neighs/atom = 89.558923 +Neighbor list builds = 1 +Dangerous builds = 0 + +unfix 3 +fix 1 all box/relax tri 0.0 vmax 0.001 +minimize 1.0e-3 1.0e-5 1000 10000 +Switching to 'neigh_modify every 1 delay 0 check yes' setting during minimization +Per MPI rank memory allocation (min/avg/max) = 6.3 | 6.3 | 6.3 Mbytes + Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume + 100 747.6193 -41964.291 -14511.487 229.51378 -14281.973 27.5622 27.5622 32.5457 24724.15 + 101 747.6193 -39284.65 -14517.424 229.51378 -14287.91 27.569615 27.569695 32.513154 24712.789 +Loop time of 0.515558 on 1 procs for 1 steps with 2376 atoms + +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -14511.4866189158 -14511.4866189158 -14517.4235162115 + Force two-norm initial, final = 5602.2481 5486.9746 + Force max component initial, final = 5232.0514 5109.4284 + Final line search alpha, max atom move = 1.9112962e-07 0.00097656312 + Iterations, force evaluations = 1 1 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.51518 | 0.51518 | 0.51518 | 0.0 | 99.93 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 6.888e-05 | 6.888e-05 | 6.888e-05 | 0.0 | 0.01 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.0003093 | | | 0.06 + +Nlocal: 2376 ave 2376 max 2376 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 4449 ave 4449 max 4449 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 105639 ave 105639 max 105639 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 211278 ave 211278 max 211278 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 211278 +Ave neighs/atom = 88.921717 +Neighbor list builds = 0 +Dangerous builds = 0 + +unfix 1 +reset_timestep 0 +thermo 50 +fix 3 all npt temp 300 300 0.1 aniso 1.0 1.0 1.0 +run 500 +Per MPI rank memory allocation (min/avg/max) = 5.19 | 5.19 | 5.19 Mbytes + Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume + 0 747.6193 -39284.65 -14517.424 229.51378 -14287.91 27.569615 27.569695 32.513154 24712.789 + 50 1155.2878 30637.502 -14678.803 354.6651 -14324.138 27.608715 27.609165 32.375366 24678.238 + 100 790.04907 99856.609 -14678.837 242.53941 -14436.297 27.777983 27.777976 32.017141 24704.942 + 150 938.88715 -21502.296 -14803.769 288.23164 -14515.537 27.996567 27.995118 31.67022 24822.079 + 200 420.1181 -791.77075 -14671.671 128.97325 -14542.698 28.126851 28.125845 31.431177 24864.936 + 250 352.17802 -3234.483 -14664.99 108.11613 -14556.874 28.222575 28.223558 31.238791 24882.993 + 300 622.92198 3667.4381 -14758.193 191.23259 -14566.96 28.301663 28.304917 31.072279 24891.264 + 350 888.27299 26277.515 -14852.568 272.69345 -14579.875 28.370265 28.375054 30.937123 24904.626 + 400 735.44199 63107.92 -14823.872 225.77543 -14598.097 28.44692 28.452281 30.838022 24959.67 + 450 804.82182 6213.5499 -14861.115 247.07454 -14614.04 28.543993 28.548769 30.775738 25079.021 + 500 628.1908 -33923.393 -14814.724 192.85008 -14621.874 28.612082 28.615255 30.740711 25168.712 +Loop time of 112.349 on 1 procs for 500 steps with 2376 atoms + +Performance: 0.077 ns/day, 312.081 hours/ns, 4.450 timesteps/s, 10.574 katom-step/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 112.15 | 112.15 | 112.15 | 0.0 | 99.82 +Neigh | 0.13243 | 0.13243 | 0.13243 | 0.0 | 0.12 +Comm | 0.01269 | 0.01269 | 0.01269 | 0.0 | 0.01 +Output | 0.00029334 | 0.00029334 | 0.00029334 | 0.0 | 0.00 +Modify | 0.053182 | 0.053182 | 0.053182 | 0.0 | 0.05 +Other | | 0.005153 | | | 0.00 + +Nlocal: 2376 ave 2376 max 2376 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 4358 ave 4358 max 4358 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 102634 ave 102634 max 102634 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 205268 ave 205268 max 205268 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 205268 +Ave neighs/atom = 86.392256 +Neighbor list builds = 16 +Dangerous builds = 0 + +Total wall time: 0:02:19 diff --git a/examples/PACKAGES/meam_spline/log.17Dec2022.meam-spline.TiO2.g++.4 b/examples/PACKAGES/meam_spline/log.17Dec2022.meam-spline.TiO2.g++.4 new file mode 100644 index 0000000000..f5ec6e5d8e --- /dev/null +++ b/examples/PACKAGES/meam_spline/log.17Dec2022.meam-spline.TiO2.g++.4 @@ -0,0 +1,253 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# + +variable T_depart equal 300 + +variable dt equal 0.0002 + +variable a equal 4.5937 +variable c equal 2.9587 +variable ca equal ${c}/${a} +variable ca equal 2.9587/${a} +variable ca equal 2.9587/4.5937 + +variable nx equal 6 +variable ny equal 6 +variable nz equal 11 + +variable bx equal ${a}*${nx} +variable bx equal 4.5937*${nx} +variable bx equal 4.5937*6 +variable by equal ${a}*${ny} +variable by equal 4.5937*${ny} +variable by equal 4.5937*6 +variable bz equal ${c}*${nz} +variable bz equal 2.9587*${nz} +variable bz equal 2.9587*11 +# ======================================================================= + +units metal +atom_style atomic +dimension 3 +boundary p p p + + +lattice sc 1.0 +Lattice spacing in x,y,z = 1 1 1 +region box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0 +region box_vide prism 0 27.5622 0 ${by} 0 ${bz} 0.0 0.0 0.0 +region box_vide prism 0 27.5622 0 27.5622 0 ${bz} 0.0 0.0 0.0 +region box_vide prism 0 27.5622 0 27.5622 0 32.5457 0.0 0.0 0.0 +create_box 2 box_vide +Created triclinic box = (0 0 0) to (27.5622 27.5622 32.5457) with tilt (0 0 0) + 1 by 2 by 2 MPI processor grid + +#lattice sc 1.0 +#region box_TiO2 block 0 ${bx} 0 ${by} 0 ${bz} + +# titanium atoms +lattice custom ${a} origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.0 0.0 0.0 basis 0.5 0.5 0.5 +lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.0 0.0 0.0 basis 0.5 0.5 0.5 +lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.644077758669482 basis 0.0 0.0 0.0 basis 0.5 0.5 0.5 +Lattice spacing in x,y,z = 4.5937 4.5937 2.9587 + +create_atoms 2 region box_vide +Created 792 atoms + using lattice units in triclinic box = (0 0 0) to (27.5622 27.5622 32.5457) with tilt (0 0 0) + create_atoms CPU = 0.000 seconds + +# Oxygen atoms +lattice custom ${a} origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5 +lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5 +lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.644077758669482 basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5 +Lattice spacing in x,y,z = 4.5937 4.5937 2.9587 + +create_atoms 1 region box_vide +Created 1584 atoms + using lattice units in triclinic box = (0 0 0) to (27.5622 27.5622 32.5457) with tilt (0 0 0) + create_atoms CPU = 0.000 seconds + + +mass 1 16.00 +group Oxy type 1 +1584 atoms in group Oxy + +mass 2 47.867 +group Ti type 2 +792 atoms in group Ti + +velocity all create ${T_depart} 277387 +velocity all create 300 277387 + +pair_style meam/spline +pair_coeff * * TiO.meam.spline O Ti +Reading meam/spline potential file TiO.meam.spline with DATE: 2016-06-05 + +neighbor 0.5 bin +neigh_modify every 2 delay 0 check yes + +timestep ${dt} +timestep 0.0002 + +thermo_style custom step temp press pe ke etotal lx ly lz vol +thermo 10 + + +#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z + +fix 3 all nve +run 100 +Neighbor list info ... + update: every = 2 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 10 10 11 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.934 | 3.934 | 3.934 Mbytes + Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume + 0 300 22403.656 -14374.073 92.097853 -14281.975 27.5622 27.5622 32.5457 24724.15 + 10 301.16725 23582.084 -14374.431 92.456192 -14281.975 27.5622 27.5622 32.5457 24724.15 + 20 304.58237 25059.749 -14375.479 93.504609 -14281.974 27.5622 27.5622 32.5457 24724.15 + 30 312.41477 26504.358 -14377.883 95.9091 -14281.974 27.5622 27.5622 32.5457 24724.15 + 40 327.67099 26687.057 -14382.566 100.59265 -14281.974 27.5622 27.5622 32.5457 24724.15 + 50 352.32125 22677.292 -14390.134 108.1601 -14281.974 27.5622 27.5622 32.5457 24724.15 + 60 388.40592 12472.705 -14401.211 119.23784 -14281.973 27.5622 27.5622 32.5457 24724.15 + 70 439.97199 -1520.4694 -14417.04 135.06825 -14281.972 27.5622 27.5622 32.5457 24724.15 + 80 513.34361 -16733.316 -14439.564 157.59282 -14281.971 27.5622 27.5622 32.5457 24724.15 + 90 613.3542 -31099.591 -14470.267 188.29535 -14281.971 27.5622 27.5622 32.5457 24724.15 + 100 741.02836 -42358.226 -14509.464 227.4904 -14281.973 27.5622 27.5622 32.5457 24724.15 +Loop time of 6.2168 on 4 procs for 100 steps with 2376 atoms + +Performance: 0.278 ns/day, 86.344 hours/ns, 16.085 timesteps/s, 38.219 katom-step/s +99.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.1958 | 6.2012 | 6.2089 | 0.2 | 99.75 +Neigh | 0.0021079 | 0.0021422 | 0.0021639 | 0.0 | 0.03 +Comm | 0.0038617 | 0.011586 | 0.017042 | 4.9 | 0.19 +Output | 0.00027671 | 0.00029064 | 0.00032183 | 0.0 | 0.00 +Modify | 0.00078288 | 0.0008221 | 0.00085066 | 0.0 | 0.01 +Other | | 0.0007406 | | | 0.01 + +Nlocal: 594 ave 599 max 589 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 2290.25 ave 2296 max 2282 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +Neighs: 26671.5 ave 26934 max 26495 min +Histogram: 1 0 0 2 0 0 0 0 0 1 +FullNghs: 53343 ave 53828 max 52922 min +Histogram: 1 0 0 0 2 0 0 0 0 1 + +Total # of neighbors = 213372 +Ave neighs/atom = 89.80303 +Neighbor list builds = 1 +Dangerous builds = 0 + +unfix 3 +fix 1 all box/relax tri 0.0 vmax 0.001 +minimize 1.0e-3 1.0e-5 1000 10000 +Switching to 'neigh_modify every 1 delay 0 check yes' setting during minimization +Per MPI rank memory allocation (min/avg/max) = 5.059 | 5.059 | 5.059 Mbytes + Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume + 100 741.02836 -42358.226 -14509.464 227.4904 -14281.973 27.5622 27.5622 32.5457 24724.15 + 101 741.02836 -39686.588 -14515.398 227.4904 -14287.907 27.569587 27.569656 32.513154 24712.729 +Loop time of 0.129231 on 4 procs for 1 steps with 2376 atoms + +99.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -14509.4635100091 -14509.4635100091 -14515.3978891321 + Force two-norm initial, final = 5602.6938 5487.7658 + Force max component initial, final = 5235.2654 5113.0611 + Final line search alpha, max atom move = 1.9101228e-07 0.00097665746 + Iterations, force evaluations = 1 1 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.12891 | 0.12896 | 0.129 | 0.0 | 99.79 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 5.5406e-05 | 9.5992e-05 | 0.00015051 | 0.0 | 0.07 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.0001737 | | | 0.13 + +Nlocal: 594 ave 601 max 586 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Nghost: 2263.25 ave 2271 max 2251 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +Neighs: 26425.8 ave 26807 max 26121 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +FullNghs: 52851.5 ave 53580 max 52175 min +Histogram: 1 0 0 0 2 0 0 0 0 1 + +Total # of neighbors = 211406 +Ave neighs/atom = 88.975589 +Neighbor list builds = 0 +Dangerous builds = 0 + +unfix 1 +reset_timestep 0 +thermo 50 +fix 3 all npt temp 300 300 0.1 aniso 1.0 1.0 1.0 +run 500 +Per MPI rank memory allocation (min/avg/max) = 3.95 | 3.95 | 3.95 Mbytes + Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume + 0 741.02836 -39686.588 -14515.398 227.4904 -14287.907 27.569587 27.569656 32.513154 24712.729 + 50 1157.3495 29319.762 -14679.318 355.29803 -14324.02 27.609057 27.60935 32.375563 24678.86 + 100 777.56728 101869.39 -14674.833 238.70759 -14436.125 27.778509 27.77736 32.017401 24705.064 + 150 945.51255 -18319.494 -14806.675 290.26559 -14516.409 27.998296 27.995331 31.670366 24823.916 + 200 427.47153 -4045.9984 -14674.872 131.2307 -14543.641 28.130223 28.127085 31.431723 24869.445 + 250 362.817 -7274.2701 -14669.054 111.38222 -14557.672 28.225123 28.222595 31.238594 24884.233 + 300 626.29209 7236.0808 -14760.119 192.26719 -14567.852 28.302278 28.299838 31.070157 24885.639 + 350 859.86407 30087.808 -14845.065 263.97212 -14581.093 28.372301 28.369278 30.934494 24899.226 + 400 755.2581 54745.968 -14830.701 231.85883 -14598.842 28.450314 28.448368 30.836162 24957.71 + 450 802.52878 5682.9998 -14860.196 246.37059 -14613.826 28.542362 28.541716 30.773281 25069.392 + 500 631.84048 -31484.881 -14816.098 193.97051 -14622.127 28.605943 28.605973 30.737856 25152.813 +Loop time of 27.3207 on 4 procs for 500 steps with 2376 atoms + +Performance: 0.316 ns/day, 75.891 hours/ns, 18.301 timesteps/s, 43.484 katom-step/s +99.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 27.21 | 27.221 | 27.237 | 0.2 | 99.64 +Neigh | 0.036501 | 0.036849 | 0.037083 | 0.1 | 0.13 +Comm | 0.02089 | 0.036492 | 0.047866 | 5.1 | 0.13 +Output | 0.00023096 | 0.00024391 | 0.00027788 | 0.0 | 0.00 +Modify | 0.022565 | 0.022706 | 0.022764 | 0.1 | 0.08 +Other | | 0.003102 | | | 0.01 + +Nlocal: 594 ave 606 max 582 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Nghost: 2226 ave 2238 max 2214 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Neighs: 25652.8 ave 26129 max 25153 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +FullNghs: 51305.5 ave 52398 max 50251 min +Histogram: 1 0 0 0 1 1 0 0 0 1 + +Total # of neighbors = 205222 +Ave neighs/atom = 86.372896 +Neighbor list builds = 16 +Dangerous builds = 0 + +Total wall time: 0:00:33 diff --git a/examples/PACKAGES/meam_spline/log.4May2017.meam-spline.Si.g++.1 b/examples/PACKAGES/meam_spline/log.4May2017.meam-spline.Si.g++.1 deleted file mode 100644 index ebf0855029..0000000000 --- a/examples/PACKAGES/meam_spline/log.4May2017.meam-spline.Si.g++.1 +++ /dev/null @@ -1,88 +0,0 @@ -LAMMPS (13 Apr 2017) - using 1 OpenMP thread(s) per MPI task -# Si fcc phase - -units metal -boundary p p p - -atom_style atomic -lattice fcc 3.98 -Lattice spacing in x,y,z = 3.98 3.98 3.98 -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (19.9 19.9 19.9) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 500 atoms - -pair_style meam/spline -pair_coeff * * Si_1.meam.spline Si -Reading potential file Si_1.meam.spline with DATE: 2012-02-01 -mass * 28.085 - -velocity all create 500.0 44226611 - -fix 1 all nvt temp 500.0 500.0 1.0 - -thermo 50 -run 500 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 6.5 - ghost atom cutoff = 6.5 - binsize = 3.25, bins = 7 7 7 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam/spline, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard - (2) pair meam/spline, perpetual, half/full from (1) - attributes: half, newton on - pair build: halffull/newton - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 3.892 | 3.892 | 3.892 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 500 -1847.729 0 -1815.4786 1813162.7 - 50 1934.0932 -1940.8016 0 -1816.051 -48657.676 - 100 2570.1286 -1984.8725 0 -1819.0971 8002.4248 - 150 2566.7917 -1990.2724 0 -1824.7123 16819.447 - 200 2555.1319 -1995.2233 0 -1830.4152 5891.5313 - 250 2487.2881 -1995.8302 0 -1835.3981 -4339.7172 - 300 2381.4836 -1994.2492 0 -1840.6415 16508.04 - 350 2330.8663 -1996.6588 0 -1846.3161 24194.447 - 400 2212.6035 -1994.9278 0 -1852.2131 -9856.3709 - 450 2257.7531 -2003.8187 0 -1858.1918 -8029.6019 - 500 2211.4385 -2006.9846 0 -1864.345 4152.4867 -Loop time of 5.13837 on 1 procs for 500 steps with 500 atoms - -Performance: 8.407 ns/day, 2.855 hours/ns, 97.307 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 | 5.0952 | 5.0952 | 5.0952 | 0.0 | 99.16 -Neigh | 0.026447 | 0.026447 | 0.026447 | 0.0 | 0.51 -Comm | 0.0063307 | 0.0063307 | 0.0063307 | 0.0 | 0.12 -Output | 0.0001905 | 0.0001905 | 0.0001905 | 0.0 | 0.00 -Modify | 0.0082877 | 0.0082877 | 0.0082877 | 0.0 | 0.16 -Other | | 0.00187 | | | 0.04 - -Nlocal: 500 ave 500 max 500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1767 ave 1767 max 1767 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 18059 ave 18059 max 18059 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 36118 ave 36118 max 36118 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 36118 -Ave neighs/atom = 72.236 -Neighbor list builds = 14 -Dangerous builds = 0 - -Total wall time: 0:00:05 diff --git a/examples/PACKAGES/meam_spline/log.4May2017.meam-spline.Si.g++.4 b/examples/PACKAGES/meam_spline/log.4May2017.meam-spline.Si.g++.4 deleted file mode 100644 index 3f059d7cee..0000000000 --- a/examples/PACKAGES/meam_spline/log.4May2017.meam-spline.Si.g++.4 +++ /dev/null @@ -1,88 +0,0 @@ -LAMMPS (13 Apr 2017) - using 1 OpenMP thread(s) per MPI task -# Si fcc phase - -units metal -boundary p p p - -atom_style atomic -lattice fcc 3.98 -Lattice spacing in x,y,z = 3.98 3.98 3.98 -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (19.9 19.9 19.9) - 1 by 2 by 2 MPI processor grid -create_atoms 1 box -Created 500 atoms - -pair_style meam/spline -pair_coeff * * Si_1.meam.spline Si -Reading potential file Si_1.meam.spline with DATE: 2012-02-01 -mass * 28.085 - -velocity all create 500.0 44226611 - -fix 1 all nvt temp 500.0 500.0 1.0 - -thermo 50 -run 500 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 6.5 - ghost atom cutoff = 6.5 - binsize = 3.25, bins = 7 7 7 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam/spline, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard - (2) pair meam/spline, perpetual, half/full from (1) - attributes: half, newton on - pair build: halffull/newton - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 3.861 | 3.861 | 3.861 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 500 -1847.729 0 -1815.4786 1813162.7 - 50 1923.4262 -1940.0936 0 -1816.0311 -38700.835 - 100 2535.2542 -1982.6249 0 -1819.0989 10216.821 - 150 2592.8247 -1992.1569 0 -1824.9176 4839.3385 - 200 2484.7391 -1990.8452 0 -1830.5775 14040.141 - 250 2597.4401 -2003.1619 0 -1835.625 1261.5199 - 300 2513.0793 -2002.942 0 -1840.8463 6690.9815 - 350 2390.933 -2001.0761 0 -1846.859 -4880.1146 - 400 2269.0782 -1999.3441 0 -1852.9867 -4921.4391 - 450 2287.5096 -2006.8236 0 -1859.2774 -7313.6151 - 500 2303.0918 -2014.0693 0 -1865.518 -9995.1789 -Loop time of 1.46588 on 4 procs for 500 steps with 500 atoms - -Performance: 29.470 ns/day, 0.814 hours/ns, 341.093 timesteps/s -99.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.4273 | 1.4292 | 1.432 | 0.1 | 97.50 -Neigh | 0.0068567 | 0.0070301 | 0.0073655 | 0.2 | 0.48 -Comm | 0.019111 | 0.022127 | 0.024148 | 1.2 | 1.51 -Output | 0.00023174 | 0.00024784 | 0.00029206 | 0.0 | 0.02 -Modify | 0.005043 | 0.0052016 | 0.0054417 | 0.2 | 0.35 -Other | | 0.002066 | | | 0.14 - -Nlocal: 125 ave 131 max 118 min -Histogram: 1 0 0 1 0 0 0 0 1 1 -Nghost: 979.25 ave 986 max 975 min -Histogram: 1 1 0 1 0 0 0 0 0 1 -Neighs: 4541.75 ave 4712 max 4362 min -Histogram: 1 1 0 0 0 0 0 0 0 2 -FullNghs: 9083.5 ave 9485 max 8601 min -Histogram: 1 0 0 1 0 0 0 0 1 1 - -Total # of neighbors = 36334 -Ave neighs/atom = 72.668 -Neighbor list builds = 14 -Dangerous builds = 0 - -Total wall time: 0:00:01 diff --git a/examples/PACKAGES/meam_spline/log.4May2017.meam-spline.TiO2.g++.1 b/examples/PACKAGES/meam_spline/log.4May2017.meam-spline.TiO2.g++.1 deleted file mode 100644 index aaeadec668..0000000000 --- a/examples/PACKAGES/meam_spline/log.4May2017.meam-spline.TiO2.g++.1 +++ /dev/null @@ -1,248 +0,0 @@ -LAMMPS (13 Apr 2017) - using 1 OpenMP thread(s) per MPI task -# - -variable T_depart equal 300 - -variable dt equal 0.0002 - -variable a equal 4.5937 -variable c equal 2.9587 -variable ca equal ${c}/${a} -variable ca equal 2.9587/${a} -variable ca equal 2.9587/4.5937 - -variable nx equal 6 -variable ny equal 6 -variable nz equal 11 - -variable bx equal ${a}*${nx} -variable bx equal 4.5937*${nx} -variable bx equal 4.5937*6 -variable by equal ${a}*${ny} -variable by equal 4.5937*${ny} -variable by equal 4.5937*6 -variable bz equal ${c}*${nz} -variable bz equal 2.9587*${nz} -variable bz equal 2.9587*11 -# ======================================================================= - -units metal -atom_style atomic -dimension 3 -boundary p p p - - -lattice sc 1.0 -Lattice spacing in x,y,z = 1 1 1 -region box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0 -region box_vide prism 0 27.5622 0 ${by} 0 ${bz} 0.0 0.0 0.0 -region box_vide prism 0 27.5622 0 27.5622 0 ${bz} 0.0 0.0 0.0 -region box_vide prism 0 27.5622 0 27.5622 0 32.5457 0.0 0.0 0.0 -create_box 2 box_vide -Created triclinic box = (0 0 0) to (27.5622 27.5622 32.5457) with tilt (0 0 0) - 1 by 1 by 1 MPI processor grid - -#lattice sc 1.0 -#region box_TiO2 block 0 ${bx} 0 ${by} 0 ${bz} - -# titanium atoms -lattice custom ${a} origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.0 0.0 0.0 basis 0.5 0.5 0.5 -lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.0 0.0 0.0 basis 0.5 0.5 0.5 -lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.644077758669482 basis 0.0 0.0 0.0 basis 0.5 0.5 0.5 -Lattice spacing in x,y,z = 4.5937 4.5937 2.9587 - -create_atoms 2 region box_vide -Created 792 atoms - -# Oxygen atoms -lattice custom ${a} origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5 -lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5 -lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.644077758669482 basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5 -Lattice spacing in x,y,z = 4.5937 4.5937 2.9587 - -create_atoms 1 region box_vide -Created 1584 atoms - - -mass 1 16.00 -group Oxy type 1 -1584 atoms in group Oxy - -mass 2 47.867 -group Ti type 2 -792 atoms in group Ti - -velocity all create ${T_depart} 277387 -velocity all create 300 277387 - -pair_style meam/spline -pair_coeff * * TiO.meam.spline O Ti -Reading potential file TiO.meam.spline with DATE: 2016-06-05 - -neighbor 0.5 bin -neigh_modify every 2 delay 0 check yes - -timestep ${dt} -timestep 0.0002 - -thermo_style custom step temp press pe ke etotal lx ly lz vol -thermo 10 - - -#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z - -fix 3 all nve -run 100 -Neighbor list info ... - update every 2 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 6 - ghost atom cutoff = 6 - binsize = 3, bins = 10 10 11 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam/spline, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard - (2) pair meam/spline, perpetual, half/full from (1) - attributes: half, newton on - pair build: halffull/newton - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 5.146 | 5.146 | 5.146 Mbytes -Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume - 0 300 22403.656 -14374.073 92.097853 -14281.975 27.5622 27.5622 32.5457 24724.15 - 10 301.41345 23612.297 -14374.507 92.531772 -14281.975 27.5622 27.5622 32.5457 24724.15 - 20 305.11674 25127.832 -14375.643 93.668657 -14281.974 27.5622 27.5622 32.5457 24724.15 - 30 313.28903 26655.89 -14378.151 96.17749 -14281.974 27.5622 27.5622 32.5457 24724.15 - 40 328.94567 26999.049 -14382.957 100.98397 -14281.974 27.5622 27.5622 32.5457 24724.15 - 50 354.05827 23023.294 -14390.667 108.69336 -14281.974 27.5622 27.5622 32.5457 24724.15 - 60 390.48404 13594.655 -14401.849 119.87581 -14281.973 27.5622 27.5622 32.5457 24724.15 - 70 442.69928 151.15709 -14417.877 135.90551 -14281.972 27.5622 27.5622 32.5457 24724.15 - 80 516.89551 -14984.124 -14440.654 158.68322 -14281.971 27.5622 27.5622 32.5457 24724.15 - 90 618.22135 -29948.066 -14471.76 189.78953 -14281.971 27.5622 27.5622 32.5457 24724.15 - 100 747.6193 -41964.291 -14511.487 229.51378 -14281.973 27.5622 27.5622 32.5457 24724.15 -Loop time of 38.7948 on 1 procs for 100 steps with 2376 atoms - -Performance: 0.045 ns/day, 538.817 hours/ns, 2.578 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 | 38.774 | 38.774 | 38.774 | 0.0 | 99.95 -Neigh | 0.010751 | 0.010751 | 0.010751 | 0.0 | 0.03 -Comm | 0.0039313 | 0.0039313 | 0.0039313 | 0.0 | 0.01 -Output | 0.00048804 | 0.00048804 | 0.00048804 | 0.0 | 0.00 -Modify | 0.0039241 | 0.0039241 | 0.0039241 | 0.0 | 0.01 -Other | | 0.001809 | | | 0.00 - -Nlocal: 2376 ave 2376 max 2376 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 4479 ave 4479 max 4479 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 106396 ave 106396 max 106396 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 212792 ave 212792 max 212792 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 212792 -Ave neighs/atom = 89.5589 -Neighbor list builds = 1 -Dangerous builds = 0 - -unfix 3 -fix 1 all box/relax tri 0.0 vmax 0.001 -minimize 1.0e-3 1.0e-5 1000 10000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) -Per MPI rank memory allocation (min/avg/max) = 6.271 | 6.271 | 6.271 Mbytes -Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume - 100 747.6193 -41964.291 -14511.487 229.51378 -14281.973 27.5622 27.5622 32.5457 24724.15 - 101 747.6193 -39284.65 -14517.424 229.51378 -14287.91 27.569615 27.569695 32.513154 24712.789 -Loop time of 0.814693 on 1 procs for 1 steps with 2376 atoms - -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads - -Minimization stats: - Stopping criterion = energy tolerance - Energy initial, next-to-last, final = - -14511.4866189 -14511.4866189 -14517.4235162 - Force two-norm initial, final = 5602.25 5486.97 - Force max component initial, final = 5232.05 5109.43 - Final line search alpha, max atom move = 1.9113e-07 0.000976563 - Iterations, force evaluations = 1 1 - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.81429 | 0.81429 | 0.81429 | 0.0 | 99.95 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 6.485e-05 | 6.485e-05 | 6.485e-05 | 0.0 | 0.01 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0.0003347 | | | 0.04 - -Nlocal: 2376 ave 2376 max 2376 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 4449 ave 4449 max 4449 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 105639 ave 105639 max 105639 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 211278 ave 211278 max 211278 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 211278 -Ave neighs/atom = 88.9217 -Neighbor list builds = 0 -Dangerous builds = 0 - -unfix 1 -reset_timestep 0 -thermo 50 -fix 3 all npt temp 300 300 0.1 aniso 1.0 1.0 1.0 -run 500 -Per MPI rank memory allocation (min/avg/max) = 5.162 | 5.162 | 5.162 Mbytes -Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume - 0 747.6193 -39284.65 -14517.424 229.51378 -14287.91 27.569615 27.569695 32.513154 24712.789 - 50 1155.2849 30650.319 -14678.807 354.6642 -14324.143 27.608688 27.60914 32.375311 24678.15 - 100 790.03926 99869.991 -14678.858 242.5364 -14436.322 27.777994 27.77799 32.017001 24704.857 - 150 938.86463 -21488.442 -14803.782 288.22472 -14515.557 27.996584 27.995139 31.67008 24822.003 - 200 420.11331 -790.80799 -14671.687 128.97178 -14542.715 28.126911 28.125909 31.431033 24864.93 - 250 352.18149 -3244.2491 -14665.007 108.1172 -14556.889 28.222686 28.223673 31.238649 24883.078 - 300 622.91245 3657.7097 -14758.201 191.22967 -14566.972 28.301771 28.30503 31.07216 24891.363 - 350 888.25374 26274.358 -14852.568 272.68754 -14579.881 28.370312 28.375107 30.937051 24904.656 - 400 735.44163 63109.066 -14823.872 225.77532 -14598.097 28.446905 28.45227 30.838015 24959.642 - 450 804.81905 6221.0364 -14861.113 247.07369 -14614.039 28.543942 28.548719 30.775793 25078.977 - 500 628.19106 -33912.026 -14814.726 192.85016 -14621.876 28.611997 28.615169 30.74081 25168.642 -Loop time of 176.167 on 1 procs for 500 steps with 2376 atoms - -Performance: 0.049 ns/day, 489.353 hours/ns, 2.838 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 | 175.9 | 175.9 | 175.9 | 0.0 | 99.85 -Neigh | 0.17043 | 0.17043 | 0.17043 | 0.0 | 0.10 -Comm | 0.018243 | 0.018243 | 0.018243 | 0.0 | 0.01 -Output | 0.00040984 | 0.00040984 | 0.00040984 | 0.0 | 0.00 -Modify | 0.067142 | 0.067142 | 0.067142 | 0.0 | 0.04 -Other | | 0.00828 | | | 0.00 - -Nlocal: 2376 ave 2376 max 2376 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 4358 ave 4358 max 4358 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 102634 ave 102634 max 102634 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 205268 ave 205268 max 205268 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 205268 -Ave neighs/atom = 86.3923 -Neighbor list builds = 16 -Dangerous builds = 0 - -Total wall time: 0:03:37 diff --git a/examples/PACKAGES/meam_spline/log.4May2017.meam-spline.TiO2.g++.4 b/examples/PACKAGES/meam_spline/log.4May2017.meam-spline.TiO2.g++.4 deleted file mode 100644 index 6c2c949acb..0000000000 --- a/examples/PACKAGES/meam_spline/log.4May2017.meam-spline.TiO2.g++.4 +++ /dev/null @@ -1,248 +0,0 @@ -LAMMPS (13 Apr 2017) - using 1 OpenMP thread(s) per MPI task -# - -variable T_depart equal 300 - -variable dt equal 0.0002 - -variable a equal 4.5937 -variable c equal 2.9587 -variable ca equal ${c}/${a} -variable ca equal 2.9587/${a} -variable ca equal 2.9587/4.5937 - -variable nx equal 6 -variable ny equal 6 -variable nz equal 11 - -variable bx equal ${a}*${nx} -variable bx equal 4.5937*${nx} -variable bx equal 4.5937*6 -variable by equal ${a}*${ny} -variable by equal 4.5937*${ny} -variable by equal 4.5937*6 -variable bz equal ${c}*${nz} -variable bz equal 2.9587*${nz} -variable bz equal 2.9587*11 -# ======================================================================= - -units metal -atom_style atomic -dimension 3 -boundary p p p - - -lattice sc 1.0 -Lattice spacing in x,y,z = 1 1 1 -region box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0 -region box_vide prism 0 27.5622 0 ${by} 0 ${bz} 0.0 0.0 0.0 -region box_vide prism 0 27.5622 0 27.5622 0 ${bz} 0.0 0.0 0.0 -region box_vide prism 0 27.5622 0 27.5622 0 32.5457 0.0 0.0 0.0 -create_box 2 box_vide -Created triclinic box = (0 0 0) to (27.5622 27.5622 32.5457) with tilt (0 0 0) - 1 by 2 by 2 MPI processor grid - -#lattice sc 1.0 -#region box_TiO2 block 0 ${bx} 0 ${by} 0 ${bz} - -# titanium atoms -lattice custom ${a} origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.0 0.0 0.0 basis 0.5 0.5 0.5 -lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.0 0.0 0.0 basis 0.5 0.5 0.5 -lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.644077758669482 basis 0.0 0.0 0.0 basis 0.5 0.5 0.5 -Lattice spacing in x,y,z = 4.5937 4.5937 2.9587 - -create_atoms 2 region box_vide -Created 792 atoms - -# Oxygen atoms -lattice custom ${a} origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5 -lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5 -lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.644077758669482 basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5 -Lattice spacing in x,y,z = 4.5937 4.5937 2.9587 - -create_atoms 1 region box_vide -Created 1584 atoms - - -mass 1 16.00 -group Oxy type 1 -1584 atoms in group Oxy - -mass 2 47.867 -group Ti type 2 -792 atoms in group Ti - -velocity all create ${T_depart} 277387 -velocity all create 300 277387 - -pair_style meam/spline -pair_coeff * * TiO.meam.spline O Ti -Reading potential file TiO.meam.spline with DATE: 2016-06-05 - -neighbor 0.5 bin -neigh_modify every 2 delay 0 check yes - -timestep ${dt} -timestep 0.0002 - -thermo_style custom step temp press pe ke etotal lx ly lz vol -thermo 10 - - -#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z - -fix 3 all nve -run 100 -Neighbor list info ... - update every 2 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 6 - ghost atom cutoff = 6 - binsize = 3, bins = 10 10 11 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam/spline, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard - (2) pair meam/spline, perpetual, half/full from (1) - attributes: half, newton on - pair build: halffull/newton - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 3.922 | 3.922 | 3.922 Mbytes -Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume - 0 300 22403.656 -14374.073 92.097853 -14281.975 27.5622 27.5622 32.5457 24724.15 - 10 301.16725 23582.084 -14374.431 92.456192 -14281.975 27.5622 27.5622 32.5457 24724.15 - 20 304.58237 25059.749 -14375.479 93.504609 -14281.974 27.5622 27.5622 32.5457 24724.15 - 30 312.41477 26504.358 -14377.883 95.9091 -14281.974 27.5622 27.5622 32.5457 24724.15 - 40 327.67099 26687.057 -14382.566 100.59265 -14281.974 27.5622 27.5622 32.5457 24724.15 - 50 352.32125 22677.292 -14390.134 108.1601 -14281.974 27.5622 27.5622 32.5457 24724.15 - 60 388.40592 12472.705 -14401.211 119.23784 -14281.973 27.5622 27.5622 32.5457 24724.15 - 70 439.97199 -1520.4694 -14417.04 135.06825 -14281.972 27.5622 27.5622 32.5457 24724.15 - 80 513.34361 -16733.316 -14439.564 157.59282 -14281.971 27.5622 27.5622 32.5457 24724.15 - 90 613.3542 -31099.591 -14470.267 188.29535 -14281.971 27.5622 27.5622 32.5457 24724.15 - 100 741.02836 -42358.226 -14509.464 227.4904 -14281.973 27.5622 27.5622 32.5457 24724.15 -Loop time of 8.92317 on 4 procs for 100 steps with 2376 atoms - -Performance: 0.194 ns/day, 123.933 hours/ns, 11.207 timesteps/s -99.5% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 8.8912 | 8.9 | 8.9064 | 0.2 | 99.74 -Neigh | 0.0027034 | 0.0028808 | 0.0032032 | 0.4 | 0.03 -Comm | 0.010964 | 0.017648 | 0.026568 | 5.0 | 0.20 -Output | 0.00037575 | 0.00047809 | 0.00053835 | 0.0 | 0.01 -Modify | 0.00099134 | 0.001001 | 0.0010085 | 0.0 | 0.01 -Other | | 0.001162 | | | 0.01 - -Nlocal: 594 ave 599 max 589 min -Histogram: 1 0 0 0 0 2 0 0 0 1 -Nghost: 2290.25 ave 2296 max 2282 min -Histogram: 1 0 0 0 1 0 0 0 1 1 -Neighs: 26671.5 ave 26934 max 26495 min -Histogram: 1 0 0 2 0 0 0 0 0 1 -FullNghs: 53343 ave 53828 max 52922 min -Histogram: 1 0 0 0 2 0 0 0 0 1 - -Total # of neighbors = 213372 -Ave neighs/atom = 89.803 -Neighbor list builds = 1 -Dangerous builds = 0 - -unfix 3 -fix 1 all box/relax tri 0.0 vmax 0.001 -minimize 1.0e-3 1.0e-5 1000 10000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) -Per MPI rank memory allocation (min/avg/max) = 5.047 | 5.047 | 5.047 Mbytes -Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume - 100 741.02836 -42358.226 -14509.464 227.4904 -14281.973 27.5622 27.5622 32.5457 24724.15 - 101 741.02836 -39686.588 -14515.398 227.4904 -14287.907 27.569587 27.569656 32.513154 24712.729 -Loop time of 0.193516 on 4 procs for 1 steps with 2376 atoms - -99.5% CPU use with 4 MPI tasks x 1 OpenMP threads - -Minimization stats: - Stopping criterion = energy tolerance - Energy initial, next-to-last, final = - -14509.46351 -14509.46351 -14515.3978891 - Force two-norm initial, final = 5602.69 5487.77 - Force max component initial, final = 5235.27 5113.06 - Final line search alpha, max atom move = 1.91012e-07 0.000976657 - Iterations, force evaluations = 1 1 - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.19287 | 0.19299 | 0.19318 | 0.0 | 99.73 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00014043 | 0.00033247 | 0.00045896 | 0.0 | 0.17 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0.0001886 | | | 0.10 - -Nlocal: 594 ave 601 max 586 min -Histogram: 1 0 0 0 0 1 1 0 0 1 -Nghost: 2263.25 ave 2271 max 2251 min -Histogram: 1 0 0 0 0 0 1 0 1 1 -Neighs: 26425.8 ave 26807 max 26121 min -Histogram: 1 0 0 1 1 0 0 0 0 1 -FullNghs: 52851.5 ave 53580 max 52175 min -Histogram: 1 0 0 0 2 0 0 0 0 1 - -Total # of neighbors = 211406 -Ave neighs/atom = 88.9756 -Neighbor list builds = 0 -Dangerous builds = 0 - -unfix 1 -reset_timestep 0 -thermo 50 -fix 3 all npt temp 300 300 0.1 aniso 1.0 1.0 1.0 -run 500 -Per MPI rank memory allocation (min/avg/max) = 3.937 | 3.937 | 3.937 Mbytes -Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume - 0 741.02836 -39686.588 -14515.398 227.4904 -14287.907 27.569587 27.569656 32.513154 24712.729 - 50 1157.347 29332.549 -14679.321 355.29725 -14324.024 27.60903 27.609325 32.375509 24678.772 - 100 777.55858 101883.12 -14674.854 238.70492 -14436.149 27.778518 27.777373 32.017262 24704.976 - 150 945.49014 -18305.383 -14806.687 290.25871 -14516.428 27.998313 27.99535 31.670225 24823.838 - 200 427.46608 -4045.0095 -14674.887 131.22903 -14543.658 28.130283 28.127147 31.431578 24869.438 - 250 362.82166 -7283.1332 -14669.07 111.38365 -14557.687 28.225232 28.222707 31.238451 24884.314 - 300 626.2858 7228.0309 -14760.128 192.26526 -14567.862 28.302384 28.299949 31.070038 24885.734 - 350 859.84293 30084.735 -14845.064 263.96563 -14581.099 28.372349 28.369334 30.934424 24899.261 - 400 755.26136 54745.408 -14830.701 231.85983 -14598.842 28.450301 28.448361 30.836159 24957.691 - 450 802.52344 5690.2863 -14860.193 246.36895 -14613.824 28.542311 28.541672 30.773339 25069.354 - 500 631.84734 -31473.795 -14816.101 193.97261 -14622.128 28.605857 28.605891 30.737955 25152.746 -Loop time of 39.7881 on 4 procs for 500 steps with 2376 atoms - -Performance: 0.217 ns/day, 110.522 hours/ns, 12.567 timesteps/s -99.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 39.617 | 39.633 | 39.653 | 0.2 | 99.61 -Neigh | 0.043624 | 0.046792 | 0.051708 | 1.4 | 0.12 -Comm | 0.05215 | 0.072616 | 0.092142 | 5.6 | 0.18 -Output | 0.00042915 | 0.00045079 | 0.00051546 | 0.0 | 0.00 -Modify | 0.029836 | 0.030341 | 0.03094 | 0.2 | 0.08 -Other | | 0.004489 | | | 0.01 - -Nlocal: 594 ave 606 max 582 min -Histogram: 1 0 0 0 1 1 0 0 0 1 -Nghost: 2226 ave 2238 max 2214 min -Histogram: 1 0 0 0 1 1 0 0 0 1 -Neighs: 25652.8 ave 26129 max 25153 min -Histogram: 1 0 0 0 1 1 0 0 0 1 -FullNghs: 51305.5 ave 52398 max 50251 min -Histogram: 1 0 0 0 1 1 0 0 0 1 - -Total # of neighbors = 205222 -Ave neighs/atom = 86.3729 -Neighbor list builds = 16 -Dangerous builds = 0 - -Total wall time: 0:00:49 diff --git a/examples/PACKAGES/meam_sw_spline/Si/Si.b.meam.sw.spline b/examples/PACKAGES/meam_sw_spline/Si/Si.b.meam.sw.spline new file mode 120000 index 0000000000..0ef2cbf6fb --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/Si.b.meam.sw.spline @@ -0,0 +1 @@ +../../../../potentials/Si.b.meam.sw.spline \ No newline at end of file diff --git a/examples/PACKAGES/meam_sw_spline/Si/bcc.in b/examples/PACKAGES/meam_sw_spline/Si/bcc.in deleted file mode 100644 index 03ac20a024..0000000000 --- a/examples/PACKAGES/meam_sw_spline/Si/bcc.in +++ /dev/null @@ -1,33 +0,0 @@ -# Si bcc - -units metal -boundary p p p - -atom_style atomic -lattice bcc 3.245 -region box block 0 1 0 1 0 1 -create_box 1 box -create_atoms 1 box - -pair_style meam/sw/spline -pair_coeff * * ../../potentials/Si.b.meam.sw.spline Si -mass * 28.085 - -variable cohesive_energy equal pe/atoms -variable atmVol equal vol/atoms -variable aLatt equal (2*vol/atoms)^0.333333333333 - -run 0 - -print "====================================================" -print "Calculated cohesive energy: ${cohesive_energy} eV/atom" -print "Reference cohesive energy: -4.37 eV/atom" -print "Atomic volume ${atmVol} A^3" -print "Lattice constant ${aLatt} A" -print "Reference lattice constant 3.245 A" -print "====================================================" - -#dump 1 all custom 1 bcc.dump id type x y z fx fy fz -#run 0 - - diff --git a/examples/PACKAGES/meam_sw_spline/Si/bcc_relax.in b/examples/PACKAGES/meam_sw_spline/Si/bcc_relax.in deleted file mode 100644 index 12299d7629..0000000000 --- a/examples/PACKAGES/meam_sw_spline/Si/bcc_relax.in +++ /dev/null @@ -1,37 +0,0 @@ -# Si bcc - -units metal -boundary p p p - -atom_style atomic -lattice bcc 3.2488516 -region box block 0 1 0 1 0 1 -create_box 1 box -create_atoms 1 box - -pair_style meam/sw/spline -pair_coeff * * ../../potentials/Si.b.meam.sw.spline Si -mass * 28.085 - -fix relax all box/relax aniso 0 -thermo 1 -minimize 0 0 10000 100000 - -variable cohesive_energy equal pe/atoms -variable atmVol equal vol/atoms -variable aLatt equal (2*vol/atoms)^0.333333333333 - -run 0 - -print "====================================================" -print "Calculated cohesive energy: ${cohesive_energy} eV/atom" -print "Reference cohesive energy: -4.37 eV/atom" -print "Atomic volume ${atmVol} A^3" -print "Lattice constant ${aLatt} A" -print "Reference lattice constant 3.238 A" -print "====================================================" - -#dump 1 all custom 1 bcc.dump id type x y z fx fy fz -#run 0 - - diff --git a/examples/PACKAGES/meam_sw_spline/Si/dc.in b/examples/PACKAGES/meam_sw_spline/Si/dc.in deleted file mode 100644 index 8807dcfd74..0000000000 --- a/examples/PACKAGES/meam_sw_spline/Si/dc.in +++ /dev/null @@ -1,34 +0,0 @@ -# Si dc phase - -units metal -boundary p p p - -atom_style atomic -lattice diamond 5.431 -region box block 0 1 0 1 0 1 -create_box 1 box -create_atoms 1 box - -pair_style meam/sw/spline -pair_coeff * * ../../potentials/Si.b.meam.sw.spline Si -mass * 28.085 - -variable cohesive_energy equal pe/atoms -variable atmVol equal vol/atoms -variable aLatt equal (8*vol/atoms)^0.33333333333 - -run 0 - -print "====================================================" -print "Calculated cohesive energy: ${cohesive_energy} eV/atom" -print "Reference cohesive energy: -4.63 eV/atom" -print "Atomic volume ${atmVol} A^3" -print "Lattice constant ${aLatt} A" -print "Reference lattice constant 5.431 A" -print "====================================================" - - -#dump 1 all custom 1 dc.dump id type x y z fx fy fz -#run 0 - - diff --git a/examples/PACKAGES/meam_sw_spline/Si/fcc.in b/examples/PACKAGES/meam_sw_spline/Si/fcc.in deleted file mode 100644 index 21d5247b31..0000000000 --- a/examples/PACKAGES/meam_sw_spline/Si/fcc.in +++ /dev/null @@ -1,34 +0,0 @@ -# Si fcc phase - -units metal -boundary p p p - -atom_style atomic -lattice fcc 4.147 -region box block 0 1 0 1 0 1 -create_box 1 box -create_atoms 1 box - -pair_style meam/sw/spline -pair_coeff * * ../../potentials/Si.b.meam.sw.spline Si -mass * 28.085 - -variable cohesive_energy equal pe/atoms -variable atmVol equal vol/atoms -variable aLatt equal (4*vol/atoms)^0.3333333333 - -run 0 - -print "====================================================" -print "Calculated cohesive energy: ${cohesive_energy} eV/atom" -print "Reference cohesive energy: -4.288 eV/atom" -print "Atomic volume ${atmVol} A^3" -print "Lattice constant ${aLatt} A" -print "Reference lattice constant 4.147 A" -print "====================================================" - - -#dump 1 all custom 1 fcc.dump id type x y z fx fy fz -#run 0 - - diff --git a/examples/PACKAGES/meam_sw_spline/Si/fcc_relax.in b/examples/PACKAGES/meam_sw_spline/Si/fcc_relax.in deleted file mode 100644 index f6e967df06..0000000000 --- a/examples/PACKAGES/meam_sw_spline/Si/fcc_relax.in +++ /dev/null @@ -1,38 +0,0 @@ -# Si fcc phase - -units metal -boundary p p p - -atom_style atomic -lattice fcc 4.309793856093661 -region box block 0 1 0 1 0 1 -create_box 1 box -create_atoms 1 box - -pair_style meam/sw/spline -pair_coeff * * ../../potentials/Si.b.meam.sw.spline Si -mass * 28.085 - -fix relax all box/relax aniso 0 -thermo 1 -minimize 0 0 10000 100000 - -variable cohesive_energy equal pe/atoms -variable atmVol equal vol/atoms -variable aLatt equal (4*vol/atoms)^0.3333333333 - -run 0 - -print "====================================================" -print "Calculated cohesive energy: ${cohesive_energy} eV/atom" -print "Reference cohesive energy: -4.289 eV/atom" -print "Atomic volume ${atmVol} A^3" -print "Lattice constant ${aLatt} A" -print "Reference lattice constant 4.137 A" -print "====================================================" - - -#dump 1 all custom 1 fcc.dump id type x y z fx fy fz -#run 0 - - diff --git a/examples/PACKAGES/meam_sw_spline/Si/hcp_relax.in b/examples/PACKAGES/meam_sw_spline/Si/hcp_relax.in deleted file mode 100644 index 4944dbec03..0000000000 --- a/examples/PACKAGES/meam_sw_spline/Si/hcp_relax.in +++ /dev/null @@ -1,40 +0,0 @@ -# Si hcp - -units metal -boundary p p p - -atom_style atomic -#lattice custom 2.93093 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 1.596 basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75 -lattice custom 2.93093 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 1.7 basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75 -region box block 0 1 0 1 0 1 -create_box 1 box -create_atoms 1 box - -pair_style meam/sw/spline -pair_coeff * * ../../potentials/Si.b.meam.sw.spline Si -mass * 28.085 - -fix relax all box/relax aniso 0 -thermo 1 -minimize 0 0 10000 100000 - -variable cohesive_energy equal pe/atoms -variable lattice_parameter equal lx -variable c_to_a equal lz/lx -variable atmVol equal vol/atoms -run 0 - -print "====================================================" -print "Calculated cohesive energy: ${cohesive_energy} eV/atom" -print "Reference cohesive energy: -4.290 eV/atom" -print "Calculated lattice parameter: ${lattice_parameter} A" -print "Reference lattice parameter: 2.925 A" -print "Atomic volume ${atmVol} A^3" -print "c/a ratio: ${c_to_a}" -print "Reference c/a ratio: 1.633" -print "====================================================" - -#dump 1 all custom 1 hcp.dump id type x y z fx fy fz -#run 0 - - diff --git a/examples/PACKAGES/meam_sw_spline/Si/in.bcc b/examples/PACKAGES/meam_sw_spline/Si/in.bcc new file mode 100644 index 0000000000..235821fa42 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/in.bcc @@ -0,0 +1,33 @@ +# Si bcc + +units metal +boundary p p p + +atom_style atomic +lattice bcc 3.245 +region box block 0 1 0 1 0 1 +create_box 1 box +create_atoms 1 box + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +mass * 28.085 + +variable cohesive_energy equal pe/atoms +variable atmVol equal vol/atoms +variable aLatt equal (2*vol/atoms)^0.333333333333 + +run 0 + +print "====================================================" +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +print "Reference cohesive energy: -4.37 eV/atom" +print "Atomic volume ${atmVol} A^3" +print "Lattice constant ${aLatt} A" +print "Reference lattice constant 3.245 A" +print "====================================================" + +#dump 1 all custom 1 bcc.dump id type x y z fx fy fz +#run 0 + + diff --git a/examples/PACKAGES/meam_sw_spline/Si/in.bcc_relax b/examples/PACKAGES/meam_sw_spline/Si/in.bcc_relax new file mode 100644 index 0000000000..b58b01dc92 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/in.bcc_relax @@ -0,0 +1,37 @@ +# Si bcc + +units metal +boundary p p p + +atom_style atomic +lattice bcc 3.2488516 +region box block 0 1 0 1 0 1 +create_box 1 box +create_atoms 1 box + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +mass * 28.085 + +fix relax all box/relax aniso 0 +thermo 1 +minimize 0 0 10000 100000 + +variable cohesive_energy equal pe/atoms +variable atmVol equal vol/atoms +variable aLatt equal (2*vol/atoms)^0.333333333333 + +run 0 + +print "====================================================" +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +print "Reference cohesive energy: -4.37 eV/atom" +print "Atomic volume ${atmVol} A^3" +print "Lattice constant ${aLatt} A" +print "Reference lattice constant 3.238 A" +print "====================================================" + +#dump 1 all custom 1 bcc.dump id type x y z fx fy fz +#run 0 + + diff --git a/examples/PACKAGES/meam_sw_spline/Si/in.dc b/examples/PACKAGES/meam_sw_spline/Si/in.dc new file mode 100644 index 0000000000..a1e49b1535 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/in.dc @@ -0,0 +1,34 @@ +# Si dc phase + +units metal +boundary p p p + +atom_style atomic +lattice diamond 5.431 +region box block 0 1 0 1 0 1 +create_box 1 box +create_atoms 1 box + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +mass * 28.085 + +variable cohesive_energy equal pe/atoms +variable atmVol equal vol/atoms +variable aLatt equal (8*vol/atoms)^0.33333333333 + +run 0 + +print "====================================================" +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +print "Reference cohesive energy: -4.63 eV/atom" +print "Atomic volume ${atmVol} A^3" +print "Lattice constant ${aLatt} A" +print "Reference lattice constant 5.431 A" +print "====================================================" + + +#dump 1 all custom 1 dc.dump id type x y z fx fy fz +#run 0 + + diff --git a/examples/PACKAGES/meam_sw_spline/Si/dc_relax.in b/examples/PACKAGES/meam_sw_spline/Si/in.dc_relax similarity index 65% rename from examples/PACKAGES/meam_sw_spline/Si/dc_relax.in rename to examples/PACKAGES/meam_sw_spline/Si/in.dc_relax index 7d74be796b..d9ccfa7bd1 100644 --- a/examples/PACKAGES/meam_sw_spline/Si/dc_relax.in +++ b/examples/PACKAGES/meam_sw_spline/Si/in.dc_relax @@ -1,16 +1,16 @@ # Si dc phase -units metal -boundary p p p +units metal +boundary p p p -atom_style atomic -lattice diamond 5.43 -region box block 0 1 0 1 0 1 -create_box 1 box -create_atoms 1 box +atom_style atomic +lattice diamond 5.43 +region box block 0 1 0 1 0 1 +create_box 1 box +create_atoms 1 box pair_style meam/sw/spline -pair_coeff * * ../../potentials/Si.b.meam.sw.spline Si +pair_coeff * * Si.b.meam.sw.spline Si mass * 28.085 fix relax all box/relax aniso 0 @@ -29,10 +29,10 @@ print "Reference cohesive energy: -4.63 eV/atom" print "Atomic volume ${atmVol} A^3" print "Lattice constant ${aLatt} A" print "Reference lattice constant 5.431 A" -print "====================================================" +print "====================================================" -#dump 1 all custom 1 dc.dump id type x y z fx fy fz -#run 0 +#dump 1 all custom 1 dc.dump id type x y z fx fy fz +#run 0 diff --git a/examples/PACKAGES/meam_sw_spline/Si/energy_conservation.meam.sw.in b/examples/PACKAGES/meam_sw_spline/Si/in.energy_conservation.meam.sw similarity index 58% rename from examples/PACKAGES/meam_sw_spline/Si/energy_conservation.meam.sw.in rename to examples/PACKAGES/meam_sw_spline/Si/in.energy_conservation.meam.sw index 2babed50c8..b05245abf0 100644 --- a/examples/PACKAGES/meam_sw_spline/Si/energy_conservation.meam.sw.in +++ b/examples/PACKAGES/meam_sw_spline/Si/in.energy_conservation.meam.sw @@ -1,16 +1,16 @@ # bulk Si lattice -variable x index 1 -variable y index 1 -variable z index 1 +variable x index 1 +variable y index 1 +variable z index 1 -units metal -atom_style atomic +units metal +atom_style atomic atom_style atomic lattice diamond 5.431 -region box block 0 20 0 20 0 20 +region box block 0 5 0 5 0 5 boundary p p p create_box 1 box @@ -18,15 +18,15 @@ create_atoms 1 box pair_style meam/sw/spline -pair_coeff * * ../../potentials/Si.b.meam.sw.spline Si +pair_coeff * * Si.b.meam.sw.spline Si mass * 28.085 -velocity all create 300.0 376847 loop geom +velocity all create 300.0 376847 loop geom -neighbor 1.0 bin +neighbor 1.0 bin neigh_modify every 1 delay 5 check yes -fix 1 all nve +fix 1 all nve thermo 1 thermo_style custom step vol etotal press pxx pyy pxz @@ -38,8 +38,8 @@ thermo_modify format 6 %14.8f thermo_modify format 7 %14.8f -timestep 0.002 -thermo 10 +timestep 0.002 +thermo 10 -run 20000 +run 2000 diff --git a/examples/PACKAGES/meam_sw_spline/Si/in.fcc b/examples/PACKAGES/meam_sw_spline/Si/in.fcc new file mode 100644 index 0000000000..13afac29ce --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/in.fcc @@ -0,0 +1,34 @@ +# Si fcc phase + +units metal +boundary p p p + +atom_style atomic +lattice fcc 4.147 +region box block 0 1 0 1 0 1 +create_box 1 box +create_atoms 1 box + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +mass * 28.085 + +variable cohesive_energy equal pe/atoms +variable atmVol equal vol/atoms +variable aLatt equal (4*vol/atoms)^0.3333333333 + +run 0 + +print "====================================================" +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +print "Reference cohesive energy: -4.288 eV/atom" +print "Atomic volume ${atmVol} A^3" +print "Lattice constant ${aLatt} A" +print "Reference lattice constant 4.147 A" +print "====================================================" + + +#dump 1 all custom 1 fcc.dump id type x y z fx fy fz +#run 0 + + diff --git a/examples/PACKAGES/meam_sw_spline/Si/in.fcc_relax b/examples/PACKAGES/meam_sw_spline/Si/in.fcc_relax new file mode 100644 index 0000000000..389d2e73b7 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/in.fcc_relax @@ -0,0 +1,38 @@ +# Si fcc phase + +units metal +boundary p p p + +atom_style atomic +lattice fcc 4.309793856093661 +region box block 0 1 0 1 0 1 +create_box 1 box +create_atoms 1 box + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +mass * 28.085 + +fix relax all box/relax aniso 0 +thermo 1 +minimize 0 0 10000 100000 + +variable cohesive_energy equal pe/atoms +variable atmVol equal vol/atoms +variable aLatt equal (4*vol/atoms)^0.3333333333 + +run 0 + +print "====================================================" +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +print "Reference cohesive energy: -4.289 eV/atom" +print "Atomic volume ${atmVol} A^3" +print "Lattice constant ${aLatt} A" +print "Reference lattice constant 4.137 A" +print "====================================================" + + +#dump 1 all custom 1 fcc.dump id type x y z fx fy fz +#run 0 + + diff --git a/examples/PACKAGES/meam_sw_spline/Si/in.hcp_relax b/examples/PACKAGES/meam_sw_spline/Si/in.hcp_relax new file mode 100644 index 0000000000..a2a91ffb22 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/in.hcp_relax @@ -0,0 +1,40 @@ +# Si hcp + +units metal +boundary p p p + +atom_style atomic +#lattice custom 2.93093 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 1.596 basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75 +lattice custom 2.93093 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 1.7 basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75 +region box block 0 1 0 1 0 1 +create_box 1 box +create_atoms 1 box + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +mass * 28.085 + +fix relax all box/relax aniso 0 +thermo 1 +minimize 0 0 10000 100000 + +variable cohesive_energy equal pe/atoms +variable lattice_parameter equal lx +variable c_to_a equal lz/lx +variable atmVol equal vol/atoms +run 0 + +print "====================================================" +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +print "Reference cohesive energy: -4.352 eV/atom" +print "Calculated lattice parameter: ${lattice_parameter} A" +print "Reference lattice parameter: 2.736 A" +print "Atomic volume ${atmVol} A^3" +print "c/a ratio: ${c_to_a}" +print "Reference c/a ratio: 1.633" +print "====================================================" + +#dump 1 all custom 1 hcp.dump id type x y z fx fy fz +#run 0 + + diff --git a/examples/PACKAGES/meam_sw_spline/Si/in.sc b/examples/PACKAGES/meam_sw_spline/Si/in.sc new file mode 100644 index 0000000000..6f235a933d --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/in.sc @@ -0,0 +1,34 @@ +# Si fcc phase + +units metal +boundary p p p + +atom_style atomic +lattice sc 2.612 +region box block 0 1 0 1 0 1 +create_box 1 box +create_atoms 1 box + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +mass * 28.085 + +variable cohesive_energy equal pe/atoms +variable atmVol equal vol/atoms +variable aLatt equal (vol/atoms)^0.3333333333 + +run 0 + +print "====================================================" +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +print "Reference cohesive energy: -4.337 eV/atom" +print "Atomic volume ${atmVol} A^3" +print "Lattice constant ${aLatt} A" +print "Reference lattice constant 2.612 A" +print "====================================================" + + +#dump 1 all custom 1 sc.dump id type x y z fx fy fz +#run 0 + + diff --git a/examples/PACKAGES/meam_sw_spline/Si/in.sc_relax b/examples/PACKAGES/meam_sw_spline/Si/in.sc_relax new file mode 100644 index 0000000000..82a017acfe --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/in.sc_relax @@ -0,0 +1,38 @@ +# Si fcc phase + +units metal +boundary p p p + +atom_style atomic +lattice sc 2.612 +region box block 0 1 0 1 0 1 +create_box 1 box +create_atoms 1 box + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +mass * 28.085 + +fix relax all box/relax aniso 0 +thermo 1 +minimize 0 0 10000 100000 + +variable cohesive_energy equal pe/atoms +variable atmVol equal vol/atoms +variable aLatt equal (vol/atoms)^0.3333333333 + +run 0 + +print "====================================================" +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +print "Reference cohesive energy: -4.337 eV/atom" +print "Atomic volume ${atmVol} A^3" +print "Lattice constant ${aLatt} A" +print "Reference lattice constant 2.612 A" +print "====================================================" + + +#dump 1 all custom 1 fcc.dump id type x y z fx fy fz +#run 0 + + diff --git a/examples/PACKAGES/meam_sw_spline/Si/in.single_atom b/examples/PACKAGES/meam_sw_spline/Si/in.single_atom new file mode 100644 index 0000000000..b145e68e0f --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/in.single_atom @@ -0,0 +1,27 @@ +# Si single atom in vacuum + +units metal +boundary f f f + +atom_style atomic +region box block -100 100 -100 100 -100 100 units box +create_box 1 box +create_atoms 1 single 0 0 0 units box + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +mass * 28.085 + +variable cohesive_energy equal pe/atoms +run 0 + +print "====================================================" +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +print "Reference cohesive energy: 0 eV/atom" +print "====================================================" + + +#dump 1 all custom 1 single_atom.dump id type x y z fx fy fz +#run 0 + + diff --git a/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.bcc.g++.1 b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.bcc.g++.1 new file mode 100644 index 0000000000..5ba7d5ed55 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.bcc.g++.1 @@ -0,0 +1,99 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Si bcc + +units metal +boundary p p p + +atom_style atomic +lattice bcc 3.245 +Lattice spacing in x,y,z = 3.245 3.245 3.245 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (3.245 3.245 3.245) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 2 atoms + using lattice units in orthogonal box = (0 0 0) to (3.245 3.245 3.245) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +Reading meam/sw/spline potential file Si.b.meam.sw.spline with DATE: 2012-10-26 +mass * 28.085 + +variable cohesive_energy equal pe/atoms +variable atmVol equal vol/atoms +variable aLatt equal (2*vol/atoms)^0.333333333333 + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.4 + ghost atom cutoff = 6.4 + binsize = 3.2, bins = 2 2 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.714 | 3.714 | 3.714 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -8.7453652 0 -8.7453652 -50884.003 +Loop time of 1.393e-06 on 1 procs for 0 steps with 2 atoms + +71.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.393e-06 | | |100.00 + +Nlocal: 2 ave 2 max 2 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 187 ave 187 max 187 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 58 ave 58 max 58 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 116 ave 116 max 116 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 116 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.37268261764397 eV/atom +print "Reference cohesive energy: -4.37 eV/atom" +Reference cohesive energy: -4.37 eV/atom +print "Atomic volume ${atmVol} A^3" +Atomic volume 17.0849655625 A^3 +print "Lattice constant ${aLatt} A" +Lattice constant 3.24499999999618 A +print "Reference lattice constant 3.245 A" +Reference lattice constant 3.245 A +print "====================================================" +==================================================== + +#dump 1 all custom 1 bcc.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.bcc.g++.4 b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.bcc.g++.4 new file mode 100644 index 0000000000..be0e7cbfe5 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.bcc.g++.4 @@ -0,0 +1,100 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Si bcc + +units metal +boundary p p p + +atom_style atomic +lattice bcc 3.245 +Lattice spacing in x,y,z = 3.245 3.245 3.245 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (3.245 3.245 3.245) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 2 atoms + using lattice units in orthogonal box = (0 0 0) to (3.245 3.245 3.245) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +Reading meam/sw/spline potential file Si.b.meam.sw.spline with DATE: 2012-10-26 +mass * 28.085 + +variable cohesive_energy equal pe/atoms +variable atmVol equal vol/atoms +variable aLatt equal (2*vol/atoms)^0.333333333333 + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.4 + ghost atom cutoff = 6.4 + binsize = 3.2, bins = 2 2 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966) +Per MPI rank memory allocation (min/avg/max) = 3.745 | 3.745 | 3.745 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -8.7453652 0 -8.7453652 -50884.003 +Loop time of 5.23625e-06 on 4 procs for 0 steps with 2 atoms + +81.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 5.236e-06 | | |100.00 + +Nlocal: 0.5 ave 1 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 143.5 ave 144 max 143 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 14.5 ave 29 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 29 ave 58 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 116 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.37268261764397 eV/atom +print "Reference cohesive energy: -4.37 eV/atom" +Reference cohesive energy: -4.37 eV/atom +print "Atomic volume ${atmVol} A^3" +Atomic volume 17.0849655625 A^3 +print "Lattice constant ${aLatt} A" +Lattice constant 3.24499999999618 A +print "Reference lattice constant 3.245 A" +Reference lattice constant 3.245 A +print "====================================================" +==================================================== + +#dump 1 all custom 1 bcc.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.bcc_relax.g++.1 b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.bcc_relax.g++.1 new file mode 100644 index 0000000000..ac73d239f3 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.bcc_relax.g++.1 @@ -0,0 +1,3489 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Si bcc + +units metal +boundary p p p + +atom_style atomic +lattice bcc 3.2488516 +Lattice spacing in x,y,z = 3.2488516 3.2488516 3.2488516 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (3.2488516 3.2488516 3.2488516) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 2 atoms + using lattice units in orthogonal box = (0 0 0) to (3.2488516 3.2488516 3.2488516) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +Reading meam/sw/spline potential file Si.b.meam.sw.spline with DATE: 2012-10-26 +mass * 28.085 + +fix relax all box/relax aniso 0 +thermo 1 +minimize 0 0 10000 100000 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.4 + ghost atom cutoff = 6.4 + binsize = 3.2, bins = 2 2 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 4.839 | 4.839 | 4.839 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 0 -8.7404875 0 -8.7404875 -77295.383 34.291748 + 1 0 -8.7409767 0 -8.7409767 -75094.498 34.281461 + 2 0 -8.7414517 0 -8.7414517 -72888.657 34.271177 + 3 0 -8.7419124 0 -8.7419124 -70677.857 34.260895 + 4 0 -8.7423588 0 -8.7423588 -68462.093 34.250614 + 5 0 -8.7427909 0 -8.7427909 -66241.362 34.240336 + 6 0 -8.7432086 0 -8.7432086 -64015.66 34.23006 + 7 0 -8.743612 0 -8.743612 -61784.983 34.219786 + 8 0 -8.7440009 0 -8.7440009 -59549.327 34.209514 + 9 0 -8.7443755 0 -8.7443755 -57308.688 34.199244 + 10 0 -8.7447355 0 -8.7447355 -55063.062 34.188976 + 11 0 -8.7450812 0 -8.7450812 -52812.505 34.17871 + 12 0 -8.7454123 0 -8.7454123 -50557.316 34.168446 + 13 0 -8.7457288 0 -8.7457288 -48297.534 34.158184 + 14 0 -8.7460309 0 -8.7460309 -46033.158 34.147924 + 15 0 -8.7463183 0 -8.7463183 -43764.184 34.137666 + 16 0 -8.7465912 0 -8.7465912 -41490.611 34.127411 + 17 0 -8.7468494 0 -8.7468494 -39212.436 34.117157 + 18 0 -8.747093 0 -8.747093 -36929.656 34.106906 + 19 0 -8.747322 0 -8.747322 -34642.27 34.096656 + 20 0 -8.7475362 0 -8.7475362 -32350.275 34.086409 + 21 0 -8.7477357 0 -8.7477357 -30053.669 34.076163 + 22 0 -8.7479205 0 -8.7479205 -27752.449 34.06592 + 23 0 -8.7480906 0 -8.7480906 -25446.613 34.055679 + 24 0 -8.7482458 0 -8.7482458 -23136.159 34.045439 + 25 0 -8.7483863 0 -8.7483863 -20821.084 34.035202 + 26 0 -8.7485119 0 -8.7485119 -18501.386 34.024967 + 27 0 -8.7486226 0 -8.7486226 -16177.063 34.014734 + 28 0 -8.7487185 0 -8.7487185 -13848.113 34.004503 + 29 0 -8.7487994 0 -8.7487994 -11514.532 33.994274 + 30 0 -8.7488655 0 -8.7488655 -9176.3196 33.984047 + 31 0 -8.7489166 0 -8.7489166 -6833.4722 33.973822 + 32 0 -8.7489527 0 -8.7489527 -4485.9879 33.963599 + 33 0 -8.7489738 0 -8.7489738 -2133.8643 33.953379 + 34 0 -8.74898 0 -8.74898 -0.15827233 33.944126 + 35 0 -8.74898 0 -8.74898 -4.1653555e-06 33.944126 + 36 0 -8.74898 0 -8.74898 9.222924e-10 33.944126 + 37 0 -8.74898 0 -8.74898 -1.3380227e-09 33.944126 + 38 0 -8.74898 0 -8.74898 -1.9424037e-09 33.944126 + 39 0 -8.74898 0 -8.74898 3.4935318e-10 33.944126 + 40 0 -8.74898 0 -8.74898 -1.2926068e-10 33.944126 + 41 0 -8.74898 0 -8.74898 1.0131242e-10 33.944126 + 42 0 -8.74898 0 -8.74898 1.0131242e-10 33.944126 + 43 0 -8.74898 0 -8.74898 -7.4761581e-10 33.944126 + 44 0 -8.74898 0 -8.74898 1.2926068e-10 33.944126 + 45 0 -8.74898 0 -8.74898 -7.4761581e-10 33.944126 + 46 0 -8.74898 0 -8.74898 -5.5547156e-10 33.944126 + 47 0 -8.74898 0 -8.74898 -9.2578593e-10 33.944126 + 48 0 -8.74898 0 -8.74898 4.9608152e-10 33.944126 + 49 0 -8.74898 0 -8.74898 -9.2578593e-10 33.944126 + 50 0 -8.74898 0 -8.74898 1.0201113e-09 33.944126 + 51 0 -8.74898 0 -8.74898 -4.2271735e-10 33.944126 + 52 0 -8.74898 0 -8.74898 -2.6201489e-10 33.944126 + 53 0 -8.74898 0 -8.74898 6.5329045e-10 33.944126 + 54 0 -8.74898 0 -8.74898 -4.2271735e-10 33.944126 + 55 0 -8.74898 0 -8.74898 -2.6201489e-10 33.944126 + 56 0 -8.74898 0 -8.74898 6.5329045e-10 33.944126 + 57 0 -8.74898 0 -8.74898 -4.2271735e-10 33.944126 + 58 0 -8.74898 0 -8.74898 -2.6201489e-10 33.944126 + 59 0 -8.74898 0 -8.74898 6.5329045e-10 33.944126 + 60 0 -8.74898 0 -8.74898 -4.2271735e-10 33.944126 + 61 0 -8.74898 0 -8.74898 1.0480595e-10 33.944126 + 62 0 -8.74898 0 -8.74898 -2.6201489e-10 33.944126 + 63 0 -8.74898 0 -8.74898 1.5860634e-09 33.944126 + 64 0 -8.74898 0 -8.74898 -5.8341981e-10 33.944126 + 65 0 -8.74898 0 -8.74898 -4.2271735e-10 33.944126 + 66 0 -8.74898 0 -8.74898 1.0480595e-10 33.944126 + 67 0 -8.74898 0 -8.74898 -2.6201489e-10 33.944126 + 68 0 -8.74898 0 -8.74898 1.3974127e-10 33.944126 + 69 0 -8.74898 0 -8.74898 -2.3406663e-10 33.944126 + 70 0 -8.74898 0 -8.74898 1.0131242e-09 33.944126 + 71 0 -8.74898 0 -8.74898 -4.2271735e-10 33.944126 + 72 0 -8.74898 0 -8.74898 -4.2271735e-10 33.944126 + 73 0 -8.74898 0 -8.74898 3.5983378e-10 33.944126 + 74 0 -8.74898 0 -8.74898 -4.2271735e-10 33.944126 + 75 0 -8.74898 0 -8.74898 -1.7467659e-10 33.944126 + 76 0 -8.74898 0 -8.74898 1.0131242e-09 33.944126 + 77 0 -8.74898 0 -8.74898 -4.2271735e-10 33.944126 + 78 0 -8.74898 0 -8.74898 -7.1617402e-10 33.944126 + 79 0 -8.74898 0 -8.74898 1.6768953e-10 33.944126 + 80 0 -8.74898 0 -8.74898 1.537154e-10 33.944126 + 81 0 -8.74898 0 -8.74898 3.5983378e-10 33.944126 + 82 0 -8.74898 0 -8.74898 -2.1659897e-10 33.944126 + 83 0 -8.74898 0 -8.74898 9.7120185e-10 33.944126 + 84 0 -8.74898 0 -8.74898 -4.2271735e-10 33.944126 + 85 0 -8.74898 0 -8.74898 -4.2271735e-10 33.944126 + 86 0 -8.74898 0 -8.74898 9.7120185e-10 33.944126 + 87 0 -8.74898 0 -8.74898 -4.716268e-10 33.944126 + 88 0 -8.74898 0 -8.74898 -4.2271735e-10 33.944126 + 89 0 -8.74898 0 -8.74898 2.4454723e-11 33.944126 + 90 0 -8.74898 0 -8.74898 -1.0480595e-11 33.944126 + 91 0 -8.74898 0 -8.74898 8.4892823e-10 33.944126 + 92 0 -8.74898 0 -8.74898 3.7730144e-10 33.944126 + 93 0 -8.74898 0 -8.74898 -1.2332167e-09 33.944126 + 94 0 -8.74898 0 -8.74898 1.484751e-09 33.944126 + 95 0 -8.74898 0 -8.74898 -1.2332167e-09 33.944126 + 96 0 -8.74898 0 -8.74898 9.0133121e-10 33.944126 + 97 0 -8.74898 0 -8.74898 -1.2332167e-09 33.944126 + 98 0 -8.74898 0 -8.74898 1.484751e-09 33.944126 + 99 0 -8.74898 0 -8.74898 1.6070246e-10 33.944126 + 100 0 -8.74898 0 -8.74898 -7.4761581e-10 33.944126 + 101 0 -8.74898 0 -8.74898 3.9826263e-10 33.944126 + 102 0 -8.74898 0 -8.74898 1.6070246e-10 33.944126 + 103 0 -8.74898 0 -8.74898 -3.1092433e-10 33.944126 + 104 0 -8.74898 0 -8.74898 3.9826263e-10 33.944126 + 105 0 -8.74898 0 -8.74898 -3.1092433e-10 33.944126 + 106 0 -8.74898 0 -8.74898 6.4979692e-10 33.944126 + 107 0 -8.74898 0 -8.74898 -3.1092433e-10 33.944126 + 108 0 -8.74898 0 -8.74898 9.6421478e-10 33.944126 + 109 0 -8.74898 0 -8.74898 -1.3275421e-10 33.944126 + 110 0 -8.74898 0 -8.74898 -1.2926068e-10 33.944126 + 111 0 -8.74898 0 -8.74898 -4.0175616e-10 33.944126 + 112 0 -8.74898 0 -8.74898 -8.7338296e-10 33.944126 + 113 0 -8.74898 0 -8.74898 -3.5634025e-10 33.944126 + 114 0 -8.74898 0 -8.74898 2.969502e-10 33.944126 + 115 0 -8.74898 0 -8.74898 -3.5634025e-10 33.944126 + 116 0 -8.74898 0 -8.74898 2.969502e-10 33.944126 + 117 0 -8.74898 0 -8.74898 -4.8210739e-10 33.944126 + 118 0 -8.74898 0 -8.74898 2.969502e-10 33.944126 + 119 0 -8.74898 0 -8.74898 2.969502e-10 33.944126 + 120 0 -8.74898 0 -8.74898 -4.8210739e-10 33.944126 + 121 0 -8.74898 0 -8.74898 2.969502e-10 33.944126 + 122 0 -8.74898 0 -8.74898 -2.0611838e-10 33.944126 + 123 0 -8.74898 0 -8.74898 2.969502e-10 33.944126 + 124 0 -8.74898 0 -8.74898 -2.0611838e-10 33.944126 + 125 0 -8.74898 0 -8.74898 -2.0611838e-10 33.944126 + 126 0 -8.74898 0 -8.74898 2.969502e-10 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2.1799639e-09 33.944126 + 3320 0 -8.74898 0 -8.74898 -1.0934755e-09 33.944126 + 3321 0 -8.74898 0 -8.74898 -1.2017749e-09 33.944126 + 3322 0 -8.74898 0 -8.74898 1.5755829e-09 33.944126 + 3323 0 -8.74898 0 -8.74898 -1.2576715e-09 33.944126 + 3324 0 -8.74898 0 -8.74898 1.2367103e-09 33.944126 + 3325 0 -8.74898 0 -8.74898 -4.611462e-10 33.944126 + 3326 0 -8.74898 0 -8.74898 -1.2926068e-10 33.944126 + 3327 0 -8.74898 0 -8.74898 1.8026624e-09 33.944126 + 3328 0 -8.74898 0 -8.74898 -1.0795013e-09 33.944126 + 3329 0 -8.74898 0 -8.74898 -3.4935318e-10 33.944126 + 3330 0 -8.74898 0 -8.74898 2.082145e-09 33.944126 + 3331 0 -8.74898 0 -8.74898 -2.0087808e-09 33.944126 + 3332 0 -8.74898 0 -8.74898 -6.9870636e-12 33.944126 + 3333 0 -8.74898 0 -8.74898 3.0044374e-10 33.944126 + 3334 0 -8.74898 0 -8.74898 3.0044374e-10 33.944126 + 3335 0 -8.74898 0 -8.74898 1.096969e-09 33.944126 + 3336 0 -8.74898 0 -8.74898 -6.8473224e-10 33.944126 + 3337 0 -8.74898 0 -8.74898 8.4892823e-10 33.944126 + 3338 0 -8.74898 0 -8.74898 -1.4148804e-09 33.944126 + 3339 0 -8.74898 0 -8.74898 3.9127556e-10 33.944126 + 3340 0 -8.74898 0 -8.74898 3.9127556e-10 33.944126 + 3341 0 -8.74898 0 -8.74898 4.9957505e-10 33.944126 + 3342 0 -8.74898 0 -8.74898 3.8079497e-10 33.944126 + 3343 0 -8.74898 0 -8.74898 -1.0795013e-09 33.944126 + 3344 0 -8.74898 0 -8.74898 -1.2017749e-09 33.944126 + 3345 0 -8.74898 0 -8.74898 2.0961191e-09 33.944126 + 3346 0 -8.74898 0 -8.74898 3.4935318e-12 33.944126 + 3347 0 -8.74898 0 -8.74898 3.4935318e-12 33.944126 +Loop time of 0.148794 on 1 procs for 3347 steps with 2 atoms + +94.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = quadratic factors are zero + Energy initial, next-to-last, final = + -8.74048754954825 -8.74897996145753 -8.74897996145753 + Force two-norm initial, final = 2.865454 2.407019e-15 + Force max component initial, final = 1.6543707 1.3322676e-15 + Final line search alpha, max atom move = 1 1.3322676e-15 + Iterations, force evaluations = 3347 6661 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.090718 | 0.090718 | 0.090718 | 0.0 | 60.97 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0076926 | 0.0076926 | 0.0076926 | 0.0 | 5.17 +Output | 0.017918 | 0.017918 | 0.017918 | 0.0 | 12.04 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.03247 | | | 21.82 + +Nlocal: 2 ave 2 max 2 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 187 ave 187 max 187 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 58 ave 58 max 58 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 116 ave 116 max 116 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 116 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + +variable cohesive_energy equal pe/atoms +variable atmVol equal vol/atoms +variable aLatt equal (2*vol/atoms)^0.333333333333 + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Per MPI rank memory allocation (min/avg/max) = 3.714 | 3.714 | 3.714 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 3347 0 -8.74898 0 -8.74898 9.4325359e-11 33.944126 +Loop time of 5.89e-07 on 1 procs for 0 steps with 2 atoms + +169.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 5.89e-07 | | |100.00 + +Nlocal: 2 ave 2 max 2 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 187 ave 187 max 187 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 58 ave 58 max 58 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 116 ave 116 max 116 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 116 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.37448998072876 eV/atom +print "Reference cohesive energy: -4.37 eV/atom" +Reference cohesive energy: -4.37 eV/atom +print "Atomic volume ${atmVol} A^3" +Atomic volume 16.9720627605584 A^3 +print "Lattice constant ${aLatt} A" +Lattice constant 3.23783620452874 A +print "Reference lattice constant 3.238 A" +Reference lattice constant 3.238 A +print "====================================================" +==================================================== + +#dump 1 all custom 1 bcc.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.bcc_relax.g++.4 b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.bcc_relax.g++.4 new file mode 100644 index 0000000000..ffd774cba5 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.bcc_relax.g++.4 @@ -0,0 +1,8809 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Si bcc + +units metal +boundary p p p + +atom_style atomic +lattice bcc 3.2488516 +Lattice spacing in x,y,z = 3.2488516 3.2488516 3.2488516 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (3.2488516 3.2488516 3.2488516) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 2 atoms + using lattice units in orthogonal box = (0 0 0) to (3.2488516 3.2488516 3.2488516) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +Reading meam/sw/spline potential file Si.b.meam.sw.spline with DATE: 2012-10-26 +mass * 28.085 + +fix relax all box/relax aniso 0 +thermo 1 +minimize 0 0 10000 100000 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.4 + ghost atom cutoff = 6.4 + binsize = 3.2, bins = 2 2 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966) +Per MPI rank memory allocation (min/avg/max) = 4.87 | 4.87 | 4.87 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 0 -8.7404875 0 -8.7404875 -77295.383 34.291748 + 1 0 -8.7409767 0 -8.7409767 -75094.498 34.281461 + 2 0 -8.7414517 0 -8.7414517 -72888.657 34.271177 + 3 0 -8.7419124 0 -8.7419124 -70677.857 34.260895 + 4 0 -8.7423588 0 -8.7423588 -68462.093 34.250614 + 5 0 -8.7427909 0 -8.7427909 -66241.362 34.240336 + 6 0 -8.7432086 0 -8.7432086 -64015.66 34.23006 + 7 0 -8.743612 0 -8.743612 -61784.983 34.219786 + 8 0 -8.7440009 0 -8.7440009 -59549.327 34.209514 + 9 0 -8.7443755 0 -8.7443755 -57308.688 34.199244 + 10 0 -8.7447355 0 -8.7447355 -55063.062 34.188976 + 11 0 -8.7450812 0 -8.7450812 -52812.505 34.17871 + 12 0 -8.7454123 0 -8.7454123 -50557.316 34.168446 + 13 0 -8.7457288 0 -8.7457288 -48297.534 34.158184 + 14 0 -8.7460309 0 -8.7460309 -46033.158 34.147924 + 15 0 -8.7463183 0 -8.7463183 -43764.184 34.137666 + 16 0 -8.7465912 0 -8.7465912 -41490.611 34.127411 + 17 0 -8.7468494 0 -8.7468494 -39212.436 34.117157 + 18 0 -8.747093 0 -8.747093 -36929.656 34.106906 + 19 0 -8.747322 0 -8.747322 -34642.27 34.096656 + 20 0 -8.7475362 0 -8.7475362 -32350.275 34.086409 + 21 0 -8.7477357 0 -8.7477357 -30053.669 34.076163 + 22 0 -8.7479205 0 -8.7479205 -27752.449 34.06592 + 23 0 -8.7480906 0 -8.7480906 -25446.613 34.055679 + 24 0 -8.7482458 0 -8.7482458 -23136.159 34.045439 + 25 0 -8.7483863 0 -8.7483863 -20821.084 34.035202 + 26 0 -8.7485119 0 -8.7485119 -18501.386 34.024967 + 27 0 -8.7486226 0 -8.7486226 -16177.063 34.014734 + 28 0 -8.7487185 0 -8.7487185 -13848.113 34.004503 + 29 0 -8.7487994 0 -8.7487994 -11514.532 33.994274 + 30 0 -8.7488655 0 -8.7488655 -9176.3196 33.984047 + 31 0 -8.7489166 0 -8.7489166 -6833.4722 33.973822 + 32 0 -8.7489527 0 -8.7489527 -4485.9879 33.963599 + 33 0 -8.7489738 0 -8.7489738 -2133.8643 33.953379 + 34 0 -8.74898 0 -8.74898 -0.15827233 33.944126 + 35 0 -8.74898 0 -8.74898 -4.165364e-06 33.944126 + 36 0 -8.74898 0 -8.74898 7.5475462e-10 33.944126 + 37 0 -8.74898 0 -8.74898 -1.1072621e-09 33.944126 + 38 0 -8.74898 0 -8.74898 -3.440686e-10 33.944126 + 39 0 -8.74898 0 -8.74898 2.6000133e-10 33.944126 + 40 0 -8.74898 0 -8.74898 -3.0882658e-10 33.944126 + 41 0 -8.74898 0 -8.74898 2.6038343e-10 33.944126 + 42 0 -8.74898 0 -8.74898 -3.0841718e-10 33.944126 + 43 0 -8.74898 0 -8.74898 1.1685158e-09 33.944126 + 44 0 -8.74898 0 -8.74898 -3.4208984e-10 33.944126 + 45 0 -8.74898 0 -8.74898 6.0400204e-10 33.944126 + 46 0 -8.74898 0 -8.74898 -6.4554544e-10 33.944126 + 47 0 -8.74898 0 -8.74898 6.0422039e-10 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33.944126 + 8480 0 -8.74898 0 -8.74898 1.3048799e-09 33.944126 + 8481 0 -8.74898 0 -8.74898 2.0706164e-10 33.944126 + 8482 0 -8.74898 0 -8.74898 -1.3920314e-09 33.944126 + 8483 0 -8.74898 0 -8.74898 6.5972781e-10 33.944126 + 8484 0 -8.74898 0 -8.74898 -6.9135753e-10 33.944126 + 8485 0 -8.74898 0 -8.74898 5.6961959e-10 33.944126 + 8486 0 -8.74898 0 -8.74898 -6.732605e-10 33.944126 + 8487 0 -8.74898 0 -8.74898 1.4489066e-09 33.944126 + 8488 0 -8.74898 0 -8.74898 2.0815337e-10 33.944126 + 8489 0 -8.74898 0 -8.74898 -8.4305544e-10 33.944126 + 8490 0 -8.74898 0 -8.74898 2.2124047e-10 33.944126 + 8491 0 -8.74898 0 -8.74898 -6.7301486e-10 33.944126 + 8492 0 -8.74898 0 -8.74898 -6.5945176e-10 33.944126 + 8493 0 -8.74898 0 -8.74898 1.9838143e-09 33.944126 + 8494 0 -8.74898 0 -8.74898 -4.8248441e-10 33.944126 + 8495 0 -8.74898 0 -8.74898 -1.1297982e-09 33.944126 + 8496 0 -8.74898 0 -8.74898 1.4490021e-09 33.944126 + 8497 0 -8.74898 0 -8.74898 -1.1296071e-09 33.944126 + 8498 0 -8.74898 0 -8.74898 6.6759032e-10 33.944126 + 8499 0 -8.74898 0 -8.74898 2.5283237e-10 33.944126 + 8500 0 -8.74898 0 -8.74898 2.5359658e-10 33.944126 + 8501 0 -8.74898 0 -8.74898 -1.1431173e-09 33.944126 + 8502 0 -8.74898 0 -8.74898 -7.2307225e-10 33.944126 + 8503 0 -8.74898 0 -8.74898 1.5947871e-09 33.944126 + 8504 0 -8.74898 0 -8.74898 8.9236389e-11 33.944126 + 8505 0 -8.74898 0 -8.74898 -1.0992804e-09 33.944126 + 8506 0 -8.74898 0 -8.74898 -1.1332596e-09 33.944126 + 8507 0 -8.74898 0 -8.74898 -6.356299e-10 33.944126 + 8508 0 -8.74898 0 -8.74898 2.3812956e-09 33.944126 + 8509 0 -8.74898 0 -8.74898 -1.1009726e-09 33.944126 + 8510 0 -8.74898 0 -8.74898 6.2981824e-10 33.944126 + 8511 0 -8.74898 0 -8.74898 -1.5176458e-09 33.944126 + 8512 0 -8.74898 0 -8.74898 2.3672668e-09 33.944126 + 8513 0 -8.74898 0 -8.74898 -1.114974e-09 33.944126 + 8514 0 -8.74898 0 -8.74898 2.4917109e-10 33.944126 + 8515 0 -8.74898 0 -8.74898 -1.2733998e-10 33.944126 + 8516 0 -8.74898 0 -8.74898 -1.1472064e-09 33.944126 + 8517 0 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33.944126 + 8536 0 -8.74898 0 -8.74898 6.3029587e-10 33.944126 + 8537 0 -8.74898 0 -8.74898 -1.1332869e-09 33.944126 + 8538 0 -8.74898 0 -8.74898 6.4291898e-10 33.944126 + 8539 0 -8.74898 0 -8.74898 2.7747416e-10 33.944126 + 8540 0 -8.74898 0 -8.74898 2.7821107e-10 33.944126 + 8541 0 -8.74898 0 -8.74898 -1.1470973e-09 33.944126 + 8542 0 -8.74898 0 -8.74898 6.2910862e-10 33.944126 + 8543 0 -8.74898 0 -8.74898 2.7761062e-10 33.944126 + 8544 0 -8.74898 0 -8.74898 2.5041293e-10 33.944126 + 8545 0 -8.74898 0 -8.74898 -8.5685612e-10 33.944126 + 8546 0 -8.74898 0 -8.74898 2.7703747e-10 33.944126 + 8547 0 -8.74898 0 -8.74898 2.7780168e-10 33.944126 + 8548 0 -8.74898 0 -8.74898 2.5060398e-10 33.944126 + 8549 0 -8.74898 0 -8.74898 -8.5666506e-10 33.944126 + 8550 0 -8.74898 0 -8.74898 2.7722852e-10 33.944126 + 8551 0 -8.74898 0 -8.74898 2.7799273e-10 33.944126 + 8552 0 -8.74898 0 -8.74898 -1.1612897e-09 33.944126 + 8553 0 -8.74898 0 -8.74898 1.6375812e-09 33.944126 + 8554 0 -8.74898 0 -8.74898 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0 -8.74898 2.3782234e-09 33.944126 + 8574 0 -8.74898 0 -8.74898 -1.1138277e-09 33.944126 + 8575 0 -8.74898 0 -8.74898 2.5031741e-10 33.944126 + 8576 0 -8.74898 0 -8.74898 -1.1084641e-09 33.944126 + 8577 0 -8.74898 0 -8.74898 2.3647951e-09 33.944126 + 8578 0 -8.74898 0 -8.74898 -3.5867199e-10 33.944126 + 8579 0 -8.74898 0 -8.74898 3.4005315e-10 33.944126 + 8580 0 -8.74898 0 -8.74898 -1.5492402e-09 33.944126 + 8581 0 -8.74898 0 -8.74898 -9.0274883e-10 33.944126 + 8582 0 -8.74898 0 -8.74898 1.7847205e-09 33.944126 + 8583 0 -8.74898 0 -8.74898 -1.7189979e-09 33.944126 + 8584 0 -8.74898 0 -8.74898 2.5351871e-09 33.944126 + 8585 0 -8.74898 0 -8.74898 -2.8744925e-09 33.944126 + 8586 0 -8.74898 0 -8.74898 2.0245068e-09 33.944126 + 8587 0 -8.74898 0 -8.74898 -2.0379481e-09 33.944126 + 8588 0 -8.74898 0 -8.74898 2.0096456e-09 33.944126 + 8589 0 -8.74898 0 -8.74898 -1.2385285e-09 33.944126 + 8590 0 -8.74898 0 -8.74898 -9.8929968e-10 33.944126 + 8591 0 -8.74898 0 -8.74898 2.0367614e-09 33.944126 + 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9.2245634e-10 33.944126 + 8611 0 -8.74898 0 -8.74898 -7.9712756e-10 33.944126 + 8612 0 -8.74898 0 -8.74898 1.7767097e-09 33.944126 + 8613 0 -8.74898 0 -8.74898 -1.0426967e-09 33.944126 + 8614 0 -8.74898 0 -8.74898 -7.8301697e-10 33.944126 + 8615 0 -8.74898 0 -8.74898 9.2322055e-10 33.944126 + 8616 0 -8.74898 0 -8.74898 -7.8238922e-10 33.944126 + 8617 0 -8.74898 0 -8.74898 9.2383464e-10 33.944126 + 8618 0 -8.74898 0 -8.74898 -7.8178877e-10 33.944126 + 8619 0 -8.74898 0 -8.74898 1.7781016e-09 33.944126 + 8620 0 -8.74898 0 -8.74898 2.8651794e-10 33.944126 + 8621 0 -8.74898 0 -8.74898 -1.0197959e-09 33.944126 + 8622 0 -8.74898 0 -8.74898 -8.2308341e-10 33.944126 + 8623 0 -8.74898 0 -8.74898 1.7785383e-09 33.944126 + 8624 0 -8.74898 0 -8.74898 -1.0199597e-09 33.944126 + 8625 0 -8.74898 0 -8.74898 -8.2324717e-10 33.944126 + 8626 0 -8.74898 0 -8.74898 1.7783746e-09 33.944126 + 8627 0 -8.74898 0 -8.74898 2.7283039e-10 33.944126 + 8628 0 -8.74898 0 -8.74898 -1.0195094e-09 33.944126 + 8629 0 -8.74898 0 -8.74898 -1.1743169e-10 33.944126 + 8630 0 -8.74898 0 -8.74898 -7.957629e-10 33.944126 + 8631 0 -8.74898 0 -8.74898 1.7781016e-09 33.944126 + 8632 0 -8.74898 0 -8.74898 2.7254382e-10 33.944126 + 8633 0 -8.74898 0 -8.74898 -1.1106005e-09 33.944126 + 8634 0 -8.74898 0 -8.74898 -1.1775921e-10 33.944126 + 8635 0 -8.74898 0 -8.74898 -7.9606313e-10 33.944126 + 8636 0 -8.74898 0 -8.74898 1.7764913e-09 33.944126 + 8637 0 -8.74898 0 -8.74898 -1.1686685e-09 33.944126 + 8638 0 -8.74898 0 -8.74898 1.7639091e-09 33.944126 + 8639 0 -8.74898 0 -8.74898 -3.6715554e-10 33.944126 + 8640 0 -8.74898 0 -8.74898 -3.6786516e-10 33.944126 + 8641 0 -8.74898 0 -8.74898 -1.1686958e-09 33.944126 + 8642 0 -8.74898 0 -8.74898 1.7638819e-09 33.944126 + 8643 0 -8.74898 0 -8.74898 -3.6718283e-10 33.944126 + 8644 0 -8.74898 0 -8.74898 3.3735415e-10 33.944126 + 8645 0 -8.74898 0 -8.74898 -5.6280437e-10 33.944126 + 8646 0 -8.74898 0 -8.74898 2.1094146e-10 33.944126 + 8647 0 -8.74898 0 -8.74898 -3.6800163e-10 33.944126 + 8648 0 -8.74898 0 -8.74898 2.1070947e-10 33.944126 + 8649 0 -8.74898 0 -8.74898 3.3699934e-10 33.944126 + 8650 0 -8.74898 0 -8.74898 -3.6775599e-10 33.944126 + 8651 0 -8.74898 0 -8.74898 3.3679464e-10 33.944126 + 8652 0 -8.74898 0 -8.74898 -3.681108e-10 33.944126 + 8653 0 -8.74898 0 -8.74898 3.3643983e-10 33.944126 + 8654 0 -8.74898 0 -8.74898 -5.6373234e-10 33.944126 + 8655 0 -8.74898 0 -8.74898 -1.9168212e-10 33.944126 + 8656 0 -8.74898 0 -8.74898 -1.7789905e-10 33.944126 + 8657 0 -8.74898 0 -8.74898 -1.6411597e-10 33.944126 + 8658 0 -8.74898 0 -8.74898 -7.9663628e-10 33.944126 + 8659 0 -8.74898 0 -8.74898 2.5490278e-09 33.944126 + 8660 0 -8.74898 0 -8.74898 -1.1243017e-09 33.944126 + 8661 0 -8.74898 0 -8.74898 -2.270822e-11 33.944126 + 8662 0 -8.74898 0 -8.74898 -1.8054649e-10 33.944126 + 8663 0 -8.74898 0 -8.74898 -6.5114247e-12 33.944126 + 8664 0 -8.74898 0 -8.74898 4.9790198e-12 33.944126 + 8665 0 -8.74898 0 -8.74898 4.9790198e-12 33.944126 +Loop time of 0.729027 on 4 procs for 8665 steps with 2 atoms + +98.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = quadratic factors are zero + Energy initial, next-to-last, final = + -8.74048754954826 -8.74897996145753 -8.74897996145753 + Force two-norm initial, final = 2.865454 2.7720348e-15 + Force max component initial, final = 1.6543707 1.7824284e-15 + Final line search alpha, max atom move = 1 1.7824284e-15 + Iterations, force evaluations = 8665 17297 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.20421 | 0.20854 | 0.21363 | 0.9 | 28.61 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.19107 | 0.192 | 0.19353 | 0.2 | 26.34 +Output | 0.067404 | 0.071837 | 0.084073 | 2.6 | 9.85 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.2567 | | | 35.20 + +Nlocal: 0.5 ave 1 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 143.5 ave 144 max 143 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 14.5 ave 29 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 29 ave 58 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 116 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + +variable cohesive_energy equal pe/atoms +variable atmVol equal vol/atoms +variable aLatt equal (2*vol/atoms)^0.333333333333 + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966) +Per MPI rank memory allocation (min/avg/max) = 3.745 | 3.745 | 3.745 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 8665 0 -8.74898 0 -8.74898 9.8078051e-11 33.944126 +Loop time of 2.501e-06 on 4 procs for 0 steps with 2 atoms + +120.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.501e-06 | | |100.00 + +Nlocal: 0.5 ave 1 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 143.5 ave 144 max 143 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 14.5 ave 29 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 29 ave 58 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 116 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.37448998072876 eV/atom +print "Reference cohesive energy: -4.37 eV/atom" +Reference cohesive energy: -4.37 eV/atom +print "Atomic volume ${atmVol} A^3" +Atomic volume 16.9720627605584 A^3 +print "Lattice constant ${aLatt} A" +Lattice constant 3.23783620452874 A +print "Reference lattice constant 3.238 A" +Reference lattice constant 3.238 A +print "====================================================" +==================================================== + +#dump 1 all custom 1 bcc.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.dc.g++.1 b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.dc.g++.1 new file mode 100644 index 0000000000..4b8118d3a7 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.dc.g++.1 @@ -0,0 +1,100 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Si dc phase + +units metal +boundary p p p + +atom_style atomic +lattice diamond 5.431 +Lattice spacing in x,y,z = 5.431 5.431 5.431 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (5.431 5.431 5.431) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 8 atoms + using lattice units in orthogonal box = (0 0 0) to (5.431 5.431 5.431) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +Reading meam/sw/spline potential file Si.b.meam.sw.spline with DATE: 2012-10-26 +mass * 28.085 + +variable cohesive_energy equal pe/atoms +variable atmVol equal vol/atoms +variable aLatt equal (8*vol/atoms)^0.33333333333 + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.4 + ghost atom cutoff = 6.4 + binsize = 3.2, bins = 2 2 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.715 | 3.715 | 3.715 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -37.039999 0 -37.039999 -32.742245 +Loop time of 1.31e-06 on 1 procs for 0 steps with 8 atoms + +76.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.31e-06 | | |100.00 + +Nlocal: 8 ave 8 max 8 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 272 ave 272 max 272 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 184 ave 184 max 184 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 368 ave 368 max 368 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 368 +Ave neighs/atom = 46 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.62999988298102 eV/atom +print "Reference cohesive energy: -4.63 eV/atom" +Reference cohesive energy: -4.63 eV/atom +print "Atomic volume ${atmVol} A^3" +Atomic volume 20.023934748875 A^3 +print "Lattice constant ${aLatt} A" +Lattice constant 5.4309999999081 A +print "Reference lattice constant 5.431 A" +Reference lattice constant 5.431 A +print "====================================================" +==================================================== + + +#dump 1 all custom 1 dc.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.dc.g++.4 b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.dc.g++.4 new file mode 100644 index 0000000000..e69d02e438 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.dc.g++.4 @@ -0,0 +1,100 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Si dc phase + +units metal +boundary p p p + +atom_style atomic +lattice diamond 5.431 +Lattice spacing in x,y,z = 5.431 5.431 5.431 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (5.431 5.431 5.431) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 8 atoms + using lattice units in orthogonal box = (0 0 0) to (5.431 5.431 5.431) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +Reading meam/sw/spline potential file Si.b.meam.sw.spline with DATE: 2012-10-26 +mass * 28.085 + +variable cohesive_energy equal pe/atoms +variable atmVol equal vol/atoms +variable aLatt equal (8*vol/atoms)^0.33333333333 + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.4 + ghost atom cutoff = 6.4 + binsize = 3.2, bins = 2 2 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.729 | 3.729 | 3.729 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -37.039999 0 -37.039999 -32.742245 +Loop time of 5.486e-06 on 4 procs for 0 steps with 8 atoms + +86.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 5.486e-06 | | |100.00 + +Nlocal: 2 ave 2 max 2 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 199 ave 199 max 199 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46 ave 46 max 46 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 92 ave 92 max 92 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 368 +Ave neighs/atom = 46 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.62999988298102 eV/atom +print "Reference cohesive energy: -4.63 eV/atom" +Reference cohesive energy: -4.63 eV/atom +print "Atomic volume ${atmVol} A^3" +Atomic volume 20.023934748875 A^3 +print "Lattice constant ${aLatt} A" +Lattice constant 5.4309999999081 A +print "Reference lattice constant 5.431 A" +Reference lattice constant 5.431 A +print "====================================================" +==================================================== + + +#dump 1 all custom 1 dc.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.dc_relax.g++.1 b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.dc_relax.g++.1 new file mode 100644 index 0000000000..ce55a5d547 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.dc_relax.g++.1 @@ -0,0 +1,10143 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Si dc phase + +units metal +boundary p p p + +atom_style atomic +lattice diamond 5.43 +Lattice spacing in x,y,z = 5.43 5.43 5.43 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (5.43 5.43 5.43) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 8 atoms + using lattice units in orthogonal box = (0 0 0) to (5.43 5.43 5.43) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +Reading meam/sw/spline potential file Si.b.meam.sw.spline with DATE: 2012-10-26 +mass * 28.085 + +fix relax all box/relax aniso 0 +thermo 1 +minimize 0 0 10000 100000 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.4 + ghost atom cutoff = 6.4 + binsize = 3.2, bins = 2 2 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 4.84 | 4.84 | 4.84 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 0 -37.039984 0 -37.039984 563.98821 160.10301 + 1 0 -37.039996 0 -37.039996 239.83776 160.15104 + 2 0 -37.039999 0 -37.039999 -0.016271308 160.18662 + 3 0 -37.039999 0 -37.039999 -6.9259589e-08 160.18662 + 4 0 -37.039999 0 -37.039999 -1.1280581e-10 160.18662 + 5 0 -37.039999 0 -37.039999 -3.6428172e-11 160.18662 + 6 0 -37.039999 0 -37.039999 -3.6428172e-11 160.18662 + 7 0 -37.039999 0 -37.039999 -7.4503225e-11 160.18662 + 8 0 -37.039999 0 -37.039999 8.0104998e-10 160.18662 + 9 0 -37.039999 0 -37.039999 -5.7309202e-10 160.18662 + 10 0 -37.039999 0 -37.039999 1.8959357e-10 160.18662 + 11 0 -37.039999 0 -37.039999 1.1066779e-09 160.18662 + 12 0 -37.039999 0 -37.039999 8.7818648e-10 160.18662 + 13 0 -37.039999 0 -37.039999 -1.5267825e-10 160.18662 + 14 0 -37.039999 0 -37.039999 -8.4092618e-10 160.18662 + 15 0 -37.039999 0 -37.039999 1.9014707e-10 160.18662 + 16 0 -37.039999 0 -37.039999 1.9074697e-10 160.18662 + 17 0 -37.039999 0 -37.039999 -1.9019753e-10 160.18662 + 18 0 -37.039999 0 -37.039999 -4.5756449e-10 160.18662 + 19 0 -37.039999 0 -37.039999 1.9176395e-10 160.18662 + 20 0 -37.039999 0 -37.039999 7.5899556e-11 160.18662 + 21 0 -37.039999 0 -37.039999 -5.3512833e-10 160.18662 + 22 0 -37.039999 0 -37.039999 -2.2832699e-10 160.18662 + 23 0 -37.039999 0 -37.039999 7.6305734e-10 160.18662 + 24 0 -37.039999 0 -37.039999 8.7754334e-10 160.18662 + 25 0 -37.039999 0 -37.039999 -2.2831546e-10 160.18662 + 26 0 -37.039999 0 -37.039999 -9.1743243e-10 160.18662 + 27 0 -37.039999 0 -37.039999 3.8413973e-11 160.18662 + 28 0 -37.039999 0 -37.039999 2.6669401e-10 160.18662 + 29 0 -37.039999 0 -37.039999 1.1614517e-10 160.18662 + 30 0 -37.039999 0 -37.039999 5.6716209e-13 160.18662 + 31 0 -37.039999 0 -37.039999 1.5268114e-10 160.18662 + 32 0 -37.039999 0 -37.039999 -3.4366573e-10 160.18662 + 33 0 -37.039999 0 -37.039999 -3.4358944e-10 160.18662 + 34 0 -37.039999 0 -37.039999 3.4281134e-10 160.18662 + 35 0 -37.039999 0 -37.039999 4.1941126e-10 160.18662 + 36 0 -37.039999 0 -37.039999 -4.9621484e-10 160.18662 + 37 0 -37.039999 0 -37.039999 -5.3551075e-10 160.18662 + 38 0 -37.039999 0 -37.039999 6.4910762e-10 160.18662 + 39 0 -37.039999 0 -37.039999 8.3948064e-10 160.18662 + 40 0 -37.039999 0 -37.039999 -3.8250738e-10 160.18662 + 41 0 -37.039999 0 -37.039999 -6.1163055e-10 160.18662 + 42 0 -37.039999 0 -37.039999 4.1836409e-10 160.18662 + 43 0 -37.039999 0 -37.039999 4.9659714e-10 160.18662 + 44 0 -37.039999 0 -37.039999 7.6099144e-11 160.18662 + 45 0 -37.039999 0 -37.039999 -3.8144143e-10 160.18662 + 46 0 -37.039999 0 -37.039999 -1.5182952e-10 160.18662 + 47 0 -37.039999 0 -37.039999 4.962909e-10 160.18662 + 48 0 -37.039999 0 -37.039999 6.1048003e-10 160.18662 + 49 0 -37.039999 0 -37.039999 -1.9118372e-10 160.18662 + 50 0 -37.039999 0 -37.039999 -7.6469627e-10 160.18662 + 51 0 -37.039999 0 -37.039999 3.4264137e-10 160.18662 + 52 0 -37.039999 0 -37.039999 -4.9849368e-10 160.18662 + 53 0 -37.039999 0 -37.039999 -6.8957981e-10 160.18662 + 54 0 -37.039999 0 -37.039999 5.3519843e-10 160.18662 + 55 0 -37.039999 0 -37.039999 5.344042e-10 160.18662 + 56 0 -37.039999 0 -37.039999 -4.592235e-10 160.18662 + 57 0 -37.039999 0 -37.039999 -4.592235e-10 160.18662 + 58 0 -37.039999 0 -37.039999 4.9567537e-10 160.18662 + 59 0 -37.039999 0 -37.039999 6.1080891e-10 160.18662 + 60 0 -37.039999 0 -37.039999 -3.810327e-10 160.18662 + 61 0 -37.039999 0 -37.039999 -5.3319564e-10 160.18662 + 62 0 -37.039999 0 -37.039999 6.4849268e-10 160.18662 + 63 0 -37.039999 0 -37.039999 -5.7157083e-10 160.18662 + 64 0 -37.039999 0 -37.039999 2.2787674e-10 160.18662 + 65 0 -37.039999 0 -37.039999 6.1038737e-10 160.18662 + 66 0 -37.039999 0 -37.039999 -4.5631345e-10 160.18662 + 67 0 -37.039999 0 -37.039999 -4.5741481e-10 160.18662 + 68 0 -37.039999 0 -37.039999 1.5118168e-10 160.18662 + 69 0 -37.039999 0 -37.039999 6.1050529e-10 160.18662 + 70 0 -37.039999 0 -37.039999 1.5333149e-10 160.18662 + 71 0 -37.039999 0 -37.039999 -4.19097e-10 160.18662 + 72 0 -37.039999 0 -37.039999 -3.4321814e-10 160.18662 + 73 0 -37.039999 0 -37.039999 3.8344667e-10 160.18662 + 74 0 -37.039999 0 -37.039999 3.8602003e-11 160.18662 + 75 0 -37.039999 0 -37.039999 -2.669362e-10 160.18662 + 76 0 -37.039999 0 -37.039999 -3.838145e-11 160.18662 + 77 0 -37.039999 0 -37.039999 5.732389e-10 160.18662 + 78 0 -37.039999 0 -37.039999 -4.9653059e-10 160.18662 + 79 0 -37.039999 0 -37.039999 -5.3360999e-10 160.18662 + 80 0 -37.039999 0 -37.039999 4.5838144e-10 160.18662 + 81 0 -37.039999 0 -37.039999 -3.4451549e-10 160.18662 + 82 0 -37.039999 0 -37.039999 -2.6862907e-10 160.18662 + 83 0 -37.039999 0 -37.039999 1.1472676e-10 160.18662 + 84 0 -37.039999 0 -37.039999 3.0518717e-10 160.18662 + 85 0 -37.039999 0 -37.039999 3.7939474e-11 160.18662 + 86 0 -37.039999 0 -37.039999 -4.9689102e-10 160.18662 + 87 0 -37.039999 0 -37.039999 -5.3507453e-10 160.18662 + 88 0 -37.039999 0 -37.039999 4.2021773e-10 160.18662 + 89 0 -37.039999 0 -37.039999 6.8730619e-10 160.18662 + 90 0 -37.039999 0 -37.039999 -2.2876438e-10 160.18662 + 91 0 -37.039999 0 -37.039999 -3.8108085e-10 160.18662 + 92 0 -37.039999 0 -37.039999 -4.5672754e-10 160.18662 + 93 0 -37.039999 0 -37.039999 1.4359492e-12 160.18662 + 94 0 -37.039999 0 -37.039999 4.2011352e-10 160.18662 + 95 0 -37.039999 0 -37.039999 3.4393145e-10 160.18662 + 96 0 -37.039999 0 -37.039999 7.6644047e-11 160.18662 + 97 0 -37.039999 0 -37.039999 -3.4233941e-10 160.18662 + 98 0 -37.039999 0 -37.039999 -2.6662425e-10 160.18662 + 99 0 -37.039999 0 -37.039999 -7.4713838e-11 160.18662 + 100 0 -37.039999 0 -37.039999 7.8066152e-11 160.18662 + 101 0 -37.039999 0 -37.039999 -7.4170309e-11 160.18662 + 102 0 -37.039999 0 -37.039999 -7.5142443e-11 160.18662 + 103 0 -37.039999 0 -37.039999 3.0502161e-10 160.18662 + 104 0 -37.039999 0 -37.039999 3.9230151e-11 160.18662 + 105 0 -37.039999 0 -37.039999 -7.4715832e-11 160.18662 + 106 0 -37.039999 0 -37.039999 1.1617675e-12 160.18662 + 107 0 -37.039999 0 -37.039999 1.1520779e-10 160.18662 + 108 0 -37.039999 0 -37.039999 -5.7131409e-10 160.18662 + 109 0 -37.039999 0 -37.039999 4.2063857e-10 160.18662 + 110 0 -37.039999 0 -37.039999 3.8016176e-10 160.18662 + 111 0 -37.039999 0 -37.039999 -2.2771719e-10 160.18662 + 112 0 -37.039999 0 -37.039999 -3.8119192e-10 160.18662 + 113 0 -37.039999 0 -37.039999 2.6660289e-10 160.18662 + 114 0 -37.039999 0 -37.039999 1.9137526e-10 160.18662 + 115 0 -37.039999 0 -37.039999 2.2828831e-10 160.18662 + 116 0 -37.039999 0 -37.039999 1.0410212e-12 160.18662 + 117 0 -37.039999 0 -37.039999 -1.1399254e-10 160.18662 + 118 0 -37.039999 0 -37.039999 7.7368615e-11 160.18662 + 119 0 -37.039999 0 -37.039999 3.989204e-11 160.18662 + 120 0 -37.039999 0 -37.039999 -2.2892627e-10 160.18662 + 121 0 -37.039999 0 -37.039999 7.9698584e-13 160.18662 + 122 0 -37.039999 0 -37.039999 -1.5278451e-10 160.18662 + 123 0 -37.039999 0 -37.039999 1.0497785e-12 160.18662 + 124 0 -37.039999 0 -37.039999 7.7220313e-11 160.18662 + 125 0 -37.039999 0 -37.039999 3.9395875e-11 160.18662 + 126 0 -37.039999 0 -37.039999 -1.1294719e-10 160.18662 + 127 0 -37.039999 0 -37.039999 -1.8868772e-10 160.18662 + 128 0 -37.039999 0 -37.039999 1.4969987e-12 160.18662 + 129 0 -37.039999 0 -37.039999 7.8089994e-11 160.18662 + 130 0 -37.039999 0 -37.039999 -7.4877041e-11 160.18662 + 131 0 -37.039999 0 -37.039999 -3.6441306e-11 160.18662 + 132 0 -37.039999 0 -37.039999 6.8914635e-13 160.18662 + 133 0 -37.039999 0 -37.039999 -7.4989693e-11 160.18662 + 134 0 -37.039999 0 -37.039999 3.2729915e-13 160.18662 + 135 0 -37.039999 0 -37.039999 -3.6247729e-11 160.18662 + 136 0 -37.039999 0 -37.039999 3.0546791e-10 160.18662 + 137 0 -37.039999 0 -37.039999 1.9018793e-10 160.18662 + 138 0 -37.039999 0 -37.039999 -3.7888564e-11 160.18662 + 139 0 -37.039999 0 -37.039999 7.6022826e-11 160.18662 + 140 0 -37.039999 0 -37.039999 -5.3374735e-10 160.18662 + 141 0 -37.039999 0 -37.039999 -5.3379628e-10 160.18662 + 142 0 -37.039999 0 -37.039999 5.3496604e-10 160.18662 + 143 0 -37.039999 0 -37.039999 5.7303445e-10 160.18662 + 144 0 -37.039999 0 -37.039999 1.1455065e-10 160.18662 + 145 0 -37.039999 0 -37.039999 -1.0705497e-09 160.18662 + 146 0 -37.039999 0 -37.039999 -1.0692533e-09 160.18662 + 147 0 -37.039999 0 -37.039999 1.1465881e-10 160.18662 + 148 0 -37.039999 0 -37.039999 -1.2509957e-12 160.18662 + 149 0 -37.039999 0 -37.039999 2.2897367e-10 160.18662 + 150 0 -37.039999 0 -37.039999 -3.8557307e-11 160.18662 + 151 0 -37.039999 0 -37.039999 -1.8851574e-10 160.18662 + 152 0 -37.039999 0 -37.039999 3.0536076e-10 160.18662 + 153 0 -37.039999 0 -37.039999 4.1978479e-10 160.18662 + 154 0 -37.039999 0 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160.18662 + 9825 0 -37.039999 0 -37.039999 4.2071864e-10 160.18662 + 9826 0 -37.039999 0 -37.039999 6.1147149e-10 160.18662 + 9827 0 -37.039999 0 -37.039999 -2.6723406e-10 160.18662 + 9828 0 -37.039999 0 -37.039999 1.9118085e-10 160.18662 + 9829 0 -37.039999 0 -37.039999 -1.5568605e-13 160.18662 + 9830 0 -37.039999 0 -37.039999 -3.4264165e-10 160.18662 + 9831 0 -37.039999 0 -37.039999 3.4270989e-10 160.18662 + 9832 0 -37.039999 0 -37.039999 4.1926889e-10 160.18662 + 9833 0 -37.039999 0 -37.039999 -3.4319038e-10 160.18662 + 9834 0 -37.039999 0 -37.039999 -3.8180833e-11 160.18662 + 9835 0 -37.039999 0 -37.039999 1.1522574e-10 160.18662 + 9836 0 -37.039999 0 -37.039999 -4.20177e-10 160.18662 + 9837 0 -37.039999 0 -37.039999 -5.7328023e-10 160.18662 + 9838 0 -37.039999 0 -37.039999 3.4327646e-10 160.18662 + 9839 0 -37.039999 0 -37.039999 5.7299818e-10 160.18662 + 9840 0 -37.039999 0 -37.039999 1.1389479e-10 160.18662 + 9841 0 -37.039999 0 -37.039999 -3.6593852e-11 160.18662 + 9842 0 -37.039999 0 -37.039999 1.3857892e-12 160.18662 + 9843 0 -37.039999 0 -37.039999 7.8109068e-11 160.18662 + 9844 0 -37.039999 0 -37.039999 -7.4557695e-11 160.18662 + 9845 0 -37.039999 0 -37.039999 -1.1293226e-10 160.18662 + 9846 0 -37.039999 0 -37.039999 7.7891876e-11 160.18662 + 9847 0 -37.039999 0 -37.039999 1.5959203e-12 160.18662 + 9848 0 -37.039999 0 -37.039999 2.6750888e-10 160.18662 + 9849 0 -37.039999 0 -37.039999 2.2903803e-10 160.18662 + 9850 0 -37.039999 0 -37.039999 1.5299246e-10 160.18662 + 9851 0 -37.039999 0 -37.039999 -3.0585473e-10 160.18662 + 9852 0 -37.039999 0 -37.039999 5.3332443e-10 160.18662 + 9853 0 -37.039999 0 -37.039999 6.1170069e-10 160.18662 + 9854 0 -37.039999 0 -37.039999 -1.1400339e-10 160.18662 + 9855 0 -37.039999 0 -37.039999 1.9107203e-10 160.18662 + 9856 0 -37.039999 0 -37.039999 1.1539147e-10 160.18662 + 9857 0 -37.039999 0 -37.039999 1.5232704e-10 160.18662 + 9858 0 -37.039999 0 -37.039999 -4.5825183e-10 160.18662 + 9859 0 -37.039999 0 -37.039999 4.2025485e-10 160.18662 + 9860 0 -37.039999 0 -37.039999 3.0479497e-10 160.18662 + 9861 0 -37.039999 0 -37.039999 3.8486804e-11 160.18662 + 9862 0 -37.039999 0 -37.039999 -3.8220142e-10 160.18662 + 9863 0 -37.039999 0 -37.039999 4.9587881e-10 160.18662 + 9864 0 -37.039999 0 -37.039999 5.3419739e-10 160.18662 + 9865 0 -37.039999 0 -37.039999 -2.6699273e-10 160.18662 + 9866 0 -37.039999 0 -37.039999 -5.3498372e-10 160.18662 + 9867 0 -37.039999 0 -37.039999 6.4811091e-10 160.18662 + 9868 0 -37.039999 0 -37.039999 7.2471145e-10 160.18662 + 9869 0 -37.039999 0 -37.039999 -5.7328906e-10 160.18662 + 9870 0 -37.039999 0 -37.039999 3.4395406e-10 160.18662 + 9871 0 -37.039999 0 -37.039999 4.5756515e-10 160.18662 + 9872 0 -37.039999 0 -37.039999 5.337283e-10 160.18662 + 9873 0 -37.039999 0 -37.039999 -4.1883713e-10 160.18662 + 9874 0 -37.039999 0 -37.039999 6.0946853e-10 160.18662 + 9875 0 -37.039999 0 -37.039999 -4.5815153e-10 160.18662 + 9876 0 -37.039999 0 -37.039999 2.6716092e-10 160.18662 + 9877 0 -37.039999 0 -37.039999 3.4294407e-10 160.18662 + 9878 0 -37.039999 0 -37.039999 -5.3359733e-10 160.18662 + 9879 0 -37.039999 0 -37.039999 6.0925749e-10 160.18662 + 9880 0 -37.039999 0 -37.039999 -5.3359733e-10 160.18662 + 9881 0 -37.039999 0 -37.039999 6.0925749e-10 160.18662 + 9882 0 -37.039999 0 -37.039999 -5.3370825e-10 160.18662 + 9883 0 -37.039999 0 -37.039999 6.0925749e-10 160.18662 + 9884 0 -37.039999 0 -37.039999 -5.3367271e-10 160.18662 + 9885 0 -37.039999 0 -37.039999 8.0101674e-10 160.18662 + 9886 0 -37.039999 0 -37.039999 -5.7177454e-10 160.18662 + 9887 0 -37.039999 0 -37.039999 -3.841742e-11 160.18662 + 9888 0 -37.039999 0 -37.039999 9.545356e-10 160.18662 + 9889 0 -37.039999 0 -37.039999 1.1823633e-09 160.18662 + 9890 0 -37.039999 0 -37.039999 1.5246046e-10 160.18662 + 9891 0 -37.039999 0 -37.039999 -5.3542356e-10 160.18662 + 9892 0 -37.039999 0 -37.039999 -9.5508021e-10 160.18662 + 9893 0 -37.039999 0 -37.039999 3.8162708e-10 160.18662 + 9894 0 -37.039999 0 -37.039999 3.0573331e-10 160.18662 + 9895 0 -37.039999 0 -37.039999 -3.821356e-10 160.18662 + 9896 0 -37.039999 0 -37.039999 8.0015554e-10 160.18662 + 9897 0 -37.039999 0 -37.039999 1.143891e-09 160.18662 + 9898 0 -37.039999 0 -37.039999 -6.5082629e-10 160.18662 + 9899 0 -37.039999 0 -37.039999 -1.184523e-09 160.18662 + 9900 0 -37.039999 0 -37.039999 -1.1506245e-10 160.18662 + 9901 0 -37.039999 0 -37.039999 1.9171127e-10 160.18662 + 9902 0 -37.039999 0 -37.039999 1.1417789e-10 160.18662 + 9903 0 -37.039999 0 -37.039999 -3.0521317e-10 160.18662 + 9904 0 -37.039999 0 -37.039999 -4.9673728e-10 160.18662 + 9905 0 -37.039999 0 -37.039999 4.9470372e-10 160.18662 + 9906 0 -37.039999 0 -37.039999 5.7312101e-10 160.18662 + 9907 0 -37.039999 0 -37.039999 -8.6505428e-13 160.18662 + 9908 0 -37.039999 0 -37.039999 -1.5230572e-10 160.18662 + 9909 0 -37.039999 0 -37.039999 2.2913715e-10 160.18662 + 9910 0 -37.039999 0 -37.039999 3.0627423e-10 160.18662 + 9911 0 -37.039999 0 -37.039999 -3.4270797e-10 160.18662 + 9912 0 -37.039999 0 -37.039999 3.4352405e-10 160.18662 + 9913 0 -37.039999 0 -37.039999 3.4352405e-10 160.18662 + 9914 0 -37.039999 0 -37.039999 -2.6738837e-10 160.18662 + 9915 0 -37.039999 0 -37.039999 2.2865463e-10 160.18662 + 9916 0 -37.039999 0 -37.039999 2.2924137e-10 160.18662 + 9917 0 -37.039999 0 -37.039999 6.0828967e-13 160.18662 + 9918 0 -37.039999 0 -37.039999 -3.049977e-10 160.18662 + 9919 0 -37.039999 0 -37.039999 -3.8895816e-11 160.18662 + 9920 0 -37.039999 0 -37.039999 -7.5761028e-11 160.18662 + 9921 0 -37.039999 0 -37.039999 3.052567e-10 160.18662 + 9922 0 -37.039999 0 -37.039999 1.155309e-10 160.18662 + 9923 0 -37.039999 0 -37.039999 -3.7864146e-11 160.18662 + 9924 0 -37.039999 0 -37.039999 -3.0365512e-10 160.18662 + 9925 0 -37.039999 0 -37.039999 -3.0455328e-10 160.18662 + 9926 0 -37.039999 0 -37.039999 -1.8914741e-10 160.18662 + 9927 0 -37.039999 0 -37.039999 -1.8972954e-10 160.18662 + 9928 0 -37.039999 0 -37.039999 5.7265208e-10 160.18662 + 9929 0 -37.039999 0 -37.039999 -5.7343119e-10 160.18662 + 9930 0 -37.039999 0 -37.039999 6.4773111e-10 160.18662 + 9931 0 -37.039999 0 -37.039999 -4.9671452e-10 160.18662 + 9932 0 -37.039999 0 -37.039999 4.9540543e-10 160.18662 + 9933 0 -37.039999 0 -37.039999 4.9539697e-10 160.18662 + 9934 0 -37.039999 0 -37.039999 -3.4347236e-10 160.18662 + 9935 0 -37.039999 0 -37.039999 -3.4514128e-10 160.18662 + 9936 0 -37.039999 0 -37.039999 5.7277773e-10 160.18662 + 9937 0 -37.039999 0 -37.039999 4.5820606e-10 160.18662 + 9938 0 -37.039999 0 -37.039999 -6.4937991e-10 160.18662 + 9939 0 -37.039999 0 -37.039999 -5.3566476e-10 160.18662 + 9940 0 -37.039999 0 -37.039999 6.4855815e-10 160.18662 + 9941 0 -37.039999 0 -37.039999 -4.2145548e-10 160.18662 + 9942 0 -37.039999 0 -37.039999 -8.7784712e-10 160.18662 + 9943 0 -37.039999 0 -37.039999 1.9029583e-10 160.18662 + 9944 0 -37.039999 0 -37.039999 1.5286217e-10 160.18662 + 9945 0 -37.039999 0 -37.039999 -5.3281493e-10 160.18662 + 9946 0 -37.039999 0 -37.039999 -4.5622931e-10 160.18662 + 9947 0 -37.039999 0 -37.039999 -4.9639951e-10 160.18662 + 9948 0 -37.039999 0 -37.039999 5.3495586e-10 160.18662 + 9949 0 -37.039999 0 -37.039999 -4.9639951e-10 160.18662 + 9950 0 -37.039999 0 -37.039999 6.1072086e-10 160.18662 + 9951 0 -37.039999 0 -37.039999 -5.7291066e-10 160.18662 + 9952 0 -37.039999 0 -37.039999 6.1072086e-10 160.18662 + 9953 0 -37.039999 0 -37.039999 -5.3451734e-10 160.18662 + 9954 0 -37.039999 0 -37.039999 5.3451156e-10 160.18662 + 9955 0 -37.039999 0 -37.039999 -4.9627968e-10 160.18662 + 9956 0 -37.039999 0 -37.039999 5.3451156e-10 160.18662 + 9957 0 -37.039999 0 -37.039999 -3.4315581e-10 160.18662 + 9958 0 -37.039999 0 -37.039999 -1.1375268e-10 160.18662 + 9959 0 -37.039999 0 -37.039999 1.449475e-12 160.18662 + 9960 0 -37.039999 0 -37.039999 1.0917772e-12 160.18662 + 9961 0 -37.039999 0 -37.039999 2.3021075e-10 160.18662 + 9962 0 -37.039999 0 -37.039999 2.3010768e-10 160.18662 + 9963 0 -37.039999 0 -37.039999 -3.0558861e-10 160.18662 + 9964 0 -37.039999 0 -37.039999 6.8663486e-10 160.18662 + 9965 0 -37.039999 0 -37.039999 1.1072345e-09 160.18662 + 9966 0 -37.039999 0 -37.039999 1.1495768e-10 160.18662 + 9967 0 -37.039999 0 -37.039999 -4.9658332e-10 160.18662 + 9968 0 -37.039999 0 -37.039999 -5.3556345e-10 160.18662 + 9969 0 -37.039999 0 -37.039999 6.8708588e-10 160.18662 + 9970 0 -37.039999 0 -37.039999 -4.2084767e-10 160.18662 + 9971 0 -37.039999 0 -37.039999 -4.2063662e-10 160.18662 + 9972 0 -37.039999 0 -37.039999 2.6729497e-10 160.18662 + 9973 0 -37.039999 0 -37.039999 8.4002573e-10 160.18662 + 9974 0 -37.039999 0 -37.039999 -2.3016276e-10 160.18662 + 9975 0 -37.039999 0 -37.039999 -1.5351499e-10 160.18662 + 9976 0 -37.039999 0 -37.039999 4.9606484e-10 160.18662 + 9977 0 -37.039999 0 -37.039999 1.9180748e-10 160.18662 + 9978 0 -37.039999 0 -37.039999 -1.9144332e-10 160.18662 + 9979 0 -37.039999 0 -37.039999 -2.6701265e-10 160.18662 + 9980 0 -37.039999 0 -37.039999 4.2060264e-10 160.18662 + 9981 0 -37.039999 0 -37.039999 8.0177047e-10 160.18662 + 9982 0 -37.039999 0 -37.039999 -1.5233816e-10 160.18662 + 9983 0 -37.039999 0 -37.039999 -3.053057e-10 160.18662 + 9984 0 -37.039999 0 -37.039999 4.3389674e-13 160.18662 + 9985 0 -37.039999 0 -37.039999 7.2394514e-10 160.18662 + 9986 0 -37.039999 0 -37.039999 6.4988998e-10 160.18662 + 9987 0 -37.039999 0 -37.039999 7.6909837e-11 160.18662 + 9988 0 -37.039999 0 -37.039999 -1.1084821e-09 160.18662 + 9989 0 -37.039999 0 -37.039999 -1.224561e-09 160.18662 + 9990 0 -37.039999 0 -37.039999 4.9653808e-10 160.18662 + 9991 0 -37.039999 0 -37.039999 6.4875657e-10 160.18662 + 9992 0 -37.039999 0 -37.039999 -3.8268848e-10 160.18662 + 9993 0 -37.039999 0 -37.039999 -6.8735249e-10 160.18662 + 9994 0 -37.039999 0 -37.039999 3.6773141e-11 160.18662 + 9995 0 -37.039999 0 -37.039999 6.8755037e-10 160.18662 + 9996 0 -37.039999 0 -37.039999 5.34258e-10 160.18662 + 9997 0 -37.039999 0 -37.039999 -2.2950669e-10 160.18662 + 9998 0 -37.039999 0 -37.039999 -2.2934342e-10 160.18662 + 9999 0 -37.039999 0 -37.039999 5.349295e-10 160.18662 + 10000 0 -37.039999 0 -37.039999 4.1936348e-10 160.18662 +Loop time of 1.41021 on 1 procs for 10000 steps with 8 atoms + +97.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = max iterations + Energy initial, next-to-last, final = + -37.0399844020227 -37.0399991134996 -37.0399991134996 + Force two-norm initial, final = 0.097615725 8.9871009e-14 + Force max component initial, final = 0.056358465 6.0455736e-14 + Final line search alpha, max atom move = 1 6.0455736e-14 + Iterations, force evaluations = 10000 19999 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.1989 | 1.1989 | 1.1989 | 0.0 | 85.01 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.030148 | 0.030148 | 0.030148 | 0.0 | 2.14 +Output | 0.062376 | 0.062376 | 0.062376 | 0.0 | 4.42 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.1188 | | | 8.42 + +Nlocal: 8 ave 8 max 8 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 272 ave 272 max 272 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 184 ave 184 max 184 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 368 ave 368 max 368 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 368 +Ave neighs/atom = 46 +Neighbor list builds = 0 +Dangerous builds = 0 + +variable cohesive_energy equal pe/atoms +variable atmVol equal vol/atoms +variable aLatt equal (8*vol/atoms)^0.333333333333 + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Per MPI rank memory allocation (min/avg/max) = 3.715 | 3.715 | 3.715 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 10000 0 -37.039999 0 -37.039999 4.192055e-10 160.18662 +Loop time of 5.32e-07 on 1 procs for 0 steps with 8 atoms + +188.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 5.32e-07 | | |100.00 + +Nlocal: 8 ave 8 max 8 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 272 ave 272 max 272 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 184 ave 184 max 184 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 368 ave 368 max 368 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 368 +Ave neighs/atom = 46 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.62999988918745 eV/atom +print "Reference cohesive energy: -4.63 eV/atom" +Reference cohesive energy: -4.63 eV/atom +print "Atomic volume ${atmVol} A^3" +Atomic volume 20.0233273617701 A^3 +print "Lattice constant ${aLatt} A" +Lattice constant 5.43094508649583 A +print "Reference lattice constant 5.431 A" +Reference lattice constant 5.431 A +print "====================================================" +==================================================== + + +#dump 1 all custom 1 dc.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.dc_relax.g++.4 b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.dc_relax.g++.4 new file mode 100644 index 0000000000..de3c137e49 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.dc_relax.g++.4 @@ -0,0 +1,10143 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Si dc phase + +units metal +boundary p p p + +atom_style atomic +lattice diamond 5.43 +Lattice spacing in x,y,z = 5.43 5.43 5.43 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (5.43 5.43 5.43) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 8 atoms + using lattice units in orthogonal box = (0 0 0) to (5.43 5.43 5.43) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +Reading meam/sw/spline potential file Si.b.meam.sw.spline with DATE: 2012-10-26 +mass * 28.085 + +fix relax all box/relax aniso 0 +thermo 1 +minimize 0 0 10000 100000 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.4 + ghost atom cutoff = 6.4 + binsize = 3.2, bins = 2 2 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 4.854 | 4.854 | 4.854 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 0 -37.039984 0 -37.039984 563.98821 160.10301 + 1 0 -37.039996 0 -37.039996 239.83776 160.15104 + 2 0 -37.039999 0 -37.039999 -0.016271308 160.18662 + 3 0 -37.039999 0 -37.039999 -6.9259589e-08 160.18662 + 4 0 -37.039999 0 -37.039999 -1.1280581e-10 160.18662 + 5 0 -37.039999 0 -37.039999 -3.6428172e-11 160.18662 + 6 0 -37.039999 0 -37.039999 -3.6428172e-11 160.18662 + 7 0 -37.039999 0 -37.039999 -7.4503225e-11 160.18662 + 8 0 -37.039999 0 -37.039999 8.0104998e-10 160.18662 + 9 0 -37.039999 0 -37.039999 -5.7309202e-10 160.18662 + 10 0 -37.039999 0 -37.039999 1.8959357e-10 160.18662 + 11 0 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-37.039999 0 -37.039999 3.8255634e-10 160.18662 + 9913 0 -37.039999 0 -37.039999 -7.4948866e-11 160.18662 + 9914 0 -37.039999 0 -37.039999 -7.4939489e-11 160.18662 + 9915 0 -37.039999 0 -37.039999 -1.5121761e-10 160.18662 + 9916 0 -37.039999 0 -37.039999 -3.806536e-11 160.18662 + 9917 0 -37.039999 0 -37.039999 4.2018766e-10 160.18662 + 9918 0 -37.039999 0 -37.039999 3.0580699e-10 160.18662 + 9919 0 -37.039999 0 -37.039999 1.5359114e-10 160.18662 + 9920 0 -37.039999 0 -37.039999 1.5347099e-10 160.18662 + 9921 0 -37.039999 0 -37.039999 -1.9054001e-10 160.18662 + 9922 0 -37.039999 0 -37.039999 1.1734592e-12 160.18662 + 9923 0 -37.039999 0 -37.039999 3.9437575e-11 160.18662 + 9924 0 -37.039999 0 -37.039999 -3.6108987e-11 160.18662 + 9925 0 -37.039999 0 -37.039999 3.9409882e-11 160.18662 + 9926 0 -37.039999 0 -37.039999 -7.4015405e-11 160.18662 + 9927 0 -37.039999 0 -37.039999 -3.6864641e-11 160.18662 + 9928 0 -37.039999 0 -37.039999 4.1923212e-10 160.18662 + 9929 0 -37.039999 0 -37.039999 -3.0557972e-10 160.18662 + 9930 0 -37.039999 0 -37.039999 3.443919e-10 160.18662 + 9931 0 -37.039999 0 -37.039999 1.5310552e-10 160.18662 + 9932 0 -37.039999 0 -37.039999 -2.6650037e-10 160.18662 + 9933 0 -37.039999 0 -37.039999 -3.0414173e-10 160.18662 + 9934 0 -37.039999 0 -37.039999 -3.0543722e-10 160.18662 + 9935 0 -37.039999 0 -37.039999 1.9139178e-10 160.18662 + 9936 0 -37.039999 0 -37.039999 -3.0500554e-10 160.18662 + 9937 0 -37.039999 0 -37.039999 -1.9065594e-10 160.18662 + 9938 0 -37.039999 0 -37.039999 -1.5221028e-10 160.18662 + 9939 0 -37.039999 0 -37.039999 2.6776406e-10 160.18662 + 9940 0 -37.039999 0 -37.039999 1.5339078e-10 160.18662 + 9941 0 -37.039999 0 -37.039999 -1.9006335e-10 160.18662 + 9942 0 -37.039999 0 -37.039999 1.9125391e-10 160.18662 + 9943 0 -37.039999 0 -37.039999 1.9094825e-10 160.18662 + 9944 0 -37.039999 0 -37.039999 -4.9722689e-10 160.18662 + 9945 0 -37.039999 0 -37.039999 -4.9712983e-10 160.18662 + 9946 0 -37.039999 0 -37.039999 4.1859302e-10 160.18662 + 9947 0 -37.039999 0 -37.039999 4.1880564e-10 160.18662 + 9948 0 -37.039999 0 -37.039999 -4.9701735e-10 160.18662 + 9949 0 -37.039999 0 -37.039999 -3.7942495e-10 160.18662 + 9950 0 -37.039999 0 -37.039999 -1.9048197e-10 160.18662 + 9951 0 -37.039999 0 -37.039999 1.5439263e-12 160.18662 + 9952 0 -37.039999 0 -37.039999 -2.2839029e-10 160.18662 + 9953 0 -37.039999 0 -37.039999 3.9852654e-11 160.18662 + 9954 0 -37.039999 0 -37.039999 7.6599827e-11 160.18662 + 9955 0 -37.039999 0 -37.039999 7.6803399e-11 160.18662 + 9956 0 -37.039999 0 -37.039999 -3.8104691e-10 160.18662 + 9957 0 -37.039999 0 -37.039999 -3.044696e-10 160.18662 + 9958 0 -37.039999 0 -37.039999 1.5379394e-10 160.18662 + 9959 0 -37.039999 0 -37.039999 -7.4464321e-11 160.18662 + 9960 0 -37.039999 0 -37.039999 -1.5026838e-10 160.18662 + 9961 0 -37.039999 0 -37.039999 1.9399318e-12 160.18662 + 9962 0 -37.039999 0 -37.039999 6.4830972e-10 160.18662 + 9963 0 -37.039999 0 -37.039999 -5.3408119e-10 160.18662 + 9964 0 -37.039999 0 -37.039999 6.1014081e-10 160.18662 + 9965 0 -37.039999 0 -37.039999 -6.4919625e-10 160.18662 + 9966 0 -37.039999 0 -37.039999 -6.4919625e-10 160.18662 + 9967 0 -37.039999 0 -37.039999 3.8072433e-10 160.18662 + 9968 0 -37.039999 0 -37.039999 9.5558024e-10 160.18662 + 9969 0 -37.039999 0 -37.039999 3.7666574e-11 160.18662 + 9970 0 -37.039999 0 -37.039999 -6.8815495e-10 160.18662 + 9971 0 -37.039999 0 -37.039999 -4.9796152e-10 160.18662 + 9972 0 -37.039999 0 -37.039999 1.905376e-10 160.18662 + 9973 0 -37.039999 0 -37.039999 -3.4248954e-10 160.18662 + 9974 0 -37.039999 0 -37.039999 -2.2781599e-10 160.18662 + 9975 0 -37.039999 0 -37.039999 5.3427199e-10 160.18662 + 9976 0 -37.039999 0 -37.039999 -4.9709273e-10 160.18662 + 9977 0 -37.039999 0 -37.039999 6.4763047e-10 160.18662 + 9978 0 -37.039999 0 -37.039999 6.4763047e-10 160.18662 + 9979 0 -37.039999 0 -37.039999 -3.8212808e-10 160.18662 + 9980 0 -37.039999 0 -37.039999 -8.7790884e-10 160.18662 + 9981 0 -37.039999 0 -37.039999 7.7046197e-11 160.18662 + 9982 0 -37.039999 0 -37.039999 3.4368579e-10 160.18662 + 9983 0 -37.039999 0 -37.039999 -6.0983172e-10 160.18662 + 9984 0 -37.039999 0 -37.039999 1.1592e-10 160.18662 + 9985 0 -37.039999 0 -37.039999 8.7845658e-10 160.18662 + 9986 0 -37.039999 0 -37.039999 5.7262696e-10 160.18662 + 9987 0 -37.039999 0 -37.039999 -1.5181735e-10 160.18662 + 9988 0 -37.039999 0 -37.039999 -4.5921841e-10 160.18662 + 9989 0 -37.039999 0 -37.039999 -3.9147304e-11 160.18662 + 9990 0 -37.039999 0 -37.039999 4.2038969e-10 160.18662 + 9991 0 -37.039999 0 -37.039999 2.2781133e-10 160.18662 + 9992 0 -37.039999 0 -37.039999 -6.1112411e-10 160.18662 + 9993 0 -37.039999 0 -37.039999 -9.9309419e-10 160.18662 + 9994 0 -37.039999 0 -37.039999 -7.5413694e-11 160.18662 + 9995 0 -37.039999 0 -37.039999 4.5785173e-10 160.18662 + 9996 0 -37.039999 0 -37.039999 5.3530437e-10 160.18662 + 9997 0 -37.039999 0 -37.039999 -7.6372505e-10 160.18662 + 9998 0 -37.039999 0 -37.039999 4.9479496e-10 160.18662 + 9999 0 -37.039999 0 -37.039999 8.3908505e-10 160.18662 + 10000 0 -37.039999 0 -37.039999 -3.0599622e-10 160.18662 +Loop time of 1.03759 on 4 procs for 10000 steps with 8 atoms + +97.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = max iterations + Energy initial, next-to-last, final = + -37.0399844020227 -37.0399991134996 -37.0399991134996 + Force two-norm initial, final = 0.097615725 8.8447233e-14 + Force max component initial, final = 0.056358465 3.2597809e-14 + Final line search alpha, max atom move = 1 3.2597809e-14 + Iterations, force evaluations = 10000 19999 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.44823 | 0.45046 | 0.45413 | 0.3 | 43.41 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.20218 | 0.20534 | 0.20767 | 0.4 | 19.79 +Output | 0.083459 | 0.089103 | 0.10315 | 2.7 | 8.59 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.2927 | | | 28.21 + +Nlocal: 2 ave 2 max 2 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 199 ave 199 max 199 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46 ave 46 max 46 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 92 ave 92 max 92 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 368 +Ave neighs/atom = 46 +Neighbor list builds = 0 +Dangerous builds = 0 + +variable cohesive_energy equal pe/atoms +variable atmVol equal vol/atoms +variable aLatt equal (8*vol/atoms)^0.333333333333 + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Per MPI rank memory allocation (min/avg/max) = 3.729 | 3.729 | 3.729 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 10000 0 -37.039999 0 -37.039999 -2.6824491e-10 160.18662 +Loop time of 2.371e-06 on 4 procs for 0 steps with 8 atoms + +126.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.371e-06 | | |100.00 + +Nlocal: 2 ave 2 max 2 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 199 ave 199 max 199 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 46 ave 48 max 44 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +FullNghs: 92 ave 92 max 92 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 368 +Ave neighs/atom = 46 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.62999988918745 eV/atom +print "Reference cohesive energy: -4.63 eV/atom" +Reference cohesive energy: -4.63 eV/atom +print "Atomic volume ${atmVol} A^3" +Atomic volume 20.0233273617701 A^3 +print "Lattice constant ${aLatt} A" +Lattice constant 5.43094508649583 A +print "Reference lattice constant 5.431 A" +Reference lattice constant 5.431 A +print "====================================================" +==================================================== + + +#dump 1 all custom 1 dc.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.energy_conservation.meam.sw.g++.1 b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.energy_conservation.meam.sw.g++.1 new file mode 100644 index 0000000000..1888ab474f --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.energy_conservation.meam.sw.g++.1 @@ -0,0 +1,304 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# bulk Si lattice + +variable x index 1 +variable y index 1 +variable z index 1 + +units metal +atom_style atomic + + +atom_style atomic +lattice diamond 5.431 +Lattice spacing in x,y,z = 5.431 5.431 5.431 +region box block 0 5 0 5 0 5 +boundary p p p + +create_box 1 box +Created orthogonal box = (0 0 0) to (27.155 27.155 27.155) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 1000 atoms + using lattice units in orthogonal box = (0 0 0) to (27.155 27.155 27.155) + create_atoms CPU = 0.000 seconds + + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +Reading meam/sw/spline potential file Si.b.meam.sw.spline with DATE: 2012-10-26 +mass * 28.085 + +velocity all create 300.0 376847 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 5 check yes + +fix 1 all nve + +thermo 1 +thermo_style custom step vol etotal press pxx pyy pxz +thermo_modify format 2 %14.8f +thermo_modify format 3 %14.8f +thermo_modify format 4 %14.8f +thermo_modify format 5 %14.8f +thermo_modify format 6 %14.8f +thermo_modify format 7 %14.8f + + +timestep 0.002 +thermo 10 + +run 2000 +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.4 + ghost atom cutoff = 5.4 + binsize = 2.7, bins = 11 11 11 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.882 | 3.882 | 3.882 Mbytes + Step Volume TotEng Press Pxx Pyy Pxz + 0 20023.93474888 -4591.26061752 2033.68946971 2021.11445194 1952.17782797 -97.47450759 + 10 20023.93474888 -4591.06635027 2106.23969322 2152.04799431 2155.92194220 12.68865715 + 20 20023.93474888 -4591.08410781 1520.06153315 1492.61610264 1497.10285778 106.41609464 + 30 20023.93474888 -4591.20090599 1491.31281700 1502.41875599 1432.20332178 -220.78939631 + 40 20023.93474888 -4591.12407583 2061.65437359 2086.56902463 2156.12774891 133.73119636 + 50 20023.93474888 -4591.07086388 1998.55985680 2023.28426545 1940.19019547 -154.08048062 + 60 20023.93474888 -4591.17588927 1598.13531474 1534.49237825 1668.01401046 -30.47944201 + 70 20023.93474888 -4591.14658914 1774.80198893 1761.97777404 1785.46768303 265.88782944 + 80 20023.93474888 -4591.07344257 2005.07361554 2086.14231294 1947.20619069 -215.28622700 + 90 20023.93474888 -4591.16235879 1688.39497858 1707.61777360 1644.33608005 -164.72130224 + 100 20023.93474888 -4591.14061103 1841.94537985 1773.73213126 1872.51475381 270.59501062 + 110 20023.93474888 -4591.10220075 1929.22145308 1909.87270800 1904.88051163 -225.24314462 + 120 20023.93474888 -4591.13680660 1781.93134139 1866.38642644 1768.89564107 99.86322623 + 130 20023.93474888 -4591.14594757 1822.72100705 1800.47495717 1820.60642574 80.95885439 + 140 20023.93474888 -4591.10390676 1910.20395959 1955.77665062 1995.74598843 -90.83622328 + 150 20023.93474888 -4591.14245989 1806.86945717 1826.66971108 1792.88598455 109.51618275 + 160 20023.93474888 -4591.13052367 1788.16506016 1720.21348685 1791.47937216 -21.37756610 + 170 20023.93474888 -4591.11781009 1807.71365716 1900.29204203 1719.93993616 -188.87504172 + 180 20023.93474888 -4591.13704844 1743.08721343 1658.19411470 1778.16073808 259.52251154 + 190 20023.93474888 -4591.13308836 1922.54250327 2098.60870590 1929.55744997 -258.20774060 + 200 20023.93474888 -4591.11910322 1948.92068139 1792.61227410 1942.76349531 -13.04781205 + 210 20023.93474888 -4591.13284135 1783.61066563 1820.43796850 1760.07633603 159.07171405 + 220 20023.93474888 -4591.13715614 1662.49241020 1659.81600936 1681.59150854 -132.96912515 + 230 20023.93474888 -4591.11129339 1856.01542680 1850.81261755 1867.66185416 52.30767173 + 240 20023.93474888 -4591.13924088 1891.58063505 1873.70129244 1956.58093826 98.93914776 + 250 20023.93474888 -4591.13115836 1860.91219630 1879.89822419 1879.31544524 -206.02783594 + 260 20023.93474888 -4591.12006308 1818.08099684 1941.33545552 1695.61949198 135.96435310 + 270 20023.93474888 -4591.13331488 1745.21920087 1632.20932864 1841.75237705 -14.79711037 + 280 20023.93474888 -4591.12668399 1922.27473363 1983.53049663 1801.16867887 -31.89499092 + 290 20023.93474888 -4591.12976814 1897.55799948 1827.64752799 1980.45982095 2.76502468 + 300 20023.93474888 -4591.13041107 1825.92142175 1878.68168429 1802.25725197 -38.06898013 + 310 20023.93474888 -4591.12342070 1743.43519435 1729.85694627 1756.42228046 -60.06468142 + 320 20023.93474888 -4591.13442022 1763.60998541 1802.84007786 1758.08838840 143.69519620 + 330 20023.93474888 -4591.12695785 1845.27144767 1808.79851160 1834.73311592 -121.25298963 + 340 20023.93474888 -4591.12739037 1824.35911264 1832.04065906 1890.80248509 133.62517019 + 350 20023.93474888 -4591.12837932 1846.72083448 1835.30033595 1798.95928707 4.24639304 + 360 20023.93474888 -4591.13622705 1815.71663299 1841.77777220 1827.49780217 -143.29464941 + 370 20023.93474888 -4591.11509215 1875.67484263 1827.27976696 1896.21161847 45.76662873 + 380 20023.93474888 -4591.13911382 1797.59606691 1812.24811799 1794.04473228 -41.59509792 + 390 20023.93474888 -4591.13044234 1898.76664850 1956.19730294 1860.25003173 50.92492249 + 400 20023.93474888 -4591.11980093 1844.92592342 1784.40892834 1906.40469373 43.28606683 + 410 20023.93474888 -4591.13203164 1712.71494613 1814.06280558 1635.86741674 -103.93631537 + 420 20023.93474888 -4591.13931019 1733.36385225 1744.49160982 1807.86989588 133.74823990 + 430 20023.93474888 -4591.11091920 1949.42231060 1909.20892751 1975.13043695 -14.29575994 + 440 20023.93474888 -4591.13618833 1864.59807598 1877.62852076 1843.27438001 -89.29004851 + 450 20023.93474888 -4591.14065042 1792.33232906 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2129.50862093 1891.59140452 -174.84268771 + 1660 20023.93474888 -4591.12623477 1937.01570743 1858.01901653 2010.43954630 262.44914826 + 1670 20023.93474888 -4591.13072559 1694.39186347 1719.93995818 1664.78730910 -145.83592220 + 1680 20023.93474888 -4591.12856494 1668.28855671 1605.96305541 1655.07886827 -142.62923930 + 1690 20023.93474888 -4591.12284600 1970.77558510 1970.04100693 2023.90407383 345.77356846 + 1700 20023.93474888 -4591.13613310 1866.78766162 1829.21192148 1874.14168461 -348.93449367 + 1710 20023.93474888 -4591.12999014 1699.05790295 1794.09077236 1679.36565966 178.31013280 + 1720 20023.93474888 -4591.11591976 1782.98025612 1700.01516442 1839.71274928 70.34469196 + 1730 20023.93474888 -4591.14002514 1828.78788640 1977.52189719 1827.54175302 -277.62511918 + 1740 20023.93474888 -4591.13058733 1798.70721142 1684.56540042 1750.52641931 233.57737288 + 1750 20023.93474888 -4591.11769219 1851.38818281 1927.22480022 1826.49368852 -71.98649667 + 1760 20023.93474888 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20023.93474888 -4591.13265210 1806.29161872 1787.78341130 1766.71844421 -34.60592395 + 1880 20023.93474888 -4591.14209985 1740.88195157 1752.31650148 1773.74624207 343.80423723 + 1890 20023.93474888 -4591.11622075 1861.70663705 1810.81638169 1911.13160086 -309.99090581 + 1900 20023.93474888 -4591.12680903 1858.70135891 2003.32077130 1814.47948340 26.70054215 + 1910 20023.93474888 -4591.14366548 1806.10434545 1792.54775377 1864.38160004 301.24438764 + 1920 20023.93474888 -4591.11781857 1833.48848596 1766.77497003 1815.64080638 -293.06438183 + 1930 20023.93474888 -4591.12285278 1839.11335622 1929.28055650 1841.52147596 59.60052069 + 1940 20023.93474888 -4591.14018804 1796.22184540 1744.26853225 1746.83391971 40.37326649 + 1950 20023.93474888 -4591.12901254 1816.28164897 1873.15646355 1849.53951502 -206.15332558 + 1960 20023.93474888 -4591.10959346 1829.95888178 1759.19881131 1818.96147638 140.43862743 + 1970 20023.93474888 -4591.15041597 1695.66220939 1759.10227856 1713.31191846 1.48998705 + 1980 20023.93474888 -4591.12373926 1839.11714441 1819.64176487 1799.65559207 -171.07051582 + 1990 20023.93474888 -4591.11065302 1930.61206830 1898.47853948 1985.20466055 305.47151137 + 2000 20023.93474888 -4591.15175708 1707.09302769 1754.70782606 1717.76389055 -259.68475322 +Loop time of 14.4074 on 1 procs for 2000 steps with 1000 atoms + +Performance: 23.988 ns/day, 1.001 hours/ns, 138.817 timesteps/s, 138.817 katom-step/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 | 14.354 | 14.354 | 14.354 | 0.0 | 99.63 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.017188 | 0.017188 | 0.017188 | 0.0 | 0.12 +Output | 0.0050332 | 0.0050332 | 0.0050332 | 0.0 | 0.03 +Modify | 0.021505 | 0.021505 | 0.021505 | 0.0 | 0.15 +Other | | 0.009614 | | | 0.07 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1470 ave 1470 max 1470 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 14000 ave 14000 max 14000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 28000 ave 28000 max 28000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 28000 +Ave neighs/atom = 28 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:14 diff --git a/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.energy_conservation.meam.sw.g++.4 b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.energy_conservation.meam.sw.g++.4 new file mode 100644 index 0000000000..0b38bb676e --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.energy_conservation.meam.sw.g++.4 @@ -0,0 +1,304 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# bulk Si lattice + +variable x index 1 +variable y index 1 +variable z index 1 + +units metal +atom_style atomic + + +atom_style atomic +lattice diamond 5.431 +Lattice spacing in x,y,z = 5.431 5.431 5.431 +region box block 0 5 0 5 0 5 +boundary p p p + +create_box 1 box +Created orthogonal box = (0 0 0) to (27.155 27.155 27.155) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 1000 atoms + using lattice units in orthogonal box = (0 0 0) to (27.155 27.155 27.155) + create_atoms CPU = 0.000 seconds + + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +Reading meam/sw/spline potential file Si.b.meam.sw.spline with DATE: 2012-10-26 +mass * 28.085 + +velocity all create 300.0 376847 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 5 check yes + +fix 1 all nve + +thermo 1 +thermo_style custom step vol etotal press pxx pyy pxz +thermo_modify format 2 %14.8f +thermo_modify format 3 %14.8f +thermo_modify format 4 %14.8f +thermo_modify format 5 %14.8f +thermo_modify format 6 %14.8f +thermo_modify format 7 %14.8f + + +timestep 0.002 +thermo 10 + +run 2000 +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.4 + ghost atom cutoff = 5.4 + binsize = 2.7, bins = 11 11 11 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.844 | 3.844 | 3.844 Mbytes + Step Volume TotEng Press Pxx Pyy Pxz + 0 20023.93474888 -4591.26061752 2033.68946971 2021.11445194 1952.17782797 -97.47450759 + 10 20023.93474888 -4591.06635027 2106.23969322 2152.04799431 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2129.50862093 1891.59140452 -174.84268771 + 1660 20023.93474888 -4591.12623477 1937.01570743 1858.01901653 2010.43954630 262.44914826 + 1670 20023.93474888 -4591.13072559 1694.39186347 1719.93995818 1664.78730910 -145.83592220 + 1680 20023.93474888 -4591.12856494 1668.28855671 1605.96305541 1655.07886827 -142.62923930 + 1690 20023.93474888 -4591.12284600 1970.77558510 1970.04100693 2023.90407383 345.77356846 + 1700 20023.93474888 -4591.13613310 1866.78766162 1829.21192148 1874.14168461 -348.93449367 + 1710 20023.93474888 -4591.12999014 1699.05790295 1794.09077236 1679.36565966 178.31013280 + 1720 20023.93474888 -4591.11591976 1782.98025612 1700.01516442 1839.71274928 70.34469196 + 1730 20023.93474888 -4591.14002514 1828.78788640 1977.52189719 1827.54175302 -277.62511918 + 1740 20023.93474888 -4591.13058733 1798.70721142 1684.56540042 1750.52641931 233.57737288 + 1750 20023.93474888 -4591.11769219 1851.38818281 1927.22480022 1826.49368852 -71.98649667 + 1760 20023.93474888 -4591.14007689 1883.09481847 1852.22751222 1980.94397520 -186.99017028 + 1770 20023.93474888 -4591.12640655 1894.21954462 1854.80842095 1863.10559976 245.84910078 + 1780 20023.93474888 -4591.12667944 1783.63681589 1763.81183224 1762.03364824 -313.41414175 + 1790 20023.93474888 -4591.13111090 1787.61153134 1881.28039744 1851.63506346 105.01216221 + 1800 20023.93474888 -4591.12970750 1803.03035944 1787.16231095 1760.00551047 314.84058979 + 1810 20023.93474888 -4591.12225161 1812.82894513 1745.83085735 1834.29341515 -340.09732132 + 1820 20023.93474888 -4591.13716194 1775.41292525 1771.18484944 1813.93798001 70.81021199 + 1830 20023.93474888 -4591.12268274 1837.06086954 1854.30962384 1844.39144552 145.53217438 + 1840 20023.93474888 -4591.12375023 1837.54812558 1877.01563366 1835.09263974 -272.38620552 + 1850 20023.93474888 -4591.14592434 1799.83851836 1722.86830853 1788.44737857 224.62763516 + 1860 20023.93474888 -4591.11203857 1905.18247850 1950.95536684 1931.86453236 -124.44793867 + 1870 20023.93474888 -4591.13265210 1806.29161872 1787.78341130 1766.71844421 -34.60592396 + 1880 20023.93474888 -4591.14209985 1740.88195157 1752.31650148 1773.74624207 343.80423723 + 1890 20023.93474888 -4591.11622075 1861.70663705 1810.81638169 1911.13160086 -309.99090581 + 1900 20023.93474888 -4591.12680903 1858.70135891 2003.32077130 1814.47948340 26.70054215 + 1910 20023.93474888 -4591.14366548 1806.10434545 1792.54775377 1864.38160004 301.24438764 + 1920 20023.93474888 -4591.11781857 1833.48848596 1766.77497003 1815.64080638 -293.06438183 + 1930 20023.93474888 -4591.12285278 1839.11335622 1929.28055650 1841.52147596 59.60052069 + 1940 20023.93474888 -4591.14018804 1796.22184540 1744.26853225 1746.83391971 40.37326649 + 1950 20023.93474888 -4591.12901254 1816.28164897 1873.15646355 1849.53951502 -206.15332558 + 1960 20023.93474888 -4591.10959346 1829.95888177 1759.19881131 1818.96147637 140.43862743 + 1970 20023.93474888 -4591.15041597 1695.66220939 1759.10227856 1713.31191846 1.48998705 + 1980 20023.93474888 -4591.12373926 1839.11714441 1819.64176487 1799.65559207 -171.07051582 + 1990 20023.93474888 -4591.11065302 1930.61206830 1898.47853948 1985.20466055 305.47151137 + 2000 20023.93474888 -4591.15175708 1707.09302769 1754.70782606 1717.76389055 -259.68475322 +Loop time of 3.74224 on 4 procs for 2000 steps with 1000 atoms + +Performance: 92.351 ns/day, 0.260 hours/ns, 534.439 timesteps/s, 534.439 katom-step/s +99.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.6818 | 3.6824 | 3.683 | 0.0 | 98.40 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.035276 | 0.035759 | 0.036375 | 0.2 | 0.96 +Output | 0.0048602 | 0.0051628 | 0.0059413 | 0.6 | 0.14 +Modify | 0.00711 | 0.00726 | 0.0074246 | 0.1 | 0.19 +Other | | 0.01162 | | | 0.31 + +Nlocal: 250 ave 250 max 250 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 733 ave 733 max 733 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 3500 ave 3500 max 3500 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 7000 ave 7000 max 7000 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 28000 +Ave neighs/atom = 28 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:03 diff --git a/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.fcc.g++.1 b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.fcc.g++.1 new file mode 100644 index 0000000000..96e9d34066 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.fcc.g++.1 @@ -0,0 +1,100 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Si fcc phase + +units metal +boundary p p p + +atom_style atomic +lattice fcc 4.147 +Lattice spacing in x,y,z = 4.147 4.147 4.147 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (4.147 4.147 4.147) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4 atoms + using lattice units in orthogonal box = (0 0 0) to (4.147 4.147 4.147) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +Reading meam/sw/spline potential file Si.b.meam.sw.spline with DATE: 2012-10-26 +mass * 28.085 + +variable cohesive_energy equal pe/atoms +variable atmVol equal vol/atoms +variable aLatt equal (4*vol/atoms)^0.3333333333 + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.4 + ghost atom cutoff = 6.4 + binsize = 3.2, bins = 2 2 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.715 | 3.715 | 3.715 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -17.15065 0 -17.15065 -53071.74 +Loop time of 1.463e-06 on 1 procs for 0 steps with 4 atoms + +136.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.463e-06 | | |100.00 + +Nlocal: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 360 ave 360 max 360 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 108 ave 108 max 108 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 216 ave 216 max 216 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 216 +Ave neighs/atom = 54 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.28766254199965 eV/atom +print "Reference cohesive energy: -4.288 eV/atom" +Reference cohesive energy: -4.288 eV/atom +print "Atomic volume ${atmVol} A^3" +Atomic volume 17.82962113075 A^3 +print "Lattice constant ${aLatt} A" +Lattice constant 4.14699999941014 A +print "Reference lattice constant 4.147 A" +Reference lattice constant 4.147 A +print "====================================================" +==================================================== + + +#dump 1 all custom 1 fcc.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.fcc.g++.4 b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.fcc.g++.4 new file mode 100644 index 0000000000..cc7d68f71d --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.fcc.g++.4 @@ -0,0 +1,100 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Si fcc phase + +units metal +boundary p p p + +atom_style atomic +lattice fcc 4.147 +Lattice spacing in x,y,z = 4.147 4.147 4.147 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (4.147 4.147 4.147) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 4 atoms + using lattice units in orthogonal box = (0 0 0) to (4.147 4.147 4.147) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +Reading meam/sw/spline potential file Si.b.meam.sw.spline with DATE: 2012-10-26 +mass * 28.085 + +variable cohesive_energy equal pe/atoms +variable atmVol equal vol/atoms +variable aLatt equal (4*vol/atoms)^0.3333333333 + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.4 + ghost atom cutoff = 6.4 + binsize = 3.2, bins = 2 2 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.746 | 3.746 | 3.746 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -17.15065 0 -17.15065 -53071.74 +Loop time of 3.73975e-06 on 4 procs for 0 steps with 4 atoms + +86.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.74e-06 | | |100.00 + +Nlocal: 1 ave 1 max 1 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 287 ave 287 max 287 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 27 ave 27 max 27 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 54 ave 54 max 54 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 216 +Ave neighs/atom = 54 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.28766254199965 eV/atom +print "Reference cohesive energy: -4.288 eV/atom" +Reference cohesive energy: -4.288 eV/atom +print "Atomic volume ${atmVol} A^3" +Atomic volume 17.82962113075 A^3 +print "Lattice constant ${aLatt} A" +Lattice constant 4.14699999941014 A +print "Reference lattice constant 4.147 A" +Reference lattice constant 4.147 A +print "====================================================" +==================================================== + + +#dump 1 all custom 1 fcc.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.fcc_relax.g++.1 b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.fcc_relax.g++.1 new file mode 100644 index 0000000000..5935017d22 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.fcc_relax.g++.1 @@ -0,0 +1,563 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Si fcc phase + +units metal +boundary p p p + +atom_style atomic +lattice fcc 4.309793856093661 +Lattice spacing in x,y,z = 4.3097939 4.3097939 4.3097939 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (4.3097939 4.3097939 4.3097939) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4 atoms + using lattice units in orthogonal box = (0 0 0) to (4.3097939 4.3097939 4.3097939) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +Reading meam/sw/spline potential file Si.b.meam.sw.spline with DATE: 2012-10-26 +mass * 28.085 + +fix relax all box/relax aniso 0 +thermo 1 +minimize 0 0 10000 100000 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.4 + ghost atom cutoff = 6.4 + binsize = 3.2, bins = 2 2 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 4.839 | 4.839 | 4.839 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 0 -14.885032 0 -14.885032 -693238.94 80.051503 + 1 0 -14.895414 0 -14.895414 -692151.97 80.02749 + 2 0 -14.905777 0 -14.905777 -691061.83 80.003482 + 3 0 -14.916122 0 -14.916122 -689968.51 79.979479 + 4 0 -14.926449 0 -14.926449 -688872.02 79.95548 + 5 0 -14.936757 0 -14.936757 -687772.36 79.931486 + 6 0 -14.947047 0 -14.947047 -686669.52 79.907497 + 7 0 -14.957318 0 -14.957318 -685563.5 79.883513 + 8 0 -14.96757 0 -14.96757 -684454.31 79.859534 + 9 0 -14.977804 0 -14.977804 -683341.94 79.835559 + 10 0 -14.988019 0 -14.988019 -682226.39 79.811589 + 11 0 -14.998215 0 -14.998215 -681107.66 79.787624 + 12 0 -15.008393 0 -15.008393 -679985.75 79.763664 + 13 0 -15.018551 0 -15.018551 -678860.66 79.739708 + 14 0 -15.028691 0 -15.028691 -677732.39 79.715758 + 15 0 -15.038812 0 -15.038812 -676600.93 79.691812 + 16 0 -15.048914 0 -15.048914 -675466.29 79.667871 + 17 0 -15.058997 0 -15.058997 -674328.46 79.643934 + 18 0 -15.06906 0 -15.06906 -673187.45 79.620003 + 19 0 -15.079105 0 -15.079105 -672043.25 79.596076 + 20 0 -15.089131 0 -15.089131 -670895.86 79.572154 + 21 0 -15.099137 0 -15.099137 -669745.28 79.548237 + 22 0 -15.109125 0 -15.109125 -668591.52 79.524325 + 23 0 -15.119093 0 -15.119093 -667434.56 79.500418 + 24 0 -15.129041 0 -15.129041 -666274.42 79.476515 + 25 0 -15.138971 0 -15.138971 -665111.08 79.452617 + 26 0 -15.148881 0 -15.148881 -663944.55 79.428724 + 27 0 -15.158771 0 -15.158771 -662774.82 79.404835 + 28 0 -15.168643 0 -15.168643 -661601.9 79.380952 + 29 0 -15.178494 0 -15.178494 -660425.79 79.357073 + 30 0 -15.188327 0 -15.188327 -659246.47 79.333199 + 31 0 -15.198139 0 -15.198139 -658063.97 79.30933 + 32 0 -15.207932 0 -15.207932 -656878.26 79.285466 + 33 0 -15.217706 0 -15.217706 -655689.36 79.261606 + 34 0 -15.227459 0 -15.227459 -654497.25 79.237751 + 35 0 -15.237193 0 -15.237193 -653301.95 79.213901 + 36 0 -15.246907 0 -15.246907 -652103.44 79.190056 + 37 0 -15.256602 0 -15.256602 -650901.73 79.166215 + 38 0 -15.266276 0 -15.266276 -649696.82 79.14238 + 39 0 -15.275931 0 -15.275931 -648488.71 79.118549 + 40 0 -15.285566 0 -15.285566 -647277.39 79.094723 + 41 0 -15.295181 0 -15.295181 -646062.87 79.070901 + 42 0 -15.304775 0 -15.304775 -644845.14 79.047085 + 43 0 -15.31435 0 -15.31435 -643624.2 79.023273 + 44 0 -15.323905 0 -15.323905 -642400.06 78.999466 + 45 0 -15.333439 0 -15.333439 -641172.71 78.975664 + 46 0 -15.342953 0 -15.342953 -639942.14 78.951867 + 47 0 -15.352447 0 -15.352447 -638708.37 78.928074 + 48 0 -15.361921 0 -15.361921 -637471.39 78.904286 + 49 0 -15.371375 0 -15.371375 -636231.2 78.880503 + 50 0 -15.380808 0 -15.380808 -634987.79 78.856725 + 51 0 -15.390221 0 -15.390221 -633741.17 78.832951 + 52 0 -15.399613 0 -15.399613 -632491.34 78.809183 + 53 0 -15.408985 0 -15.408985 -631238.3 78.785419 + 54 0 -15.418337 0 -15.418337 -629982.03 78.761659 + 55 0 -15.427668 0 -15.427668 -628722.56 78.737905 + 56 0 -15.436978 0 -15.436978 -627459.86 78.714155 + 57 0 -15.446268 0 -15.446268 -626193.95 78.690411 + 58 0 -15.455537 0 -15.455537 -624924.82 78.666671 + 59 0 -15.464786 0 -15.464786 -623652.47 78.642935 + 60 0 -15.474014 0 -15.474014 -622376.9 78.619205 + 61 0 -15.483221 0 -15.483221 -621098.11 78.595479 + 62 0 -15.492407 0 -15.492407 -619816.1 78.571758 + 63 0 -15.501572 0 -15.501572 -618530.86 78.548042 + 64 0 -15.510716 0 -15.510716 -617242.41 78.52433 + 65 0 -15.51984 0 -15.51984 -615950.73 78.500624 + 66 0 -15.528942 0 -15.528942 -614655.82 78.476922 + 67 0 -15.538024 0 -15.538024 -613357.7 78.453225 + 68 0 -15.547084 0 -15.547084 -612056.34 78.429532 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-17.157878 -19900.891 71.001656 + 393 0 -17.158137 0 -17.158137 -17551.954 70.979488 + 394 0 -17.158363 0 -17.158363 -15199.82 70.957326 + 395 0 -17.158557 0 -17.158557 -12844.489 70.935168 + 396 0 -17.158719 0 -17.158719 -10485.962 70.913014 + 397 0 -17.158847 0 -17.158847 -8124.2386 70.890866 + 398 0 -17.158943 0 -17.158943 -5759.3193 70.868722 + 399 0 -17.159006 0 -17.159006 -3391.2043 70.846582 + 400 0 -17.159037 0 -17.159037 -1019.8937 70.824447 + 401 0 -17.15904 0 -17.15904 -0.27024801 70.81494 + 402 0 -17.15904 0 -17.15904 -1.5603989e-05 70.814937 + 403 0 -17.15904 0 -17.15904 3.4008317e-09 70.814937 + 404 0 -17.15904 0 -17.15904 3.2564181e-09 70.814937 + 405 0 -17.15904 0 -17.15904 2.3373282e-09 70.814937 + 406 0 -17.15904 0 -17.15904 -9.4785189e-10 70.814937 + 407 0 -17.15904 0 -17.15904 -1.238317e-10 70.814937 + 408 0 -17.15904 0 -17.15904 -1.6373305e-10 70.814937 + 409 0 -17.15904 0 -17.15904 9.4335021e-11 70.814937 + 410 0 -17.15904 0 -17.15904 -4.6124262e-10 70.814937 + 411 0 -17.15904 0 -17.15904 3.3870854e-09 70.814937 + 412 0 -17.15904 0 -17.15904 -1.3077808e-09 70.814937 + 413 0 -17.15904 0 -17.15904 -2.0897946e-09 70.814937 + 414 0 -17.15904 0 -17.15904 3.3870854e-09 70.814937 + 415 0 -17.15904 0 -17.15904 -1.5433105e-09 70.814937 + 416 0 -17.15904 0 -17.15904 -2.0629924e-09 70.814937 + 417 0 -17.15904 0 -17.15904 3.3870854e-09 70.814937 + 418 0 -17.15904 0 -17.15904 -1.8838344e-09 70.814937 + 419 0 -17.15904 0 -17.15904 3.5418108e-12 70.814937 + 420 0 -17.15904 0 -17.15904 3.5418108e-12 70.814937 +Loop time of 0.0241749 on 1 procs for 420 steps with 4 atoms + +95.2% CPU use with 1 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = linesearch alpha is zero + Energy initial, next-to-last, final = + -14.8850317162759 -17.1590398301299 -17.1590398301299 + Force two-norm initial, final = 59.993295 1.0284199e-14 + Force max component initial, final = 34.637145 6.9392045e-15 + Final line search alpha, max atom move = 0.5 3.4696022e-15 + Iterations, force evaluations = 420 440 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.018593 | 0.018593 | 0.018593 | 0.0 | 76.91 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00049936 | 0.00049936 | 0.00049936 | 0.0 | 2.07 +Output | 0.0027008 | 0.0027008 | 0.0027008 | 0.0 | 11.17 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.002382 | | | 9.85 + +Nlocal: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 168 ave 168 max 168 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 108 ave 108 max 108 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 216 ave 216 max 216 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 216 +Ave neighs/atom = 54 +Neighbor list builds = 0 +Dangerous builds = 0 + +variable cohesive_energy equal pe/atoms +variable atmVol equal vol/atoms +variable aLatt equal (4*vol/atoms)^0.3333333333 + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Per MPI rank memory allocation (min/avg/max) = 3.715 | 3.715 | 3.715 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 420 0 -17.15904 0 -17.15904 3.8874134e-10 70.814937 +Loop time of 1.22e-06 on 1 procs for 0 steps with 4 atoms + +163.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.22e-06 | | |100.00 + +Nlocal: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 360 ave 360 max 360 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 108 ave 108 max 108 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 216 ave 216 max 216 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 216 +Ave neighs/atom = 54 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.28975995753248 eV/atom +print "Reference cohesive energy: -4.289 eV/atom" +Reference cohesive energy: -4.289 eV/atom +print "Atomic volume ${atmVol} A^3" +Atomic volume 17.7037343507869 A^3 +print "Lattice constant ${aLatt} A" +Lattice constant 4.13721691666803 A +print "Reference lattice constant 4.137 A" +Reference lattice constant 4.137 A +print "====================================================" +==================================================== + + +#dump 1 all custom 1 fcc.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.fcc_relax.g++.4 b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.fcc_relax.g++.4 new file mode 100644 index 0000000000..1c3e31302a --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.fcc_relax.g++.4 @@ -0,0 +1,10143 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Si fcc phase + +units metal +boundary p p p + +atom_style atomic +lattice fcc 4.309793856093661 +Lattice spacing in x,y,z = 4.3097939 4.3097939 4.3097939 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (4.3097939 4.3097939 4.3097939) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 4 atoms + using lattice units in orthogonal box = (0 0 0) to (4.3097939 4.3097939 4.3097939) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +Reading meam/sw/spline potential file Si.b.meam.sw.spline with DATE: 2012-10-26 +mass * 28.085 + +fix relax all box/relax aniso 0 +thermo 1 +minimize 0 0 10000 100000 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.4 + ghost atom cutoff = 6.4 + binsize = 3.2, bins = 2 2 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 4.854 | 4.854 | 4.854 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 0 -14.885032 0 -14.885032 -693238.94 80.051503 + 1 0 -14.895414 0 -14.895414 -692151.97 80.02749 + 2 0 -14.905777 0 -14.905777 -691061.83 80.003482 + 3 0 -14.916122 0 -14.916122 -689968.51 79.979479 + 4 0 -14.926449 0 -14.926449 -688872.02 79.95548 + 5 0 -14.936757 0 -14.936757 -687772.36 79.931486 + 6 0 -14.947047 0 -14.947047 -686669.52 79.907497 + 7 0 -14.957318 0 -14.957318 -685563.5 79.883513 + 8 0 -14.96757 0 -14.96757 -684454.31 79.859534 + 9 0 -14.977804 0 -14.977804 -683341.94 79.835559 + 10 0 -14.988019 0 -14.988019 -682226.39 79.811589 + 11 0 -14.998215 0 -14.998215 -681107.66 79.787624 + 12 0 -15.008393 0 -15.008393 -679985.75 79.763664 + 13 0 -15.018551 0 -15.018551 -678860.66 79.739708 + 14 0 -15.028691 0 -15.028691 -677732.39 79.715758 + 15 0 -15.038812 0 -15.038812 -676600.93 79.691812 + 16 0 -15.048914 0 -15.048914 -675466.29 79.667871 + 17 0 -15.058997 0 -15.058997 -674328.46 79.643934 + 18 0 -15.06906 0 -15.06906 -673187.45 79.620003 + 19 0 -15.079105 0 -15.079105 -672043.25 79.596076 + 20 0 -15.089131 0 -15.089131 -670895.86 79.572154 + 21 0 -15.099137 0 -15.099137 -669745.28 79.548237 + 22 0 -15.109125 0 -15.109125 -668591.52 79.524325 + 23 0 -15.119093 0 -15.119093 -667434.56 79.500418 + 24 0 -15.129041 0 -15.129041 -666274.42 79.476515 + 25 0 -15.138971 0 -15.138971 -665111.08 79.452617 + 26 0 -15.148881 0 -15.148881 -663944.55 79.428724 + 27 0 -15.158771 0 -15.158771 -662774.82 79.404835 + 28 0 -15.168643 0 -15.168643 -661601.9 79.380952 + 29 0 -15.178494 0 -15.178494 -660425.79 79.357073 + 30 0 -15.188327 0 -15.188327 -659246.47 79.333199 + 31 0 -15.198139 0 -15.198139 -658063.97 79.30933 + 32 0 -15.207932 0 -15.207932 -656878.26 79.285466 + 33 0 -15.217706 0 -15.217706 -655689.36 79.261606 + 34 0 -15.227459 0 -15.227459 -654497.25 79.237751 + 35 0 -15.237193 0 -15.237193 -653301.95 79.213901 + 36 0 -15.246907 0 -15.246907 -652103.44 79.190056 + 37 0 -15.256602 0 -15.256602 -650901.73 79.166215 + 38 0 -15.266276 0 -15.266276 -649696.82 79.14238 + 39 0 -15.275931 0 -15.275931 -648488.71 79.118549 + 40 0 -15.285566 0 -15.285566 -647277.39 79.094723 + 41 0 -15.295181 0 -15.295181 -646062.87 79.070901 + 42 0 -15.304775 0 -15.304775 -644845.14 79.047085 + 43 0 -15.31435 0 -15.31435 -643624.2 79.023273 + 44 0 -15.323905 0 -15.323905 -642400.06 78.999466 + 45 0 -15.333439 0 -15.333439 -641172.71 78.975664 + 46 0 -15.342953 0 -15.342953 -639942.14 78.951867 + 47 0 -15.352447 0 -15.352447 -638708.37 78.928074 + 48 0 -15.361921 0 -15.361921 -637471.39 78.904286 + 49 0 -15.371375 0 -15.371375 -636231.2 78.880503 + 50 0 -15.380808 0 -15.380808 -634987.79 78.856725 + 51 0 -15.390221 0 -15.390221 -633741.17 78.832951 + 52 0 -15.399613 0 -15.399613 -632491.34 78.809183 + 53 0 -15.408985 0 -15.408985 -631238.3 78.785419 + 54 0 -15.418337 0 -15.418337 -629982.03 78.761659 + 55 0 -15.427668 0 -15.427668 -628722.56 78.737905 + 56 0 -15.436978 0 -15.436978 -627459.86 78.714155 + 57 0 -15.446268 0 -15.446268 -626193.95 78.690411 + 58 0 -15.455537 0 -15.455537 -624924.82 78.666671 + 59 0 -15.464786 0 -15.464786 -623652.47 78.642935 + 60 0 -15.474014 0 -15.474014 -622376.9 78.619205 + 61 0 -15.483221 0 -15.483221 -621098.11 78.595479 + 62 0 -15.492407 0 -15.492407 -619816.1 78.571758 + 63 0 -15.501572 0 -15.501572 -618530.86 78.548042 + 64 0 -15.510716 0 -15.510716 -617242.41 78.52433 + 65 0 -15.51984 0 -15.51984 -615950.73 78.500624 + 66 0 -15.528942 0 -15.528942 -614655.82 78.476922 + 67 0 -15.538024 0 -15.538024 -613357.7 78.453225 + 68 0 -15.547084 0 -15.547084 -612056.34 78.429532 + 69 0 -15.556124 0 -15.556124 -610751.76 78.405845 + 70 0 -15.565142 0 -15.565142 -609443.95 78.382162 + 71 0 -15.574139 0 -15.574139 -608132.92 78.358484 + 72 0 -15.583115 0 -15.583115 -606818.65 78.334811 + 73 0 -15.59207 0 -15.59207 -605501.16 78.311142 + 74 0 -15.601003 0 -15.601003 -604180.44 78.287479 + 75 0 -15.609915 0 -15.609915 -602856.49 78.26382 + 76 0 -15.618806 0 -15.618806 -601529.3 78.240165 + 77 0 -15.627675 0 -15.627675 -600198.88 78.216516 + 78 0 -15.636523 0 -15.636523 -598865.24 78.192871 + 79 0 -15.645349 0 -15.645349 -597528.35 78.169231 + 80 0 -15.654154 0 -15.654154 -596188.24 78.145596 + 81 0 -15.662937 0 -15.662937 -594844.89 78.121966 + 82 0 -15.671699 0 -15.671699 -593498.3 78.09834 + 83 0 -15.680439 0 -15.680439 -592148.48 78.07472 + 84 0 -15.689157 0 -15.689157 -590795.42 78.051103 + 85 0 -15.697854 0 -15.697854 -589439.12 78.027492 + 86 0 -15.706528 0 -15.706528 -588079.59 78.003886 + 87 0 -15.715181 0 -15.715181 -586716.81 77.980284 + 88 0 -15.723812 0 -15.723812 -585350.8 77.956687 + 89 0 -15.732422 0 -15.732422 -583981.55 77.933095 + 90 0 -15.741009 0 -15.741009 -582609.05 77.909507 + 91 0 -15.749575 0 -15.749575 -581233.32 77.885924 + 92 0 -15.758118 0 -15.758118 -579854.34 77.862346 + 93 0 -15.766639 0 -15.766639 -578472.13 77.838773 + 94 0 -15.775139 0 -15.775139 -577086.66 77.815205 + 95 0 -15.783616 0 -15.783616 -575697.96 77.791641 + 96 0 -15.792071 0 -15.792071 -574306.01 77.768082 + 97 0 -15.800504 0 -15.800504 -572910.81 77.744528 + 98 0 -15.808914 0 -15.808914 -571512.37 77.720978 + 99 0 -15.817303 0 -15.817303 -570110.68 77.697434 + 100 0 -15.825669 0 -15.825669 -568705.75 77.673894 + 101 0 -15.834012 0 -15.834012 -567297.57 77.650359 + 102 0 -15.842334 0 -15.842334 -565886.14 77.626828 + 103 0 -15.850632 0 -15.850632 -564471.46 77.603303 + 104 0 -15.858909 0 -15.858909 -563053.53 77.579782 + 105 0 -15.867163 0 -15.867163 -561632.35 77.556266 + 106 0 -15.875394 0 -15.875394 -560207.92 77.532754 + 107 0 -15.883603 0 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-16.035225 0 -16.035225 -531035.84 77.063523 + 127 0 -16.042974 0 -16.042974 -529543.02 77.040112 + 128 0 -16.0507 0 -16.0507 -528046.94 77.016705 + 129 0 -16.058402 0 -16.058402 -526547.6 76.993303 + 130 0 -16.06608 0 -16.06608 -525044.99 76.969905 + 131 0 -16.073735 0 -16.073735 -523539.12 76.946512 + 132 0 -16.081366 0 -16.081366 -522029.98 76.923124 + 133 0 -16.088974 0 -16.088974 -520517.58 76.899741 + 134 0 -16.096559 0 -16.096559 -519001.91 76.876363 + 135 0 -16.104119 0 -16.104119 -517482.98 76.852989 + 136 0 -16.111656 0 -16.111656 -515960.78 76.82962 + 137 0 -16.119169 0 -16.119169 -514435.32 76.806255 + 138 0 -16.126658 0 -16.126658 -512906.59 76.782896 + 139 0 -16.134124 0 -16.134124 -511374.59 76.759541 + 140 0 -16.141565 0 -16.141565 -509839.32 76.736191 + 141 0 -16.148983 0 -16.148983 -508300.78 76.712846 + 142 0 -16.156377 0 -16.156377 -506758.97 76.689505 + 143 0 -16.163746 0 -16.163746 -505213.89 76.666169 + 144 0 -16.171092 0 -16.171092 -503665.55 76.642838 + 145 0 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-17.15904 0 -17.15904 1.1615549e-09 70.814937 + 10000 0 -17.15904 0 -17.15904 -1.1922665e-09 70.814937 +Loop time of 0.852954 on 4 procs for 10000 steps with 4 atoms + +98.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = max iterations + Energy initial, next-to-last, final = + -14.8850317162759 -17.1590398301299 -17.1590398301299 + Force two-norm initial, final = 59.993295 9.581849e-14 + Force max component initial, final = 34.637145 6.0848149e-14 + Final line search alpha, max atom move = 1 6.0848149e-14 + Iterations, force evaluations = 10000 19600 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.30002 | 0.30136 | 0.30326 | 0.2 | 35.33 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.1786 | 0.18075 | 0.18225 | 0.4 | 21.19 +Output | 0.082981 | 0.087714 | 0.10035 | 2.5 | 10.28 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.2831 | | | 33.19 + +Nlocal: 1 ave 1 max 1 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 125 ave 125 max 125 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 27 ave 27 max 27 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 54 ave 54 max 54 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 216 +Ave neighs/atom = 54 +Neighbor list builds = 0 +Dangerous builds = 0 + +variable cohesive_energy equal pe/atoms +variable atmVol equal vol/atoms +variable aLatt equal (4*vol/atoms)^0.3333333333 + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Per MPI rank memory allocation (min/avg/max) = 3.746 | 3.746 | 3.746 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 10000 0 -17.15904 0 -17.15904 -6.9517313e-10 70.814937 +Loop time of 2.1825e-06 on 4 procs for 0 steps with 4 atoms + +114.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.183e-06 | | |100.00 + +Nlocal: 1 ave 2 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 287 ave 288 max 286 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 27 ave 54 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 54 ave 108 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 216 +Ave neighs/atom = 54 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.28975995753248 eV/atom +print "Reference cohesive energy: -4.289 eV/atom" +Reference cohesive energy: -4.289 eV/atom +print "Atomic volume ${atmVol} A^3" +Atomic volume 17.7037343507869 A^3 +print "Lattice constant ${aLatt} A" +Lattice constant 4.13721691666803 A +print "Reference lattice constant 4.137 A" +Reference lattice constant 4.137 A +print "====================================================" +==================================================== + + +#dump 1 all custom 1 fcc.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.hcp_relax.g++.1 b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.hcp_relax.g++.1 new file mode 100644 index 0000000000..105ffcd178 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.hcp_relax.g++.1 @@ -0,0 +1,10147 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Si hcp + +units metal +boundary p p p + +atom_style atomic +#lattice custom 2.93093 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 1.596 basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75 +lattice custom 2.93093 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 1.7 basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75 +Lattice spacing in x,y,z = 2.93093 5.0765173 4.982581 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (2.93093 5.0765173 4.982581) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4 atoms + using lattice units in orthogonal box = (0 0 0) to (2.93093 5.0765173 4.982581) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +Reading meam/sw/spline potential file Si.b.meam.sw.spline with DATE: 2012-10-26 +mass * 28.085 + +fix relax all box/relax aniso 0 +thermo 1 +minimize 0 0 10000 100000 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.4 + ghost atom cutoff = 6.4 + binsize = 3.2, bins = 1 2 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 4.849 | 4.849 | 4.849 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 0 -16.762227 0 -16.762227 -314547.95 74.135408 + 1 0 -16.765928 0 -16.765928 -313024.59 74.116882 + 2 0 -16.769609 0 -16.769609 -311500.27 74.098373 + 3 0 -16.773269 0 -16.773269 -309975.01 74.079883 + 4 0 -16.776908 0 -16.776908 -308448.82 74.061411 + 5 0 -16.780526 0 -16.780526 -306921.71 74.042957 + 6 0 -16.784123 0 -16.784123 -305393.7 74.024521 + 7 0 -16.787699 0 -16.787699 -303864.8 74.006104 + 8 0 -16.791255 0 -16.791255 -302335.03 73.987706 + 9 0 -16.79479 0 -16.79479 -300804.41 73.969326 + 10 0 -16.798304 0 -16.798304 -299272.94 73.950965 + 11 0 -16.801797 0 -16.801797 -297740.64 73.932623 + 12 0 -16.80527 0 -16.80527 -296207.52 73.9143 + 13 0 -16.808721 0 -16.808721 -294673.61 73.895996 + 14 0 -16.812152 0 -16.812152 -293138.91 73.877711 + 15 0 -16.815562 0 -16.815562 -291603.45 73.859446 + 16 0 -16.818952 0 -16.818952 -290067.23 73.8412 + 17 0 -16.822321 0 -16.822321 -288530.28 73.822974 + 18 0 -16.825669 0 -16.825669 -286992.6 73.804767 + 19 0 -16.828996 0 -16.828996 -285454.22 73.786581 + 20 0 -16.832302 0 -16.832302 -283915.16 73.768414 + 21 0 -16.835588 0 -16.835588 -282375.42 73.750267 + 22 0 -16.838853 0 -16.838853 -280835.03 73.732141 + 23 0 -16.842098 0 -16.842098 -279294 73.714034 + 24 0 -16.845322 0 -16.845322 -277752.35 73.695949 + 25 0 -16.848525 0 -16.848525 -276210.1 73.677884 + 26 0 -16.851708 0 -16.851708 -274667.26 73.659839 + 27 0 -16.854869 0 -16.854869 -273123.86 73.641815 + 28 0 -16.858011 0 -16.858011 -271579.9 73.623813 + 29 0 -16.861132 0 -16.861132 -270035.42 73.605831 + 30 0 -16.864232 0 -16.864232 -268490.42 73.587871 + 31 0 -16.867311 0 -16.867311 -266944.93 73.569932 + 32 0 -16.87037 0 -16.87037 -265398.97 73.552014 + 33 0 -16.873409 0 -16.873409 -263852.55 73.534118 + 34 0 -16.876427 0 -16.876427 -262305.69 73.516244 + 35 0 -16.879424 0 -16.879424 -260758.42 73.498392 + 36 0 -16.882401 0 -16.882401 -259210.75 73.480562 + 37 0 -16.885358 0 -16.885358 -257662.7 73.462754 + 38 0 -16.888294 0 -16.888294 -256114.3 73.444969 + 39 0 -16.891209 0 -16.891209 -254565.56 73.427206 + 40 0 -16.894105 0 -16.894105 -253016.51 73.409466 + 41 0 -16.896979 0 -16.896979 -251467.17 73.391749 + 42 0 -16.899834 0 -16.899834 -249917.56 73.374055 + 43 0 -16.902668 0 -16.902668 -248367.69 73.356384 + 44 0 -16.905481 0 -16.905481 -246817.6 73.338736 + 45 0 -16.908275 0 -16.908275 -245267.3 73.321112 + 46 0 -16.911048 0 -16.911048 -243716.82 73.303511 + 47 0 -16.9138 0 -16.9138 -242166.18 73.285935 + 48 0 -16.916533 0 -16.916533 -240615.4 73.268382 + 49 0 -16.919245 0 -16.919245 -239064.51 73.250854 + 50 0 -16.921937 0 -16.921937 -237513.53 73.23335 + 51 0 -16.924609 0 -16.924609 -235962.49 73.215871 + 52 0 -16.92726 0 -16.92726 -234411.41 73.198416 + 53 0 -16.929892 0 -16.929892 -232860.31 73.180987 + 54 0 -16.932503 0 -16.932503 -231309.21 73.163582 + 55 0 -16.935094 0 -16.935094 -229758.16 73.146203 + 56 0 -16.937665 0 -16.937665 -228207.16 73.12885 + 57 0 -16.940216 0 -16.940216 -226656.25 73.111522 + 58 0 -16.942747 0 -16.942747 -225105.46 73.09422 + 59 0 -16.945258 0 -16.945258 -223554.8 73.076944 + 60 0 -16.947749 0 -16.947749 -222004.31 73.059695 + 61 0 -16.95022 0 -16.95022 -220454.02 73.042472 + 62 0 -16.952671 0 -16.952671 -218903.95 73.025276 + 63 0 -16.955102 0 -16.955102 -217354.13 73.008107 + 64 0 -16.957513 0 -16.957513 -215804.59 72.990965 + 65 0 -16.959904 0 -16.959904 -214255.36 72.973851 + 66 0 -16.962276 0 -16.962276 -212706.47 72.956764 + 67 0 -16.964628 0 -16.964628 -211157.95 72.939705 + 68 0 -16.96696 0 -16.96696 -209609.83 72.922675 + 69 0 -16.969272 0 -16.969272 -208062.14 72.905673 + 70 0 -16.971564 0 -16.971564 -206514.91 72.888699 + 71 0 -16.973837 0 -16.973837 -204968.17 72.871754 + 72 0 -16.97609 0 -16.97609 -203421.96 72.854838 + 73 0 -16.978324 0 -16.978324 -201876.3 72.837952 + 74 0 -16.980538 0 -16.980538 -200331.24 72.821095 + 75 0 -16.982733 0 -16.982733 -198786.8 72.804269 + 76 0 -16.984908 0 -16.984908 -197243.02 72.787472 + 77 0 -16.987063 0 -16.987063 -195699.94 72.770706 + 78 0 -16.989199 0 -16.989199 -194157.58 72.75397 + 79 0 -16.991316 0 -16.991316 -192615.99 72.737265 + 80 0 -16.993413 0 -16.993413 -191075.19 72.720592 + 81 0 -16.995491 0 -16.995491 -189535.24 72.70395 + 82 0 -16.99755 0 -16.99755 -187996.16 72.68734 + 83 0 -16.99959 0 -16.99959 -186457.99 72.670762 + 84 0 -17.00161 0 -17.00161 -184920.77 72.654217 + 85 0 -17.003611 0 -17.003611 -183384.54 72.637704 + 86 0 -17.005593 0 -17.005593 -181849.34 72.621225 + 87 0 -17.007556 0 -17.007556 -180315.2 72.604778 + 88 0 -17.0095 0 -17.0095 -178782.18 72.588365 + 89 0 -17.011425 0 -17.011425 -177250.31 72.571987 + 90 0 -17.013331 0 -17.013331 -175719.63 72.555642 + 91 0 -17.015218 0 -17.015218 -174190.18 72.539333 + 92 0 -17.017086 0 -17.017086 -172662.02 72.523058 + 93 0 -17.018936 0 -17.018936 -171135.18 72.506819 + 94 0 -17.020766 0 -17.020766 -169609.7 72.490615 + 95 0 -17.022578 0 -17.022578 -168085.64 72.474447 + 96 0 -17.024372 0 -17.024372 -166563.03 72.458316 + 97 0 -17.026147 0 -17.026147 -165041.93 72.442222 + 98 0 -17.027903 0 -17.027903 -163522.38 72.426164 + 99 0 -17.02964 0 -17.02964 -162004.43 72.410145 + 100 0 -17.03136 0 -17.03136 -160488.14 72.394163 + 101 0 -17.03306 0 -17.03306 -158973.54 72.378219 + 102 0 -17.034743 0 -17.034743 -157460.69 72.362315 + 103 0 -17.036407 0 -17.036407 -155949.64 72.346449 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123 0 -17.065946 0 -17.065946 -126197.63 72.038049 + 124 0 -17.067241 0 -17.067241 -124738.49 72.023113 + 125 0 -17.068519 0 -17.068519 -123282.56 72.008227 + 126 0 -17.069781 0 -17.069781 -121829.92 71.993392 + 127 0 -17.071026 0 -17.071026 -120380.64 71.978608 + 128 0 -17.072254 0 -17.072254 -118934.81 71.963876 + 129 0 -17.073466 0 -17.073466 -117492.5 71.949197 + 130 0 -17.074661 0 -17.074661 -116053.78 71.934571 + 131 0 -17.075841 0 -17.075841 -114618.75 71.919999 + 132 0 -17.077004 0 -17.077004 -113187.47 71.905481 + 133 0 -17.078151 0 -17.078151 -111760.05 71.891019 + 134 0 -17.079282 0 -17.079282 -110336.55 71.876612 + 135 0 -17.080397 0 -17.080397 -108917.07 71.862262 + 136 0 -17.081496 0 -17.081496 -107501.7 71.84797 + 137 0 -17.08258 0 -17.08258 -106090.52 71.833735 + 138 0 -17.083647 0 -17.083647 -104683.62 71.81956 + 139 0 -17.0847 0 -17.0847 -103281.1 71.805444 + 140 0 -17.085737 0 -17.085737 -101883.05 71.791388 + 141 0 -17.086759 0 -17.086759 -100489.56 71.777393 + 142 0 -17.087765 0 -17.087765 -99100.741 71.763461 + 143 0 -17.088757 0 -17.088757 -97716.679 71.749591 + 144 0 -17.089733 0 -17.089733 -96337.477 71.735784 + 145 0 -17.090695 0 -17.090695 -94963.236 71.722042 + 146 0 -17.091642 0 -17.091642 -93594.06 71.708365 + 147 0 -17.092574 0 -17.092574 -92230.053 71.694754 + 148 0 -17.093491 0 -17.093491 -90871.322 71.68121 + 149 0 -17.094395 0 -17.094395 -89517.976 71.667734 + 150 0 -17.095284 0 -17.095284 -88170.122 71.654327 + 151 0 -17.096159 0 -17.096159 -86827.875 71.640989 + 152 0 -17.097019 0 -17.097019 -85491.345 71.627722 + 153 0 -17.097866 0 -17.097866 -84160.649 71.614526 + 154 0 -17.098699 0 -17.098699 -82835.907 71.601403 + 155 0 -17.099519 0 -17.099519 -81517.242 71.588353 + 156 0 -17.100325 0 -17.100325 -80204.773 71.575377 + 157 0 -17.101117 0 -17.101117 -78898.623 71.562477 + 158 0 -17.101896 0 -17.101896 -77598.914 71.549654 + 159 0 -17.102662 0 -17.102662 -76305.772 71.536908 + 160 0 -17.103415 0 -17.103415 -75019.324 71.52424 + 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-17.781718 0 -17.781718 -1.1416058e-09 66.486818 +Loop time of 1.20503 on 1 procs for 10000 steps with 4 atoms + +98.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = max iterations + Energy initial, next-to-last, final = + -16.7622269576344 -17.7817183149305 -17.7817183149305 + Force two-norm initial, final = 25.461198 8.8878297e-14 + Force max component initial, final = 17.471035 6.2703592e-14 + Final line search alpha, max atom move = 1 6.2703592e-14 + Iterations, force evaluations = 10000 18031 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.98806 | 0.98806 | 0.98806 | 0.0 | 81.99 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.033461 | 0.033461 | 0.033461 | 0.0 | 2.78 +Output | 0.061824 | 0.061824 | 0.061824 | 0.0 | 5.13 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.1217 | | | 10.10 + +Nlocal: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 300 ave 300 max 300 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 112 ave 112 max 112 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 224 ave 224 max 224 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 224 +Ave neighs/atom = 56 +Neighbor list builds = 0 +Dangerous builds = 0 + +variable cohesive_energy equal pe/atoms +variable lattice_parameter equal lx +variable c_to_a equal lz/lx +variable atmVol equal vol/atoms +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Per MPI rank memory allocation (min/avg/max) = 3.724 | 3.724 | 3.724 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 10000 0 -17.781718 0 -17.781718 -1.0779541e-09 66.486818 +Loop time of 8.81e-07 on 1 procs for 0 steps with 4 atoms + +113.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 8.81e-07 | | |100.00 + +Nlocal: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 300 ave 300 max 300 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 128 ave 128 max 128 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 256 ave 256 max 256 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 256 +Ave neighs/atom = 64 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.44542957873261 eV/atom +print "Reference cohesive energy: -4.352 eV/atom" +Reference cohesive energy: -4.352 eV/atom +print "Calculated lattice parameter: ${lattice_parameter} A" +Calculated lattice parameter: 2.76079963615789 A +print "Reference lattice parameter: 2.736 A" +Reference lattice parameter: 2.736 A +print "Atomic volume ${atmVol} A^3" +Atomic volume 16.6217045402861 A^3 +print "c/a ratio: ${c_to_a}" +c/a ratio: 1.71820967774805 +print "Reference c/a ratio: 1.633" +Reference c/a ratio: 1.633 +print "====================================================" +==================================================== + +#dump 1 all custom 1 hcp.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.hcp_relax.g++.4 b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.hcp_relax.g++.4 new file mode 100644 index 0000000000..683a19c280 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.hcp_relax.g++.4 @@ -0,0 +1,1510 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Si hcp + +units metal +boundary p p p + +atom_style atomic +#lattice custom 2.93093 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 1.596 basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75 +lattice custom 2.93093 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 1.7 basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75 +Lattice spacing in x,y,z = 2.93093 5.0765173 4.982581 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (2.93093 5.0765173 4.982581) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 4 atoms + using lattice units in orthogonal box = (0 0 0) to (2.93093 5.0765173 4.982581) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +Reading meam/sw/spline potential file Si.b.meam.sw.spline with DATE: 2012-10-26 +mass * 28.085 + +fix relax all box/relax aniso 0 +thermo 1 +minimize 0 0 10000 100000 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.4 + ghost atom cutoff = 6.4 + binsize = 3.2, bins = 1 2 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 4.864 | 4.864 | 4.864 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 0 -16.762227 0 -16.762227 -314547.95 74.135408 + 1 0 -16.765928 0 -16.765928 -313024.59 74.116882 + 2 0 -16.769609 0 -16.769609 -311500.27 74.098373 + 3 0 -16.773269 0 -16.773269 -309975.01 74.079883 + 4 0 -16.776908 0 -16.776908 -308448.82 74.061411 + 5 0 -16.780526 0 -16.780526 -306921.71 74.042957 + 6 0 -16.784123 0 -16.784123 -305393.7 74.024521 + 7 0 -16.787699 0 -16.787699 -303864.8 74.006104 + 8 0 -16.791255 0 -16.791255 -302335.03 73.987706 + 9 0 -16.79479 0 -16.79479 -300804.41 73.969326 + 10 0 -16.798304 0 -16.798304 -299272.94 73.950965 + 11 0 -16.801797 0 -16.801797 -297740.64 73.932623 + 12 0 -16.80527 0 -16.80527 -296207.52 73.9143 + 13 0 -16.808721 0 -16.808721 -294673.61 73.895996 + 14 0 -16.812152 0 -16.812152 -293138.91 73.877711 + 15 0 -16.815562 0 -16.815562 -291603.45 73.859446 + 16 0 -16.818952 0 -16.818952 -290067.23 73.8412 + 17 0 -16.822321 0 -16.822321 -288530.28 73.822974 + 18 0 -16.825669 0 -16.825669 -286992.6 73.804767 + 19 0 -16.828996 0 -16.828996 -285454.22 73.786581 + 20 0 -16.832302 0 -16.832302 -283915.16 73.768414 + 21 0 -16.835588 0 -16.835588 -282375.42 73.750267 + 22 0 -16.838853 0 -16.838853 -280835.03 73.732141 + 23 0 -16.842098 0 -16.842098 -279294 73.714034 + 24 0 -16.845322 0 -16.845322 -277752.35 73.695949 + 25 0 -16.848525 0 -16.848525 -276210.1 73.677884 + 26 0 -16.851708 0 -16.851708 -274667.26 73.659839 + 27 0 -16.854869 0 -16.854869 -273123.86 73.641815 + 28 0 -16.858011 0 -16.858011 -271579.9 73.623813 + 29 0 -16.861132 0 -16.861132 -270035.42 73.605831 + 30 0 -16.864232 0 -16.864232 -268490.42 73.587871 + 31 0 -16.867311 0 -16.867311 -266944.93 73.569932 + 32 0 -16.87037 0 -16.87037 -265398.97 73.552014 + 33 0 -16.873409 0 -16.873409 -263852.55 73.534118 + 34 0 -16.876427 0 -16.876427 -262305.69 73.516244 + 35 0 -16.879424 0 -16.879424 -260758.42 73.498392 + 36 0 -16.882401 0 -16.882401 -259210.75 73.480562 + 37 0 -16.885358 0 -16.885358 -257662.7 73.462754 + 38 0 -16.888294 0 -16.888294 -256114.3 73.444969 + 39 0 -16.891209 0 -16.891209 -254565.56 73.427206 + 40 0 -16.894105 0 -16.894105 -253016.51 73.409466 + 41 0 -16.896979 0 -16.896979 -251467.17 73.391749 + 42 0 -16.899834 0 -16.899834 -249917.56 73.374055 + 43 0 -16.902668 0 -16.902668 -248367.69 73.356384 + 44 0 -16.905481 0 -16.905481 -246817.6 73.338736 + 45 0 -16.908275 0 -16.908275 -245267.3 73.321112 + 46 0 -16.911048 0 -16.911048 -243716.82 73.303511 + 47 0 -16.9138 0 -16.9138 -242166.18 73.285935 + 48 0 -16.916533 0 -16.916533 -240615.4 73.268382 + 49 0 -16.919245 0 -16.919245 -239064.51 73.250854 + 50 0 -16.921937 0 -16.921937 -237513.53 73.23335 + 51 0 -16.924609 0 -16.924609 -235962.49 73.215871 + 52 0 -16.92726 0 -16.92726 -234411.41 73.198416 + 53 0 -16.929892 0 -16.929892 -232860.31 73.180987 + 54 0 -16.932503 0 -16.932503 -231309.21 73.163582 + 55 0 -16.935094 0 -16.935094 -229758.16 73.146203 + 56 0 -16.937665 0 -16.937665 -228207.16 73.12885 + 57 0 -16.940216 0 -16.940216 -226656.25 73.111522 + 58 0 -16.942747 0 -16.942747 -225105.46 73.09422 + 59 0 -16.945258 0 -16.945258 -223554.8 73.076944 + 60 0 -16.947749 0 -16.947749 -222004.31 73.059695 + 61 0 -16.95022 0 -16.95022 -220454.02 73.042472 + 62 0 -16.952671 0 -16.952671 -218903.95 73.025276 + 63 0 -16.955102 0 -16.955102 -217354.13 73.008107 + 64 0 -16.957513 0 -16.957513 -215804.59 72.990965 + 65 0 -16.959904 0 -16.959904 -214255.36 72.973851 + 66 0 -16.962276 0 -16.962276 -212706.47 72.956764 + 67 0 -16.964628 0 -16.964628 -211157.95 72.939705 + 68 0 -16.96696 0 -16.96696 -209609.83 72.922675 + 69 0 -16.969272 0 -16.969272 -208062.14 72.905673 + 70 0 -16.971564 0 -16.971564 -206514.91 72.888699 + 71 0 -16.973837 0 -16.973837 -204968.17 72.871754 + 72 0 -16.97609 0 -16.97609 -203421.96 72.854838 + 73 0 -16.978324 0 -16.978324 -201876.3 72.837952 + 74 0 -16.980538 0 -16.980538 -200331.24 72.821095 + 75 0 -16.982733 0 -16.982733 -198786.8 72.804269 + 76 0 -16.984908 0 -16.984908 -197243.02 72.787472 + 77 0 -16.987063 0 -16.987063 -195699.94 72.770706 + 78 0 -16.989199 0 -16.989199 -194157.58 72.75397 + 79 0 -16.991316 0 -16.991316 -192615.99 72.737265 + 80 0 -16.993413 0 -16.993413 -191075.19 72.720592 + 81 0 -16.995491 0 -16.995491 -189535.24 72.70395 + 82 0 -16.99755 0 -16.99755 -187996.16 72.68734 + 83 0 -16.99959 0 -16.99959 -186457.99 72.670762 + 84 0 -17.00161 0 -17.00161 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-17.407164 -0.0012055293 68.739514 + 1358 0 -17.407164 0 -17.407164 0.00010604666 68.739514 + 1359 0 -17.407164 0 -17.407164 0.00014373194 68.739514 + 1360 0 -17.407164 0 -17.407164 -1.9445639e-07 68.739514 + 1361 0 -17.407164 0 -17.407164 4.2739214e-08 68.739514 + 1362 0 -17.407164 0 -17.407164 3.3994737e-07 68.739514 + 1363 0 -17.407164 0 -17.407164 3.3994737e-07 68.739514 +Loop time of 0.10075 on 4 procs for 1363 steps with 4 atoms + +97.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = linesearch alpha is zero + Energy initial, next-to-last, final = + -16.7622269576344 -17.4071637400335 -17.4071637400335 + Force two-norm initial, final = 25.461198 2.6317686e-09 + Force max component initial, final = 17.471035 2.1004698e-09 + Final line search alpha, max atom move = 0.5 1.0502349e-09 + Iterations, force evaluations = 1363 1432 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.029396 | 0.030078 | 0.030836 | 0.4 | 29.85 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.01925 | 0.020056 | 0.020717 | 0.5 | 19.91 +Output | 0.014407 | 0.016235 | 0.019321 | 1.6 | 16.11 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.03438 | | | 34.13 + +Nlocal: 1 ave 1 max 1 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 230 ave 230 max 230 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 28 ave 28 max 28 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 56 ave 56 max 56 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 224 +Ave neighs/atom = 56 +Neighbor list builds = 0 +Dangerous builds = 0 + +variable cohesive_energy equal pe/atoms +variable lattice_parameter equal lx +variable c_to_a equal lz/lx +variable atmVol equal vol/atoms +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Per MPI rank memory allocation (min/avg/max) = 3.739 | 3.739 | 3.739 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 1363 0 -17.407164 0 -17.407164 3.398773e-07 68.739514 +Loop time of 2.618e-06 on 4 procs for 0 steps with 4 atoms + +124.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.618e-06 | | |100.00 + +Nlocal: 1 ave 1 max 1 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 230 ave 230 max 230 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 32 ave 36 max 28 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 64 ave 64 max 64 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 256 +Ave neighs/atom = 64 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.35179093500837 eV/atom +print "Reference cohesive energy: -4.352 eV/atom" +Reference cohesive energy: -4.352 eV/atom +print "Calculated lattice parameter: ${lattice_parameter} A" +Calculated lattice parameter: 2.73621887141886 A +print "Reference lattice parameter: 2.736 A" +Reference lattice parameter: 2.736 A +print "Atomic volume ${atmVol} A^3" +Atomic volume 17.1848785131775 A^3 +print "c/a ratio: ${c_to_a}" +c/a ratio: 1.73054348005468 +print "Reference c/a ratio: 1.633" +Reference c/a ratio: 1.633 +print "====================================================" +==================================================== + +#dump 1 all custom 1 hcp.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.sc.g++.1 b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.sc.g++.1 new file mode 100644 index 0000000000..b9272ab376 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.sc.g++.1 @@ -0,0 +1,100 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Si fcc phase + +units metal +boundary p p p + +atom_style atomic +lattice sc 2.612 +Lattice spacing in x,y,z = 2.612 2.612 2.612 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (2.612 2.612 2.612) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 1 atoms + using lattice units in orthogonal box = (0 0 0) to (2.612 2.612 2.612) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +Reading meam/sw/spline potential file Si.b.meam.sw.spline with DATE: 2012-10-26 +mass * 28.085 + +variable cohesive_energy equal pe/atoms +variable atmVol equal vol/atoms +variable aLatt equal (vol/atoms)^0.3333333333 + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.4 + ghost atom cutoff = 6.4 + binsize = 3.2, bins = 1 1 1 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.744 | 3.744 | 3.744 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -4.3368757 0 -4.3368757 -41.869135 +Loop time of 1.328e-06 on 1 procs for 0 steps with 1 atoms + +75.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.328e-06 | | |100.00 + +Nlocal: 1 ave 1 max 1 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 215 ave 215 max 215 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 40 ave 40 max 40 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 80 ave 80 max 80 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 80 +Ave neighs/atom = 80 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.33687572290858 eV/atom +print "Reference cohesive energy: -4.337 eV/atom" +Reference cohesive energy: -4.337 eV/atom +print "Atomic volume ${atmVol} A^3" +Atomic volume 17.820484928 A^3 +print "Lattice constant ${aLatt} A" +Lattice constant 2.61199999974922 A +print "Reference lattice constant 2.612 A" +Reference lattice constant 2.612 A +print "====================================================" +==================================================== + + +#dump 1 all custom 1 sc.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.sc.g++.4 b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.sc.g++.4 new file mode 100644 index 0000000000..5e41e2467d --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.sc.g++.4 @@ -0,0 +1,101 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Si fcc phase + +units metal +boundary p p p + +atom_style atomic +lattice sc 2.612 +Lattice spacing in x,y,z = 2.612 2.612 2.612 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (2.612 2.612 2.612) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 1 atoms + using lattice units in orthogonal box = (0 0 0) to (2.612 2.612 2.612) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +Reading meam/sw/spline potential file Si.b.meam.sw.spline with DATE: 2012-10-26 +mass * 28.085 + +variable cohesive_energy equal pe/atoms +variable atmVol equal vol/atoms +variable aLatt equal (vol/atoms)^0.3333333333 + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.4 + ghost atom cutoff = 6.4 + binsize = 3.2, bins = 1 1 1 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966) +Per MPI rank memory allocation (min/avg/max) = 3.774 | 3.774 | 3.774 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -4.3368757 0 -4.3368757 -41.869135 +Loop time of 3.492e-06 on 4 procs for 0 steps with 1 atoms + +85.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.492e-06 | | |100.00 + +Nlocal: 0.25 ave 1 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 149.75 ave 150 max 149 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 10 ave 40 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +FullNghs: 20 ave 80 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 80 +Ave neighs/atom = 80 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.33687572290858 eV/atom +print "Reference cohesive energy: -4.337 eV/atom" +Reference cohesive energy: -4.337 eV/atom +print "Atomic volume ${atmVol} A^3" +Atomic volume 17.820484928 A^3 +print "Lattice constant ${aLatt} A" +Lattice constant 2.61199999974922 A +print "Reference lattice constant 2.612 A" +Reference lattice constant 2.612 A +print "====================================================" +==================================================== + + +#dump 1 all custom 1 sc.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.sc_relax.g++.1 b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.sc_relax.g++.1 new file mode 100644 index 0000000000..9868af99d9 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.sc_relax.g++.1 @@ -0,0 +1,4402 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Si fcc phase + +units metal +boundary p p p + +atom_style atomic +lattice sc 2.612 +Lattice spacing in x,y,z = 2.612 2.612 2.612 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (2.612 2.612 2.612) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 1 atoms + using lattice units in orthogonal box = (0 0 0) to (2.612 2.612 2.612) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +Reading meam/sw/spline potential file Si.b.meam.sw.spline with DATE: 2012-10-26 +mass * 28.085 + +fix relax all box/relax aniso 0 +thermo 1 +minimize 0 0 10000 100000 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.4 + ghost atom cutoff = 6.4 + binsize = 3.2, bins = 1 1 1 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 4.869 | 4.869 | 4.869 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 0 -4.3368757 0 -4.3368757 -41.869135 17.820485 + 1 0 -4.3368757 0 -4.3368757 -0.0064151392 17.820115 + 2 0 -4.3368757 0 -4.3368757 -1.5832709e-09 17.820115 + 3 0 -4.3368757 0 -4.3368757 3.3909505e-10 17.820115 + 4 0 -4.3368757 0 -4.3368757 3.2578595e-10 17.820115 + 5 0 -4.3368757 0 -4.3368757 -1.9080803e-10 17.820115 + 6 0 -4.3368757 0 -4.3368757 3.3909495e-10 17.820115 + 7 0 -4.3368757 0 -4.3368757 -1.9079854e-10 17.820115 + 8 0 -4.3368757 0 -4.3368757 -1.9079854e-10 17.820115 + 9 0 -4.3368757 0 -4.3368757 1.0118722e-10 17.820115 + 10 0 -4.3368757 0 -4.3368757 -2.3072585e-10 17.820115 + 11 0 -4.3368757 0 -4.3368757 3.5240418e-10 17.820115 + 12 0 -4.3368757 0 -4.3368757 -1.6419005e-10 17.820115 + 13 0 -4.3368757 0 -4.3368757 -1.6419005e-10 17.820115 + 14 0 -4.3368757 0 -4.3368757 1.1449508e-10 17.820115 + 15 0 -4.3368757 0 -4.3368757 -1.9080803e-10 17.820115 + 16 0 -4.3368757 0 -4.3368757 3.7902891e-10 17.820115 + 17 0 -4.3368757 0 -4.3368757 -5.5015387e-10 17.820115 + 18 0 -4.3368757 0 -4.3368757 3.7902891e-10 17.820115 + 19 0 -4.3368757 0 -4.3368757 -1.9080803e-10 17.820115 + 20 0 -4.3368757 0 -4.3368757 3.9233792e-10 17.820115 + 21 0 -4.3368757 0 -4.3368757 -5.3684477e-10 17.820115 + 22 0 -4.3368757 0 -4.3368757 3.7902891e-10 17.820115 + 23 0 -4.3368757 0 -4.3368757 -5.3684477e-10 17.820115 + 24 0 -4.3368757 0 -4.3368757 3.5241068e-10 17.820115 + 25 0 -4.3368757 0 -4.3368757 1.1448328e-10 17.820115 + 26 0 -4.3368757 0 -4.3368757 -5.5015387e-10 17.820115 + 27 0 -4.3368757 0 -4.3368757 3.5240418e-10 17.820115 + 28 0 -4.3368757 0 -4.3368757 1.0118725e-10 17.820115 + 29 0 -4.3368757 0 -4.3368757 -5.3684477e-10 17.820115 + 30 0 -4.3368757 0 -4.3368757 3.6571981e-10 17.820115 + 31 0 -4.3368757 0 -4.3368757 1.2779228e-10 17.820115 + 32 0 -4.3368757 0 -4.3368757 -5.5015387e-10 17.820115 + 33 0 -4.3368757 0 -4.3368757 3.7902891e-10 17.820115 + 34 0 -4.3368757 0 -4.3368757 -5.5015387e-10 17.820115 + 35 0 -4.3368757 0 -4.3368757 3.7902891e-10 17.820115 + 36 0 -4.3368757 0 -4.3368757 -2.0411714e-10 17.820115 + 37 0 -4.3368757 0 -4.3368757 3.5241071e-10 17.820115 + 38 0 -4.3368757 0 -4.3368757 -5.5015387e-10 17.820115 + 39 0 -4.3368757 0 -4.3368757 3.7902891e-10 17.820115 + 40 0 -4.3368757 0 -4.3368757 3.391016e-10 17.820115 + 41 0 -4.3368757 0 -4.3368757 -5.5015387e-10 17.820115 + 42 0 -4.3368757 0 -4.3368757 3.6571981e-10 17.820115 + 43 0 -4.3368757 0 -4.3368757 -5.6346277e-10 17.820115 + 44 0 -4.3368757 0 -4.3368757 3.6571981e-10 17.820115 + 45 0 -4.3368757 0 -4.3368757 1.0117418e-10 17.820115 + 46 0 -4.3368757 0 -4.3368757 -2.307128e-10 17.820115 + 47 0 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4171 0 -4.3368757 0 -4.3368757 -2.1742406e-10 17.820115 + 4172 0 -4.3368757 0 -4.3368757 1.0116664e-10 17.820115 + 4173 0 -4.3368757 0 -4.3368757 3.5241606e-10 17.820115 + 4174 0 -4.3368757 0 -4.3368757 1.0116664e-10 17.820115 + 4175 0 -4.3368757 0 -4.3368757 -2.1743708e-10 17.820115 + 4176 0 -4.3368757 0 -4.3368757 8.7844586e-11 17.820115 + 4177 0 -4.3368757 0 -4.3368757 1.0116664e-10 17.820115 + 4178 0 -4.3368757 0 -4.3368757 -2.1743708e-10 17.820115 + 4179 0 -4.3368757 0 -4.3368757 3.5241606e-10 17.820115 + 4180 0 -4.3368757 0 -4.3368757 -5.6348339e-10 17.820115 + 4181 0 -4.3368757 0 -4.3368757 3.6572517e-10 17.820115 + 4182 0 -4.3368757 0 -4.3368757 1.0116664e-10 17.820115 + 4183 0 -4.3368757 0 -4.3368757 -2.0412798e-10 17.820115 + 4184 0 -4.3368757 0 -4.3368757 1.0116664e-10 17.820115 + 4185 0 -4.3368757 0 -4.3368757 -2.1743708e-10 17.820115 + 4186 0 -4.3368757 0 -4.3368757 7.4535482e-11 17.820115 + 4187 0 -4.3368757 0 -4.3368757 1.0116664e-10 17.820115 + 4188 0 -4.3368757 0 -4.3368757 8.7844586e-11 17.820115 + 4189 0 -4.3368757 0 -4.3368757 -2.1743708e-10 17.820115 + 4190 0 -4.3368757 0 -4.3368757 1.0119799e-10 17.820115 + 4191 0 -4.3368757 0 -4.3368757 -1.9082867e-10 17.820115 + 4192 0 -4.3368757 0 -4.3368757 3.6572517e-10 17.820115 + 4193 0 -4.3368757 0 -4.3368757 -2.0412798e-10 17.820115 + 4194 0 -4.3368757 0 -4.3368757 1.0116664e-10 17.820115 + 4195 0 -4.3368757 0 -4.3368757 -2.0412798e-10 17.820115 + 4196 0 -4.3368757 0 -4.3368757 3.6572517e-10 17.820115 + 4197 0 -4.3368757 0 -4.3368757 3.6572517e-10 17.820115 + 4198 0 -4.3368757 0 -4.3368757 -1.9082867e-10 17.820115 + 4199 0 -4.3368757 0 -4.3368757 -1.9082867e-10 17.820115 + 4200 0 -4.3368757 0 -4.3368757 1.1450709e-10 17.820115 + 4201 0 -4.3368757 0 -4.3368757 -2.0413777e-10 17.820115 + 4202 0 -4.3368757 0 -4.3368757 3.6572517e-10 17.820115 + 4203 0 -4.3368757 0 -4.3368757 -5.6348339e-10 17.820115 + 4204 0 -4.3368757 0 -4.3368757 3.7903427e-10 17.820115 + 4205 0 -4.3368757 0 -4.3368757 8.7857533e-11 17.820115 + 4206 0 -4.3368757 0 -4.3368757 -1.9081887e-10 17.820115 + 4207 0 -4.3368757 0 -4.3368757 1.0115369e-10 17.820115 + 4208 0 -4.3368757 0 -4.3368757 7.4548428e-11 17.820115 + 4209 0 -4.3368757 0 -4.3368757 -2.0412798e-10 17.820115 + 4210 0 -4.3368757 0 -4.3368757 3.6572517e-10 17.820115 + 4211 0 -4.3368757 0 -4.3368757 3.6572517e-10 17.820115 + 4212 0 -4.3368757 0 -4.3368757 7.4548428e-11 17.820115 + 4213 0 -4.3368757 0 -4.3368757 -5.6348339e-10 17.820115 + 4214 0 -4.3368757 0 -4.3368757 3.6572517e-10 17.820115 + 4215 0 -4.3368757 0 -4.3368757 1.277719e-10 17.820115 + 4216 0 -4.3368757 0 -4.3368757 -5.6348339e-10 17.820115 + 4217 0 -4.3368757 0 -4.3368757 3.6572517e-10 17.820115 + 4218 0 -4.3368757 0 -4.3368757 -2.4404227e-10 17.820115 + 4219 0 -4.3368757 0 -4.3368757 1.277719e-10 17.820115 + 4220 0 -4.3368757 0 -4.3368757 7.4548428e-11 17.820115 + 4221 0 -4.3368757 0 -4.3368757 7.4548428e-11 17.820115 + 4222 0 -4.3368757 0 -4.3368757 -1.9081887e-10 17.820115 + 4223 0 -4.3368757 0 -4.3368757 3.5241606e-10 17.820115 + 4224 0 -4.3368757 0 -4.3368757 -5.5017428e-10 17.820115 + 4225 0 -4.3368757 0 -4.3368757 3.6572517e-10 17.820115 + 4226 0 -4.3368757 0 -4.3368757 -1.7751957e-10 17.820115 + 4227 0 -4.3368757 0 -4.3368757 -1.7751957e-10 17.820115 + 4228 0 -4.3368757 0 -4.3368757 1.1450709e-10 17.820115 + 4229 0 -4.3368757 0 -4.3368757 -1.9082867e-10 17.820115 + 4230 0 -4.3368757 0 -4.3368757 3.6572517e-10 17.820115 + 4231 0 -4.3368757 0 -4.3368757 -2.1743708e-10 17.820115 + 4232 0 -4.3368757 0 -4.3368757 -5.7679249e-10 17.820115 + 4233 0 -4.3368757 0 -4.3368757 -5.6348339e-10 17.820115 + 4234 0 -4.3368757 0 -4.3368757 3.6572517e-10 17.820115 + 4235 0 -4.3368757 0 -4.3368757 3.7902777e-10 17.820115 + 4236 0 -4.3368757 0 -4.3368757 -5.7679249e-10 17.820115 + 4237 0 -4.3368757 0 -4.3368757 3.7902777e-10 17.820115 + 4238 0 -4.3368757 0 -4.3368757 -1.9082867e-10 17.820115 + 4239 0 -4.3368757 0 -4.3368757 -1.9082867e-10 17.820115 + 4240 0 -4.3368757 0 -4.3368757 1.411188e-10 17.820115 + 4241 0 -4.3368757 0 -4.3368757 -1.9082867e-10 17.820115 + 4242 0 -4.3368757 0 -4.3368757 1.1446279e-10 17.820115 + 4243 0 -4.3368757 0 -4.3368757 1.0119799e-10 17.820115 + 4244 0 -4.3368757 0 -4.3368757 -1.9082867e-10 17.820115 + 4245 0 -4.3368757 0 -4.3368757 3.9233688e-10 17.820115 + 4246 0 -4.3368757 0 -4.3368757 -2.1743708e-10 17.820115 + 4247 0 -4.3368757 0 -4.3368757 -2.1743708e-10 17.820115 + 4248 0 -4.3368757 0 -4.3368757 1.0116664e-10 17.820115 + 4249 0 -4.3368757 0 -4.3368757 1.0115369e-10 17.820115 + 4250 0 -4.3368757 0 -4.3368757 -2.1743708e-10 17.820115 + 4251 0 -4.3368757 0 -4.3368757 1.0115369e-10 17.820115 + 4252 0 -4.3368757 0 -4.3368757 1.0116664e-10 17.820115 + 4253 0 -4.3368757 0 -4.3368757 1.1446279e-10 17.820115 + 4254 0 -4.3368757 0 -4.3368757 1.1450059e-10 17.820115 + 4255 0 -4.3368757 0 -4.3368757 -2.1742406e-10 17.820115 + 4256 0 -4.3368757 0 -4.3368757 7.4548428e-11 17.820115 + 4257 0 -4.3368757 0 -4.3368757 -2.1743708e-10 17.820115 + 4258 0 -4.3368757 0 -4.3368757 8.7844586e-11 17.820115 + 4259 0 -4.3368757 0 -4.3368757 8.7844586e-11 17.820115 +Loop time of 0.172347 on 1 procs for 4259 steps with 1 atoms + +92.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = quadratic factors are zero + Energy initial, next-to-last, final = + -4.33687572290858 -4.33687572774504 -4.33687572774504 + Force two-norm initial, final = 0.00080661032 5.9264807e-15 + Force max component initial, final = 0.00046569669 3.9192579e-15 + Final line search alpha, max atom move = 1 3.9192579e-15 + Iterations, force evaluations = 4259 8518 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.096254 | 0.096254 | 0.096254 | 0.0 | 55.85 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.01149 | 0.01149 | 0.01149 | 0.0 | 6.67 +Output | 0.022004 | 0.022004 | 0.022004 | 0.0 | 12.77 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.0426 | | | 24.72 + +Nlocal: 1 ave 1 max 1 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 215 ave 215 max 215 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 40 ave 40 max 40 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 80 ave 80 max 80 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 80 +Ave neighs/atom = 80 +Neighbor list builds = 0 +Dangerous builds = 0 + +variable cohesive_energy equal pe/atoms +variable atmVol equal vol/atoms +variable aLatt equal (vol/atoms)^0.3333333333 + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Per MPI rank memory allocation (min/avg/max) = 3.744 | 3.744 | 3.744 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 4259 0 -4.3368757 0 -4.3368757 4.121405e-10 17.820115 +Loop time of 9.82e-07 on 1 procs for 0 steps with 1 atoms + +101.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 9.82e-07 | | |100.00 + +Nlocal: 1 ave 1 max 1 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 215 ave 215 max 215 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 40 ave 40 max 40 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 80 ave 80 max 80 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 80 +Ave neighs/atom = 80 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.33687572774504 eV/atom +print "Reference cohesive energy: -4.337 eV/atom" +Reference cohesive energy: -4.337 eV/atom +print "Atomic volume ${atmVol} A^3" +Atomic volume 17.8201147853823 A^3 +print "Lattice constant ${aLatt} A" +Lattice constant 2.61198191533279 A +print "Reference lattice constant 2.612 A" +Reference lattice constant 2.612 A +print "====================================================" +==================================================== + + +#dump 1 all custom 1 fcc.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.sc_relax.g++.4 b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.sc_relax.g++.4 new file mode 100644 index 0000000000..52e51b7563 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.sc_relax.g++.4 @@ -0,0 +1,4404 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Si fcc phase + +units metal +boundary p p p + +atom_style atomic +lattice sc 2.612 +Lattice spacing in x,y,z = 2.612 2.612 2.612 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (2.612 2.612 2.612) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 1 atoms + using lattice units in orthogonal box = (0 0 0) to (2.612 2.612 2.612) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +Reading meam/sw/spline potential file Si.b.meam.sw.spline with DATE: 2012-10-26 +mass * 28.085 + +fix relax all box/relax aniso 0 +thermo 1 +minimize 0 0 10000 100000 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.4 + ghost atom cutoff = 6.4 + binsize = 3.2, bins = 1 1 1 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966) +Per MPI rank memory allocation (min/avg/max) = 4.899 | 4.899 | 4.899 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 0 -4.3368757 0 -4.3368757 -41.869135 17.820485 + 1 0 -4.3368757 0 -4.3368757 -0.0064151392 17.820115 + 2 0 -4.3368757 0 -4.3368757 -1.5832709e-09 17.820115 + 3 0 -4.3368757 0 -4.3368757 3.3909505e-10 17.820115 + 4 0 -4.3368757 0 -4.3368757 3.2578595e-10 17.820115 + 5 0 -4.3368757 0 -4.3368757 -1.9080803e-10 17.820115 + 6 0 -4.3368757 0 -4.3368757 3.3909495e-10 17.820115 + 7 0 -4.3368757 0 -4.3368757 -1.9079854e-10 17.820115 + 8 0 -4.3368757 0 -4.3368757 -1.9079854e-10 17.820115 + 9 0 -4.3368757 0 -4.3368757 1.0118722e-10 17.820115 + 10 0 -4.3368757 0 -4.3368757 -2.3072585e-10 17.820115 + 11 0 -4.3368757 0 -4.3368757 3.5240418e-10 17.820115 + 12 0 -4.3368757 0 -4.3368757 -1.6419005e-10 17.820115 + 13 0 -4.3368757 0 -4.3368757 -1.6419005e-10 17.820115 + 14 0 -4.3368757 0 -4.3368757 1.1449508e-10 17.820115 + 15 0 -4.3368757 0 -4.3368757 -1.9080803e-10 17.820115 + 16 0 -4.3368757 0 -4.3368757 3.7902891e-10 17.820115 + 17 0 -4.3368757 0 -4.3368757 -5.5015387e-10 17.820115 + 18 0 -4.3368757 0 -4.3368757 3.7902891e-10 17.820115 + 19 0 -4.3368757 0 -4.3368757 -1.9080803e-10 17.820115 + 20 0 -4.3368757 0 -4.3368757 3.9233792e-10 17.820115 + 21 0 -4.3368757 0 -4.3368757 -5.3684477e-10 17.820115 + 22 0 -4.3368757 0 -4.3368757 3.7902891e-10 17.820115 + 23 0 -4.3368757 0 -4.3368757 -5.3684477e-10 17.820115 + 24 0 -4.3368757 0 -4.3368757 3.5241068e-10 17.820115 + 25 0 -4.3368757 0 -4.3368757 1.1448328e-10 17.820115 + 26 0 -4.3368757 0 -4.3368757 -5.5015387e-10 17.820115 + 27 0 -4.3368757 0 -4.3368757 3.5240418e-10 17.820115 + 28 0 -4.3368757 0 -4.3368757 1.0118725e-10 17.820115 + 29 0 -4.3368757 0 -4.3368757 -5.3684477e-10 17.820115 + 30 0 -4.3368757 0 -4.3368757 3.6571981e-10 17.820115 + 31 0 -4.3368757 0 -4.3368757 1.2779228e-10 17.820115 + 32 0 -4.3368757 0 -4.3368757 -5.5015387e-10 17.820115 + 33 0 -4.3368757 0 -4.3368757 3.7902891e-10 17.820115 + 34 0 -4.3368757 0 -4.3368757 -5.5015387e-10 17.820115 + 35 0 -4.3368757 0 -4.3368757 3.7902891e-10 17.820115 + 36 0 -4.3368757 0 -4.3368757 -2.0411714e-10 17.820115 + 37 0 -4.3368757 0 -4.3368757 3.5241071e-10 17.820115 + 38 0 -4.3368757 0 -4.3368757 -5.5015387e-10 17.820115 + 39 0 -4.3368757 0 -4.3368757 3.7902891e-10 17.820115 + 40 0 -4.3368757 0 -4.3368757 3.391016e-10 17.820115 + 41 0 -4.3368757 0 -4.3368757 -5.5015387e-10 17.820115 + 42 0 -4.3368757 0 -4.3368757 3.6571981e-10 17.820115 + 43 0 -4.3368757 0 -4.3368757 -5.6346277e-10 17.820115 + 44 0 -4.3368757 0 -4.3368757 3.6571981e-10 17.820115 + 45 0 -4.3368757 0 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8.7844586e-11 17.820115 + 4170 0 -4.3368757 0 -4.3368757 -2.0412798e-10 17.820115 + 4171 0 -4.3368757 0 -4.3368757 -2.1742406e-10 17.820115 + 4172 0 -4.3368757 0 -4.3368757 1.0116664e-10 17.820115 + 4173 0 -4.3368757 0 -4.3368757 3.5241606e-10 17.820115 + 4174 0 -4.3368757 0 -4.3368757 1.0116664e-10 17.820115 + 4175 0 -4.3368757 0 -4.3368757 -2.1743708e-10 17.820115 + 4176 0 -4.3368757 0 -4.3368757 8.7844586e-11 17.820115 + 4177 0 -4.3368757 0 -4.3368757 1.0116664e-10 17.820115 + 4178 0 -4.3368757 0 -4.3368757 -2.1743708e-10 17.820115 + 4179 0 -4.3368757 0 -4.3368757 3.5241606e-10 17.820115 + 4180 0 -4.3368757 0 -4.3368757 -5.6348339e-10 17.820115 + 4181 0 -4.3368757 0 -4.3368757 3.6572517e-10 17.820115 + 4182 0 -4.3368757 0 -4.3368757 1.0116664e-10 17.820115 + 4183 0 -4.3368757 0 -4.3368757 -2.0412798e-10 17.820115 + 4184 0 -4.3368757 0 -4.3368757 1.0116664e-10 17.820115 + 4185 0 -4.3368757 0 -4.3368757 -2.1743708e-10 17.820115 + 4186 0 -4.3368757 0 -4.3368757 7.4535482e-11 17.820115 + 4187 0 -4.3368757 0 -4.3368757 1.0116664e-10 17.820115 + 4188 0 -4.3368757 0 -4.3368757 8.7844586e-11 17.820115 + 4189 0 -4.3368757 0 -4.3368757 -2.1743708e-10 17.820115 + 4190 0 -4.3368757 0 -4.3368757 1.0119799e-10 17.820115 + 4191 0 -4.3368757 0 -4.3368757 -1.9082867e-10 17.820115 + 4192 0 -4.3368757 0 -4.3368757 3.6572517e-10 17.820115 + 4193 0 -4.3368757 0 -4.3368757 -2.0412798e-10 17.820115 + 4194 0 -4.3368757 0 -4.3368757 1.0116664e-10 17.820115 + 4195 0 -4.3368757 0 -4.3368757 -2.0412798e-10 17.820115 + 4196 0 -4.3368757 0 -4.3368757 3.6572517e-10 17.820115 + 4197 0 -4.3368757 0 -4.3368757 3.6572517e-10 17.820115 + 4198 0 -4.3368757 0 -4.3368757 -1.9082867e-10 17.820115 + 4199 0 -4.3368757 0 -4.3368757 -1.9082867e-10 17.820115 + 4200 0 -4.3368757 0 -4.3368757 1.1450709e-10 17.820115 + 4201 0 -4.3368757 0 -4.3368757 -2.0413777e-10 17.820115 + 4202 0 -4.3368757 0 -4.3368757 3.6572517e-10 17.820115 + 4203 0 -4.3368757 0 -4.3368757 -5.6348339e-10 17.820115 + 4204 0 -4.3368757 0 -4.3368757 3.7903427e-10 17.820115 + 4205 0 -4.3368757 0 -4.3368757 8.7857533e-11 17.820115 + 4206 0 -4.3368757 0 -4.3368757 -1.9081887e-10 17.820115 + 4207 0 -4.3368757 0 -4.3368757 1.0115369e-10 17.820115 + 4208 0 -4.3368757 0 -4.3368757 7.4548428e-11 17.820115 + 4209 0 -4.3368757 0 -4.3368757 -2.0412798e-10 17.820115 + 4210 0 -4.3368757 0 -4.3368757 3.6572517e-10 17.820115 + 4211 0 -4.3368757 0 -4.3368757 3.6572517e-10 17.820115 + 4212 0 -4.3368757 0 -4.3368757 7.4548428e-11 17.820115 + 4213 0 -4.3368757 0 -4.3368757 -5.6348339e-10 17.820115 + 4214 0 -4.3368757 0 -4.3368757 3.6572517e-10 17.820115 + 4215 0 -4.3368757 0 -4.3368757 1.277719e-10 17.820115 + 4216 0 -4.3368757 0 -4.3368757 -5.6348339e-10 17.820115 + 4217 0 -4.3368757 0 -4.3368757 3.6572517e-10 17.820115 + 4218 0 -4.3368757 0 -4.3368757 -2.4404227e-10 17.820115 + 4219 0 -4.3368757 0 -4.3368757 1.277719e-10 17.820115 + 4220 0 -4.3368757 0 -4.3368757 7.4548428e-11 17.820115 + 4221 0 -4.3368757 0 -4.3368757 7.4548428e-11 17.820115 + 4222 0 -4.3368757 0 -4.3368757 -1.9081887e-10 17.820115 + 4223 0 -4.3368757 0 -4.3368757 3.5241606e-10 17.820115 + 4224 0 -4.3368757 0 -4.3368757 -5.5017428e-10 17.820115 + 4225 0 -4.3368757 0 -4.3368757 3.6572517e-10 17.820115 + 4226 0 -4.3368757 0 -4.3368757 -1.7751957e-10 17.820115 + 4227 0 -4.3368757 0 -4.3368757 -1.7751957e-10 17.820115 + 4228 0 -4.3368757 0 -4.3368757 1.1450709e-10 17.820115 + 4229 0 -4.3368757 0 -4.3368757 -1.9082867e-10 17.820115 + 4230 0 -4.3368757 0 -4.3368757 3.6572517e-10 17.820115 + 4231 0 -4.3368757 0 -4.3368757 -2.1743708e-10 17.820115 + 4232 0 -4.3368757 0 -4.3368757 -5.7679249e-10 17.820115 + 4233 0 -4.3368757 0 -4.3368757 -5.6348339e-10 17.820115 + 4234 0 -4.3368757 0 -4.3368757 3.6572517e-10 17.820115 + 4235 0 -4.3368757 0 -4.3368757 3.7902777e-10 17.820115 + 4236 0 -4.3368757 0 -4.3368757 -5.7679249e-10 17.820115 + 4237 0 -4.3368757 0 -4.3368757 3.7902777e-10 17.820115 + 4238 0 -4.3368757 0 -4.3368757 -1.9082867e-10 17.820115 + 4239 0 -4.3368757 0 -4.3368757 -1.9082867e-10 17.820115 + 4240 0 -4.3368757 0 -4.3368757 1.411188e-10 17.820115 + 4241 0 -4.3368757 0 -4.3368757 -1.9082867e-10 17.820115 + 4242 0 -4.3368757 0 -4.3368757 1.1446279e-10 17.820115 + 4243 0 -4.3368757 0 -4.3368757 1.0119799e-10 17.820115 + 4244 0 -4.3368757 0 -4.3368757 -1.9082867e-10 17.820115 + 4245 0 -4.3368757 0 -4.3368757 3.9233688e-10 17.820115 + 4246 0 -4.3368757 0 -4.3368757 -2.1743708e-10 17.820115 + 4247 0 -4.3368757 0 -4.3368757 -2.1743708e-10 17.820115 + 4248 0 -4.3368757 0 -4.3368757 1.0116664e-10 17.820115 + 4249 0 -4.3368757 0 -4.3368757 1.0115369e-10 17.820115 + 4250 0 -4.3368757 0 -4.3368757 -2.1743708e-10 17.820115 + 4251 0 -4.3368757 0 -4.3368757 1.0115369e-10 17.820115 + 4252 0 -4.3368757 0 -4.3368757 1.0116664e-10 17.820115 + 4253 0 -4.3368757 0 -4.3368757 1.1446279e-10 17.820115 + 4254 0 -4.3368757 0 -4.3368757 1.1450059e-10 17.820115 + 4255 0 -4.3368757 0 -4.3368757 -2.1742406e-10 17.820115 + 4256 0 -4.3368757 0 -4.3368757 7.4548428e-11 17.820115 + 4257 0 -4.3368757 0 -4.3368757 -2.1743708e-10 17.820115 + 4258 0 -4.3368757 0 -4.3368757 8.7844586e-11 17.820115 + 4259 0 -4.3368757 0 -4.3368757 8.7844586e-11 17.820115 +Loop time of 0.402665 on 4 procs for 4259 steps with 1 atoms + +97.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = quadratic factors are zero + Energy initial, next-to-last, final = + -4.33687572290858 -4.33687572774504 -4.33687572774504 + Force two-norm initial, final = 0.00080661032 5.9264807e-15 + Force max component initial, final = 0.00046569669 3.9192579e-15 + Final line search alpha, max atom move = 1 3.9192579e-15 + Iterations, force evaluations = 4259 8518 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.12945 | 0.13161 | 0.13583 | 0.7 | 32.68 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.083513 | 0.098512 | 0.11322 | 4.3 | 24.47 +Output | 0.032878 | 0.03501 | 0.041178 | 1.9 | 8.69 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.1375 | | | 34.16 + +Nlocal: 0.25 ave 1 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 149.75 ave 150 max 149 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 10 ave 40 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +FullNghs: 20 ave 80 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 80 +Ave neighs/atom = 80 +Neighbor list builds = 0 +Dangerous builds = 0 + +variable cohesive_energy equal pe/atoms +variable atmVol equal vol/atoms +variable aLatt equal (vol/atoms)^0.3333333333 + +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966) +Per MPI rank memory allocation (min/avg/max) = 3.774 | 3.774 | 3.774 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 4259 0 -4.3368757 0 -4.3368757 4.121405e-10 17.820115 +Loop time of 3.46025e-06 on 4 procs for 0 steps with 1 atoms + +101.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.46e-06 | | |100.00 + +Nlocal: 0.25 ave 1 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 149.75 ave 150 max 149 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 10 ave 40 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +FullNghs: 20 ave 80 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 80 +Ave neighs/atom = 80 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.33687572774504 eV/atom +print "Reference cohesive energy: -4.337 eV/atom" +Reference cohesive energy: -4.337 eV/atom +print "Atomic volume ${atmVol} A^3" +Atomic volume 17.8201147853823 A^3 +print "Lattice constant ${aLatt} A" +Lattice constant 2.61198191533279 A +print "Reference lattice constant 2.612 A" +Reference lattice constant 2.612 A +print "====================================================" +==================================================== + + +#dump 1 all custom 1 fcc.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.single_atom.g++.1 b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.single_atom.g++.1 new file mode 100644 index 0000000000..7ba1798e37 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.single_atom.g++.1 @@ -0,0 +1,89 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Si single atom in vacuum + +units metal +boundary f f f + +atom_style atomic +region box block -100 100 -100 100 -100 100 units box +create_box 1 box +Created orthogonal box = (-100 -100 -100) to (100 100 100) + 1 by 1 by 1 MPI processor grid +create_atoms 1 single 0 0 0 units box +Created 1 atoms + using box units in orthogonal box = (-100 -100 -100) to (100 100 100) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +Reading meam/sw/spline potential file Si.b.meam.sw.spline with DATE: 2012-10-26 +mass * 28.085 + +variable cohesive_energy equal pe/atoms +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.4 + ghost atom cutoff = 6.4 + binsize = 3.2, bins = 63 63 63 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 4.364 | 4.364 | 4.364 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 0 0 0 0 +Loop time of 1.903e-06 on 1 procs for 0 steps with 1 atoms + +157.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.903e-06 | | |100.00 + +Nlocal: 1 ave 1 max 1 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: 0 eV/atom +print "Reference cohesive energy: 0 eV/atom" +Reference cohesive energy: 0 eV/atom +print "====================================================" +==================================================== + + +#dump 1 all custom 1 single_atom.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.single_atom.g++.4 b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.single_atom.g++.4 new file mode 100644 index 0000000000..f5e0ac22d8 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Si/log.17Dec2022.single_atom.g++.4 @@ -0,0 +1,89 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Si single atom in vacuum + +units metal +boundary f f f + +atom_style atomic +region box block -100 100 -100 100 -100 100 units box +create_box 1 box +Created orthogonal box = (-100 -100 -100) to (100 100 100) + 1 by 2 by 2 MPI processor grid +create_atoms 1 single 0 0 0 units box +Created 1 atoms + using box units in orthogonal box = (-100 -100 -100) to (100 100 100) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Si.b.meam.sw.spline Si +Reading meam/sw/spline potential file Si.b.meam.sw.spline with DATE: 2012-10-26 +mass * 28.085 + +variable cohesive_energy equal pe/atoms +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.4 + ghost atom cutoff = 6.4 + binsize = 3.2, bins = 63 63 63 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 1.16 | 1.754 | 3.535 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 0 0 0 0 +Loop time of 4.06575e-06 on 4 procs for 0 steps with 1 atoms + +79.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 4.066e-06 | | |100.00 + +Nlocal: 0.25 ave 1 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 0.75 ave 1 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: 0 eV/atom +print "Reference cohesive energy: 0 eV/atom" +Reference cohesive energy: 0 eV/atom +print "====================================================" +==================================================== + + +#dump 1 all custom 1 single_atom.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Si/sc.in b/examples/PACKAGES/meam_sw_spline/Si/sc.in deleted file mode 100644 index 8c14be356c..0000000000 --- a/examples/PACKAGES/meam_sw_spline/Si/sc.in +++ /dev/null @@ -1,34 +0,0 @@ -# Si fcc phase - -units metal -boundary p p p - -atom_style atomic -lattice sc 2.612 -region box block 0 1 0 1 0 1 -create_box 1 box -create_atoms 1 box - -pair_style meam/sw/spline -pair_coeff * * ../../potentials/Si.b.meam.sw.spline Si -mass * 28.085 - -variable cohesive_energy equal pe/atoms -variable atmVol equal vol/atoms -variable aLatt equal (vol/atoms)^0.3333333333 - -run 0 - -print "====================================================" -print "Calculated cohesive energy: ${cohesive_energy} eV/atom" -print "Reference cohesive energy: -4.337 eV/atom" -print "Atomic volume ${atmVol} A^3" -print "Lattice constant ${aLatt} A" -print "Reference lattice constant 2.612 A" -print "====================================================" - - -#dump 1 all custom 1 sc.dump id type x y z fx fy fz -#run 0 - - diff --git a/examples/PACKAGES/meam_sw_spline/Si/sc_relax.in b/examples/PACKAGES/meam_sw_spline/Si/sc_relax.in deleted file mode 100644 index 6fea88a931..0000000000 --- a/examples/PACKAGES/meam_sw_spline/Si/sc_relax.in +++ /dev/null @@ -1,38 +0,0 @@ -# Si fcc phase - -units metal -boundary p p p - -atom_style atomic -lattice sc 2.612 -region box block 0 1 0 1 0 1 -create_box 1 box -create_atoms 1 box - -pair_style meam/sw/spline -pair_coeff * * ../../potentials/Si.b.meam.sw.spline Si -mass * 28.085 - -fix relax all box/relax aniso 0 -thermo 1 -minimize 0 0 10000 100000 - -variable cohesive_energy equal pe/atoms -variable atmVol equal vol/atoms -variable aLatt equal (vol/atoms)^0.3333333333 - -run 0 - -print "====================================================" -print "Calculated cohesive energy: ${cohesive_energy} eV/atom" -print "Reference cohesive energy: -4.337 eV/atom" -print "Atomic volume ${atmVol} A^3" -print "Lattice constant ${aLatt} A" -print "Reference lattice constant 2.612 A" -print "====================================================" - - -#dump 1 all custom 1 fcc.dump id type x y z fx fy fz -#run 0 - - diff --git a/examples/PACKAGES/meam_sw_spline/Si/single_atom.in b/examples/PACKAGES/meam_sw_spline/Si/single_atom.in deleted file mode 100644 index 8ed7c7ae4e..0000000000 --- a/examples/PACKAGES/meam_sw_spline/Si/single_atom.in +++ /dev/null @@ -1,27 +0,0 @@ -# Si single atom in vacuum - -units metal -boundary f f f - -atom_style atomic -region box block -100 100 -100 100 -100 100 units box -create_box 1 box -create_atoms 1 single 0 0 0 units box - -pair_style meam/sw/spline -pair_coeff * * ../../potentials/Si.b.meam.sw.spline Si -mass * 28.085 - -variable cohesive_energy equal pe/atoms -run 0 - -print "====================================================" -print "Calculated cohesive energy: ${cohesive_energy} eV/atom" -print "Reference cohesive energy: 0 eV/atom" -print "====================================================" - - -#dump 1 all custom 1 single_atom.dump id type x y z fx fy fz -#run 0 - - diff --git a/examples/PACKAGES/meam_sw_spline/Ti/Ti.meam.sw.spline b/examples/PACKAGES/meam_sw_spline/Ti/Ti.meam.sw.spline new file mode 120000 index 0000000000..0bba5b911d --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Ti/Ti.meam.sw.spline @@ -0,0 +1 @@ +../../../../potentials/Ti.meam.sw.spline \ No newline at end of file diff --git a/examples/PACKAGES/meam_sw_spline/Ti/alpha.in b/examples/PACKAGES/meam_sw_spline/Ti/alpha.in deleted file mode 100644 index 5f1c79736d..0000000000 --- a/examples/PACKAGES/meam_sw_spline/Ti/alpha.in +++ /dev/null @@ -1,27 +0,0 @@ -# Ti alpha phase (hcp) - -units metal -boundary p p p - -atom_style atomic -lattice custom 2.93093 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 1.596 basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75 -region box block 0 1 0 1 0 1 -create_box 1 box -create_atoms 1 box - -pair_style meam/sw/spline -pair_coeff * * ../../potentials/Ti.meam.sw.spline Ti -mass * 47.90 - -variable cohesive_energy equal pe/atoms -run 0 - -print "====================================================" -print "Calculated cohesive energy: ${cohesive_energy} eV/atom" -print "Reference cohesive energy: -4.831 eV/atom" -print "====================================================" - -#dump 1 all custom 1 alpha.dump id type x y z fx fy fz -#run 0 - - diff --git a/examples/PACKAGES/meam_sw_spline/Ti/alpha_relaxation.in b/examples/PACKAGES/meam_sw_spline/Ti/alpha_relaxation.in deleted file mode 100644 index 726ef3b693..0000000000 --- a/examples/PACKAGES/meam_sw_spline/Ti/alpha_relaxation.in +++ /dev/null @@ -1,38 +0,0 @@ -# Ti alpha phase (hcp) - -units metal -boundary p p p - -atom_style atomic -#lattice custom 2.93093 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 1.596 basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75 -lattice custom 2.93093 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 1.7 basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75 -region box block 0 1 0 1 0 1 -create_box 1 box -create_atoms 1 box - -pair_style meam/sw/spline -pair_coeff * * ../../potentials/Ti.meam.sw.spline Ti -mass * 47.90 - -fix relax all box/relax aniso 0 -thermo 1 -minimize 0 0 10000 100000 - -variable cohesive_energy equal pe/atoms -variable lattice_parameter equal lx -variable c_to_a equal lz/lx -run 0 - -print "====================================================" -print "Calculated cohesive energy: ${cohesive_energy} eV/atom" -print "Reference cohesive energy: -4.831 eV/atom" -print "Calculated lattice parameter: ${lattice_parameter} A" -print "Reference lattice parameter: 2.9304 A" -print "C/A ratio: ${c_to_a}" -print "Reference c/a ratio: 1.596" -print "====================================================" - -#dump 1 all custom 1 alpha_relaxed.dump id type x y z fx fy fz -#run 0 - - diff --git a/examples/PACKAGES/meam_sw_spline/Ti/beta.in b/examples/PACKAGES/meam_sw_spline/Ti/beta.in deleted file mode 100644 index 8569d7f380..0000000000 --- a/examples/PACKAGES/meam_sw_spline/Ti/beta.in +++ /dev/null @@ -1,27 +0,0 @@ -# Ti beta phase (bcc) - -units metal -boundary p p p - -atom_style atomic -lattice bcc 3.27169 -region box block 0 1 0 1 0 1 -create_box 1 box -create_atoms 1 box - -pair_style meam/sw/spline -pair_coeff * * ../../potentials/Ti.meam.sw.spline Ti -mass * 47.90 - -variable cohesive_energy equal pe/atoms -run 0 - -print "====================================================" -print "Calculated cohesive energy: ${cohesive_energy} eV/atom" -print "Reference cohesive energy: -4.720 eV/atom" -print "====================================================" - -#dump 1 all custom 1 beta.dump id type x y z fx fy fz -#run 0 - - diff --git a/examples/PACKAGES/meam_sw_spline/Ti/fcc.in b/examples/PACKAGES/meam_sw_spline/Ti/fcc.in deleted file mode 100644 index a40cb1acdc..0000000000 --- a/examples/PACKAGES/meam_sw_spline/Ti/fcc.in +++ /dev/null @@ -1,28 +0,0 @@ -# Ti fcc phase - -units metal -boundary p p p - -atom_style atomic -lattice fcc 4.147029 -region box block 0 1 0 1 0 1 -create_box 1 box -create_atoms 1 box - -pair_style meam/sw/spline -pair_coeff * * ../../potentials/Ti.meam.sw.spline Ti -mass * 47.90 - -variable cohesive_energy equal pe/atoms -run 0 - -print "====================================================" -print "Calculated cohesive energy: ${cohesive_energy} eV/atom" -print "Reference cohesive energy: -4.792 eV/atom" -print "====================================================" - - -#dump 1 all custom 1 fcc.dump id type x y z fx fy fz -#run 0 - - diff --git a/examples/PACKAGES/meam_sw_spline/Ti/hexagonal.in b/examples/PACKAGES/meam_sw_spline/Ti/hexagonal.in deleted file mode 100644 index 1487b06e8c..0000000000 --- a/examples/PACKAGES/meam_sw_spline/Ti/hexagonal.in +++ /dev/null @@ -1,28 +0,0 @@ -# Ti omega phase (hexagonal) - -units metal -boundary p p p - -atom_style atomic -lattice custom 2.727192 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 0.982 basis 0 0 0 -region box block 0 1 0 1 0 1 -create_box 1 box -create_atoms 1 box - -pair_style meam/sw/spline -pair_coeff * * ../../potentials/Ti.meam.sw.spline Ti -mass * 47.90 - -variable cohesive_energy equal pe/atoms -run 0 - -print "====================================================" -print "Calculated cohesive energy: ${cohesive_energy} eV/atom" -print "Reference cohesive energy: -4.435 eV/atom" -print "====================================================" - - -#dump 1 all custom 1 hexagonal.dump id type x y z fx fy fz -#run 0 - - diff --git a/examples/PACKAGES/meam_sw_spline/Ti/in.alpha b/examples/PACKAGES/meam_sw_spline/Ti/in.alpha new file mode 100644 index 0000000000..2aff0624ed --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Ti/in.alpha @@ -0,0 +1,27 @@ +# Ti alpha phase (hcp) + +units metal +boundary p p p + +atom_style atomic +lattice custom 2.93093 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 1.596 basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75 +region box block 0 1 0 1 0 1 +create_box 1 box +create_atoms 1 box + +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +mass * 47.90 + +variable cohesive_energy equal pe/atoms +run 0 + +print "====================================================" +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +print "Reference cohesive energy: -4.831 eV/atom" +print "====================================================" + +#dump 1 all custom 1 alpha.dump id type x y z fx fy fz +#run 0 + + diff --git a/examples/PACKAGES/meam_sw_spline/Ti/in.alpha_relaxation b/examples/PACKAGES/meam_sw_spline/Ti/in.alpha_relaxation new file mode 100644 index 0000000000..56301d6ab0 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Ti/in.alpha_relaxation @@ -0,0 +1,38 @@ +# Ti alpha phase (hcp) + +units metal +boundary p p p + +atom_style atomic +#lattice custom 2.93093 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 1.596 basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75 +lattice custom 2.93093 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 1.7 basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75 +region box block 0 1 0 1 0 1 +create_box 1 box +create_atoms 1 box + +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +mass * 47.90 + +fix relax all box/relax aniso 0 +thermo 1 +minimize 0 0 10000 100000 + +variable cohesive_energy equal pe/atoms +variable lattice_parameter equal lx +variable c_to_a equal lz/lx +run 0 + +print "====================================================" +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +print "Reference cohesive energy: -4.831 eV/atom" +print "Calculated lattice parameter: ${lattice_parameter} A" +print "Reference lattice parameter: 2.9304 A" +print "C/A ratio: ${c_to_a}" +print "Reference c/a ratio: 1.596" +print "====================================================" + +#dump 1 all custom 1 alpha_relaxed.dump id type x y z fx fy fz +#run 0 + + diff --git a/examples/PACKAGES/meam_sw_spline/Ti/in.beta b/examples/PACKAGES/meam_sw_spline/Ti/in.beta new file mode 100644 index 0000000000..e73f8ed2b6 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Ti/in.beta @@ -0,0 +1,27 @@ +# Ti beta phase (bcc) + +units metal +boundary p p p + +atom_style atomic +lattice bcc 3.27169 +region box block 0 1 0 1 0 1 +create_box 1 box +create_atoms 1 box + +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +mass * 47.90 + +variable cohesive_energy equal pe/atoms +run 0 + +print "====================================================" +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +print "Reference cohesive energy: -4.720 eV/atom" +print "====================================================" + +#dump 1 all custom 1 beta.dump id type x y z fx fy fz +#run 0 + + diff --git a/examples/PACKAGES/meam_sw_spline/Ti/energy_conservation.meam.sw.in b/examples/PACKAGES/meam_sw_spline/Ti/in.energy_conservation.meam.sw similarity index 58% rename from examples/PACKAGES/meam_sw_spline/Ti/energy_conservation.meam.sw.in rename to examples/PACKAGES/meam_sw_spline/Ti/in.energy_conservation.meam.sw index 1816dc0dee..bb73b2d264 100644 --- a/examples/PACKAGES/meam_sw_spline/Ti/energy_conservation.meam.sw.in +++ b/examples/PACKAGES/meam_sw_spline/Ti/in.energy_conservation.meam.sw @@ -1,22 +1,22 @@ # bulk Ti lattice -variable x index 1 -variable y index 1 -variable z index 1 +variable x index 1 +variable y index 1 +variable z index 1 -variable xx equal 20*$x -variable yy equal 20*$y -variable zz equal 20*$z +variable xx equal 20*$x +variable yy equal 20*$y +variable zz equal 20*$z -units metal -atom_style atomic +units metal +atom_style atomic variable a equal 2.28806 variable covera equal 1.58111 variable sqrt3 equal sqrt(3.) variable theta equal PI/2. -variable cos_theta equal cos(${theta}) -variable sin_theta equal sin(${theta}) +variable cos_theta equal round(cos(${theta})) +variable sin_theta equal round(sin(${theta})) variable Dx equal 1. variable Dy equal ${covera} variable Dz equal sqrt(3.) @@ -32,30 +32,30 @@ lattice custom ${a} a1 1 0 0 a2 0 ${sqrt3} 0 a3 0 0 ${covera} & spacing ${Dx} ${Dy} ${Dz} & origin 0.25 0.25 0.15 -variable Xlo equal -round(90./(${a}*${Dx})) -variable Xhi equal round(90./(${a}*${Dx})) -variable Ylo equal -round(90./(${a}*${Dy})) -variable Yhi equal round(90./(${a}*${Dy})) -variable Zlo equal -round(30./(${a}*${Dz})) -variable Zhi equal round(30./(${a}*${Dz})) +variable Xlo equal -round(9./(${a}*${Dx})) +variable Xhi equal round(9./(${a}*${Dx})) +variable Ylo equal -round(9./(${a}*${Dy})) +variable Yhi equal round(9./(${a}*${Dy})) +variable Zlo equal -round(3./(${a}*${Dz})) +variable Zhi equal round(3./(${a}*${Dz})) region box prism ${Xlo} ${Xhi} ${Ylo} ${Yhi} ${Zlo} ${Zhi} 0.0 0.0 0.0 boundary p p p -create_box 1 box -create_atoms 1 box +create_box 1 box +create_atoms 1 box pair_style meam/sw/spline -pair_coeff * * ../../potentials/Ti.meam.sw.spline Ti +pair_coeff * * Ti.meam.sw.spline Ti mass * 47.90 -velocity all create 300.0 376847 loop geom +velocity all create 300.0 376847 loop geom -neighbor 1.0 bin +neighbor 1.0 bin neigh_modify every 1 delay 5 check yes -fix 1 all nve +fix 1 all nve thermo 1 thermo_style custom step vol etotal press pxx pyy pxz @@ -67,8 +67,8 @@ thermo_modify format 6 %14.8f thermo_modify format 7 %14.8f -timestep 0.002 -thermo 10 +timestep 0.002 +thermo 10 -run 20000 +run 2000 diff --git a/examples/PACKAGES/meam_sw_spline/Ti/in.fcc b/examples/PACKAGES/meam_sw_spline/Ti/in.fcc new file mode 100644 index 0000000000..7c440f9027 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Ti/in.fcc @@ -0,0 +1,28 @@ +# Ti fcc phase + +units metal +boundary p p p + +atom_style atomic +lattice fcc 4.147029 +region box block 0 1 0 1 0 1 +create_box 1 box +create_atoms 1 box + +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +mass * 47.90 + +variable cohesive_energy equal pe/atoms +run 0 + +print "====================================================" +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +print "Reference cohesive energy: -4.792 eV/atom" +print "====================================================" + + +#dump 1 all custom 1 fcc.dump id type x y z fx fy fz +#run 0 + + diff --git a/examples/PACKAGES/meam_sw_spline/Ti/in.hexagonal b/examples/PACKAGES/meam_sw_spline/Ti/in.hexagonal new file mode 100644 index 0000000000..4f10b9bdc7 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Ti/in.hexagonal @@ -0,0 +1,28 @@ +# Ti omega phase (hexagonal) + +units metal +boundary p p p + +atom_style atomic +lattice custom 2.727192 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 0.982 basis 0 0 0 +region box block 0 1 0 1 0 1 +create_box 1 box +create_atoms 1 box + +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +mass * 47.90 + +variable cohesive_energy equal pe/atoms +run 0 + +print "====================================================" +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +print "Reference cohesive energy: -4.435 eV/atom" +print "====================================================" + + +#dump 1 all custom 1 hexagonal.dump id type x y z fx fy fz +#run 0 + + diff --git a/examples/PACKAGES/meam_sw_spline/Ti/in.omega b/examples/PACKAGES/meam_sw_spline/Ti/in.omega new file mode 100644 index 0000000000..e0117ae376 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Ti/in.omega @@ -0,0 +1,27 @@ +# Ti omega phase + +units metal +boundary p p p + +atom_style atomic +lattice custom 4.6064061 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 0.611 basis 0 0 0 basis 0.3333333 0.66666666 0.5 basis 0.6666666 0.3333333 0.5 +region box block 0 1 0 1 0 1 +create_box 1 box +create_atoms 1 box + +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +mass * 47.90 + +variable cohesive_energy equal pe/atoms +run 0 + +print "====================================================" +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +print "Reference cohesive energy: -4.836 eV/atom" +print "====================================================" + +#dump 1 all custom 1 omega.dump id type x y z fx fy fz +#run 0 + + diff --git a/examples/PACKAGES/meam_sw_spline/Ti/in.single_atom b/examples/PACKAGES/meam_sw_spline/Ti/in.single_atom new file mode 100644 index 0000000000..5088354fce --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Ti/in.single_atom @@ -0,0 +1,27 @@ +# Ti single atom in vacuum + +units metal +boundary f f f + +atom_style atomic +region box block -100 100 -100 100 -100 100 units box +create_box 1 box +create_atoms 1 single 0 0 0 units box + +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +mass * 47.90 + +variable cohesive_energy equal pe/atoms +run 0 + +print "====================================================" +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +print "Reference cohesive energy: 0 eV/atom" +print "====================================================" + + +#dump 1 all custom 1 single_atom.dump id type x y z fx fy fz +#run 0 + + diff --git a/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.alpha.g++.1 b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.alpha.g++.1 new file mode 100644 index 0000000000..bfe9dc6405 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.alpha.g++.1 @@ -0,0 +1,90 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Ti alpha phase (hcp) + +units metal +boundary p p p + +atom_style atomic +lattice custom 2.93093 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 1.596 basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75 +Lattice spacing in x,y,z = 2.93093 5.0765173 4.6777643 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (2.93093 5.0765173 4.6777643) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4 atoms + using lattice units in orthogonal box = (0 0 0) to (2.93093 5.0765173 4.6777643) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +Reading meam/sw/spline potential file Ti.meam.sw.spline with DATE: 2012-02-01 +mass * 47.90 + +variable cohesive_energy equal pe/atoms +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.5 + ghost atom cutoff = 7.5 + binsize = 3.75, bins = 1 2 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.725 | 3.725 | 3.725 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -19.324733 0 -19.324733 -214.33961 +Loop time of 1.853e-06 on 1 procs for 0 steps with 4 atoms + +107.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.853e-06 | | |100.00 + +Nlocal: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 412 ave 412 max 412 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 208 ave 208 max 208 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 416 ave 416 max 416 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 416 +Ave neighs/atom = 104 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.83118326640309 eV/atom +print "Reference cohesive energy: -4.831 eV/atom" +Reference cohesive energy: -4.831 eV/atom +print "====================================================" +==================================================== + +#dump 1 all custom 1 alpha.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.alpha.g++.4 b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.alpha.g++.4 new file mode 100644 index 0000000000..f757be4331 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.alpha.g++.4 @@ -0,0 +1,90 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Ti alpha phase (hcp) + +units metal +boundary p p p + +atom_style atomic +lattice custom 2.93093 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 1.596 basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75 +Lattice spacing in x,y,z = 2.93093 5.0765173 4.6777643 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (2.93093 5.0765173 4.6777643) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 4 atoms + using lattice units in orthogonal box = (0 0 0) to (2.93093 5.0765173 4.6777643) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +Reading meam/sw/spline potential file Ti.meam.sw.spline with DATE: 2012-02-01 +mass * 47.90 + +variable cohesive_energy equal pe/atoms +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.5 + ghost atom cutoff = 7.5 + binsize = 3.75, bins = 1 2 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.747 | 3.747 | 3.747 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -19.324733 0 -19.324733 -214.33961 +Loop time of 7.63575e-06 on 4 procs for 0 steps with 4 atoms + +75.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 7.636e-06 | | |100.00 + +Nlocal: 1 ave 1 max 1 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 317.5 ave 318 max 317 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 52 ave 52 max 52 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 104 ave 104 max 104 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 416 +Ave neighs/atom = 104 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.83118326640308 eV/atom +print "Reference cohesive energy: -4.831 eV/atom" +Reference cohesive energy: -4.831 eV/atom +print "====================================================" +==================================================== + +#dump 1 all custom 1 alpha.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.alpha_relaxation.g++.1 b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.alpha_relaxation.g++.1 new file mode 100644 index 0000000000..4d17d2fef1 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.alpha_relaxation.g++.1 @@ -0,0 +1,3567 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Ti alpha phase (hcp) + +units metal +boundary p p p + +atom_style atomic +#lattice custom 2.93093 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 1.596 basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75 +lattice custom 2.93093 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 1.7 basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75 +Lattice spacing in x,y,z = 2.93093 5.0765173 4.982581 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (2.93093 5.0765173 4.982581) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4 atoms + using lattice units in orthogonal box = (0 0 0) to (2.93093 5.0765173 4.982581) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +Reading meam/sw/spline potential file Ti.meam.sw.spline with DATE: 2012-02-01 +mass * 47.90 + +fix relax all box/relax aniso 0 +thermo 1 +minimize 0 0 10000 100000 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.5 + ghost atom cutoff = 7.5 + binsize = 3.75, bins = 1 2 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 4.85 | 4.85 | 4.85 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 0 -19.186187 0 -19.186187 -52654.105 74.135408 + 1 0 -19.186725 0 -19.186725 -52527.113 74.121586 + 2 0 -19.187261 0 -19.187261 -52400.121 74.107782 + 3 0 -19.187796 0 -19.187796 -52273.129 74.093995 + 4 0 -19.18833 0 -19.18833 -52146.139 74.080225 + 5 0 -19.188862 0 -19.188862 -52019.151 74.066473 + 6 0 -19.189393 0 -19.189393 -51892.165 74.052739 + 7 0 -19.189922 0 -19.189922 -51765.183 74.039023 + 8 0 -19.19045 0 -19.19045 -51638.205 74.025324 + 9 0 -19.190976 0 -19.190976 -51511.232 74.011642 + 10 0 -19.191501 0 -19.191501 -51384.265 73.997979 + 11 0 -19.192024 0 -19.192024 -51257.305 73.984333 + 12 0 -19.192546 0 -19.192546 -51130.351 73.970705 + 13 0 -19.193067 0 -19.193067 -51003.406 73.957094 + 14 0 -19.193586 0 -19.193586 -50876.469 73.943502 + 15 0 -19.194103 0 -19.194103 -50749.542 73.929927 + 16 0 -19.19462 0 -19.19462 -50622.625 73.916369 + 17 0 -19.195134 0 -19.195134 -50495.719 73.90283 + 18 0 -19.195648 0 -19.195648 -50368.824 73.889309 + 19 0 -19.19616 0 -19.19616 -50241.942 73.875805 + 20 0 -19.19667 0 -19.19667 -50115.073 73.862319 + 21 0 -19.197179 0 -19.197179 -49988.218 73.848851 + 22 0 -19.197687 0 -19.197687 -49861.378 73.835401 + 23 0 -19.198193 0 -19.198193 -49734.553 73.821968 + 24 0 -19.198698 0 -19.198698 -49607.744 73.808554 + 25 0 -19.199202 0 -19.199202 -49480.953 73.795157 + 26 0 -19.199704 0 -19.199704 -49354.178 73.781779 + 27 0 -19.200204 0 -19.200204 -49227.422 73.768418 + 28 0 -19.200704 0 -19.200704 -49100.685 73.755075 + 29 0 -19.201201 0 -19.201201 -48973.968 73.741751 + 30 0 -19.201698 0 -19.201698 -48847.272 73.728444 + 31 0 -19.202193 0 -19.202193 -48720.597 73.715155 + 32 0 -19.202687 0 -19.202687 -48593.943 73.701884 + 33 0 -19.203179 0 -19.203179 -48467.313 73.688632 + 34 0 -19.20367 0 -19.20367 -48340.706 73.675397 + 35 0 -19.204159 0 -19.204159 -48214.123 73.66218 + 36 0 -19.204647 0 -19.204647 -48087.566 73.648982 + 37 0 -19.205134 0 -19.205134 -47961.034 73.635801 + 38 0 -19.20562 0 -19.20562 -47834.528 73.622639 + 39 0 -19.206104 0 -19.206104 -47708.05 73.609495 + 40 0 -19.206586 0 -19.206586 -47581.599 73.596368 + 41 0 -19.207067 0 -19.207067 -47455.177 73.58326 + 42 0 -19.207547 0 -19.207547 -47328.785 73.570171 + 43 0 -19.208026 0 -19.208026 -47202.423 73.557099 + 44 0 -19.208503 0 -19.208503 -47076.091 73.544045 + 45 0 -19.208979 0 -19.208979 -46949.791 73.53101 + 46 0 -19.209453 0 -19.209453 -46823.524 73.517993 + 47 0 -19.209927 0 -19.209927 -46697.289 73.504994 + 48 0 -19.210398 0 -19.210398 -46571.088 73.492013 + 49 0 -19.210869 0 -19.210869 -46444.922 73.479051 + 50 0 -19.211338 0 -19.211338 -46318.791 73.466107 + 51 0 -19.211806 0 -19.211806 -46192.696 73.453181 + 52 0 -19.212272 0 -19.212272 -46066.637 73.440273 + 53 0 -19.212737 0 -19.212737 -45940.617 73.427384 + 54 0 -19.213201 0 -19.213201 -45814.634 73.414513 + 55 0 -19.213663 0 -19.213663 -45688.69 73.401661 + 56 0 -19.214124 0 -19.214124 -45562.785 73.388826 + 57 0 -19.214584 0 -19.214584 -45436.921 73.37601 + 58 0 -19.215043 0 -19.215043 -45311.098 73.363213 + 59 0 -19.2155 0 -19.2155 -45185.2 73.350434 + 60 0 -19.215956 0 -19.215956 -45059.109 73.337673 + 61 0 -19.21641 0 -19.21641 -44932.827 73.32493 + 62 0 -19.216863 0 -19.216863 -44806.355 73.312206 + 63 0 -19.217315 0 -19.217315 -44679.693 73.299501 + 64 0 -19.217766 0 -19.217766 -44552.844 73.286813 + 65 0 -19.218215 0 -19.218215 -44425.808 73.274145 + 66 0 -19.218663 0 -19.218663 -44298.587 73.261494 + 67 0 -19.219109 0 -19.219109 -44171.181 73.248862 + 68 0 -19.219555 0 -19.219555 -44043.595 73.236249 + 69 0 -19.219999 0 -19.219999 -43915.928 73.223653 + 70 0 -19.220441 0 -19.220441 -43788.226 73.211077 + 71 0 -19.220883 0 -19.220883 -43660.491 73.198518 + 72 0 -19.221323 0 -19.221323 -43532.724 73.185978 + 73 0 -19.221761 0 -19.221761 -43404.926 73.173457 + 74 0 -19.222199 0 -19.222199 -43277.098 73.160954 + 75 0 -19.222635 0 -19.222635 -43149.24 73.148469 + 76 0 -19.22307 0 -19.22307 -43021.355 73.136003 + 77 0 -19.223503 0 -19.223503 -42893.443 73.123556 + 78 0 -19.223936 0 -19.223936 -42765.506 73.111127 + 79 0 -19.224367 0 -19.224367 -42637.543 73.098716 + 80 0 -19.224796 0 -19.224796 -42509.558 73.086324 + 81 0 -19.225225 0 -19.225225 -42381.55 73.073951 + 82 0 -19.225652 0 -19.225652 -42253.52 73.061596 + 83 0 -19.226077 0 -19.226077 -42125.47 73.049259 + 84 0 -19.226502 0 -19.226502 -41997.402 73.036941 + 85 0 -19.226925 0 -19.226925 -41869.315 73.024642 + 86 0 -19.227347 0 -19.227347 -41741.211 73.012362 + 87 0 -19.227768 0 -19.227768 -41613.091 73.0001 + 88 0 -19.228187 0 -19.228187 -41484.957 72.987856 + 89 0 -19.228605 0 -19.228605 -41356.809 72.975632 + 90 0 -19.229022 0 -19.229022 -41228.649 72.963426 + 91 0 -19.229438 0 -19.229438 -41100.477 72.951238 + 92 0 -19.229852 0 -19.229852 -40972.295 72.939069 + 93 0 -19.230265 0 -19.230265 -40844.103 72.926919 + 94 0 -19.230677 0 -19.230677 -40715.903 72.914788 + 95 0 -19.231087 0 -19.231087 -40587.697 72.902675 + 96 0 -19.231497 0 -19.231497 -40459.484 72.890582 + 97 0 -19.231905 0 -19.231905 -40331.267 72.878506 + 98 0 -19.232311 0 -19.232311 -40203.046 72.86645 + 99 0 -19.232717 0 -19.232717 -40074.822 72.854412 + 100 0 -19.233121 0 -19.233121 -39946.597 72.842393 + 101 0 -19.233524 0 -19.233524 -39818.371 72.830393 + 102 0 -19.233926 0 -19.233926 -39690.147 72.818412 + 103 0 -19.234326 0 -19.234326 -39561.924 72.80645 + 104 0 -19.234725 0 -19.234725 -39433.704 72.794506 + 105 0 -19.235123 0 -19.235123 -39305.488 72.782581 + 106 0 -19.23552 0 -19.23552 -39177.277 72.770675 + 107 0 -19.235916 0 -19.235916 -39049.072 72.758788 + 108 0 -19.23631 0 -19.23631 -38920.875 72.74692 + 109 0 -19.236703 0 -19.236703 -38792.687 72.735071 + 110 0 -19.237095 0 -19.237095 -38664.508 72.723241 + 111 0 -19.237486 0 -19.237486 -38536.339 72.711429 + 112 0 -19.237875 0 -19.237875 -38408.183 72.699637 + 113 0 -19.238263 0 -19.238263 -38280.054 72.687863 + 114 0 -19.23865 0 -19.23865 -38151.984 72.676109 + 115 0 -19.239036 0 -19.239036 -38023.973 72.664373 + 116 0 -19.23942 0 -19.23942 -37896.022 72.652656 + 117 0 -19.239804 0 -19.239804 -37768.133 72.640959 + 118 0 -19.240186 0 -19.240186 -37640.306 72.62928 + 119 0 -19.240567 0 -19.240567 -37512.541 72.617621 + 120 0 -19.240946 0 -19.240946 -37384.84 72.60598 + 121 0 -19.241325 0 -19.241325 -37257.203 72.594359 + 122 0 -19.241702 0 -19.241702 -37129.632 72.582756 + 123 0 -19.242078 0 -19.242078 -37002.126 72.571173 + 124 0 -19.242453 0 -19.242453 -36874.688 72.559608 + 125 0 -19.242827 0 -19.242827 -36747.317 72.548063 + 126 0 -19.243199 0 -19.243199 -36620.014 72.536537 + 127 0 -19.243571 0 -19.243571 -36492.781 72.52503 + 128 0 -19.243941 0 -19.243941 -36365.617 72.513542 + 129 0 -19.24431 0 -19.24431 -36238.525 72.502073 + 130 0 -19.244678 0 -19.244678 -36111.504 72.490623 + 131 0 -19.245044 0 -19.245044 -35984.556 72.479192 + 132 0 -19.24541 0 -19.24541 -35857.681 72.467781 + 133 0 -19.245774 0 -19.245774 -35730.88 72.456388 + 134 0 -19.246137 0 -19.246137 -35604.154 72.445015 + 135 0 -19.246499 0 -19.246499 -35477.504 72.433661 + 136 0 -19.24686 0 -19.24686 -35350.93 72.422326 + 137 0 -19.247219 0 -19.247219 -35224.434 72.411011 + 138 0 -19.247578 0 -19.247578 -35098.016 72.399714 + 139 0 -19.247935 0 -19.247935 -34971.677 72.388437 + 140 0 -19.248291 0 -19.248291 -34845.417 72.377179 + 141 0 -19.248646 0 -19.248646 -34719.239 72.36594 + 142 0 -19.249 0 -19.249 -34593.141 72.35472 + 143 0 -19.249353 0 -19.249353 -34467.126 72.34352 + 144 0 -19.249704 0 -19.249704 -34341.194 72.332339 + 145 0 -19.250055 0 -19.250055 -34215.346 72.321177 + 146 0 -19.250404 0 -19.250404 -34089.583 72.310034 + 147 0 -19.250752 0 -19.250752 -33963.905 72.298911 + 148 0 -19.251099 0 -19.251099 -33838.314 72.287807 + 149 0 -19.251445 0 -19.251445 -33712.81 72.276722 + 150 0 -19.25179 0 -19.25179 -33587.394 72.265657 + 151 0 -19.252133 0 -19.252133 -33462.066 72.254611 + 152 0 -19.252476 0 -19.252476 -33336.829 72.243584 + 153 0 -19.252817 0 -19.252817 -33211.682 72.232577 + 154 0 -19.253158 0 -19.253158 -33086.626 72.221589 + 155 0 -19.253497 0 -19.253497 -32961.662 72.210621 + 156 0 -19.253835 0 -19.253835 -32836.791 72.199672 + 157 0 -19.254172 0 -19.254172 -32712.014 72.188742 + 158 0 -19.254508 0 -19.254508 -32587.332 72.177832 + 159 0 -19.254842 0 -19.254842 -32462.745 72.166941 + 160 0 -19.255176 0 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-19.324735 -3.0150787e-11 69.587141 + 3402 0 -19.324735 0 -19.324735 1.1145515e-10 69.587141 + 3403 0 -19.324735 0 -19.324735 1.4522303e-10 69.587141 + 3404 0 -19.324735 0 -19.324735 -1.1998324e-10 69.587141 + 3405 0 -19.324735 0 -19.324735 1.4522303e-10 69.587141 + 3406 0 -19.324735 0 -19.324735 -8.5196046e-11 69.587141 + 3407 0 -19.324735 0 -19.324735 2.1608549e-11 69.587141 + 3408 0 -19.324735 0 -19.324735 -1.4154186e-10 69.587141 + 3409 0 -19.324735 0 -19.324735 -1.4940095e-10 69.587141 + 3410 0 -19.324735 0 -19.324735 -9.8061824e-11 69.587141 + 3411 0 -19.324735 0 -19.324735 9.0820143e-11 69.587141 + 3412 0 -19.324735 0 -19.324735 5.0507872e-11 69.587141 + 3413 0 -19.324735 0 -19.324735 6.0218364e-11 69.587141 + 3414 0 -19.324735 0 -19.324735 -9.2515111e-11 69.587141 + 3415 0 -19.324735 0 -19.324735 -9.5091262e-11 69.587141 + 3416 0 -19.324735 0 -19.324735 -1.2408212e-10 69.587141 + 3417 0 -19.324735 0 -19.324735 2.7185633e-10 69.587141 + 3418 0 -19.324735 0 -19.324735 -3.8475848e-11 69.587141 + 3419 0 -19.324735 0 -19.324735 -9.5091262e-11 69.587141 + 3420 0 -19.324735 0 -19.324735 -1.0926841e-10 69.587141 + 3421 0 -19.324735 0 -19.324735 1.4819359e-10 69.587141 + 3422 0 -19.324735 0 -19.324735 -1.7758468e-11 69.587141 + 3423 0 -19.324735 0 -19.324735 -1.7758468e-11 69.587141 +Loop time of 1.06201 on 1 procs for 3423 steps with 4 atoms + +99.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = quadratic factors are zero + Energy initial, next-to-last, final = + -19.1861867348158 -19.3247351111814 -19.3247351111814 + Force two-norm initial, final = 4.5945611 3.5266103e-15 + Force max component initial, final = 3.9200702 2.0376244e-15 + Final line search alpha, max atom move = 1 2.0376244e-15 + Iterations, force evaluations = 3423 6236 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.98145 | 0.98145 | 0.98145 | 0.0 | 92.41 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.014136 | 0.014136 | 0.014136 | 0.0 | 1.33 +Output | 0.021117 | 0.021117 | 0.021117 | 0.0 | 1.99 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.04531 | | | 4.27 + +Nlocal: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 412 ave 412 max 412 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 172 ave 172 max 172 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 344 ave 344 max 344 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 344 +Ave neighs/atom = 86 +Neighbor list builds = 0 +Dangerous builds = 0 + +variable cohesive_energy equal pe/atoms +variable lattice_parameter equal lx +variable c_to_a equal lz/lx +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Per MPI rank memory allocation (min/avg/max) = 3.725 | 3.725 | 3.725 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 3423 0 -19.324735 0 -19.324735 -1.7758468e-11 69.587141 +Loop time of 1.173e-06 on 1 procs for 0 steps with 4 atoms + +255.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.173e-06 | | |100.00 + +Nlocal: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 412 ave 412 max 412 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 208 ave 208 max 208 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 416 ave 416 max 416 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 416 +Ave neighs/atom = 104 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.83118377779534 eV/atom +print "Reference cohesive energy: -4.831 eV/atom" +Reference cohesive energy: -4.831 eV/atom +print "Calculated lattice parameter: ${lattice_parameter} A" +Calculated lattice parameter: 2.9304937210165 A +print "Reference lattice parameter: 2.9304 A" +Reference lattice parameter: 2.9304 A +print "C/A ratio: ${c_to_a}" +C/A ratio: 1.59641567225833 +print "Reference c/a ratio: 1.596" +Reference c/a ratio: 1.596 +print "====================================================" +==================================================== + +#dump 1 all custom 1 alpha_relaxed.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.alpha_relaxation.g++.4 b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.alpha_relaxation.g++.4 new file mode 100644 index 0000000000..f9b16bf4f3 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.alpha_relaxation.g++.4 @@ -0,0 +1,1187 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Ti alpha phase (hcp) + +units metal +boundary p p p + +atom_style atomic +#lattice custom 2.93093 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 1.596 basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75 +lattice custom 2.93093 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 1.7 basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75 +Lattice spacing in x,y,z = 2.93093 5.0765173 4.982581 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (2.93093 5.0765173 4.982581) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 4 atoms + using lattice units in orthogonal box = (0 0 0) to (2.93093 5.0765173 4.982581) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +Reading meam/sw/spline potential file Ti.meam.sw.spline with DATE: 2012-02-01 +mass * 47.90 + +fix relax all box/relax aniso 0 +thermo 1 +minimize 0 0 10000 100000 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.5 + ghost atom cutoff = 7.5 + binsize = 3.75, bins = 1 2 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 4.872 | 4.872 | 4.872 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 0 -19.186187 0 -19.186187 -52654.105 74.135408 + 1 0 -19.186725 0 -19.186725 -52527.113 74.121586 + 2 0 -19.187261 0 -19.187261 -52400.121 74.107782 + 3 0 -19.187796 0 -19.187796 -52273.129 74.093995 + 4 0 -19.18833 0 -19.18833 -52146.139 74.080225 + 5 0 -19.188862 0 -19.188862 -52019.151 74.066473 + 6 0 -19.189393 0 -19.189393 -51892.165 74.052739 + 7 0 -19.189922 0 -19.189922 -51765.183 74.039023 + 8 0 -19.19045 0 -19.19045 -51638.205 74.025324 + 9 0 -19.190976 0 -19.190976 -51511.232 74.011642 + 10 0 -19.191501 0 -19.191501 -51384.265 73.997979 + 11 0 -19.192024 0 -19.192024 -51257.305 73.984333 + 12 0 -19.192546 0 -19.192546 -51130.351 73.970705 + 13 0 -19.193067 0 -19.193067 -51003.406 73.957094 + 14 0 -19.193586 0 -19.193586 -50876.469 73.943502 + 15 0 -19.194103 0 -19.194103 -50749.542 73.929927 + 16 0 -19.19462 0 -19.19462 -50622.625 73.916369 + 17 0 -19.195134 0 -19.195134 -50495.719 73.90283 + 18 0 -19.195648 0 -19.195648 -50368.824 73.889309 + 19 0 -19.19616 0 -19.19616 -50241.942 73.875805 + 20 0 -19.19667 0 -19.19667 -50115.073 73.862319 + 21 0 -19.197179 0 -19.197179 -49988.218 73.848851 + 22 0 -19.197687 0 -19.197687 -49861.378 73.835401 + 23 0 -19.198193 0 -19.198193 -49734.553 73.821968 + 24 0 -19.198698 0 -19.198698 -49607.744 73.808554 + 25 0 -19.199202 0 -19.199202 -49480.953 73.795157 + 26 0 -19.199704 0 -19.199704 -49354.178 73.781779 + 27 0 -19.200204 0 -19.200204 -49227.422 73.768418 + 28 0 -19.200704 0 -19.200704 -49100.685 73.755075 + 29 0 -19.201201 0 -19.201201 -48973.968 73.741751 + 30 0 -19.201698 0 -19.201698 -48847.272 73.728444 + 31 0 -19.202193 0 -19.202193 -48720.597 73.715155 + 32 0 -19.202687 0 -19.202687 -48593.943 73.701884 + 33 0 -19.203179 0 -19.203179 -48467.313 73.688632 + 34 0 -19.20367 0 -19.20367 -48340.706 73.675397 + 35 0 -19.204159 0 -19.204159 -48214.123 73.66218 + 36 0 -19.204647 0 -19.204647 -48087.566 73.648982 + 37 0 -19.205134 0 -19.205134 -47961.034 73.635801 + 38 0 -19.20562 0 -19.20562 -47834.528 73.622639 + 39 0 -19.206104 0 -19.206104 -47708.05 73.609495 + 40 0 -19.206586 0 -19.206586 -47581.599 73.596368 + 41 0 -19.207067 0 -19.207067 -47455.177 73.58326 + 42 0 -19.207547 0 -19.207547 -47328.785 73.570171 + 43 0 -19.208026 0 -19.208026 -47202.423 73.557099 + 44 0 -19.208503 0 -19.208503 -47076.091 73.544045 + 45 0 -19.208979 0 -19.208979 -46949.791 73.53101 + 46 0 -19.209453 0 -19.209453 -46823.524 73.517993 + 47 0 -19.209927 0 -19.209927 -46697.289 73.504994 + 48 0 -19.210398 0 -19.210398 -46571.088 73.492013 + 49 0 -19.210869 0 -19.210869 -46444.922 73.479051 + 50 0 -19.211338 0 -19.211338 -46318.791 73.466107 + 51 0 -19.211806 0 -19.211806 -46192.696 73.453181 + 52 0 -19.212272 0 -19.212272 -46066.637 73.440273 + 53 0 -19.212737 0 -19.212737 -45940.617 73.427384 + 54 0 -19.213201 0 -19.213201 -45814.634 73.414513 + 55 0 -19.213663 0 -19.213663 -45688.69 73.401661 + 56 0 -19.214124 0 -19.214124 -45562.785 73.388826 + 57 0 -19.214584 0 -19.214584 -45436.921 73.37601 + 58 0 -19.215043 0 -19.215043 -45311.098 73.363213 + 59 0 -19.2155 0 -19.2155 -45185.2 73.350434 + 60 0 -19.215956 0 -19.215956 -45059.109 73.337673 + 61 0 -19.21641 0 -19.21641 -44932.827 73.32493 + 62 0 -19.216863 0 -19.216863 -44806.355 73.312206 + 63 0 -19.217315 0 -19.217315 -44679.693 73.299501 + 64 0 -19.217766 0 -19.217766 -44552.844 73.286813 + 65 0 -19.218215 0 -19.218215 -44425.808 73.274145 + 66 0 -19.218663 0 -19.218663 -44298.587 73.261494 + 67 0 -19.219109 0 -19.219109 -44171.181 73.248862 + 68 0 -19.219555 0 -19.219555 -44043.595 73.236249 + 69 0 -19.219999 0 -19.219999 -43915.928 73.223653 + 70 0 -19.220441 0 -19.220441 -43788.226 73.211077 + 71 0 -19.220883 0 -19.220883 -43660.491 73.198518 + 72 0 -19.221323 0 -19.221323 -43532.724 73.185978 + 73 0 -19.221761 0 -19.221761 -43404.926 73.173457 + 74 0 -19.222199 0 -19.222199 -43277.098 73.160954 + 75 0 -19.222635 0 -19.222635 -43149.24 73.148469 + 76 0 -19.22307 0 -19.22307 -43021.355 73.136003 + 77 0 -19.223503 0 -19.223503 -42893.443 73.123556 + 78 0 -19.223936 0 -19.223936 -42765.506 73.111127 + 79 0 -19.224367 0 -19.224367 -42637.543 73.098716 + 80 0 -19.224796 0 -19.224796 -42509.558 73.086324 + 81 0 -19.225225 0 -19.225225 -42381.55 73.073951 + 82 0 -19.225652 0 -19.225652 -42253.52 73.061596 + 83 0 -19.226077 0 -19.226077 -42125.47 73.049259 + 84 0 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+ 1041 0 -19.324735 0 -19.324735 6.2336579e-11 69.587141 + 1042 0 -19.324735 0 -19.324735 -4.6001569e-12 69.587141 + 1043 0 -19.324735 0 -19.324735 -4.6001569e-12 69.587141 +Loop time of 0.150191 on 4 procs for 1043 steps with 4 atoms + +98.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = quadratic factors are zero + Energy initial, next-to-last, final = + -19.1861867348158 -19.3247351111814 -19.3247351111814 + Force two-norm initial, final = 4.5945611 2.9927541e-15 + Force max component initial, final = 3.9200702 1.4432899e-15 + Final line search alpha, max atom move = 1 1.4432899e-15 + Iterations, force evaluations = 1043 1476 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.089089 | 0.089556 | 0.090042 | 0.1 | 59.63 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.020347 | 0.020795 | 0.021239 | 0.3 | 13.85 +Output | 0.010127 | 0.011086 | 0.012102 | 0.7 | 7.38 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.02875 | | | 19.14 + +Nlocal: 1 ave 1 max 1 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 317.5 ave 318 max 317 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 43 ave 43 max 43 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 86 ave 86 max 86 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 344 +Ave neighs/atom = 86 +Neighbor list builds = 0 +Dangerous builds = 0 + +variable cohesive_energy equal pe/atoms +variable lattice_parameter equal lx +variable c_to_a equal lz/lx +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Per MPI rank memory allocation (min/avg/max) = 3.747 | 3.747 | 3.747 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 1043 0 -19.324735 0 -19.324735 -4.6001569e-12 69.587141 +Loop time of 2.4425e-06 on 4 procs for 0 steps with 4 atoms + +112.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.442e-06 | | |100.00 + +Nlocal: 1 ave 1 max 1 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 317.5 ave 318 max 317 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 52 ave 52 max 52 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 104 ave 104 max 104 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 416 +Ave neighs/atom = 104 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.83118377779534 eV/atom +print "Reference cohesive energy: -4.831 eV/atom" +Reference cohesive energy: -4.831 eV/atom +print "Calculated lattice parameter: ${lattice_parameter} A" +Calculated lattice parameter: 2.9304937210165 A +print "Reference lattice parameter: 2.9304 A" +Reference lattice parameter: 2.9304 A +print "C/A ratio: ${c_to_a}" +C/A ratio: 1.59641567225833 +print "Reference c/a ratio: 1.596" +Reference c/a ratio: 1.596 +print "====================================================" +==================================================== + +#dump 1 all custom 1 alpha_relaxed.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.beta.g++.1 b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.beta.g++.1 new file mode 100644 index 0000000000..84513c9cd8 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.beta.g++.1 @@ -0,0 +1,90 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Ti beta phase (bcc) + +units metal +boundary p p p + +atom_style atomic +lattice bcc 3.27169 +Lattice spacing in x,y,z = 3.27169 3.27169 3.27169 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (3.27169 3.27169 3.27169) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 2 atoms + using lattice units in orthogonal box = (0 0 0) to (3.27169 3.27169 3.27169) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +Reading meam/sw/spline potential file Ti.meam.sw.spline with DATE: 2012-02-01 +mass * 47.90 + +variable cohesive_energy equal pe/atoms +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.5 + ghost atom cutoff = 7.5 + binsize = 3.75, bins = 1 1 1 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.745 | 3.745 | 3.745 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -9.4401327 0 -9.4401327 -116.39305 +Loop time of 1.843e-06 on 1 procs for 0 steps with 2 atoms + +108.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.843e-06 | | |100.00 + +Nlocal: 2 ave 2 max 2 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 339 ave 339 max 339 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 112 ave 112 max 112 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 224 ave 224 max 224 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 224 +Ave neighs/atom = 112 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.72006633828534 eV/atom +print "Reference cohesive energy: -4.720 eV/atom" +Reference cohesive energy: -4.720 eV/atom +print "====================================================" +==================================================== + +#dump 1 all custom 1 beta.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.beta.g++.4 b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.beta.g++.4 new file mode 100644 index 0000000000..287628ca4f --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.beta.g++.4 @@ -0,0 +1,91 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Ti beta phase (bcc) + +units metal +boundary p p p + +atom_style atomic +lattice bcc 3.27169 +Lattice spacing in x,y,z = 3.27169 3.27169 3.27169 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (3.27169 3.27169 3.27169) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 2 atoms + using lattice units in orthogonal box = (0 0 0) to (3.27169 3.27169 3.27169) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +Reading meam/sw/spline potential file Ti.meam.sw.spline with DATE: 2012-02-01 +mass * 47.90 + +variable cohesive_energy equal pe/atoms +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.5 + ghost atom cutoff = 7.5 + binsize = 3.75, bins = 1 1 1 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966) +Per MPI rank memory allocation (min/avg/max) = 3.775 | 3.775 | 3.775 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -9.4401327 0 -9.4401327 -116.39305 +Loop time of 3.81775e-06 on 4 procs for 0 steps with 2 atoms + +91.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.818e-06 | | |100.00 + +Nlocal: 0.5 ave 1 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 274.5 ave 275 max 274 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 28 ave 56 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 56 ave 112 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 224 +Ave neighs/atom = 112 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.72006633828534 eV/atom +print "Reference cohesive energy: -4.720 eV/atom" +Reference cohesive energy: -4.720 eV/atom +print "====================================================" +==================================================== + +#dump 1 all custom 1 beta.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.energy_conservation.meam.sw.g++.1 b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.energy_conservation.meam.sw.g++.1 new file mode 100644 index 0000000000..c32d6b82e1 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.energy_conservation.meam.sw.g++.1 @@ -0,0 +1,358 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# bulk Ti lattice + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable xx equal 20*1 +variable yy equal 20*$y +variable yy equal 20*1 +variable zz equal 20*$z +variable zz equal 20*1 + +units metal +atom_style atomic + +variable a equal 2.28806 +variable covera equal 1.58111 +variable sqrt3 equal sqrt(3.) +variable theta equal PI/2. +variable cos_theta equal round(cos(${theta})) +variable cos_theta equal round(cos(1.5707963267949)) +variable sin_theta equal round(sin(${theta})) +variable sin_theta equal round(sin(1.5707963267949)) +variable Dx equal 1. +variable Dy equal ${covera} +variable Dy equal 1.58111 +variable Dz equal sqrt(3.) + +lattice custom ${a} a1 1 0 0 a2 0 ${sqrt3} 0 a3 0 0 ${covera} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.833333 0.5 basis 0.0 0.333333 0.5 orient x 1 0 0 orient y 0 ${cos_theta} ${sin_theta} orient z 0 -${sin_theta} ${cos_theta} spacing ${Dx} ${Dy} ${Dz} origin 0.25 0.25 0.15 +lattice custom 2.28806 a1 1 0 0 a2 0 ${sqrt3} 0 a3 0 0 ${covera} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.833333 0.5 basis 0.0 0.333333 0.5 orient x 1 0 0 orient y 0 ${cos_theta} ${sin_theta} orient z 0 -${sin_theta} ${cos_theta} spacing ${Dx} ${Dy} ${Dz} origin 0.25 0.25 0.15 +lattice custom 2.28806 a1 1 0 0 a2 0 1.73205080756888 0 a3 0 0 ${covera} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.833333 0.5 basis 0.0 0.333333 0.5 orient x 1 0 0 orient y 0 ${cos_theta} ${sin_theta} orient z 0 -${sin_theta} ${cos_theta} spacing ${Dx} ${Dy} ${Dz} origin 0.25 0.25 0.15 +lattice custom 2.28806 a1 1 0 0 a2 0 1.73205080756888 0 a3 0 0 1.58111 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.833333 0.5 basis 0.0 0.333333 0.5 orient x 1 0 0 orient y 0 ${cos_theta} ${sin_theta} orient z 0 -${sin_theta} ${cos_theta} spacing ${Dx} ${Dy} ${Dz} origin 0.25 0.25 0.15 +lattice custom 2.28806 a1 1 0 0 a2 0 1.73205080756888 0 a3 0 0 1.58111 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.833333 0.5 basis 0.0 0.333333 0.5 orient x 1 0 0 orient y 0 -0 ${sin_theta} orient z 0 -${sin_theta} ${cos_theta} spacing ${Dx} ${Dy} ${Dz} origin 0.25 0.25 0.15 +lattice custom 2.28806 a1 1 0 0 a2 0 1.73205080756888 0 a3 0 0 1.58111 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.833333 0.5 basis 0.0 0.333333 0.5 orient x 1 0 0 orient y 0 -0 1 orient z 0 -${sin_theta} ${cos_theta} spacing ${Dx} ${Dy} ${Dz} origin 0.25 0.25 0.15 +lattice custom 2.28806 a1 1 0 0 a2 0 1.73205080756888 0 a3 0 0 1.58111 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.833333 0.5 basis 0.0 0.333333 0.5 orient x 1 0 0 orient y 0 -0 1 orient z 0 -1 ${cos_theta} spacing ${Dx} ${Dy} ${Dz} origin 0.25 0.25 0.15 +lattice custom 2.28806 a1 1 0 0 a2 0 1.73205080756888 0 a3 0 0 1.58111 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.833333 0.5 basis 0.0 0.333333 0.5 orient x 1 0 0 orient y 0 -0 1 orient z 0 -1 -0 spacing ${Dx} ${Dy} ${Dz} origin 0.25 0.25 0.15 +lattice custom 2.28806 a1 1 0 0 a2 0 1.73205080756888 0 a3 0 0 1.58111 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.833333 0.5 basis 0.0 0.333333 0.5 orient x 1 0 0 orient y 0 -0 1 orient z 0 -1 -0 spacing 1 ${Dy} ${Dz} origin 0.25 0.25 0.15 +lattice custom 2.28806 a1 1 0 0 a2 0 1.73205080756888 0 a3 0 0 1.58111 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.833333 0.5 basis 0.0 0.333333 0.5 orient x 1 0 0 orient y 0 -0 1 orient z 0 -1 -0 spacing 1 1.58111 ${Dz} origin 0.25 0.25 0.15 +lattice custom 2.28806 a1 1 0 0 a2 0 1.73205080756888 0 a3 0 0 1.58111 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.833333 0.5 basis 0.0 0.333333 0.5 orient x 1 0 0 orient y 0 -0 1 orient z 0 -1 -0 spacing 1 1.58111 1.73205080756888 origin 0.25 0.25 0.15 +Lattice spacing in x,y,z = 2.28806 3.6176745 3.9630362 + +variable Xlo equal -round(9./(${a}*${Dx})) +variable Xlo equal -round(9./(2.28806*${Dx})) +variable Xlo equal -round(9./(2.28806*1)) +variable Xhi equal round(9./(${a}*${Dx})) +variable Xhi equal round(9./(2.28806*${Dx})) +variable Xhi equal round(9./(2.28806*1)) +variable Ylo equal -round(9./(${a}*${Dy})) +variable Ylo equal -round(9./(2.28806*${Dy})) +variable Ylo equal -round(9./(2.28806*1.58111)) +variable Yhi equal round(9./(${a}*${Dy})) +variable Yhi equal round(9./(2.28806*${Dy})) +variable Yhi equal round(9./(2.28806*1.58111)) +variable Zlo equal -round(3./(${a}*${Dz})) +variable Zlo equal -round(3./(2.28806*${Dz})) +variable Zlo equal -round(3./(2.28806*1.73205080756888)) +variable Zhi equal round(3./(${a}*${Dz})) +variable Zhi equal round(3./(2.28806*${Dz})) +variable Zhi equal round(3./(2.28806*1.73205080756888)) + +region box prism ${Xlo} ${Xhi} ${Ylo} ${Yhi} ${Zlo} ${Zhi} 0.0 0.0 0.0 +region box prism -4 ${Xhi} ${Ylo} ${Yhi} ${Zlo} ${Zhi} 0.0 0.0 0.0 +region box prism -4 4 ${Ylo} ${Yhi} ${Zlo} ${Zhi} 0.0 0.0 0.0 +region box prism -4 4 -2 ${Yhi} ${Zlo} ${Zhi} 0.0 0.0 0.0 +region box prism -4 4 -2 2 ${Zlo} ${Zhi} 0.0 0.0 0.0 +region box prism -4 4 -2 2 -1 ${Zhi} 0.0 0.0 0.0 +region box prism -4 4 -2 2 -1 1 0.0 0.0 0.0 + +boundary p p p + +create_box 1 box +Created triclinic box = (-9.15224 -7.2353491 -3.9630362) to (9.15224 7.2353491 3.9630362) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 256 atoms + using lattice units in triclinic box = (-9.15224 -7.2353491 -3.9630362) to (9.15224 7.2353491 3.9630362) with tilt (0 0 0) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +Reading meam/sw/spline potential file Ti.meam.sw.spline with DATE: 2012-02-01 +mass * 47.90 + +velocity all create 300.0 376847 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 5 check yes + +fix 1 all nve + +thermo 1 +thermo_style custom step vol etotal press pxx pyy pxz +thermo_modify format 2 %14.8f +thermo_modify format 3 %14.8f +thermo_modify format 4 %14.8f +thermo_modify format 5 %14.8f +thermo_modify format 6 %14.8f +thermo_modify format 7 %14.8f + + +timestep 0.002 +thermo 10 + +run 2000 +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.5 + ghost atom cutoff = 6.5 + binsize = 3.25, bins = 6 5 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.91 | 3.91 | 3.91 Mbytes + Step Volume TotEng Press Pxx Pyy Pxz + 0 2099.44698923 141.95084453 2770269.20500733 1849461.67282887 4612443.51948809 -200.92314181 + 10 2099.44698923 136.33077653 1958557.36795408 2434513.67914763 1325202.13170667 -68176.03310424 + 20 2099.44698923 140.14870590 2034227.20290597 2181759.00797868 1957240.30079100 -24556.64622746 + 30 2099.44698923 141.93445362 2143757.61334882 2130997.29062662 2194778.91443186 -2919.77630179 + 40 2099.44698923 142.77365516 2147955.66088043 2109635.72653715 2156587.62644743 -14244.60118806 + 50 2099.44698923 142.87043233 2033334.38628842 1937442.59449182 2075504.44620003 37419.59959355 + 60 2099.44698923 142.38830676 2138363.39987139 2004531.45133533 2210079.04632844 -163393.77296844 + 70 2099.44698923 142.29741561 2074195.97510129 2006685.04815304 2111763.84115527 77094.68966752 + 80 2099.44698923 142.49220468 2123101.40630001 2047646.63928723 2197988.27561128 -18271.98124007 + 90 2099.44698923 142.67434162 2223896.82123570 2253076.13758682 2250603.62272739 -114786.38067562 + 100 2099.44698923 144.11596935 2221059.47057083 2166972.05033758 2124132.88128236 14103.01463135 + 110 2099.44698923 144.59582155 2178294.89834435 2136419.99945026 2293362.65352157 83796.79384278 + 120 2099.44698923 145.31467921 2088728.12438738 2073042.17202669 2099497.34361092 18785.33875339 + 130 2099.44698923 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177.98638560 2050837.55770902 2048454.09614426 2087208.10668847 -13898.23829272 + 1930 2099.44698923 178.93053376 2048451.40218711 1893347.24530875 2168389.36568868 49250.32625701 + 1940 2099.44698923 177.67065278 2003989.31997591 1961857.54065587 2030080.76278604 -6629.82955803 + 1950 2099.44698923 177.85891746 1988335.82805743 1967759.98325713 1907343.68480253 45814.50149073 + 1960 2099.44698923 177.62160576 2111910.66096559 2159786.98657515 2103028.53323572 51946.56425808 + 1970 2099.44698923 176.27935973 2127731.34314723 2178583.14275802 2056629.63951371 -87198.67992398 + 1980 2099.44698923 176.80499887 2156411.08886277 2172212.65624708 2155875.63215539 65355.23567098 + 1990 2099.44698923 178.35434641 2100169.69201692 2092393.03883065 2073013.15142734 47946.05896865 + 2000 2099.44698923 179.03920352 2085120.39659205 2119204.00544264 2038171.77865358 -4801.17973982 +Loop time of 87.4745 on 1 procs for 2000 steps with 256 atoms + +Performance: 3.951 ns/day, 6.075 hours/ns, 22.864 timesteps/s, 5.853 katom-step/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 | 86.87 | 86.87 | 86.87 | 0.0 | 99.31 +Neigh | 0.55118 | 0.55118 | 0.55118 | 0.0 | 0.63 +Comm | 0.03131 | 0.03131 | 0.03131 | 0.0 | 0.04 +Output | 0.0056033 | 0.0056033 | 0.0056033 | 0.0 | 0.01 +Modify | 0.0070439 | 0.0070439 | 0.0070439 | 0.0 | 0.01 +Other | | 0.008988 | | | 0.01 + +Nlocal: 256 ave 256 max 256 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1935 ave 1935 max 1935 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 17836 ave 17836 max 17836 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 35672 ave 35672 max 35672 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 35672 +Ave neighs/atom = 139.34375 +Neighbor list builds = 397 +Dangerous builds = 391 + +Total wall time: 0:01:27 diff --git a/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.energy_conservation.meam.sw.g++.4 b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.energy_conservation.meam.sw.g++.4 new file mode 100644 index 0000000000..76250350af --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.energy_conservation.meam.sw.g++.4 @@ -0,0 +1,358 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# bulk Ti lattice + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable xx equal 20*1 +variable yy equal 20*$y +variable yy equal 20*1 +variable zz equal 20*$z +variable zz equal 20*1 + +units metal +atom_style atomic + +variable a equal 2.28806 +variable covera equal 1.58111 +variable sqrt3 equal sqrt(3.) +variable theta equal PI/2. +variable cos_theta equal round(cos(${theta})) +variable cos_theta equal round(cos(1.5707963267949)) +variable sin_theta equal round(sin(${theta})) +variable sin_theta equal round(sin(1.5707963267949)) +variable Dx equal 1. +variable Dy equal ${covera} +variable Dy equal 1.58111 +variable Dz equal sqrt(3.) + +lattice custom ${a} a1 1 0 0 a2 0 ${sqrt3} 0 a3 0 0 ${covera} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.833333 0.5 basis 0.0 0.333333 0.5 orient x 1 0 0 orient y 0 ${cos_theta} ${sin_theta} orient z 0 -${sin_theta} ${cos_theta} spacing ${Dx} ${Dy} ${Dz} origin 0.25 0.25 0.15 +lattice custom 2.28806 a1 1 0 0 a2 0 ${sqrt3} 0 a3 0 0 ${covera} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.833333 0.5 basis 0.0 0.333333 0.5 orient x 1 0 0 orient y 0 ${cos_theta} ${sin_theta} orient z 0 -${sin_theta} ${cos_theta} spacing ${Dx} ${Dy} ${Dz} origin 0.25 0.25 0.15 +lattice custom 2.28806 a1 1 0 0 a2 0 1.73205080756888 0 a3 0 0 ${covera} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.833333 0.5 basis 0.0 0.333333 0.5 orient x 1 0 0 orient y 0 ${cos_theta} ${sin_theta} orient z 0 -${sin_theta} ${cos_theta} spacing ${Dx} ${Dy} ${Dz} origin 0.25 0.25 0.15 +lattice custom 2.28806 a1 1 0 0 a2 0 1.73205080756888 0 a3 0 0 1.58111 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.833333 0.5 basis 0.0 0.333333 0.5 orient x 1 0 0 orient y 0 ${cos_theta} ${sin_theta} orient z 0 -${sin_theta} ${cos_theta} spacing ${Dx} ${Dy} ${Dz} origin 0.25 0.25 0.15 +lattice custom 2.28806 a1 1 0 0 a2 0 1.73205080756888 0 a3 0 0 1.58111 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.833333 0.5 basis 0.0 0.333333 0.5 orient x 1 0 0 orient y 0 -0 ${sin_theta} orient z 0 -${sin_theta} ${cos_theta} spacing ${Dx} ${Dy} ${Dz} origin 0.25 0.25 0.15 +lattice custom 2.28806 a1 1 0 0 a2 0 1.73205080756888 0 a3 0 0 1.58111 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.833333 0.5 basis 0.0 0.333333 0.5 orient x 1 0 0 orient y 0 -0 1 orient z 0 -${sin_theta} ${cos_theta} spacing ${Dx} ${Dy} ${Dz} origin 0.25 0.25 0.15 +lattice custom 2.28806 a1 1 0 0 a2 0 1.73205080756888 0 a3 0 0 1.58111 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.833333 0.5 basis 0.0 0.333333 0.5 orient x 1 0 0 orient y 0 -0 1 orient z 0 -1 ${cos_theta} spacing ${Dx} ${Dy} ${Dz} origin 0.25 0.25 0.15 +lattice custom 2.28806 a1 1 0 0 a2 0 1.73205080756888 0 a3 0 0 1.58111 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.833333 0.5 basis 0.0 0.333333 0.5 orient x 1 0 0 orient y 0 -0 1 orient z 0 -1 -0 spacing ${Dx} ${Dy} ${Dz} origin 0.25 0.25 0.15 +lattice custom 2.28806 a1 1 0 0 a2 0 1.73205080756888 0 a3 0 0 1.58111 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.833333 0.5 basis 0.0 0.333333 0.5 orient x 1 0 0 orient y 0 -0 1 orient z 0 -1 -0 spacing 1 ${Dy} ${Dz} origin 0.25 0.25 0.15 +lattice custom 2.28806 a1 1 0 0 a2 0 1.73205080756888 0 a3 0 0 1.58111 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.833333 0.5 basis 0.0 0.333333 0.5 orient x 1 0 0 orient y 0 -0 1 orient z 0 -1 -0 spacing 1 1.58111 ${Dz} origin 0.25 0.25 0.15 +lattice custom 2.28806 a1 1 0 0 a2 0 1.73205080756888 0 a3 0 0 1.58111 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.833333 0.5 basis 0.0 0.333333 0.5 orient x 1 0 0 orient y 0 -0 1 orient z 0 -1 -0 spacing 1 1.58111 1.73205080756888 origin 0.25 0.25 0.15 +Lattice spacing in x,y,z = 2.28806 3.6176745 3.9630362 + +variable Xlo equal -round(9./(${a}*${Dx})) +variable Xlo equal -round(9./(2.28806*${Dx})) +variable Xlo equal -round(9./(2.28806*1)) +variable Xhi equal round(9./(${a}*${Dx})) +variable Xhi equal round(9./(2.28806*${Dx})) +variable Xhi equal round(9./(2.28806*1)) +variable Ylo equal -round(9./(${a}*${Dy})) +variable Ylo equal -round(9./(2.28806*${Dy})) +variable Ylo equal -round(9./(2.28806*1.58111)) +variable Yhi equal round(9./(${a}*${Dy})) +variable Yhi equal round(9./(2.28806*${Dy})) +variable Yhi equal round(9./(2.28806*1.58111)) +variable Zlo equal -round(3./(${a}*${Dz})) +variable Zlo equal -round(3./(2.28806*${Dz})) +variable Zlo equal -round(3./(2.28806*1.73205080756888)) +variable Zhi equal round(3./(${a}*${Dz})) +variable Zhi equal round(3./(2.28806*${Dz})) +variable Zhi equal round(3./(2.28806*1.73205080756888)) + +region box prism ${Xlo} ${Xhi} ${Ylo} ${Yhi} ${Zlo} ${Zhi} 0.0 0.0 0.0 +region box prism -4 ${Xhi} ${Ylo} ${Yhi} ${Zlo} ${Zhi} 0.0 0.0 0.0 +region box prism -4 4 ${Ylo} ${Yhi} ${Zlo} ${Zhi} 0.0 0.0 0.0 +region box prism -4 4 -2 ${Yhi} ${Zlo} ${Zhi} 0.0 0.0 0.0 +region box prism -4 4 -2 2 ${Zlo} ${Zhi} 0.0 0.0 0.0 +region box prism -4 4 -2 2 -1 ${Zhi} 0.0 0.0 0.0 +region box prism -4 4 -2 2 -1 1 0.0 0.0 0.0 + +boundary p p p + +create_box 1 box +Created triclinic box = (-9.15224 -7.2353491 -3.9630362) to (9.15224 7.2353491 3.9630362) with tilt (0 0 0) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 256 atoms + using lattice units in triclinic box = (-9.15224 -7.2353491 -3.9630362) to (9.15224 7.2353491 3.9630362) with tilt (0 0 0) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +Reading meam/sw/spline potential file Ti.meam.sw.spline with DATE: 2012-02-01 +mass * 47.90 + +velocity all create 300.0 376847 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 5 check yes + +fix 1 all nve + +thermo 1 +thermo_style custom step vol etotal press pxx pyy pxz +thermo_modify format 2 %14.8f +thermo_modify format 3 %14.8f +thermo_modify format 4 %14.8f +thermo_modify format 5 %14.8f +thermo_modify format 6 %14.8f +thermo_modify format 7 %14.8f + + +timestep 0.002 +thermo 10 + +run 2000 +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.5 + ghost atom cutoff = 6.5 + binsize = 3.25, bins = 6 5 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.858 | 3.858 | 3.858 Mbytes + Step Volume TotEng Press Pxx Pyy Pxz + 0 2099.44698923 141.95084453 2770269.20500732 1849461.67282887 4612443.51948808 -200.92314181 + 10 2099.44698923 136.33077653 1958557.36795408 2434513.67914763 1325202.13170667 -68176.03310424 + 20 2099.44698923 140.14870590 2034227.20290596 2181759.00797869 1957240.30079099 -24556.64622746 + 30 2099.44698923 141.93445362 2143757.61334881 2130997.29062662 2194778.91443186 -2919.77630181 + 40 2099.44698923 142.77365516 2147955.66088040 2109635.72653706 2156587.62644742 -14244.60118813 + 50 2099.44698923 142.87043233 2033334.38628833 1937442.59449175 2075504.44619994 37419.59959355 + 60 2099.44698923 142.38830676 2138363.39987169 2004531.45133575 2210079.04632873 -163393.77296846 + 70 2099.44698923 142.29741561 2074195.97510078 2006685.04815312 2111763.84115463 77094.68966760 + 80 2099.44698923 142.49220468 2123101.40630225 2047646.63928832 2197988.27561440 -18271.98124070 + 90 2099.44698923 142.67434162 2223896.82123525 2253076.13758849 2250603.62272579 -114786.38067492 + 100 2099.44698923 144.11596935 2221059.47057347 2166972.05033401 2124132.88129360 14103.01464350 + 110 2099.44698923 144.59582155 2178294.89836371 2136419.99948096 2293362.65354383 83796.79380109 + 120 2099.44698923 145.31467921 2088728.12433774 2073042.17194525 2099497.34358516 18785.33874898 + 130 2099.44698923 145.06214272 2057214.50998047 1975241.78773798 2142250.09661757 12591.75358550 + 140 2099.44698923 146.28976141 2096554.50714041 2077376.79791019 2142990.52214906 -16791.54385812 + 150 2099.44698923 144.80731478 2087150.62683918 2191868.17773523 2168208.12598483 -14365.74223176 + 160 2099.44698923 145.18230266 2159234.15408580 2119660.90519269 2188266.39986483 -80465.21876555 + 170 2099.44698923 145.79888252 2017869.97022458 2064331.05014382 1942513.99621364 25331.49140276 + 180 2099.44698923 146.27160994 2130307.51823101 2094999.32517748 2178097.30498862 62391.17754372 + 190 2099.44698923 146.32542554 2124318.95029165 2214623.23659909 2082878.63036191 14551.70875737 + 200 2099.44698923 145.73872298 2042854.40973869 2024038.60437399 1915826.45551365 -71026.91764224 + 210 2099.44698923 145.76568225 2092101.45554806 1983388.98993370 2303152.68801411 -73909.73010597 + 220 2099.44698923 146.64904419 2090212.89038279 2042185.53538746 2115055.60532560 -153112.29584318 + 230 2099.44698923 147.09053340 2084690.04858681 2031410.13404116 2211340.69045831 77369.53366492 + 240 2099.44698923 147.67271853 2183052.86060754 2223423.96234103 2134816.50040790 -28488.09896454 + 250 2099.44698923 148.33439298 2147377.33501386 2130068.16925358 2202199.30403281 -69590.71932265 + 260 2099.44698923 147.93766985 1960315.29017707 1885818.49153399 1963070.63466385 -304.74207464 + 270 2099.44698923 148.42074323 2136915.72369958 2002301.03150437 2181853.47259660 32891.51187756 + 280 2099.44698923 148.83182039 2113177.87179107 2106572.69813513 2025541.98226176 43884.75263681 + 290 2099.44698923 149.84123587 2066057.87938847 2120536.41652421 2036036.27802384 -7753.03550030 + 300 2099.44698923 149.93519488 2082917.77052997 2215396.92339865 1930080.36365132 53283.89373792 + 310 2099.44698923 150.75843446 2092470.86960937 2117852.59481063 2136827.27534212 -1569.53945649 + 320 2099.44698923 151.20710387 2058465.58471811 2080842.80934031 2044743.13738705 -50352.29022320 + 330 2099.44698923 152.02079947 2082586.16120456 2077785.24127540 2080243.44467767 -23505.10974102 + 340 2099.44698923 151.94256411 2138640.79109189 2205134.92688846 2073382.51330172 -6346.14896403 + 350 2099.44698923 153.35120137 2049296.08564107 2048099.01481015 2015276.01240142 50311.76483843 + 360 2099.44698923 152.18557005 2179623.03566902 2166151.50942126 2166314.82981672 -9944.36477934 + 370 2099.44698923 153.13753244 2077401.52438283 2112096.89379137 1950942.85039910 47066.87229881 + 380 2099.44698923 153.08647659 2176530.90642283 2261131.27063450 2157678.11405844 -24995.41302255 + 390 2099.44698923 155.24509173 2033974.69202180 2115192.39498879 1952897.09183643 6715.22283440 + 400 2099.44698923 154.20793035 2025032.28456425 2141991.33897200 1914474.96773135 62202.43565548 + 410 2099.44698923 154.94234461 1996133.65762731 1974020.15046901 1996940.07884260 239.74906146 + 420 2099.44698923 154.99405444 2064983.96082068 1918497.27779035 2158170.05680229 5085.80305921 + 430 2099.44698923 153.91000310 2207981.74818522 2278997.68895500 2247746.90343778 60886.21505091 + 440 2099.44698923 153.52617582 2093267.92694548 2111990.93489840 2002795.19296691 35059.46041020 + 450 2099.44698923 153.14138095 2095959.88265135 2028364.62675497 2182407.21039516 64933.12797967 + 460 2099.44698923 153.25625074 1980636.76405223 1956318.99832973 2042506.35203898 -87295.45961447 + 470 2099.44698923 153.32728915 2120132.83496282 2083262.56294551 2085135.52248661 6129.44292274 + 480 2099.44698923 153.73432577 2140771.27971295 2241489.04786541 2050362.67696813 20490.93815606 + 490 2099.44698923 154.27692159 2076056.78527870 2040574.26951869 2135225.80445834 -76411.31637446 + 500 2099.44698923 156.07088715 2099340.68853421 1926544.45359856 2231296.56154476 100291.40590457 + 510 2099.44698923 156.50466217 1949722.86446108 2068961.44409942 1847132.64447129 -47563.38576439 + 520 2099.44698923 157.05444228 2093777.44522219 2146198.75329716 2133612.82068735 74969.01818818 + 530 2099.44698923 157.57378530 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hours/ns, 85.851 timesteps/s, 21.978 katom-step/s +99.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 23.099 | 23.099 | 23.1 | 0.0 | 99.15 +Neigh | 0.1338 | 0.13473 | 0.13581 | 0.2 | 0.58 +Comm | 0.046095 | 0.047331 | 0.048475 | 0.5 | 0.20 +Output | 0.0056511 | 0.0059203 | 0.0067023 | 0.6 | 0.03 +Modify | 0.0025324 | 0.0026458 | 0.0028537 | 0.2 | 0.01 +Other | | 0.006341 | | | 0.03 + +Nlocal: 64 ave 66 max 61 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +Nghost: 1075.75 ave 1093 max 1064 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +Neighs: 4453.5 ave 4642 max 4225 min +Histogram: 1 0 0 0 1 0 0 1 0 1 +FullNghs: 8907 ave 9266 max 8455 min +Histogram: 1 0 0 0 1 0 0 1 0 1 + +Total # of neighbors = 35628 +Ave neighs/atom = 139.17188 +Neighbor list builds = 396 +Dangerous builds = 386 + +Total wall time: 0:00:23 diff --git a/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.fcc.g++.1 b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.fcc.g++.1 new file mode 100644 index 0000000000..09a6a75d0c --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.fcc.g++.1 @@ -0,0 +1,91 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Ti fcc phase + +units metal +boundary p p p + +atom_style atomic +lattice fcc 4.147029 +Lattice spacing in x,y,z = 4.147029 4.147029 4.147029 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (4.147029 4.147029 4.147029) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4 atoms + using lattice units in orthogonal box = (0 0 0) to (4.147029 4.147029 4.147029) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +Reading meam/sw/spline potential file Ti.meam.sw.spline with DATE: 2012-02-01 +mass * 47.90 + +variable cohesive_energy equal pe/atoms +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.5 + ghost atom cutoff = 7.5 + binsize = 3.75, bins = 2 2 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.715 | 3.715 | 3.715 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -19.169864 0 -19.169864 -239.58594 +Loop time of 1.97e-06 on 1 procs for 0 steps with 4 atoms + +152.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.97e-06 | | |100.00 + +Nlocal: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 360 ave 360 max 360 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 172 ave 172 max 172 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 344 ave 344 max 344 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 344 +Ave neighs/atom = 86 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.79246596281897 eV/atom +print "Reference cohesive energy: -4.792 eV/atom" +Reference cohesive energy: -4.792 eV/atom +print "====================================================" +==================================================== + + +#dump 1 all custom 1 fcc.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.fcc.g++.4 b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.fcc.g++.4 new file mode 100644 index 0000000000..3c9bcb10aa --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.fcc.g++.4 @@ -0,0 +1,91 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Ti fcc phase + +units metal +boundary p p p + +atom_style atomic +lattice fcc 4.147029 +Lattice spacing in x,y,z = 4.147029 4.147029 4.147029 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (4.147029 4.147029 4.147029) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 4 atoms + using lattice units in orthogonal box = (0 0 0) to (4.147029 4.147029 4.147029) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +Reading meam/sw/spline potential file Ti.meam.sw.spline with DATE: 2012-02-01 +mass * 47.90 + +variable cohesive_energy equal pe/atoms +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.5 + ghost atom cutoff = 7.5 + binsize = 3.75, bins = 2 2 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.746 | 3.746 | 3.746 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -19.169864 0 -19.169864 -239.58594 +Loop time of 3.42925e-06 on 4 procs for 0 steps with 4 atoms + +87.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.429e-06 | | |100.00 + +Nlocal: 1 ave 1 max 1 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 287 ave 287 max 287 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 43 ave 43 max 43 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 86 ave 86 max 86 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 344 +Ave neighs/atom = 86 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.79246596281896 eV/atom +print "Reference cohesive energy: -4.792 eV/atom" +Reference cohesive energy: -4.792 eV/atom +print "====================================================" +==================================================== + + +#dump 1 all custom 1 fcc.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.hexagonal.g++.1 b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.hexagonal.g++.1 new file mode 100644 index 0000000000..86589eef10 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.hexagonal.g++.1 @@ -0,0 +1,91 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Ti omega phase (hexagonal) + +units metal +boundary p p p + +atom_style atomic +lattice custom 2.727192 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 0.982 basis 0 0 0 +Lattice spacing in x,y,z = 2.727192 4.7236329 2.6781025 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (2.727192 4.7236329 2.6781025) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 2 atoms + using lattice units in orthogonal box = (0 0 0) to (2.727192 4.7236329 2.6781025) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +Reading meam/sw/spline potential file Ti.meam.sw.spline with DATE: 2012-02-01 +mass * 47.90 + +variable cohesive_energy equal pe/atoms +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.5 + ghost atom cutoff = 7.5 + binsize = 3.75, bins = 1 2 1 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.734 | 3.734 | 3.734 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -8.8695224 0 -8.8695224 262.05359 +Loop time of 1.196e-06 on 1 procs for 0 steps with 2 atoms + +167.2% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.196e-06 | | |100.00 + +Nlocal: 2 ave 2 max 2 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 352 ave 352 max 352 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 94 ave 94 max 94 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 188 ave 188 max 188 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 188 +Ave neighs/atom = 94 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.43476118506642 eV/atom +print "Reference cohesive energy: -4.435 eV/atom" +Reference cohesive energy: -4.435 eV/atom +print "====================================================" +==================================================== + + +#dump 1 all custom 1 hexagonal.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.hexagonal.g++.4 b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.hexagonal.g++.4 new file mode 100644 index 0000000000..8d116a6d9f --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.hexagonal.g++.4 @@ -0,0 +1,92 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Ti omega phase (hexagonal) + +units metal +boundary p p p + +atom_style atomic +lattice custom 2.727192 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 0.982 basis 0 0 0 +Lattice spacing in x,y,z = 2.727192 4.7236329 2.6781025 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (2.727192 4.7236329 2.6781025) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 2 atoms + using lattice units in orthogonal box = (0 0 0) to (2.727192 4.7236329 2.6781025) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +Reading meam/sw/spline potential file Ti.meam.sw.spline with DATE: 2012-02-01 +mass * 47.90 + +variable cohesive_energy equal pe/atoms +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.5 + ghost atom cutoff = 7.5 + binsize = 3.75, bins = 1 2 1 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966) +Per MPI rank memory allocation (min/avg/max) = 3.773 | 3.773 | 3.773 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -8.8695224 0 -8.8695224 262.05359 +Loop time of 8.48775e-06 on 4 procs for 0 steps with 2 atoms + +82.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 8.488e-06 | | |100.00 + +Nlocal: 0.5 ave 1 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 287.5 ave 288 max 287 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 23.5 ave 47 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 47 ave 94 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 188 +Ave neighs/atom = 94 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.43476118506641 eV/atom +print "Reference cohesive energy: -4.435 eV/atom" +Reference cohesive energy: -4.435 eV/atom +print "====================================================" +==================================================== + + +#dump 1 all custom 1 hexagonal.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.omega.g++.1 b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.omega.g++.1 new file mode 100644 index 0000000000..d0855fc984 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.omega.g++.1 @@ -0,0 +1,90 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Ti omega phase + +units metal +boundary p p p + +atom_style atomic +lattice custom 4.6064061 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 0.611 basis 0 0 0 basis 0.3333333 0.66666666 0.5 basis 0.6666666 0.3333333 0.5 +Lattice spacing in x,y,z = 4.6064061 7.9785257 2.8145141 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (4.6064061 7.9785257 2.8145141) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 6 atoms + using lattice units in orthogonal box = (0 0 0) to (4.6064061 7.9785257 2.8145141) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +Reading meam/sw/spline potential file Ti.meam.sw.spline with DATE: 2012-02-01 +mass * 47.90 + +variable cohesive_energy equal pe/atoms +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.5 + ghost atom cutoff = 7.5 + binsize = 3.75, bins = 2 3 1 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.843 | 3.843 | 3.843 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -29.016539 0 -29.016539 103.20055 +Loop time of 1.858e-06 on 1 procs for 0 steps with 6 atoms + +107.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.858e-06 | | |100.00 + +Nlocal: 6 ave 6 max 6 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 510 ave 510 max 510 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 306 ave 306 max 306 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 612 ave 612 max 612 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 612 +Ave neighs/atom = 102 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.8360898853642 eV/atom +print "Reference cohesive energy: -4.836 eV/atom" +Reference cohesive energy: -4.836 eV/atom +print "====================================================" +==================================================== + +#dump 1 all custom 1 omega.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.omega.g++.4 b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.omega.g++.4 new file mode 100644 index 0000000000..4179f4b4df --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.omega.g++.4 @@ -0,0 +1,90 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Ti omega phase + +units metal +boundary p p p + +atom_style atomic +lattice custom 4.6064061 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 0.611 basis 0 0 0 basis 0.3333333 0.66666666 0.5 basis 0.6666666 0.3333333 0.5 +Lattice spacing in x,y,z = 4.6064061 7.9785257 2.8145141 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (4.6064061 7.9785257 2.8145141) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 6 atoms + using lattice units in orthogonal box = (0 0 0) to (4.6064061 7.9785257 2.8145141) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +Reading meam/sw/spline potential file Ti.meam.sw.spline with DATE: 2012-02-01 +mass * 47.90 + +variable cohesive_energy equal pe/atoms +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.5 + ghost atom cutoff = 7.5 + binsize = 3.75, bins = 2 3 1 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.74 | 3.74 | 3.74 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -29.016539 0 -29.016539 103.20055 +Loop time of 9.049e-06 on 4 procs for 0 steps with 6 atoms + +77.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 9.049e-06 | | |100.00 + +Nlocal: 1.5 ave 2 max 1 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 374.5 ave 375 max 374 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 76.5 ave 104 max 49 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 153 ave 206 max 100 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 612 +Ave neighs/atom = 102 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: -4.8360898853642 eV/atom +print "Reference cohesive energy: -4.836 eV/atom" +Reference cohesive energy: -4.836 eV/atom +print "====================================================" +==================================================== + +#dump 1 all custom 1 omega.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.single_atom.g++.1 b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.single_atom.g++.1 new file mode 100644 index 0000000000..f62101d5b5 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.single_atom.g++.1 @@ -0,0 +1,89 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Ti single atom in vacuum + +units metal +boundary f f f + +atom_style atomic +region box block -100 100 -100 100 -100 100 units box +create_box 1 box +Created orthogonal box = (-100 -100 -100) to (100 100 100) + 1 by 1 by 1 MPI processor grid +create_atoms 1 single 0 0 0 units box +Created 1 atoms + using box units in orthogonal box = (-100 -100 -100) to (100 100 100) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +Reading meam/sw/spline potential file Ti.meam.sw.spline with DATE: 2012-02-01 +mass * 47.90 + +variable cohesive_energy equal pe/atoms +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.5 + ghost atom cutoff = 7.5 + binsize = 3.75, bins = 54 54 54 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.948 | 3.948 | 3.948 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 0 0 0 0 +Loop time of 1.424e-06 on 1 procs for 0 steps with 1 atoms + +70.2% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.424e-06 | | |100.00 + +Nlocal: 1 ave 1 max 1 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: 0 eV/atom +print "Reference cohesive energy: 0 eV/atom" +Reference cohesive energy: 0 eV/atom +print "====================================================" +==================================================== + + +#dump 1 all custom 1 single_atom.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.single_atom.g++.4 b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.single_atom.g++.4 new file mode 100644 index 0000000000..ceb6abf7b7 --- /dev/null +++ b/examples/PACKAGES/meam_sw_spline/Ti/log.17Dec2022.single_atom.g++.4 @@ -0,0 +1,89 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Ti single atom in vacuum + +units metal +boundary f f f + +atom_style atomic +region box block -100 100 -100 100 -100 100 units box +create_box 1 box +Created orthogonal box = (-100 -100 -100) to (100 100 100) + 1 by 2 by 2 MPI processor grid +create_atoms 1 single 0 0 0 units box +Created 1 atoms + using box units in orthogonal box = (-100 -100 -100) to (100 100 100) + create_atoms CPU = 0.000 seconds + +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +Reading meam/sw/spline potential file Ti.meam.sw.spline with DATE: 2012-02-01 +mass * 47.90 + +variable cohesive_energy equal pe/atoms +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.5 + ghost atom cutoff = 7.5 + binsize = 3.75, bins = 54 54 54 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/sw/spline, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/sw/spline, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 1.05 | 1.644 | 3.425 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 0 0 0 0 +Loop time of 3.81e-06 on 4 procs for 0 steps with 1 atoms + +85.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.81e-06 | | |100.00 + +Nlocal: 0.25 ave 1 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 0.75 ave 1 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "====================================================" +==================================================== +print "Calculated cohesive energy: ${cohesive_energy} eV/atom" +Calculated cohesive energy: 0 eV/atom +print "Reference cohesive energy: 0 eV/atom" +Reference cohesive energy: 0 eV/atom +print "====================================================" +==================================================== + + +#dump 1 all custom 1 single_atom.dump id type x y z fx fy fz +#run 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/meam_sw_spline/Ti/omega.in b/examples/PACKAGES/meam_sw_spline/Ti/omega.in deleted file mode 100644 index 8e19c6a208..0000000000 --- a/examples/PACKAGES/meam_sw_spline/Ti/omega.in +++ /dev/null @@ -1,27 +0,0 @@ -# Ti omega phase - -units metal -boundary p p p - -atom_style atomic -lattice custom 4.6064061 a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 0.611 basis 0 0 0 basis 0.3333333 0.66666666 0.5 basis 0.6666666 0.3333333 0.5 -region box block 0 1 0 1 0 1 -create_box 1 box -create_atoms 1 box - -pair_style meam/sw/spline -pair_coeff * * ../../potentials/Ti.meam.sw.spline Ti -mass * 47.90 - -variable cohesive_energy equal pe/atoms -run 0 - -print "====================================================" -print "Calculated cohesive energy: ${cohesive_energy} eV/atom" -print "Reference cohesive energy: -4.836 eV/atom" -print "====================================================" - -#dump 1 all custom 1 omega.dump id type x y z fx fy fz -#run 0 - - diff --git a/examples/PACKAGES/meam_sw_spline/Ti/single_atom.in b/examples/PACKAGES/meam_sw_spline/Ti/single_atom.in deleted file mode 100644 index 65243de23c..0000000000 --- a/examples/PACKAGES/meam_sw_spline/Ti/single_atom.in +++ /dev/null @@ -1,27 +0,0 @@ -# Ti single atom in vacuum - -units metal -boundary f f f - -atom_style atomic -region box block -100 100 -100 100 -100 100 units box -create_box 1 box -create_atoms 1 single 0 0 0 units box - -pair_style meam/sw/spline -pair_coeff * * ../../potentials/Ti.meam.sw.spline Ti -mass * 47.90 - -variable cohesive_energy equal pe/atoms -run 0 - -print "====================================================" -print "Calculated cohesive energy: ${cohesive_energy} eV/atom" -print "Reference cohesive energy: 0 eV/atom" -print "====================================================" - - -#dump 1 all custom 1 single_atom.dump id type x y z fx fy fz -#run 0 - - diff --git a/examples/PACKAGES/pace/plugin/CMakeLists.txt b/examples/PACKAGES/pace/plugin/CMakeLists.txt index 6ad9c791ba..25fa877ffc 100644 --- a/examples/PACKAGES/pace/plugin/CMakeLists.txt +++ b/examples/PACKAGES/pace/plugin/CMakeLists.txt @@ -38,9 +38,15 @@ elseif(CMAKE_SYSTEM_NAME STREQUAL "Windows") execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_SOURCE_DIR}/lammps.ico ${CMAKE_SOURCE_DIR}/lammps-text-logo-wide.bmp ${CMAKE_SOURCE_DIR}/paceplugin.nsis ${CMAKE_BINARY_DIR}) if(BUILD_MPI) - add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION}-MPI paceplugin.nsis - DEPENDS paceplugin - BYPRODUCTS LAMMPS-ML-PACE-plugin-${LAMMPS_VERSION}-MPI.exe) + if(USE_MSMPI) + add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION}-MSMPI paceplugin.nsis + DEPENDS paceplugin + BYPRODUCTS LAMMPS-ML-PACE-plugin-${LAMMPS_VERSION}-MSMPI.exe) + else() + add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION}-MPI paceplugin.nsis + DEPENDS paceplugin + BYPRODUCTS LAMMPS-ML-PACE-plugin-${LAMMPS_VERSION}-MPI.exe) + endif() else() add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION} paceplugin.nsis COMMAND ${CMAKE_COMMAND} -E echo ${PWD} diff --git a/examples/PACKAGES/pod/README.md b/examples/PACKAGES/pod/README.md new file mode 100644 index 0000000000..2c6db69200 --- /dev/null +++ b/examples/PACKAGES/pod/README.md @@ -0,0 +1,21 @@ +### Compile LAMMPS/POD + +Go to `lammps` directory and build with the POD package: + + cd path/to/lammps + mkdir build-pod + cd build-pod + cmake -C ../cmake/presets/basic.cmake -D PKG_ML-POD=on ../cmake + cmake --build . + +### Fit a POD potential for tantalum + +Go to `lammps/examples/PACKAGES/pod/Ta` directory and run + + lmp -in in.podfit + +See the README in `lammps/examples/PACKAGES/pod/Ta` for instructions on how to run MD with the potential. + +### Examples for other materials + +See [https://github.com/cesmix-mit/pod-examples](https://github.com/cesmix-mit/pod-examples) diff --git a/examples/PACKAGES/pod/Ta/README.md b/examples/PACKAGES/pod/Ta/README.md new file mode 100644 index 0000000000..031698550c --- /dev/null +++ b/examples/PACKAGES/pod/Ta/README.md @@ -0,0 +1,15 @@ +### POD example for Ta + +We will fit a potential to the `Ta` training data in the `XYZ` directory, which houses `.xyz` files +of the training data taken from [the FitSNAP repo](https://github.com/FitSNAP/FitSNAP/tree/master/examples/Ta_XYZ/XYZ) + +Fit POD with + + lmp -in in.fitpod + +This creates `Ta_coefficients.pod` for the linear model, which we can use to run MD with + + lmp -in in.pod + + + diff --git a/examples/PACKAGES/pod/Ta/Ta_coeff.pod b/examples/PACKAGES/pod/Ta/Ta_coeff.pod new file mode 120000 index 0000000000..ddf9c1426d --- /dev/null +++ b/examples/PACKAGES/pod/Ta/Ta_coeff.pod @@ -0,0 +1 @@ +../../../../potentials/Ta_coeff.pod \ No newline at end of file diff --git a/examples/PACKAGES/pod/Ta/Ta_coefficients.pod b/examples/PACKAGES/pod/Ta/Ta_coefficients.pod new file mode 100644 index 0000000000..c8943bb889 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/Ta_coefficients.pod @@ -0,0 +1,33 @@ +POD_coefficients: 32 +-4.44242 +4.10219 +-2.36987 +-3.92184 +0.83796 +-0.79457 +0.26230 +-21.24294 +-15.38460 +-38.44056 +8.29872 +-42.54514 +2.79976 +3.76109 +5.23499 +0.04878 +2.96006 +0.09101 +-0.19257 +-0.24326 +-0.16735 +0.53738 +0.02236 +-0.00154 +0.02488 +-0.00565 +0.07672 +-0.05894 +-0.05604 +-0.12664 +0.11723 +0.00262 diff --git a/examples/PACKAGES/pod/Ta/Ta_data.pod b/examples/PACKAGES/pod/Ta/Ta_data.pod new file mode 100644 index 0000000000..0933f3e79a --- /dev/null +++ b/examples/PACKAGES/pod/Ta/Ta_data.pod @@ -0,0 +1,20 @@ +file_format extxyz +file_extension xyz + +path_to_training_data_set "XYZ" +path_to_test_data_set "XYZ" + +fitting_weight_energy 100.0 +fitting_weight_force 1.0 +fitting_regularization_parameter 1e-10 + +error_analysis_for_training_data_set 1 +error_analysis_for_test_data_set 0 + +# Add the following basename to the name of output files +basename_for_output_files Ta + +# number of digits after the decimal point for pod coefficients +precision_for_pod_coefficients 5 + + diff --git a/examples/PACKAGES/pod/Ta/Ta_param.pod b/examples/PACKAGES/pod/Ta/Ta_param.pod new file mode 100644 index 0000000000..00c01b01a6 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/Ta_param.pod @@ -0,0 +1,32 @@ +# DATE: 2022-11-30 UNITS: metal CONTRIBUTOR: Ngoc Cuong Nguyen, exapde@gmail.com CITATION: https://arxiv.org/abs/2209.02362 +# chemical element symbols +species Ta + +# periodic boundary conditions +pbc 1 1 1 + +# inner cut-off radius +rin 1.0 + +# outer cut-off radius +rcut 5.0 + +# polynomial degrees for radial basis functions +bessel_polynomial_degree 3 +inverse_polynomial_degree 6 + +# one-body potential +onebody 1 + +# two-body linear POD potential +twobody_number_radial_basis_functions 6 + +# three-body linear POD potential +threebody_number_radial_basis_functions 5 +threebody_number_angular_basis_functions 5 + +# four-body linear SNAP potential +fourbody_snap_twojmax 0 + +# quadratic POD potential +quadratic_pod_potential 0 diff --git a/examples/PACKAGES/pod/Ta/Ta_training_analysis.pod b/examples/PACKAGES/pod/Ta/Ta_training_analysis.pod new file mode 100644 index 0000000000..d5bbec1cb8 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/Ta_training_analysis.pod @@ -0,0 +1,387 @@ +# Displaced_A15.xyz + config # atoms energy DFT energy energy error force DFT force force error + 1 64 -753.4412087 -754.220443 0.01217553565 7.734608752 8.398670477 0.1147177501 + 2 64 -752.99206 -753.865255 0.01364367179 8.845831302 9.134430545 0.128875643 + 3 64 -753.3230789 -754.0221 0.01092220404 8.320493902 9.017261102 0.1155421197 + 4 64 -753.5972757 -754.279613 0.01066151964 7.709417685 8.381725092 0.1058659753 + 5 64 -753.0554721 -753.777209 0.01127713895 8.89827564 9.478314477 0.1191609049 + 6 64 -753.3515905 -754.048643 0.01089144564 7.808950564 8.465317938 0.1128142237 + 7 64 -753.6515992 -754.317603 0.01040630929 7.441773668 8.127690491 0.1024025645 + 8 64 -753.3305668 -753.969161 0.009978033993 8.524333384 9.425464952 0.1066300011 + 9 64 -753.3982699 -754.141988 0.01162059587 8.165654685 8.821346913 0.1141641875 +# Displaced_BCC.xyz + config # atoms energy DFT energy energy error force DFT force force error + 10 54 -631.72742 -631.019667 0.01310653789 15.42892812 16.625876 0.264811012 + 11 54 -632.2725892 -631.719595 0.01024063328 14.51788198 15.58666626 0.2236637006 + 12 54 -631.9431698 -631.386255 0.01031323642 15.21539049 15.92378883 0.2259171686 + 13 54 -633.0728554 -632.575826 0.009204247811 13.38472946 14.55977162 0.2050161952 + 14 54 -630.8933737 -630.450212 0.008206698429 16.5539163 16.96340726 0.2366453149 + 15 54 -632.0739208 -631.669379 0.007491515673 15.23887638 16.05757315 0.2280333831 + 16 54 -632.8030856 -632.431277 0.006885343815 14.21127984 14.69810718 0.2026063598 + 17 54 -631.6814096 -630.960068 0.01335817778 14.70924474 15.99073148 0.2283605143 + 18 54 -625.0410285 -623.378198 0.03079315656 23.39224423 24.67640432 0.3504654115 +# Displaced_FCC.xyz + config # atoms energy DFT energy energy error force DFT force force error + 19 48 -555.9696753 -555.899463 0.001462755232 6.079460735 6.084617063 0.07083484607 + 20 48 -555.9506355 -555.922478 0.0005866147697 6.28112122 6.297071211 0.09285822038 + 21 48 -555.8344979 -555.800269 0.0007131011841 6.153574445 6.021098636 0.08137696888 + 22 48 -556.2639568 -556.196151 0.001412620461 5.066504178 5.127955094 0.08649299664 + 23 48 -555.6269121 -555.488929 0.002874647697 6.848109842 7.050223459 0.08116202322 + 24 48 -556.1089332 -556.027926 0.001687649405 5.662035842 5.611881174 0.07953916327 + 25 48 -556.0580873 -555.968399 0.001868505799 5.879931332 5.979217189 0.07470196866 + 26 48 -556.0083267 -556.047132 0.0008084440258 5.752828608 5.544452585 0.08224848502 + 27 48 -555.82441 -555.747848 0.001595040721 6.367423657 6.47892568 0.09497869851 +# Elastic_BCC.xyz + config # atoms energy DFT energy energy error force DFT force force error + 28 2 -23.68353253 -23.689367 0.002917237243 0.0006486347527 0.0006222748589 7.696560647e-06 + 29 2 -23.68281295 -23.689888 0.003537526523 0.0006442481331 0.0006166052222 7.353613433e-06 + 30 2 -23.68293438 -23.689996 0.00353080996 0.0009115876426 0.0008810425642 1.183334558e-05 + 31 2 -23.68108003 -23.690957 0.004938485589 1.044193546e-06 0 4.166083011e-07 + 32 2 -23.67919793 -23.690521 0.005661535829 0.0006261455712 0.0005982273815 7.573309962e-06 + 33 2 -23.67785535 -23.69038 0.006262326378 0.0006219476538 0.0005925723585 8.098703345e-06 + 34 2 -23.68415292 -23.689202 0.00252453823 0.0006520193214 0.0006279363025 7.128171198e-06 + 35 2 -23.68169552 -23.690482 0.004393238412 0.0009021557258 0.0008640138888 1.329061297e-05 + 36 2 -23.68301023 -23.689902 0.003445886213 0.0006432418939 0.0006152154094 8.589463686e-06 + 37 2 -23.68063814 -23.690563 0.004962429905 0.0006318669831 0.0006038725031 7.463726891e-06 + 38 2 -23.68337588 -23.690207 0.003415557958 0.001118071502 0.00107369735 1.811741272e-05 + 39 2 -23.68369233 -23.689285 0.00279633424 0.0009215683923 0.000890013483 1.127366011e-05 + 40 2 -23.68344234 -23.689768 0.003162828655 0.001120158205 0.001080249045 1.630224161e-05 + 41 2 -23.68224173 -23.68968 0.003719136062 0.0009070521506 0.0008680034562 1.339908745e-05 + 42 2 -23.68259685 -23.690074 0.003738573623 0.00143649564 0.001373818765 2.432187597e-05 + 43 2 -23.68469428 -23.688108 0.001706858485 0.0006587619148 0.0006336134468 7.932733886e-06 + 44 2 -23.68405177 -23.689241 0.002594615211 0.0009223784492 0.0008880101351 1.189350098e-05 + 45 2 -23.68384626 -23.68952 0.002836868987 0.0009181252225 0.0008860011287 1.116431522e-05 + 46 2 -23.68524763 -23.686278 0.0005151850612 0.0006668258323 0.0006406777661 8.585622872e-06 + 47 2 -23.67629396 -23.690097 0.006901518594 0.0008737523828 0.0008410160522 1.125104926e-05 + 48 2 -23.67835169 -23.690811 0.006229654604 0.0008814028122 0.0008500070588 1.103963422e-05 + 49 2 -23.67981574 -23.690266 0.005225130991 0.001091936388 0.001044322747 1.944706281e-05 + 50 2 -23.68209703 -23.690597 0.004249983197 0.001105769275 0.001050833003 2.242828166e-05 + 51 2 -23.68050418 -23.690673 0.005084408246 0.000631172526 0.0006038907186 7.85857762e-06 + 52 2 -23.68185505 -23.690551 0.00434797299 0.0009022813915 0.0008590064028 1.486707593e-05 + 53 2 -23.68191508 -23.690693 0.004388958442 0.0009013677777 0.0008590110593 1.516503239e-05 + 54 2 -23.68097184 -23.69021 0.004619081961 0.0009000307855 0.0008730051546 9.670733045e-06 + 55 2 -23.68426495 -23.688943 0.002339025274 0.0009232115961 0.0008800306813 1.619629586e-05 + 56 2 -23.67842316 -23.690136 0.00585641942 0.0006239138245 0.000593996633 8.394193459e-06 + 57 2 -23.6849427 -23.687444 0.001250651312 0.0009347957747 0.000903059245 1.290489522e-05 + 58 2 -23.6836322 -23.689801 0.003084401813 0.0009160470298 0.0008740011442 1.424271291e-05 + 59 2 -23.6814842 -23.690408 0.00446190038 8.690218922e-07 0 3.245696982e-07 + 60 2 -23.68115817 -23.690362 0.004601914896 0.0006345480975 0.0006067503605 9.377221837e-06 + 61 2 -23.67229452 -23.688881 0.008293240443 0.0008566684404 0.0008250054545 1.108928728e-05 + 62 2 -23.6791352 -23.690515 0.005689901939 0.001534883496 0.001475779794 2.12469595e-05 + 63 2 -23.67786743 -23.690551 0.006341785918 0.0006228264143 0.0005996599036 7.295416678e-06 + 64 2 -23.68316372 -23.689487 0.003161641446 0.0006469755816 0.0006194384554 7.530154689e-06 + 65 2 -23.6834063 -23.68986 0.003226849907 0.0009142334935 0.0008860124153 1.052672488e-05 + 66 2 -23.68377813 -23.689288 0.002754934411 0.00145229412 0.001396479144 1.7028268e-05 + 67 2 -23.67700773 -23.690457 0.006724637324 0.0006187196638 0.0005939831647 7.080762894e-06 + 68 2 -23.67552804 -23.689792 0.007131981721 0.0008698720997 0.0008340587509 1.418233126e-05 + 69 2 -23.67583966 -23.690006 0.007083167889 0.0006146073806 0.0005897694465 8.070657469e-06 + 70 2 -23.6777397 -23.690571 0.006415648131 0.0006207500925 0.0005939781141 7.401996527e-06 + 71 2 -23.68270064 -23.690213 0.003756180649 0.001112284016 0.001084315452 1.142137177e-05 + 72 2 -23.67870666 -23.690617 0.005955171449 0.0006250314539 0.0006024682564 6.623275773e-06 + 73 2 -23.68231586 -23.689761 0.00372256923 0.0009095463313 0.0008790688255 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-46.43668282 -46.426557 0.00253145389 0.0007326220467 0.001359624213 0.0001251472548 + 213 4 -46.44485583 -46.434009 0.002711707903 0.000870647096 0.001391131194 0.0001541542453 + 214 4 -46.44732696 -46.436262 0.002766239028 0.001116549362 0.002503347159 0.0003211377445 + 215 4 -46.44414241 -46.434505 0.002409352177 0.0008685662223 0.001041637173 4.942106462e-05 + 216 4 -46.45095913 -46.438768 0.003047783488 0.0008482298138 0.001098285027 8.657909629e-05 + 217 4 -46.45111242 -46.440254 0.002714605501 0.0004892442432 0.0006069892915 5.824568303e-05 + 218 4 -46.43463407 -46.42286 0.002943517186 0.0004976409931 0.0007365242698 7.564906264e-05 + 219 4 -46.42611144 -46.418078 0.002008360417 0.001053243552 0.002028412187 0.0002473380313 + 220 4 -46.45344976 -46.440513 0.003234189608 0.0007024129954 0.001158189967 0.0001371889048 + 221 4 -46.41584187 -46.409824 0.001504467167 0.0007558580012 0.001759573812 0.0002386003087 + 222 4 -46.45494987 -46.440329 0.003655216631 0.0005034620022 0.0009534044263 0.0001064495091 + 223 4 -46.45000759 -46.43773 0.003069396495 0.0006831478015 0.000926180328 7.390298375e-05 + 224 4 -46.42538863 -46.416525 0.002215907169 0.0005605993692 0.0007573664899 5.946405938e-05 + 225 4 -46.45386072 -46.440293 0.003391930454 0.0006980795454 0.0007725386722 1.864508071e-05 + 226 4 -46.4527969 -46.43839 0.003601726069 0.0005103417187 0.0005612022808 1.656002337e-05 + 227 4 -46.45374294 -46.438916 0.00370673382 0.0006956794369 0.001650878554 0.0002154167998 +# GSF_110.xyz + config # atoms energy DFT energy energy error force DFT force force error + 228 24 -278.7403996 -279.068761 0.01368172569 2.282668754 1.756353161 0.04745635589 + 229 24 -279.902595 -279.784296 0.004929123883 0.9479314831 0.9057668891 0.02403120774 + 230 24 -279.9942014 -279.901657 0.003856015841 0.2795933118 0.001565946359 0.01120665859 + 231 24 -279.6335344 -279.584238 0.002054016532 1.573004204 1.035572248 0.05514377891 + 232 24 -279.9025974 -279.784283 0.004929767703 0.947921084 0.9056396189 0.02406018404 + 233 24 -279.1817177 -279.302158 0.005018345952 2.388096516 1.771965137 0.06275542538 + 234 24 -279.5900705 -279.55564 0.001434605813 1.950503627 1.405626506 0.05370441115 + 235 24 -279.0106063 -279.246939 0.00984719392 1.577003357 0.4813964151 0.08190583543 + 236 24 -279.1817217 -279.302157 0.005018138375 2.388094324 1.771953347 0.06275588675 + 237 24 -279.0107548 -279.246935 0.009840841347 1.576191869 0.4809484798 0.0819682416 + 238 24 -279.9941671 -279.896025 0.004089255845 0.2809227604 0.01060549839 0.01118927817 + 239 24 -279.6337951 -279.584237 0.002064919631 1.571895405 1.035836121 0.05510997377 + 240 24 -278.8616595 -279.124427 0.0109486445 2.383512182 1.809545887 0.06232801199 + 241 24 -279.2927133 -279.379366 0.003610531084 1.779238829 0.8982692706 0.07658702105 + 242 24 -279.292656 -279.37937 0.003613082676 1.779203263 0.898081355 0.0765940488 + 243 24 -278.8616573 -279.124427 0.01094873842 2.383511745 1.809523374 0.06232387507 + 244 24 -279.9942014 -279.901657 0.003856015842 0.27959331 0.001570374478 0.01120603916 + 245 24 -279.9072278 -279.79264 0.004774491325 0.8361247356 0.8392614852 0.02418251879 + 246 24 -279.9941671 -279.896025 0.004089255843 0.2809227622 0.01060243293 0.01118973247 + 247 24 -278.8973689 -279.206496 0.01288029691 1.390234609 0.005326518563 0.06648378416 + 248 24 -279.590075 -279.55564 0.001434791018 1.950495712 1.4056319 0.05370353355 + 249 24 -279.9072386 -279.79264 0.004774943229 0.8361385582 0.8392625708 0.02418484015 +# GSF_112.xyz + config # atoms energy DFT energy energy error force DFT force force error + 250 30 -345.1428414 -345.175835 0.001099787279 2.717783384 1.057395322 0.1393371019 + 251 30 -346.8213325 -346.361714 0.01532061701 1.6320981 1.220284939 0.1010819808 + 252 30 -346.3061373 -345.795524 0.01702044399 2.435031121 2.112860875 0.1171529224 + 253 30 -344.8834516 -345.164602 0.009371679669 3.314987489 1.765832199 0.1576958872 + 254 30 -346.9668291 -346.593523 0.01244353764 1.327935537 0.01148867129 0.08670065177 + 255 30 -346.7938009 -346.396186 0.01325383111 1.743989434 0.9954683928 0.09783463277 + 256 30 -345.0939055 -345.319406 0.007516682785 3.756566851 1.772040852 0.1806000978 + 257 30 -345.6468551 -345.594794 0.00173536844 3.432645857 1.516014157 0.1670589876 + 258 30 -346.2843474 -345.98566 0.00995624537 2.709563559 1.406252265 0.1356658489 + 259 30 -345.7058793 -345.383994 0.01072951129 2.464665654 0.963574308 0.13389942 + 260 30 -346.9664564 -346.582564 0.01279641284 1.32870642 0.0126740587 0.08670344939 + 261 30 -345.3305431 -345.452139 0.004053195139 4.515828739 2.787719406 0.1519418929 + 262 30 -346.966836 -346.593523 0.01244376534 1.327919807 0.01148834 0.08669988209 + 263 30 -345.5935851 -345.281949 0.01038786965 2.922665543 1.873142686 0.1300383724 + 264 30 -346.157169 -345.928661 0.007616932828 3.42803556 2.100874472 0.1330089569 + 265 30 -344.6836135 -345.111657 0.01426811685 4.87813643 3.358068319 0.1517605655 + 266 30 -346.8140968 -346.367123 0.01489912587 1.700448289 1.335797131 0.1014030448 + 267 30 -346.9664062 -346.582565 0.0127947081 1.328695393 0.01254743735 0.08670444025 + 268 30 -344.5284456 -344.91356 0.012837147 4.30679737 3.441834403 0.1293440404 + 269 30 -346.3471173 -345.836703 0.01701381162 2.177883948 1.608769148 0.1178087924 + 270 30 -344.9135302 -344.984307 0.002359225817 3.517317775 2.542628782 0.122092966 + 271 30 -346.7846048 -346.393931 0.01302245877 1.941770224 1.211680725 0.09898842713 +# Liquid.xyz + config # atoms energy DFT energy energy error force DFT force force error + 272 100 -1104.74829 -1105.601723 0.008534329546 31.13590643 31.39853886 0.5826598142 + 273 100 -1099.007356 -1099.673012 0.006656557481 34.30763539 32.03167218 0.6355970492 + 274 100 -1123.744375 -1121.31506 0.0242931528 23.69463257 20.81076453 0.4843518851 +# Surface.xyz + config # atoms energy DFT energy energy error force DFT force force error + 275 24 -279.9941674 -279.911828 0.003430809358 0.2809230273 0.002753093533 0.01155715982 + 276 48 -551.0953781 -555.359452 0.08883487284 6.541312712 0.003020630398 0.1949601982 + 277 40 -458.209131 -459.216162 0.02517577443 5.605061426 5.0461364 0.1098503638 + 278 40 -459.8554229 -461.144076 0.03221632783 2.691145822 0.005582740008 0.08174930001 + 279 24 -279.8970746 -279.635146 0.01091369091 1.238573481 1.288799837 0.008644383713 + 280 30 -346.9668295 -346.592525 0.01247681774 1.32793475 0.008446203407 0.08664452133 + 281 30 -345.8871537 -345.744506 0.004754921864 3.992236552 3.124961367 0.08594721633 +# Volume_A15.xyz + config # atoms energy DFT energy energy error force DFT force force error + 282 8 -66.46788051 -66.990732 0.06535643627 9.752469663e-15 0 1.665479097e-15 + 283 8 -72.67646146 -72.957807 0.03516819273 2.586146435e-14 0 4.592824963e-15 + 284 8 -94.20621366 -94.145745 0.00755858243 1.888003685e-14 0 2.536262854e-15 + 285 8 -94.43981933 -94.554682 0.01435783313 5.386472433e-15 0 7.930900378e-16 + 286 8 -79.39814886 -79.438363 0.005026767697 2.732255702e-14 0 4.777139332e-15 + 287 8 -69.38946962 -69.627817 0.02979342197 4.097415198e-15 0 6.093939011e-16 + 288 8 -83.05531805 -82.604907 0.05630138147 5.707505975e-15 0 9.444123724e-16 + 289 8 14.36690687 14.89048 0.0654466408 4.4225873e-14 0 6.966360359e-15 + 290 8 -94.13472519 -94.367599 0.02910922586 1.366361161e-14 0 1.887762444e-15 + 291 8 -89.38757156 -89.248227 0.01741807051 7.77370779e-15 0 1.130389185e-15 + 292 8 -87.49741165 -87.211997 0.03567683079 6.822093797e-15 0 9.11308066e-16 + 293 8 -93.42285179 -93.66897 0.03076477666 2.411445427e-15 0 4.058488494e-16 + 294 8 -8.05187323 -7.989166 0.007838403786 7.012640574e-14 0 1.102472786e-14 + 295 8 -85.3779751 -84.982834 0.04939263793 2.716993442e-15 0 4.647613313e-16 + 296 8 -92.37490481 -92.536373 0.0201835236 1.315958485e-14 0 1.882608652e-15 + 297 8 -26.56925158 -26.77612 0.02585855302 5.079538464e-14 0 8.697279448e-15 + 298 8 -77.90929192 -77.544107 0.04564811452 4.172342826e-15 0 7.131159089e-16 + 299 8 -80.55632181 -80.114217 0.05526310126 7.985686614e-15 0 1.195874996e-15 + 300 8 -41.83202596 -42.143041 0.03887688062 4.657987766e-14 0 8.540891409e-15 + 301 8 -91.02235339 -91.040671 0.002289700674 5.29233855e-15 0 8.086702604e-16 + 302 8 -84.76781055 -84.499231 0.03357244376 3.520461367e-14 0 6.70250169e-15 + 303 8 -60.71236154 -61.825173 0.1391014324 7.011275997e-15 0 1.104512893e-15 + 304 8 -91.5794594 -91.156873 0.05282330009 3.722647197e-15 0 6.096739866e-16 + 305 8 -54.28408457 -54.658744 0.04683242815 1.027218023e-13 0 1.699815447e-14 + 306 8 -72.29317827 -72.277255 0.00199040924 2.147214247e-15 0 3.631173776e-16 + 307 8 -75.14428628 -74.923334 0.02761903549 4.875315485e-15 0 8.058016421e-16 + 308 8 -64.41647714 -64.798066 0.04769860741 8.515566542e-15 0 1.300175245e-15 + 309 8 -93.29905733 -93.048342 0.03133941583 1.392455458e-14 0 1.75636545e-15 + 310 8 -63.56375833 -64.38702 0.1029077093 3.169925692e-15 0 4.425351867e-16 + 311 8 -88.81067445 -88.352871 0.05722543104 1.824573667e-14 0 3.223116218e-15 +# Volume_BCC.xyz + config # atoms energy DFT energy energy error force DFT force force error + 312 2 -16.38936242 -16.763625 0.1871312901 8.438105833e-16 0 3.261280135e-16 + 313 2 16.19675433 16.314145 0.05869533665 6.012211515e-14 0 2.140301825e-14 + 314 2 -21.24238574 -21.209071 0.01665736942 3.105315998e-15 0 1.031580172e-15 + 315 2 -15.80560502 -15.780524 0.01254051028 3.075772419e-14 0 1.04682611e-14 + 316 2 -19.05526774 -19.002205 0.02653137193 5.049484454e-15 0 1.840167643e-15 + 317 2 -22.67434567 -22.620568 0.02688883674 8.42211374e-16 0 2.844946501e-16 + 318 2 4.04311049 4.096885 0.02688725502 1.697721462e-14 0 5.111651843e-15 + 319 2 56.2105911 56.26276 0.02608445186 2.167345189e-13 0 8.162180947e-14 + 320 2 -22.55797904 -22.585113 0.01356697915 1.62710774e-15 0 5.666763355e-16 + 321 2 -21.75972417 -21.795501 0.0178884163 1.403784713e-15 0 3.978299172e-16 + 322 2 33.30678917 33.110078 0.09835558332 4.389819223e-14 0 1.229051583e-14 + 323 2 -20.82125169 -20.885998 0.0323731563 1.078546098e-15 0 2.960594732e-16 + 324 2 -23.55239721 -23.601336 0.02446939304 1.098352585e-15 0 3.53350523e-16 + 325 2 -23.17147126 -23.207313 0.01792086946 1.690886327e-15 0 6.164070796e-16 + 326 2 -19.78146338 -19.898089 0.05831281177 3.071791199e-15 0 1.188863822e-15 + 327 2 -23.45038238 -23.405474 0.02245418985 1.35097431e-15 0 4.949744318e-16 + 328 2 -4.653232293 -4.781324 0.06404585371 8.217105136e-15 0 2.951342874e-15 + 329 2 -18.67517238 -18.864936 0.09488180756 5.14040454e-16 0 1.896631e-16 + 330 2 -17.53439276 -17.813086 0.1393466189 6.912475817e-16 0 2.521131452e-16 + 331 2 -11.04889659 -11.197201 0.07415220345 1.082601284e-14 0 4.046820749e-15 + 332 2 -23.68489671 -23.696705 0.00590414498 1.843452652e-15 0 5.315481851e-16 +# Volume_FCC.xyz + config # atoms energy DFT energy energy error force DFT force force error + 333 4 -19.13390887 -19.075994 0.01447871809 1.517335469e-14 0 3.900232098e-15 + 334 4 -35.26038882 -34.873619 0.0966924543 3.754176171e-16 0 8.829019691e-17 + 335 4 -43.93272346 -43.950003 0.004319884817 1.957527644e-15 0 4.836987292e-16 + 336 4 -41.03733831 -40.991909 0.01135732773 2.229474894e-15 0 5.093220406e-16 + 337 4 -43.4228254 -43.453929 0.00777589967 2.787997321e-14 0 8.011425939e-15 + 338 4 -42.67289278 -42.686077 0.003296054 9.84568285e-16 0 2.229119667e-16 + 339 4 -33.58842759 -33.224653 0.09094364633 5.773580884e-16 0 1.303933813e-16 + 340 4 -27.01189372 -26.862709 0.03729618105 5.151726288e-15 0 1.109453787e-15 + 341 4 -25.59030438 -25.519883 0.01760534598 2.863765244e-16 0 7.531591092e-17 + 342 4 3.441093749 3.463071 0.005494312716 2.696629063e-14 0 6.828072631e-15 + 343 4 -31.9073245 -31.59595 0.07784362479 8.890859753e-16 0 1.682681772e-16 + 344 4 -45.06068744 -45.100466 0.009944641012 1.71159984e-15 0 3.996665291e-16 + 345 4 -46.03981427 -46.052258 0.0031109323 1.705627547e-15 0 4.273202162e-16 + 346 4 -30.24326213 -30.001189 0.06051828302 8.403226845e-16 0 2.104797818e-16 + 347 4 -22.957351 -22.8504 0.02673775024 6.125121657e-16 0 1.416690839e-16 + 348 4 -9.130654755 -9.164691 0.008509061334 1.894766019e-14 0 4.742914684e-15 + 349 4 -24.21746226 -24.150343 0.01677981454 1.777054657e-16 0 4.452456922e-17 + 350 4 -46.44761241 -46.426795 0.005204351765 2.043289244e-15 0 5.31981866e-16 + 351 4 -28.62111495 -28.451145 0.04249248833 8.802221276e-15 0 2.537755885e-15 + 352 4 40.31615798 40.341566 0.006352005141 2.120221165e-14 0 5.59689556e-15 + 353 4 19.51151427 19.617912 0.02659943252 6.461385682e-14 0 1.647388493e-14 + 354 4 -27.06356399 -26.954384 0.02729499736 3.089999778e-16 0 7.849623729e-17 + 355 4 -46.3678929 -46.323696 0.01104922394 2.195905041e-15 0 5.105869431e-16 + 356 4 -45.87221055 -45.828947 0.01081588677 1.843344298e-15 0 4.174901166e-16 + 357 4 -38.47076405 -38.16029 0.0776185126 2.683812325e-15 0 6.998163623e-16 + 358 4 -33.06813795 -32.919741 0.03709923634 1.577584492e-14 0 4.412991963e-15 + 359 4 -41.34431995 -41.272675 0.01791123821 2.234618078e-15 0 5.98499928e-16 + 360 4 -39.95757678 -39.753322 0.05106369446 1.172665551e-15 0 2.900618248e-16 + 361 4 -37.66252943 -37.547435 0.02877360828 6.430065721e-15 0 1.652468671e-15 + 362 4 -36.89659259 -36.52595 0.09266064636 3.213653781e-15 0 8.769027171e-16 + 363 4 -45.03250721 -45.016087 0.004105053074 1.112789617e-15 0 2.434395278e-16 diff --git a/examples/PACKAGES/pod/Ta/Ta_training_errors.pod b/examples/PACKAGES/pod/Ta/Ta_training_errors.pod new file mode 100644 index 0000000000..39b7af3723 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/Ta_training_errors.pod @@ -0,0 +1,20 @@ +**************** Begin of Error Analysis for the Training Data Set **************** +--------------------------------------------------------------------------------------------------- + File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force +--------------------------------------------------------------------------------------------------- +Displaced_A15.xyz 9 576 0.011286 0.011334 0.113353 0.141650 +Displaced_BCC.xyz 9 486 0.012178 0.014005 0.240613 0.312191 +Displaced_FCC.xyz 9 432 0.001445 0.001591 0.082688 0.103800 +Elastic_BCC.xyz 100 200 0.004452 0.004783 0.000010 0.000013 +Elastic_FCC.xyz 100 400 0.002865 0.002923 0.000146 0.000207 +GSF_110.xyz 22 528 0.005804 0.006853 0.047276 0.097819 +GSF_112.xyz 22 660 0.010588 0.011555 0.123342 0.191090 +Liquid.xyz 3 300 0.013161 0.015355 0.567536 0.757847 +Surface.xyz 7 236 0.025400 0.037555 0.096121 0.295623 +Volume_A15.xyz 30 240 0.039281 0.048678 0.000000 0.000000 +Volume_BCC.xyz 21 42 0.049766 0.067554 0.000000 0.000000 +Volume_FCC.xyz 31 124 0.030056 0.041738 0.000000 0.000000 +--------------------------------------------------------------------------------------------------- +All files 363 4224 0.012917 0.025797 0.122473 0.260052 +--------------------------------------------------------------------------------------------------- +**************** End of Error Analysis for the Training Data Set **************** diff --git a/examples/PACKAGES/pod/Ta/XYZ/Displaced_A15.xyz b/examples/PACKAGES/pod/Ta/XYZ/Displaced_A15.xyz new file mode 100644 index 0000000000..b144703144 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/XYZ/Displaced_A15.xyz @@ -0,0 +1,594 @@ +64 +Lattice="10.6000003815 0.0 0.0 0.0 10.6000003815 0.0 0.0 0.0 10.6000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-754.220443 stress="23963.03 -518.08 331.99 -518.08 26158.899999999998 289.93 331.99 289.93 26014.94" +Ta 10.54497 10.54551 10.5956 0.738379 0.48581 0.018519 +Ta 2.6058 2.59577 2.66276 0.983004 0.695353 -0.423917 +Ta 1.29338 2.62737 0.06659 0.967488 0.116743 -0.589823 +Ta 3.97859 2.60074 0.05226 -0.084389 0.137046 -0.423367 +Ta 0.06826 1.26322 2.67108 -0.470328 1.296441 -0.423078 +Ta 0.03489 4.006 2.58088 -0.263493 -1.182047 0.521328 +Ta 2.60404 0.03209 1.27573 0.332524 -0.382338 0.466834 +Ta 2.61384 0.03978 4.00017 0.19652 -0.552756 -0.617059 +Ta 5.26731 10.53909 0.0525 0.340753 0.932737 -1.082711 +Ta 8.00375 2.64902 2.69207 -0.352834 -0.034069 -0.546853 +Ta 6.64426 2.6613 10.54 0.209447 -0.170553 0.255905 +Ta 9.33824 2.64457 0.03106 -1.248523 0.1324 -0.277314 +Ta 5.3522 1.2665 2.5671 -0.296298 1.327488 0.591352 +Ta 5.27655 4.04903 2.65011 0.225842 -1.705193 -0.220596 +Ta 7.9997 10.54384 1.3323 -0.602859 0.598417 0.360383 +Ta 7.97961 10.59814 4.02363 -0.487819 0.018537 -0.681676 +Ta 0.07703 5.36114 0.02699 -0.850702 -0.481463 -0.618219 +Ta 2.6646 7.93725 2.60955 -0.375888 0.3131 0.609637 +Ta 1.40379 7.96668 10.52251 -1.425719 -0.081346 0.714056 +Ta 3.99035 7.99423 10.59771 -0.152265 -0.539619 0.318009 +Ta 0.04355 6.56889 2.62727 -0.178473 1.482119 0.427439 +Ta 0.00703 9.28757 2.68364 0.269104 -1.208309 -0.327712 +Ta 2.56957 5.34141 1.33893 0.850349 -0.517951 0.275559 +Ta 2.72447 5.25375 4.04037 -0.588363 0.226576 -0.96233 +Ta 10.53684 10.5759 5.2221 0.629328 0.101208 1.170955 +Ta 2.66913 2.7096 7.94723 0.175608 -0.725726 0.018084 +Ta 1.35438 2.68364 5.23358 -0.672848 -0.376194 0.690747 +Ta 3.92914 2.57652 5.21831 1.314233 0.49323 0.453261 +Ta 0.08152 1.31737 7.90103 -0.403463 -0.248525 0.230807 +Ta 0.01596 3.94268 7.99393 -0.081478 0.863863 -0.071733 +Ta 2.6785 10.52779 6.63557 -0.387653 0.744336 -0.69563 +Ta 2.57563 10.5398 9.20066 0.204661 1.016501 1.272453 +Ta 5.28026 5.2908 10.53874 0.210489 -0.369673 0.610136 +Ta 8.02116 8.00301 2.56791 -0.618631 -0.801014 1.16881 +Ta 6.56126 7.9104 0.04457 1.247918 -0.045758 -0.325354 +Ta 9.26485 7.95508 10.58594 0.342738 -0.215167 -0.069832 +Ta 5.26103 6.62842 2.63265 0.441032 0.314676 -0.03073 +Ta 5.28955 9.23968 2.5673 0.215784 0.14419 0.976532 +Ta 8.00221 5.33276 1.34132 -0.277749 -0.258368 -0.418189 +Ta 7.91864 5.28423 3.97891 0.132647 0.303744 -0.143621 +Ta 5.27037 0.01177 5.31967 0.293403 0.10204 -0.586267 +Ta 7.97577 2.58846 7.90284 -0.0766 0.318418 0.741565 +Ta 6.67111 2.70945 5.31433 -1.193866 -0.235149 -0.180348 +Ta 9.29025 2.58105 5.29066 0.286858 0.294859 0.204099 +Ta 5.2532 1.26795 7.91799 0.289819 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6.62358 0.295654 0.152651 -0.023568 +Ta 8.00072 5.28621 9.26356 -0.210447 -0.178269 0.331507 +64 +Lattice = "10.6000003815 0.0 0.0 0.0 10.6000003815 0.0 0.0 0.0 10.6000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-753.865255 stress="25885.719999999998 -817.02 -36.62 -817.02 23024.370000000003 -107.14 -36.62 -107.14 29257.940000000002" +Ta 0.04908 0.00115 10.57826 -0.437757 -0.090743 0.15803 +Ta 2.61654 2.71455 2.72901 0.449605 -0.435267 -0.828991 +Ta 1.39595 2.61446 10.52477 -2.072616 -0.051825 0.877711 +Ta 3.90381 2.6756 0.06766 2.144694 -0.090086 0.075882 +Ta 0.05742 1.31249 2.58872 -0.607352 0.532786 0.378598 +Ta 0.05697 4.05163 2.67585 -0.777264 -1.885963 -0.048956 +Ta 2.58852 10.55529 1.39238 0.39704 0.642203 -1.068312 +Ta 2.6599 0.00552 4.01733 0.064098 0.179003 -0.177005 +Ta 5.26427 10.58342 10.56227 -0.033574 0.346172 0.680676 +Ta 7.89236 2.6016 2.71779 0.82825 0.497825 -0.656618 +Ta 6.6321 2.63976 10.53024 -0.906833 -0.010611 0.365963 +Ta 9.21243 2.59505 0.06665 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7.9791 10.56722 9.28911 -0.274024 0.193096 0.130562 +Ta 0.08155 5.37803 5.24262 -1.153238 -0.394578 0.405264 +Ta 2.69772 8.006 7.99419 -0.445287 -0.699603 -0.114074 +Ta 1.38725 7.96453 5.37281 -1.117986 -0.159911 -0.252436 +Ta 3.9138 7.92522 5.25427 1.483723 -0.15328 0.336593 +Ta 10.54558 6.64409 7.90011 0.381189 -0.437364 0.391497 +Ta 0.0414 9.23222 7.94529 -0.069632 0.550601 0.135542 +Ta 2.6176 5.26509 6.55154 0.497368 0.356473 1.817883 +Ta 2.67779 5.27183 9.34564 -0.09738 0.356697 -2.092389 +Ta 5.37167 5.22358 5.28383 -1.082933 0.58337 0.189313 +Ta 7.97831 7.95033 7.98746 -0.334998 -0.148464 -0.752988 +Ta 6.58772 7.97118 5.22845 0.250508 -0.279802 0.963668 +Ta 9.29703 7.96398 5.22074 -0.269342 -0.065478 0.796032 +Ta 5.35894 6.66603 8.02645 -0.160453 -0.945482 -0.543903 +Ta 5.25491 9.2658 7.91135 0.540075 0.33829 0.275545 +Ta 7.86723 5.29649 6.61035 0.852005 0.19428 0.109663 +Ta 8.01927 5.21862 9.29005 -0.365475 0.483588 -0.393695 +64 +Lattice = "10.6000003815 0.0 0.0 0.0 10.6000003815 0.0 0.0 0.0 10.6000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-754.0221 stress="26594.42 1368.85 19.48 1368.85 26417.43 -1442.27 19.48 -1442.27 23937.75" +Ta 10.59872 10.5966 0.05505 -0.231571 0.031614 -0.560153 +Ta 2.72054 2.66769 2.56793 -0.779697 -0.12909 0.784258 +Ta 1.2783 2.60895 0.03547 0.744629 0.548126 -0.214124 +Ta 3.95508 2.65628 10.5551 -0.165396 0.001128 0.026529 +Ta 0.03293 1.39934 2.6967 0.072305 -0.873594 -0.208971 +Ta 10.5651 4.05678 2.65596 0.527021 -1.331302 0.031311 +Ta 2.60171 10.52714 1.285 0.350354 0.537482 0.600499 +Ta 2.68709 10.58122 3.91851 -0.372039 0.361715 0.809071 +Ta 5.31795 0.08026 0.03906 -0.106989 -0.635521 -0.720814 +Ta 8.02486 2.64122 2.59891 -0.739467 0.359337 0.641206 +Ta 6.60369 2.73118 0.06843 0.678906 -0.310297 -0.697991 +Ta 9.30745 2.57138 10.58055 -1.01243 0.693756 -0.108245 +Ta 5.35248 1.38217 2.58572 -0.13929 -0.071214 0.685498 +Ta 5.27678 4.05493 2.58839 0.361124 -1.418968 0.248615 +Ta 7.97704 10.56983 1.33943 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10.52268 0.567659 0.751713 1.05061 +Ta 7.92372 7.92335 2.69137 -0.276611 0.573618 -0.487148 +Ta 6.67129 7.91947 0.00781 -1.67251 0.193902 0.064344 +Ta 9.22152 8.02659 0.00287 0.769306 -0.25307 0.030428 +Ta 5.33288 6.56827 2.67559 -0.356132 1.879818 -0.275818 +Ta 5.21843 9.3313 2.61368 0.313957 -1.184708 0.134729 +Ta 7.93465 5.34206 1.38987 -0.27093 -0.232294 -1.254009 +Ta 7.94771 5.35777 3.99603 -0.441572 -0.509412 0.402878 +Ta 5.28258 10.54181 5.27443 0.165589 0.546578 -0.181307 +Ta 7.87019 2.58685 7.88448 0.864444 0.720171 0.90474 +Ta 6.61351 2.69961 5.33299 -0.298459 -0.117041 -0.655843 +Ta 9.20963 2.61413 5.29428 0.646321 0.352518 0.003302 +Ta 5.381 1.3824 7.94181 -1.162347 -0.755975 0.017657 +Ta 5.28467 4.01816 7.99502 0.024319 -0.640279 -0.524219 +Ta 8.00243 10.5584 6.55969 -0.64714 0.462493 1.495007 +Ta 7.92724 0.03497 9.30326 0.221614 -0.134477 -0.661187 +Ta 10.55391 5.32768 5.23195 0.476568 -0.381016 0.980462 +Ta 2.64406 7.95567 7.93345 0.001297 0.120229 0.191712 +Ta 1.2986 7.9027 5.33624 0.708615 0.289977 -0.158132 +Ta 4.04604 7.87659 5.36207 -1.974177 0.710669 -0.438506 +Ta 0.04337 6.69689 8.01066 -0.426712 -1.619512 -0.55647 +Ta 10.54014 9.26136 7.89857 0.447195 1.282555 0.234867 +Ta 2.68344 5.29148 6.55058 -0.713159 0.045261 0.661323 +Ta 2.61535 5.26646 9.22004 -0.124682 0.621019 0.504493 +Ta 5.22677 5.33996 5.32711 1.047955 -1.01859 -0.083156 +Ta 7.93781 8.02504 7.94133 -0.089305 -0.92943 0.174588 +Ta 6.58943 7.89688 5.28857 1.109411 0.43459 0.232028 +Ta 9.26138 8.02661 5.25779 -0.279333 -0.594174 0.435718 +Ta 5.27411 6.62462 8.02195 0.25952 0.675178 -0.659935 +Ta 5.30985 9.30627 7.88256 -0.174466 -0.148032 0.732729 +Ta 7.99384 5.30652 6.67382 -0.405756 0.105152 -0.448951 +Ta 7.89346 5.23521 9.29012 0.232414 0.496659 0.293761 +64 +Lattice = "10.6000003815 0.0 0.0 0.0 10.6000003815 0.0 0.0 0.0 10.6000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-754.279613 stress="23907.050000000003 444.79 -765.15 444.79 24515.940000000002 375.59 -765.15 375.59 27487.829999999998" +Ta 0.00046 10.54735 10.58932 0.114704 0.911029 0.002417 +Ta 2.73129 2.71027 2.64805 -1.312269 -0.768934 0.192601 +Ta 1.30416 2.70676 0.05081 -0.549542 -0.385376 -0.090451 +Ta 3.9224 2.56802 0.05914 1.338111 0.432571 -0.522326 +Ta 10.52754 1.32714 2.64946 0.526452 0.497736 0.118023 +Ta 10.58917 3.98207 2.62548 0.027974 -0.098405 0.015828 +Ta 2.64792 0.02452 1.38081 -0.204416 -0.141407 -1.100083 +Ta 2.59488 0.05512 3.95199 0.552837 -0.178236 0.473214 +Ta 5.22138 10.52799 0.03746 0.576453 0.970244 -0.579639 +Ta 7.88634 2.63138 2.61996 0.902337 0.559648 1.080475 +Ta 6.69452 2.7219 0.06773 -2.02583 -0.335157 -0.878841 +Ta 9.21373 2.71014 0.05862 1.514389 -0.315085 -0.524943 +Ta 5.3281 1.39418 2.60417 -0.26237 -1.230172 0.420769 +Ta 5.2637 3.95414 2.69271 0.464892 1.262082 -0.270578 +Ta 7.90795 0.06254 1.39383 0.167236 -0.202524 -1.058609 +Ta 7.94511 10.51799 3.98105 0.185425 0.426977 0.087026 +Ta 10.57577 5.37732 10.54307 0.605017 -0.422613 0.786988 +Ta 2.70528 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5.35239 -0.118786 -0.470272 -0.408554 +Ta 5.32938 1.27255 7.97134 -0.303978 0.286044 0.13783 +Ta 5.30418 3.93812 7.93568 0.040155 0.762457 0.076378 +Ta 7.95987 10.54938 6.61642 -0.218528 0.46405 0.105442 +Ta 7.87538 0.02651 9.23341 0.304713 -0.390603 0.650333 +Ta 0.01871 5.23215 5.21873 -0.275057 0.30265 1.189576 +Ta 2.58005 8.01801 8.00091 0.903103 -0.811538 -0.942974 +Ta 1.35622 7.90716 5.21911 -0.69223 0.095275 0.734107 +Ta 3.91664 8.00527 5.23273 1.355059 -0.299637 0.764864 +Ta 0.05597 6.54262 7.99991 -0.53468 1.450745 -0.817521 +Ta 0.05678 9.22328 7.97883 -0.723123 0.147795 -0.085492 +Ta 2.66025 5.35371 6.64491 0.12943 -0.14096 -0.631864 +Ta 2.64384 5.23012 9.2296 0.184014 0.70864 1.326423 +Ta 5.34418 5.35604 5.295 -0.670333 -0.337693 0.183358 +Ta 7.96554 7.96325 7.88581 0.240713 -0.060137 0.461609 +Ta 6.67445 7.93954 5.26624 -0.870954 0.115388 0.099246 +Ta 9.32253 7.94305 5.27672 -0.121051 -0.177459 -0.101598 +Ta 5.37998 6.62136 8.01604 -0.697928 -0.125018 -0.551236 +Ta 5.23732 9.22012 7.8725 0.142822 0.596726 0.634521 +Ta 7.90914 5.35867 6.63564 0.470037 -0.554497 -0.783277 +Ta 7.8945 5.29107 9.20052 0.619005 0.147575 1.411797 +64 +Lattice = "10.6000003815 0.0 0.0 0.0 10.6000003815 0.0 0.0 0.0 10.6000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-753.969161 stress="24114.940000000002 317.58 426.17 317.58 28035.48 -838.5899999999999 426.17 -838.5899999999999 25020.420000000002" +Ta 10.59947 10.59661 10.52413 -0.226907 -0.080536 0.902052 +Ta 2.59454 2.65092 2.68446 0.776819 0.171288 -0.551025 +Ta 1.33041 2.674 10.58143 0.176394 -0.183256 0.204614 +Ta 3.95295 2.58315 10.54506 0.854273 0.68598 0.610189 +Ta 10.59883 1.31774 2.66978 -0.091936 0.35913 -0.579748 +Ta 10.57967 3.96662 2.60593 0.084104 0.473431 0.095227 +Ta 2.59254 0.00678 1.31972 0.598698 0.099657 -0.823976 +Ta 2.59169 0.03133 3.90382 0.425043 -0.081448 1.419933 +Ta 5.37939 0.04023 0.07113 -1.005574 -0.469543 -0.545443 +Ta 7.94984 2.73234 2.65636 0.080843 -0.503649 -0.229292 +Ta 6.7035 2.71875 10.57105 -1.075835 -0.284081 0.217795 +Ta 9.33869 2.66536 10.5534 -0.645726 -0.07901 0.309219 +Ta 5.38144 1.37363 2.59678 -0.660687 -0.7539 0.448111 +Ta 5.27263 3.99656 2.66272 0.021249 -0.323657 0.146107 +Ta 7.96657 0.06435 1.30009 0.116005 -0.264227 0.267969 +Ta 7.99235 0.04847 3.89505 -0.241556 -0.152596 0.888561 +Ta 0.0218 5.29659 10.5698 0.190539 -0.014165 0.267054 +Ta 2.73175 8.00138 2.71285 -1.053594 -0.284418 -0.953258 +Ta 1.31806 7.96372 10.54256 -0.136246 -0.133944 0.366015 +Ta 3.91844 7.96217 10.56452 0.996651 0.062808 0.124581 +Ta 0.03602 6.66478 2.64422 0.197253 -0.463833 -0.145331 +Ta 10.5258 9.31439 2.65344 0.724814 -0.437657 -0.379722 +Ta 2.66149 5.31748 1.25965 -0.022671 0.017877 1.049002 +Ta 2.71043 5.3142 3.96356 -0.229855 -0.004722 -0.591605 +Ta 0.01714 0.02895 5.25397 -0.154714 -0.160145 0.666203 +Ta 2.64597 2.62331 8.00147 0.380032 0.718636 -0.704725 +Ta 1.34375 2.63266 5.31467 0.392862 -0.03449 -0.003614 +Ta 4.01969 2.72066 5.33483 -1.339879 -0.221236 -0.290386 +Ta 0.05334 1.28072 7.94153 -0.439149 1.033607 -0.306897 +Ta 10.56225 3.9163 7.87893 0.077647 0.175986 0.172003 +Ta 2.67491 10.58095 6.65598 -0.034472 0.357047 -1.370013 +Ta 2.61935 0.04143 9.225 0.449865 -0.403463 1.302128 +Ta 5.37858 5.37062 0.02738 -0.971327 -1.005554 -0.649326 +Ta 8.01211 7.93604 2.73 -0.650844 -0.187724 -0.927616 +Ta 6.6093 7.90613 0.06492 0.276128 0.710737 -0.478142 +Ta 9.28311 7.87808 10.53355 -0.273083 0.488493 0.413712 +Ta 5.22651 6.57935 2.58919 0.641086 0.512876 0.520235 +Ta 5.36331 9.19414 2.65024 0.022943 1.480425 0.177898 +Ta 7.9726 5.27207 1.2508 0.18907 0.389324 1.308572 +Ta 7.89187 5.26738 3.98139 0.703866 0.272666 -0.675214 +Ta 5.30786 0.02387 5.37311 -0.441452 -0.182156 -1.394336 +Ta 7.90554 2.64139 7.96721 0.778455 0.069504 -0.485925 +Ta 6.54626 2.62801 5.34703 1.838904 0.098736 -0.497372 +Ta 9.30386 2.63489 5.25676 -1.018893 -0.04522 0.187076 +Ta 5.34196 1.30641 7.91047 -0.440112 1.103483 0.738039 +Ta 5.33435 4.01755 7.93742 -0.433146 -1.463369 0.322362 +Ta 7.87923 10.59827 6.57191 0.570104 -0.011791 0.650285 +Ta 7.91667 0.07787 9.29291 0.417554 -0.726222 -0.85977 +Ta 0.00407 5.21804 5.29085 -0.306761 0.830359 -0.270748 +Ta 2.64244 8.01096 7.89122 -0.154505 -0.65194 -0.071913 +Ta 1.27073 7.96757 5.24059 1.78038 -0.289728 0.312266 +Ta 4.05652 7.94422 5.24628 -1.766243 -0.059655 0.397705 +Ta 10.55504 6.5449 8.02866 0.326135 1.292787 -0.813062 +Ta 10.54757 9.32356 7.97367 0.218025 -1.545104 -0.663048 +Ta 2.57132 5.31124 6.54943 0.638753 -0.09298 1.309355 +Ta 2.70552 5.36844 9.25923 -0.31279 -0.257789 -0.758911 +Ta 5.37917 5.32156 5.36422 -1.051024 0.088554 -0.982928 +Ta 7.96636 7.91391 7.89315 -0.365514 0.575159 0.279003 +Ta 6.60266 8.02328 5.30029 1.44818 -0.312672 -0.021217 +Ta 9.34959 7.99431 5.26212 -1.787702 -0.359966 0.327963 +Ta 5.27917 6.54337 7.93235 -0.08343 2.464228 0.472227 +Ta 5.31647 9.3383 7.99422 -0.013579 -1.711441 -0.018178 +Ta 7.90244 5.24771 6.59897 0.734729 0.047141 0.508435 +Ta 7.93795 5.34891 9.25032 0.301803 -0.342634 -0.33915 +64 +Lattice = "10.6000003815 0.0 0.0 0.0 10.6000003815 0.0 0.0 0.0 10.6000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-754.141988 stress="22301.33 -285.37 -20.8 -285.37 25600.899999999998 162.91 -20.8 162.91 28086.86" +Ta 10.53107 10.5509 0.0015 0.70485 0.845648 -0.070019 +Ta 2.70215 2.61155 2.65638 -0.286099 0.325604 -0.074327 +Ta 1.39743 2.61545 0.05847 -1.474313 -0.095142 -0.280113 +Ta 3.97713 2.68268 10.5346 0.156378 -0.098493 0.356179 +Ta 0.03222 1.38317 2.60891 -0.081506 -1.587414 0.159126 +Ta 10.56764 3.92107 2.7266 0.259373 1.331992 -0.73363 +Ta 2.59022 10.55975 1.32456 0.049236 0.371753 0.102809 +Ta 2.70858 0.00916 4.05153 -0.701193 -0.070601 -1.695173 +Ta 5.26413 10.53793 0.03804 0.195324 0.197551 -0.279303 +Ta 7.92699 2.58218 2.67357 -0.196352 0.687631 -0.299411 +Ta 6.56938 2.58335 0.00915 0.481385 0.355506 0.054864 +Ta 9.21553 2.70158 0.00339 1.079668 -0.370583 0.25622 +Ta 5.29644 1.25773 2.66315 0.219113 1.844104 -0.251113 +Ta 5.25049 4.05699 2.72857 0.405022 -1.35655 -0.365109 +Ta 7.95797 0.00795 1.26652 -0.349291 -0.012386 0.95892 +Ta 7.95876 0.0029 3.97425 -0.085176 -0.246415 0.146522 +Ta 0.00111 5.29169 0.0101 0.244936 -0.074089 0.083447 +Ta 2.62824 7.99165 2.57985 0.090964 -0.453594 0.8187 +Ta 1.27056 8.03072 0.02474 0.413629 -0.598829 -0.229027 +Ta 3.95298 7.86756 0.04116 0.152752 0.468204 -0.422925 +Ta 10.52695 6.6817 2.6853 0.300417 -1.266839 -0.375852 +Ta 0.02498 9.27815 2.68712 -0.304899 0.803536 -0.158136 +Ta 2.65962 5.24127 1.35865 -0.043804 0.363366 -0.570782 +Ta 2.68315 5.34774 4.00482 -0.286335 -0.186484 -0.056142 +Ta 10.59249 0.03152 5.33264 0.313027 -0.429223 -0.38406 +Ta 2.58832 2.58393 7.94631 0.844596 0.451826 -0.031232 +Ta 1.37297 2.61641 5.29619 -0.990905 0.328928 -0.096763 +Ta 3.95207 2.62642 5.27401 1.187182 0.414363 0.303667 +Ta 0.01362 1.29568 7.93105 -0.217583 0.454567 0.400647 +Ta 0.06717 3.99538 7.88147 -0.472589 -0.121955 0.480331 +Ta 2.72677 10.57217 6.60708 -0.58854 0.058778 0.860541 +Ta 2.713 10.58575 9.24417 -0.506506 0.039032 0.567002 +Ta 5.30308 5.35945 0.05831 -0.152176 -0.937176 -0.30934 +Ta 7.87019 7.94183 2.57359 1.036899 0.327117 1.33664 +Ta 6.65928 7.9017 0.0785 -1.124811 0.536497 -0.907975 +Ta 9.22504 7.86881 10.58464 0.924083 0.364728 -0.065373 +Ta 5.29923 6.68288 2.66667 -0.266393 -0.338893 0.356213 +Ta 5.34057 9.3156 2.71909 -0.369711 -1.091863 -0.151577 +Ta 7.9974 5.33778 1.31662 -0.337005 -0.510079 -0.103385 +Ta 8.0053 5.25623 3.92597 -0.472408 0.14717 1.386647 +Ta 5.25104 0.03317 5.26596 1.390735 -0.14389 0.946126 +Ta 7.98045 2.60832 7.99115 0.289511 0.923595 -0.088863 +Ta 6.70353 2.60779 5.33602 -1.549564 0.47403 -0.141706 +Ta 9.2746 2.58651 5.33229 0.918837 0.547058 -0.191653 +Ta 5.38008 1.39809 7.98274 -0.530078 -0.860802 -0.130916 +Ta 5.33862 3.99447 7.94033 -0.428322 -0.31397 0.179289 +Ta 7.95961 0.05884 6.68706 -0.114391 -0.600564 -1.150373 +Ta 7.95876 0.02794 9.26141 -0.363392 -0.320188 0.423549 +Ta 0.06343 5.2606 5.22321 -0.328214 0.242764 0.905362 +Ta 2.68463 7.97169 7.9776 -0.420291 -0.285961 -0.011666 +Ta 1.29864 7.91228 5.24043 0.869986 0.358854 0.269282 +Ta 3.95071 8.01668 5.34254 0.539614 -0.279841 -0.051604 +Ta 10.52651 6.66919 7.95196 0.773319 -0.746678 -0.127338 +Ta 10.55688 9.28857 7.96148 0.62099 -0.258731 -0.038343 +Ta 2.70803 5.32339 6.70382 -0.389582 -0.121461 -1.219023 +Ta 2.57492 5.22962 9.24619 0.509556 0.339673 1.192371 +Ta 5.22267 5.3038 5.33156 1.3354 0.250454 0.009213 +Ta 7.98999 7.90061 7.96163 -0.945486 0.84251 -0.352597 +Ta 6.68533 8.02176 5.30974 -0.632817 -0.296567 -0.005138 +Ta 9.34825 7.99677 5.29878 -1.180526 -0.264671 -0.130746 +Ta 5.33163 6.57634 7.98884 -0.009265 1.176676 -0.00019 +Ta 5.29614 9.34403 7.95803 0.264039 -1.003617 -0.12967 +Ta 8.00726 5.27369 6.70227 -0.286454 -0.101025 -2.091338 +Ta 7.97483 5.326 9.24028 -0.084847 -0.42894 1.218267 diff --git a/examples/PACKAGES/pod/Ta/XYZ/Displaced_BCC.xyz b/examples/PACKAGES/pod/Ta/XYZ/Displaced_BCC.xyz new file mode 100644 index 0000000000..f2de497d5e --- /dev/null +++ b/examples/PACKAGES/pod/Ta/XYZ/Displaced_BCC.xyz @@ -0,0 +1,504 @@ +54 +Lattice = "9.96000003815 0.0 0.0 0.0 9.96000003815 0.0 0.0 0.0 9.96000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-631.019667 stress="48457.11 -1136.2 -2351.6499999999996 -1136.2 49582.49 -508.49999999999994 -2351.6499999999996 -508.49999999999994 49591.75" +Ta 0.03088 9.94467 0.03567 -0.612376 -0.402684 -1.345349 +Ta 1.76644 1.66184 1.44089 -1.2057 1.054325 2.428563 +Ta 3.15336 9.91786 0.09806 1.832799 -0.872674 -1.263279 +Ta 9.90797 3.4076 9.86152 0.297218 -1.020932 0.904226 +Ta 3.35029 3.41556 0.08196 -0.474781 -0.303924 -0.630438 +Ta 9.87659 0.24016 3.2897 1.017582 -2.732856 0.243285 +Ta 3.19754 9.8139 3.31195 1.086563 0.951134 0.062863 +Ta 0.08403 3.3137 3.13958 -0.885405 -1.158694 1.624432 +Ta 3.39974 3.48704 3.44694 -0.379616 -1.521174 -1.132181 +Ta 5.07318 1.57764 1.57293 -1.924629 1.561628 0.647121 +Ta 6.63264 0.09181 0.15115 -0.072574 -1.323405 -2.650495 +Ta 8.39478 1.48796 1.58174 -0.843688 3.259658 -0.417314 +Ta 6.7258 3.35837 9.78756 -1.038348 -0.281612 2.282876 +Ta 6.62212 0.16031 3.16166 -0.465928 -0.905667 2.675349 +Ta 6.62042 3.31664 3.31262 0.200967 -0.07823 0.521868 +Ta 1.54439 4.91527 1.83097 0.997719 1.072497 -2.393149 +Ta 9.86899 6.74766 0.03204 0.130914 -0.582942 0.03917 +Ta 1.53276 8.30182 1.78092 0.418129 0.388694 -1.393579 +Ta 3.20199 6.66207 0.08252 0.203286 -0.527057 -0.549649 +Ta 9.8179 6.83547 3.1511 0.116081 -1.993238 2.124523 +Ta 3.2641 6.51799 3.20131 0.251868 1.623578 1.121764 +Ta 5.01293 5.01666 1.65694 -0.60696 -1.008076 -0.05693 +Ta 8.3041 4.93065 1.67994 -0.477682 0.619238 -0.426472 +Ta 4.92858 8.36431 1.64619 -0.219331 -0.900422 0.085838 +Ta 6.45171 6.49288 9.86487 2.179344 0.818455 1.969854 +Ta 8.17019 8.46521 1.78178 0.066493 -1.369324 -1.060782 +Ta 6.49459 6.44867 3.32152 1.495401 1.861587 -0.033194 +Ta 1.68005 1.47471 4.81754 0.149108 1.822933 1.469216 +Ta 9.84583 0.19765 6.76751 0.42718 -1.609424 -1.224098 +Ta 1.69522 1.63512 8.38002 0.084742 0.557896 -0.456487 +Ta 3.48664 0.05215 6.57542 -1.934503 -0.752789 1.48785 +Ta 0.12798 3.32081 6.73112 -1.229494 -0.484439 -1.358874 +Ta 3.10095 3.36454 6.48278 1.921122 -0.938531 0.820666 +Ta 4.85343 1.62817 5.0425 1.234126 0.870681 -0.99265 +Ta 8.36737 1.67732 5.00314 -0.975535 1.13482 0.108656 +Ta 4.90899 1.80105 8.38128 -0.039766 -0.878359 -0.651697 +Ta 6.62609 9.89334 6.61756 -0.816596 1.409513 -0.309355 +Ta 8.0983 1.79178 8.16645 1.859748 -1.248881 0.899404 +Ta 6.55346 3.46095 6.83157 0.395776 -0.669972 -2.721461 +Ta 1.66233 5.09512 5.00854 -0.671291 0.362604 -0.539021 +Ta 1.62699 8.17655 5.00487 -0.188259 1.341073 -0.158559 +Ta 1.55751 4.87741 8.21882 1.446618 1.907859 1.214679 +Ta 0.00182 6.68339 6.71874 -0.827626 -0.053836 -0.695514 +Ta 1.55288 8.27814 8.30093 0.682118 0.586247 -0.235491 +Ta 3.53869 6.81025 6.55411 -2.996765 -1.824506 1.97593 +Ta 4.93422 5.11727 5.01126 0.811714 -1.188027 0.493333 +Ta 8.47308 4.97388 4.90308 -0.996458 0.210843 0.346855 +Ta 4.85618 8.3031 5.00957 1.943666 0.394624 -1.649648 +Ta 8.16403 8.34109 4.92427 0.91047 0.263158 0.079445 +Ta 4.93491 4.96157 8.29899 -1.172036 0.51008 -0.179543 +Ta 8.30629 4.96656 8.34881 0.344097 1.095134 -0.874028 +Ta 5.1789 8.11229 8.35024 -3.233148 3.075485 0.666856 +Ta 6.73281 6.78612 6.82621 -0.949494 -3.102187 -3.614177 +Ta 8.11993 8.34071 8.16079 2.733141 0.980114 2.718789 +54 +Lattice = "9.96000003815 0.0 0.0 0.0 9.96000003815 0.0 0.0 0.0 9.96000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-631.719595 stress="44221.5 1652.1999999999998 85.95 1652.1999999999998 46661.8 2659.1800000000003 85.95 2659.1800000000003 45398.76" +Ta 9.88176 9.87945 0.1862 0.078511 0.774502 -3.074145 +Ta 1.72277 1.64067 1.45897 -0.388557 1.148359 1.788807 +Ta 3.29248 9.91934 0.1304 0.320177 -0.192327 -1.925714 +Ta 9.9322 3.28625 9.92067 0.151826 0.305556 0.342341 +Ta 3.39626 3.47237 0.027 -1.172443 -1.196633 -0.381029 +Ta 9.82641 0.17857 3.34651 1.471988 -1.800854 -0.398222 +Ta 3.18421 9.75374 3.20228 1.172612 2.338131 1.461522 +Ta 0.0643 3.32106 3.21026 -0.524353 -0.677178 0.569751 +Ta 3.36095 3.52794 3.46046 0.265224 -1.853189 -1.194265 +Ta 5.05551 1.59902 1.56265 -1.305786 1.821863 0.915691 +Ta 6.55573 0.10614 0.0715 0.473027 -1.331628 -1.56567 +Ta 8.32355 1.55377 1.58678 -0.34357 2.420135 0.231492 +Ta 6.79062 3.46987 9.80057 -2.578904 -2.079435 2.539246 +Ta 6.65472 0.19462 3.23542 -0.854033 -1.11806 1.182547 +Ta 6.68241 3.29629 3.38474 -0.467825 0.142616 -0.130294 +Ta 1.6702 4.89369 1.79281 -0.731988 0.661803 -1.877031 +Ta 9.93781 6.83545 0.11497 -0.079074 -1.393283 -0.700726 +Ta 1.55467 8.44593 1.70683 -0.318713 -2.059723 0.143176 +Ta 3.12799 6.70462 0.09695 0.649317 -0.982046 -0.987759 +Ta 9.87365 6.726 3.29089 0.358887 -0.808113 0.020022 +Ta 3.21735 6.54561 3.18977 1.043621 1.493821 1.154247 +Ta 5.01268 5.00658 1.62783 -0.475689 -0.239773 0.337642 +Ta 8.30126 4.99697 1.66463 -0.164073 0.238569 0.134521 +Ta 4.9138 8.33572 1.62276 0.337469 -0.531079 0.293633 +Ta 6.4397 6.55776 9.88777 1.902994 0.646598 1.055407 +Ta 8.2046 8.46737 1.69724 -0.705785 -1.624672 0.59768 +Ta 6.47327 6.53333 3.348 1.087057 0.860747 -0.071448 +Ta 1.63781 1.56651 4.86513 0.303333 0.759117 0.988318 +Ta 9.7163 0.09312 6.79336 1.972395 -0.68173 -1.740951 +Ta 1.61582 1.57397 8.30893 0.534301 0.691166 0.33332 +Ta 3.49451 0.05066 6.70224 -2.318362 -0.853012 0.193493 +Ta 9.94977 3.38199 6.78886 -0.299979 -1.645948 -1.888923 +Ta 3.18672 3.36165 6.43952 0.586136 -0.962061 1.644513 +Ta 4.89114 1.58583 5.10545 0.895504 0.96948 -1.159718 +Ta 8.35054 1.66148 5.06446 -0.650427 1.385707 -0.230145 +Ta 4.86816 1.73116 8.31179 0.899776 0.423663 0.126451 +Ta 6.68153 9.92387 6.63426 -0.794656 0.815228 0.039522 +Ta 8.19213 1.74268 8.29407 0.709237 -0.766675 0.419655 +Ta 6.68538 3.41569 6.73237 -1.039762 -0.942693 -1.573563 +Ta 1.62301 5.03369 4.94072 -0.479437 0.708177 0.454442 +Ta 1.67811 8.17661 4.94845 -0.43286 1.033108 0.702773 +Ta 1.50449 4.90497 8.12727 2.157996 1.39217 2.121635 +Ta 9.95522 6.68722 6.7223 -1.207088 -1.014513 -2.023602 +Ta 1.45061 8.21644 8.20658 1.867458 1.404377 0.979038 +Ta 3.56471 6.75841 6.62207 -3.094311 -0.309955 1.003355 +Ta 4.86687 5.12412 5.14144 1.869234 -0.95749 -1.296573 +Ta 8.38876 4.88961 4.89775 -0.647449 1.012711 0.567511 +Ta 4.92136 8.45113 5.01625 0.770451 -1.088974 -1.090266 +Ta 8.20783 8.3489 4.81321 0.21963 0.005286 1.165586 +Ta 4.94875 4.9618 8.28572 -0.426832 0.599091 -0.345599 +Ta 8.20464 4.88251 8.34235 2.170673 2.829715 -0.757157 +Ta 5.07191 8.2117 8.40225 -1.362796 1.673933 -0.46401 +Ta 6.76974 6.82114 6.74241 -1.906068 -2.251947 -1.927455 +Ta 8.24859 8.29304 8.12672 0.501988 0.80736 3.296928 +54 +Lattice = "9.96000003815 0.0 0.0 0.0 9.96000003815 0.0 0.0 0.0 9.96000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-631.386255 stress="48618.67 -1616.79 -530.36 -1616.79 47533.82 1218.01 -530.36 1218.01 48883.18" +Ta 9.92016 0.01438 0.03854 0.556788 -0.67783 -1.5106 +Ta 1.82311 1.70936 1.41659 -1.918774 0.138683 2.301326 +Ta 3.28553 9.91893 0.14739 0.748737 -0.469771 -1.769605 +Ta 9.87507 3.32337 9.83154 0.793708 -0.519091 0.991363 +Ta 3.3031 3.46518 0.07875 0.443248 -0.426577 -0.905273 +Ta 9.95947 0.08218 3.34696 0.739427 -0.726997 -0.766983 +Ta 3.1684 9.75979 3.2356 1.642308 1.605642 1.000091 +Ta 0.02998 3.22821 3.21978 0.370247 0.48123 0.316324 +Ta 3.32428 3.45789 3.46471 0.337827 -1.517721 -1.355537 +Ta 5.13331 1.59317 1.61007 -2.537997 2.199599 0.12697 +Ta 6.66564 0.10058 0.15795 -0.170102 -1.253786 -3.131771 +Ta 8.39979 1.53376 1.55197 -0.736293 2.568367 0.959357 +Ta 6.699 3.46643 9.78218 -1.357883 -2.290461 2.801884 +Ta 6.55739 0.19963 3.22195 1.010984 -1.898276 1.569223 +Ta 6.6614 3.19875 3.40136 0.28987 0.883996 -0.281886 +Ta 1.65474 4.95752 1.79601 -0.834231 0.053286 -1.593869 +Ta 9.95302 6.80511 0.03196 -0.079769 -1.229448 0.075092 +Ta 1.56181 8.37445 1.75774 0.103273 -1.036598 -1.620168 +Ta 3.25788 6.58258 9.89943 -0.15681 0.002856 0.109545 +Ta 9.81575 6.84635 3.22839 0.491934 -1.902197 0.607502 +Ta 3.26659 6.5421 3.20775 1.051845 1.685557 0.716388 +Ta 4.961 4.94444 1.67842 0.154733 0.132572 -0.385023 +Ta 8.39914 5.00135 1.64081 -0.85754 -0.046821 0.044073 +Ta 4.981 8.40495 1.52317 -0.154277 -1.618489 1.137429 +Ta 6.59095 6.57229 9.81082 0.516853 -0.031072 2.168022 +Ta 8.23079 8.50453 1.71947 -0.19104 -1.640479 -0.218034 +Ta 6.5189 6.4527 3.26946 1.051143 1.341567 0.195318 +Ta 1.69996 1.52396 4.92178 -0.286649 1.057284 0.327442 +Ta 9.71449 0.20654 6.76983 2.454386 -2.330371 -0.861132 +Ta 1.75395 1.54634 8.40434 -0.369274 0.99695 -0.846145 +Ta 3.36184 9.91466 6.55661 -0.545145 -0.225476 0.969587 +Ta 0.07017 3.38145 6.72746 -0.97093 -1.700112 -1.838196 +Ta 3.188 3.32611 6.41893 0.788188 -0.658484 1.70621 +Ta 4.88158 1.53321 4.98105 0.344727 0.704928 0.157548 +Ta 8.47411 1.59131 4.94665 -1.939704 1.794052 0.479038 +Ta 4.88901 1.78086 8.34967 0.243383 -0.808705 -0.52527 +Ta 6.73425 9.77434 6.70175 -1.485362 1.795728 -1.262133 +Ta 8.06248 1.71241 8.15301 1.263397 0.222212 1.789119 +Ta 6.58956 3.39493 6.70849 -0.327807 -0.793748 -1.979357 +Ta 1.72658 5.14855 4.93998 -1.319359 -0.168591 0.474034 +Ta 1.56142 8.14402 4.97342 0.414502 1.370212 0.309023 +Ta 1.49024 4.85879 8.1549 2.112914 2.183214 1.555991 +Ta 9.89805 6.74264 6.68864 -0.638427 -1.761151 -1.247128 +Ta 1.51881 8.19293 8.20586 1.126883 1.771936 0.731665 +Ta 3.53422 6.78757 6.63995 -2.202411 -1.241629 0.531987 +Ta 4.91797 5.05055 5.07395 0.97697 -0.452695 -0.680973 +Ta 8.37523 4.90856 4.86905 -0.569914 0.544987 0.445982 +Ta 4.96025 8.30839 4.98936 0.640131 -0.024991 -0.918091 +Ta 8.25393 8.41481 4.85824 -0.321351 -0.771339 0.862505 +Ta 4.98338 4.92238 8.25755 -1.037048 0.701643 -0.025492 +Ta 8.20041 4.82836 8.34047 1.93369 2.92161 -1.499861 +Ta 5.14911 8.22565 8.35035 -2.453675 1.564843 0.655552 +Ta 6.67583 6.74955 6.82036 -0.298729 -2.031929 -2.821342 +Ta 8.24568 8.22146 8.24391 1.158405 1.531882 1.928281 +54 +Lattice = "9.96000003815 0.0 0.0 0.0 9.96000003815 0.0 0.0 0.0 9.96000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-632.575826 stress="37007.6 -3335.61 -654.2900000000001 -3335.61 41350.14000000001 729.9499999999999 -654.2900000000001 729.9499999999999 42032.22" +Ta 9.89658 0.05915 0.05605 1.036339 -0.553602 -1.509413 +Ta 1.84029 1.75247 1.5692 -1.142381 -0.38124 0.773395 +Ta 3.2103 9.87745 0.03021 0.881726 0.55755 -0.326543 +Ta 0.02515 3.41269 9.87251 -0.122739 -0.795043 1.221499 +Ta 3.43008 3.44154 0.03351 -1.7763 -1.011632 -0.445853 +Ta 9.87697 0.19214 3.32206 1.584106 -2.293162 0.196284 +Ta 3.22174 9.87812 3.28991 0.769286 0.831055 0.301207 +Ta 0.1052 3.26647 3.18262 -0.190214 0.336725 0.865636 +Ta 3.41777 3.41426 3.37277 -0.455402 -0.720753 -0.151548 +Ta 5.17196 1.58588 1.62527 -2.939961 2.107641 0.562846 +Ta 6.60208 0.22971 0.08742 0.803627 -2.595707 -2.375381 +Ta 8.43127 1.4925 1.61697 -1.259463 3.750632 -0.106891 +Ta 6.76348 3.3785 9.80186 -2.03401 -1.195377 2.585494 +Ta 6.65909 0.1949 3.2601 -0.56741 -1.409525 1.503945 +Ta 6.6316 3.23626 3.37906 0.319 0.938546 -0.113448 +Ta 1.62284 5.00729 1.75386 -0.237159 -0.599216 -1.433498 +Ta 9.93301 6.82006 0.07168 -0.603293 -1.11764 -0.086884 +Ta 1.52042 8.42173 1.76252 0.366653 -0.814026 -0.80013 +Ta 3.21357 6.59587 0.05473 -0.149533 0.25932 -0.610436 +Ta 9.80178 6.73879 3.20649 0.278464 -0.754372 0.931782 +Ta 3.18872 6.5548 3.14659 1.331155 1.227953 1.549942 +Ta 4.90812 4.89326 1.56359 1.415424 1.204801 1.175799 +Ta 8.30391 4.92482 1.63948 -0.141538 0.852068 0.296628 +Ta 4.96767 8.43868 1.50927 -0.390065 -1.085888 1.127117 +Ta 6.58605 6.61068 9.88944 0.61683 -0.473365 1.726223 +Ta 8.16049 8.53247 1.75295 0.195242 -1.799944 -0.538088 +Ta 6.52605 6.5329 3.27653 0.530753 0.627982 -0.045421 +Ta 1.62199 1.50417 4.93639 0.838566 1.316864 0.614038 +Ta 9.80755 0.13028 6.79412 0.867567 -1.141378 -1.30953 +Ta 1.7363 1.62901 8.31191 -0.210323 0.210696 0.384316 +Ta 3.35607 9.88966 6.63602 -0.80484 0.044494 0.395101 +Ta 0.10319 3.2834 6.73662 -1.43873 -0.584218 -1.316375 +Ta 3.23105 3.25793 6.54382 0.621854 0.133901 0.243236 +Ta 4.92957 1.63938 4.99734 0.279261 -0.276038 0.237899 +Ta 8.42481 1.65711 4.95454 -1.326796 1.057458 1.098206 +Ta 4.84069 1.75925 8.38234 0.745716 -0.829046 -0.859739 +Ta 6.64597 9.80629 6.69075 -0.741154 2.128175 -0.430751 +Ta 8.19543 1.78177 8.30388 1.200953 -1.19775 -0.25616 +Ta 6.57343 3.34206 6.80779 0.135786 -0.186078 -2.215599 +Ta 1.6324 5.02772 5.04564 -0.039204 0.36717 -0.650982 +Ta 1.56954 8.11698 4.93801 0.230278 1.550094 0.24251 +Ta 1.44091 4.90529 8.17235 2.716493 1.617542 1.20799 +Ta 9.93346 6.67194 6.71914 -1.022256 -0.17536 -0.867865 +Ta 1.47975 8.31024 8.36713 1.004335 0.238704 -0.734919 +Ta 3.48998 6.76276 6.56515 -1.924801 -0.712464 1.159232 +Ta 4.9581 5.06922 5.0693 0.337345 -0.924942 -0.538749 +Ta 8.40596 4.88849 4.85949 -0.874232 0.467588 0.615094 +Ta 4.91272 8.41158 4.96637 0.732014 -1.112804 -0.699182 +Ta 8.15337 8.43609 4.86865 0.839591 -1.003948 0.68469 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-1.979508 -0.962122 +Ta 5.04991 1.63426 1.4814 -1.341163 1.468593 1.819665 +Ta 6.63167 0.11405 0.21537 -0.12109 -1.761401 -4.075404 +Ta 8.31494 1.42157 1.60574 0.368731 4.528905 0.569883 +Ta 6.74419 3.49221 9.84811 -2.007412 -2.167313 2.65689 +Ta 6.63412 0.20045 3.26587 -0.684628 -1.087473 1.050812 +Ta 6.74149 3.29744 3.34049 -0.536207 0.257368 0.20051 +Ta 1.65629 4.91473 1.70491 -0.099545 0.910351 -0.802777 +Ta 9.8848 6.82698 0.05792 0.376337 -1.495085 -0.415922 +Ta 1.52902 8.3382 1.76782 0.639344 -0.53398 -1.01794 +Ta 3.2842 6.59888 0.05835 -0.561013 0.262988 -0.786249 +Ta 9.8388 6.70884 3.26058 0.554427 -0.634265 0.300656 +Ta 3.29697 6.67135 3.2332 0.752046 -0.215397 0.311965 +Ta 4.97002 4.96577 1.62011 0.05044 0.104913 0.434502 +Ta 8.33172 4.99905 1.67588 -0.034233 0.026594 -0.111203 +Ta 4.97516 8.44565 1.55002 -0.020779 -1.935482 0.889879 +Ta 6.57558 6.51621 9.81153 1.066759 1.429994 2.384917 +Ta 8.25006 8.48199 1.74936 -0.452919 -1.834688 -0.031687 +Ta 6.44899 6.4711 3.23262 1.703195 1.475113 0.740876 +Ta 1.66863 1.57808 4.93069 0.431628 0.338513 0.161788 +Ta 9.72144 0.20932 6.75785 1.958848 -2.154971 -0.993231 +Ta 1.63635 1.60616 8.35046 0.463086 0.37157 -0.091186 +Ta 3.48302 0.00215 6.71334 -1.509435 -0.172883 0.010894 +Ta 9.93596 3.25148 6.70143 0.237451 -0.065117 -1.344746 +Ta 3.08129 3.29628 6.51691 2.160928 -0.13483 0.507974 +Ta 4.96743 1.5573 5.07437 0.055528 1.049799 -0.152912 +Ta 8.45292 1.6707 5.00536 -1.761269 1.037855 -0.291955 +Ta 4.94629 1.85995 8.30452 -0.162188 -1.40003 0.218906 +Ta 6.73739 9.79788 6.73002 -1.360293 2.553733 -1.038778 +Ta 8.13299 1.84164 8.23538 1.255041 -2.346864 1.564886 +Ta 6.66656 3.37782 6.84701 -0.835313 0.379035 -3.422381 +Ta 1.68024 5.12154 4.98734 -0.660796 0.080462 0.142574 +Ta 1.60982 8.10644 4.87313 0.325313 1.774663 1.223699 +Ta 1.43945 4.82885 8.10227 2.085236 1.993105 1.922899 +Ta 9.9461 6.81388 6.73985 -0.837177 -1.923205 -1.883599 +Ta 1.46223 8.29911 8.22847 1.981531 0.926889 0.882329 +Ta 3.56097 6.69411 6.63008 -2.368401 -0.099926 0.349055 +Ta 4.97662 5.05599 5.0457 0.641095 -0.663324 -0.062532 +Ta 8.47313 4.93262 4.89931 -1.205654 0.412649 0.354766 +Ta 4.99461 8.38381 5.00182 0.283353 -0.567275 -0.555014 +Ta 8.15164 8.40758 4.84002 1.070067 -0.7384 0.47295 +Ta 5.02489 5.02411 8.3462 -1.295414 -0.424201 -1.125591 +Ta 8.29233 4.81641 8.42543 1.342299 3.650693 -2.347555 +Ta 5.13768 8.20531 8.35183 -1.942023 1.3521 0.356008 +Ta 6.7424 6.82181 6.74362 -1.121731 -2.790179 -1.913012 +Ta 8.24574 8.2733 8.18525 1.245134 1.248761 2.999274 +54 +Lattice = "9.96000003815 0.0 0.0 0.0 9.96000003815 0.0 0.0 0.0 9.96000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-631.669379 stress="43133.57 -1318.24 471.24 -1318.24 48697.43 3329.94 471.24 3329.94 47363.12" +Ta 9.94799 9.88693 0.10122 -0.263284 1.216688 -1.883794 +Ta 1.86889 1.76555 1.56581 -1.932894 -0.197466 0.799563 +Ta 3.18914 9.88171 0.13041 0.610905 0.517831 -1.648338 +Ta 9.92665 3.38968 9.84955 0.317542 -1.257416 1.688263 +Ta 3.43358 3.54499 0.1688 -1.726787 -2.050304 -2.386849 +Ta 9.82474 0.16394 3.32778 2.216383 -1.538245 -0.264099 +Ta 3.17727 9.89254 3.26737 1.70172 0.460024 0.157384 +Ta 0.07445 3.24025 3.20793 -0.069552 0.434181 0.546568 +Ta 3.36565 3.516 3.35675 0.112956 -1.917705 -0.223914 +Ta 5.16123 1.6239 1.55508 -3.303498 2.564182 1.651578 +Ta 6.55575 0.21191 0.17217 1.231731 -2.686607 -3.911866 +Ta 8.29508 1.55441 1.6632 0.089146 2.52746 -0.701653 +Ta 6.73309 3.48714 9.89848 -2.274779 -2.67868 1.66594 +Ta 6.59035 0.09173 3.21496 -0.0633 -0.576713 2.012973 +Ta 6.64791 3.2176 3.34745 0.160139 1.027979 0.160616 +Ta 1.65171 4.94471 1.7425 -0.713082 0.706387 -1.212205 +Ta 9.93323 6.79042 0.0161 -0.225077 -1.132914 -0.016869 +Ta 1.4431 8.3808 1.76113 1.378961 -0.749711 -0.52572 +Ta 3.21108 6.66508 0.00376 -0.00978 -0.476703 -0.29896 +Ta 9.81714 6.70548 3.17335 0.208961 -0.701521 1.301811 +Ta 3.21572 6.591 3.22023 1.033304 1.008256 0.532303 +Ta 4.91106 4.93792 1.58572 1.678571 2.009249 1.603115 +Ta 8.26464 4.94698 1.60854 0.497683 0.531052 0.869356 +Ta 4.90809 8.44903 1.49243 0.088267 -1.613979 1.633781 +Ta 6.59154 6.59584 9.95944 0.505361 0.227865 0.830287 +Ta 8.21527 8.54264 1.72812 -0.429569 -2.313543 -0.559364 +Ta 6.55385 6.57757 3.26324 0.271827 0.622681 0.181604 +Ta 1.75661 1.52675 4.84155 -0.633945 1.321519 1.006441 +Ta 9.87636 0.21376 6.70268 0.45418 -1.893615 -0.40218 +Ta 1.6521 1.61415 8.35169 0.600238 0.373907 0.119151 +Ta 3.44156 0.04311 6.6096 -1.495661 -0.599002 0.704379 +Ta 0.09339 3.37032 6.65029 -1.099312 -1.412438 -0.819685 +Ta 3.18042 3.28906 6.45515 0.992949 0.211285 1.220556 +Ta 5.00918 1.65807 5.12559 0.127178 -0.0364 -1.088507 +Ta 8.38565 1.61267 4.93819 -1.405672 1.604515 0.911956 +Ta 4.81649 1.82535 8.27026 1.005288 -0.428096 0.38029 +Ta 6.74177 9.88632 6.6854 -1.192978 0.733832 -0.379597 +Ta 8.06265 1.81199 8.23079 2.096046 -1.128412 0.494263 +Ta 6.62079 3.42161 6.7044 -0.241025 -0.422289 -1.432335 +Ta 1.71584 5.10974 5.01063 -0.952074 0.094302 -0.330628 +Ta 1.6423 8.21258 4.88283 -0.325763 0.887706 0.945961 +Ta 1.49636 4.82702 8.22043 2.120092 2.257811 0.840294 +Ta 9.95578 6.72188 6.72066 -0.190571 -0.973108 -1.045394 +Ta 1.57396 8.29892 8.32339 0.49698 0.587894 -0.638339 +Ta 3.53534 6.71052 6.61516 -2.080422 -0.439087 0.577691 +Ta 4.91158 5.00762 4.99897 1.141976 -0.039622 -0.08708 +Ta 8.42976 4.87775 4.88036 -0.952974 0.858021 0.171909 +Ta 4.90384 8.41136 4.98652 0.894637 -0.884584 -0.741048 +Ta 8.2864 8.42598 4.87128 -0.087899 -0.922239 0.910409 +Ta 5.03024 4.97737 8.34689 -1.018587 0.572925 -0.691072 +Ta 8.23151 4.84154 8.4374 1.578619 3.115272 -2.575512 +Ta 5.1302 8.08126 8.35768 -1.750753 2.547363 0.298061 +Ta 6.65325 6.73813 6.7005 0.162071 -1.670992 -1.976694 +Ta 8.2436 8.19187 8.19738 0.665528 1.721207 1.625195 +54 +Lattice = "9.96000003815 0.0 0.0 0.0 9.96000003815 0.0 0.0 0.0 9.96000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-632.431277 stress="39332.07 -484.03000000000003 -591.5 -484.03000000000003 42463.85 -935.67 -591.5 -935.67 44557.78" +Ta 0.01093 0.07201 0.09451 -0.133033 -0.624676 -1.390718 +Ta 1.86279 1.76064 1.51659 -1.592195 -0.069139 1.205785 +Ta 3.2078 9.79995 0.13153 0.540433 1.454104 -1.58264 +Ta 9.85766 3.40762 9.89988 1.024661 -1.342485 0.791698 +Ta 3.38902 3.43935 0.04627 -0.448466 -0.286011 -0.80136 +Ta 9.90188 0.13348 3.29636 1.537302 -1.039386 0.836358 +Ta 3.22408 9.86832 3.24936 1.3552 0.851114 0.539138 +Ta 0.12559 3.29783 3.20677 -1.020326 -0.682337 1.223972 +Ta 3.36531 3.39767 3.43601 0.009962 -0.529326 -1.103499 +Ta 5.15746 1.68746 1.60975 -2.532105 1.453447 0.682011 +Ta 6.67484 0.22558 0.19511 -0.045042 -2.082264 -2.946332 +Ta 8.39432 1.57083 1.68829 -0.326523 2.974804 -0.552053 +Ta 6.7901 3.4905 9.84778 -2.280421 -1.914956 1.902637 +Ta 6.66098 0.16369 3.1821 -0.458515 -1.404543 2.285847 +Ta 6.68975 3.33374 3.35351 -0.189956 -0.055081 0.175264 +Ta 1.51952 4.8757 1.72333 1.250032 1.568243 -1.070974 +Ta 9.93504 6.80931 0.00911 -0.545334 -1.102829 0.05256 +Ta 1.53614 8.31731 1.75831 0.412055 0.075595 -1.050824 +Ta 3.19933 6.67436 9.9199 -0.185239 -1.027413 0.207555 +Ta 9.87719 6.84896 3.30936 0.023055 -2.415004 0.073182 +Ta 3.27549 6.6063 3.18917 0.469425 0.419811 0.76263 +Ta 5.00755 4.96297 1.63652 -0.168999 0.238458 0.154223 +Ta 8.27314 4.95228 1.66284 0.330644 1.338439 0.511823 +Ta 4.91774 8.42919 1.48115 0.474143 -1.326573 1.888404 +Ta 6.55832 6.62377 9.94221 1.26809 -0.236095 1.051695 +Ta 8.27021 8.49129 1.78853 -0.55743 -1.432265 -0.989698 +Ta 6.39844 6.56795 3.35477 1.561076 0.83826 -0.364502 +Ta 1.77582 1.5455 4.9351 -1.060253 0.494227 0.023332 +Ta 9.87126 0.15154 6.74741 0.212135 -1.347122 -0.696834 +Ta 1.74456 1.52234 8.31732 0.085858 1.095537 0.038296 +Ta 3.45815 9.88882 6.55866 -1.684608 0.594275 1.383549 +Ta 0.03304 3.29479 6.73355 -0.261879 -0.877624 -1.394156 +Ta 3.18079 3.30298 6.42253 1.207944 0.171277 1.336295 +Ta 4.9603 1.57723 4.99617 0.634253 0.567922 -0.173103 +Ta 8.3559 1.62409 5.03154 -0.530634 1.162549 -0.066204 +Ta 4.7903 1.73365 8.2792 1.03526 -0.144088 0.183756 +Ta 6.74404 9.77079 6.64995 -1.450453 2.324287 -0.166798 +Ta 8.09234 1.79785 8.24264 1.673615 -1.361805 0.313033 +Ta 6.57421 3.42967 6.77064 0.019605 -0.880931 -1.798564 +Ta 1.57913 5.11576 4.95243 0.306594 -0.25138 -0.080154 +Ta 1.69273 8.20716 4.92075 -0.341052 1.046973 0.557303 +Ta 1.43354 4.91751 8.16401 2.287861 1.338427 1.255018 +Ta 0.01425 6.67723 6.65523 -1.147897 -0.077148 -0.417608 +Ta 1.58291 8.27957 8.26309 0.342823 0.685693 0.016051 +Ta 3.42748 6.83665 6.641 -1.510001 -2.239526 0.838695 +Ta 4.97343 5.04097 5.00585 -0.037888 -0.412025 0.456637 +Ta 8.4039 4.8646 4.9179 -0.583261 0.965744 0.28682 +Ta 4.91928 8.3318 5.11892 1.250045 -0.399127 -2.452135 +Ta 8.20159 8.28199 4.88507 0.813012 0.601139 0.388164 +Ta 5.04212 4.99253 8.32778 -1.424968 0.603147 -0.546645 +Ta 8.29629 4.88656 8.35075 0.628928 2.792969 -1.330955 +Ta 5.08862 8.21773 8.50315 -0.984696 1.400694 -1.476016 +Ta 6.79769 6.74824 6.68609 -1.854116 -2.150746 -0.908504 +Ta 8.1091 8.29833 8.26479 2.601277 0.654768 1.938542 +54 +Lattice = "9.96000003815 0.0 0.0 0.0 9.96000003815 0.0 0.0 0.0 9.96000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-630.960068 stress="47457.030000000006 -1005.83 -232.22 -1005.83 51553.91 452.42 -232.22 452.42 48272.9" +Ta 0.05485 9.94068 0.04882 -0.759723 0.349463 -1.073784 +Ta 1.85805 1.77201 1.5217 -1.724392 -0.312777 1.581767 +Ta 3.16512 9.83319 0.13832 1.061743 0.568667 -1.386846 +Ta 9.93006 3.33808 9.91253 -0.064995 -0.093866 0.630283 +Ta 3.35014 3.4521 0.05567 -0.390836 -0.380588 -0.755337 +Ta 9.83256 0.11516 3.3997 1.419777 -1.102908 -0.922237 +Ta 3.23053 9.80404 3.17024 0.958769 1.69459 1.532703 +Ta 0.01161 3.22748 3.27368 0.022937 0.373478 0.292145 +Ta 3.35601 3.5215 3.45824 0.330549 -1.676711 -0.671565 +Ta 5.17312 1.6729 1.58962 -2.671903 1.121811 0.197691 +Ta 6.67768 0.12311 0.12029 -0.440876 -1.26923 -2.349462 +Ta 8.34051 1.56504 1.62363 0.168904 1.957241 -0.015229 +Ta 6.78008 3.36169 9.8788 -1.638783 -0.833959 1.395422 +Ta 6.60936 0.19924 3.21319 -0.445878 -1.774358 1.382608 +Ta 6.66488 3.23598 3.33678 -0.05205 1.041637 0.440105 +Ta 1.55882 4.89699 1.83484 0.420221 0.664634 -1.787995 +Ta 9.92966 6.74077 0.07931 -0.240379 -0.888703 -0.594008 +Ta 1.46294 8.36123 1.80347 1.383538 -0.598636 -1.619561 +Ta 3.27604 6.65474 9.90339 -0.790555 -1.047873 0.411754 +Ta 9.88531 6.85002 3.21939 -0.582286 -2.052939 1.256318 +Ta 3.29061 6.52643 3.19139 0.073936 1.783087 1.280681 +Ta 4.89996 4.99982 1.70189 1.223371 -0.15804 -0.71227 +Ta 8.31065 5.01116 1.69232 -0.087953 0.030026 -0.109796 +Ta 4.88784 8.33857 1.51732 0.850961 -0.596673 1.090247 +Ta 6.50104 6.53275 9.80774 2.177734 -0.433205 2.899269 +Ta 8.2643 8.49938 1.67302 -0.503687 -1.58688 0.09942 +Ta 6.55463 6.57827 3.32912 0.424308 0.463881 -0.236654 +Ta 1.62393 1.56011 4.84451 0.739422 0.750623 1.039514 +Ta 9.83601 0.23425 6.80872 1.000448 -2.657832 -1.896794 +Ta 1.61133 1.59769 8.41214 1.032998 0.937424 -0.476098 +Ta 3.35598 0.02593 6.56637 -1.123068 -0.410917 1.065083 +Ta 0.09395 3.33379 6.73292 -1.590772 -1.594874 -2.032464 +Ta 3.10315 3.36912 6.45924 1.749889 -0.890546 1.008948 +Ta 4.94948 1.60844 5.13297 0.326327 0.438573 -0.854681 +Ta 8.3112 1.6084 4.98866 -0.787743 1.376575 0.740112 +Ta 4.84637 1.81183 8.24772 0.358933 -1.184604 0.522666 +Ta 6.65846 9.76479 6.73502 -0.922055 2.08298 -0.978385 +Ta 8.20906 1.73062 8.14887 0.457034 -0.533352 2.19381 +Ta 6.58641 3.34768 6.84906 -0.07115 -0.232275 -3.047979 +Ta 1.68643 5.13518 4.9899 -0.983213 0.345899 0.008163 +Ta 1.66974 8.17852 4.94291 -0.25579 1.350395 0.365493 +Ta 1.47384 4.8564 8.10261 2.294153 2.563508 2.527259 +Ta 9.88912 6.80164 6.77309 -0.120678 -1.620395 -1.826051 +Ta 1.55837 8.19547 8.30267 0.878074 1.467856 0.015021 +Ta 3.56356 6.83284 6.56625 -2.486358 -1.682642 1.765681 +Ta 4.99706 5.12232 5.11423 0.43805 -1.159229 -0.988294 +Ta 8.4671 4.91132 4.92219 -1.21811 0.738609 0.182139 +Ta 4.87329 8.34516 4.9908 1.555301 0.282701 -1.632594 +Ta 8.1534 8.37445 4.79401 0.515688 -0.19719 1.530097 +Ta 5.00952 4.94855 8.26218 -1.33193 0.185129 -0.033086 +Ta 8.21481 4.8505 8.29903 1.753267 2.042376 0.013681 +Ta 5.14988 8.12501 8.49478 -2.325196 2.631836 -1.723209 +Ta 6.79841 6.70737 6.74515 -1.373171 -1.292054 -2.073736 +Ta 8.2086 8.27306 8.2346 1.367197 1.020256 2.330032 +54 +Lattice = "9.96000003815 0.0 0.0 0.0 9.96000003815 0.0 0.0 0.0 9.96000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-623.378198 stress="80008.25 -785.4100000000001 1601.25 -785.4100000000001 86520.39 4960.87 1601.25 4960.87 85233.93000000001" +Ta 9.95615 9.94979 0.16514 -0.137356 -0.028883 -3.40463 +Ta 1.87163 1.71307 1.41378 -1.76357 0.590114 2.267852 +Ta 3.17989 9.83685 0.10642 1.277421 0.225697 -1.841016 +Ta 9.90024 3.33884 9.82529 0.735381 -0.941566 1.77777 +Ta 3.4188 3.54303 0.14009 -1.606974 -1.518343 -1.948061 +Ta 9.8553 0.24533 3.33787 2.112303 -3.154318 -0.288821 +Ta 3.17514 9.74142 3.2 1.589191 1.94113 1.194543 +Ta 0.11128 3.26365 3.15053 -0.364264 -0.441607 0.999143 +Ta 3.37385 3.56077 3.43718 -0.10161 -1.946969 -0.790652 +Ta 5.20458 1.63365 1.50672 -4.374578 3.807338 1.826632 +Ta 6.57608 0.24353 0.2053 1.355941 -3.643228 -5.429459 +Ta 8.39734 1.42414 1.60164 -0.6903 5.287807 -0.169411 +Ta 6.79744 3.4915 9.76717 -3.482997 -2.71942 3.817554 +Ta 6.57033 0.23978 3.13517 0.116586 -1.988113 3.629484 +Ta 6.72113 3.22949 3.3633 -0.338679 0.658098 0.181119 +Ta 1.57149 4.94775 1.80091 0.075728 0.493399 -1.98724 +Ta 9.92064 6.87072 0.13795 -0.725063 -1.775537 -0.966934 +Ta 1.41785 8.41983 1.76001 1.411759 -1.132459 -0.69594 +Ta 3.14851 6.64163 0.03349 0.008652 -0.525052 -0.43074 +Ta 9.7788 6.83849 3.18243 0.240296 -2.124804 1.273631 +Ta 3.16533 6.57739 3.14068 1.48579 1.371308 1.35272 +Ta 4.90709 4.92946 1.61468 1.153866 1.203555 0.949633 +Ta 8.33316 4.92031 1.59073 -0.391861 0.974553 0.849438 +Ta 4.9596 8.47655 1.51542 -0.546245 -2.139501 1.15131 +Ta 6.44823 6.51342 9.85247 2.586298 -0.265344 3.052647 +Ta 8.17315 8.54045 1.75264 -0.705353 -2.252394 -0.493293 +Ta 6.39303 6.44322 3.27828 1.523627 1.285888 -0.061445 +Ta 1.70938 1.43709 4.84222 0.306581 1.628448 1.044131 +Ta 9.71238 0.24769 6.81385 1.995125 -2.589965 -0.973181 +Ta 1.68921 1.55889 8.35846 0.351955 0.61258 -0.208928 +Ta 3.47749 9.92814 6.63177 -2.081328 0.048903 1.244886 +Ta 0.07656 3.32278 6.77536 -1.946033 -1.979053 -2.885009 +Ta 3.07793 3.27871 6.40803 1.81774 -0.328617 1.303887 +Ta 4.90115 1.58004 5.10411 0.818241 0.705137 -0.829745 +Ta 8.43888 1.56841 5.00344 -2.225694 2.689319 0.426868 +Ta 4.81957 1.88977 8.30861 0.398342 -1.185455 -0.079158 +Ta 6.73863 9.78981 6.71678 -2.05864 2.854477 -1.371358 +Ta 8.05528 1.82891 8.19103 1.951662 -1.704639 1.321716 +Ta 6.59394 3.44619 6.83462 -0.445378 -0.730496 -3.696673 +Ta 1.65312 5.15331 5.0431 -0.703206 0.151193 -0.646398 +Ta 1.60774 8.12544 4.90328 -0.101304 1.629949 1.006095 +Ta 1.42058 4.79056 8.10344 3.354131 3.342928 2.609888 +Ta 9.92554 6.78882 6.73898 -1.110388 -1.85868 -1.874234 +Ta 1.4639 8.19238 8.28284 1.738894 1.866439 0.339074 +Ta 3.56301 6.81221 6.61544 -3.063945 -1.111905 1.132298 +Ta 4.934 5.10947 5.11506 0.832308 -0.890416 -0.494106 +Ta 8.45728 4.85519 4.78408 -1.053171 0.965832 0.968872 +Ta 4.91173 8.4049 5.06479 1.33012 -0.900003 -2.085329 +Ta 8.16172 8.38305 4.77586 0.217903 -0.195045 1.235079 +Ta 4.96219 4.997 8.25034 -1.340837 0.253721 -0.064669 +Ta 8.22081 4.83811 8.40873 2.589217 4.367823 -2.571794 +Ta 5.19313 8.07977 8.4862 -3.823089 3.630743 -0.94626 +Ta 6.77011 6.85567 6.82197 -2.081899 -4.511915 -4.402203 +Ta 8.12043 8.25909 8.1457 3.888707 1.997353 4.680418 diff --git a/examples/PACKAGES/pod/Ta/XYZ/Displaced_FCC.xyz b/examples/PACKAGES/pod/Ta/XYZ/Displaced_FCC.xyz new file mode 100644 index 0000000000..e1fbb58bbc --- /dev/null +++ b/examples/PACKAGES/pod/Ta/XYZ/Displaced_FCC.xyz @@ -0,0 +1,450 @@ +48 +Lattice = "8.39999961853 0.0 0.0 0.0 8.39999961853 0.0 0.0 0.0 12.6000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-555.899463 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-0.432403 +Ta 4.26826 8.33822 0.02108 -0.755392 0.804853 0.059577 +Ta 6.33489 2.131 12.53088 -0.426566 -0.592698 0.445778 +Ta 6.25404 0.03209 2.05073 0.258429 0.220942 0.825671 +Ta 4.16384 2.13978 2.12517 0.060709 -0.255028 -0.249772 +Ta 8.36731 4.13909 0.0525 0.331667 0.645722 -0.10797 +Ta 2.15375 6.29902 0.04207 -0.223718 0.33025 -0.423847 +Ta 2.11926 4.2113 2.04 0.077389 -0.274763 0.060731 +Ta 0.06324 6.29457 2.13106 -0.639548 -0.256039 -0.611666 +Ta 0.0522 8.3415 4.1171 -0.688958 0.522915 0.942873 +Ta 2.07655 2.17403 4.20011 -0.235656 -0.209697 0.072817 +Ta 2.1497 8.34384 6.3073 -0.390747 0.045154 -0.212304 +Ta 0.02961 2.09814 6.34863 -0.334421 -0.350008 -0.633984 +Ta 0.07703 0.06114 8.42699 -0.48162 -0.529725 -0.105918 +Ta 2.1146 2.08725 8.35955 0.000134 0.091763 0.144876 +Ta 2.17879 0.01668 10.42251 -0.327921 -0.945931 0.74699 +Ta 0.01535 2.14423 10.49771 0.421563 -0.107154 0.042196 +Ta 4.24355 4.14389 12.57727 -0.490707 -0.151469 0.150492 +Ta 6.30703 6.31257 0.03364 0.317513 -0.514173 0.21469 +Ta 6.21957 4.24141 2.11393 0.747501 -0.932063 -0.27685 +Ta 4.27447 6.25375 2.16537 -0.54996 0.359185 -0.634042 +Ta 4.13684 8.3759 4.1221 0.976955 0.422783 0.46928 +Ta 6.31913 2.1596 4.19723 -0.042125 -0.448326 0.0636 +Ta 6.32938 0.03364 6.23358 0.112289 -0.022674 -0.410219 +Ta 4.15414 2.02652 6.21831 0.551165 0.522365 0.208895 +Ta 4.28152 8.39237 8.35103 -0.247267 -0.367146 -0.056108 +Ta 6.31596 2.06768 8.44393 -0.115638 0.184021 -0.398675 +Ta 6.3285 8.32779 10.51057 -0.165051 0.47747 -0.199364 +Ta 4.12563 2.0398 10.42566 0.443476 0.125337 0.61432 +Ta 8.38026 4.1908 4.13874 0.589643 0.264679 0.088241 +Ta 2.17116 6.35301 4.11791 -0.570772 -1.315435 0.985555 +Ta 2.03626 4.1604 6.34457 0.154161 0.572819 -0.628519 +Ta 8.38985 6.30508 6.28594 0.326379 0.413925 -0.417146 +Ta 8.36103 4.20342 8.38265 -0.217143 0.101356 0.728482 +Ta 2.08955 6.26468 8.3173 0.243414 0.178383 0.814981 +Ta 2.15221 4.23276 10.51632 -0.473082 0.143977 0.127608 +Ta 8.36864 6.28423 10.50391 0.518348 -0.281377 0.03593 +Ta 4.17037 4.21177 4.21967 -0.156993 -0.293509 0.422478 +Ta 6.32577 6.23846 4.15284 0.005152 0.74102 0.318444 +Ta 6.34611 4.25945 6.31433 -0.335588 -0.895129 0.197851 +Ta 4.21525 6.23105 6.29066 0.022941 0.346622 -0.028249 +Ta 4.1532 4.14295 8.36799 0.730355 0.232327 -0.123611 +Ta 6.32703 6.37247 8.32622 -0.158654 -0.470012 0.487803 +Ta 6.2491 4.16576 10.55905 0.217972 0.346985 -0.975743 +Ta 4.26539 6.24873 10.54677 -0.405539 0.323408 -0.750301 +48 +Lattice = "8.39999961853 0.0 0.0 0.0 8.39999961853 0.0 0.0 0.0 12.6000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-555.968399 stress="43047.68 454.90999999999997 -179.26 454.90999999999997 45952.240000000005 326.2 -179.26 326.2 41269.62" +Ta 8.33107 8.3509 0.0015 0.920711 0.047635 0.466085 +Ta 2.15215 2.06155 0.00638 0.013766 0.114377 0.114976 +Ta 2.17243 8.36545 2.15847 -0.432619 0.744561 -0.543999 +Ta 0.00213 2.13268 2.0346 0.046002 -1.061264 0.961179 +Ta 4.23222 0.05817 12.55891 -0.409962 -0.778639 -0.063284 +Ta 6.26764 2.04607 0.0766 -0.214809 0.598564 -0.689581 +Ta 6.24022 8.35975 2.09956 0.446009 0.343529 0.506397 +Ta 4.25858 2.10916 2.17653 -0.950565 0.012664 -0.279387 +Ta 8.36413 4.13793 0.03804 0.227157 0.360461 -0.615113 +Ta 2.07699 6.23218 0.02357 -0.035908 0.836465 0.1878 +Ta 2.04438 4.13335 2.10915 0.215365 0.362086 -0.128602 +Ta 8.34053 6.35158 2.10339 0.192164 -0.413234 -0.37135 +Ta 8.39644 8.33273 4.21315 -0.029012 0.821143 -0.309048 +Ta 2.05049 2.18199 4.27857 -0.15645 -0.41091 -0.813722 +Ta 2.10797 0.00795 6.24152 -0.317156 -0.701413 0.424479 +Ta 0.00876 2.1029 6.29925 -0.221688 -0.231517 -0.287747 +Ta 0.00111 8.39169 8.41011 0.358727 -0.010756 -0.601951 +Ta 2.07824 2.14165 8.32985 0.262314 -0.445469 0.887731 +Ta 2.04556 0.08072 10.52474 0.5264 -0.285219 -0.083721 +Ta 8.37798 2.01756 10.54116 -0.140639 1.218338 -0.186234 +Ta 4.12695 4.2567 0.0353 0.753601 -0.317693 0.037295 +Ta 6.32498 6.30315 0.03712 -0.388071 -0.337876 -0.313802 +Ta 6.30962 4.14127 2.13365 -0.135269 0.601454 0.056099 +Ta 4.23315 6.34774 2.12982 -0.212883 -0.527314 -0.160335 +Ta 4.19249 0.03152 4.23264 -0.076723 -0.943434 0.376392 +Ta 6.23832 2.03393 4.19631 1.15411 0.515942 0.335054 +Ta 6.34797 8.36641 6.29619 -0.34515 0.166198 -0.034551 +Ta 4.17707 2.07642 6.27401 0.591806 0.420296 0.519899 +Ta 4.21362 8.37068 8.38105 -0.080896 0.523146 -0.053202 +Ta 6.36717 2.12038 8.33147 -0.401482 -0.340538 0.569328 +Ta 6.37677 8.37217 10.48208 -0.574779 0.057651 -0.218756 +Ta 4.263 2.08575 10.46917 0.085217 0.16737 -0.392696 +Ta 0.00308 4.25945 4.25831 -0.216132 -0.940307 -0.693366 +Ta 2.02019 6.29183 4.12359 0.782573 -0.22301 0.653063 +Ta 2.13428 4.1517 6.3785 0.043308 1.139429 -0.121789 +Ta 8.35004 6.21881 6.28464 1.158421 0.740718 0.664429 +Ta 8.39923 4.25788 8.41667 0.108854 -0.46318 0.567778 +Ta 2.14057 6.3406 8.46909 -0.263525 0.035096 -0.867844 +Ta 2.1474 4.23778 10.49162 -0.289223 -1.035858 0.015625 +Ta 0.0553 6.25623 10.45097 -0.282479 0.0763 0.811523 +Ta 4.15104 4.23317 4.16596 0.281648 0.167552 0.379349 +Ta 6.33045 6.25832 4.24115 -0.699707 0.07144 -0.17646 +Ta 6.37853 4.15779 6.33602 -1.073636 -0.112077 -0.599552 +Ta 4.1996 6.23651 6.33229 -0.262227 0.289885 -0.585827 +Ta 4.28008 4.27309 8.43274 -0.041823 -0.686192 -0.088247 +Ta 6.33862 6.31947 8.39033 -0.051946 -0.054734 0.085119 +Ta 6.30961 4.25884 10.56206 0.075121 -0.542769 0.057588 +Ta 4.20876 6.32794 10.48641 0.061486 0.431101 0.602978 +48 +Lattice = "8.39999961853 0.0 0.0 0.0 8.39999961853 0.0 0.0 0.0 12.6000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-556.047132 stress="42983.7 837.4200000000001 145.2 837.4200000000001 43867.59 -1054.67 145.2 -1054.67 42053.840000000004" +Ta 8.35391 0.02768 12.53195 0.2996 0.097159 -0.189691 +Ta 2.09406 2.10567 12.58345 -0.566566 -0.276803 -0.258138 +Ta 2.0736 8.3527 2.13624 0.431138 0.069631 -0.176146 +Ta 0.07104 2.02659 2.16207 -0.798628 0.179308 -0.911212 +Ta 4.24337 0.07189 0.06066 -0.667104 -1.01187 -0.253714 +Ta 6.24014 2.08636 12.54857 0.783637 0.195082 0.154676 +Ta 6.33344 8.39148 2.02558 -0.303788 0.247493 1.015414 +Ta 4.16535 2.06646 2.04504 0.073468 0.186828 0.468777 +Ta 8.32677 4.23996 0.02711 0.81379 -0.478646 0.053713 +Ta 2.08781 6.37504 12.59133 0.032354 -0.135994 0.303608 +Ta 2.06443 4.14688 2.08857 -0.166601 0.775039 -0.532869 +Ta 8.38638 6.37661 2.05779 -0.182172 -0.557039 0.479008 +Ta 8.37411 8.39962 4.27195 0.241148 -0.01589 -0.246337 +Ta 2.10985 2.13127 4.13256 0.516219 -0.39379 1.293154 +Ta 2.14384 0.00652 6.34882 0.125171 0.286979 -0.653648 +Ta 8.34346 2.03521 6.31512 0.018758 0.590464 0.348758 +Ta 0.03525 8.32946 8.41429 -0.219143 0.55592 0.013803 +Ta 2.12988 2.0852 8.36064 -0.099944 0.308003 0.252642 +Ta 2.08083 8.32403 10.45611 0.15963 0.438777 0.611576 +Ta 0.02857 2.10046 10.46488 0.00465 0.06223 -0.163579 +Ta 4.12633 4.25698 12.56375 -0.253803 -0.345212 0.164038 +Ta 6.24339 6.25677 0.07703 0.214297 0.405605 -0.193076 +Ta 6.23523 4.15385 2.04007 0.673655 -0.032667 0.435699 +Ta 4.23419 6.22194 2.15425 -0.259175 0.88278 -0.155619 +Ta 4.19632 0.02098 4.26019 0.256837 0.15204 -0.517119 +Ta 6.2787 2.16315 4.12282 -0.232405 -0.499866 0.253482 +Ta 6.34721 8.31974 6.30085 -0.979334 0.910385 0.303536 +Ta 4.28154 2.17035 6.32716 -0.15794 -0.615192 -0.1244 +Ta 4.18199 8.39045 8.46612 0.325504 0.011668 -0.623247 +Ta 6.26218 2.04661 8.48258 0.1676 0.725305 -0.25923 +Ta 6.23956 8.33727 10.47655 0.418626 0.454527 0.207051 +Ta 4.15476 2.10491 10.56002 -0.313925 0.116788 -0.527027 +Ta 0.01924 4.13985 4.22933 -0.14445 0.528571 -0.009114 +Ta 2.08713 6.26332 4.12939 -0.556542 0.338386 0.377019 +Ta 2.15091 4.23252 6.31161 -0.453388 -0.485864 -0.240866 +Ta 0.01574 6.34253 6.34105 0.560159 -0.626169 -0.553544 +Ta 0.06165 4.27339 8.34091 -0.693509 -0.695001 0.015426 +Ta 2.17693 6.29896 8.40088 -0.096806 0.060357 0.058203 +Ta 2.04233 4.27207 10.49743 -0.170105 0.047304 0.328134 +Ta 8.326 6.32148 10.47975 0.051179 -0.370901 0.321938 +Ta 4.17478 4.27838 4.20752 -0.040763 -0.935827 -0.576582 +Ta 6.33594 6.28787 4.27554 0.307038 0.027247 -1.208419 +Ta 6.22034 4.2468 6.22637 0.65603 -0.422269 1.121308 +Ta 4.16145 6.31917 6.2391 0.094184 0.321459 0.407157 +Ta 4.14417 4.25682 8.46183 0.755121 -0.328996 0.17207 +Ta 6.30692 6.29958 8.38648 -0.576112 -0.600141 0.013593 +Ta 6.30183 4.19292 10.57602 0.207371 0.051704 -0.883456 +Ta 4.25713 6.3237 10.54986 -0.254962 -0.198902 0.083246 +48 +Lattice = "8.39999961853 0.0 0.0 0.0 8.39999961853 0.0 0.0 0.0 12.6000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-555.747848 stress="44613.38 397.28000000000003 -242.23 397.28000000000003 46401.21 -102.86 -242.23 -102.86 43613.280000000006" +Ta 0.02479 8.34418 0.01275 -0.16642 0.336623 -0.17578 +Ta 2.12361 2.14989 0.01237 -0.405458 -0.253401 -0.541818 +Ta 2.15668 0.05545 2.03048 -1.000877 -0.537193 0.264476 +Ta 8.38488 2.15096 2.04122 -0.226412 -0.742284 -0.216619 +Ta 4.26822 0.07709 0.05369 -1.051454 -0.974093 -0.658846 +Ta 6.22169 2.03316 12.57305 1.255557 0.920651 0.507841 +Ta 6.25622 8.38573 2.18037 0.795872 0.410847 -0.509558 +Ta 4.16678 2.07023 2.1321 0.423587 0.619136 0.258117 +Ta 0.05908 4.28115 12.57632 -0.514548 -0.229495 0.223581 +Ta 2.15681 6.25911 12.52611 -0.187265 0.793507 0.590029 +Ta 2.10607 4.20234 2.1649 -0.204517 0.52787 -0.182255 +Ta 8.33964 6.36799 2.06365 0.524674 -0.464522 0.434211 +Ta 8.32432 8.32625 4.27611 0.592658 0.021054 -0.297495 +Ta 2.02168 2.04529 4.16312 0.026264 -0.221166 0.743869 +Ta 2.16588 0.04144 6.35945 -0.460731 -0.235445 -0.58949 +Ta 0.01204 2.05369 6.35048 0.259091 0.326814 -0.495643 +Ta 0.01039 0.00368 8.3336 -0.673018 -0.236784 0.607724 +Ta 2.0362 2.11502 8.41459 0.695682 0.392328 0.347056 +Ta 2.06078 8.33946 10.46227 0.422497 0.624614 0.395156 +Ta 8.39011 2.13863 10.50323 0.037882 -0.407402 0.601189 +Ta 4.20505 4.24743 0.06234 -0.328867 -0.887587 -0.011584 +Ta 6.2258 6.25659 0.00484 0.425855 0.635452 0.199651 +Ta 6.25834 4.14378 2.03463 0.154989 0.155997 0.516394 +Ta 4.15865 6.35101 2.06568 0.13635 -0.562846 0.542472 +Ta 4.24566 0.03553 4.16912 -0.27687 0.238692 0.561637 +Ta 6.36116 2.13477 4.23864 -0.0672 0.263837 -0.212871 +Ta 6.28832 0.03663 6.33587 -0.054626 -0.825117 0.073016 +Ta 4.26921 2.03519 6.33887 -0.525339 0.940356 -0.102505 +Ta 4.20405 0.04164 8.423 0.312009 0.161766 0.440029 +Ta 6.3561 2.16604 8.38015 -0.556637 -0.443675 0.656518 +Ta 6.22231 0.06354 10.57462 0.749122 -0.629719 -0.896467 +Ta 4.23446 2.05368 10.5626 -0.759888 0.841158 -0.975855 +Ta 0.00046 4.14735 4.18932 0.123745 1.012572 -0.167229 +Ta 2.18129 6.36027 4.19805 -0.666359 0.064525 -0.022031 +Ta 2.07916 4.25676 6.35081 0.158957 -0.818787 -0.400517 +Ta 8.3474 6.21802 6.35914 0.325132 0.928801 -0.633002 +Ta 8.32754 4.20214 8.39946 0.837886 0.30854 0.750161 +Ta 2.08917 6.30707 8.37548 -0.142599 -0.403183 0.505543 +Ta 2.09792 4.22452 10.55581 0.108204 -0.342607 -0.998745 +Ta 8.34488 6.35512 10.47699 0.002323 -0.149774 0.008416 +Ta 4.12138 4.12799 4.23746 0.523048 0.17672 0.272443 +Ta 6.23634 6.28138 4.16996 -0.092966 -0.776434 0.306905 +Ta 6.36952 4.2719 6.36773 -1.008562 -0.323291 -1.151597 +Ta 4.13873 6.36014 6.35862 0.771311 -0.156347 -0.591177 +Ta 4.2281 4.26918 8.35417 -0.447945 -1.108738 0.194339 +Ta 6.2637 6.27914 8.44271 -0.036946 0.834555 0.001538 +Ta 6.25795 4.26254 10.56883 0.196157 -0.749479 0.01619 +Ta 4.19511 6.21799 10.50605 -0.003346 0.942955 -0.187417 diff --git a/examples/PACKAGES/pod/Ta/XYZ/Elastic_BCC.xyz b/examples/PACKAGES/pod/Ta/XYZ/Elastic_BCC.xyz new file mode 100644 index 0000000000..ba2d560f43 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/XYZ/Elastic_BCC.xyz @@ -0,0 +1,400 @@ +2 +Lattice = "3.31180000305 0.0 0.0 0.0131999999285 3.32649993896 0.0 -0.00789999961853 -0.00710000004619 3.30480003357" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689367 stress="4063.55 -2978.6600000000003 1761.76 -2978.6600000000003 -667.64 1596.31 1761.76 1596.31 6346.89" +Ta 0.0 0.0 0.0 -0.00044 3e-06 -2e-06 +Ta 1.6585 1.6597 1.6524 0.00044 -3e-06 2e-06 +2 +Lattice = "3.31170010567 0.0 0.0 -0.00419999985024 3.30890011787 0.0 -0.00920000020415 -0.0154999997467 3.328799963" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689888 stress="1032.59 906.63 2045.1999999999998 906.63 1918.6499999999999 3453.7599999999998 2045.1999999999998 3453.7599999999998 -4437.12" +Ta 0.0 0.0 0.0 -0.000436 -1e-06 -2e-06 +Ta 1.6491 1.6467 1.6644 0.000436 1e-06 2e-06 +2 +Lattice = "3.3111000061 0.0 0.0 0.00810000021011 3.3273999691 0.0 -0.00889999978244 0.00870000012219 3.31040000916" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689996 stress="1447.25 -1793.1 1960.95 -1793.1 -3771.35 -1928.0900000000001 1960.95 -1928.0900000000001 1685.23" +Ta 0.0 0.0 0.0 0.000438 -0.000443 5e-06 +Ta 1.6552 1.668 1.6552 -0.000438 0.000443 -5e-06 +2 +Lattice = "3.32399988174 0.0 0.0 -0.00179999996908 3.32139992714 0.0 -0.00359999993816 -0.00600000005215 3.31699991226" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690957 stress="-9165.53 392.27 787.5 392.27 -8350.429999999998 1310.7 787.5 1310.7 -6953.2" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.6593 1.6577 1.6585 0.0 0.0 0.0 +2 +Lattice = "3.31089997292 0.0 0.0 0.0124000003561 3.32559990883 0.0 -0.001200000057 -0.0124000003561 3.3341999054" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690521 stress="-8949.18 -2681.52 276.69 -2681.52 -13545.81 2724.27 276.69 2724.27 -16201.730000000001" +Ta 0.0 0.0 0.0 -0.000423 3e-06 0.0 +Ta 1.661 1.6566 1.6671 0.000423 -3e-06 0.0 +2 +Lattice = "3.30999994278 0.0 0.0 0.0110999997705 3.33330011368 0.0 0.00200000009499 -0.00749999983236 3.33319997787" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.69038 stress="-11410.16 -2387.02 -421.38 -2387.02 -18621.670000000002 1636.99 -421.38 1636.99 -18577.07" +Ta 0.0 0.0 0.0 0.000419 -3e-06 -1e-06 +Ta 1.6616 1.6629 1.6666 -0.000419 3e-06 1e-06 +2 +Lattice = "3.31480002403 0.0 0.0 -0.00130000000354 3.30679988861 0.0 0.0152000002563 -0.00179999996908 3.31760001183" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689202 stress="4967.67 296.10999999999996 -3428.94 296.10999999999996 7593.91 406.16 -3428.94 406.16 4075.8900000000003" +Ta 0.0 0.0 0.0 0.000444 0.0 -4e-06 +Ta 1.6644 1.6525 1.6588 -0.000444 0.0 4e-06 +2 +Lattice = "3.30529999733 0.0 0.0 -0.00170000002254 3.32520008087 0.0 0.00170000002254 -0.00829999987036 3.32640004158" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690482 stress="-550.9 376.95 -376.77 376.95 -6880.99 1848.91 -376.77 1848.91 -7253.42" +Ta 0.0 0.0 0.0 0.00043 -0.000434 -2e-06 +Ta 1.6527 1.6584 1.6632 -0.00043 0.000434 2e-06 +2 +Lattice = "3.32270002365 0.0 0.0 -0.00240000011399 3.32060003281 0.0 -0.0148999998346 0.00600000005215 3.30489993095" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689902 stress="-1938.73 553.61 3301.04 553.61 -1240.33 -1332.82 3301.04 -1332.82 3793.0" +Ta 0.0 0.0 0.0 -4e-06 2e-06 -0.000435 +Ta 1.6527 1.6633 1.6524 4e-06 -2e-06 0.000435 +2 +Lattice = "3.3232998848 0.0 0.0 0.00380000006407 3.30970001221 0.0 -0.0163000002503 -0.00340000004508 3.33060002327" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690563 stress="-9502.029999999999 -833.58 3604.52 -833.58 -5183.259999999999 750.48 3604.52 750.48 -11765.68" +Ta 0.0 0.0 0.0 -1e-06 0.000427 1e-06 +Ta 1.6554 1.6532 1.6653 1e-06 -0.000427 -1e-06 +2 +Lattice = "3.31620001793 0.0 0.0 0.00319999991916 3.31369996071 0.0 -0.00190000003204 0.00400000018999 3.31730008125" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690207 stress="617.27 -708.54 421.95 -708.54 1415.16 -887.75 421.95 -887.75 266.22" +Ta 0.0 0.0 0.0 -0.000437 -0.000438 0.00044 +Ta 1.6587 1.6588 1.6587 0.000437 0.000438 -0.00044 +2 +Lattice = "3.32719993591 0.0 0.0 0.00240000011399 3.30349993706 0.0 0.00430000014603 -0.0038999998942 3.31030011177" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689285 stress="138.79 -534.2 -967.78 -534.2 7805.76 865.88 -967.78 865.88 5611.4" +Ta 0.0 0.0 0.0 0.000447 -2e-06 -0.000443 +Ta 1.667 1.6498 1.6551 -0.000447 2e-06 0.000443 +2 +Lattice = "3.3218998909 0.0 0.0 0.00930000003427 3.30679988861 0.0 0.0109000001103 0.00510000018403 3.31669998169" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689768 stress="-340.25 -2080.88 -2448.95 -2080.88 4545.72 -1144.55 -2448.95 -1144.55 1351.01" +Ta 0.0 0.0 0.0 -0.000442 -0.000437 0.000444 +Ta 1.671 1.6559 1.6584 0.000442 0.000437 -0.000444 +2 +Lattice = "3.31170010567 0.0 0.0 0.0164999999106 3.3343000412 0.0 -9.99999974738e-05 0.0138999996707 3.30570006371" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.68968 stress="-50.55 -3689.6800000000003 -1.47 -3689.6800000000003 -7274.5199999999995 -3083.4 -1.47 -3083.4 1889.91" +Ta 0.0 0.0 0.0 -0.000435 1e-06 0.000433 +Ta 1.664 1.6741 1.6529 0.000435 -1e-06 -0.000433 +2 +Lattice = "3.32259988785 0.0 0.0 0.0109999999404 3.30929994583 0.0 -0.0142000000924 -0.0140000004321 3.32019996643" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690074 stress="-3803.7000000000003 -2463.9700000000003 3178.14 -2463.9700000000003 463.82 3109.52 3178.14 3109.52 -3014.8100000000004" +Ta 0.0 0.0 0.0 0.000872 0.000428 1.1e-05 +Ta 1.6598 1.6477 1.6601 -0.000872 -0.000428 -1.1e-05 +2 +Lattice = "3.31579995155 0.0 0.0 0.0163000002503 3.31240010262 0.0 0.00620000017807 -0.00879999995232 3.30360007286" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.688108 stress="8273.59 -3695.21 -1386.53 -3695.21 9410.130000000001 1972.81 -1386.53 1972.81 12301.0" +Ta 0.0 0.0 0.0 0.000448 -5e-06 -2e-06 +Ta 1.6692 1.6518 1.6518 -0.000448 5e-06 2e-06 +2 +Lattice = "3.31279993057 0.0 0.0 0.000699999975041 3.3220000267 0.0 -0.00209999992512 0.00410000002012 3.30430006981" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689241 stress="5705.93 -155.59 468.56 -155.59 2710.42 -920.27 468.56 -920.27 8460.77" +Ta 0.0 0.0 0.0 -1e-06 0.000446 -0.000442 +Ta 1.6557 1.6631 1.6521 1e-06 -0.000446 0.000442 +2 +Lattice = "3.31509995461 0.0 0.0 -0.0077999997884 3.31060004234 0.0 0.0136000001803 -0.0110999997705 3.31699991226" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.68952 stress="3143.69 1764.0800000000002 -3057.7000000000003 1764.0800000000002 4618.12 2493.02 -3057.7000000000003 2493.02 2546.3" +Ta 0.0 0.0 0.0 0.000443 0.000443 -1e-06 +Ta 1.6605 1.6498 1.6585 -0.000443 -0.000443 1e-06 +2 +Lattice = "3.30970001221 0.0 0.0 -0.0141000002623 3.30669999123 0.0 -0.00380000006407 -0.0109999999404 3.30399990082" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.686278 stress="15948.689999999999 3229.23 856.13 3229.23 16943.010000000002 2508.75 856.13 2508.75 17860.57" +Ta 0.0 0.0 0.0 -4e-06 -0.000453 -3e-06 +Ta 1.6459 1.6478 1.652 4e-06 0.000453 3e-06 +2 +Lattice = "3.31279993057 0.0 0.0 0.00680000009015 3.33550000191 0.0 -0.00949999969453 -0.00449999980628 3.33489990234" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690097 stress="-15440.51 -1462.0800000000002 2035.5400000000002 -1462.0800000000002 -22399.3 982.8 2035.5400000000002 982.8 -22219.22" +Ta 0.0 0.0 0.0 0.000418 -1e-06 0.000423 +Ta 1.6551 1.6655 1.6675 -0.000418 1e-06 -0.000423 +2 +Lattice = "3.33060002327 0.0 0.0 -0.00740000000224 3.32299995422 0.0 0.00570000009611 0.00219999998808 3.32229995728" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690811 stress="-17578.07 1606.3700000000001 -1235.27 1606.3700000000001 -15218.79 -469.97 -1235.27 -469.97 -14998.810000000001" +Ta 0.0 0.0 0.0 0.000426 2e-06 -0.000424 +Ta 1.6645 1.6626 1.6611 -0.000426 -2e-06 0.000424 +2 +Lattice = "3.30460000038 0.0 0.0 0.00960000045598 3.32699990273 0.0 -0.0129000004381 0.00889999978244 3.33470010757" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690266 stress="-4850.61 -2063.29 2800.95 -2063.29 -11849.39 -1958.39 2800.95 -1958.39 -14262.01" +Ta 0.0 0.0 0.0 0.000423 -0.00043 -0.000426 +Ta 1.6507 1.6679 1.6673 -0.000423 0.00043 0.000426 +2 +Lattice = "3.3166000843 0.0 0.0 0.00989999994636 3.32179999352 0.0 0.00899999961257 0.00829999987036 3.3178999424" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690597 stress="-3926.0299999999997 -2198.55 -1990.1100000000001 -2198.55 -5568.17 -1841.1599999999999 -1990.1100000000001 -1841.1599999999999 -4321.4800000000005" +Ta 0.0 0.0 0.0 0.000428 0.00043 0.000429 +Ta 1.6678 1.6651 1.659 -0.000428 -0.00043 -0.000429 +2 +Lattice = "3.32559990883 0.0 0.0 0.0149999996647 3.32439994812 0.0 -0.0102000003681 -0.00879999995232 3.31529998779" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690673 stress="-11060.560000000001 -3311.08 2234.96 -3311.08 -10663.09 1930.59 2234.96 1930.59 -7793.1" +Ta 0.0 0.0 0.0 3e-06 2e-06 0.000427 +Ta 1.6652 1.6578 1.6577 -3e-06 -2e-06 -0.000427 +2 +Lattice = "3.32710003853 0.0 0.0 0.0142999999225 3.31200003624 0.0 0.00529999984428 -0.00150000001304 3.3180000782" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690551 stress="-7626.490000000001 -3148.54 -1170.5 -3148.54 -2813.94 319.88 -1170.5 319.88 -4708.87" +Ta 0.0 0.0 0.0 -0.000431 -0.000428 1e-06 +Ta 1.6733 1.6552 1.659 0.000431 0.000428 -1e-06 +2 +Lattice = "3.3218998909 0.0 0.0 0.00829999987036 3.31850004196 0.0 0.0119000002742 0.00230000005104 3.31710004807" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690693 stress="-6193.7300000000005 -1837.26 -2623.8700000000003 -1837.26 -5083.38 -517.81 -2623.8700000000003 -517.81 -4646.26" +Ta 0.0 0.0 0.0 -0.00043 3e-06 -0.000429 +Ta 1.671 1.6604 1.6585 0.00043 -3e-06 0.000429 +2 +Lattice = "3.32940006256 0.0 0.0 -0.00769999995828 3.30390000343 0.0 -0.0120000001043 0.0147000001743 3.32710003853" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.69021 stress="-9842.3 1710.3600000000001 2678.2400000000002 1710.3600000000001 -1794.44 -3224.8100000000004 2678.2400000000002 -3224.8100000000004 -9105.6" +Ta 0.0 0.0 0.0 -0.000437 2e-06 -0.000436 +Ta 1.6548 1.6593 1.6635 0.000437 -2e-06 0.000436 +2 +Lattice = "3.30669999123 0.0 0.0 -0.0122999995947 3.31839990616 0.0 0.00789999961853 -0.0104999998584 3.31259989738" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.688943 stress="8333.89 2780.83 -1785.3000000000002 2780.83 4535.25 2375.9700000000003 -1785.3000000000002 2375.9700000000003 6440.179999999999" +Ta 0.0 0.0 0.0 0.000439 -0.000441 -5e-06 +Ta 1.6512 1.6539 1.6563 -0.000439 0.000441 5e-06 +2 +Lattice = "3.33619999886 0.0 0.0 0.00150000001304 3.30669999123 0.0 0.0163000002503 0.0137999998406 3.33039999008" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690136 stress="-18003.329999999998 -360.51 -3576.72 -360.51 -8835.43 -2976.33 -3576.72 -2976.33 -16192.060000000001" +Ta 0.0 0.0 0.0 0.0 0.00042 -4e-06 +Ta 1.677 1.6603 1.6652 0.0 -0.00042 4e-06 +2 +Lattice = "3.30349993706 0.0 0.0 0.0162000004202 3.30900001526 0.0 -0.00700000021607 0.00680000009015 3.31489992142" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.687444 stress="14486.06 -3661.95 1582.35 -3661.95 12701.029999999999 -1541.32 1582.35 -1541.32 10767.84" +Ta 0.0 0.0 0.0 -0.00045 7e-06 -0.000453 +Ta 1.6563 1.6579 1.6574 0.00045 -7e-06 0.000453 +2 +Lattice = "3.31089997292 0.0 0.0 -0.00889999978244 3.31270003319 0.0 0.00829999987036 0.00520000001416 3.32080006599" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689801 stress="3684.26 1974.24 -1852.3799999999999 1974.24 3114.35 -1156.8400000000001 -1852.3799999999999 -1156.8400000000001 502.12999999999994" +Ta 0.0 0.0 0.0 0.000437 -0.000437 -1e-06 +Ta 1.6552 1.6589 1.6604 -0.000437 0.000437 1e-06 +2 +Lattice = "3.31879997253 0.0 0.0 -0.0110999997705 3.31049990654 0.0 -0.0164999999106 -0.00410000002012 3.32960009575" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690408 stress="-5855.900000000001 2413.85 3653.84 2413.85 -3177.2999999999997 882.09 3653.84 882.09 -9230.779999999999" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.6456 1.6532 1.6648 0.0 0.0 0.0 +2 +Lattice = "3.33170008659 0.0 0.0 0.00689999992028 3.3178999424 0.0 -0.0148000000045 0.0147000001743 3.31089997292" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690362 stress="-10662.19 -1488.5900000000001 3240.34 -1488.5900000000001 -6300.3099999999995 -3192.45 3240.34 -3192.45 -4075.9999999999995" +Ta 0.0 0.0 0.0 4e-06 -4e-06 0.000429 +Ta 1.6619 1.6663 1.6555 -4e-06 4e-06 -0.000429 +2 +Lattice = "3.3343000412 0.0 0.0 0.00540000014007 3.32949995995 0.0 -0.0140000004321 -0.00460000010207 3.33520007133" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.688881 stress="-29339.85 -1153.21 2967.17 -1153.21 -27876.05 983.26 2967.17 983.26 -29592.94" +Ta 0.0 0.0 0.0 -0.000413 0.000412 -2e-06 +Ta 1.6628 1.6625 1.6676 0.000413 -0.000412 2e-06 +2 +Lattice = "3.31089997292 0.0 0.0 0.0131999999285 3.32349991798 0.0 -0.00669999979436 -0.00520000001416 3.33629989624" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690515 stress="-8945.37 -2854.2900000000004 1466.4299999999998 -2854.2900000000004 -12870.23 1153.96 1466.4299999999998 1153.96 -16851.88" +Ta 0.0 0.0 0.0 0.000847 -0.000435 -0.000427 +Ta 1.6588 1.6591 1.6681 -0.000847 0.000435 0.000427 +2 +Lattice = "3.33450007439 0.0 0.0 0.0136000001803 3.32259988785 0.0 0.00700000021607 0.00400000018999 3.32060003281" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690551 stress="-19623.16 -2954.7799999999997 -1523.28 -2954.7799999999997 -15920.310000000001 -868.95 -1523.28 -868.95 -15295.98" +Ta 0.0 0.0 0.0 -0.000424 4e-06 2e-06 +Ta 1.6775 1.6633 1.6603 0.000424 -4e-06 -2e-06 +2 +Lattice = "3.30719995499 0.0 0.0 0.00600000005215 3.30640006065 0.0 -0.00870000012219 -0.00480000022799 3.33119988441" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689487 stress="4760.94 -1330.3100000000002 1958.3200000000002 -1330.3100000000002 5030.59 1081.68 1958.3200000000002 1081.68 -2959.67" +Ta 0.0 0.0 0.0 0.000438 -2e-06 2e-06 +Ta 1.6523 1.6508 1.6656 -0.000438 2e-06 -2e-06 +2 +Lattice = "3.32150006294 0.0 0.0 -0.000699999975041 3.30979990959 0.0 0.0129000004381 -0.0104000000283 3.31489992142" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.68986 stress="-609.8 175.89 -2883.99 175.89 3169.7000000000003 2312.35 -2883.99 2312.35 1528.81" +Ta 0.0 0.0 0.0 0.000444 -3e-06 -0.000442 +Ta 1.6669 1.6497 1.6574 -0.000444 3e-06 0.000442 +2 +Lattice = "3.30480003357 0.0 0.0 -0.00669999979436 3.31340003014 0.0 -0.00689999992028 0.0142999999225 3.3234000206" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689288 stress="7065.76 1506.72 1557.04 1506.72 4265.53 -3227.4500000000003 1557.04 -3227.4500000000003 1046.89" +Ta 0.0 0.0 0.0 -0.000881 -0.000446 0.0 +Ta 1.6455 1.6638 1.6617 0.000881 0.000446 0.0 +2 +Lattice = "3.32389998436 0.0 0.0 -0.00850000046194 3.32249999046 0.0 -0.00889999978244 -0.00329999998212 3.33500003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690457 stress="-18069.48 1814.44 1923.43 1814.44 -17623.8 707.29 1923.43 707.29 -21466.73" +Ta 0.0 0.0 0.0 -0.00042 -2e-06 -2e-06 +Ta 1.6532 1.6596 1.6675 0.00042 2e-06 2e-06 +2 +Lattice = "3.33189988136 0.0 0.0 0.0142999999225 3.31990003586 0.0 -0.00710000004619 -0.0148999998346 3.33529996872" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689792 stress="-23150.59 -3063.23 1550.5800000000002 -3063.23 -19490.46 3197.18 1550.5800000000002 3197.18 -24167.48" +Ta 0.0 0.0 0.0 0.000417 -7e-06 -0.000417 +Ta 1.6696 1.6525 1.6676 -0.000417 7e-06 0.000417 +2 +Lattice = "3.33060002327 0.0 0.0 -0.0143999997526 3.32369995117 0.0 -0.00139999995008 -0.0136000001803 3.33200001717" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690006 stress="-22406.35 3075.85 283.12 3075.85 -20306.539999999997 2912.28 283.12 2912.28 -22816.16" +Ta 0.0 0.0 0.0 -4e-06 -0.000417 -3e-06 +Ta 1.6574 1.655 1.666 4e-06 0.000417 3e-06 +2 +Lattice = "3.3259999752 0.0 0.0 -0.00749999983236 3.33489990234 0.0 -0.0097000002861 0.00089999998454 3.31710004807" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690571 stress="-17118.0 1635.28 2081.98 1635.28 -19844.84 -203.19 2081.98 -203.19 -14345.72" +Ta 0.0 0.0 0.0 2e-06 -1e-06 0.00042 +Ta 1.6544 1.6679 1.6586 -2e-06 1e-06 -0.00042 +2 +Lattice = "3.31739997864 0.0 0.0 -0.0156999994069 3.31970000267 0.0 0.00499999988824 0.0146000003442 3.31509995461" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690213 stress="-2208.17 3473.14 -1080.09 3473.14 -2950.43 -3225.5600000000004 -1080.09 -3225.5600000000004 -1446.74" +Ta 0.0 0.0 0.0 -0.000442 -0.000445 0.000441 +Ta 1.6533 1.6671 1.6576 0.000442 0.000445 -0.000441 +2 +Lattice = "3.31410002708 0.0 0.0 0.0126000000164 3.32780003548 0.0 0.00749999983236 -0.00620000017807 3.33170008659" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690617 stress="-11356.33 -2713.87 -1615.29 -2713.87 -15605.029999999999 1345.96 -1615.29 1345.96 -16800.52" +Ta 0.0 0.0 0.0 -2e-06 2e-06 0.000426 +Ta 1.6671 1.6608 1.6659 2e-06 -2e-06 -0.000426 +2 +Lattice = "3.33410000801 0.0 0.0 -0.00949999969453 3.30469989777 0.0 -0.0119000002742 -0.00879999995232 3.31220006943" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689761 stress="-6865.599999999999 2087.9500000000003 2646.9 2087.9500000000003 2545.62 1920.39 2646.9 1920.39 148.10000000000002" +Ta 0.0 0.0 0.0 0.000443 0.000436 6e-06 +Ta 1.6564 1.648 1.6561 -0.000443 -0.000436 -6e-06 +2 +Lattice = "3.32760000229 0.0 0.0 -0.00190000003204 3.31820011139 0.0 0.000500000023749 -0.0155999995768 3.33640003204" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.69027 stress="-19541.46 406.28 -110.74000000000001 406.28 -16673.960000000003 3361.5 -110.74000000000001 3361.5 -22262.14" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.6631 1.6513 1.6682 0.0 0.0 0.0 +2 +Lattice = "3.30819988251 0.0 0.0 0.00719999987632 3.32559990883 0.0 0.00159999995958 0.00719999987632 3.32410001755" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690599 stress="-1982.3500000000001 -1585.1200000000001 -358.04999999999995 -1585.1200000000001 -7502.34 -1599.04 -358.04999999999995 -1599.04 -7019.8099999999995" +Ta 0.0 0.0 0.0 0.0 -2e-06 0.000434 +Ta 1.6585 1.6664 1.6621 0.0 2e-06 -0.000434 +2 +Lattice = "3.31769990921 0.0 0.0 -0.00579999992624 3.31699991226 0.0 0.00889999978244 0.0162000004202 3.3327999115" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.69061 stress="-9577.12 1230.78 -1945.3100000000002 1230.78 -9380.55 -3550.1800000000003 -1945.3100000000002 -3550.1800000000003 -14308.38" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.6604 1.6666 1.6664 0.0 0.0 0.0 +2 +Lattice = "3.31329989433 0.0 0.0 -0.000399999989895 3.31690001488 0.0 0.0135000003502 0.0 3.33590006828" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690603 stress="-7520.4800000000005 87.73 -2963.21 87.73 -8622.48 0.69 -2963.21 0.69 -14592.02" +Ta 0.0 0.0 0.0 -4e-06 -0.000427 0.000432 +Ta 1.6632 1.6584 1.668 4e-06 0.000427 -0.000432 +2 +Lattice = "3.31369996071 0.0 0.0 -0.00350000010803 3.30380010605 0.0 -0.00719999987632 -0.0097000002861 3.31170010567" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.687908 stress="10264.31 780.75 1638.34 780.75 13511.390000000001 2195.65 1638.34 2195.65 10923.89" +Ta 0.0 0.0 0.0 -3e-06 -0.00045 -0.000451 +Ta 1.6515 1.647 1.6558 3e-06 0.00045 0.000451 +2 +Lattice = "3.31100010872 0.0 0.0 0.00730000017211 3.32240009308 0.0 0.00260000000708 0.00310000008903 3.33559989929" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690688 stress="-8159.87 -1578.8500000000001 -569.48 -1578.8500000000001 -11732.89 -685.38 -569.48 -685.38 -15843.04" +Ta 0.0 0.0 0.0 -0.000422 -0.000425 1e-06 +Ta 1.6604 1.6627 1.6678 0.000422 0.000425 -1e-06 +2 +Lattice = "3.32010006905 0.0 0.0 0.0153999999166 3.31189990044 0.0 0.00710000004619 -0.0116999996826 3.3164999485" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689988 stress="-1287.79 -3409.17 -1564.98 -3409.17 1359.31 2585.44 -1564.98 2585.44 -98.57000000000001" +Ta 0.0 0.0 0.0 -2e-06 3e-06 0.000438 +Ta 1.6713 1.6501 1.6583 2e-06 -3e-06 -0.000438 +2 +Lattice = "3.31150007248 0.0 0.0 -0.0038999998942 3.30809998512 0.0 0.0154999997467 -0.0133999995887 3.32680010796" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689613 stress="2542.36 898.2 -3478.91 898.2 3649.25 3002.21 -3478.91 3002.21 -2359.93" +Ta 0.0 0.0 0.0 0.000437 -0.000437 -8e-06 +Ta 1.6616 1.6473 1.6634 -0.000437 0.000437 8e-06 +2 +Lattice = "3.31990003586 0.0 0.0 0.0131000000983 3.32010006905 0.0 -0.00529999984428 0.00910000037402 3.31820011139" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690678 stress="-5888.5 -2879.58 1153.4 -2879.58 -5946.5 -1998.02 1153.4 -1998.02 -5325.56" +Ta 0.0 0.0 0.0 -0.000433 3e-06 -2e-06 +Ta 1.6638 1.6646 1.6591 0.000433 -3e-06 2e-06 +2 +Lattice = "3.3194000721 0.0 0.0 -0.00700000021607 3.3289000988 0.0 0.0137000000104 -0.0137999998406 3.3069999218" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.69017 stress="-4282.71 1592.26 -3010.8799999999997 1592.26 -7298.28 3048.75 -3010.8799999999997 3048.75 -325.23" +Ta 0.0 0.0 0.0 0.000436 0.000439 0.0 +Ta 1.6631 1.6576 1.6535 -0.000436 -0.000439 0.0 +2 +Lattice = "3.30819988251 0.0 0.0 -0.0120000001043 3.30579996109 0.0 -0.00590000022203 -0.0113000003621 3.31590008736" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.687892 stress="11705.5 2699.26 1327.81 2699.26 12498.38 2559.92 1327.81 2559.92 9195.539999999999" +Ta 0.0 0.0 0.0 -0.000453 -0.000454 -0.000455 +Ta 1.6451 1.6472 1.6579 0.000453 0.000454 0.000455 +2 +Lattice = "3.32249999046 0.0 0.0 -0.0121999997646 3.30819988251 0.0 0.0137999998406 -0.00240000011399 3.320499897" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690132 stress="-3343.01 2704.11 -3081.23 2704.11 1270.1899999999998 549.12 -3081.23 549.12 -2672.32" +Ta 0.0 0.0 0.0 -0.000434 -4e-06 -0.000434 +Ta 1.662 1.6529 1.6602 0.000434 4e-06 0.000434 +2 +Lattice = "3.31189990044 0.0 0.0 -0.00439999997616 3.32540011406 0.0 -0.0063000000082 0.00219999998808 3.32909989357" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690843 stress="-7235.45 958.77 1373.71 958.77 -11469.4 -487.27 1373.71 -487.27 -12631.220000000001" +Ta 0.0 0.0 0.0 -1e-06 0.0 -0.00043 +Ta 1.6506 1.6638 1.6645 1e-06 0.0 0.00043 +2 +Lattice = "3.33640003204 0.0 0.0 0.0120000001043 3.31399989128 0.0 0.00639999983832 -0.00499999988824 3.31839990616" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690598 stress="-16030.460000000001 -2615.3 -1399.57 -2615.3 -9011.369999999999 1069.71 -1399.57 1069.71 -10383.800000000001" +Ta 0.0 0.0 0.0 -0.000861 6e-06 3e-06 +Ta 1.6773 1.6545 1.6592 0.000861 -6e-06 -3e-06 +2 +Lattice = "3.31769990921 0.0 0.0 -0.00949999969453 3.32529997826 0.0 0.0105999996886 0.00949999969453 3.33109998703" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690656 stress="-12733.07 2033.6599999999999 -2291.25 2033.6599999999999 -15085.44 -2061.68 -2291.25 -2061.68 -16870.989999999998" +Ta 0.0 0.0 0.0 -3e-06 -2e-06 0.000426 +Ta 1.6594 1.6674 1.6656 3e-06 2e-06 -0.000426 +2 +Lattice = "3.32620000839 0.0 0.0 0.00270000007004 3.30970001221 0.0 0.01600000076 0.0155999995768 3.33610010147" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690254 stress="-14323.800000000001 -620.5899999999999 -3515.58 -620.5899999999999 -9188.58 -3392.86 -3515.58 -3392.86 -17392.0" +Ta 0.0 0.0 0.0 -0.000423 0.000427 -0.000428 +Ta 1.6724 1.6627 1.668 0.000423 -0.000427 0.000428 +2 +Lattice = "3.31920003891 0.0 0.0 -0.00730000017211 3.32259988785 0.0 -0.0133999995887 -0.0131999999285 3.32820010185" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690694 stress="-11276.81 1552.73 2911.96 1552.73 -12332.94 2876.65 2911.96 2876.65 -14073.7" +Ta 0.0 0.0 0.0 0.000425 2e-06 4e-06 +Ta 1.6493 1.6547 1.6641 -0.000425 -2e-06 -4e-06 +2 +Lattice = "3.33060002327 0.0 0.0 0.00170000002254 3.30550003052 0.0 -0.0154999997467 -0.0108000002801 3.31830000877" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690097 stress="-7398.2 -404.2 3456.2400000000002 -404.2 607.84 2374.71 3456.2400000000002 2374.71 -3477.02" +Ta 0.0 0.0 0.0 4e-06 0.000435 0.000438 +Ta 1.6584 1.6474 1.6592 -4e-06 -0.000435 -0.000438 +2 +Lattice = "3.30870008469 0.0 0.0 0.00079999997979 3.3125 0.0 0.0129000004381 -0.0046999999322 3.3111000061" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.688402 stress="10344.23 -170.68 -2918.0299999999997 -170.68 9114.35 1063.15 -2918.0299999999997 1063.15 9572.1" +Ta 0.0 0.0 0.0 4e-06 -1e-06 -0.000447 +Ta 1.6612 1.6539 1.6555 -4e-06 1e-06 0.000447 +2 +Lattice = "3.32299995422 0.0 0.0 -0.00439999997616 3.3085000515 0.0 0.00289999996312 0.0137999998406 3.304500103" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.688669 stress="3910.4 988.25 -648.7 988.25 8614.3 -3085.0 -648.7 -3085.0 9933.490000000002" +Ta 0.0 0.0 0.0 0.000445 -0.000447 0.000446 +Ta 1.6608 1.6611 1.6523 -0.000445 0.000447 -0.000446 +2 +Lattice = "3.31419992447 0.0 0.0 -0.0108000002801 3.31520009041 0.0 0.0114000001922 -0.00249999994412 3.33610010147" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690538 stress="-7515.75 2343.1000000000004 -2512.81 2343.1000000000004 -7800.79 565.26 -2512.81 565.26 -14362.84" +Ta 0.0 0.0 0.0 0.0 0.000428 0.000433 +Ta 1.6574 1.6564 1.6681 0.0 -0.000428 -0.000433 +2 +Lattice = "3.30870008469 0.0 0.0 -0.0105999996886 3.31060004234 0.0 0.00710000004619 -0.0164000000805 3.32909989357" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689722 stress="2494.02 2358.67 -1602.8700000000001 2358.67 1865.98 3675.35 -1602.8700000000001 3675.35 -4043.8799999999997" +Ta 0.0 0.0 0.0 -2e-06 5e-06 0.000442 +Ta 1.6526 1.6471 1.6646 2e-06 -5e-06 -0.000442 +2 +Lattice = "3.33130002022 0.0 0.0 0.0153999999166 3.3259999752 0.0 0.00669999979436 0.00999999977648 3.31539988518" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690581 stress="-16296.82 -3376.3999999999996 -1468.21 -3376.3999999999996 -14640.43 -2166.98 -1468.21 -2166.98 -11322.16" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.6767 1.668 1.6577 0.0 0.0 0.0 +2 +Lattice = "3.30430006981 0.0 0.0 0.0136000001803 3.32470011711 0.0 0.00740000000224 0.00650000013411 3.3083999157" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.688755 stress="9299.8 -3078.46 -1660.51 -3078.46 2679.5 -1477.71 -1660.51 -1477.71 7991.16" +Ta 0.0 0.0 0.0 0.000442 -4e-06 -2e-06 +Ta 1.6627 1.6656 1.6542 -0.000442 4e-06 2e-06 +2 +Lattice = "3.3273999691 0.0 0.0 0.0126999998465 3.33459997177 0.0 -0.00460000010207 0.0146000003442 3.33229994774" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689312 stress="-25105.09 -2688.4 959.13 -2688.4 -27291.81 -3105.23 959.13 -3105.23 -26574.49" +Ta 0.0 0.0 0.0 0.000414 -7e-06 0.000415 +Ta 1.6678 1.6746 1.6662 -0.000414 7e-06 -0.000415 +2 +Lattice = "3.30520009995 0.0 0.0 -0.0137000000104 3.31570005417 0.0 -0.0162000004202 -0.0124000003561 3.30730009079" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.687388 stress="13516.93 3087.18 3651.46 3087.18 10100.35 2802.34 3651.46 2802.34 12865.9" +Ta 0.0 0.0 0.0 -0.000456 -0.000459 -0.000457 +Ta 1.6376 1.6516 1.6536 0.000456 0.000459 0.000457 +2 +Lattice = "3.31599998474 0.0 0.0 0.000699999975041 3.31730008125 0.0 0.000600000028498 -0.0154999997467 3.32500004768" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690664 stress="-4661.23 -151.07000000000002 -130.38 -151.07000000000002 -5113.86 3419.6 -130.38 3419.6 -7531.63" +Ta 0.0 0.0 0.0 -0.000432 0.0 0.0 +Ta 1.6586 1.6509 1.6625 0.000432 0.0 0.0 +2 +Lattice = "3.3273999691 0.0 0.0 -0.0148999998346 3.32949995995 0.0 0.0137000000104 0.0154999997467 3.33450007439" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.68941 stress="-23795.190000000002 3133.63 -2900.7000000000003 3133.63 -24418.25 -3288.91 -2900.7000000000003 -3288.91 -25917.71" +Ta 0.0 0.0 0.0 3e-06 4e-06 -0.000416 +Ta 1.6631 1.6725 1.6672 -3e-06 -4e-06 0.000416 +2 +Lattice = "3.32439994812 0.0 0.0 0.00760000012815 3.31010007858 0.0 0.00590000022203 0.0038999998942 3.31290006638" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690035 stress="-2106.9399999999996 -1695.3400000000001 -1317.1299999999999 -1695.3400000000001 2496.5299999999997 -868.58 -1317.1299999999999 -868.58 1598.99" +Ta 0.0 0.0 0.0 -0.000442 1e-06 0.000439 +Ta 1.6689 1.657 1.6565 0.000442 -1e-06 -0.000439 +2 +Lattice = "3.32430005074 0.0 0.0 0.00910000037402 3.3289000988 0.0 -0.00740000000224 0.01600000076 3.33310008049" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690015 stress="-20472.059999999998 -1926.96 1574.3700000000001 -1926.96 -21891.98 -3433.3999999999996 1574.3700000000001 -3433.3999999999996 -23153.19" +Ta 0.0 0.0 0.0 4e-06 -0.000422 0.000423 +Ta 1.663 1.6724 1.6666 -4e-06 0.000422 -0.000423 +2 +Lattice = "3.32279992104 0.0 0.0 0.0130000002682 3.32789993286 0.0 -0.00899999961257 -0.001200000057 3.32439994812" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690752 stress="-14810.21 -2823.7999999999997 1946.96 -2823.7999999999997 -16361.699999999999 271.0 1946.96 271.0 -15278.02" +Ta 0.0 0.0 0.0 -3e-06 0.000424 0.0 +Ta 1.6634 1.6634 1.6622 3e-06 -0.000424 0.0 +2 +Lattice = "3.30900001526 0.0 0.0 -0.0046999999322 3.33019995689 0.0 -0.00850000046194 0.00170000002254 3.30809998512" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689825 stress="2936.71 1055.66 1878.49 1055.66 -3856.89 -383.2 1878.49 -383.2 3236.96" +Ta 0.0 0.0 0.0 -1e-06 0.000443 -0.000437 +Ta 1.6479 1.666 1.654 1e-06 -0.000443 0.000437 +2 +Lattice = "3.32730007172 0.0 0.0 -0.0148000000045 3.31719994545 0.0 0.00960000045598 -0.0111999996006 3.32929992676" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690562 stress="-15582.82 3214.2400000000002 -2112.58 3214.2400000000002 -12428.97 2441.49 -2112.58 2441.49 -16168.56" +Ta 0.0 0.0 0.0 -0.000428 -1e-06 0.000428 +Ta 1.661 1.653 1.6647 0.000428 1e-06 -0.000428 +2 +Lattice = "3.31780004501 0.0 0.0 -0.0141000002623 3.31990003586 0.0 -0.000199999994948 -0.00460000010207 3.33559989929" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690622 stress="-12368.81 3035.58 36.589999999999996 3035.58 -13009.29 1003.22 36.589999999999996 1003.22 -17869.59" +Ta 0.0 0.0 0.0 0.000419 -0.00042 -1e-06 +Ta 1.6518 1.6576 1.6678 -0.000419 0.00042 1e-06 +2 +Lattice = "3.31019997597 0.0 0.0 0.0127999996766 3.32069993019 0.0 0.0063000000082 -0.00170000002254 3.30509996414" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.688764 stress="8054.89 -2896.21 -1408.45 -2896.21 4644.51 375.59999999999997 -1408.45 375.59999999999997 9733.77" +Ta 0.0 0.0 0.0 -0.000446 4e-06 0.000445 +Ta 1.6646 1.6595 1.6526 0.000446 -4e-06 -0.000445 +2 +Lattice = "3.31080007553 0.0 0.0 -0.00319999991916 3.31229996681 0.0 -0.00240000011399 0.00359999993816 3.32299995422" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690011 stress="2899.77 713.48 536.4100000000001 713.48 2419.23 -804.18 536.4100000000001 -804.18 -1023.68" +Ta 0.0 0.0 0.0 1e-06 0.000438 -1e-06 +Ta 1.6526 1.658 1.6615 -1e-06 -0.000438 1e-06 +2 +Lattice = "3.30539989471 0.0 0.0 0.00359999993816 3.31970000267 0.0 -0.0097000002861 -0.0120000001043 3.30390000343" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.687696 stress="13108.67 -840.56 2187.26 -840.56 8404.43 2733.05 2187.26 2733.05 13609.949999999999" +Ta 0.0 0.0 0.0 0.000444 0.000447 -0.000441 +Ta 1.6497 1.6539 1.6519 -0.000444 -0.000447 0.000441 +2 +Lattice = "3.31929993629 0.0 0.0 0.00240000011399 3.32459998131 0.0 0.00540000014007 0.00109999999404 3.32540011406" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.691019 stress="-10964.99 -525.81 -1177.09 -525.81 -12623.84 -241.71 -1177.09 -241.71 -12870.95" +Ta 0.0 0.0 0.0 0.000426 -0.000428 -1e-06 +Ta 1.6636 1.6628 1.6627 -0.000426 0.000428 1e-06 +2 +Lattice = "3.31080007553 0.0 0.0 0.00350000010803 3.31130003929 0.0 -0.0135000003502 0.00310000008903 3.31500005722" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689025 stress="7287.55 -782.66 3041.1000000000004 -782.66 7135.919999999999 -692.63 3041.1000000000004 -692.63 5936.740000000001" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.6504 1.6572 1.6575 0.0 0.0 0.0 +2 +Lattice = "3.30800008774 0.0 0.0 -0.00200000009499 3.33439993858 0.0 0.0111999996006 0.0130000002682 3.31060004234" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689952 stress="508.71 421.52 -2451.6800000000003 421.52 -7909.360000000001 -2885.62 -2451.6800000000003 -2885.62 -315.85999999999996" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.6586 1.6737 1.6553 0.0 0.0 0.0 +2 +Lattice = "3.3289000988 0.0 0.0 0.00820000004023 3.32640004158 0.0 -0.0105999996886 -0.0156999994069 3.31559991837" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.69061 stress="-14693.78 -1821.97 2311.93 -1821.97 -13931.74 3407.2 2311.93 3407.2 -10544.75" +Ta 0.0 0.0 0.0 0.000429 -0.000429 -1e-06 +Ta 1.6633 1.6553 1.6578 -0.000429 0.000429 1e-06 +2 +Lattice = "3.32290005684 0.0 0.0 0.0154999997467 3.31669998169 0.0 0.00870000012219 0.0142000000924 3.32319998741" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690595 stress="-9023.58 -3411.2599999999998 -1934.4099999999999 -3411.2599999999998 -7071.44 -3121.81 -1934.4099999999999 -3121.81 -9087.630000000001" +Ta 0.0 0.0 0.0 0.000435 -0.000433 2e-06 +Ta 1.6736 1.6654 1.6616 -0.000435 0.000433 -2e-06 +2 +Lattice = "3.3303000927 0.0 0.0 0.0146000003442 3.31329989433 0.0 0.0110999997705 0.00760000012815 3.33520007133" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690231 stress="-18800.98 -3140.71 -2429.11 -3140.71 -13532.06 -1652.97 -2429.11 -1652.97 -20281.1" +Ta 0.0 0.0 0.0 4e-06 -0.000419 2e-06 +Ta 1.678 1.6604 1.6676 -4e-06 0.000419 -2e-06 +2 +Lattice = "3.33489990234 0.0 0.0 0.0162000004202 3.32060003281 0.0 -0.00230000005104 0.01070000045 3.32109999657" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690469 stress="-19225.86 -3508.14 482.12 -3508.14 -14795.67 -2294.36 482.12 -2294.36 -14933.130000000001" +Ta 0.0 0.0 0.0 -5e-06 0.000425 -0.000425 +Ta 1.6744 1.6657 1.6605 5e-06 -0.000425 0.000425 +2 +Lattice = "3.31529998779 0.0 0.0 -0.00449999980628 3.31590008736 0.0 -0.00150000001304 -0.0077999997884 3.32039999962" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690482 stress="-1223.53 989.7099999999999 330.42 989.7099999999999 -1425.84 1726.31 330.42 1726.31 -2854.88" +Ta 0.0 0.0 0.0 0.000437 0.000437 3e-06 +Ta 1.6547 1.6541 1.6602 -0.000437 -0.000437 -3e-06 +2 +Lattice = "3.33599996567 0.0 0.0 0.0127999996766 3.31879997253 0.0 0.0046999999322 0.00219999998808 3.33610010147" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689613 stress="-26129.239999999998 -2719.4500000000003 -1009.22 -2719.4500000000003 -20885.58 -474.41 -1009.22 -474.41 -26139.41" +Ta 0.0 0.0 0.0 0.000416 -4e-06 0.000416 +Ta 1.6768 1.6605 1.6681 -0.000416 4e-06 -0.000416 +2 +Lattice = "3.30529999733 0.0 0.0 -0.0137000000104 3.31130003929 0.0 -0.0113000003621 -0.00879999995232 3.31049990654" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.687426 stress="14036.429999999998 3100.8300000000004 2557.21 3100.8300000000004 12085.73 1993.28 2557.21 1993.28 12358.140000000001" +Ta 0.0 0.0 0.0 0.000442 -0.00045 -0.00045 +Ta 1.6402 1.6512 1.6552 -0.000442 0.00045 0.00045 +2 +Lattice = "3.30550003052 0.0 0.0 -0.00620000017807 3.30990004539 0.0 0.0144999995828 -0.00209999992512 3.33089995384" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689562 stress="4550.63 1373.71 -3248.75 1373.71 3169.0 478.2 -3248.75 478.2 -3584.6" +Ta 0.0 0.0 0.0 4e-06 -1e-06 -0.000443 +Ta 1.6569 1.6539 1.6654 -4e-06 1e-06 0.000443 +2 +Lattice = "3.31920003891 0.0 0.0 0.0109999999404 3.31369996071 0.0 0.0155999995768 0.0151000004262 3.3273999691" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.6904 stress="-6656.91 -2444.4 -3459.77 -2444.4 -4902.92 -3339.7000000000003 -3459.77 -3339.7000000000003 -9220.65" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.6729 1.6644 1.6637 0.0 0.0 0.0 +2 +Lattice = "3.32829999924 0.0 0.0 0.00159999995958 3.32319998741 0.0 0.0164999999106 -0.0138999996707 3.32419991493" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690561 stress="-16787.82 -307.25 -3575.27 -307.25 -15202.7 3000.58 -3575.27 3000.58 -15509.24" +Ta 0.0 0.0 0.0 0.0 0.000423 3e-06 +Ta 1.6732 1.6547 1.6621 0.0 -0.000423 -3e-06 +2 +Lattice = "3.33509993553 0.0 0.0 0.0 3.32529997826 0.0 0.00889999978244 0.0130000002682 3.33629989624" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689107 stress="-28509.83 -17.12 -1893.91 -17.12 -25562.52 -2751.32 -1893.91 -2751.32 -28867.920000000002" +Ta 0.0 0.0 0.0 -2e-06 0.000408 0.00041 +Ta 1.672 1.6692 1.6682 2e-06 -0.000408 -0.00041 +2 +Lattice = "3.33400011063 0.0 0.0 -0.0162000004202 3.30960011482 0.0 -0.0131000000983 -0.0115000000224 3.31579995155" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690145 stress="-10872.289999999999 3539.75 2881.95 3539.75 -3120.2999999999997 2484.82 2881.95 2484.82 -5070.15" +Ta 0.0 0.0 0.0 -0.00044 -0.000434 -7e-06 +Ta 1.6523 1.649 1.6579 0.00044 0.000434 7e-06 +2 +Lattice = "3.32870006561 0.0 0.0 0.00930000003427 3.33170008659 0.0 -0.00400000018999 -0.0147000001743 3.31769990921" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.690482 stress="-17992.4 -2032.8300000000002 873.85 -2032.8300000000002 -18940.809999999998 3171.19 873.85 3171.19 -14593.14" +Ta 0.0 0.0 0.0 1e-06 4e-06 0.00042 +Ta 1.667 1.6585 1.6589 -1e-06 -4e-06 -0.00042 +2 +Lattice = "3.32459998131 0.0 0.0 -0.00170000002254 3.30690002441 0.0 0.0126000000164 0.00930000003427 3.31570005417" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.689864 stress="-2068.5699999999997 357.16999999999996 -2815.44 357.16999999999996 3633.85 -2059.7599999999998 -2815.44 -2059.7599999999998 802.9" +Ta 0.0 0.0 0.0 0.000444 3e-06 -0.000442 +Ta 1.6678 1.6581 1.6578 -0.000444 -3e-06 0.000442 diff --git a/examples/PACKAGES/pod/Ta/XYZ/Elastic_FCC.xyz b/examples/PACKAGES/pod/Ta/XYZ/Elastic_FCC.xyz new file mode 100644 index 0000000000..b0f70e3e0c --- /dev/null +++ b/examples/PACKAGES/pod/Ta/XYZ/Elastic_FCC.xyz @@ -0,0 +1,600 @@ +4 +Lattice = "4.20979976654 0.0 0.0 0.00079999997979 4.19229984283 0.0 0.00139999995008 -0.00289999996312 4.20120000839" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.437936 stress="32125.329999999998 -282.22 -267.48 -282.22 28704.550000000003 301.20000000000005 -267.48 301.20000000000005 19406.25" +Ta 2.1056 -0.0014 2.1006 -0.00024 -0.000831 -4.2e-05 +Ta 2.1053 2.0961 0.0 0.00024 0.000831 4.2e-05 +Ta 0.0011 2.0947 2.1006 0.000211 -2.8e-05 -7.8e-05 +Ta 0.0 0.0 0.0 -0.000211 2.8e-05 7.8e-05 +4 +Lattice = "4.21169996262 0.0 0.0 -0.0197000000626 4.18310022354 0.0 0.0122999995947 -0.0172000005841 4.21549987793" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.438504 stress="28580.99 4661.44 -2537.73 4661.44 21736.13 3777.39 -2537.73 3777.39 15422.61" +Ta 2.112 -0.0086 2.1078 -8.5e-05 0.000609 -0.000432 +Ta 2.096 2.0916 0.0 8.5e-05 -0.000609 0.000432 +Ta -0.0037 2.083 2.1078 -7.9e-05 -0.000591 -0.00044 +Ta 0.0 0.0 0.0 7.9e-05 0.000591 0.00044 +4 +Lattice = "4.20760011673 0.0 0.0 0.00839999970049 4.19579982758 0.0 -0.0108000002801 0.00989999994636 4.19500017166" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.436378 stress="32906.770000000004 -1998.4299999999998 2448.51 -1998.4299999999998 31390.95 -2209.73 2448.51 -2209.73 20534.55" +Ta 2.1068 4.2007 2.0975 4.9e-05 0.00037 -0.000158 +Ta 2.108 2.0979 0.0 -4.9e-05 -0.00037 0.000158 +Ta -0.0012 2.1028 2.0975 4.9e-05 0.00037 -0.000158 +Ta 0.0 0.0 0.0 -4.9e-05 -0.00037 0.000158 +4 +Lattice = "4.21610021591 0.0 0.0 -0.0186000000685 4.20079994202 0.0 -0.0110999997705 -0.0149999996647 4.195499897" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.441551 stress="27882.2 4157.13 2708.72 4157.13 24066.9 3156.97 2708.72 3156.97 13737.52" +Ta 2.0839 4.1933 2.0977 6.8e-05 -4.7e-05 0.000367 +Ta 2.0987 2.1004 0.0 0.000703 0.000158 -0.000404 +Ta -0.0148 2.0929 2.0977 -0.000703 -0.000158 0.000404 +Ta 0.0 0.0 0.0 -6.8e-05 4.7e-05 -0.000367 +4 +Lattice = "4.18009996414 0.0 0.0 -0.00079999997979 4.19099998474 0.0 -0.00109999999404 -0.0186000000685 4.19029998779" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.416957 stress="47483.73 251.66 89.96 251.66 51115.740000000005 3817.67 89.96 3817.67 39271.009999999995" +Ta 2.0895 -0.0093 2.0952 -0.000287 7.5e-05 -0.000462 +Ta 2.0896 2.0955 0.0 0.000287 -7.5e-05 0.000462 +Ta 4.1791 2.0862 2.0952 0.00038 6.8e-05 -0.000503 +Ta 0.0 0.0 0.0 -0.00038 -6.8e-05 0.000503 +4 +Lattice = "4.21759986877 0.0 0.0 0.00989999994636 4.20160007477 0.0 -0.0164999999106 0.000600000028498 4.1861000061" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.440495 stress="30412.84 -2230.41 3936.28 -2230.41 27956.19 -314.22 3936.28 -314.22 16511.39" +Ta 2.1006 0.0003 2.093 -0.000512 -1.6e-05 0.000315 +Ta 2.1138 2.1008 0.0 -0.000516 -1.4e-05 -0.000327 +Ta 4.2143 2.1011 2.093 0.000516 1.4e-05 0.000327 +Ta 0.0 0.0 0.0 0.000512 1.6e-05 -0.000315 +4 +Lattice = "4.20800018311 0.0 0.0 -0.00609999988228 4.19269990921 0.0 0.0185000002384 0.00510000018403 4.20429992676" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.437972 stress="30692.39 1017.5300000000001 -3953.9 1017.5300000000001 27371.22 -937.5 -3953.9 -937.5 18526.5" +Ta 2.1071 4.1952 2.1022 0.000867 0.001178 -0.000599 +Ta 2.101 2.0964 0.0 -0.000867 -0.001178 0.000599 +Ta 4.2142 2.0989 2.1022 -3.6e-05 -0.000335 -0.000411 +Ta 0.0 0.0 0.0 3.6e-05 0.000335 0.000411 +4 +Lattice = "4.20389986038 0.0 0.0 0.0109999999404 4.21560001373 0.0 -0.0149999996647 -0.0195000004023 4.21710014343" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.44586 stress="13322.5 -1851.3999999999999 2698.2400000000002 -1851.3999999999999 15084.53 4168.71 2698.2400000000002 4168.71 3183.15" +Ta 2.0944 -0.0097 2.1085 0.000605 -0.001004 0.000354 +Ta 2.1075 2.1078 0.0 -0.000787 0.00036 -0.000493 +Ta 4.2019 2.098 2.1085 0.000145 0.000977 0.000593 +Ta 0.0 0.0 0.0 3.7e-05 -0.000333 -0.000454 +4 +Lattice = "4.20989990234 0.0 0.0 0.0194000005722 4.18979978561 0.0 0.0187999997288 -0.00710000004619 4.1998000145" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.435744 stress="32866.979999999996 -4705.08 -4510.19 -4705.08 27538.81 1684.04 -4510.19 1684.04 19619.25" +Ta 2.1338 4.1862 2.0999 -0.000654 0.000551 -0.000151 +Ta 2.1146 2.0949 0.0 0.000654 -0.000551 0.000151 +Ta 0.0191 2.0913 2.0999 0.000168 0.00073 -0.000338 +Ta 0.0 0.0 0.0 -0.000168 -0.00073 0.000338 +4 +Lattice = "4.20370006561 0.0 0.0 -0.00999999977648 4.18909978867 0.0 0.0038999998942 0.0115999998525 4.21619987488" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.438209 stress="27954.8 2323.13 -793.2399999999999 2323.13 23969.38 -2424.6400000000003 -793.2399999999999 -2424.6400000000003 15680.8" +Ta 2.1038 0.0058 2.1081 0.000328 -0.000478 -1.9e-05 +Ta 2.0969 2.0945 0.0 -0.000328 0.000478 1.9e-05 +Ta -0.003 2.1003 2.1081 -0.000328 0.000478 1.9e-05 +Ta 0.0 0.0 0.0 0.000328 -0.000478 -1.9e-05 +4 +Lattice = "4.19409990311 0.0 0.0 -0.00949999969453 4.18279981613 0.0 -0.00359999993816 0.0146000003442 4.20279979706" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.42629 stress="40994.259999999995 1984.0500000000002 678.41 1984.0500000000002 38515.95 -2950.21 678.41 -2950.21 30369.28" +Ta 2.0953 0.0073 2.1014 -0.000264 2.1e-05 -3e-06 +Ta 2.0923 2.0914 0.0 0.000264 -2.1e-05 3e-06 +Ta -0.0065 2.0987 2.1014 -0.000264 2.1e-05 -3e-06 +Ta 0.0 0.0 0.0 0.000264 -2.1e-05 3e-06 +4 +Lattice = "4.21500015259 0.0 0.0 0.00240000011399 4.2077999115 0.0 0.00559999980032 -0.00430000014603 4.19150018692" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.443301 stress="25318.89 -582.25 -1370.1399999999999 -582.25 24260.940000000002 1009.18 -1370.1399999999999 1009.18 11853.45" +Ta 2.1103 -0.0021 2.0957 2.5e-05 -0.00092 0.000616 +Ta 2.1087 2.1039 0.0 -3.1e-05 0.000243 -0.000622 +Ta 0.004 2.1017 2.0957 4e-05 0.000897 0.000626 +Ta 0.0 0.0 0.0 -3.4e-05 -0.00022 -0.000621 +4 +Lattice = "4.21619987488 0.0 0.0 -0.0207000002265 4.1875 0.0 -0.00230000005104 0.00730000017211 4.20310020447" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.439002 stress="30242.61 4765.59 418.83 4765.59 23708.24 -1576.43 418.83 -1576.43 16414.149999999998" +Ta 2.0863 4.1911 2.1015 -0.00067 0.000288 0.000472 +Ta 2.0977 2.0937 0.0 0.000637 0.000248 -0.000453 +Ta 4.2047 2.0974 2.1015 6.7e-05 -0.00028 0.000455 +Ta 0.0 0.0 0.0 -3.3e-05 -0.000255 -0.000474 +4 +Lattice = "4.21169996262 0.0 0.0 -0.0137999998406 4.18540000916 0.0 0.00350000010803 0.016799999401 4.19210004807" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.432438 stress="38865.54 2976.27 -1187.3700000000001 2976.27 32433.36 -3670.5899999999997 -1187.3700000000001 -3670.5899999999997 24012.71" +Ta 2.0938 4.1938 2.0961 0.000109 1.5e-05 -0.000266 +Ta 2.0989 2.0927 0.0 0.000626 -5.5e-05 0.000181 +Ta -0.0051 2.1011 2.0961 -0.000626 5.5e-05 -0.000181 +Ta 0.0 0.0 0.0 -0.000109 -1.5e-05 0.000266 +4 +Lattice = "4.18310022354 0.0 0.0 -0.00300000002608 4.18790006638 0.0 0.0161000005901 -0.0153999999166 4.18289995193" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.412654 stress="53423.5 705.21 -3760.97 705.21 56329.25 3452.61 -3760.97 3452.61 44823.36" +Ta 2.0996 -0.0077 2.0915 0.000209 0.000715 -0.000359 +Ta 2.09 2.094 0.0 0.000554 -0.000722 0.000333 +Ta 0.0066 2.0863 2.0915 -0.000628 -0.000725 -0.000262 +Ta 0.0 0.0 0.0 -0.000135 0.000731 0.000288 +4 +Lattice = "4.19859981537 0.0 0.0 -0.00520000001416 4.21680021286 0.0 -0.000199999994948 0.00190000003204 4.20230007172" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.443231 stress="21408.78 997.66 2.63 997.66 23951.809999999998 -420.08 2.63 -420.08 10910.34" +Ta 2.094 4.2177 2.1012 -4.8e-05 0.000221 -0.000815 +Ta 2.0967 2.1084 0.0 4.8e-05 -0.000221 0.000815 +Ta 4.1959 2.1093 2.1012 -4.8e-05 0.000221 -0.000815 +Ta 0.0 0.0 0.0 4.8e-05 -0.000221 0.000815 +4 +Lattice = "4.21309995651 0.0 0.0 0.00989999994636 4.17939996719 0.0 -0.0111999996006 -0.0109000001103 4.19469976425" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.431513 stress="38571.840000000004 -2057.94 2001.0400000000002 -2057.94 31128.620000000003 2212.8199999999997 2001.0400000000002 2212.8199999999997 25395.620000000003" +Ta 2.101 -0.0054 2.0973 -0.000812 -0.000699 0.000382 +Ta 2.1115 2.0897 0.0 -5.2e-05 0.000172 -0.000317 +Ta 4.2124 2.0842 2.0973 0.000823 0.000706 0.000273 +Ta 0.0 0.0 0.0 4.1e-05 -0.000179 -0.000337 +4 +Lattice = "4.21220016479 0.0 0.0 0.00730000017211 4.19630002975 0.0 0.00209999992512 -0.0115000000224 4.18480014801" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.435608 stress="35907.1 -1805.28 -643.2900000000001 -1805.28 32898.1 2687.74 -643.2900000000001 2687.74 21620.26" +Ta 2.1144 4.1905 2.0924 0.000371 0.000304 -3e-06 +Ta 2.1097 2.0981 0.0 0.000371 0.000304 -3e-06 +Ta 0.0047 2.0924 2.0924 -0.000371 -0.000304 3e-06 +Ta 0.0 0.0 0.0 -0.000371 -0.000304 3e-06 +4 +Lattice = "4.18069982529 0.0 0.0 -0.0109000001103 4.21169996262 0.0 -0.00529999984428 0.00520000001416 4.21330022812" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.437689 stress="23769.33 2509.14 1235.52 2509.14 31281.32 -1087.23 1235.52 -1087.23 17393.4" +Ta 2.0768 4.2143 2.1067 -0.000106 -0.000368 -0.000493 +Ta 2.0849 2.1058 0.0 0.000106 0.000368 0.000493 +Ta 4.1726 2.1084 2.1067 0.000104 0.000319 -0.000489 +Ta 0.0 0.0 0.0 -0.000104 -0.000319 0.000489 +4 +Lattice = "4.18959999084 0.0 0.0 0.0164999999106 4.20200014114 0.0 0.00899999961257 -0.0188999995589 4.19029998779" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.428447 stress="39131.659999999996 -3973.89 -2296.86 -3973.89 42258.21 4597.84 -2296.86 4597.84 29361.260000000002" +Ta 2.0993 -0.0094 2.0951 0.000613 -0.000529 0.000975 +Ta 2.1031 2.101 0.0 -0.000613 0.000529 -0.000975 +Ta 0.0128 2.0916 2.0951 -0.000208 -0.000185 0.000662 +Ta 0.0 0.0 0.0 0.000208 0.000185 -0.000662 +4 +Lattice = "4.18120002747 0.0 0.0 -0.000399999989895 4.21000003815 0.0 0.00460000010207 0.0187999997288 4.19910001755" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.432255 stress="29757.62 -182.62 -536.07 -182.62 36285.020000000004 -3344.74 -536.07 -3344.74 22592.0" +Ta 2.0929 0.0094 2.0995 -0.00013 1.7e-05 0.000285 +Ta 2.0904 2.105 0.0 0.00013 -1.7e-05 -0.000285 +Ta 0.0021 2.1144 2.0995 -0.00013 1.7e-05 0.000285 +Ta 0.0 0.0 0.0 0.00013 -1.7e-05 -0.000285 +4 +Lattice = "4.21250009537 0.0 0.0 -0.0190999992192 4.2062997818 0.0 0.0172000005841 0.0121999997646 4.1968998909" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.442315 stress="24536.86 4406.19 -4080.28 4406.19 23952.329999999998 -2854.26 -4080.28 -2854.26 11636.13" +Ta 2.1149 0.0061 2.0984 -0.00079 -0.000901 0.000821 +Ta 2.0967 2.1031 0.0 0.00079 0.000901 -0.000821 +Ta -0.0009 2.1092 2.0984 -0.00026 0.000434 0.000757 +Ta 0.0 0.0 0.0 0.00026 -0.000434 -0.000757 +4 +Lattice = "4.18179988861 0.0 0.0 0.0136000001803 4.21280002594 0.0 0.00310000008903 -0.0118000004441 4.20720005035" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.436613 stress="25874.06 -3205.31 -821.0 -3205.31 32985.54 2726.66 -821.0 2726.66 19695.18" +Ta 2.0925 -0.0059 2.1036 -0.000254 -3.3e-05 -7.2e-05 +Ta 2.0977 2.1064 0.0 0.000254 3.3e-05 7.2e-05 +Ta 0.0084 2.1005 2.1036 -0.000254 -3.3e-05 -7.2e-05 +Ta 0.0 0.0 0.0 0.000254 3.3e-05 7.2e-05 +4 +Lattice = "4.20440006256 0.0 0.0 -0.00430000014603 4.18720006943 0.0 0.0116999996826 0.0206000003964 4.19589996338" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.430825 stress="38754.51 1016.0100000000001 -2801.6 1016.0100000000001 34556.35 -4530.67 -2801.6 -4530.67 26227.129999999997" +Ta 2.108 0.0103 2.0979 0.000384 -3.4e-05 0.000554 +Ta 2.1 2.0936 0.0 0.000373 -0.000115 -0.00061 +Ta 0.0037 2.1039 2.0979 -0.000373 0.000115 0.00061 +Ta 0.0 0.0 0.0 -0.000384 3.4e-05 -0.000554 +4 +Lattice = "4.1888999939 0.0 0.0 0.0038999998942 4.20720005035 0.0 -0.0144999995828 0.0156999994069 4.19560003281" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.43312 stress="29781.53 -523.96 3434.8399999999997 -523.96 33821.21 -3382.98 3434.8399999999997 -3382.98 20448.34" +Ta 2.0911 4.215 2.0978 2.8e-05 0.00036 4.3e-05 +Ta 2.0964 2.1036 0.0 -2.8e-05 -0.00036 -4.3e-05 +Ta -0.0053 2.1114 2.0978 2.8e-05 0.00036 4.3e-05 +Ta 0.0 0.0 0.0 -2.8e-05 -0.00036 -4.3e-05 +4 +Lattice = "4.21330022812 0.0 0.0 0.000699999975041 4.1810002327 0.0 0.0054999999702 -0.00949999969453 4.19969987869" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.434347 stress="37957.909999999996 -320.79 -1076.83 -320.79 30562.539999999997 2073.23 -1076.83 2073.23 23518.02" +Ta 2.1094 -0.0047 2.0998 -8.7e-05 -0.000391 0.000502 +Ta 2.107 2.0905 0.0 8.7e-05 0.000391 -0.000502 +Ta 0.0031 2.0858 2.0998 -8.7e-05 -0.000391 0.000502 +Ta 0.0 0.0 0.0 8.7e-05 0.000391 -0.000502 +4 +Lattice = "4.20370006561 0.0 0.0 0.00340000004508 4.18830013275 0.0 -0.00089999998454 0.00980000011623 4.19320011139" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.430573 stress="38159.329999999994 -261.17 350.0 -261.17 35372.36 -2364.75 350.0 -2364.75 25174.510000000002" +Ta 2.1014 0.0049 2.0966 0.000389 -0.00053 2.4e-05 +Ta 2.1036 2.0941 0.0 -0.000389 0.00053 -2.4e-05 +Ta 0.0013 2.099 2.0966 -0.000389 0.00053 -2.4e-05 +Ta 0.0 0.0 0.0 0.000389 -0.00053 2.4e-05 +4 +Lattice = "4.20860004425 0.0 0.0 -0.00989999994636 4.20669984818 0.0 -0.0154999997467 0.00520000001416 4.21969985962" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.445665 stress="14174.23 2425.32 3028.21 2425.32 15030.34 -809.6999999999999 3028.21 -809.6999999999999 2911.0299999999997" +Ta 2.0966 0.0026 2.1098 -0.000412 -0.000614 0.000581 +Ta 2.0994 2.1033 0.0 -0.00059 0.000627 -0.000659 +Ta 4.1959 2.1059 2.1098 0.000541 0.000424 0.000445 +Ta 0.0 0.0 0.0 0.000461 -0.000437 -0.000367 +4 +Lattice = "4.19920015335 0.0 0.0 0.0185000002384 4.19920015335 0.0 -0.0126000000164 0.00540000014007 4.20139980316" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.435898 stress="32203.23 -4272.68 2945.41 -4272.68 31706.99 -1474.9 2945.41 -1474.9 21250.72" +Ta 2.0933 0.0027 2.1007 0.00043 -1.3e-05 0.000192 +Ta 2.1088 2.0996 0.0 0.00122 -8.7e-05 -0.000171 +Ta 0.003 2.1023 2.1007 -0.00122 8.7e-05 0.000171 +Ta 0.0 0.0 0.0 -0.00043 1.3e-05 -0.000192 +4 +Lattice = "4.2108001709 0.0 0.0 0.0163000002503 4.21479988098 0.0 0.01070000045 0.00499999988824 4.18380022049" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.442107 stress="28916.579999999998 -3579.5699999999997 -2277.82 -3579.5699999999997 29458.98 -1392.66 -2277.82 -1392.66 14592.84" +Ta 2.1108 0.0025 2.0919 -0.000298 4e-05 1.5e-05 +Ta 2.1136 2.1074 0.0 -0.000298 4e-05 1.5e-05 +Ta 0.0135 2.1099 2.0919 0.000298 -4e-05 -1.5e-05 +Ta 0.0 0.0 0.0 0.000298 -4e-05 -1.5e-05 +4 +Lattice = "4.19960021973 0.0 0.0 0.00079999997979 4.18790006638 0.0 -0.0054999999702 0.00499999988824 4.21040010452" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.434432 stress="33222.78 -147.47 1254.14 -147.47 29633.84 -1145.8 1254.14 -1145.8 20687.69" +Ta 2.097 0.0025 2.1052 0.00033 -1.2e-05 0.000134 +Ta 2.1002 2.094 0.0 -0.000357 -0.00057 -0.000134 +Ta 4.1972 2.0964 2.1052 0.000357 0.00057 0.000134 +Ta 0.0 0.0 0.0 -0.00033 1.2e-05 -0.000134 +4 +Lattice = "4.18860006332 0.0 0.0 0.00829999987036 4.19880008698 0.0 0.00680000009015 -0.0104999998584 4.21710014343" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.436308 stress="26865.34 -1570.0700000000002 -1633.81 -1570.0700000000002 30088.280000000002 2199.78 -1633.81 2199.78 18762.14" +Ta 2.0977 -0.0052 2.1086 0.000219 -0.000492 -0.000515 +Ta 2.0984 2.0994 0.0 0.000816 0.000404 0.000554 +Ta 0.0076 2.0942 2.1086 -0.000816 -0.000404 -0.000554 +Ta 0.0 0.0 0.0 -0.000219 0.000492 0.000515 +4 +Lattice = "4.1999001503 0.0 0.0 0.01600000076 4.18179988861 0.0 0.0184000004083 0.00219999998808 4.19189977646" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.423938 stress="45156.3 -3736.32 -4044.29 -3736.32 42163.939999999995 -272.71000000000004 -4044.29 -272.71000000000004 33401.829999999994" +Ta 2.1091 0.0011 2.0959 0.00063 0.000124 0.000424 +Ta 2.1079 2.0909 0.0 0.000645 0.000127 -0.000216 +Ta 0.0172 2.092 2.0959 -0.000645 -0.000127 0.000216 +Ta 0.0 0.0 0.0 -0.00063 -0.000124 -0.000424 +4 +Lattice = "4.18540000916 0.0 0.0 0.00910000037402 4.20340013504 0.0 -0.00449999980628 0.0206000003964 4.19199991226" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.428115 stress="33159.950000000004 -2037.96 1037.3300000000002 -2037.96 36902.979999999996 -4264.8 1037.3300000000002 -4264.8 24342.199999999997" +Ta 2.0905 0.0103 2.096 -0.000408 0.000133 9e-06 +Ta 2.0973 2.1017 0.0 -0.000408 0.000133 9e-06 +Ta 0.0023 2.112 2.096 0.000408 -0.000133 -9e-06 +Ta 0.0 0.0 0.0 0.000408 -0.000133 -9e-06 +4 +Lattice = "4.20219993591 0.0 0.0 -0.0137000000104 4.18510007858 0.0 0.0170000009239 0.000399999989895 4.19110012054" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.4269 stress="42344.0 2996.3700000000003 -4106.58 2996.3700000000003 39499.920000000006 161.89000000000001 -4106.58 161.89000000000001 29485.66" +Ta 2.1096 0.0002 2.0955 3.6e-05 -2.9e-05 0.000575 +Ta 2.0943 2.0925 0.0 -0.000498 0.000956 -0.000492 +Ta 0.0017 2.0928 2.0955 5e-06 -0.000949 0.000486 +Ta 0.0 0.0 0.0 0.000457 2.2e-05 -0.000569 +4 +Lattice = "4.18289995193 0.0 0.0 0.00159999995958 4.179500103 0.0 -0.00310000008903 0.0133999995887 4.209400177" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.421142 stress="44099.57 -461.53 789.15 -461.53 41820.810000000005 -2469.31 789.15 -2469.31 34193.81" +Ta 2.0899 0.0067 2.1047 0.000191 0.000394 1e-06 +Ta 2.0922 2.0898 0.0 0.000613 -0.00044 1.7e-05 +Ta -0.0007 2.0965 2.1047 -0.000794 -0.000378 -7e-06 +Ta 0.0 0.0 0.0 -1e-05 0.000423 -1e-05 +4 +Lattice = "4.21260023117 0.0 0.0 0.0207000002265 4.19000005722 0.0 0.00159999995958 -0.00769999995828 4.18440008163" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.432233 stress="39750.03 -4610.75 -478.2 -4610.75 34854.11 1877.37 -478.2 1877.37 25710.550000000003" +Ta 2.1071 -0.0038 2.0922 0.000289 -0.000207 -3e-06 +Ta 2.1167 2.095 0.0 -0.000289 0.000207 3e-06 +Ta 0.0112 2.0912 2.0922 -0.000287 -0.000233 1e-06 +Ta 0.0 0.0 0.0 0.000287 0.000233 -1e-06 +4 +Lattice = "4.19710016251 0.0 0.0 0.017899999395 4.18270015717 0.0 -0.00960000045598 -0.01600000076 4.20739984512" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.429408 stress="37387.92 -3190.48 1878.9499999999998 -3190.48 32357.480000000003 3103.4700000000003 1878.9499999999998 3103.4700000000003 25220.76" +Ta 2.0938 -0.008 2.1037 -0.000335 0.000327 5.2e-05 +Ta 2.1075 2.0914 0.0 0.000335 -0.000327 -5.2e-05 +Ta 0.0042 2.0834 2.1037 -0.000324 -0.000492 4.2e-05 +Ta 0.0 0.0 0.0 0.000324 0.000492 -4.2e-05 +4 +Lattice = "4.21169996262 0.0 0.0 -0.00689999992028 4.20370006561 0.0 0.00150000001304 -0.00920000020415 4.21269989014" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.445145 stress="18335.4 1673.0 -228.65 1673.0 16239.820000000002 2082.03 -228.65 2082.03 6136.77" +Ta 2.0997 4.1991 2.1063 6.7e-05 -0.000114 0.000643 +Ta 2.1024 2.1018 0.0 -9e-05 0.000831 -0.000669 +Ta -0.0027 2.0973 2.1063 9e-05 -0.000831 0.000669 +Ta 0.0 0.0 0.0 -6.7e-05 0.000114 -0.000643 +4 +Lattice = "4.19729995728 0.0 0.0 0.00370000000112 4.20749998093 0.0 0.0143999997526 -0.00310000008903 4.19150018692" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.435868 stress="32126.109999999997 -1008.08 -3338.91 -1008.08 34042.35 685.31 -3338.91 685.31 21906.06" +Ta 2.1095 4.2059 2.0958 0.000735 0.000174 -0.00065 +Ta 2.1005 2.1037 0.0 0.000783 0.000746 0.000651 +Ta 0.0091 2.1022 2.0958 -0.00125 -0.00074 -0.00065 +Ta 0.0 0.0 0.0 -0.000268 -0.00018 0.00065 +4 +Lattice = "4.18669986725 0.0 0.0 0.018200000748 4.22060012817 0.0 0.00449999980628 -0.00139999995008 4.19939994812" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.439663 stress="24909.960000000003 -4206.58 -1004.1899999999999 -4206.58 31036.64 543.86 -1004.1899999999999 543.86 16832.42" +Ta 2.0956 -0.0007 2.0997 0.000559 -2.8e-05 1e-06 +Ta 2.1025 2.1103 0.0 -0.000559 2.8e-05 -1e-06 +Ta 0.0114 2.1096 2.0997 -0.000559 2.8e-05 -1e-06 +Ta 0.0 0.0 0.0 0.000559 -2.8e-05 1e-06 +4 +Lattice = "4.1998000145 0.0 0.0 -0.0163000002503 4.19570016861 0.0 0.01070000045 -0.0124000003561 4.18389987946" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.428287 stress="41731.25 3757.21 -2445.36 3757.21 41051.920000000006 2856.2799999999997 -2445.36 2856.2799999999997 30297.370000000003" +Ta 2.1053 -0.0062 2.092 -0.00054 -0.000412 -0.000306 +Ta 2.0917 2.0978 0.0 0.00054 0.000412 0.000306 +Ta 4.197 2.0916 2.092 2.3e-05 0.0004 -0.000316 +Ta 0.0 0.0 0.0 -2.3e-05 -0.0004 0.000316 +4 +Lattice = "4.1970000267 0.0 0.0 0.0194000005722 4.1888999939 0.0 -0.00179999996908 -0.0136000001803 4.18779993057" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.424584 stress="44875.270000000004 -4458.47 289.83 -4458.47 43234.76 3197.07 289.83 3197.07 33469.479999999996" +Ta 2.0976 -0.0068 2.0939 5.4e-05 -0.000398 -1e-06 +Ta 2.1082 2.0944 0.0 -5.4e-05 0.000398 1e-06 +Ta 0.0088 2.0876 2.0939 -5.4e-05 0.000398 1e-06 +Ta 0.0 0.0 0.0 5.4e-05 -0.000398 -1e-06 +4 +Lattice = "4.18450021744 0.0 0.0 0.0130000002682 4.18849992752 0.0 -0.0195000004023 -0.00370000000112 4.18139982224" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.413045 stress="50367.32 -3261.88 3822.1099999999997 -3261.88 50402.17 705.52 3822.1099999999997 705.52 39882.66" +Ta 2.0825 -0.0018 2.0907 -5.1e-05 -0.000344 -1e-06 +Ta 2.0988 2.0943 0.0 -0.000738 -0.000336 2.6e-05 +Ta 4.1812 2.0924 2.0907 0.000738 0.000336 -2.6e-05 +Ta 0.0 0.0 0.0 5.1e-05 0.000344 1e-06 +4 +Lattice = "4.20609998703 0.0 0.0 0.0121999997646 4.20860004425 0.0 0.0104000000283 0.00490000005811 4.1810002327" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.436994 stress="32291.899999999998 -2490.73 -2201.86 -2490.73 33006.25 -463.13 -2201.86 -463.13 19860.08" +Ta 2.1204 4.211 2.0905 0.000646 0.000444 0.000147 +Ta 2.1092 2.1043 0.0 -0.000646 -0.000444 -0.000147 +Ta 0.0113 2.1067 2.0905 0.000171 0.000448 0.000145 +Ta 0.0 0.0 0.0 -0.000171 -0.000448 -0.000145 +4 +Lattice = "4.1939997673 0.0 0.0 -0.0175999999046 4.21909999847 0.0 -0.00359999993816 0.00300000002608 4.2079000473" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.443604 stress="18084.66 3671.56 781.26 3671.56 24730.91 -432.39 781.26 -432.39 9828.4" +Ta 2.0776 4.2206 2.104 0.000117 0.000438 -0.0005 +Ta 2.0882 2.1096 0.0 -0.000117 -0.000438 0.0005 +Ta -0.0106 2.1111 2.104 -1.1e-05 -0.000248 -0.000419 +Ta 0.0 0.0 0.0 1.1e-05 0.000248 0.000419 +4 +Lattice = "4.19670009613 0.0 0.0 0.0144999995828 4.20499992371 0.0 -0.0154999997467 -0.00319999991916 4.21000003815" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.439718 stress="23536.32 -3142.14 3304.68 -3142.14 26048.2 678.5 3304.68 678.5 13870.050000000001" +Ta 2.0906 -0.0016 2.105 0.0 0.0 0.0 +Ta 2.1056 2.1025 0.0 0.0 0.0 0.0 +Ta -0.0005 2.1009 2.105 0.0 0.0 0.0 +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +4 +Lattice = "4.18400001526 0.0 0.0 -0.00139999995008 4.20389986038 0.0 -0.0186000000685 -0.0144999995828 4.21430015564" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.435527 stress="26601.199999999997 224.89999999999998 3984.39 224.89999999999998 32506.140000000003 3199.5499999999997 3984.39 3199.5499999999997 20323.48" +Ta 2.0813 4.1966 2.1072 -5.7e-05 0.000574 -0.000235 +Ta 2.0913 2.102 0.0 5.7e-05 -0.000574 0.000235 +Ta -0.01 2.0947 2.1072 7.8e-05 -6.3e-05 -0.000195 +Ta 0.0 0.0 0.0 -7.8e-05 6.3e-05 0.000195 +4 +Lattice = "4.1810002327 0.0 0.0 0.00600000005215 4.22009992599 0.0 -0.00669999979436 -0.0204000007361 4.19239997864" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.434787 stress="30521.97 -1467.91 1403.6 -1467.91 38595.36 4398.91 1403.6 4398.91 23894.760000000002" +Ta 2.0872 -0.0102 2.0962 -0.000704 0.000292 6e-05 +Ta 2.0935 2.1101 0.0 -0.000115 -0.000301 -1e-06 +Ta 4.1806 2.0999 2.0962 0.000704 -0.000292 -6e-05 +Ta 0.0 0.0 0.0 0.000115 0.000301 1e-06 +4 +Lattice = "4.2076997757 0.0 0.0 -0.00329999998212 4.18240022659 0.0 0.0197999998927 -0.0142999999225 4.20949983597" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.434929 stress="33106.05 400.43 -4376.98 400.43 26345.52 2747.71 -4376.98 2747.71 20304.05" +Ta 2.1104 4.1752 2.1048 0.000619 0.000224 -0.00034 +Ta 2.1022 2.0912 0.0 0.000185 -0.00027 0.000324 +Ta 0.0083 2.084 2.1048 -0.000828 0.000293 -0.000329 +Ta 0.0 0.0 0.0 2.4e-05 -0.000248 0.000344 +4 +Lattice = "4.18709993362 0.0 0.0 -0.0137000000104 4.19210004807 0.0 -0.0206000003964 -0.00300000002608 4.2013001442" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.426499 stress="39883.59 3131.64 4730.58 3131.64 40703.380000000005 736.94 4730.58 736.94 30183.84" +Ta 2.0695 4.1906 2.1006 0.000281 -0.00046 0.000374 +Ta 2.0867 2.096 0.0 -0.000281 0.00046 -0.000374 +Ta 4.1699 2.0945 2.1006 0.000239 0.000426 0.000333 +Ta 0.0 0.0 0.0 -0.000239 -0.000426 -0.000333 +4 +Lattice = "4.19180011749 0.0 0.0 0.00350000010803 4.20699977875 0.0 0.0201999992132 -0.0141000002623 4.20459985733" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.437025 stress="28895.21 -1353.89 -4533.7300000000005 -1353.89 33286.0 2779.0699999999997 -4533.7300000000005 2779.0699999999997 20380.649999999998" +Ta 2.1095 4.1999 2.1023 0.000444 0.000256 2.5e-05 +Ta 2.0977 2.1035 0.0 -0.000444 -0.000256 -2.5e-05 +Ta 0.0119 2.0964 2.1023 -0.000371 0.000196 3.1e-05 +Ta 0.0 0.0 0.0 0.000371 -0.000196 -3.1e-05 +4 +Lattice = "4.19680023193 0.0 0.0 -0.019999999553 4.19010019302 0.0 0.0148000000045 0.00449999980628 4.19729995728" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.428937 stress="38946.02 4281.84 -3402.34 4281.84 36868.95 -1152.93 -3402.34 -1152.93 27927.85" +Ta 2.0858 4.1923 2.0986 -3.4e-05 0.000667 0.000439 +Ta 2.0884 2.0951 0.0 3.4e-05 -0.000667 -0.000439 +Ta -0.0026 2.0973 2.0986 -7.3e-05 -0.000101 0.000416 +Ta 0.0 0.0 0.0 7.3e-05 0.000101 -0.000416 +4 +Lattice = "4.21390008926 0.0 0.0 -0.0159000009298 4.2077999115 0.0 -0.0115000000224 0.00680000009015 4.19169998169" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.442516 stress="26548.37 3415.7000000000003 2464.46 3415.7000000000003 25895.34 -1426.55 2464.46 -1426.55 12731.93" +Ta 2.1012 0.0034 2.0958 -0.000117 -0.000115 0.000445 +Ta 2.099 2.1039 0.0 0.000117 0.000115 -0.000445 +Ta 4.2002 2.1073 2.0958 -0.000117 -0.000115 0.000445 +Ta 0.0 0.0 0.0 0.000117 0.000115 -0.000445 +4 +Lattice = "4.18620014191 0.0 0.0 0.00319999991916 4.18989992142 0.0 0.00359999993816 0.0201999992132 4.21029996872" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.428736 stress="36533.26 -472.27000000000004 -599.63 -472.27000000000004 38503.49 -4878.59 -599.63 -4878.59 28242.54" +Ta 2.0949 0.0101 2.1051 7.8e-05 0.000472 0.000488 +Ta 2.0947 2.095 0.0 -7.8e-05 -0.000472 -0.000488 +Ta 0.0034 2.1051 2.1051 3e-06 -0.000581 0.000458 +Ta 0.0 0.0 0.0 -3e-06 0.000581 -0.000458 +4 +Lattice = "4.18650007248 0.0 0.0 -0.020300000906 4.20889997482 0.0 0.0177999995649 -0.0108000002801 4.19799995422" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.433359 stress="31456.3 4402.04 -3820.04 4402.04 36583.71000000001 2243.03 -3820.04 2243.03 23228.44" +Ta 2.1021 -0.0054 2.099 0.000683 0.000409 2.2e-05 +Ta 2.0831 2.1045 0.0 0.000136 -0.000401 -3.2e-05 +Ta -0.0012 2.0991 2.099 -0.000683 -0.000409 -2.2e-05 +Ta 0.0 0.0 0.0 -0.000136 0.000401 3.2e-05 +4 +Lattice = "4.18569993973 0.0 0.0 -0.0201999992132 4.21250009537 0.0 0.0132999997586 -0.0038999998942 4.21120023727" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.438799 stress="22841.29 4506.599999999999 -2944.67 4506.599999999999 28994.420000000002 787.89 -2944.67 787.89 15742.92" +Ta 2.0793 4.2105 2.1056 0.00025 0.000338 -9e-06 +Ta 2.0828 2.1062 0.0 -0.000222 0.00033 -1.1e-05 +Ta -0.0034 2.1043 2.1056 -0.00025 -0.000338 9e-06 +Ta 0.0 0.0 0.0 0.000222 -0.00033 1.1e-05 +4 +Lattice = "4.20319986343 0.0 0.0 0.0133999995887 4.21220016479 0.0 0.0153000000864 0.016799999401 4.20030021667" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.441993 stress="22767.3 -2987.04 -3341.07 -2987.04 24394.9 -3697.02 -3341.07 -3697.02 11782.27" +Ta 2.1226 4.2206 2.1002 0.000406 4.3e-05 -0.000851 +Ta 2.1083 2.1061 0.0 -0.000406 -4.3e-05 0.000851 +Ta 4.2175 2.1145 2.1002 0.000406 4.3e-05 -0.000851 +Ta 0.0 0.0 0.0 -0.000406 -4.3e-05 0.000851 +4 +Lattice = "4.20020008087 0.0 0.0 0.0159000009298 4.21250009537 0.0 0.00839999970049 0.00270000007004 4.19059991837" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.439033 stress="31311.34 -2962.04 -2118.77 -2962.04 33332.84 -497.0 -2118.77 -497.0 19397.95" +Ta 2.1043 0.0014 2.0953 -0.000169 -0.000336 2e-06 +Ta 2.108 2.1063 0.0 0.000307 -0.000319 4e-06 +Ta 4.2123 2.1076 2.0953 0.000169 0.000336 -2e-06 +Ta 0.0 0.0 0.0 -0.000307 0.000319 -4e-06 +4 +Lattice = "4.19460010529 0.0 0.0 -0.00380000006407 4.20300006866 0.0 0.00710000004619 0.00289999996312 4.20419979095" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.436967 stress="28199.07 1077.27 -1364.09 1077.27 30335.760000000002 -742.39 -1364.09 -742.39 18938.510000000002" +Ta 2.1009 0.0015 2.1021 -0.000397 -0.000899 -0.000183 +Ta 2.0954 2.1015 0.0 0.000341 0.000174 0.00019 +Ta 0.0017 2.1029 2.1021 -0.000267 0.000862 -0.0002 +Ta 0.0 0.0 0.0 0.000324 -0.000137 0.000193 +4 +Lattice = "4.19649982452 0.0 0.0 0.0170000009239 4.18389987946 0.0 0.000500000023749 0.0197000000626 4.20139980316" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.427245 stress="39200.850000000006 -3187.19 -498.29 -3187.19 36589.530000000006 -4530.76 -498.29 -4530.76 27001.34" +Ta 2.0985 0.0099 2.1007 1e-05 -0.00045 2.8e-05 +Ta 2.1067 2.092 0.0 0.000706 -0.000365 -4.5e-05 +Ta 0.0088 2.1018 2.1007 -0.000706 0.000365 4.5e-05 +Ta 0.0 0.0 0.0 -1e-05 0.00045 -2.8e-05 +4 +Lattice = "4.19409990311 0.0 0.0 -0.0157999992371 4.20200014114 0.0 -0.00249999994412 -0.00449999980628 4.21129989624" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.438046 stress="26136.06 3578.57 621.48 3578.57 27841.36 1030.6 621.48 1030.6 16177.720000000001" +Ta 2.08 4.1997 2.1057 0.000264 0.000278 -0.000459 +Ta 2.0891 2.101 0.0 0.000831 -0.000264 0.000454 +Ta -0.0091 2.0987 2.1057 -0.000831 0.000264 -0.000454 +Ta 0.0 0.0 0.0 -0.000264 -0.000278 0.000459 +4 +Lattice = "4.18219995499 0.0 0.0 -0.0186999998987 4.19169998169 0.0 0.00850000046194 -0.00270000007004 4.19329977036" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.420083 stress="45896.659999999996 4350.44 -1715.56 4350.44 48179.94 571.0699999999999 -1715.56 571.0699999999999 36393.41" +Ta 2.0766 4.1903 2.0967 0.00046 0.001197 -0.000615 +Ta 2.0818 2.0959 0.0 -0.00046 -0.001197 0.000615 +Ta 4.1771 2.0945 2.0967 -0.000243 -0.00048 -0.000746 +Ta 0.0 0.0 0.0 0.000243 0.00048 0.000746 +4 +Lattice = "4.21379995346 0.0 0.0 -0.00889999978244 4.20090007782 0.0 0.00829999987036 -0.0121999997646 4.2157998085" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.445247 stress="17199.95 2060.92 -1868.0 2060.92 14754.65 2656.7 -1868.0 2656.7 4564.79" +Ta 2.111 -0.0061 2.1079 0.000429 -0.000346 -2e-05 +Ta 2.1024 2.1004 0.0 0.000445 0.000491 -1.1e-05 +Ta 4.2135 2.0943 2.1079 -0.000429 0.000346 2e-05 +Ta 0.0 0.0 0.0 -0.000445 -0.000491 1.1e-05 +4 +Lattice = "4.2171998024 0.0 0.0 -0.00249999994412 4.21280002594 0.0 0.0010000000475 -0.0208000000566 4.19570016861" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.446044 stress="19496.41 709.2 -122.84 709.2 18308.6 4583.75 -122.84 4583.75 6100.4" +Ta 2.1091 -0.0104 2.0979 0.000565 1.3e-05 -0.000312 +Ta 2.1074 2.1064 0.0 -0.000565 -1.3e-05 0.000312 +Ta -0.0007 2.096 2.0979 -0.000564 -1.2e-05 -0.000342 +Ta 0.0 0.0 0.0 0.000564 1.2e-05 0.000342 +4 +Lattice = "4.20889997482 0.0 0.0 0.0163000002503 4.17980003357 0.0 -0.00310000008903 -0.017899999395 4.2093000412" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.434472 stress="34887.090000000004 -3559.16 445.12 -3559.16 27517.510000000002 4000.3399999999997 445.12 4000.3399999999997 21214.9" +Ta 2.1029 -0.0089 2.1046 -4.5e-05 -0.000191 0.000367 +Ta 2.1126 2.0899 0.0 4.5e-05 0.000191 -0.000367 +Ta 4.2155 2.081 2.1046 -4.5e-05 -0.000191 0.000367 +Ta 0.0 0.0 0.0 4.5e-05 0.000191 -0.000367 +4 +Lattice = "4.21549987793 0.0 0.0 -0.0132999997586 4.21330022812 0.0 -0.0054999999702 0.0157999992371 4.18979978561" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.44458 stress="23231.31 2911.85 1091.22 2911.85 22696.98 -3466.5499999999997 1091.22 -3466.5499999999997 9663.7" +Ta 2.105 0.0079 2.0949 1.3e-05 0.000487 6e-06 +Ta 2.1011 2.1067 0.0 -1.3e-05 -0.000487 -6e-06 +Ta -0.0094 2.1146 2.0949 -1.3e-05 -0.000487 -6e-06 +Ta 0.0 0.0 0.0 1.3e-05 0.000487 6e-06 +4 +Lattice = "4.20329999924 0.0 0.0 0.0104000000283 4.2093000412 0.0 0.00359999993816 -0.00270000007004 4.20109987259" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.441776 stress="25420.61 -1768.14 -1189.8899999999999 -1768.14 27462.18 568.28 -1189.8899999999999 568.28 14665.82" +Ta 2.1139 4.2079 2.1005 -0.00054 0.0004 0.000307 +Ta 2.1069 2.1046 0.0 -0.000437 0.000188 -0.000353 +Ta 0.007 2.1033 2.1005 0.000437 -0.000188 0.000353 +Ta 0.0 0.0 0.0 0.00054 -0.0004 -0.000307 +4 +Lattice = "4.19390010834 0.0 0.0 -0.0154999997467 4.20030021667 0.0 0.0118000004441 -0.017100000754 4.2093000412" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.436389 stress="28175.18 3461.97 -2554.14 3461.97 29398.74 3490.6600000000003 -2554.14 3490.6600000000003 18104.420000000002" +Ta 2.1028 -0.0085 2.1047 0.000405 -0.000951 -0.000355 +Ta 2.0892 2.1001 0.0 -0.000405 0.000951 0.000355 +Ta 4.192 2.0916 2.1047 0.000387 0.000179 -0.000469 +Ta 0.0 0.0 0.0 -0.000387 -0.000179 0.000469 +4 +Lattice = "4.2079000473 0.0 0.0 -0.0097000002861 4.21920013428 0.0 -0.00490000005811 -0.00999999977648 4.20109987259" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.446416 stress="19209.399999999998 2025.1299999999999 1589.1299999999999 2025.1299999999999 20626.989999999998 2446.81 1589.1299999999999 2446.81 6438.570000000001" +Ta 2.1015 -0.005 2.1006 -2.8e-05 -0.000105 -0.000311 +Ta 2.0991 2.1096 0.0 2.8e-05 0.000105 0.000311 +Ta -0.0073 2.1046 2.1006 -2.8e-05 -0.000105 -0.000311 +Ta 0.0 0.0 0.0 2.8e-05 0.000105 0.000311 +4 +Lattice = "4.21920013428 0.0 0.0 0.00370000000112 4.21530008316 0.0 -0.001200000057 -9.99999974738e-05 4.21350002289" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.449806 stress="9066.92 -618.3199999999999 80.69 -618.3199999999999 8795.18 242.32000000000002 80.69 242.32000000000002 -3831.06" +Ta 2.109 0.0 2.1067 -0.000377 -0.000342 0.00055 +Ta 2.1115 2.1077 0.0 -0.001167 -0.000182 -0.000568 +Ta 4.2204 2.1076 2.1067 0.001167 0.000182 0.000568 +Ta 0.0 0.0 0.0 0.000377 0.000342 -0.00055 +4 +Lattice = "4.20060014725 0.0 0.0 0.00680000009015 4.19710016251 0.0 -0.0146000003442 0.0186000000685 4.17910003662" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.427189 stress="44173.07 -1484.73 3360.38 -1484.73 43201.93 -4284.93 3360.38 -4284.93 31256.18" +Ta 2.0998 4.2064 2.0896 -2.2e-05 -0.000426 -0.000366 +Ta 2.1037 2.0985 0.0 2.2e-05 0.000426 0.000366 +Ta -0.0039 2.1078 2.0896 -2.5e-05 0.000364 -0.000321 +Ta 0.0 0.0 0.0 2.5e-05 -0.000364 0.000321 +4 +Lattice = "4.18919992447 0.0 0.0 0.0135000003502 4.20279979706 0.0 -0.0119000002742 0.00999999977648 4.1875" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.427857 stress="39322.19 -2611.56 2676.7 -2611.56 42055.02 -2182.03 2676.7 -2182.03 28576.71" +Ta 2.1022 4.2078 2.0938 -0.000527 -0.000167 -0.000317 +Ta 2.1014 2.1014 0.0 -0.000703 1.2e-05 0.000454 +Ta 0.0008 2.1064 2.0938 0.000703 -1.2e-05 -0.000454 +Ta 0.0 0.0 0.0 0.000527 0.000167 0.000317 +4 +Lattice = "4.2079000473 0.0 0.0 -0.00980000011623 4.18940019608 0.0 0.0206000003964 0.0189999993891 4.21960020065" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.44004 stress="24518.6 2270.46 -4602.22 2270.46 19823.78 -4164.55 -4602.22 -4164.55 12729.210000000001" +Ta 2.1142 0.0095 2.1098 0.000377 -3.3e-05 1.1e-05 +Ta 2.099 2.0947 0.0 0.000377 -3.3e-05 1.1e-05 +Ta 0.0054 2.1042 2.1098 -0.000377 3.3e-05 -1.1e-05 +Ta 0.0 0.0 0.0 -0.000377 3.3e-05 -1.1e-05 +4 +Lattice = "4.18559980392 0.0 0.0 -0.0141000002623 4.21939992905 0.0 0.00270000007004 -0.0183000005782 4.19519996643" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.437214 stress="27548.75 3217.5699999999997 -517.42 3217.5699999999997 33898.46 4094.8900000000003 -517.42 4094.8900000000003 19872.68" +Ta 2.0941 -0.0091 2.0976 0.00078 -0.000197 -3.2e-05 +Ta 2.0857 2.1097 0.0 0.000496 0.000489 5e-06 +Ta -0.0057 2.1006 2.0976 -0.000496 -0.000489 -5e-06 +Ta 0.0 0.0 0.0 -0.00078 0.000197 3.2e-05 +4 +Lattice = "4.18179988861 0.0 0.0 -0.00949999969453 4.19159984589 0.0 0.0148000000045 0.00139999995008 4.19890022278" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.422628 stress="43385.56 2136.82 -3260.5400000000004 2136.82 46015.15 -518.6500000000001 -3260.5400000000004 -518.6500000000001 33939.47" +Ta 2.0888 4.1923 2.0995 -0.000281 -0.00027 -0.000582 +Ta 2.0861 2.0958 0.0 0.000281 0.00027 0.000582 +Ta 4.1844 2.0965 2.0995 0.000629 0.000286 -0.000561 +Ta 0.0 0.0 0.0 -0.000629 -0.000286 0.000561 +4 +Lattice = "4.20370006561 0.0 0.0 -0.0200999993831 4.21630001068 0.0 -0.0164000000805 -0.0195000004023 4.20209980011" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.443535 stress="20218.039999999997 4818.6900000000005 3580.07 4818.6900000000005 21841.62 4429.02 3580.07 4429.02 8549.369999999999" +Ta 2.0736 4.2065 2.1011 -0.000398 0.000783 -0.000458 +Ta 2.0918 2.1082 0.0 0.000398 -0.000783 0.000458 +Ta -0.0182 2.0984 2.1011 -0.000248 -0.000173 -0.000438 +Ta 0.0 0.0 0.0 0.000248 0.000173 0.000438 +4 +Lattice = "4.20109987259 0.0 0.0 0.00289999996312 4.2077999115 0.0 0.00179999996908 0.00260000000708 4.19890022278" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.439922 stress="27455.690000000002 -990.9599999999999 -176.72 -990.9599999999999 29472.14 -256.46000000000004 -176.72 -256.46000000000004 15890.19" +Ta 2.1015 0.0013 2.0994 -0.000776 -9.4e-05 0.000494 +Ta 2.102 2.1039 0.0 -0.00018 1.1e-05 -0.000461 +Ta 4.2034 2.1052 2.0994 0.000991 9.2e-05 0.000337 +Ta 0.0 0.0 0.0 -3.5e-05 -9e-06 -0.00037 +4 +Lattice = "4.20909976959 0.0 0.0 0.00279999990016 4.19089984894 0.0 0.0129000004381 0.0113000003621 4.20370006561" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.437675 stress="30559.32 -328.34999999999997 -2999.48 -328.34999999999997 26504.989999999998 -2563.55 -2999.48 -2563.55 18218.93" +Ta 2.1138 4.1965 2.1019 0.000516 0.001068 -0.000754 +Ta 2.1059 2.0955 0.0 0.000599 -0.000983 0.000746 +Ta 0.0079 2.1011 2.1019 -0.000833 -0.000415 -0.000718 +Ta 0.0 0.0 0.0 -0.000282 0.000331 0.000726 +4 +Lattice = "4.21960020065 0.0 0.0 -0.0164999999106 4.20809984207 0.0 0.00209999992512 -0.0104999998584 4.19619989395" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.445558 stress="21138.43 3552.79 -295.98 3552.79 19496.949999999997 2230.2599999999998 -295.98 2230.2599999999998 7402.18" +Ta 2.0944 4.2028 2.0981 -0.000489 0.000278 7.1e-05 +Ta 2.1016 2.104 0.0 -0.000489 0.000278 7.1e-05 +Ta -0.0072 2.0988 2.0981 0.000489 -0.000278 -7.1e-05 +Ta 0.0 0.0 0.0 0.000489 -0.000278 -7.1e-05 +4 +Lattice = "4.18620014191 0.0 0.0 0.0142000000924 4.21759986877 0.0 0.00529999984428 0.000699999975041 4.20249986649" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.439106 stress="24311.969999999998 -3207.16 -1065.08 -3207.16 30723.109999999997 -53.699999999999996 -1065.08 -53.699999999999996 16577.88" +Ta 2.11 4.2179 2.1012 -0.000734 0.000343 0.000586 +Ta 2.1002 2.1088 0.0 -0.000395 -0.000327 -0.000614 +Ta 4.1959 2.1091 2.1012 0.000856 0.000318 0.000602 +Ta 0.0 0.0 0.0 0.000273 -0.000334 -0.000574 +4 +Lattice = "4.19910001755 0.0 0.0 -0.0100999996066 4.21040010452 0.0 0.0163000002503 0.0195000004023 4.21479988098" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.443073 stress="21214.73 1620.02 -3139.49 1620.02 23804.07 -3361.12 -3139.49 -3361.12 11182.08" +Ta 2.0976 4.2201 2.1074 1.7e-05 0.000287 -2.2e-05 +Ta 2.0945 2.1052 0.0 -1.7e-05 -0.000287 2.2e-05 +Ta 4.2022 2.1149 2.1074 1.7e-05 0.000287 -2.2e-05 +Ta 0.0 0.0 0.0 -1.7e-05 -0.000287 2.2e-05 +4 +Lattice = "4.20900011063 0.0 0.0 -0.0132999997586 4.19000005722 0.0 -0.00510000018403 0.0116999996826 4.21299982071" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.4397 stress="27256.09 2922.24 1093.0500000000002 2922.24 22439.64 -2593.18 1093.0500000000002 -2593.18 14372.06" +Ta 2.102 0.0059 2.1065 -0.000435 -0.000338 0.0 +Ta 2.0979 2.095 0.0 -0.000572 0.000306 2.7e-05 +Ta -0.0092 2.1009 2.1065 0.000572 -0.000306 -2.7e-05 +Ta 0.0 0.0 0.0 0.000435 0.000338 0.0 +4 +Lattice = "4.18540000916 0.0 0.0 0.00499999988824 4.21269989014 0.0 -0.0170000009239 -0.0157999992371 4.20230007172" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.436374 stress="29413.82 -848.39 3021.03 -848.39 35818.05 3586.5499999999997 3021.03 3586.5499999999997 22359.57" +Ta 2.0892 4.2048 2.1011 0.000247 -0.000509 0.000473 +Ta 2.0952 2.1063 0.0 -0.000247 0.000509 -0.000473 +Ta 4.1794 2.0984 2.1011 0.000198 0.000499 0.000486 +Ta 0.0 0.0 0.0 -0.000198 -0.000499 -0.000486 +4 +Lattice = "4.19089984894 0.0 0.0 0.00889999978244 4.18580007553 0.0 -0.00769999995828 -0.00370000000112 4.20340013504" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.426557 stress="41786.9 -1592.19 1901.3 -1592.19 40672.780000000006 565.31 1901.3 565.31 31476.21" +Ta 2.0916 -0.0018 2.1017 9.5e-05 -0.000938 -7.3e-05 +Ta 2.0999 2.0929 0.0 -9e-06 0.000173 9e-06 +Ta 0.0006 2.091 2.1017 -9.5e-05 0.000938 7.3e-05 +Ta 0.0 0.0 0.0 9e-06 -0.000173 -9e-06 +4 +Lattice = "4.1985001564 0.0 0.0 -0.0179999992251 4.19869995117 0.0 -0.00079999997979 0.0184000004083 4.19780015945" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.434009 stress="33693.26 4132.23 124.97999999999999 4132.23 32953.46 -4050.66 124.97999999999999 -4050.66 22096.65" +Ta 2.0988 0.0092 2.0989 0.000663 0.000517 0.000224 +Ta 2.0903 2.0994 0.0 -0.000663 -0.000517 -0.000224 +Ta -0.0094 2.1086 2.0989 1.4e-05 -0.000453 7.2e-05 +Ta 0.0 0.0 0.0 -1.4e-05 0.000453 -7.2e-05 +4 +Lattice = "4.20100021362 0.0 0.0 -0.00910000037402 4.19759988785 0.0 -0.00689999992028 0.00609999988228 4.20090007782" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.436262 stress="32759.129999999997 2409.49 1583.58 2409.49 32101.69 -912.27 1583.58 -912.27 21073.66" +Ta 2.088 4.2006 2.1005 -0.001062 0.001392 -0.000497 +Ta 2.0959 2.0988 0.0 0.000982 -0.000276 0.000312 +Ta -0.008 2.1019 2.1005 -4.7e-05 -0.001302 -6.7e-05 +Ta 0.0 0.0 0.0 0.000128 0.000186 0.000252 +4 +Lattice = "4.21759986877 0.0 0.0 0.0156999994069 4.18800020218 0.0 0.00659999996424 0.0181000009179 4.18650007248" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.434505 stress="37654.36 -3876.7999999999997 -1440.8799999999999 -3876.7999999999997 32519.67 -4103.17 -1440.8799999999999 -4103.17 23829.38" +Ta 2.1278 4.197 2.0932 -0.000269 0.000298 0.000324 +Ta 2.1166 2.094 0.0 0.000269 -0.000298 -0.000324 +Ta 4.2287 2.103 2.0932 0.000297 0.000285 0.000327 +Ta 0.0 0.0 0.0 -0.000297 -0.000285 -0.000327 +4 +Lattice = "4.19199991226 0.0 0.0 0.01070000045 4.21519994736 0.0 -0.0195000004023 0.0172000005841 4.19929981232" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.438768 stress="27465.83 -1845.49 4487.129999999999 -1845.49 32725.54 -3897.0099999999998 4487.129999999999 -3897.0099999999998 17774.13" +Ta 2.0863 0.0086 2.0996 -0.000554 6.9e-05 0.000378 +Ta 2.1013 2.1076 0.0 0.000554 -6.9e-05 -0.000378 +Ta 4.1876 2.1162 2.0996 -9.3e-05 3.9e-05 0.000372 +Ta 0.0 0.0 0.0 9.3e-05 -3.9e-05 -0.000372 +4 +Lattice = "4.20120000839 0.0 0.0 -0.00980000011623 4.21460008621 0.0 0.0137000000104 -0.0104000000283 4.19080018997" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.440254 stress="26850.75 1979.56 -3070.84 1979.56 30335.71 2128.91 -3070.84 2128.91 16599.23" +Ta 2.1074 -0.0052 2.0954 0.000286 -4.3e-05 -9.2e-05 +Ta 2.0957 2.1073 0.0 -0.000286 4.3e-05 9.2e-05 +Ta 4.2031 2.1021 2.0954 0.000286 -4.3e-05 -9.2e-05 +Ta 0.0 0.0 0.0 -0.000286 4.3e-05 9.2e-05 +4 +Lattice = "4.18440008163 0.0 0.0 -0.0175000000745 4.18079996109 0.0 -0.0194000005722 0.0108000002801 4.21099996567" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.42286 stress="40368.11 3432.0 3719.6699999999996 3432.0 39974.420000000006 -1873.58 3719.6699999999996 -1873.58 31423.030000000002" +Ta 2.0825 0.0054 2.1055 -0.000359 6e-05 5.6e-05 +Ta 2.0834 2.0904 0.0 0.000359 -6e-05 -5.6e-05 +Ta 4.1659 2.0958 2.1055 0.000359 -6e-05 -5.6e-05 +Ta 0.0 0.0 0.0 -0.000359 6e-05 5.6e-05 +4 +Lattice = "4.18879985809 0.0 0.0 -0.0208000000566 4.18480014801 0.0 -0.00730000017211 -0.0186999998987 4.19089984894" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.418078 stress="45790.12 4993.91 1730.1100000000001 4993.91 45930.82 3649.4300000000003 1730.1100000000001 3649.4300000000003 35583.67" +Ta 2.0907 -0.0093 2.0955 0.000623 -0.000961 -0.000332 +Ta 2.084 2.0924 0.0 -0.000626 -0.000189 0.000487 +Ta 4.1747 2.083 2.0955 0.000372 0.001139 -0.000549 +Ta 0.0 0.0 0.0 -0.000369 1e-05 0.000393 +4 +Lattice = "4.19479990005 0.0 0.0 -0.00620000017807 4.21269989014 0.0 -0.01600000076 -0.0153000000864 4.20469999313" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.440513 stress="22841.39 1639.92 3610.02 1639.92 27085.86 3356.16 3610.02 3356.16 13927.91" +Ta 2.0894 -0.0076 2.1024 -0.000112 -0.000351 -0.000518 +Ta 2.0943 2.1064 0.0 0.00016 -0.000267 0.000412 +Ta -0.0111 2.0987 2.1024 -0.00016 0.000267 -0.000412 +Ta 0.0 0.0 0.0 0.000112 0.000351 0.000518 +4 +Lattice = "4.18660020828 0.0 0.0 -0.0172000005841 4.17999982834 0.0 -0.0137000000104 0.0121999997646 4.18389987946" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.409824 stress="54573.9 3803.25 2849.0 3803.25 53362.96 -2844.54 2849.0 -2844.54 43325.58" +Ta 2.0692 4.1861 2.092 0.000705 -1.8e-05 -0.000526 +Ta 2.0847 2.09 0.0 -0.000705 1.8e-05 0.000526 +Ta 4.1711 2.0961 2.092 0.000705 -1.8e-05 -0.000526 +Ta 0.0 0.0 0.0 -0.000705 1.8e-05 0.000526 +4 +Lattice = "4.20060014725 0.0 0.0 0.00219999998808 4.19719982147 0.0 -0.0162000004202 -0.00079999997979 4.21750020981" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.440329 stress="24420.449999999997 -556.41 3615.46 -556.41 22664.89 379.38 3615.46 379.38 13111.85" +Ta 2.0922 -0.0004 2.1088 1.1e-05 9e-05 -0.000468 +Ta 2.1014 2.0986 0.0 -1.1e-05 -9e-05 0.000468 +Ta -0.007 2.0982 2.1088 1.1e-05 9e-05 -0.000468 +Ta 0.0 0.0 0.0 -1.1e-05 -9e-05 0.000468 +4 +Lattice = "4.19640016556 0.0 0.0 0.00889999978244 4.20380020142 0.0 -0.0110999997705 0.0162000004202 4.20480012894" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.43773 stress="26565.65 -1735.6799999999998 2480.6400000000003 -1735.6799999999998 28315.010000000002 -3741.6200000000003 2480.6400000000003 -3741.6200000000003 17263.329999999998" +Ta 2.0927 0.0081 2.1024 -0.00063 -0.000147 2e-05 +Ta 2.1026 2.1019 0.0 0.00063 0.000147 -2e-05 +Ta -0.0011 2.11 2.1024 9.4e-05 3.4e-05 -2e-06 +Ta 0.0 0.0 0.0 -9.4e-05 -3.4e-05 2e-06 +4 +Lattice = "4.18130016327 0.0 0.0 0.0177999995649 4.18319988251 0.0 -0.00340000004508 -0.0187999997288 4.19859981537" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.416525 stress="45103.520000000004 -3012.21 864.34 -3012.21 46101.13 4242.0 864.34 4242.0 36460.39" +Ta 2.089 -0.0094 2.0993 -0.000372 -6.9e-05 -1.6e-05 +Ta 2.0996 2.0916 0.0 -0.000372 -6.9e-05 -1.6e-05 +Ta 0.0072 2.0822 2.0993 0.000372 6.9e-05 1.6e-05 +Ta 0.0 0.0 0.0 0.000372 6.9e-05 1.6e-05 +4 +Lattice = "4.19229984283 0.0 0.0 0.001200000057 4.20900011063 0.0 -0.0151000004262 -0.00659999996424 4.21150016785" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.440293 stress="27393.899999999998 -151.45 2769.0 -151.45 30944.28 1878.31 2769.0 1878.31 18332.49" +Ta 2.0886 -0.0033 2.1058 -0.00024 0.0 -0.000304 +Ta 2.0967 2.1045 0.0 0.00024 0.0 0.000304 +Ta 4.1853 2.1012 2.1058 0.000234 0.0 -0.000306 +Ta 0.0 0.0 0.0 -0.000234 0.0 0.000306 +4 +Lattice = "4.18419981003 0.0 0.0 0.0206000003964 4.209400177 0.0 -0.0109999999404 -0.00480000022799 4.21589994431" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.43839 stress="21338.170000000002 -4162.9 2184.87 -4162.9 28153.19 1038.1 2184.87 1038.1 15498.07" +Ta 2.1072 4.207 2.1079 -1.6e-05 9e-06 0.00028 +Ta 2.1024 2.1047 0.0 1.6e-05 -9e-06 -0.00028 +Ta 4.189 2.1023 2.1079 -1.6e-05 9e-06 0.00028 +Ta 0.0 0.0 0.0 1.6e-05 -9e-06 -0.00028 +4 +Lattice = "4.17980003357 0.0 0.0 0.00789999961853 4.21220016479 0.0 0.0197000000626 -0.00270000007004 4.2185997963" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.438916 stress="20722.52 -1865.4599999999998 -4386.49 -1865.4599999999998 29240.06 779.2900000000001 -4386.49 779.2900000000001 15461.880000000001" +Ta 2.0998 -0.0013 2.1093 -0.00064 -0.000286 9e-05 +Ta 2.0939 2.1061 0.0 -0.000872 0.000312 -7.4e-05 +Ta 4.1936 2.1048 2.1093 0.000872 -0.000312 7.4e-05 +Ta 0.0 0.0 0.0 0.00064 0.000286 -9e-05 diff --git a/examples/PACKAGES/pod/Ta/XYZ/GSF_110.xyz b/examples/PACKAGES/pod/Ta/XYZ/GSF_110.xyz new file mode 100644 index 0000000000..378878ef80 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/XYZ/GSF_110.xyz @@ -0,0 +1,572 @@ +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.068761 stress="-2699.74 -3225.67 0.0 -3225.67 -11966.73 0.0 0.0 0.0 8811.74" +Ta 2.34759 1.66 0.09121 0.0 0.0 0.002389 +Ta 0.0 0.0 0.09121 0.0 0.0 0.002389 +Ta 0.0 1.66 2.3361 0.0 0.0 -0.010927 +Ta 2.34759 0.0 2.3361 0.0 0.0 -0.010927 +Ta 2.34759 1.66 4.68536 0.0 0.0 -0.004142 +Ta 0.0 0.0 4.68536 0.0 0.0 -0.004142 +Ta 0.0 1.66 7.03392 0.0 0.0 0.078092 +Ta 2.34759 0.0 7.03392 0.0 0.0 0.078092 +Ta 2.34759 1.66 9.38594 0.0 0.0 -0.152903 +Ta 0.0 0.0 9.38594 0.0 0.0 -0.152903 +Ta 0.0 1.66 11.73648 0.0 0.0 -0.861147 +Ta 2.34759 0.0 11.73648 0.0 0.0 -0.861147 +Ta 3.52139 2.49 14.08712 0.0 0.0 0.861147 +Ta 1.1738 0.83 14.08712 0.0 0.0 0.861147 +Ta 1.1738 2.49 16.43764 0.0 0.0 0.152903 +Ta 3.52139 0.83 16.43764 0.0 0.0 0.152903 +Ta 3.52139 2.49 18.78966 0.0 0.0 -0.078092 +Ta 1.1738 0.83 18.78966 0.0 0.0 -0.078092 +Ta 1.1738 2.49 21.13823 0.0 0.0 0.004142 +Ta 3.52139 0.83 21.13823 0.0 0.0 0.004142 +Ta 3.52139 2.49 23.48739 0.0 0.0 0.010927 +Ta 1.1738 0.83 23.48739 0.0 0.0 0.010927 +Ta 1.1738 2.49 25.73229 0.0 0.0 -0.002389 +Ta 3.52139 0.83 25.73229 0.0 0.0 -0.002389 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.784296 stress="-9310.84 -724.11 -1802.3100000000002 -724.11 -7581.28 -1731.35 -1802.3100000000002 -1731.35 -145.04" +Ta 2.34759 1.66 0.09121 -0.000195 -0.00161 0.000812 +Ta 0.0 0.0 0.09121 -0.000195 -0.00161 0.000812 +Ta 0.0 1.66 2.3361 -0.000284 0.000353 -0.002185 +Ta 2.34759 0.0 2.3361 -0.000284 0.000353 -0.002185 +Ta 2.34759 1.66 4.68536 0.008799 -0.00141 -0.002306 +Ta 0.0 0.0 4.68536 0.008799 -0.00141 -0.002306 +Ta 0.0 1.66 7.03392 -0.006695 0.021282 0.017658 +Ta 2.34759 0.0 7.03392 -0.006695 0.021282 0.017658 +Ta 2.34759 1.66 9.38594 -0.014885 -0.089566 0.000145 +Ta 0.0 0.0 9.38594 -0.014885 -0.089566 0.000145 +Ta 0.0 1.66 11.73648 0.220002 0.367425 -0.11205 +Ta 2.34759 0.0 11.73648 0.220002 0.367425 -0.11205 +Ta 2.58235 1.826 14.08712 -0.220002 -0.367425 0.11205 +Ta 0.23476 0.166 14.08712 -0.220002 -0.367425 0.11205 +Ta 0.23476 1.826 16.43764 0.014885 0.089566 -0.000145 +Ta 2.58235 0.166 16.43764 0.014885 0.089566 -0.000145 +Ta 2.58235 1.826 18.78966 0.006695 -0.021282 -0.017658 +Ta 0.23476 0.166 18.78966 0.006695 -0.021282 -0.017658 +Ta 0.23476 1.826 21.13823 -0.008799 0.00141 0.002306 +Ta 2.58235 0.166 21.13823 -0.008799 0.00141 0.002306 +Ta 2.58235 1.826 23.48739 0.000284 -0.000353 0.002185 +Ta 0.23476 0.166 23.48739 0.000284 -0.000353 0.002185 +Ta 0.23476 1.826 25.73229 0.000195 0.00161 -0.000812 +Ta 2.58235 0.166 25.73229 0.000195 0.00161 -0.000812 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.901657 stress="-9711.95 0.0 0.0 0.0 -7971.759999999999 0.0 0.0 0.0 -387.39" +Ta 2.34759 1.66 0.09122 0.0 0.0 -2.1e-05 +Ta 0.0 0.0 0.09122 0.0 0.0 -2.1e-05 +Ta 0.0 1.66 2.33609 0.0 0.0 0.000332 +Ta 2.34759 0.0 2.33609 0.0 0.0 0.000332 +Ta 2.34759 1.66 4.68537 0.0 0.0 0.000393 +Ta 0.0 0.0 4.68537 0.0 0.0 0.000393 +Ta 0.0 1.66 7.03419 0.0 0.0 8.4e-05 +Ta 2.34759 0.0 7.03419 0.0 0.0 8.4e-05 +Ta 2.34759 1.66 9.38555 0.0 0.0 -0.000286 +Ta 0.0 0.0 9.38555 0.0 0.0 -0.000286 +Ta 0.0 1.66 11.73665 0.0 0.0 -0.000509 +Ta 2.34759 0.0 11.73665 0.0 0.0 -0.000509 +Ta 4.69519 0.0 14.08695 0.0 0.0 0.000509 +Ta 2.3476 1.66 14.08695 0.0 0.0 0.000509 +Ta 2.3476 0.0 16.43803 0.0 0.0 0.000286 +Ta 4.69519 1.66 16.43803 0.0 0.0 0.000286 +Ta 4.69519 0.0 18.78939 0.0 0.0 -8.4e-05 +Ta 2.3476 1.66 18.78939 0.0 0.0 -8.4e-05 +Ta 2.3476 0.0 21.13822 0.0 0.0 -0.000393 +Ta 4.69519 1.66 21.13822 0.0 0.0 -0.000393 +Ta 4.69519 0.0 23.4874 0.0 0.0 -0.000332 +Ta 2.3476 1.66 23.4874 0.0 0.0 -0.000332 +Ta 2.3476 0.0 25.73228 0.0 0.0 2.1e-05 +Ta 4.69519 1.66 25.73228 0.0 0.0 2.1e-05 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.584238 stress="-8455.84 -1472.71 2162.92 -1472.71 -8121.589999999999 1800.64 2162.92 1800.64 -338.96" +Ta 2.34759 1.66 0.07452 -0.000101 0.002118 -0.001067 +Ta 0.0 0.0 0.07452 -0.000101 0.002118 -0.001067 +Ta 0.0 1.66 2.31914 0.000559 -0.002302 0.001125 +Ta 2.34759 0.0 2.31914 0.000559 -0.002302 0.001125 +Ta 2.34759 1.66 4.6683 -0.011564 0.001165 -0.001122 +Ta 0.0 0.0 4.6683 -0.011564 0.001165 -0.001122 +Ta 0.0 1.66 7.0214 0.010839 -0.033575 -0.000333 +Ta 2.34759 0.0 7.0214 0.010839 -0.033575 -0.000333 +Ta 2.34759 1.66 9.36328 0.008027 0.132954 0.000561 +Ta 0.0 0.0 9.36328 0.008027 0.132954 0.000561 +Ta 0.0 1.66 11.70268 -0.232266 -0.441609 -0.001106 +Ta 2.34759 0.0 11.70268 -0.232266 -0.441609 -0.001106 +Ta 4.22567 2.988 14.12092 0.232266 0.441609 0.001106 +Ta 1.87808 1.328 14.12092 0.232266 0.441609 0.001106 +Ta 1.87808 2.988 16.4603 -0.008027 -0.132954 -0.000561 +Ta 4.22567 1.328 16.4603 -0.008027 -0.132954 -0.000561 +Ta 4.22567 2.988 18.80218 -0.010839 0.033575 0.000333 +Ta 1.87808 1.328 18.80218 -0.010839 0.033575 0.000333 +Ta 1.87808 2.988 21.15529 0.011564 -0.001165 0.001122 +Ta 4.22567 1.328 21.15529 0.011564 -0.001165 0.001122 +Ta 4.22567 2.988 23.50435 -0.000559 0.002302 -0.001125 +Ta 1.87808 1.328 23.50435 -0.000559 0.002302 -0.001125 +Ta 1.87808 2.988 25.74898 0.000101 -0.002118 0.001067 +Ta 4.22567 1.328 25.74898 0.000101 -0.002118 0.001067 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.784283 stress="-9315.08 -723.62 1802.65 -723.62 -7584.349999999999 1731.7800000000002 1802.65 1731.7800000000002 -137.97" +Ta 2.34759 1.66 0.09121 0.000196 0.00161 0.000943 +Ta 0.0 0.0 0.09121 0.000196 0.00161 0.000943 +Ta 0.0 1.66 2.3361 0.000284 -0.000353 -0.002245 +Ta 2.34759 0.0 2.3361 0.000284 -0.000353 -0.002245 +Ta 2.34759 1.66 4.68536 -0.008799 0.00141 -0.002392 +Ta 0.0 0.0 4.68536 -0.008799 0.00141 -0.002392 +Ta 0.0 1.66 7.03392 0.006694 -0.021282 0.017465 +Ta 2.34759 0.0 7.03392 0.006694 -0.021282 0.017465 +Ta 2.34759 1.66 9.38594 0.014872 0.089556 -4.7e-05 +Ta 0.0 0.0 9.38594 0.014872 0.089556 -4.7e-05 +Ta 0.0 1.66 11.73648 -0.219937 -0.367391 -0.112068 +Ta 2.34759 0.0 11.73648 -0.219937 -0.367391 -0.112068 +Ta 4.46043 3.154 14.08712 0.219937 0.367391 0.112068 +Ta 2.11284 1.494 14.08712 0.219937 0.367391 0.112068 +Ta 2.11284 3.154 16.43764 -0.014872 -0.089556 4.7e-05 +Ta 4.46043 1.494 16.43764 -0.014872 -0.089556 4.7e-05 +Ta 4.46043 3.154 18.78966 -0.006694 0.021282 -0.017465 +Ta 2.11284 1.494 18.78966 -0.006694 0.021282 -0.017465 +Ta 2.11284 3.154 21.13823 0.008799 -0.00141 0.002392 +Ta 4.46043 1.494 21.13823 0.008799 -0.00141 0.002392 +Ta 4.46043 3.154 23.48739 -0.000284 0.000353 0.002245 +Ta 2.11284 1.494 23.48739 -0.000284 0.000353 0.002245 +Ta 2.11284 3.154 25.73229 -0.000196 -0.00161 -0.000943 +Ta 4.46043 1.494 25.73229 -0.000196 -0.00161 -0.000943 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.302158 stress="-5999.0 -2091.5499999999997 -2060.3199999999997 -2091.5499999999997 -8316.509999999998 -1933.87 -2060.3199999999997 -1933.87 4767.089999999999" +Ta 2.34759 1.66 0.09121 0.000338 -0.000764 0.003013 +Ta 0.0 0.0 0.09121 0.000338 -0.000764 0.003013 +Ta 0.0 1.66 2.3361 -0.000192 0.002217 -0.008533 +Ta 2.34759 0.0 2.3361 -0.000192 0.002217 -0.008533 +Ta 2.34759 1.66 4.68536 0.007402 -0.005681 -0.01113 +Ta 0.0 0.0 4.68536 0.007402 -0.005681 -0.01113 +Ta 0.0 1.66 7.03392 -0.010084 0.035505 0.068653 +Ta 2.34759 0.0 7.03392 -0.010084 0.035505 0.068653 +Ta 2.34759 1.66 9.38594 0.009421 -0.162853 -0.055133 +Ta 0.0 0.0 9.38594 0.009421 -0.162853 -0.055133 +Ta 0.0 1.66 11.73648 0.194592 0.543144 -0.645035 +Ta 2.34759 0.0 11.73648 0.194592 0.543144 -0.645035 +Ta 3.05187 2.158 14.08712 -0.194592 -0.543144 0.645035 +Ta 0.70428 0.498 14.08712 -0.194592 -0.543144 0.645035 +Ta 0.70428 2.158 16.43764 -0.009421 0.162853 0.055133 +Ta 3.05187 0.498 16.43764 -0.009421 0.162853 0.055133 +Ta 3.05187 2.158 18.78966 0.010084 -0.035505 -0.068653 +Ta 0.70428 0.498 18.78966 0.010084 -0.035505 -0.068653 +Ta 0.70428 2.158 21.13823 -0.007402 0.005681 0.01113 +Ta 3.05187 0.498 21.13823 -0.007402 0.005681 0.01113 +Ta 3.05187 2.158 23.48739 0.000192 -0.002217 0.008533 +Ta 0.70428 0.498 23.48739 0.000192 -0.002217 0.008533 +Ta 0.70428 2.158 25.73229 -0.000338 0.000764 -0.003013 +Ta 3.05187 0.498 25.73229 -0.000338 0.000764 -0.003013 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.55564 stress="-7951.990000000001 -1470.47 -2323.28 -1470.47 -7087.54 -2242.19 -2323.28 -2242.19 1393.38" +Ta 2.34759 1.66 0.09121 6.8e-05 -0.00218 0.002247 +Ta 0.0 0.0 0.09121 6.8e-05 -0.00218 0.002247 +Ta 0.0 1.66 2.3361 -0.000373 0.001531 -0.005318 +Ta 2.34759 0.0 2.3361 -0.000373 0.001531 -0.005318 +Ta 2.34759 1.66 4.68536 0.011743 -0.002192 -0.00859 +Ta 0.0 0.0 4.68536 0.011743 -0.002192 -0.00859 +Ta 0.0 1.66 7.03392 -0.010535 0.038081 0.052269 +Ta 2.34759 0.0 7.03392 -0.010535 0.038081 0.052269 +Ta 2.34759 1.66 9.38594 -0.00905 -0.147322 -0.015198 +Ta 0.0 0.0 9.38594 -0.00905 -0.147322 -0.015198 +Ta 0.0 1.66 11.73648 0.255618 0.52958 -0.348689 +Ta 2.34759 0.0 11.73648 0.255618 0.52958 -0.348689 +Ta 2.81711 1.992 14.08712 -0.255618 -0.52958 0.348689 +Ta 0.46952 0.332 14.08712 -0.255618 -0.52958 0.348689 +Ta 0.46952 1.992 16.43764 0.00905 0.147322 0.015198 +Ta 2.81711 0.332 16.43764 0.00905 0.147322 0.015198 +Ta 2.81711 1.992 18.78966 0.010535 -0.038081 -0.052269 +Ta 0.46952 0.332 18.78966 0.010535 -0.038081 -0.052269 +Ta 0.46952 1.992 21.13823 -0.011743 0.002192 0.00859 +Ta 2.81711 0.332 21.13823 -0.011743 0.002192 0.00859 +Ta 2.81711 1.992 23.48739 0.000373 -0.001531 0.005318 +Ta 0.46952 0.332 23.48739 0.000373 -0.001531 0.005318 +Ta 0.46952 1.992 25.73229 -6.8e-05 0.00218 -0.002247 +Ta 2.81711 0.332 25.73229 -6.8e-05 0.00218 -0.002247 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.246939 stress="-7247.110000000001 -2088.01 900.26 -2088.01 -12867.95 522.24 900.26 522.24 -343.87" +Ta 2.34759 1.66 0.0313 -0.000299 2.9e-05 0.000555 +Ta 0.0 0.0 0.0313 -0.000299 2.9e-05 0.000555 +Ta 0.0 1.66 2.27588 0.000225 -0.001627 0.00115 +Ta 2.34759 0.0 2.27588 0.000225 -0.001627 0.00115 +Ta 2.34759 1.66 4.62506 -0.002747 0.002713 0.000254 +Ta 0.0 0.0 4.62506 -0.002747 0.002713 0.000254 +Ta 0.0 1.66 6.98061 0.004373 -0.018318 9.6e-05 +Ta 2.34759 0.0 6.98061 0.004373 -0.018318 9.6e-05 +Ta 2.34759 1.66 9.31312 -0.010337 0.080996 -2e-06 +Ta 0.0 0.0 9.31312 -0.010337 0.080996 -2e-06 +Ta 0.0 1.66 11.6666 -0.064509 -0.216178 0.000109 +Ta 2.34759 0.0 11.6666 -0.064509 -0.216178 0.000109 +Ta 3.75615 2.656 14.157 0.064509 0.216178 -0.000109 +Ta 1.40856 0.996 14.157 0.064509 0.216178 -0.000109 +Ta 1.40856 2.656 16.51046 0.010337 -0.080996 2e-06 +Ta 3.75615 0.996 16.51046 0.010337 -0.080996 2e-06 +Ta 3.75615 2.656 18.84297 -0.004373 0.018318 -9.6e-05 +Ta 1.40856 0.996 18.84297 -0.004373 0.018318 -9.6e-05 +Ta 1.40856 2.656 21.19853 0.002747 -0.002713 -0.000254 +Ta 3.75615 0.996 21.19853 0.002747 -0.002713 -0.000254 +Ta 3.75615 2.656 23.54761 -0.000225 0.001627 -0.00115 +Ta 1.40856 0.996 23.54761 -0.000225 0.001627 -0.00115 +Ta 1.40856 2.656 25.7922 0.000299 -2.9e-05 -0.000555 +Ta 3.75615 0.996 25.7922 0.000299 -2.9e-05 -0.000555 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.302157 stress="-5999.4800000000005 -2091.2000000000003 2059.81 -2091.2000000000003 -8317.08 1933.52 2059.81 1933.52 4766.58" +Ta 2.34759 1.66 0.09121 -0.000338 0.000764 0.003027 +Ta 0.0 0.0 0.09121 -0.000338 0.000764 0.003027 +Ta 0.0 1.66 2.3361 0.000192 -0.002217 -0.008526 +Ta 2.34759 0.0 2.3361 0.000192 -0.002217 -0.008526 +Ta 2.34759 1.66 4.68536 -0.007402 0.005681 -0.011124 +Ta 0.0 0.0 4.68536 -0.007402 0.005681 -0.011124 +Ta 0.0 1.66 7.03392 0.010084 -0.035505 0.068661 +Ta 2.34759 0.0 7.03392 0.010084 -0.035505 0.068661 +Ta 2.34759 1.66 9.38594 -0.009421 0.162854 -0.055124 +Ta 0.0 0.0 9.38594 -0.009421 0.162854 -0.055124 +Ta 0.0 1.66 11.73648 -0.194591 -0.543144 -0.645027 +Ta 2.34759 0.0 11.73648 -0.194591 -0.543144 -0.645027 +Ta 3.99091 2.822 14.08712 0.194591 0.543144 0.645027 +Ta 1.64332 1.162 14.08712 0.194591 0.543144 0.645027 +Ta 1.64332 2.822 16.43764 0.009421 -0.162854 0.055124 +Ta 3.99091 1.162 16.43764 0.009421 -0.162854 0.055124 +Ta 3.99091 2.822 18.78966 -0.010084 0.035505 -0.068661 +Ta 1.64332 1.162 18.78966 -0.010084 0.035505 -0.068661 +Ta 1.64332 2.822 21.13823 0.007402 -0.005681 0.011124 +Ta 3.99091 1.162 21.13823 0.007402 -0.005681 0.011124 +Ta 3.99091 2.822 23.48739 -0.000192 0.002217 0.008526 +Ta 1.64332 1.162 23.48739 -0.000192 0.002217 0.008526 +Ta 1.64332 2.822 25.73229 0.000338 -0.000764 -0.003027 +Ta 3.99091 1.162 25.73229 0.000338 -0.000764 -0.003027 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.246935 stress="-7243.7300000000005 -2085.2 -898.75 -2085.2 -12860.99 -521.24 -898.75 -521.24 -339.14" +Ta 2.34759 1.66 0.03138 0.000299 -3.1e-05 0.000674 +Ta 0.0 0.0 0.03138 0.000299 -3.1e-05 0.000674 +Ta 0.0 1.66 2.276 -0.000225 0.001628 -0.00088 +Ta 2.34759 0.0 2.276 -0.000225 0.001628 -0.00088 +Ta 2.34759 1.66 4.62485 0.002741 -0.002715 0.000469 +Ta 0.0 0.0 4.62485 0.002741 -0.002715 0.000469 +Ta 0.0 1.66 6.98003 -0.004361 0.018297 0.002362 +Ta 2.34759 0.0 6.98003 -0.004361 0.018297 0.002362 +Ta 2.34759 1.66 9.31271 0.010328 -0.080927 0.000615 +Ta 0.0 0.0 9.31271 0.010328 -0.080927 0.000615 +Ta 0.0 1.66 11.66645 0.064416 0.215971 0.000489 +Ta 2.34759 0.0 11.66645 0.064416 0.215971 0.000489 +Ta 3.28663 2.324 14.15715 -0.064416 -0.215971 -0.000489 +Ta 0.93904 0.664 14.15715 -0.064416 -0.215971 -0.000489 +Ta 0.93904 2.324 16.51087 -0.010328 0.080927 -0.000615 +Ta 3.28663 0.664 16.51087 -0.010328 0.080927 -0.000615 +Ta 3.28663 2.324 18.84355 0.004361 -0.018297 -0.002362 +Ta 0.93904 0.664 18.84355 0.004361 -0.018297 -0.002362 +Ta 0.93904 2.324 21.19874 -0.002741 0.002715 -0.000469 +Ta 3.28663 0.664 21.19874 -0.002741 0.002715 -0.000469 +Ta 3.28663 2.324 23.54749 0.000225 -0.001628 0.00088 +Ta 0.93904 0.664 23.54749 0.000225 -0.001628 0.00088 +Ta 0.93904 2.324 25.79212 -0.000299 3.1e-05 -0.000674 +Ta 3.28663 0.664 25.79212 -0.000299 3.1e-05 -0.000674 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.896025 stress="-9869.42 0.0 0.0 0.0 -8124.2 0.0 0.0 0.0 -554.5600000000001" +Ta 2.34759 1.66 0.09121 0.0 0.0 0.000102 +Ta 0.0 0.0 0.09121 0.0 0.0 0.000102 +Ta 0.0 1.66 2.3361 0.0 0.0 -0.000104 +Ta 2.34759 0.0 2.3361 0.0 0.0 -0.000104 +Ta 2.34759 1.66 4.68536 0.0 0.0 0.000115 +Ta 0.0 0.0 4.68536 0.0 0.0 0.000115 +Ta 0.0 1.66 7.03392 0.0 0.0 0.002828 +Ta 2.34759 0.0 7.03392 0.0 0.0 0.002828 +Ta 2.34759 1.66 9.38594 0.0 0.0 -0.004132 +Ta 0.0 0.0 9.38594 0.0 0.0 -0.004132 +Ta 0.0 1.66 11.73648 0.0 0.0 0.001736 +Ta 2.34759 0.0 11.73648 0.0 0.0 0.001736 +Ta 2.34759 1.66 14.08712 0.0 0.0 -0.001736 +Ta 0.0 0.0 14.08712 0.0 0.0 -0.001736 +Ta 0.0 1.66 16.43764 0.0 0.0 0.004132 +Ta 2.34759 0.0 16.43764 0.0 0.0 0.004132 +Ta 2.34759 1.66 18.78966 0.0 0.0 -0.002828 +Ta 0.0 0.0 18.78966 0.0 0.0 -0.002828 +Ta 0.0 1.66 21.13823 0.0 0.0 -0.000115 +Ta 2.34759 0.0 21.13823 0.0 0.0 -0.000115 +Ta 2.34759 1.66 23.48739 0.0 0.0 0.000104 +Ta 0.0 0.0 23.48739 0.0 0.0 0.000104 +Ta 0.0 1.66 25.73229 0.0 0.0 -0.000102 +Ta 2.34759 0.0 25.73229 0.0 0.0 -0.000102 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.584237 stress="-8428.63 -1472.9 -2164.32 -1472.9 -8091.21 -1800.0100000000002 -2164.32 -1800.0100000000002 -288.22999999999996" +Ta 2.34759 1.66 0.07506 0.000102 -0.002133 -0.000914 +Ta 0.0 0.0 0.07506 0.000102 -0.002133 -0.000914 +Ta 0.0 1.66 2.31974 -0.000559 0.002291 0.000397 +Ta 2.34759 0.0 2.31974 -0.000559 0.002291 0.000397 +Ta 2.34759 1.66 4.6688 0.011573 -0.001165 -0.000831 +Ta 0.0 0.0 4.6688 0.011573 -0.001165 -0.000831 +Ta 0.0 1.66 7.02184 -0.010852 0.033591 -0.000593 +Ta 2.34759 0.0 7.02184 -0.010852 0.033591 -0.000593 +Ta 2.34759 1.66 9.36366 -0.008031 -0.133014 -0.000394 +Ta 0.0 0.0 9.36366 -0.008031 -0.133014 -0.000394 +Ta 0.0 1.66 11.70273 0.232392 0.441681 -0.000156 +Ta 2.34759 0.0 11.70273 0.232392 0.441681 -0.000156 +Ta 2.81711 1.992 14.12087 -0.232392 -0.441681 0.000156 +Ta 0.46952 0.332 14.12087 -0.232392 -0.441681 0.000156 +Ta 0.46952 1.992 16.45992 0.008031 0.133014 0.000394 +Ta 2.81711 0.332 16.45992 0.008031 0.133014 0.000394 +Ta 2.81711 1.992 18.80174 0.010852 -0.033591 0.000593 +Ta 0.46952 0.332 18.80174 0.010852 -0.033591 0.000593 +Ta 0.46952 1.992 21.15479 -0.011573 0.001165 0.000831 +Ta 2.81711 0.332 21.15479 -0.011573 0.001165 0.000831 +Ta 2.81711 1.992 23.50375 0.000559 -0.002291 -0.000397 +Ta 0.46952 0.332 23.50375 0.000559 -0.002291 -0.000397 +Ta 0.46952 1.992 25.74844 -0.000102 0.002133 0.000914 +Ta 2.81711 0.332 25.74844 -0.000102 0.002133 0.000914 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.124427 stress="-3757.0899999999997 -2887.24 902.0 -2887.24 -10640.1 866.64 902.0 866.64 7774.740000000001" +Ta 2.34759 1.66 0.09121 -0.000483 -0.000237 0.002307 +Ta 0.0 0.0 0.09121 -0.000483 -0.000237 0.002307 +Ta 0.0 1.66 2.3361 8.9e-05 -0.001539 -0.010324 +Ta 2.34759 0.0 2.3361 8.9e-05 -0.001539 -0.010324 +Ta 2.34759 1.66 4.68536 -0.003111 0.003535 -0.007613 +Ta 0.0 0.0 4.68536 -0.003111 0.003535 -0.007613 +Ta 0.0 1.66 7.03392 0.007146 -0.021127 0.073738 +Ta 2.34759 0.0 7.03392 0.007146 -0.021127 0.073738 +Ta 2.34759 1.66 9.38594 -0.013663 0.107342 -0.116996 +Ta 0.0 0.0 9.38594 -0.013663 0.107342 -0.116996 +Ta 0.0 1.66 11.73648 -0.067743 -0.32857 -0.821304 +Ta 2.34759 0.0 11.73648 -0.067743 -0.32857 -0.821304 +Ta 3.75615 2.656 14.08712 0.067743 0.32857 0.821304 +Ta 1.40856 0.996 14.08712 0.067743 0.32857 0.821304 +Ta 1.40856 2.656 16.43764 0.013663 -0.107342 0.116996 +Ta 3.75615 0.996 16.43764 0.013663 -0.107342 0.116996 +Ta 3.75615 2.656 18.78966 -0.007146 0.021127 -0.073738 +Ta 1.40856 0.996 18.78966 -0.007146 0.021127 -0.073738 +Ta 1.40856 2.656 21.13823 0.003111 -0.003535 0.007613 +Ta 3.75615 0.996 21.13823 0.003111 -0.003535 0.007613 +Ta 3.75615 2.656 23.48739 -8.9e-05 0.001539 0.010324 +Ta 1.40856 0.996 23.48739 -8.9e-05 0.001539 0.010324 +Ta 1.40856 2.656 25.73229 0.000483 0.000237 -0.002307 +Ta 3.75615 0.996 25.73229 0.000483 0.000237 -0.002307 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.379366 stress="-7763.09 -1797.51 1889.74 -1797.51 -10164.59 1320.57 1889.74 1320.57 34.12" +Ta 2.34759 1.66 0.05376 -0.000259 0.002166 -0.001263 +Ta 0.0 0.0 0.05376 -0.000259 0.002166 -0.001263 +Ta 0.0 1.66 2.29821 0.000506 -0.00178 0.000245 +Ta 2.34759 0.0 2.29821 0.000506 -0.00178 0.000245 +Ta 2.34759 1.66 4.64698 -0.007327 0.004782 -0.001824 +Ta 0.0 0.0 4.64698 -0.007327 0.004782 -0.001824 +Ta 0.0 1.66 7.00162 0.008163 -0.030937 -0.001313 +Ta 2.34759 0.0 7.00162 0.008163 -0.030937 -0.001313 +Ta 2.34759 1.66 9.33764 -0.007098 0.132381 -0.001661 +Ta 0.0 0.0 9.33764 -0.007098 0.132381 -0.001661 +Ta 0.0 1.66 11.67998 -0.168672 -0.393164 0.000838 +Ta 2.34759 0.0 11.67998 -0.168672 -0.393164 0.000838 +Ta 3.99091 2.822 14.14362 0.168672 0.393164 -0.000838 +Ta 1.64332 1.162 14.14362 0.168672 0.393164 -0.000838 +Ta 1.64332 2.822 16.48594 0.007098 -0.132381 0.001661 +Ta 3.99091 1.162 16.48594 0.007098 -0.132381 0.001661 +Ta 3.99091 2.822 18.82196 -0.008163 0.030937 0.001313 +Ta 1.64332 1.162 18.82196 -0.008163 0.030937 0.001313 +Ta 1.64332 2.822 21.17661 0.007327 -0.004782 0.001824 +Ta 3.99091 1.162 21.17661 0.007327 -0.004782 0.001824 +Ta 3.99091 2.822 23.52528 -0.000506 0.00178 -0.000245 +Ta 1.64332 1.162 23.52528 -0.000506 0.00178 -0.000245 +Ta 1.64332 2.822 25.76974 0.000259 -0.002166 0.001263 +Ta 3.99091 1.162 25.76974 0.000259 -0.002166 0.001263 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.37937 stress="-7778.34 -1797.1200000000001 -1889.07 -1797.1200000000001 -10180.85 -1319.78 -1889.07 -1319.78 5.64" +Ta 2.34759 1.66 0.0535 0.000258 -0.00217 -0.000937 +Ta 0.0 0.0 0.0535 0.000258 -0.00217 -0.000937 +Ta 0.0 1.66 2.29801 -0.000506 0.00178 -2.1e-05 +Ta 2.34759 0.0 2.29801 -0.000506 0.00178 -2.1e-05 +Ta 2.34759 1.66 4.64678 0.007324 -0.004781 -0.001649 +Ta 0.0 0.0 4.64678 0.007324 -0.004781 -0.001649 +Ta 0.0 1.66 7.00147 -0.00816 0.030933 -0.001233 +Ta 2.34759 0.0 7.00147 -0.00816 0.030933 -0.001233 +Ta 2.34759 1.66 9.33754 0.0071 -0.132353 -0.001629 +Ta 0.0 0.0 9.33754 0.0071 -0.132353 -0.001629 +Ta 0.0 1.66 11.67995 0.168627 0.393088 0.00081 +Ta 2.34759 0.0 11.67995 0.168627 0.393088 0.00081 +Ta 3.05187 2.158 14.14365 -0.168627 -0.393088 -0.00081 +Ta 0.70428 0.498 14.14365 -0.168627 -0.393088 -0.00081 +Ta 0.70428 2.158 16.48604 -0.0071 0.132353 0.001629 +Ta 3.05187 0.498 16.48604 -0.0071 0.132353 0.001629 +Ta 3.05187 2.158 18.82211 0.00816 -0.030933 0.001233 +Ta 0.70428 0.498 18.82211 0.00816 -0.030933 0.001233 +Ta 0.70428 2.158 21.17681 -0.007324 0.004781 0.001649 +Ta 3.05187 0.498 21.17681 -0.007324 0.004781 0.001649 +Ta 3.05187 2.158 23.52548 0.000506 -0.00178 2.1e-05 +Ta 0.70428 0.498 23.52548 0.000506 -0.00178 2.1e-05 +Ta 0.70428 2.158 25.77 -0.000258 0.00217 0.000937 +Ta 3.05187 0.498 25.77 -0.000258 0.00217 0.000937 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.124427 stress="-3756.4 -2886.7400000000002 -901.71 -2886.7400000000002 -10639.47 -867.12 -901.71 -867.12 7774.14" +Ta 2.34759 1.66 0.09121 0.000483 0.000237 0.002314 +Ta 0.0 0.0 0.09121 0.000483 0.000237 0.002314 +Ta 0.0 1.66 2.3361 -8.8e-05 0.001538 -0.010267 +Ta 2.34759 0.0 2.3361 -8.8e-05 0.001538 -0.010267 +Ta 2.34759 1.66 4.68536 0.003111 -0.003535 -0.007607 +Ta 0.0 0.0 4.68536 0.003111 -0.003535 -0.007607 +Ta 0.0 1.66 7.03392 -0.007146 0.021127 0.073723 +Ta 2.34759 0.0 7.03392 -0.007146 0.021127 0.073723 +Ta 2.34759 1.66 9.38594 0.013663 -0.10734 -0.116992 +Ta 0.0 0.0 9.38594 0.013663 -0.10734 -0.116992 +Ta 0.0 1.66 11.73648 0.067747 0.328568 -0.821295 +Ta 2.34759 0.0 11.73648 0.067747 0.328568 -0.821295 +Ta 3.28663 2.324 14.08712 -0.067747 -0.328568 0.821295 +Ta 0.93904 0.664 14.08712 -0.067747 -0.328568 0.821295 +Ta 0.93904 2.324 16.43764 -0.013663 0.10734 0.116992 +Ta 3.28663 0.664 16.43764 -0.013663 0.10734 0.116992 +Ta 3.28663 2.324 18.78966 0.007146 -0.021127 -0.073723 +Ta 0.93904 0.664 18.78966 0.007146 -0.021127 -0.073723 +Ta 0.93904 2.324 21.13823 -0.003111 0.003535 0.007607 +Ta 3.28663 0.664 21.13823 -0.003111 0.003535 0.007607 +Ta 3.28663 2.324 23.48739 8.8e-05 -0.001538 0.010267 +Ta 0.93904 0.664 23.48739 8.8e-05 -0.001538 0.010267 +Ta 0.93904 2.324 25.73229 -0.000483 -0.000237 -0.002314 +Ta 3.28663 0.664 25.73229 -0.000483 -0.000237 -0.002314 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.901657 stress="-9712.87 0.0 0.0 0.0 -7972.25 0.0 0.0 0.0 -388.31" +Ta 2.34759 1.66 0.09122 0.0 0.0 -1.6e-05 +Ta 0.0 0.0 0.09122 0.0 0.0 -1.6e-05 +Ta 0.0 1.66 2.33609 0.0 0.0 0.000319 +Ta 2.34759 0.0 2.33609 0.0 0.0 0.000319 +Ta 2.34759 1.66 4.68537 0.0 0.0 0.0004 +Ta 0.0 0.0 4.68537 0.0 0.0 0.0004 +Ta 0.0 1.66 7.03419 0.0 0.0 9.3e-05 +Ta 2.34759 0.0 7.03419 0.0 0.0 9.3e-05 +Ta 2.34759 1.66 9.38555 0.0 0.0 -0.000298 +Ta 0.0 0.0 9.38555 0.0 0.0 -0.000298 +Ta 0.0 1.66 11.73665 0.0 0.0 -0.000507 +Ta 2.34759 0.0 11.73665 0.0 0.0 -0.000507 +Ta 2.34759 1.66 14.08695 0.0 0.0 0.000507 +Ta 0.0 0.0 14.08695 0.0 0.0 0.000507 +Ta 0.0 1.66 16.43803 0.0 0.0 0.000298 +Ta 2.34759 0.0 16.43803 0.0 0.0 0.000298 +Ta 2.34759 1.66 18.78939 0.0 0.0 -9.3e-05 +Ta 0.0 0.0 18.78939 0.0 0.0 -9.3e-05 +Ta 0.0 1.66 21.13822 0.0 0.0 -0.0004 +Ta 2.34759 0.0 21.13822 0.0 0.0 -0.0004 +Ta 2.34759 1.66 23.4874 0.0 0.0 -0.000319 +Ta 0.0 0.0 23.4874 0.0 0.0 -0.000319 +Ta 0.0 1.66 25.73228 0.0 0.0 1.6e-05 +Ta 2.34759 0.0 25.73228 0.0 0.0 1.6e-05 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.79264 stress="-9277.630000000001 -706.52 -1762.12 -706.52 -7720.29 -1609.51 -1762.12 -1609.51 -420.21999999999997" +Ta 2.34759 1.66 0.0871 -0.000184 -0.001656 0.000674 +Ta 0.0 0.0 0.0871 -0.000184 -0.001656 0.000674 +Ta 0.0 1.66 2.332 -0.000294 0.000423 0.000306 +Ta 2.34759 0.0 2.332 -0.000294 0.000423 0.000306 +Ta 2.34759 1.66 4.68156 0.008643 -0.001357 -0.001853 +Ta 0.0 0.0 4.68156 0.008643 -0.001357 -0.001853 +Ta 0.0 1.66 7.03137 -0.006924 0.020397 -0.000275 +Ta 2.34759 0.0 7.03137 -0.006924 0.020397 -0.000275 +Ta 2.34759 1.66 9.38022 -0.01463 -0.087628 0.000622 +Ta 0.0 0.0 9.38022 -0.01463 -0.087628 0.000622 +Ta 0.0 1.66 11.72434 0.214497 0.348769 -0.000686 +Ta 2.34759 0.0 11.72434 0.214497 0.348769 -0.000686 +Ta 2.58235 1.826 14.09926 -0.214497 -0.348769 0.000686 +Ta 0.23476 0.166 14.09926 -0.214497 -0.348769 0.000686 +Ta 0.23476 1.826 16.44336 0.01463 0.087628 -0.000622 +Ta 2.58235 0.166 16.44336 0.01463 0.087628 -0.000622 +Ta 2.58235 1.826 18.79221 0.006924 -0.020397 0.000275 +Ta 0.23476 0.166 18.79221 0.006924 -0.020397 0.000275 +Ta 0.23476 1.826 21.14203 -0.008643 0.001357 0.001853 +Ta 2.58235 0.166 21.14203 -0.008643 0.001357 0.001853 +Ta 2.58235 1.826 23.49149 0.000294 -0.000423 -0.000306 +Ta 0.23476 0.166 23.49149 0.000294 -0.000423 -0.000306 +Ta 0.23476 1.826 25.7364 0.000184 0.001656 -0.000674 +Ta 2.58235 0.166 25.7364 0.000184 0.001656 -0.000674 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.896025 stress="-9868.86 0.0 0.0 0.0 -8124.259999999999 0.0 0.0 0.0 -554.9" +Ta 2.34759 1.66 0.09121 0.0 0.0 0.000107 +Ta 0.0 0.0 0.09121 0.0 0.0 0.000107 +Ta 0.0 1.66 2.3361 0.0 0.0 -9.8e-05 +Ta 2.34759 0.0 2.3361 0.0 0.0 -9.8e-05 +Ta 2.34759 1.66 4.68536 0.0 0.0 0.000111 +Ta 0.0 0.0 4.68536 0.0 0.0 0.000111 +Ta 0.0 1.66 7.03392 0.0 0.0 0.002832 +Ta 2.34759 0.0 7.03392 0.0 0.0 0.002832 +Ta 2.34759 1.66 9.38594 0.0 0.0 -0.004127 +Ta 0.0 0.0 9.38594 0.0 0.0 -0.004127 +Ta 0.0 1.66 11.73648 0.0 0.0 0.001737 +Ta 2.34759 0.0 11.73648 0.0 0.0 0.001737 +Ta 4.69519 0.0 14.08712 0.0 0.0 -0.001737 +Ta 2.3476 1.66 14.08712 0.0 0.0 -0.001737 +Ta 2.3476 0.0 16.43764 0.0 0.0 0.004127 +Ta 4.69519 1.66 16.43764 0.0 0.0 0.004127 +Ta 4.69519 0.0 18.78966 0.0 0.0 -0.002832 +Ta 2.3476 1.66 18.78966 0.0 0.0 -0.002832 +Ta 2.3476 0.0 21.13823 0.0 0.0 -0.000111 +Ta 4.69519 1.66 21.13823 0.0 0.0 -0.000111 +Ta 4.69519 0.0 23.48739 0.0 0.0 9.8e-05 +Ta 2.3476 1.66 23.48739 0.0 0.0 9.8e-05 +Ta 2.3476 0.0 25.73229 0.0 0.0 -0.000107 +Ta 4.69519 1.66 25.73229 0.0 0.0 -0.000107 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.206496 stress="-6761.16 -2211.9399999999996 0.0 -2211.9399999999996 -14026.06 0.0 0.0 0.0 -201.45" +Ta 2.34759 1.66 0.026 0.0 0.0 -0.000166 +Ta 0.0 0.0 0.026 0.0 0.0 -0.000166 +Ta 0.0 1.66 2.2705 0.0 0.0 -0.000442 +Ta 2.34759 0.0 2.2705 0.0 0.0 -0.000442 +Ta 2.34759 1.66 4.61955 0.0 0.0 -0.001018 +Ta 0.0 0.0 4.61955 0.0 0.0 -0.001018 +Ta 0.0 1.66 6.97451 0.0 0.0 0.001141 +Ta 2.34759 0.0 6.97451 0.0 0.0 0.001141 +Ta 2.34759 1.66 9.30496 0.0 0.0 0.000143 +Ta 0.0 0.0 9.30496 0.0 0.0 0.000143 +Ta 0.0 1.66 11.66343 0.0 0.0 0.002124 +Ta 2.34759 0.0 11.66343 0.0 0.0 0.002124 +Ta 3.52139 2.49 14.16017 0.0 0.0 -0.002124 +Ta 1.1738 0.83 14.16017 0.0 0.0 -0.002124 +Ta 1.1738 2.49 16.51862 0.0 0.0 -0.000143 +Ta 3.52139 0.83 16.51862 0.0 0.0 -0.000143 +Ta 3.52139 2.49 18.84907 0.0 0.0 -0.001141 +Ta 1.1738 0.83 18.84907 0.0 0.0 -0.001141 +Ta 1.1738 2.49 21.20404 0.0 0.0 0.001018 +Ta 3.52139 0.83 21.20404 0.0 0.0 0.001018 +Ta 3.52139 2.49 23.55299 0.0 0.0 0.000442 +Ta 1.1738 0.83 23.55299 0.0 0.0 0.000442 +Ta 1.1738 2.49 25.7975 0.0 0.0 0.000166 +Ta 3.52139 0.83 25.7975 0.0 0.0 0.000166 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.55564 stress="-7951.26 -1470.33 2322.88 -1470.33 -7086.45 2241.6200000000003 2322.88 2241.6200000000003 1394.24" +Ta 2.34759 1.66 0.09121 -6.8e-05 0.00218 0.002238 +Ta 0.0 0.0 0.09121 -6.8e-05 0.00218 0.002238 +Ta 0.0 1.66 2.3361 0.000372 -0.001531 -0.005316 +Ta 2.34759 0.0 2.3361 0.000372 -0.001531 -0.005316 +Ta 2.34759 1.66 4.68536 -0.011743 0.002192 -0.008604 +Ta 0.0 0.0 4.68536 -0.011743 0.002192 -0.008604 +Ta 0.0 1.66 7.03392 0.010535 -0.038081 0.05226 +Ta 2.34759 0.0 7.03392 0.010535 -0.038081 0.05226 +Ta 2.34759 1.66 9.38594 0.00905 0.147322 -0.015204 +Ta 0.0 0.0 9.38594 0.00905 0.147322 -0.015204 +Ta 0.0 1.66 11.73648 -0.255617 -0.52958 -0.348696 +Ta 2.34759 0.0 11.73648 -0.255617 -0.52958 -0.348696 +Ta 4.22567 2.988 14.08712 0.255617 0.52958 0.348696 +Ta 1.87808 1.328 14.08712 0.255617 0.52958 0.348696 +Ta 1.87808 2.988 16.43764 -0.00905 -0.147322 0.015204 +Ta 4.22567 1.328 16.43764 -0.00905 -0.147322 0.015204 +Ta 4.22567 2.988 18.78966 -0.010535 0.038081 -0.05226 +Ta 1.87808 1.328 18.78966 -0.010535 0.038081 -0.05226 +Ta 1.87808 2.988 21.13823 0.011743 -0.002192 0.008604 +Ta 4.22567 1.328 21.13823 0.011743 -0.002192 0.008604 +Ta 4.22567 2.988 23.48739 -0.000372 0.001531 0.005316 +Ta 1.87808 1.328 23.48739 -0.000372 0.001531 0.005316 +Ta 1.87808 2.988 25.73229 6.8e-05 -0.00218 -0.002238 +Ta 4.22567 1.328 25.73229 6.8e-05 -0.00218 -0.002238 +24 +Lattice = "4.69519042969 0.0 0.0 0.0 3.31999993324 0.0 0.0 0.0 53.1199989319" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.79264 stress="-9276.56 -705.96 1761.7 -705.96 -7718.9800000000005 1609.3500000000001 1761.7 1609.3500000000001 -417.65000000000003" +Ta 2.34759 1.66 0.08713 0.000184 0.001656 0.000681 +Ta 0.0 0.0 0.08713 0.000184 0.001656 0.000681 +Ta 0.0 1.66 2.33202 0.000294 -0.000424 0.000309 +Ta 2.34759 0.0 2.33202 0.000294 -0.000424 0.000309 +Ta 2.34759 1.66 4.68158 -0.008643 0.001357 -0.001844 +Ta 0.0 0.0 4.68158 -0.008643 0.001357 -0.001844 +Ta 0.0 1.66 7.03138 0.006924 -0.020398 -0.000267 +Ta 2.34759 0.0 7.03138 0.006924 -0.020398 -0.000267 +Ta 2.34759 1.66 9.38023 0.01463 0.087629 0.00063 +Ta 0.0 0.0 9.38023 0.01463 0.087629 0.00063 +Ta 0.0 1.66 11.72434 -0.214496 -0.34877 -0.000676 +Ta 2.34759 0.0 11.72434 -0.214496 -0.34877 -0.000676 +Ta 4.46043 3.154 14.09926 0.214496 0.34877 0.000676 +Ta 2.11284 1.494 14.09926 0.214496 0.34877 0.000676 +Ta 2.11284 3.154 16.44335 -0.01463 -0.087629 -0.00063 +Ta 4.46043 1.494 16.44335 -0.01463 -0.087629 -0.00063 +Ta 4.46043 3.154 18.7922 -0.006924 0.020398 0.000267 +Ta 2.11284 1.494 18.7922 -0.006924 0.020398 0.000267 +Ta 2.11284 3.154 21.14201 0.008643 -0.001357 0.001844 +Ta 4.46043 1.494 21.14201 0.008643 -0.001357 0.001844 +Ta 4.46043 3.154 23.49147 -0.000294 0.000424 -0.000309 +Ta 2.11284 1.494 23.49147 -0.000294 0.000424 -0.000309 +Ta 2.11284 3.154 25.73637 -0.000184 -0.001656 -0.000681 +Ta 4.46043 1.494 25.73637 -0.000184 -0.001656 -0.000681 diff --git a/examples/PACKAGES/pod/Ta/XYZ/GSF_112.xyz b/examples/PACKAGES/pod/Ta/XYZ/GSF_112.xyz new file mode 100644 index 0000000000..71e317e259 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/XYZ/GSF_112.xyz @@ -0,0 +1,704 @@ +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-345.175835 stress="-13147.16 0.0 -3780.86 0.0 -8634.359999999999 0.0 -3780.86 0.0 -262.94" +Ta 0.9892 0.0 2.67612 0.024552 0.0 -0.00195 +Ta 0.00727 2.34759 4.02628 0.020645 0.0 9.3e-05 +Ta 2.88247 2.34759 4.02628 0.020645 0.0 9.3e-05 +Ta 0.17997 0.0 0.13381 0.04617 0.0 -0.000386 +Ta 3.05517 0.0 0.13381 0.04617 0.0 -0.000386 +Ta 1.87083 2.34759 1.2728 -0.032821 0.0 -0.001196 +Ta 4.74604 2.34759 1.2728 -0.032821 0.0 -0.001196 +Ta 3.86441 0.0 2.67612 0.024552 0.0 -0.00195 +Ta 0.94648 2.34759 6.72012 0.031811 0.0 0.000572 +Ta 0.00117 0.0 8.09323 0.426675 0.0 0.000202 +Ta 2.87637 0.0 8.09323 0.426675 0.0 0.000202 +Ta 1.91123 0.0 5.35809 -0.1254 0.0 0.000587 +Ta 4.78644 0.0 5.35809 -0.1254 0.0 0.000587 +Ta 3.82169 2.34759 6.72012 0.031811 0.0 0.000572 +Ta 1.9168 2.34759 9.40413 -0.175762 0.0 0.000278 +Ta 4.79201 2.34759 9.40413 -0.175762 0.0 0.000278 +Ta 2.10731 0.0 10.91795 0.187758 0.0 0.000468 +Ta 1.162 2.34759 12.2439 -0.520663 0.0 0.000295 +Ta 4.0372 2.34759 12.2439 -0.520663 0.0 0.000295 +Ta 4.98252 0.0 10.91795 0.187758 0.0 0.000468 +Ta 2.10121 2.34759 14.96595 0.131217 0.0 0.000175 +Ta 1.11928 0.0 16.30656 -0.015432 0.0 6e-06 +Ta 3.99448 0.0 16.30656 -0.015432 0.0 6e-06 +Ta 3.11285 2.34759 17.71541 0.007977 0.0 0.000401 +Ta 0.23765 2.34759 17.71541 0.007977 0.0 0.000401 +Ta 3.07245 0.0 13.62798 0.021452 0.0 0.000107 +Ta 0.19725 0.0 13.62798 0.021452 0.0 0.000107 +Ta 4.97642 2.34759 14.96595 0.131217 0.0 0.000175 +Ta 1.92851 0.0 18.85304 -0.028176 0.0 0.00035 +Ta 4.80372 0.0 18.85304 -0.028176 0.0 0.00035 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-346.361714 stress="-10339.27 0.0 -4235.839999999999 0.0 -10300.0 0.0 -4235.839999999999 0.0 -143.8" +Ta 0.9892 0.0 2.71788 0.039491 0.0 -0.003174 +Ta 0.00727 2.34759 4.0686 -0.006941 0.0 0.000225 +Ta 2.88247 2.34759 4.0686 -0.006941 0.0 0.000225 +Ta 0.17997 0.0 0.18084 0.006017 0.0 -0.000536 +Ta 3.05517 0.0 0.18084 0.006017 0.0 -0.000536 +Ta 1.87083 2.34759 1.32379 -0.009843 0.0 -0.001904 +Ta 4.74604 2.34759 1.32379 -0.009843 0.0 -0.001904 +Ta 3.86441 0.0 2.71788 0.039491 0.0 -0.003174 +Ta 0.94648 2.34759 6.76401 0.031952 0.0 0.001417 +Ta 0.00117 0.0 8.13836 0.170121 0.0 0.00142 +Ta 2.87637 0.0 8.13836 0.170121 0.0 0.00142 +Ta 1.91123 0.0 5.41435 -0.068665 0.0 0.001093 +Ta 4.78644 0.0 5.41435 -0.068665 0.0 0.001093 +Ta 3.82169 2.34759 6.76401 0.031952 0.0 0.001417 +Ta 1.9168 2.34759 9.47269 0.56983 0.0 0.001115 +Ta 4.79201 2.34759 9.47269 0.56983 0.0 0.001115 +Ta 1.24475 0.0 10.85237 -0.591123 0.0 0.000193 +Ta 0.29944 2.34759 12.20261 -0.170693 0.0 -0.00076 +Ta 3.17464 2.34759 12.20261 -0.170693 0.0 -0.00076 +Ta 4.11996 0.0 10.85237 -0.591123 0.0 0.000193 +Ta 1.23865 2.34759 14.90362 0.062003 0.0 -0.000147 +Ta 0.25672 0.0 16.25811 0.014238 0.0 6.7e-05 +Ta 3.13192 0.0 16.25811 0.014238 0.0 6.7e-05 +Ta 2.25029 2.34759 17.65366 -0.022348 0.0 0.000828 +Ta 5.1255 2.34759 17.65366 -0.022348 0.0 0.000828 +Ta 2.20989 0.0 13.56973 -0.01066 0.0 -0.000183 +Ta 5.0851 0.0 13.56973 -0.01066 0.0 -0.000183 +Ta 4.11386 2.34759 14.90362 0.062003 0.0 -0.000147 +Ta 1.06595 0.0 18.79472 -0.01338 0.0 0.000344 +Ta 3.94116 0.0 18.79472 -0.01338 0.0 0.000344 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-345.795524 stress="-11480.130000000001 0.0 -5932.89 0.0 -5542.72 0.0 -5932.89 0.0 3462.38" +Ta 0.9892 0.0 2.7203 0.054393 0.0 0.051613 +Ta 0.00727 2.34759 4.07239 0.011422 0.0 0.01044 +Ta 2.88247 2.34759 4.07239 0.011422 0.0 0.01044 +Ta 0.17997 0.0 0.18449 0.010146 0.0 -0.022298 +Ta 3.05517 0.0 0.18449 0.010146 0.0 -0.022298 +Ta 1.87083 2.34759 1.32776 -0.011079 0.0 -0.021669 +Ta 4.74604 2.34759 1.32776 -0.011079 0.0 -0.021669 +Ta 3.86441 0.0 2.7203 0.054393 0.0 0.051613 +Ta 0.94648 2.34759 6.77133 0.038911 0.0 -0.069106 +Ta 0.00117 0.0 8.1367 0.287747 0.0 -0.1262 +Ta 2.87637 0.0 8.1367 0.287747 0.0 -0.1262 +Ta 1.91123 0.0 5.41489 -0.141892 0.0 0.03774 +Ta 4.78644 0.0 5.41489 -0.141892 0.0 0.03774 +Ta 3.82169 2.34759 6.77133 0.038911 0.0 -0.069106 +Ta 1.9168 2.34759 9.48769 0.847487 0.0 -0.484094 +Ta 4.79201 2.34759 9.48769 0.847487 0.0 -0.484094 +Ta 1.53227 0.0 10.83871 -0.88891 0.0 0.460491 +Ta 0.58696 2.34759 12.20409 -0.291722 0.0 0.122028 +Ta 3.46216 2.34759 12.20409 -0.291722 0.0 0.122028 +Ta 4.40748 0.0 10.83871 -0.88891 0.0 0.460491 +Ta 1.52617 2.34759 14.90296 0.134409 0.0 -0.060843 +Ta 0.54424 0.0 16.25507 -0.007639 0.0 -0.054033 +Ta 3.41944 0.0 16.25507 -0.007639 0.0 -0.054033 +Ta 2.53781 2.34759 17.64762 -0.034954 0.0 0.011635 +Ta 5.41302 2.34759 17.64762 -0.034954 0.0 0.011635 +Ta 2.49741 0.0 13.56045 -0.007731 0.0 0.131746 +Ta 5.37262 0.0 13.56045 -0.007731 0.0 0.131746 +Ta 4.40138 2.34759 14.90296 0.134409 0.0 -0.060843 +Ta 1.35347 0.0 18.79091 -0.000588 0.0 0.012548 +Ta 4.22868 0.0 18.79091 -0.000588 0.0 0.012548 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-345.164602 stress="-11863.390000000001 0.0 -2699.1299999999997 0.0 -8952.85 0.0 -2699.1299999999997 0.0 -224.73000000000002" +Ta 0.9892 0.0 2.67528 0.007638 0.0 0.001035 +Ta 0.00727 2.34759 4.02882 0.030305 0.0 -0.001775 +Ta 2.88247 2.34759 4.02882 0.030305 0.0 -0.001775 +Ta 0.17997 0.0 0.13405 0.029187 0.0 -0.000966 +Ta 3.05517 0.0 0.13405 0.029187 0.0 -0.000966 +Ta 1.87083 2.34759 1.27454 -0.02274 0.0 0.00023 +Ta 4.74604 2.34759 1.27454 -0.02274 0.0 0.00023 +Ta 3.86441 0.0 2.67528 0.007638 0.0 0.001035 +Ta 0.94648 2.34759 6.72231 -0.027764 0.0 -0.000181 +Ta 0.00117 0.0 8.09205 0.529066 0.0 -0.000552 +Ta 2.87637 0.0 8.09205 0.529066 0.0 -0.000552 +Ta 1.91123 0.0 5.3597 -0.091215 0.0 -0.000447 +Ta 4.78644 0.0 5.3597 -0.091215 0.0 -0.000447 +Ta 3.82169 2.34759 6.72231 -0.027764 0.0 -0.000181 +Ta 1.9168 2.34759 9.39558 -0.613631 0.0 -0.000278 +Ta 4.79201 2.34759 9.39558 -0.613631 0.0 -0.000278 +Ta 2.39483 0.0 10.92856 0.685544 0.0 -0.000982 +Ta 1.44952 2.34759 12.2419 -0.636467 0.0 0.000459 +Ta 4.32472 2.34759 12.2419 -0.636467 0.0 0.000459 +Ta 5.27004 0.0 10.92856 0.685544 0.0 -0.000982 +Ta 2.38873 2.34759 14.96563 0.083017 0.0 0.000884 +Ta 1.4068 0.0 16.30385 -0.037081 0.0 0.000794 +Ta 4.282 0.0 16.30385 -0.037081 0.0 0.000794 +Ta 3.40038 2.34759 17.71704 0.037388 0.0 0.000623 +Ta 0.52518 2.34759 17.71704 0.037388 0.0 0.000623 +Ta 3.35997 0.0 13.62371 0.068589 0.0 -0.000292 +Ta 0.48477 0.0 13.62371 0.068589 0.0 -0.000292 +Ta 5.26394 2.34759 14.96563 0.083017 0.0 0.000884 +Ta 2.21604 0.0 18.85233 -0.041835 0.0 0.001449 +Ta 5.09124 0.0 18.85233 -0.041835 0.0 0.001449 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-346.593523 stress="-9414.98 0.0 -281.99 0.0 -11857.62 0.0 -281.99 0.0 174.60999999999999" +Ta 0.9892 0.0 2.7203 0.00126 0.0 -0.000952 +Ta 0.00727 2.34759 4.07239 0.002425 0.0 -0.000721 +Ta 2.88247 2.34759 4.07239 0.002425 0.0 -0.000721 +Ta 0.17997 0.0 0.18449 0.003483 0.0 -0.001569 +Ta 3.05517 0.0 0.18449 0.003483 0.0 -0.001569 +Ta 1.87083 2.34759 1.32776 -0.001158 0.0 -0.001292 +Ta 4.74604 2.34759 1.32776 -0.001158 0.0 -0.001292 +Ta 3.86441 0.0 2.7203 0.00126 0.0 -0.000952 +Ta 0.94648 2.34759 6.77133 -0.000275 0.0 -0.000556 +Ta 0.00117 0.0 8.1367 0.001745 0.0 0.000187 +Ta 2.87637 0.0 8.1367 0.001745 0.0 0.000187 +Ta 1.91123 0.0 5.41489 0.00171 0.0 -0.000333 +Ta 4.78644 0.0 5.41489 0.00171 0.0 -0.000333 +Ta 3.82169 2.34759 6.77133 -0.000275 0.0 -0.000556 +Ta 1.9168 2.34759 9.48769 0.0 0.0 0.0 +Ta 4.79201 2.34759 9.48769 0.0 0.0 0.0 +Ta 0.95723 0.0 10.83871 -0.001745 0.0 -0.000187 +Ta 0.01192 2.34759 12.20409 0.000275 0.0 0.000556 +Ta 2.88712 2.34759 12.20409 0.000275 0.0 0.000556 +Ta 3.83244 0.0 10.83871 -0.001745 0.0 -0.000187 +Ta 0.95113 2.34759 14.90296 -0.002425 0.0 0.000721 +Ta 5.71961 0.0 16.25507 -0.00126 0.0 0.000952 +Ta 2.8444 0.0 16.25507 -0.00126 0.0 0.000952 +Ta 1.96277 2.34759 17.64762 0.001158 0.0 0.001292 +Ta 4.83798 2.34759 17.64762 0.001158 0.0 0.001292 +Ta 1.92237 0.0 13.56045 -0.00171 0.0 0.000333 +Ta 4.79758 0.0 13.56045 -0.00171 0.0 0.000333 +Ta 3.82634 2.34759 14.90296 -0.002425 0.0 0.000721 +Ta 0.77843 0.0 18.79091 -0.003483 0.0 0.001569 +Ta 3.65364 0.0 18.79091 -0.003483 0.0 0.001569 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-346.396186 stress="-10475.46 0.0 3307.63 0.0 -12303.68 0.0 3307.63 0.0 -222.97" +Ta 0.9892 0.0 2.7089 -0.03377 0.0 0.000745 +Ta 0.00727 2.34759 4.06352 0.026744 0.0 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16.2663 -0.029184 0.0 8.5e-05 +Ta 4.55046 2.34759 17.66134 0.026269 0.0 -0.000704 +Ta 1.67526 2.34759 17.66134 0.026269 0.0 -0.000704 +Ta 4.51005 0.0 13.57023 0.044788 0.0 0.000159 +Ta 1.63485 0.0 13.57023 0.044788 0.0 0.000159 +Ta 0.66361 2.34759 14.91622 -0.038582 0.0 0.000491 +Ta 3.36612 0.0 18.80388 0.004104 0.0 0.000717 +Ta 0.49092 0.0 18.80388 0.004104 0.0 0.000717 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-345.319406 stress="-11416.52 0.0 -757.17 0.0 -9138.949999999999 0.0 -757.17 0.0 -340.37" +Ta 0.9892 0.0 2.6792 -0.016362 0.0 0.000549 +Ta 0.00727 2.34759 4.0346 0.061621 0.0 0.000282 +Ta 2.88247 2.34759 4.0346 0.061621 0.0 0.000282 +Ta 0.17997 0.0 0.13955 0.017834 0.0 -0.000235 +Ta 3.05517 0.0 0.13955 0.017834 0.0 -0.000235 +Ta 1.87083 2.34759 1.28166 -0.013104 0.0 -5.3e-05 +Ta 4.74604 2.34759 1.28166 -0.013104 0.0 -5.3e-05 +Ta 3.86441 0.0 2.6792 -0.016362 0.0 0.000549 +Ta 0.94648 2.34759 6.7292 -0.109435 0.0 -0.002041 +Ta 0.00117 0.0 8.07884 0.457863 0.0 0.000169 +Ta 2.87637 0.0 8.07884 0.457863 0.0 0.000169 +Ta 1.91123 0.0 5.36942 -0.062934 0.0 -0.000236 +Ta 4.78644 0.0 5.36942 -0.062934 0.0 -0.000236 +Ta 3.82169 2.34759 6.7292 -0.109435 0.0 -0.002041 +Ta 1.9168 2.34759 9.41051 -0.711692 0.0 0.000101 +Ta 4.79201 2.34759 9.41051 -0.711692 0.0 0.000101 +Ta 2.68235 0.0 10.91706 0.761406 0.0 -0.00084 +Ta 1.73705 2.34759 12.25543 -0.48479 0.0 0.001087 +Ta 4.61225 2.34759 12.25543 -0.48479 0.0 0.001087 +Ta 5.55756 0.0 10.91706 0.761406 0.0 -0.00084 +Ta 2.67625 2.34759 14.95587 0.044573 0.0 0.001069 +Ta 1.69432 0.0 16.29727 -0.054726 0.0 0.000221 +Ta 4.56952 0.0 16.29727 -0.054726 0.0 0.000221 +Ta 3.6879 2.34759 17.70919 0.045804 0.0 -0.000493 +Ta 0.8127 2.34759 17.70919 0.045804 0.0 -0.000493 +Ta 3.64749 0.0 13.61175 0.101011 0.0 0.001537 +Ta 0.77229 0.0 13.61175 0.101011 0.0 0.001537 +Ta 5.55146 2.34759 14.95587 0.044573 0.0 0.001069 +Ta 2.50356 0.0 18.84582 -0.037068 0.0 -0.001117 +Ta 5.37876 0.0 18.84582 -0.037068 0.0 -0.001117 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-345.594794 stress="-11819.76 0.0 1952.92 0.0 -9519.769999999999 0.0 1952.92 0.0 -130.88" +Ta 0.9892 0.0 2.68665 -0.031396 0.0 0.000256 +Ta 0.00727 2.34759 4.04268 0.07751 0.0 -0.000764 +Ta 2.88247 2.34759 4.04268 0.07751 0.0 -0.000764 +Ta 0.17997 0.0 0.14906 0.014641 0.0 -0.00412 +Ta 3.05517 0.0 0.14906 0.014641 0.0 -0.00412 +Ta 1.87083 2.34759 1.29212 -0.010131 0.0 -0.002448 +Ta 4.74604 2.34759 1.29212 -0.010131 0.0 -0.002448 +Ta 3.86441 0.0 2.68665 -0.031396 0.0 0.000256 +Ta 0.94648 2.34759 6.73839 -0.134831 0.0 0.001428 +Ta 0.00117 0.0 8.07155 0.239952 0.0 0.002962 +Ta 2.87637 0.0 8.07155 0.239952 0.0 0.002962 +Ta 1.91123 0.0 5.38052 -0.030029 0.0 -0.000509 +Ta 4.78644 0.0 5.38052 -0.030029 0.0 -0.000509 +Ta 3.82169 2.34759 6.73839 -0.134831 0.0 0.001428 +Ta 1.9168 2.34759 9.43202 -0.708973 0.0 0.000446 +Ta 4.79201 2.34759 9.43202 -0.708973 0.0 0.000446 +Ta 2.96987 0.0 10.89606 0.708813 0.0 0.000528 +Ta 2.02457 2.34759 12.26428 -0.203649 0.0 0.002064 +Ta 4.89977 2.34759 12.26428 -0.203649 0.0 0.002064 +Ta 0.09467 0.0 10.89606 0.708813 0.0 0.000528 +Ta 2.96377 2.34759 14.9433 0.014742 0.0 -0.000587 +Ta 1.98184 0.0 16.28932 -0.077212 0.0 0.001835 +Ta 4.85704 0.0 16.28932 -0.077212 0.0 0.001835 +Ta 3.97542 2.34759 17.69607 0.052551 0.0 -9.3e-05 +Ta 1.10022 2.34759 17.69607 0.052551 0.0 -9.3e-05 +Ta 3.93501 0.0 13.59778 0.097817 0.0 0.000127 +Ta 1.05981 0.0 13.59778 0.097817 0.0 0.000127 +Ta 0.08857 2.34759 14.9433 0.014742 0.0 -0.000587 +Ta 2.79108 0.0 18.83554 -0.009805 0.0 -0.001124 +Ta 5.66629 0.0 18.83554 -0.009805 0.0 -0.001124 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-345.98566 stress="-11481.859999999999 0.0 3919.02 0.0 -10708.259999999998 0.0 3919.02 0.0 -234.91" +Ta 0.9892 0.0 2.69672 -0.042372 0.0 -0.001938 +Ta 0.00727 2.34759 4.05296 0.05908 0.0 0.000592 +Ta 2.88247 2.34759 4.05296 0.05908 0.0 0.000592 +Ta 0.17997 0.0 0.16008 0.012695 0.0 0.000742 +Ta 3.05517 0.0 0.16008 0.012695 0.0 0.000742 +Ta 1.87083 2.34759 1.30375 -0.006266 0.0 -0.00108 +Ta 4.74604 2.34759 1.30375 -0.006266 0.0 -0.00108 +Ta 3.86441 0.0 2.69672 -0.042372 0.0 -0.001938 +Ta 0.94648 2.34759 6.75108 -0.115544 0.0 0.001071 +Ta 0.00117 0.0 8.08344 0.015442 0.0 7e-06 +Ta 2.87637 0.0 8.08344 0.015442 0.0 7e-06 +Ta 1.91123 0.0 5.39189 0.017023 0.0 -0.000768 +Ta 4.78644 0.0 5.39189 0.017023 0.0 -0.000768 +Ta 3.82169 2.34759 6.75108 -0.115544 0.0 0.001071 +Ta 1.9168 2.34759 9.45911 -0.69384 0.0 0.000691 +Ta 4.79201 2.34759 9.45911 -0.69384 0.0 0.000691 +Ta 3.25739 0.0 10.86943 0.687279 0.0 -0.000892 +Ta 2.31209 2.34759 12.25603 0.025406 0.0 0.001977 +Ta 5.18729 2.34759 12.25603 0.025406 0.0 0.001977 +Ta 0.38219 0.0 10.86943 0.687279 0.0 -0.000892 +Ta 3.25129 2.34759 14.92962 -0.021568 0.0 -0.000155 +Ta 2.26936 0.0 16.27869 -0.069625 0.0 6e-05 +Ta 5.14456 0.0 16.27869 -0.069625 0.0 6e-05 +Ta 4.26294 2.34759 17.67903 0.042589 0.0 -0.000517 +Ta 1.38774 2.34759 17.67903 0.042589 0.0 -0.000517 +Ta 4.22253 0.0 13.58337 0.088627 0.0 -0.000326 +Ta 1.34733 0.0 13.58337 0.088627 0.0 -0.000326 +Ta 0.37609 2.34759 14.92962 -0.021568 0.0 -0.000155 +Ta 3.0786 0.0 18.82016 0.001073 0.0 0.000537 +Ta 0.2034 0.0 18.82016 0.001073 0.0 0.000537 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-345.383994 stress="-14034.28 0.0 -4327.110000000001 0.0 -7778.13 0.0 -4327.110000000001 0.0 -145.71" +Ta 0.9892 0.0 2.68561 0.041017 0.0 -0.001969 +Ta 0.00727 2.34759 4.03469 0.0126 0.0 -0.000764 +Ta 2.88247 2.34759 4.03469 0.0126 0.0 -0.000764 +Ta 0.17997 0.0 0.14398 0.044685 0.0 -0.000337 +Ta 3.05517 0.0 0.14398 0.044685 0.0 -0.000337 +Ta 1.87083 2.34759 1.28198 -0.034873 0.0 -0.000989 +Ta 4.74604 2.34759 1.28198 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+Ta 4.6889 2.34759 14.95092 0.137584 0.0 0.001218 +Ta 1.64099 0.0 18.83881 -0.017303 0.0 0.002258 +Ta 4.5162 0.0 18.83881 -0.017303 0.0 0.002258 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-346.582564 stress="-9591.91 0.0 -296.03000000000003 0.0 -12027.84 0.0 -296.03000000000003 0.0 -17.44" +Ta 0.9892 0.0 2.72001 0.001297 0.0 -0.000868 +Ta 0.00727 2.34759 4.07221 0.002338 0.0 -0.000918 +Ta 2.88247 2.34759 4.07221 0.002338 0.0 -0.000918 +Ta 0.17997 0.0 0.18416 0.004037 0.0 -0.001343 +Ta 3.05517 0.0 0.18416 0.004037 0.0 -0.001343 +Ta 1.87083 2.34759 1.32742 -0.00151 0.0 -0.00104 +Ta 4.74604 2.34759 1.32742 -0.00151 0.0 -0.00104 +Ta 3.86441 0.0 2.72001 0.001297 0.0 -0.000868 +Ta 0.94648 2.34759 6.77122 -0.000493 0.0 -5.2e-05 +Ta 0.00117 0.0 8.13674 0.002006 0.0 -0.000634 +Ta 2.87637 0.0 8.13674 0.002006 0.0 -0.000634 +Ta 1.91123 0.0 5.41485 0.001966 0.0 -0.001189 +Ta 4.78644 0.0 5.41485 0.001966 0.0 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2195.0699999999997 0.0 -6268.24 0.0 2195.0699999999997 0.0 6817.8099999999995" +Ta 0.9892 0.0 2.7203 -0.023223 0.0 0.001016 +Ta 0.00727 2.34759 4.07239 0.069003 0.0 0.068642 +Ta 2.88247 2.34759 4.07239 0.069003 0.0 0.068642 +Ta 0.17997 0.0 0.18449 0.005805 0.0 -0.024588 +Ta 3.05517 0.0 0.18449 0.005805 0.0 -0.024588 +Ta 1.87083 2.34759 1.32776 -0.003386 0.0 0.004796 +Ta 4.74604 2.34759 1.32776 -0.003386 0.0 0.004796 +Ta 3.86441 0.0 2.7203 -0.023223 0.0 0.001016 +Ta 0.94648 2.34759 6.77133 -0.15941 0.0 0.086585 +Ta 0.00117 0.0 8.1367 0.254346 0.0 -0.687398 +Ta 2.87637 0.0 8.1367 0.254346 0.0 -0.687398 +Ta 1.91123 0.0 5.41489 -0.007273 0.0 0.083064 +Ta 4.78644 0.0 5.41489 -0.007273 0.0 0.083064 +Ta 3.82169 2.34759 6.77133 -0.15941 0.0 0.086585 +Ta 1.9168 2.34759 9.48769 -0.854831 0.0 -0.81341 +Ta 4.79201 2.34759 9.48769 -0.854831 0.0 -0.81341 +Ta 2.96987 0.0 10.83871 0.856404 0.0 0.869919 +Ta 2.02457 2.34759 12.20409 -0.204616 0.0 0.570902 +Ta 4.89977 2.34759 12.20409 -0.204616 0.0 0.570902 +Ta 0.09467 0.0 10.83871 0.856404 0.0 0.869919 +Ta 2.96377 2.34759 14.90296 -0.014831 0.0 -0.080565 +Ta 1.98184 0.0 16.25507 -0.069492 0.0 -0.116436 +Ta 4.85704 0.0 16.25507 -0.069492 0.0 -0.116436 +Ta 3.97542 2.34759 17.64762 0.035331 0.0 0.046498 +Ta 1.10022 2.34759 17.64762 0.035331 0.0 0.046498 +Ta 3.93501 0.0 13.56045 0.105163 0.0 -0.067164 +Ta 1.05981 0.0 13.56045 0.105163 0.0 -0.067164 +Ta 0.08857 2.34759 14.90296 -0.014831 0.0 -0.080565 +Ta 2.79108 0.0 18.79091 0.011012 0.0 0.058138 +Ta 5.66629 0.0 18.79091 0.011012 0.0 0.058138 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-346.593523 stress="-9415.82 0.0 -282.14 0.0 -11858.18 0.0 -282.14 0.0 174.85" +Ta 0.9892 0.0 2.7203 0.00126 0.0 -0.000951 +Ta 0.00727 2.34759 4.07239 0.002425 0.0 -0.000721 +Ta 2.88247 2.34759 4.07239 0.002425 0.0 -0.000721 +Ta 0.17997 0.0 0.18449 0.003483 0.0 -0.001569 +Ta 3.05517 0.0 0.18449 0.003483 0.0 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-0.00171 0.0 0.000333 +Ta 1.92238 0.0 13.56045 -0.00171 0.0 0.000333 +Ta 0.95113 2.34759 14.90296 -0.002425 0.0 0.000721 +Ta 3.65364 0.0 18.79091 -0.003483 0.0 0.001569 +Ta 0.77844 0.0 18.79091 -0.003483 0.0 0.001569 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-345.281949 stress="-11560.39 0.0 -4653.08 0.0 -2434.16 0.0 -4653.08 0.0 6566.94" +Ta 0.9892 0.0 2.7203 0.050194 0.0 0.096189 +Ta 0.00727 2.34759 4.07239 0.024666 0.0 0.022454 +Ta 2.88247 2.34759 4.07239 0.024666 0.0 0.022454 +Ta 0.17997 0.0 0.18449 0.022221 0.0 -0.035876 +Ta 3.05517 0.0 0.18449 0.022221 0.0 -0.035876 +Ta 1.87083 2.34759 1.32776 -0.018007 0.0 -0.028654 +Ta 4.74604 2.34759 1.32776 -0.018007 0.0 -0.028654 +Ta 3.86441 0.0 2.7203 0.050194 0.0 0.096189 +Ta 0.94648 2.34759 6.77133 0.035097 0.0 -0.05687 +Ta 0.00117 0.0 8.1367 0.39639 0.0 -0.242712 +Ta 2.87637 0.0 8.1367 0.39639 0.0 -0.242712 +Ta 1.91123 0.0 5.41489 -0.174932 0.0 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Properties=species:S:1:pos:R:3:forces:R:3 energy=-345.928661 stress="-9145.630000000001 0.0 4495.89 0.0 -8704.09 0.0 4495.89 0.0 4121.84" +Ta 0.9892 0.0 2.7203 -0.037192 0.0 -0.008535 +Ta 0.00727 2.34759 4.07239 0.046799 0.0 0.059571 +Ta 2.88247 2.34759 4.07239 0.046799 0.0 0.059571 +Ta 0.17997 0.0 0.18449 0.009422 0.0 -0.012097 +Ta 3.05517 0.0 0.18449 0.009422 0.0 -0.012097 +Ta 1.87083 2.34759 1.32776 -0.005981 0.0 0.006654 +Ta 4.74604 2.34759 1.32776 -0.005981 0.0 0.006654 +Ta 3.86441 0.0 2.7203 -0.037192 0.0 -0.008535 +Ta 0.94648 2.34759 6.77133 -0.141158 0.0 0.065062 +Ta 0.00117 0.0 8.1367 -0.005041 0.0 -0.535781 +Ta 2.87637 0.0 8.1367 -0.005041 0.0 -0.535781 +Ta 1.91123 0.0 5.41489 0.047966 0.0 0.052967 +Ta 4.78644 0.0 5.41489 0.047966 0.0 0.052967 +Ta 3.82169 2.34759 6.77133 -0.141158 0.0 0.065062 +Ta 1.9168 2.34759 9.48769 -0.807767 0.0 -0.37656 +Ta 4.79201 2.34759 9.48769 -0.807767 0.0 -0.37656 +Ta 3.25739 0.0 10.83871 0.80662 0.0 0.413175 +Ta 2.31209 2.34759 12.20409 0.049763 0.0 0.478936 +Ta 5.18729 2.34759 12.20409 0.049763 0.0 0.478936 +Ta 0.38219 0.0 10.83871 0.80662 0.0 0.413175 +Ta 3.25129 2.34759 14.90296 -0.059966 0.0 -0.070617 +Ta 2.26936 0.0 16.25507 -0.058332 0.0 -0.070148 +Ta 5.14456 0.0 16.25507 -0.058332 0.0 -0.070148 +Ta 4.26294 2.34759 17.64762 0.034688 0.0 0.021628 +Ta 1.38774 2.34759 17.64762 0.034688 0.0 0.021628 +Ta 4.22253 0.0 13.56045 0.107399 0.0 -0.061704 +Ta 1.34733 0.0 13.56045 0.107399 0.0 -0.061704 +Ta 0.37609 2.34759 14.90296 -0.059966 0.0 -0.070617 +Ta 3.0786 0.0 18.79091 0.01278 0.0 0.037448 +Ta 0.2034 0.0 18.79091 0.01278 0.0 0.037448 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-345.111657 stress="-8100.32 0.0 -1129.41 0.0 -4564.69 0.0 -1129.41 0.0 8777.64" +Ta 0.9892 0.0 2.7203 -0.002999 0.0 0.02667 +Ta 0.00727 2.34759 4.07239 0.054882 0.0 0.061699 +Ta 2.88247 2.34759 4.07239 0.054882 0.0 0.061699 +Ta 0.17997 0.0 0.18449 -0.00101 0.0 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0.8127 2.34759 17.64762 0.020235 0.0 0.058633 +Ta 3.64749 0.0 13.56045 0.091771 0.0 -0.007909 +Ta 0.77229 0.0 13.56045 0.091771 0.0 -0.007909 +Ta 5.55146 2.34759 14.90296 0.046884 0.0 -0.018316 +Ta 2.50356 0.0 18.79091 -0.009823 0.0 0.055977 +Ta 5.37876 0.0 18.79091 -0.009823 0.0 0.055977 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-346.367123 stress="-9925.11 0.0 -4252.58 0.0 -9690.35 0.0 -4252.58 0.0 528.8000000000001" +Ta 0.9892 0.0 2.7203 0.036893 0.0 0.011121 +Ta 0.00727 2.34759 4.07239 0.003739 0.0 -0.008403 +Ta 2.88247 2.34759 4.07239 0.003739 0.0 -0.008403 +Ta 0.17997 0.0 0.18449 0.001677 0.0 -0.008529 +Ta 3.05517 0.0 0.18449 0.001677 0.0 -0.008529 +Ta 1.87083 2.34759 1.32776 -0.006125 0.0 -0.007305 +Ta 4.74604 2.34759 1.32776 -0.006125 0.0 -0.007305 +Ta 3.86441 0.0 2.7203 0.036893 0.0 0.011121 +Ta 0.94648 2.34759 6.77133 0.047105 0.0 -0.045187 +Ta 0.00117 0.0 8.1367 0.149771 0.0 0.043481 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"5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-346.582565 stress="-9596.72 0.0 -296.27 0.0 -12032.57 0.0 -296.27 0.0 -26.450000000000003" +Ta 0.9892 0.0 2.71997 0.001254 0.0 -0.000998 +Ta 0.00727 2.34759 4.07216 0.002375 0.0 -0.000846 +Ta 2.88247 2.34759 4.07216 0.002375 0.0 -0.000846 +Ta 0.17997 0.0 0.18409 0.004062 0.0 -0.001188 +Ta 3.05517 0.0 0.18409 0.004062 0.0 -0.001188 +Ta 1.87083 2.34759 1.32736 -0.001515 0.0 -0.001063 +Ta 4.74604 2.34759 1.32736 -0.001515 0.0 -0.001063 +Ta 3.86441 0.0 2.71997 0.001254 0.0 -0.000998 +Ta 0.94648 2.34759 6.77121 -0.000474 0.0 -0.000276 +Ta 0.00117 0.0 8.13671 0.001992 0.0 -0.000431 +Ta 2.87637 0.0 8.13671 0.001992 0.0 -0.000431 +Ta 1.91123 0.0 5.41479 0.001951 0.0 -0.000915 +Ta 4.78644 0.0 5.41479 0.001951 0.0 -0.000915 +Ta 3.82169 2.34759 6.77121 -0.000474 0.0 -0.000276 +Ta 1.9168 2.34759 9.48769 0.0 0.0 0.0 +Ta 4.79201 2.34759 9.48769 0.0 0.0 0.0 +Ta 0.95723 0.0 10.8387 -0.001992 0.0 0.000431 +Ta 0.01192 2.34759 12.20421 0.000474 0.0 0.000276 +Ta 2.88712 2.34759 12.20421 0.000474 0.0 0.000276 +Ta 3.83244 0.0 10.8387 -0.001992 0.0 0.000431 +Ta 0.95113 2.34759 14.90319 -0.002375 0.0 0.000846 +Ta 5.71961 0.0 16.2554 -0.001254 0.0 0.000998 +Ta 2.8444 0.0 16.2554 -0.001254 0.0 0.000998 +Ta 1.96277 2.34759 17.64802 0.001515 0.0 0.001063 +Ta 4.83798 2.34759 17.64802 0.001515 0.0 0.001063 +Ta 1.92237 0.0 13.56055 -0.001951 0.0 0.000915 +Ta 4.79758 0.0 13.56055 -0.001951 0.0 0.000915 +Ta 3.82634 2.34759 14.90319 -0.002375 0.0 0.000846 +Ta 0.77843 0.0 18.79131 -0.004062 0.0 0.001188 +Ta 3.65364 0.0 18.79131 -0.004062 0.0 0.001188 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-344.91356 stress="-9331.87 0.0 -3483.6 0.0 -3070.65 0.0 -3483.6 0.0 10023.91" +Ta 0.9892 0.0 2.7203 0.020761 0.0 0.069829 +Ta 0.00727 2.34759 4.07239 0.031416 0.0 0.042888 +Ta 2.88247 2.34759 4.07239 0.031416 0.0 0.042888 +Ta 0.17997 0.0 0.18449 0.008231 0.0 -0.040672 +Ta 3.05517 0.0 0.18449 0.008231 0.0 -0.040672 +Ta 1.87083 2.34759 1.32776 -0.006968 0.0 -0.013357 +Ta 4.74604 2.34759 1.32776 -0.006968 0.0 -0.013357 +Ta 3.86441 0.0 2.7203 0.020761 0.0 0.069829 +Ta 0.94648 2.34759 6.77133 -0.012614 0.0 0.0322 +Ta 0.00117 0.0 8.1367 0.6286 0.0 -0.362527 +Ta 2.87637 0.0 8.1367 0.6286 0.0 -0.362527 +Ta 1.91123 0.0 5.41489 -0.117602 0.0 -0.047411 +Ta 4.78644 0.0 5.41489 -0.117602 0.0 -0.047411 +Ta 3.82169 2.34759 6.77133 -0.012614 0.0 0.0322 +Ta 1.9168 2.34759 9.48769 -0.731669 0.0 -1.341165 +Ta 4.79201 2.34759 9.48769 -0.731669 0.0 -1.341165 +Ta 2.39483 0.0 10.83871 0.796655 0.0 1.335154 +Ta 1.44952 2.34759 12.20409 -0.719661 0.0 0.218469 +Ta 4.32472 2.34759 12.20409 -0.719661 0.0 0.218469 +Ta 5.27004 0.0 10.83871 0.796655 0.0 1.335154 +Ta 2.38873 2.34759 14.90296 0.115505 0.0 0.057838 +Ta 1.4068 0.0 16.25507 -0.048364 0.0 -0.136512 +Ta 4.282 0.0 16.25507 -0.048364 0.0 -0.136512 +Ta 3.40038 2.34759 17.64762 0.008342 0.0 0.049918 +Ta 0.52518 2.34759 17.64762 0.008342 0.0 0.049918 +Ta 3.35997 0.0 13.56045 0.043395 0.0 0.085984 +Ta 0.48477 0.0 13.56045 0.043395 0.0 0.085984 +Ta 5.26394 2.34759 14.90296 0.115505 0.0 0.057838 +Ta 2.21604 0.0 18.79091 -0.016029 0.0 0.049364 +Ta 5.09124 0.0 18.79091 -0.016029 0.0 0.049364 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-345.836703 stress="-13121.27 0.0 -5634.91 0.0 -8850.33 0.0 -5634.91 0.0 -251.82" +Ta 0.9892 0.0 2.69946 0.050014 0.0 0.000282 +Ta 0.00727 2.34759 4.05025 0.000899 0.0 -0.000628 +Ta 2.88247 2.34759 4.05025 0.000899 0.0 -0.000628 +Ta 0.17997 0.0 0.16024 0.025286 0.0 -0.000329 +Ta 3.05517 0.0 0.16024 0.025286 0.0 -0.000329 +Ta 1.87083 2.34759 1.30033 -0.022784 0.0 0.0001 +Ta 4.74604 2.34759 1.30033 -0.022784 0.0 0.0001 +Ta 3.86441 0.0 2.69946 0.050014 0.0 0.000282 +Ta 0.94648 2.34759 6.74132 0.018982 0.0 0.000803 +Ta 0.00117 0.0 8.1136 0.294678 0.0 -7e-05 +Ta 2.87637 0.0 8.1136 0.294678 0.0 -7e-05 +Ta 1.91123 0.0 5.39201 -0.117735 0.0 -0.000184 +Ta 4.78644 0.0 5.39201 -0.117735 0.0 -0.000184 +Ta 3.82169 2.34759 6.74132 0.018982 0.0 0.000803 +Ta 1.9168 2.34759 9.44202 0.717113 0.0 3.7e-05 +Ta 4.79201 2.34759 9.44202 0.717113 0.0 3.7e-05 +Ta 1.53227 0.0 10.88381 -0.754498 0.0 3.7e-05 +Ta 0.58696 2.34759 12.229 -0.304417 0.0 -0.000673 +Ta 3.46216 2.34759 12.229 -0.304417 0.0 -0.000673 +Ta 4.40748 0.0 10.88381 -0.754498 0.0 3.7e-05 +Ta 1.52617 2.34759 14.92821 0.111991 0.0 0.000677 +Ta 0.54424 0.0 16.27854 0.000794 0.0 -0.00097 +Ta 3.41944 0.0 16.27854 0.000794 0.0 -0.00097 +Ta 2.53781 2.34759 17.67931 -0.020042 0.0 -0.001378 +Ta 5.41302 2.34759 17.67931 -0.020042 0.0 -0.001378 +Ta 2.49741 0.0 13.59913 0.010142 0.0 0.001166 +Ta 5.37262 0.0 13.59913 0.010142 0.0 0.001166 +Ta 4.40138 2.34759 14.92821 0.111991 0.0 0.000677 +Ta 1.35347 0.0 18.81813 -0.010421 0.0 0.001129 +Ta 4.22868 0.0 18.81813 -0.010421 0.0 0.001129 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-344.984307 stress="-10564.03 0.0 -4829.4 0.0 -2612.55 0.0 -4829.4 0.0 9464.02" +Ta 0.9892 0.0 2.7203 0.037412 0.0 0.099042 +Ta 0.00727 2.34759 4.07239 0.028536 0.0 0.023468 +Ta 2.88247 2.34759 4.07239 0.028536 0.0 0.023468 +Ta 0.17997 0.0 0.18449 0.023555 0.0 -0.042618 +Ta 3.05517 0.0 0.18449 0.023555 0.0 -0.042618 +Ta 1.87083 2.34759 1.32776 -0.016108 0.0 -0.021017 +Ta 4.74604 2.34759 1.32776 -0.016108 0.0 -0.021017 +Ta 3.86441 0.0 2.7203 0.037412 0.0 0.099042 +Ta 0.94648 2.34759 6.77133 0.046477 0.0 0.002765 +Ta 0.00117 0.0 8.1367 0.514609 0.0 -0.283847 +Ta 2.87637 0.0 8.1367 0.514609 0.0 -0.283847 +Ta 1.91123 0.0 5.41489 -0.163272 0.0 -0.078622 +Ta 4.78644 0.0 5.41489 -0.163272 0.0 -0.078622 +Ta 3.82169 2.34759 6.77133 0.046477 0.0 0.002765 +Ta 1.9168 2.34759 9.48769 -0.094634 0.0 -1.114901 +Ta 4.79201 2.34759 9.48769 -0.094634 0.0 -1.114901 +Ta 2.10731 0.0 10.83871 0.096153 0.0 1.054366 +Ta 1.162 2.34759 12.20409 -0.593943 0.0 0.202897 +Ta 4.0372 2.34759 12.20409 -0.593943 0.0 0.202897 +Ta 4.98252 0.0 10.83871 0.096153 0.0 1.054366 +Ta 2.10121 2.34759 14.90296 0.169155 0.0 0.056551 +Ta 1.11928 0.0 16.25507 -0.031734 0.0 -0.113985 +Ta 3.99448 0.0 16.25507 -0.031734 0.0 -0.113985 +Ta 3.11285 2.34759 17.64762 -0.01565 0.0 0.02811 +Ta 0.23765 2.34759 17.64762 -0.01565 0.0 0.02811 +Ta 3.07245 0.0 13.56045 0.006275 0.0 0.144107 +Ta 0.19725 0.0 13.56045 0.006275 0.0 0.144107 +Ta 4.97642 2.34759 14.90296 0.169155 0.0 0.056551 +Ta 1.92851 0.0 18.79091 -0.00683 0.0 0.043685 +Ta 4.80372 0.0 18.79091 -0.00683 0.0 0.043685 +30 +Lattice = "5.75041007996 0.0 0.0 0.0 4.69518995285 0.0 0.0 0.0 39.8400001526" Properties=species:S:1:pos:R:3:forces:R:3 energy=-346.393931 stress="-9438.37 0.0 3529.1 0.0 -11318.58 0.0 3529.1 0.0 1838.01" +Ta 0.9892 0.0 2.7203 -0.028288 0.0 -0.004272 +Ta 0.00727 2.34759 4.07239 0.01665 0.0 0.029245 +Ta 2.88247 2.34759 4.07239 0.01665 0.0 0.029245 +Ta 0.17997 0.0 0.18449 0.006746 0.0 -0.001633 +Ta 3.05517 0.0 0.18449 0.006746 0.0 -0.001633 +Ta 1.87083 2.34759 1.32776 -0.000473 0.0 -3e-05 +Ta 4.74604 2.34759 1.32776 -0.000473 0.0 -3e-05 +Ta 3.86441 0.0 2.7203 -0.028288 0.0 -0.004272 +Ta 0.94648 2.34759 6.77133 -0.081349 0.0 0.034571 +Ta 0.00117 0.0 8.1367 -0.101274 0.0 -0.252924 +Ta 2.87637 0.0 8.1367 -0.101274 0.0 -0.252924 +Ta 1.91123 0.0 5.41489 0.063888 0.0 0.002877 +Ta 4.78644 0.0 5.41489 0.063888 0.0 0.002877 +Ta 3.82169 2.34759 6.77133 -0.081349 0.0 0.034571 +Ta 1.9168 2.34759 9.48769 -0.523826 0.0 -0.065241 +Ta 4.79201 2.34759 9.48769 -0.523826 0.0 -0.065241 +Ta 3.54491 0.0 10.83871 0.531471 0.0 0.075625 +Ta 2.59961 2.34759 12.20409 0.108678 0.0 0.237898 +Ta 5.47481 2.34759 12.20409 0.108678 0.0 0.237898 +Ta 0.66971 0.0 10.83871 0.531471 0.0 0.075625 +Ta 3.53881 2.34759 14.90296 -0.061771 0.0 -0.016484 +Ta 2.55688 0.0 16.25507 -0.022115 0.0 -0.025346 +Ta 5.43208 0.0 16.25507 -0.022115 0.0 -0.025346 +Ta 4.55046 2.34759 17.64762 0.021554 0.0 0.004745 +Ta 1.67526 2.34759 17.64762 0.021554 0.0 0.004745 +Ta 4.51005 0.0 13.56045 0.060372 0.0 -0.032886 +Ta 1.63485 0.0 13.56045 0.060372 0.0 -0.032886 +Ta 0.66361 2.34759 14.90296 -0.061771 0.0 -0.016484 +Ta 3.36612 0.0 18.79091 0.009737 0.0 0.013855 +Ta 0.49092 0.0 18.79091 0.009737 0.0 0.013855 diff --git a/examples/PACKAGES/pod/Ta/XYZ/Liquid.xyz b/examples/PACKAGES/pod/Ta/XYZ/Liquid.xyz new file mode 100644 index 0000000000..1bf7814567 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/XYZ/Liquid.xyz @@ -0,0 +1,306 @@ +100 +Lattice = "12.6055002213 0.0 0.0 0.0 12.6055002213 0.0 0.0 0.0 12.6055002213" Properties=species:S:1:pos:R:3:forces:R:3 energy=-1105.601723 stress="41522.36 -10028.6 5843.19 -10028.6 44080.57 10402.62 5843.19 10402.62 34745.600000000006" +Ta 0.43107 3.74888 0.07776 -0.335192 0.399751 2.053897 +Ta 1.60366 2.09108 2.35693 -3.868362 -1.228623 -1.515572 +Ta 4.15329 1.55338 2.45739 1.505017 -0.176525 -0.218711 +Ta 2.64801 1.89114 12.39607 0.25781 1.51672 2.137521 +Ta 7.24215 1.70209 1.79979 -0.11292 -2.198189 -0.337499 +Ta 10.95446 2.67458 1.59213 -0.965217 -1.195646 -0.253554 +Ta 9.27673 0.87789 3.43116 1.643765 0.347467 -1.593945 +Ta 2.03607 6.61594 1.61137 2.535752 0.592029 1.82052 +Ta 5.49317 3.20146 0.58262 -0.862046 0.984883 -1.598913 +Ta 3.04231 4.31908 2.00353 0.620511 -1.092947 -1.508929 +Ta 4.95339 6.14708 0.65118 -1.365205 -2.865106 2.363303 +Ta 7.52643 4.18623 2.31722 0.746021 1.167867 -1.110257 +Ta 12.27295 5.1198 2.52809 0.765074 0.812857 1.098129 +Ta 9.25719 7.32072 1.58199 0.215508 0.987987 1.690552 +Ta 10.53635 5.29937 0.6285 -0.28915 -1.601915 -1.639854 +Ta 1.90384 9.1638 3.00286 0.22302 2.303078 2.48401 +Ta 3.80372 8.76382 0.84403 -1.139535 0.518969 0.980714 +Ta 6.20544 8.3316 1.50988 2.193636 0.909931 -1.013726 +Ta 8.06784 5.83681 12.25104 -1.350407 0.626007 -0.379155 +Ta 0.31897 6.90336 0.10643 -5.3666 -0.250563 -1.141097 +Ta 11.55436 9.51362 3.34931 0.547949 -2.202531 -1.917224 +Ta 10.78092 9.16961 0.43619 2.93789 -2.957858 -2.910142 +Ta 1.24862 9.5832 0.57435 -1.713064 -0.323209 -1.423673 +Ta 5.81406 11.77176 1.54406 1.638754 0.219842 1.61986 +Ta 10.13103 11.22875 1.38321 -1.800705 4.539384 2.649159 +Ta 0.34899 0.35649 6.1042 -1.407332 -2.793672 0.622672 +Ta 2.3232 1.67801 4.77877 -0.05644 2.09227 -0.734316 +Ta 7.49734 2.52339 4.64715 -2.007496 -0.115682 0.14042 +Ta 9.77964 2.17772 5.83529 3.713057 -1.608783 0.411426 +Ta 12.08877 2.91076 4.07847 -1.520526 -1.704707 -0.587973 +Ta 1.76078 4.6877 4.47668 1.413545 -7.499735 -1.858957 +Ta 4.98999 4.11433 3.79876 0.289553 -1.316969 -0.292034 +Ta 6.76353 5.11499 5.45587 -3.138755 0.635253 -4.508867 +Ta 8.18843 6.66761 6.69958 1.823722 2.515733 1.945463 +Ta 9.26522 5.32398 3.90117 2.522311 -2.914637 0.434012 +Ta 11.70087 5.41848 5.49634 -0.91363 0.599933 0.511554 +Ta 1.65165 6.89091 4.56552 -4.64308 7.078545 2.907672 +Ta 3.88906 7.3482 3.69272 4.376913 -1.607122 -3.387251 +Ta 3.78056 9.22669 5.62637 -1.173755 -0.484115 1.473183 +Ta 7.2778 6.86119 3.31305 -1.712746 -0.762926 0.612453 +Ta 8.43315 9.5977 2.96474 -0.068906 0.588767 0.305611 +Ta 8.32391 9.49805 7.04669 1.283119 0.857479 -0.056213 +Ta 9.74646 7.68415 4.88166 1.553537 2.838279 -1.262714 +Ta 0.20242 11.9595 3.59124 0.480807 0.704331 -0.139582 +Ta 0.92234 9.81536 5.6286 -0.676685 -0.718246 -1.353345 +Ta 2.97319 11.83837 4.92159 0.124172 -2.5278 -0.825427 +Ta 4.81042 10.11638 3.25804 -0.00158 0.832634 1.353808 +Ta 5.10938 0.86525 4.93901 1.123663 0.063599 1.236154 +Ta 7.61412 11.73973 4.74754 -0.814736 -0.047356 -0.545511 +Ta 10.33697 11.30643 4.67815 -0.528432 -0.050872 2.228917 +Ta 0.27884 2.84477 6.49144 0.360201 1.903395 2.778998 +Ta 2.01197 0.93667 8.3625 1.378708 0.191326 -1.606266 +Ta 5.95649 1.56866 7.7316 -3.530422 2.114153 0.082888 +Ta 7.99571 0.37668 7.3238 3.086708 -0.94535 -1.566298 +Ta 9.75758 2.05273 9.00324 -1.78926 -0.869367 -0.765594 +Ta 7.0553 1.30554 10.35383 -0.468981 0.451781 -0.424135 +Ta 3.31072 3.02847 6.68212 2.374838 -0.044278 1.652536 +Ta 1.94786 5.25704 7.02637 -4.869392 -0.604143 3.206895 +Ta 5.58301 4.41656 7.69055 -0.012085 -1.275371 2.405145 +Ta 8.49696 4.09995 6.94038 1.731209 -2.887879 -0.17644 +Ta 11.05285 4.3866 7.9546 0.367601 1.162168 1.374681 +Ta 0.98645 7.70557 8.0109 1.110298 0.078167 -0.561606 +Ta 4.08075 5.84992 6.03442 1.908693 2.469334 -1.250813 +Ta 6.48069 8.76967 5.22823 0.114255 -0.523517 -0.733113 +Ta 3.57803 8.81681 8.5928 -0.66732 -1.171187 1.154754 +Ta 7.84056 7.36674 9.41266 2.673183 -2.160921 0.812097 +Ta 5.68236 7.53635 7.81446 0.283447 -0.99061 -1.738751 +Ta 10.93798 7.78281 7.44991 -0.183664 0.008309 0.251959 +Ta 9.9392 9.29803 9.66467 -1.179107 -2.844565 -1.936143 +Ta 3.27502 11.20914 7.71694 -1.605014 0.866048 -1.920371 +Ta 5.80571 11.2039 6.87956 0.570374 -0.917997 -1.21799 +Ta 6.62643 9.54017 9.251 -2.194588 1.730297 1.398058 +Ta 8.37506 11.43578 9.44763 -1.003205 1.254061 1.409533 +Ta 10.64763 11.60302 8.34425 0.22912 1.878017 -4.253745 +Ta 0.62444 10.81341 7.95926 -0.845854 -0.025244 3.548273 +Ta 1.3128 0.0772 10.94202 1.021441 -1.772357 0.971535 +Ta 3.66982 2.58827 9.88588 2.775855 -0.901529 -1.133165 +Ta 4.9029 0.55814 12.14694 0.745195 -0.14623 -0.925343 +Ta 10.71412 0.70352 12.01211 -0.821757 1.855819 -0.172903 +Ta 0.09616 11.95074 0.94667 -0.073589 1.703385 -0.8464 +Ta 12.24445 1.18229 9.52752 -4.911344 -2.238124 -2.990827 +Ta 0.56652 5.73639 10.25403 -1.285215 0.56972 -1.80217 +Ta 1.04406 2.95713 10.2879 0.54537 1.767964 -1.435358 +Ta 2.78879 4.62903 11.50554 1.816283 1.761154 1.997143 +Ta 3.64576 5.81754 9.10448 -0.291727 0.525333 1.415918 +Ta 6.14975 4.49268 10.80918 -3.938361 -1.263146 1.537617 +Ta 8.46844 3.03493 11.91111 -0.260212 -0.549013 1.590318 +Ta 7.95371 4.47804 9.32882 3.486802 -0.184534 -0.465321 +Ta 10.60265 3.91791 10.65025 1.584639 0.666232 1.28596 +Ta 2.41835 7.66344 11.35717 3.582823 -2.530851 -1.921205 +Ta 5.6897 7.16124 11.11328 -0.724382 2.649569 -1.819833 +Ta 8.24854 8.99729 11.81822 -0.58882 -1.012186 0.957519 +Ta 10.50201 6.92143 10.75604 -0.179214 -0.360035 0.514513 +Ta 0.20749 8.75375 10.46189 -1.586508 0.42554 -0.709369 +Ta 2.55072 10.18804 10.88287 1.336488 2.096133 -1.047152 +Ta 4.96405 12.00073 9.46535 1.226786 1.399389 2.14847 +Ta 2.9582 11.89523 1.24555 -0.497007 -1.084677 0.372878 +Ta 5.43899 10.20671 12.04447 0.457816 0.156284 -2.53866 +Ta 7.88861 11.67933 12.19294 -0.209863 1.614617 -0.260277 +Ta 11.22489 11.04751 10.7648 2.246152 1.517056 4.384995 +100 +Lattice = "12.6055002213 0.0 0.0 0.0 12.6055002213 0.0 0.0 0.0 12.6055002213" Properties=species:S:1:pos:R:3:forces:R:3 energy=-1099.673012 stress="64329.38 4705.339999999999 16428.34 4705.339999999999 41963.4 -4448.86 16428.34 -4448.86 54142.01" +Ta 0.38188 4.35838 0.74564 -0.727255 -2.684915 -1.502186 +Ta 1.34891 1.23814 1.97516 -0.901556 -0.105425 1.00657 +Ta 3.91629 1.3428 2.33074 3.786054 2.848263 -0.971111 +Ta 2.50882 2.14034 12.20579 -0.262289 0.109978 0.538412 +Ta 8.20217 1.50457 1.09255 -0.492384 -1.785903 2.601547 +Ta 10.36593 3.31163 1.41537 1.881298 -2.609227 -1.324217 +Ta 10.4022 0.62792 3.78647 -0.90696 3.879838 -1.72804 +Ta 1.89782 6.78766 2.24739 0.610213 0.257066 0.30111 +Ta 5.50184 3.35273 0.83641 -0.560965 -1.138714 0.441504 +Ta 2.32284 3.6359 2.17719 2.602499 1.961671 1.752727 +Ta 5.3072 5.9129 1.35024 -1.807728 1.348974 1.869601 +Ta 7.97916 4.52402 2.2256 -1.448678 0.224978 0.932881 +Ta 12.08411 5.36653 3.17826 1.407869 -0.153369 -2.235907 +Ta 9.93622 6.94867 2.71342 -0.96168 -0.819272 -0.695758 +Ta 9.90617 5.56065 0.39246 1.437756 2.22277 -1.483484 +Ta 2.03145 9.47094 3.47002 -0.365866 -1.501921 0.223241 +Ta 3.89512 9.09235 1.57401 -0.289378 -1.595243 -0.704364 +Ta 6.55755 9.06145 1.13007 1.481441 -1.964278 0.317382 +Ta 7.19441 5.95163 12.15045 5.313352 -0.388306 3.350518 +Ta 0.47731 6.73144 12.49172 -2.324959 2.468907 0.162569 +Ta 11.99106 8.65573 2.136 0.320078 0.329798 0.427882 +Ta 10.46579 8.3526 12.36863 0.469025 0.961865 1.106144 +Ta 1.09582 9.74623 0.42674 -0.367347 0.331195 0.683008 +Ta 6.08716 11.81081 1.97743 -0.347952 0.939564 0.150091 +Ta 10.03534 11.67059 1.4824 1.765295 -0.063423 0.419687 +Ta 0.08024 12.16929 6.35254 3.013201 1.559359 -1.565584 +Ta 2.71663 1.31896 5.17141 1.289295 0.727934 -0.294145 +Ta 7.31848 1.89673 4.23838 -0.731578 2.730215 -0.825462 +Ta 10.8977 1.28949 6.47917 -5.83876 3.773198 -2.47763 +Ta 0.45432 2.51989 4.22159 -3.64939 -0.925817 -2.950598 +Ta 1.70947 4.66775 4.8384 0.462076 1.170048 -2.403113 +Ta 4.57205 3.37193 4.25893 -0.109762 0.615399 0.386449 +Ta 6.6353 4.9693 5.07404 -0.677674 0.753118 -0.691499 +Ta 9.08878 7.33531 5.79768 -1.926322 -3.675185 0.927457 +Ta 9.91121 3.22337 3.84582 -0.878305 0.821935 2.646587 +Ta 11.32221 4.97359 5.54846 -1.015803 -0.259629 1.700732 +Ta 0.53406 7.05513 5.42905 4.213154 0.915513 -0.387097 +Ta 4.46164 6.80136 4.09833 -0.176562 -0.533475 -2.129646 +Ta 3.93041 8.596 5.90044 -2.349383 1.463451 1.214532 +Ta 7.45709 7.32471 3.28984 -1.580622 -0.59473 -0.153408 +Ta 8.73043 9.80728 2.84372 -0.269419 -1.581451 0.380496 +Ta 8.3667 9.63065 6.92756 1.753511 2.485611 1.143484 +Ta 11.10448 8.19971 4.67383 -2.984282 1.041303 -1.700702 +Ta 12.33138 11.59365 3.22318 2.360024 -1.006585 -0.789645 +Ta 12.53349 9.89403 5.63928 3.735451 -1.567194 1.41596 +Ta 3.05157 11.96433 3.46769 -2.586656 -4.605553 1.003837 +Ta 5.53812 9.74587 3.73544 -0.624627 0.711032 0.321477 +Ta 5.17764 0.08755 4.56072 0.792806 1.090161 2.480897 +Ta 7.64882 11.92872 4.33422 1.371203 -2.646937 -1.592811 +Ta 10.26273 11.13472 4.99862 -1.516508 -2.562682 1.139746 +Ta 0.63147 2.19678 6.67724 -1.933442 4.953146 -0.194708 +Ta 2.39775 1.15536 7.89766 1.566886 -5.944045 0.931194 +Ta 5.33276 1.28983 7.19797 -1.126761 0.854886 -2.020746 +Ta 7.89352 0.43228 6.56287 1.13823 0.267818 2.364431 +Ta 8.88305 1.54913 9.09168 1.934009 3.681926 -0.69568 +Ta 6.00124 2.16677 9.5598 8.252345 -1.117748 2.215338 +Ta 2.66739 3.83317 7.06559 2.190193 -4.842621 2.418064 +Ta 0.44413 5.53507 7.53921 0.172202 -0.843263 -0.144565 +Ta 6.07444 4.29758 7.92983 -1.04507 0.569502 -0.853121 +Ta 8.61236 4.26866 6.45192 0.842947 -0.703065 0.93539 +Ta 10.50987 4.11989 8.35507 0.547985 -0.173489 -1.269773 +Ta 2.02897 8.56787 8.24972 -1.223362 -0.887987 -0.332769 +Ta 3.57963 5.79304 6.48017 2.842291 5.01202 -1.423259 +Ta 6.53156 8.37515 5.75214 -0.50131 -0.78674 -2.188556 +Ta 4.51454 9.02305 9.28712 -1.887242 0.583318 -0.321074 +Ta 8.34047 6.94108 8.77392 2.702214 0.628662 0.365051 +Ta 6.01989 7.16828 7.91506 -2.736883 -1.03701 0.87708 +Ta 11.52313 8.08118 8.00297 0.861961 -0.750437 -2.832105 +Ta 9.87066 9.68884 9.34964 -0.418705 -1.344113 0.080437 +Ta 2.69897 11.01376 6.90606 0.624985 0.222953 -0.025436 +Ta 5.56553 10.9604 7.05448 1.478972 -0.881736 -1.62077 +Ta 6.91858 9.87487 9.3601 -0.933279 -1.508382 -2.062547 +Ta 7.56671 12.23671 9.78063 -0.406385 -0.308972 0.183521 +Ta 10.22294 11.87342 7.79903 -1.175658 -1.688479 1.642029 +Ta 0.04509 10.83657 8.74612 1.380926 -0.290325 -0.323702 +Ta 0.94632 0.06721 10.62363 1.061812 0.946373 0.815892 +Ta 3.83384 2.56871 9.64718 -1.450486 1.088741 1.78581 +Ta 4.91898 0.74942 12.23402 2.069575 0.652415 -1.682263 +Ta 10.35682 1.29618 11.60881 -1.007516 -0.380767 -0.681798 +Ta 12.25089 0.25724 0.5674 -1.167993 -0.553636 -1.082113 +Ta 12.05792 1.27062 8.79257 -1.958821 -0.199606 3.512891 +Ta 0.94154 6.36726 9.79464 -0.470327 -1.562595 2.388469 +Ta 1.55131 2.94376 9.49017 -5.482202 3.713318 2.157258 +Ta 2.83736 5.28335 12.23429 0.21999 -0.856343 -0.328898 +Ta 3.28912 5.72925 9.20121 2.590913 0.102617 0.278337 +Ta 5.23966 4.63128 11.01018 -0.510883 -1.107745 -0.843113 +Ta 8.09196 3.41706 12.13822 -0.502547 -2.144772 0.04882 +Ta 8.1563 4.57839 10.05093 0.383882 0.414866 -3.808578 +Ta 10.79442 4.02679 10.93553 1.752466 -1.881501 1.268269 +Ta 2.71931 8.02403 11.22143 2.049893 -0.963189 1.387113 +Ta 5.73731 7.44013 11.32002 -4.676222 3.883048 -2.762461 +Ta 8.16217 8.96831 11.31638 0.374044 -1.476354 1.757164 +Ta 10.92094 6.50569 10.08481 -2.942535 0.663572 0.583517 +Ta 0.13295 8.72748 10.50938 -1.244418 2.69593 0.1167 +Ta 2.76073 10.72733 11.03757 0.159817 -0.598944 -1.675276 +Ta 4.565 12.20225 9.16074 -0.475524 -0.325595 2.074182 +Ta 3.333 11.65103 0.9196 -2.017399 0.539865 -1.533111 +Ta 5.52052 10.58245 11.86999 -0.929433 -0.112136 -1.59182 +Ta 7.97547 11.45742 0.05805 -0.0746 0.038856 -1.899211 +Ta 11.12836 11.17255 11.09073 -0.284488 0.783851 1.570373 +100 +Lattice = "12.6055002213 0.0 0.0 0.0 12.6055002213 0.0 0.0 0.0 12.6055002213" Properties=species:S:1:pos:R:3:forces:R:3 energy=-1121.31506 stress="6315.33 3551.01 1290.84 3551.01 7373.36 -1793.4699999999998 1290.84 -1793.4699999999998 -4190.5599999999995" +Ta 0.64937 3.12625 0.43144 -0.384771 0.95129 0.165479 +Ta 1.36715 0.72175 2.1191 -0.396084 1.361974 -0.172418 +Ta 4.5846 1.15642 2.6142 -0.373595 0.78336 -1.848167 +Ta 3.4656 2.34361 0.38597 -2.224767 -1.381119 -1.370954 +Ta 7.88853 1.1719 1.55114 -0.598212 -0.078923 1.145428 +Ta 10.07282 2.82479 1.63047 1.639511 -1.074148 -1.081096 +Ta 10.53174 0.56802 2.94785 0.257895 1.267816 1.941643 +Ta 2.10362 6.2679 1.6589 0.701345 0.454084 2.496936 +Ta 5.6154 3.59317 1.03035 0.195919 -1.236583 -0.019497 +Ta 3.32731 3.74082 2.62776 -1.283076 0.780111 0.884303 +Ta 4.82978 6.12805 1.02771 1.04951 2.209193 2.462833 +Ta 7.60239 4.46941 2.24663 1.036576 0.558243 2.859549 +Ta 12.48993 4.97942 2.67215 -0.349711 -0.000505 0.40415 +Ta 9.84709 6.20394 2.82647 -0.257749 1.429134 0.922074 +Ta 10.38504 5.10677 0.57401 -0.209053 1.4898 -1.696587 +Ta 2.12734 8.88431 2.41071 -0.896766 0.496609 1.485094 +Ta 4.37717 9.21766 1.21522 -0.870196 -1.493612 0.07125 +Ta 7.07182 9.00281 1.02655 0.183737 -1.129029 -0.559981 +Ta 7.71788 6.33342 0.33272 -0.30082 1.581148 -1.075768 +Ta 12.44465 6.65378 0.30277 0.556355 -0.191302 -1.493292 +Ta 12.09046 8.23945 2.26765 -0.509885 1.361164 -0.650694 +Ta 9.81566 8.34073 0.27729 0.6859 1.115843 0.637478 +Ta 0.91684 11.16462 0.54206 0.073874 -1.819993 0.221407 +Ta 5.69432 11.50075 1.29392 1.279331 1.42035 2.206812 +Ta 10.71239 11.30092 1.18755 -0.759539 -2.842687 -0.44627 +Ta 0.12647 0.57355 5.6744 1.485357 -0.339908 0.72473 +Ta 2.40387 1.53268 4.75274 0.971096 -0.38073 0.869134 +Ta 6.4354 2.09058 4.44464 1.8115 0.323829 -0.954613 +Ta 10.29448 1.87908 6.14933 -0.973544 0.673823 0.524211 +Ta 12.13409 2.64826 3.96133 1.041975 -0.146906 -0.101053 +Ta 1.89139 4.2711 5.14514 -1.126257 1.765095 -1.172303 +Ta 4.29285 3.26764 5.49838 1.359585 0.954058 -0.894642 +Ta 6.22054 4.99782 4.76901 -0.57103 0.193676 0.659475 +Ta 8.73015 5.75307 5.41647 0.977001 1.137808 0.707847 +Ta 9.46292 3.6411 4.00924 0.208171 -0.619736 1.487252 +Ta 11.80799 5.28602 5.31887 -1.14111 -1.708079 1.708749 +Ta 1.42351 7.04153 5.51044 0.442962 1.999421 -1.932131 +Ta 3.99608 6.77694 4.00068 0.020115 -0.082585 -0.562723 +Ta 3.50684 9.23442 5.21977 0.277684 0.652346 0.809939 +Ta 6.82787 7.1376 3.15953 0.461297 -1.023286 -0.200358 +Ta 9.15017 9.16521 3.22539 0.975528 -0.406877 -2.361923 +Ta 9.03229 9.22399 5.76536 -0.96211 0.660671 1.97306 +Ta 11.42908 7.93297 4.71336 -1.075725 2.179405 -1.299081 +Ta 0.05087 11.06881 3.63544 0.18806 -0.894103 -2.497085 +Ta 0.61823 10.14934 5.99785 0.964288 -1.323025 0.615744 +Ta 2.87244 11.55729 3.56061 -0.950735 -1.383789 -0.752604 +Ta 6.21349 9.52465 3.78915 -1.000365 1.509307 0.554842 +Ta 5.15602 12.31549 4.62675 0.565237 -0.704465 1.119632 +Ta 8.08827 11.62648 3.35101 -0.339071 0.461047 0.284645 +Ta 10.68985 11.76775 5.34052 -2.452377 -2.887406 0.054989 +Ta 0.14268 2.96019 7.28952 -1.17741 0.302926 -1.013001 +Ta 1.79625 1.2317 8.73242 1.145361 -3.820996 -0.45811 +Ta 5.07039 1.39926 7.46358 -0.781338 0.724617 -1.541559 +Ta 7.57216 0.49788 6.56353 0.962384 0.05587 -0.04513 +Ta 9.27827 2.61852 8.92732 0.176007 -0.879678 -0.926458 +Ta 6.54771 2.47044 9.38651 2.190569 0.166399 1.077573 +Ta 2.76284 3.40149 7.77645 3.137421 -0.183358 -0.704336 +Ta 1.46964 5.59388 7.81661 -3.887251 -0.228325 -0.342894 +Ta 5.28247 4.64737 8.03918 0.338155 -1.923057 0.116762 +Ta 7.44449 3.18893 6.73322 1.141594 1.207491 -0.292546 +Ta 11.12935 5.21434 8.64857 -1.612825 -2.999306 -1.714386 +Ta 1.54461 8.15093 8.61321 0.347763 2.086893 -0.257285 +Ta 3.74639 6.51293 6.87702 0.959722 -0.501443 -1.452222 +Ta 6.16432 8.04946 6.35417 0.023322 -2.311879 -2.364886 +Ta 4.17774 8.81779 8.33178 -1.45671 1.390508 1.192928 +Ta 8.79674 7.34098 7.76356 0.744674 0.017978 0.615727 +Ta 6.3995 6.81915 8.95492 -2.56268 0.245528 -0.18037 +Ta 11.65865 7.47829 7.15549 -0.141642 0.63044 2.199066 +Ta 10.36878 9.3845 9.0403 -0.66872 0.230975 -0.20666 +Ta 3.44367 12.01539 7.00233 -1.966426 -2.282219 -0.555493 +Ta 6.18022 10.72879 6.38769 -0.159595 0.636574 0.422497 +Ta 6.60979 9.53788 8.62428 1.893523 1.309962 1.811685 +Ta 7.82809 11.91798 9.44419 -1.75495 0.501787 1.526707 +Ta 9.83162 12.15132 7.88212 0.675577 0.0338 -0.256919 +Ta 12.33473 11.37557 8.23941 1.476837 0.086277 1.652827 +Ta 1.26867 0.5664 11.43089 0.552369 0.109749 -1.014297 +Ta 4.11323 2.51574 10.31659 -0.216484 0.602173 -0.337403 +Ta 6.1981 1.3171 12.07577 -0.840924 -1.268238 -1.122831 +Ta 8.93316 0.96241 11.49866 0.200771 0.591493 -0.447815 +Ta 11.51202 0.95161 12.55636 0.023759 0.436473 0.983974 +Ta 11.74771 1.34839 9.48403 -0.672837 0.114932 -0.4313 +Ta 0.37088 6.14613 10.23785 1.469982 0.175809 2.274858 +Ta 1.53343 3.45239 10.16056 -2.401632 0.95373 1.427778 +Ta 2.97984 4.88656 12.27482 -1.163376 -0.933805 -0.832442 +Ta 3.23113 5.88226 9.89191 1.644345 0.515055 -2.001086 +Ta 5.83202 4.76093 11.09154 -1.265112 -0.209543 -0.313576 +Ta 8.18149 3.7694 12.32031 -0.908072 -2.871898 -1.645014 +Ta 8.28389 5.18304 9.86813 1.06209 -0.729605 -0.590042 +Ta 10.60165 3.38032 11.14631 2.294652 0.864636 -1.210164 +Ta 2.16602 8.04842 12.06324 1.617599 0.103075 -0.814791 +Ta 5.19763 7.5131 11.34985 -0.346409 1.752742 -0.487937 +Ta 7.92875 8.24785 10.61624 0.728867 1.077493 1.692555 +Ta 10.42049 6.95313 10.57826 -0.286476 0.160363 0.370268 +Ta 12.38682 9.14199 11.43376 -0.594871 0.767297 -0.960584 +Ta 2.2479 10.73902 9.80504 -0.028268 0.335889 0.421595 +Ta 4.91854 12.45236 9.55661 -0.382663 -1.868957 -0.192626 +Ta 3.60604 12.29562 12.33442 -0.6243 -0.490257 0.799831 +Ta 5.45536 10.4337 11.30531 0.355343 -0.806764 -0.469902 +Ta 8.0691 11.11452 12.46882 0.894574 0.749785 -0.70888 +Ta 10.68626 11.50854 10.77779 0.440455 -1.251201 0.450872 diff --git a/examples/PACKAGES/pod/Ta/XYZ/Surface.xyz b/examples/PACKAGES/pod/Ta/XYZ/Surface.xyz new file mode 100644 index 0000000000..d22d2ee956 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/XYZ/Surface.xyz @@ -0,0 +1,250 @@ +24 +Lattice = "4.69519013405 0.0 0.0 0.0 3.32 0.0 0.0 0.0 53.12" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.911828 stress="-9651.84 0.0 0.0 0.0 -7622.87 0.0 0.0 0.0 -272.58" +Ta 2.34759 1.66 0.09121 0.0 0.0 0.001057 +Ta 0.0 0.0 0.09121 0.0 0.0 0.001057 +Ta 0.0 1.66 2.3361 0.0 0.0 0.000335 +Ta 2.34759 0.0 2.3361 0.0 0.0 0.000335 +Ta 2.34759 1.66 4.68536 0.0 0.0 0.000274 +Ta 0.0 0.0 4.68536 0.0 0.0 0.000274 +Ta 0.0 1.66 7.03392 0.0 0.0 0.000349 +Ta 2.34759 0.0 7.03392 0.0 0.0 0.000349 +Ta 2.34759 1.66 9.38594 0.0 0.0 -0.000481 +Ta 0.0 0.0 9.38594 0.0 0.0 -0.000481 +Ta 0.0 1.66 11.73648 0.0 0.0 -0.000487 +Ta 2.34759 0.0 11.73648 0.0 0.0 -0.000487 +Ta 2.34759 1.66 14.08712 0.0 0.0 0.000487 +Ta 0.0 0.0 14.08712 0.0 0.0 0.000487 +Ta 0.0 1.66 16.43764 0.0 0.0 0.000481 +Ta 2.34759 0.0 16.43764 0.0 0.0 0.000481 +Ta 2.34759 1.66 18.78966 0.0 0.0 -0.000349 +Ta 0.0 0.0 18.78966 0.0 0.0 -0.000349 +Ta 0.0 1.66 21.13823 0.0 0.0 -0.000274 +Ta 2.34759 0.0 21.13823 0.0 0.0 -0.000274 +Ta 2.34759 1.66 23.48739 0.0 0.0 -0.000335 +Ta 0.0 0.0 23.48739 0.0 0.0 -0.000335 +Ta 0.0 1.66 25.73229 0.0 0.0 -0.001057 +Ta 2.34759 0.0 25.73229 0.0 0.0 -0.001057 +48 +Lattice = "6.64001325846 0.0 0.0 0.0 6.64001325846 0.0 0.0 0.0 39.84" Properties=species:S:1:pos:R:3:forces:R:3 energy=-555.359452 stress="-6438.73 0.0 0.0 0.0 -6438.73 0.0 0.0 0.0 -286.5" +Ta 1.66001 1.66 1.62137 0.0 0.0 -3e-05 +Ta 0.0 0.0 0.17247 0.0 0.0 0.00038 +Ta 1.66001 1.66 4.98756 0.0 0.0 0.000833 +Ta 0.0 0.0 3.27999 0.0 0.0 0.000359 +Ta 1.66001 1.66 8.28844 0.0 0.0 0.00041 +Ta 0.0 0.0 6.62582 0.0 0.0 6.6e-05 +Ta 1.66001 1.66 11.63419 0.0 0.0 -6.6e-05 +Ta 0.0 0.0 9.97156 0.0 0.0 -0.00041 +Ta 1.66001 1.66 14.98001 0.0 0.0 -0.000359 +Ta 0.0 0.0 13.27244 0.0 0.0 -0.000833 +Ta 1.66001 1.66 18.08753 0.0 0.0 -0.00038 +Ta 0.0 0.0 16.63864 0.0 0.0 3e-05 +Ta 1.66001 4.98001 1.62137 0.0 0.0 -3e-05 +Ta 0.0 3.32001 0.17247 0.0 0.0 0.00038 +Ta 1.66001 4.98001 4.98756 0.0 0.0 0.000833 +Ta 0.0 3.32001 3.27999 0.0 0.0 0.000359 +Ta 1.66001 4.98001 8.28844 0.0 0.0 0.00041 +Ta 0.0 3.32001 6.62582 0.0 0.0 6.6e-05 +Ta 1.66001 4.98001 11.63419 0.0 0.0 -6.6e-05 +Ta 0.0 3.32001 9.97156 0.0 0.0 -0.00041 +Ta 1.66001 4.98001 14.98001 0.0 0.0 -0.000359 +Ta 0.0 3.32001 13.27244 0.0 0.0 -0.000833 +Ta 1.66001 4.98001 18.08753 0.0 0.0 -0.00038 +Ta 0.0 3.32001 16.63864 0.0 0.0 3e-05 +Ta 4.98002 1.66 1.62137 0.0 0.0 -3e-05 +Ta 3.32001 0.0 0.17247 0.0 0.0 0.00038 +Ta 4.98002 1.66 4.98756 0.0 0.0 0.000833 +Ta 3.32001 0.0 3.27999 0.0 0.0 0.000359 +Ta 4.98002 1.66 8.28844 0.0 0.0 0.00041 +Ta 3.32001 0.0 6.62582 0.0 0.0 6.6e-05 +Ta 4.98002 1.66 11.63419 0.0 0.0 -6.6e-05 +Ta 3.32001 0.0 9.97156 0.0 0.0 -0.00041 +Ta 4.98002 1.66 14.98001 0.0 0.0 -0.000359 +Ta 3.32001 0.0 13.27244 0.0 0.0 -0.000833 +Ta 4.98002 1.66 18.08753 0.0 0.0 -0.00038 +Ta 3.32001 0.0 16.63864 0.0 0.0 3e-05 +Ta 4.98002 4.98001 1.62137 0.0 0.0 -3e-05 +Ta 3.32001 3.32001 0.17247 0.0 0.0 0.00038 +Ta 4.98002 4.98001 4.98756 0.0 0.0 0.000833 +Ta 3.32001 3.32001 3.27999 0.0 0.0 0.000359 +Ta 4.98002 4.98001 8.28844 0.0 0.0 0.00041 +Ta 3.32001 3.32001 6.62582 0.0 0.0 6.6e-05 +Ta 4.98002 4.98001 11.63419 0.0 0.0 -6.6e-05 +Ta 3.32001 3.32001 9.97156 0.0 0.0 -0.00041 +Ta 4.98002 4.98001 14.98001 0.0 0.0 -0.000359 +Ta 3.32001 3.32001 13.27244 0.0 0.0 -0.000833 +Ta 4.98002 4.98001 18.08753 0.0 0.0 -0.00038 +Ta 3.32001 3.32001 16.63864 0.0 0.0 3e-05 +40 +Lattice = "4.69518993616 0.0 0.0 0.0 8.13231015027 0.0 0.0 0.0 36.52" Properties=species:S:1:pos:R:3:forces:R:3 energy=-459.216162 stress="-27041.87 0.0 0.0 0.0 -26744.41 19.599999999999998 0.0 19.599999999999998 -29530.539999999997" +Ta 2.34759 6.77692 0.9584 0.0 0.00104 0.266836 +Ta 0.0 2.71077 0.9584 0.0 0.00104 0.266836 +Ta 2.34759 4.06615 0.0 0.0 -0.000781 2.01398 +Ta 2.34759 4.06615 2.8752 0.0 0.002127 -0.707743 +Ta 0.0 5.42154 1.9168 0.0 -0.0035 -1.222398 +Ta 2.34759 6.77692 3.83361 0.0 0.000551 -0.353108 +Ta 0.0 0.0 0.0 0.0 -0.000781 2.01398 +Ta 0.0 0.0 2.8752 0.0 0.002127 -0.707743 +Ta 2.34759 1.35538 1.9168 0.0 -0.0035 -1.222398 +Ta 0.0 2.71077 3.83361 0.0 0.000551 -0.353108 +Ta 0.0 5.42154 4.79201 0.0 0.001693 -0.22097 +Ta 2.34759 6.77692 6.70881 0.0 0.000422 -0.070866 +Ta 2.34759 1.35538 4.79201 0.0 0.001693 -0.22097 +Ta 0.0 2.71077 6.70881 0.0 0.000422 -0.070866 +Ta 2.34759 4.06615 5.75041 0.0 -0.000841 0.251247 +Ta 2.34759 4.06615 8.62561 0.0 -0.000554 0.023395 +Ta 0.0 5.42154 7.66721 0.0 -0.000869 -0.03418 +Ta 0.0 0.0 5.75041 0.0 -0.000841 0.251247 +Ta 0.0 0.0 8.62561 0.0 -0.000554 0.023395 +Ta 2.34759 1.35538 7.66721 0.0 -0.000869 -0.03418 +Ta 0.0 5.42154 10.5424 0.0 0.000869 0.03418 +Ta 2.34759 6.77692 9.58401 0.0 0.000554 -0.023395 +Ta 2.34759 6.77692 12.4592 0.0 0.000841 -0.251247 +Ta 2.34759 1.35538 10.5424 0.0 0.000869 0.03418 +Ta 0.0 2.71077 9.58401 0.0 0.000554 -0.023395 +Ta 0.0 2.71077 12.4592 0.0 0.000841 -0.251247 +Ta 2.34759 4.06615 11.5008 0.0 -0.000422 0.070866 +Ta 0.0 5.42154 13.4176 0.0 -0.001693 0.22097 +Ta 0.0 0.0 11.5008 0.0 -0.000422 0.070866 +Ta 2.34759 1.35538 13.4176 0.0 -0.001693 0.22097 +Ta 2.34759 4.06615 14.376 0.0 -0.000551 0.353108 +Ta 0.0 5.42154 16.2928 0.0 0.0035 1.222398 +Ta 2.34759 6.77692 15.3344 0.0 -0.002127 0.707743 +Ta 2.34759 6.77692 18.2096 0.0 0.000781 -2.01398 +Ta 0.0 0.0 14.376 0.0 -0.000551 0.353108 +Ta 2.34759 1.35538 16.2928 0.0 0.0035 1.222398 +Ta 0.0 2.71077 15.3344 0.0 -0.002127 0.707743 +Ta 0.0 2.71077 18.2096 0.0 0.000781 -2.01398 +Ta 2.34759 4.06615 17.2512 0.0 -0.00104 -0.266836 +Ta 0.0 0.0 17.2512 0.0 -0.00104 -0.266836 +40 +Lattice = "4.69518993616 0.0 0.0 0.0 8.13231015027 0.0 0.0 0.0 36.52" Properties=species:S:1:pos:R:3:forces:R:3 energy=-461.144076 stress="-6214.78 0.0 0.0 0.0 -6110.78 11.43 0.0 11.43 -124.44" +Ta 2.34759 6.77677 1.02996 0.0 4.9e-05 0.000956 +Ta 0.0 2.71062 1.02996 0.0 4.9e-05 0.000956 +Ta 2.34759 4.06617 0.30181 0.0 -0.000436 0.000304 +Ta 2.34759 4.0661 2.9333 0.0 0.000405 -0.000621 +Ta 0.0 5.42161 1.81457 0.0 -0.000256 -0.000454 +Ta 2.34759 6.77673 3.82136 0.0 0.000483 0.001188 +Ta 0.0 2e-05 0.30181 0.0 -0.000436 0.000304 +Ta 0.0 8.13226 2.9333 0.0 0.000405 -0.000621 +Ta 2.34759 1.35545 1.81457 0.0 -0.000256 -0.000454 +Ta 0.0 2.71058 3.82136 0.0 0.000483 0.001188 +Ta 0.0 5.42171 4.75865 0.0 -0.000286 3.9e-05 +Ta 2.34759 6.77697 6.68474 0.0 0.000174 0.001115 +Ta 2.34759 1.35555 4.75865 0.0 -0.000286 3.9e-05 +Ta 0.0 2.71082 6.68474 0.0 0.000174 0.001115 +Ta 2.34759 4.06631 5.76725 0.0 0.000154 -0.0006 +Ta 2.34759 4.0661 8.64133 0.0 0.000311 0.000365 +Ta 0.0 5.42175 7.66351 0.0 -0.000264 -0.00059 +Ta 0.0 0.00016 5.76725 0.0 0.000154 -0.0006 +Ta 0.0 -5e-05 8.64133 0.0 0.000311 0.000365 +Ta 2.34759 1.35559 7.66351 0.0 -0.000264 -0.00059 +Ta 0.0 5.42176 10.5454 0.0 -0.000164 0.000261 +Ta 2.34759 6.77681 9.56856 0.0 0.000347 -0.001383 +Ta 2.34759 6.77657 12.44226 0.0 0.000206 0.000791 +Ta 2.34759 1.3556 10.5454 0.0 -0.000164 0.000261 +Ta 0.0 2.71066 9.56856 0.0 0.000347 -0.001383 +Ta 0.0 2.71042 12.44226 0.0 0.000206 0.000791 +Ta 2.34759 4.06598 11.52478 0.0 0.000279 -0.00135 +Ta 0.0 5.42175 13.45118 0.0 -0.000329 -0.001033 +Ta 0.0 8.13214 11.52478 0.0 0.000279 -0.00135 +Ta 2.34759 1.35559 13.45118 0.0 -0.000329 -0.001033 +Ta 2.34759 4.06624 14.38799 0.0 0.000351 -0.000576 +Ta 0.0 5.4218 16.39523 0.0 -0.000453 0.0004 +Ta 2.34759 6.77687 15.2766 0.0 0.000189 0.001532 +Ta 2.34759 6.77657 17.90814 0.0 -0.000603 -0.00011 +Ta 0.0 9e-05 14.38799 0.0 0.000351 -0.000576 +Ta 2.34759 1.35564 16.39523 0.0 -0.000453 0.0004 +Ta 0.0 2.71072 15.2766 0.0 0.000189 0.001532 +Ta 0.0 2.71042 17.90814 0.0 -0.000603 -0.00011 +Ta 2.34759 4.06617 17.17945 0.0 -0.000157 -0.000235 +Ta 0.0 2e-05 17.17945 0.0 -0.000157 -0.000235 +24 +Lattice = "4.69519013405 0.0 0.0 0.0 3.32 0.0 0.0 0.0 53.12" Properties=species:S:1:pos:R:3:forces:R:3 energy=-279.635146 stress="-21250.23 0.0 0.0 0.0 -20345.210000000003 0.0 0.0 0.0 -14676.96" +Ta 2.34759 1.66 0.0 0.0 0.0 0.48507 +Ta 0.0 0.0 0.0 0.0 0.0 0.48507 +Ta 0.0 1.66 2.34759 0.0 0.0 -0.412878 +Ta 2.34759 0.0 2.34759 0.0 0.0 -0.412878 +Ta 2.34759 1.66 4.69519 0.0 0.0 -0.096961 +Ta 0.0 0.0 4.69519 0.0 0.0 -0.096961 +Ta 0.0 1.66 7.04278 0.0 0.0 0.008179 +Ta 2.34759 0.0 7.04278 0.0 0.0 0.008179 +Ta 2.34759 1.66 9.39038 0.0 0.0 -0.003881 +Ta 0.0 0.0 9.39038 0.0 0.0 -0.003881 +Ta 0.0 1.66 11.738 0.0 0.0 0.002591 +Ta 2.34759 0.0 11.738 0.0 0.0 0.002591 +Ta 2.34759 1.66 14.0856 0.0 0.0 -0.002591 +Ta 0.0 0.0 14.0856 0.0 0.0 -0.002591 +Ta 0.0 1.66 16.4332 0.0 0.0 0.003881 +Ta 2.34759 0.0 16.4332 0.0 0.0 0.003881 +Ta 2.34759 1.66 18.7808 0.0 0.0 -0.008179 +Ta 0.0 0.0 18.7808 0.0 0.0 -0.008179 +Ta 0.0 1.66 21.1284 0.0 0.0 0.096961 +Ta 2.34759 0.0 21.1284 0.0 0.0 0.096961 +Ta 2.34759 1.66 23.4759 0.0 0.0 0.412878 +Ta 0.0 0.0 23.4759 0.0 0.0 0.412878 +Ta 0.0 1.66 25.8235 0.0 0.0 -0.48507 +Ta 2.34759 0.0 25.8235 0.0 0.0 -0.48507 +30 +Lattice = "5.75040976524 0.0 0.0 0.0 4.69518993616 0.0 0.0 0.0 39.84" Properties=species:S:1:pos:R:3:forces:R:3 energy=-346.592525 stress="-9399.49 0.0 -208.25 0.0 -11819.32 0.0 -208.25 0.0 132.24" +Ta 0.9892 0.0 2.7203 0.001551 0.0 -0.000488 +Ta 0.00727 2.34759 4.07239 0.001169 0.0 -0.000766 +Ta 2.88247 2.34759 4.07239 0.001169 0.0 -0.000766 +Ta 0.17997 0.0 0.18449 0.002466 0.0 -0.001108 +Ta 3.05517 0.0 0.18449 0.002466 0.0 -0.001108 +Ta 1.87083 2.34759 1.32776 -0.000874 0.0 -0.001517 +Ta 4.74604 2.34759 1.32776 -0.000874 0.0 -0.001517 +Ta 3.86441 0.0 2.7203 0.001551 0.0 -0.000488 +Ta 0.94648 2.34759 6.77133 0.00042 0.0 -0.000294 +Ta 0.00117 0.0 8.1367 0.000452 0.0 9.6e-05 +Ta 2.87637 0.0 8.1367 0.000452 0.0 9.6e-05 +Ta 1.91123 0.0 5.41489 0.001544 0.0 -5.7e-05 +Ta 4.78644 0.0 5.41489 0.001544 0.0 -5.7e-05 +Ta 3.82169 2.34759 6.77133 0.00042 0.0 -0.000294 +Ta 0.95723 0.0 10.83871 -0.000452 0.0 -9.6e-05 +Ta 0.01192 2.34759 12.20409 -0.00042 0.0 0.000294 +Ta 2.88712 2.34759 12.20409 -0.00042 0.0 0.000294 +Ta 1.9168 2.34759 9.48769 0.0 0.0 0.0 +Ta 4.79201 2.34759 9.48769 0.0 0.0 0.0 +Ta 3.83244 0.0 10.83871 -0.000452 0.0 -9.6e-05 +Ta 0.95113 2.34759 14.90296 -0.001169 0.0 0.000766 +Ta 5.71961 0.0 16.25507 -0.001551 0.0 0.000488 +Ta 2.8444 0.0 16.25507 -0.001551 0.0 0.000488 +Ta 1.96277 2.34759 17.64762 0.000874 0.0 0.001517 +Ta 4.83798 2.34759 17.64762 0.000874 0.0 0.001517 +Ta 1.92237 0.0 13.56045 -0.001544 0.0 5.7e-05 +Ta 4.79758 0.0 13.56045 -0.001544 0.0 5.7e-05 +Ta 3.82634 2.34759 14.90296 -0.001169 0.0 0.000766 +Ta 0.77843 0.0 18.79091 -0.002466 0.0 0.001108 +Ta 3.65364 0.0 18.79091 -0.002466 0.0 0.001108 +30 +Lattice = "5.75040976524 0.0 0.0 0.0 4.69518993616 0.0 0.0 0.0 39.84" Properties=species:S:1:pos:R:3:forces:R:3 energy=-345.744506 stress="-26530.08 0.0 -2915.02 0.0 -25603.77 0.0 -2915.02 0.0 -21262.54" +Ta 0.9584 0.0 2.71077 0.048753 0.0 -0.789488 +Ta 0.0 2.34759 4.06615 0.000543 0.0 0.103698 +Ta 2.8752 2.34759 4.06615 0.000543 0.0 0.103698 +Ta 0.0 0.0 0.0 0.302653 0.0 1.1858 +Ta 2.8752 0.0 0.0 0.302653 0.0 1.1858 +Ta 1.9168 2.34759 1.35538 -0.326078 0.0 -0.402735 +Ta 4.79201 2.34759 1.35538 -0.326078 0.0 -0.402735 +Ta 3.83361 0.0 2.71077 0.048753 0.0 -0.789488 +Ta 0.9584 2.34759 6.77692 -0.058605 0.0 -0.050501 +Ta 0.0 0.0 8.13231 0.022525 0.0 0.111412 +Ta 2.8752 0.0 8.13231 0.022525 0.0 0.111412 +Ta 1.9168 0.0 5.42154 0.017191 0.0 -0.139574 +Ta 4.79201 0.0 5.42154 0.017191 0.0 -0.139574 +Ta 3.83361 2.34759 6.77692 -0.058605 0.0 -0.050501 +Ta 0.9584 0.0 10.8431 -0.022525 0.0 -0.111412 +Ta 0.0 2.34759 12.1985 0.058605 0.0 0.050501 +Ta 2.8752 2.34759 12.1985 0.058605 0.0 0.050501 +Ta 1.9168 2.34759 9.48769 0.0 0.0 0.0 +Ta 4.79201 2.34759 9.48769 0.0 0.0 0.0 +Ta 3.83361 0.0 10.8431 -0.022525 0.0 -0.111412 +Ta 0.9584 2.34759 14.9092 -0.000543 0.0 -0.103698 +Ta 0.0 0.0 16.2646 -0.048753 0.0 0.789488 +Ta 2.8752 0.0 16.2646 -0.048753 0.0 0.789488 +Ta 1.9168 2.34759 17.62 0.326078 0.0 0.402735 +Ta 4.79201 2.34759 17.62 0.326078 0.0 0.402735 +Ta 1.9168 0.0 13.5538 -0.017191 0.0 0.139574 +Ta 4.79201 0.0 13.5538 -0.017191 0.0 0.139574 +Ta 3.83361 2.34759 14.9092 -0.000543 0.0 -0.103698 +Ta 0.9584 0.0 18.9754 -0.302653 0.0 -1.1858 +Ta 3.83361 0.0 18.9754 -0.302653 0.0 -1.1858 diff --git a/examples/PACKAGES/pod/Ta/XYZ/Volume_A15.xyz b/examples/PACKAGES/pod/Ta/XYZ/Volume_A15.xyz new file mode 100644 index 0000000000..41e9be5a6d --- /dev/null +++ b/examples/PACKAGES/pod/Ta/XYZ/Volume_A15.xyz @@ -0,0 +1,300 @@ +8 +Lattice = "6.7 0.0 0.0 0.0 6.7 0.0 0.0 0.0 6.7" Properties=species:S:1:pos:R:3:forces:R:3 energy=-66.990732 stress="-312387.88 0.0 -0.0 0.0 -312387.88 0.0 -0.0 0.0 -312387.88" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 3.35 3.35 3.35 0.0 0.0 0.0 +Ta 1.675 3.35 0.0 0.0 0.0 0.0 +Ta 5.025 3.35 0.0 0.0 0.0 0.0 +Ta 0.0 1.675 3.35 0.0 0.0 0.0 +Ta 0.0 5.025 3.35 0.0 0.0 0.0 +Ta 3.35 0.0 1.675 0.0 0.0 0.0 +Ta 3.35 0.0 5.025 0.0 0.0 0.0 +8 +Lattice = "4.6 0.0 0.0 0.0 4.6 0.0 0.0 0.0 4.6" Properties=species:S:1:pos:R:3:forces:R:3 energy=-72.957807 stress="1835613.98 0.0 -0.0 0.0 1835613.98 0.0 -0.0 0.0 1835613.98" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.3 2.3 2.3 0.0 0.0 0.0 +Ta 1.15 2.3 0.0 0.0 0.0 0.0 +Ta 3.45 2.3 0.0 0.0 0.0 0.0 +Ta 0.0 1.15 2.3 0.0 0.0 0.0 +Ta 0.0 3.45 2.3 0.0 0.0 0.0 +Ta 2.3 0.0 1.15 0.0 0.0 0.0 +Ta 2.3 0.0 3.45 0.0 0.0 0.0 +8 +Lattice = "5.2 0.0 0.0 0.0 5.2 0.0 0.0 0.0 5.2" Properties=species:S:1:pos:R:3:forces:R:3 energy=-94.145745 stress="145354.31 0.0 0.0 0.0 145354.31 -0.0 0.0 -0.0 145354.31" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.6 2.6 2.6 0.0 0.0 0.0 +Ta 1.3 2.6 0.0 0.0 0.0 0.0 +Ta 3.9 2.6 0.0 0.0 0.0 0.0 +Ta 0.0 1.3 2.6 0.0 0.0 0.0 +Ta 0.0 3.9 2.6 0.0 0.0 0.0 +Ta 2.6 0.0 1.3 0.0 0.0 0.0 +Ta 2.6 0.0 3.9 0.0 0.0 0.0 +8 +Lattice = "5.3 0.0 0.0 0.0 5.3 0.0 0.0 0.0 5.3" Properties=species:S:1:pos:R:3:forces:R:3 energy=-94.554682 stress="18038.98 0.0 -0.0 0.0 18038.98 -0.0 -0.0 -0.0 18038.98" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.65 2.65 2.65 0.0 0.0 0.0 +Ta 1.325 2.65 0.0 0.0 0.0 0.0 +Ta 3.975 2.65 0.0 0.0 0.0 0.0 +Ta 0.0 1.325 2.65 0.0 0.0 0.0 +Ta 0.0 3.975 2.65 0.0 0.0 0.0 +Ta 2.65 0.0 1.325 0.0 0.0 0.0 +Ta 2.65 0.0 3.975 0.0 0.0 0.0 +8 +Lattice = "4.7 0.0 0.0 0.0 4.7 0.0 0.0 0.0 4.7" Properties=species:S:1:pos:R:3:forces:R:3 energy=-79.438363 stress="1385239.49 0.0 0.0 0.0 1385239.49 0.0 0.0 0.0 1385239.49" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.35 2.35 2.35 0.0 0.0 0.0 +Ta 1.175 2.35 0.0 0.0 0.0 0.0 +Ta 3.525 2.35 0.0 0.0 0.0 0.0 +Ta 0.0 1.175 2.35 0.0 0.0 0.0 +Ta 0.0 3.525 2.35 0.0 0.0 0.0 +Ta 2.35 0.0 1.175 0.0 0.0 0.0 +Ta 2.35 0.0 3.525 0.0 0.0 0.0 +8 +Lattice = "6.6 0.0 0.0 0.0 6.6 0.0 0.0 0.0 6.6" Properties=species:S:1:pos:R:3:forces:R:3 energy=-69.627817 stress="-324717.99 0.0 0.0 0.0 -324717.99 0.0 0.0 0.0 -324717.99" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 3.3 3.3 3.3 0.0 0.0 0.0 +Ta 1.65 3.3 0.0 0.0 0.0 0.0 +Ta 4.95 3.3 0.0 0.0 0.0 0.0 +Ta 0.0 1.65 3.3 0.0 0.0 0.0 +Ta 0.0 4.95 3.3 0.0 0.0 0.0 +Ta 3.3 0.0 1.65 0.0 0.0 0.0 +Ta 3.3 0.0 4.95 0.0 0.0 0.0 +8 +Lattice = "6.1 0.0 0.0 0.0 6.1 0.0 0.0 0.0 6.1" Properties=species:S:1:pos:R:3:forces:R:3 energy=-82.604907 stress="-350351.07 0.0 0.0 0.0 -350351.07 0.0 0.0 0.0 -350351.07" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 3.05 3.05 3.05 0.0 0.0 0.0 +Ta 1.525 3.05 0.0 0.0 0.0 0.0 +Ta 4.575 3.05 0.0 0.0 0.0 0.0 +Ta 0.0 1.525 3.05 0.0 0.0 0.0 +Ta 0.0 4.575 3.05 0.0 0.0 0.0 +Ta 3.05 0.0 1.525 0.0 0.0 0.0 +Ta 3.05 0.0 4.575 0.0 0.0 0.0 +8 +Lattice = "4.0 0.0 0.0 0.0 4.0 0.0 0.0 0.0 4.0" Properties=species:S:1:pos:R:3:forces:R:3 energy=14.89048 stress="8403695.620000001 0.0 0.0 0.0 8403695.620000001 0.0 0.0 0.0 8403695.620000001" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.0 2.0 2.0 0.0 0.0 0.0 +Ta 1.0 2.0 0.0 0.0 0.0 0.0 +Ta 3.0 2.0 0.0 0.0 0.0 0.0 +Ta 0.0 1.0 2.0 0.0 0.0 0.0 +Ta 0.0 3.0 2.0 0.0 0.0 0.0 +Ta 2.0 0.0 1.0 0.0 0.0 0.0 +Ta 2.0 0.0 3.0 0.0 0.0 0.0 +8 +Lattice = "5.4 0.0 0.0 0.0 5.4 0.0 0.0 0.0 5.4" Properties=species:S:1:pos:R:3:forces:R:3 energy=-94.367599 stress="-83756.66 -0.0 0.0 -0.0 -83756.66 -0.0 0.0 -0.0 -83756.66" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.7 2.7 2.7 0.0 0.0 0.0 +Ta 1.35 2.7 0.0 0.0 0.0 0.0 +Ta 4.05 2.7 0.0 0.0 0.0 0.0 +Ta 0.0 1.35 2.7 0.0 0.0 0.0 +Ta 0.0 4.05 2.7 0.0 0.0 0.0 +Ta 2.7 0.0 1.35 0.0 0.0 0.0 +Ta 2.7 0.0 4.05 0.0 0.0 0.0 +8 +Lattice = "5.8 0.0 0.0 0.0 5.8 0.0 0.0 0.0 5.8" Properties=species:S:1:pos:R:3:forces:R:3 energy=-89.248227 stress="-305522.26 0.0 0.0 0.0 -305522.26 -0.0 0.0 -0.0 -305522.26" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.9 2.9 2.9 0.0 0.0 0.0 +Ta 1.45 2.9 0.0 0.0 0.0 0.0 +Ta 4.35 2.9 0.0 0.0 0.0 0.0 +Ta 0.0 1.45 2.9 0.0 0.0 0.0 +Ta 0.0 4.35 2.9 0.0 0.0 0.0 +Ta 2.9 0.0 1.45 0.0 0.0 0.0 +Ta 2.9 0.0 4.35 0.0 0.0 0.0 +8 +Lattice = "5.9 0.0 0.0 0.0 5.9 0.0 0.0 0.0 5.9" Properties=species:S:1:pos:R:3:forces:R:3 energy=-87.211997 stress="-328516.14999999997 -0.0 0.0 -0.0 -328516.14999999997 0.0 0.0 0.0 -328516.14999999997" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.95 2.95 2.95 0.0 0.0 0.0 +Ta 1.475 2.95 0.0 0.0 0.0 0.0 +Ta 4.425 2.95 0.0 0.0 0.0 0.0 +Ta 0.0 1.475 2.95 0.0 0.0 0.0 +Ta 0.0 4.425 2.95 0.0 0.0 0.0 +Ta 2.95 0.0 1.475 0.0 0.0 0.0 +Ta 2.95 0.0 4.425 0.0 0.0 0.0 +8 +Lattice = "5.5 0.0 0.0 0.0 5.5 0.0 0.0 0.0 5.5" Properties=species:S:1:pos:R:3:forces:R:3 energy=-93.66897 stress="-164011.68000000002 -0.0 0.0 -0.0 -164011.68000000002 0.0 0.0 0.0 -164011.68000000002" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.75 2.75 2.75 0.0 0.0 0.0 +Ta 1.375 2.75 0.0 0.0 0.0 0.0 +Ta 4.125 2.75 0.0 0.0 0.0 0.0 +Ta 0.0 1.375 2.75 0.0 0.0 0.0 +Ta 0.0 4.125 2.75 0.0 0.0 0.0 +Ta 2.75 0.0 1.375 0.0 0.0 0.0 +Ta 2.75 0.0 4.125 0.0 0.0 0.0 +8 +Lattice = "4.1 0.0 0.0 0.0 4.1 0.0 0.0 0.0 4.1" Properties=species:S:1:pos:R:3:forces:R:3 energy=-7.989166 stress="6580211.09 0.0 0.0 0.0 6580211.09 0.0 0.0 0.0 6580211.09" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.05 2.05 2.05 0.0 0.0 0.0 +Ta 1.025 2.05 0.0 0.0 0.0 0.0 +Ta 3.075 2.05 0.0 0.0 0.0 0.0 +Ta 0.0 1.025 2.05 0.0 0.0 0.0 +Ta 0.0 3.075 2.05 0.0 0.0 0.0 +Ta 2.05 0.0 1.025 0.0 0.0 0.0 +Ta 2.05 0.0 3.075 0.0 0.0 0.0 +8 +Lattice = "6.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3:forces:R:3 energy=-84.982834 stress="-342905.56 0.0 -0.0 0.0 -342905.56 -0.0 -0.0 -0.0 -342905.56" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 3.0 3.0 3.0 0.0 0.0 0.0 +Ta 1.5 3.0 0.0 0.0 0.0 0.0 +Ta 4.5 3.0 0.0 0.0 0.0 0.0 +Ta 0.0 1.5 3.0 0.0 0.0 0.0 +Ta 0.0 4.5 3.0 0.0 0.0 0.0 +Ta 3.0 0.0 1.5 0.0 0.0 0.0 +Ta 3.0 0.0 4.5 0.0 0.0 0.0 +8 +Lattice = "5.6 0.0 0.0 0.0 5.6 0.0 0.0 0.0 5.6" Properties=species:S:1:pos:R:3:forces:R:3 energy=-92.536373 stress="-225855.3 0.0 -0.0 0.0 -225855.3 0.0 -0.0 0.0 -225855.3" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.8 2.8 2.8 0.0 0.0 0.0 +Ta 1.4 2.8 0.0 0.0 0.0 0.0 +Ta 4.2 2.8 0.0 0.0 0.0 0.0 +Ta 0.0 1.4 2.8 0.0 0.0 0.0 +Ta 0.0 4.2 2.8 0.0 0.0 0.0 +Ta 2.8 0.0 1.4 0.0 0.0 0.0 +Ta 2.8 0.0 4.2 0.0 0.0 0.0 +8 +Lattice = "4.2 0.0 0.0 0.0 4.2 0.0 0.0 0.0 4.2" Properties=species:S:1:pos:R:3:forces:R:3 energy=-26.77612 stress="5138714.33 -0.0 -0.0 -0.0 5138714.33 0.0 -0.0 0.0 5138714.33" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.1 2.1 2.1 0.0 0.0 0.0 +Ta 1.05 2.1 0.0 0.0 0.0 0.0 +Ta 3.15 2.1 0.0 0.0 0.0 0.0 +Ta 0.0 1.05 2.1 0.0 0.0 0.0 +Ta 0.0 3.15 2.1 0.0 0.0 0.0 +Ta 2.1 0.0 1.05 0.0 0.0 0.0 +Ta 2.1 0.0 3.15 0.0 0.0 0.0 +8 +Lattice = "6.3 0.0 0.0 0.0 6.3 0.0 0.0 0.0 6.3" Properties=species:S:1:pos:R:3:forces:R:3 energy=-77.544107 stress="-349968.45 0.0 0.0 0.0 -349968.45 0.0 0.0 0.0 -349968.45" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 3.15 3.15 3.15 0.0 0.0 0.0 +Ta 1.575 3.15 0.0 0.0 0.0 0.0 +Ta 4.725 3.15 0.0 0.0 0.0 0.0 +Ta 0.0 1.575 3.15 0.0 0.0 0.0 +Ta 0.0 4.725 3.15 0.0 0.0 0.0 +Ta 3.15 0.0 1.575 0.0 0.0 0.0 +Ta 3.15 0.0 4.725 0.0 0.0 0.0 +8 +Lattice = "6.2 0.0 0.0 0.0 6.2 0.0 0.0 0.0 6.2" Properties=species:S:1:pos:R:3:forces:R:3 energy=-80.114217 stress="-352410.12 0.0 0.0 0.0 -352410.12 0.0 0.0 0.0 -352410.12" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 3.1 3.1 3.1 0.0 0.0 0.0 +Ta 1.55 3.1 0.0 0.0 0.0 0.0 +Ta 4.65 3.1 0.0 0.0 0.0 0.0 +Ta 0.0 1.55 3.1 0.0 0.0 0.0 +Ta 0.0 4.65 3.1 0.0 0.0 0.0 +Ta 3.1 0.0 1.55 0.0 0.0 0.0 +Ta 3.1 0.0 4.65 0.0 0.0 0.0 +8 +Lattice = "4.3 0.0 0.0 0.0 4.3 0.0 0.0 0.0 4.3" Properties=species:S:1:pos:R:3:forces:R:3 energy=-42.143041 stress="4001608.1 -0.0 -0.0 -0.0 4001608.1 -0.0 -0.0 -0.0 4001608.1" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.15 2.15 2.15 0.0 0.0 0.0 +Ta 1.075 2.15 0.0 0.0 0.0 0.0 +Ta 3.225 2.15 0.0 0.0 0.0 0.0 +Ta 0.0 1.075 2.15 0.0 0.0 0.0 +Ta 0.0 3.225 2.15 0.0 0.0 0.0 +Ta 2.15 0.0 1.075 0.0 0.0 0.0 +Ta 2.15 0.0 3.225 0.0 0.0 0.0 +8 +Lattice = "5.7 0.0 0.0 0.0 5.7 0.0 0.0 0.0 5.7" Properties=species:S:1:pos:R:3:forces:R:3 energy=-91.040671 stress="-272236.58 -0.0 0.0 -0.0 -272236.58 -0.0 0.0 -0.0 -272236.58" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.85 2.85 2.85 0.0 0.0 0.0 +Ta 1.425 2.85 0.0 0.0 0.0 0.0 +Ta 4.275 2.85 0.0 0.0 0.0 0.0 +Ta 0.0 1.425 2.85 0.0 0.0 0.0 +Ta 0.0 4.275 2.85 0.0 0.0 0.0 +Ta 2.85 0.0 1.425 0.0 0.0 0.0 +Ta 2.85 0.0 4.275 0.0 0.0 0.0 +8 +Lattice = "4.8 0.0 0.0 0.0 4.8 0.0 0.0 0.0 4.8" Properties=species:S:1:pos:R:3:forces:R:3 energy=-84.499231 stress="1025744.96 -0.0 -0.0 -0.0 1025744.96 -0.0 -0.0 -0.0 1025744.96" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.4 2.4 2.4 0.0 0.0 0.0 +Ta 1.2 2.4 0.0 0.0 0.0 0.0 +Ta 3.6 2.4 0.0 0.0 0.0 0.0 +Ta 0.0 1.2 2.4 0.0 0.0 0.0 +Ta 0.0 3.6 2.4 0.0 0.0 0.0 +Ta 2.4 0.0 1.2 0.0 0.0 0.0 +Ta 2.4 0.0 3.6 0.0 0.0 0.0 +8 +Lattice = "6.9 0.0 0.0 0.0 6.9 0.0 0.0 0.0 6.9" Properties=species:S:1:pos:R:3:forces:R:3 energy=-61.825173 stress="-284789.87 -0.0 -0.0 -0.0 -284789.87 -0.0 -0.0 -0.0 -284789.87" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 3.45 3.45 3.45 0.0 0.0 0.0 +Ta 1.725 3.45 0.0 0.0 0.0 0.0 +Ta 5.175 3.45 0.0 0.0 0.0 0.0 +Ta 0.0 1.725 3.45 0.0 0.0 0.0 +Ta 0.0 5.175 3.45 0.0 0.0 0.0 +Ta 3.45 0.0 1.725 0.0 0.0 0.0 +Ta 3.45 0.0 5.175 0.0 0.0 0.0 +8 +Lattice = "5.0 0.0 0.0 0.0 5.0 0.0 0.0 0.0 5.0" Properties=species:S:1:pos:R:3:forces:R:3 energy=-91.156873 stress="496748.23 -0.0 0.0 -0.0 496748.23 0.0 0.0 0.0 496748.23" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.5 2.5 2.5 0.0 0.0 0.0 +Ta 1.25 2.5 0.0 0.0 0.0 0.0 +Ta 3.75 2.5 0.0 0.0 0.0 0.0 +Ta 0.0 1.25 2.5 0.0 0.0 0.0 +Ta 0.0 3.75 2.5 0.0 0.0 0.0 +Ta 2.5 0.0 1.25 0.0 0.0 0.0 +Ta 2.5 0.0 3.75 0.0 0.0 0.0 +8 +Lattice = "4.4 0.0 0.0 0.0 4.4 0.0 0.0 0.0 4.4" Properties=species:S:1:pos:R:3:forces:R:3 energy=-54.658744 stress="3103602.33 0.0 -0.0 0.0 3103602.33 -0.0 -0.0 -0.0 3103602.33" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.2 2.2 2.2 0.0 0.0 0.0 +Ta 1.1 2.2 0.0 0.0 0.0 0.0 +Ta 3.3 2.2 0.0 0.0 0.0 0.0 +Ta 0.0 1.1 2.2 0.0 0.0 0.0 +Ta 0.0 3.3 2.2 0.0 0.0 0.0 +Ta 2.2 0.0 1.1 0.0 0.0 0.0 +Ta 2.2 0.0 3.3 0.0 0.0 0.0 +8 +Lattice = "6.5 0.0 0.0 0.0 6.5 0.0 0.0 0.0 6.5" Properties=species:S:1:pos:R:3:forces:R:3 energy=-72.277255 stress="-335267.83999999997 -0.0 -0.0 -0.0 -335267.83999999997 -0.0 -0.0 -0.0 -335267.83999999997" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 3.25 3.25 3.25 0.0 0.0 0.0 +Ta 1.625 3.25 0.0 0.0 0.0 0.0 +Ta 4.875 3.25 0.0 0.0 0.0 0.0 +Ta 0.0 1.625 3.25 0.0 0.0 0.0 +Ta 0.0 4.875 3.25 0.0 0.0 0.0 +Ta 3.25 0.0 1.625 0.0 0.0 0.0 +Ta 3.25 0.0 4.875 0.0 0.0 0.0 +8 +Lattice = "6.4 0.0 0.0 0.0 6.4 0.0 0.0 0.0 6.4" Properties=species:S:1:pos:R:3:forces:R:3 energy=-74.923334 stress="-344004.72000000003 -0.0 -0.0 -0.0 -344004.72000000003 -0.0 -0.0 -0.0 -344004.72000000003" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 3.2 3.2 3.2 0.0 0.0 0.0 +Ta 1.6 3.2 0.0 0.0 0.0 0.0 +Ta 4.8 3.2 0.0 0.0 0.0 0.0 +Ta 0.0 1.6 3.2 0.0 0.0 0.0 +Ta 0.0 4.8 3.2 0.0 0.0 0.0 +Ta 3.2 0.0 1.6 0.0 0.0 0.0 +Ta 3.2 0.0 4.8 0.0 0.0 0.0 +8 +Lattice = "4.5 0.0 0.0 0.0 4.5 0.0 0.0 0.0 4.5" Properties=species:S:1:pos:R:3:forces:R:3 energy=-64.798066 stress="2398125.0500000003 0.0 0.0 0.0 2398125.0500000003 0.0 0.0 0.0 2398125.0500000003" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.25 2.25 2.25 0.0 0.0 0.0 +Ta 1.125 2.25 0.0 0.0 0.0 0.0 +Ta 3.375 2.25 0.0 0.0 0.0 0.0 +Ta 0.0 1.125 2.25 0.0 0.0 0.0 +Ta 0.0 3.375 2.25 0.0 0.0 0.0 +Ta 2.25 0.0 1.125 0.0 0.0 0.0 +Ta 2.25 0.0 3.375 0.0 0.0 0.0 +8 +Lattice = "5.1 0.0 0.0 0.0 5.1 0.0 0.0 0.0 5.1" Properties=species:S:1:pos:R:3:forces:R:3 energy=-93.048342 stress="302698.75 0.0 -0.0 0.0 302698.75 -0.0 -0.0 -0.0 302698.75" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.55 2.55 2.55 0.0 0.0 0.0 +Ta 1.275 2.55 0.0 0.0 0.0 0.0 +Ta 3.825 2.55 0.0 0.0 0.0 0.0 +Ta 0.0 1.275 2.55 0.0 0.0 0.0 +Ta 0.0 3.825 2.55 0.0 0.0 0.0 +Ta 2.55 0.0 1.275 0.0 0.0 0.0 +Ta 2.55 0.0 3.825 0.0 0.0 0.0 +8 +Lattice = "6.8 0.0 0.0 0.0 6.8 0.0 0.0 0.0 6.8" Properties=species:S:1:pos:R:3:forces:R:3 energy=-64.38702 stress="-298814.67 0.0 0.0 0.0 -298814.67 0.0 0.0 0.0 -298814.67" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 3.4 3.4 3.4 0.0 0.0 0.0 +Ta 1.7 3.4 0.0 0.0 0.0 0.0 +Ta 5.1 3.4 0.0 0.0 0.0 0.0 +Ta 0.0 1.7 3.4 0.0 0.0 0.0 +Ta 0.0 5.1 3.4 0.0 0.0 0.0 +Ta 3.4 0.0 1.7 0.0 0.0 0.0 +Ta 3.4 0.0 5.1 0.0 0.0 0.0 +8 +Lattice = "4.9 0.0 0.0 0.0 4.9 0.0 0.0 0.0 4.9" Properties=species:S:1:pos:R:3:forces:R:3 energy=-88.352871 stress="734688.7400000001 0.0 0.0 0.0 734688.7400000001 -0.0 0.0 -0.0 734688.7400000001" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.45 2.45 2.45 0.0 0.0 0.0 +Ta 1.225 2.45 0.0 0.0 0.0 0.0 +Ta 3.675 2.45 0.0 0.0 0.0 0.0 +Ta 0.0 1.225 2.45 0.0 0.0 0.0 +Ta 0.0 3.675 2.45 0.0 0.0 0.0 +Ta 2.45 0.0 1.225 0.0 0.0 0.0 +Ta 2.45 0.0 3.675 0.0 0.0 0.0 diff --git a/examples/PACKAGES/pod/Ta/XYZ/Volume_BCC.xyz b/examples/PACKAGES/pod/Ta/XYZ/Volume_BCC.xyz new file mode 100644 index 0000000000..1a43270892 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/XYZ/Volume_BCC.xyz @@ -0,0 +1,84 @@ +2 +Lattice = "4.2 0.0 0.0 0.0 4.2 0.0 0.0 0.0 4.2" Properties=species:S:1:pos:R:3:forces:R:3 energy=-16.763625 stress="-315811.75 0.0 0.0 0.0 -315811.75 0.0 0.0 0.0 -315811.75" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.1 2.1 2.1 0.0 0.0 0.0 +2 +Lattice = "2.4 0.0 0.0 0.0 2.4 0.0 0.0 0.0 2.4" Properties=species:S:1:pos:R:3:forces:R:3 energy=16.314145 stress="13221145.45 0.0 -0.0 0.0 13221145.45 0.0 -0.0 0.0 13221145.45" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.2 1.2 1.2 0.0 0.0 0.0 +2 +Lattice = "3.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 3.0" Properties=species:S:1:pos:R:3:forces:R:3 energy=-21.209071 stress="1054433.87 -0.0 0.0 -0.0 1054433.87 -0.0 0.0 -0.0 1054433.87" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.5 1.5 1.5 0.0 0.0 0.0 +2 +Lattice = "2.8 0.0 0.0 0.0 2.8 0.0 0.0 0.0 2.8" Properties=species:S:1:pos:R:3:forces:R:3 energy=-15.780524 stress="2609201.0100000002 0.0 -0.0 0.0 2609201.0100000002 0.0 -0.0 0.0 2609201.0100000002" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.4 1.4 1.4 0.0 0.0 0.0 +2 +Lattice = "2.9 0.0 0.0 0.0 2.9 0.0 0.0 0.0 2.9" Properties=species:S:1:pos:R:3:forces:R:3 energy=-19.002205 stress="1696212.8900000001 0.0 0.0 0.0 1696212.8900000001 0.0 0.0 0.0 1696212.8900000001" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.45 1.45 1.45 0.0 0.0 0.0 +2 +Lattice = "3.1 0.0 0.0 0.0 3.1 0.0 0.0 0.0 3.1" Properties=species:S:1:pos:R:3:forces:R:3 energy=-22.620568 stress="596204.8200000001 0.0 0.0 0.0 596204.8200000001 0.0 0.0 0.0 596204.8200000001" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.55 1.55 1.55 0.0 0.0 0.0 +2 +Lattice = "2.5 0.0 0.0 0.0 2.5 0.0 0.0 0.0 2.5" Properties=species:S:1:pos:R:3:forces:R:3 energy=4.096885 stress="8866538.459999999 0.0 0.0 0.0 8866538.459999999 -0.0 0.0 -0.0 8866538.459999999" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.25 1.25 1.25 0.0 0.0 0.0 +2 +Lattice = "2.2 0.0 0.0 0.0 2.2 0.0 0.0 0.0 2.2" Properties=species:S:1:pos:R:3:forces:R:3 energy=56.26276 stress="29925857.27 -0.0 -0.0 -0.0 29925857.27 -0.0 -0.0 -0.0 29925857.27" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.1 1.1 1.1 0.0 0.0 0.0 +2 +Lattice = "3.6 0.0 0.0 0.0 3.6 0.0 0.0 0.0 3.6" Properties=species:S:1:pos:R:3:forces:R:3 energy=-22.585113 stress="-294769.07 0.0 0.0 0.0 -294769.07 0.0 0.0 0.0 -294769.07" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.8 1.8 1.8 0.0 0.0 0.0 +2 +Lattice = "3.7 0.0 0.0 0.0 3.7 0.0 0.0 0.0 3.7" Properties=species:S:1:pos:R:3:forces:R:3 energy=-21.795501 stress="-334343.07 0.0 0.0 0.0 -334343.07 -0.0 0.0 -0.0 -334343.07" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.85 1.85 1.85 0.0 0.0 0.0 +2 +Lattice = "2.3 0.0 0.0 0.0 2.3 0.0 0.0 0.0 2.3" Properties=species:S:1:pos:R:3:forces:R:3 energy=33.110078 stress="19804876.43 0.0 0.0 0.0 19804876.43 -0.0 0.0 -0.0 19804876.43" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.15 1.15 1.15 0.0 0.0 0.0 +2 +Lattice = "3.8 0.0 0.0 0.0 3.8 0.0 0.0 0.0 3.8" Properties=species:S:1:pos:R:3:forces:R:3 energy=-20.885998 stress="-353363.87 -0.0 0.0 -0.0 -353363.87 -0.0 0.0 -0.0 -353363.87" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.9 1.9 1.9 0.0 0.0 0.0 +2 +Lattice = "3.4 0.0 0.0 0.0 3.4 0.0 0.0 0.0 3.4" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.601336 stress="-119086.12999999999 0.0 -0.0 0.0 -119086.12999999999 0.0 -0.0 0.0 -119086.12999999999" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.7 1.7 1.7 0.0 0.0 0.0 +2 +Lattice = "3.5 0.0 0.0 0.0 3.5 0.0 0.0 0.0 3.5" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.207313 stress="-226389.97 0.0 -0.0 0.0 -226389.97 0.0 -0.0 0.0 -226389.97" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.75 1.75 1.75 0.0 0.0 0.0 +2 +Lattice = "3.9 0.0 0.0 0.0 3.9 0.0 0.0 0.0 3.9" Properties=species:S:1:pos:R:3:forces:R:3 energy=-19.898089 stress="-356527.42 0.0 -0.0 0.0 -356527.42 0.0 -0.0 0.0 -356527.42" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.95 1.95 1.95 0.0 0.0 0.0 +2 +Lattice = "3.2 0.0 0.0 0.0 3.2 0.0 0.0 0.0 3.2" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.405474 stress="270245.51 -0.0 0.0 -0.0 270245.51 -0.0 0.0 -0.0 270245.51" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.6 1.6 1.6 0.0 0.0 0.0 +2 +Lattice = "2.6 0.0 0.0 0.0 2.6 0.0 0.0 0.0 2.6" Properties=species:S:1:pos:R:3:forces:R:3 energy=-4.781324 stress="5944705.43 -0.0 0.0 -0.0 5944705.43 -0.0 0.0 -0.0 5944705.43" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.3 1.3 1.3 0.0 0.0 0.0 +2 +Lattice = "4.0 0.0 0.0 0.0 4.0 0.0 0.0 0.0 4.0" Properties=species:S:1:pos:R:3:forces:R:3 energy=-18.864936 stress="-349512.61 -0.0 -0.0 -0.0 -349512.61 0.0 -0.0 0.0 -349512.61" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.0 2.0 2.0 0.0 0.0 0.0 +2 +Lattice = "4.1 0.0 0.0 0.0 4.1 0.0 0.0 0.0 4.1" Properties=species:S:1:pos:R:3:forces:R:3 energy=-17.813086 stress="-334971.81 0.0 0.0 0.0 -334971.81 0.0 0.0 0.0 -334971.81" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.05 2.05 2.05 0.0 0.0 0.0 +2 +Lattice = "2.7 0.0 0.0 0.0 2.7 0.0 0.0 0.0 2.7" Properties=species:S:1:pos:R:3:forces:R:3 energy=-11.197201 stress="3964027.36 0.0 0.0 0.0 3964027.36 0.0 0.0 0.0 3964027.36" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.35 1.35 1.35 0.0 0.0 0.0 +2 +Lattice = "3.3 0.0 0.0 0.0 3.3 0.0 0.0 0.0 3.3" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.696705 stress="39945.84 -0.0 -0.0 -0.0 39945.84 0.0 -0.0 0.0 39945.84" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.65 1.65 1.65 0.0 0.0 0.0 diff --git a/examples/PACKAGES/pod/Ta/XYZ/Volume_FCC.xyz b/examples/PACKAGES/pod/Ta/XYZ/Volume_FCC.xyz new file mode 100644 index 0000000000..48c577b507 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/XYZ/Volume_FCC.xyz @@ -0,0 +1,186 @@ +4 +Lattice = "3.4 0.0 0.0 0.0 3.4 0.0 0.0 0.0 3.4" Properties=species:S:1:pos:R:3:forces:R:3 energy=-19.075994 stress="4059178.91 0.0 -0.0 0.0 4059178.91 0.0 -0.0 0.0 4059178.91" +Ta 0.0 0.0 0.0 0 0 0 +Ta 1.7 1.7 0.0 0 0 0 +Ta 1.7 0.0 1.7 0 0 0 +Ta 0.0 1.7 1.7 0 0 0 +4 +Lattice = "5.2 0.0 0.0 0.0 5.2 0.0 0.0 0.0 5.2" Properties=species:S:1:pos:R:3:forces:R:3 energy=-34.873619 stress="-326647.94999999995 0.0 0.0 0.0 -326647.94999999995 -0.0 0.0 -0.0 -326647.94999999995" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.6 2.6 0.0 0.0 0.0 0.0 +Ta 2.6 0.0 2.6 0.0 0.0 0.0 +Ta 0.0 2.6 2.6 0.0 0.0 0.0 +4 +Lattice = "4.6 0.0 0.0 0.0 4.6 0.0 0.0 0.0 4.6" Properties=species:S:1:pos:R:3:forces:R:3 energy=-43.950003 stress="-296256.79000000004 -0.0 -0.0 -0.0 -296256.79000000004 0.0 -0.0 0.0 -296256.79000000004" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.3 2.3 0.0 0.0 0.0 0.0 +Ta 2.3 0.0 2.3 0.0 0.0 0.0 +Ta 0.0 2.3 2.3 0.0 0.0 0.0 +4 +Lattice = "3.8 0.0 0.0 0.0 3.8 0.0 0.0 0.0 3.8" Properties=species:S:1:pos:R:3:forces:R:3 energy=-40.991909 stress="1079302.71 0.0 0.0 0.0 1079302.71 0.0 0.0 0.0 1079302.71" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.9 1.9 0.0 0.0 0.0 0.0 +Ta 1.9 0.0 1.9 0.0 0.0 0.0 +Ta 0.0 1.9 1.9 0.0 0.0 0.0 +4 +Lattice = "3.9 0.0 0.0 0.0 3.9 0.0 0.0 0.0 3.9" Properties=species:S:1:pos:R:3:forces:R:3 energy=-43.453929 stress="713769.5499999999 0.0 0.0 0.0 713769.5499999999 -0.0 0.0 -0.0 713769.5499999999" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.95 1.95 0.0 0.0 0.0 0.0 +Ta 1.95 0.0 1.95 0.0 0.0 0.0 +Ta 0.0 1.95 1.95 0.0 0.0 0.0 +4 +Lattice = "4.7 0.0 0.0 0.0 4.7 0.0 0.0 0.0 4.7" Properties=species:S:1:pos:R:3:forces:R:3 energy=-42.686077 stress="-325547.88 0.0 0.0 0.0 -325547.88 0.0 0.0 0.0 -325547.88" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.35 2.35 0.0 0.0 0.0 0.0 +Ta 2.35 0.0 2.35 0.0 0.0 0.0 +Ta 0.0 2.35 2.35 0.0 0.0 0.0 +4 +Lattice = "5.3 0.0 0.0 0.0 5.3 0.0 0.0 0.0 5.3" Properties=species:S:1:pos:R:3:forces:R:3 energy=-33.224653 stress="-312088.68 0.0 0.0 0.0 -312088.68 0.0 0.0 0.0 -312088.68" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.65 2.65 0.0 0.0 0.0 0.0 +Ta 2.65 0.0 2.65 0.0 0.0 0.0 +Ta 0.0 2.65 2.65 0.0 0.0 0.0 +4 +Lattice = "3.5 0.0 0.0 0.0 3.5 0.0 0.0 0.0 3.5" Properties=species:S:1:pos:R:3:forces:R:3 energy=-26.862709 stress="2990127.38 0.0 0.0 0.0 2990127.38 -0.0 0.0 -0.0 2990127.38" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.75 1.75 0.0 0.0 0.0 0.0 +Ta 1.75 0.0 1.75 0.0 0.0 0.0 +Ta 0.0 1.75 1.75 0.0 0.0 0.0 +4 +Lattice = "5.8 0.0 0.0 0.0 5.8 0.0 0.0 0.0 5.8" Properties=species:S:1:pos:R:3:forces:R:3 energy=-25.519883 stress="-222839.06 0.0 -0.0 0.0 -222839.06 -0.0 -0.0 -0.0 -222839.06" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.9 2.9 0.0 0.0 0.0 0.0 +Ta 2.9 0.0 2.9 0.0 0.0 0.0 +Ta 0.0 2.9 2.9 0.0 0.0 0.0 +4 +Lattice = "3.2 0.0 0.0 0.0 3.2 0.0 0.0 0.0 3.2" Properties=species:S:1:pos:R:3:forces:R:3 energy=3.463071 stress="7429287.470000001 0.0 -0.0 0.0 7429287.470000001 -0.0 -0.0 -0.0 7429287.470000001" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.6 1.6 0.0 0.0 0.0 0.0 +Ta 1.6 0.0 1.6 0.0 0.0 0.0 +Ta 0.0 1.6 1.6 0.0 0.0 0.0 +4 +Lattice = "5.4 0.0 0.0 0.0 5.4 0.0 0.0 0.0 5.4" Properties=species:S:1:pos:R:3:forces:R:3 energy=-31.59595 stress="-295489.55 0.0 0.0 0.0 -295489.55 -0.0 0.0 -0.0 -295489.55" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.7 2.7 0.0 0.0 0.0 0.0 +Ta 2.7 0.0 2.7 0.0 0.0 0.0 +Ta 0.0 2.7 2.7 0.0 0.0 0.0 +4 +Lattice = "4.0 0.0 0.0 0.0 4.0 0.0 0.0 0.0 4.0" Properties=species:S:1:pos:R:3:forces:R:3 energy=-45.100466 stress="426831.86 0.0 -0.0 0.0 426831.86 0.0 -0.0 0.0 426831.86" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.0 2.0 0.0 0.0 0.0 0.0 +Ta 2.0 0.0 2.0 0.0 0.0 0.0 +Ta 0.0 2.0 2.0 0.0 0.0 0.0 +4 +Lattice = "4.1 0.0 0.0 0.0 4.1 0.0 0.0 0.0 4.1" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.052258 stress="204707.15999999997 -0.0 0.0 -0.0 204707.15999999997 -0.0 0.0 -0.0 204707.15999999997" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.05 2.05 0.0 0.0 0.0 0.0 +Ta 2.05 0.0 2.05 0.0 0.0 0.0 +Ta 0.0 2.05 2.05 0.0 0.0 0.0 +4 +Lattice = "5.5 0.0 0.0 0.0 5.5 0.0 0.0 0.0 5.5" Properties=species:S:1:pos:R:3:forces:R:3 energy=-30.001189 stress="-277646.68 0.0 0.0 0.0 -277646.68 -0.0 0.0 -0.0 -277646.68" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.75 2.75 0.0 0.0 0.0 0.0 +Ta 2.75 0.0 2.75 0.0 0.0 0.0 +Ta 0.0 2.75 2.75 0.0 0.0 0.0 +4 +Lattice = "6.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3:forces:R:3 energy=-22.8504 stress="-187574.33000000002 -0.0 -0.0 -0.0 -187574.33000000002 0.0 -0.0 0.0 -187574.33000000002" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 3.0 3.0 0.0 0.0 0.0 0.0 +Ta 3.0 0.0 3.0 0.0 0.0 0.0 +Ta 0.0 3.0 3.0 0.0 0.0 0.0 +4 +Lattice = "3.3 0.0 0.0 0.0 3.3 0.0 0.0 0.0 3.3" Properties=species:S:1:pos:R:3:forces:R:3 energy=-9.164691 stress="5458905.82 0.0 -0.0 0.0 5458905.82 0.0 -0.0 0.0 5458905.82" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.65 1.65 0.0 0.0 0.0 0.0 +Ta 1.65 0.0 1.65 0.0 0.0 0.0 +Ta 0.0 1.65 1.65 0.0 0.0 0.0 +4 +Lattice = "5.9 0.0 0.0 0.0 5.9 0.0 0.0 0.0 5.9" Properties=species:S:1:pos:R:3:forces:R:3 energy=-24.150343 stress="-204945.0 0.0 -0.0 0.0 -204945.0 0.0 -0.0 0.0 -204945.0" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.95 2.95 0.0 0.0 0.0 0.0 +Ta 2.95 0.0 2.95 0.0 0.0 0.0 +Ta 0.0 2.95 2.95 0.0 0.0 0.0 +4 +Lattice = "4.2 0.0 0.0 0.0 4.2 0.0 0.0 0.0 4.2" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.426795 stress="36447.14 -0.0 0.0 -0.0 36447.14 -0.0 0.0 -0.0 36447.14" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.1 2.1 0.0 0.0 0.0 0.0 +Ta 2.1 0.0 2.1 0.0 0.0 0.0 +Ta 0.0 2.1 2.1 0.0 0.0 0.0 +4 +Lattice = "5.6 0.0 0.0 0.0 5.6 0.0 0.0 0.0 5.6" Properties=species:S:1:pos:R:3:forces:R:3 energy=-28.451145 stress="-259709.67 0.0 0.0 0.0 -259709.67 -0.0 0.0 -0.0 -259709.67" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.8 2.8 0.0 0.0 0.0 0.0 +Ta 2.8 0.0 2.8 0.0 0.0 0.0 +Ta 0.0 2.8 2.8 0.0 0.0 0.0 +4 +Lattice = "3.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 3.0" Properties=species:S:1:pos:R:3:forces:R:3 energy=40.341566 stress="13905054.1 0.0 0.0 0.0 13905054.1 0.0 0.0 0.0 13905054.1" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.5 1.5 0.0 0.0 0.0 0.0 +Ta 1.5 0.0 1.5 0.0 0.0 0.0 +Ta 0.0 1.5 1.5 0.0 0.0 0.0 +4 +Lattice = "3.1 0.0 0.0 0.0 3.1 0.0 0.0 0.0 3.1" Properties=species:S:1:pos:R:3:forces:R:3 energy=19.617912 stress="10138102.870000001 -0.0 0.0 -0.0 10138102.870000001 -0.0 0.0 -0.0 10138102.870000001" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.55 1.55 0.0 0.0 0.0 0.0 +Ta 1.55 0.0 1.55 0.0 0.0 0.0 +Ta 0.0 1.55 1.55 0.0 0.0 0.0 +4 +Lattice = "5.7 0.0 0.0 0.0 5.7 0.0 0.0 0.0 5.7" Properties=species:S:1:pos:R:3:forces:R:3 energy=-26.954384 stress="-241322.06 0.0 -0.0 0.0 -241322.06 0.0 -0.0 0.0 -241322.06" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.85 2.85 0.0 0.0 0.0 0.0 +Ta 2.85 0.0 2.85 0.0 0.0 0.0 +Ta 0.0 2.85 2.85 0.0 0.0 0.0 +4 +Lattice = "4.3 0.0 0.0 0.0 4.3 0.0 0.0 0.0 4.3" Properties=species:S:1:pos:R:3:forces:R:3 energy=-46.323696 stress="-90447.06999999999 0.0 0.0 0.0 -90447.06999999999 -0.0 0.0 -0.0 -90447.06999999999" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.15 2.15 0.0 0.0 0.0 0.0 +Ta 2.15 0.0 2.15 0.0 0.0 0.0 +Ta 0.0 2.15 2.15 0.0 0.0 0.0 +4 +Lattice = "4.4 0.0 0.0 0.0 4.4 0.0 0.0 0.0 4.4" Properties=species:S:1:pos:R:3:forces:R:3 energy=-45.828947 stress="-183778.61 0.0 0.0 0.0 -183778.61 0.0 0.0 0.0 -183778.61" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.2 2.2 0.0 0.0 0.0 0.0 +Ta 2.2 0.0 2.2 0.0 0.0 0.0 +Ta 0.0 2.2 2.2 0.0 0.0 0.0 +4 +Lattice = "5.0 0.0 0.0 0.0 5.0 0.0 0.0 0.0 5.0" Properties=species:S:1:pos:R:3:forces:R:3 energy=-38.16029 stress="-345892.4 -0.0 -0.0 -0.0 -345892.4 0.0 -0.0 0.0 -345892.4" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.5 2.5 0.0 0.0 0.0 0.0 +Ta 2.5 0.0 2.5 0.0 0.0 0.0 +Ta 0.0 2.5 2.5 0.0 0.0 0.0 +4 +Lattice = "3.6 0.0 0.0 0.0 3.6 0.0 0.0 0.0 3.6" Properties=species:S:1:pos:R:3:forces:R:3 energy=-32.919741 stress="2180370.41 0.0 0.0 0.0 2180370.41 -0.0 0.0 -0.0 2180370.41" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.8 1.8 0.0 0.0 0.0 0.0 +Ta 1.8 0.0 1.8 0.0 0.0 0.0 +Ta 0.0 1.8 1.8 0.0 0.0 0.0 +4 +Lattice = "4.8 0.0 0.0 0.0 4.8 0.0 0.0 0.0 4.8" Properties=species:S:1:pos:R:3:forces:R:3 energy=-41.272675 stress="-341505.95 0.0 0.0 0.0 -341505.95 -0.0 0.0 -0.0 -341505.95" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.4 2.4 0.0 0.0 0.0 0.0 +Ta 2.4 0.0 2.4 0.0 0.0 0.0 +Ta 0.0 2.4 2.4 0.0 0.0 0.0 +4 +Lattice = "4.9 0.0 0.0 0.0 4.9 0.0 0.0 0.0 4.9" Properties=species:S:1:pos:R:3:forces:R:3 energy=-39.753322 stress="-347458.42 0.0 -0.0 0.0 -347458.42 0.0 -0.0 0.0 -347458.42" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.45 2.45 0.0 0.0 0.0 0.0 +Ta 2.45 0.0 2.45 0.0 0.0 0.0 +Ta 0.0 2.45 2.45 0.0 0.0 0.0 +4 +Lattice = "3.7 0.0 0.0 0.0 3.7 0.0 0.0 0.0 3.7" Properties=species:S:1:pos:R:3:forces:R:3 energy=-37.547435 stress="1562535.85 0.0 0.0 0.0 1562535.85 -0.0 0.0 -0.0 1562535.85" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 1.85 1.85 0.0 0.0 0.0 0.0 +Ta 1.85 0.0 1.85 0.0 0.0 0.0 +Ta 0.0 1.85 1.85 0.0 0.0 0.0 +4 +Lattice = "5.1 0.0 0.0 0.0 5.1 0.0 0.0 0.0 5.1" Properties=species:S:1:pos:R:3:forces:R:3 energy=-36.52595 stress="-338327.71 -0.0 -0.0 -0.0 -338327.71 0.0 -0.0 0.0 -338327.71" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.55 2.55 0.0 0.0 0.0 0.0 +Ta 2.55 0.0 2.55 0.0 0.0 0.0 +Ta 0.0 2.55 2.55 0.0 0.0 0.0 +4 +Lattice = "4.5 0.0 0.0 0.0 4.5 0.0 0.0 0.0 4.5" Properties=species:S:1:pos:R:3:forces:R:3 energy=-45.016087 stress="-250456.02 -0.0 -0.0 -0.0 -250456.02 0.0 -0.0 0.0 -250456.02" +Ta 0.0 0.0 0.0 0.0 0.0 0.0 +Ta 2.25 2.25 0.0 0.0 0.0 0.0 +Ta 2.25 0.0 2.25 0.0 0.0 0.0 +Ta 0.0 2.25 2.25 0.0 0.0 0.0 diff --git a/examples/PACKAGES/pod/Ta/in.fitpod b/examples/PACKAGES/pod/Ta/in.fitpod new file mode 100644 index 0000000000..7b932558ea --- /dev/null +++ b/examples/PACKAGES/pod/Ta/in.fitpod @@ -0,0 +1,5 @@ +# Demonstrate fitpod for POD potential + +units metal +fitpod Ta_param.pod Ta_data.pod + diff --git a/examples/PACKAGES/pod/Ta/in.pod b/examples/PACKAGES/pod/Ta/in.pod new file mode 100644 index 0000000000..866ee40549 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/in.pod @@ -0,0 +1,47 @@ +# Demonstrate POD Ta potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable ny equal ${nrep} +variable nz equal ${nrep} + +boundary p p p + +lattice bcc $a +region box block 0 ${nx} 0 ${ny} 0 ${nz} +create_box 1 box +create_atoms 1 box + +mass 1 180.88 + + +# POD potential +pair_style pod +pair_coeff * * Ta_param.pod Ta_coeff.pod Ta + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} + + diff --git a/examples/PACKAGES/pod/Ta/log.1Dec22.fitpod.g++.1 b/examples/PACKAGES/pod/Ta/log.1Dec22.fitpod.g++.1 new file mode 100644 index 0000000000..92bf7ede2d --- /dev/null +++ b/examples/PACKAGES/pod/Ta/log.1Dec22.fitpod.g++.1 @@ -0,0 +1,114 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate fitpod for POD potential + +units metal +fitpod Ta_param.pod Ta_data.pod +Reading potential file Ta_param.pod with DATE: 2022-11-30 +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body potential: 3 6 6 +three-body potential: 3 6 5 5 +four-body SNAP potential: 0 0 +quadratic POD potential: 0 +number of basis functions for one-body potential: 1 +number of basis functions for two-body potential: 6 +number of basis functions for three-body potential: 25 +number of basis functions for four-body potential: 0 +number of descriptors for one-body potential: 1 +number of descriptors for two-body potential: 6 +number of descriptors for three-body potential: 25 +number of descriptors for four-body potential: 0 +number of descriptors for quadratic POD potential: 0 +total number of descriptors for all potentials: 32 +**************** End of POD Potentials **************** + +**************** Begin of Data File **************** +file format: extxyz +file extension: xyz +path to training data set: XYZ +path to test data set: XYZ +training fraction: 1 +test fraction: 1 +randomize training data set: 1 +randomize test data set: 1 +error analysis for training data set: 1 +error analysis for test data set: 0 +energy/force calculation for training data set: 0 +energy/force calculation for test data set: 0 +fitting weight for energy: 100 +fitting weight for force: 1 +fitting weight for stress: 0 +**************** End of Data File **************** +**************** Begin of Training Data Set **************** +--------------------------------------------------------------- + data file | number of configurations | number of atoms +--------------------------------------------------------------- + Displaced_A15.xyz | 9 | 576 + Displaced_BCC.xyz | 9 | 486 + Displaced_FCC.xyz | 9 | 432 + Elastic_BCC.xyz | 100 | 200 + Elastic_FCC.xyz | 100 | 400 + GSF_110.xyz | 22 | 528 + GSF_112.xyz | 22 | 660 + Liquid.xyz | 3 | 300 + Surface.xyz | 7 | 236 + Volume_A15.xyz | 30 | 240 + Volume_BCC.xyz | 21 | 42 + Volume_FCC.xyz | 31 | 124 +--------------------------------------------------------------- +number of files: 12 +number of configurations in all files: 363 +number of atoms in all files: 4224 +minimum number of atoms: 2 +maximum number of atoms: 100 +**************** End of Training Data Set **************** +**************** Begin of Memory Allocation **************** +maximum number of atoms in periodic domain: 100 +maximum number of atoms in extended domain: 2700 +maximum number of neighbors in extended domain: 270000 +size of double memory: 223201 +size of int memory: 14709 +size of descriptor matrix: 32 x 32 +**************** End of Memory Allocation **************** +**************** Begin of Least-Squares Fitting **************** +Configuration: # 1 +Configuration: # 101 +Configuration: # 201 +Configuration: # 301 +**************** End of Least-Squares Fitting **************** +**************** Begin of Error Calculation **************** +Configuration: # 1 +Configuration: # 101 +Configuration: # 201 +Configuration: # 301 +**************** End of Error Calculation **************** +**************** Begin of Error Analysis for the Training Data Set **************** +--------------------------------------------------------------------------------------------------- + File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force +--------------------------------------------------------------------------------------------------- +Displaced_A15.xyz 9 576 0.011286 0.011334 0.113353 0.141650 +Displaced_BCC.xyz 9 486 0.012178 0.014005 0.240613 0.312191 +Displaced_FCC.xyz 9 432 0.001445 0.001591 0.082688 0.103800 +Elastic_BCC.xyz 100 200 0.004452 0.004783 0.000010 0.000013 +Elastic_FCC.xyz 100 400 0.002865 0.002923 0.000146 0.000207 +GSF_110.xyz 22 528 0.005804 0.006853 0.047276 0.097819 +GSF_112.xyz 22 660 0.010588 0.011555 0.123342 0.191090 +Liquid.xyz 3 300 0.013161 0.015355 0.567536 0.757847 +Surface.xyz 7 236 0.025400 0.037555 0.096121 0.295623 +Volume_A15.xyz 30 240 0.039281 0.048678 0.000000 0.000000 +Volume_BCC.xyz 21 42 0.049766 0.067554 0.000000 0.000000 +Volume_FCC.xyz 31 124 0.030056 0.041738 0.000000 0.000000 +--------------------------------------------------------------------------------------------------- +All files 363 4224 0.012917 0.025797 0.122473 0.260052 +--------------------------------------------------------------------------------------------------- +**************** End of Error Analysis for the Training Data Set **************** + +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/pod/Ta/log.1Dec22.fitpod.g++.4 b/examples/PACKAGES/pod/Ta/log.1Dec22.fitpod.g++.4 new file mode 100644 index 0000000000..698636c4ba --- /dev/null +++ b/examples/PACKAGES/pod/Ta/log.1Dec22.fitpod.g++.4 @@ -0,0 +1,114 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate fitpod for POD potential + +units metal +fitpod Ta_param.pod Ta_data.pod +Reading potential file Ta_param.pod with DATE: 2022-11-30 +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body potential: 3 6 6 +three-body potential: 3 6 5 5 +four-body SNAP potential: 0 0 +quadratic POD potential: 0 +number of basis functions for one-body potential: 1 +number of basis functions for two-body potential: 6 +number of basis functions for three-body potential: 25 +number of basis functions for four-body potential: 0 +number of descriptors for one-body potential: 1 +number of descriptors for two-body potential: 6 +number of descriptors for three-body potential: 25 +number of descriptors for four-body potential: 0 +number of descriptors for quadratic POD potential: 0 +total number of descriptors for all potentials: 32 +**************** End of POD Potentials **************** + +**************** Begin of Data File **************** +file format: extxyz +file extension: xyz +path to training data set: XYZ +path to test data set: XYZ +training fraction: 1 +test fraction: 1 +randomize training data set: 1 +randomize test data set: 1 +error analysis for training data set: 1 +error analysis for test data set: 0 +energy/force calculation for training data set: 0 +energy/force calculation for test data set: 0 +fitting weight for energy: 100 +fitting weight for force: 1 +fitting weight for stress: 0 +**************** End of Data File **************** +**************** Begin of Training Data Set **************** +--------------------------------------------------------------- + data file | number of configurations | number of atoms +--------------------------------------------------------------- + Displaced_A15.xyz | 9 | 576 + Displaced_BCC.xyz | 9 | 486 + Displaced_FCC.xyz | 9 | 432 + Elastic_BCC.xyz | 100 | 200 + Elastic_FCC.xyz | 100 | 400 + GSF_110.xyz | 22 | 528 + GSF_112.xyz | 22 | 660 + Liquid.xyz | 3 | 300 + Surface.xyz | 7 | 236 + Volume_A15.xyz | 30 | 240 + Volume_BCC.xyz | 21 | 42 + Volume_FCC.xyz | 31 | 124 +--------------------------------------------------------------- +number of files: 12 +number of configurations in all files: 363 +number of atoms in all files: 4224 +minimum number of atoms: 2 +maximum number of atoms: 100 +**************** End of Training Data Set **************** +**************** Begin of Memory Allocation **************** +maximum number of atoms in periodic domain: 100 +maximum number of atoms in extended domain: 2700 +maximum number of neighbors in extended domain: 270000 +size of double memory: 223201 +size of int memory: 14709 +size of descriptor matrix: 32 x 32 +**************** End of Memory Allocation **************** +**************** Begin of Least-Squares Fitting **************** +Configuration: # 1 +Configuration: # 101 +Configuration: # 201 +Configuration: # 301 +**************** End of Least-Squares Fitting **************** +**************** Begin of Error Calculation **************** +Configuration: # 1 +Configuration: # 101 +Configuration: # 201 +Configuration: # 301 +**************** End of Error Calculation **************** +**************** Begin of Error Analysis for the Training Data Set **************** +--------------------------------------------------------------------------------------------------- + File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force +--------------------------------------------------------------------------------------------------- +Displaced_A15.xyz 9 576 0.011286 0.011334 0.113353 0.141650 +Displaced_BCC.xyz 9 486 0.012178 0.014005 0.240613 0.312191 +Displaced_FCC.xyz 9 432 0.001445 0.001591 0.082688 0.103800 +Elastic_BCC.xyz 100 200 0.004452 0.004783 0.000010 0.000013 +Elastic_FCC.xyz 100 400 0.002865 0.002923 0.000146 0.000207 +GSF_110.xyz 22 528 0.005804 0.006853 0.047276 0.097819 +GSF_112.xyz 22 660 0.010588 0.011555 0.123342 0.191090 +Liquid.xyz 3 300 0.013161 0.015355 0.567536 0.757847 +Surface.xyz 7 236 0.025400 0.037555 0.096121 0.295623 +Volume_A15.xyz 30 240 0.039281 0.048678 0.000000 0.000000 +Volume_BCC.xyz 21 42 0.049766 0.067554 0.000000 0.000000 +Volume_FCC.xyz 31 124 0.030056 0.041738 0.000000 0.000000 +--------------------------------------------------------------------------------------------------- +All files 363 4224 0.012917 0.025797 0.122473 0.260052 +--------------------------------------------------------------------------------------------------- +**************** End of Error Analysis for the Training Data Set **************** + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pod/Ta/log.1Dec22.pod.g++.1 b/examples/PACKAGES/pod/Ta/log.1Dec22.pod.g++.1 new file mode 100644 index 0000000000..eceb9f5dec --- /dev/null +++ b/examples/PACKAGES/pod/Ta/log.1Dec22.pod.g++.1 @@ -0,0 +1,143 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate POD Ta potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.316 +Lattice spacing in x,y,z = 3.316 3.316 3.316 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 128 atoms + using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264) + create_atoms CPU = 0.000 seconds + +mass 1 180.88 + + +# POD potential +pair_style pod +pair_coeff * * Ta_param.pod Ta_coeff.pod Ta +Reading potential file Ta_param.pod with DATE: 2022-11-30 +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body potential: 3 6 6 +three-body potential: 3 6 5 5 +four-body SNAP potential: 0 0 +quadratic POD potential: 0 +number of basis functions for one-body potential: 1 +number of basis functions for two-body potential: 6 +number of basis functions for three-body potential: 25 +number of basis functions for four-body potential: 0 +number of descriptors for one-body potential: 1 +number of descriptors for two-body potential: 6 +number of descriptors for three-body potential: 25 +number of descriptors for four-body potential: 0 +number of descriptors for quadratic POD potential: 0 +total number of descriptors for all potentials: 32 +**************** End of POD Potentials **************** + + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair pod, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.082 | 3.082 | 3.082 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -11.841512 0 -11.803037 -15933.622 + 10 296.91721 -11.841117 0 -11.803037 -15691.904 + 20 287.83555 -11.839952 0 -11.803037 -14982.977 + 30 273.25574 -11.838082 0 -11.803037 -13853.44 + 40 253.98821 -11.835611 0 -11.803037 -12375.459 + 50 231.10664 -11.832676 0 -11.803037 -10639.774 + 60 205.8844 -11.829441 0 -11.803037 -8747.2222 + 70 179.71599 -11.826085 0 -11.803037 -6799.8371 + 80 154.02711 -11.822791 0 -11.803037 -4892.7805 + 90 130.17821 -11.819732 0 -11.803036 -3108.1226 + 100 109.36842 -11.817063 0 -11.803036 -1510.9592 +Loop time of 2.21355 on 1 procs for 100 steps with 128 atoms + +Performance: 1.952 ns/day, 12.298 hours/ns, 45.176 timesteps/s, 5.783 katom-step/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.2126 | 2.2126 | 2.2126 | 0.0 | 99.96 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00039011 | 0.00039011 | 0.00039011 | 0.0 | 0.02 +Output | 0.00018205 | 0.00018205 | 0.00018205 | 0.0 | 0.01 +Modify | 0.00014707 | 0.00014707 | 0.00014707 | 0.0 | 0.01 +Other | | 0.0002439 | | | 0.01 + +Nlocal: 128 ave 128 max 128 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 727 ave 727 max 727 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 7424 ave 7424 max 7424 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7424 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + + +Total wall time: 0:00:02 diff --git a/examples/PACKAGES/pod/Ta/log.1Dec22.pod.g++.4 b/examples/PACKAGES/pod/Ta/log.1Dec22.pod.g++.4 new file mode 100644 index 0000000000..ace3943c12 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/log.1Dec22.pod.g++.4 @@ -0,0 +1,143 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate POD Ta potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.316 +Lattice spacing in x,y,z = 3.316 3.316 3.316 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 128 atoms + using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264) + create_atoms CPU = 0.000 seconds + +mass 1 180.88 + + +# POD potential +pair_style pod +pair_coeff * * Ta_param.pod Ta_coeff.pod Ta +Reading potential file Ta_param.pod with DATE: 2022-11-30 +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body potential: 3 6 6 +three-body potential: 3 6 5 5 +four-body SNAP potential: 0 0 +quadratic POD potential: 0 +number of basis functions for one-body potential: 1 +number of basis functions for two-body potential: 6 +number of basis functions for three-body potential: 25 +number of basis functions for four-body potential: 0 +number of descriptors for one-body potential: 1 +number of descriptors for two-body potential: 6 +number of descriptors for three-body potential: 25 +number of descriptors for four-body potential: 0 +number of descriptors for quadratic POD potential: 0 +total number of descriptors for all potentials: 32 +**************** End of POD Potentials **************** + + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair pod, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.062 | 3.062 | 3.062 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -11.841512 0 -11.803037 -15933.622 + 10 296.91721 -11.841117 0 -11.803037 -15691.904 + 20 287.83555 -11.839952 0 -11.803037 -14982.977 + 30 273.25574 -11.838082 0 -11.803037 -13853.44 + 40 253.98821 -11.835611 0 -11.803037 -12375.459 + 50 231.10664 -11.832676 0 -11.803037 -10639.774 + 60 205.8844 -11.829441 0 -11.803037 -8747.2222 + 70 179.71599 -11.826085 0 -11.803037 -6799.8371 + 80 154.02711 -11.822791 0 -11.803037 -4892.7805 + 90 130.17821 -11.819732 0 -11.803036 -3108.1226 + 100 109.36842 -11.817063 0 -11.803036 -1510.9592 +Loop time of 0.638221 on 4 procs for 100 steps with 128 atoms + +Performance: 6.769 ns/day, 3.546 hours/ns, 156.686 timesteps/s, 20.056 katom-step/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.59009 | 0.60345 | 0.61657 | 1.3 | 94.55 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.020708 | 0.033858 | 0.047324 | 5.5 | 5.31 +Output | 0.00021209 | 0.00022669 | 0.00026379 | 0.0 | 0.04 +Modify | 0.00012321 | 0.00012709 | 0.00013646 | 0.0 | 0.02 +Other | | 0.00056 | | | 0.09 + +Nlocal: 32 ave 32 max 32 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 431 ave 431 max 431 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 1856 ave 1856 max 1856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7424 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pod/Ta_Quadratic/Ta_coefficients.pod b/examples/PACKAGES/pod/Ta_Quadratic/Ta_coefficients.pod new file mode 100644 index 0000000000..19a1263bff --- /dev/null +++ b/examples/PACKAGES/pod/Ta_Quadratic/Ta_coefficients.pod @@ -0,0 +1,183 @@ +POD_coefficients: 182 +-4.35181 +3.57833 +-2.25499 +-4.84612 +2.06319 +-1.17070 +0.23842 +9.17159 +36.02380 +16.65293 +-141.18389 +37.17631 +0.46029 +-9.76145 +-0.03678 +15.64520 +2.29801 +0.02143 +2.69734 +-0.35337 +0.51108 +-2.36290 +0.18617 +-0.13079 +1.02665 +0.21514 +0.08076 +-0.28347 +-0.45059 +-0.24762 +-1.13671 +-0.30577 +0.60504 +-0.31285 +0.10638 +0.06958 +0.21962 +0.10426 +0.80241 +11.41434 +10.26118 +0.03871 +-18.86071 +4.47376 +-1.76865 +0.92507 +-0.42650 +-0.35847 +0.56613 +0.79353 +5.65244 +-8.75326 +6.22216 +4.34659 +10.19995 +-6.53345 +7.16628 +-2.19246 +-5.90780 +-3.52168 +7.97278 +-0.21108 +-0.01016 +-0.01023 +-0.03088 +-0.10222 +0.05366 +0.08037 +-3.17607 +3.45670 +0.79279 +2.38325 +-0.69796 +1.44779 +-0.03351 +0.05645 +-0.01901 +0.01923 +0.05401 +0.02095 +1.45657 +-1.58808 +-1.41187 +-2.18121 +3.04892 +-1.09293 +3.03780 +-1.07247 +-0.50261 +-0.81151 +0.35996 +-0.64601 +-0.04245 +-0.00112 +0.02894 +-0.04382 +-0.06556 +-0.00052 +4.67527 +-0.11816 +-1.52428 +0.17075 +0.20231 +-0.36857 +0.61745 +-0.20190 +0.00816 +-0.16194 +-0.12948 +0.02136 +-2.19267 +-0.62508 +-0.20029 +0.27620 +-0.58116 +0.21791 +-1.82301 +0.32164 +0.64550 +0.11580 +-0.02438 +0.08056 +0.19537 +-0.04119 +-0.00323 +-0.06530 +-0.02547 +0.01404 +0.22333 +0.48190 +0.10715 +0.25684 +-0.65069 +0.31428 +-0.06946 +-0.11924 +-0.05467 +-0.12105 +-0.03980 +0.00295 +-2.14415 +-0.82347 +-0.23084 +0.24926 +-0.36679 +0.16710 +1.20411 +0.47757 +0.11104 +-0.09587 +0.03722 +-0.00309 +-0.29879 +0.06463 +0.10236 +0.02276 +-0.06012 +0.02985 +12.06878 +3.39996 +-0.85590 +0.77481 +-1.13392 +0.40511 +-0.08006 +0.07161 +0.05978 +0.02407 +-0.06031 +0.02307 +-10.24102 +-2.49354 +1.14053 +-0.70454 +0.99990 +-0.33863 +2.43470 +1.16557 +0.23708 +-0.03482 +-0.05280 +0.02735 diff --git a/examples/PACKAGES/pod/Ta_Quadratic/Ta_data.pod b/examples/PACKAGES/pod/Ta_Quadratic/Ta_data.pod new file mode 100644 index 0000000000..2aed5d60dd --- /dev/null +++ b/examples/PACKAGES/pod/Ta_Quadratic/Ta_data.pod @@ -0,0 +1,20 @@ +file_format extxyz +file_extension xyz + +path_to_training_data_set "../Ta/XYZ" +path_to_test_data_set "../Ta/XYZ" + +fitting_weight_energy 100.0 +fitting_weight_force 1.0 +fitting_regularization_parameter 1e-10 + +error_analysis_for_training_data_set 1 +error_analysis_for_test_data_set 0 + +# Add the following basename to the name of output files +basename_for_output_files Ta + +# number of digits after the decimal point for pod coefficients +precision_for_pod_coefficients 5 + + diff --git a/examples/PACKAGES/pod/Ta_Quadratic/Ta_param.pod b/examples/PACKAGES/pod/Ta_Quadratic/Ta_param.pod new file mode 100644 index 0000000000..adfe772d10 --- /dev/null +++ b/examples/PACKAGES/pod/Ta_Quadratic/Ta_param.pod @@ -0,0 +1,33 @@ +# DATE: 2022-11-30 UNITS: metal CONTRIBUTOR: Ngoc Cuong Nguyen, exapde@gmail.com CITATION: https://arxiv.org/abs/2209.02362 +# chemical element symbols +species Ta + +# periodic boundary conditions +pbc 1 1 1 + +# inner cut-off radius +rin 1.0 + +# outer cut-off radius +rcut 5.0 + +# polynomial degrees for radial basis functions +bessel_polynomial_degree 3 +inverse_polynomial_degree 6 + +# one-body potential +onebody 1 + +# two-body linear POD potential +twobody_number_radial_basis_functions 6 + +# three-body linear POD potential +threebody_number_radial_basis_functions 5 +threebody_number_angular_basis_functions 5 + +# four-body linear SNAP potential +fourbody_snap_twojmax 0 + +# quadratic POD potential +quadratic_pod_potential 1 + diff --git a/examples/PACKAGES/pod/Ta_Quadratic/Ta_training_analysis.pod b/examples/PACKAGES/pod/Ta_Quadratic/Ta_training_analysis.pod new file mode 100644 index 0000000000..f7f3910f93 --- /dev/null +++ b/examples/PACKAGES/pod/Ta_Quadratic/Ta_training_analysis.pod @@ -0,0 +1,387 @@ +# Displaced_A15.xyz + config # atoms energy DFT energy energy error force DFT force force error + 1 64 -754.2481469 -754.220443 0.0004328736542 8.011514932 8.398670477 0.06376626471 + 2 64 -753.8045627 -753.865255 0.0009483170919 9.036675474 9.134430545 0.07283331622 + 3 64 -754.1013213 -754.0221 0.001237833587 8.637024563 9.017261102 0.06364803016 + 4 64 -754.2847415 -754.279613 8.013259279e-05 8.107730847 8.381725092 0.0651017527 + 5 64 -753.8382044 -753.777209 0.0009530524751 9.104259346 9.478314477 0.07200166218 + 6 64 -754.0793448 -754.048643 0.0004797149516 8.152199121 8.465317938 0.06707944664 + 7 64 -754.3310528 -754.317603 0.0002101527451 7.944092757 8.127690491 0.05987173847 + 8 64 -754.0070856 -753.969161 0.0005925723559 9.179444115 9.425464952 0.06695321977 + 9 64 -754.1450603 -754.141988 4.800421744e-05 8.574171053 8.821346913 0.06628509806 +# Displaced_BCC.xyz + config # atoms energy DFT energy energy error force DFT force force error + 10 54 -630.8081936 -631.019667 0.003916173668 15.97497492 16.625876 0.1021118884 + 11 54 -631.4580137 -631.719595 0.004844098796 15.24068909 15.58666626 0.1043856899 + 12 54 -631.1667565 -631.386255 0.004064786135 15.46091763 15.92378883 0.1062824237 + 13 54 -632.3004944 -632.575826 0.005098733889 14.42619736 14.55977162 0.09839143245 + 14 54 -630.0894752 -630.450212 0.006680311898 16.78432817 16.96340726 0.108510231 + 15 54 -631.3402507 -631.669379 0.006094968579 15.82894198 16.05757315 0.1000888506 + 16 54 -632.0447348 -632.431277 0.007158188469 14.73098392 14.69810718 0.09621570623 + 17 54 -630.7186534 -630.960068 0.004470640569 15.62236513 15.99073148 0.1063789504 + 18 54 -623.3884972 -623.378198 0.0001907256206 23.97393076 24.67640432 0.1519105242 +# Displaced_FCC.xyz + config # atoms energy DFT energy energy error force DFT force force error + 19 48 -556.0112402 -555.899463 0.002328692595 5.300795182 6.084617063 0.07215984282 + 20 48 -555.9884375 -555.922478 0.001374155755 5.509767105 6.297071211 0.08438733778 + 21 48 -555.8765557 -555.800269 0.001589305952 5.420812181 6.021098636 0.07404420713 + 22 48 -556.2511473 -556.196151 0.00114575707 4.54185517 5.127955094 0.06609457327 + 23 48 -555.6590667 -555.488929 0.003544534966 6.087062872 7.050223459 0.09107544933 + 24 48 -556.1020654 -556.027926 0.001544570012 5.048523316 5.611881174 0.06751585758 + 25 48 -556.0607473 -555.968399 0.001923922354 5.20975666 5.979217189 0.08024051191 + 26 48 -556.0598013 -556.047132 0.0002639447837 4.995519809 5.544452585 0.07745365182 + 27 48 -555.8256423 -555.747848 0.001620713741 5.762702449 6.47892568 0.08480579641 +# Elastic_BCC.xyz + config # atoms energy DFT energy energy error force DFT force force error + 28 2 -23.69025375 -23.689367 0.0004433760298 0.0006229109944 0.0006222748589 9.850145246e-07 + 29 2 -23.690768 -23.689888 0.000440000226 0.000618183093 0.0006166052222 1.005028422e-06 + 30 2 -23.69082186 -23.689996 0.0004129297806 0.0008798074771 0.0008810425642 1.74843114e-06 + 31 2 -23.69166748 -23.690957 0.0003552393384 1.000599337e-06 0 4.011213572e-07 + 32 2 -23.69137648 -23.690521 0.0004277400529 0.0005992883433 0.0005982273815 7.219128625e-07 + 33 2 -23.69120607 -23.69038 0.0004130356748 0.0005947953498 0.0005925723585 9.949545518e-07 + 34 2 -23.6900782 -23.689202 0.0004381010976 0.000626333442 0.0006279363025 1.11150918e-06 + 35 2 -23.69121642 -23.690482 0.0003672088756 0.0008635087452 0.0008640138888 1.400552377e-06 + 36 2 -23.69074792 -23.689902 0.0004229607524 0.0006176587851 0.0006152154094 9.894653378e-07 + 37 2 -23.6914111 -23.690563 0.0004240511901 0.00060523674 0.0006038725031 4.148446495e-07 + 38 2 -23.69095105 -23.690207 0.0003720260028 0.001071999141 0.00107369735 7.195432847e-07 + 39 2 -23.69007856 -23.689285 0.0003967815187 0.0008875288751 0.000890013483 1.187800698e-06 + 40 2 -23.69061639 -23.689768 0.0004241948328 0.001078744596 0.001080249045 1.098539288e-06 + 41 2 -23.69064479 -23.68968 0.0004823961198 0.0008702112502 0.0008680034562 8.482029159e-07 + 42 2 -23.6910243 -23.690074 0.0004751500988 0.00136892629 0.001373818765 2.351923075e-06 + 43 2 -23.68910107 -23.688108 0.0004965356565 0.0006334703054 0.0006336134468 5.99047899e-07 + 44 2 -23.69003986 -23.689241 0.0003994297476 0.0008886652258 0.0008880101351 1.319383612e-06 + 45 2 -23.69042994 -23.68952 0.0004549687915 0.0008868886746 0.0008860011287 4.687853177e-07 + 46 2 -23.68738487 -23.686278 0.0005534349406 0.0006426679338 0.0006406777661 9.71847259e-07 + 47 2 -23.69095089 -23.690097 0.000426944902 0.0008409063968 0.0008410160522 1.331156612e-06 + 48 2 -23.6915816 -23.690811 0.0003853023262 0.0008464479016 0.0008500070588 1.611941107e-06 + 49 2 -23.69114597 -23.690266 0.0004399833623 0.001039354426 0.001044322747 3.354790597e-06 + 50 2 -23.69142231 -23.690597 0.0004126527557 0.001045528808 0.001050833003 2.164976718e-06 + 51 2 -23.69157045 -23.690673 0.0004487231875 0.000604541849 0.0006038907186 7.137781043e-07 + 52 2 -23.69135377 -23.690551 0.0004013839772 0.0008554940241 0.0008590064028 1.199877126e-06 + 53 2 -23.6914855 -23.690693 0.0003962483174 0.0008561039044 0.0008590110593 1.062367199e-06 + 54 2 -23.69110782 -23.69021 0.0004489099543 0.0008699574153 0.0008730051546 1.100986285e-06 + 55 2 -23.68987142 -23.688943 0.0004642118095 0.0008789739049 0.0008800306813 8.920178193e-07 + 56 2 -23.69108099 -23.690136 0.0004724929669 0.000597100569 0.000593996633 9.80915639e-07 + 57 2 -23.6884849 -23.687444 0.0005204507995 0.0009046496679 0.000903059245 1.159810957e-06 + 58 2 -23.69061659 -23.689801 0.0004077972116 0.0008734820883 0.0008740011442 2.826546206e-07 + 59 2 -23.69129673 -23.690408 0.0004443660476 8.294236971e-07 0 3.094976021e-07 + 60 2 -23.69128183 -23.690362 0.0004599146498 0.0006083805154 0.0006067503605 7.610258412e-07 + 61 2 -23.68992957 -23.688881 0.0005242861565 0.0008210298141 0.0008250054545 1.716902102e-06 + 62 2 -23.6913441 -23.690515 0.0004145511761 0.001475621115 0.001475779794 2.846782756e-06 + 63 2 -23.69141171 -23.690551 0.0004303554398 0.0005957864934 0.0005996599036 1.205169041e-06 + 64 2 -23.69029628 -23.689487 0.0004046409478 0.0006212224483 0.0006194384554 9.873569794e-07 + 65 2 -23.69072139 -23.68986 0.0004306953753 0.0008858826742 0.0008860124153 5.860307089e-07 + 66 2 -23.69018379 -23.689288 0.0004478958682 0.001400962673 0.001396479144 1.244220213e-06 + 67 2 -23.69129611 -23.690457 0.0004195533333 0.0005914018694 0.0005939831647 1.147206273e-06 + 68 2 -23.6908455 -23.689792 0.0005267514192 0.0008274901181 0.0008340587509 2.92351135e-06 + 69 2 -23.69101454 -23.690006 0.000504270969 0.0005874525941 0.0005897694465 1.183929198e-06 + 70 2 -23.69137638 -23.690571 0.0004026908865 0.000593505398 0.0005939781141 8.885138938e-07 + 71 2 -23.69114123 -23.690213 0.0004641149057 0.001085936923 0.001084315452 6.622719884e-07 + 72 2 -23.69146017 -23.690617 0.0004215861743 0.0005980164348 0.0006024682564 1.268431385e-06 + 73 2 -23.69063494 -23.689761 0.000436969988 0.0008787869884 0.0008790688255 2.274049903e-06 + 74 2 -23.69116059 -23.69027 0.0004452945331 6.913231892e-07 0 2.06028124e-07 + 75 2 -23.69134793 -23.690599 0.0003744660856 0.0006108389518 0.0006137752031 6.965603905e-07 + 76 2 -23.69149586 -23.69061 0.0004429280005 9.198411365e-07 0 3.754400665e-07 + 77 2 -23.69139951 -23.690603 0.000398256099 0.0008543318552 0.0008590331775 1.578689348e-06 + 78 2 -23.68884519 -23.687908 0.0004685950581 0.0009053954566 0.0009010105438 1.65775018e-06 + 79 2 -23.6914255 -23.690688 0.0003687521098 0.0008461958108 0.0008470064935 1.24650271e-06 + 80 2 -23.69088798 -23.689988 0.0004499890418 0.0006191456007 0.0006194465272 7.975009516e-07 + 81 2 -23.69054504 -23.689613 0.000466018941 0.0008740606753 0.0008740732235 7.595178952e-07 + 82 2 -23.69150291 -23.690678 0.0004124549265 0.000610815433 0.0006123757017 8.072128622e-07 + 83 2 -23.69107508 -23.69017 0.0004525408662 0.0008712162343 0.0008750051428 1.392028307e-06 + 84 2 -23.68888775 -23.687892 0.0004978736601 0.001115255007 0.001112070142 1.300142654e-06 + 85 2 -23.69100617 -23.690132 0.0004370859053 0.0008623538074 0.000868018433 1.989858339e-06 + 86 2 -23.6915696 -23.690843 0.0003633021835 0.0006034842936 0.0006081134763 1.367591325e-06 + 87 2 -23.6914135 -23.690598 0.0004077489269 0.001205622222 0.001217674833 4.139631643e-06 + 88 2 -23.69152569 -23.690656 0.0004348445802 0.00059822098 0.0006024765556 1.339932217e-06 + 89 2 -23.69122964 -23.690254 0.0004878211992 0.001039614315 0.001043496047 2.818924297e-06 + 90 2 -23.69160573 -23.690694 0.0004558637161 0.0006005236901 0.0006010740387 4.468420123e-07 + 91 2 -23.69097667 -23.690097 0.0004398330703 0.0008742194238 0.0008730234819 9.401050256e-07 + 92 2 -23.68931979 -23.688402 0.0004588927364 0.0006323490707 0.000632180354 2.788475676e-07 + 93 2 -23.68957637 -23.688669 0.0004536826549 0.00109306805 0.001092474256 1.597364093e-06 + 94 2 -23.69136079 -23.690538 0.0004113947461 0.0008559690445 0.0008610145179 1.717539372e-06 + 95 2 -23.69064046 -23.689722 0.0004592303219 0.0006203234131 0.0006251287867 1.466461168e-06 + 96 2 -23.69148676 -23.690581 0.0004528821164 7.127209296e-07 0 2.255862749e-07 + 97 2 -23.68967251 -23.688755 0.0004587573049 0.0006269090495 0.0006251143895 8.455647387e-07 + 98 2 -23.69038245 -23.689312 0.0005352239912 0.000826073741 0.0008290597083 1.434612139e-06 + 99 2 -23.6885155 -23.687388 0.0005637521677 0.001127067737 0.001120237475 2.789972117e-06 + 100 2 -23.69147138 -23.690664 0.0004036885172 0.0006101342417 0.0006109402589 2.333615197e-07 + 101 2 -23.69059185 -23.68941 0.0005909249423 0.0005851627123 0.0005883553348 1.578374866e-06 + 102 2 -23.69082355 -23.690035 0.0003942736357 0.0008795917739 0.0008810062429 8.322936553e-07 + 103 2 -23.69101815 -23.690015 0.0005015752118 0.0008420115266 0.0008450195264 1.339974338e-06 + 104 2 -23.6915919 -23.690752 0.0004199489474 0.0005974769534 0.0005996415596 9.70832204e-07 + 105 2 -23.69060481 -23.689825 0.0003899071047 0.0008774615458 0.0008800215906 1.681763497e-06 + 106 2 -23.69149833 -23.690562 0.0004681669348 0.0008527073264 0.0008560011682 1.112325585e-06 + 107 2 -23.69145561 -23.690622 0.0004168042562 0.0008363622912 0.0008390017878 8.931080404e-07 + 108 2 -23.68965306 -23.688764 0.0004445309599 0.0008936261428 0.0008910185183 1.309260409e-06 + 109 2 -23.69077552 -23.690011 0.0003822599475 0.000620379228 0.0006194287691 3.13320397e-07 + 110 2 -23.68867102 -23.687696 0.000487511551 0.00108606805 0.001087589996 1.326985668e-06 + 111 2 -23.69172933 -23.691019 0.0003551640965 0.000852012982 0.0008540035129 9.847228238e-07 + 112 2 -23.68991099 -23.689025 0.0004429972401 6.462272267e-07 0 2.557212251e-07 + 113 2 -23.69080506 -23.689952 0.0004265320817 7.01277621e-07 0 2.758977153e-07 + 114 2 -23.69152793 -23.69061 0.0004589649051 0.0008542964546 0.0008580011655 1.338538453e-06 + 115 2 -23.69153556 -23.690595 0.0004702784057 0.0008679746125 0.0008680069124 6.687400365e-07 + 116 2 -23.69117399 -23.690231 0.0004714925881 0.0005924022792 0.0005925892338 1.259966552e-07 + 117 2 -23.69139497 -23.690469 0.0004629847699 0.0008486905112 0.0008500294113 6.345373178e-07 + 118 2 -23.69122801 -23.690482 0.0003730074478 0.0008734799561 0.0008740102974 2.172848871e-07 + 119 2 -23.69055118 -23.689613 0.0004690900383 0.0008237357642 0.0008320192305 2.927979209e-06 + 120 2 -23.68847553 -23.687426 0.0005247674818 0.00109373942 0.00109577735 8.309003636e-07 + 121 2 -23.69041353 -23.689562 0.0004257635066 0.0006210722843 0.0006265237426 1.574787587e-06 + 122 2 -23.69137916 -23.6904 0.0004895816263 3.712921572e-07 0 1.509058152e-07 + 123 2 -23.69152028 -23.690561 0.0004796420104 0.0005964910689 0.0005982273815 1.201534101e-06 + 124 2 -23.69012376 -23.689107 0.0005083815771 0.0008124995056 0.0008180073349 1.978492784e-06 + 125 2 -23.69112303 -23.690145 0.0004890142327 0.0008742243294 0.0008740766557 1.981009549e-06 + 126 2 -23.6913827 -23.690482 0.0004503495661 0.0005944562314 0.0005939983165 2.226897955e-07 + 127 2 -23.69071568 -23.689864 0.0004258395345 0.0008855409145 0.0008860124153 7.974979118e-07 +# Elastic_FCC.xyz + config # atoms energy DFT energy energy error force DFT force force error + 128 4 -46.43709855 -46.437936 0.0002093612883 0.0008950060736 0.001265949446 0.000146452977 + 129 4 -46.4407039 -46.438504 0.0005499748573 0.000997595139 0.001492549497 0.0001384061782 + 130 4 -46.43497365 -46.436378 0.0003510862834 0.0005521282519 0.000810592376 9.989142068e-05 + 131 4 -46.44077415 -46.441551 0.0001942119059 0.001132198228 0.001283675193 6.296962032e-05 + 132 4 -46.41517164 -46.416957 0.0004463405792 0.0009179900208 0.001186145859 8.226328068e-05 + 133 4 -46.43849879 -46.440495 0.0004990525813 0.001000780392 0.001212440514 6.935589607e-05 + 134 4 -46.43777706 -46.437972 4.873549652e-05 0.001389269894 0.002358226452 0.0002414826841 + 135 4 -46.44772061 -46.44586 0.0004651531137 0.001363793596 0.002033949852 0.0001874007898 + 136 4 -46.43566097 -46.435744 2.075817254e-05 0.000953167535 0.001690849491 0.0002499304679 + 137 4 -46.4397151 -46.438209 0.00037652527 0.0008871613375 0.001160049999 6.827988406e-05 + 138 4 -46.42609455 -46.42629 4.886318637e-05 0.0005556350354 0.0005297018029 1.216514421e-05 + 139 4 -46.44149051 -46.443301 0.000452621879 0.001132511065 0.001818421568 0.0001734412183 + 140 4 -46.43896893 -46.439002 8.267057767e-06 0.00117987933 0.001416973535 6.937475084e-05 + 141 4 -46.43123556 -46.432438 0.0003006109725 0.001147766863 0.001010469198 6.008541597e-05 + 142 4 -46.41017485 -46.412654 0.0006197881873 0.001371501038 0.001801959766 0.0001610014005 + 143 4 -46.44246774 -46.443231 0.0001908139315 0.0008879090598 0.001691590967 0.0001867981606 + 144 4 -46.43057135 -46.431513 0.0002354125917 0.001455115673 0.001680544852 7.970584941e-05 + 145 4 -46.43314849 -46.435608 0.0006148762889 0.000895665118 0.0009593039143 1.661567686e-05 + 146 4 -46.43895751 -46.437689 0.0003171274211 0.001001645194 0.001217708504 8.864742137e-05 + 147 4 -46.42711221 -46.428447 0.0003336986888 0.001053852558 0.002060081552 0.0002791878112 + 148 4 -46.43182739 -46.432255 0.0001069024683 0.0007125257042 0.0006274201144 7.371629444e-05 + 149 4 -46.44177162 -46.442315 0.0001358457811 0.001140464208 0.002424436842 0.0003371036569 + 150 4 -46.43717254 -46.436613 0.0001398846117 0.0005515470177 0.0005321240457 4.259807028e-05 + 151 4 -46.43004027 -46.430825 0.0001961820031 0.001008903044 0.001399987143 0.0001075255526 + 152 4 -46.43208405 -46.43312 0.0002589878074 0.0005518527942 0.0007272771136 5.274203403e-05 + 153 4 -46.43371444 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4.994080216e-05 + 164 4 -46.4302643 -46.432233 0.0004921740977 0.0007882965793 0.0007253109678 2.466489667e-05 + 165 4 -46.43017474 -46.429408 0.0001916838665 0.0008990219519 0.001068327665 6.20865224e-05 + 166 4 -46.44541887 -46.445145 6.846696931e-05 0.001028604655 0.001776038288 0.0001975508878 + 167 4 -46.43410132 -46.435868 0.0004416694333 0.00126629656 0.002376074704 0.000327900749 + 168 4 -46.43919494 -46.439663 0.000117015505 0.0005441673063 0.001119403413 0.0001039537782 + 169 4 -46.42584101 -46.428287 0.0006114965752 0.001286554786 0.001277000392 3.606394767e-05 + 170 4 -46.42254993 -46.424584 0.0005085169742 0.0007166928162 0.0008032957114 3.058247108e-05 + 171 4 -46.41053526 -46.413045 0.0006274343113 0.001077488513 0.001248322074 4.395077903e-05 + 172 4 -46.43440112 -46.436994 0.0006482188049 0.0009567631791 0.001331939188 0.0001491134555 + 173 4 -46.44377744 -46.443604 4.335960636e-05 0.0009956177543 0.001177046303 8.761451233e-05 + 174 4 -46.44028269 -46.439718 0.0001411721588 9.067047531e-07 0 2.475505668e-07 + 175 4 -46.43723548 -46.435527 0.0004271210489 0.001133620592 0.0009338393866 8.014318869e-05 + 176 4 -46.43396161 -46.434787 0.0002063463028 0.001150111497 0.00117329195 4.934566521e-05 + 177 4 -46.43612253 -46.434929 0.0002983827305 0.001267527163 0.001349491756 5.093505267e-05 + 178 4 -46.42638491 -46.426499 2.852212041e-05 0.001164859731 0.001248937949 4.347948673e-05 + 179 4 -46.43717201 -46.437025 3.675291261e-05 0.0007725497049 0.000938418883 6.831038145e-05 + 180 4 -46.4281895 -46.428937 0.0001868753733 0.001151244017 0.001286352984 4.994280583e-05 + 181 4 -46.44116364 -46.442516 0.0003380888012 0.0007032389703 0.00094855469 0.000108860383 + 182 4 -46.42978258 -46.428736 0.000261644323 0.001009630039 0.001424321593 0.0001089615374 + 183 4 -46.43305551 -46.433359 7.587324757e-05 0.001156683005 0.001276381604 4.128762871e-05 + 184 4 -46.44006475 -46.438799 0.0003164387002 0.0007752996484 0.0008186940821 3.548756759e-05 + 185 4 -46.44169053 -46.441993 7.561811334e-05 0.0008970971352 0.001887735151 0.000222339744 + 186 4 -46.43727222 -46.439033 0.0004401950631 0.0007708721421 0.000821568013 4.107006528e-05 + 187 4 -46.43632517 -46.436967 0.0001604569693 0.001052390429 0.001482323514 0.0001388091175 + 188 4 -46.42718259 -46.427245 1.560321473e-05 0.001072419719 0.001293885621 7.709436807e-05 + 189 4 -46.43874841 -46.438046 0.0001756028841 0.001260671466 0.001627288542 0.0001002073731 + 190 4 -46.41877429 -46.420083 0.0003271766028 0.001421603027 0.002395244873 0.0003233098337 + 191 4 -46.44621445 -46.445247 0.0002418621169 0.0009904379233 0.001219330964 5.687300364e-05 + 192 4 -46.44511464 -46.446044 0.0002323405647 0.0008790841215 0.001305329077 0.0001107509546 + 193 4 -46.43564394 -46.434472 0.0002929855068 0.0008903788205 0.0008323340675 4.743676385e-05 + 194 4 -46.44317175 -46.44458 0.0003520614781 0.0007034017538 0.0009744208536 5.172011109e-05 + 195 4 -46.44087095 -46.441776 0.0002262619087 0.001139223456 0.001339231869 8.765048343e-05 + 196 4 -46.43719327 -46.436389 0.0002010663787 0.001277509155 0.001786741168 0.0001303767139 + 197 4 -46.44563996 -46.446416 0.0001940092562 0.000700739078 0.0006588778339 5.645492682e-05 + 198 4 -46.44980864 -46.449806 6.612381167e-07 0.001232827144 0.002135055034 0.000238485636 + 199 4 -46.42466674 -46.427189 0.000630565232 0.001011828268 0.001050788276 2.797047063e-05 + 200 4 -46.42588994 -46.427857 0.0004917661001 0.00101091552 0.001487666629 0.0001398462851 + 201 4 -46.44273693 -46.44004 0.0006742322248 0.0007050797939 0.000757202747 2.506453736e-05 + 202 4 -46.43659247 -46.437214 0.0001553826468 0.0008924047139 0.001505586265 0.0001475570783 + 203 4 -46.42189527 -46.422628 0.0001831832406 0.0009120248401 0.001601713458 0.000220735026 + 204 4 -46.44387014 -46.443535 8.378488419e-05 0.001253187877 0.001590304373 0.0001006146179 + 205 4 -46.4386991 -46.439922 0.0003057250066 0.001138308596 0.001530493385 0.0001018467448 + 206 4 -46.4373267 -46.437675 8.707593122e-05 0.001448336679 0.002440246094 0.0003149340449 + 207 4 -46.44459348 -46.445558 0.0002411298298 0.0008716896548 0.00113392416 7.56133778e-05 + 208 4 -46.43888137 -46.439106 5.615857123e-05 0.001259801506 0.001830731002 0.0001709221809 + 209 4 -46.44452218 -46.443073 0.0003622950507 0.0005355234286 0.0005766870902 1.79131694e-05 + 210 4 -46.44072829 -46.4397 0.0002570731957 0.0008912596243 0.001204174406 7.190944969e-05 + 211 4 -46.43632905 -46.436374 1.123662554e-05 0.001004541694 0.001461656594 0.0001640759015 + 212 4 -46.42622449 -46.426557 8.312803221e-05 0.0009090508284 0.001359624213 9.61864457e-05 + 213 4 -46.43334095 -46.434009 0.0001670113496 0.001064727188 0.001391131194 0.0001118380498 + 214 4 -46.43528491 -46.436262 0.0002442731151 0.001381671346 0.002503347159 0.0002862586044 + 215 4 -46.43302209 -46.434505 0.0003707284248 0.001050895839 0.001041637173 1.89496147e-05 + 216 4 -46.43866543 -46.438768 2.564310569e-05 0.001038218766 0.001098285027 4.514347826e-05 + 217 4 -46.43867092 -46.440254 0.0003957707004 0.0005510961941 0.0006069892915 4.783704875e-05 + 218 4 -46.42481604 -46.42286 0.0004890088296 0.0005673661233 0.0007365242698 6.506186378e-05 + 219 4 -46.41707211 -46.418078 0.0002514713405 0.001292943112 0.002028412187 0.0002017017778 + 220 4 -46.44058128 -46.440513 1.707010597e-05 0.0008917164568 0.001158189967 9.459267259e-05 + 221 4 -46.40786735 -46.409824 0.0004891615343 0.0009159953828 0.001759573812 0.0002027400844 + 222 4 -46.44176165 -46.440329 0.0003581620037 0.0007050786772 0.0009534044263 7.330941275e-05 + 223 4 -46.43764613 -46.43773 2.096713934e-05 0.0007747180798 0.000926180328 6.358620118e-05 + 224 4 -46.41646676 -46.416525 1.456051792e-05 0.0007183861299 0.0007573664899 3.367542767e-05 + 225 4 -46.44086814 -46.440293 0.0001437847792 0.0008909027165 0.0007725386722 2.803789995e-05 + 226 4 -46.44027214 -46.43839 0.0004705341364 0.000707862255 0.0005612022808 3.305825174e-05 + 227 4 -46.44117428 -46.438916 0.0005645709574 0.0008843760681 0.001650878554 0.0001728225821 +# GSF_110.xyz + config # atoms energy DFT energy energy error force DFT force force error + 228 24 -278.9717069 -279.068761 0.00404392159 1.716820058 1.756353161 0.02195806777 + 229 24 -279.8354387 -279.784296 0.002130947259 0.8360146768 0.9057668891 0.02306494032 + 230 24 -279.920921 -279.901657 0.0008026665456 0.2958425102 0.001565946359 0.01411644012 + 231 24 -279.6113309 -279.584238 0.001128868858 1.136927341 1.035572248 0.02681094686 + 232 24 -279.8354404 -279.784283 0.002131557037 0.8360110766 0.9056396189 0.0230536352 + 233 24 -279.3024349 -279.302158 1.153693867e-05 1.736732164 1.771965137 0.0337612822 + 234 24 -279.5958842 -279.55564 0.001676842348 1.457718728 1.405626506 0.02601747541 + 235 24 -279.1575825 -279.246939 0.003723188855 0.7701800349 0.4813964151 0.04047321686 + 236 24 -279.3024374 -279.302157 1.168449864e-05 1.736735452 1.771953347 0.03376037562 + 237 24 -279.1575945 -279.246935 0.003722519724 0.7692674812 0.4809484798 0.04044518496 + 238 24 -279.9208868 -279.896025 0.001035908286 0.2963183655 0.01060549839 0.01410249268 + 239 24 -279.6115694 -279.584237 0.001138851225 1.137705592 1.035836121 0.02686761868 + 240 24 -279.0645289 -279.124427 0.002495753535 1.763755884 1.809545887 0.03536481445 + 241 24 -279.3562358 -279.379366 0.0009637580399 1.070359709 0.8982692706 0.03586364626 + 242 24 -279.3561336 -279.37937 0.0009681812755 1.070186817 0.898081355 0.03582333417 + 243 24 -279.0645273 -279.124427 0.002495821471 1.76375235 1.809523374 0.03536506787 + 244 24 -279.920921 -279.901657 0.0008026665457 0.2958425115 0.001570374478 0.01411414901 + 245 24 -279.835369 -279.79264 0.001780376458 0.7694167211 0.8392614852 0.02365582641 + 246 24 -279.9208868 -279.896025 0.001035908286 0.2963183642 0.01060243293 0.01410272845 + 247 24 -279.0819585 -279.206496 0.005189062307 0.5487881184 0.005326518563 0.03225762846 + 248 24 -279.5958869 -279.55564 0.001676953548 1.457718908 1.4056319 0.0260184492 + 249 24 -279.8353874 -279.79264 0.00178114169 0.7694019544 0.8392625708 0.02365755724 +# GSF_112.xyz + config # atoms energy DFT energy energy error force DFT force force error + 250 30 -345.1958147 -345.175835 0.0006659891847 1.417828523 1.057395322 0.04924265533 + 251 30 -346.4091655 -346.361714 0.00158171544 1.014644749 1.220284939 0.04659092137 + 252 30 -345.9623041 -345.795524 0.00555933642 1.67846042 2.112860875 0.06265038152 + 253 30 -345.1047773 -345.164602 0.001994155137 1.81758407 1.765832199 0.05258058282 + 254 30 -346.5687926 -346.593523 0.0008243469243 0.5266157132 0.01148867129 0.03755503081 + 255 30 -346.4165138 -346.396186 0.000677592277 1.101956155 0.9954683928 0.04399110273 + 256 30 -345.2521555 -345.319406 0.002241683384 2.024012114 1.772040852 0.05936121329 + 257 30 -345.5898529 -345.594794 0.0001647017128 2.048144748 1.516014157 0.06040124074 + 258 30 -346.0297766 -345.98566 0.001470553801 1.767327567 1.406252265 0.0524370388 + 259 30 -345.5053827 -345.383994 0.004046291647 1.336428827 0.963574308 0.05104898331 + 260 30 -346.5686343 -346.582564 0.0004643235194 0.5264211967 0.0126740587 0.03760970063 + 261 30 -345.4208874 -345.452139 0.001041721437 3.011664984 2.787719406 0.06345649604 + 262 30 -346.5687923 -346.593523 0.0008243564189 0.5266290267 0.01148834 0.03755658657 + 263 30 -345.4303119 -345.281949 0.004945431293 1.947208693 1.873142686 0.05337068276 + 264 30 -345.9593201 -345.928661 0.001021971125 2.36272379 2.100874472 0.0500210761 + 265 30 -345.0137679 -345.111657 0.003262969466 3.193781636 3.358068319 0.0653642582 + 266 30 -346.4078757 -346.367123 0.00135842305 1.085591177 1.335797131 0.04639233515 + 267 30 -346.5685865 -346.582565 0.000465950677 0.5264876602 0.01254743735 0.03760888491 + 268 30 -344.8663405 -344.91356 0.00157398253 2.930409434 3.441834403 0.06926997464 + 269 30 -345.9709087 -345.836703 0.00447352268 1.391835322 1.608769148 0.05570538969 + 270 30 -345.0229889 -344.984307 0.001289396737 2.372017585 2.542628782 0.05571754983 + 271 30 -346.4089446 -346.393931 0.0005004538568 1.297845709 1.211680725 0.04319349627 +# Liquid.xyz + config # atoms energy DFT energy energy error force DFT force force error + 272 100 -1105.559726 -1105.601723 0.0004199685213 30.70196318 31.39853886 0.2273901981 + 273 100 -1099.629534 -1099.673012 0.0004347839505 31.9864667 32.03167218 0.2226202822 + 274 100 -1121.431681 -1121.31506 0.001166208152 21.23863487 20.81076453 0.2037539182 +# Surface.xyz + config # atoms energy DFT energy energy error force DFT force force error + 275 24 -279.9208871 -279.911828 0.0003774638802 0.296319206 0.002753093533 0.01433131366 + 276 48 -554.2414777 -555.359452 0.02329113138 1.363109763 0.003020630398 0.05738251122 + 277 40 -459.5808396 -459.216162 0.009116939427 3.331498127 5.0461364 0.07877996732 + 278 40 -460.5932468 -461.144076 0.01377073069 0.885446861 0.005582740008 0.03813346389 + 279 24 -279.8214987 -279.635146 0.007764695863 0.9820115882 1.288799837 0.01857542284 + 280 30 -346.5687934 -346.592525 0.000791054458 0.5266151802 0.008446203407 0.03726635334 + 281 30 -346.0051972 -345.744506 0.008689705343 2.2667395 3.124961367 0.06591070418 +# Volume_A15.xyz + config # atoms energy DFT energy energy error force DFT force force error + 282 8 -67.00264006 -66.990732 0.001488507429 1.215939804e-14 0 2.243358855e-15 + 283 8 -72.95775649 -72.957807 6.314313802e-06 8.336427488e-14 0 1.123457519e-14 + 284 8 -94.15079086 -94.145745 0.0006307320297 1.643238761e-14 0 2.292400473e-15 + 285 8 -94.55576973 -94.554682 0.0001359665592 8.781810015e-15 0 1.347934763e-15 + 286 8 -79.41651001 -79.438363 0.002731624081 2.791146139e-14 0 4.283068402e-15 + 287 8 -69.63190551 -69.627817 0.0005110639107 2.797159709e-15 0 4.945407509e-16 + 288 8 -82.61402421 -82.604907 0.001139651578 5.50518588e-15 0 8.533393899e-16 + 289 8 14.88715331 14.89048 0.0004158363277 2.277623074e-13 0 3.606918366e-14 + 290 8 -94.356027 -94.367599 0.001446500568 1.370656518e-14 0 1.897531383e-15 + 291 8 -89.24943611 -89.248227 0.0001511386032 1.664774127e-14 0 2.375992921e-15 + 292 8 -87.22359359 -87.211997 0.001449574005 7.983033839e-15 0 1.375635716e-15 + 293 8 -93.64917628 -93.66897 0.002474215442 2.161830962e-15 0 3.67529118e-16 + 294 8 -7.974970933 -7.989166 0.001774383436 5.099416125e-13 0 6.946546112e-14 + 295 8 -84.99735699 -84.982834 0.001815374179 2.170443421e-15 0 3.781697178e-16 + 296 8 -92.51696438 -92.536373 0.002426077641 3.718860295e-14 0 5.973231169e-15 + 297 8 -26.79883513 -26.77612 0.002839390901 2.233715834e-13 0 3.517493235e-14 + 298 8 -77.53738471 -77.544107 0.0008402860664 4.491324709e-15 0 6.054184931e-16 + 299 8 -80.11476756 -80.114217 6.882047834e-05 5.913998758e-15 0 9.669637776e-16 + 300 8 -42.12903277 -42.143041 0.00175102843 2.422750345e-13 0 3.585193613e-14 + 301 8 -91.02990945 -91.040671 0.001345193709 6.975614512e-15 0 1.271552308e-15 + 302 8 -84.50933128 -84.499231 0.001262535287 7.403156156e-14 0 1.406889651e-14 + 303 8 -61.79844785 -61.825173 0.00334064406 6.607450367e-15 0 1.159662644e-15 + 304 8 -91.13057634 -91.156873 0.003287081921 4.951266629e-15 0 8.926959288e-16 + 305 8 -54.64916673 -54.658744 0.001197159343 1.762087937e-13 0 2.65881147e-14 + 306 8 -72.27319254 -72.277255 0.000507807722 1.012753197e-15 0 1.548963504e-16 + 307 8 -74.91471828 -74.923334 0.001076965039 5.031158658e-15 0 8.218252467e-16 + 308 8 -64.81833234 -64.798066 0.002533292377 2.413198886e-14 0 3.886792508e-15 + 309 8 -93.03489737 -93.048342 0.001680578381 1.933770811e-14 0 2.823007783e-15 + 310 8 -64.39098016 -64.38702 0.0004950203573 5.491439235e-15 0 7.035387897e-16 + 311 8 -88.36401111 -88.352871 0.001392513469 2.448818319e-14 0 4.111150078e-15 +# Volume_BCC.xyz + config # atoms energy DFT energy energy error force DFT force force error + 312 2 -16.76594324 -16.763625 0.001159120926 6.976263305e-16 0 2.428612866e-16 + 313 2 16.313727 16.314145 0.0002090019872 8.554299543e-13 0 3.258747439e-13 + 314 2 -21.21034404 -21.209071 0.0006365184639 6.640073969e-15 0 2.236638531e-15 + 315 2 -15.78459679 -15.780524 0.002036394156 5.203101774e-14 0 1.833927975e-14 + 316 2 -18.99841037 -19.002205 0.001897313323 1.54524867e-14 0 5.273488075e-15 + 317 2 -22.62451928 -22.620568 0.001975641435 2.616505909e-15 0 8.627358087e-16 + 318 2 4.098164524 4.096885 0.0006397621932 1.343238339e-13 0 4.308474873e-14 + 319 2 56.26275599 56.26276 2.005140033e-06 4.519068948e-12 0 1.619606237e-12 + 320 2 -22.58944013 -22.585113 0.002163564374 5.342497709e-16 0 1.665334537e-16 + 321 2 -21.79724015 -21.795501 0.0008695727187 1.356336346e-15 0 5.088522196e-16 + 322 2 33.11015633 33.110078 3.916319966e-05 9.447550921e-13 0 3.146094496e-13 + 323 2 -20.88315873 -20.885998 0.001419633105 7.79136136e-16 0 2.683038976e-16 + 324 2 -23.59568896 -23.601336 0.002823519876 1.786193989e-15 0 4.786425072e-16 + 325 2 -23.20858072 -23.207313 0.0006338593044 1.587616402e-15 0 5.168500994e-16 + 326 2 -19.89310508 -19.898089 0.002491959911 5.484204741e-15 0 2.212350673e-15 + 327 2 -23.40543383 -23.405474 2.008348612e-05 1.53358588e-15 0 5.31475905e-16 + 328 2 -4.78389031 -4.781324 0.001283154883 1.032154003e-13 0 2.824014171e-14 + 329 2 -18.86311291 -18.864936 0.0009115426575 7.879846534e-16 0 3.053113318e-16 + 330 2 -17.81642586 -17.813086 0.001669928234 3.605555037e-16 0 9.945747929e-17 + 331 2 -11.19369732 -11.197201 0.001751838472 4.930421981e-14 0 1.82568081e-14 + 332 2 -23.68308621 -23.696705 0.00680939721 1.854348399e-15 0 6.493648212e-16 +# Volume_FCC.xyz + config # atoms energy DFT energy energy error force DFT force force error + 333 4 -19.07363593 -19.075994 0.0005895165228 4.539228243e-14 0 9.571047658e-15 + 334 4 -34.87911159 -34.873619 0.001373146366 4.198460887e-16 0 9.425330886e-17 + 335 4 -43.95312211 -43.950003 0.0007797776247 2.024630393e-15 0 4.763261544e-16 + 336 4 -40.99484531 -40.991909 0.0007340787492 7.390350347e-15 0 1.496325488e-15 + 337 4 -43.44688588 -43.453929 0.001760780713 4.008514517e-15 0 1.003087756e-15 + 338 4 -42.69057262 -42.686077 0.00112390473 2.201304978e-15 0 5.507566336e-16 + 339 4 -33.2256766 -33.224653 0.0002559009775 2.053725049e-16 0 5.088522196e-17 + 340 4 -26.86518979 -26.862709 0.0006201985978 3.140235603e-14 0 7.073764388e-15 + 341 4 -25.52095379 -25.519883 0.000267698747 6.385007894e-16 0 1.350193105e-16 + 342 4 3.462101351 3.463071 0.0002424122902 9.859120235e-14 0 2.313607928e-14 + 343 4 -31.59322682 -31.59595 0.0006807955537 2.683163594e-16 0 6.85215773e-17 + 344 4 -45.10086835 -45.100466 0.0001005869681 1.851345213e-15 0 4.233676619e-16 + 345 4 -46.05341345 -46.052258 0.0002888617397 5.706396539e-16 0 1.230208065e-16 + 346 4 -29.99832747 -30.001189 0.000715381888 4.217055326e-16 0 9.772275581e-17 + 347 4 -22.85257323 -22.8504 0.0005433065144 5.289057803e-16 0 1.249000903e-16 + 348 4 -9.165925355 -9.164691 0.0003085886251 6.994099953e-14 0 1.740903428e-14 + 349 4 -24.14844551 -24.150343 0.0004743734227 3.331030455e-16 0 7.459310947e-17 + 350 4 -46.43546878 -46.426795 0.002168446119 3.110946892e-15 0 8.45388574e-16 + 351 4 -28.4512672 -28.451145 3.054899355e-05 7.027034849e-15 0 2.024133176e-15 + 352 4 40.34134283 40.341566 5.579222461e-05 4.132267104e-13 0 1.032726433e-13 + 353 4 19.61887601 19.617912 0.0002410019119 1.957059783e-13 0 4.973561211e-14 + 354 4 -26.95747285 -26.954384 0.0007722115981 4.151755412e-16 0 1.006139616e-16 + 355 4 -46.33491981 -46.323696 0.002805952031 2.472781231e-15 0 6.375108774e-16 + 356 4 -45.83316789 -45.828947 0.001055221357 1.149213664e-14 0 3.283108739e-15 + 357 4 -38.16058672 -38.16029 7.417901943e-05 5.394515869e-16 0 1.214306433e-16 + 358 4 -32.91257361 -32.919741 0.001791847013 3.667266479e-14 0 9.583190722e-15 + 359 4 -41.2675262 -41.272675 0.001287200608 1.447869656e-14 0 4.164533482e-15 + 360 4 -39.74460491 -39.753322 0.002179272067 5.980937198e-16 0 1.292283933e-16 + 361 4 -37.55548161 -37.547435 0.002011651484 1.56813803e-14 0 3.793478841e-15 + 362 4 -36.53186907 -36.52595 0.00147976637 2.125160163e-16 0 4.741577501e-17 + 363 4 -45.01550152 -45.016087 0.0001463706371 1.97327102e-15 0 4.891920202e-16 diff --git a/examples/PACKAGES/pod/Ta_Quadratic/Ta_training_errors.pod b/examples/PACKAGES/pod/Ta_Quadratic/Ta_training_errors.pod new file mode 100644 index 0000000000..78f600d5cb --- /dev/null +++ b/examples/PACKAGES/pod/Ta_Quadratic/Ta_training_errors.pod @@ -0,0 +1,20 @@ +**************** Begin of Error Analysis for the Training Data Set **************** +--------------------------------------------------------------------------------------------------- + File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force +--------------------------------------------------------------------------------------------------- +Displaced_A15.xyz 9 576 0.000554 0.000680 0.066393 0.083014 +Displaced_BCC.xyz 9 486 0.004724 0.005103 0.108253 0.139461 +Displaced_FCC.xyz 9 432 0.001704 0.001900 0.077531 0.097471 +Elastic_BCC.xyz 100 200 0.000444 0.000446 0.000001 0.000002 +Elastic_FCC.xyz 100 400 0.000273 0.000327 0.000110 0.000163 +GSF_110.xyz 22 528 0.001852 0.002260 0.027302 0.044765 +GSF_112.xyz 22 660 0.001839 0.002404 0.051415 0.080350 +Liquid.xyz 3 300 0.000674 0.000758 0.217921 0.276109 +Surface.xyz 7 236 0.009115 0.011661 0.047949 0.105123 +Volume_A15.xyz 30 240 0.001407 0.001693 0.000000 0.000000 +Volume_BCC.xyz 21 42 0.001497 0.002077 0.000000 0.000000 +Volume_FCC.xyz 31 124 0.000870 0.001139 0.000000 0.000000 +--------------------------------------------------------------------------------------------------- +All files 363 4224 0.001053 0.002171 0.059051 0.106960 +--------------------------------------------------------------------------------------------------- +**************** End of Error Analysis for the Training Data Set **************** diff --git a/examples/PACKAGES/pod/Ta_Quadratic/in.fitpod b/examples/PACKAGES/pod/Ta_Quadratic/in.fitpod new file mode 100644 index 0000000000..7b932558ea --- /dev/null +++ b/examples/PACKAGES/pod/Ta_Quadratic/in.fitpod @@ -0,0 +1,5 @@ +# Demonstrate fitpod for POD potential + +units metal +fitpod Ta_param.pod Ta_data.pod + diff --git a/examples/PACKAGES/pod/Ta_Quadratic/in.pod b/examples/PACKAGES/pod/Ta_Quadratic/in.pod new file mode 100644 index 0000000000..bde2df00a1 --- /dev/null +++ b/examples/PACKAGES/pod/Ta_Quadratic/in.pod @@ -0,0 +1,47 @@ +# Demonstrate POD Ta potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable ny equal ${nrep} +variable nz equal ${nrep} + +boundary p p p + +lattice bcc $a +region box block 0 ${nx} 0 ${ny} 0 ${nz} +create_box 1 box +create_atoms 1 box + +mass 1 180.88 + + +# POD potential +pair_style pod +pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} + + diff --git a/examples/PACKAGES/pod/Ta_Quadratic/log.1Dec22.fitpod.g++.1 b/examples/PACKAGES/pod/Ta_Quadratic/log.1Dec22.fitpod.g++.1 new file mode 100644 index 0000000000..6e5e4cd78b --- /dev/null +++ b/examples/PACKAGES/pod/Ta_Quadratic/log.1Dec22.fitpod.g++.1 @@ -0,0 +1,114 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate fitpod for POD potential + +units metal +fitpod Ta_param.pod Ta_data.pod +Reading potential file Ta_param.pod with DATE: 2022-11-30 +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body potential: 3 6 6 +three-body potential: 3 6 5 5 +four-body SNAP potential: 0 0 +quadratic POD potential: 1 +number of basis functions for one-body potential: 1 +number of basis functions for two-body potential: 6 +number of basis functions for three-body potential: 25 +number of basis functions for four-body potential: 0 +number of descriptors for one-body potential: 1 +number of descriptors for two-body potential: 6 +number of descriptors for three-body potential: 25 +number of descriptors for four-body potential: 0 +number of descriptors for quadratic POD potential: 150 +total number of descriptors for all potentials: 182 +**************** End of POD Potentials **************** + +**************** Begin of Data File **************** +file format: extxyz +file extension: xyz +path to training data set: ../Ta/XYZ +path to test data set: ../Ta/XYZ +training fraction: 1 +test fraction: 1 +randomize training data set: 1 +randomize test data set: 1 +error analysis for training data set: 1 +error analysis for test data set: 0 +energy/force calculation for training data set: 0 +energy/force calculation for test data set: 0 +fitting weight for energy: 100 +fitting weight for force: 1 +fitting weight for stress: 0 +**************** End of Data File **************** +**************** Begin of Training Data Set **************** +--------------------------------------------------------------- + data file | number of configurations | number of atoms +--------------------------------------------------------------- + Displaced_A15.xyz | 9 | 576 + Displaced_BCC.xyz | 9 | 486 + Displaced_FCC.xyz | 9 | 432 + Elastic_BCC.xyz | 100 | 200 + Elastic_FCC.xyz | 100 | 400 + GSF_110.xyz | 22 | 528 + GSF_112.xyz | 22 | 660 + Liquid.xyz | 3 | 300 + Surface.xyz | 7 | 236 + Volume_A15.xyz | 30 | 240 + Volume_BCC.xyz | 21 | 42 + Volume_FCC.xyz | 31 | 124 +--------------------------------------------------------------- +number of files: 12 +number of configurations in all files: 363 +number of atoms in all files: 4224 +minimum number of atoms: 2 +maximum number of atoms: 100 +**************** End of Training Data Set **************** +**************** Begin of Memory Allocation **************** +maximum number of atoms in periodic domain: 100 +maximum number of atoms in extended domain: 2700 +maximum number of neighbors in extended domain: 270000 +size of double memory: 223201 +size of int memory: 14709 +size of descriptor matrix: 182 x 182 +**************** End of Memory Allocation **************** +**************** Begin of Least-Squares Fitting **************** +Configuration: # 1 +Configuration: # 101 +Configuration: # 201 +Configuration: # 301 +**************** End of Least-Squares Fitting **************** +**************** Begin of Error Calculation **************** +Configuration: # 1 +Configuration: # 101 +Configuration: # 201 +Configuration: # 301 +**************** End of Error Calculation **************** +**************** Begin of Error Analysis for the Training Data Set **************** +--------------------------------------------------------------------------------------------------- + File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force +--------------------------------------------------------------------------------------------------- +Displaced_A15.xyz 9 576 0.000554 0.000680 0.066393 0.083014 +Displaced_BCC.xyz 9 486 0.004724 0.005103 0.108253 0.139461 +Displaced_FCC.xyz 9 432 0.001704 0.001900 0.077531 0.097471 +Elastic_BCC.xyz 100 200 0.000444 0.000446 0.000001 0.000002 +Elastic_FCC.xyz 100 400 0.000273 0.000327 0.000110 0.000163 +GSF_110.xyz 22 528 0.001852 0.002260 0.027302 0.044765 +GSF_112.xyz 22 660 0.001839 0.002404 0.051415 0.080350 +Liquid.xyz 3 300 0.000674 0.000758 0.217921 0.276109 +Surface.xyz 7 236 0.009115 0.011661 0.047949 0.105123 +Volume_A15.xyz 30 240 0.001407 0.001693 0.000000 0.000000 +Volume_BCC.xyz 21 42 0.001497 0.002077 0.000000 0.000000 +Volume_FCC.xyz 31 124 0.000870 0.001139 0.000000 0.000000 +--------------------------------------------------------------------------------------------------- +All files 363 4224 0.001053 0.002171 0.059051 0.106960 +--------------------------------------------------------------------------------------------------- +**************** End of Error Analysis for the Training Data Set **************** + +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/pod/Ta_Quadratic/log.1Dec22.fitpod.g++.4 b/examples/PACKAGES/pod/Ta_Quadratic/log.1Dec22.fitpod.g++.4 new file mode 100644 index 0000000000..ddc559c6c0 --- /dev/null +++ b/examples/PACKAGES/pod/Ta_Quadratic/log.1Dec22.fitpod.g++.4 @@ -0,0 +1,114 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate fitpod for POD potential + +units metal +fitpod Ta_param.pod Ta_data.pod +Reading potential file Ta_param.pod with DATE: 2022-11-30 +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body potential: 3 6 6 +three-body potential: 3 6 5 5 +four-body SNAP potential: 0 0 +quadratic POD potential: 1 +number of basis functions for one-body potential: 1 +number of basis functions for two-body potential: 6 +number of basis functions for three-body potential: 25 +number of basis functions for four-body potential: 0 +number of descriptors for one-body potential: 1 +number of descriptors for two-body potential: 6 +number of descriptors for three-body potential: 25 +number of descriptors for four-body potential: 0 +number of descriptors for quadratic POD potential: 150 +total number of descriptors for all potentials: 182 +**************** End of POD Potentials **************** + +**************** Begin of Data File **************** +file format: extxyz +file extension: xyz +path to training data set: ../Ta/XYZ +path to test data set: ../Ta/XYZ +training fraction: 1 +test fraction: 1 +randomize training data set: 1 +randomize test data set: 1 +error analysis for training data set: 1 +error analysis for test data set: 0 +energy/force calculation for training data set: 0 +energy/force calculation for test data set: 0 +fitting weight for energy: 100 +fitting weight for force: 1 +fitting weight for stress: 0 +**************** End of Data File **************** +**************** Begin of Training Data Set **************** +--------------------------------------------------------------- + data file | number of configurations | number of atoms +--------------------------------------------------------------- + Displaced_A15.xyz | 9 | 576 + Displaced_BCC.xyz | 9 | 486 + Displaced_FCC.xyz | 9 | 432 + Elastic_BCC.xyz | 100 | 200 + Elastic_FCC.xyz | 100 | 400 + GSF_110.xyz | 22 | 528 + GSF_112.xyz | 22 | 660 + Liquid.xyz | 3 | 300 + Surface.xyz | 7 | 236 + Volume_A15.xyz | 30 | 240 + Volume_BCC.xyz | 21 | 42 + Volume_FCC.xyz | 31 | 124 +--------------------------------------------------------------- +number of files: 12 +number of configurations in all files: 363 +number of atoms in all files: 4224 +minimum number of atoms: 2 +maximum number of atoms: 100 +**************** End of Training Data Set **************** +**************** Begin of Memory Allocation **************** +maximum number of atoms in periodic domain: 100 +maximum number of atoms in extended domain: 2700 +maximum number of neighbors in extended domain: 270000 +size of double memory: 223201 +size of int memory: 14709 +size of descriptor matrix: 182 x 182 +**************** End of Memory Allocation **************** +**************** Begin of Least-Squares Fitting **************** +Configuration: # 1 +Configuration: # 101 +Configuration: # 201 +Configuration: # 301 +**************** End of Least-Squares Fitting **************** +**************** Begin of Error Calculation **************** +Configuration: # 1 +Configuration: # 101 +Configuration: # 201 +Configuration: # 301 +**************** End of Error Calculation **************** +**************** Begin of Error Analysis for the Training Data Set **************** +--------------------------------------------------------------------------------------------------- + File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force +--------------------------------------------------------------------------------------------------- +Displaced_A15.xyz 9 576 0.000554 0.000680 0.066393 0.083014 +Displaced_BCC.xyz 9 486 0.004724 0.005103 0.108253 0.139461 +Displaced_FCC.xyz 9 432 0.001704 0.001900 0.077531 0.097471 +Elastic_BCC.xyz 100 200 0.000444 0.000446 0.000001 0.000002 +Elastic_FCC.xyz 100 400 0.000273 0.000327 0.000110 0.000163 +GSF_110.xyz 22 528 0.001852 0.002260 0.027302 0.044765 +GSF_112.xyz 22 660 0.001839 0.002404 0.051415 0.080350 +Liquid.xyz 3 300 0.000674 0.000758 0.217921 0.276109 +Surface.xyz 7 236 0.009115 0.011661 0.047949 0.105123 +Volume_A15.xyz 30 240 0.001407 0.001693 0.000000 0.000000 +Volume_BCC.xyz 21 42 0.001497 0.002077 0.000000 0.000000 +Volume_FCC.xyz 31 124 0.000870 0.001139 0.000000 0.000000 +--------------------------------------------------------------------------------------------------- +All files 363 4224 0.001053 0.002171 0.059051 0.106960 +--------------------------------------------------------------------------------------------------- +**************** End of Error Analysis for the Training Data Set **************** + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pod/Ta_Quadratic/log.1Dec22.pod.g++.1 b/examples/PACKAGES/pod/Ta_Quadratic/log.1Dec22.pod.g++.1 new file mode 100644 index 0000000000..1635479223 --- /dev/null +++ b/examples/PACKAGES/pod/Ta_Quadratic/log.1Dec22.pod.g++.1 @@ -0,0 +1,143 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate POD Ta potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.316 +Lattice spacing in x,y,z = 3.316 3.316 3.316 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 128 atoms + using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264) + create_atoms CPU = 0.000 seconds + +mass 1 180.88 + + +# POD potential +pair_style pod +pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta +Reading potential file Ta_param.pod with DATE: 2022-11-30 +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body potential: 3 6 6 +three-body potential: 3 6 5 5 +four-body SNAP potential: 0 0 +quadratic POD potential: 1 +number of basis functions for one-body potential: 1 +number of basis functions for two-body potential: 6 +number of basis functions for three-body potential: 25 +number of basis functions for four-body potential: 0 +number of descriptors for one-body potential: 1 +number of descriptors for two-body potential: 6 +number of descriptors for three-body potential: 25 +number of descriptors for four-body potential: 0 +number of descriptors for quadratic POD potential: 150 +total number of descriptors for all potentials: 182 +**************** End of POD Potentials **************** + + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair pod, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.082 | 3.082 | 3.082 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -11.84932 0 -11.810845 12965.331 + 10 296.47479 -11.848868 0 -11.810845 12992.863 + 20 286.0912 -11.847536 0 -11.810845 13077.505 + 30 269.42142 -11.845399 0 -11.810845 13223.909 + 40 247.39188 -11.842573 0 -11.810845 13436.937 + 50 221.23616 -11.839219 0 -11.810845 13718.879 + 60 192.42749 -11.835524 0 -11.810845 14066.912 + 70 162.5922 -11.831697 0 -11.810845 14471.57 + 80 133.40727 -11.827954 0 -11.810845 14916.653 + 90 106.48844 -11.824502 0 -11.810844 15380.602 + 100 83.277725 -11.821525 0 -11.810844 15838.941 +Loop time of 2.21094 on 1 procs for 100 steps with 128 atoms + +Performance: 1.954 ns/day, 12.283 hours/ns, 45.230 timesteps/s, 5.789 katom-step/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.21 | 2.21 | 2.21 | 0.0 | 99.96 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00036776 | 0.00036776 | 0.00036776 | 0.0 | 0.02 +Output | 0.00019486 | 0.00019486 | 0.00019486 | 0.0 | 0.01 +Modify | 0.00016419 | 0.00016419 | 0.00016419 | 0.0 | 0.01 +Other | | 0.0002416 | | | 0.01 + +Nlocal: 128 ave 128 max 128 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 727 ave 727 max 727 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 7424 ave 7424 max 7424 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7424 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + + +Total wall time: 0:00:02 diff --git a/examples/PACKAGES/pod/Ta_Quadratic/log.1Dec22.pod.g++.4 b/examples/PACKAGES/pod/Ta_Quadratic/log.1Dec22.pod.g++.4 new file mode 100644 index 0000000000..0a9472c23e --- /dev/null +++ b/examples/PACKAGES/pod/Ta_Quadratic/log.1Dec22.pod.g++.4 @@ -0,0 +1,143 @@ +LAMMPS (3 Nov 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate POD Ta potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.316 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.316 +Lattice spacing in x,y,z = 3.316 3.316 3.316 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 128 atoms + using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264) + create_atoms CPU = 0.000 seconds + +mass 1 180.88 + + +# POD potential +pair_style pod +pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta +Reading potential file Ta_param.pod with DATE: 2022-11-30 +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body potential: 3 6 6 +three-body potential: 3 6 5 5 +four-body SNAP potential: 0 0 +quadratic POD potential: 1 +number of basis functions for one-body potential: 1 +number of basis functions for two-body potential: 6 +number of basis functions for three-body potential: 25 +number of basis functions for four-body potential: 0 +number of descriptors for one-body potential: 1 +number of descriptors for two-body potential: 6 +number of descriptors for three-body potential: 25 +number of descriptors for four-body potential: 0 +number of descriptors for quadratic POD potential: 150 +total number of descriptors for all potentials: 182 +**************** End of POD Potentials **************** + + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 loop geom +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6 + ghost atom cutoff = 6 + binsize = 3, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair pod, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.062 | 3.062 | 3.062 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -11.84932 0 -11.810845 12965.331 + 10 296.47479 -11.848868 0 -11.810845 12992.863 + 20 286.0912 -11.847536 0 -11.810845 13077.505 + 30 269.42142 -11.845399 0 -11.810845 13223.909 + 40 247.39188 -11.842573 0 -11.810845 13436.937 + 50 221.23616 -11.839219 0 -11.810845 13718.879 + 60 192.42749 -11.835524 0 -11.810845 14066.912 + 70 162.5922 -11.831697 0 -11.810845 14471.57 + 80 133.40727 -11.827954 0 -11.810845 14916.653 + 90 106.48844 -11.824502 0 -11.810844 15380.602 + 100 83.277725 -11.821525 0 -11.810844 15838.941 +Loop time of 0.680827 on 4 procs for 100 steps with 128 atoms + +Performance: 6.345 ns/day, 3.782 hours/ns, 146.880 timesteps/s, 18.801 katom-step/s +99.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.66292 | 0.66527 | 0.66845 | 0.3 | 97.72 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.011041 | 0.014313 | 0.01666 | 1.9 | 2.10 +Output | 0.00023806 | 0.00027584 | 0.00038453 | 0.0 | 0.04 +Modify | 0.00015182 | 0.00015927 | 0.00016433 | 0.0 | 0.02 +Other | | 0.0008078 | | | 0.12 + +Nlocal: 32 ave 32 max 32 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 431 ave 431 max 431 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 1856 ave 1856 max 1856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7424 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/sph/shock_tube/shock2d.lmp b/examples/PACKAGES/sph/shock_tube/shock2d.lmp index 32cfd8067b..c63b537bc7 100644 --- a/examples/PACKAGES/sph/shock_tube/shock2d.lmp +++ b/examples/PACKAGES/sph/shock_tube/shock2d.lmp @@ -22,7 +22,7 @@ pair_style hybrid/overlay sph/rhosum 1 sph/idealgas pair_coeff * * sph/rhosum 4.0 pair_coeff * * sph/idealgas 0.75 4.0 -compute rhoatom all shp/rho/atom +compute rhoatom all sph/rho/atom compute ieatom all sph/e/atom compute esph all reduce sum c_ieatom # total internal energy compute ke all ke diff --git a/examples/README b/examples/README index b563fd818e..c1c1c7dcd5 100644 --- a/examples/README +++ b/examples/README @@ -78,6 +78,7 @@ flow: Couette and Poiseuille flow in a 2d channel friction: frictional contact of spherical asperities between 2d surfaces gjf: use of fix langevin Gronbech-Jensen/Farago option granregion: use of fix wall/region/gran as boundary on granular particles +grid use of commands which overlay grids on the simulation domain hugoniostat: Hugoniostat shock dynamics hyper: global and local hyperdynamics of diffusion on Pt surface indent: spherical indenter into a 2d solid diff --git a/examples/grid/README b/examples/grid/README new file mode 100644 index 0000000000..4d65325308 --- /dev/null +++ b/examples/grid/README @@ -0,0 +1,23 @@ +These input scripts illustrate the use of several commands that +overlay grids on the simulation domain. + +fix ave/grid +compute property/grid +dump grid +dump grid/vtk + +The in.grid.2d and in.grid.3d scripts model simple Lennard Jones +liquids. The in.sph script models SPH water flowing over a dam. All +the scripts use dynamic load balancing to illustrate that the grid +cells can be dynamically partitioned across processors similar to how +particles are. + +To produce output dump files and image files, you will need to +uncomment the various "dump" commands that produce them. 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tiled +fix 100 all balance 100 0.9 rcb + +# fix ave/grid + +fix ave all ave/grid 10 10 100 10 10 1 vx vy + +# dump grid + +compute ave all property/grid 10 10 1 id ix iy +#dump ave all grid 100 tmp.dump.2d & +# c_ave:grid:data[*] f_ave:grid:count f_ave:grid:data[*] +#dump_modify ave sort 1 + +#dump vtk1 all grid/vtk 100 tmp.dump1.2d.*.vtr f_ave:grid:count + +#dump vtk2 all grid/vtk 100 tmp.dump2.2d.*.vtr f_ave:grid:data[2] + +#dump 10 all image 100 tmp.image.*.2d.png type type & +# zoom 1.6 grid f_ave:grid:count adiam 0.6 shiny 0.0 & +# subbox yes 0.01 + +# run + +thermo 100 + +run 500 diff --git a/examples/grid/in.grid.3d b/examples/grid/in.grid.3d new file mode 100644 index 0000000000..dc67f64cb5 --- /dev/null +++ b/examples/grid/in.grid.3d @@ -0,0 +1,50 @@ +# 3d Lennard-Jones melt + +units lj +atom_style atomic + +lattice fcc 0.8442 +region box block 0 10 0 10 0 10 +create_box 1 box +create_atoms 1 box +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +fix 1 all nve + +# load balancing + +comm_style tiled +fix 100 all balance 100 0.9 rcb + +# fix ave/grid + +fix ave all ave/grid 10 10 100 5 5 5 vx vy vz + +# dump grid + +compute ave all property/grid 5 5 5 id ix iy +#dump ave all grid 100 tmp.dump.3d & +# c_ave:grid:data[*] f_ave:grid:count f_ave:grid:data[*] +#dump_modify ave sort 1 + +#dump vtk1 all grid/vtk 100 tmp.dump1.3d.*.vtr f_ave:grid:count + +#dump vtk2 all grid/vtk 100 tmp.dump2.3d.*.vtr f_ave:grid:data[*] + +#dump 10 all image 100 tmp.image.*.3d.png type type & +# grid f_ave:grid:count view 60 -30 shiny 0.0 & +# subbox yes 0.01 + +# run + +thermo 100 + +run 500 diff --git a/examples/grid/in.sph b/examples/grid/in.sph new file mode 100644 index 0000000000..172b5be7d6 --- /dev/null +++ b/examples/grid/in.sph @@ -0,0 +1,112 @@ +# SPH water over dam + +atom_style sph +dimension 2 +newton on +boundary s s p +units lj + +read_data data.sph + +# upper limit of timestep based on CFL-like criterion +# roughly estimate number of timesteps needed for 7.5 seconds + +variable h equal 0.03 +variable c equal 10.0 # soundspeed for Tait's EOS +variable dt equal 0.1*${h}/${c} +variable nrun equal 15.0/${dt} + +# assign group name "bc" to boundary particles (type 2) +# assign group name "water" to water particles (type 1) + +group bc type 2 +group water type 1 + +# use hybrid pairstyle which does density summation +# with cutoff ${h} every timestep (1) +# use target density of 1000, soundspeed ${c} for Tait's EOS + +pair_style hybrid/overlay sph/rhosum 1 sph/taitwater +pair_coeff * * sph/taitwater 1000.0 ${c} 1.0 ${h} +pair_coeff 1 1 sph/rhosum ${h} + +# add gravity. This fix also computes potential energy of mass in gravity field + +fix gfix water gravity -9.81 vector 0 1 0 +fix 2d_fix all enforce2d + +compute rho_peratom all sph/rho/atom +compute e_peratom all sph/e/atom +compute esph all reduce sum c_e_peratom +compute ke all ke +variable etot equal c_esph+c_ke+f_gfix +compute ke_peratom all ke/atom + +# adjust nevery | min. allowed dt | max. allowed dt | +# max. travel distance per dt +# ${dt} ~= CFL criterion 0.1*h/c + +# remove top atoms + +region cut block INF INF 2.5 INF INF INF +delete_atoms region cut + +# use a variable timestep + +fix dtfix all dt/reset 1 NULL ${dt} 0.0005 units box + +# time-integrate position, velocities, +# internal energy and density of water particles + +fix integrate_water_fix water sph + +# time-integrate only internal energy and density of boundary particles + +fix integrate_bc_fix bc sph/stationary + +thermo 500 +thermo_style custom step ke c_esph v_etot f_gfix press time f_dtfix +thermo_modify norm no + +# load balancing + +comm_style tiled +fix 100 all balance 100 0.9 rcb + +# fix ave/grid + +fix ave all ave/grid 50 5 250 10 10 1 vx vy + +# dump particles + +#dump dump_id all custom 100 tmp.dump & +# id type x y z c_ke_peratom +#dump_modify dump_id first yes + +# dump grid + +#compute ave all property/grid 10 10 1 id ix iy +#dump ave all grid 250 tmp.grid c_ave:grid:data[*] f_ave:grid:data[*] +#dump_modify ave sort 1 + +# dump image + +#compute 1 all property/atom proc +#variable p atom c_1%10 + +#dump 3 all image 500 tmp.*.png c_ke_peratom type & +# adiam 0.015 view 0 0 zoom 2.5 subbox yes 0.01 & +# center d 0.5 0.5 0.5 size 1024 768 box no 0.0 & +# grid f_ave:grid:count +#variable colors string & +# "min blue 0.25 green 0.5 orange 0.75 yellow max red" +#dump_modify 3 pad 5 amap 0 1.5 cf 1 5 ${colors} + +# run + +neigh_modify every 5 delay 0 check no +variable skin equal 0.3*${h} +neighbor ${skin} bin + +run 6000 + diff --git a/examples/grid/log.1Dec22.grid.2d.g++.1 b/examples/grid/log.1Dec22.grid.2d.g++.1 new file mode 100644 index 0000000000..174225b1b9 --- /dev/null +++ b/examples/grid/log.1Dec22.grid.2d.g++.1 @@ -0,0 +1,104 @@ +LAMMPS (3 Nov 2022) +# 2d Lennard-Jones melt + +units lj +atom_style atomic +dimension 2 + +lattice sq 0.5 +Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136 +region box block 0 50 0 50 -0.5 0.5 +create_box 1 box +Created orthogonal box = (0 0 -0.70710678) to (70.710678 70.710678 0.70710678) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 2500 atoms + using lattice units in orthogonal box = (0 0 -0.70710678) to (70.710678 70.710678 0.70710678) + create_atoms CPU = 0.001 seconds +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +fix 1 all nve +fix 2 all enforce2d + +# load balancing + +comm_style tiled +fix 100 all balance 100 0.9 rcb + +# fix ave/grid + +fix ave all ave/grid 10 10 100 10 10 1 vx vy + +# dump grid + +compute ave all property/grid 10 10 1 id ix iy +#dump ave all grid 100 tmp.dump.2d # c_ave:grid:data[*] f_ave:grid:count f_ave:grid:data[*] +#dump_modify ave sort 1 + +#dump vtk1 all grid/vtk 100 tmp.dump1.2d.*.vtr f_ave:grid:count + +#dump vtk2 all grid/vtk 100 tmp.dump2.2d.*.vtr f_ave:grid:data[2] + +#dump 10 all image 100 tmp.image.*.2d.png type type # zoom 1.6 grid f_ave:grid:count adiam 0.6 shiny 0.0 # subbox yes 0.01 + +# run + +thermo 100 + +run 500 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 20 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 51 51 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.6 | 2.6 | 2.6 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 1.44 -0.99804688 0 0.44137713 -0.58692862 5000 + 100 1.5598149 -1.1263538 0 0.43283708 1.5290994 5000 + 200 1.6032951 -1.1706712 0 0.43198254 1.3417115 5000 + 300 1.6027535 -1.1702899 0 0.43182248 1.3590294 5000 + 400 1.6099053 -1.1774853 0 0.43177606 1.3305193 5000 + 500 1.6163874 -1.184699 0 0.43104185 1.346977 5000 +Loop time of 0.0605938 on 1 procs for 500 steps with 2500 atoms + +Performance: 3564723.496 tau/day, 8251.675 timesteps/s, 20.629 Matom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.042252 | 0.042252 | 0.042252 | 0.0 | 69.73 +Neigh | 0.0080564 | 0.0080564 | 0.0080564 | 0.0 | 13.30 +Comm | 0.00092699 | 0.00092699 | 0.00092699 | 0.0 | 1.53 +Output | 5.6077e-05 | 5.6077e-05 | 5.6077e-05 | 0.0 | 0.09 +Modify | 0.0087579 | 0.0087579 | 0.0087579 | 0.0 | 14.45 +Other | | 0.000544 | | | 0.90 + +Nlocal: 2500 ave 2500 max 2500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 405 ave 405 max 405 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 14487 ave 14487 max 14487 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 14487 +Ave neighs/atom = 5.7948 +Neighbor list builds = 25 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/grid/log.1Dec22.grid.2d.g++.12 b/examples/grid/log.1Dec22.grid.2d.g++.12 new file mode 100644 index 0000000000..0e9892e327 --- /dev/null +++ b/examples/grid/log.1Dec22.grid.2d.g++.12 @@ -0,0 +1,105 @@ +LAMMPS (3 Nov 2022) +WARNING: Using I/O redirection is unreliable with parallel runs. Better use -in switch to read input file. (../lammps.cpp:528) +# 2d Lennard-Jones melt + +units lj +atom_style atomic +dimension 2 + +lattice sq 0.5 +Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136 +region box block 0 50 0 50 -0.5 0.5 +create_box 1 box +Created orthogonal box = (0 0 -0.70710678) to (70.710678 70.710678 0.70710678) + 4 by 3 by 1 MPI processor grid +create_atoms 1 box +Created 2500 atoms + using lattice units in orthogonal box = (0 0 -0.70710678) to (70.710678 70.710678 0.70710678) + create_atoms CPU = 0.000 seconds +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +fix 1 all nve +fix 2 all enforce2d + +# load balancing + +comm_style tiled +fix 100 all balance 100 0.9 rcb + +# fix ave/grid + +fix ave all ave/grid 10 10 100 10 10 1 vx vy + +# dump grid + +compute ave all property/grid 10 10 1 id ix iy +#dump ave all grid 100 tmp.dump.2d # c_ave:grid:data[*] f_ave:grid:count f_ave:grid:data[*] +#dump_modify ave sort 1 + +#dump vtk1 all grid/vtk 100 tmp.dump1.2d.*.vtr f_ave:grid:count + +#dump vtk2 all grid/vtk 100 tmp.dump2.2d.*.vtr f_ave:grid:data[2] + +#dump 10 all image 100 tmp.image.*.2d.png type type # zoom 1.6 grid f_ave:grid:count adiam 0.6 shiny 0.0 # subbox yes 0.01 + +# run + +thermo 100 + +run 500 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 20 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 51 51 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.546 | 2.573 | 2.595 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 1.44 -0.99804687 0 0.44137713 -0.58692863 5000 + 100 1.5598149 -1.1263538 0 0.43283708 1.5290994 5000 + 200 1.6032951 -1.1706712 0 0.43198254 1.3417115 5000 + 300 1.6027535 -1.1702899 0 0.43182248 1.3590294 5000 + 400 1.6099053 -1.1774853 0 0.43177606 1.3305193 5000 + 500 1.6163874 -1.184699 0 0.43104185 1.346977 5000 +Loop time of 0.0234746 on 12 procs for 500 steps with 2500 atoms + +Performance: 9201451.891 tau/day, 21299.657 timesteps/s, 53.249 Matom-step/s +99.2% CPU use with 12 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0037768 | 0.006317 | 0.0074702 | 1.7 | 26.91 +Neigh | 0.0010967 | 0.0013082 | 0.0014397 | 0.3 | 5.57 +Comm | 0.0096964 | 0.011159 | 0.0145 | 1.7 | 47.54 +Output | 9.5604e-05 | 0.00012067 | 0.00016341 | 0.0 | 0.51 +Modify | 0.0034389 | 0.0039338 | 0.0041602 | 0.4 | 16.76 +Other | | 0.0006358 | | | 2.71 + +Nlocal: 208.333 ave 210 max 207 min +Histogram: 2 0 0 6 0 0 2 0 0 2 +Nghost: 137.333 ave 155 max 121 min +Histogram: 1 1 2 1 3 1 0 0 1 2 +Neighs: 1207.25 ave 1253 max 1169 min +Histogram: 2 1 2 0 3 1 0 0 1 2 + +Total # of neighbors = 14487 +Ave neighs/atom = 5.7948 +Neighbor list builds = 25 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/grid/log.1Dec22.grid.2d.g++.4 b/examples/grid/log.1Dec22.grid.2d.g++.4 new file mode 100644 index 0000000000..06e17d7bb1 --- /dev/null +++ b/examples/grid/log.1Dec22.grid.2d.g++.4 @@ -0,0 +1,105 @@ +LAMMPS (3 Nov 2022) +WARNING: Using I/O redirection is unreliable with parallel runs. Better use -in switch to read input file. (../lammps.cpp:528) +# 2d Lennard-Jones melt + +units lj +atom_style atomic +dimension 2 + +lattice sq 0.5 +Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136 +region box block 0 50 0 50 -0.5 0.5 +create_box 1 box +Created orthogonal box = (0 0 -0.70710678) to (70.710678 70.710678 0.70710678) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 2500 atoms + using lattice units in orthogonal box = (0 0 -0.70710678) to (70.710678 70.710678 0.70710678) + create_atoms CPU = 0.000 seconds +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +fix 1 all nve +fix 2 all enforce2d + +# load balancing + +comm_style tiled +fix 100 all balance 100 0.9 rcb + +# fix ave/grid + +fix ave all ave/grid 10 10 100 10 10 1 vx vy + +# dump grid + +compute ave all property/grid 10 10 1 id ix iy +#dump ave all grid 100 tmp.dump.2d # c_ave:grid:data[*] f_ave:grid:count f_ave:grid:data[*] +#dump_modify ave sort 1 + +#dump vtk1 all grid/vtk 100 tmp.dump1.2d.*.vtr f_ave:grid:count + +#dump vtk2 all grid/vtk 100 tmp.dump2.2d.*.vtr f_ave:grid:data[2] + +#dump 10 all image 100 tmp.image.*.2d.png type type # zoom 1.6 grid f_ave:grid:count adiam 0.6 shiny 0.0 # subbox yes 0.01 + +# run + +thermo 100 + +run 500 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 20 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 51 51 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.555 | 2.556 | 2.557 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 1.44 -0.99804687 0 0.44137712 -0.58692863 5000 + 100 1.5598149 -1.1263538 0 0.43283708 1.5290994 5000 + 200 1.6032951 -1.1706712 0 0.43198254 1.3417115 5000 + 300 1.6027535 -1.1702899 0 0.43182248 1.3590294 5000 + 400 1.6099053 -1.1774853 0 0.43177606 1.3305193 5000 + 500 1.6163874 -1.184699 0 0.43104185 1.346977 5000 +Loop time of 0.031365 on 4 procs for 500 steps with 2500 atoms + +Performance: 6886659.462 tau/day, 15941.341 timesteps/s, 39.853 Matom-step/s +100.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0098202 | 0.01197 | 0.018294 | 3.3 | 38.16 +Neigh | 0.0023502 | 0.0025479 | 0.0030895 | 0.6 | 8.12 +Comm | 0.0046956 | 0.012744 | 0.015481 | 4.1 | 40.63 +Output | 5.6153e-05 | 6.3163e-05 | 7.3849e-05 | 0.0 | 0.20 +Modify | 0.0032687 | 0.0036046 | 0.0046066 | 1.0 | 11.49 +Other | | 0.0004358 | | | 1.39 + +Nlocal: 625 ave 627 max 623 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 212 ave 216 max 207 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Neighs: 3621.75 ave 3673 max 3585 min +Histogram: 1 0 0 2 0 0 0 0 0 1 + +Total # of neighbors = 14487 +Ave neighs/atom = 5.7948 +Neighbor list builds = 25 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/grid/log.1Dec22.grid.3d.g++.1 b/examples/grid/log.1Dec22.grid.3d.g++.1 new file mode 100644 index 0000000000..603189c013 --- /dev/null +++ b/examples/grid/log.1Dec22.grid.3d.g++.1 @@ -0,0 +1,102 @@ +LAMMPS (3 Nov 2022) +# 3d Lennard-Jones melt + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 10 0 10 0 10 +create_box 1 box +Created orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4000 atoms + using lattice units in orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962) + create_atoms CPU = 0.001 seconds +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +fix 1 all nve + +# load balancing + +comm_style tiled +fix 100 all balance 100 0.9 rcb + +# fix ave/grid + +fix ave all ave/grid 10 10 100 5 5 5 vx vy vz + +# dump grid + +compute ave all property/grid 5 5 5 id ix iy +#dump ave all grid 100 tmp.dump.3d # c_ave:grid:data[*] f_ave:grid:count f_ave:grid:data[*] +#dump_modify ave sort 1 + +#dump vtk1 all grid/vtk 100 tmp.dump1.3d.*.vtr f_ave:grid:count + +#dump vtk2 all grid/vtk 100 tmp.dump2.3d.*.vtr f_ave:grid:data[*] + +#dump 10 all image 100 tmp.image.*.3d.png type type # grid f_ave:grid:count view 60 -30 shiny 0.0 # subbox yes 0.01 + +# run + +thermo 100 + +run 500 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 20 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.072 | 3.072 | 3.072 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 1.44 -6.7733681 0 -4.6139081 -5.0199732 4738.2137 + 100 0.75715334 -5.7581426 0 -4.6226965 0.20850222 4738.2137 + 200 0.75139921 -5.7500924 0 -4.6232753 0.25362795 4738.2137 + 300 0.73979146 -5.7326964 0 -4.6232866 0.37781798 4738.2137 + 400 0.73834687 -5.7300319 0 -4.6227884 0.41282909 4738.2137 + 500 0.72941121 -5.7153612 0 -4.6215179 0.49793402 4738.2137 +Loop time of 0.531792 on 1 procs for 500 steps with 4000 atoms + +Performance: 406174.160 tau/day, 940.218 timesteps/s, 3.761 Matom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.42996 | 0.42996 | 0.42996 | 0.0 | 80.85 +Neigh | 0.082407 | 0.082407 | 0.082407 | 0.0 | 15.50 +Comm | 0.007947 | 0.007947 | 0.007947 | 0.0 | 1.49 +Output | 8.9375e-05 | 8.9375e-05 | 8.9375e-05 | 0.0 | 0.02 +Modify | 0.009507 | 0.009507 | 0.009507 | 0.0 | 1.79 +Other | | 0.001879 | | | 0.35 + +Nlocal: 4000 ave 4000 max 4000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5657 ave 5657 max 5657 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 149883 ave 149883 max 149883 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 149883 +Ave neighs/atom = 37.47075 +Neighbor list builds = 25 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/grid/log.1Dec22.grid.3d.g++.10 b/examples/grid/log.1Dec22.grid.3d.g++.10 new file mode 100644 index 0000000000..816db23d5d --- /dev/null +++ b/examples/grid/log.1Dec22.grid.3d.g++.10 @@ -0,0 +1,103 @@ +LAMMPS (3 Nov 2022) +WARNING: Using I/O redirection is unreliable with parallel runs. Better use -in switch to read input file. (../lammps.cpp:528) +# 3d Lennard-Jones melt + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 10 0 10 0 10 +create_box 1 box +Created orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962) + 1 by 2 by 5 MPI processor grid +create_atoms 1 box +Created 4000 atoms + using lattice units in orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962) + create_atoms CPU = 0.000 seconds +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +fix 1 all nve + +# load balancing + +comm_style tiled +fix 100 all balance 100 0.9 rcb + +# fix ave/grid + +fix ave all ave/grid 10 10 100 5 5 5 vx vy vz + +# dump grid + +compute ave all property/grid 5 5 5 id ix iy +#dump ave all grid 100 tmp.dump.3d # c_ave:grid:data[*] f_ave:grid:count f_ave:grid:data[*] +#dump_modify ave sort 1 + +#dump vtk1 all grid/vtk 100 tmp.dump1.3d.*.vtr f_ave:grid:count + +#dump vtk2 all grid/vtk 100 tmp.dump2.3d.*.vtr f_ave:grid:data[*] + +#dump 10 all image 100 tmp.image.*.3d.png type type # grid f_ave:grid:count view 60 -30 shiny 0.0 # subbox yes 0.01 + +# run + +thermo 100 + +run 500 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 20 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.613 | 2.651 | 2.686 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 1.44 -6.7733681 0 -4.6139081 -5.0199732 4738.2137 + 100 0.75715334 -5.7581426 0 -4.6226965 0.20850222 4738.2137 + 200 0.75139921 -5.7500924 0 -4.6232753 0.25362795 4738.2137 + 300 0.73979146 -5.7326964 0 -4.6232866 0.37781798 4738.2137 + 400 0.73834687 -5.7300319 0 -4.6227884 0.41282909 4738.2137 + 500 0.72941121 -5.7153612 0 -4.6215179 0.49793402 4738.2137 +Loop time of 0.192284 on 10 procs for 500 steps with 4000 atoms + +Performance: 1123340.176 tau/day, 2600.324 timesteps/s, 10.401 Matom-step/s +94.0% CPU use with 10 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.059331 | 0.090145 | 0.11296 | 7.8 | 46.88 +Neigh | 0.0129 | 0.016371 | 0.019414 | 2.1 | 8.51 +Comm | 0.048952 | 0.07696 | 0.1131 | 9.9 | 40.02 +Output | 0.00012204 | 0.00013855 | 0.00019358 | 0.0 | 0.07 +Modify | 0.0053527 | 0.0062584 | 0.0070699 | 0.9 | 3.25 +Other | | 0.00241 | | | 1.25 + +Nlocal: 400 ave 402 max 398 min +Histogram: 2 0 1 0 0 3 0 3 0 1 +Nghost: 1709.1 ave 1774 max 1663 min +Histogram: 1 2 4 0 0 0 0 0 1 2 +Neighs: 14988.3 ave 15609 max 14496 min +Histogram: 3 1 0 0 1 1 1 2 0 1 + +Total # of neighbors = 149883 +Ave neighs/atom = 37.47075 +Neighbor list builds = 25 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/grid/log.1Dec22.grid.3d.g++.4 b/examples/grid/log.1Dec22.grid.3d.g++.4 new file mode 100644 index 0000000000..d302d9ab2e --- /dev/null +++ b/examples/grid/log.1Dec22.grid.3d.g++.4 @@ -0,0 +1,103 @@ +LAMMPS (3 Nov 2022) +WARNING: Using I/O redirection is unreliable with parallel runs. Better use -in switch to read input file. (../lammps.cpp:528) +# 3d Lennard-Jones melt + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 10 0 10 0 10 +create_box 1 box +Created orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 4000 atoms + using lattice units in orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962) + create_atoms CPU = 0.000 seconds +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +fix 1 all nve + +# load balancing + +comm_style tiled +fix 100 all balance 100 0.9 rcb + +# fix ave/grid + +fix ave all ave/grid 10 10 100 5 5 5 vx vy vz + +# dump grid + +compute ave all property/grid 5 5 5 id ix iy +#dump ave all grid 100 tmp.dump.3d # c_ave:grid:data[*] f_ave:grid:count f_ave:grid:data[*] +#dump_modify ave sort 1 + +#dump vtk1 all grid/vtk 100 tmp.dump1.3d.*.vtr f_ave:grid:count + +#dump vtk2 all grid/vtk 100 tmp.dump2.3d.*.vtr f_ave:grid:data[*] + +#dump 10 all image 100 tmp.image.*.3d.png type type # grid f_ave:grid:count view 60 -30 shiny 0.0 # subbox yes 0.01 + +# run + +thermo 100 + +run 500 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 20 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.748 | 2.797 | 2.844 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 1.44 -6.7733681 0 -4.6139081 -5.0199732 4738.2137 + 100 0.75715334 -5.7581426 0 -4.6226965 0.20850222 4738.2137 + 200 0.75139921 -5.7500924 0 -4.6232753 0.25362795 4738.2137 + 300 0.73979146 -5.7326964 0 -4.6232866 0.37781798 4738.2137 + 400 0.73834687 -5.7300319 0 -4.6227884 0.41282909 4738.2137 + 500 0.72941121 -5.7153612 0 -4.6215179 0.49793402 4738.2137 +Loop time of 0.198482 on 4 procs for 500 steps with 4000 atoms + +Performance: 1088259.442 tau/day, 2519.119 timesteps/s, 10.076 Matom-step/s +96.4% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.13322 | 0.13586 | 0.13838 | 0.5 | 68.45 +Neigh | 0.027201 | 0.027464 | 0.027811 | 0.1 | 13.84 +Comm | 0.025899 | 0.028681 | 0.031618 | 1.4 | 14.45 +Output | 7.6799e-05 | 8.8378e-05 | 0.00011635 | 0.0 | 0.04 +Modify | 0.0050217 | 0.0051246 | 0.0053789 | 0.2 | 2.58 +Other | | 0.001269 | | | 0.64 + +Nlocal: 1000 ave 1002 max 998 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 2797.75 ave 2810 max 2790 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Neighs: 37470.8 ave 38366 max 36995 min +Histogram: 2 0 0 1 0 0 0 0 0 1 + +Total # of neighbors = 149883 +Ave neighs/atom = 37.47075 +Neighbor list builds = 25 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/grid/log.1Dec22.sph.g++.1 b/examples/grid/log.1Dec22.sph.g++.1 new file mode 100644 index 0000000000..a0d2f4260d --- /dev/null +++ b/examples/grid/log.1Dec22.sph.g++.1 @@ -0,0 +1,193 @@ +LAMMPS (3 Nov 2022) +# SPH water over dam + +atom_style sph +dimension 2 +newton on +boundary s s p +units lj + +read_data data.sph +Reading data file ... + orthogonal box = (0 0 -0.001) to (4.001 8.001 0.001) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 15702 atoms + reading velocities ... + 15702 velocities + read_data CPU = 0.037 seconds + +# upper limit of timestep based on CFL-like criterion +# roughly estimate number of timesteps needed for 7.5 seconds + +variable h equal 0.03 +variable c equal 10.0 # soundspeed for Tait's EOS +variable dt equal 0.1*${h}/${c} +variable dt equal 0.1*0.03/${c} +variable dt equal 0.1*0.03/10 +variable nrun equal 15.0/${dt} +variable nrun equal 15.0/0.0003 + +# assign group name "bc" to boundary particles (type 2) +# assign group name "water" to water particles (type 1) + +group bc type 2 +6000 atoms in group bc +group water type 1 +9702 atoms in group water + +# use hybrid pairstyle which does density summation +# with cutoff ${h} every timestep (1) +# use target density of 1000, soundspeed ${c} for Tait's EOS + +pair_style hybrid/overlay sph/rhosum 1 sph/taitwater +pair_coeff * * sph/taitwater 1000.0 ${c} 1.0 ${h} +pair_coeff * * sph/taitwater 1000.0 10 1.0 ${h} +pair_coeff * * sph/taitwater 1000.0 10 1.0 0.03 +pair_coeff 1 1 sph/rhosum ${h} +pair_coeff 1 1 sph/rhosum 0.03 + +# add gravity. This fix also computes potential energy of mass in gravity field + +fix gfix water gravity -9.81 vector 0 1 0 +fix 2d_fix all enforce2d + +compute rho_peratom all sph/rho/atom +compute e_peratom all sph/e/atom +compute esph all reduce sum c_e_peratom +compute ke all ke +variable etot equal c_esph+c_ke+f_gfix +compute ke_peratom all ke/atom + +# adjust nevery | min. allowed dt | max. allowed dt | +# max. travel distance per dt +# ${dt} ~= CFL criterion 0.1*h/c + +# remove top atoms + +region cut block INF INF 2.5 INF INF INF +delete_atoms region cut +Deleted 3174 atoms, new total = 12528 + +# use a variable timestep + +fix dtfix all dt/reset 1 NULL ${dt} 0.0005 units box +fix dtfix all dt/reset 1 NULL 0.0003 0.0005 units box + +# time-integrate position, velocities, +# internal energy and density of water particles + +fix integrate_water_fix water sph + +# time-integrate only internal energy and density of boundary particles + +fix integrate_bc_fix bc sph/stationary + +thermo 500 +thermo_style custom step ke c_esph v_etot f_gfix press time f_dtfix +thermo_modify norm no + +# load balancing + +comm_style tiled +fix 100 all balance 100 0.9 rcb + +# fix ave/grid + +fix ave all ave/grid 50 5 250 10 10 1 vx vy + +# dump particles + +#dump dump_id all custom 100 tmp.dump # id type x y z c_ke_peratom +#dump_modify dump_id first yes + +# dump grid + +#compute ave all property/grid 10 10 1 id ix iy +#dump ave all grid 250 tmp.grid c_ave:grid:data[*] f_ave:grid:data[*] +#dump_modify ave sort 1 + +# dump image + +#compute 1 all property/atom proc +#variable p atom c_1%10 + +#dump 3 all image 500 tmp.*.png c_ke_peratom type # adiam 0.015 view 0 0 zoom 2.5 subbox yes 0.01 # center d 0.5 0.5 0.5 size 1024 768 box no 0.0 # grid f_ave:grid:count +#variable colors string # "min blue 0.25 green 0.5 orange 0.75 yellow max red" +#dump_modify 3 pad 5 amap 0 1.5 cf 1 5 ${colors} + +# run + +neigh_modify every 5 delay 0 check no +variable skin equal 0.3*${h} +variable skin equal 0.3*0.03 +neighbor ${skin} bin +neighbor 0.009 bin + +run 6000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 5 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0.039 + ghost atom cutoff = 0.039 + binsize = 0.0195, bins = 205 411 1 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair sph/rhosum, perpetual, skip from (3) + attributes: full, newton on + pair build: skip + stencil: none + bin: none + (2) pair sph/taitwater, perpetual, half/full from (3) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.755 | 6.755 | 6.755 Mbytes + Step KinEng c_esph v_etot f_gfix Press Time f_dtfix + 0 0 0 19320.854 19320.854 -3.624517 0 0 + 500 1274.8192 226.44643 19320.367 17819.101 754.35811 0.14057754 500 + 1000 2793.9358 410.18897 19320.367 16116.242 1184.8364 0.21912692 1000 + 1500 4227.2566 547.60309 19320.367 14545.508 1290.9567 0.27943572 1500 + 2000 5515.6545 763.42902 19320.367 13041.284 1468.5449 0.33279685 2000 + 2500 6595.5906 1087.0212 19320.368 11637.756 1878.9882 0.38198106 2500 + 3000 7053.147 1574.0538 19320.369 10693.168 2250.759 0.41605101 3000 + 3500 7396.4079 2058.4224 19320.369 9865.539 2517.1665 0.45034972 3500 + 4000 7690.0468 2419.389 19320.369 9210.9336 2615.8142 0.48685712 4000 + 4500 7986.5331 2529.7094 19320.369 8804.1268 2453.9595 0.52464306 4500 + 5000 8206.3658 2497.1242 19320.369 8616.879 1998.6296 0.56308208 5000 + 5500 8264.0602 2487.5778 19320.369 8568.7309 1614.3683 0.60225589 5500 + 6000 8185.7128 2570.3178 19320.369 8564.3383 1463.8307 0.64295437 6000 +Loop time of 22.4589 on 1 procs for 6000 steps with 12528 atoms + +Performance: 1919.324 tau/day, 267.155 timesteps/s, 3.347 Matom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 15.365 | 15.365 | 15.365 | 0.0 | 68.41 +Neigh | 5.2774 | 5.2774 | 5.2774 | 0.0 | 23.50 +Comm | 0.021675 | 0.021675 | 0.021675 | 0.0 | 0.10 +Output | 0.0011944 | 0.0011944 | 0.0011944 | 0.0 | 0.01 +Modify | 1.6991 | 1.6991 | 1.6991 | 0.0 | 7.57 +Other | | 0.09478 | | | 0.42 + +Nlocal: 12528 ave 12528 max 12528 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 153317 ave 153317 max 153317 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 153317 +Ave neighs/atom = 12.237947 +Neighbor list builds = 1200 +Dangerous builds not checked + +Total wall time: 0:00:22 diff --git a/examples/grid/log.1Dec22.sph.g++.12 b/examples/grid/log.1Dec22.sph.g++.12 new file mode 100644 index 0000000000..b2890cee3b --- /dev/null +++ b/examples/grid/log.1Dec22.sph.g++.12 @@ -0,0 +1,194 @@ +LAMMPS (3 Nov 2022) +WARNING: Using I/O redirection is unreliable with parallel runs. Better use -in switch to read input file. (../lammps.cpp:528) +# SPH water over dam + +atom_style sph +dimension 2 +newton on +boundary s s p +units lj + +read_data data.sph +Reading data file ... + orthogonal box = (0 0 -0.001) to (4.001 8.001 0.001) + 3 by 4 by 1 MPI processor grid + reading atoms ... + 15702 atoms + reading velocities ... + 15702 velocities + read_data CPU = 0.075 seconds + +# upper limit of timestep based on CFL-like criterion +# roughly estimate number of timesteps needed for 7.5 seconds + +variable h equal 0.03 +variable c equal 10.0 # soundspeed for Tait's EOS +variable dt equal 0.1*${h}/${c} +variable dt equal 0.1*0.03/${c} +variable dt equal 0.1*0.03/10 +variable nrun equal 15.0/${dt} +variable nrun equal 15.0/0.0003 + +# assign group name "bc" to boundary particles (type 2) +# assign group name "water" to water particles (type 1) + +group bc type 2 +6000 atoms in group bc +group water type 1 +9702 atoms in group water + +# use hybrid pairstyle which does density summation +# with cutoff ${h} every timestep (1) +# use target density of 1000, soundspeed ${c} for Tait's EOS + +pair_style hybrid/overlay sph/rhosum 1 sph/taitwater +pair_coeff * * sph/taitwater 1000.0 ${c} 1.0 ${h} +pair_coeff * * sph/taitwater 1000.0 10 1.0 ${h} +pair_coeff * * sph/taitwater 1000.0 10 1.0 0.03 +pair_coeff 1 1 sph/rhosum ${h} +pair_coeff 1 1 sph/rhosum 0.03 + +# add gravity. This fix also computes potential energy of mass in gravity field + +fix gfix water gravity -9.81 vector 0 1 0 +fix 2d_fix all enforce2d + +compute rho_peratom all sph/rho/atom +compute e_peratom all sph/e/atom +compute esph all reduce sum c_e_peratom +compute ke all ke +variable etot equal c_esph+c_ke+f_gfix +compute ke_peratom all ke/atom + +# adjust nevery | min. allowed dt | max. allowed dt | +# max. travel distance per dt +# ${dt} ~= CFL criterion 0.1*h/c + +# remove top atoms + +region cut block INF INF 2.5 INF INF INF +delete_atoms region cut +Deleted 3174 atoms, new total = 12528 + +# use a variable timestep + +fix dtfix all dt/reset 1 NULL ${dt} 0.0005 units box +fix dtfix all dt/reset 1 NULL 0.0003 0.0005 units box + +# time-integrate position, velocities, +# internal energy and density of water particles + +fix integrate_water_fix water sph + +# time-integrate only internal energy and density of boundary particles + +fix integrate_bc_fix bc sph/stationary + +thermo 500 +thermo_style custom step ke c_esph v_etot f_gfix press time f_dtfix +thermo_modify norm no + +# load balancing + +comm_style tiled +fix 100 all balance 100 0.9 rcb + +# fix ave/grid + +fix ave all ave/grid 50 5 250 10 10 1 vx vy + +# dump particles + +#dump dump_id all custom 100 tmp.dump # id type x y z c_ke_peratom +#dump_modify dump_id first yes + +# dump grid + +#compute ave all property/grid 10 10 1 id ix iy +#dump ave all grid 250 tmp.grid c_ave:grid:data[*] f_ave:grid:data[*] +#dump_modify ave sort 1 + +# dump image + +#compute 1 all property/atom proc +#variable p atom c_1%10 + +#dump 3 all image 500 tmp.*.png c_ke_peratom type # adiam 0.015 view 0 0 zoom 2.5 subbox yes 0.01 # center d 0.5 0.5 0.5 size 1024 768 box no 0.0 # grid f_ave:grid:count +#variable colors string # "min blue 0.25 green 0.5 orange 0.75 yellow max red" +#dump_modify 3 pad 5 amap 0 1.5 cf 1 5 ${colors} + +# run + +neigh_modify every 5 delay 0 check no +variable skin equal 0.3*${h} +variable skin equal 0.3*0.03 +neighbor ${skin} bin +neighbor 0.009 bin + +run 6000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 5 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0.039 + ghost atom cutoff = 0.039 + binsize = 0.0195, bins = 205 411 1 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair sph/rhosum, perpetual, skip from (3) + attributes: full, newton on + pair build: skip + stencil: none + bin: none + (2) pair sph/taitwater, perpetual, half/full from (3) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.06 | 5.302 | 6.72 Mbytes + Step KinEng c_esph v_etot f_gfix Press Time f_dtfix + 0 0 0 19320.854 19320.854 -3.624517 0 0 + 500 1274.8192 226.44643 19320.367 17819.101 754.35811 0.14057754 500 + 1000 2793.9358 410.18897 19320.367 16116.242 1184.8364 0.21912692 1000 + 1500 4227.2566 547.60309 19320.367 14545.508 1290.9567 0.27943572 1500 + 2000 5515.6545 763.42902 19320.367 13041.284 1468.5449 0.33279685 2000 + 2500 6595.5906 1087.0212 19320.368 11637.756 1878.9882 0.38198106 2500 + 3000 7053.147 1574.0538 19320.369 10693.168 2250.759 0.41605101 3000 + 3500 7396.4079 2058.4224 19320.369 9865.539 2517.1665 0.45034972 3500 + 4000 7690.0468 2419.389 19320.369 9210.9336 2615.8142 0.48685712 4000 + 4500 7986.5331 2529.7094 19320.369 8804.1268 2453.9595 0.52464306 4500 + 5000 8206.3658 2497.1242 19320.369 8616.879 1998.6296 0.56308208 5000 + 5500 8264.0602 2487.5778 19320.369 8568.7309 1614.3683 0.60225589 5500 + 6000 8185.7128 2570.3178 19320.369 8564.3383 1463.8307 0.64295437 6000 +Loop time of 5.47224 on 12 procs for 6000 steps with 12528 atoms + +Performance: 7877.181 tau/day, 1096.443 timesteps/s, 13.736 Matom-step/s +99.2% CPU use with 12 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.8469 | 3.1632 | 3.4316 | 11.3 | 57.80 +Neigh | 0.56431 | 0.78494 | 0.95346 | 14.2 | 14.34 +Comm | 0.4559 | 0.89439 | 1.4747 | 35.4 | 16.34 +Output | 0.0005864 | 0.00060563 | 0.00074071 | 0.0 | 0.01 +Modify | 0.51006 | 0.57563 | 0.65636 | 4.9 | 10.52 +Other | | 0.05352 | | | 0.98 + +Nlocal: 1044 ave 1046 max 1043 min +Histogram: 2 0 0 9 0 0 0 0 0 1 +Nghost: 244.75 ave 320 max 120 min +Histogram: 2 1 0 1 0 0 1 1 1 5 +Neighs: 12776.4 ave 16885 max 9467 min +Histogram: 1 1 1 2 3 1 0 2 0 1 + +Total # of neighbors = 153317 +Ave neighs/atom = 12.237947 +Neighbor list builds = 1200 +Dangerous builds not checked + +Total wall time: 0:00:05 diff --git a/examples/grid/log.1Dec22.sph.g++.4 b/examples/grid/log.1Dec22.sph.g++.4 new file mode 100644 index 0000000000..621249ed3a --- /dev/null +++ b/examples/grid/log.1Dec22.sph.g++.4 @@ -0,0 +1,194 @@ +LAMMPS (3 Nov 2022) +WARNING: Using I/O redirection is unreliable with parallel runs. Better use -in switch to read input file. (../lammps.cpp:528) +# SPH water over dam + +atom_style sph +dimension 2 +newton on +boundary s s p +units lj + +read_data data.sph +Reading data file ... + orthogonal box = (0 0 -0.001) to (4.001 8.001 0.001) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 15702 atoms + reading velocities ... + 15702 velocities + read_data CPU = 0.043 seconds + +# upper limit of timestep based on CFL-like criterion +# roughly estimate number of timesteps needed for 7.5 seconds + +variable h equal 0.03 +variable c equal 10.0 # soundspeed for Tait's EOS +variable dt equal 0.1*${h}/${c} +variable dt equal 0.1*0.03/${c} +variable dt equal 0.1*0.03/10 +variable nrun equal 15.0/${dt} +variable nrun equal 15.0/0.0003 + +# assign group name "bc" to boundary particles (type 2) +# assign group name "water" to water particles (type 1) + +group bc type 2 +6000 atoms in group bc +group water type 1 +9702 atoms in group water + +# use hybrid pairstyle which does density summation +# with cutoff ${h} every timestep (1) +# use target density of 1000, soundspeed ${c} for Tait's EOS + +pair_style hybrid/overlay sph/rhosum 1 sph/taitwater +pair_coeff * * sph/taitwater 1000.0 ${c} 1.0 ${h} +pair_coeff * * sph/taitwater 1000.0 10 1.0 ${h} +pair_coeff * * sph/taitwater 1000.0 10 1.0 0.03 +pair_coeff 1 1 sph/rhosum ${h} +pair_coeff 1 1 sph/rhosum 0.03 + +# add gravity. This fix also computes potential energy of mass in gravity field + +fix gfix water gravity -9.81 vector 0 1 0 +fix 2d_fix all enforce2d + +compute rho_peratom all sph/rho/atom +compute e_peratom all sph/e/atom +compute esph all reduce sum c_e_peratom +compute ke all ke +variable etot equal c_esph+c_ke+f_gfix +compute ke_peratom all ke/atom + +# adjust nevery | min. allowed dt | max. allowed dt | +# max. travel distance per dt +# ${dt} ~= CFL criterion 0.1*h/c + +# remove top atoms + +region cut block INF INF 2.5 INF INF INF +delete_atoms region cut +Deleted 3174 atoms, new total = 12528 + +# use a variable timestep + +fix dtfix all dt/reset 1 NULL ${dt} 0.0005 units box +fix dtfix all dt/reset 1 NULL 0.0003 0.0005 units box + +# time-integrate position, velocities, +# internal energy and density of water particles + +fix integrate_water_fix water sph + +# time-integrate only internal energy and density of boundary particles + +fix integrate_bc_fix bc sph/stationary + +thermo 500 +thermo_style custom step ke c_esph v_etot f_gfix press time f_dtfix +thermo_modify norm no + +# load balancing + +comm_style tiled +fix 100 all balance 100 0.9 rcb + +# fix ave/grid + +fix ave all ave/grid 50 5 250 10 10 1 vx vy + +# dump particles + +#dump dump_id all custom 100 tmp.dump # id type x y z c_ke_peratom +#dump_modify dump_id first yes + +# dump grid + +#compute ave all property/grid 10 10 1 id ix iy +#dump ave all grid 250 tmp.grid c_ave:grid:data[*] f_ave:grid:data[*] +#dump_modify ave sort 1 + +# dump image + +#compute 1 all property/atom proc +#variable p atom c_1%10 + +#dump 3 all image 500 tmp.*.png c_ke_peratom type # adiam 0.015 view 0 0 zoom 2.5 subbox yes 0.01 # center d 0.5 0.5 0.5 size 1024 768 box no 0.0 # grid f_ave:grid:count +#variable colors string # "min blue 0.25 green 0.5 orange 0.75 yellow max red" +#dump_modify 3 pad 5 amap 0 1.5 cf 1 5 ${colors} + +# run + +neigh_modify every 5 delay 0 check no +variable skin equal 0.3*${h} +variable skin equal 0.3*0.03 +neighbor ${skin} bin +neighbor 0.009 bin + +run 6000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 5 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0.039 + ghost atom cutoff = 0.039 + binsize = 0.0195, bins = 205 411 1 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair sph/rhosum, perpetual, skip from (3) + attributes: full, newton on + pair build: skip + stencil: none + bin: none + (2) pair sph/taitwater, perpetual, half/full from (3) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.607 | 5.957 | 6.474 Mbytes + Step KinEng c_esph v_etot f_gfix Press Time f_dtfix + 0 0 0 19320.854 19320.854 -3.624517 0 0 + 500 1274.8192 226.44643 19320.367 17819.101 754.35811 0.14057754 500 + 1000 2793.9358 410.18897 19320.367 16116.242 1184.8364 0.21912692 1000 + 1500 4227.2566 547.60309 19320.367 14545.508 1290.9567 0.27943572 1500 + 2000 5515.6545 763.42902 19320.367 13041.284 1468.5449 0.33279685 2000 + 2500 6595.5906 1087.0212 19320.368 11637.756 1878.9882 0.38198106 2500 + 3000 7053.147 1574.0538 19320.369 10693.168 2250.759 0.41605101 3000 + 3500 7396.4079 2058.4224 19320.369 9865.539 2517.1665 0.45034972 3500 + 4000 7690.0468 2419.389 19320.369 9210.9336 2615.8142 0.48685712 4000 + 4500 7986.5331 2529.7094 19320.369 8804.1268 2453.9595 0.52464306 4500 + 5000 8206.3658 2497.1242 19320.369 8616.879 1998.6296 0.56308208 5000 + 5500 8264.0602 2487.5778 19320.369 8568.7309 1614.3683 0.60225589 5500 + 6000 8185.7128 2570.3178 19320.369 8564.3383 1463.8307 0.64295437 6000 +Loop time of 8.44486 on 4 procs for 6000 steps with 12528 atoms + +Performance: 5104.390 tau/day, 710.492 timesteps/s, 8.901 Matom-step/s +99.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.3618 | 5.4752 | 5.5857 | 3.5 | 64.83 +Neigh | 1.607 | 1.7333 | 1.8496 | 6.6 | 20.53 +Comm | 0.36438 | 0.60163 | 0.70886 | 18.0 | 7.12 +Output | 0.00062026 | 0.00064412 | 0.00071499 | 0.0 | 0.01 +Modify | 0.57676 | 0.59785 | 0.60941 | 1.6 | 7.08 +Other | | 0.03618 | | | 0.43 + +Nlocal: 3132 ave 3134 max 3131 min +Histogram: 2 0 0 1 0 0 0 0 0 1 +Nghost: 248.25 ave 333 max 165 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +Neighs: 38329.2 ave 41127 max 35425 min +Histogram: 1 0 1 0 0 0 0 1 0 1 + +Total # of neighbors = 153317 +Ave neighs/atom = 12.237947 +Neighbor list builds = 1200 +Dangerous builds not checked + +Total wall time: 0:00:08 diff --git a/examples/mc/FeCu.pasianot.eamfs b/examples/mc/FeCu.pasianot.eamfs new file mode 100644 index 0000000000..a5633bacaf --- /dev/null +++ b/examples/mc/FeCu.pasianot.eamfs @@ -0,0 +1,9007 @@ +Fe-Cu potential by Pasianot and Malerba, JNM 360, 118 (2007) +Fe potential by Mendelev, Cu potential by Mishin +PE, 05/27/2009 +2 Fe Cu +5000 0.3000000000E-02 5000 0.1101358000E-02 5.506790000 +26 55.847 2.8553 BCC + 0.000000000000000e+00 -2.502338715878852e-01 -3.915852477615788e-01 -4.541520341263603e-01 -5.270235795086948e-01 + -5.820137813191907e-01 -6.334511319245772e-01 -6.793141998726575e-01 -7.215324706414761e-01 -7.606131975312557e-01 + -7.970827725223445e-01 -8.313329919387222e-01 -8.636549303943222e-01 -8.942886450128376e-01 -9.234251076248214e-01 + -9.512229825062409e-01 -9.778144791806214e-01 -1.003311523498760e+00 -1.027809755065672e+00 -1.051391697497198e+00 + -1.074129154477209e+00 -1.096085058497037e+00 -1.117314932647117e+00 -1.137868055905411e+00 -1.157788403784776e+00 + -1.177115413961566e+00 -1.195884611609660e+00 -1.214128134799185e+00 -1.231875173682360e+00 -1.249152335150178e+00 + 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1.937705190701948e-10 6.137307387111768e-11 1.213548138731746e-11 7.592420426160233e-13 diff --git a/examples/mc/in.sgcmc.eam b/examples/mc/in.sgcmc.eam new file mode 100644 index 0000000000..c649da8e8f --- /dev/null +++ b/examples/mc/in.sgcmc.eam @@ -0,0 +1,48 @@ +# general variables +variable temperature equal 700 +variable size equal 20 + +# variables for 'fix sgcmc' +variable nsteps_mc equal 100 +variable swap_fraction equal 0.2 +variable temperature_mc equal ${temperature} +variable deltamu equal -0.70 +variable target_concentration equal 0.02 +variable kappa equal 1e3 + +# general settings +units metal +atom_style atomic + +# set up structure +boundary p p p +lattice bcc 2.88 +region box block 0 ${size} 0 ${size} 0 ${size} +create_box 2 box +create_atoms 1 box +reset_timestep 0 +timestep 0.0025 + +# set up interaction +pair_style eam/fs +pair_coeff * * FeCu.pasianot.eamfs Fe Cu + +# initialize velocities +variable double_temp equal ${temperature}*2 +velocity all create ${double_temp} 428459 dist gaussian + +# what and how to run +fix integrate all npt & + temp ${temperature} ${temperature} 1.7 & + aniso 0.0 0.0 1.5 +fix mc all sgcmc ${nsteps_mc} ${swap_fraction} ${temperature_mc} ${deltamu} & + randseed 324234 & + variance ${kappa} ${target_concentration} + +# set up output +thermo 100 +thermo_style custom step temp atoms pe press & + lx ly lz f_mc[1] f_mc[2] f_mc[3] f_mc[4] +#dump 1 all custom 200 mc.*.dump id type x y z + +run 2000 diff --git a/examples/mc/log.13Dec22.sgcmc.eam.g++.1 b/examples/mc/log.13Dec22.sgcmc.eam.g++.1 new file mode 100644 index 0000000000..4c242f266a --- /dev/null +++ b/examples/mc/log.13Dec22.sgcmc.eam.g++.1 @@ -0,0 +1,143 @@ +LAMMPS (3 Nov 2022) + using 1 OpenMP thread(s) per MPI task +# general variables +variable temperature equal 700 +variable size equal 20 + +# variables for 'fix sgcmc' +variable nsteps_mc equal 100 +variable swap_fraction equal 0.2 +variable temperature_mc equal ${temperature} +variable temperature_mc equal 700 +variable deltamu equal -0.70 +variable target_concentration equal 0.02 +variable kappa equal 1e3 + +# general settings +units metal +atom_style atomic + +# set up structure +boundary p p p +lattice bcc 2.88 +Lattice spacing in x,y,z = 2.88 2.88 2.88 +region box block 0 ${size} 0 ${size} 0 ${size} +region box block 0 20 0 ${size} 0 ${size} +region box block 0 20 0 20 0 ${size} +region box block 0 20 0 20 0 20 +create_box 2 box +Created orthogonal box = (0 0 0) to (57.6 57.6 57.6) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 16000 atoms + using lattice units in orthogonal box = (0 0 0) to (57.6 57.6 57.6) + create_atoms CPU = 0.001 seconds +reset_timestep 0 +timestep 0.0025 + +# set up interaction +pair_style eam/fs +pair_coeff * * FeCu.pasianot.eamfs Fe Cu + +# initialize velocities +variable double_temp equal ${temperature}*2 +variable double_temp equal 700*2 +velocity all create ${double_temp} 428459 dist gaussian +velocity all create 1400 428459 dist gaussian + +# what and how to run +fix integrate all npt temp ${temperature} ${temperature} 1.7 aniso 0.0 0.0 1.5 +fix integrate all npt temp 700 ${temperature} 1.7 aniso 0.0 0.0 1.5 +fix integrate all npt temp 700 700 1.7 aniso 0.0 0.0 1.5 +fix mc all sgcmc ${nsteps_mc} ${swap_fraction} ${temperature_mc} ${deltamu} randseed 324234 variance ${kappa} ${target_concentration} +fix mc all sgcmc 100 ${swap_fraction} ${temperature_mc} ${deltamu} randseed 324234 variance ${kappa} ${target_concentration} +fix mc all sgcmc 100 0.2 ${temperature_mc} ${deltamu} randseed 324234 variance ${kappa} ${target_concentration} +fix mc all sgcmc 100 0.2 700 ${deltamu} randseed 324234 variance ${kappa} ${target_concentration} +fix mc all sgcmc 100 0.2 700 -0.7 randseed 324234 variance ${kappa} ${target_concentration} +fix mc all sgcmc 100 0.2 700 -0.7 randseed 324234 variance 1000 ${target_concentration} +fix mc all sgcmc 100 0.2 700 -0.7 randseed 324234 variance 1000 0.02 + SGC - Number of MD timesteps: 100 + SGC - Fraction of swap atoms: 0.2 + SGC - Temperature: %f + SGC - Chemical potential of species 2: -0.7 + SGC - Random number seed: 324234 + SGC - Kappa: 1000 + SGC - Target concentration of species 2: 0.02 + SGC - Target concentration of species 1: 0.98 + +# set up output +thermo 100 +thermo_style custom step temp atoms pe press lx ly lz f_mc[1] f_mc[2] f_mc[3] f_mc[4] +#dump 1 all custom 200 mc.*.dump id type x y z + +run 2000 + SGC - Interaction radius: 5.50679 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.50679 + ghost atom cutoff = 7.50679 + binsize = 3.753395, bins = 16 16 16 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/fs, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) fix sgcmc, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 25.06 | 25.06 | 25.06 Mbytes + Step Temp Atoms PotEng Press Lx Ly Lz f_mc[1] f_mc[2] f_mc[3] f_mc[4] + 0 1400 16000 -65889.786 -28854.541 57.6 57.6 57.6 0 0 1 0 + 100 734.32713 16000 -64514.143 5439.4277 57.327173 57.322333 57.318848 12 3188 0.99925 0.00075 + 200 678.63428 16000 -64386.224 -920.7819 57.423954 57.409111 57.412727 22 3178 0.997875 0.002125 + 300 683.24749 16000 -64370.598 -1609.0429 57.427441 57.424568 57.426831 20 3180 0.996625 0.003375 + 400 689.28007 16000 -64359.115 2489.3933 57.376537 57.379856 57.372895 27 3173 0.9949375 0.0050625 + 500 693.85333 16000 -64337.222 -1935.9815 57.435754 57.43493 57.427453 18 3182 0.9938125 0.0061875 + 600 693.52855 16000 -64314.465 380.8264 57.410314 57.397604 57.408337 21 3179 0.9925 0.0075 + 700 690.62721 16000 -64284.369 208.21986 57.412407 57.407285 57.410684 31 3169 0.9905625 0.0094375 + 800 687.08129 16000 -64244.443 -936.31731 57.425765 57.438983 57.421321 31 3169 0.988625 0.011375 + 900 696.07347 16000 -64230.523 932.65537 57.414588 57.413865 57.402817 27 3173 0.9869375 0.0130625 + 1000 691.70667 16000 -64194.151 -690.02055 57.429033 57.420053 57.443245 23 3177 0.9855 0.0145 + 1100 691.21797 16000 -64169.016 -86.623524 57.42147 57.424262 57.436841 35 3165 0.9833125 0.0166875 + 1200 691.27155 16000 -64134.443 411.68129 57.425111 57.432481 57.4118 42 3158 0.9806875 0.0193125 + 1300 693.76194 16000 -64098.615 -943.9013 57.446704 57.448382 57.440727 64 3136 0.9800625 0.0199375 + 1400 691.16411 16000 -64080.423 1248.7921 57.417118 57.409651 57.435099 104 3096 0.9799375 0.0200625 + 1500 694.49681 16000 -64084.428 -179.5269 57.440533 57.432581 57.434409 68 3132 0.9799375 0.0200625 + 1600 697.58329 16000 -64089.682 -761.14401 57.450616 57.450654 57.422293 97 3103 0.98 0.02 + 1700 697.57549 16000 -64090.2 1370.3938 57.399319 57.423969 57.426788 85 3115 0.9801875 0.0198125 + 1800 694.18435 16000 -64083.812 -1381.5398 57.446114 57.438096 57.475109 84 3116 0.9799375 0.0200625 + 1900 702.82577 16000 -64096.005 918.83968 57.452789 57.404638 57.408161 70 3130 0.9799375 0.0200625 + 2000 696.02963 16000 -64080.059 276.99031 57.443085 57.452012 57.403928 81 3119 0.980125 0.019875 +Loop time of 48.793 on 1 procs for 2000 steps with 16000 atoms + +Performance: 8.854 ns/day, 2.711 hours/ns, 40.989 timesteps/s, 655.831 katom-step/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 | 47.46 | 47.46 | 47.46 | 0.0 | 97.27 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.13269 | 0.13269 | 0.13269 | 0.0 | 0.27 +Output | 0.0011432 | 0.0011432 | 0.0011432 | 0.0 | 0.00 +Modify | 1.0996 | 1.0996 | 1.0996 | 0.0 | 2.25 +Other | | 0.0993 | | | 0.20 + +Nlocal: 16000 ave 16000 max 16000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 17201 ave 17201 max 17201 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1.344e+06 ave 1.344e+06 max 1.344e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 2.688e+06 ave 2.688e+06 max 2.688e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2688000 +Ave neighs/atom = 168 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:48 diff --git a/examples/mc/log.13Dec22.sgcmc.eam.g++.4 b/examples/mc/log.13Dec22.sgcmc.eam.g++.4 new file mode 100644 index 0000000000..403a40ebae --- /dev/null +++ b/examples/mc/log.13Dec22.sgcmc.eam.g++.4 @@ -0,0 +1,143 @@ +LAMMPS (3 Nov 2022) + using 1 OpenMP thread(s) per MPI task +# general variables +variable temperature equal 700 +variable size equal 20 + +# variables for 'fix sgcmc' +variable nsteps_mc equal 100 +variable swap_fraction equal 0.2 +variable temperature_mc equal ${temperature} +variable temperature_mc equal 700 +variable deltamu equal -0.70 +variable target_concentration equal 0.02 +variable kappa equal 1e3 + +# general settings +units metal +atom_style atomic + +# set up structure +boundary p p p +lattice bcc 2.88 +Lattice spacing in x,y,z = 2.88 2.88 2.88 +region box block 0 ${size} 0 ${size} 0 ${size} +region box block 0 20 0 ${size} 0 ${size} +region box block 0 20 0 20 0 ${size} +region box block 0 20 0 20 0 20 +create_box 2 box +Created orthogonal box = (0 0 0) to (57.6 57.6 57.6) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 16000 atoms + using lattice units in orthogonal box = (0 0 0) to (57.6 57.6 57.6) + create_atoms CPU = 0.001 seconds +reset_timestep 0 +timestep 0.0025 + +# set up interaction +pair_style eam/fs +pair_coeff * * FeCu.pasianot.eamfs Fe Cu + +# initialize velocities +variable double_temp equal ${temperature}*2 +variable double_temp equal 700*2 +velocity all create ${double_temp} 428459 dist gaussian +velocity all create 1400 428459 dist gaussian + +# what and how to run +fix integrate all npt temp ${temperature} ${temperature} 1.7 aniso 0.0 0.0 1.5 +fix integrate all npt temp 700 ${temperature} 1.7 aniso 0.0 0.0 1.5 +fix integrate all npt temp 700 700 1.7 aniso 0.0 0.0 1.5 +fix mc all sgcmc ${nsteps_mc} ${swap_fraction} ${temperature_mc} ${deltamu} randseed 324234 variance ${kappa} ${target_concentration} +fix mc all sgcmc 100 ${swap_fraction} ${temperature_mc} ${deltamu} randseed 324234 variance ${kappa} ${target_concentration} +fix mc all sgcmc 100 0.2 ${temperature_mc} ${deltamu} randseed 324234 variance ${kappa} ${target_concentration} +fix mc all sgcmc 100 0.2 700 ${deltamu} randseed 324234 variance ${kappa} ${target_concentration} +fix mc all sgcmc 100 0.2 700 -0.7 randseed 324234 variance ${kappa} ${target_concentration} +fix mc all sgcmc 100 0.2 700 -0.7 randseed 324234 variance 1000 ${target_concentration} +fix mc all sgcmc 100 0.2 700 -0.7 randseed 324234 variance 1000 0.02 + SGC - Number of MD timesteps: 100 + SGC - Fraction of swap atoms: 0.2 + SGC - Temperature: %f + SGC - Chemical potential of species 2: -0.7 + SGC - Random number seed: 324234 + SGC - Kappa: 1000 + SGC - Target concentration of species 2: 0.02 + SGC - Target concentration of species 1: 0.98 + +# set up output +thermo 100 +thermo_style custom step temp atoms pe press lx ly lz f_mc[1] f_mc[2] f_mc[3] f_mc[4] +#dump 1 all custom 200 mc.*.dump id type x y z + +run 2000 + SGC - Interaction radius: 5.50679 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.50679 + ghost atom cutoff = 7.50679 + binsize = 3.753395, bins = 16 16 16 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/fs, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) fix sgcmc, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.809 | 7.809 | 7.809 Mbytes + Step Temp Atoms PotEng Press Lx Ly Lz f_mc[1] f_mc[2] f_mc[3] f_mc[4] + 0 1400 16000 -65889.786 -28854.541 57.6 57.6 57.6 0 0 1 0 + 100 741.39222 16000 -64528.923 5317.2919 57.324639 57.32318 57.314928 19 3181 0.9988125 0.0011875 + 200 691.21024 16000 -64405.429 -1238.5107 57.421346 57.415516 57.412006 16 3184 0.9978125 0.0021875 + 300 686.85178 16000 -64377.312 -1816.799 57.424469 57.424335 57.425065 25 3175 0.996375 0.003625 + 400 690.93203 16000 -64358.609 2211.7763 57.376246 57.38185 57.381742 16 3184 0.995375 0.004625 + 500 696.77972 16000 -64350.3 -1583.8383 57.432929 57.426928 57.425935 22 3178 0.994125 0.005875 + 600 694.13567 16000 -64320.831 144.2514 57.420097 57.403531 57.401394 19 3181 0.9930625 0.0069375 + 700 691.79625 16000 -64295.155 384.47869 57.410637 57.412957 57.40707 25 3175 0.991625 0.008375 + 800 692.12887 16000 -64270.053 -764.91901 57.415576 57.43037 57.428708 21 3179 0.9903125 0.0096875 + 900 693.26555 16000 -64249.904 666.65335 57.408245 57.407059 57.417437 34 3166 0.9885625 0.0114375 + 1000 697.97016 16000 -64230.234 -562.91022 57.432317 57.424316 57.423668 28 3172 0.9868125 0.0131875 + 1100 686.52149 16000 -64177.536 -267.21801 57.429 57.434594 57.419878 35 3165 0.984875 0.015125 + 1200 691.55047 16000 -64156.268 810.17844 57.422282 57.413529 57.422883 37 3163 0.9828125 0.0171875 + 1300 691.91944 16000 -64124.602 -1012.7184 57.441793 57.433848 57.446947 32 3168 0.9810625 0.0189375 + 1400 701.78807 16000 -64116.475 180.93518 57.425156 57.438679 57.419575 76 3124 0.9799375 0.0200625 + 1500 692.75501 16000 -64080.481 176.96902 57.429275 57.442405 57.426519 81 3119 0.980125 0.019875 + 1600 694.11818 16000 -64083.435 -785.49617 57.442143 57.432114 57.458304 86 3114 0.98 0.02 + 1700 697.72576 16000 -64088.874 1227.5194 57.423225 57.408678 57.427056 75 3125 0.9800625 0.0199375 + 1800 697.24171 16000 -64086.742 -1166.4832 57.447168 57.47416 57.425229 67 3133 0.98025 0.01975 + 1900 699.53558 16000 -64092.97 214.99908 57.425459 57.437864 57.431139 86 3114 0.98025 0.01975 + 2000 699.00277 16000 -64089.117 978.69672 57.429266 57.39107 57.448289 81 3119 0.9798125 0.0201875 +Loop time of 15.2907 on 4 procs for 2000 steps with 16000 atoms + +Performance: 28.252 ns/day, 0.849 hours/ns, 130.798 timesteps/s, 2.093 Matom-step/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 14.31 | 14.404 | 14.479 | 1.6 | 94.20 +Neigh | 0.090756 | 0.091006 | 0.091258 | 0.1 | 0.60 +Comm | 0.27623 | 0.35113 | 0.44457 | 10.4 | 2.30 +Output | 0.0006002 | 0.0013338 | 0.0035331 | 3.5 | 0.01 +Modify | 0.38023 | 0.38128 | 0.38228 | 0.2 | 2.49 +Other | | 0.06148 | | | 0.40 + +Nlocal: 4000 ave 4017 max 3970 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +Nghost: 8274.75 ave 8305 max 8257 min +Histogram: 1 1 0 1 0 0 0 0 0 1 +Neighs: 311257 ave 313506 max 308273 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +FullNghs: 622514 ave 626251 max 616896 min +Histogram: 1 0 0 0 0 0 1 1 0 1 + +Total # of neighbors = 2490056 +Ave neighs/atom = 155.6285 +Neighbor list builds = 6 +Dangerous builds = 0 +Total wall time: 0:00:15 diff --git a/examples/plugins/LAMMPSInterfaceCXX.cmake b/examples/plugins/LAMMPSInterfaceCXX.cmake index a3313215d6..7eef5bd6e4 100644 --- a/examples/plugins/LAMMPSInterfaceCXX.cmake +++ b/examples/plugins/LAMMPSInterfaceCXX.cmake @@ -45,45 +45,80 @@ if(BUILD_MPI) 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 "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball") - set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball") - set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball") - mark_as_advanced(MPICH2_WIN64_DEVEL_URL) - mark_as_advanced(MPICH2_WIN32_DEVEL_URL) - mark_as_advanced(MPICH2_WIN64_DEVEL_MD5) - mark_as_advanced(MPICH2_WIN32_DEVEL_MD5) + # Download and configure MinGW compatible MPICH development files for Windows + option(USE_MSMPI "Use Microsoft's MS-MPI SDK instead of MPICH2-1.4.1" OFF) + if(USE_MSMPI) + message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation") + set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball") + set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball") + mark_as_advanced(MPICH2_WIN64_DEVEL_URL) + mark_as_advanced(MPICH2_WIN64_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) + include(ExternalProject) + if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64") + ExternalProject_Add(mpi4win_build + URL ${MPICH2_WIN64_DEVEL_URL} + URL_MD5 ${MPICH2_WIN64_DEVEL_MD5} + CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" + BUILD_BYPRODUCTS /lib/libmsmpi.a) + else() + message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI") + endif() + + ExternalProject_get_property(mpi4win_build SOURCE_DIR) + file(MAKE_DIRECTORY "${SOURCE_DIR}/include") + add_library(MPI::MPI_CXX UNKNOWN IMPORTED) + set_target_properties(MPI::MPI_CXX PROPERTIES + IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a" + INTERFACE_INCLUDE_DIRECTORIES "${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/libmsmpi.a") else() - ExternalProject_Add(mpi4win_build - URL ${MPICH2_WIN32_DEVEL_URL} - URL_MD5 ${MPICH2_WIN32_DEVEL_MD5} - CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" - BUILD_BYPRODUCTS /lib/libmpi.a) + # Download and configure custom MPICH files for Windows + message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows") + set(MPICH2_WIN64_DEVEL_URL "${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") 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) diff --git a/examples/plugins/angle_zero2.cpp b/examples/plugins/angle_zero2.cpp index bc2f6869dc..2db7645245 100644 --- a/examples/plugins/angle_zero2.cpp +++ b/examples/plugins/angle_zero2.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/plugins/angle_zero2.h b/examples/plugins/angle_zero2.h index e9a5df3ae4..1bdda7472d 100644 --- a/examples/plugins/angle_zero2.h +++ b/examples/plugins/angle_zero2.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/plugins/bond_zero2.cpp b/examples/plugins/bond_zero2.cpp index 768f176c63..7ca904b31d 100644 --- a/examples/plugins/bond_zero2.cpp +++ b/examples/plugins/bond_zero2.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/plugins/bond_zero2.h b/examples/plugins/bond_zero2.h index e01ec8c1fc..52b919567a 100644 --- a/examples/plugins/bond_zero2.h +++ b/examples/plugins/bond_zero2.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/plugins/dihedral_zero2.cpp b/examples/plugins/dihedral_zero2.cpp index a597d7a48e..df4e873993 100644 --- a/examples/plugins/dihedral_zero2.cpp +++ b/examples/plugins/dihedral_zero2.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/plugins/dihedral_zero2.h b/examples/plugins/dihedral_zero2.h index ca0e49b21a..2e28d6e943 100644 --- a/examples/plugins/dihedral_zero2.h +++ b/examples/plugins/dihedral_zero2.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/plugins/fix_nve2.cpp b/examples/plugins/fix_nve2.cpp index 498cb40d21..321dd802b6 100644 --- a/examples/plugins/fix_nve2.cpp +++ b/examples/plugins/fix_nve2.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/plugins/fix_nve2.h b/examples/plugins/fix_nve2.h index 3be0131d28..83c334c658 100644 --- a/examples/plugins/fix_nve2.h +++ b/examples/plugins/fix_nve2.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/plugins/improper_zero2.cpp b/examples/plugins/improper_zero2.cpp index 9b0335df8b..c2b9203832 100644 --- a/examples/plugins/improper_zero2.cpp +++ b/examples/plugins/improper_zero2.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/plugins/improper_zero2.h b/examples/plugins/improper_zero2.h index f561a4ae19..8ce2f2d001 100644 --- a/examples/plugins/improper_zero2.h +++ b/examples/plugins/improper_zero2.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/plugins/pair_morse2.cpp b/examples/plugins/pair_morse2.cpp index 738fd53e87..f09be36585 100644 --- a/examples/plugins/pair_morse2.cpp +++ b/examples/plugins/pair_morse2.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/plugins/pair_morse2.h b/examples/plugins/pair_morse2.h index c796cd1164..149a518908 100644 --- a/examples/plugins/pair_morse2.h +++ b/examples/plugins/pair_morse2.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/plugins/pair_morse2_omp.cpp b/examples/plugins/pair_morse2_omp.cpp index 9c81bad970..71313bd5f3 100644 --- a/examples/plugins/pair_morse2_omp.cpp +++ b/examples/plugins/pair_morse2_omp.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/examples/plugins/pair_morse2_omp.h b/examples/plugins/pair_morse2_omp.h index ec8f28e074..79f729efde 100644 --- a/examples/plugins/pair_morse2_omp.h +++ b/examples/plugins/pair_morse2_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/plugins/pair_zero2.cpp b/examples/plugins/pair_zero2.cpp index c5197a67a6..ed264aa00b 100644 --- a/examples/plugins/pair_zero2.cpp +++ b/examples/plugins/pair_zero2.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/plugins/pair_zero2.h b/examples/plugins/pair_zero2.h index 8c8ed6f59e..6be0c5b0f1 100644 --- a/examples/plugins/pair_zero2.h +++ b/examples/plugins/pair_zero2.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/examples/ttm/in.ttm.grid b/examples/ttm/in.ttm.grid index 2e3c622823..5c3b9c41fb 100644 --- a/examples/ttm/in.ttm.grid +++ b/examples/ttm/in.ttm.grid @@ -40,4 +40,22 @@ thermo 100 thermo_style custom step temp etotal f_twotemp[1] f_twotemp[2] thermo_modify format float "%20.16g" +# dump output + +#compute 1 all property/grid 10 10 10 id ix iy iz +#dump 1 all grid 100 tmp.dump c_1:grid:data[*] f_twotemp:grid:data +#dump_modify 1 sort 1 + +#compute 10 all property/grid 10 10 10 id xc yc zc +#fix ave all ave/grid 10 10 100 10 10 10 f_twotemp:grid:data + +#dump ave all grid 100 tmp.dump.ave & +# c_10:grid:data[*] f_ave:grid:data +#dump_modify ave sort id + +#dump vtk all grid/vtk 100 tmp.dump.*.vtk f_ave:grid:data +#dump_modify vtk sort id buffer no + +# run simulation + run 1000 diff --git a/examples/ttm/log.26Aug21.ttm.grid.g++.1 b/examples/ttm/log.1Dec22.ttm.grid.g++.1 similarity index 53% rename from examples/ttm/log.26Aug21.ttm.grid.g++.1 rename to examples/ttm/log.1Dec22.ttm.grid.g++.1 index a576583557..9d4a91cf55 100644 --- a/examples/ttm/log.26Aug21.ttm.grid.g++.1 +++ b/examples/ttm/log.1Dec22.ttm.grid.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (30 Jul 2021) +LAMMPS (3 Nov 2022) units metal atom_style atomic boundary p p p @@ -6,7 +6,7 @@ boundary p p p variable latc equal 2.87 lattice bcc ${latc} lattice bcc 2.87 -Lattice spacing in x,y,z = 2.8700000 2.8700000 2.8700000 +Lattice spacing in x,y,z = 2.87 2.87 2.87 variable xmax equal 10.0 variable xmin equal -10.0 variable ymax equal 10.0 @@ -22,7 +22,7 @@ region sim_box block -10 10 -10 10 ${zmin} ${zmax} units latti region sim_box block -10 10 -10 10 -10 ${zmax} units lattice region sim_box block -10 10 -10 10 -10 10 units lattice create_box 1 sim_box -Created orthogonal box = (-28.700000 -28.700000 -28.700000) to (28.700000 28.700000 28.700000) +Created orthogonal box = (-28.7 -28.7 -28.7) to (28.7 28.7 28.7) 1 by 1 by 1 MPI processor grid region atom_box block ${xmin} ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} units lattice region atom_box block -10 ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} units lattice @@ -33,14 +33,14 @@ region atom_box block -10 10 -10 10 -10 ${zmax} units lattice region atom_box block -10 10 -10 10 -10 10 units lattice create_atoms 1 region atom_box Created 16000 atoms - using lattice units in orthogonal box = (-28.700000 -28.700000 -28.700000) to (28.700000 28.700000 28.700000) - create_atoms CPU = 0.005 seconds + using lattice units in orthogonal box = (-28.7 -28.7 -28.7) to (28.7 28.7 28.7) + create_atoms CPU = 0.002 seconds mass 1 55.845 -include pot_iron.mod pair_style eam/fs pair_coeff * * FeVoter-ChenRecheck.fs Fe +Reading eam/fs potential file FeVoter-ChenRecheck.fs with DATE: 2016-04-04 neighbor 2.0 bin neigh_modify every 5 delay 0 check yes @@ -58,9 +58,26 @@ thermo 100 thermo_style custom step temp etotal f_twotemp[1] f_twotemp[2] thermo_modify format float "%20.16g" +# dump output + +#compute 1 all property/grid 10 10 10 id ix iy iz +#dump 1 all grid 100 tmp.dump c_1:grid:data[*] f_twotemp:grid:data +#dump_modify 1 sort 1 + +#compute 10 all property/grid 10 10 10 id xc yc zc +#fix ave all ave/grid 10 10 100 10 10 10 f_twotemp:grid:data + +#dump ave all grid 100 tmp.dump.ave # c_10:grid:data[*] f_ave:grid:data +#dump_modify ave sort id + +#dump vtk all grid/vtk 100 tmp.dump.*.vtk f_ave:grid:data +#dump_modify vtk sort id buffer no + +# run simulation + run 1000 Neighbor list info ... - update every 5 steps, delay 0 steps, check yes + update: every = 5 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.524 ghost atom cutoff = 6.524 @@ -72,42 +89,42 @@ Neighbor list info ... stencil: half/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.99 | 10.99 | 10.99 Mbytes -Step Temp TotEng f_twotemp[1] f_twotemp[2] - 0 0 -68483.52254543516 371.9188105082105 0 - 100 17.01353086098387 -68446.50228930202 334.6217068813629 0.3763710887774046 - 200 27.91331236535322 -68413.16008042906 301.3181773007303 0.3165912892484031 - 300 32.20115656493125 -68383.19634217303 271.3756381838045 0.2901111802983097 - 400 33.46056398887347 -68355.73057141017 243.9344715501159 0.2548133388123378 - 500 35.5346204243821 -68331.63060947017 219.84946888619 0.2388591367999414 - 600 40.61692458441596 -68309.36124792948 197.5527667607886 0.3056696014124338 - 700 46.20303146200326 -68290.12727395598 178.3775768561405 0.1982123493608406 - 800 50.4375018189932 -68272.72651051797 160.995046695269 0.1708386295858845 - 900 52.17011714635106 -68257.85059865142 146.1567281868867 0.1032829304640776 - 1000 53.49296457217382 -68244.38715993936 132.7166474251702 0.06428993394665769 -Loop time of 14.8767 on 1 procs for 1000 steps with 16000 atoms + Step Temp TotEng f_twotemp[1] f_twotemp[2] + 0 0 -68483.52254543516 371.9188105082105 0 + 100 17.01353086098387 -68446.50228930202 334.6217068813629 0.3763710887774046 + 200 27.91331236535322 -68413.16008042906 301.3181773007303 0.3165912892484031 + 300 32.20115656493125 -68383.19634217303 271.3756381838045 0.2901111802983097 + 400 33.46056398887347 -68355.73057141017 243.9344715501159 0.2548133388123378 + 500 35.5346204243821 -68331.63060947017 219.84946888619 0.2388591367999414 + 600 40.61692458441596 -68309.36124792948 197.5527667607886 0.3056696014124338 + 700 46.20303146200326 -68290.12727395598 178.3775768561405 0.1982123493608406 + 800 50.4375018189932 -68272.72651051797 160.995046695269 0.1708386295858845 + 900 52.17011714635106 -68257.85059865142 146.1567281868867 0.1032829304640776 + 1000 53.49296457217382 -68244.38715993936 132.7166474251702 0.06428993394665769 +Loop time of 5.99191 on 1 procs for 1000 steps with 16000 atoms -Performance: 0.581 ns/day, 41.324 hours/ns, 67.219 timesteps/s +Performance: 1.442 ns/day, 16.644 hours/ns, 166.892 timesteps/s, 2.670 Matom-step/s 100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 13.759 | 13.759 | 13.759 | 0.0 | 92.49 +Pair | 5.3136 | 5.3136 | 5.3136 | 0.0 | 88.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.087429 | 0.087429 | 0.087429 | 0.0 | 0.59 -Output | 0.00063941 | 0.00063941 | 0.00063941 | 0.0 | 0.00 -Modify | 0.98561 | 0.98561 | 0.98561 | 0.0 | 6.63 -Other | | 0.04396 | | | 0.30 +Comm | 0.035738 | 0.035738 | 0.035738 | 0.0 | 0.60 +Output | 0.00049119 | 0.00049119 | 0.00049119 | 0.0 | 0.01 +Modify | 0.62365 | 0.62365 | 0.62365 | 0.0 | 10.41 +Other | | 0.01844 | | | 0.31 -Nlocal: 16000.0 ave 16000 max 16000 min +Nlocal: 16000 ave 16000 max 16000 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 13449.0 ave 13449 max 13449 min +Nghost: 13449 ave 13449 max 13449 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 896000.0 ave 896000 max 896000 min +Neighs: 896000 ave 896000 max 896000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 896000 -Ave neighs/atom = 56.000000 +Ave neighs/atom = 56 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:14 +Total wall time: 0:00:06 diff --git a/examples/ttm/log.26Aug21.ttm.grid.g++.4 b/examples/ttm/log.1Dec22.ttm.grid.g++.4 similarity index 51% rename from examples/ttm/log.26Aug21.ttm.grid.g++.4 rename to examples/ttm/log.1Dec22.ttm.grid.g++.4 index b603c66df9..4bcce5365e 100644 --- a/examples/ttm/log.26Aug21.ttm.grid.g++.4 +++ b/examples/ttm/log.1Dec22.ttm.grid.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (30 Jul 2021) +LAMMPS (3 Nov 2022) +WARNING: Using I/O redirection is unreliable with parallel runs. Better use -in switch to read input file. (../lammps.cpp:528) units metal atom_style atomic boundary p p p @@ -6,7 +7,7 @@ boundary p p p variable latc equal 2.87 lattice bcc ${latc} lattice bcc 2.87 -Lattice spacing in x,y,z = 2.8700000 2.8700000 2.8700000 +Lattice spacing in x,y,z = 2.87 2.87 2.87 variable xmax equal 10.0 variable xmin equal -10.0 variable ymax equal 10.0 @@ -22,7 +23,7 @@ region sim_box block -10 10 -10 10 ${zmin} ${zmax} units latti region sim_box block -10 10 -10 10 -10 ${zmax} units lattice region sim_box block -10 10 -10 10 -10 10 units lattice create_box 1 sim_box -Created orthogonal box = (-28.700000 -28.700000 -28.700000) to (28.700000 28.700000 28.700000) +Created orthogonal box = (-28.7 -28.7 -28.7) to (28.7 28.7 28.7) 1 by 2 by 2 MPI processor grid region atom_box block ${xmin} ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} units lattice region atom_box block -10 ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} units lattice @@ -33,14 +34,14 @@ region atom_box block -10 10 -10 10 -10 ${zmax} units lattice region atom_box block -10 10 -10 10 -10 10 units lattice create_atoms 1 region atom_box Created 16000 atoms - using lattice units in orthogonal box = (-28.700000 -28.700000 -28.700000) to (28.700000 28.700000 28.700000) - create_atoms CPU = 0.002 seconds + using lattice units in orthogonal box = (-28.7 -28.7 -28.7) to (28.7 28.7 28.7) + create_atoms CPU = 0.001 seconds mass 1 55.845 -include pot_iron.mod pair_style eam/fs pair_coeff * * FeVoter-ChenRecheck.fs Fe +Reading eam/fs potential file FeVoter-ChenRecheck.fs with DATE: 2016-04-04 neighbor 2.0 bin neigh_modify every 5 delay 0 check yes @@ -58,9 +59,26 @@ thermo 100 thermo_style custom step temp etotal f_twotemp[1] f_twotemp[2] thermo_modify format float "%20.16g" +# dump output + +#compute 1 all property/grid 10 10 10 id ix iy iz +#dump 1 all grid 100 tmp.dump c_1:grid:data[*] f_twotemp:grid:data +#dump_modify 1 sort 1 + +#compute 10 all property/grid 10 10 10 id xc yc zc +#fix ave all ave/grid 10 10 100 10 10 10 f_twotemp:grid:data + +#dump ave all grid 100 tmp.dump.ave # c_10:grid:data[*] f_ave:grid:data +#dump_modify ave sort id + +#dump vtk all grid/vtk 100 tmp.dump.*.vtk f_ave:grid:data +#dump_modify vtk sort id buffer no + +# run simulation + run 1000 Neighbor list info ... - update every 5 steps, delay 0 steps, check yes + update: every = 5 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.524 ghost atom cutoff = 6.524 @@ -72,42 +90,42 @@ Neighbor list info ... stencil: half/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.843 | 4.843 | 4.843 Mbytes -Step Temp TotEng f_twotemp[1] f_twotemp[2] - 0 0 -68483.52254530673 371.9188105082186 0 - 100 16.95536995775684 -68446.64765713879 334.7745598327931 0.3602932995006087 - 200 27.82619298359641 -68413.48663012494 301.6568409464847 0.2922875754523593 - 300 32.28660976355901 -68383.41369945828 271.6030085280586 0.26987388247804 - 400 33.33119316198579 -68356.74598240001 244.9747750036311 0.2061586600914003 - 500 35.14534756499593 -68332.73504057307 220.9328922343961 0.2800368538794578 - 600 39.58922469808521 -68311.03191758461 199.2602622784512 0.2310303196166884 - 700 45.34652315787151 -68291.65247941404 179.9297699858464 0.1438135463248855 - 800 49.66707856481075 -68274.98092841901 163.2540575286425 0.1600890300738265 - 900 52.17692450487317 -68259.8031091165 148.1017576370548 0.1177316234407941 - 1000 54.24228199265479 -68245.58589458198 133.8816957314364 0.1314999893461343 -Loop time of 4.95173 on 4 procs for 1000 steps with 16000 atoms + Step Temp TotEng f_twotemp[1] f_twotemp[2] + 0 0 -68483.52254530673 371.9188105082186 0 + 100 16.95536995775684 -68446.64765713879 334.7745598327931 0.3602932995006087 + 200 27.82619298359641 -68413.48663012494 301.6568409464847 0.2922875754523593 + 300 32.28660976355901 -68383.41369945828 271.6030085280586 0.26987388247804 + 400 33.33119316198579 -68356.74598240001 244.9747750036311 0.2061586600914003 + 500 35.14534756499593 -68332.73504057307 220.9328922343961 0.2800368538794578 + 600 39.58922469808521 -68311.03191758461 199.2602622784512 0.2310303196166884 + 700 45.34652315787151 -68291.65247941404 179.9297699858464 0.1438135463248855 + 800 49.66707856481075 -68274.98092841901 163.2540575286425 0.1600890300738265 + 900 52.17692450487317 -68259.8031091165 148.1017576370548 0.1177316234407941 + 1000 54.24228199265479 -68245.58589458198 133.8816957314364 0.1314999893461343 +Loop time of 2.16917 on 4 procs for 1000 steps with 16000 atoms -Performance: 1.745 ns/day, 13.755 hours/ns, 201.949 timesteps/s -98.2% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 3.983 ns/day, 6.025 hours/ns, 461.006 timesteps/s, 7.376 Matom-step/s +97.7% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 4.1159 | 4.2665 | 4.4446 | 7.1 | 86.16 +Pair | 1.8638 | 1.8826 | 1.9014 | 1.0 | 86.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.14618 | 0.32518 | 0.47663 | 25.8 | 6.57 -Output | 0.00030633 | 0.00034695 | 0.00044693 | 0.0 | 0.01 -Modify | 0.33258 | 0.3333 | 0.33402 | 0.1 | 6.73 -Other | | 0.0264 | | | 0.53 +Comm | 0.057938 | 0.076258 | 0.094755 | 4.8 | 3.52 +Output | 0.00020722 | 0.00022911 | 0.00029186 | 0.0 | 0.01 +Modify | 0.20222 | 0.20238 | 0.20256 | 0.0 | 9.33 +Other | | 0.007738 | | | 0.36 -Nlocal: 4000.00 ave 4000 max 4000 min +Nlocal: 4000 ave 4000 max 4000 min Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 6329.00 ave 6329 max 6329 min +Nghost: 6329 ave 6329 max 6329 min Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 224000.0 ave 227436 max 220450 min +Neighs: 224000 ave 227436 max 220450 min Histogram: 1 0 1 0 0 0 0 1 0 1 Total # of neighbors = 896000 -Ave neighs/atom = 56.000000 +Ave neighs/atom = 56 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:05 +Total wall time: 0:00:02 diff --git a/fortran/lammps.f90 b/fortran/lammps.f90 index 3355db5209..e25b5ec206 100644 --- a/fortran/lammps.f90 +++ b/fortran/lammps.f90 @@ -1,7 +1,7 @@ ! ------------------------------------------------------------------------- ! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator ! https://www.lammps.org/ Sandia National Laboratories -! Steve Plimpton, sjplimp@sandia.gov +! LAMMPS Development team: developers@lammps.org ! ! Copyright (2003) Sandia Corporation. Under the terms of Contract ! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -19,8 +19,12 @@ ! Karl D. Hammond ! University of Missouri, 2012-2020 ! +! Contributing authors: +! - Axel Kohlmeyer , Temple University, 2020-2022 +! - Karl D. Hammond , University of Missouri, 2022 +! ! The Fortran module tries to follow the API of the C library interface -! closely, but like the Python wrapper it employs an object-oriented +! closely, but like the Python wrapper, it employs an object-oriented ! approach. To accommodate the object-oriented approach, all exported ! subroutines and functions have to be implemented in Fortran and ! call the interfaced C-style functions with adapted calling conventions @@ -31,7 +35,7 @@ MODULE LIBLAMMPS USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_ptr, c_null_ptr, C_ASSOCIATED, & C_LOC, c_int, c_int64_t, c_char, c_null_char, c_double, c_size_t, & - C_F_POINTER + C_F_POINTER, c_funptr, C_FUNLOC IMPLICIT NONE PRIVATE @@ -40,17 +44,18 @@ MODULE LIBLAMMPS ! Data type constants for extracting data from global, atom, compute, and fix ! ! Must be kept in sync with the equivalent declarations in - ! src/library.h and python/lammps/constants.py + ! src/library.h, python/lammps/constants.py, tools/swig/lammps.i, + ! and examples/COUPLE/plugin/liblammpsplugin.h ! ! These are NOT part of the API (the part the user sees) INTEGER(c_int), PARAMETER :: & - LAMMPS_INT = 0, & ! 32-bit integer (array) + LAMMPS_INT = 0, & ! 32-bit integer (or array) LAMMPS_INT_2D = 1, & ! two-dimensional 32-bit integer array - LAMMPS_DOUBLE = 2, & ! 64-bit double (array) + LAMMPS_DOUBLE = 2, & ! 64-bit double (or array) LAMMPS_DOUBLE_2D = 3, & ! two-dimensional 64-bit double array - LAMMPS_INT64 = 4, & ! 64-bit integer (array) + LAMMPS_INT64 = 4, & ! 64-bit integer (or array) LAMMPS_INT64_2D = 5, & ! two-dimensional 64-bit integer array - LAMMPS_STRING = 6, & ! C-String + LAMMPS_STRING = 6, & ! string LMP_STYLE_GLOBAL = 0, & ! request global compute/fix/etc. data LMP_STYLE_ATOM = 1, & ! request per-atom compute/fix/etc. data LMP_STYLE_LOCAL = 2, & ! request local compute/fix/etc. data @@ -59,7 +64,7 @@ MODULE LIBLAMMPS LMP_TYPE_ARRAY = 2, & ! request array LMP_SIZE_VECTOR = 3, & ! request size of vector LMP_SIZE_ROWS = 4, & ! request rows (actually columns) - LMP_SIZE_COLS = 5, & ! request colums (actually rows) + LMP_SIZE_COLS = 5, & ! request columns (actually rows) LMP_ERROR_WARNING = 0, & ! call Error::warning() LMP_ERROR_ONE = 1, & ! call Error::one() (from this MPI rank) LMP_ERROR_ALL = 2, & ! call Error::all() (from all MPI ranks) @@ -70,6 +75,9 @@ MODULE LIBLAMMPS LMP_VAR_VECTOR = 2, & ! vector variables LMP_VAR_STRING = 3 ! string variables (everything else) + ! Constants we set once (in the constructor) and never need to check again + INTEGER(c_int), SAVE :: SIZE_TAGINT, SIZE_BIGINT, SIZE_IMAGEINT + ! "Constants" to use with extract_compute and friends TYPE lammps_style INTEGER(c_int) :: global, atom, local @@ -119,25 +127,83 @@ MODULE LIBLAMMPS PROCEDURE, PRIVATE :: lmp_scatter_atoms_double GENERIC :: scatter_atoms => lmp_scatter_atoms_int, & lmp_scatter_atoms_double -! PROCEDURE, PRIVATE :: lmp_scatter_atoms_subset_int PROCEDURE, PRIVATE :: lmp_scatter_atoms_subset_double GENERIC :: scatter_atoms_subset => lmp_scatter_atoms_subset_int, & lmp_scatter_atoms_subset_double + PROCEDURE, PRIVATE :: lmp_gather_bonds_small + PROCEDURE, PRIVATE :: lmp_gather_bonds_big + GENERIC :: gather_bonds => lmp_gather_bonds_small, & + lmp_gather_bonds_big + PROCEDURE, PRIVATE :: lmp_gather_int + PROCEDURE, PRIVATE :: lmp_gather_double + GENERIC :: gather => lmp_gather_int, lmp_gather_double + PROCEDURE, PRIVATE :: lmp_gather_concat_int + PROCEDURE, PRIVATE :: lmp_gather_concat_double + GENERIC :: gather_concat => lmp_gather_concat_int, & + lmp_gather_concat_double + PROCEDURE, PRIVATE :: lmp_gather_subset_int + PROCEDURE, PRIVATE :: lmp_gather_subset_double + GENERIC :: gather_subset => lmp_gather_subset_int, & + lmp_gather_subset_double + PROCEDURE, PRIVATE :: lmp_scatter_int + PROCEDURE, PRIVATE :: lmp_scatter_double + GENERIC :: scatter => lmp_scatter_int, lmp_scatter_double + PROCEDURE, PRIVATE :: lmp_scatter_subset_int + PROCEDURE, PRIVATE :: lmp_scatter_subset_double + GENERIC :: scatter_subset => lmp_scatter_subset_int, & + lmp_scatter_subset_double + PROCEDURE, PRIVATE :: lmp_create_atoms_int + PROCEDURE, PRIVATE :: lmp_create_atoms_bigbig + GENERIC :: create_atoms => lmp_create_atoms_int, & + lmp_create_atoms_bigbig + PROCEDURE :: find_pair_neighlist => lmp_find_pair_neighlist + PROCEDURE :: find_fix_neighlist => lmp_find_fix_neighlist + PROCEDURE :: find_compute_neighlist => lmp_find_compute_neighlist + PROCEDURE :: neighlist_num_elements => lmp_neighlist_num_elements + PROCEDURE :: neighlist_element_neighbors => lmp_neighlist_element_neighbors PROCEDURE :: version => lmp_version - PROCEDURE,NOPASS :: get_os_info => lmp_get_os_info - PROCEDURE,NOPASS :: config_has_mpi_support => lmp_config_has_mpi_support - PROCEDURE,NOPASS :: config_has_gzip_support => lmp_config_has_gzip_support - PROCEDURE,NOPASS :: config_has_png_support => lmp_config_has_png_support - PROCEDURE,NOPASS :: config_has_jpeg_support => lmp_config_has_jpeg_support - PROCEDURE,NOPASS :: config_has_ffmpeg_support & - => lmp_config_has_ffmpeg_support - PROCEDURE,NOPASS :: config_has_exceptions => lmp_config_has_exceptions - PROCEDURE,NOPASS :: config_has_package => lmp_config_has_package - PROCEDURE,NOPASS :: config_package_count => lammps_config_package_count - PROCEDURE,NOPASS :: config_package_name => lmp_config_package_name - PROCEDURE,NOPASS :: installed_packages => lmp_installed_packages -! + PROCEDURE, NOPASS :: get_os_info => lmp_get_os_info + PROCEDURE, NOPASS :: config_has_mpi_support => lmp_config_has_mpi_support + PROCEDURE, NOPASS :: config_has_gzip_support => lmp_config_has_gzip_support + PROCEDURE, NOPASS :: config_has_png_support => lmp_config_has_png_support + PROCEDURE, NOPASS :: config_has_jpeg_support => lmp_config_has_jpeg_support + PROCEDURE, NOPASS :: config_has_ffmpeg_support & + => lmp_config_has_ffmpeg_support + PROCEDURE, NOPASS :: config_has_exceptions => lmp_config_has_exceptions + PROCEDURE, NOPASS :: config_has_package => lmp_config_has_package + PROCEDURE, NOPASS :: config_package_count => lammps_config_package_count + PROCEDURE :: config_package_name => lmp_config_package_name + PROCEDURE :: installed_packages => lmp_installed_packages + PROCEDURE, NOPASS :: config_accelerator => lmp_config_accelerator + PROCEDURE, NOPASS :: has_gpu_device => lmp_has_gpu_device + PROCEDURE, NOPASS :: get_gpu_device_info => lmp_get_gpu_device_info + PROCEDURE :: has_style => lmp_has_style + PROCEDURE :: style_count => lmp_style_count + PROCEDURE :: style_name => lmp_style_name + PROCEDURE :: has_id => lmp_has_id + PROCEDURE :: id_count => lmp_id_count + PROCEDURE :: id_name => lmp_id_name + PROCEDURE, NOPASS :: plugin_count => lammps_plugin_count + PROCEDURE :: plugin_name => lmp_plugin_name + PROCEDURE :: encode_image_flags => lmp_encode_image_flags + PROCEDURE, PRIVATE :: lmp_decode_image_flags + PROCEDURE, PRIVATE :: lmp_decode_image_flags_bigbig + GENERIC :: decode_image_flags => lmp_decode_image_flags, & + lmp_decode_image_flags_bigbig + PROCEDURE :: set_fix_external_callback => lmp_set_fix_external_callback + PROCEDURE :: fix_external_get_force => lmp_fix_external_get_force + PROCEDURE :: fix_external_set_energy_global & + => lmp_fix_external_set_energy_global + PROCEDURE :: fix_external_set_virial_global & + => lmp_fix_external_set_virial_global + PROCEDURE :: fix_external_set_energy_peratom & + => lmp_fix_external_set_energy_peratom + PROCEDURE :: fix_external_set_virial_peratom & + => lmp_fix_external_set_virial_peratom + PROCEDURE :: fix_external_set_vector_length & + => lmp_fix_external_set_vector_length + PROCEDURE :: fix_external_set_vector => lmp_fix_external_set_vector PROCEDURE :: flush_buffers => lmp_flush_buffers PROCEDURE :: is_running => lmp_is_running PROCEDURE :: force_timeout => lmp_force_timeout @@ -197,6 +263,11 @@ MODULE LIBLAMMPS CHARACTER(LEN=:), ALLOCATABLE :: str END TYPE lammps_variable_data + TYPE, EXTENDS(lammps_data_baseclass) :: lammps_image_data + INTEGER(c_int) :: i32 + INTEGER(c_int64_t) :: i64 + END TYPE lammps_image_data + ! This overloads the assignment operator (=) so that assignments of the ! form ! nlocal = extract_global('nlocal') @@ -217,8 +288,55 @@ MODULE LIBLAMMPS MODULE PROCEDURE assign_double_to_lammps_variable_data, & assign_doublevec_to_lammps_variable_data, & assign_string_to_lammps_variable_data + ! Image data, too + MODULE PROCEDURE assign_int_to_lammps_image_data, & + assign_int64_to_lammps_image_data END INTERFACE + ! Interface templates for fix external callbacks + ABSTRACT INTERFACE + SUBROUTINE external_callback_smallsmall(caller, timestep, ids, x, fexternal) + IMPORT :: c_int, c_double + CLASS(*), INTENT(INOUT) :: caller + INTEGER(c_int), INTENT(IN) :: timestep + INTEGER(c_int), DIMENSION(:), INTENT(IN) :: ids + REAL(c_double), DIMENSION(:,:), INTENT(IN) :: x + REAL(c_double), DIMENSION(:,:), INTENT(OUT) :: fexternal + END SUBROUTINE external_callback_smallsmall + SUBROUTINE external_callback_smallbig(caller, timestep, ids, x, fexternal) + IMPORT :: c_int, c_double, c_int64_t + CLASS(*), INTENT(INOUT) :: caller + INTEGER(c_int64_t), INTENT(IN) :: timestep + INTEGER(c_int), DIMENSION(:), INTENT(IN) :: ids + REAL(c_double), DIMENSION(:,:), INTENT(IN) :: x + REAL(c_double), DIMENSION(:,:), INTENT(OUT) :: fexternal + END SUBROUTINE external_callback_smallbig + SUBROUTINE external_callback_bigbig(caller, timestep, ids, x, fexternal) + IMPORT :: c_double, c_int64_t + CLASS(*), INTENT(INOUT) :: caller + INTEGER(c_int64_t), INTENT(IN) :: timestep + INTEGER(c_int64_t), DIMENSION(:), INTENT(IN) :: ids + REAL(c_double), DIMENSION(:,:), INTENT(IN) :: x + REAL(c_double), DIMENSION(:,:), INTENT(OUT) :: fexternal + END SUBROUTINE external_callback_bigbig + END INTERFACE + + ! Derived type for fix external callback data + TYPE fix_external_data + CHARACTER(LEN=:), ALLOCATABLE :: id + PROCEDURE(external_callback_smallsmall), NOPASS, POINTER :: & + callback_smallsmall => NULL() + PROCEDURE(external_callback_smallbig), NOPASS, POINTER :: & + callback_smallbig => NULL() + PROCEDURE(external_callback_bigbig), NOPASS, POINTER :: & + callback_bigbig => NULL() + CLASS(*), POINTER :: caller => NULL() + CLASS(lammps), POINTER :: lammps_instance => NULL() + END TYPE fix_external_data + + ! Array used to store Fortran-facing callback functions for fix external + TYPE(fix_external_data), DIMENSION(:), ALLOCATABLE, TARGET, SAVE :: ext_data + ! interface definitions for calling functions in library.cpp INTERFACE FUNCTION lammps_open(argc, argv, comm) BIND(C,name='lammps_open_fortran') @@ -349,13 +467,6 @@ MODULE LIBLAMMPS INTEGER(c_int) :: lammps_extract_global_datatype END FUNCTION lammps_extract_global_datatype - FUNCTION c_strlen(str) BIND(C,name='strlen') - IMPORT :: c_ptr, c_size_t - IMPLICIT NONE - TYPE(c_ptr), INTENT(IN), VALUE :: str - INTEGER(c_size_t) :: c_strlen - END FUNCTION c_strlen - FUNCTION lammps_extract_global(handle, name) BIND(C) IMPORT :: c_ptr IMPLICIT NONE @@ -452,28 +563,98 @@ MODULE LIBLAMMPS INTEGER(c_int), VALUE :: count, ndata, type END SUBROUTINE lammps_scatter_atoms_subset - !SUBROUTINE lammps_gather_bonds + SUBROUTINE lammps_gather_bonds(handle, data) BIND(C) + IMPORT :: c_ptr + IMPLICIT NONE + TYPE(c_ptr), VALUE :: handle, data + END SUBROUTINE lammps_gather_bonds - !SUBROUTINE lammps_gather + SUBROUTINE lammps_gather(handle, name, type, count, data) BIND(C) + IMPORT :: c_ptr, c_int + IMPLICIT NONE + TYPE(c_ptr), VALUE :: handle, name, data + INTEGER(c_int), VALUE :: type, count + END SUBROUTINE lammps_gather - !SUBROUTINE lammps_gather_concat + SUBROUTINE lammps_gather_concat(handle, name, type, count, data) BIND(C) + IMPORT :: c_ptr, c_int + IMPLICIT NONE + TYPE(c_ptr), VALUE :: handle, name, data + INTEGER(c_int), VALUE :: type, count + END SUBROUTINE lammps_gather_concat - !SUBROUTINE lammps_gather_subset + SUBROUTINE lammps_gather_subset(handle, name, type, count, ndata, ids, & + data) BIND(C) + IMPORT :: c_ptr, c_int + IMPLICIT NONE + TYPE(c_ptr), VALUE :: handle, name, ids, data + INTEGER(c_int), VALUE :: type, count, ndata + END SUBROUTINE lammps_gather_subset - !SUBROUTINE lammps_scatter_subset + SUBROUTINE lammps_scatter(handle, name, type, count, data) BIND(C) + IMPORT :: c_ptr, c_int + IMPLICIT NONE + TYPE(c_ptr), VALUE :: handle, name, data + INTEGER(c_int), VALUE :: type, count + END SUBROUTINE lammps_scatter - !(generic / id, type, and image are special) / requires LAMMPS_BIGBIG - !INTEGER(c_int) FUNCTION lammps_create_atoms + SUBROUTINE lammps_scatter_subset(handle, name, type, count, ndata, ids, & + data) BIND(C) + IMPORT :: c_ptr, c_int + IMPLICIT NONE + TYPE(c_ptr), VALUE :: handle, name, ids, data + INTEGER(c_int), VALUE :: count, ndata, type + END SUBROUTINE lammps_scatter_subset - !INTEGER(c_int) FUNCTION lammps_find_pair_neighlist + FUNCTION lammps_create_atoms(handle, n, id, type, x, v, image, bexpand) & + BIND(C) + IMPORT :: c_ptr, c_int + IMPLICIT NONE + TYPE(c_ptr), VALUE :: handle, id, type, x, v, image + INTEGER(c_int), VALUE :: n, bexpand + INTEGER(c_int) :: lammps_create_atoms + END FUNCTION lammps_create_atoms - !INTEGER(c_int) FUNCTION lammps_find_fix_neighlist + FUNCTION lammps_find_pair_neighlist(handle, style, exact, nsub, reqid) & + BIND(C) + IMPORT :: c_ptr, c_int + IMPLICIT NONE + TYPE(c_ptr), VALUE :: handle, style + INTEGER(c_int), VALUE :: exact, nsub, reqid + INTEGER(c_int) :: lammps_find_pair_neighlist + END FUNCTION lammps_find_pair_neighlist - !INTEGER(c_int) FUNCTION lammps_find_compute_neighlist + FUNCTION lammps_find_fix_neighlist(handle, id, reqid) BIND(C) + IMPORT :: c_int, c_ptr + IMPLICIT NONE + TYPE(c_ptr), VALUE :: handle, id + INTEGER(c_int), VALUE :: reqid + INTEGER(c_int) :: lammps_find_fix_neighlist + END FUNCTION lammps_find_fix_neighlist - !INTEGER(c_int) FUNCTION lammps_neighlist_num_elements + FUNCTION lammps_find_compute_neighlist(handle, id, reqid) BIND(C) + IMPORT :: c_int, c_ptr + IMPLICIT NONE + TYPE(c_ptr), VALUE :: handle, id + INTEGER(c_int), VALUE :: reqid + INTEGER(c_int) :: lammps_find_compute_neighlist + END FUNCTION lammps_find_compute_neighlist - !SUBROUTINE lammps_neighlist_element_neighbors + FUNCTION lammps_neighlist_num_elements(handle, idx) BIND(C) + IMPORT :: c_ptr, c_int + TYPE(c_ptr), VALUE :: handle + INTEGER(c_int), VALUE :: idx + INTEGER(c_int) :: lammps_neighlist_num_elements + END FUNCTION lammps_neighlist_num_elements + + SUBROUTINE lammps_neighlist_element_neighbors(handle, idx, element, & + iatom, numneigh, neighbors) BIND(C) + IMPORT :: c_ptr, c_int + TYPE(c_ptr), VALUE :: handle + INTEGER(c_int), VALUE :: idx, element + INTEGER(c_int) :: iatom, numneigh + TYPE(c_ptr) :: neighbors + END SUBROUTINE lammps_neighlist_element_neighbors FUNCTION lammps_version(handle) BIND(C) IMPORT :: c_ptr, c_int @@ -546,30 +727,138 @@ MODULE LIBLAMMPS TYPE(c_ptr), VALUE :: buffer END FUNCTION lammps_config_package_name - !LOGICAL FUNCTION lammps_config_accelerator - !LOGICAL FUNCTION lammps_has_gpu_device - !SUBROUTINE lammps_get_gpu_device + FUNCTION lammps_config_accelerator(package, category, setting) BIND(C) + IMPORT :: c_int, c_ptr + IMPLICIT NONE + TYPE(c_ptr), VALUE :: package, category, setting + INTEGER(c_int) :: lammps_config_accelerator + END FUNCTION lammps_config_accelerator - !LOGICAL FUNCTION lammps_has_id - !INTEGER(c_int) FUNCTION lammps_id_count - !SUBROUTINE lammps_id_name + FUNCTION lammps_has_gpu_device() BIND(C) + IMPORT :: c_int + IMPLICIT NONE + INTEGER(c_int) :: lammps_has_gpu_device + END FUNCTION lammps_has_gpu_device - !INTEGER(c_int) FUNCTION lammps_plugin_count - !SUBROUTINE lammps_plugin_name + SUBROUTINE lammps_get_gpu_device_info(buffer, buf_size) BIND(C) + IMPORT :: c_int, c_ptr + IMPLICIT NONE + TYPE(c_ptr), VALUE :: buffer + INTEGER(c_int), VALUE :: buf_size + END SUBROUTINE lammps_get_gpu_device_info - !Both of these use LAMMPS_BIGBIG - !INTEGER(LAMMPS_imageint) FUNCTION lammps_encode_image_flags - !SUBROUTINE lammps_decode_image_flags + FUNCTION lammps_has_style(handle, category, name) BIND(C) + IMPORT :: c_ptr, c_int + IMPLICIT NONE + TYPE(c_ptr), VALUE :: handle, category, name + INTEGER(c_int) :: lammps_has_style + END FUNCTION lammps_has_style - !SUBROUTINE lammps_set_fix_external_callback ! may have trouble.... - !FUNCTION lammps_fix_external_get_force() ! returns real(c_double)(:) + FUNCTION lammps_style_count(handle, category) BIND(C) + IMPORT :: c_ptr, c_int + IMPLICIT NONE + TYPE(c_ptr), VALUE :: handle, category + INTEGER(c_int) :: lammps_style_count + END FUNCTION lammps_style_count - !SUBROUTINE lammps_fix_external_set_energy_global - !SUBROUTINE lammps_fix_external_set_energy_peratom - !SUBROUTINE lammps_fix_external_set_virial_global - !SUBROUTINE lammps_fix_external_set_virial_peratom - !SUBROUTINE lammps_fix_external_set_vector_length - !SUBROUTINE lammps_fix_external_set_vector + FUNCTION lammps_style_name(handle, category, idx, buffer, buf_size) BIND(C) + IMPORT :: c_ptr, c_int + IMPLICIT NONE + TYPE(c_ptr), VALUE :: handle, category, buffer + INTEGER(c_int), VALUE :: idx, buf_size + INTEGER(c_int) :: lammps_style_name + END FUNCTION lammps_style_name + + FUNCTION lammps_has_id(handle, category, name) BIND(C) + IMPORT :: c_ptr, c_int + IMPLICIT NONE + TYPE(c_ptr), VALUE :: handle, category, name + INTEGER(c_int) :: lammps_has_id + END FUNCTION lammps_has_id + + FUNCTION lammps_id_count(handle, category) BIND(C) + IMPORT :: c_ptr, c_int + IMPLICIT NONE + TYPE(c_ptr), VALUE :: handle, category + INTEGER(c_int) :: lammps_id_count + END FUNCTION lammps_id_count + + FUNCTION lammps_id_name(handle, category, idx, buffer, buf_size) BIND(C) + IMPORT :: c_ptr, c_int + IMPLICIT NONE + TYPE(c_ptr), VALUE :: handle, category, buffer + INTEGER(c_int), VALUE :: idx, buf_size + INTEGER(c_int) :: lammps_id_name + END FUNCTION lammps_id_name + + FUNCTION lammps_plugin_count() BIND(C) + IMPORT :: c_int + IMPLICIT NONE + INTEGER(c_int) :: lammps_plugin_count + END FUNCTION lammps_plugin_count + + FUNCTION lammps_plugin_name(idx, stylebuf, namebuf, buf_size) BIND(C) + IMPORT :: c_int, c_ptr + IMPLICIT NONE + INTEGER(c_int), VALUE :: idx, buf_size + TYPE(c_ptr), VALUE :: stylebuf, namebuf + INTEGER(c_int) :: lammps_plugin_name + END FUNCTION lammps_plugin_name + + ! We don't call lammps_encode_image_flags because its interface is + ! ambiguous: we don't know sizeof(imageint) prior to compile time. + ! It is re-written in Fortran below. It was easier to do the same for + ! lammps_decode_image_flags's equivalent. + + SUBROUTINE lammps_set_fix_external_callback(handle, id, funcptr, ptr) & + BIND(C) + IMPORT :: c_ptr, c_funptr + TYPE(c_ptr), VALUE :: handle, id, ptr + TYPE(c_funptr), VALUE :: funcptr + END SUBROUTINE lammps_set_fix_external_callback + + FUNCTION lammps_fix_external_get_force(handle, id) BIND(C) + IMPORT :: c_ptr + TYPE(c_ptr), VALUE :: handle, id + TYPE(c_ptr) :: lammps_fix_external_get_force + END FUNCTION lammps_fix_external_get_force + + SUBROUTINE lammps_fix_external_set_energy_global(handle, id, eng) BIND(C) + IMPORT :: c_ptr, c_double + TYPE(c_ptr), VALUE :: handle, id + REAL(c_double), VALUE :: eng + END SUBROUTINE lammps_fix_external_set_energy_global + + SUBROUTINE lammps_fix_external_set_virial_global(handle, id, virial) & + BIND(C) + IMPORT :: c_ptr + TYPE(c_ptr), VALUE :: handle, id, virial + END SUBROUTINE lammps_fix_external_set_virial_global + + SUBROUTINE lammps_fix_external_set_energy_peratom(handle, id, eng) BIND(C) + IMPORT :: c_ptr + TYPE(c_ptr), VALUE :: handle, id, eng + END SUBROUTINE lammps_fix_external_set_energy_peratom + + SUBROUTINE lammps_fix_external_set_virial_peratom(handle, id, virial) & + BIND(C) + IMPORT :: c_ptr + TYPE(c_ptr), VALUE :: handle, id, virial + END SUBROUTINE lammps_fix_external_set_virial_peratom + + SUBROUTINE lammps_fix_external_set_vector_length(handle, id, length) & + BIND(C) + IMPORT :: c_ptr, c_int + TYPE(c_ptr), VALUE :: handle, id + INTEGER(c_int), VALUE :: length + END SUBROUTINE lammps_fix_external_set_vector_length + + SUBROUTINE lammps_fix_external_set_vector(handle, id, idx, val) BIND(C) + IMPORT :: c_ptr, c_int, c_double + TYPE(c_ptr), VALUE :: handle, id + INTEGER(c_int), VALUE :: idx + REAL(c_double), VALUE :: val + END SUBROUTINE lammps_fix_external_set_vector SUBROUTINE lammps_flush_buffers(handle) BIND(C) IMPORT :: c_ptr @@ -577,13 +866,6 @@ MODULE LIBLAMMPS TYPE(c_ptr), VALUE :: handle END SUBROUTINE lammps_flush_buffers - FUNCTION lammps_malloc(size) BIND(C, name='malloc') - IMPORT :: c_ptr, c_size_t - IMPLICIT NONE - INTEGER(c_size_t), VALUE :: size - TYPE(c_ptr) :: lammps_malloc - END FUNCTION lammps_malloc - SUBROUTINE lammps_free(ptr) BIND(C) IMPORT :: c_ptr IMPLICIT NONE @@ -616,6 +898,23 @@ MODULE LIBLAMMPS INTEGER(c_int), VALUE :: buf_size END FUNCTION lammps_get_last_error_message + !--------------------------------------------------------------------- + ! Utility functions imported for convenience (not in library.h) + !--------------------------------------------------------------------- + FUNCTION lammps_malloc(size) BIND(C, name='malloc') + IMPORT :: c_ptr, c_size_t + IMPLICIT NONE + INTEGER(c_size_t), VALUE :: size + TYPE(c_ptr) :: lammps_malloc + END FUNCTION lammps_malloc + + FUNCTION c_strlen(str) BIND(C, name='strlen') + IMPORT :: c_ptr, c_size_t + IMPLICIT NONE + TYPE(c_ptr), INTENT(IN), VALUE :: str + INTEGER(c_size_t) :: c_strlen + END FUNCTION c_strlen + END INTERFACE CONTAINS @@ -630,28 +929,28 @@ CONTAINS INTEGER(c_int) :: i, c_comm, argc IF (PRESENT(args)) THEN - ! convert fortran argument list to c style - argc = SIZE(args) - ALLOCATE(argv(argc)) - DO i=1, argc - argv(i) = f2c_string(args(i)) - END DO + ! convert fortran argument list to c style + argc = SIZE(args) + ALLOCATE(argv(argc)) + DO i=1, argc + argv(i) = f2c_string(args(i)) + END DO ELSE - argc = 1 - ALLOCATE(argv(1)) - argv(1) = f2c_string("liblammps") + argc = 1 + ALLOCATE(argv(1)) + argv(1) = f2c_string("liblammps") ENDIF IF (PRESENT(comm)) THEN - c_comm = comm - lmp_open%handle = lammps_open(argc, argv, c_comm) + c_comm = comm + lmp_open%handle = lammps_open(argc, argv, c_comm) ELSE - lmp_open%handle = lammps_open_no_mpi(argc, argv, c_null_ptr) + lmp_open%handle = lammps_open_no_mpi(argc, argv, c_null_ptr) END IF ! Clean up allocated memory DO i=1, argc - CALL lammps_free(argv(i)) + CALL lammps_free(argv(i)) END DO DEALLOCATE(argv) @@ -662,6 +961,11 @@ CONTAINS lmp_open%type%scalar = LMP_TYPE_SCALAR lmp_open%type%vector = LMP_TYPE_VECTOR lmp_open%type%array = LMP_TYPE_ARRAY + + ! Assign constants for bigint and tagint for use elsewhere + SIZE_TAGINT = lmp_extract_setting(lmp_open, 'tagint') + SIZE_BIGINT = lmp_extract_setting(lmp_open, 'bigint') + SIZE_IMAGEINT = lmp_extract_setting(lmp_open, 'imageint') END FUNCTION lmp_open ! Combined Fortran wrapper around lammps_close() and lammps_mpi_finalize() @@ -672,17 +976,17 @@ CONTAINS CALL lammps_close(self%handle) IF (PRESENT(finalize)) THEN - IF (finalize) THEN - CALL lammps_kokkos_finalize() - CALL lammps_mpi_finalize() - END IF + IF (finalize) THEN + CALL lammps_kokkos_finalize() + CALL lammps_mpi_finalize() + END IF END IF END SUBROUTINE lmp_close ! equivalent function to lammps_error() SUBROUTINE lmp_error(self, error_type, error_text) CLASS(lammps) :: self - INTEGER :: error_type + INTEGER(c_int) :: error_type CHARACTER(len=*) :: error_text TYPE(c_ptr) :: str @@ -830,11 +1134,9 @@ CONTAINS CLASS(lammps), INTENT(IN), TARGET :: self CHARACTER(LEN=*), INTENT(IN) :: name TYPE(lammps_data) :: global_data - INTEGER(c_int) :: datatype TYPE(c_ptr) :: Cname, Cptr - INTEGER(c_size_t) :: length, i - CHARACTER(KIND=c_char, LEN=1), DIMENSION(:), POINTER :: Fptr + INTEGER(c_size_t) :: length ! Determine vector length ! FIXME Is there a way to get the length of the vector from C rather @@ -845,7 +1147,7 @@ CONTAINS length = 3 CASE DEFAULT length = 1 - ! string cases are overridden later + ! string cases do not use "length" END SELECT Cname = f2c_string(name) @@ -882,12 +1184,7 @@ CONTAINS END IF CASE (LAMMPS_STRING) global_data%datatype = DATA_STRING - length = c_strlen(Cptr) - CALL C_F_POINTER(Cptr, Fptr, [length]) - ALLOCATE(CHARACTER(LEN=length) :: global_data%str) - DO i = 1, length - global_data%str(i:i) = Fptr(i) - END DO + global_data%str = c2f_string(Cptr) CASE DEFAULT CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & 'Unknown pointer type in extract_global') @@ -955,6 +1252,7 @@ CONTAINS CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & 'per-atom property ' // name // 'not found in extract_setting') CASE DEFAULT + error_msg = '' WRITE(error_msg,'(A,I0,A)') 'return value ', datatype, & ' from lammps_extract_atom_datatype not known [Fortran/extract_atom]' CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, error_msg) @@ -1134,8 +1432,7 @@ CONTAINS TYPE(lammps_variable_data) :: variable_data TYPE(c_ptr) :: Cptr, Cname, Cgroup, Cveclength - INTEGER(c_size_t) :: length, i - CHARACTER(KIND=c_char, LEN=1), DIMENSION(:), POINTER :: Cstring + INTEGER(c_size_t) :: length INTEGER(c_int) :: datatype REAL(c_double), POINTER :: double => NULL() REAL(c_double), DIMENSION(:), POINTER :: double_vec => NULL() @@ -1186,11 +1483,8 @@ CONTAINS CASE (LMP_VAR_STRING) variable_data%datatype = DATA_STRING length = c_strlen(Cptr) - CALL C_F_POINTER(Cptr, Cstring, [length]) ALLOCATE(CHARACTER(LEN=length) :: variable_data%str) - DO i = 1, length - variable_data%str(i:i) = Cstring(i) - END DO + variable_data%str = c2f_string(Cptr) ! DO NOT deallocate the C pointer CASE (-1) CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & @@ -1374,7 +1668,7 @@ CONTAINS IF (count /= 1 .AND. count /= 3) THEN CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & 'gather_atoms_subset requires "count" to be 1 or 3 & - &[Fortran/gather_atoms]') + &[Fortran/gather_atoms_subset]') END IF ndata = SIZE(ids, KIND=c_int) @@ -1404,7 +1698,7 @@ CONTAINS IF (count /= 1 .AND. count /= 3) THEN CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & 'gather_atoms_subset requires "count" to be 1 or 3 & - &[Fortran/gather_atoms]') + &[Fortran/gather_atoms_subset]') END IF ndata = SIZE(ids, KIND=c_int) @@ -1484,6 +1778,7 @@ CONTAINS CALL lammps_free(Cname) END SUBROUTINE lmp_scatter_atoms_double + ! equivalent function to lammps_scatter_atoms_subset (for integers) SUBROUTINE lmp_scatter_atoms_subset_int(self, name, ids, data) CLASS(lammps), INTENT(IN) :: self CHARACTER(LEN=*), INTENT(IN) :: name @@ -1497,7 +1792,8 @@ CONTAINS Ccount = SIZE(data, KIND=c_int) / Cndata IF (Ccount /= 1 .AND. Ccount /= 3) THEN CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & - 'scatter_atoms_subset requires either 1 or 3 data per atom') + 'scatter_atoms_subset requires either 1 or 3 data per atom & + &[Fortran/scatter_atoms_subset]') END IF Cname = f2c_string(name) @@ -1508,6 +1804,7 @@ CONTAINS CALL lammps_free(Cname) END SUBROUTINE lmp_scatter_atoms_subset_int + ! equivalent function to lammps_scatter_atoms_subset (for doubles) SUBROUTINE lmp_scatter_atoms_subset_double(self, name, ids, data) CLASS(lammps), INTENT(IN) :: self CHARACTER(LEN=*), INTENT(IN) :: name @@ -1521,7 +1818,8 @@ CONTAINS Ccount = SIZE(data, KIND=c_int) / Cndata IF (Ccount /= 1 .AND. Ccount /= 3) THEN CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & - 'scatter_atoms_subset requires either 1 or 3 data per atom') + 'scatter_atoms_subset requires either 1 or 3 data per atom & + &[Fortran/scatter_atoms_subset]') END IF Cname = f2c_string(name) @@ -1532,6 +1830,590 @@ CONTAINS CALL lammps_free(Cname) END SUBROUTINE lmp_scatter_atoms_subset_double + ! equivalent function to lammps_gather_bonds (LAMMPS_SMALLSMALL or SMALLBIG) + SUBROUTINE lmp_gather_bonds_small(self, data) + CLASS(lammps), INTENT(IN) :: self + INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET, INTENT(OUT) :: data + INTEGER(c_int), POINTER :: nbonds_small + INTEGER(c_int64_t), POINTER :: nbonds_big + TYPE(c_ptr) :: Cdata + + IF (SIZE_TAGINT /= 4_c_int) THEN + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & + 'Incompatible integer kind in gather_bonds [Fortran/gather_bonds]') + END IF + IF (ALLOCATED(data)) DEALLOCATE(data) + IF (SIZE_BIGINT == 4_c_int) THEN + nbonds_small = lmp_extract_global(self, 'nbonds') + ALLOCATE(data(3*nbonds_small)) + ELSE + nbonds_big = lmp_extract_global(self, 'nbonds') + ALLOCATE(data(3*nbonds_big)) + END IF + Cdata = C_LOC(data(1)) + CALL lammps_gather_bonds(self%handle, Cdata) + END SUBROUTINE lmp_gather_bonds_small + + ! equivalent function to lammps_gather_bonds (LAMMPS_BIGBIG) + SUBROUTINE lmp_gather_bonds_big(self, data) + CLASS(lammps), INTENT(IN) :: self + INTEGER(c_int64_t), DIMENSION(:), ALLOCATABLE, TARGET, INTENT(OUT) :: data + INTEGER(c_int64_t), POINTER :: nbonds + TYPE(c_ptr) :: Cdata + + IF (SIZE_TAGINT /= 8_c_int) THEN + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & + 'Incompatible integer kind in gather_bonds [Fortran/gather_bonds]') + END IF + nbonds = lmp_extract_global(self, 'nbonds') + IF (ALLOCATED(data)) DEALLOCATE(data) + ALLOCATE(data(3*nbonds)) + Cdata = C_LOC(data(1)) + CALL lammps_gather_bonds(self%handle, Cdata) + END SUBROUTINE lmp_gather_bonds_big + + ! equivalent function to lammps_gather (for int data) + SUBROUTINE lmp_gather_int(self, name, count, data) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: name + INTEGER(c_int), INTENT(IN) :: count + INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET, INTENT(OUT) :: data + TYPE(c_ptr) :: Cdata, Cname + INTEGER(c_int) :: natoms + INTEGER(c_int), PARAMETER :: Ctype = 0_c_int + REAL(c_double) :: dnatoms + CHARACTER(LEN=100) :: error_msg + + IF (count /= 1 .AND. count /= 3) THEN + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & + 'gather requires "count" to be 1 or 3 [Fortran/gather]') + END IF + + dnatoms = lmp_get_natoms(self) + IF (dnatoms > HUGE(1_c_int)) THEN + WRITE(error_msg,'(A,1X,I0,1X,A)') & + 'Cannot use library function gather with more than', & + HUGE(0_c_int), 'atoms [Fortran/gather]' + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, error_msg) + END IF + natoms = NINT(dnatoms, c_int) + + Cname = f2c_string(name) + IF (ALLOCATED(data)) DEALLOCATE(data) + ALLOCATE(data(natoms*count)) + Cdata = C_LOC(data(1)) + CALL lammps_gather(self%handle, Cname, Ctype, count, Cdata) + CALL lammps_free(Cname) + END SUBROUTINE lmp_gather_int + + ! equivalent function to lammps_gather_atoms (for doubles) + SUBROUTINE lmp_gather_double(self, name, count, data) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: name + INTEGER(c_int), INTENT(IN) :: count + REAL(c_double), DIMENSION(:), ALLOCATABLE, TARGET, INTENT(OUT) :: data + TYPE(c_ptr) :: Cdata, Cname + INTEGER(c_int) :: natoms + INTEGER(c_int), PARAMETER :: Ctype = 1_c_int + REAL(c_double) :: dnatoms + CHARACTER(LEN=100) :: error_msg + + IF (count /= 1 .AND. count /= 3) THEN + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & + 'gather requires "count" to be 1 or 3 [Fortran/gather]') + END IF + + dnatoms = lmp_get_natoms(self) + IF (dnatoms > HUGE(1_c_int)) THEN + WRITE(error_msg,'(A,1X,I0,1X,A)') & + 'Cannot use library function gather with more than', & + HUGE(0_c_int), 'atoms [Fortran/gather]' + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, error_msg) + END IF + natoms = NINT(dnatoms, c_int) + + Cname = f2c_string(name) + IF (ALLOCATED(data)) DEALLOCATE(data) + ALLOCATE(data(natoms*count)) + Cdata = C_LOC(data(1)) + CALL lammps_gather(self%handle, Cname, Ctype, count, Cdata) + CALL lammps_free(Cname) + END SUBROUTINE lmp_gather_double + + ! equivalent function to lammps_gather_concat (for ints) + SUBROUTINE lmp_gather_concat_int(self, name, count, data) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: name + INTEGER(c_int), INTENT(IN) :: count + INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET, INTENT(OUT) :: data + TYPE(c_ptr) :: Cdata, Cname + INTEGER(c_int) :: natoms + INTEGER(c_int), PARAMETER :: Ctype = 0_c_int + REAL(c_double) :: dnatoms + CHARACTER(LEN=100) :: error_msg + + IF (count /= 1 .AND. count /= 3) THEN + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & + 'gather_concat requires "count" to be 1 or 3 [Fortran/gather_concat]') + END IF + + dnatoms = lmp_get_natoms(self) + IF (dnatoms > HUGE(1_c_int)) THEN + WRITE(error_msg,'(A,1X,I0,1X,A)') & + 'Cannot use library function gather_concat with more than', & + HUGE(0_c_int), 'atoms [Fortran/gather_concat]' + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, error_msg) + END IF + natoms = NINT(dnatoms, c_int) + + Cname = f2c_string(name) + IF (ALLOCATED(data)) DEALLOCATE(data) + ALLOCATE(data(natoms*count)) + Cdata = C_LOC(data(1)) + CALL lammps_gather_concat(self%handle, Cname, Ctype, count, Cdata) + CALL lammps_free(Cname) + END SUBROUTINE lmp_gather_concat_int + + ! equivalent function to lammps_gather_concat (for doubles) + SUBROUTINE lmp_gather_concat_double(self, name, count, data) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: name + INTEGER(c_int), INTENT(IN) :: count + REAL(c_double), DIMENSION(:), ALLOCATABLE, TARGET, INTENT(OUT) :: data + TYPE(c_ptr) :: Cdata, Cname + INTEGER(c_int) :: natoms + INTEGER(c_int), PARAMETER :: Ctype = 1_c_int + REAL(c_double) :: dnatoms + CHARACTER(LEN=100) :: error_msg + + IF (count /= 1 .AND. count /= 3) THEN + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & + 'gather_concat requires "count" to be 1 or 3 [Fortran/gather_concat]') + END IF + + dnatoms = lmp_get_natoms(self) + IF (dnatoms > HUGE(1_c_int)) THEN + WRITE(error_msg,'(A,1X,I0,1X,A)') & + 'Cannot use library function gather_concat with more than', & + HUGE(0_c_int), 'atoms [Fortran/gather_concat]' + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, error_msg) + END IF + natoms = NINT(dnatoms, c_int) + + Cname = f2c_string(name) + IF (ALLOCATED(data)) DEALLOCATE(data) + ALLOCATE(data(natoms*count)) + Cdata = C_LOC(data(1)) + CALL lammps_gather_concat(self%handle, Cname, Ctype, count, Cdata) + CALL lammps_free(Cname) + END SUBROUTINE lmp_gather_concat_double + + ! equivalent function to lammps_gather_subset (for integers) + SUBROUTINE lmp_gather_subset_int(self, name, count, ids, data) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: name + INTEGER(c_int), INTENT(IN) :: count + INTEGER(c_int), DIMENSION(:), TARGET, INTENT(IN) :: ids + INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET, INTENT(OUT) :: data + INTEGER(c_int) :: ndata + TYPE(c_ptr) :: Cdata, Cname, Cids + INTEGER(c_int), PARAMETER :: Ctype = 0_c_int + + IF (count /= 1 .AND. count /= 3) THEN + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & + 'gather_subset requires "count" to be 1 or 3 [Fortran/gather_subset]') + END IF + + ndata = SIZE(ids, KIND=c_int) + + Cname = f2c_string(name) + IF (ALLOCATED(data)) DEALLOCATE(data) + ALLOCATE(data(ndata*count)) + data = -1_c_int + Cdata = C_LOC(data(1)) + Cids = C_LOC(ids(1)) + CALL lammps_gather_subset(self%handle, Cname, Ctype, count, & + ndata, Cids, Cdata) + CALL lammps_free(Cname) + END SUBROUTINE lmp_gather_subset_int + + ! equivalent function to lammps_gather_subset (for doubles) + SUBROUTINE lmp_gather_subset_double(self, name, count, ids, data) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: name + INTEGER(c_int), INTENT(IN) :: count + INTEGER(c_int), DIMENSION(:), TARGET, INTENT(IN) :: ids + REAL(c_double), DIMENSION(:), ALLOCATABLE, TARGET, INTENT(OUT) :: data + INTEGER(c_int) :: ndata + TYPE(c_ptr) :: Cdata, Cname, Cids + INTEGER(c_int), PARAMETER :: Ctype = 1_c_int + + IF (count /= 1 .AND. count /= 3) THEN + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & + 'gather_subset requires "count" to be 1 or 3 [Fortran/gather_subset]') + END IF + + ndata = SIZE(ids, KIND=c_int) + + Cname = f2c_string(name) + IF (ALLOCATED(data)) DEALLOCATE(data) + ALLOCATE(data(ndata*count)) + Cdata = C_LOC(data(1)) + Cids = C_LOC(ids(1)) + CALL lammps_gather_subset(self%handle, Cname, Ctype, count, & + ndata, Cids, Cdata) + CALL lammps_free(Cname) + END SUBROUTINE lmp_gather_subset_double + + ! equivalent function to lammps_scatter (for integers) + SUBROUTINE lmp_scatter_int(self, name, data) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: name + INTEGER(c_int), DIMENSION(:), TARGET :: data + INTEGER(c_int) :: natoms, Ccount + INTEGER(c_int), PARAMETER :: Ctype = 0_c_int + TYPE(c_ptr) :: Cname, Cdata + REAL(c_double) :: dnatoms + CHARACTER(LEN=100) :: error_msg + + dnatoms = lmp_get_natoms(self) + IF (dnatoms > HUGE(1_c_int)) THEN + WRITE(error_msg,'(A,1X,I0,1X,A)') & + 'Cannot use library function scatter with more than', & + HUGE(0_c_int), 'atoms [Fortran/scatter]' + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, error_msg) + END IF + natoms = NINT(dnatoms, c_int) + + Cname = f2c_string(name) + Cdata = C_LOC(data(1)) + Ccount = SIZE(data) / natoms + + IF (Ccount /= 1 .AND. Ccount /= 3) THEN + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & + 'lammps_scatter requires either 1 or 3 data per atom') + END IF + CALL lammps_scatter(self%handle, Cname, Ctype, Ccount, Cdata) + CALL lammps_free(Cname) + END SUBROUTINE lmp_scatter_int + + ! equivalent function to lammps_scatter (for doubles) + SUBROUTINE lmp_scatter_double(self, name, data) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: name + REAL(c_double), DIMENSION(:), TARGET :: data + INTEGER(c_int) :: natoms, Ccount + INTEGER(c_int), PARAMETER :: Ctype = 1_c_int + TYPE(c_ptr) :: Cname, Cdata + REAL(c_double) :: dnatoms + CHARACTER(LEN=100) :: error_msg + + dnatoms = lmp_get_natoms(self) + IF (dnatoms > HUGE(1_c_int)) THEN + WRITE(error_msg,'(A,1X,I0,1X,A)') & + 'Cannot use library function scatter with more than', & + HUGE(0_c_int), 'atoms [Fortran/scatter]' + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, error_msg) + END IF + natoms = NINT(dnatoms, c_int) + + Cname = f2c_string(name) + Cdata = C_LOC(data(1)) + Ccount = SIZE(data) / natoms + + IF (Ccount /= 1 .AND. Ccount /= 3) THEN + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & + 'scatter requires either 1 or 3 data per atom [Fortran/scatter]') + END IF + CALL lammps_scatter(self%handle, Cname, Ctype, Ccount, Cdata) + CALL lammps_free(Cname) + END SUBROUTINE lmp_scatter_double + + ! equivalent function to lammps_scatter_subset (for integers) + SUBROUTINE lmp_scatter_subset_int(self, name, ids, data) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: name + INTEGER(c_int), DIMENSION(:), TARGET :: ids + INTEGER(c_int), DIMENSION(:), TARGET :: data + INTEGER(c_int), PARAMETER :: Ctype = 0_c_int + INTEGER(c_int) :: Cndata, Ccount + TYPE(c_ptr) :: Cdata, Cname, Cids + + Cndata = SIZE(ids, KIND=c_int) + Ccount = SIZE(data, KIND=c_int) / Cndata + IF (Ccount /= 1 .AND. Ccount /= 3) THEN + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & + 'scatter_subset requires either 1 or 3 data per atom & + &[Fortran/scatter_subset]') + END IF + + Cname = f2c_string(name) + Cdata = C_LOC(data(1)) + Cids = C_LOC(ids(1)) + CALL lammps_scatter_subset(self%handle, Cname, Ctype, Ccount, & + Cndata, Cids, Cdata) + CALL lammps_free(Cname) + END SUBROUTINE lmp_scatter_subset_int + + ! equivalent function to lammps_scatter_subset (for doubles) + SUBROUTINE lmp_scatter_subset_double(self, name, ids, data) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: name + INTEGER(c_int), DIMENSION(:), TARGET :: ids + REAL(c_double), DIMENSION(:), TARGET :: data + INTEGER(c_int), PARAMETER :: Ctype = 1_c_int + INTEGER(c_int) :: Cndata, Ccount + TYPE(c_ptr) :: Cdata, Cname, Cids + + Cndata = SIZE(ids, KIND=c_int) + Ccount = SIZE(data, KIND=c_int) / Cndata + IF (Ccount /= 1 .AND. Ccount /= 3) THEN + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & + 'scatter_subset requires either 1 or 3 data per atom') + END IF + + Cname = f2c_string(name) + Cdata = C_LOC(data(1)) + Cids = C_LOC(ids(1)) + CALL lammps_scatter_subset(self%handle, Cname, Ctype, Ccount, & + Cndata, Cids, Cdata) + CALL lammps_free(Cname) + END SUBROUTINE lmp_scatter_subset_double + + ! equivalent function to lammps_create_atoms (int ids or id absent) + SUBROUTINE lmp_create_atoms_int(self, id, type, x, v, image, bexpand) + CLASS(lammps), INTENT(IN) :: self + INTEGER(c_int), DIMENSION(:), TARGET, OPTIONAL :: id, image + INTEGER(c_int), DIMENSION(:), TARGET, OPTIONAL :: type + REAL(c_double), DIMENSION(:), TARGET, OPTIONAL :: x, v + LOGICAL, OPTIONAL :: bexpand + INTEGER(c_int) :: n, Cbexpand + TYPE(c_ptr) :: Cid, Ctype, Cx, Cv, Cimage + INTEGER(c_int) :: tagint_size, atoms_created + + ! type is actually NOT optional, but we can't make id optional without it, + ! so we check at run-time + IF (.NOT. PRESENT(type)) THEN + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & + 'the "type" argument to create_atoms is required& + & [Fortran/create_atoms]') + END IF + + tagint_size = lmp_extract_setting(self, 'tagint') + IF (tagint_size /= 4_c_int .AND. (PRESENT(id) .OR. PRESENT(image))) THEN + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & + 'Unable to create_atoms; your id/image array types are incompatible& + & with LAMMPS_SMALLBIG and LAMMPS_SMALLSMALL [Fortran/create_atoms]') + END IF + n = SIZE(type, KIND=c_int) + IF (PRESENT(bexpand)) THEN + IF (bexpand) THEN + Cbexpand = 1_c_int + ELSE + Cbexpand = 0_c_int + END IF + ELSE + Cbexpand = 0_c_int + END IF + IF (PRESENT(id)) THEN + Cid = C_LOC(id(1)) + ELSE + Cid = c_null_ptr + END IF + IF (PRESENT(type)) THEN + Ctype = C_LOC(type(1)) + END IF + IF (PRESENT(image)) THEN + Cimage = C_LOC(image(1)) + ELSE + Cimage = c_null_ptr + END IF + IF (PRESENT(x)) THEN + Cx = C_LOC(x(1)) + ELSE + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & + 'the argument "x" to create_atoms is required') + END IF + IF (PRESENT(v)) THEN + Cv = C_LOC(v(1)) + ELSE + Cv = c_null_ptr + END IF + atoms_created = lammps_create_atoms(self%handle, n, Cid, Ctype, Cx, Cv, & + Cimage, Cbexpand) + IF ( atoms_created < 0_c_int ) THEN + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & + 'error when trying to create atoms [Fortran/create_atoms]') + ELSE IF ( atoms_created /= n ) THEN + CALL lmp_error(self, LMP_ERROR_WARNING + LMP_ERROR_WORLD, & + 'atoms created /= atoms asked to create [Fortran/create_atoms]') + END IF + END SUBROUTINE lmp_create_atoms_int + + ! equivalent function to lammps_create_atoms (long int ids and images) + SUBROUTINE lmp_create_atoms_bigbig(self, id, type, x, v, image, bexpand) + CLASS(lammps), INTENT(IN) :: self + INTEGER(c_int64_t), DIMENSION(:), TARGET :: id + INTEGER(c_int), DIMENSION(:), TARGET :: type + REAL(c_double), DIMENSION(:), TARGET :: x + REAL(c_double), DIMENSION(:), OPTIONAL, TARGET :: v + INTEGER(c_int64_t), DIMENSION(:), OPTIONAL, TARGET :: image + LOGICAL, OPTIONAL :: bexpand + INTEGER(c_int) :: n, Cbexpand + TYPE(c_ptr) :: Cid, Ctype, Cx, Cv, Cimage + INTEGER(c_int) :: tagint_size, atoms_created + + tagint_size = lmp_extract_setting(self, 'tagint') + IF ( tagint_size /= 8_c_int ) THEN + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & + 'Unable to create_atoms; your id/image array types are incompatible& + & with LAMMPS_BIGBIG') + END IF + n = SIZE(type, KIND=c_int) + IF (PRESENT(bexpand)) THEN + IF (bexpand) THEN + Cbexpand = 1_c_int + ELSE + Cbexpand = 0_c_int + END IF + ELSE + Cbexpand = 0_c_int + END IF + Cid = C_LOC(id(1)) + Ctype = C_LOC(type(1)) + IF (PRESENT(image)) THEN + Cimage = C_LOC(image(1)) + ELSE + Cimage = c_null_ptr + END IF + Cx = C_LOC(x(1)) + IF (PRESENT(v)) THEN + Cv = C_LOC(v(1)) + ELSE + Cv = c_null_ptr + END IF + atoms_created = lammps_create_atoms(self%handle, n, Cid, Ctype, Cx, Cv, & + Cimage, Cbexpand) + IF ( atoms_created < 0_c_int ) THEN + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & + 'error when trying to create atoms [Fortran/create_atoms]') + ELSE IF ( atoms_created /= n ) THEN + CALL lmp_error(self, LMP_ERROR_WARNING + LMP_ERROR_WORLD, & + 'atoms created /= atoms asked to create [Fortran/create_atoms]') + END IF + END SUBROUTINE lmp_create_atoms_bigbig + + ! equivalent function to lammps_find_pair_neighlist + INTEGER(c_int) FUNCTION lmp_find_pair_neighlist(self, style, exact, nsub, & + reqid) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: style + LOGICAL, INTENT(IN), OPTIONAL :: exact + INTEGER(c_int), INTENT(IN), OPTIONAL :: nsub, reqid + TYPE(c_ptr) :: Cstyle + INTEGER(c_int) :: Cexact, Cnsub, Creqid + + Cexact = 0_c_int + IF (PRESENT(exact)) THEN + IF (exact) THEN + Cexact = 1_c_int + END IF + END IF + IF (PRESENT(nsub)) THEN + Cnsub = nsub + ELSE + Cnsub = 0_c_int + END IF + IF (PRESENT(reqid)) THEN + Creqid = reqid + ELSE + Creqid = 0_c_int + END IF + Cstyle = f2c_string(style) + lmp_find_pair_neighlist = lammps_find_pair_neighlist(self%handle, Cstyle, & + Cexact, Cnsub, Creqid) + IF (lmp_find_pair_neighlist < 0) THEN + CALL lmp_error(self, LMP_ERROR_WARNING + LMP_ERROR_WORLD, & + 'unable to find pair neighbor list [Fortran/find_pair_neighlist]') + END IF + CALL lammps_free(Cstyle) + END FUNCTION lmp_find_pair_neighlist + + ! equivalent function to lammps_find_fix_neighlist + INTEGER(c_int) FUNCTION lmp_find_fix_neighlist(self, id, reqid) RESULT(idx) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: id + INTEGER(c_int), INTENT(IN), OPTIONAL :: reqid + TYPE(c_ptr) :: Cid + INTEGER(c_int) :: Creqid + + IF (PRESENT(reqid)) THEN + Creqid = reqid + ELSE + Creqid = 0_c_int + END IF + Cid = f2c_string(id) + idx = lammps_find_fix_neighlist(self%handle, Cid, Creqid) + IF (idx < 0) THEN + CALL lmp_error(self, LMP_ERROR_WARNING + LMP_ERROR_WORLD, & + 'neighbor list not found [Fortran/find_fix_neighlist]') + END IF + CALL lammps_free(Cid) + END FUNCTION lmp_find_fix_neighlist + + ! equivalent function to lammps_find_compute_neighlist + INTEGER(c_int) FUNCTION lmp_find_compute_neighlist(self, id, reqid) & + RESULT(idx) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: id + INTEGER(c_int), INTENT(IN), OPTIONAL :: reqid + TYPE(c_ptr) :: Cid + INTEGER(c_int) :: Creqid + + IF (PRESENT(reqid)) THEN + Creqid = reqid + ELSE + Creqid = 0_c_int + END IF + Cid = f2c_string(id) + idx = lammps_find_compute_neighlist(self%handle, Cid, Creqid) + IF (idx < 0) THEN + CALL lmp_error(self, LMP_ERROR_WARNING + LMP_ERROR_WORLD, & + 'neighbor list not found [Fortran/find_compute_neighlist]') + END IF + CALL lammps_free(Cid) + END FUNCTION lmp_find_compute_neighlist + + INTEGER(c_int) FUNCTION lmp_neighlist_num_elements(self, idx) RESULT(inum) + CLASS(lammps), INTENT(IN) :: self + INTEGER(c_int), INTENT(IN) :: idx + + inum = lammps_neighlist_num_elements(self%handle, idx) + IF (inum < 0) THEN + CALL lmp_error(self, LMP_ERROR_WARNING + LMP_ERROR_WORLD, & + 'neighbor list not found [Fortran/neighlist_num_elements]') + END IF + END FUNCTION lmp_neighlist_num_elements + + SUBROUTINE lmp_neighlist_element_neighbors(self, idx, element, iatom, & + neighbors) + CLASS(lammps), INTENT(IN) :: self + INTEGER(c_int), INTENT(IN) :: idx, element + INTEGER(c_int), INTENT(OUT) :: iatom + INTEGER(c_int), DIMENSION(:), POINTER, INTENT(OUT) :: neighbors + INTEGER(c_int) :: numneigh + TYPE(c_ptr) :: Cneighbors + + CALL lammps_neighlist_element_neighbors(self%handle, idx, element, iatom, & + numneigh, Cneighbors) + IF (C_ASSOCIATED(Cneighbors)) THEN + CALL C_F_POINTER(Cneighbors, neighbors, [numneigh]) + ELSE + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & + 'Pointer returned from lammps_neighlist_element_neighbors is NULL') + END IF + END SUBROUTINE lmp_neighlist_element_neighbors + ! equivalent function to lammps_version INTEGER FUNCTION lmp_version(self) CLASS(lammps), INTENT(IN) :: self @@ -1543,18 +2425,14 @@ CONTAINS SUBROUTINE lmp_get_os_info(buffer) CHARACTER(LEN=*) :: buffer INTEGER(c_int) :: buf_size - CHARACTER(LEN=1,KIND=c_char), DIMENSION(LEN(buffer)), TARGET :: Cbuffer + CHARACTER(LEN=1, KIND=c_char), DIMENSION(LEN(buffer)+1), TARGET :: Cbuffer TYPE(c_ptr) :: ptr - INTEGER :: i - buffer = ' ' + buffer = '' + buf_size = LEN(buffer, KIND=c_int) + 1_c_int ptr = C_LOC(Cbuffer(1)) - buf_size = LEN(buffer) - CALL lammps_get_os_info(ptr, buf_size) - DO i=1,buf_size - IF (Cbuffer(i) == c_null_char) EXIT - buffer(i:i) = Cbuffer(i) - END DO + CALL lammps_get_os_info(ptr, INT(buf_size, KIND=c_int)) + buffer = array2string(Cbuffer) END SUBROUTINE lmp_get_os_info ! equivalent function to lammps_config_has_mpi_support @@ -1618,28 +2496,29 @@ CONTAINS END FUNCTION lmp_config_has_package ! equivalent subroutine to lammps_config_package_name - SUBROUTINE lmp_config_package_name(idx, buffer) + SUBROUTINE lmp_config_package_name(self, idx, buffer) + CLASS(lammps), INTENT(IN) :: self INTEGER, INTENT(IN) :: idx CHARACTER(LEN=*), INTENT(OUT) :: buffer + CHARACTER(LEN=1, KIND=c_char), DIMENSION(LEN(buffer)+1), TARGET :: Cbuffer INTEGER(c_int) :: Cidx, Csuccess TYPE(c_ptr) :: Cptr - CHARACTER(LEN=1,KIND=c_char), TARGET :: Cbuffer(LEN(buffer)+1) - INTEGER(c_size_t) :: i, strlen Cidx = idx - 1 Cptr = C_LOC(Cbuffer(1)) Csuccess = lammps_config_package_name(Cidx, Cptr, LEN(buffer)+1) - buffer = ' ' + buffer = '' IF (Csuccess /= 0_c_int) THEN - strlen = c_strlen(Cptr) - DO i = 1, strlen - buffer(i:i) = Cbuffer(i) - END DO + buffer = array2string(Cbuffer) + ELSE + CALL lmp_error(self, LMP_ERROR_WARNING + LMP_ERROR_WORLD, & + 'failure of lammps_config_package_name [Fortran/config_package_name]') END IF END SUBROUTINE lmp_config_package_name - ! equivalent function to Python routine .installed_packages() - SUBROUTINE lmp_installed_packages(package, length) + ! equivalent function to Python routine lammps.installed_packages() + SUBROUTINE lmp_installed_packages(self, package, length) + CLASS(lammps), INTENT(IN) :: self CHARACTER(LEN=:), DIMENSION(:), ALLOCATABLE, INTENT(OUT) :: package INTEGER, INTENT(IN), OPTIONAL :: length INTEGER, PARAMETER :: MAX_BUFFER_LENGTH = 31 @@ -1655,10 +2534,558 @@ CONTAINS npackage = lammps_config_package_count() ALLOCATE(CHARACTER(LEN=MAX_BUFFER_LENGTH) :: package(npackage)) DO i=1, npackage - CALL lmp_config_package_name(i, package(i)) + CALL lmp_config_package_name(self, i, package(i)) END DO END SUBROUTINE lmp_installed_packages + ! equivalent function to lammps_config_accelerator + LOGICAL FUNCTION lmp_config_accelerator(package, category, setting) + CHARACTER(LEN=*), INTENT(IN) :: package, category, setting + TYPE(c_ptr) :: Cpackage, Ccategory, Csetting + INTEGER(c_int) :: is_configured + + Cpackage = f2c_string(package) + Ccategory = f2c_string(category) + Csetting = f2c_string(setting) + is_configured = lammps_config_accelerator(Cpackage, Ccategory, Csetting) + CALL lammps_free(Cpackage) + CALL lammps_free(Ccategory) + CALL lammps_free(Csetting) + lmp_config_accelerator = (is_configured /= 0_c_int) + END FUNCTION lmp_config_accelerator + + ! equivalent function to lammps_has_gpu_device + LOGICAL FUNCTION lmp_has_gpu_device() + lmp_has_gpu_device = (lammps_has_gpu_device() /= 0_c_int) + END FUNCTION lmp_has_gpu_device + + ! equivalent subroutine to lammps_get_gpu_device_info + SUBROUTINE lmp_get_gpu_device_info(buffer) + CHARACTER(LEN=*), INTENT(OUT) :: buffer + INTEGER(c_int) :: buf_size + CHARACTER(LEN=1, KIND=c_char), DIMENSION(LEN(buffer)+1), TARGET :: Cbuffer + TYPE(c_ptr) :: Cptr + + buffer = '' + buf_size = LEN(buffer) + 1 + Cptr = C_LOC(Cbuffer) + CALL lammps_get_gpu_device_info(Cptr, buf_size) + buffer = array2string(Cbuffer) + END SUBROUTINE lmp_get_gpu_device_info + + ! equivalent function to lammps_has_style + LOGICAL FUNCTION lmp_has_style(self, category, name) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: category, name + TYPE(c_ptr) :: Ccategory, Cname + INTEGER(c_int) :: has_style + + Ccategory = f2c_string(category) + Cname = f2c_string(name) + has_style = lammps_has_style(self%handle, Ccategory, Cname) + CALL lammps_free(Ccategory) + CALL lammps_free(Cname) + lmp_has_style = (has_style /= 0_c_int) + END FUNCTION + + ! equivalent function to lammps_style_count + INTEGER(c_int) FUNCTION lmp_style_count(self, category) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: category + TYPE(c_ptr) :: Ccategory + + Ccategory = f2c_string(category) + lmp_style_count = lammps_style_count(self%handle, Ccategory) + CALL lammps_free(Ccategory) + END FUNCTION lmp_style_count + + ! equivalent function to lammps_style_name + SUBROUTINE lmp_style_name(self, category, idx, buffer) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: category + INTEGER(c_int), INTENT(IN) :: idx + CHARACTER(LEN=*), INTENT(OUT) :: buffer + INTEGER(c_int) :: buf_size, success + CHARACTER(LEN=1, KIND=c_char), DIMENSION(LEN(buffer)+1), TARGET :: Cbuffer + TYPE(c_ptr) :: Ccategory, Cptr + + buffer = '' + buf_size = LEN(buffer, KIND=c_int) + 1_c_int + Ccategory = f2c_string(category) + Cptr = C_LOC(Cbuffer) + success = lammps_style_name(self%handle, Ccategory, idx - 1, Cptr, buf_size) + IF (success == 1_c_int) THEN + buffer = array2string(Cbuffer) + ELSE + CALL lmp_error(self, LMP_ERROR_WARNING + LMP_ERROR_WORLD, & + 'idx value not in range [Fortran/style_name]') + END IF + CALL lammps_free(Ccategory) + END SUBROUTINE lmp_style_name + + ! equivalent function to lammps_has_id + LOGICAL FUNCTION lmp_has_id(self, category, name) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: category, name + TYPE(c_ptr) :: Ccategory, Cname + INTEGER(c_int) :: has_id + + Ccategory = f2c_string(category) + Cname = f2c_string(name) + has_id = lammps_has_id(self%handle, Ccategory, Cname) + CALL lammps_free(Ccategory) + CALL lammps_free(Cname) + lmp_has_id = (has_id /= 0_c_int) + END FUNCTION lmp_has_id + + ! equivalent function to lammps_id_count + INTEGER(c_int) FUNCTION lmp_id_count(self, category) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: category + TYPE(c_ptr) :: Ccategory + + Ccategory = f2c_string(category) + lmp_id_count = lammps_id_count(self%handle, Ccategory) + CALL lammps_free(Ccategory) + END FUNCTION lmp_id_count + + ! equivalent function to lammps_id_name + SUBROUTINE lmp_id_name(self, category, idx, buffer) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: category + INTEGER(c_int), INTENT(IN) :: idx + CHARACTER(LEN=*), INTENT(OUT) :: buffer + INTEGER(c_int) :: success + INTEGER(c_int) :: buf_size + TYPE(c_ptr) :: Ccategory, Cptr + CHARACTER(LEN=1, KIND=c_char), DIMENSION(LEN(buffer)+1), TARGET :: Cbuffer + + buffer = '' + Ccategory = f2c_string(category) + buf_size = LEN(buffer, KIND=c_int) + Cptr = C_LOC(Cbuffer(1)) + success = lammps_id_name(self%handle, Ccategory, idx - 1, Cptr, buf_size) + IF (success /= 0) THEN + buffer = array2string(Cbuffer) + ELSE + CALL lmp_error(self, LMP_ERROR_WARNING + LMP_ERROR_WORLD, & + 'lammps_id_name failed [Fortran/id_name]') + END IF + CALL lammps_free(Ccategory) + END SUBROUTINE lmp_id_name + + ! equivalent function to lammps_plugin_name + SUBROUTINE lmp_plugin_name(self, idx, stylebuf, namebuf) + CLASS(lammps), INTENT(IN) :: self + INTEGER(c_int), INTENT(IN) :: idx + CHARACTER(LEN=*), INTENT(OUT) :: stylebuf, namebuf + INTEGER(c_int) :: buf_size, success + TYPE(c_ptr) :: Cstylebuf, Cnamebuf + + buf_size = MIN(LEN(stylebuf, KIND=c_int), LEN(namebuf, KIND=c_int)) + Cstylebuf = lammps_malloc(INT(buf_size, KIND=c_size_t)) + Cnamebuf = lammps_malloc(INT(buf_size, KIND=c_size_t)) + success = lammps_plugin_name(idx - 1, Cstylebuf, Cnamebuf, buf_size) + IF (success /= 0_c_int) THEN + stylebuf = c2f_string(Cstylebuf) + namebuf = c2f_string(Cnamebuf) + ELSE + stylebuf = '' + namebuf = '' + CALL lmp_error(self, LMP_ERROR_WARNING + LMP_ERROR_WORLD, & + 'call to lammps_plugin_name failed [Fortran/plugin_name]') + END IF + CALL lammps_free(Cstylebuf) + CALL lammps_free(Cnamebuf) + END SUBROUTINE lmp_plugin_name + + ! equivalent function to lammps_encode_image_flags + FUNCTION lmp_encode_image_flags(self, ix, iy, iz) RESULT (image) + CLASS(lammps), INTENT(IN), TARGET :: self + INTEGER(c_int), INTENT(IN) :: ix, iy, iz + TYPE(lammps_image_data) :: image + INTEGER(c_int) :: imageint_size + INTEGER(c_int) :: IMGMAX, IMGMASK, IMGBITS, IMG2BITS + INTEGER(c_int64_t) :: ibx, iby, ibz, BIMGMAX, BIMGMASK, BIMGBITS, BIMG2BITS + + image%lammps_instance => self + IMGMASK = lmp_extract_setting(self, 'IMGMASK') + IMGMAX = lmp_extract_setting(self, 'IMGMAX') + IMGBITS = lmp_extract_setting(self, 'IMGBITS') + IMG2BITS = lmp_extract_setting(self, 'IMG2BITS') + imageint_size = lmp_extract_setting(self, 'imageint') + IF (imageint_size == 4_c_int) THEN + image%datatype = DATA_INT + image%i32 = IOR( IOR(IAND(ix + IMGMAX, IMGMASK), & + ISHFT(IAND(iy + IMGMAX, IMGMASK), IMGBITS)), & + ISHFT(IAND(iz + IMGMAX, IMGMASK), IMG2BITS) ) + ELSE + image%datatype = DATA_INT64 + ibx = ix + iby = iy + ibz = iz + BIMGMAX = IMGMAX + BIMGMASK = IMGMASK + BIMGBITS = IMGBITS + BIMG2BITS = IMG2BITS + image%i64 = IOR( IOR(IAND(ibx + BIMGMAX, BIMGMASK), & + ISHFT(IAND(iby + BIMGMAX, BIMGMASK), BIMGBITS)), & + ISHFT(IAND(ibz + BIMGMAX, BIMGMASK), BIMG2BITS) ) + END IF + END FUNCTION lmp_encode_image_flags + + ! equivalent function to lammps_decode_image_flags + SUBROUTINE lmp_decode_image_flags(self, image, flags) + CLASS(lammps), INTENT(IN) :: self + INTEGER(c_int), INTENT(IN) :: image + INTEGER(c_int), DIMENSION(3), TARGET, INTENT(OUT) :: flags + INTEGER(c_int) :: size_imageint + INTEGER(c_int) :: IMGMASK, IMGMAX, IMGBITS, IMG2BITS + + size_imageint = lmp_extract_setting(self, 'imageint') + IF (size_imageint == 4_c_int) THEN + IMGMASK = lmp_extract_setting(self, 'IMGMASK') + IMGMAX = lmp_extract_setting(self, 'IMGMAX') + IMGBITS = lmp_extract_setting(self, 'IMGBITS') + IMG2BITS = lmp_extract_setting(self, 'IMG2BITS') + flags(1) = IAND(image, IMGMASK) - IMGMAX + flags(2) = IAND(ISHFT(image, -IMGBITS), IMGMASK) - IMGMAX + flags(3) = ISHFT(image, -IMG2BITS) - IMGMAX + ELSE + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, 'Incorrect& + & integer kind passed as "image" [Fortran/decode_image_flags]') + END IF + END SUBROUTINE lmp_decode_image_flags + + ! equivalent function to lammps_decode_image_flags if -DLAMMPS_BIGBIG is used + SUBROUTINE lmp_decode_image_flags_bigbig(self, image, flags) + CLASS(lammps), INTENT(IN) :: self + INTEGER(c_int64_t), INTENT(IN) :: image + INTEGER(c_int), DIMENSION(3), TARGET, INTENT(OUT) :: flags + INTEGER(c_int) :: size_imageint + INTEGER(c_int) :: IMGMASK, IMGMAX, IMGBITS, IMG2BITS + INTEGER(c_int64_t) :: BIMGMASK, BIMGMAX, BIMGBITS, BIMG2BITS + + size_imageint = lmp_extract_setting(self, 'imageint') + IF (size_imageint == 8_c_int) THEN + IMGMASK = lmp_extract_setting(self, 'IMGMASK') + IMGMAX = lmp_extract_setting(self, 'IMGMAX') + IMGBITS = lmp_extract_setting(self, 'IMGBITS') + IMG2BITS = lmp_extract_setting(self, 'IMG2BITS') + BIMGMASK = IMGMASK + BIMGMAX = IMGMAX + BIMGBITS = IMGBITS + BIMG2BITS = IMG2BITS + flags(1) = INT(IAND(image, BIMGMASK) - BIMGMAX, KIND=c_int) + flags(2) = INT(IAND(ISHFT(image, -BIMGBITS), BIMGMASK) - BIMGMAX, & + KIND=c_int) + flags(3) = INT(ISHFT(image, -BIMG2BITS) - BIMGMAX, KIND=c_int) + ELSE + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, 'Incorrect& + & integer kind passed as "image" [Fortran/decode_image_flags]') + END IF + END SUBROUTINE lmp_decode_image_flags_bigbig + + ! equivalent function to lammps_set_fix_external_callback for -DSMALLSMALL + ! note that "caller" is wrapped into a fix_external_data derived type along + ! with the fix id and the Fortran calling function. + SUBROUTINE lmp_set_fix_external_callback(self, id, callback, caller) + CLASS(lammps), TARGET, INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: id + EXTERNAL :: callback + CLASS(*), INTENT(IN), TARGET, OPTIONAL :: caller + TYPE(c_ptr) :: c_id, c_caller + TYPE(c_funptr) :: c_callback + INTEGER :: i, this_fix + + c_id = f2c_string(id) + IF (ALLOCATED(ext_data)) THEN + this_fix = SIZE(ext_data) + 1 + DO i = 1, SIZE(ext_data) + IF (ext_data(i)%id == id) THEN + this_fix = i + EXIT + END IF + END DO + IF (this_fix > SIZE(ext_data)) THEN + ! reallocates ext_data; this requires us to re-bind "caller" on the C + ! side to the new data structure, which likely moved to a new address + ext_data = [ext_data, fix_external_data()] ! extends ext_data by 1 + CALL rebind_external_callback_data() + END IF + ELSE + ALLOCATE(ext_data(1)) + this_fix = 1 + END IF + ext_data(this_fix)%id = id + ext_data(this_fix)%lammps_instance => self + + IF (SIZE_TAGINT == 4_c_int .AND. SIZE_BIGINT == 4_c_int) THEN + ! -DSMALLSMALL + c_callback = C_FUNLOC(callback_wrapper_smallsmall) + CALL set_fix_external_callback_smallsmall(this_fix, callback) + ELSE IF (SIZE_TAGINT == 8_c_int .AND. SIZE_BIGINT == 8_c_int) THEN + ! -DBIGBIG + c_callback = C_FUNLOC(callback_wrapper_bigbig) + CALL set_fix_external_callback_bigbig(this_fix, callback) + ELSE + ! -DSMALLBIG + c_callback = C_FUNLOC(callback_wrapper_smallbig) + CALL set_fix_external_callback_smallbig(this_fix, callback) + END IF + + IF (PRESENT(caller)) THEN + ext_data(this_fix)%caller => caller + ELSE + NULLIFY(ext_data(this_fix)%caller) + END IF + c_caller = C_LOC(ext_data(this_fix)) + CALL lammps_set_fix_external_callback(self%handle, c_id, c_callback, & + c_caller) + CALL lammps_free(c_id) + END SUBROUTINE lmp_set_fix_external_callback + + ! Wrappers to assign callback pointers with explicit interfaces + SUBROUTINE set_fix_external_callback_smallsmall(id, callback) + INTEGER, INTENT(IN) :: id + PROCEDURE(external_callback_smallsmall) :: callback + + ext_data(id)%callback_smallsmall => callback + END SUBROUTINE set_fix_external_callback_smallsmall + + SUBROUTINE set_fix_external_callback_smallbig(id, callback) + INTEGER, INTENT(IN) :: id + PROCEDURE(external_callback_smallbig) :: callback + + ext_data(id)%callback_smallbig => callback + END SUBROUTINE set_fix_external_callback_smallbig + + SUBROUTINE set_fix_external_callback_bigbig(id, callback) + INTEGER, INTENT(IN) :: id + PROCEDURE(external_callback_bigbig) :: callback + + ext_data(id)%callback_bigbig => callback + END SUBROUTINE set_fix_external_callback_bigbig + + ! subroutine that re-binds all external callback data after a reallocation + SUBROUTINE rebind_external_callback_data() + INTEGER :: i + TYPE(c_ptr) :: c_id, c_caller + TYPE(c_funptr) :: c_callback + + DO i = 1, SIZE(ext_data) - 1 + c_id = f2c_string(ext_data(i)%id) + c_caller = C_LOC(ext_data(i)) + IF (SIZE_TAGINT == 4_c_int .AND. SIZE_BIGINT == 4_c_int) THEN + c_callback = C_FUNLOC(callback_wrapper_smallsmall) + ELSE IF (SIZE_TAGINT == 8_c_int .AND. SIZE_BIGINT == 8_c_int) THEN + c_callback = C_FUNLOC(callback_wrapper_bigbig) + ELSE + c_callback = C_FUNLOC(callback_wrapper_smallbig) + END IF + CALL lammps_set_fix_external_callback( & + ext_data(i)%lammps_instance%handle, c_id, c_callback, c_caller) + CALL lammps_free(c_id) + END DO + END SUBROUTINE rebind_external_callback_data + + ! companions to lmp_set_fix_external_callback to change interface + SUBROUTINE callback_wrapper_smallsmall(caller, timestep, nlocal, ids, x, & + fexternal) BIND(C) + TYPE(c_ptr), INTENT(IN), VALUE :: caller + INTEGER(c_int), INTENT(IN), VALUE :: timestep + INTEGER(c_int), INTENT(IN), VALUE :: nlocal + TYPE(c_ptr), INTENT(IN), VALUE :: ids, x, fexternal + TYPE(c_ptr), DIMENSION(:), POINTER :: x0, f0 + INTEGER(c_int), DIMENSION(:), POINTER :: f_ids => NULL() + REAL(c_double), DIMENSION(:,:), POINTER :: f_x => NULL(), & + f_fexternal => NULL() + TYPE(fix_external_data), POINTER :: f_caller => NULL() + + CALL C_F_POINTER(ids, f_ids, [nlocal]) + CALL C_F_POINTER(x, x0, [nlocal]) + CALL C_F_POINTER(x0(1), f_x, [3, nlocal]) + CALL C_F_POINTER(fexternal, f0, [nlocal]) + CALL C_F_POINTER(f0(1), f_fexternal, [3, nlocal]) + IF (C_ASSOCIATED(caller)) THEN + CALL C_F_POINTER(caller, f_caller) + CALL f_caller%callback_smallsmall(f_caller%caller, timestep, f_ids, & + f_x, f_fexternal) + ELSE + CALL lmp_error(f_caller%lammps_instance, & + LMP_ERROR_ALL + LMP_ERROR_WORLD, & + 'Got null pointer from "caller"; this should never happen;& + & please report a bug') + END IF + END SUBROUTINE callback_wrapper_smallsmall + + SUBROUTINE callback_wrapper_smallbig(caller, timestep, nlocal, ids, x, & + fexternal) BIND(C) + TYPE(c_ptr), INTENT(IN), VALUE :: caller + INTEGER(c_int64_t), INTENT(IN), VALUE :: timestep + INTEGER(c_int), INTENT(IN), VALUE :: nlocal + TYPE(c_ptr), INTENT(IN), VALUE :: ids, x, fexternal + TYPE(c_ptr), DIMENSION(:), POINTER :: x0, f0 + INTEGER(c_int), DIMENSION(:), POINTER :: f_ids => NULL() + REAL(c_double), DIMENSION(:,:), POINTER :: f_x => NULL(), & + f_fexternal => NULL() + TYPE(fix_external_data), POINTER :: f_caller => NULL() + + CALL C_F_POINTER(ids, f_ids, [nlocal]) + CALL C_F_POINTER(x, x0, [nlocal]) + CALL C_F_POINTER(x0(1), f_x, [3, nlocal]) + CALL C_F_POINTER(fexternal, f0, [nlocal]) + CALL C_F_POINTER(f0(1), f_fexternal, [3, nlocal]) + IF (C_ASSOCIATED(caller)) THEN + CALL C_F_POINTER(caller, f_caller) + CALL f_caller%callback_smallbig(f_caller%caller, timestep, f_ids, f_x, & + f_fexternal) + ELSE + CALL lmp_error(f_caller%lammps_instance, & + LMP_ERROR_ALL + LMP_ERROR_WORLD, & + 'Got null pointer from "caller"; this should never happen;& + & please report a bug') + END IF + END SUBROUTINE callback_wrapper_smallbig + + SUBROUTINE callback_wrapper_bigbig(caller, timestep, nlocal, ids, x, & + fexternal) BIND(C) + TYPE(c_ptr), INTENT(IN), VALUE :: caller + INTEGER(c_int64_t), INTENT(IN), VALUE :: timestep + INTEGER(c_int), INTENT(IN), VALUE :: nlocal + TYPE(c_ptr), INTENT(IN), VALUE :: ids, x, fexternal + TYPE(c_ptr), DIMENSION(:), POINTER :: x0, f0 + INTEGER(c_int64_t), DIMENSION(:), POINTER :: f_ids => NULL() + REAL(c_double), DIMENSION(:,:), POINTER :: f_x => NULL(), & + f_fexternal => NULL() + TYPE(fix_external_data), POINTER :: f_caller => NULL() + + CALL C_F_POINTER(ids, f_ids, [nlocal]) + CALL C_F_POINTER(x, x0, [nlocal]) + CALL C_F_POINTER(x0(1), f_x, [3, nlocal]) + CALL C_F_POINTER(fexternal, f0, [nlocal]) + CALL C_F_POINTER(f0(1), f_fexternal, [3, nlocal]) + IF (C_ASSOCIATED(caller)) THEN + CALL C_F_POINTER(caller, f_caller) + CALL f_caller%callback_bigbig(f_caller%caller, timestep, f_ids, f_x, & + f_fexternal) + ELSE + CALL lmp_error(f_caller%lammps_instance, & + LMP_ERROR_ALL + LMP_ERROR_WORLD, & + 'Got null pointer from "caller"; this should never happen;& + & please report a bug') + END IF + END SUBROUTINE callback_wrapper_bigbig + + ! equivalent function to lammps_fix_external_get_force + FUNCTION lmp_fix_external_get_force(self, id) RESULT(fexternal) + CLASS(lammps), TARGET, INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: id + TYPE(lammps_fix_data) :: fexternal + TYPE(c_ptr) :: ptr, Cid + TYPE(c_ptr), DIMENSION(:), POINTER :: f + INTEGER(c_int) :: nmax + + Cid = f2c_string(id) + ptr = lammps_fix_external_get_force(self%handle, Cid) + nmax = lmp_extract_setting(self, 'nmax') + CALL C_F_POINTER(ptr, f, [nmax]) + fexternal%datatype = DATA_DOUBLE_2D + fexternal%lammps_instance => self + CALL C_F_POINTER(f(1), fexternal%r64_mat, [3, nmax]) + CALL lammps_free(Cid) + END FUNCTION lmp_fix_external_get_force + + SUBROUTINE lmp_fix_external_set_energy_global(self, id, eng) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: id + REAL(c_double), INTENT(IN) :: eng + TYPE(c_ptr) :: Cid + + Cid = f2c_string(id) + CALL lammps_fix_external_set_energy_global(self%handle, Cid, eng) + CALL lammps_free(Cid) + END SUBROUTINE lmp_fix_external_set_energy_global + + SUBROUTINE lmp_fix_external_set_virial_global(self, id, virial) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: id + REAL(c_double), DIMENSION(6), TARGET, INTENT(IN) :: virial + TYPE(c_ptr) :: Cid, Cvirial + + Cid = f2c_string(id) + Cvirial = C_LOC(virial(1)) + CALL lammps_fix_external_set_virial_global(self%handle, Cid, Cvirial) + CALL lammps_free(Cid) + END SUBROUTINE lmp_fix_external_set_virial_global + + SUBROUTINE lmp_fix_external_set_energy_peratom(self, id, eng) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: id + REAL(c_double), DIMENSION(:), TARGET, INTENT(IN) :: eng + TYPE(c_ptr) :: Cid, Ceng + INTEGER(c_int) :: nlocal + + nlocal = lmp_extract_setting(self, 'nlocal') + IF (SIZE(eng) < nlocal) THEN + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & + 'Array "eng" should be length nlocal or greater & + &[Fortran/fix_external_set_energy_peratom]') + END IF + Cid = f2c_string(id) + Ceng = C_LOC(eng) + CALL lammps_fix_external_set_energy_peratom(self%handle, Cid, Ceng) + CALL lammps_free(Cid) + END SUBROUTINE lmp_fix_external_set_energy_peratom + + SUBROUTINE lmp_fix_external_set_virial_peratom(self, id, virial) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: id + REAL(c_double), DIMENSION(:,:), TARGET, INTENT(IN) :: virial + TYPE(c_ptr) :: Cid, Cvirial + TYPE(c_ptr), DIMENSION(:), ALLOCATABLE, TARGET :: Cptr + INTEGER(c_int) :: nlocal, i + + nlocal = lmp_extract_setting(self, 'nlocal') + IF (SIZE(virial,2) < nlocal .OR. SIZE(virial,1) /= 6) THEN + CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, & + 'Array "virial" should be size 6 x nlocal or greater & + &[Fortran/fix_external_set_energy_peratom]') + END IF + Cid = f2c_string(id) + ALLOCATE(Cptr(nlocal)) + DO i = 1, nlocal + Cptr(i) = C_LOC(virial(1,i)) + END DO + Cvirial = C_LOC(Cptr(1)) + CALL lammps_fix_external_set_virial_peratom(self%handle, Cid, Cvirial) + CALL lammps_free(Cid) + DEALLOCATE(Cptr) + END SUBROUTINE lmp_fix_external_set_virial_peratom + + SUBROUTINE lmp_fix_external_set_vector_length(self, id, length) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: id + INTEGER(c_int), INTENT(IN) :: length + TYPE(c_ptr) :: Cid + + Cid = f2c_string(id) + CALL lammps_fix_external_set_vector_length(self%handle, Cid, length) + CALL lammps_free(Cid) + END SUBROUTINE lmp_fix_external_set_vector_length + + SUBROUTINE lmp_fix_external_set_vector(self, id, idx, val) + CLASS(lammps), INTENT(IN) :: self + CHARACTER(LEN=*), INTENT(IN) :: id + INTEGER(c_int), INTENT(IN) :: idx + REAL(c_double), INTENT(IN) :: val + TYPE(c_ptr) :: Cid + + Cid = f2c_string(id) + CALL lammps_fix_external_set_vector(self%handle, Cid, idx, val) + CALL lammps_free(Cid) + END SUBROUTINE lmp_fix_external_set_vector + ! equivalent function to lammps_flush_buffers SUBROUTINE lmp_flush_buffers(self) CLASS(lammps), INTENT(IN) :: self @@ -1695,27 +3122,20 @@ CONTAINS CHARACTER(LEN=*), INTENT(OUT) :: buffer INTEGER, INTENT(OUT), OPTIONAL :: status INTEGER(c_int) :: buflen, Cstatus - INTEGER(c_size_t) :: i, length + CHARACTER(LEN=1, KIND=c_char), DIMENSION(LEN(buffer)+1), TARGET :: Cbuffer TYPE(c_ptr) :: Cptr - CHARACTER(LEN=1, KIND=c_char), POINTER :: c_string(:) - buffer = ' ' + buffer = '' IF (lmp_has_error(self)) THEN - buflen = LEN(buffer) - length = buflen - Cptr = lammps_malloc(length) + buflen = LEN(buffer, KIND=c_int) + 1_c_int + Cptr = C_LOC(Cbuffer(1)) Cstatus = lammps_get_last_error_message(self%handle, Cptr, buflen) - CALL C_F_POINTER(Cptr, c_string, [1]) - DO i=1, length - buffer(i:i) = c_string(i) - IF (c_string(i) == c_null_char) EXIT - END DO + buffer = array2string(Cbuffer) IF (PRESENT(status)) THEN status = Cstatus END IF - CALL lammps_free(Cptr) ELSE - buffer = ' ' + buffer = '' IF (PRESENT(status)) THEN status = 0 END IF @@ -1895,6 +3315,28 @@ CONTAINS END IF END SUBROUTINE assign_string_to_lammps_variable_data + SUBROUTINE assign_int_to_lammps_image_data(lhs, rhs) + INTEGER(c_int), INTENT(OUT) :: lhs + CLASS(lammps_image_data), INTENT(IN) :: rhs + + IF (rhs%datatype == DATA_INT) THEN + lhs = rhs%i32 + ELSE + CALL assignment_error(rhs, 'scalar int') + END IF + END SUBROUTINE assign_int_to_lammps_image_data + + SUBROUTINE assign_int64_to_lammps_image_data(lhs, rhs) + INTEGER(c_int64_t), INTENT(OUT) :: lhs + CLASS(lammps_image_data), INTENT(IN) :: rhs + + IF (rhs%datatype == DATA_INT64) THEN + lhs = rhs%i64 + ELSE + CALL assignment_error(rhs, 'scalar long int') + END IF + END SUBROUTINE assign_int64_to_lammps_image_data + ! ---------------------------------------------------------------------- ! Generic function to catch all errors in assignments of LAMMPS data to ! user-space variables/pointers @@ -1950,6 +3392,46 @@ CONTAINS END DO c_string(n+1) = c_null_char END FUNCTION f2c_string + + ! copy null-terminated C string to fortran string + FUNCTION c2f_string(ptr) RESULT(f_string) + TYPE(c_ptr), INTENT(IN) :: ptr + CHARACTER(LEN=:), ALLOCATABLE :: f_string + CHARACTER(LEN=1, KIND=c_char), DIMENSION(:), POINTER :: c_string + INTEGER :: n + + IF (.NOT. C_ASSOCIATED(ptr)) THEN + f_string = '' + ELSE + n = INT(c_strlen(ptr), KIND=KIND(n)) + CALL C_F_POINTER(ptr, c_string, [n+1]) + f_string = array2string(c_string, n) + END IF + END FUNCTION c2f_string + + ! Copy a known-length or null-terminated array of C characters into a string + FUNCTION array2string(array, length) RESULT(string) + CHARACTER(LEN=1, KIND=c_char), DIMENSION(:) :: array +! NOTE: giving "length" the VALUE attribute reveals a bug in gfortran 12.2.1 +! https://gcc.gnu.org/bugzilla/show_bug.cgi?id=107441 + INTEGER, INTENT(IN), OPTIONAL :: length + CHARACTER(LEN=:), ALLOCATABLE :: string + INTEGER :: n, i + + IF (PRESENT(length)) THEN + n = length + ELSE + n = 1 + DO WHILE (n < SIZE(array) .AND. array(n+1) /= c_null_char) + n = n + 1 + END DO + END IF + ALLOCATE(CHARACTER(LEN=n) :: string) + DO i = 1, n + string(i:i) = array(i) + END DO + END FUNCTION array2string + END MODULE LIBLAMMPS ! vim: ts=2 sts=2 sw=2 et diff --git a/lib/electrode/Makefile.serial b/lib/electrode/Makefile.serial index 8bdd02bae3..0bcc22a58a 100644 --- a/lib/electrode/Makefile.serial +++ b/lib/electrode/Makefile.serial @@ -11,7 +11,7 @@ OBJ = $(SRC:.cpp=.o) # ------ SETTINGS ------ -# include any MPI settings needed for the ATC library to build with +# include any MPI settings needed for the electrode library to build with # the same MPI library that LAMMPS is built with CC = g++ diff --git a/lib/gpu/geryon/ocl_device.h b/lib/gpu/geryon/ocl_device.h index 095c1395f2..4163d40881 100644 --- a/lib/gpu/geryon/ocl_device.h +++ b/lib/gpu/geryon/ocl_device.h @@ -184,7 +184,7 @@ class UCL_Device { _cq.back()=clCreateCommandQueueWithProperties(_context, _cl_device, props, &errorv); } else { - cl_queue_properties props[] = {CL_QUEUE_PROPERTIES, 0}; + cl_queue_properties props[] = {0}; _cq.back()=clCreateCommandQueueWithProperties(_context, _cl_device, props, &errorv); } @@ -536,9 +536,9 @@ int UCL_Device::create_context() { cl_int errorv; cl_context_properties props[3]; props[0]=CL_CONTEXT_PLATFORM; - props[1]=_platform; + props[1]=(cl_context_properties)_cl_platform; props[2]=0; - _context=clCreateContext(0,1,&_cl_device,nullptr,nullptr,&errorv); + _context=clCreateContext(props,1,&_cl_device,nullptr,nullptr,&errorv); if (errorv!=CL_SUCCESS) { #ifndef UCL_NO_EXIT std::cerr << "UCL Error: Could not access accelerator number " << _device diff --git a/lib/gpu/geryon/ocl_texture.h b/lib/gpu/geryon/ocl_texture.h index 43de4b258c..8ddde5b2a3 100644 --- a/lib/gpu/geryon/ocl_texture.h +++ b/lib/gpu/geryon/ocl_texture.h @@ -76,7 +76,7 @@ class UCL_Const { /// Copy from array on host to const memory template inline void update_device(UCL_H_Vec &src, const int numel) { - const int bytes=numel*sizeof(numtyp); + const size_t bytes=numel*sizeof(numtyp); if (_global_bytes < bytes) { if (_global_bytes) CL_SAFE_CALL(clReleaseMemObject(_global)); cl_int e; @@ -84,7 +84,7 @@ class UCL_Const { CL_SAFE_CALL(e); } CL_SAFE_CALL(clEnqueueWriteBuffer(_cq, _global, CL_FALSE, 0, bytes, - (void *)src.begin(), 0, NULL, NULL)); + (void *)src.begin(), 0, NULL, NULL)); } /// Get device ptr associated with object inline const cl_mem * begin() const { return &_global; } diff --git a/lib/gpu/geryon/ucl_d_vec.h b/lib/gpu/geryon/ucl_d_vec.h index 6c10568f86..9158e145b3 100644 --- a/lib/gpu/geryon/ucl_d_vec.h +++ b/lib/gpu/geryon/ucl_d_vec.h @@ -375,7 +375,7 @@ class UCL_D_Vec : public UCL_BaseMat { /// Resize (only if bigger) the allocation to contain cols elements /** \note Cannot be used on views **/ inline int resize_ib(const int cols) - { if (cols>_cols) return resize(cols); else return UCL_SUCCESS; } + { if (cols > (int)_cols) return resize(cols); else return UCL_SUCCESS; } /// Set each element to zero asynchronously in the default command_queue inline void zero() { zero(_cq); } diff --git a/lib/gpu/lal_base_atomic.cpp b/lib/gpu/lal_base_atomic.cpp index b668399a48..bb0e815b3f 100644 --- a/lib/gpu/lal_base_atomic.cpp +++ b/lib/gpu/lal_base_atomic.cpp @@ -340,8 +340,7 @@ void BaseAtomicT::compile_kernels(UCL_Device &dev, const void *pair_str, #if defined(LAL_OCL_EV_JIT) mx_subgroup_sz = std::min(mx_subgroup_sz, k_pair_noev.max_subgroup_size(_block_size)); #endif - if (_threads_per_atom > mx_subgroup_sz) - _threads_per_atom = mx_subgroup_sz; + if (_threads_per_atom > (int)mx_subgroup_sz) _threads_per_atom = mx_subgroup_sz; device->set_simd_size(mx_subgroup_sz); } #endif diff --git a/lib/gpu/lal_base_charge.cpp b/lib/gpu/lal_base_charge.cpp index 84fbddd4e9..4a59f70d83 100644 --- a/lib/gpu/lal_base_charge.cpp +++ b/lib/gpu/lal_base_charge.cpp @@ -359,8 +359,7 @@ void BaseChargeT::compile_kernels(UCL_Device &dev, const void *pair_str, #if defined(LAL_OCL_EV_JIT) mx_subgroup_sz = std::min(mx_subgroup_sz, k_pair_noev.max_subgroup_size(_block_size)); #endif - if (_threads_per_atom > mx_subgroup_sz) - _threads_per_atom = mx_subgroup_sz; + if (_threads_per_atom > (int)mx_subgroup_sz) _threads_per_atom = mx_subgroup_sz; device->set_simd_size(mx_subgroup_sz); } #endif diff --git a/lib/gpu/lal_base_dipole.cpp b/lib/gpu/lal_base_dipole.cpp index 439637cbde..66e03de651 100644 --- a/lib/gpu/lal_base_dipole.cpp +++ b/lib/gpu/lal_base_dipole.cpp @@ -361,8 +361,7 @@ void BaseDipoleT::compile_kernels(UCL_Device &dev, const void *pair_str, #if defined(LAL_OCL_EV_JIT) mx_subgroup_sz = std::min(mx_subgroup_sz, k_pair_noev.max_subgroup_size(_block_size)); #endif - if (_threads_per_atom > mx_subgroup_sz) - _threads_per_atom = mx_subgroup_sz; + if (_threads_per_atom > (int)mx_subgroup_sz) _threads_per_atom = mx_subgroup_sz; device->set_simd_size(mx_subgroup_sz); } #endif diff --git a/lib/gpu/lal_base_dpd.cpp b/lib/gpu/lal_base_dpd.cpp index d3c3353415..44b86abeeb 100644 --- a/lib/gpu/lal_base_dpd.cpp +++ b/lib/gpu/lal_base_dpd.cpp @@ -361,8 +361,7 @@ void BaseDPDT::compile_kernels(UCL_Device &dev, const void *pair_str, #if defined(LAL_OCL_EV_JIT) mx_subgroup_sz = std::min(mx_subgroup_sz, k_pair_noev.max_subgroup_size(_block_size)); #endif - if (_threads_per_atom > mx_subgroup_sz) - _threads_per_atom = mx_subgroup_sz; + if (_threads_per_atom > (int)mx_subgroup_sz) _threads_per_atom = mx_subgroup_sz; device->set_simd_size(mx_subgroup_sz); } #endif diff --git a/lib/gpu/lal_base_ellipsoid.cpp b/lib/gpu/lal_base_ellipsoid.cpp index ca7dc645bc..0bc20615a1 100644 --- a/lib/gpu/lal_base_ellipsoid.cpp +++ b/lib/gpu/lal_base_ellipsoid.cpp @@ -569,8 +569,7 @@ void BaseEllipsoidT::compile_kernels(UCL_Device &dev, if (e_s) mx_subgroup_sz = std::min(mx_subgroup_sz, k_ellipsoid_sphere_noev.max_subgroup_size(_block_size)); #endif - if (_threads_per_atom > mx_subgroup_sz) - _threads_per_atom = mx_subgroup_sz; + if (_threads_per_atom > (int)mx_subgroup_sz) _threads_per_atom = mx_subgroup_sz; device->set_simd_size(mx_subgroup_sz); } #endif diff --git a/lib/gpu/lal_base_three.cpp b/lib/gpu/lal_base_three.cpp index 8ba6147582..3457955b3e 100644 --- a/lib/gpu/lal_base_three.cpp +++ b/lib/gpu/lal_base_three.cpp @@ -471,8 +471,7 @@ void BaseThreeT::compile_kernels(UCL_Device &dev, const void *pair_str, mx_subgroup_sz = std::min(mx_subgroup_sz, k_three_center_noev.max_subgroup_size(_block_size)); mx_subgroup_sz = std::min(mx_subgroup_sz, k_three_end_noev.max_subgroup_size(_block_size)); #endif - if (_threads_per_atom > mx_subgroup_sz) - _threads_per_atom = mx_subgroup_sz; + if (_threads_per_atom > (int)mx_subgroup_sz) _threads_per_atom = mx_subgroup_sz; device->set_simd_size(mx_subgroup_sz); } #endif diff --git a/lib/gpu/lal_device.cpp b/lib/gpu/lal_device.cpp index c28404ab78..0d9578b491 100644 --- a/lib/gpu/lal_device.cpp +++ b/lib/gpu/lal_device.cpp @@ -86,7 +86,7 @@ int DeviceT::init_device(MPI_Comm world, MPI_Comm replica, const int ngpu, #ifdef LAL_OCL_EXTRA_ARGS extra_args+=":" LAL_PRE_STRINGIFY(LAL_OCL_EXTRA_ARGS); #endif - for (int i=0; iplatform_name(); - for (int i=0; i='a') pname[i]=toupper(pname[i]); if (pname.find("NVIDIA")!=std::string::npos) @@ -741,6 +741,7 @@ void DeviceT::estimate_gpu_overhead(const int kernel_calls, } gpu_overhead/=10.0; gpu_driver_overhead/=10.0; + gpu->sync(); if (_data_in_estimate>0) { delete [] host_data_in; @@ -793,6 +794,7 @@ void DeviceT::output_times(UCL_Timer &time_pair, Answer &ans, #ifdef USE_OPENCL // Workaround for timing issue on Intel OpenCL if (times[0] > 80e6) times[0]=0.0; + if (times[1] > 80e6) times[1]=0.0; if (times[3] > 80e6) times[3]=0.0; if (times[5] > 80e6) times[5]=0.0; #endif @@ -806,9 +808,8 @@ void DeviceT::output_times(UCL_Timer &time_pair, Answer &ans, fprintf(screen,"--------------------------------\n"); if (time_device() && (times[3] > 0.0)) { - if (times[0] > 0.0) - fprintf(screen,"Data Transfer: %.4f s.\n",times[0]/_replica_size); - fprintf(screen,"Neighbor copy: %.4f s.\n",times[1]/_replica_size); + if (times[0] > 0.0) fprintf(screen,"Data Transfer: %.4f s.\n",times[0]/_replica_size); + if (times[1] > 0.0) fprintf(screen,"Neighbor copy: %.4f s.\n",times[1]/_replica_size); if (nbor.gpu_nbor() > 0.0) fprintf(screen,"Neighbor build: %.4f s.\n",times[2]/_replica_size); else @@ -862,32 +863,34 @@ void DeviceT::output_kspace_times(UCL_Timer &time_in, double max_mb=mpi_max_bytes/(1024.0*1024.0); #ifdef USE_OPENCL // Workaround for timing issue on Intel OpenCL + if (times[0] > 80e6) times[0]=0.0; + if (times[1] > 80e6) times[1]=0.0; if (times[3] > 80e6) times[3]=0.0; + if (times[5] > 80e6) times[5]=0.0; #endif if (replica_me()==0) - if (screen && times[6]>0.0) { + if (screen && (times[6] > 0.0)) { fprintf(screen,"\n\n-------------------------------------"); fprintf(screen,"--------------------------------\n"); fprintf(screen," Device Time Info (average) for kspace: "); fprintf(screen,"\n-------------------------------------"); fprintf(screen,"--------------------------------\n"); - if (time_device() && times[3]>0) { - fprintf(screen,"Data Out: %.4f s.\n",times[0]/_replica_size); - fprintf(screen,"Data In: %.4f s.\n",times[1]/_replica_size); + if (time_device() && (times[3] > 0.0)) { + if (times[0] > 0.0) fprintf(screen,"Data Out: %.4f s.\n",times[0]/_replica_size); + if (times[1] > 0.0) fprintf(screen,"Data In: %.4f s.\n",times[1]/_replica_size); fprintf(screen,"Kernel (map): %.4f s.\n",times[2]/_replica_size); fprintf(screen,"Kernel (rho): %.4f s.\n",times[3]/_replica_size); fprintf(screen,"Force interp: %.4f s.\n",times[4]/_replica_size); - fprintf(screen,"Total rho: %.4f s.\n", - (times[0]+times[2]+times[3])/_replica_size); - fprintf(screen,"Total interp: %.4f s.\n", - (times[1]+times[4])/_replica_size); - fprintf(screen,"Force copy: %.4f s.\n",times[5]/_replica_size); + if (times[0] > 0.0) + fprintf(screen,"Total rho: %.4f s.\n", (times[0]+times[2]+times[3])/_replica_size); + if (times[1] > 0.0) + fprintf(screen,"Total interp: %.4f s.\n", (times[1]+times[4])/_replica_size); + if (times[5] > 0.0) fprintf(screen,"Force copy: %.4f s.\n",times[5]/_replica_size); fprintf(screen,"Total: %.4f s.\n", - (times[0]+times[1]+times[2]+times[3]+times[4]+times[5])/ - _replica_size); + (times[0]+times[1]+times[2]+times[3]+times[4]+times[5])/_replica_size); } fprintf(screen,"CPU Poisson: %.4f s.\n",times[6]/_replica_size); fprintf(screen,"CPU Data Cast: %.4f s.\n",times[8]/_replica_size); diff --git a/lib/gpu/lal_lj_tip4p_long.cu b/lib/gpu/lal_lj_tip4p_long.cu index 07a7ae7913..063daf7256 100644 --- a/lib/gpu/lal_lj_tip4p_long.cu +++ b/lib/gpu/lal_lj_tip4p_long.cu @@ -257,7 +257,7 @@ __kernel void k_lj_tip4p_reneigh( } if (i subgroup2cell.numel()) { + if (subgroup_count > (int)subgroup2cell.numel()) { subgroup2cell.clear(); success = success && (subgroup2cell.alloc(1.1*subgroup_count,*dev, UCL_READ_WRITE,UCL_READ_ONLY) == UCL_SUCCESS); @@ -702,7 +702,7 @@ void Neighbor::build_nbor_list(double **x, const int inum, const int host_inum, _old_ncellz = ncellz; const int bin_stencil_stride = cells_in_cutoff * 2 + 1; const int bin_stencil_size = bin_stencil_stride * bin_stencil_stride; - if (bin_stencil_size > _host_bin_stencil.numel()) + if (bin_stencil_size > (int)_host_bin_stencil.numel()) _host_bin_stencil.alloc(bin_stencil_size,*dev); for (int s = 0; s_nall; - if (nall*this->nbor->max_nbors() > _zetaij.cols()) { + if (nall*this->nbor->max_nbors() > (int)_zetaij.cols()) { int _nmax=static_cast(static_cast(nall)*1.10); _zetaij.clear(); _zetaij_eng.clear(); diff --git a/lib/gpu/lal_tersoff_mod.cpp b/lib/gpu/lal_tersoff_mod.cpp index 7f050c8eee..4c5e60f737 100644 --- a/lib/gpu/lal_tersoff_mod.cpp +++ b/lib/gpu/lal_tersoff_mod.cpp @@ -252,7 +252,7 @@ int TersoffMT::loop(const int eflag, const int vflag, const int evatom, // re-allocate zetaij if necessary int nall = this->_nall; - if (nall*this->nbor->max_nbors() > _zetaij.cols()) { + if (nall*this->nbor->max_nbors() > (int)_zetaij.cols()) { int _nmax=static_cast(static_cast(nall)*1.10); _zetaij.clear(); success = success && (_zetaij.alloc(this->nbor->max_nbors()*_nmax, diff --git a/lib/gpu/lal_tersoff_zbl.cpp b/lib/gpu/lal_tersoff_zbl.cpp index b3d7df9a3e..1499416b66 100644 --- a/lib/gpu/lal_tersoff_zbl.cpp +++ b/lib/gpu/lal_tersoff_zbl.cpp @@ -276,7 +276,7 @@ int TersoffZT::loop(const int eflag, const int vflag, const int evatom, // re-allocate zetaij if necessary int nall = this->_nall; - if (nall*this->nbor->max_nbors() > _zetaij.cols()) { + if (nall*this->nbor->max_nbors() > (int)_zetaij.cols()) { int _nmax=static_cast(static_cast(nall)*1.10); _zetaij.clear(); success = success && (_zetaij.alloc(this->nbor->max_nbors()*_nmax, diff --git a/lib/linalg/README b/lib/linalg/README index de2d83dcbd..e3b817cacc 100644 --- a/lib/linalg/README +++ b/lib/linalg/README @@ -1,13 +1,16 @@ -This directory has BLAS and LAPACK files needed by the ATC and -AWPMD packages, and possibly by other packages in the future. +This directory has generic BLAS and LAPACK source files needed by the +ATC, AWPMD, ELECTRODE, LATTE, and ML-POD packages (and possibly by other +packages) in the future that can be used instead of platform or vendor +optimized BLAS/LAPACK library. Note that this is an *incomplete* subset of full BLAS/LAPACK. +The files correspond to LAPACK version 3.11.0. + You should only need to build and use the library in this directory if -you want to build LAMMPS with the ATC and/or AWPMD packages -AND you do not have any other suitable BLAS and LAPACK libraries -installed on your system. E.g. ATLAS, GOTO-BLAS, OpenBLAS, ACML, or -MKL. +you want to build LAMMPS with one of the listed packages AND you do not +have any other suitable BLAS and LAPACK libraries installed on your +system (like ATLAS, GOTO-BLAS, OpenBLAS, ACML, MKL and so on). You can type "make lib-linalg" from the src directory to see help on how to build this library via make commands, or you can do the same @@ -27,3 +30,4 @@ liblinalg.a the library LAMMPS will link against You can then include this library and its path in the Makefile.lammps file of any packages that need it. As an example, see the lib/atc/Makefile.lammps.linalg file. + diff --git a/lib/linalg/dgelss.f b/lib/linalg/dgelss.f index 8ed703fcf2..c4190f2e09 100644 --- a/lib/linalg/dgelss.f +++ b/lib/linalg/dgelss.f @@ -254,11 +254,11 @@ * * Compute space needed for DGEQRF CALL DGEQRF( M, N, A, LDA, DUM(1), DUM(1), -1, INFO ) - LWORK_DGEQRF=DUM(1) + LWORK_DGEQRF = INT( DUM(1) ) * Compute space needed for DORMQR CALL DORMQR( 'L', 'T', M, NRHS, N, A, LDA, DUM(1), B, $ LDB, DUM(1), -1, INFO ) - LWORK_DORMQR=DUM(1) + LWORK_DORMQR = INT( DUM(1) ) MM = N MAXWRK = MAX( MAXWRK, N + LWORK_DGEQRF ) MAXWRK = MAX( MAXWRK, N + LWORK_DORMQR ) @@ -273,15 +273,15 @@ * Compute space needed for DGEBRD CALL DGEBRD( MM, N, A, LDA, S, DUM(1), DUM(1), $ DUM(1), DUM(1), -1, INFO ) - LWORK_DGEBRD=DUM(1) + LWORK_DGEBRD = INT( DUM(1) ) * Compute space needed for DORMBR CALL DORMBR( 'Q', 'L', 'T', MM, NRHS, N, A, LDA, DUM(1), $ B, LDB, DUM(1), -1, INFO ) - LWORK_DORMBR=DUM(1) + LWORK_DORMBR = INT( DUM(1) ) * Compute space needed for DORGBR CALL DORGBR( 'P', N, N, N, A, LDA, DUM(1), $ DUM(1), -1, INFO ) - LWORK_DORGBR=DUM(1) + LWORK_DORGBR = INT( DUM(1) ) * Compute total workspace needed MAXWRK = MAX( MAXWRK, 3*N + LWORK_DGEBRD ) MAXWRK = MAX( MAXWRK, 3*N + LWORK_DORMBR ) @@ -305,23 +305,23 @@ * Compute space needed for DGELQF CALL DGELQF( M, N, A, LDA, DUM(1), DUM(1), $ -1, INFO ) - LWORK_DGELQF=DUM(1) + LWORK_DGELQF = INT( DUM(1) ) * Compute space needed for DGEBRD CALL DGEBRD( M, M, A, LDA, S, DUM(1), DUM(1), $ DUM(1), DUM(1), -1, INFO ) - LWORK_DGEBRD=DUM(1) + LWORK_DGEBRD = INT( DUM(1) ) * Compute space needed for DORMBR CALL DORMBR( 'Q', 'L', 'T', M, NRHS, N, A, LDA, $ DUM(1), B, LDB, DUM(1), -1, INFO ) - LWORK_DORMBR=DUM(1) + LWORK_DORMBR = INT( DUM(1) ) * Compute space needed for DORGBR CALL DORGBR( 'P', M, M, M, A, LDA, DUM(1), $ DUM(1), -1, INFO ) - LWORK_DORGBR=DUM(1) + LWORK_DORGBR = INT( DUM(1) ) * Compute space needed for DORMLQ CALL DORMLQ( 'L', 'T', N, NRHS, M, A, LDA, DUM(1), $ B, LDB, DUM(1), -1, INFO ) - LWORK_DORMLQ=DUM(1) + LWORK_DORMLQ = INT( DUM(1) ) * Compute total workspace needed MAXWRK = M + LWORK_DGELQF MAXWRK = MAX( MAXWRK, M*M + 4*M + LWORK_DGEBRD ) @@ -341,15 +341,15 @@ * Compute space needed for DGEBRD CALL DGEBRD( M, N, A, LDA, S, DUM(1), DUM(1), $ DUM(1), DUM(1), -1, INFO ) - LWORK_DGEBRD=DUM(1) + LWORK_DGEBRD = INT( DUM(1) ) * Compute space needed for DORMBR CALL DORMBR( 'Q', 'L', 'T', M, NRHS, M, A, LDA, $ DUM(1), B, LDB, DUM(1), -1, INFO ) - LWORK_DORMBR=DUM(1) + LWORK_DORMBR = INT( DUM(1) ) * Compute space needed for DORGBR CALL DORGBR( 'P', M, N, M, A, LDA, DUM(1), $ DUM(1), -1, INFO ) - LWORK_DORGBR=DUM(1) + LWORK_DORGBR = INT( DUM(1) ) MAXWRK = 3*M + LWORK_DGEBRD MAXWRK = MAX( MAXWRK, 3*M + LWORK_DORMBR ) MAXWRK = MAX( MAXWRK, 3*M + LWORK_DORGBR ) diff --git a/lib/linalg/dlaed4.f b/lib/linalg/dlaed4.f index 3ee3ef920f..b51e23d850 100644 --- a/lib/linalg/dlaed4.f +++ b/lib/linalg/dlaed4.f @@ -328,9 +328,12 @@ IF( C.LT.ZERO ) $ C = ABS( C ) IF( C.EQ.ZERO ) THEN -* ETA = B/A +* ETA = B/A * ETA = RHO - TAU - ETA = DLTUB - TAU +* ETA = DLTUB - TAU +* +* Update proposed by Li, Ren-Cang: + ETA = -W / ( DPSI+DPHI ) ELSE IF( A.GE.ZERO ) THEN ETA = ( A+SQRT( ABS( A*A-FOUR*B*C ) ) ) / ( TWO*C ) ELSE diff --git a/lib/linalg/dlascl.f b/lib/linalg/dlascl.f index 05ad1c4f3c..0a4bf21ce1 100644 --- a/lib/linalg/dlascl.f +++ b/lib/linalg/dlascl.f @@ -272,6 +272,8 @@ ELSE MUL = CTOC / CFROMC DONE = .TRUE. + IF (MUL .EQ. ONE) + $ RETURN END IF END IF * diff --git a/lib/linalg/dlatrs.f b/lib/linalg/dlatrs.f index 43f92911d7..be156bee20 100644 --- a/lib/linalg/dlatrs.f +++ b/lib/linalg/dlatrs.f @@ -264,8 +264,8 @@ * .. External Functions .. LOGICAL LSAME INTEGER IDAMAX - DOUBLE PRECISION DASUM, DDOT, DLAMCH - EXTERNAL LSAME, IDAMAX, DASUM, DDOT, DLAMCH + DOUBLE PRECISION DASUM, DDOT, DLAMCH, DLANGE + EXTERNAL LSAME, IDAMAX, DASUM, DDOT, DLAMCH, DLANGE * .. * .. External Subroutines .. EXTERNAL DAXPY, DSCAL, DTRSV, XERBLA @@ -304,6 +304,7 @@ * * Quick return if possible * + SCALE = ONE IF( N.EQ.0 ) $ RETURN * @@ -311,7 +312,6 @@ * SMLNUM = DLAMCH( 'Safe minimum' ) / DLAMCH( 'Precision' ) BIGNUM = ONE / SMLNUM - SCALE = ONE * IF( LSAME( NORMIN, 'N' ) ) THEN * @@ -343,8 +343,67 @@ IF( TMAX.LE.BIGNUM ) THEN TSCAL = ONE ELSE - TSCAL = ONE / ( SMLNUM*TMAX ) - CALL DSCAL( N, TSCAL, CNORM, 1 ) +* +* Avoid NaN generation if entries in CNORM exceed the +* overflow threshold +* + IF( TMAX.LE.DLAMCH('Overflow') ) THEN +* Case 1: All entries in CNORM are valid floating-point numbers + TSCAL = ONE / ( SMLNUM*TMAX ) + CALL DSCAL( N, TSCAL, CNORM, 1 ) + ELSE +* Case 2: At least one column norm of A cannot be represented +* as floating-point number. Find the offdiagonal entry A( I, J ) +* with the largest absolute value. If this entry is not +/- Infinity, +* use this value as TSCAL. + TMAX = ZERO + IF( UPPER ) THEN +* +* A is upper triangular. +* + DO J = 2, N + TMAX = MAX( DLANGE( 'M', J-1, 1, A( 1, J ), 1, SUMJ ), + $ TMAX ) + END DO + ELSE +* +* A is lower triangular. +* + DO J = 1, N - 1 + TMAX = MAX( DLANGE( 'M', N-J, 1, A( J+1, J ), 1, + $ SUMJ ), TMAX ) + END DO + END IF +* + IF( TMAX.LE.DLAMCH('Overflow') ) THEN + TSCAL = ONE / ( SMLNUM*TMAX ) + DO J = 1, N + IF( CNORM( J ).LE.DLAMCH('Overflow') ) THEN + CNORM( J ) = CNORM( J )*TSCAL + ELSE +* Recompute the 1-norm without introducing Infinity +* in the summation + CNORM( J ) = ZERO + IF( UPPER ) THEN + DO I = 1, J - 1 + CNORM( J ) = CNORM( J ) + + $ TSCAL * ABS( A( I, J ) ) + END DO + ELSE + DO I = J + 1, N + CNORM( J ) = CNORM( J ) + + $ TSCAL * ABS( A( I, J ) ) + END DO + END IF + END IF + END DO + ELSE +* At least one entry of A is not a valid floating-point entry. +* Rely on TRSV to propagate Inf and NaN. + CALL DTRSV( UPLO, TRANS, DIAG, N, A, LDA, X, 1 ) + RETURN + END IF + END IF END IF * * Compute a bound on the computed solution vector to see if the diff --git a/lib/linalg/dorgbr.f b/lib/linalg/dorgbr.f index 1b242ff97f..7dfd03961e 100644 --- a/lib/linalg/dorgbr.f +++ b/lib/linalg/dorgbr.f @@ -232,7 +232,7 @@ END IF END IF END IF - LWKOPT = WORK( 1 ) + LWKOPT = INT( WORK( 1 ) ) LWKOPT = MAX (LWKOPT, MN) END IF * diff --git a/lib/linalg/dposv.f b/lib/linalg/dposv.f new file mode 100644 index 0000000000..ee2988e6fd --- /dev/null +++ b/lib/linalg/dposv.f @@ -0,0 +1,190 @@ +*> \brief DPOSV computes the solution to system of linear equations A * X = B for PO matrices +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download DPOSV + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE DPOSV( UPLO, N, NRHS, A, LDA, B, LDB, INFO ) +* +* .. Scalar Arguments .. +* CHARACTER UPLO +* INTEGER INFO, LDA, LDB, N, NRHS +* .. +* .. Array Arguments .. +* DOUBLE PRECISION A( LDA, * ), B( LDB, * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> DPOSV computes the solution to a real system of linear equations +*> A * X = B, +*> where A is an N-by-N symmetric positive definite matrix and X and B +*> are N-by-NRHS matrices. +*> +*> The Cholesky decomposition is used to factor A as +*> A = U**T* U, if UPLO = 'U', or +*> A = L * L**T, if UPLO = 'L', +*> where U is an upper triangular matrix and L is a lower triangular +*> matrix. The factored form of A is then used to solve the system of +*> equations A * X = B. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] UPLO +*> \verbatim +*> UPLO is CHARACTER*1 +*> = 'U': Upper triangle of A is stored; +*> = 'L': Lower triangle of A is stored. +*> \endverbatim +*> +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> The number of linear equations, i.e., the order of the +*> matrix A. N >= 0. +*> \endverbatim +*> +*> \param[in] NRHS +*> \verbatim +*> NRHS is INTEGER +*> The number of right hand sides, i.e., the number of columns +*> of the matrix B. NRHS >= 0. +*> \endverbatim +*> +*> \param[in,out] A +*> \verbatim +*> A is DOUBLE PRECISION array, dimension (LDA,N) +*> On entry, the symmetric matrix A. If UPLO = 'U', the leading +*> N-by-N upper triangular part of A contains the upper +*> triangular part of the matrix A, and the strictly lower +*> triangular part of A is not referenced. If UPLO = 'L', the +*> leading N-by-N lower triangular part of A contains the lower +*> triangular part of the matrix A, and the strictly upper +*> triangular part of A is not referenced. +*> +*> On exit, if INFO = 0, the factor U or L from the Cholesky +*> factorization A = U**T*U or A = L*L**T. +*> \endverbatim +*> +*> \param[in] LDA +*> \verbatim +*> LDA is INTEGER +*> The leading dimension of the array A. LDA >= max(1,N). +*> \endverbatim +*> +*> \param[in,out] B +*> \verbatim +*> B is DOUBLE PRECISION array, dimension (LDB,NRHS) +*> On entry, the N-by-NRHS right hand side matrix B. +*> On exit, if INFO = 0, the N-by-NRHS solution matrix X. +*> \endverbatim +*> +*> \param[in] LDB +*> \verbatim +*> LDB is INTEGER +*> The leading dimension of the array B. LDB >= max(1,N). +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> = 0: successful exit +*> < 0: if INFO = -i, the i-th argument had an illegal value +*> > 0: if INFO = i, the leading minor of order i of A is not +*> positive definite, so the factorization could not be +*> completed, and the solution has not been computed. +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \ingroup doublePOsolve +* +* ===================================================================== + SUBROUTINE DPOSV( UPLO, N, NRHS, A, LDA, B, LDB, INFO ) +* +* -- LAPACK driver routine -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* +* .. Scalar Arguments .. + CHARACTER UPLO + INTEGER INFO, LDA, LDB, N, NRHS +* .. +* .. Array Arguments .. + DOUBLE PRECISION A( LDA, * ), B( LDB, * ) +* .. +* +* ===================================================================== +* +* .. External Functions .. + LOGICAL LSAME + EXTERNAL LSAME +* .. +* .. External Subroutines .. + EXTERNAL DPOTRF, DPOTRS, XERBLA +* .. +* .. Intrinsic Functions .. + INTRINSIC MAX +* .. +* .. Executable Statements .. +* +* Test the input parameters. +* + INFO = 0 + IF( .NOT.LSAME( UPLO, 'U' ) .AND. .NOT.LSAME( UPLO, 'L' ) ) THEN + INFO = -1 + ELSE IF( N.LT.0 ) THEN + INFO = -2 + ELSE IF( NRHS.LT.0 ) THEN + INFO = -3 + ELSE IF( LDA.LT.MAX( 1, N ) ) THEN + INFO = -5 + ELSE IF( LDB.LT.MAX( 1, N ) ) THEN + INFO = -7 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DPOSV ', -INFO ) + RETURN + END IF +* +* Compute the Cholesky factorization A = U**T*U or A = L*L**T. +* + CALL DPOTRF( UPLO, N, A, LDA, INFO ) + IF( INFO.EQ.0 ) THEN +* +* Solve the system A*X = B, overwriting B with X. +* + CALL DPOTRS( UPLO, N, NRHS, A, LDA, B, LDB, INFO ) +* + END IF + RETURN +* +* End of DPOSV +* + END diff --git a/lib/linalg/dpotrs.f b/lib/linalg/dpotrs.f new file mode 100644 index 0000000000..862ee078fd --- /dev/null +++ b/lib/linalg/dpotrs.f @@ -0,0 +1,201 @@ +*> \brief \b DPOTRS +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download DPOTRS + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE DPOTRS( UPLO, N, NRHS, A, LDA, B, LDB, INFO ) +* +* .. Scalar Arguments .. +* CHARACTER UPLO +* INTEGER INFO, LDA, LDB, N, NRHS +* .. +* .. Array Arguments .. +* DOUBLE PRECISION A( LDA, * ), B( LDB, * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> DPOTRS solves a system of linear equations A*X = B with a symmetric +*> positive definite matrix A using the Cholesky factorization +*> A = U**T*U or A = L*L**T computed by DPOTRF. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] UPLO +*> \verbatim +*> UPLO is CHARACTER*1 +*> = 'U': Upper triangle of A is stored; +*> = 'L': Lower triangle of A is stored. +*> \endverbatim +*> +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> The order of the matrix A. N >= 0. +*> \endverbatim +*> +*> \param[in] NRHS +*> \verbatim +*> NRHS is INTEGER +*> The number of right hand sides, i.e., the number of columns +*> of the matrix B. NRHS >= 0. +*> \endverbatim +*> +*> \param[in] A +*> \verbatim +*> A is DOUBLE PRECISION array, dimension (LDA,N) +*> The triangular factor U or L from the Cholesky factorization +*> A = U**T*U or A = L*L**T, as computed by DPOTRF. +*> \endverbatim +*> +*> \param[in] LDA +*> \verbatim +*> LDA is INTEGER +*> The leading dimension of the array A. LDA >= max(1,N). +*> \endverbatim +*> +*> \param[in,out] B +*> \verbatim +*> B is DOUBLE PRECISION array, dimension (LDB,NRHS) +*> On entry, the right hand side matrix B. +*> On exit, the solution matrix X. +*> \endverbatim +*> +*> \param[in] LDB +*> \verbatim +*> LDB is INTEGER +*> The leading dimension of the array B. LDB >= max(1,N). +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> = 0: successful exit +*> < 0: if INFO = -i, the i-th argument had an illegal value +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \ingroup doublePOcomputational +* +* ===================================================================== + SUBROUTINE DPOTRS( UPLO, N, NRHS, A, LDA, B, LDB, INFO ) +* +* -- LAPACK computational routine -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* +* .. Scalar Arguments .. + CHARACTER UPLO + INTEGER INFO, LDA, LDB, N, NRHS +* .. +* .. Array Arguments .. + DOUBLE PRECISION A( LDA, * ), B( LDB, * ) +* .. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ONE + PARAMETER ( ONE = 1.0D+0 ) +* .. +* .. Local Scalars .. + LOGICAL UPPER +* .. +* .. External Functions .. + LOGICAL LSAME + EXTERNAL LSAME +* .. +* .. External Subroutines .. + EXTERNAL DTRSM, XERBLA +* .. +* .. Intrinsic Functions .. + INTRINSIC MAX +* .. +* .. Executable Statements .. +* +* Test the input parameters. +* + INFO = 0 + UPPER = LSAME( UPLO, 'U' ) + IF( .NOT.UPPER .AND. .NOT.LSAME( UPLO, 'L' ) ) THEN + INFO = -1 + ELSE IF( N.LT.0 ) THEN + INFO = -2 + ELSE IF( NRHS.LT.0 ) THEN + INFO = -3 + ELSE IF( LDA.LT.MAX( 1, N ) ) THEN + INFO = -5 + ELSE IF( LDB.LT.MAX( 1, N ) ) THEN + INFO = -7 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DPOTRS', -INFO ) + RETURN + END IF +* +* Quick return if possible +* + IF( N.EQ.0 .OR. NRHS.EQ.0 ) + $ RETURN +* + IF( UPPER ) THEN +* +* Solve A*X = B where A = U**T *U. +* +* Solve U**T *X = B, overwriting B with X. +* + CALL DTRSM( 'Left', 'Upper', 'Transpose', 'Non-unit', N, NRHS, + $ ONE, A, LDA, B, LDB ) +* +* Solve U*X = B, overwriting B with X. +* + CALL DTRSM( 'Left', 'Upper', 'No transpose', 'Non-unit', N, + $ NRHS, ONE, A, LDA, B, LDB ) + ELSE +* +* Solve A*X = B where A = L*L**T. +* +* Solve L*X = B, overwriting B with X. +* + CALL DTRSM( 'Left', 'Lower', 'No transpose', 'Non-unit', N, + $ NRHS, ONE, A, LDA, B, LDB ) +* +* Solve L**T *X = B, overwriting B with X. +* + CALL DTRSM( 'Left', 'Lower', 'Transpose', 'Non-unit', N, NRHS, + $ ONE, A, LDA, B, LDB ) + END IF +* + RETURN +* +* End of DPOTRS +* + END diff --git a/lib/linalg/dscal.f b/lib/linalg/dscal.f index 3713427334..e055d198af 100644 --- a/lib/linalg/dscal.f +++ b/lib/linalg/dscal.f @@ -93,11 +93,14 @@ * * .. Local Scalars .. INTEGER I,M,MP1,NINCX +* .. Parameters .. + DOUBLE PRECISION ONE + PARAMETER (ONE=1.0D+0) * .. * .. Intrinsic Functions .. INTRINSIC MOD * .. - IF (N.LE.0 .OR. INCX.LE.0) RETURN + IF (N.LE.0 .OR. INCX.LE.0 .OR. DA.EQ.ONE) RETURN IF (INCX.EQ.1) THEN * * code for increment equal to 1 diff --git a/lib/linalg/dsyevd.f b/lib/linalg/dsyevd.f index edbe896fe8..eaaecd8d98 100644 --- a/lib/linalg/dsyevd.f +++ b/lib/linalg/dsyevd.f @@ -257,7 +257,7 @@ LWMIN = 2*N + 1 END IF LOPT = MAX( LWMIN, 2*N + - $ ILAENV( 1, 'DSYTRD', UPLO, N, -1, -1, -1 ) ) + $ N*ILAENV( 1, 'DSYTRD', UPLO, N, -1, -1, -1 ) ) LIOPT = LIWMIN END IF WORK( 1 ) = LOPT diff --git a/lib/linalg/dsygvd.f b/lib/linalg/dsygvd.f index 61134bedce..3b38665a75 100644 --- a/lib/linalg/dsygvd.f +++ b/lib/linalg/dsygvd.f @@ -330,8 +330,8 @@ CALL DSYGST( ITYPE, UPLO, N, A, LDA, B, LDB, INFO ) CALL DSYEVD( JOBZ, UPLO, N, A, LDA, W, WORK, LWORK, IWORK, LIWORK, $ INFO ) - LOPT = MAX( DBLE( LOPT ), DBLE( WORK( 1 ) ) ) - LIOPT = MAX( DBLE( LIOPT ), DBLE( IWORK( 1 ) ) ) + LOPT = INT( MAX( DBLE( LOPT ), DBLE( WORK( 1 ) ) ) ) + LIOPT = INT( MAX( DBLE( LIOPT ), DBLE( IWORK( 1 ) ) ) ) * IF( WANTZ .AND. INFO.EQ.0 ) THEN * diff --git a/lib/linalg/ieeeck.f b/lib/linalg/ieeeck.f index 74065c3b4e..f9f6332ecf 100644 --- a/lib/linalg/ieeeck.f +++ b/lib/linalg/ieeeck.f @@ -41,7 +41,7 @@ *> \param[in] ISPEC *> \verbatim *> ISPEC is INTEGER -*> Specifies whether to test just for inifinity arithmetic +*> Specifies whether to test just for infinity arithmetic *> or whether to test for infinity and NaN arithmetic. *> = 0: Verify infinity arithmetic only. *> = 1: Verify infinity and NaN arithmetic. diff --git a/lib/linalg/ilaenv.f b/lib/linalg/ilaenv.f index af28503986..a639e0375a 100644 --- a/lib/linalg/ilaenv.f +++ b/lib/linalg/ilaenv.f @@ -469,6 +469,15 @@ ELSE NB = 64 END IF + ELSE IF( C3.EQ.'SYL' ) THEN +* The upper bound is to prevent overly aggressive scaling. + IF( SNAME ) THEN + NB = MIN( MAX( 48, INT( ( MIN( N1, N2 ) * 16 ) / 100) ), + $ 240 ) + ELSE + NB = MIN( MAX( 24, INT( ( MIN( N1, N2 ) * 8 ) / 100) ), + $ 80 ) + END IF END IF ELSE IF( C2.EQ.'LA' ) THEN IF( C3.EQ.'UUM' ) THEN @@ -477,6 +486,12 @@ ELSE NB = 64 END IF + ELSE IF( C3.EQ.'TRS' ) THEN + IF( SNAME ) THEN + NB = 32 + ELSE + NB = 32 + END IF END IF ELSE IF( SNAME .AND. C2.EQ.'ST' ) THEN IF( C3.EQ.'EBZ' ) THEN diff --git a/lib/linalg/zdscal.f b/lib/linalg/zdscal.f index b3546ba206..5a16048771 100644 --- a/lib/linalg/zdscal.f +++ b/lib/linalg/zdscal.f @@ -92,17 +92,20 @@ * * .. Local Scalars .. INTEGER I,NINCX +* .. Parameters .. + DOUBLE PRECISION ONE + PARAMETER (ONE=1.0D+0) * .. * .. Intrinsic Functions .. - INTRINSIC DCMPLX + INTRINSIC DBLE, DCMPLX, DIMAG * .. - IF (N.LE.0 .OR. INCX.LE.0) RETURN + IF (N.LE.0 .OR. INCX.LE.0 .OR. DA.EQ.ONE) RETURN IF (INCX.EQ.1) THEN * * code for increment equal to 1 * DO I = 1,N - ZX(I) = DCMPLX(DA,0.0d0)*ZX(I) + ZX(I) = DCMPLX(DA*DBLE(ZX(I)),DA*DIMAG(ZX(I))) END DO ELSE * @@ -110,7 +113,7 @@ * NINCX = N*INCX DO I = 1,NINCX,INCX - ZX(I) = DCMPLX(DA,0.0d0)*ZX(I) + ZX(I) = DCMPLX(DA*DBLE(ZX(I)),DA*DIMAG(ZX(I))) END DO END IF RETURN diff --git a/lib/linalg/zheevd.f b/lib/linalg/zheevd.f index a6484eb032..7f58c7f726 100644 --- a/lib/linalg/zheevd.f +++ b/lib/linalg/zheevd.f @@ -284,7 +284,7 @@ LIWMIN = 1 END IF LOPT = MAX( LWMIN, N + - $ ILAENV( 1, 'ZHETRD', UPLO, N, -1, -1, -1 ) ) + $ N*ILAENV( 1, 'ZHETRD', UPLO, N, -1, -1, -1 ) ) LROPT = LRWMIN LIOPT = LIWMIN END IF diff --git a/lib/linalg/zlascl.f b/lib/linalg/zlascl.f index 3d53f5ae60..4cce5ff5e0 100644 --- a/lib/linalg/zlascl.f +++ b/lib/linalg/zlascl.f @@ -272,6 +272,8 @@ ELSE MUL = CTOC / CFROMC DONE = .TRUE. + IF (MUL .EQ. ONE) + $ RETURN END IF END IF * diff --git a/lib/linalg/zscal.f b/lib/linalg/zscal.f index 8085f5a399..8b8c2c8ab5 100644 --- a/lib/linalg/zscal.f +++ b/lib/linalg/zscal.f @@ -93,7 +93,11 @@ * .. Local Scalars .. INTEGER I,NINCX * .. - IF (N.LE.0 .OR. INCX.LE.0) RETURN +* .. Parameters .. + COMPLEX*16 ONE + PARAMETER (ONE= (1.0D+0,0.0D+0)) +* .. + IF (N.LE.0 .OR. INCX.LE.0 .OR. ZA.EQ.ONE) RETURN IF (INCX.EQ.1) THEN * * code for increment equal to 1 diff --git a/lib/mesont/CNTPot.f90 b/lib/mesont/CNTPot.f90 index 5c83ce63e5..296c436049 100644 --- a/lib/mesont/CNTPot.f90 +++ b/lib/mesont/CNTPot.f90 @@ -1,7 +1,7 @@ ! ------------ ---------------------------------------------------------- ! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator ! https://www.lammps.org/ Sandia National Laboratories -! Steve Plimpton, sjplimp@sandia.gov +! LAMMPS development team: developers@lammps.org ! ! Copyright (2003) Sandia Corporation. Under the terms of Contract ! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/lib/mesont/ExportCNT.f90 b/lib/mesont/ExportCNT.f90 index 039503d51e..e86ada0c7c 100644 --- a/lib/mesont/ExportCNT.f90 +++ b/lib/mesont/ExportCNT.f90 @@ -1,7 +1,7 @@ ! ------------ ---------------------------------------------------------- ! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator ! https://www.lammps.org/ Sandia National Laboratories -! Steve Plimpton, sjplimp@sandia.gov +! LAMMPS development team: developers@lammps.org ! ! Copyright (2003) Sandia Corporation. Under the terms of Contract ! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/lib/mesont/LinFun2.f90 b/lib/mesont/LinFun2.f90 index d0c10088e9..2bf1d2872a 100644 --- a/lib/mesont/LinFun2.f90 +++ b/lib/mesont/LinFun2.f90 @@ -1,7 +1,7 @@ ! ------------ ---------------------------------------------------------- ! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator ! https://www.lammps.org/ Sandia National Laboratories -! Steve Plimpton, sjplimp@sandia.gov +! LAMMPS development team: developers@lammps.org ! ! Copyright (2003) Sandia Corporation. Under the terms of Contract ! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/lib/mesont/Spline1.f90 b/lib/mesont/Spline1.f90 index 95d7317049..77731383b6 100644 --- a/lib/mesont/Spline1.f90 +++ b/lib/mesont/Spline1.f90 @@ -1,7 +1,7 @@ ! ------------ ---------------------------------------------------------- ! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator ! https://www.lammps.org/ Sandia National Laboratories -! Steve Plimpton, sjplimp@sandia.gov +! LAMMPS development team: developers@lammps.org ! ! Copyright (2003) Sandia Corporation. Under the terms of Contract ! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/lib/mesont/Spline2.f90 b/lib/mesont/Spline2.f90 index 2dd7fb131b..12ed56ab1e 100644 --- a/lib/mesont/Spline2.f90 +++ b/lib/mesont/Spline2.f90 @@ -1,7 +1,7 @@ ! ------------ ---------------------------------------------------------- ! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator ! https://www.lammps.org/ Sandia National Laboratories -! Steve Plimpton, sjplimp@sandia.gov +! LAMMPS development team: developers@lammps.org ! ! Copyright (2003) Sandia Corporation. Under the terms of Contract ! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/lib/mesont/TPMForceField.f90 b/lib/mesont/TPMForceField.f90 index 5fa0514eea..cc797b3440 100644 --- a/lib/mesont/TPMForceField.f90 +++ b/lib/mesont/TPMForceField.f90 @@ -1,7 +1,7 @@ ! ------------ ---------------------------------------------------------- ! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator ! https://www.lammps.org/ Sandia National Laboratories -! Steve Plimpton, sjplimp@sandia.gov +! LAMMPS development team: developers@lammps.org ! ! Copyright (2003) Sandia Corporation. Under the terms of Contract ! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/lib/mesont/TPMGeom.f90 b/lib/mesont/TPMGeom.f90 index 638f2cd27e..5e8ab73645 100644 --- a/lib/mesont/TPMGeom.f90 +++ b/lib/mesont/TPMGeom.f90 @@ -1,7 +1,7 @@ ! ------------ ---------------------------------------------------------- ! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator ! https://www.lammps.org/ Sandia National Laboratories -! Steve Plimpton, sjplimp@sandia.gov +! LAMMPS development team: developers@lammps.org ! ! Copyright (2003) Sandia Corporation. Under the terms of Contract ! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/lib/mesont/TPMLib.f90 b/lib/mesont/TPMLib.f90 index c3c9f5eb4d..c8abaa40b4 100644 --- a/lib/mesont/TPMLib.f90 +++ b/lib/mesont/TPMLib.f90 @@ -1,7 +1,7 @@ ! ------------ ---------------------------------------------------------- ! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator ! https://www.lammps.org/ Sandia National Laboratories -! Steve Plimpton, sjplimp@sandia.gov +! LAMMPS development team: developers@lammps.org ! ! Copyright (2003) Sandia Corporation. Under the terms of Contract ! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/lib/mesont/TPMM0.f90 b/lib/mesont/TPMM0.f90 index d2b38fe558..175e1c4cce 100644 --- a/lib/mesont/TPMM0.f90 +++ b/lib/mesont/TPMM0.f90 @@ -1,7 +1,7 @@ ! ------------ ---------------------------------------------------------- ! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator ! https://www.lammps.org/ Sandia National Laboratories -! Steve Plimpton, sjplimp@sandia.gov +! LAMMPS development team: developers@lammps.org ! ! Copyright (2003) Sandia Corporation. Under the terms of Contract ! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/lib/mesont/TPMM1.f90 b/lib/mesont/TPMM1.f90 index d8186683ca..c27c239d8b 100644 --- a/lib/mesont/TPMM1.f90 +++ b/lib/mesont/TPMM1.f90 @@ -1,7 +1,7 @@ ! ------------ ---------------------------------------------------------- ! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator ! https://www.lammps.org/ Sandia National Laboratories -! Steve Plimpton, sjplimp@sandia.gov +! LAMMPS development team: developers@lammps.org ! ! Copyright (2003) Sandia Corporation. Under the terms of Contract ! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/lib/mesont/TubePotBase.f90 b/lib/mesont/TubePotBase.f90 index d278a2390f..3c65d19d4e 100644 --- a/lib/mesont/TubePotBase.f90 +++ b/lib/mesont/TubePotBase.f90 @@ -1,7 +1,7 @@ ! ------------ ---------------------------------------------------------- ! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator ! https://www.lammps.org/ Sandia National Laboratories -! Steve Plimpton, sjplimp@sandia.gov +! LAMMPS development team: developers@lammps.org ! ! Copyright (2003) Sandia Corporation. Under the terms of Contract ! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/lib/mesont/TubePotMono.f90 b/lib/mesont/TubePotMono.f90 index f59c810e4f..049b5bcb26 100644 --- a/lib/mesont/TubePotMono.f90 +++ b/lib/mesont/TubePotMono.f90 @@ -1,7 +1,7 @@ ! ------------ ---------------------------------------------------------- ! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator ! https://www.lammps.org/ Sandia National Laboratories -! Steve Plimpton, sjplimp@sandia.gov +! LAMMPS development team: developers@lammps.org ! ! Copyright (2003) Sandia Corporation. Under the terms of Contract ! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/lib/mesont/TubePotTrue.f90 b/lib/mesont/TubePotTrue.f90 index 98e7450a99..4631cc1a1c 100644 --- a/lib/mesont/TubePotTrue.f90 +++ b/lib/mesont/TubePotTrue.f90 @@ -1,7 +1,7 @@ ! ------------ ---------------------------------------------------------- ! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator ! https://www.lammps.org/ Sandia National Laboratories -! Steve Plimpton, sjplimp@sandia.gov +! LAMMPS development team: developers@lammps.org ! ! Copyright (2003) Sandia Corporation. Under the terms of Contract ! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/lib/mlpod/Install.py b/lib/mlpod/Install.py new file mode 100644 index 0000000000..0a0979c2ee --- /dev/null +++ b/lib/mlpod/Install.py @@ -0,0 +1,97 @@ +#!/usr/bin/env python + +""" +Install.py tool to do a generic build of a library +soft linked to by many of the lib/Install.py files +used to automate the steps described in the corresponding lib/README +""" + +from __future__ import print_function +import sys, os, subprocess +from argparse import ArgumentParser + +sys.path.append('..') +from install_helpers import get_cpus, fullpath + +parser = ArgumentParser(prog='Install.py', + description="LAMMPS library build wrapper script") + +HELP = """ +Syntax from src dir: make lib-libname args="-m machine -e suffix" +Syntax from lib dir: python Install.py -m machine -e suffix + +libname = name of lib dir (e.g. atc, h5md, meam, poems, etc) +specify -m and optionally -e, order does not matter + +Examples: + +make lib-poems args="-m serial" # build POEMS lib with same settings as in the serial Makefile in src +make lib-colvars args="-m mpi" # build COLVARS lib with same settings as in the mpi Makefile in src +make lib-meam args="-m ifort" # build MEAM lib with custom Makefile.ifort (using Intel Fortran) +""" + +# parse and process arguments + +parser.add_argument("-m", "--machine", + help="suffix of a /Makefile.* file used for compiling this library") +parser.add_argument("-e", "--extramake", + help="set EXTRAMAKE variable in /Makefile. to Makefile.lammps.") + +args = parser.parse_args() + +# print help message and exit, if neither build nor path options are given +if not args.machine and not args.extramake: + parser.print_help() + sys.exit(HELP) + +machine = args.machine +extraflag = args.extramake +if extraflag: + suffix = args.extramake +else: + suffix = 'empty' + +# set lib from working dir + +cwd = fullpath('.') +lib = os.path.basename(cwd) + +# create Makefile.auto as copy of Makefile.machine +# reset EXTRAMAKE if requested + +if not os.path.exists("Makefile.%s" % machine): + sys.exit("lib/%s/Makefile.%s does not exist" % (lib, machine)) + +lines = open("Makefile.%s" % machine, 'r').readlines() +fp = open("Makefile.auto", 'w') + +has_extramake = False +for line in lines: + words = line.split() + if len(words) == 3 and words[0] == "EXTRAMAKE" and words[1] == '=': + has_extramake = True + if extraflag: + line = line.replace(words[2], "Makefile.lammps.%s" % suffix) + fp.write(line) + +fp.close() + +# make the library via Makefile.auto optionally with parallel make +n_cpus = get_cpus() + +print("Building lib%s.a ..." % lib) +cmd = "make -f Makefile.auto clean; make -f Makefile.auto -j%d" % n_cpus +try: + txt = subprocess.check_output(cmd, shell=True, stderr=subprocess.STDOUT) + print(txt.decode('UTF-8')) +except subprocess.CalledProcessError as e: + print("Make failed with:\n %s" % e.output.decode('UTF-8')) + sys.exit(1) + +if os.path.exists("lib%s.a" % lib): + print("Build was successful") +else: + sys.exit("Build of lib/%s/lib%s.a was NOT successful" % (lib, lib)) + +if has_extramake and not os.path.exists("Makefile.lammps"): + print("WARNING: lib/%s/Makefile.lammps was NOT created" % lib) diff --git a/lib/mlpod/Makefile.lammps.empty b/lib/mlpod/Makefile.lammps.empty new file mode 100644 index 0000000000..bf467a20c3 --- /dev/null +++ b/lib/mlpod/Makefile.lammps.empty @@ -0,0 +1,5 @@ +# Settings that the LAMMPS build will import when this package library is used + +mlpod_SYSINC = +mlpod_SYSLIB = +mlpod_SYSPATH = diff --git a/lib/mlpod/Makefile.lammps.installed b/lib/mlpod/Makefile.lammps.installed new file mode 100644 index 0000000000..d8b0d41225 --- /dev/null +++ b/lib/mlpod/Makefile.lammps.installed @@ -0,0 +1,5 @@ +# Settings that the LAMMPS build will import when this package library is used + +mlpod_SYSINC = +mlpod_SYSLIB = -lblas -llapack +mlpod_SYSPATH = diff --git a/lib/mlpod/Makefile.lammps.linalg b/lib/mlpod/Makefile.lammps.linalg new file mode 100644 index 0000000000..cb4d78df99 --- /dev/null +++ b/lib/mlpod/Makefile.lammps.linalg @@ -0,0 +1,5 @@ +# Settings that the LAMMPS build will import when this package library is used + +mlpod_SYSINC = +mlpod_SYSLIB = -llinalg -lgfortran +mlpod_SYSPATH = -L../../lib/linalg$(LIBOBJDIR) diff --git a/lib/mlpod/Makefile.mpi b/lib/mlpod/Makefile.mpi new file mode 100644 index 0000000000..05b6ee642a --- /dev/null +++ b/lib/mlpod/Makefile.mpi @@ -0,0 +1,48 @@ +SHELL = /bin/sh + +# which file will be copied to Makefile.lammps + +EXTRAMAKE = Makefile.lammps.linalg + +# ------ DEFINITIONS ------ + +LIB = libmlpod.a +OBJ = $(SRC:.cpp=.o) + +# ------ SETTINGS ------ + +# include any MPI settings needed for the ELECTRODE library to build with +# the same MPI library that LAMMPS is built with + +CC = mpicxx +CCFLAGS = -O3 -fPIC -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 + +ARCHIVE = ar +ARCHFLAG = -rc +DEPFLAGS = -M +#LINK = +#LINKFLAGS = +USRLIB = +SYSLIB = + +# ------ MAKE PROCEDURE ------ + +lib: $(OBJ) + $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ) + @cp $(EXTRAMAKE) Makefile.lammps + +# ------ COMPILE RULES ------ + +%.o:%.cpp + $(CC) $(CCFLAGS) -c $< -o $@ +%.d:%.cpp + $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@ + +# ------ DEPENDENCIES ------ + +DEPENDS = $(OBJ:.o=.d) + +# ------ CLEAN ------ + +clean: + -rm -f *.d *~ $(OBJ) $(LIB) diff --git a/lib/mlpod/Makefile.serial b/lib/mlpod/Makefile.serial new file mode 100644 index 0000000000..54e819ee38 --- /dev/null +++ b/lib/mlpod/Makefile.serial @@ -0,0 +1,48 @@ +SHELL = /bin/sh + +# which file will be copied to Makefile.lammps + +EXTRAMAKE = Makefile.lammps.linalg + +# ------ DEFINITIONS ------ + +LIB = libmlpod.a +OBJ = $(SRC:.cpp=.o) + +# ------ SETTINGS ------ + +# include any MPI settings needed for the mlpod library to build with +# the same MPI library that LAMMPS is built with + +CC = g++ +CCFLAGS = -O3 -fPIC -I../../src/STUBS + +ARCHIVE = ar +ARCHFLAG = -rc +DEPFLAGS = -M +#LINK = +#LINKFLAGS = +USRLIB = +SYSLIB = + +# ------ MAKE PROCEDURE ------ + +lib: $(OBJ) + $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ) + @cp $(EXTRAMAKE) Makefile.lammps + +# ------ COMPILE RULES ------ + +%.o:%.cpp + $(CC) $(CCFLAGS) -c $< -o $@ +%.d:%.cpp + $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@ + +# ------ DEPENDENCIES ------ + +DEPENDS = $(OBJ:.o=.d) + +# ------ CLEAN ------ + +clean: + -rm -f *.d *~ $(OBJ) $(LIB) diff --git a/lib/plumed/Install.py b/lib/plumed/Install.py index 772f09ca51..bb3a158bd4 100644 --- a/lib/plumed/Install.py +++ b/lib/plumed/Install.py @@ -17,7 +17,7 @@ parser = ArgumentParser(prog='Install.py', # settings -version = "2.7.4" +version = "2.8.1" mode = "static" # help message @@ -58,7 +58,9 @@ checksums = { \ '2.7.2' : 'cfa0b4dd90a81c25d3302e8d97bfeaea', \ '2.7.3' : 'f00cc82edfefe6bb3df934911dbe32fb', \ '2.7.4' : 'f858e0b6aed173748fc85b6bc8a9dcb3', \ + '2.7.5' : '2aca1986d6c1ca3ba7e9eb51b1102792', \ '2.8.0' : '489b23daba70da78cf0506cbc31689c6', \ + '2.8.1' : '6bfe72ebdae63dc38a9ca27d9b0e08f8', \ } # parse and process arguments diff --git a/potentials/README b/potentials/README index 4df315a7f2..c234f5f48b 100644 --- a/potentials/README +++ b/potentials/README @@ -104,6 +104,7 @@ mliap MLIAP potential mliap.descriptor MLIAP potential descriptor mliap.model MLIAP potential model nb3b.harmonic nonbonded 3-body harmonic potential +pod ML potential with proper orthogonal descriptors (POD) poly polymorphic 3-body potential reax ReaxFF potential (see README.reax for more info) smtbq second moment tight binding QEq (SMTBQ) potential diff --git a/potentials/Si.b.meam.sw.spline b/potentials/Si.b.meam.sw.spline index 8affba6ab5..6e6ef2ac45 100644 --- a/potentials/Si.b.meam.sw.spline +++ b/potentials/Si.b.meam.sw.spline @@ -1,6 +1,6 @@ # DATE: 2012-10-26 UNITS: metal CONTRIBUTOR: Robert Rudd, robert.rudd@llnl.gov CITATION: Balamane et al, Phys Rev B 46, 2250 (1992) COMMENT: Spline-based MEAM+SW potential for Si (F.H. Stillinger and T.A. Weber, Phys. Rev. B 31, 5262 (1985) with Balamane parameters: Balamane et al., Phys Rev B 46, 2250 (1992)). 37 --5.511362311759948+02 0.000000000000000000e+00 +-5.511362311759948e+02 0.000000000000000000e+00 1 0 1 0 9.2969999999999997E-01 1.1344841447915871E+02 2.9969523122045521E+03 1.0086299999999999E+00 7.8058660789969480E+01 1.8181346482323115E+03 diff --git a/potentials/Si_1.meam.spline b/potentials/Si_1.meam.spline index 827b0ad59b..31268ca44b 100644 --- a/potentials/Si_1.meam.spline +++ b/potentials/Si_1.meam.spline @@ -1,4 +1,4 @@ -DATE: 2012-02-01 UNITS: metal CONTRIBUTOR: Alexander Stukowski, stukowski@mm.tu-darmstadt.de CITATION: Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter and Kress, Modell Simul Mater Sci Eng, 8, 825 (2000) COMMENT: Spline-based MEAM potential for Si. Reference: T. J. Lenosky, B. Sadigh, E. Alonso, V. V. Bulatov, T. D. de la Rubia, J. Kim, A. F. Voter, and J. D. Kress, Modell. Simul. Mater. Sci. Eng. 8, 825 (2000) +# DATE: 2012-02-01 UNITS: metal CONTRIBUTOR: Alexander Stukowski, stukowski@mm.tu-darmstadt.de CITATION: Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter and Kress, Modell Simul Mater Sci Eng, 8, 825 (2000) COMMENT: Spline-based MEAM potential for Si. Reference: T. J. Lenosky, B. Sadigh, E. Alonso, V. V. Bulatov, T. D. de la Rubia, J. Kim, A. F. Voter, and J. D. Kress, Modell. Simul. Mater. Sci. Eng. 8, 825 (2000) 10 -4.266966781858503300e+01 0.000000000000000000e+00 1 0 1 0 diff --git a/potentials/Ta_coeff.pod b/potentials/Ta_coeff.pod new file mode 100644 index 0000000000..c8943bb889 --- /dev/null +++ b/potentials/Ta_coeff.pod @@ -0,0 +1,33 @@ +POD_coefficients: 32 +-4.44242 +4.10219 +-2.36987 +-3.92184 +0.83796 +-0.79457 +0.26230 +-21.24294 +-15.38460 +-38.44056 +8.29872 +-42.54514 +2.79976 +3.76109 +5.23499 +0.04878 +2.96006 +0.09101 +-0.19257 +-0.24326 +-0.16735 +0.53738 +0.02236 +-0.00154 +0.02488 +-0.00565 +0.07672 +-0.05894 +-0.05604 +-0.12664 +0.11723 +0.00262 diff --git a/potentials/Ta_param.pod b/potentials/Ta_param.pod new file mode 100644 index 0000000000..888dcb1b34 --- /dev/null +++ b/potentials/Ta_param.pod @@ -0,0 +1,38 @@ +# DATE: 2022-11-30 UNITS: metal CONTRIBUTOR: Ngoc Cuong Nguyen, exapde@gmail.com CITATION: https://arxiv.org/abs/2209.02362 +# chemical element symbols +species Ta + +# periodic boundary conditions +pbc 1 1 1 + +# inner cut-off radius +rin 1.0 + +# outer cut-off radius +rcut 5.0 + +# polynomial degrees for radial basis functions +bessel_polynomial_degree 3 +inverse_polynomial_degree 6 + +# one-body potential +onebody 1 + +# two-body linear POD potential +twobody_number_radial_basis_functions 6 + +# three-body linear POD potential +threebody_number_radial_basis_functions 5 +threebody_number_angular_basis_functions 5 + +# four-body linear SNAP potential +fourbody_snap_twojmax 0 + +# quadratic POD potential +quadratic_pod_potential 0 + +# Add the following basename to the name of output files +basename_for_output_files Ta + +# number of digits after the decimal point +precision_for_pod_coefficients 5 diff --git a/potentials/TiO.meam.spline b/potentials/TiO.meam.spline index e2b2bd7a53..1de0f7eb49 100644 --- a/potentials/TiO.meam.spline +++ b/potentials/TiO.meam.spline @@ -1,4 +1,4 @@ -# Ti-O cubic spline potential where O is in the dilute limit. DATE: 2016-06-05 UNITS: metal CONTRIBUTOR: Pinchao Zhang, Dallas R. Trinkle +# Ti-O cubic spline potential where O is in the dilute limit. UNITS: metal DATE: 2016-06-05 CONTRIBUTOR: Pinchao Zhang, Dallas R. Trinkle meam/spline 2 Ti O spline3eq 13 diff --git a/python/examples/pizza/gl.py b/python/examples/pizza/gl.py index c567c0805f..2eaa2a61af 100644 --- a/python/examples/pizza/gl.py +++ b/python/examples/pizza/gl.py @@ -1,5 +1,5 @@ # Pizza.py toolkit, https://lammps.github.io/pizza -# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# LAMMPS Development team: developers@lammps.org, Sandia National Laboratories # # Copyright (2005) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/python/examples/pizza/vizinfo.py b/python/examples/pizza/vizinfo.py index e3a05d71ce..147dd6a1db 100644 --- a/python/examples/pizza/vizinfo.py +++ b/python/examples/pizza/vizinfo.py @@ -1,5 +1,5 @@ # Pizza.py toolkit, https://lammps.github.io/pizza -# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# LAMMPS Development team: developers@lammps.org, Sandia National Laboratories # # Copyright (2005) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/python/examples/pizza/vmd.py b/python/examples/pizza/vmd.py index 5c8461f6ca..6a1abd246d 100644 --- a/python/examples/pizza/vmd.py +++ b/python/examples/pizza/vmd.py @@ -1,5 +1,5 @@ # Pizza.py toolkit, https://lammps.github.io/pizza -# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# LAMMPS Development team: developers@lammps.org, Sandia National Laboratories # # Copyright (2005) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/python/lammps/constants.py b/python/lammps/constants.py index 6fe7750326..8fd6a9eaf5 100644 --- a/python/lammps/constants.py +++ b/python/lammps/constants.py @@ -1,7 +1,7 @@ # ---------------------------------------------------------------------- # LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator # https://www.lammps.org/ Sandia National Laboratories -# Steve Plimpton, sjplimp@sandia.gov +# LAMMPS Development team: developers@lammps.org # # Copyright (2003) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -22,8 +22,8 @@ LAMMPS_INT64 = 4 LAMMPS_INT64_2D = 5 LAMMPS_STRING = 6 -# these must be kept in sync with the enums in src/library.h, tools/swig/lammps.i -# and the constants in fortran/lammps.f90 +# these must be kept in sync with the enums in src/library.h, tools/swig/lammps.i, +# examples/COUPLE/plugin/liblammpsplugin.h, and the constants in fortran/lammps.f90 LMP_STYLE_GLOBAL = 0 LMP_STYLE_ATOM = 1 LMP_STYLE_LOCAL = 2 diff --git a/python/lammps/core.py b/python/lammps/core.py index 074e579d13..dba7dda4dc 100644 --- a/python/lammps/core.py +++ b/python/lammps/core.py @@ -1,7 +1,7 @@ # ---------------------------------------------------------------------- # LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator # https://www.lammps.org/ Sandia National Laboratories -# Steve Plimpton, sjplimp@sandia.gov +# LAMMPS Development team: developers@lammps.org # # Copyright (2003) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -265,6 +265,7 @@ class lammps(object): self.lib.lammps_encode_image_flags.restype = self.c_imageint + self.lib.lammps_config_has_package.argtypes = [c_char_p] self.lib.lammps_config_package_name.argtypes = [c_int, c_char_p, c_int] self.lib.lammps_config_accelerator.argtypes = [c_char_p, c_char_p, c_char_p] @@ -1627,6 +1628,23 @@ class lammps(object): # ------------------------------------------------------------------------- + def has_package(self, name): + """ Report if the named package has been enabled in the LAMMPS shared library. + + This is a wrapper around the :cpp:func:`lammps_config_has_package` + function of the library interface. + + .. versionadded:: TBD + + :param name: name of the package + :type name: string + + :return: state of package availability + :rtype: bool + """ + return self.lib.lammps_config_has_package(name.encode()) != 0 + # ------------------------------------------------------------------------- + @property def accelerator_config(self): """ Return table with available accelerator configuration settings. diff --git a/python/lammps/data.py b/python/lammps/data.py index 731a8c514a..9d217d3c39 100644 --- a/python/lammps/data.py +++ b/python/lammps/data.py @@ -1,7 +1,7 @@ # ---------------------------------------------------------------------- # LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator # https://www.lammps.org/ Sandia National Laboratories -# Steve Plimpton, sjplimp@sandia.gov +# LAMMPS Development team: developers@lammps.org # # Copyright (2003) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/python/lammps/formats.py b/python/lammps/formats.py index b7c267466f..3641a89558 100644 --- a/python/lammps/formats.py +++ b/python/lammps/formats.py @@ -1,7 +1,7 @@ # ---------------------------------------------------------------------- # LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator # https://www.lammps.org/ Sandia National Laboratories -# Steve Plimpton, sjplimp@sandia.gov +# LAMMPS Development team: developers@lammps.org # # Copyright (2003) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/python/lammps/mliap/__init__.py b/python/lammps/mliap/__init__.py index b888eb55ce..3e50f43098 100644 --- a/python/lammps/mliap/__init__.py +++ b/python/lammps/mliap/__init__.py @@ -10,15 +10,15 @@ import warnings py_ver = sysconfig.get_config_vars('VERSION')[0] OS_name = platform.system() -if OS_name == "Linux": - SHLIB_SUFFIX = '.so' - library = 'libpython' + py_ver + SHLIB_SUFFIX -elif OS_name == "Darwin": +if OS_name == "Darwin": SHLIB_SUFFIX = '.dylib' library = 'libpython' + py_ver + SHLIB_SUFFIX elif OS_name == "Windows": SHLIB_SUFFIX = '.dll' library = 'python' + py_ver + SHLIB_SUFFIX +else: + SHLIB_SUFFIX = '.so' + library = 'libpython' + py_ver + SHLIB_SUFFIX try: pylib = ctypes.CDLL(library) diff --git a/python/lammps/mliap/loader.py b/python/lammps/mliap/loader.py index e1e60c4f50..0d44413371 100644 --- a/python/lammps/mliap/loader.py +++ b/python/lammps/mliap/loader.py @@ -1,7 +1,7 @@ # ---------------------------------------------------------------------- # LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator # https://www.lammps.org/ Sandia National Laboratories -# Steve Plimpton, sjplimp@sandia.gov +# LAMMPS Development team: developers@lammps.org # # Copyright (2003) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/python/lammps/mliap/pytorch.py b/python/lammps/mliap/pytorch.py index 51b953fd61..b02d5ee3dd 100644 --- a/python/lammps/mliap/pytorch.py +++ b/python/lammps/mliap/pytorch.py @@ -1,7 +1,7 @@ # ---------------------------------------------------------------------- # LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator # https://www.lammps.org/ Sandia National Laboratories -# Steve Plimpton, sjplimp@sandia.gov +# LAMMPS Development team: developers@lammps.org # # Copyright (2003) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/python/lammps/numpy_wrapper.py b/python/lammps/numpy_wrapper.py index ce0cb35e47..b16c359d7e 100644 --- a/python/lammps/numpy_wrapper.py +++ b/python/lammps/numpy_wrapper.py @@ -1,7 +1,7 @@ # ---------------------------------------------------------------------- # LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator # https://www.lammps.org/ Sandia National Laboratories -# Steve Plimpton, sjplimp@sandia.gov +# LAMMPS Development team: developers@lammps.org # # Copyright (2003) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/python/lammps/pylammps.py b/python/lammps/pylammps.py index 1fe1f2452b..d0ff7ab1aa 100644 --- a/python/lammps/pylammps.py +++ b/python/lammps/pylammps.py @@ -1,7 +1,7 @@ # ---------------------------------------------------------------------- # LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator # https://www.lammps.org/ Sandia National Laboratories -# Steve Plimpton, sjplimp@sandia.gov +# LAMMPS Development team: developers@lammps.org # # Copyright (2003) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/python/setup.py b/python/setup.py index 7794119930..722230d477 100644 --- a/python/setup.py +++ b/python/setup.py @@ -46,8 +46,8 @@ else: setup( name = "lammps", version = get_lammps_version(), - author = "Steve Plimpton", - author_email = "sjplimp@sandia.gov", + author = "The LAMMPS Developers", + author_email = "developers@lammps.org", url = "https://www.lammps.org", project_urls = { "Bug Tracker": "https://github.com/lammps/lammps/issues", diff --git a/src/.gitignore b/src/.gitignore index 0d3cb2ff4a..c5a7eed911 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -37,8 +37,8 @@ /library_mdi.h /mdi_engine.cpp /mdi_engine.h -/fix_mdi_aimd.cpp -/fix_mdi_aimd.h +/fix_mdi_qm.cpp +/fix_mdi_qm.h /mdi_command.cpp /mdi_command.h /mdi_plugin.cpp @@ -56,6 +56,15 @@ /pair_pace.cpp /pair_pace.h +/pair_pace_extrapolation.cpp +/pair_pace_extrapolation.h + +/pair_pod.cpp +/pair_pod.h +/fitpod_command.cpp +/fitpod_command.h +/mlpod.cpp +/mlpod.h /fix_polarize*.cpp /fix_polarize*.h @@ -87,7 +96,7 @@ /compute_mliap.h /mliap_*.cpp /mliap_*.h -/mliap_model_python_couple.pyx +/mliap_*.pyx /pair_mliap.cpp /pair_mliap.h @@ -913,6 +922,8 @@ /fix_rigid_nvt_small.h /fix_rigid_small.cpp /fix_rigid_small.h +/fix_sgcmc.cpp +/fix_sgcmc.h /fix_shake.cpp /fix_shake.h /fix_shardlow.cpp @@ -1336,6 +1347,8 @@ /pair_yukawa_colloid.h /pair_wf_cut.cpp /pair_wf_cut.h +/pair_ylz.cpp +/pair_ylz.h /pair_momb.cpp /pair_momb.h /pppm.cpp diff --git a/src/ADIOS/Install.sh b/src/ADIOS/Install.sh index bd0acb1414..0ee2c5428e 100644 --- a/src/ADIOS/Install.sh +++ b/src/ADIOS/Install.sh @@ -69,7 +69,7 @@ adios_SYSLIB=${ADIOS2_LIB} fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*ADIOS.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*ADIOS.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ../ADIOS/Makefile.lammps @@ -85,7 +85,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*ADIOS.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*ADIOS.*$/d' ../Makefile.package.settings fi rm -f Makefile.lammps diff --git a/src/ADIOS/adios_common.h b/src/ADIOS/adios_common.h index 9b0fb357ea..3345b1e071 100644 --- a/src/ADIOS/adios_common.h +++ b/src/ADIOS/adios_common.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ADIOS/dump_atom_adios.cpp b/src/ADIOS/dump_atom_adios.cpp index 1be03a7b2d..8e92300591 100644 --- a/src/ADIOS/dump_atom_adios.cpp +++ b/src/ADIOS/dump_atom_adios.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -62,7 +62,11 @@ DumpAtomADIOS::DumpAtomADIOS(LAMMPS *lmp, int narg, char **arg) : DumpAtom(lmp, internal = new DumpAtomADIOSInternal(); try { +#if defined(MPI_STUBS) + internal->ad = new adios2::ADIOS("adios2_config.xml", adios2::DebugON); +#else internal->ad = new adios2::ADIOS("adios2_config.xml", world, adios2::DebugON); +#endif } catch (std::ios_base::failure &e) { error->all(FLERR, "ADIOS initialization failed with error: {}", e.what()); } @@ -84,11 +88,19 @@ void DumpAtomADIOS::openfile() if (multifile) { // if one file per timestep, replace '*' with current timestep auto filecurrent = utils::star_subst(filename, update->ntimestep, padflag); +#if defined(MPI_STUBS) + internal->fh = internal->io.Open(filecurrent, adios2::Mode::Write); +#else internal->fh = internal->io.Open(filecurrent, adios2::Mode::Write, world); +#endif if (!internal->fh) error->one(FLERR, "Cannot open dump file {}", filecurrent); } else { if (!singlefile_opened) { +#if defined(MPI_STUBS) + internal->fh = internal->io.Open(filename, adios2::Mode::Write); +#else internal->fh = internal->io.Open(filename, adios2::Mode::Write, world); +#endif if (!internal->fh) error->one(FLERR, "Cannot open dump file {}", filename); singlefile_opened = 1; } @@ -256,61 +268,63 @@ void DumpAtomADIOS::init_style() else if (scale_flag == 0 && image_flag == 1) pack_choice = &DumpAtomADIOS::pack_noscale_image; - /* Define the group of variables for the atom style here since it's a fixed - * set */ - internal->io = internal->ad->DeclareIO(internal->ioName); - if (!internal->io.InConfigFile()) { - // if not defined by user, we can change the default settings - // BPFile is the default writer - internal->io.SetEngine("BPFile"); - int num_aggregators = multiproc; - if (num_aggregators == 0) num_aggregators = 1; - auto nstreams = std::to_string(num_aggregators); - internal->io.SetParameters({{"substreams", nstreams}}); - if (me == 0) - utils::logmesg(lmp, "ADIOS method for {} is n-to-m (aggregation with {} writers)\n", filename, - nstreams); - } + /* Define the group of variables for the atom style here since it's a fixed set */ - internal->io.DefineVariable("ntimestep"); - internal->io.DefineVariable("natoms"); + if (!internal->io) { + internal->io = internal->ad->DeclareIO(internal->ioName); + if (!internal->io.InConfigFile()) { + // if not defined by user, we can change the default settings + // BPFile is the default writer + internal->io.SetEngine("BPFile"); + int num_aggregators = multiproc; + if (num_aggregators == 0) num_aggregators = 1; + auto nstreams = std::to_string(num_aggregators); + internal->io.SetParameters({{"substreams", nstreams}}); + if (me == 0) + utils::logmesg(lmp, "ADIOS method for {} is n-to-m (aggregation with {} writers)\n", filename, + nstreams); + } - internal->io.DefineVariable("nprocs"); - internal->io.DefineVariable("ncolumns"); + internal->io.DefineVariable("ntimestep"); + internal->io.DefineVariable("natoms"); - internal->io.DefineVariable("boxxlo"); - internal->io.DefineVariable("boxxhi"); - internal->io.DefineVariable("boxylo"); - internal->io.DefineVariable("boxyhi"); - internal->io.DefineVariable("boxzlo"); - internal->io.DefineVariable("boxzhi"); + internal->io.DefineVariable("nprocs"); + internal->io.DefineVariable("ncolumns"); - internal->io.DefineVariable("boxxy"); - internal->io.DefineVariable("boxxz"); - internal->io.DefineVariable("boxyz"); + internal->io.DefineVariable("boxxlo"); + internal->io.DefineVariable("boxxhi"); + internal->io.DefineVariable("boxylo"); + internal->io.DefineVariable("boxyhi"); + internal->io.DefineVariable("boxzlo"); + internal->io.DefineVariable("boxzhi"); - internal->io.DefineAttribute("triclinic", domain->triclinic); - internal->io.DefineAttribute("scaled", scale_flag); - internal->io.DefineAttribute("image", image_flag); + internal->io.DefineVariable("boxxy"); + internal->io.DefineVariable("boxxz"); + internal->io.DefineVariable("boxyz"); - int *boundaryptr = reinterpret_cast(domain->boundary); - internal->io.DefineAttribute("boundary", boundaryptr, 6); + internal->io.DefineAttribute("triclinic", domain->triclinic); + internal->io.DefineAttribute("scaled", scale_flag); + internal->io.DefineAttribute("image", image_flag); - auto nColumns = static_cast(size_one); - internal->io.DefineAttribute("columns", columnNames.data(), nColumns); - internal->io.DefineAttribute("columnstr", columns); - internal->io.DefineAttribute("boundarystr", boundstr); - internal->io.DefineAttribute("LAMMPS/dump_style", "atom"); - internal->io.DefineAttribute("LAMMPS/version", lmp->version); - internal->io.DefineAttribute("LAMMPS/num_ver", std::to_string(lmp->num_ver)); + int *boundaryptr = reinterpret_cast(domain->boundary); + internal->io.DefineAttribute("boundary", boundaryptr, 6); - // local dimension variables - internal->io.DefineVariable("nme", {adios2::LocalValueDim}); - internal->io.DefineVariable("offset", {adios2::LocalValueDim}); + auto nColumns = static_cast(size_one); + internal->io.DefineAttribute("columns", columnNames.data(), nColumns); + internal->io.DefineAttribute("columnstr", columns); + internal->io.DefineAttribute("boundarystr", boundstr); + internal->io.DefineAttribute("LAMMPS/dump_style", "atom"); + internal->io.DefineAttribute("LAMMPS/version", lmp->version); + internal->io.DefineAttribute("LAMMPS/num_ver", std::to_string(lmp->num_ver)); - // atom table size is not known at the moment - // it will be correctly defined at the moment of write - size_t UnknownSizeYet = 1; - internal->varAtoms = internal->io.DefineVariable( + // local dimension variables + internal->io.DefineVariable("nme", {adios2::LocalValueDim}); + internal->io.DefineVariable("offset", {adios2::LocalValueDim}); + + // atom table size is not known at the moment + // it will be correctly defined at the moment of write + size_t UnknownSizeYet = 1; + internal->varAtoms = internal->io.DefineVariable( "atoms", {UnknownSizeYet, nColumns}, {UnknownSizeYet, 0}, {UnknownSizeYet, nColumns}); + } } diff --git a/src/ADIOS/dump_atom_adios.h b/src/ADIOS/dump_atom_adios.h index 294a0d1519..727bfd5937 100644 --- a/src/ADIOS/dump_atom_adios.h +++ b/src/ADIOS/dump_atom_adios.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ADIOS/dump_custom_adios.cpp b/src/ADIOS/dump_custom_adios.cpp index 305f3d3032..be827f507d 100644 --- a/src/ADIOS/dump_custom_adios.cpp +++ b/src/ADIOS/dump_custom_adios.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -70,7 +70,11 @@ DumpCustomADIOS::DumpCustomADIOS(LAMMPS *lmp, int narg, char **arg) : DumpCustom internal = new DumpCustomADIOSInternal(); try { +#if defined(MPI_STUBS) + internal->ad = new adios2::ADIOS("adios2_config.xml", adios2::DebugON); +#else internal->ad = new adios2::ADIOS("adios2_config.xml", world, adios2::DebugON); +#endif } catch (std::ios_base::failure &e) { error->all(FLERR, "ADIOS initialization failed with error: {}", e.what()); } @@ -96,11 +100,19 @@ void DumpCustomADIOS::openfile() if (multifile) { // if one file per timestep, replace '*' with current timestep auto filecurrent = utils::star_subst(filename, update->ntimestep, padflag); +#if defined(MPI_STUBS) + internal->fh = internal->io.Open(filecurrent, adios2::Mode::Write); +#else internal->fh = internal->io.Open(filecurrent, adios2::Mode::Write, world); +#endif if (!internal->fh) error->one(FLERR, "Cannot open dump file {}", filecurrent); } else { if (!singlefile_opened) { +#if defined(MPI_STUBS) + internal->fh = internal->io.Open(filename, adios2::Mode::Write); +#else internal->fh = internal->io.Open(filename, adios2::Mode::Write, world); +#endif if (!internal->fh) error->one(FLERR, "Cannot open dump file {}", filename); singlefile_opened = 1; } diff --git a/src/ADIOS/dump_custom_adios.h b/src/ADIOS/dump_custom_adios.h index b0232defed..7f6c9b7dca 100644 --- a/src/ADIOS/dump_custom_adios.h +++ b/src/ADIOS/dump_custom_adios.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ADIOS/reader_adios.cpp b/src/ADIOS/reader_adios.cpp index 09a3ffd2b0..655df98d26 100644 --- a/src/ADIOS/reader_adios.cpp +++ b/src/ADIOS/reader_adios.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -82,7 +82,11 @@ ReaderADIOS::ReaderADIOS(LAMMPS *lmp) : Reader(lmp) internal = new ReadADIOSInternal(); try { +#if defined(MPI_STUBS) + internal->ad = new adios2::ADIOS("adios2_config.xml", adios2::DebugON); +#else internal->ad = new adios2::ADIOS("adios2_config.xml", world, adios2::DebugON); +#endif } catch (std::ios_base::failure &e) { error->one(FLERR, "ADIOS initialization failed with error: {}", e.what()); } @@ -134,7 +138,11 @@ void ReaderADIOS::open_file(const std::string &file) if (internal->fh) internal->fh.Close(); try { +#if defined(MPI_STUBS) + internal->fh = internal->io.Open(file, adios2::Mode::Read); +#else internal->fh = internal->io.Open(file, adios2::Mode::Read, world); +#endif } catch (std::ios_base::failure &e) { error->one(FLERR, "Error opening file {}: {}", file, e.what()); } diff --git a/src/ADIOS/reader_adios.h b/src/ADIOS/reader_adios.h index 18748a8584..07d5333ca2 100644 --- a/src/ADIOS/reader_adios.h +++ b/src/ADIOS/reader_adios.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/AMOEBA/amoeba_charge_transfer.cpp b/src/AMOEBA/amoeba_charge_transfer.cpp index 1528ea348f..718d5c5b22 100644 --- a/src/AMOEBA/amoeba_charge_transfer.cpp +++ b/src/AMOEBA/amoeba_charge_transfer.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -15,7 +15,6 @@ #include "pair_amoeba.h" #include "atom.h" -#include "memory.h" #include "neigh_list.h" #include diff --git a/src/AMOEBA/amoeba_convolution.cpp b/src/AMOEBA/amoeba_convolution.cpp index 9d08dd6e79..68da7ca7e5 100644 --- a/src/AMOEBA/amoeba_convolution.cpp +++ b/src/AMOEBA/amoeba_convolution.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -17,11 +17,14 @@ #include "comm.h" #include "domain.h" #include "fft3d_wrap.h" -#include "gridcomm.h" +#include "grid3d.h" +#include "math_extra.h" #include "memory.h" #include "neighbor.h" #include "remap_wrap.h" -#include "update.h" + +#include +#include using namespace LAMMPS_NS; @@ -76,82 +79,58 @@ AmoebaConvolution::AmoebaConvolution(LAMMPS *lmp, Pair *pair, nfft_global = (bigint) nx * ny * nz; - // global indices of grid range from 0 to N-1 - // nlo_in,nhi_in = lower/upper limits of the 3d sub-brick of - // global grid that I own without ghost cells - // both non-tiled and tiled proc layouts use 0-1 fractional subdomain info + allocate_grid(); +} - if (comm->layout != Comm::LAYOUT_TILED) { - nxlo_in = static_cast (comm->xsplit[comm->myloc[0]] * nx); - nxhi_in = static_cast (comm->xsplit[comm->myloc[0]+1] * nx) - 1; - nylo_in = static_cast (comm->ysplit[comm->myloc[1]] * ny); - nyhi_in = static_cast (comm->ysplit[comm->myloc[1]+1] * ny) - 1; - nzlo_in = static_cast (comm->zsplit[comm->myloc[2]] * nz); - nzhi_in = static_cast (comm->zsplit[comm->myloc[2]+1] * nz) - 1; +/* ---------------------------------------------------------------------- + free all memory +------------------------------------------------------------------------- */ - } else { - nxlo_in = static_cast (comm->mysplit[0][0] * nx); - nxhi_in = static_cast (comm->mysplit[0][1] * nx) - 1; - nylo_in = static_cast (comm->mysplit[1][0] * ny); - nyhi_in = static_cast (comm->mysplit[1][1] * ny) - 1; - nzlo_in = static_cast (comm->mysplit[2][0] * nz); - nzhi_in = static_cast (comm->mysplit[2][1] * nz) - 1; - } +AmoebaConvolution::~AmoebaConvolution() +{ + deallocate_grid(); +} +/* ---------------------------------------------------------------------- + subset of FFT grids assigned to each proc may have changed + called by load balancer when proc subdomains are adjusted +------------------------------------------------------------------------- */ + +void AmoebaConvolution::reset_grid() +{ + deallocate_grid(); + allocate_grid(); +} + +/* ---------------------------------------------------------------------- + allocate all local grid data structs: FFT, Grid3d, Remap +------------------------------------------------------------------------- */ + +void AmoebaConvolution::allocate_grid() +{ + // maxdist = max distance outside of subbox my owned atom may be // nlower,nupper = stencil size for mapping particles to FFT grid + double maxdist = 0.5*neighbor->skin; int nlower = -(order-1)/2; int nupper = order/2; - // nlo_out,nhi_out = lower/upper limits of the 3d sub-brick of - // global grid that my particles can contribute charge to - // effectively nlo_in,nhi_in + ghost cells - // nlo,nhi = global coords of grid pt to "lower left" of smallest/largest - // position a particle in my box can be at - // dist[3] = particle position bound = subbox + skin/2.0 - // convert to triclinic if necessary - // nlo_out,nhi_out = nlo,nhi + stencil size for particle mapping + // Grid3d determines my owned + ghost grid cells + // ghost cell extent depends on maxdist, nlower, nupper - double *prd,*boxlo,*sublo,*subhi; - int triclinic = domain->triclinic; + gc = new Grid3d(lmp,world,nx,ny,nz); + gc->set_distance(maxdist); + gc->set_stencil_atom(-nlower,nupper); - if (triclinic == 0) { - prd = domain->prd; - boxlo = domain->boxlo; - sublo = domain->sublo; - subhi = domain->subhi; - } else { - prd = domain->prd_lamda; - boxlo = domain->boxlo_lamda; - sublo = domain->sublo_lamda; - subhi = domain->subhi_lamda; - } + gc->setup_grid(nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, + nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out); - double xprd = prd[0]; - double yprd = prd[1]; - double zprd = prd[2]; + int nqty = flag3d ? 1 : 2; + int ngc_buf1,ngc_buf2; - double dist[3] = {0.0,0.0,0.0}; - double cuthalf = 0.5*neighbor->skin; - if (triclinic == 0) dist[0] = dist[1] = dist[2] = cuthalf; - else kspacebbox(cuthalf,&dist[0]); - - int nlo,nhi; - - nlo = static_cast ((sublo[0]-dist[0]-boxlo[0]) * nx/xprd); - nhi = static_cast ((subhi[0]+dist[0]-boxlo[0]) * nx/xprd); - nxlo_out = nlo + nlower; - nxhi_out = nhi + nupper; - - nlo = static_cast ((sublo[1]-dist[1]-boxlo[1]) * ny/yprd); - nhi = static_cast ((subhi[1]+dist[1]-boxlo[1]) * ny/yprd); - nylo_out = nlo + nlower; - nyhi_out = nhi + nupper; - - nlo = static_cast ((sublo[2]-dist[2]-boxlo[2]) * nz/zprd); - nhi = static_cast ((subhi[2]+dist[2]-boxlo[2]) * nz/zprd); - nzlo_out = nlo + nlower; - nzhi_out = nhi + nupper; + gc->setup_comm(ngc_buf1,ngc_buf2); + memory->create(gc_buf1,nqty*ngc_buf1,"amoeba:gc_buf1"); + memory->create(gc_buf2,nqty*ngc_buf2,"amoeba:gc_buf2"); // x-pencil decomposition of FFT mesh // global indices range from 0 to N-1 @@ -182,7 +161,7 @@ AmoebaConvolution::AmoebaConvolution(LAMMPS *lmp, Pair *pair, nzlo_fft = me_z*nz/npez_fft; nzhi_fft = (me_z+1)*nz/npez_fft - 1; - // grid sizes + // FFT grid sizes // nbrick_owned = owned grid points in brick decomp // nbrick_ghosts = owned + ghost grid points in grid decomp // nfft_owned = owned grid points in FFT decomp @@ -198,27 +177,20 @@ AmoebaConvolution::AmoebaConvolution(LAMMPS *lmp, Pair *pair, ngrid_either = MAX(nbrick_owned,nfft_owned); - // instantiate FFT, GridComm, and Remap + // instantiate FFT and Remap int tmp; fft1 = new FFT3d(lmp,world,nx,ny,nz, nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft, nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft, - 1,0,&tmp,0); - // 0,0,&tmp,0); + 1,0,&tmp,0); fft2 = new FFT3d(lmp,world,nx,ny,nz, nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft, nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, - //1,0,&tmp,0); 0,0,&tmp,0); - gc = new GridComm(lmp,world,nx,ny,nz, - nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, - nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out); - - int nqty = flag3d ? 1 : 2; remap = new Remap(lmp,world, nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft, @@ -240,33 +212,27 @@ AmoebaConvolution::AmoebaConvolution(LAMMPS *lmp, Pair *pair, memory->create(grid_fft,ngrid_either,"amoeba:grid_fft"); memory->create(cfft,2*ngrid_either,"amoeba:cfft"); - - int ngc_buf1,ngc_buf2; - gc->setup(ngc_buf1,ngc_buf2); - memory->create(gc_buf1,nqty*ngc_buf1,"amoeba:gc_buf1"); - memory->create(gc_buf2,nqty*ngc_buf2,"amoeba:gc_buf2"); - memory->create(remap_buf,nqty*nfft_owned,"amoeba:remap_buf"); } -/* ---------------------------------------------------------------------- - free all memory -------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- */ -AmoebaConvolution::~AmoebaConvolution() +void AmoebaConvolution::deallocate_grid() { + delete gc; + + memory->destroy(gc_buf1); + memory->destroy(gc_buf2); + + delete fft1; + delete fft2; + delete remap; + memory->destroy3d_offset(grid_brick,nzlo_out,nylo_out,nxlo_out); memory->destroy4d_offset_last(cgrid_brick,nzlo_out,nylo_out,nxlo_out); memory->destroy(grid_fft); memory->destroy(cfft); - memory->destroy(gc_buf1); - memory->destroy(gc_buf2); memory->destroy(remap_buf); - - delete fft1; - delete fft2; - delete gc; - delete remap; } /* ---------------------------------------------------------------------- @@ -324,15 +290,15 @@ FFT_SCALAR *AmoebaConvolution::pre_convolution_3d() // reverse comm for 3d brick grid + ghosts #if DEBUG_AMOEBA - debug_scalar(GRIDBRICK_OUT,"PRE Convo / PRE GridComm"); + debug_scalar(GRIDBRICK_OUT,"PRE Convo / PRE Grid3d"); #endif - gc->reverse_comm(GridComm::PAIR,amoeba,1,sizeof(FFT_SCALAR),which, + gc->reverse_comm(Grid3d::PAIR,amoeba,which,1,sizeof(FFT_SCALAR), gc_buf1,gc_buf2,MPI_FFT_SCALAR); #if DEBUG_AMOEBA - debug_scalar(GRIDBRICK_IN,"PRE Convo / POST GridComm"); - debug_file(GRIDBRICK_IN,"pre.convo.post.gridcomm"); + debug_scalar(GRIDBRICK_IN,"PRE Convo / POST Grid3d"); + debug_file(GRIDBRICK_IN,"pre.convo.post.grid3d"); #endif // copy owned 3d brick grid values to FFT grid @@ -387,15 +353,15 @@ FFT_SCALAR *AmoebaConvolution::pre_convolution_4d() // reverse comm for 4d brick grid + ghosts #if DEBUG_AMOEBA - debug_scalar(GRIDBRICK_OUT,"PRE Convo / PRE GridComm"); + debug_scalar(GRIDBRICK_OUT,"PRE Convo / PRE Grid3d"); #endif - gc->reverse_comm(GridComm::PAIR,amoeba,2,sizeof(FFT_SCALAR),which, + gc->reverse_comm(Grid3d::PAIR,amoeba,which,2,sizeof(FFT_SCALAR), gc_buf1,gc_buf2,MPI_FFT_SCALAR); #if DEBUG_AMOEBA - debug_scalar(GRIDBRICK_IN,"PRE Convo / POST GridComm"); - debug_file(GRIDBRICK_IN,"pre.convo.post.gridcomm"); + debug_scalar(GRIDBRICK_IN,"PRE Convo / POST Grid3d"); + debug_file(GRIDBRICK_IN,"pre.convo.post.grid3d"); #endif // copy owned 4d brick grid values to FFT grid @@ -476,10 +442,10 @@ void *AmoebaConvolution::post_convolution_3d() // forward comm to populate ghost grid values #if DEBUG_AMOEBA - debug_scalar(GRIDBRICK_IN,"POST Convo / PRE gridcomm"); - debug_file(GRIDBRICK_IN,"post.convo.pre.gridcomm"); + debug_scalar(GRIDBRICK_IN,"POST Convo / PRE grid3d"); + debug_file(GRIDBRICK_IN,"post.convo.pre.grid3d"); #endif - gc->forward_comm(GridComm::PAIR,amoeba,1,sizeof(FFT_SCALAR),which, + gc->forward_comm(Grid3d::PAIR,amoeba,which,1,sizeof(FFT_SCALAR), gc_buf1,gc_buf2,MPI_FFT_SCALAR); return (void *) grid_brick; @@ -518,38 +484,15 @@ void *AmoebaConvolution::post_convolution_4d() // forward comm to populate ghost grid values #if DEBUG_AMOEBA - debug_scalar(GRIDBRICK_IN,"POST Convo / PRE gridcomm"); - debug_file(GRIDBRICK_IN,"post.convo.pre.gridcomm"); + debug_scalar(GRIDBRICK_IN,"POST Convo / PRE grid3d"); + debug_file(GRIDBRICK_IN,"post.convo.pre.grid3d"); #endif - gc->forward_comm(GridComm::PAIR,amoeba,2,sizeof(FFT_SCALAR),which, + gc->forward_comm(Grid3d::PAIR,amoeba,which,2,sizeof(FFT_SCALAR), gc_buf1,gc_buf2,MPI_FFT_SCALAR); return (void *) cgrid_brick; } -/* ---------------------------------------------------------------------- - convert a sphere in box coords to an ellipsoid in lamda (0-1) - coords and return the tight (axis-aligned) bounding box, does not - preserve vector magnitude - see http://www.loria.fr/~shornus/ellipsoid-bbox.html and - http://yiningkarlli.blogspot.com/2013/02/ - bounding-boxes-for-ellipsoidsfigure.html -------------------------------------------------------------------------- */ - -void AmoebaConvolution::kspacebbox(double r, double *b) -{ - double *h = domain->h; - double lx,ly,lz,xy,xz,yz; - - lx = h[0]; ly = h[1]; lz = h[2]; - yz = h[3]; xz = h[4]; xy = h[5]; - - b[0] = r*sqrt(ly*ly*lz*lz + ly*ly*xz*xz - 2.0*ly*xy*xz*yz + lz*lz*xy*xy + - xy*xy*yz*yz)/(lx*ly*lz); - b[1] = r*sqrt(lz*lz + yz*yz)/(ly*lz); - b[2] = r/lz; -} - /* ---------------------------------------------------------------------- map nprocs to NX by NY grid as PX by PY procs - return optimal px,py copy of PPPM::procs2grid2d() diff --git a/src/AMOEBA/amoeba_convolution.h b/src/AMOEBA/amoeba_convolution.h index d7c4f9fbd7..99ad11ade4 100644 --- a/src/AMOEBA/amoeba_convolution.h +++ b/src/AMOEBA/amoeba_convolution.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -42,6 +42,7 @@ class AmoebaConvolution : protected Pointers { AmoebaConvolution(class LAMMPS *, class Pair *, int, int, int, int, int); ~AmoebaConvolution(); + void reset_grid(); void *zero(); FFT_SCALAR *pre_convolution(); void *post_convolution(); @@ -55,7 +56,7 @@ class AmoebaConvolution : protected Pointers { class Pair *amoeba; class FFT3d *fft1, *fft2; - class GridComm *gc; + class Grid3d *gc; class Remap *remap; double ***grid_brick; // 3d real brick grid with ghosts @@ -67,13 +68,14 @@ class AmoebaConvolution : protected Pointers { double *gc_buf1, *gc_buf2; // buffers for GridComm double *remap_buf; // buffer for Remap + void allocate_grid(); + void deallocate_grid(); void *zero_3d(); void *zero_4d(); FFT_SCALAR *pre_convolution_3d(); FFT_SCALAR *pre_convolution_4d(); void *post_convolution_3d(); void *post_convolution_4d(); - void kspacebbox(double, double *); void procs2grid2d(int, int, int, int &, int &); // DEBUG diff --git a/src/AMOEBA/amoeba_dispersion.cpp b/src/AMOEBA/amoeba_dispersion.cpp index 4005c3b1bd..f3af921d85 100644 --- a/src/AMOEBA/amoeba_dispersion.cpp +++ b/src/AMOEBA/amoeba_dispersion.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -18,10 +18,8 @@ #include "atom.h" #include "comm.h" #include "domain.h" -#include "fft3d_wrap.h" #include "math_const.h" #include "math_special.h" -#include "memory.h" #include "neigh_list.h" #include diff --git a/src/AMOEBA/amoeba_file.cpp b/src/AMOEBA/amoeba_file.cpp index 2089ab3a27..6bf961cdab 100644 --- a/src/AMOEBA/amoeba_file.cpp +++ b/src/AMOEBA/amoeba_file.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel ator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -17,14 +17,11 @@ #include "comm.h" #include "domain.h" #include "error.h" -#include "force.h" #include "memory.h" -#include "utils.h" #include "tokenizer.h" #include #include -#include using namespace LAMMPS_NS; diff --git a/src/AMOEBA/amoeba_hal.cpp b/src/AMOEBA/amoeba_hal.cpp index 896595945e..a3cfeceb06 100644 --- a/src/AMOEBA/amoeba_hal.cpp +++ b/src/AMOEBA/amoeba_hal.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/AMOEBA/amoeba_induce.cpp b/src/AMOEBA/amoeba_induce.cpp index ae801e5a62..a6724e2bb7 100644 --- a/src/AMOEBA/amoeba_induce.cpp +++ b/src/AMOEBA/amoeba_induce.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -19,16 +19,13 @@ #include "comm.h" #include "domain.h" #include "error.h" -#include "fft3d_wrap.h" #include "fix_store_peratom.h" #include "math_const.h" #include "math_special.h" -#include "memory.h" #include "my_page.h" #include "neigh_list.h" #include -#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/AMOEBA/amoeba_kspace.cpp b/src/AMOEBA/amoeba_kspace.cpp index 51b206b6d8..da6483ef40 100644 --- a/src/AMOEBA/amoeba_kspace.cpp +++ b/src/AMOEBA/amoeba_kspace.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -217,6 +217,10 @@ void PairAmoeba::bspline_fill() // NOTE: could subtract off nlpts to start with // NOTE: this is place to check that stencil size does not // go out of bounds relative to igrid for a proc's sub-domain + // similar to PPPM::particle_map() + // subtracting eps is strange, and could mess up the check + // better to check here than in methods like grid_mpole() + // but check needs to be valid for all KSpace terms // NOTE: could convert x -> lamda for entire set of Nlocal atoms domain->x2lamda(x[i],lamda); diff --git a/src/AMOEBA/amoeba_multipole.cpp b/src/AMOEBA/amoeba_multipole.cpp index 8466a8fe1d..f58395aa1c 100644 --- a/src/AMOEBA/amoeba_multipole.cpp +++ b/src/AMOEBA/amoeba_multipole.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -18,14 +18,11 @@ #include "atom.h" #include "comm.h" #include "domain.h" -#include "fft3d_wrap.h" #include "math_const.h" #include "math_special.h" -#include "memory.h" #include "neigh_list.h" #include -#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/AMOEBA/amoeba_polar.cpp b/src/AMOEBA/amoeba_polar.cpp index ad6b585f25..4d143c7a22 100644 --- a/src/AMOEBA/amoeba_polar.cpp +++ b/src/AMOEBA/amoeba_polar.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -18,10 +18,8 @@ #include "atom.h" #include "comm.h" #include "domain.h" -#include "fft3d_wrap.h" #include "math_const.h" #include "math_special.h" -#include "memory.h" #include "neigh_list.h" #include @@ -250,10 +248,12 @@ void PairAmoeba::polar_real() double drc3[3],drc5[3],drc7[3]; double urc3[3],urc5[3],tep[3]; double fix[3],fiy[3],fiz[3]; +#if 0 // for poltyp TCG which is currently not supported double uax[3],uay[3],uaz[3]; double ubx[3],uby[3],ubz[3]; double uaxp[3],uayp[3],uazp[3]; double ubxp[3],ubyp[3],ubzp[3]; +#endif double dmpi[9],dmpk[9]; double dmpik[9]; double bn[5]; @@ -320,6 +320,7 @@ void PairAmoeba::polar_real() uixp = uinp[i][0]; uiyp = uinp[i][1]; uizp = uinp[i][2]; +#if 0 // for poltyp TCG which is currently not supported for (m = 0; m < tcgnab; m++) { uax[m] = uad[m][i][0]; uay[m] = uad[m][i][1]; @@ -334,7 +335,7 @@ void PairAmoeba::polar_real() ubyp[m] = ubp[m][i][1]; ubzp[m] = ubp[m][i][2]; } - +#endif if (amoeba) { pdi = pdamp[itype]; pti = thole[itype]; @@ -1030,7 +1031,8 @@ void PairAmoeba::polar_real() // get the dtau/dr terms used for TCG polarization force } else if (poltyp == TCG) { - /* +#if 0 + // poltyp TCG not yet supported for AMOEBA/HIPPO for (m = 0; m < tcgnab; m++) { ukx = ubd[m][j][0]; uky = ubd[m][j][1]; @@ -1131,8 +1133,7 @@ void PairAmoeba::polar_real() frcx += depx; frcy += depy; frcz += depz; - } - */ +#endif } // increment force-based gradient on the interaction sites diff --git a/src/AMOEBA/amoeba_repulsion.cpp b/src/AMOEBA/amoeba_repulsion.cpp index 041d74e54d..789674bb8d 100644 --- a/src/AMOEBA/amoeba_repulsion.cpp +++ b/src/AMOEBA/amoeba_repulsion.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -16,7 +16,6 @@ #include "atom.h" #include "comm.h" -#include "memory.h" #include "neigh_list.h" #include diff --git a/src/AMOEBA/amoeba_utils.cpp b/src/AMOEBA/amoeba_utils.cpp index dedeaffb09..5a4057930c 100644 --- a/src/AMOEBA/amoeba_utils.cpp +++ b/src/AMOEBA/amoeba_utils.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -15,7 +15,6 @@ #include "pair_amoeba.h" #include "atom.h" -#include "comm.h" #include "domain.h" #include "error.h" #include "fix_store_peratom.h" diff --git a/src/AMOEBA/angle_amoeba.cpp b/src/AMOEBA/angle_amoeba.cpp index c77cf99518..e6ee7b579e 100644 --- a/src/AMOEBA/angle_amoeba.cpp +++ b/src/AMOEBA/angle_amoeba.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/AMOEBA/angle_amoeba.h b/src/AMOEBA/angle_amoeba.h index de9bd42ca5..24cf12c50e 100644 --- a/src/AMOEBA/angle_amoeba.h +++ b/src/AMOEBA/angle_amoeba.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/AMOEBA/atom_vec_amoeba.cpp b/src/AMOEBA/atom_vec_amoeba.cpp index 71f614dc40..0907718102 100644 --- a/src/AMOEBA/atom_vec_amoeba.cpp +++ b/src/AMOEBA/atom_vec_amoeba.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/AMOEBA/atom_vec_amoeba.h b/src/AMOEBA/atom_vec_amoeba.h index a80d4c4b61..04e4650b4a 100644 --- a/src/AMOEBA/atom_vec_amoeba.h +++ b/src/AMOEBA/atom_vec_amoeba.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,7 @@ AtomStyle(amoeba,AtomVecAmoeba); namespace LAMMPS_NS { -class AtomVecAmoeba : public AtomVec { +class AtomVecAmoeba : virtual public AtomVec { public: AtomVecAmoeba(class LAMMPS *); ~AtomVecAmoeba() override; diff --git a/src/AMOEBA/fix_amoeba_bitorsion.cpp b/src/AMOEBA/fix_amoeba_bitorsion.cpp index 711ac7e05d..aeba26fb4d 100644 --- a/src/AMOEBA/fix_amoeba_bitorsion.cpp +++ b/src/AMOEBA/fix_amoeba_bitorsion.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/AMOEBA/fix_amoeba_bitorsion.h b/src/AMOEBA/fix_amoeba_bitorsion.h index f9d1da3b52..c936fe987d 100644 --- a/src/AMOEBA/fix_amoeba_bitorsion.h +++ b/src/AMOEBA/fix_amoeba_bitorsion.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -119,7 +119,7 @@ class FixAmoebaBiTorsion : public Fix { void chkttor(int, int, int, double &, double &, double &); void bcuint1(double *, double *, double *, double *, double, double, double, double, double, double, double &, double &, double &); - void bcucof(double *, double *, double *, double *, double, double, double[][4]); + void bcucof(double *, double *, double *, double *, double, double, double[4][4]); }; } // namespace LAMMPS_NS #endif diff --git a/src/AMOEBA/fix_amoeba_pitorsion.cpp b/src/AMOEBA/fix_amoeba_pitorsion.cpp index d8d712cfcb..445845c075 100644 --- a/src/AMOEBA/fix_amoeba_pitorsion.cpp +++ b/src/AMOEBA/fix_amoeba_pitorsion.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/AMOEBA/fix_amoeba_pitorsion.h b/src/AMOEBA/fix_amoeba_pitorsion.h index 6f78cbe34c..631bac8604 100644 --- a/src/AMOEBA/fix_amoeba_pitorsion.h +++ b/src/AMOEBA/fix_amoeba_pitorsion.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/AMOEBA/improper_amoeba.cpp b/src/AMOEBA/improper_amoeba.cpp index 93e07f662f..b1e403da78 100644 --- a/src/AMOEBA/improper_amoeba.cpp +++ b/src/AMOEBA/improper_amoeba.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -22,7 +22,6 @@ #include "memory.h" #include "neighbor.h" #include "pair.h" -#include "update.h" #include diff --git a/src/AMOEBA/improper_amoeba.h b/src/AMOEBA/improper_amoeba.h index 36fdcf4da9..d5a783a82f 100644 --- a/src/AMOEBA/improper_amoeba.h +++ b/src/AMOEBA/improper_amoeba.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/AMOEBA/pair_amoeba.cpp b/src/AMOEBA/pair_amoeba.cpp index a717416524..e8b7a18dba 100644 --- a/src/AMOEBA/pair_amoeba.cpp +++ b/src/AMOEBA/pair_amoeba.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -19,25 +19,20 @@ #include "comm.h" #include "domain.h" #include "error.h" -#include "fft3d_wrap.h" #include "fix.h" #include "fix_store_peratom.h" #include "force.h" -#include "gridcomm.h" #include "group.h" #include "math_special.h" #include "memory.h" #include "modify.h" #include "my_page.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "update.h" -#include "utils.h" -#include +#include #include -#include using namespace LAMMPS_NS; @@ -832,7 +827,7 @@ void PairAmoeba::init_style() // initialize KSpace Ewald settings and FFTs and parallel grid objects // Coulombic grid is used with two orders: bseorder and bsporder - // so need two GridComm instantiations for ghost comm + // so need two Grid3d instantiations for ghost comm if (first_flag) { kewald(); @@ -1418,38 +1413,65 @@ void PairAmoeba::unpack_reverse_comm(int n, int *list, double *buf) } } +/* ---------------------------------------------------------------------- + subset of FFT grids assigned to each proc may have changed + notify each instance of AmoebaConvolution class + called by load balancer when proc subdomains are adjusted +------------------------------------------------------------------------- */ + +void PairAmoeba::reset_grid() +{ + if (use_ewald) { + m_kspace->reset_grid(); + p_kspace->reset_grid(); + pc_kspace->reset_grid(); + i_kspace->reset_grid(); + ic_kspace->reset_grid(); + } + if (use_dewald) d_kspace->reset_grid(); + + // qfac is shared by induce and polar + // gridfft1 is copy of FFT grid used within polar + + memory->destroy(qfac); + memory->destroy(gridfft1); + int nmine = p_kspace->nfft_owned; + memory->create(qfac,nmine,"ameoba/induce:qfac"); + memory->create(gridfft1,2*nmine,"amoeba/polar:gridfft1"); +} + /* ---------------------------------------------------------------------- pack own values to buf to send to another proc ------------------------------------------------------------------------- */ -void PairAmoeba::pack_forward_grid(int flag, void *vbuf, int nlist, int *list) +void PairAmoeba::pack_forward_grid(int which, void *vbuf, int nlist, int *list) { FFT_SCALAR *buf = (FFT_SCALAR *) vbuf; - if (flag == MPOLE_GRID) { + if (which == MPOLE_GRID) { FFT_SCALAR *src = m_kspace->grid_brick_start; for (int i = 0; i < nlist; i++) buf[i] = src[list[i]]; - } else if (flag == POLAR_GRID) { + } else if (which == POLAR_GRID) { FFT_SCALAR *src = p_kspace->grid_brick_start; for (int i = 0; i < nlist; i++) buf[i] = src[list[i]]; - } else if (flag == POLAR_GRIDC) { + } else if (which == POLAR_GRIDC) { FFT_SCALAR *src = pc_kspace->grid_brick_start; int n = 0; for (int i = 0; i < nlist; i++) { buf[n++] = src[2*list[i]]; buf[n++] = src[2*list[i]+1]; } - } else if (flag == DISP_GRID) { + } else if (which == DISP_GRID) { FFT_SCALAR *src = d_kspace->grid_brick_start; for (int i = 0; i < nlist; i++) buf[i] = src[list[i]]; - } else if (flag == INDUCE_GRID) { + } else if (which == INDUCE_GRID) { FFT_SCALAR *src = i_kspace->grid_brick_start; for (int i = 0; i < nlist; i++) buf[i] = src[list[i]]; - } else if (flag == INDUCE_GRIDC) { + } else if (which == INDUCE_GRIDC) { FFT_SCALAR *src = ic_kspace->grid_brick_start; int n = 0; for (int i = 0; i < nlist; i++) { @@ -1463,34 +1485,34 @@ void PairAmoeba::pack_forward_grid(int flag, void *vbuf, int nlist, int *list) unpack another proc's own values from buf and set own ghost values ------------------------------------------------------------------------- */ -void PairAmoeba::unpack_forward_grid(int flag, void *vbuf, int nlist, int *list) +void PairAmoeba::unpack_forward_grid(int which, void *vbuf, int nlist, int *list) { FFT_SCALAR *buf = (FFT_SCALAR *) vbuf; - if (flag == MPOLE_GRID) { + if (which == MPOLE_GRID) { FFT_SCALAR *dest = m_kspace->grid_brick_start; for (int i = 0; i < nlist; i++) dest[list[i]] = buf[i]; - } else if (flag == POLAR_GRID) { + } else if (which == POLAR_GRID) { FFT_SCALAR *dest = p_kspace->grid_brick_start; for (int i = 0; i < nlist; i++) dest[list[i]] = buf[i]; - } else if (flag == POLAR_GRIDC) { + } else if (which == POLAR_GRIDC) { FFT_SCALAR *dest = pc_kspace->grid_brick_start; int n = 0; for (int i = 0; i < nlist; i++) { dest[2*list[i]] = buf[n++]; dest[2*list[i]+1] = buf[n++]; } - } else if (flag == DISP_GRID) { + } else if (which == DISP_GRID) { FFT_SCALAR *dest = d_kspace->grid_brick_start; for (int i = 0; i < nlist; i++) dest[list[i]] = buf[i]; - } else if (flag == INDUCE_GRID) { + } else if (which == INDUCE_GRID) { FFT_SCALAR *dest = i_kspace->grid_brick_start; for (int i = 0; i < nlist; i++) dest[list[i]] = buf[i]; - } else if (flag == INDUCE_GRIDC) { + } else if (which == INDUCE_GRIDC) { FFT_SCALAR *dest = ic_kspace->grid_brick_start; int n = 0; for (int i = 0; i < nlist; i++) { @@ -1504,34 +1526,34 @@ void PairAmoeba::unpack_forward_grid(int flag, void *vbuf, int nlist, int *list) pack ghost values into buf to send to another proc ------------------------------------------------------------------------- */ -void PairAmoeba::pack_reverse_grid(int flag, void *vbuf, int nlist, int *list) +void PairAmoeba::pack_reverse_grid(int which, void *vbuf, int nlist, int *list) { FFT_SCALAR *buf = (FFT_SCALAR *) vbuf; - if (flag == MPOLE_GRID) { + if (which == MPOLE_GRID) { FFT_SCALAR *src = m_kspace->grid_brick_start; for (int i = 0; i < nlist; i++) buf[i] = src[list[i]]; - } else if (flag == POLAR_GRID) { + } else if (which == POLAR_GRID) { FFT_SCALAR *src = p_kspace->grid_brick_start; for (int i = 0; i < nlist; i++) buf[i] = src[list[i]]; - } else if (flag == POLAR_GRIDC) { + } else if (which == POLAR_GRIDC) { FFT_SCALAR *src = pc_kspace->grid_brick_start; int n = 0; for (int i = 0; i < nlist; i++) { buf[n++] = src[2*list[i]]; buf[n++] = src[2*list[i]+1]; } - } else if (flag == DISP_GRID) { + } else if (which == DISP_GRID) { FFT_SCALAR *src = d_kspace->grid_brick_start; for (int i = 0; i < nlist; i++) buf[i] = src[list[i]]; - } else if (flag == INDUCE_GRID) { + } else if (which == INDUCE_GRID) { FFT_SCALAR *src = i_kspace->grid_brick_start; for (int i = 0; i < nlist; i++) buf[i] = src[list[i]]; - } else if (flag == INDUCE_GRIDC) { + } else if (which == INDUCE_GRIDC) { FFT_SCALAR *src = ic_kspace->grid_brick_start; int n = 0; for (int i = 0; i < nlist; i++) { @@ -1545,34 +1567,34 @@ void PairAmoeba::pack_reverse_grid(int flag, void *vbuf, int nlist, int *list) unpack another proc's ghost values from buf and add to own values ------------------------------------------------------------------------- */ -void PairAmoeba::unpack_reverse_grid(int flag, void *vbuf, int nlist, int *list) +void PairAmoeba::unpack_reverse_grid(int which, void *vbuf, int nlist, int *list) { FFT_SCALAR *buf = (FFT_SCALAR *) vbuf; - if (flag == MPOLE_GRID) { + if (which == MPOLE_GRID) { FFT_SCALAR *dest = m_kspace->grid_brick_start; for (int i = 0; i < nlist; i++) dest[list[i]] += buf[i]; - } else if (flag == POLAR_GRID) { + } else if (which == POLAR_GRID) { FFT_SCALAR *dest = p_kspace->grid_brick_start; for (int i = 0; i < nlist; i++) dest[list[i]] += buf[i]; - } else if (flag == POLAR_GRIDC) { + } else if (which == POLAR_GRIDC) { FFT_SCALAR *dest = pc_kspace->grid_brick_start; int n = 0; for (int i = 0; i < nlist; i++) { dest[2*list[i]] += buf[n++]; dest[2*list[i]+1] += buf[n++]; } - } else if (flag == DISP_GRID) { + } else if (which == DISP_GRID) { FFT_SCALAR *dest = d_kspace->grid_brick_start; for (int i = 0; i < nlist; i++) dest[list[i]] += buf[i]; - } else if (flag == INDUCE_GRID) { + } else if (which == INDUCE_GRID) { FFT_SCALAR *dest = i_kspace->grid_brick_start; for (int i = 0; i < nlist; i++) dest[list[i]] += buf[i]; - } else if (flag == INDUCE_GRIDC) { + } else if (which == INDUCE_GRIDC) { FFT_SCALAR *dest = ic_kspace->grid_brick_start; int n = 0; for (int i = 0; i < nlist; i++) { diff --git a/src/AMOEBA/pair_amoeba.h b/src/AMOEBA/pair_amoeba.h index 7f6596c3bd..847764244b 100644 --- a/src/AMOEBA/pair_amoeba.h +++ b/src/AMOEBA/pair_amoeba.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -44,6 +44,8 @@ class PairAmoeba : public Pair { int pack_reverse_comm(int, int, double *) override; void unpack_reverse_comm(int, int *, double *) override; + void reset_grid() override; + void pack_forward_grid(int, void *, int, int *) override; void unpack_forward_grid(int, void *, int, int *) override; void pack_reverse_grid(int, void *, int, int *) override; diff --git a/src/AMOEBA/pair_hippo.cpp b/src/AMOEBA/pair_hippo.cpp index d798ce2d4b..9a85a801e5 100644 --- a/src/AMOEBA/pair_hippo.cpp +++ b/src/AMOEBA/pair_hippo.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/AMOEBA/pair_hippo.h b/src/AMOEBA/pair_hippo.h index e8ad7a14ab..e7e6a87fea 100644 --- a/src/AMOEBA/pair_hippo.h +++ b/src/AMOEBA/pair_hippo.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/compute_erotate_asphere.cpp b/src/ASPHERE/compute_erotate_asphere.cpp index d98ef4efb2..82249a1db5 100644 --- a/src/ASPHERE/compute_erotate_asphere.cpp +++ b/src/ASPHERE/compute_erotate_asphere.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/compute_erotate_asphere.h b/src/ASPHERE/compute_erotate_asphere.h index c8ae5ca709..0cb8e9be65 100644 --- a/src/ASPHERE/compute_erotate_asphere.h +++ b/src/ASPHERE/compute_erotate_asphere.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/compute_temp_asphere.cpp b/src/ASPHERE/compute_temp_asphere.cpp index 36ef8af338..707938b2b9 100644 --- a/src/ASPHERE/compute_temp_asphere.cpp +++ b/src/ASPHERE/compute_temp_asphere.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/compute_temp_asphere.h b/src/ASPHERE/compute_temp_asphere.h index 8ac9cb1d00..c8c09b445b 100644 --- a/src/ASPHERE/compute_temp_asphere.h +++ b/src/ASPHERE/compute_temp_asphere.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/fix_nh_asphere.cpp b/src/ASPHERE/fix_nh_asphere.cpp index 07461ba365..45bf011e04 100644 --- a/src/ASPHERE/fix_nh_asphere.cpp +++ b/src/ASPHERE/fix_nh_asphere.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/fix_nh_asphere.h b/src/ASPHERE/fix_nh_asphere.h index 5cc49c4cc2..e4889d9d57 100644 --- a/src/ASPHERE/fix_nh_asphere.h +++ b/src/ASPHERE/fix_nh_asphere.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/fix_nph_asphere.cpp b/src/ASPHERE/fix_nph_asphere.cpp index 6ca263b8e6..6c25277d6a 100644 --- a/src/ASPHERE/fix_nph_asphere.cpp +++ b/src/ASPHERE/fix_nph_asphere.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/fix_nph_asphere.h b/src/ASPHERE/fix_nph_asphere.h index 52b2cdd879..e82c1f1987 100644 --- a/src/ASPHERE/fix_nph_asphere.h +++ b/src/ASPHERE/fix_nph_asphere.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/fix_npt_asphere.cpp b/src/ASPHERE/fix_npt_asphere.cpp index e7648bc32b..9d240a1b9a 100644 --- a/src/ASPHERE/fix_npt_asphere.cpp +++ b/src/ASPHERE/fix_npt_asphere.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/fix_npt_asphere.h b/src/ASPHERE/fix_npt_asphere.h index ccaa9c0313..2fdd891231 100644 --- a/src/ASPHERE/fix_npt_asphere.h +++ b/src/ASPHERE/fix_npt_asphere.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/fix_nve_asphere.cpp b/src/ASPHERE/fix_nve_asphere.cpp index d969796f89..f4080493c8 100644 --- a/src/ASPHERE/fix_nve_asphere.cpp +++ b/src/ASPHERE/fix_nve_asphere.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/fix_nve_asphere.h b/src/ASPHERE/fix_nve_asphere.h index 78c49fa2c7..b614f4083f 100644 --- a/src/ASPHERE/fix_nve_asphere.h +++ b/src/ASPHERE/fix_nve_asphere.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/fix_nve_asphere_noforce.cpp b/src/ASPHERE/fix_nve_asphere_noforce.cpp index 2be23a644c..aaa21d9550 100644 --- a/src/ASPHERE/fix_nve_asphere_noforce.cpp +++ b/src/ASPHERE/fix_nve_asphere_noforce.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/fix_nve_asphere_noforce.h b/src/ASPHERE/fix_nve_asphere_noforce.h index b46ed400f0..8f7548633c 100644 --- a/src/ASPHERE/fix_nve_asphere_noforce.h +++ b/src/ASPHERE/fix_nve_asphere_noforce.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/fix_nve_line.cpp b/src/ASPHERE/fix_nve_line.cpp index 5d9251d541..d7adf0a963 100644 --- a/src/ASPHERE/fix_nve_line.cpp +++ b/src/ASPHERE/fix_nve_line.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/fix_nve_line.h b/src/ASPHERE/fix_nve_line.h index 40b18e5ab1..b31228f6cb 100644 --- a/src/ASPHERE/fix_nve_line.h +++ b/src/ASPHERE/fix_nve_line.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/fix_nve_tri.cpp b/src/ASPHERE/fix_nve_tri.cpp index d594f6a854..b8d5bf1b89 100644 --- a/src/ASPHERE/fix_nve_tri.cpp +++ b/src/ASPHERE/fix_nve_tri.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/fix_nve_tri.h b/src/ASPHERE/fix_nve_tri.h index b1e91d712c..dc2bc1cefa 100644 --- a/src/ASPHERE/fix_nve_tri.h +++ b/src/ASPHERE/fix_nve_tri.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/fix_nvt_asphere.cpp b/src/ASPHERE/fix_nvt_asphere.cpp index dc98d97dcf..16b7c65b38 100644 --- a/src/ASPHERE/fix_nvt_asphere.cpp +++ b/src/ASPHERE/fix_nvt_asphere.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/fix_nvt_asphere.h b/src/ASPHERE/fix_nvt_asphere.h index 78c9e0a156..7ee6caeda9 100644 --- a/src/ASPHERE/fix_nvt_asphere.h +++ b/src/ASPHERE/fix_nvt_asphere.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/pair_gayberne.cpp b/src/ASPHERE/pair_gayberne.cpp index 025de0975b..600889e0d1 100644 --- a/src/ASPHERE/pair_gayberne.cpp +++ b/src/ASPHERE/pair_gayberne.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/pair_gayberne.h b/src/ASPHERE/pair_gayberne.h index d8975e6ad0..1549d14c17 100644 --- a/src/ASPHERE/pair_gayberne.h +++ b/src/ASPHERE/pair_gayberne.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/pair_line_lj.cpp b/src/ASPHERE/pair_line_lj.cpp index 6784f3341d..2d6dc557f3 100644 --- a/src/ASPHERE/pair_line_lj.cpp +++ b/src/ASPHERE/pair_line_lj.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/pair_line_lj.h b/src/ASPHERE/pair_line_lj.h index 064e2520c6..6f230eb871 100644 --- a/src/ASPHERE/pair_line_lj.h +++ b/src/ASPHERE/pair_line_lj.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/pair_resquared.cpp b/src/ASPHERE/pair_resquared.cpp index 473489632a..9322425a88 100644 --- a/src/ASPHERE/pair_resquared.cpp +++ b/src/ASPHERE/pair_resquared.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/pair_resquared.h b/src/ASPHERE/pair_resquared.h index 4fd3312001..ec74eab36b 100644 --- a/src/ASPHERE/pair_resquared.h +++ b/src/ASPHERE/pair_resquared.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/pair_tri_lj.cpp b/src/ASPHERE/pair_tri_lj.cpp index a62e4f253d..4fe999f039 100644 --- a/src/ASPHERE/pair_tri_lj.cpp +++ b/src/ASPHERE/pair_tri_lj.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/pair_tri_lj.h b/src/ASPHERE/pair_tri_lj.h index aaf0d4e7ae..b31e73f609 100644 --- a/src/ASPHERE/pair_tri_lj.h +++ b/src/ASPHERE/pair_tri_lj.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ASPHERE/pair_ylz.cpp b/src/ASPHERE/pair_ylz.cpp new file mode 100644 index 0000000000..31cbf3f929 --- /dev/null +++ b/src/ASPHERE/pair_ylz.cpp @@ -0,0 +1,509 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + 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: Hongyan Yuan (SUSTech) +------------------------------------------------------------------------- */ + +#include "pair_ylz.h" + +#include "atom.h" +#include "atom_vec_ellipsoid.h" +#include "citeme.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "math_const.h" +#include "math_extra.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" + +#include + +using namespace LAMMPS_NS; +using MathConst::MY_4PI; +using MathConst::MY_PI2; +using MathConst::MY_TWOBYSIXTH; + +static const char cite_pair_ylz[] = + "pair ylz command:\n\n" + "@Article{Yuan10,\n" + " author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},\n" + " title = {One-particle-thick, solvent-free, coarse-grained model for biological and " + "biomimetic fluid membranes},\n" + " journal = {Phys. Rev. E},\n" + " year = 2010,\n" + " volume = 82,\n" + " pages = {011905}\n" + "}\n\n"; + +/* ---------------------------------------------------------------------- */ + +PairYLZ::PairYLZ(LAMMPS *lmp) : + Pair(lmp), epsilon(nullptr), sigma(nullptr), cut(nullptr), zeta(nullptr), mu(nullptr), + beta(nullptr), avec(nullptr) +{ + if (lmp->citeme) lmp->citeme->add(cite_pair_ylz); + + single_enable = 0; + writedata = 1; +} + +/* ---------------------------------------------------------------------- + free all arrays +------------------------------------------------------------------------- */ + +PairYLZ::~PairYLZ() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(epsilon); + memory->destroy(sigma); + memory->destroy(cut); + memory->destroy(zeta); + memory->destroy(mu); + memory->destroy(beta); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairYLZ::compute(int eflag, int vflag) +{ + int i, j, ii, jj, inum, jnum, itype, jtype; + double evdwl, one_eng, rsq, factor_lj; + double fforce[3], ttor[3], rtor[3], r12[3]; + double a1[3][3], a2[3][3]; + int *ilist, *jlist, *numneigh, **firstneigh; + double *iquat, *jquat; + + evdwl = 0.0; + ev_init(eflag, vflag); + + AtomVecEllipsoid::Bonus *bonus = avec->bonus; + int *ellipsoid = atom->ellipsoid; + double **x = atom->x; + double **f = atom->f; + double **tor = atom->torque; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + itype = type[i]; + + iquat = bonus[ellipsoid[i]].quat; + MathExtra::quat_to_mat_trans(iquat, a1); + + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + // r12 = center to center vector + + r12[0] = x[j][0] - x[i][0]; + r12[1] = x[j][1] - x[i][1]; + r12[2] = x[j][2] - x[i][2]; + rsq = MathExtra::dot3(r12, r12); + jtype = type[j]; + + // compute if less than cutoff + + if (rsq < cutsq[itype][jtype]) { + + jquat = bonus[ellipsoid[j]].quat; + MathExtra::quat_to_mat_trans(jquat, a2); + one_eng = ylz_analytic(i, j, a1, a2, r12, rsq, fforce, ttor, rtor); + + fforce[0] *= factor_lj; + fforce[1] *= factor_lj; + fforce[2] *= factor_lj; + ttor[0] *= factor_lj; + ttor[1] *= factor_lj; + ttor[2] *= factor_lj; + + f[i][0] += fforce[0]; + f[i][1] += fforce[1]; + f[i][2] += fforce[2]; + tor[i][0] += ttor[0]; + tor[i][1] += ttor[1]; + tor[i][2] += ttor[2]; + + if (newton_pair || j < nlocal) { + rtor[0] *= factor_lj; + rtor[1] *= factor_lj; + rtor[2] *= factor_lj; + f[j][0] -= fforce[0]; + f[j][1] -= fforce[1]; + f[j][2] -= fforce[2]; + tor[j][0] += rtor[0]; + tor[j][1] += rtor[1]; + tor[j][2] += rtor[2]; + } + + if (eflag) evdwl = factor_lj * one_eng; + + if (evflag) + ev_tally_xyz(i, j, nlocal, newton_pair, evdwl, 0.0, fforce[0], fforce[1], fforce[2], + -r12[0], -r12[1], -r12[2]); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairYLZ::allocate() +{ + allocated = 1; + int np1 = atom->ntypes + 1; + + memory->create(setflag, np1, np1, "pair:setflag"); + for (int i = 1; i < np1; i++) + for (int j = i; j < np1; j++) setflag[i][j] = 0; + + memory->create(cutsq, np1, np1, "pair:cutsq"); + memory->create(epsilon, np1, np1, "pair:epsilon"); + memory->create(sigma, np1, np1, "pair:sigma"); + memory->create(cut, np1, np1, "pair:cut"); + memory->create(zeta, np1, np1, "pair:zeta"); + memory->create(mu, np1, np1, "pair:mu"); + memory->create(beta, np1, np1, "pair:beta"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairYLZ::settings(int narg, char **arg) +{ + if (narg != 1) error->all(FLERR, "Illegal pair_style command"); + + cut_global = utils::numeric(FLERR, arg[0], false, lmp); +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairYLZ::coeff(int narg, char **arg) +{ + if (narg < 8 || narg > 8) error->all(FLERR, "Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo, ihi, jlo, jhi; + utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error); + utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error); + + double epsilon_one = utils::numeric(FLERR, arg[2], false, lmp); + double sigma_one = utils::numeric(FLERR, arg[3], false, lmp); + double zeta_one = utils::numeric(FLERR, arg[4], false, lmp); + double mu_one = utils::numeric(FLERR, arg[5], false, lmp); + double beta_one = utils::numeric(FLERR, arg[6], false, lmp); + double cut_one = utils::numeric(FLERR, arg[7], false, lmp); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo, i); j <= jhi; j++) { + epsilon[i][j] = epsilon_one; + sigma[i][j] = sigma_one; + cut[i][j] = cut_one; + zeta[i][j] = zeta_one; + mu[i][j] = mu_one; + beta[i][j] = beta_one; + + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairYLZ::init_style() +{ + avec = dynamic_cast(atom->style_match("ellipsoid")); + if (!avec) error->all(FLERR, "Pair style ylz requires atom style ellipsoid"); + + neighbor->request(this, instance_me); + + // check that all atoms are ellipsoids + + int flag_all, flag = 0; + const int *ellipsoid = atom->ellipsoid; + const int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; ++i) + if (ellipsoid[i] < 0) flag = 1; + MPI_Allreduce(&flag, &flag_all, 1, MPI_INT, MPI_MAX, world); + if (flag_all) error->all(FLERR, "All atoms must be ellipsoids for pair style ylz"); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairYLZ::init_one(int i, int j) +{ + if (setflag[i][j] == 0) { + epsilon[i][j] = mix_energy(epsilon[i][i], epsilon[j][j], sigma[i][i], sigma[j][j]); + sigma[i][j] = mix_distance(sigma[i][i], sigma[j][j]); + cut[i][j] = mix_distance(cut[i][i], cut[j][j]); + } + + epsilon[j][i] = epsilon[i][j]; + sigma[j][i] = sigma[i][j]; + zeta[j][i] = zeta[i][j]; + mu[j][i] = mu[i][j]; + beta[j][i] = beta[i][j]; + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairYLZ::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + for (int i = 1; i <= atom->ntypes; i++) { + for (int j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j], sizeof(int), 1, fp); + if (setflag[i][j]) { + fwrite(&epsilon[i][j], sizeof(double), 1, fp); + fwrite(&sigma[i][j], sizeof(double), 1, fp); + fwrite(&cut[i][j], sizeof(double), 1, fp); + fwrite(&zeta[i][j], sizeof(double), 1, fp); + fwrite(&mu[i][j], sizeof(double), 1, fp); + fwrite(&beta[i][j], sizeof(double), 1, fp); + } + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairYLZ::read_restart(FILE *fp) +{ + read_restart_settings(fp); + allocate(); + + for (int i = 1; i <= atom->ntypes; i++) { + for (int j = i; j <= atom->ntypes; j++) { + if (comm->me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error); + MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world); + if (setflag[i][j]) { + if (comm->me == 0) { + utils::sfread(FLERR, &epsilon[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &sigma[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &zeta[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &mu[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &beta[i][j], sizeof(double), 1, fp, nullptr, error); + } + + MPI_Bcast(&epsilon[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&sigma[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&zeta[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&mu[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&beta[i][j], 1, MPI_DOUBLE, 0, world); + } + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairYLZ::write_restart_settings(FILE *fp) +{ + fwrite(&cut_global, sizeof(double), 1, fp); + fwrite(&offset_flag, sizeof(int), 1, fp); + fwrite(&mix_flag, sizeof(int), 1, fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairYLZ::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + + utils::sfread(FLERR, &cut_global, sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &offset_flag, sizeof(int), 1, fp, nullptr, error); + utils::sfread(FLERR, &mix_flag, sizeof(int), 1, fp, nullptr, error); + } + + MPI_Bcast(&cut_global, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&offset_flag, 1, MPI_INT, 0, world); + MPI_Bcast(&mix_flag, 1, MPI_INT, 0, world); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairYLZ::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp, "%d %g %g %g %g %g %g\n", i, epsilon[i][i], sigma[i][i], cut[i][i], zeta[i][i], + mu[i][i], beta[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairYLZ::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp, "%d %d %g %g %g %g %g %g\n", i, j, epsilon[i][i], sigma[i][i], cut[i][j], + zeta[i][j], mu[i][j], beta[i][j]); +} + +/* ---------------------------------------------------------------------- + compute analytic energy, force (fforce), and torque (ttor & rtor) + based on rotation matrices a + if newton is off, rtor is not calculated for ghost atoms +------------------------------------------------------------------------- */ + +double PairYLZ::ylz_analytic(const int i, const int j, double a1[3][3], double a2[3][3], + double *r12, const double rsq, double *fforce, double *ttor, + double *rtor) + +{ + int *type = atom->type; + int newton_pair = force->newton_pair; + int nlocal = atom->nlocal; + + double r12hat[3]; + MathExtra::normalize3(r12, r12hat); + double r = sqrt(rsq); + + double ni1[3], nj1[3], dphi_drhat[3], dUdrhat[3], dUdni1[3], dUdnj1[3]; + double dphi_dni1[3], dphi_dnj1[3]; + double t, t1, t2, t4, cos_t, U, uR, uA, dUdr, dUdphi; + const double energy_well = epsilon[type[i]][type[j]]; + const double rmin = MY_TWOBYSIXTH * sigma[type[i]][type[j]]; + const double rcut = cut[type[i]][type[j]]; + const double zt = zeta[type[i]][type[j]]; + const double muu = mu[type[i]][type[j]]; + const double sint = beta[type[i]][type[j]]; + + ni1[0] = a1[0][0]; + ni1[1] = a1[0][1]; + ni1[2] = a1[0][2]; + + nj1[0] = a2[0][0]; + nj1[1] = a2[0][1]; + nj1[2] = a2[0][2]; + + const double ninj = MathExtra::dot3(ni1, nj1); + const double ni1rhat = MathExtra::dot3(ni1, r12hat); + const double nj1rhat = MathExtra::dot3(nj1, r12hat); + + const double a = ninj + (sint - ni1rhat) * (sint + nj1rhat) - 2.0 * sint * sint; + const double phi = 1.0 + (a - 1.0) * muu; + + dphi_drhat[0] = muu * ((sint - ni1rhat) * nj1[0] - ni1[0] * (sint + nj1rhat)); + dphi_drhat[1] = muu * ((sint - ni1rhat) * nj1[1] - ni1[1] * (sint + nj1rhat)); + dphi_drhat[2] = muu * ((sint - ni1rhat) * nj1[2] - ni1[2] * (sint + nj1rhat)); + + dphi_dni1[0] = muu * (nj1[0] - r12hat[0] * (sint + nj1rhat)); + dphi_dni1[1] = muu * (nj1[1] - r12hat[1] * (sint + nj1rhat)); + dphi_dni1[2] = muu * (nj1[2] - r12hat[2] * (sint + nj1rhat)); + + dphi_dnj1[0] = muu * (ni1[0] + r12hat[0] * (sint - ni1rhat)); + dphi_dnj1[1] = muu * (ni1[1] + r12hat[1] * (sint - ni1rhat)); + dphi_dnj1[2] = muu * (ni1[2] + r12hat[2] * (sint - ni1rhat)); + + if (r < rmin) { + t = rmin / r; + t2 = t * t; + t4 = t2 * t2; + uR = (t4 - 2.0 * t2) * energy_well; + U = uR + (1.0 - phi) * energy_well; + dUdr = 4.0 * (t2 - t4) / r * energy_well; + dUdphi = -energy_well; + } else { + t = MY_PI2 * (r - rmin) / (rcut - rmin); + cos_t = cos(t); + t1 = cos_t; + + for (int k = 1; k <= 2 * zt - 2; k++) t1 *= cos_t; // get cos()^(2zt-1) + + uA = -energy_well * t1 * cos_t; + U = uA * phi; + dUdr = MY_4PI / (rcut - rmin) * (t1) *sin(t) * phi * energy_well; + dUdphi = uA; + } + + dUdrhat[0] = dUdphi * dphi_drhat[0]; + dUdrhat[1] = dUdphi * dphi_drhat[1]; + dUdrhat[2] = dUdphi * dphi_drhat[2]; + + double dUdrhatrhat = MathExtra::dot3(dUdrhat, r12hat); + + fforce[0] = dUdr * r12hat[0] + (dUdrhat[0] - dUdrhatrhat * r12hat[0]) / r; + fforce[1] = dUdr * r12hat[1] + (dUdrhat[1] - dUdrhatrhat * r12hat[1]) / r; + fforce[2] = dUdr * r12hat[2] + (dUdrhat[2] - dUdrhatrhat * r12hat[2]) / r; + + // torque i + + dUdni1[0] = dUdphi * dphi_dni1[0]; + dUdni1[1] = dUdphi * dphi_dni1[1]; + dUdni1[2] = dUdphi * dphi_dni1[2]; + + MathExtra::cross3(dUdni1, ni1, ttor); //minus sign is replace by swapping ni1 and dUdni1 + + if (newton_pair || j < nlocal) { + + dUdnj1[0] = dUdphi * dphi_dnj1[0]; + dUdnj1[1] = dUdphi * dphi_dnj1[1]; + dUdnj1[2] = dUdphi * dphi_dnj1[2]; + + MathExtra::cross3(dUdnj1, nj1, rtor); //minus sign is replace by swapping ni1 and dUdni1 + } + return U; +} diff --git a/src/ASPHERE/pair_ylz.h b/src/ASPHERE/pair_ylz.h new file mode 100644 index 0000000000..976a4d2465 --- /dev/null +++ b/src/ASPHERE/pair_ylz.h @@ -0,0 +1,56 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + 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(ylz,PairYLZ); +// clang-format on + +#else + +#ifndef LMP_PAIR_YLZ_H +#define LMP_PAIR_YLZ_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairYLZ : public Pair { + public: + PairYLZ(LAMMPS *lmp); + virtual ~PairYLZ(); + virtual void compute(int, int); + virtual void settings(int, char **); + void coeff(int, char **); + virtual void init_style(); + double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + void write_data(FILE *); + void write_data_all(FILE *); + + protected: + double cut_global; + double **epsilon, **sigma, **cut, **zeta, **mu, **beta; + + class AtomVecEllipsoid *avec; + + void allocate(); + double ylz_analytic(const int i, const int j, double a1[3][3], double a2[3][3], double *r12, + const double rsq, double *fforce, double *ttor, double *rtor); +}; +} // namespace LAMMPS_NS +#endif +#endif diff --git a/src/ATC/Install.sh b/src/ATC/Install.sh index e1dacdd7d6..2194685f92 100755 --- a/src/ATC/Install.sh +++ b/src/ATC/Install.sh @@ -60,7 +60,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*atc.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*atc.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/atc\/Makefile.lammps @@ -74,7 +74,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*atc.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*atc.*$/d' ../Makefile.package.settings fi fi diff --git a/src/ATC/fix_atc.cpp b/src/ATC/fix_atc.cpp index 356aa2596c..436ffc9555 100644 --- a/src/ATC/fix_atc.cpp +++ b/src/ATC/fix_atc.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + LAMMPS development team: developers@lammps.org, Sandia National Laboratories Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ATC/fix_atc.h b/src/ATC/fix_atc.h index 6b7a5ff8d9..9df0a55aab 100644 --- a/src/ATC/fix_atc.h +++ b/src/ATC/fix_atc.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/AWPMD/Install.sh b/src/AWPMD/Install.sh index 70e87c3fbc..0e2e2d3473 100755 --- a/src/AWPMD/Install.sh +++ b/src/AWPMD/Install.sh @@ -46,7 +46,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*awpmd.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*awpmd.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/awpmd\/Makefile.lammps @@ -60,7 +60,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*awpmd.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*awpmd.*$/d' ../Makefile.package.settings fi fi diff --git a/src/AWPMD/atom_vec_wavepacket.cpp b/src/AWPMD/atom_vec_wavepacket.cpp index b904410cd3..ff0d660fb6 100644 --- a/src/AWPMD/atom_vec_wavepacket.cpp +++ b/src/AWPMD/atom_vec_wavepacket.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/AWPMD/atom_vec_wavepacket.h b/src/AWPMD/atom_vec_wavepacket.h index 9ceaadbb5a..cc7c34191c 100644 --- a/src/AWPMD/atom_vec_wavepacket.h +++ b/src/AWPMD/atom_vec_wavepacket.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,7 @@ AtomStyle(wavepacket,AtomVecWavepacket); namespace LAMMPS_NS { -class AtomVecWavepacket : public AtomVec { +class AtomVecWavepacket : virtual public AtomVec { public: AtomVecWavepacket(class LAMMPS *); diff --git a/src/AWPMD/fix_nve_awpmd.cpp b/src/AWPMD/fix_nve_awpmd.cpp index f9931d5302..739c983b83 100644 --- a/src/AWPMD/fix_nve_awpmd.cpp +++ b/src/AWPMD/fix_nve_awpmd.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/AWPMD/fix_nve_awpmd.h b/src/AWPMD/fix_nve_awpmd.h index 182470a702..96f2bba512 100644 --- a/src/AWPMD/fix_nve_awpmd.h +++ b/src/AWPMD/fix_nve_awpmd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/AWPMD/pair_awpmd_cut.cpp b/src/AWPMD/pair_awpmd_cut.cpp index fcce6006fd..e0ce319ebd 100644 --- a/src/AWPMD/pair_awpmd_cut.cpp +++ b/src/AWPMD/pair_awpmd_cut.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/AWPMD/pair_awpmd_cut.h b/src/AWPMD/pair_awpmd_cut.h index 203552dcab..17abbd74f1 100644 --- a/src/AWPMD/pair_awpmd_cut.h +++ b/src/AWPMD/pair_awpmd_cut.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BOCS/compute_pressure_bocs.cpp b/src/BOCS/compute_pressure_bocs.cpp index 19b1ef7d99..db63b4597e 100644 --- a/src/BOCS/compute_pressure_bocs.cpp +++ b/src/BOCS/compute_pressure_bocs.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BOCS/compute_pressure_bocs.h b/src/BOCS/compute_pressure_bocs.h index 820ca3bff6..00a2394c5a 100644 --- a/src/BOCS/compute_pressure_bocs.h +++ b/src/BOCS/compute_pressure_bocs.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BOCS/fix_bocs.cpp b/src/BOCS/fix_bocs.cpp index de55019be0..d17884855a 100644 --- a/src/BOCS/fix_bocs.cpp +++ b/src/BOCS/fix_bocs.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BOCS/fix_bocs.h b/src/BOCS/fix_bocs.h index 5419506fd3..fd47fda4d7 100644 --- a/src/BOCS/fix_bocs.h +++ b/src/BOCS/fix_bocs.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/body_nparticle.cpp b/src/BODY/body_nparticle.cpp index ccd0c55619..62e6ee802a 100644 --- a/src/BODY/body_nparticle.cpp +++ b/src/BODY/body_nparticle.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/body_nparticle.h b/src/BODY/body_nparticle.h index 3e814543c4..496c15a486 100644 --- a/src/BODY/body_nparticle.h +++ b/src/BODY/body_nparticle.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/body_rounded_polygon.cpp b/src/BODY/body_rounded_polygon.cpp index 88cf03e76b..2fb2a991f1 100644 --- a/src/BODY/body_rounded_polygon.cpp +++ b/src/BODY/body_rounded_polygon.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/body_rounded_polygon.h b/src/BODY/body_rounded_polygon.h index c6b1cd134f..499aebc90f 100644 --- a/src/BODY/body_rounded_polygon.h +++ b/src/BODY/body_rounded_polygon.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/body_rounded_polyhedron.cpp b/src/BODY/body_rounded_polyhedron.cpp index aa71b89529..1d11644618 100644 --- a/src/BODY/body_rounded_polyhedron.cpp +++ b/src/BODY/body_rounded_polyhedron.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/body_rounded_polyhedron.h b/src/BODY/body_rounded_polyhedron.h index f49bce9574..40e7cf53db 100644 --- a/src/BODY/body_rounded_polyhedron.h +++ b/src/BODY/body_rounded_polyhedron.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/compute_body_local.cpp b/src/BODY/compute_body_local.cpp index d3d28a7ea0..4fda71afaa 100644 --- a/src/BODY/compute_body_local.cpp +++ b/src/BODY/compute_body_local.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/compute_body_local.h b/src/BODY/compute_body_local.h index 7462d5cedd..95af881900 100644 --- a/src/BODY/compute_body_local.h +++ b/src/BODY/compute_body_local.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/compute_temp_body.cpp b/src/BODY/compute_temp_body.cpp index 084b715b25..319c2ff986 100644 --- a/src/BODY/compute_temp_body.cpp +++ b/src/BODY/compute_temp_body.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/compute_temp_body.h b/src/BODY/compute_temp_body.h index df64211174..7518951032 100644 --- a/src/BODY/compute_temp_body.h +++ b/src/BODY/compute_temp_body.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/fix_nh_body.cpp b/src/BODY/fix_nh_body.cpp index 2b462f1f4c..5e56c29312 100644 --- a/src/BODY/fix_nh_body.cpp +++ b/src/BODY/fix_nh_body.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/fix_nh_body.h b/src/BODY/fix_nh_body.h index e442d47097..08661774d6 100644 --- a/src/BODY/fix_nh_body.h +++ b/src/BODY/fix_nh_body.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/fix_nph_body.cpp b/src/BODY/fix_nph_body.cpp index 31964df496..14dea9d36b 100644 --- a/src/BODY/fix_nph_body.cpp +++ b/src/BODY/fix_nph_body.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/fix_nph_body.h b/src/BODY/fix_nph_body.h index 6bc734a43d..b5314b5c20 100644 --- a/src/BODY/fix_nph_body.h +++ b/src/BODY/fix_nph_body.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/fix_npt_body.cpp b/src/BODY/fix_npt_body.cpp index 97e06d6166..b6c774223f 100644 --- a/src/BODY/fix_npt_body.cpp +++ b/src/BODY/fix_npt_body.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/fix_npt_body.h b/src/BODY/fix_npt_body.h index 1e977fb688..6763eb542e 100644 --- a/src/BODY/fix_npt_body.h +++ b/src/BODY/fix_npt_body.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/fix_nve_body.cpp b/src/BODY/fix_nve_body.cpp index a0c2430f18..6332993228 100644 --- a/src/BODY/fix_nve_body.cpp +++ b/src/BODY/fix_nve_body.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/fix_nve_body.h b/src/BODY/fix_nve_body.h index c37f6218cd..6bff18634a 100644 --- a/src/BODY/fix_nve_body.h +++ b/src/BODY/fix_nve_body.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/fix_nvt_body.cpp b/src/BODY/fix_nvt_body.cpp index a0d269da8c..aec808d1ea 100644 --- a/src/BODY/fix_nvt_body.cpp +++ b/src/BODY/fix_nvt_body.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/fix_nvt_body.h b/src/BODY/fix_nvt_body.h index fbed640a6f..d5df628b89 100644 --- a/src/BODY/fix_nvt_body.h +++ b/src/BODY/fix_nvt_body.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/fix_wall_body_polygon.cpp b/src/BODY/fix_wall_body_polygon.cpp index be1d89468b..4d0517e527 100644 --- a/src/BODY/fix_wall_body_polygon.cpp +++ b/src/BODY/fix_wall_body_polygon.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/fix_wall_body_polygon.h b/src/BODY/fix_wall_body_polygon.h index 971fdcfe1b..0fa4ee743b 100644 --- a/src/BODY/fix_wall_body_polygon.h +++ b/src/BODY/fix_wall_body_polygon.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/fix_wall_body_polyhedron.cpp b/src/BODY/fix_wall_body_polyhedron.cpp index f739d9d682..212830eb81 100644 --- a/src/BODY/fix_wall_body_polyhedron.cpp +++ b/src/BODY/fix_wall_body_polyhedron.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/fix_wall_body_polyhedron.h b/src/BODY/fix_wall_body_polyhedron.h index 9125820fcd..2cd80e2947 100644 --- a/src/BODY/fix_wall_body_polyhedron.h +++ b/src/BODY/fix_wall_body_polyhedron.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/pair_body_nparticle.cpp b/src/BODY/pair_body_nparticle.cpp index d056dd2840..9e1e640015 100644 --- a/src/BODY/pair_body_nparticle.cpp +++ b/src/BODY/pair_body_nparticle.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/pair_body_nparticle.h b/src/BODY/pair_body_nparticle.h index 419028e49c..d1959af3c9 100644 --- a/src/BODY/pair_body_nparticle.h +++ b/src/BODY/pair_body_nparticle.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp index a7a83049a2..0e83b63f99 100644 --- a/src/BODY/pair_body_rounded_polygon.cpp +++ b/src/BODY/pair_body_rounded_polygon.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/pair_body_rounded_polygon.h b/src/BODY/pair_body_rounded_polygon.h index 06b5c6b3f2..314e3633f7 100644 --- a/src/BODY/pair_body_rounded_polygon.h +++ b/src/BODY/pair_body_rounded_polygon.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp index db8d6baf5d..2c23199e33 100644 --- a/src/BODY/pair_body_rounded_polyhedron.cpp +++ b/src/BODY/pair_body_rounded_polyhedron.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BODY/pair_body_rounded_polyhedron.h b/src/BODY/pair_body_rounded_polyhedron.h index a137ebd4fa..a407e192df 100644 --- a/src/BODY/pair_body_rounded_polyhedron.h +++ b/src/BODY/pair_body_rounded_polyhedron.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BPM/atom_vec_bpm_sphere.cpp b/src/BPM/atom_vec_bpm_sphere.cpp index f2116aefa3..3d2ced5429 100644 --- a/src/BPM/atom_vec_bpm_sphere.cpp +++ b/src/BPM/atom_vec_bpm_sphere.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -20,7 +20,6 @@ #include "fix_adapt.h" #include "math_const.h" #include "modify.h" -#include "utils.h" #include diff --git a/src/BPM/atom_vec_bpm_sphere.h b/src/BPM/atom_vec_bpm_sphere.h index 5bd40cc5c0..38ce3d9bca 100644 --- a/src/BPM/atom_vec_bpm_sphere.h +++ b/src/BPM/atom_vec_bpm_sphere.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,7 @@ AtomStyle(bpm/sphere,AtomVecBPMSphere); namespace LAMMPS_NS { -class AtomVecBPMSphere : public AtomVec { +class AtomVecBPMSphere : virtual public AtomVec { public: AtomVecBPMSphere(class LAMMPS *); void process_args(int, char **) override; diff --git a/src/BPM/bond_bpm.cpp b/src/BPM/bond_bpm.cpp index 5a20059860..4d65fe7684 100644 --- a/src/BPM/bond_bpm.cpp +++ b/src/BPM/bond_bpm.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -25,7 +25,8 @@ #include "modify.h" #include "update.h" -#include +#include +#include using namespace LAMMPS_NS; @@ -319,8 +320,7 @@ void BondBPM::write_restart(FILE *fp) void BondBPM::read_restart(FILE *fp) { - if (comm->me == 0) - utils::sfread(FLERR, &overlay_flag, sizeof(int), 1, fp, nullptr, error); + if (comm->me == 0) utils::sfread(FLERR, &overlay_flag, sizeof(int), 1, fp, nullptr, error); MPI_Bcast(&overlay_flag, 1, MPI_INT, 0, world); } diff --git a/src/BPM/bond_bpm.h b/src/BPM/bond_bpm.h index 7a32ec2d0d..cc2e46d5d3 100644 --- a/src/BPM/bond_bpm.h +++ b/src/BPM/bond_bpm.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -16,8 +16,6 @@ #include "bond.h" -#include - namespace LAMMPS_NS { class BondBPM : public Bond { diff --git a/src/BPM/bond_bpm_rotational.cpp b/src/BPM/bond_bpm_rotational.cpp index d86caf0eb6..3085488ef9 100644 --- a/src/BPM/bond_bpm_rotational.cpp +++ b/src/BPM/bond_bpm_rotational.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -19,13 +19,13 @@ #include "error.h" #include "fix_bond_history.h" #include "force.h" -#include "math_const.h" #include "math_extra.h" #include "memory.h" #include "modify.h" #include "neighbor.h" #include +#include #define EPSILON 1e-10 diff --git a/src/BPM/bond_bpm_rotational.h b/src/BPM/bond_bpm_rotational.h index 8b9338d7db..0fb38e7343 100644 --- a/src/BPM/bond_bpm_rotational.h +++ b/src/BPM/bond_bpm_rotational.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -43,8 +43,8 @@ class BondBPMRotational : public BondBPM { double *Fcr, *Fcs, *Tct, *Tcb; int smooth_flag; - double elastic_forces(int, int, int, double, double, double, double *, double *, - double *, double *, double *, double *); + double elastic_forces(int, int, int, double, double, double, double *, double *, double *, + double *, double *, double *); void damping_forces(int, int, int, double *, double *, double *, double *, double *); void allocate(); diff --git a/src/BPM/bond_bpm_spring.cpp b/src/BPM/bond_bpm_spring.cpp index e87419e178..ed4e71daf1 100644 --- a/src/BPM/bond_bpm_spring.cpp +++ b/src/BPM/bond_bpm_spring.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -23,6 +23,9 @@ #include "modify.h" #include "neighbor.h" +#include +#include + #define EPSILON 1e-10 using namespace LAMMPS_NS; @@ -356,8 +359,7 @@ void BondBPMSpring::write_restart_settings(FILE *fp) void BondBPMSpring::read_restart_settings(FILE *fp) { - if (comm->me == 0) - utils::sfread(FLERR, &smooth_flag, sizeof(int), 1, fp, nullptr, error); + if (comm->me == 0) utils::sfread(FLERR, &smooth_flag, sizeof(int), 1, fp, nullptr, error); MPI_Bcast(&smooth_flag, 1, MPI_INT, 0, world); } diff --git a/src/BPM/bond_bpm_spring.h b/src/BPM/bond_bpm_spring.h index 4bea7266a5..409469bef3 100644 --- a/src/BPM/bond_bpm_spring.h +++ b/src/BPM/bond_bpm_spring.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BPM/compute_nbond_atom.cpp b/src/BPM/compute_nbond_atom.cpp index b0fbacf038..4f0fc4c3f0 100644 --- a/src/BPM/compute_nbond_atom.cpp +++ b/src/BPM/compute_nbond_atom.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -15,12 +15,8 @@ #include "atom.h" #include "comm.h" -#include "error.h" #include "force.h" #include "memory.h" -#include "update.h" - -#include using namespace LAMMPS_NS; @@ -29,7 +25,7 @@ using namespace LAMMPS_NS; ComputeNBondAtom::ComputeNBondAtom(LAMMPS *_lmp, int narg, char **arg) : Compute(_lmp, narg, arg), nbond(nullptr) { - if (narg < 3) error->all(FLERR, "Illegal compute nbond/atom command"); + if (narg < 3) utils::missing_cmd_args(FLERR, "compute nbond/atom", error); peratom_flag = 1; size_peratom_cols = 0; diff --git a/src/BPM/compute_nbond_atom.h b/src/BPM/compute_nbond_atom.h index 32d4ca2462..e0c2d7ce01 100644 --- a/src/BPM/compute_nbond_atom.h +++ b/src/BPM/compute_nbond_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BPM/fix_nve_bpm_sphere.cpp b/src/BPM/fix_nve_bpm_sphere.cpp index 77e2441618..ceab07822e 100644 --- a/src/BPM/fix_nve_bpm_sphere.cpp +++ b/src/BPM/fix_nve_bpm_sphere.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -14,13 +14,10 @@ #include "fix_nve_bpm_sphere.h" #include "atom.h" -#include "atom_vec.h" #include "domain.h" #include "error.h" -#include "force.h" #include "math_extra.h" -#include #include using namespace LAMMPS_NS; diff --git a/src/BPM/fix_nve_bpm_sphere.h b/src/BPM/fix_nve_bpm_sphere.h index 5f96f33df5..ec52615122 100644 --- a/src/BPM/fix_nve_bpm_sphere.h +++ b/src/BPM/fix_nve_bpm_sphere.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BPM/pair_bpm_spring.cpp b/src/BPM/pair_bpm_spring.cpp index 40f40b8a3b..1177156359 100644 --- a/src/BPM/pair_bpm_spring.cpp +++ b/src/BPM/pair_bpm_spring.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -19,7 +19,8 @@ #include "force.h" #include "memory.h" #include "neigh_list.h" -#include "neighbor.h" + +#include using namespace LAMMPS_NS; diff --git a/src/BPM/pair_bpm_spring.h b/src/BPM/pair_bpm_spring.h index 97d7995f14..3cb281bff3 100644 --- a/src/BPM/pair_bpm_spring.h +++ b/src/BPM/pair_bpm_spring.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BROWNIAN/fix_brownian.cpp b/src/BROWNIAN/fix_brownian.cpp index 9284126676..0b73858f29 100644 --- a/src/BROWNIAN/fix_brownian.cpp +++ b/src/BROWNIAN/fix_brownian.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BROWNIAN/fix_brownian.h b/src/BROWNIAN/fix_brownian.h index 703a49cd69..6e8b1302b8 100644 --- a/src/BROWNIAN/fix_brownian.h +++ b/src/BROWNIAN/fix_brownian.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BROWNIAN/fix_brownian_asphere.cpp b/src/BROWNIAN/fix_brownian_asphere.cpp index 46c58e7877..5ce57df7ce 100644 --- a/src/BROWNIAN/fix_brownian_asphere.cpp +++ b/src/BROWNIAN/fix_brownian_asphere.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -27,6 +27,8 @@ #include "math_extra.h" #include "random_mars.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/BROWNIAN/fix_brownian_asphere.h b/src/BROWNIAN/fix_brownian_asphere.h index a9c24d17a2..7ce4657e17 100644 --- a/src/BROWNIAN/fix_brownian_asphere.h +++ b/src/BROWNIAN/fix_brownian_asphere.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BROWNIAN/fix_brownian_base.cpp b/src/BROWNIAN/fix_brownian_base.cpp index 730b9a0c41..b2e89a096a 100644 --- a/src/BROWNIAN/fix_brownian_base.cpp +++ b/src/BROWNIAN/fix_brownian_base.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BROWNIAN/fix_brownian_base.h b/src/BROWNIAN/fix_brownian_base.h index 6f6be89b0c..9fab2a54ce 100644 --- a/src/BROWNIAN/fix_brownian_base.h +++ b/src/BROWNIAN/fix_brownian_base.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BROWNIAN/fix_brownian_sphere.cpp b/src/BROWNIAN/fix_brownian_sphere.cpp index 5a20c4c0ec..220a3b9735 100644 --- a/src/BROWNIAN/fix_brownian_sphere.cpp +++ b/src/BROWNIAN/fix_brownian_sphere.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BROWNIAN/fix_brownian_sphere.h b/src/BROWNIAN/fix_brownian_sphere.h index 258c4cbf0d..712285a4e3 100644 --- a/src/BROWNIAN/fix_brownian_sphere.h +++ b/src/BROWNIAN/fix_brownian_sphere.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BROWNIAN/fix_propel_self.cpp b/src/BROWNIAN/fix_propel_self.cpp index 55fce754a6..8d97b828a9 100644 --- a/src/BROWNIAN/fix_propel_self.cpp +++ b/src/BROWNIAN/fix_propel_self.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/BROWNIAN/fix_propel_self.h b/src/BROWNIAN/fix_propel_self.h index 887b042051..3acaed31d2 100644 --- a/src/BROWNIAN/fix_propel_self.h +++ b/src/BROWNIAN/fix_propel_self.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/atom_vec_oxdna.cpp b/src/CG-DNA/atom_vec_oxdna.cpp index 52380eca57..d7aa7a3d01 100644 --- a/src/CG-DNA/atom_vec_oxdna.cpp +++ b/src/CG-DNA/atom_vec_oxdna.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/atom_vec_oxdna.h b/src/CG-DNA/atom_vec_oxdna.h index 4c439dc3a6..91318574eb 100644 --- a/src/CG-DNA/atom_vec_oxdna.h +++ b/src/CG-DNA/atom_vec_oxdna.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,7 @@ AtomStyle(oxdna,AtomVecOxdna); namespace LAMMPS_NS { -class AtomVecOxdna : public AtomVec { +class AtomVecOxdna : virtual public AtomVec { public: AtomVecOxdna(class LAMMPS *); diff --git a/src/CG-DNA/bond_oxdna2_fene.cpp b/src/CG-DNA/bond_oxdna2_fene.cpp index 54f2dab9d2..ace0742963 100644 --- a/src/CG-DNA/bond_oxdna2_fene.cpp +++ b/src/CG-DNA/bond_oxdna2_fene.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/bond_oxdna2_fene.h b/src/CG-DNA/bond_oxdna2_fene.h index 89e291505f..a342ea1c67 100644 --- a/src/CG-DNA/bond_oxdna2_fene.h +++ b/src/CG-DNA/bond_oxdna2_fene.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/bond_oxdna_fene.cpp b/src/CG-DNA/bond_oxdna_fene.cpp index acaa26b7e1..2d471cbbe6 100644 --- a/src/CG-DNA/bond_oxdna_fene.cpp +++ b/src/CG-DNA/bond_oxdna_fene.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/bond_oxdna_fene.h b/src/CG-DNA/bond_oxdna_fene.h index 1f754e817a..ad5c913e97 100644 --- a/src/CG-DNA/bond_oxdna_fene.h +++ b/src/CG-DNA/bond_oxdna_fene.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/bond_oxrna2_fene.cpp b/src/CG-DNA/bond_oxrna2_fene.cpp index 24de5f7714..5d28f744a8 100644 --- a/src/CG-DNA/bond_oxrna2_fene.cpp +++ b/src/CG-DNA/bond_oxrna2_fene.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/bond_oxrna2_fene.h b/src/CG-DNA/bond_oxrna2_fene.h index 638fea394e..7c8222f7e8 100644 --- a/src/CG-DNA/bond_oxrna2_fene.h +++ b/src/CG-DNA/bond_oxrna2_fene.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/fix_nve_dot.cpp b/src/CG-DNA/fix_nve_dot.cpp index 47506874a7..a9d288eb16 100644 --- a/src/CG-DNA/fix_nve_dot.cpp +++ b/src/CG-DNA/fix_nve_dot.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/fix_nve_dot.h b/src/CG-DNA/fix_nve_dot.h index 86562f5b74..c2e30a43d5 100644 --- a/src/CG-DNA/fix_nve_dot.h +++ b/src/CG-DNA/fix_nve_dot.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/fix_nve_dotc_langevin.cpp b/src/CG-DNA/fix_nve_dotc_langevin.cpp index 0c48df32ce..56436a3a98 100644 --- a/src/CG-DNA/fix_nve_dotc_langevin.cpp +++ b/src/CG-DNA/fix_nve_dotc_langevin.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/fix_nve_dotc_langevin.h b/src/CG-DNA/fix_nve_dotc_langevin.h index ab74e13ab5..afb1f15b41 100644 --- a/src/CG-DNA/fix_nve_dotc_langevin.h +++ b/src/CG-DNA/fix_nve_dotc_langevin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/mf_oxdna.h b/src/CG-DNA/mf_oxdna.h index 0dcd236773..c583abf3ab 100644 --- a/src/CG-DNA/mf_oxdna.h +++ b/src/CG-DNA/mf_oxdna.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxdna2_coaxstk.cpp b/src/CG-DNA/pair_oxdna2_coaxstk.cpp index 1e53104003..844ba56577 100644 --- a/src/CG-DNA/pair_oxdna2_coaxstk.cpp +++ b/src/CG-DNA/pair_oxdna2_coaxstk.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxdna2_coaxstk.h b/src/CG-DNA/pair_oxdna2_coaxstk.h index 4030194c19..6dca466b46 100644 --- a/src/CG-DNA/pair_oxdna2_coaxstk.h +++ b/src/CG-DNA/pair_oxdna2_coaxstk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxdna2_dh.cpp b/src/CG-DNA/pair_oxdna2_dh.cpp index 19b158ea61..dcfe3f9ea1 100644 --- a/src/CG-DNA/pair_oxdna2_dh.cpp +++ b/src/CG-DNA/pair_oxdna2_dh.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxdna2_dh.h b/src/CG-DNA/pair_oxdna2_dh.h index aca5391122..375a19a351 100644 --- a/src/CG-DNA/pair_oxdna2_dh.h +++ b/src/CG-DNA/pair_oxdna2_dh.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxdna2_excv.cpp b/src/CG-DNA/pair_oxdna2_excv.cpp index cde2af65da..f0f9ca904e 100644 --- a/src/CG-DNA/pair_oxdna2_excv.cpp +++ b/src/CG-DNA/pair_oxdna2_excv.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxdna2_excv.h b/src/CG-DNA/pair_oxdna2_excv.h index c24239d343..9c96676876 100644 --- a/src/CG-DNA/pair_oxdna2_excv.h +++ b/src/CG-DNA/pair_oxdna2_excv.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxdna_coaxstk.cpp b/src/CG-DNA/pair_oxdna_coaxstk.cpp index 1976de0f62..b9b34338fe 100644 --- a/src/CG-DNA/pair_oxdna_coaxstk.cpp +++ b/src/CG-DNA/pair_oxdna_coaxstk.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxdna_coaxstk.h b/src/CG-DNA/pair_oxdna_coaxstk.h index 67c8b34a9c..89406926c1 100644 --- a/src/CG-DNA/pair_oxdna_coaxstk.h +++ b/src/CG-DNA/pair_oxdna_coaxstk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxdna_excv.cpp b/src/CG-DNA/pair_oxdna_excv.cpp index 73386f3fe4..254b8e18d8 100644 --- a/src/CG-DNA/pair_oxdna_excv.cpp +++ b/src/CG-DNA/pair_oxdna_excv.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxdna_excv.h b/src/CG-DNA/pair_oxdna_excv.h index 17f35b848b..e9d59d996a 100644 --- a/src/CG-DNA/pair_oxdna_excv.h +++ b/src/CG-DNA/pair_oxdna_excv.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxdna_hbond.cpp b/src/CG-DNA/pair_oxdna_hbond.cpp index 3f563767c5..5b121a9113 100644 --- a/src/CG-DNA/pair_oxdna_hbond.cpp +++ b/src/CG-DNA/pair_oxdna_hbond.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxdna_hbond.h b/src/CG-DNA/pair_oxdna_hbond.h index 8850e1bd9b..9208fc3e59 100644 --- a/src/CG-DNA/pair_oxdna_hbond.h +++ b/src/CG-DNA/pair_oxdna_hbond.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxdna_stk.cpp b/src/CG-DNA/pair_oxdna_stk.cpp index 0f17d332d6..99ddf9c96a 100644 --- a/src/CG-DNA/pair_oxdna_stk.cpp +++ b/src/CG-DNA/pair_oxdna_stk.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxdna_stk.h b/src/CG-DNA/pair_oxdna_stk.h index ae74ee77ac..dcba19d97a 100644 --- a/src/CG-DNA/pair_oxdna_stk.h +++ b/src/CG-DNA/pair_oxdna_stk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxdna_xstk.cpp b/src/CG-DNA/pair_oxdna_xstk.cpp index f50d5219f9..d95004f537 100644 --- a/src/CG-DNA/pair_oxdna_xstk.cpp +++ b/src/CG-DNA/pair_oxdna_xstk.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxdna_xstk.h b/src/CG-DNA/pair_oxdna_xstk.h index ae808679f9..21e4bf154a 100644 --- a/src/CG-DNA/pair_oxdna_xstk.h +++ b/src/CG-DNA/pair_oxdna_xstk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxrna2_dh.cpp b/src/CG-DNA/pair_oxrna2_dh.cpp index f19dbb249b..eceda90768 100644 --- a/src/CG-DNA/pair_oxrna2_dh.cpp +++ b/src/CG-DNA/pair_oxrna2_dh.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxrna2_dh.h b/src/CG-DNA/pair_oxrna2_dh.h index 157bc0ae8e..29c91eed6b 100644 --- a/src/CG-DNA/pair_oxrna2_dh.h +++ b/src/CG-DNA/pair_oxrna2_dh.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxrna2_excv.cpp b/src/CG-DNA/pair_oxrna2_excv.cpp index 422c7e2d89..a49497ef5a 100644 --- a/src/CG-DNA/pair_oxrna2_excv.cpp +++ b/src/CG-DNA/pair_oxrna2_excv.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxrna2_excv.h b/src/CG-DNA/pair_oxrna2_excv.h index 2185e17ada..3e2caccfe2 100644 --- a/src/CG-DNA/pair_oxrna2_excv.h +++ b/src/CG-DNA/pair_oxrna2_excv.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxrna2_hbond.cpp b/src/CG-DNA/pair_oxrna2_hbond.cpp index dfa9997af3..14ecc6c659 100644 --- a/src/CG-DNA/pair_oxrna2_hbond.cpp +++ b/src/CG-DNA/pair_oxrna2_hbond.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxrna2_hbond.h b/src/CG-DNA/pair_oxrna2_hbond.h index e84295afb3..de61e7926d 100644 --- a/src/CG-DNA/pair_oxrna2_hbond.h +++ b/src/CG-DNA/pair_oxrna2_hbond.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxrna2_stk.cpp b/src/CG-DNA/pair_oxrna2_stk.cpp index a14f78e715..f6e12fffe1 100644 --- a/src/CG-DNA/pair_oxrna2_stk.cpp +++ b/src/CG-DNA/pair_oxrna2_stk.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxrna2_stk.h b/src/CG-DNA/pair_oxrna2_stk.h index 1cf404e73b..85f7064e5c 100644 --- a/src/CG-DNA/pair_oxrna2_stk.h +++ b/src/CG-DNA/pair_oxrna2_stk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxrna2_xstk.cpp b/src/CG-DNA/pair_oxrna2_xstk.cpp index 09f8e68943..cdba56e33a 100644 --- a/src/CG-DNA/pair_oxrna2_xstk.cpp +++ b/src/CG-DNA/pair_oxrna2_xstk.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-DNA/pair_oxrna2_xstk.h b/src/CG-DNA/pair_oxrna2_xstk.h index 919ee22857..0264a50236 100644 --- a/src/CG-DNA/pair_oxrna2_xstk.h +++ b/src/CG-DNA/pair_oxrna2_xstk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-SPICA/angle_spica.cpp b/src/CG-SPICA/angle_spica.cpp index ff19f29b75..3f8a506ed2 100644 --- a/src/CG-SPICA/angle_spica.cpp +++ b/src/CG-SPICA/angle_spica.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -297,7 +297,7 @@ void AngleSPICA::init_style() repflag = 0; for (int i = 1; i <= atom->nangletypes; i++) - if (repscale[i] > 0.0) repflag = 1; + if (repscale && (repscale[i] > 0.0)) repflag = 1; // set up pointers to access SPICA LJ parameters for 1-3 interactions diff --git a/src/CG-SPICA/angle_spica.h b/src/CG-SPICA/angle_spica.h index e270ee5de5..f0085fe2fd 100644 --- a/src/CG-SPICA/angle_spica.h +++ b/src/CG-SPICA/angle_spica.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-SPICA/lj_spica_common.h b/src/CG-SPICA/lj_spica_common.h index 656b5dedb6..0967782d58 100644 --- a/src/CG-SPICA/lj_spica_common.h +++ b/src/CG-SPICA/lj_spica_common.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-SPICA/pair_lj_spica.cpp b/src/CG-SPICA/pair_lj_spica.cpp index 32af30cd2b..03fab85954 100644 --- a/src/CG-SPICA/pair_lj_spica.cpp +++ b/src/CG-SPICA/pair_lj_spica.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-SPICA/pair_lj_spica.h b/src/CG-SPICA/pair_lj_spica.h index 6c016ccd7c..0da9ea60f4 100644 --- a/src/CG-SPICA/pair_lj_spica.h +++ b/src/CG-SPICA/pair_lj_spica.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-SPICA/pair_lj_spica_coul_long.cpp b/src/CG-SPICA/pair_lj_spica_coul_long.cpp index 968f1aad74..b95dde5ef5 100644 --- a/src/CG-SPICA/pair_lj_spica_coul_long.cpp +++ b/src/CG-SPICA/pair_lj_spica_coul_long.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-SPICA/pair_lj_spica_coul_long.h b/src/CG-SPICA/pair_lj_spica_coul_long.h index dce60e5e77..e6ef5ea539 100644 --- a/src/CG-SPICA/pair_lj_spica_coul_long.h +++ b/src/CG-SPICA/pair_lj_spica_coul_long.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-SPICA/pair_lj_spica_coul_msm.cpp b/src/CG-SPICA/pair_lj_spica_coul_msm.cpp index 536c01595c..8078380a75 100644 --- a/src/CG-SPICA/pair_lj_spica_coul_msm.cpp +++ b/src/CG-SPICA/pair_lj_spica_coul_msm.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CG-SPICA/pair_lj_spica_coul_msm.h b/src/CG-SPICA/pair_lj_spica_coul_msm.h index be43b5ba52..503421e77f 100644 --- a/src/CG-SPICA/pair_lj_spica_coul_msm.h +++ b/src/CG-SPICA/pair_lj_spica_coul_msm.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CLASS2/angle_class2.cpp b/src/CLASS2/angle_class2.cpp index c37c5a8f65..c731a4d5c9 100644 --- a/src/CLASS2/angle_class2.cpp +++ b/src/CLASS2/angle_class2.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CLASS2/angle_class2.h b/src/CLASS2/angle_class2.h index 9503a35c70..f5fbd62b57 100644 --- a/src/CLASS2/angle_class2.h +++ b/src/CLASS2/angle_class2.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CLASS2/bond_class2.cpp b/src/CLASS2/bond_class2.cpp index 2b33039a13..e49607f6ee 100644 --- a/src/CLASS2/bond_class2.cpp +++ b/src/CLASS2/bond_class2.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CLASS2/bond_class2.h b/src/CLASS2/bond_class2.h index 1ca65a8628..894a60f684 100644 --- a/src/CLASS2/bond_class2.h +++ b/src/CLASS2/bond_class2.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CLASS2/dihedral_class2.cpp b/src/CLASS2/dihedral_class2.cpp index 7b5406a7e9..d49d50f0e6 100644 --- a/src/CLASS2/dihedral_class2.cpp +++ b/src/CLASS2/dihedral_class2.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CLASS2/dihedral_class2.h b/src/CLASS2/dihedral_class2.h index 5dafe8e043..ad42c5c3a1 100644 --- a/src/CLASS2/dihedral_class2.h +++ b/src/CLASS2/dihedral_class2.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CLASS2/improper_class2.cpp b/src/CLASS2/improper_class2.cpp index 72e146f76d..6e6541919a 100644 --- a/src/CLASS2/improper_class2.cpp +++ b/src/CLASS2/improper_class2.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CLASS2/improper_class2.h b/src/CLASS2/improper_class2.h index 8646b44735..6102ef945c 100644 --- a/src/CLASS2/improper_class2.h +++ b/src/CLASS2/improper_class2.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp index d6348bafa7..c2f79c6333 100644 --- a/src/CLASS2/pair_lj_class2.cpp +++ b/src/CLASS2/pair_lj_class2.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org 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 diff --git a/src/CLASS2/pair_lj_class2.h b/src/CLASS2/pair_lj_class2.h index a709be3f54..2aff62851c 100644 --- a/src/CLASS2/pair_lj_class2.h +++ b/src/CLASS2/pair_lj_class2.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org 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 diff --git a/src/CLASS2/pair_lj_class2_coul_cut.cpp b/src/CLASS2/pair_lj_class2_coul_cut.cpp index 6b5ffe9e65..d05eb9acae 100644 --- a/src/CLASS2/pair_lj_class2_coul_cut.cpp +++ b/src/CLASS2/pair_lj_class2_coul_cut.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CLASS2/pair_lj_class2_coul_cut.h b/src/CLASS2/pair_lj_class2_coul_cut.h index c9da2222ea..ca5d6830f5 100644 --- a/src/CLASS2/pair_lj_class2_coul_cut.h +++ b/src/CLASS2/pair_lj_class2_coul_cut.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CLASS2/pair_lj_class2_coul_long.cpp b/src/CLASS2/pair_lj_class2_coul_long.cpp index 839586abcf..10b42588db 100644 --- a/src/CLASS2/pair_lj_class2_coul_long.cpp +++ b/src/CLASS2/pair_lj_class2_coul_long.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CLASS2/pair_lj_class2_coul_long.h b/src/CLASS2/pair_lj_class2_coul_long.h index 9d1aeb711d..5e524d4a4b 100644 --- a/src/CLASS2/pair_lj_class2_coul_long.h +++ b/src/CLASS2/pair_lj_class2_coul_long.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COLLOID/fix_wall_colloid.cpp b/src/COLLOID/fix_wall_colloid.cpp index 6f6374e2ac..02b747a8cc 100644 --- a/src/COLLOID/fix_wall_colloid.cpp +++ b/src/COLLOID/fix_wall_colloid.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COLLOID/fix_wall_colloid.h b/src/COLLOID/fix_wall_colloid.h index 7e6adf6308..58ed5fedd2 100644 --- a/src/COLLOID/fix_wall_colloid.h +++ b/src/COLLOID/fix_wall_colloid.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COLLOID/pair_brownian.cpp b/src/COLLOID/pair_brownian.cpp index 12362dab6f..4d78145207 100644 --- a/src/COLLOID/pair_brownian.cpp +++ b/src/COLLOID/pair_brownian.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -92,7 +92,6 @@ void PairBrownian::compute(int eflag, int vflag) double prethermostat; double xl[3], a_sq, a_sh, a_pu, Fbmag; double p1[3], p2[3], p3[3]; - int overlaps = 0; // This section of code adjusts R0/RT0/RS0 if necessary due to changes // in the volume fraction as a result of fix deform or moving walls @@ -187,10 +186,6 @@ void PairBrownian::compute(int eflag, int vflag) h_sep = r - 2.0 * radi; - // check for overlaps - - if (h_sep < 0.0) overlaps++; - // if less than minimum gap, use minimum gap instead if (r < cut_inner[itype][jtype]) h_sep = cut_inner[itype][jtype] - 2.0 * radi; @@ -336,9 +331,6 @@ void PairBrownian::compute(int eflag, int vflag) } } - int print_overlaps = 0; - if (print_overlaps && overlaps) printf("Number of overlaps=%d\n", overlaps); - if (vflag_fdotr) virial_fdotr_compute(); } diff --git a/src/COLLOID/pair_brownian.h b/src/COLLOID/pair_brownian.h index 110e0aec77..a6a08db699 100644 --- a/src/COLLOID/pair_brownian.h +++ b/src/COLLOID/pair_brownian.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COLLOID/pair_brownian_poly.cpp b/src/COLLOID/pair_brownian_poly.cpp index 69af4ae769..2654410c03 100644 --- a/src/COLLOID/pair_brownian_poly.cpp +++ b/src/COLLOID/pair_brownian_poly.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -72,7 +72,6 @@ void PairBrownianPoly::compute(int eflag, int vflag) int nlocal = atom->nlocal; double vxmu2f = force->vxmu2f; - int overlaps = 0; double randr; double prethermostat; double xl[3],a_sq,a_sh,a_pu,Fbmag; @@ -176,10 +175,6 @@ void PairBrownianPoly::compute(int eflag, int vflag) h_sep = r - radi-radj; - // check for overlaps - - if (h_sep < 0.0) overlaps++; - // if less than minimum gap, use minimum gap instead if (r < cut_inner[itype][jtype]) diff --git a/src/COLLOID/pair_brownian_poly.h b/src/COLLOID/pair_brownian_poly.h index aef5a5c13d..aec379a61b 100644 --- a/src/COLLOID/pair_brownian_poly.h +++ b/src/COLLOID/pair_brownian_poly.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COLLOID/pair_colloid.cpp b/src/COLLOID/pair_colloid.cpp index 891aae9233..55424fa398 100644 --- a/src/COLLOID/pair_colloid.cpp +++ b/src/COLLOID/pair_colloid.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COLLOID/pair_colloid.h b/src/COLLOID/pair_colloid.h index 27057665e5..bf8c6cac0d 100644 --- a/src/COLLOID/pair_colloid.h +++ b/src/COLLOID/pair_colloid.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COLLOID/pair_lubricate.cpp b/src/COLLOID/pair_lubricate.cpp index 7e15bc563a..6f07d63bfb 100644 --- a/src/COLLOID/pair_lubricate.cpp +++ b/src/COLLOID/pair_lubricate.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COLLOID/pair_lubricate.h b/src/COLLOID/pair_lubricate.h index a783312e5e..8097eb76dd 100644 --- a/src/COLLOID/pair_lubricate.h +++ b/src/COLLOID/pair_lubricate.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COLLOID/pair_lubricateU.cpp b/src/COLLOID/pair_lubricateU.cpp index f263b18a86..ac1e62c2a2 100644 --- a/src/COLLOID/pair_lubricateU.cpp +++ b/src/COLLOID/pair_lubricateU.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COLLOID/pair_lubricateU.h b/src/COLLOID/pair_lubricateU.h index 24be18710e..8712a18321 100644 --- a/src/COLLOID/pair_lubricateU.h +++ b/src/COLLOID/pair_lubricateU.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COLLOID/pair_lubricateU_poly.cpp b/src/COLLOID/pair_lubricateU_poly.cpp index 7598baa88e..b91f7bb730 100644 --- a/src/COLLOID/pair_lubricateU_poly.cpp +++ b/src/COLLOID/pair_lubricateU_poly.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COLLOID/pair_lubricateU_poly.h b/src/COLLOID/pair_lubricateU_poly.h index ed5aab3aed..e47b2132e9 100644 --- a/src/COLLOID/pair_lubricateU_poly.h +++ b/src/COLLOID/pair_lubricateU_poly.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COLLOID/pair_lubricate_poly.cpp b/src/COLLOID/pair_lubricate_poly.cpp index 8ce3e8e110..e6a0606e87 100644 --- a/src/COLLOID/pair_lubricate_poly.cpp +++ b/src/COLLOID/pair_lubricate_poly.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COLLOID/pair_lubricate_poly.h b/src/COLLOID/pair_lubricate_poly.h index 1df27834b7..018a0cf20d 100644 --- a/src/COLLOID/pair_lubricate_poly.h +++ b/src/COLLOID/pair_lubricate_poly.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COLLOID/pair_yukawa_colloid.cpp b/src/COLLOID/pair_yukawa_colloid.cpp index 67b518fe70..ad63292e33 100644 --- a/src/COLLOID/pair_yukawa_colloid.cpp +++ b/src/COLLOID/pair_yukawa_colloid.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COLLOID/pair_yukawa_colloid.h b/src/COLLOID/pair_yukawa_colloid.h index 55f86f9e13..e215af0c4c 100644 --- a/src/COLLOID/pair_yukawa_colloid.h +++ b/src/COLLOID/pair_yukawa_colloid.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COLVARS/Install.sh b/src/COLVARS/Install.sh index d67883a416..ebabfd7a1e 100755 --- a/src/COLVARS/Install.sh +++ b/src/COLVARS/Install.sh @@ -47,7 +47,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*colvars.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*colvars.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/colvars\/Makefile.lammps @@ -62,7 +62,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*colvars.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*colvars.*$/d' ../Makefile.package.settings fi fi diff --git a/src/COLVARS/fix_colvars.cpp b/src/COLVARS/fix_colvars.cpp index a46e6318d0..3a613a6785 100644 --- a/src/COLVARS/fix_colvars.cpp +++ b/src/COLVARS/fix_colvars.cpp @@ -11,7 +11,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COLVARS/fix_colvars.h b/src/COLVARS/fix_colvars.h index 4d5f19e9a9..715ee64a7f 100644 --- a/src/COLVARS/fix_colvars.h +++ b/src/COLVARS/fix_colvars.h @@ -10,7 +10,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COLVARS/group_ndx.cpp b/src/COLVARS/group_ndx.cpp index c4c37c8d8b..05a50a1596 100644 --- a/src/COLVARS/group_ndx.cpp +++ b/src/COLVARS/group_ndx.cpp @@ -4,7 +4,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COLVARS/group_ndx.h b/src/COLVARS/group_ndx.h index 524d2d6c03..685ad82d91 100644 --- a/src/COLVARS/group_ndx.h +++ b/src/COLVARS/group_ndx.h @@ -3,7 +3,7 @@ /* ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COLVARS/ndx_group.cpp b/src/COLVARS/ndx_group.cpp index 34b3bd7dae..4f8a682a2a 100644 --- a/src/COLVARS/ndx_group.cpp +++ b/src/COLVARS/ndx_group.cpp @@ -4,7 +4,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COLVARS/ndx_group.h b/src/COLVARS/ndx_group.h index 484c53f109..0b35fb62a0 100644 --- a/src/COLVARS/ndx_group.h +++ b/src/COLVARS/ndx_group.h @@ -3,7 +3,7 @@ /* ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COMPRESS/Install.sh b/src/COMPRESS/Install.sh index ab9dac33dc..c0d926cba4 100755 --- a/src/COMPRESS/Install.sh +++ b/src/COMPRESS/Install.sh @@ -44,7 +44,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*compress.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*compress.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/compress\/Makefile.lammps @@ -58,7 +58,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*compress.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*compress.*$/d' ../Makefile.package.settings fi fi diff --git a/src/COMPRESS/dump_atom_gz.cpp b/src/COMPRESS/dump_atom_gz.cpp index 3e15d6240d..d4fb01a3e6 100644 --- a/src/COMPRESS/dump_atom_gz.cpp +++ b/src/COMPRESS/dump_atom_gz.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COMPRESS/dump_atom_gz.h b/src/COMPRESS/dump_atom_gz.h index fcf27464be..637074d560 100644 --- a/src/COMPRESS/dump_atom_gz.h +++ b/src/COMPRESS/dump_atom_gz.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COMPRESS/dump_atom_zstd.cpp b/src/COMPRESS/dump_atom_zstd.cpp index 453efb6972..a1a098eb19 100644 --- a/src/COMPRESS/dump_atom_zstd.cpp +++ b/src/COMPRESS/dump_atom_zstd.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COMPRESS/dump_atom_zstd.h b/src/COMPRESS/dump_atom_zstd.h index 35143a983f..82e9d2e026 100644 --- a/src/COMPRESS/dump_atom_zstd.h +++ b/src/COMPRESS/dump_atom_zstd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COMPRESS/dump_cfg_gz.cpp b/src/COMPRESS/dump_cfg_gz.cpp index 43b24d7bdb..259056c013 100644 --- a/src/COMPRESS/dump_cfg_gz.cpp +++ b/src/COMPRESS/dump_cfg_gz.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COMPRESS/dump_cfg_gz.h b/src/COMPRESS/dump_cfg_gz.h index b1376861c6..4b46cea2c9 100644 --- a/src/COMPRESS/dump_cfg_gz.h +++ b/src/COMPRESS/dump_cfg_gz.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COMPRESS/dump_cfg_zstd.cpp b/src/COMPRESS/dump_cfg_zstd.cpp index 865a8ccf87..e3f9a7c1f9 100644 --- a/src/COMPRESS/dump_cfg_zstd.cpp +++ b/src/COMPRESS/dump_cfg_zstd.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COMPRESS/dump_cfg_zstd.h b/src/COMPRESS/dump_cfg_zstd.h index 3b056141a0..75bd2c93a3 100644 --- a/src/COMPRESS/dump_cfg_zstd.h +++ b/src/COMPRESS/dump_cfg_zstd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COMPRESS/dump_custom_gz.cpp b/src/COMPRESS/dump_custom_gz.cpp index 42b15c4146..3ff0124b24 100644 --- a/src/COMPRESS/dump_custom_gz.cpp +++ b/src/COMPRESS/dump_custom_gz.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COMPRESS/dump_custom_gz.h b/src/COMPRESS/dump_custom_gz.h index 51ac402050..10f3b06522 100644 --- a/src/COMPRESS/dump_custom_gz.h +++ b/src/COMPRESS/dump_custom_gz.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COMPRESS/dump_custom_zstd.cpp b/src/COMPRESS/dump_custom_zstd.cpp index e3effe1744..10d6d3e440 100644 --- a/src/COMPRESS/dump_custom_zstd.cpp +++ b/src/COMPRESS/dump_custom_zstd.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COMPRESS/dump_custom_zstd.h b/src/COMPRESS/dump_custom_zstd.h index 56f8022704..52e9804bce 100644 --- a/src/COMPRESS/dump_custom_zstd.h +++ b/src/COMPRESS/dump_custom_zstd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COMPRESS/dump_local_gz.cpp b/src/COMPRESS/dump_local_gz.cpp index 9c04f0cd61..b39f6bc7ac 100644 --- a/src/COMPRESS/dump_local_gz.cpp +++ b/src/COMPRESS/dump_local_gz.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COMPRESS/dump_local_gz.h b/src/COMPRESS/dump_local_gz.h index ebfb57cd58..8848620d57 100644 --- a/src/COMPRESS/dump_local_gz.h +++ b/src/COMPRESS/dump_local_gz.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COMPRESS/dump_local_zstd.cpp b/src/COMPRESS/dump_local_zstd.cpp index 4e65702b0e..cb805750e1 100644 --- a/src/COMPRESS/dump_local_zstd.cpp +++ b/src/COMPRESS/dump_local_zstd.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COMPRESS/dump_local_zstd.h b/src/COMPRESS/dump_local_zstd.h index 0dfcf87660..f5be60ef6f 100644 --- a/src/COMPRESS/dump_local_zstd.h +++ b/src/COMPRESS/dump_local_zstd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COMPRESS/dump_xyz_gz.cpp b/src/COMPRESS/dump_xyz_gz.cpp index 4b544c0d67..f4d4361de4 100644 --- a/src/COMPRESS/dump_xyz_gz.cpp +++ b/src/COMPRESS/dump_xyz_gz.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COMPRESS/dump_xyz_gz.h b/src/COMPRESS/dump_xyz_gz.h index cd4e22c0ef..ab1dc0d1e9 100644 --- a/src/COMPRESS/dump_xyz_gz.h +++ b/src/COMPRESS/dump_xyz_gz.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COMPRESS/dump_xyz_zstd.cpp b/src/COMPRESS/dump_xyz_zstd.cpp index ed87bb3f2c..976979675a 100644 --- a/src/COMPRESS/dump_xyz_zstd.cpp +++ b/src/COMPRESS/dump_xyz_zstd.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COMPRESS/dump_xyz_zstd.h b/src/COMPRESS/dump_xyz_zstd.h index 97380f6c95..705e058ed5 100644 --- a/src/COMPRESS/dump_xyz_zstd.h +++ b/src/COMPRESS/dump_xyz_zstd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COMPRESS/gz_file_writer.cpp b/src/COMPRESS/gz_file_writer.cpp index a796568e70..d458027fe6 100644 --- a/src/COMPRESS/gz_file_writer.cpp +++ b/src/COMPRESS/gz_file_writer.cpp @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COMPRESS/gz_file_writer.h b/src/COMPRESS/gz_file_writer.h index 2356675921..b43b3a9487 100644 --- a/src/COMPRESS/gz_file_writer.h +++ b/src/COMPRESS/gz_file_writer.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COMPRESS/zstd_file_writer.cpp b/src/COMPRESS/zstd_file_writer.cpp index 2485074ad9..dd7020c740 100644 --- a/src/COMPRESS/zstd_file_writer.cpp +++ b/src/COMPRESS/zstd_file_writer.cpp @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/COMPRESS/zstd_file_writer.h b/src/COMPRESS/zstd_file_writer.h index 77b3838f83..90437a2574 100644 --- a/src/COMPRESS/zstd_file_writer.h +++ b/src/COMPRESS/zstd_file_writer.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CORESHELL/compute_temp_cs.cpp b/src/CORESHELL/compute_temp_cs.cpp index e9778489fd..49e8a4dd47 100644 --- a/src/CORESHELL/compute_temp_cs.cpp +++ b/src/CORESHELL/compute_temp_cs.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -31,9 +31,6 @@ #include "modify.h" #include "update.h" -#include - - using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/CORESHELL/compute_temp_cs.h b/src/CORESHELL/compute_temp_cs.h index d8368827d5..3fdf0f3711 100644 --- a/src/CORESHELL/compute_temp_cs.h +++ b/src/CORESHELL/compute_temp_cs.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CORESHELL/pair_born_coul_dsf_cs.cpp b/src/CORESHELL/pair_born_coul_dsf_cs.cpp index bb9b9693e4..9e0ac11c78 100644 --- a/src/CORESHELL/pair_born_coul_dsf_cs.cpp +++ b/src/CORESHELL/pair_born_coul_dsf_cs.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CORESHELL/pair_born_coul_dsf_cs.h b/src/CORESHELL/pair_born_coul_dsf_cs.h index afb4becfbb..665eaa252f 100644 --- a/src/CORESHELL/pair_born_coul_dsf_cs.h +++ b/src/CORESHELL/pair_born_coul_dsf_cs.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CORESHELL/pair_born_coul_long_cs.cpp b/src/CORESHELL/pair_born_coul_long_cs.cpp index 2a89241e5f..3a3dc39d69 100644 --- a/src/CORESHELL/pair_born_coul_long_cs.cpp +++ b/src/CORESHELL/pair_born_coul_long_cs.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CORESHELL/pair_born_coul_long_cs.h b/src/CORESHELL/pair_born_coul_long_cs.h index a5b44d1729..3036306fbe 100644 --- a/src/CORESHELL/pair_born_coul_long_cs.h +++ b/src/CORESHELL/pair_born_coul_long_cs.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CORESHELL/pair_born_coul_wolf_cs.cpp b/src/CORESHELL/pair_born_coul_wolf_cs.cpp index 00d557a14e..4765e1575c 100644 --- a/src/CORESHELL/pair_born_coul_wolf_cs.cpp +++ b/src/CORESHELL/pair_born_coul_wolf_cs.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CORESHELL/pair_born_coul_wolf_cs.h b/src/CORESHELL/pair_born_coul_wolf_cs.h index 8f052ef8a7..0cda153a36 100644 --- a/src/CORESHELL/pair_born_coul_wolf_cs.h +++ b/src/CORESHELL/pair_born_coul_wolf_cs.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CORESHELL/pair_buck_coul_long_cs.cpp b/src/CORESHELL/pair_buck_coul_long_cs.cpp index 44a2f37ae8..6b15e8dfe5 100644 --- a/src/CORESHELL/pair_buck_coul_long_cs.cpp +++ b/src/CORESHELL/pair_buck_coul_long_cs.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CORESHELL/pair_buck_coul_long_cs.h b/src/CORESHELL/pair_buck_coul_long_cs.h index 0366b748a3..8f1a6ed243 100644 --- a/src/CORESHELL/pair_buck_coul_long_cs.h +++ b/src/CORESHELL/pair_buck_coul_long_cs.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CORESHELL/pair_coul_long_cs.cpp b/src/CORESHELL/pair_coul_long_cs.cpp index 9e2b87b659..5148ffda2d 100644 --- a/src/CORESHELL/pair_coul_long_cs.cpp +++ b/src/CORESHELL/pair_coul_long_cs.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CORESHELL/pair_coul_long_cs.h b/src/CORESHELL/pair_coul_long_cs.h index 6850152d2b..38f438ef0c 100644 --- a/src/CORESHELL/pair_coul_long_cs.h +++ b/src/CORESHELL/pair_coul_long_cs.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CORESHELL/pair_coul_wolf_cs.cpp b/src/CORESHELL/pair_coul_wolf_cs.cpp index 19798dd034..5e15493aad 100644 --- a/src/CORESHELL/pair_coul_wolf_cs.cpp +++ b/src/CORESHELL/pair_coul_wolf_cs.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CORESHELL/pair_coul_wolf_cs.h b/src/CORESHELL/pair_coul_wolf_cs.h index 47f3e1a716..8c44986865 100644 --- a/src/CORESHELL/pair_coul_wolf_cs.h +++ b/src/CORESHELL/pair_coul_wolf_cs.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CORESHELL/pair_lj_class2_coul_long_cs.cpp b/src/CORESHELL/pair_lj_class2_coul_long_cs.cpp index 266b91d5e3..1cbddf0614 100644 --- a/src/CORESHELL/pair_lj_class2_coul_long_cs.cpp +++ b/src/CORESHELL/pair_lj_class2_coul_long_cs.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CORESHELL/pair_lj_class2_coul_long_cs.h b/src/CORESHELL/pair_lj_class2_coul_long_cs.h index 39548f51a9..a9339959ea 100644 --- a/src/CORESHELL/pair_lj_class2_coul_long_cs.h +++ b/src/CORESHELL/pair_lj_class2_coul_long_cs.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp index 52a37f7fa0..253ae440b0 100644 --- a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp +++ b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/CORESHELL/pair_lj_cut_coul_long_cs.h b/src/CORESHELL/pair_lj_cut_coul_long_cs.h index aa47b7710b..177dab348a 100644 --- a/src/CORESHELL/pair_lj_cut_coul_long_cs.h +++ b/src/CORESHELL/pair_lj_cut_coul_long_cs.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/atom_vec_dielectric.cpp b/src/DIELECTRIC/atom_vec_dielectric.cpp index 18fcac8d1c..3b25ad4e17 100644 --- a/src/DIELECTRIC/atom_vec_dielectric.cpp +++ b/src/DIELECTRIC/atom_vec_dielectric.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/atom_vec_dielectric.h b/src/DIELECTRIC/atom_vec_dielectric.h index 9e1bff8c4d..28bf7abb33 100644 --- a/src/DIELECTRIC/atom_vec_dielectric.h +++ b/src/DIELECTRIC/atom_vec_dielectric.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,7 @@ AtomStyle(dielectric,AtomVecDielectric); namespace LAMMPS_NS { -class AtomVecDielectric : public AtomVec { +class AtomVecDielectric : virtual public AtomVec { friend class PairLJCutCoulDebyeDielectric; friend class PairLJLongCoulLongDielectric; diff --git a/src/DIELECTRIC/compute_efield_atom.cpp b/src/DIELECTRIC/compute_efield_atom.cpp index 24c29321ed..a6f2ff6d2c 100644 --- a/src/DIELECTRIC/compute_efield_atom.cpp +++ b/src/DIELECTRIC/compute_efield_atom.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/compute_efield_atom.h b/src/DIELECTRIC/compute_efield_atom.h index c38cd5860e..1c4e4ad35c 100644 --- a/src/DIELECTRIC/compute_efield_atom.h +++ b/src/DIELECTRIC/compute_efield_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/fix_polarize_bem_gmres.cpp b/src/DIELECTRIC/fix_polarize_bem_gmres.cpp index 1e5d39e828..85b23cb667 100644 --- a/src/DIELECTRIC/fix_polarize_bem_gmres.cpp +++ b/src/DIELECTRIC/fix_polarize_bem_gmres.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/fix_polarize_bem_gmres.h b/src/DIELECTRIC/fix_polarize_bem_gmres.h index e590b1b35e..a2fcfdf34f 100644 --- a/src/DIELECTRIC/fix_polarize_bem_gmres.h +++ b/src/DIELECTRIC/fix_polarize_bem_gmres.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/fix_polarize_bem_icc.cpp b/src/DIELECTRIC/fix_polarize_bem_icc.cpp index 3b30c1d0f0..0d503d87a7 100644 --- a/src/DIELECTRIC/fix_polarize_bem_icc.cpp +++ b/src/DIELECTRIC/fix_polarize_bem_icc.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/fix_polarize_bem_icc.h b/src/DIELECTRIC/fix_polarize_bem_icc.h index 4ca182259f..2d13f2dfb1 100644 --- a/src/DIELECTRIC/fix_polarize_bem_icc.h +++ b/src/DIELECTRIC/fix_polarize_bem_icc.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/fix_polarize_functional.cpp b/src/DIELECTRIC/fix_polarize_functional.cpp index af922d9168..d751bcd6ce 100644 --- a/src/DIELECTRIC/fix_polarize_functional.cpp +++ b/src/DIELECTRIC/fix_polarize_functional.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/fix_polarize_functional.h b/src/DIELECTRIC/fix_polarize_functional.h index c4cf8366e8..77acde439d 100644 --- a/src/DIELECTRIC/fix_polarize_functional.h +++ b/src/DIELECTRIC/fix_polarize_functional.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/msm_dielectric.cpp b/src/DIELECTRIC/msm_dielectric.cpp index 102f0421ca..fd09e40acc 100644 --- a/src/DIELECTRIC/msm_dielectric.cpp +++ b/src/DIELECTRIC/msm_dielectric.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -20,10 +20,9 @@ #include "atom.h" #include "atom_vec_dielectric.h" -#include "comm.h" #include "domain.h" #include "error.h" -#include "gridcomm.h" +#include "grid3d.h" #include "math_const.h" #include "memory.h" @@ -130,7 +129,7 @@ void MSMDielectric::compute(int eflag, int vflag) // to fully sum contribution in their 3d grid current_level = 0; - gcall->reverse_comm(GridComm::KSPACE,this,1,sizeof(double),REVERSE_RHO, + gcall->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(double), gcall_buf1,gcall_buf2,MPI_DOUBLE); // forward communicate charge density values to fill ghost grid points @@ -139,7 +138,7 @@ void MSMDielectric::compute(int eflag, int vflag) for (int n=0; n<=levels-2; n++) { if (!active_flag[n]) continue; current_level = n; - gc[n]->forward_comm(GridComm::KSPACE,this,1,sizeof(double),FORWARD_RHO, + gc[n]->forward_comm(Grid3d::KSPACE,this,FORWARD_RHO,1,sizeof(double), gc_buf1[n],gc_buf2[n],MPI_DOUBLE); direct(n); restriction(n); @@ -152,15 +151,15 @@ void MSMDielectric::compute(int eflag, int vflag) if (domain->nonperiodic) { current_level = levels-1; gc[levels-1]-> - forward_comm(GridComm::KSPACE,this,1,sizeof(double),FORWARD_RHO, + forward_comm(Grid3d::KSPACE,this,FORWARD_RHO,1,sizeof(double), gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE); direct_top(levels-1); gc[levels-1]-> - reverse_comm(GridComm::KSPACE,this,1,sizeof(double),REVERSE_AD, + reverse_comm(Grid3d::KSPACE,this,REVERSE_AD,1,sizeof(double), gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE); if (vflag_atom) gc[levels-1]-> - reverse_comm(GridComm::KSPACE,this,6,sizeof(double),REVERSE_AD_PERATOM, + reverse_comm(Grid3d::KSPACE,this,REVERSE_AD_PERATOM,6,sizeof(double), gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE); } else { @@ -171,7 +170,7 @@ void MSMDielectric::compute(int eflag, int vflag) current_level = levels-1; if (vflag_atom) gc[levels-1]-> - reverse_comm(GridComm::KSPACE,this,6,sizeof(double),REVERSE_AD_PERATOM, + reverse_comm(Grid3d::KSPACE,this,REVERSE_AD_PERATOM,6,sizeof(double), gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE); } } @@ -184,27 +183,27 @@ void MSMDielectric::compute(int eflag, int vflag) prolongation(n); current_level = n; - gc[n]->reverse_comm(GridComm::KSPACE,this,1,sizeof(double),REVERSE_AD, + gc[n]->reverse_comm(Grid3d::KSPACE,this,REVERSE_AD,1,sizeof(double), gc_buf1[n],gc_buf2[n],MPI_DOUBLE); // extra per-atom virial communication if (vflag_atom) - gc[n]->reverse_comm(GridComm::KSPACE,this,6,sizeof(double), - REVERSE_AD_PERATOM,gc_buf1[n],gc_buf2[n],MPI_DOUBLE); + gc[n]->reverse_comm(Grid3d::KSPACE,this,REVERSE_AD_PERATOM,6,sizeof(double), + gc_buf1[n],gc_buf2[n],MPI_DOUBLE); } // all procs communicate E-field values // to fill ghost cells surrounding their 3d bricks current_level = 0; - gcall->forward_comm(GridComm::KSPACE,this,1,sizeof(double),FORWARD_AD, + gcall->forward_comm(Grid3d::KSPACE,this,FORWARD_AD,1,sizeof(double), gcall_buf1,gcall_buf2,MPI_DOUBLE); // extra per-atom energy/virial communication if (vflag_atom) - gcall->forward_comm(GridComm::KSPACE,this,6,sizeof(double),FORWARD_AD_PERATOM, + gcall->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_PERATOM,6,sizeof(double), gcall_buf1,gcall_buf2,MPI_DOUBLE); // calculate the force on my particles (interpolation) diff --git a/src/DIELECTRIC/msm_dielectric.h b/src/DIELECTRIC/msm_dielectric.h index f5a18ec1d0..b67d64efc5 100644 --- a/src/DIELECTRIC/msm_dielectric.h +++ b/src/DIELECTRIC/msm_dielectric.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/pair_coul_cut_dielectric.cpp b/src/DIELECTRIC/pair_coul_cut_dielectric.cpp index e9d7ac3455..c44552176d 100644 --- a/src/DIELECTRIC/pair_coul_cut_dielectric.cpp +++ b/src/DIELECTRIC/pair_coul_cut_dielectric.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/pair_coul_cut_dielectric.h b/src/DIELECTRIC/pair_coul_cut_dielectric.h index 50268936b7..14959a502b 100644 --- a/src/DIELECTRIC/pair_coul_cut_dielectric.h +++ b/src/DIELECTRIC/pair_coul_cut_dielectric.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/pair_coul_long_dielectric.cpp b/src/DIELECTRIC/pair_coul_long_dielectric.cpp index da9528f8a2..a30bd6e45e 100644 --- a/src/DIELECTRIC/pair_coul_long_dielectric.cpp +++ b/src/DIELECTRIC/pair_coul_long_dielectric.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/pair_coul_long_dielectric.h b/src/DIELECTRIC/pair_coul_long_dielectric.h index 41dbeb2964..fb858fd424 100644 --- a/src/DIELECTRIC/pair_coul_long_dielectric.h +++ b/src/DIELECTRIC/pair_coul_long_dielectric.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/pair_lj_cut_coul_cut_dielectric.cpp b/src/DIELECTRIC/pair_lj_cut_coul_cut_dielectric.cpp index d02cbc0562..7433b653d9 100644 --- a/src/DIELECTRIC/pair_lj_cut_coul_cut_dielectric.cpp +++ b/src/DIELECTRIC/pair_lj_cut_coul_cut_dielectric.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/pair_lj_cut_coul_cut_dielectric.h b/src/DIELECTRIC/pair_lj_cut_coul_cut_dielectric.h index 5d88bf59ce..402d854c58 100644 --- a/src/DIELECTRIC/pair_lj_cut_coul_cut_dielectric.h +++ b/src/DIELECTRIC/pair_lj_cut_coul_cut_dielectric.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/pair_lj_cut_coul_debye_dielectric.cpp b/src/DIELECTRIC/pair_lj_cut_coul_debye_dielectric.cpp index 3f39206251..edc5ede368 100644 --- a/src/DIELECTRIC/pair_lj_cut_coul_debye_dielectric.cpp +++ b/src/DIELECTRIC/pair_lj_cut_coul_debye_dielectric.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/pair_lj_cut_coul_debye_dielectric.h b/src/DIELECTRIC/pair_lj_cut_coul_debye_dielectric.h index c70d86368d..6fcbed7452 100644 --- a/src/DIELECTRIC/pair_lj_cut_coul_debye_dielectric.h +++ b/src/DIELECTRIC/pair_lj_cut_coul_debye_dielectric.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/pair_lj_cut_coul_long_dielectric.cpp b/src/DIELECTRIC/pair_lj_cut_coul_long_dielectric.cpp index a99699883a..ab64d2bd10 100644 --- a/src/DIELECTRIC/pair_lj_cut_coul_long_dielectric.cpp +++ b/src/DIELECTRIC/pair_lj_cut_coul_long_dielectric.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/pair_lj_cut_coul_long_dielectric.h b/src/DIELECTRIC/pair_lj_cut_coul_long_dielectric.h index 139b3bc763..b7ca2cb07d 100644 --- a/src/DIELECTRIC/pair_lj_cut_coul_long_dielectric.h +++ b/src/DIELECTRIC/pair_lj_cut_coul_long_dielectric.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/pair_lj_cut_coul_msm_dielectric.cpp b/src/DIELECTRIC/pair_lj_cut_coul_msm_dielectric.cpp index ade05ddb04..4bec063e78 100644 --- a/src/DIELECTRIC/pair_lj_cut_coul_msm_dielectric.cpp +++ b/src/DIELECTRIC/pair_lj_cut_coul_msm_dielectric.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/pair_lj_cut_coul_msm_dielectric.h b/src/DIELECTRIC/pair_lj_cut_coul_msm_dielectric.h index a7cebc94c1..64a6c38639 100644 --- a/src/DIELECTRIC/pair_lj_cut_coul_msm_dielectric.h +++ b/src/DIELECTRIC/pair_lj_cut_coul_msm_dielectric.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/pair_lj_long_coul_long_dielectric.cpp b/src/DIELECTRIC/pair_lj_long_coul_long_dielectric.cpp index 1de5e8afcf..c1696170cc 100644 --- a/src/DIELECTRIC/pair_lj_long_coul_long_dielectric.cpp +++ b/src/DIELECTRIC/pair_lj_long_coul_long_dielectric.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/pair_lj_long_coul_long_dielectric.h b/src/DIELECTRIC/pair_lj_long_coul_long_dielectric.h index 50521cee60..3c1fbee3b8 100644 --- a/src/DIELECTRIC/pair_lj_long_coul_long_dielectric.h +++ b/src/DIELECTRIC/pair_lj_long_coul_long_dielectric.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/pppm_dielectric.cpp b/src/DIELECTRIC/pppm_dielectric.cpp index 589ea58a90..6b274e773d 100644 --- a/src/DIELECTRIC/pppm_dielectric.cpp +++ b/src/DIELECTRIC/pppm_dielectric.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -25,7 +25,7 @@ #include "error.h" #include "fft3d_wrap.h" #include "force.h" -#include "gridcomm.h" +#include "grid3d.h" #include "math_const.h" #include "math_special.h" #include "memory.h" @@ -134,8 +134,8 @@ void PPPMDielectric::compute(int eflag, int vflag) // to fully sum contribution in their 3d bricks // remap from 3d decomposition to FFT decomposition - gc->reverse_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR), - REVERSE_RHO,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); brick2fft(); // compute potential gradient on my FFT grid and @@ -150,21 +150,21 @@ void PPPMDielectric::compute(int eflag, int vflag) // to fill ghost cells surrounding their 3d bricks if (differentiation_flag == 1) - gc->forward_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR), - FORWARD_AD,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_AD,1,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); else - gc->forward_comm(GridComm::KSPACE,this,3,sizeof(FFT_SCALAR), - FORWARD_IK,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK,3,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); // extra per-atom energy/virial communication if (evflag_atom) { if (differentiation_flag == 1 && vflag_atom) - gc->forward_comm(GridComm::KSPACE,this,6,sizeof(FFT_SCALAR), - FORWARD_AD_PERATOM,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_PERATOM,6,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); else if (differentiation_flag == 0) - gc->forward_comm(GridComm::KSPACE,this,7,sizeof(FFT_SCALAR), - FORWARD_IK_PERATOM,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_PERATOM,7,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); } // calculate the force on my particles @@ -196,8 +196,8 @@ void PPPMDielectric::compute(int eflag, int vflag) // communicate for charge density - gc->reverse_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR), - REVERSE_RHO,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); brick2fft(); @@ -698,7 +698,6 @@ void PPPMDielectric::slabcorr() double *q = atom->q_scaled; double **x = atom->x; double *eps = atom->epsilon; - double zprd_slab = domain->zprd*slab_volfactor; int nlocal = atom->nlocal; @@ -715,7 +714,6 @@ void PPPMDielectric::slabcorr() double dipole_r2 = 0.0; if (eflag_atom || fabs(qsum) > SMALL) { - for (int i = 0; i < nlocal; i++) dipole_r2 += q[i]*x[i][2]*x[i][2]; diff --git a/src/DIELECTRIC/pppm_dielectric.h b/src/DIELECTRIC/pppm_dielectric.h index 637aa3dd8a..4221723b1c 100644 --- a/src/DIELECTRIC/pppm_dielectric.h +++ b/src/DIELECTRIC/pppm_dielectric.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIELECTRIC/pppm_disp_dielectric.cpp b/src/DIELECTRIC/pppm_disp_dielectric.cpp index d0eef2f1c1..e7cf2f410e 100644 --- a/src/DIELECTRIC/pppm_disp_dielectric.cpp +++ b/src/DIELECTRIC/pppm_disp_dielectric.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -18,14 +18,13 @@ #include "pppm_disp_dielectric.h" -#include "angle.h" #include "atom.h" #include "atom_vec_dielectric.h" #include "comm.h" #include "domain.h" #include "error.h" #include "force.h" -#include "gridcomm.h" +#include "grid3d.h" #include "math_const.h" #include "memory.h" @@ -149,8 +148,8 @@ void PPPMDispDielectric::compute(int eflag, int vflag) make_rho_c(); - gc->reverse_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR), - REVERSE_RHO,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); brick2fft(nxlo_in,nylo_in,nzlo_in,nxhi_in,nyhi_in,nzhi_in, density_brick,density_fft,work1,remap); @@ -164,14 +163,14 @@ void PPPMDispDielectric::compute(int eflag, int vflag) virial_1,vg,vg2, u_brick,v0_brick,v1_brick,v2_brick,v3_brick,v4_brick,v5_brick); - gc->forward_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR),FORWARD_AD, + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_AD,1,sizeof(FFT_SCALAR), gc_buf1,gc_buf2,MPI_FFT_SCALAR); fieldforce_c_ad(); if (vflag_atom) - gc->forward_comm(GridComm::KSPACE,this,6,sizeof(FFT_SCALAR), - FORWARD_AD_PERATOM,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_PERATOM,6,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); } else { poisson_ik(work1,work2,density_fft,fft1,fft2, @@ -183,14 +182,14 @@ void PPPMDispDielectric::compute(int eflag, int vflag) vdx_brick,vdy_brick,vdz_brick,virial_1,vg,vg2, u_brick,v0_brick,v1_brick,v2_brick,v3_brick,v4_brick,v5_brick); - gc->forward_comm(GridComm::KSPACE,this,3,sizeof(FFT_SCALAR),FORWARD_IK, + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK,3,sizeof(FFT_SCALAR), gc_buf1,gc_buf2,MPI_FFT_SCALAR); fieldforce_c_ik(); if (evflag_atom) - gc->forward_comm(GridComm::KSPACE,this,7,sizeof(FFT_SCALAR), - FORWARD_IK_PERATOM,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_PERATOM,7,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); } if (evflag_atom) fieldforce_c_peratom(); @@ -207,8 +206,8 @@ void PPPMDispDielectric::compute(int eflag, int vflag) make_rho_g(); - gc6->reverse_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR), - REVERSE_RHO_GEOM,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO_GEOM,1,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); brick2fft(nxlo_in_6,nylo_in_6,nzlo_in_6,nxhi_in_6,nyhi_in_6,nzhi_in_6, density_brick_g,density_fft_g,work1_6,remap_6); @@ -223,14 +222,13 @@ void PPPMDispDielectric::compute(int eflag, int vflag) u_brick_g,v0_brick_g,v1_brick_g,v2_brick_g, v3_brick_g,v4_brick_g,v5_brick_g); - gc6->forward_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR), - FORWARD_AD_GEOM,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_GEOM,1,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); fieldforce_g_ad(); if (vflag_atom) - gc6->forward_comm(GridComm::KSPACE,this,6,sizeof(FFT_SCALAR), - FORWARD_AD_PERATOM_GEOM, + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_PERATOM_GEOM,6,sizeof(FFT_SCALAR), gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); } else { @@ -244,14 +242,13 @@ void PPPMDispDielectric::compute(int eflag, int vflag) u_brick_g,v0_brick_g,v1_brick_g,v2_brick_g, v3_brick_g,v4_brick_g,v5_brick_g); - gc6->forward_comm(GridComm::KSPACE,this,3,sizeof(FFT_SCALAR), - FORWARD_IK_GEOM,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_GEOM,3,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); fieldforce_g_ik(); if (evflag_atom) - gc6->forward_comm(GridComm::KSPACE,this,7,sizeof(FFT_SCALAR), - FORWARD_IK_PERATOM_GEOM, + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_PERATOM_GEOM,7,sizeof(FFT_SCALAR), gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); } @@ -269,8 +266,8 @@ void PPPMDispDielectric::compute(int eflag, int vflag) make_rho_a(); - gc6->reverse_comm(GridComm::KSPACE,this,7,sizeof(FFT_SCALAR), - REVERSE_RHO_ARITH,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO_ARITH,7,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); brick2fft_a(); @@ -299,14 +296,13 @@ void PPPMDispDielectric::compute(int eflag, int vflag) u_brick_a4,v0_brick_a4,v1_brick_a4,v2_brick_a4, v3_brick_a4,v4_brick_a4,v5_brick_a4); - gc6->forward_comm(GridComm::KSPACE,this,7,sizeof(FFT_SCALAR), - FORWARD_AD_ARITH,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_ARITH,7,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); fieldforce_a_ad(); if (evflag_atom) - gc6->forward_comm(GridComm::KSPACE,this,42,sizeof(FFT_SCALAR), - FORWARD_AD_PERATOM_ARITH, + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_PERATOM_ARITH,42,sizeof(FFT_SCALAR), gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); } else { @@ -341,14 +337,13 @@ void PPPMDispDielectric::compute(int eflag, int vflag) u_brick_a4,v0_brick_a4,v1_brick_a4,v2_brick_a4, v3_brick_a4,v4_brick_a4,v5_brick_a4); - gc6->forward_comm(GridComm::KSPACE,this,21,sizeof(FFT_SCALAR), - FORWARD_IK_ARITH,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_ARITH,21,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); fieldforce_a_ik(); if (evflag_atom) - gc6->forward_comm(GridComm::KSPACE,this,49,sizeof(FFT_SCALAR), - FORWARD_IK_PERATOM_ARITH, + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_PERATOM_ARITH,49,sizeof(FFT_SCALAR), gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); } @@ -366,8 +361,8 @@ void PPPMDispDielectric::compute(int eflag, int vflag) make_rho_none(); - gc6->reverse_comm(GridComm::KSPACE,this,nsplit_alloc,sizeof(FFT_SCALAR), - REVERSE_RHO_NONE,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO_NONE,nsplit_alloc,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); brick2fft_none(); @@ -381,14 +376,13 @@ void PPPMDispDielectric::compute(int eflag, int vflag) n += 2; } - gc6->forward_comm(GridComm::KSPACE,this,1*nsplit_alloc,sizeof(FFT_SCALAR), - FORWARD_AD_NONE,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_NONE,1*nsplit_alloc,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); fieldforce_none_ad(); if (vflag_atom) - gc6->forward_comm(GridComm::KSPACE,this,6*nsplit_alloc,sizeof(FFT_SCALAR), - FORWARD_AD_PERATOM_NONE, + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_PERATOM_NONE,6*nsplit_alloc,sizeof(FFT_SCALAR), gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); } else { @@ -402,14 +396,13 @@ void PPPMDispDielectric::compute(int eflag, int vflag) n += 2; } - gc6->forward_comm(GridComm::KSPACE,this,3*nsplit_alloc,sizeof(FFT_SCALAR), - FORWARD_IK_NONE,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_NONE,3*nsplit_alloc,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); fieldforce_none_ik(); if (evflag_atom) - gc6->forward_comm(GridComm::KSPACE,this,7*nsplit_alloc,sizeof(FFT_SCALAR), - FORWARD_IK_PERATOM_NONE, + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_PERATOM_NONE,7*nsplit_alloc,sizeof(FFT_SCALAR), gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); } diff --git a/src/DIELECTRIC/pppm_disp_dielectric.h b/src/DIELECTRIC/pppm_disp_dielectric.h index 45e51b976f..c93fb6a65a 100644 --- a/src/DIELECTRIC/pppm_disp_dielectric.h +++ b/src/DIELECTRIC/pppm_disp_dielectric.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIFFRACTION/compute_saed.cpp b/src/DIFFRACTION/compute_saed.cpp index ba16b65352..1350257910 100644 --- a/src/DIFFRACTION/compute_saed.cpp +++ b/src/DIFFRACTION/compute_saed.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIFFRACTION/compute_saed.h b/src/DIFFRACTION/compute_saed.h index 379cb0d1e7..72cc678311 100644 --- a/src/DIFFRACTION/compute_saed.h +++ b/src/DIFFRACTION/compute_saed.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIFFRACTION/compute_saed_consts.h b/src/DIFFRACTION/compute_saed_consts.h index d7045718b5..c590e44ad6 100644 --- a/src/DIFFRACTION/compute_saed_consts.h +++ b/src/DIFFRACTION/compute_saed_consts.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIFFRACTION/compute_xrd.cpp b/src/DIFFRACTION/compute_xrd.cpp index 153f8fddb5..48152a7f68 100644 --- a/src/DIFFRACTION/compute_xrd.cpp +++ b/src/DIFFRACTION/compute_xrd.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIFFRACTION/compute_xrd.h b/src/DIFFRACTION/compute_xrd.h index 115ecfb6b4..e327a0ca11 100644 --- a/src/DIFFRACTION/compute_xrd.h +++ b/src/DIFFRACTION/compute_xrd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIFFRACTION/compute_xrd_consts.h b/src/DIFFRACTION/compute_xrd_consts.h index d033e5a662..39780b9a0a 100644 --- a/src/DIFFRACTION/compute_xrd_consts.h +++ b/src/DIFFRACTION/compute_xrd_consts.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIFFRACTION/fix_saed_vtk.cpp b/src/DIFFRACTION/fix_saed_vtk.cpp index 64c62164ef..b3f6693e9e 100644 --- a/src/DIFFRACTION/fix_saed_vtk.cpp +++ b/src/DIFFRACTION/fix_saed_vtk.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -407,7 +407,6 @@ void FixSAEDVTK::invoke_vector(bigint ntimestep) // Finding the intersection of the reciprical space and Ewald sphere int NROW1 = 0; - int NROW2 = 0; double dinv2 = 0.0; double r = 0.0; double K[3]; @@ -425,11 +424,9 @@ void FixSAEDVTK::invoke_vector(bigint ntimestep) fprintf(fp,"%g\n",vector_total[NROW1]/norm); fflush(fp); NROW1++; - NROW2++; } else { fprintf(fp,"%d\n",-1); fflush(fp); - NROW2++; } } } @@ -449,17 +446,14 @@ void FixSAEDVTK::invoke_vector(bigint ntimestep) if ( (r > (R_Ewald - dR_Ewald) ) && (r < (R_Ewald + dR_Ewald) )) { fprintf(fp,"%g\n",vector_total[NROW1]/norm); fflush(fp); - NROW2++; NROW1++; } else { fprintf(fp,"%d\n",-1); fflush(fp); - NROW2++; } } else { fprintf(fp,"%d\n",-1); fflush(fp); - NROW2++; } } } diff --git a/src/DIFFRACTION/fix_saed_vtk.h b/src/DIFFRACTION/fix_saed_vtk.h index d50ef01833..63f1bb4bf6 100644 --- a/src/DIFFRACTION/fix_saed_vtk.h +++ b/src/DIFFRACTION/fix_saed_vtk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIPOLE/angle_dipole.cpp b/src/DIPOLE/angle_dipole.cpp index b3d269fdb7..f6508022db 100644 --- a/src/DIPOLE/angle_dipole.cpp +++ b/src/DIPOLE/angle_dipole.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIPOLE/angle_dipole.h b/src/DIPOLE/angle_dipole.h index 6965e1ca5b..2e55722673 100644 --- a/src/DIPOLE/angle_dipole.h +++ b/src/DIPOLE/angle_dipole.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp index 2e9fd4226c..3f160787b2 100644 --- a/src/DIPOLE/atom_vec_dipole.cpp +++ b/src/DIPOLE/atom_vec_dipole.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIPOLE/atom_vec_dipole.h b/src/DIPOLE/atom_vec_dipole.h index 786b884cfe..923454a39f 100644 --- a/src/DIPOLE/atom_vec_dipole.h +++ b/src/DIPOLE/atom_vec_dipole.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,7 @@ AtomStyle(dipole,AtomVecDipole); namespace LAMMPS_NS { -class AtomVecDipole : public AtomVec { +class AtomVecDipole : virtual public AtomVec { public: AtomVecDipole(class LAMMPS *); diff --git a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp index 6f0ed58520..a7e5674a88 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIPOLE/pair_lj_cut_dipole_cut.h b/src/DIPOLE/pair_lj_cut_dipole_cut.h index f42662aa60..e563077835 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_cut.h +++ b/src/DIPOLE/pair_lj_cut_dipole_cut.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIPOLE/pair_lj_cut_dipole_long.cpp b/src/DIPOLE/pair_lj_cut_dipole_long.cpp index 6d6ddb748a..a1976221d0 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_long.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + LAMMPS development team: developers@lammps.org, Sandia National Laboratories Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIPOLE/pair_lj_cut_dipole_long.h b/src/DIPOLE/pair_lj_cut_dipole_long.h index 03f4c1561c..288d927da7 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_long.h +++ b/src/DIPOLE/pair_lj_cut_dipole_long.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - www.cs.sandia.gov/~sjplimp/lammps.html - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIPOLE/pair_lj_long_dipole_long.cpp b/src/DIPOLE/pair_lj_long_dipole_long.cpp index 76dc487528..1ed4a8c8d7 100644 --- a/src/DIPOLE/pair_lj_long_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_long_dipole_long.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIPOLE/pair_lj_long_dipole_long.h b/src/DIPOLE/pair_lj_long_dipole_long.h index faf0c3898c..c60b832914 100644 --- a/src/DIPOLE/pair_lj_long_dipole_long.h +++ b/src/DIPOLE/pair_lj_long_dipole_long.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIPOLE/pair_lj_sf_dipole_sf.cpp b/src/DIPOLE/pair_lj_sf_dipole_sf.cpp index f32f50461c..1cd84ed490 100644 --- a/src/DIPOLE/pair_lj_sf_dipole_sf.cpp +++ b/src/DIPOLE/pair_lj_sf_dipole_sf.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DIPOLE/pair_lj_sf_dipole_sf.h b/src/DIPOLE/pair_lj_sf_dipole_sf.h index 783ec00ad8..892c227a7a 100644 --- a/src/DIPOLE/pair_lj_sf_dipole_sf.h +++ b/src/DIPOLE/pair_lj_sf_dipole_sf.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-BASIC/pair_dpd.cpp b/src/DPD-BASIC/pair_dpd.cpp index b16be8d212..ef7b87d8c9 100644 --- a/src/DPD-BASIC/pair_dpd.cpp +++ b/src/DPD-BASIC/pair_dpd.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-BASIC/pair_dpd.h b/src/DPD-BASIC/pair_dpd.h index 4da94ae8d1..7d99726c7b 100644 --- a/src/DPD-BASIC/pair_dpd.h +++ b/src/DPD-BASIC/pair_dpd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-BASIC/pair_dpd_ext.cpp b/src/DPD-BASIC/pair_dpd_ext.cpp index 19cce06d5e..de66ab2a9a 100644 --- a/src/DPD-BASIC/pair_dpd_ext.cpp +++ b/src/DPD-BASIC/pair_dpd_ext.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-BASIC/pair_dpd_ext.h b/src/DPD-BASIC/pair_dpd_ext.h index 40377ac310..e7d86ef3bf 100644 --- a/src/DPD-BASIC/pair_dpd_ext.h +++ b/src/DPD-BASIC/pair_dpd_ext.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -49,7 +49,6 @@ class PairDPDExt : public Pair { double **sigma, **sigmaT; double **ws, **wsT; class RanMars *random; - virtual void allocate(); }; diff --git a/src/DPD-BASIC/pair_dpd_ext_tstat.cpp b/src/DPD-BASIC/pair_dpd_ext_tstat.cpp index df012065d6..c205a08c4a 100644 --- a/src/DPD-BASIC/pair_dpd_ext_tstat.cpp +++ b/src/DPD-BASIC/pair_dpd_ext_tstat.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-BASIC/pair_dpd_ext_tstat.h b/src/DPD-BASIC/pair_dpd_ext_tstat.h index 94ef466f0d..daae388aa6 100644 --- a/src/DPD-BASIC/pair_dpd_ext_tstat.h +++ b/src/DPD-BASIC/pair_dpd_ext_tstat.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -40,8 +40,6 @@ class PairDPDExtTstat : public PairDPDExt { protected: double t_start, t_stop; }; - } // namespace LAMMPS_NS - #endif #endif diff --git a/src/DPD-BASIC/pair_dpd_tstat.cpp b/src/DPD-BASIC/pair_dpd_tstat.cpp index 502241db73..fdc43de8de 100644 --- a/src/DPD-BASIC/pair_dpd_tstat.cpp +++ b/src/DPD-BASIC/pair_dpd_tstat.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-BASIC/pair_dpd_tstat.h b/src/DPD-BASIC/pair_dpd_tstat.h index b7d985253d..ab3824b55d 100644 --- a/src/DPD-BASIC/pair_dpd_tstat.h +++ b/src/DPD-BASIC/pair_dpd_tstat.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/atom_vec_edpd.cpp b/src/DPD-MESO/atom_vec_edpd.cpp index d8592d26f5..fca42e00e4 100644 --- a/src/DPD-MESO/atom_vec_edpd.cpp +++ b/src/DPD-MESO/atom_vec_edpd.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/atom_vec_edpd.h b/src/DPD-MESO/atom_vec_edpd.h index fb47fba628..43da20be70 100644 --- a/src/DPD-MESO/atom_vec_edpd.h +++ b/src/DPD-MESO/atom_vec_edpd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,7 @@ AtomStyle(edpd,AtomVecEDPD); namespace LAMMPS_NS { -class AtomVecEDPD : public AtomVec { +class AtomVecEDPD : virtual public AtomVec { public: AtomVecEDPD(class LAMMPS *); void init() override; diff --git a/src/DPD-MESO/atom_vec_mdpd.cpp b/src/DPD-MESO/atom_vec_mdpd.cpp index 4b9b58b0d6..5690b99fb6 100644 --- a/src/DPD-MESO/atom_vec_mdpd.cpp +++ b/src/DPD-MESO/atom_vec_mdpd.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/atom_vec_mdpd.h b/src/DPD-MESO/atom_vec_mdpd.h index 1d7bc3db71..9c2f293ba7 100644 --- a/src/DPD-MESO/atom_vec_mdpd.h +++ b/src/DPD-MESO/atom_vec_mdpd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,7 @@ AtomStyle(mdpd,AtomVecMDPD); namespace LAMMPS_NS { -class AtomVecMDPD : public AtomVec { +class AtomVecMDPD : virtual public AtomVec { public: AtomVecMDPD(class LAMMPS *); void init() override; diff --git a/src/DPD-MESO/atom_vec_tdpd.cpp b/src/DPD-MESO/atom_vec_tdpd.cpp index bbd6bc89bc..b401064b6a 100644 --- a/src/DPD-MESO/atom_vec_tdpd.cpp +++ b/src/DPD-MESO/atom_vec_tdpd.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/atom_vec_tdpd.h b/src/DPD-MESO/atom_vec_tdpd.h index 1daea09628..8bed9eb3a7 100644 --- a/src/DPD-MESO/atom_vec_tdpd.h +++ b/src/DPD-MESO/atom_vec_tdpd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,7 @@ AtomStyle(tdpd,AtomVecTDPD); namespace LAMMPS_NS { -class AtomVecTDPD : public AtomVec { +class AtomVecTDPD : virtual public AtomVec { public: AtomVecTDPD(class LAMMPS *); void process_args(int, char **) override; diff --git a/src/DPD-MESO/compute_edpd_temp_atom.cpp b/src/DPD-MESO/compute_edpd_temp_atom.cpp index 951473a62b..c24b726248 100644 --- a/src/DPD-MESO/compute_edpd_temp_atom.cpp +++ b/src/DPD-MESO/compute_edpd_temp_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/compute_edpd_temp_atom.h b/src/DPD-MESO/compute_edpd_temp_atom.h index a361698be9..02c11d2e78 100644 --- a/src/DPD-MESO/compute_edpd_temp_atom.h +++ b/src/DPD-MESO/compute_edpd_temp_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/compute_tdpd_cc_atom.cpp b/src/DPD-MESO/compute_tdpd_cc_atom.cpp index ccf83c9aad..4827308ef1 100644 --- a/src/DPD-MESO/compute_tdpd_cc_atom.cpp +++ b/src/DPD-MESO/compute_tdpd_cc_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/compute_tdpd_cc_atom.h b/src/DPD-MESO/compute_tdpd_cc_atom.h index 403e32c6d5..7a11d3cd6c 100644 --- a/src/DPD-MESO/compute_tdpd_cc_atom.h +++ b/src/DPD-MESO/compute_tdpd_cc_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/fix_edpd_source.cpp b/src/DPD-MESO/fix_edpd_source.cpp index 83ff896ff9..cd54521ce2 100644 --- a/src/DPD-MESO/fix_edpd_source.cpp +++ b/src/DPD-MESO/fix_edpd_source.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/fix_edpd_source.h b/src/DPD-MESO/fix_edpd_source.h index 73c0e13c56..6fd3566319 100644 --- a/src/DPD-MESO/fix_edpd_source.h +++ b/src/DPD-MESO/fix_edpd_source.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/fix_mvv_dpd.cpp b/src/DPD-MESO/fix_mvv_dpd.cpp index d96031c9f9..c475fa6651 100644 --- a/src/DPD-MESO/fix_mvv_dpd.cpp +++ b/src/DPD-MESO/fix_mvv_dpd.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/fix_mvv_dpd.h b/src/DPD-MESO/fix_mvv_dpd.h index e6cf370de6..d398adbf54 100644 --- a/src/DPD-MESO/fix_mvv_dpd.h +++ b/src/DPD-MESO/fix_mvv_dpd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/fix_mvv_edpd.cpp b/src/DPD-MESO/fix_mvv_edpd.cpp index 9b31bc4c5d..ac8ee858e3 100644 --- a/src/DPD-MESO/fix_mvv_edpd.cpp +++ b/src/DPD-MESO/fix_mvv_edpd.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/fix_mvv_edpd.h b/src/DPD-MESO/fix_mvv_edpd.h index 00b52e02b8..e2a2dbe25b 100644 --- a/src/DPD-MESO/fix_mvv_edpd.h +++ b/src/DPD-MESO/fix_mvv_edpd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/fix_mvv_tdpd.cpp b/src/DPD-MESO/fix_mvv_tdpd.cpp index 1a0dc5d520..d579dc778a 100644 --- a/src/DPD-MESO/fix_mvv_tdpd.cpp +++ b/src/DPD-MESO/fix_mvv_tdpd.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/fix_mvv_tdpd.h b/src/DPD-MESO/fix_mvv_tdpd.h index 4cdd66b01e..225055bf32 100644 --- a/src/DPD-MESO/fix_mvv_tdpd.h +++ b/src/DPD-MESO/fix_mvv_tdpd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/fix_tdpd_source.cpp b/src/DPD-MESO/fix_tdpd_source.cpp index 80848d553d..053d96568b 100644 --- a/src/DPD-MESO/fix_tdpd_source.cpp +++ b/src/DPD-MESO/fix_tdpd_source.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/fix_tdpd_source.h b/src/DPD-MESO/fix_tdpd_source.h index f20bed4f74..d19c5bb2fc 100644 --- a/src/DPD-MESO/fix_tdpd_source.h +++ b/src/DPD-MESO/fix_tdpd_source.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/pair_edpd.cpp b/src/DPD-MESO/pair_edpd.cpp index 13cbed2ece..ed99a5eac1 100644 --- a/src/DPD-MESO/pair_edpd.cpp +++ b/src/DPD-MESO/pair_edpd.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/pair_edpd.h b/src/DPD-MESO/pair_edpd.h index 055fdfdadc..d9cc10c48a 100644 --- a/src/DPD-MESO/pair_edpd.h +++ b/src/DPD-MESO/pair_edpd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/pair_mdpd.cpp b/src/DPD-MESO/pair_mdpd.cpp index c08ac2dde3..767fddd7ac 100644 --- a/src/DPD-MESO/pair_mdpd.cpp +++ b/src/DPD-MESO/pair_mdpd.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/pair_mdpd.h b/src/DPD-MESO/pair_mdpd.h index b95e257043..9ad63d7c77 100644 --- a/src/DPD-MESO/pair_mdpd.h +++ b/src/DPD-MESO/pair_mdpd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/pair_mdpd_rhosum.cpp b/src/DPD-MESO/pair_mdpd_rhosum.cpp index 773248a212..6dbeaf2125 100644 --- a/src/DPD-MESO/pair_mdpd_rhosum.cpp +++ b/src/DPD-MESO/pair_mdpd_rhosum.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/pair_mdpd_rhosum.h b/src/DPD-MESO/pair_mdpd_rhosum.h index e7bc7dec23..6dced585a4 100644 --- a/src/DPD-MESO/pair_mdpd_rhosum.h +++ b/src/DPD-MESO/pair_mdpd_rhosum.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/pair_tdpd.cpp b/src/DPD-MESO/pair_tdpd.cpp index 6efe3f4546..eac5bd1318 100644 --- a/src/DPD-MESO/pair_tdpd.cpp +++ b/src/DPD-MESO/pair_tdpd.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-MESO/pair_tdpd.h b/src/DPD-MESO/pair_tdpd.h index 34bed64abc..a1c35c52f5 100644 --- a/src/DPD-MESO/pair_tdpd.h +++ b/src/DPD-MESO/pair_tdpd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/atom_vec_dpd.cpp b/src/DPD-REACT/atom_vec_dpd.cpp index 7fae4c8ff8..a6fc81d1ee 100644 --- a/src/DPD-REACT/atom_vec_dpd.cpp +++ b/src/DPD-REACT/atom_vec_dpd.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/atom_vec_dpd.h b/src/DPD-REACT/atom_vec_dpd.h index 8710d133ad..7b50e26236 100644 --- a/src/DPD-REACT/atom_vec_dpd.h +++ b/src/DPD-REACT/atom_vec_dpd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,7 @@ AtomStyle(dpd,AtomVecDPD); namespace LAMMPS_NS { -class AtomVecDPD : public AtomVec { +class AtomVecDPD : virtual public AtomVec { public: AtomVecDPD(class LAMMPS *); @@ -32,7 +32,7 @@ class AtomVecDPD : public AtomVec { void unpack_restart_init(int) override; void data_atom_post(int) override; - private: + protected: double *rho, *dpdTheta; double *uCond, *uMech, *uChem; double *uCG, *uCGnew; diff --git a/src/DPD-REACT/compute_dpd.cpp b/src/DPD-REACT/compute_dpd.cpp index f6848b9834..1f6e6bb0ec 100644 --- a/src/DPD-REACT/compute_dpd.cpp +++ b/src/DPD-REACT/compute_dpd.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/compute_dpd.h b/src/DPD-REACT/compute_dpd.h index 269c9919a0..1e5ac77535 100644 --- a/src/DPD-REACT/compute_dpd.h +++ b/src/DPD-REACT/compute_dpd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/compute_dpd_atom.cpp b/src/DPD-REACT/compute_dpd_atom.cpp index f881612447..1c1381d27d 100644 --- a/src/DPD-REACT/compute_dpd_atom.cpp +++ b/src/DPD-REACT/compute_dpd_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/compute_dpd_atom.h b/src/DPD-REACT/compute_dpd_atom.h index 817e8145c3..5c3a8f8574 100644 --- a/src/DPD-REACT/compute_dpd_atom.h +++ b/src/DPD-REACT/compute_dpd_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/fix_dpd_energy.cpp b/src/DPD-REACT/fix_dpd_energy.cpp index c8dbf15bc4..cb74a897be 100644 --- a/src/DPD-REACT/fix_dpd_energy.cpp +++ b/src/DPD-REACT/fix_dpd_energy.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/fix_dpd_energy.h b/src/DPD-REACT/fix_dpd_energy.h index 39236e1d36..ec4be01061 100644 --- a/src/DPD-REACT/fix_dpd_energy.h +++ b/src/DPD-REACT/fix_dpd_energy.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/fix_eos_cv.cpp b/src/DPD-REACT/fix_eos_cv.cpp index 396a8b3e32..d0eb7e8db0 100644 --- a/src/DPD-REACT/fix_eos_cv.cpp +++ b/src/DPD-REACT/fix_eos_cv.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/fix_eos_cv.h b/src/DPD-REACT/fix_eos_cv.h index 9795cc763e..03ace67266 100644 --- a/src/DPD-REACT/fix_eos_cv.h +++ b/src/DPD-REACT/fix_eos_cv.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/fix_eos_table.cpp b/src/DPD-REACT/fix_eos_table.cpp index 17158e5a51..5e8ecf5536 100644 --- a/src/DPD-REACT/fix_eos_table.cpp +++ b/src/DPD-REACT/fix_eos_table.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/fix_eos_table.h b/src/DPD-REACT/fix_eos_table.h index 882b9ba284..c61cce92ce 100644 --- a/src/DPD-REACT/fix_eos_table.h +++ b/src/DPD-REACT/fix_eos_table.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/fix_eos_table_rx.cpp b/src/DPD-REACT/fix_eos_table_rx.cpp index a2f8893b82..2687a11658 100644 --- a/src/DPD-REACT/fix_eos_table_rx.cpp +++ b/src/DPD-REACT/fix_eos_table_rx.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/fix_eos_table_rx.h b/src/DPD-REACT/fix_eos_table_rx.h index bd6c1a0653..50712579c1 100644 --- a/src/DPD-REACT/fix_eos_table_rx.h +++ b/src/DPD-REACT/fix_eos_table_rx.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/fix_rx.cpp b/src/DPD-REACT/fix_rx.cpp index c54a8acee1..96eb9d4572 100644 --- a/src/DPD-REACT/fix_rx.cpp +++ b/src/DPD-REACT/fix_rx.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -390,7 +390,6 @@ void FixRX::initSparse() int mxprod = 0; int mxreac = 0; int mxspec = 0; - int nIntegral = 0; for (int i = 0; i < nreactions; ++i) { int nreac_i = 0, nprod_i = 0; std::string pstr, rstr; @@ -430,7 +429,6 @@ void FixRX::initSparse() mxreac = std::max( mxreac, nreac_i ); mxprod = std::max( mxprod, nprod_i ); mxspec = std::max( mxspec, nreac_i + nprod_i ); - if (allAreIntegral) nIntegral++; } if (comm->me == 0 && Verbosity > 1) { diff --git a/src/DPD-REACT/fix_rx.h b/src/DPD-REACT/fix_rx.h index d3e4545ed5..b6bc47dfa8 100644 --- a/src/DPD-REACT/fix_rx.h +++ b/src/DPD-REACT/fix_rx.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/fix_shardlow.cpp b/src/DPD-REACT/fix_shardlow.cpp index 824386019d..19f2c08a5f 100644 --- a/src/DPD-REACT/fix_shardlow.cpp +++ b/src/DPD-REACT/fix_shardlow.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/fix_shardlow.h b/src/DPD-REACT/fix_shardlow.h index 40cc22eec1..0086874e31 100644 --- a/src/DPD-REACT/fix_shardlow.h +++ b/src/DPD-REACT/fix_shardlow.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/nbin_ssa.cpp b/src/DPD-REACT/nbin_ssa.cpp index c6ef22fe7d..fc04021891 100644 --- a/src/DPD-REACT/nbin_ssa.cpp +++ b/src/DPD-REACT/nbin_ssa.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/nbin_ssa.h b/src/DPD-REACT/nbin_ssa.h index f6c60b1a79..7d0c069d32 100644 --- a/src/DPD-REACT/nbin_ssa.h +++ b/src/DPD-REACT/nbin_ssa.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/npair_half_bin_newton_ssa.cpp b/src/DPD-REACT/npair_half_bin_newton_ssa.cpp index 2f36b467e0..ce405da3ac 100644 --- a/src/DPD-REACT/npair_half_bin_newton_ssa.cpp +++ b/src/DPD-REACT/npair_half_bin_newton_ssa.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/npair_half_bin_newton_ssa.h b/src/DPD-REACT/npair_half_bin_newton_ssa.h index dae45742f4..5d8872c42f 100644 --- a/src/DPD-REACT/npair_half_bin_newton_ssa.h +++ b/src/DPD-REACT/npair_half_bin_newton_ssa.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/nstencil_half_bin_2d_ssa.cpp b/src/DPD-REACT/nstencil_half_bin_2d_ssa.cpp index 810802e43d..e8d487ef17 100644 --- a/src/DPD-REACT/nstencil_half_bin_2d_ssa.cpp +++ b/src/DPD-REACT/nstencil_half_bin_2d_ssa.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/nstencil_half_bin_2d_ssa.h b/src/DPD-REACT/nstencil_half_bin_2d_ssa.h index 52e3d645c1..1939fd3179 100644 --- a/src/DPD-REACT/nstencil_half_bin_2d_ssa.h +++ b/src/DPD-REACT/nstencil_half_bin_2d_ssa.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/nstencil_half_bin_3d_ssa.cpp b/src/DPD-REACT/nstencil_half_bin_3d_ssa.cpp index 9530ea44c6..877fda75d3 100644 --- a/src/DPD-REACT/nstencil_half_bin_3d_ssa.cpp +++ b/src/DPD-REACT/nstencil_half_bin_3d_ssa.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/nstencil_half_bin_3d_ssa.h b/src/DPD-REACT/nstencil_half_bin_3d_ssa.h index dcaaaa91e9..250a9da4d8 100644 --- a/src/DPD-REACT/nstencil_half_bin_3d_ssa.h +++ b/src/DPD-REACT/nstencil_half_bin_3d_ssa.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/nstencil_ssa.h b/src/DPD-REACT/nstencil_ssa.h index a1438f5dac..e2a2e5e968 100644 --- a/src/DPD-REACT/nstencil_ssa.h +++ b/src/DPD-REACT/nstencil_ssa.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/pair_dpd_fdt.cpp b/src/DPD-REACT/pair_dpd_fdt.cpp index a39198710d..e6cab0e996 100644 --- a/src/DPD-REACT/pair_dpd_fdt.cpp +++ b/src/DPD-REACT/pair_dpd_fdt.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/pair_dpd_fdt.h b/src/DPD-REACT/pair_dpd_fdt.h index 6b488d0820..4458acc41b 100644 --- a/src/DPD-REACT/pair_dpd_fdt.h +++ b/src/DPD-REACT/pair_dpd_fdt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/pair_dpd_fdt_energy.cpp b/src/DPD-REACT/pair_dpd_fdt_energy.cpp index 02396a07f1..d3371f465a 100644 --- a/src/DPD-REACT/pair_dpd_fdt_energy.cpp +++ b/src/DPD-REACT/pair_dpd_fdt_energy.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/pair_dpd_fdt_energy.h b/src/DPD-REACT/pair_dpd_fdt_energy.h index dcebc2d683..df1a98b968 100644 --- a/src/DPD-REACT/pair_dpd_fdt_energy.h +++ b/src/DPD-REACT/pair_dpd_fdt_energy.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/pair_exp6_rx.cpp b/src/DPD-REACT/pair_exp6_rx.cpp index 02d4e84e9e..c6b831f84b 100644 --- a/src/DPD-REACT/pair_exp6_rx.cpp +++ b/src/DPD-REACT/pair_exp6_rx.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/pair_exp6_rx.h b/src/DPD-REACT/pair_exp6_rx.h index d965b8031e..72350bc3a8 100644 --- a/src/DPD-REACT/pair_exp6_rx.h +++ b/src/DPD-REACT/pair_exp6_rx.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/pair_multi_lucy.cpp b/src/DPD-REACT/pair_multi_lucy.cpp index bb6792da74..db3376fb9f 100644 --- a/src/DPD-REACT/pair_multi_lucy.cpp +++ b/src/DPD-REACT/pair_multi_lucy.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/pair_multi_lucy.h b/src/DPD-REACT/pair_multi_lucy.h index a5ee9641fd..922cd49bcb 100644 --- a/src/DPD-REACT/pair_multi_lucy.h +++ b/src/DPD-REACT/pair_multi_lucy.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/pair_multi_lucy_rx.cpp b/src/DPD-REACT/pair_multi_lucy_rx.cpp index c2a3f1a55e..234cbf5ae2 100644 --- a/src/DPD-REACT/pair_multi_lucy_rx.cpp +++ b/src/DPD-REACT/pair_multi_lucy_rx.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/pair_multi_lucy_rx.h b/src/DPD-REACT/pair_multi_lucy_rx.h index 4179d5f4a8..2b68a9e2ba 100644 --- a/src/DPD-REACT/pair_multi_lucy_rx.h +++ b/src/DPD-REACT/pair_multi_lucy_rx.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/pair_table_rx.cpp b/src/DPD-REACT/pair_table_rx.cpp index fedc5fa879..dffb57d4bc 100644 --- a/src/DPD-REACT/pair_table_rx.cpp +++ b/src/DPD-REACT/pair_table_rx.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/pair_table_rx.h b/src/DPD-REACT/pair_table_rx.h index 6a97125c19..9b629c392d 100644 --- a/src/DPD-REACT/pair_table_rx.h +++ b/src/DPD-REACT/pair_table_rx.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-REACT/random_external_state.h b/src/DPD-REACT/random_external_state.h index 539a20e55a..9c5958e243 100644 --- a/src/DPD-REACT/random_external_state.h +++ b/src/DPD-REACT/random_external_state.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-SMOOTH/fix_meso_move.cpp b/src/DPD-SMOOTH/fix_meso_move.cpp index 078274416d..2c3213c3cd 100644 --- a/src/DPD-SMOOTH/fix_meso_move.cpp +++ b/src/DPD-SMOOTH/fix_meso_move.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-SMOOTH/fix_meso_move.h b/src/DPD-SMOOTH/fix_meso_move.h index 2ad945bd5b..9220f0cadf 100644 --- a/src/DPD-SMOOTH/fix_meso_move.h +++ b/src/DPD-SMOOTH/fix_meso_move.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-SMOOTH/fix_rigid_meso.cpp b/src/DPD-SMOOTH/fix_rigid_meso.cpp index 7f5a069f38..e0ad501e02 100644 --- a/src/DPD-SMOOTH/fix_rigid_meso.cpp +++ b/src/DPD-SMOOTH/fix_rigid_meso.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-SMOOTH/fix_rigid_meso.h b/src/DPD-SMOOTH/fix_rigid_meso.h index 5ef8aa7baf..ad6085ec79 100644 --- a/src/DPD-SMOOTH/fix_rigid_meso.h +++ b/src/DPD-SMOOTH/fix_rigid_meso.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.cpp b/src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.cpp index 7a36cdfc5c..2deeefe90e 100644 --- a/src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.cpp +++ b/src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.h b/src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.h index 475ac1fb53..0708497dc2 100644 --- a/src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.h +++ b/src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DRUDE/compute_temp_drude.cpp b/src/DRUDE/compute_temp_drude.cpp index 18a924ba17..b309346934 100644 --- a/src/DRUDE/compute_temp_drude.cpp +++ b/src/DRUDE/compute_temp_drude.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DRUDE/compute_temp_drude.h b/src/DRUDE/compute_temp_drude.h index 16a9a46652..096bb7ae54 100644 --- a/src/DRUDE/compute_temp_drude.h +++ b/src/DRUDE/compute_temp_drude.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DRUDE/fix_drude.cpp b/src/DRUDE/fix_drude.cpp index 70b36a63ee..56a5cd42f6 100644 --- a/src/DRUDE/fix_drude.cpp +++ b/src/DRUDE/fix_drude.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DRUDE/fix_drude.h b/src/DRUDE/fix_drude.h index fcec09a419..9629e8255b 100644 --- a/src/DRUDE/fix_drude.h +++ b/src/DRUDE/fix_drude.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DRUDE/fix_drude_transform.cpp b/src/DRUDE/fix_drude_transform.cpp index 642f5aabf8..a301a0cbea 100644 --- a/src/DRUDE/fix_drude_transform.cpp +++ b/src/DRUDE/fix_drude_transform.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DRUDE/fix_drude_transform.h b/src/DRUDE/fix_drude_transform.h index 28c2aa0643..8c154faef8 100644 --- a/src/DRUDE/fix_drude_transform.h +++ b/src/DRUDE/fix_drude_transform.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DRUDE/fix_langevin_drude.cpp b/src/DRUDE/fix_langevin_drude.cpp index 622aa77f9f..1b165c029a 100644 --- a/src/DRUDE/fix_langevin_drude.cpp +++ b/src/DRUDE/fix_langevin_drude.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DRUDE/fix_langevin_drude.h b/src/DRUDE/fix_langevin_drude.h index 38bc417929..de401aaea8 100644 --- a/src/DRUDE/fix_langevin_drude.h +++ b/src/DRUDE/fix_langevin_drude.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DRUDE/fix_tgnh_drude.cpp b/src/DRUDE/fix_tgnh_drude.cpp index 779b557fcf..273f163303 100644 --- a/src/DRUDE/fix_tgnh_drude.cpp +++ b/src/DRUDE/fix_tgnh_drude.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DRUDE/fix_tgnh_drude.h b/src/DRUDE/fix_tgnh_drude.h index 634a8a2cc1..adfa69671a 100644 --- a/src/DRUDE/fix_tgnh_drude.h +++ b/src/DRUDE/fix_tgnh_drude.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DRUDE/fix_tgnpt_drude.cpp b/src/DRUDE/fix_tgnpt_drude.cpp index f9df2ed93b..52da72708c 100644 --- a/src/DRUDE/fix_tgnpt_drude.cpp +++ b/src/DRUDE/fix_tgnpt_drude.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DRUDE/fix_tgnpt_drude.h b/src/DRUDE/fix_tgnpt_drude.h index 19b44296c0..4f1a66fe33 100644 --- a/src/DRUDE/fix_tgnpt_drude.h +++ b/src/DRUDE/fix_tgnpt_drude.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DRUDE/fix_tgnvt_drude.cpp b/src/DRUDE/fix_tgnvt_drude.cpp index ac4f8d4845..8c7354a7b8 100644 --- a/src/DRUDE/fix_tgnvt_drude.cpp +++ b/src/DRUDE/fix_tgnvt_drude.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DRUDE/fix_tgnvt_drude.h b/src/DRUDE/fix_tgnvt_drude.h index 836b2a3369..b2d266caa7 100644 --- a/src/DRUDE/fix_tgnvt_drude.h +++ b/src/DRUDE/fix_tgnvt_drude.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DRUDE/pair_coul_tt.cpp b/src/DRUDE/pair_coul_tt.cpp index 9d8395b535..b8814265b6 100644 --- a/src/DRUDE/pair_coul_tt.cpp +++ b/src/DRUDE/pair_coul_tt.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DRUDE/pair_coul_tt.h b/src/DRUDE/pair_coul_tt.h index adb86c8129..4c99c2924c 100644 --- a/src/DRUDE/pair_coul_tt.h +++ b/src/DRUDE/pair_coul_tt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DRUDE/pair_lj_cut_thole_long.cpp b/src/DRUDE/pair_lj_cut_thole_long.cpp index 581496a1f5..60913dc4f5 100644 --- a/src/DRUDE/pair_lj_cut_thole_long.cpp +++ b/src/DRUDE/pair_lj_cut_thole_long.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DRUDE/pair_lj_cut_thole_long.h b/src/DRUDE/pair_lj_cut_thole_long.h index 3cacb6222d..dd7b3f8b61 100644 --- a/src/DRUDE/pair_lj_cut_thole_long.h +++ b/src/DRUDE/pair_lj_cut_thole_long.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DRUDE/pair_thole.cpp b/src/DRUDE/pair_thole.cpp index 79f7c8557a..4039fd72fa 100644 --- a/src/DRUDE/pair_thole.cpp +++ b/src/DRUDE/pair_thole.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/DRUDE/pair_thole.h b/src/DRUDE/pair_thole.h index ef4d493ce1..18a8da5181 100644 --- a/src/DRUDE/pair_thole.h +++ b/src/DRUDE/pair_thole.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/atom_vec_electron.cpp b/src/EFF/atom_vec_electron.cpp index 83772df700..d763ff0671 100644 --- a/src/EFF/atom_vec_electron.cpp +++ b/src/EFF/atom_vec_electron.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -20,6 +20,8 @@ #include "atom.h" #include "citeme.h" +#include + using namespace LAMMPS_NS; static const char cite_user_eff_package[] = diff --git a/src/EFF/atom_vec_electron.h b/src/EFF/atom_vec_electron.h index 21015d56b0..3c268182bc 100644 --- a/src/EFF/atom_vec_electron.h +++ b/src/EFF/atom_vec_electron.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,7 @@ AtomStyle(electron,AtomVecElectron); namespace LAMMPS_NS { -class AtomVecElectron : public AtomVec { +class AtomVecElectron : virtual public AtomVec { public: AtomVecElectron(class LAMMPS *); diff --git a/src/EFF/compute_ke_atom_eff.cpp b/src/EFF/compute_ke_atom_eff.cpp index cb6e489fc1..0bf20f6d1a 100644 --- a/src/EFF/compute_ke_atom_eff.cpp +++ b/src/EFF/compute_ke_atom_eff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/compute_ke_atom_eff.h b/src/EFF/compute_ke_atom_eff.h index b5ad27b524..fcf4ec8a76 100644 --- a/src/EFF/compute_ke_atom_eff.h +++ b/src/EFF/compute_ke_atom_eff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/compute_ke_eff.cpp b/src/EFF/compute_ke_eff.cpp index 621b186887..4cb925a5e0 100644 --- a/src/EFF/compute_ke_eff.cpp +++ b/src/EFF/compute_ke_eff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/compute_ke_eff.h b/src/EFF/compute_ke_eff.h index cc5baa863f..36f99bbde9 100644 --- a/src/EFF/compute_ke_eff.h +++ b/src/EFF/compute_ke_eff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/compute_temp_deform_eff.cpp b/src/EFF/compute_temp_deform_eff.cpp index 66452bb95c..a6a841ce12 100644 --- a/src/EFF/compute_temp_deform_eff.cpp +++ b/src/EFF/compute_temp_deform_eff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/compute_temp_deform_eff.h b/src/EFF/compute_temp_deform_eff.h index 5490abd9ca..0e12304bcc 100644 --- a/src/EFF/compute_temp_deform_eff.h +++ b/src/EFF/compute_temp_deform_eff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/compute_temp_eff.cpp b/src/EFF/compute_temp_eff.cpp index 6ce6d5f671..f04f8224cf 100644 --- a/src/EFF/compute_temp_eff.cpp +++ b/src/EFF/compute_temp_eff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/compute_temp_eff.h b/src/EFF/compute_temp_eff.h index bc2bbc3597..f3a83b3ca9 100644 --- a/src/EFF/compute_temp_eff.h +++ b/src/EFF/compute_temp_eff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/compute_temp_region_eff.cpp b/src/EFF/compute_temp_region_eff.cpp index de61abc4b7..ff20d48124 100644 --- a/src/EFF/compute_temp_region_eff.cpp +++ b/src/EFF/compute_temp_region_eff.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -141,12 +141,6 @@ double ComputeTempRegionEff::compute_scalar() if (dof < 0.0 && tarray_all[0] > 0.0) error->all(FLERR, "Temperature compute degrees of freedom < 0"); - int one = 0; - for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2])) { - if (abs(spin[i]) == 1) one++; - } - if (dof > 0.0) scalar = force->mvv2e * tarray_all[1] / (dof * force->boltz); else diff --git a/src/EFF/compute_temp_region_eff.h b/src/EFF/compute_temp_region_eff.h index a3dd7e5dd4..0de3d35146 100644 --- a/src/EFF/compute_temp_region_eff.h +++ b/src/EFF/compute_temp_region_eff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/fix_langevin_eff.cpp b/src/EFF/fix_langevin_eff.cpp index e288e8732d..8c255e4348 100644 --- a/src/EFF/fix_langevin_eff.cpp +++ b/src/EFF/fix_langevin_eff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/fix_langevin_eff.h b/src/EFF/fix_langevin_eff.h index c7681fc4cf..dcc730af97 100644 --- a/src/EFF/fix_langevin_eff.h +++ b/src/EFF/fix_langevin_eff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/fix_nh_eff.cpp b/src/EFF/fix_nh_eff.cpp index fb1ab1ecca..15aaf5deb6 100644 --- a/src/EFF/fix_nh_eff.cpp +++ b/src/EFF/fix_nh_eff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/fix_nh_eff.h b/src/EFF/fix_nh_eff.h index 9860f81ba2..3bdb8dd9c4 100644 --- a/src/EFF/fix_nh_eff.h +++ b/src/EFF/fix_nh_eff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/fix_nph_eff.cpp b/src/EFF/fix_nph_eff.cpp index 9e82a50535..e5a3807d30 100644 --- a/src/EFF/fix_nph_eff.cpp +++ b/src/EFF/fix_nph_eff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/fix_nph_eff.h b/src/EFF/fix_nph_eff.h index 45e8c02ea5..3959dc9683 100644 --- a/src/EFF/fix_nph_eff.h +++ b/src/EFF/fix_nph_eff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/fix_npt_eff.cpp b/src/EFF/fix_npt_eff.cpp index e304bedd33..0d97166abf 100644 --- a/src/EFF/fix_npt_eff.cpp +++ b/src/EFF/fix_npt_eff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/fix_npt_eff.h b/src/EFF/fix_npt_eff.h index 107130685d..f01d92ff1e 100644 --- a/src/EFF/fix_npt_eff.h +++ b/src/EFF/fix_npt_eff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/fix_nve_eff.cpp b/src/EFF/fix_nve_eff.cpp index f8ce14f9f9..dadc4365c2 100644 --- a/src/EFF/fix_nve_eff.cpp +++ b/src/EFF/fix_nve_eff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/fix_nve_eff.h b/src/EFF/fix_nve_eff.h index b4fea154af..847c3df49f 100644 --- a/src/EFF/fix_nve_eff.h +++ b/src/EFF/fix_nve_eff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/fix_nvt_eff.cpp b/src/EFF/fix_nvt_eff.cpp index 05448c6697..02be397c52 100644 --- a/src/EFF/fix_nvt_eff.cpp +++ b/src/EFF/fix_nvt_eff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/fix_nvt_eff.h b/src/EFF/fix_nvt_eff.h index 602ff97eee..304748b394 100644 --- a/src/EFF/fix_nvt_eff.h +++ b/src/EFF/fix_nvt_eff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/fix_nvt_sllod_eff.cpp b/src/EFF/fix_nvt_sllod_eff.cpp index 333c98668c..15a679aa3b 100644 --- a/src/EFF/fix_nvt_sllod_eff.cpp +++ b/src/EFF/fix_nvt_sllod_eff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/fix_nvt_sllod_eff.h b/src/EFF/fix_nvt_sllod_eff.h index f014f9c956..3e56638726 100644 --- a/src/EFF/fix_nvt_sllod_eff.h +++ b/src/EFF/fix_nvt_sllod_eff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/fix_temp_rescale_eff.cpp b/src/EFF/fix_temp_rescale_eff.cpp index 579d8901c6..5970c6cba7 100644 --- a/src/EFF/fix_temp_rescale_eff.cpp +++ b/src/EFF/fix_temp_rescale_eff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/fix_temp_rescale_eff.h b/src/EFF/fix_temp_rescale_eff.h index bbcc3396aa..5b1d41d2b9 100644 --- a/src/EFF/fix_temp_rescale_eff.h +++ b/src/EFF/fix_temp_rescale_eff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/pair_eff_cut.cpp b/src/EFF/pair_eff_cut.cpp index a6a33c4972..1cfe5cd1dd 100644 --- a/src/EFF/pair_eff_cut.cpp +++ b/src/EFF/pair_eff_cut.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/pair_eff_cut.h b/src/EFF/pair_eff_cut.h index 5fcb98063b..89c9376c0a 100644 --- a/src/EFF/pair_eff_cut.h +++ b/src/EFF/pair_eff_cut.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EFF/pair_eff_inline.h b/src/EFF/pair_eff_inline.h index a6249bc4b6..c663e44b35 100644 --- a/src/EFF/pair_eff_inline.h +++ b/src/EFF/pair_eff_inline.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ELECTRODE/Install.sh b/src/ELECTRODE/Install.sh index 65d0b404da..561df0dce0 100755 --- a/src/ELECTRODE/Install.sh +++ b/src/ELECTRODE/Install.sh @@ -49,11 +49,11 @@ if (test $1 = 1) then sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(electrode_SYSLIB) |' ../Makefile.package fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*electrode.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*electrode.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ - include ..\/..\/lib\/electrode\/Makefile.lammps - ' ../Makefile.package.settings +include ..\/..\/lib\/electrode\/Makefile.lammps +' ../Makefile.package.settings fi elif (test $1 = 0) then @@ -61,7 +61,7 @@ elif (test $1 = 0) then sed -i -e 's/[^ \t]*electrode[^ \t]* //g' ../Makefile.package fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*electrode.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*electrode.*$/d' ../Makefile.package.settings fi fi diff --git a/src/ELECTRODE/boundary_correction.cpp b/src/ELECTRODE/boundary_correction.cpp index 7bc7fa4e45..8e622c170f 100644 --- a/src/ELECTRODE/boundary_correction.cpp +++ b/src/ELECTRODE/boundary_correction.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -19,34 +19,18 @@ #include "atom.h" #include "comm.h" +#include "domain.h" #include "force.h" +#include "kspace.h" using namespace LAMMPS_NS; -// use EW3DC slab correction -// BoundaryCorrection::BoundaryCorrection(LAMMPS *lmp) : Pointers(lmp) {} -void BoundaryCorrection::setup(double x, double y, double z) +double BoundaryCorrection::get_volume() { - xprd_wire = x; - yprd_wire = y; - zprd_slab = z; - volume = x * y * z; - area = x * y; - qqrd2e = force->qqrd2e; - scale = 1.0; -} -void BoundaryCorrection::setup(double x, double y, double z, double g) -{ - xprd_wire = x; - yprd_wire = y; - zprd_slab = z; - volume = x * y * z; - area = x * y; - qqrd2e = force->qqrd2e; - scale = 1.0; - g_ewald = g; + return domain->xprd * force->kspace->wire_volfactor * domain->yprd * + force->kspace->wire_volfactor * domain->zprd * force->kspace->slab_volfactor; } std::vector BoundaryCorrection::gather_recvcounts(int n) diff --git a/src/ELECTRODE/boundary_correction.h b/src/ELECTRODE/boundary_correction.h index 681db645e5..3fec90f8d2 100644 --- a/src/ELECTRODE/boundary_correction.h +++ b/src/ELECTRODE/boundary_correction.h @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -27,20 +27,10 @@ class BoundaryCorrection : protected Pointers { BoundaryCorrection(LAMMPS *); virtual void vector_corr(double *, int, int, bool){}; virtual void matrix_corr(bigint *, double **){}; - virtual void compute_corr(double, double, int, int, double &, double *){}; - void setup(double, double, double); - void setup(double, double, double, double); + virtual void compute_corr(double, int, int, double &, double *){}; protected: - double area; - double volume; - double xprd_wire; - double yprd_wire; - double zprd_slab; - double qqrd2e; - double scale; - double g_ewald; - + double get_volume(); std::vector gather_jmat(bigint *); std::vector gather_recvcounts(int); std::vector gather_displs(const std::vector &); diff --git a/src/ELECTRODE/electrode_accel_interface.h b/src/ELECTRODE/electrode_accel_interface.h index 0ff58cc9b7..bec4e0ed1f 100644 --- a/src/ELECTRODE/electrode_accel_interface.h +++ b/src/ELECTRODE/electrode_accel_interface.h @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ELECTRODE/electrode_kspace.h b/src/ELECTRODE/electrode_kspace.h index 21b3b46054..f51e61a534 100644 --- a/src/ELECTRODE/electrode_kspace.h +++ b/src/ELECTRODE/electrode_kspace.h @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ELECTRODE/electrode_math.h b/src/ELECTRODE/electrode_math.h index 5f51c8ae18..5992df2289 100644 --- a/src/ELECTRODE/electrode_math.h +++ b/src/ELECTRODE/electrode_math.h @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ELECTRODE/electrode_matrix.cpp b/src/ELECTRODE/electrode_matrix.cpp index eca497344b..5faac5a252 100644 --- a/src/ELECTRODE/electrode_matrix.cpp +++ b/src/ELECTRODE/electrode_matrix.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -29,6 +29,9 @@ #include "neigh_list.h" #include "pair.h" +#include +#include + using namespace LAMMPS_NS; using namespace MathConst; @@ -82,7 +85,9 @@ void ElectrodeMatrix::compute_array(double **array, bool timer_flag) MPI_Barrier(world); if (timer_flag && (comm->me == 0)) utils::logmesg(lmp, fmt::format("KSpace time: {:.4g} s\n", MPI_Wtime() - kspace_time)); + //cout << array[0][0] << ", " << array[0][1] << endl; pair_contribution(array); + //cout << array[0][0] << ", " << array[0][1] << endl; self_contribution(array); electrode_kspace->compute_matrix_corr(&mpos[0], array); if (tfflag) tf_contribution(array); @@ -110,7 +115,7 @@ void ElectrodeMatrix::pair_contribution(double **array) int nlocal = atom->nlocal; int newton_pair = force->newton_pair; - double etaij = eta * eta / sqrt(2.0 * eta * eta); // see mw ewald theory eq. (29)-(30) + double const etaij = eta * eta / sqrt(2.0 * eta * eta); // see mw ewald theory eq. (29)-(30) // neighbor list will be ready because called from post_neighbor inum = list->inum; diff --git a/src/ELECTRODE/electrode_matrix.h b/src/ELECTRODE/electrode_matrix.h index 7ab9ddd4cd..8499cfdb34 100644 --- a/src/ELECTRODE/electrode_matrix.h +++ b/src/ELECTRODE/electrode_matrix.h @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ELECTRODE/electrode_vector.cpp b/src/ELECTRODE/electrode_vector.cpp index 4f742df5c5..245ba57727 100644 --- a/src/ELECTRODE/electrode_vector.cpp +++ b/src/ELECTRODE/electrode_vector.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -25,10 +25,15 @@ #include "force.h" #include "group.h" #include "kspace.h" +#include "math_const.h" #include "neigh_list.h" #include "pair.h" +#include +#include + using namespace LAMMPS_NS; +using namespace MathConst; ElectrodeVector::ElectrodeVector(LAMMPS *lmp, int sensor_group, int source_group, double eta, bool invert_source) : @@ -41,6 +46,7 @@ ElectrodeVector::ElectrodeVector(LAMMPS *lmp, int sensor_group, int source_group ngroup = group->count(igroup); source_grpbit = group->bitmask[source_group]; this->eta = eta; + tfflag = false; kspace_time_total = 0; pair_time_total = 0; @@ -79,6 +85,14 @@ void ElectrodeVector::setup(class Pair *fix_pair, class NeighList *fix_neighlist /* ---------------------------------------------------------------------- */ +void ElectrodeVector::setup_tf(const std::map &tf_types) +{ + tfflag = true; + this->tf_types = tf_types; +} + +/* ---------------------------------------------------------------------- */ + void ElectrodeVector::compute_vector(double *vector) { MPI_Barrier(world); @@ -86,6 +100,8 @@ void ElectrodeVector::compute_vector(double *vector) // pair double pair_start_time = MPI_Wtime(); pair_contribution(vector); + self_contribution(vector); + if (tfflag) tf_contribution(vector); MPI_Barrier(world); pair_time_total += MPI_Wtime() - pair_start_time; // kspace @@ -105,6 +121,7 @@ void ElectrodeVector::compute_vector(double *vector) void ElectrodeVector::pair_contribution(double *vector) { + double const etaij = eta * MY_ISQRT2; double **x = atom->x; double *q = atom->q; int *type = atom->type; @@ -121,6 +138,7 @@ void ElectrodeVector::pair_contribution(double *vector) int const i = ilist[ii]; bool const i_in_sensor = (mask[i] & groupbit); bool const i_in_source = !!(mask[i] & source_grpbit) != invert_source; + if (!(i_in_sensor || i_in_source)) continue; double const xtmp = x[i][0]; double const ytmp = x[i][1]; double const ztmp = x[i][2]; @@ -144,12 +162,53 @@ void ElectrodeVector::pair_contribution(double *vector) double const rinv = 1.0 / r; double aij = rinv; aij *= ElectrodeMath::safe_erfc(g_ewald * r); - aij -= ElectrodeMath::safe_erfc(eta * r) * rinv; + if (invert_source) + aij -= ElectrodeMath::safe_erfc(eta * r) * rinv; + else + aij -= ElectrodeMath::safe_erfc(etaij * r) * rinv; if (i_in_sensor) { vector[i] += aij * q[j]; - } else if (j_in_sensor) { - vector[j] += aij * q[i]; + //} else if (j_in_sensor) { } + if (j_in_sensor && (!invert_source || !i_in_sensor)) { vector[j] += aij * q[i]; } } } } + +/* ---------------------------------------------------------------------- */ + +void ElectrodeVector::self_contribution(double *vector) +{ + int const inum = list->inum; + int *mask = atom->mask; + int *ilist = list->ilist; + double *q = atom->q; + + const double selfint = 2.0 / MY_PIS * g_ewald; + const double preta = MY_SQRT2 / MY_PIS; + + for (int ii = 0; ii < inum; ii++) { + int const i = ilist[ii]; + bool const i_in_sensor = (mask[i] & groupbit); + bool const i_in_source = !!(mask[i] & source_grpbit) != invert_source; + if (i_in_sensor && i_in_source) vector[i] += (preta * eta - selfint) * q[i]; + } +} + +/* ---------------------------------------------------------------------- */ + +void ElectrodeVector::tf_contribution(double *vector) +{ + int const inum = list->inum; + int *mask = atom->mask; + int *type = atom->type; + int *ilist = list->ilist; + double *q = atom->q; + + for (int ii = 0; ii < inum; ii++) { + int const i = ilist[ii]; + bool const i_in_sensor = (mask[i] & groupbit); + bool const i_in_source = !!(mask[i] & source_grpbit) != invert_source; + if (i_in_sensor && i_in_source) vector[i] += tf_types[type[i]] * q[i]; + } +} diff --git a/src/ELECTRODE/electrode_vector.h b/src/ELECTRODE/electrode_vector.h index f4cf533fe5..e7f637dd2d 100644 --- a/src/ELECTRODE/electrode_vector.h +++ b/src/ELECTRODE/electrode_vector.h @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -19,6 +19,7 @@ #define LMP_ELECTRODE_VECTOR_H #include "pointers.h" +#include namespace LAMMPS_NS { @@ -27,6 +28,7 @@ class ElectrodeVector : protected Pointers { ElectrodeVector(class LAMMPS *, int, int, double, bool); ~ElectrodeVector() override; void setup(class Pair *, class NeighList *, bool); + void setup_tf(const std::map &); void compute_vector(double *); int igroup, source_group; @@ -36,11 +38,15 @@ class ElectrodeVector : protected Pointers { bigint ngroup; double **cutsq; double g_ewald, eta; + bool tfflag; + std::map tf_types; class Pair *pair; class NeighList *list; class ElectrodeKSpace *electrode_kspace; void pair_contribution(double *); + void self_contribution(double *); + void tf_contribution(double *); double kspace_time_total; double pair_time_total; diff --git a/src/ELECTRODE/ewald_electrode.cpp b/src/ELECTRODE/ewald_electrode.cpp index 7a38f89f1c..99266ed450 100644 --- a/src/ELECTRODE/ewald_electrode.cpp +++ b/src/ELECTRODE/ewald_electrode.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -18,6 +18,7 @@ #include "ewald_electrode.h" #include "atom.h" +#include "boundary_correction.h" #include "comm.h" #include "domain.h" #include "error.h" @@ -40,7 +41,7 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -EwaldElectrode::EwaldElectrode(LAMMPS *lmp) : Ewald(lmp) +EwaldElectrode::EwaldElectrode(LAMMPS *lmp) : Ewald(lmp), boundcorr(nullptr) { eikr_step = -1; } @@ -88,6 +89,7 @@ void EwaldElectrode::init() }; int periodicity_2d[] = {1, 1, 0}; int periodicity_1d[] = {0, 0, 1}; + if (boundcorr != nullptr) delete boundcorr; if (slabflag == 1) { // EW3Dc dipole correction if (!equal_periodicity(periodicity_2d)) @@ -301,7 +303,6 @@ void EwaldElectrode::setup() memory->create3d_offset(sn, -kmax, kmax, 3, nmax, "ewald/electrode:sn"); kmax_created = kmax; } - boundcorr->setup(xprd_wire, yprd_wire, zprd_slab, g_ewald); // pre-compute Ewald coefficients @@ -418,7 +419,7 @@ void EwaldElectrode::compute(int eflag, int vflag) for (int j = 0; j < 6; j++) vatom[i][j] *= q[i] * qscale; } - boundcorr->compute_corr(qsum, slab_volfactor, eflag_atom, eflag_global, energy, eatom); + boundcorr->compute_corr(qsum, eflag_atom, eflag_global, energy, eatom); } /* ---------------------------------------------------------------------- */ @@ -1007,7 +1008,8 @@ void EwaldElectrode::compute_matrix(bigint *imat, double **matrix, bool /* timer n++; } - // TODO check if ((bigint) kxmax+1)*ngroup overflows ... + if (((bigint) kxmax + 1) * ngroup > INT_MAX) + error->all(FLERR, "kmax is too large, integer overflows might occur."); memory->create(csx_all, ((bigint) kxmax + 1) * ngroup, "ewald/electrode:csx_all"); memory->create(snx_all, ((bigint) kxmax + 1) * ngroup, "ewald/electrode:snx_all"); @@ -1018,15 +1020,12 @@ void EwaldElectrode::compute_matrix(bigint *imat, double **matrix, bool /* timer memory->create(jmat, ngroup, "ewald/electrode:jmat"); - int *recvcounts, *displs; // TODO allgather requires int for displs but - // displs might overflow! + int *recvcounts, *displs; memory->create(recvcounts, nprocs, "ewald/electrode:recvcounts"); memory->create(displs, nprocs, "ewald/electrode:displs"); // gather subsets global cs and sn int n = (kxmax + 1) * ngrouplocal; - // TODO check if (kxmax+1)*ngrouplocal, etc. - // overflows int n! typically kxmax small MPI_Allgather(&n, 1, MPI_INT, recvcounts, 1, MPI_INT, world); displs[0] = 0; diff --git a/src/ELECTRODE/ewald_electrode.h b/src/ELECTRODE/ewald_electrode.h index ce9284fc66..cea00fbbcf 100644 --- a/src/ELECTRODE/ewald_electrode.h +++ b/src/ELECTRODE/ewald_electrode.h @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ELECTRODE/fix_electrode_conp.cpp b/src/ELECTRODE/fix_electrode_conp.cpp index e6f15ee33d..2c39a57532 100644 --- a/src/ELECTRODE/fix_electrode_conp.cpp +++ b/src/ELECTRODE/fix_electrode_conp.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -18,8 +18,8 @@ #include "fix_electrode_conp.h" #include "atom.h" +#include "citeme.h" #include "comm.h" -#include "compute.h" #include "domain.h" #include "electrode_accel_interface.h" #include "electrode_math.h" @@ -36,44 +36,65 @@ #include "neigh_request.h" #include "neighbor.h" #include "pair.h" -#include "pointers.h" #include "text_file_reader.h" #include "variable.h" +#include #include -#include +#include +#include +#include +#include using namespace LAMMPS_NS; using namespace MathConst; +#define SMALL 1e-16 + extern "C" { void dgetrf_(const int *M, const int *N, double *A, const int *lda, int *ipiv, int *info); void dgetri_(const int *N, double *A, const int *lda, const int *ipiv, double *work, const int *lwork, int *info); } -enum { CONST, EQUAL }; -enum { - V, // voltage - QSB, // q_sb - MC, // macro_capacitance - ME // macro_elastance -}; +static const char cite_fix_electrode[] = + "fix electrode command:\n\n" + "@article{Ahrens2022\n" + "author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\\ss}ner, " + "Robert H.},\n" + "doi = {10.1063/5.0099239},\n" + "title = {{ELECTRODE: An electrochemistry package for LAMMPS}},\n" + "journal = {The Journal of Chemical Physics},\n" + "year = {2022}\n" + "volume = {157},\n" + "pages = {084801},\n" + "}\n"; // 0 1 2 3 4 // fix fxupdate group1 electrode/conp pot1 eta couple group2 pot2 FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg), f_inv(nullptr), f_mat(nullptr), f_vec(nullptr), array_compute(nullptr), - ele_vector(nullptr), capacitance(nullptr), pair(nullptr), mat_neighlist(nullptr), - vec_neighlist(nullptr), recvcounts(nullptr), displs(nullptr), iele_gathered(nullptr), - buf_gathered(nullptr), potential_i(nullptr), potential_iele(nullptr), charge_iele(nullptr) + Fix(lmp, narg, arg), elyt_vector(nullptr), elec_vector(nullptr), capacitance(nullptr), + elastance(nullptr), pair(nullptr), mat_neighlist(nullptr), vec_neighlist(nullptr), + recvcounts(nullptr), displs(nullptr), iele_gathered(nullptr), buf_gathered(nullptr), + potential_i(nullptr), potential_iele(nullptr) { - read_inv = read_mat = false; + if (lmp->citeme) lmp->citeme->add(cite_fix_electrode); + // fix.h output flags + scalar_flag = 1; + vector_flag = 1; + extscalar = 1; + extvector = 0; + extarray = 0; + + bool default_algo = true; + algo = Algo::MATRIX_INV; + matrix_algo = true; + cg_threshold = 0.; + write_inv = write_mat = write_vec = read_inv = read_mat = false; symm = false; ffield = false; thermo_time = 0.; - scalar_flag = 1; - vector_flag = 1; + top_group = 0; intelflag = false; tfflag = false; @@ -81,19 +102,20 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : update_time = 0; mult_time = 0; + n_call = n_cg_step = 0; // read fix command fixname = std::string(arg[0]); groups = std::vector(1, igroup); group_bits = std::vector(1, groupbit); group_psi_var_names = std::vector(1); - group_psi_var_styles = std::vector(1, CONST); + group_psi_var_styles = std::vector(1, VarStyle::CONST); group_psi = std::vector(1); etypes_neighlists = false; if (strstr(arg[3], "v_") == arg[3]) { std::string vname = arg[3]; group_psi_var_names[0] = vname.substr(2); - group_psi_var_styles[0] = EQUAL; + group_psi_var_styles[0] = VarStyle::EQUAL; } else group_psi[0] = utils::numeric(FLERR, arg[3], false, lmp); char *eta_str = arg[4]; @@ -110,50 +132,51 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : if (strstr(arg[iarg], "v_") == arg[iarg]) { std::string vname = arg[iarg]; group_psi_var_names.push_back(vname.substr(2)); - group_psi_var_styles.push_back(EQUAL); + group_psi_var_styles.push_back(VarStyle::EQUAL); group_psi.push_back(0.); } else { std::string null; group_psi_var_names.push_back(null); - group_psi_var_styles.push_back(CONST); + group_psi_var_styles.push_back(VarStyle::CONST); group_psi.push_back(utils::numeric(FLERR, arg[iarg], false, lmp)); } - } else if ((strncmp(arg[iarg], "symm", 4) == 0)) { - if (iarg + 2 > narg) error->all(FLERR, "Need yes/no command after symm keyword"); - char *symm_arg = arg[++iarg]; - if ((strcmp(symm_arg, "yes") == 0) || (strcmp(symm_arg, "on") == 0)) { - symm = true; - } else if ((strcmp(symm_arg, "no") == 0) || (strcmp(symm_arg, "off") == 0)) { - symm = false; + } else if ((strcmp(arg[iarg], "algo") == 0)) { + if (!default_algo) error->one(FLERR, fmt::format("Algorithm can be set once, only")); + default_algo = false; + if (iarg + 2 > narg) error->all(FLERR, "Need one argument after algo command"); + char *algo_arg = arg[++iarg]; + bool cg_algo = false; + if ((strcmp(algo_arg, "mat_inv") == 0)) { + algo = Algo::MATRIX_INV; + matrix_algo = true; + } else if ((strcmp(algo_arg, "mat_cg") == 0)) { + algo = Algo::MATRIX_CG; + matrix_algo = true; + cg_algo = true; + } else if ((strcmp(algo_arg, "cg") == 0)) { + algo = Algo::CG; + matrix_algo = false; + cg_algo = true; } else { - error->all(FLERR, "Invalid argument after symm keyword"); + error->all(FLERR, "Invalid argument after algo keyword"); + } + if (cg_algo) { + if (iarg + 2 > narg) error->all(FLERR, "Need one argument after algo *cg command"); + cg_threshold = utils::numeric(FLERR, arg[++iarg], false, lmp); } } else if ((strncmp(arg[iarg], "write", 5) == 0)) { if (iarg + 2 > narg) error->all(FLERR, "Need one argument after write command"); - if (comm->me == 0) { - if ((strcmp(arg[iarg], "write_inv") == 0)) { // capacitance matrix - f_inv = fopen(arg[++iarg], "w"); - if (f_inv == nullptr) - error->one(FLERR, - fmt::format("Cannot open capacitance matrix file {}: {}", arg[iarg], - utils::getsyserror())); - } else if ((strcmp(arg[iarg], "write_mat") == 0)) { // b vector - f_mat = fopen(arg[++iarg], "w"); - if (f_mat == nullptr) - error->one(FLERR, - fmt::format("Cannot open elastance matrix file {}: {}", arg[iarg], - utils::getsyserror())); - } else if ((strcmp(arg[iarg], "write_vec") == 0)) { // b vector - f_vec = fopen(arg[++iarg], "w"); - if (f_vec == nullptr) - error->one( - FLERR, - fmt::format("Cannot open vector file {}: {}", arg[iarg], utils::getsyserror())); - } else { - error->all(FLERR, "Illegal fix electrode/conp command with write"); - } + if ((strcmp(arg[iarg], "write_inv") == 0)) { // capacitance matrix + write_inv = true; + output_file_inv = arg[++iarg]; + } else if ((strcmp(arg[iarg], "write_mat") == 0)) { // elastance matrix + write_mat = true; + output_file_mat = arg[++iarg]; + } else if ((strcmp(arg[iarg], "write_vec") == 0)) { // b vector + write_vec = true; + output_file_vec = arg[++iarg]; } else { - iarg++; + error->all(FLERR, "Illegal fix electrode/conp command with write"); } } else if ((strncmp(arg[iarg], "read", 4) == 0)) { if (iarg + 2 > narg) error->all(FLERR, "Need one argument after read command"); @@ -166,12 +189,6 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : } else { error->all(FLERR, "Illegal fix electrode/conp command with read"); } - } else if ((strcmp(arg[iarg], "etypes") == 0)) { - if (iarg + 2 > narg) error->all(FLERR, "Need one argument after etypes command"); - int ilo, ihi; - utils::bounds(FLERR, arg[++iarg], 1, atom->ntypes, ilo, ihi, error); - for (int i = ilo; i <= ihi; ++i) etypes.push_back(i); - etypes_neighlists = true; } else if ((strcmp(arg[iarg], "temp") == 0)) { if (iarg + 4 > narg) error->all(FLERR, "Need three arguments after temp command"); if (strcmp(this->style, "electrode/thermo") != 0) @@ -179,16 +196,13 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : thermo_temp = force->boltz / force->qe2f * utils::numeric(FLERR, arg[++iarg], false, lmp); thermo_time = utils::numeric(FLERR, arg[++iarg], false, lmp); thermo_init = utils::inumeric(FLERR, arg[++iarg], false, lmp); + // toggle parameters + } else if ((strcmp(arg[iarg], "etypes") == 0)) { + etypes_neighlists = utils::logical(FLERR, arg[++iarg], false, lmp); + } else if ((strncmp(arg[iarg], "symm", 4) == 0)) { + symm = utils::logical(FLERR, arg[++iarg], false, lmp); } else if ((strcmp(arg[iarg], "ffield") == 0)) { - if (iarg + 2 > narg) error->all(FLERR, "Need yes/no command after ffield keyword"); - char *ffield_arg = arg[++iarg]; - if ((strcmp(ffield_arg, "yes") == 0) || (strcmp(ffield_arg, "on") == 0)) { - ffield = true; - } else if ((strcmp(ffield_arg, "no") == 0) || (strcmp(ffield_arg, "off") == 0)) { - ffield = false; - } else { - error->all(FLERR, "Invalid argument after ffield keyword"); - } + ffield = utils::logical(FLERR, arg[++iarg], false, lmp); } else { error->all(FLERR, "Illegal fix electrode/conp command"); } @@ -206,23 +220,38 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : igroup = group->find(union_group); if (igroup < 0) error->all(FLERR, "Failed to create union of groups"); // construct computes - ele_vector = new ElectrodeVector(lmp, igroup, igroup, eta, true); - if (!(read_inv || read_mat)) { array_compute = new ElectrodeMatrix(lmp, igroup, eta); } - - // error checks + need_array_compute = !(read_inv || read_mat) && matrix_algo; + need_elec_vector = algo == Algo::CG; + elyt_vector = new ElectrodeVector(lmp, igroup, igroup, eta, true); + if (need_elec_vector) elec_vector = new ElectrodeVector(lmp, igroup, igroup, eta, false); assert(groups.size() == group_bits.size()); assert(groups.size() == group_psi.size()); assert(groups.size() == group_psi_var_styles.size()); assert(groups.size() == group_psi_var_names.size()); - assert(igroup == ele_vector->igroup); - if (!(read_mat || read_inv)) assert(igroup == array_compute->igroup); + assert(igroup == elyt_vector->igroup); + if (need_elec_vector) assert(igroup == elec_vector->igroup); + if (algo != Algo::MATRIX_INV) { + if (read_inv || write_inv) + error->all( + FLERR, + "Selected algorithm does not use inverted matrix. Cannot read/write inverted matrix."); + } + if (!matrix_algo && (read_mat || write_mat || write_vec)) { + error->all(FLERR, + "Selected algorithm does not use matrix. Cannot read/write matrix or vector."); + } if (read_inv && read_mat) error->all(FLERR, "Cannot read matrix from two files"); - if (f_mat && read_inv) + if (write_mat && read_inv) error->all(FLERR, "Cannot write elastance matrix if reading capacitance matrix " "from file"); num_of_groups = static_cast(groups.size()); size_vector = num_of_groups; + array_flag = !!(algo == Algo::MATRIX_INV); + if (array_flag) { + size_array_rows = num_of_groups; + size_array_cols = 2 + 2 * num_of_groups; + } // check groups are consistent int *mask = atom->mask; @@ -243,15 +272,17 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : groupbit = group->bitmask[igroup]; ngroup = group->count(igroup); - accel_interface = new ElectrodeAccelInterface(lmp); + accel_interface = std::unique_ptr(new ElectrodeAccelInterface(lmp)); - memory->create(iele_gathered, ngroup, "FixElectrode:iele_gathered"); - memory->create(buf_gathered, ngroup, "FixElectrode:buf_gathered"); - memory->create(potential_iele, ngroup, "FixElectrode:potential_iele"); - memory->create(charge_iele, ngroup, "FixElectrode:charge_iele"); + if (matrix_algo) { + memory->create(iele_gathered, ngroup, "FixElectrode:iele_gathered"); + memory->create(buf_gathered, ngroup, "FixElectrode:buf_gathered"); + memory->create(potential_iele, ngroup, "FixElectrode:potential_iele"); + } atom->add_callback(Atom::GROW); // atomvec track local electrode atoms comm_reverse = 1; + comm_forward = 1; nlocalele = 0; @@ -260,12 +291,6 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) : /* ---------------------------------------------------------------------- */ -// 0 1 2 3 return 4 if successful -// fix_modify fxupdate set v [group] [var] -// fix_modify fxupdate set qsb [group] [var] -// 0 1 2 3 4 return 5 if successful -// fix_modify fxupdate set mc [group1] [group2] [var] -// fix_modify fxupdate set me [group1] [group2] [var] int FixElectrodeConp::modify_param(int narg, char **arg) { if (strcmp(arg[0], "tf") == 0) { @@ -306,49 +331,6 @@ int FixElectrodeConp::modify_param(int narg, char **arg) timer_flag = utils::logical(FLERR, arg[1], false, lmp); return 2; - } else if (strcmp(arg[0], "set") == 0) { - if (strcmp(arg[1], "v") == 0 || strcmp(arg[1], "qsb") == 0) { - if (narg != 4) - error->all(FLERR, - fmt::format("Incorrect number of arguments for fix_modify set {}", arg[1])); - int outputgrp = groupnum_from_name(arg[2]); - int outputvar = input->variable->find(arg[3]); - if (outputvar < 0) - error->all(FLERR, - fmt::format("Variable {} for fix_modify electrode does not exist", arg[3])); - if (!input->variable->internalstyle(outputvar)) - error->all(FLERR, - fmt::format("Variable {} for fix_modify electrode is invalid style", arg[3])); - if (strcmp(arg[1], "v") == 0) - setvars_types.push_back(V); - else - setvars_types.push_back(QSB); - setvars_groups.push_back(outputgrp); - setvars_vars.push_back(outputvar); - return 4; - } else if (strcmp(arg[1], "mc") == 0 || strcmp(arg[1], "me") == 0) { - if (narg != 5) - error->all(FLERR, - fmt::format("Incorrect number of arguments for fix_modify set {}", arg[1])); - int outputgrpi = groupnum_from_name(arg[2]); - int outputgrpj = groupnum_from_name(arg[3]); - int outputgrpij = outputgrpi * num_of_groups + outputgrpj; - int outputvar = input->variable->find(arg[4]); - if (outputvar < 0) - error->all(FLERR, - fmt::format("Variable {} for fix_modify electrode does not exist", arg[4])); - if (!input->variable->internalstyle(outputvar)) - error->all(FLERR, - fmt::format("Variable {} for fix_modify electrode is invalid style", arg[4])); - if (strcmp(arg[1], "mc") == 0) - setvars_types.push_back(MC); - else - setvars_types.push_back(ME); - setvars_groups.push_back(outputgrpij); - setvars_vars.push_back(outputvar); - return 5; - } else - error->all(FLERR, "Invalid set option for fix_modify electrode"); } else error->all(FLERR, "Invalid argument for fix_modify electrode"); return 0; @@ -392,6 +374,12 @@ void FixElectrodeConp::init() } if (pair == nullptr) error->all(FLERR, "Fix electrode couldn't find a Coulombic pair style"); + // error if more than one fix electrode/* + int count = 0; + for (int i = 0; i < modify->nfix; i++) + if (strncmp(modify->fix[i]->style, "electrode", 9) == 0) count++; + if (count > 1) error->all(FLERR, "More than one fix electrode"); + // check for package intel accel_interface->intel_find_fix(); if (etypes_neighlists) @@ -436,7 +424,7 @@ void FixElectrodeConp::post_constructor() input->variable->set(fmt::format("{} equal f_{}[{}]", var_vtop, fixname, 1 + top_group)); input->variable->set(fmt::format("{} equal (v_{}-v_{})/lz", var_efield, var_vbot, var_vtop)); // check for other efields and warn if found - if (modify->get_fix_by_style("efield").size() > 0) + if (modify->get_fix_by_style("efield").size() > 0 && comm->me == 0) error->warning(FLERR, "Other efield fixes found -- please make sure this is intended!"); // call fix command: // fix [varstem]_efield all efield 0.0 0.0 [var_vdiff]/lz @@ -452,10 +440,6 @@ void FixElectrodeConp::setup_post_neighbor() int *mask = atom->mask; tagint *tag = atom->tag; - // setvars asserts: - assert(setvars_groups.size() == setvars_vars.size()); - assert(setvars_groups.size() == setvars_types.size()); - // if Thomas-Fermi, make sure all electrode atoms have parameters if (tfflag) { int unset_tf = 0; @@ -471,7 +455,7 @@ void FixElectrodeConp::setup_post_neighbor() // get equal-style variable ids: group_psi_var_ids = std::vector(num_of_groups, -1); for (int g = 0; g < num_of_groups; g++) { - if (group_psi_var_styles[g] == CONST) continue; + if (group_psi_var_styles[g] == VarStyle::CONST) continue; const char *var_name = group_psi_var_names[g].c_str(); int var_id = input->variable->find(var_name); if (var_id < 0) @@ -485,22 +469,11 @@ void FixElectrodeConp::setup_post_neighbor() // pair and list setups: evscale = force->qe2f / force->qqrd2e; - ele_vector->setup(pair, vec_neighlist, timer_flag); - if (!(read_mat || read_inv)) { - if (etypes_neighlists) neighbor->build_one(mat_neighlist, 0); - array_compute->setup(tag_to_iele, pair, mat_neighlist); - if (tfflag) { array_compute->setup_tf(tf_types); } + elyt_vector->setup(pair, vec_neighlist, timer_flag); + if (need_elec_vector) { + elec_vector->setup(pair, mat_neighlist, timer_flag); + if (tfflag) elec_vector->setup_tf(tf_types); } - // setup psi with target potentials - iele_to_group = std::vector(ngroup, -1); - sd_vectors = std::vector>(num_of_groups, std::vector(ngroup)); - sb_charges = std::vector(num_of_groups); - for (int i = 0; i < nlocal; i++) { - for (int g = 0; g < num_of_groups; g++) { - if (mask[i] & group_bits[g]) { iele_to_group[tag_to_iele[tag[i]]] = g; } - } - } - MPI_Allreduce(MPI_IN_PLACE, &iele_to_group.front(), ngroup, MPI_INT, MPI_MAX, world); auto const order_matrix = [](std::vector order, double **mat) { size_t n = order.size(); @@ -512,51 +485,93 @@ void FixElectrodeConp::setup_post_neighbor() return ordered_mat; }; - // capacitance matrix - memory->create(capacitance, ngroup, ngroup, "fix_electrode:capacitance"); - if (read_inv) { - read_from_file(input_file_inv, capacitance, "capacitance"); - } else { - // temporarily hold elastance in "capacitance" + if (matrix_algo) { + + sd_vectors = std::vector>(num_of_groups, std::vector(ngroup)); + sb_charges = std::vector(num_of_groups); + iele_to_group = std::vector(ngroup, -1); + for (int i = 0; i < nlocal; i++) { + for (int g = 0; g < num_of_groups; g++) { + if (mask[i] & group_bits[g]) { iele_to_group[tag_to_iele[tag[i]]] = g; } + } + } + MPI_Allreduce(MPI_IN_PLACE, &iele_to_group.front(), ngroup, MPI_INT, MPI_MAX, world); + + memory->create(elastance, ngroup, ngroup, "fix_electrode:matrix"); if (read_mat) - read_from_file(input_file_mat, capacitance, "elastance"); - else - array_compute->compute_array(capacitance, timer_flag); - if (f_mat && !(read_inv)) - write_to_file(f_mat, taglist_bygroup, order_matrix(group_idx, capacitance)); - invert(); // TODO uncommented lots of stuff here - } - if (symm) symmetrize(); + read_from_file(input_file_mat, elastance, "elastance"); + else if (!read_inv) { + if (etypes_neighlists) neighbor->build_one(mat_neighlist, 0); + auto array_compute = std::unique_ptr(new ElectrodeMatrix(lmp, igroup, eta)); + array_compute->setup(tag_to_iele, pair, mat_neighlist); + if (tfflag) { array_compute->setup_tf(tf_types); } + array_compute->compute_array(elastance, timer_flag); + } // write_mat before proceeding + if (comm->me == 0 && write_mat) { + auto f_mat = fopen(output_file_mat.c_str(), "w"); + if (f_mat == nullptr) + error->one(FLERR, + fmt::format("Cannot open elastance matrix file {}: {}", output_file_mat, + utils::getsyserror())); + write_to_file(f_mat, taglist_bygroup, order_matrix(group_idx, elastance)); + fclose(f_mat); + } + if (algo == Algo::MATRIX_INV) { + capacitance = elastance; + elastance = nullptr; + if (read_inv) + read_from_file(input_file_inv, capacitance, "capacitance"); + else + invert(); + if (symm) symmetrize(); - // build sd vectors and macro matrices - MPI_Barrier(world); - double start = MPI_Wtime(); - if (ffield) { - compute_sd_vectors_ffield(); - } else { - compute_sd_vectors(); + // build sd vectors and macro matrices + MPI_Barrier(world); + double start = MPI_Wtime(); + if (ffield) { + compute_sd_vectors_ffield(); + } else { + compute_sd_vectors(); + } + compute_macro_matrices(); + MPI_Barrier(world); + if (timer_flag && (comm->me == 0)) + utils::logmesg( + lmp, fmt::format("SD-vector and macro matrices time: {:.4g} s\n", MPI_Wtime() - start)); + } } - compute_macro_matrices(); - MPI_Barrier(world); - if (timer_flag && (comm->me == 0)) - utils::logmesg( - lmp, fmt::format("SD-vector and macro matrices time: {:.4g} s\n", MPI_Wtime() - start)); - // initial charges and b vector update_charges(); // write to files, ordered by group - memset(potential_i, 0, atom->nmax * sizeof(double)); - ele_vector->compute_vector(potential_i); - if (force->newton_pair) comm->reverse_comm(this); - buffer_and_gather(potential_i, potential_iele); - if (comm->me == 0) { - if (f_vec) { + if (write_vec) { + memset(potential_i, 0, atom->nmax * sizeof(double)); + elyt_vector->compute_vector(potential_i); + if (force->newton_pair) comm->reverse_comm(this); + buffer_and_gather(potential_i, potential_iele); + if (comm->me == 0) { + auto f_vec = fopen(output_file_vec.c_str(), "w"); + if (f_vec == nullptr) + error->one( + FLERR, + fmt::format("Cannot open vector file {}: {}", output_file_vec, utils::getsyserror())); std::vector> vec(ngroup, std::vector(1)); for (int i = 0; i < ngroup; i++) { vec[group_idx[i]][0] = potential_iele[i]; } write_to_file(f_vec, taglist_bygroup, vec); + fclose(f_vec); + } + } + + if (write_inv) { + if (comm->me == 0) { + auto f_inv = fopen(output_file_inv.c_str(), "w"); + if (f_inv == nullptr) + error->one(FLERR, + fmt::format("Cannot open capacitance matrix file {}: {}", output_file_inv, + utils::getsyserror())); + write_to_file(f_inv, taglist_bygroup, order_matrix(group_idx, capacitance)); + fclose(f_inv); } - if (f_inv) { write_to_file(f_inv, taglist_bygroup, order_matrix(group_idx, capacitance)); } } } @@ -567,13 +582,15 @@ void FixElectrodeConp::setup_pre_reverse(int eflag, int /*vflag*/) // correct forces for initial timestep gausscorr(eflag, true); self_energy(eflag); - potential_energy(eflag); + // potential_energy(eflag); // not always part of the energy, depending on ensemble, therefore + // removed } /* ---------------------------------------------------------------------- */ void FixElectrodeConp::invert() { + assert(algo == Algo::MATRIX_INV); MPI_Barrier(world); double invert_time = MPI_Wtime(); if (timer_flag && (comm->me == 0)) utils::logmesg(lmp, "CONP inverting matrix\n"); @@ -596,6 +613,11 @@ void FixElectrodeConp::invert() void FixElectrodeConp::symmetrize() { // S matrix to enforce charge neutrality constraint + if (read_inv && comm->me == 0) + error->warning(FLERR, + "Symmetrizing matrix from file. Make sure the provided matrix has not been " + "symmetrized yet."); + assert(algo == Algo::MATRIX_INV); std::vector AinvE(ngroup, 0.); double EAinvE = 0.0; for (int i = 0; i < ngroup; i++) { @@ -614,6 +636,10 @@ void FixElectrodeConp::symmetrize() void FixElectrodeConp::setup_pre_exchange() // create_taglist { + nlocalele_outdated = 1; // force regather + // + if (!matrix_algo) return; + int *mask = atom->mask; int const nlocal = atom->nlocal; int const nprocs = comm->nprocs; @@ -626,21 +652,21 @@ void FixElectrodeConp::setup_pre_exchange() // create_taglist taglist_bygroup = std::vector(); nlocalele = 0; for (int gbit : group_bits) { - std::vector taglist_local; + std::vector taglist_local_group; for (int i = 0; i < nlocal; i++) { if (mask[i] & gbit) { - taglist_local.push_back(tag[i]); + taglist_local_group.push_back(tag[i]); nlocalele++; } } // gather from all cpus for this group - int gnum_local = taglist_local.size(); + int gnum_local = taglist_local_group.size(); MPI_Allgather(&gnum_local, 1, MPI_INT, recvcounts, 1, MPI_INT, world); displs[0] = 0; for (int i = 1; i < nprocs; i++) { displs[i] = displs[i - 1] + recvcounts[i - 1]; } int const gnum = displs[nprocs - 1] + recvcounts[nprocs - 1]; std::vector taglist_all(gnum); - MPI_Allgatherv(&taglist_local.front(), gnum_local, MPI_LMP_TAGINT, &taglist_all.front(), + MPI_Allgatherv(&taglist_local_group.front(), gnum_local, MPI_LMP_TAGINT, &taglist_all.front(), recvcounts, displs, MPI_LMP_TAGINT, world); std::sort(taglist_all.begin(), taglist_all.end()); for (tagint t : taglist_all) taglist_bygroup.push_back(t); @@ -656,8 +682,6 @@ void FixElectrodeConp::setup_pre_exchange() // create_taglist tag_to_iele.insert(std::pair(taglist[i], i)); } - nlocalele_outdated = 1; // force regather - // group_idx allows mapping a vector that is sorted by taglist to being // ordered by taglist_bygroup group_idx = std::vector(taglist_bygroup.size()); @@ -668,10 +692,10 @@ void FixElectrodeConp::setup_pre_exchange() // create_taglist // if memory_usage > 0.5 GiB, warn with expected usage double mem_needed = memory_usage(); mem_needed /= (1024 * 1024 * 1024); // convert to GiB - if (mem_needed > 0.5) + if (mem_needed > 0.5 && comm->me == 0) error->warning(FLERR, fmt::format("Please ensure there is sufficient memory for fix electrode " - "(anticipated usage is {:.1f} per proc)", + "(anticipated usage is at least {:.1f} GiB per proc)", mem_needed)); } @@ -688,13 +712,15 @@ void FixElectrodeConp::pre_reverse(int eflag, int /*vflag*/) { gausscorr(eflag, true); self_energy(eflag); - potential_energy(eflag); + //potential_energy(eflag); // not always part of the energy, depending on ensemble, therefore + // removed } /* ---------------------------------------------------------------------- */ void FixElectrodeConp::compute_sd_vectors() { + assert(algo == Algo::MATRIX_INV); for (int g = 0; g < num_of_groups; g++) { for (int j = 0; j < ngroup; j++) { if (iele_to_group[j] == g) { @@ -708,6 +734,7 @@ void FixElectrodeConp::compute_sd_vectors() void FixElectrodeConp::compute_sd_vectors_ffield() { + assert(algo == Algo::MATRIX_INV); double **x = atom->x; int *mask = atom->mask; tagint *tag = atom->tag; @@ -756,6 +783,7 @@ int FixElectrodeConp::get_top_group() void FixElectrodeConp::update_charges() { + n_call++; MPI_Barrier(world); double start = MPI_Wtime(); if (atom->nmax > nmax) { @@ -764,92 +792,214 @@ void FixElectrodeConp::update_charges() memory->create(potential_i, nmax, "FixElectrode:potential_i"); } - std::fill(sb_charges.begin(), sb_charges.end(), 0.); double *q = atom->q; - int *mask = atom->mask; - tagint *tag = atom->tag; - int const nlocal = atom->nlocal; - int const nall = nlocal + atom->nghost; - memset(potential_i, 0, atom->nmax * sizeof(double)); - ele_vector->compute_vector(potential_i); - if (force->newton_pair) comm->reverse_comm(this); - buffer_and_gather(potential_i, potential_iele); - MPI_Barrier(world); + gather_list_iele(); pre_update(); - MPI_Barrier(world); - double mult_start = MPI_Wtime(); - for (int i_iele = 0; i_iele < nlocalele; i_iele++) { - double q_tmp = 0; - int const iele = list_iele[i_iele]; - double *_noalias caprow = capacitance[iele]; - for (int j = 0; j < ngroup; j++) { q_tmp -= caprow[j] * potential_iele[j]; } - buf_iele[i_iele] = q_tmp; - sb_charges[iele_to_group[iele]] += q_tmp; + accel_interface->intel_pack_buffers(); // update buffers for pppmintel to compute potential + auto q_local = std::vector(nlocalele, 0.); + if (algo == Algo::MATRIX_INV) { + std::fill(sb_charges.begin(), sb_charges.end(), 0.); + memset(potential_i, 0, atom->nmax * sizeof(double)); + elyt_vector->compute_vector(potential_i); + if (force->newton_pair) comm->reverse_comm(this); + buffer_and_gather(potential_i, potential_iele); + MPI_Barrier(world); + double mult_start = MPI_Wtime(); + for (int i_iele = 0; i_iele < nlocalele; i_iele++) { + double q_tmp = 0; + int const iele = list_iele[i_iele]; + double *_noalias caprow = capacitance[iele]; + for (int j = 0; j < ngroup; j++) { q_tmp -= caprow[j] * potential_iele[j]; } + q_local[i_iele] = q_tmp; + sb_charges[iele_to_group[iele]] += q_tmp; + } + MPI_Allreduce(MPI_IN_PLACE, &sb_charges.front(), num_of_groups, MPI_DOUBLE, MPI_SUM, world); + update_psi(); // use for equal-style and conq + for (int g = 0; g < num_of_groups; g++) + for (int j = 0; j < nlocalele; j++) q_local[j] += sd_vectors[g][list_iele[j]] * group_psi[g]; + MPI_Barrier(world); + mult_time += MPI_Wtime() - mult_start; + } else if (algo == Algo::MATRIX_CG || algo == Algo::CG) { // conjugate gradient algorithm + update_psi(); // update group_psi if equal-style + auto b = gather_elevec_local(elyt_vector); + for (int i = 0; i < nlocalele; i++) { + b[i] -= evscale * group_psi[iele_to_group_local[i]]; + q_local[i] = q[atom->map(taglist_local[i])]; // pre-condition with current charges + } + q_local = constraint_correction(q_local); + MPI_Barrier(world); + double mult_start = MPI_Wtime(); + auto a = ele_ele_interaction(q_local); + MPI_Barrier(world); + mult_time += MPI_Wtime() - mult_start; + auto r = add_nlocalele(b, a); + auto d = constraint_projection(r); + double dot_old = dot_nlocalele(r, d); + double delta = dot_old; + for (int k = 0; k < ngroup && delta > cg_threshold; k++, n_cg_step++) { + MPI_Barrier(world); + double mult_start_loop = MPI_Wtime(); + auto y = ele_ele_interaction(d); + MPI_Barrier(world); + mult_time += MPI_Wtime() - mult_start_loop; + double alpha = dot_old / -dot_nlocalele(d, y); + q_local = add_nlocalele(q_local, scale_vector(alpha, d)); + // prepare next step + if ((k + 1) % 20 == 0) { + // avoid shifting residual. This rarely happens. + q_local = constraint_correction(q_local); + a = ele_ele_interaction(q_local); + r = add_nlocalele(b, a); + } else { + r = add_nlocalele(r, scale_vector(alpha, y)); + } + auto p = constraint_projection(r); + double dot_new = dot_nlocalele(r, p); + d = add_nlocalele(p, scale_vector(dot_new / dot_old, d)); + delta = dot_nlocalele(r, d); + dot_old = dot_new; + } + recompute_potential(b, q_local); + if (delta > cg_threshold && comm->me == 0) error->warning(FLERR, "CG threshold not reached"); + } else { + error->all(FLERR, "This algorithm is not implemented, yet"); } - gather_elevec(charge_iele); - MPI_Allreduce(MPI_IN_PLACE, &sb_charges.front(), num_of_groups, MPI_DOUBLE, MPI_SUM, world); - - update_setvars(QSB); - update_psi(); // use for equal-style and conq - update_setvars(V); // push psi into 'fix_modify set' vars - - for (int g = 0; g < num_of_groups; g++) - for (int j = 0; j < ngroup; j++) { charge_iele[j] += sd_vectors[g][j] * group_psi[g]; } - - for (int i = 0; i < nall; i++) { - if (!(groupbit & mask[i])) continue; - int const iele = tag_to_iele[tag[i]]; - q[i] = charge_iele[iele]; - } - - MPI_Barrier(world); - mult_time += MPI_Wtime() - mult_start; + set_charges(q_local); update_time += MPI_Wtime() - start; accel_interface->intel_pack_buffers(); } +std::vector FixElectrodeConp::ele_ele_interaction(const std::vector& q_local) +{ + assert(q_local.size() == nlocalele); + assert(algo == Algo::CG || algo == Algo::MATRIX_CG); + if (algo == Algo::CG) { + set_charges(q_local); + return gather_elevec_local(elec_vector); + } else { + return times_elastance(gather_ngroup(q_local)); + } +} + +/* ---------------------------------------------------------------------- */ + +void FixElectrodeConp::set_charges(std::vector q_local) +{ + assert(q_local.size() == nlocalele); + double *q = atom->q; + for (int i = 0; i < nlocalele; i++) q[atom->map(taglist_local[i])] = q_local[i]; + comm->forward_comm(this); + accel_interface->intel_pack_buffers(); +} + +/* ---------------------------------------------------------------------- */ + +std::vector FixElectrodeConp::gather_elevec_local(ElectrodeVector *vec) +{ + memset(potential_i, 0, atom->nmax * sizeof(double)); + vec->compute_vector(potential_i); + if (force->newton_pair) comm->reverse_comm(this); + auto a = std::vector(nlocalele, 0.); + for (int i = 0; i < nlocalele; i++) a[i] = potential_i[atom->map(taglist_local[i])]; + return a; +} + +/* ---------------------------------------------------------------------- */ + +std::vector FixElectrodeConp::gather_ngroup(std::vector x_local) +{ + auto x = std::vector(ngroup, 0.); + for (int i = 0; i < nlocalele; i++) { + int const iele = list_iele[i]; + x[iele] = x_local[i]; + } + MPI_Allreduce(MPI_IN_PLACE, &x.front(), ngroup, MPI_DOUBLE, MPI_SUM, world); + return x; +} + +/* ---------------------------------------------------------------------- + ensure total electrode charge is 0 if symm +------------------------------------------------------------------------- */ + +std::vector FixElectrodeConp::constraint_correction(std::vector x) +{ + return constraint_projection(x); +} + +/* ---------------------------------------------------------------------- + project into direction that conserves total charge (cf. Gingrich master thesis) +------------------------------------------------------------------------- */ + +std::vector FixElectrodeConp::constraint_projection(std::vector x) +{ + if (symm) { + double sum = 0.; + for (double xi : x) sum += xi; + MPI_Allreduce(MPI_IN_PLACE, &sum, 1, MPI_DOUBLE, MPI_SUM, world); + sum /= ngroup; + for (double &xi : x) xi -= sum; + } + return x; +} + +/* ---------------------------------------------------------------------- */ + +std::vector FixElectrodeConp::scale_vector(double alpha, std::vector x) +{ + for (double &xi : x) xi *= alpha; + return x; +} + +/* ---------------------------------------------------------------------- */ + +std::vector FixElectrodeConp::add_nlocalele(std::vector a, std::vector b) +{ + assert(a.size() == nlocalele && b.size() == nlocalele); + for (int i = 0; i < nlocalele; i++) a[i] += b[i]; + return a; +} + +/* ---------------------------------------------------------------------- */ + +double FixElectrodeConp::dot_nlocalele(std::vector a, std::vector b) +{ + assert(a.size() == nlocalele && b.size() == nlocalele); + double out = 0.; + for (int i = 0; i < nlocalele; i++) out += a[i] * b[i]; + MPI_Allreduce(MPI_IN_PLACE, &out, 1, MPI_DOUBLE, MPI_SUM, world); + return out; +} + +/* ---------------------------------------------------------------------- */ + +std::vector FixElectrodeConp::times_elastance(std::vector x) +{ + assert(x.size() == ngroup); + auto out = std::vector(nlocalele, 0.); + for (int i = 0; i < nlocalele; i++) { + double *_noalias row = elastance[list_iele[i]]; + double oi = 0; + for (int j = 0; j < ngroup; j++) oi += row[j] * x[j]; + out[i] = oi; + } + return out; +} + /* ---------------------------------------------------------------------- */ void FixElectrodeConp::update_psi() { for (int g = 0; g < num_of_groups; g++) { - if (group_psi_var_styles[g] == CONST) continue; + if (group_psi_var_styles[g] == VarStyle::CONST) continue; group_psi[g] = input->variable->compute_equal(group_psi_var_ids[g]); } } /* ---------------------------------------------------------------------- */ -void FixElectrodeConp::update_setvars(int vtype) -{ - int num_of_vars = static_cast(setvars_groups.size()); - for (int v = 0; v < num_of_vars; v++) { - if (vtype != setvars_types[v]) continue; - switch (vtype) { - case V: - input->variable->internal_set(setvars_vars[v], group_psi[setvars_groups[v]]); - break; - case QSB: - input->variable->internal_set(setvars_vars[v], sb_charges[setvars_groups[v]]); - break; - case MC: { - int groupi = setvars_groups[v] / num_of_groups; - int groupj = setvars_groups[v] % num_of_groups; - input->variable->internal_set(setvars_vars[v], macro_capacitance[groupi][groupj]); - } break; - case ME: { - int groupi = setvars_groups[v] / num_of_groups; - int groupj = setvars_groups[v] % num_of_groups; - input->variable->internal_set(setvars_vars[v], macro_elastance[groupi][groupj]); - } - } - } -} - -/* ---------------------------------------------------------------------- */ - void FixElectrodeConp::compute_macro_matrices() { + assert(algo == Algo::MATRIX_INV); macro_capacitance = std::vector>(num_of_groups, std::vector(num_of_groups)); for (int g = 0; g < num_of_groups; g++) { @@ -865,13 +1015,13 @@ void FixElectrodeConp::compute_macro_matrices() macro_elastance = std::vector>(num_of_groups, std::vector(num_of_groups)); - // TODO: does determinant ever = 0 if !symm? what to do then? if (num_of_groups == 1) { macro_elastance[0][0] = 1 / macro_capacitance[0][0]; } else if (num_of_groups == 2) { - double detinv = 1 / - (macro_capacitance[0][0] * macro_capacitance[1][1] - - macro_capacitance[0][1] * macro_capacitance[1][0]); + double const det = macro_capacitance[0][0] * macro_capacitance[1][1] - + macro_capacitance[0][1] * macro_capacitance[1][0]; + if (fabs(det) < SMALL) error->all(FLERR, "ELECTRODE macro matrix inversion failed!"); + double const detinv = 1 / det; macro_elastance[0][0] = macro_capacitance[1][1] * detinv; macro_elastance[1][1] = macro_capacitance[0][0] * detinv; macro_elastance[0][1] = -macro_capacitance[0][1] * detinv; @@ -894,7 +1044,7 @@ void FixElectrodeConp::compute_macro_matrices() int info_rf, info_ri; dgetrf_(&m, &n, &tmp.front(), &lda, &ipiv.front(), &info_rf); dgetri_(&n, &tmp.front(), &lda, &ipiv.front(), &work.front(), &lwork, &info_ri); - if (info_rf != 0 || info_ri != 0) error->all(FLERR, "CONP macro matrix inversion failed!"); + if (info_rf != 0 || info_ri != 0) error->all(FLERR, "ELECTRODE macro matrix inversion failed!"); for (int i = 0; i < num_of_groups; i++) { for (int j = 0; j < num_of_groups; j++) { int idx = i * num_of_groups + j; @@ -902,17 +1052,15 @@ void FixElectrodeConp::compute_macro_matrices() } } } - - update_setvars(MC); - update_setvars(ME); } /* ---------------------------------------------------------------------- */ double FixElectrodeConp::compute_scalar() { - return potential_energy(0); + return potential_energy(); } + /* ---------------------------------------------------------------------- */ double FixElectrodeConp::compute_vector(int i) @@ -922,24 +1070,32 @@ double FixElectrodeConp::compute_vector(int i) /* ---------------------------------------------------------------------- */ -double FixElectrodeConp::potential_energy(int eflag) +double FixElectrodeConp::compute_array(int i, int j) +{ + if (j == 0) + return sb_charges[i]; + else if (j <= num_of_groups) + return macro_capacitance[i][j - 1]; + else if (j <= 2 * num_of_groups) + return macro_elastance[i][j - num_of_groups - 1]; + else + return 0.; // avoid -Wreturn-type warning +} + +/* ---------------------------------------------------------------------- */ + +double FixElectrodeConp::potential_energy() { // corrections to energy due to potential psi double const qqrd2e = force->qqrd2e; int const nlocal = atom->nlocal; int *mask = atom->mask; - tagint *tag = atom->tag; double *q = atom->q; double energy = 0; - for (int i = 0; i < nlocal; i++) { + for (int i = 0, iele = 0; i < nlocal; i++) { if (groupbit & mask[i]) { - int const i_iele = tag_to_iele[tag[i]]; - double e = -qqrd2e * q[i] * group_psi[iele_to_group[i_iele]] * evscale; - energy += e; - if (eflag) { - force->pair->ev_tally(i, i, nlocal, force->newton_pair, 0., e, 0, 0, 0, - 0); // 0 evdwl, 0 fpair, 0 delxyz - } + energy -= qqrd2e * q[i] * group_psi[iele_to_group_local[iele]] * evscale; + iele++; } } MPI_Allreduce(MPI_IN_PLACE, &energy, 1, MPI_DOUBLE, MPI_SUM, world); @@ -1054,30 +1210,36 @@ double FixElectrodeConp::gausscorr(int eflag, bool fflag) FixElectrodeConp::~FixElectrodeConp() { - if (timer_flag && (comm->me == 0)) { + if (comm->me == 0) { try { - utils::logmesg(lmp, fmt::format("Multiplication time: {:.4g} s\n", mult_time)); - utils::logmesg(lmp, fmt::format("Update time: {:.4g} s\n", update_time)); + if (timer_flag) { + utils::logmesg(lmp, fmt::format("Multiplication time: {:.4g} s\n", mult_time)); + utils::logmesg(lmp, fmt::format("Update time: {:.4g} s\n", update_time)); + } + if (algo == Algo::CG || algo == Algo::MATRIX_CG) + utils::logmesg( + lmp, + fmt::format("Average conjugate gradient steps: {:.4g}\n", n_cg_step * 1. / n_call)); } catch (std::exception &) { } } if (!modify->get_fix_by_id(id)) // avoid segfault if derived fixes' ctor throws err atom->delete_callback(id, Atom::GROW); // atomvec track local electrode atoms - delete[] recvcounts; - delete[] displs; - memory->destroy(iele_gathered); - memory->destroy(buf_gathered); + if (matrix_algo) { + delete[] recvcounts; + delete[] displs; + memory->destroy(iele_gathered); + memory->destroy(buf_gathered); + memory->destroy(potential_iele); + } memory->destroy(potential_i); - memory->destroy(potential_iele); - memory->destroy(charge_iele); - if (!(read_mat || read_inv)) delete array_compute; - delete ele_vector; - memory->destroy(capacitance); - delete accel_interface; - if (f_inv) fclose(f_inv); - if (f_mat) fclose(f_mat); - if (f_vec) fclose(f_vec); + delete elyt_vector; + if (need_elec_vector) delete elec_vector; + if (algo == Algo::MATRIX_INV) + memory->destroy(capacitance); + else if (matrix_algo) + memory->destroy(elastance); } /* ---------------------------------------------------------------------- */ @@ -1116,7 +1278,8 @@ void FixElectrodeConp::read_from_file(const std::string &input_file, double **ar std::vector tags; try { TextFileReader reader(input_file, filetype); - reader.set_bufsize(ngroup * 20 + 4); + int bufsize = ngroup * 20 + 4; + reader.set_bufsize(bufsize > 100 ? bufsize : 100); // get line with tags auto values = reader.next_values(ngroup); @@ -1157,6 +1320,25 @@ void FixElectrodeConp::read_from_file(const std::string &input_file, double **ar void FixElectrodeConp::request_etypes_neighlists() { int const ntypes = atom->ntypes; + // construct etypes + int *mask = atom->mask; + int *type = atom->type; + auto elec = std::vector(ntypes, 0); + auto elyt = std::vector(ntypes, 0); + for (int i = 0; i < atom->nlocal; i++) { + if (mask[i] & groupbit) + elec[type[i] - 1] += 1; + else + elyt[type[i] - 1] += 1; + } + MPI_Allreduce(MPI_IN_PLACE, &elec.front(), ntypes, MPI_INT, MPI_SUM, world); + MPI_Allreduce(MPI_IN_PLACE, &elyt.front(), ntypes, MPI_INT, MPI_SUM, world); + etypes.clear(); + for (int i = 0; i < ntypes; i++) { + if (!elec[i] == !elyt[i]) error->all(FLERR, "Types overlap, cannot use etypes keyword"); + if (elec[i]) etypes.push_back(i + 1); + } + // construct skip arrays int *iskip_mat = new int[ntypes + 1]; int *iskip_vec = new int[ntypes + 1]; int **ijskip_mat; @@ -1182,11 +1364,16 @@ void FixElectrodeConp::request_etypes_neighlists() } } - if (!(read_inv || read_mat)) { + if (need_array_compute) { auto matReq = neighbor->add_request(this, NeighConst::REQ_OCCASIONAL); matReq->set_skip(iskip_mat, ijskip_mat); matReq->set_id(1); if (intelflag) matReq->enable_intel(); + } else if (need_elec_vector) { + auto matReq = neighbor->add_request(this); + matReq->set_skip(iskip_mat, ijskip_mat); + matReq->set_id(1); + if (intelflag) matReq->enable_intel(); } else { delete[] iskip_mat; memory->destroy(ijskip_mat); @@ -1224,26 +1411,39 @@ void FixElectrodeConp::gather_list_iele() int *mask = atom->mask; tagint *tag = atom->tag; int const nlocal = atom->nlocal; - list_iele.clear(); - list_iele.reserve(nlocalele); - for (int i = 0; i < nlocal; i++) { - if (mask[i] & groupbit) list_iele.push_back(tag_to_iele[tag[i]]); + if (matrix_algo) { + list_iele.clear(); + list_iele.reserve(nlocalele); } + taglist_local.clear(); + iele_to_group_local.clear(); + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + tagint const t = tag[i]; + if (matrix_algo) list_iele.push_back(tag_to_iele[t]); + taglist_local.push_back(t); + for (int g = 0; g < num_of_groups; g++) + if (mask[i] & group_bits[g]) iele_to_group_local.push_back(g); + } + } + nlocalele = static_cast(taglist_local.size()); // just for safety + assert(iele_to_group_local.size() == nlocalele); - nlocalele = static_cast(list_iele.size()); // just for safety + if (matrix_algo) { + MPI_Allgather(&nlocalele, 1, MPI_INT, recvcounts, 1, MPI_INT, world); + displs[0] = 0; + int const nprocs = comm->nprocs; + for (int i = 1; i < nprocs; i++) { displs[i] = displs[i - 1] + recvcounts[i - 1]; } - MPI_Allgather(&nlocalele, 1, MPI_INT, recvcounts, 1, MPI_INT, world); - displs[0] = 0; - int const nprocs = comm->nprocs; - for (int i = 1; i < nprocs; i++) { displs[i] = displs[i - 1] + recvcounts[i - 1]; } - - MPI_Allgatherv(&list_iele[0], nlocalele, MPI_INT, iele_gathered, recvcounts, displs, MPI_INT, - world); + MPI_Allgatherv(&list_iele[0], nlocalele, MPI_INT, iele_gathered, recvcounts, displs, MPI_INT, + world); + } nlocalele_outdated = 0; } void FixElectrodeConp::gather_elevec(double *elevec) { + assert(matrix_algo); MPI_Allgatherv(&buf_iele[0], nlocalele, MPI_DOUBLE, buf_gathered, recvcounts, displs, MPI_DOUBLE, world); @@ -1252,13 +1452,11 @@ void FixElectrodeConp::gather_elevec(double *elevec) void FixElectrodeConp::buffer_and_gather(double *ivec, double *elevec) { - gather_list_iele(); - + assert(matrix_algo); buf_iele.reserve(nlocalele); // avoid unexpected reallocs for (int i_iele = 0; i_iele < nlocalele; i_iele++) { buf_iele[i_iele] = ivec[atom->map(taglist[list_iele[i_iele]])]; } - gather_elevec(elevec); } @@ -1268,16 +1466,25 @@ double FixElectrodeConp::memory_usage() int const nmax = atom->nmax; double bytes = 0.0; bytes += nmax * (sizeof(double)); // potential_i - bytes += ngroup * - (sizeof(int) + 3 * sizeof(double)); // iele_gathered, buf_gathered, pot / charge_iele - bytes += ngroup * ngroup * sizeof(double); // capacitance - bytes += nprocs * (2 * sizeof(int)); // displs, recvcounts - bytes += list_iele.capacity() * sizeof(int); - bytes += buf_iele.capacity() * sizeof(double); + if (matrix_algo) { + bytes += ngroup * (sizeof(int) + 2 * sizeof(double)); // iele_gathered, buf_gathered, pot + bytes += ngroup * ngroup * sizeof(double); // capacitance or elastance + bytes += list_iele.capacity() * sizeof(int); + bytes += buf_iele.capacity() * sizeof(double); + bytes += nprocs * (2 * sizeof(int)); // displs, recvcounts + bytes += (tag_to_iele.size() * (sizeof(int) + sizeof(void *)) + // data list + tag_to_iele.bucket_count() * (sizeof(void *) + sizeof(size_t))); // bucket index + bytes += taglist.capacity() * sizeof(tagint); + bytes += iele_to_group.capacity() * sizeof(int); + } + bytes += taglist_local.capacity() * sizeof(tagint); + bytes += iele_to_group_local.capacity() * sizeof(int); return bytes; } +/* ---------------------------------------------------------------------- */ + int FixElectrodeConp::pack_reverse_comm(int n, int first, double *buf) { int m = 0; @@ -1287,7 +1494,30 @@ int FixElectrodeConp::pack_reverse_comm(int n, int first, double *buf) return m; } +/* ---------------------------------------------------------------------- */ + void FixElectrodeConp::unpack_reverse_comm(int n, int *list, double *buf) { for (int i = 0; i < n; i++) { potential_i[list[i]] += buf[i]; } } + +/* ---------------------------------------------------------------------- */ + +int FixElectrodeConp::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, + int * /*pbc*/) +{ + int m = 0; + for (int i = 0; i < n; i++) { + int const j = list[i]; + buf[m++] = atom->q[j]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void FixElectrodeConp::unpack_forward_comm(int n, int first, double *buf) +{ + int const last = first + n; + for (int i = first, m = 0; i < last; i++) atom->q[i] = buf[m++]; +} diff --git a/src/ELECTRODE/fix_electrode_conp.h b/src/ELECTRODE/fix_electrode_conp.h index 0ddc612d2f..5d3131bcce 100644 --- a/src/ELECTRODE/fix_electrode_conp.h +++ b/src/ELECTRODE/fix_electrode_conp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -26,16 +26,22 @@ FixStyle(electrode/conp, FixElectrodeConp); #ifndef LMP_FIX_ELECTRODE_CONP_H #define LMP_FIX_ELECTRODE_CONP_H -#include "electrode_accel_interface.h" #include "fix.h" -#include #include +#include #include namespace LAMMPS_NS { +// forward decls + +class ElectrodeAccelInterface; +class ElectrodeVector; +class NeighList; +class Pair; class FixElectrodeConp : public Fix { + public: FixElectrodeConp(class LAMMPS *, int, char **); ~FixElectrodeConp() override; @@ -47,6 +53,7 @@ class FixElectrodeConp : public Fix { void pre_reverse(int, int) override; double compute_scalar() override; double compute_vector(int) override; + double compute_array(int, int) override; int modify_param(int, char **) override; int modify_param(const std::string &); void init() override; @@ -60,56 +67,66 @@ class FixElectrodeConp : public Fix { int pack_reverse_comm(int, int, double *) override; void unpack_reverse_comm(int, int *, double *) override; + int pack_forward_comm(int, int *, double *, int, int *) override; + void unpack_forward_comm(int, int, double *) override; protected: + enum class Algo { MATRIX_INV, MATRIX_CG, CG }; + enum class VarStyle { CONST, EQUAL }; virtual void update_psi(); virtual void pre_update(){}; + virtual void recompute_potential(std::vector, std::vector){}; + virtual std::vector constraint_projection(std::vector); + virtual std::vector constraint_correction(std::vector); virtual void compute_macro_matrices(); + std::vector ele_ele_interaction(const std::vector &); std::vector group_psi; std::vector group_bits; + std::vector groups; int num_of_groups; bigint ngroup; + double evscale; std::vector> sd_vectors; std::vector sb_charges; - std::vector group_psi_var_ids, group_psi_var_styles; + std::vector group_psi_var_ids; + std::vector group_psi_var_styles; std::vector group_psi_var_names; - bool symm; // symmetrize elastance for charge neutrality - std::vector> macro_elastance; // used by conq + std::vector iele_to_group_local; + bool symm; // symmetrize elastance for charge neutrality + Algo algo; + std::vector> macro_elastance; // used by conq std::vector> macro_capacitance; // used by thermo double thermo_temp, thermo_time; // used by electrode/thermo only int thermo_init; // initializer for rng in electrode/thermo bool ffield; // possibly tweak electrode/conq's version std::string fixname; // used by electrode/ffield to set up internal efield bool intelflag; - ElectrodeAccelInterface *accel_interface; // used by /intel + std::unique_ptr accel_interface; // used by /intel private: - FILE *f_inv, *f_mat, *f_vec; // files for capacitance, eleastance and vector + std::string output_file_inv, output_file_mat, output_file_vec; std::string input_file_inv, input_file_mat; - class ElectrodeMatrix *array_compute; - class ElectrodeVector *ele_vector; - std::vector groups; - double **capacitance; - bool read_inv, read_mat; - double eta; + ElectrodeVector *elyt_vector, *elec_vector; + double **capacitance, **elastance; + bool read_inv, read_mat, write_inv, write_mat, write_vec; + bool matrix_algo, need_array_compute, need_elec_vector; + double eta, cg_threshold; double update_time, mult_time; + long n_cg_step, n_call; void create_taglist(); void invert(); void symmetrize(); double gausscorr(int, bool); void update_charges(); - double potential_energy(int); + double potential_energy(); double self_energy(int); void write_to_file(FILE *, const std::vector &, const std::vector> &); void read_from_file(const std::string &input_file, double **, const std::string &); void compute_sd_vectors(); void compute_sd_vectors_ffield(); - std::vector setvars_types, setvars_groups, setvars_vars; - void update_setvars(int); int groupnum_from_name(char *); - double evscale; - class Pair *pair; - class NeighList *mat_neighlist, *vec_neighlist; + Pair *pair; + NeighList *mat_neighlist, *vec_neighlist; std::vector etypes; int mat_request, vec_request; void request_etypes_neighlists(); @@ -119,12 +136,21 @@ class FixElectrodeConp : public Fix { bool tfflag; bool timer_flag; std::map tf_types; + // cg + std::vector scale_vector(double, std::vector); + std::vector add_nlocalele(std::vector, std::vector); + double dot_nlocalele(std::vector, std::vector); + std::vector times_elastance(std::vector); + std::vector gather_ngroup(std::vector); + std::vector gather_elevec_local(ElectrodeVector *); + void set_charges(std::vector); // fix-specific electrode ID storage system: - std::vector taglist; // global list: all tags in combined electrode group - std::vector taglist_bygroup; // taglist sorted by group - std::vector group_idx; // permutation taglist<->taglist_bygroup + std::vector taglist; // global list: all tags in combined electrode group + std::vector taglist_local; + std::vector taglist_bygroup; // taglist sorted by group + std::vector group_idx; // permutation taglist<->taglist_bygroup std::unordered_map tag_to_iele; // inverse of taglist: std::vector iele_to_group; // tag_to_iele[taglist[iele]] = iele @@ -138,7 +164,6 @@ class FixElectrodeConp : public Fix { double *buf_gathered; // buffer for MPIgathered buf_iele (NOT YET iele-ordered) double *potential_i; // potentials, i-indexed (0 for non-electrode atoms) double *potential_iele; // potentials ordered by iele - double *charge_iele; // charges ordered by iele void gather_list_iele(); // build iele_gathered void gather_elevec(double *); // gather buf_iele and rearrange into iele-order diff --git a/src/ELECTRODE/fix_electrode_conq.cpp b/src/ELECTRODE/fix_electrode_conq.cpp index fa6240816c..0d3d1d2aaf 100644 --- a/src/ELECTRODE/fix_electrode_conq.cpp +++ b/src/ELECTRODE/fix_electrode_conq.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -17,44 +17,108 @@ #include "fix_electrode_conq.h" +#include "comm.h" #include "error.h" #include "fix_electrode_conp.h" +#include "group.h" #include "input.h" #include "variable.h" using namespace LAMMPS_NS; -#define SMALL 0.00001 - -enum { CONST, EQUAL }; - -// 0 1 2 3 4 -// fix fxupdate group1 electrode/conp pot1 eta couple group2 pot2 FixElectrodeConq::FixElectrodeConq(LAMMPS *lmp, int narg, char **arg) : FixElectrodeConp(lmp, narg, arg) { // copy const-style values across because update_psi will change group_psi group_q = group_psi; - if (symm) { error->all(FLERR, "Keyword symm on not allowed in electrode/conq"); } + if (symm) { + if (num_of_groups == 1) + error->all(FLERR, "Keyword symm on not allowed in electrode/conq with only one electrode"); + if (comm->me == 0) + error->warning(FLERR, + "Fix electrode/conq with keyword symm ignores the charge setting for the last " + "electrode listed"); + if (algo != Algo::MATRIX_INV) { + double last_q = 0.; + for (int g = 0; g < num_of_groups - 1; g++) last_q -= group_q[g]; + group_q.back() = last_q; // needed for CG algos + } + } } void FixElectrodeConq::update_psi() { - // don't need MPI_Barrier because always preceded by MPI_Allreduce - for (int g = 0; g < num_of_groups; g++) { - if (group_psi_var_styles[g] == CONST) continue; + int const numsymm = num_of_groups - ((symm) ? 1 : 0); + bool symm_update_back = false; + for (int g = 0; g < numsymm; g++) { + if (group_psi_var_styles[g] == VarStyle::CONST) continue; group_q[g] = input->variable->compute_equal(group_psi_var_ids[g]); + symm_update_back = true; } - - std::vector group_remainder_q(num_of_groups); - for (int g = 0; g < num_of_groups; g++) { group_remainder_q[g] = group_q[g] - sb_charges[g]; } - - for (int g = 0; g < num_of_groups; g++) { - double vtmp = 0; - for (int h = 0; h < num_of_groups; h++) { - vtmp += macro_elastance[g][h] * group_remainder_q[h]; + if (algo == Algo::MATRIX_INV) { + std::vector group_remainder_q(num_of_groups, 0.); + for (int g = 0; g < numsymm; g++) { group_remainder_q[g] = group_q[g] - sb_charges[g]; } + for (int g = 0; g < num_of_groups; g++) { + double vtmp = 0; + for (int h = 0; h < num_of_groups; h++) { + vtmp += macro_elastance[g][h] * group_remainder_q[h]; + } + group_psi[g] = vtmp; } - group_psi[g] = vtmp; + } else { + if (symm && symm_update_back) { // needed for CG algos + double last_q = 0.; + for (int g = 0; g < num_of_groups - 1; g++) last_q -= group_q[g]; + group_q.back() = last_q; + } + for (double &g : group_psi) g = 0; } } + +/* ---------------------------------------------------------------------- + Correct charge of each electrode to target charge by adding a homogeneous charge +------------------------------------------------------------------------- */ + +std::vector FixElectrodeConq::constraint_correction(std::vector x) +{ + int const n = x.size(); + auto sums = std::vector(num_of_groups, 0); + for (int i = 0; i < n; i++) sums[iele_to_group_local[i]] += x[i]; + MPI_Allreduce(MPI_IN_PLACE, &sums.front(), num_of_groups, MPI_DOUBLE, MPI_SUM, world); + for (int g = 0; g < num_of_groups; g++) { + sums[g] -= group_q[g]; + sums[g] /= group->count(groups[g]); + } + for (int i = 0; i < n; i++) x[i] -= sums[iele_to_group_local[i]]; + return x; +} + +/* ---------------------------------------------------------------------- + Project into direction that conserves charge of each electrode (cf. M. Shariff (1995)) +------------------------------------------------------------------------- */ + +std::vector FixElectrodeConq::constraint_projection(std::vector x) +{ + int const n = x.size(); + auto sums = std::vector(num_of_groups, 0); + for (int i = 0; i < n; i++) sums[iele_to_group_local[i]] += x[i]; + MPI_Allreduce(MPI_IN_PLACE, &sums.front(), num_of_groups, MPI_DOUBLE, MPI_SUM, world); + for (int g = 0; g < num_of_groups; g++) sums[g] /= group->count(groups[g]); + for (int i = 0; i < n; i++) x[i] -= sums[iele_to_group_local[i]]; + return x; +} + +/* ---------------------------------------------------------------------- + Recompute group potential as average for output if using cg algo +------------------------------------------------------------------------- */ + +void FixElectrodeConq::recompute_potential(std::vector b, std::vector q_local) +{ + int const n = b.size(); + auto a = ele_ele_interaction(q_local); + auto psi_sums = std::vector(num_of_groups, 0); + for (int i = 0; i < n; i++) { psi_sums[iele_to_group_local[i]] += (a[i] + b[i]) / evscale; } + MPI_Allreduce(MPI_IN_PLACE, &psi_sums.front(), num_of_groups, MPI_DOUBLE, MPI_SUM, world); + for (int g = 0; g < num_of_groups; g++) group_psi[g] = psi_sums[g] / group->count(groups[g]); +} diff --git a/src/ELECTRODE/fix_electrode_conq.h b/src/ELECTRODE/fix_electrode_conq.h index 2497d12996..221ec2beff 100644 --- a/src/ELECTRODE/fix_electrode_conq.h +++ b/src/ELECTRODE/fix_electrode_conq.h @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -34,6 +34,9 @@ class FixElectrodeConq : public FixElectrodeConp { public: FixElectrodeConq(class LAMMPS *, int, char **); void update_psi() override; + void recompute_potential(std::vector, std::vector) override; + std::vector constraint_projection(std::vector) override; + std::vector constraint_correction(std::vector) override; private: std::vector group_q; diff --git a/src/ELECTRODE/fix_electrode_thermo.cpp b/src/ELECTRODE/fix_electrode_thermo.cpp index 0c2ee06816..52c0a3ce4c 100644 --- a/src/ELECTRODE/fix_electrode_thermo.cpp +++ b/src/ELECTRODE/fix_electrode_thermo.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -20,19 +20,18 @@ #include "atom.h" #include "error.h" #include "fix_electrode_conp.h" -#include "force.h" #include "input.h" #include "random_mars.h" #include "update.h" #include "variable.h" +#include + using namespace LAMMPS_NS; #define NUM_GROUPS 2 #define SMALL 0.00001 -enum { CONST, EQUAL }; - /* ----------------------------------------------------------------------- */ // 0 1 2 3 4 @@ -44,11 +43,11 @@ FixElectrodeThermo::FixElectrodeThermo(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR, "Number of electrodes != two in electrode/thermo"); if (group_psi_var_styles[0] != group_psi_var_styles[1]) error->all(FLERR, "Potentials in electrode/thermo must have same style"); - if (symm) error->all(FLERR, "Keyword symm on not allowed in electrode/thermo"); + if (algo != Algo::MATRIX_INV) error->all(FLERR, "Algorithm not allowed in electrode/thermo"); if (thermo_time < SMALL) error->all(FLERR, "Keyword temp not set or zero in electrode/thermo"); thermo_random = new RanMars(lmp, thermo_init); - if (group_psi_var_styles[0] == CONST) delta_psi_0 = group_psi[1] - group_psi[0]; + if (group_psi_var_styles[0] == VarStyle::CONST) delta_psi_0 = group_psi[1] - group_psi[0]; } /* ----------------------------------------------------------------------- */ @@ -63,9 +62,12 @@ FixElectrodeThermo::~FixElectrodeThermo() void FixElectrodeThermo::compute_macro_matrices() { FixElectrodeConp::compute_macro_matrices(); - vac_cap = (macro_capacitance[0][0] * macro_capacitance[1][1] - - macro_capacitance[0][1] * macro_capacitance[0][1]) / - (macro_capacitance[0][0] + macro_capacitance[1][1] + 2 * macro_capacitance[0][1]); + if (symm) + vac_cap = macro_capacitance[0][0]; + else + vac_cap = (macro_capacitance[0][0] * macro_capacitance[1][1] - + macro_capacitance[0][1] * macro_capacitance[0][1]) / + (macro_capacitance[0][0] + macro_capacitance[1][1] + 2 * macro_capacitance[0][1]); } /* ----------------------------------------------------------------------- */ @@ -92,18 +94,15 @@ void FixElectrodeThermo::update_psi() double const dt = update->dt; // group_q_eff is charge that corresponds to potential after previous step - double group_q_eff[NUM_GROUPS] = {0., 0.}; - for (int g = 0; g < NUM_GROUPS; g++) { group_q_eff[g] = group_q_old[g] - sb_charges[g]; } - double group_psi_old[NUM_GROUPS] = {0., 0.}; - for (int g = 0; g < NUM_GROUPS; g++) { - double vtmp = 0; - for (int h = 0; h < NUM_GROUPS; h++) { vtmp += macro_elastance[g][h] * group_q_eff[h]; } - group_psi_old[g] = vtmp; - } + double const group_q_eff[NUM_GROUPS] = {group_q_old[0] - sb_charges[0], + (symm) ? 0. : group_q_old[1] - sb_charges[1]}; + double const group_psi_old[NUM_GROUPS] = { + macro_elastance[0][0] * group_q_eff[0] + macro_elastance[0][1] * group_q_eff[1], + macro_elastance[1][0] * group_q_eff[0] + macro_elastance[1][1] * group_q_eff[1]}; double const delta_psi = group_psi_old[1] - group_psi_old[0]; // target potential difference from input parameters - if (group_psi_var_styles[0] != CONST) { + if (group_psi_var_styles[0] != VarStyle::CONST) { delta_psi_0 = input->variable->compute_equal(group_psi_var_ids[1]) - input->variable->compute_equal(group_psi_var_ids[0]); } @@ -114,11 +113,10 @@ void FixElectrodeThermo::update_psi() thermo_random->gaussian(); double const group_remainder_q[NUM_GROUPS] = {-delta_charge - sb_charges[0], - delta_charge - sb_charges[1]}; + (symm) ? 0. : delta_charge - sb_charges[1]}; - for (int g = 0; g < NUM_GROUPS; g++) { - double vtmp = 0; - for (int h = 0; h < NUM_GROUPS; h++) { vtmp += macro_elastance[g][h] * group_remainder_q[h]; } - group_psi[g] = vtmp; - } + group_psi[0] = + macro_elastance[0][0] * group_remainder_q[0] + macro_elastance[0][1] * group_remainder_q[1]; + group_psi[1] = + macro_elastance[1][0] * group_remainder_q[0] + macro_elastance[1][1] * group_remainder_q[1]; } diff --git a/src/ELECTRODE/fix_electrode_thermo.h b/src/ELECTRODE/fix_electrode_thermo.h index 72f98e04c2..81a60f4715 100644 --- a/src/ELECTRODE/fix_electrode_thermo.h +++ b/src/ELECTRODE/fix_electrode_thermo.h @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ELECTRODE/pppm_electrode.cpp b/src/ELECTRODE/pppm_electrode.cpp index 9ba76e1d6e..7418a052e6 100644 --- a/src/ELECTRODE/pppm_electrode.cpp +++ b/src/ELECTRODE/pppm_electrode.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -20,13 +20,13 @@ #include "angle.h" #include "atom.h" #include "bond.h" -#include "boundary_correction.h" +#include "citeme.h" #include "comm.h" #include "domain.h" #include "error.h" #include "fft3d_wrap.h" #include "force.h" -#include "gridcomm.h" +#include "grid3d.h" #include "math_const.h" #include "math_special.h" #include "memory.h" @@ -62,11 +62,26 @@ enum { FORWARD_IK, FORWARD_AD, FORWARD_IK_PERATOM, FORWARD_AD_PERATOM }; #define ONEF 1.0 #endif +static const char cite_pppm_electrode[] = + "kspace_style pppm/electrode command:\n\n" + "@article{Ahrens2021,\n" + "author = {Ahrens-Iwers, Ludwig J.V. and Mei{\\ss}ner, Robert H.},\n" + "doi = {10.1063/5.0063381},\n" + "title = {{Constant potential simulations on a mesh}},\n" + "journal = {Journal of Chemical Physics},\n" + "year = {2021}\n" + "volume = {155},\n" + "pages = {104104},\n" + "}\n"; + /* ---------------------------------------------------------------------- */ PPPMElectrode::PPPMElectrode(LAMMPS *lmp) : - PPPM(lmp), electrolyte_density_brick(nullptr), electrolyte_density_fft(nullptr) + PPPM(lmp), electrolyte_density_brick(nullptr), electrolyte_density_fft(nullptr), + boundcorr(nullptr) { + if (lmp->citeme) lmp->citeme->add(cite_pppm_electrode); + group_group_enable = 0; electrolyte_density_brick = nullptr; electrolyte_density_fft = nullptr; @@ -83,7 +98,6 @@ PPPMElectrode::~PPPMElectrode() if (copymode) return; deallocate(); - delete boundcorr; if (peratom_allocate_flag) deallocate_peratom(); if (group_allocate_flag) deallocate_groups(); memory->destroy(part2grid); @@ -187,10 +201,6 @@ void PPPMElectrode::init() // free all arrays previously allocated deallocate(); - delete fft1; - delete fft2; - delete remap; - delete gc; if (peratom_allocate_flag) deallocate_peratom(); if (group_allocate_flag) deallocate_groups(); @@ -200,7 +210,7 @@ void PPPMElectrode::init() // or overlap is allowed, then done // else reduce order and try again - GridComm *gctmp = nullptr; + gc = nullptr; int iteration = 0; while (order >= minorder) { @@ -214,23 +224,22 @@ void PPPMElectrode::init() set_grid_local(); if (overlap_allowed) break; - gctmp = - new GridComm(lmp, world, nx_pppm, ny_pppm, nz_pppm, nxlo_in, nxhi_in, nylo_in, nyhi_in, - nzlo_in, nzhi_in, nxlo_out, nxhi_out, nylo_out, nyhi_out, nzlo_out, nzhi_out); + gc = new Grid3d(lmp, world, nx_pppm, ny_pppm, nz_pppm, nxlo_in, nxhi_in, nylo_in, nyhi_in, + nzlo_in, nzhi_in, nxlo_out, nxhi_out, nylo_out, nyhi_out, nzlo_out, nzhi_out); int tmp1, tmp2; - gctmp->setup(tmp1, tmp2); - if (gctmp->ghost_adjacent()) break; - delete gctmp; + gc->setup_comm(tmp1, tmp2); + if (gc->ghost_adjacent()) break; + delete gc; order--; iteration++; } if (order < minorder) error->all(FLERR, "PPPM/electrode order < minimum allowed order"); - if (!overlap_allowed && !gctmp->ghost_adjacent()) + if (!overlap_allowed && !gc->ghost_adjacent()) error->all(FLERR, "PPPM/electrode grid stencil extends beyond nearest neighbor processor"); - if (gctmp) delete gctmp; + if (gc) delete gc; // adjust g_ewald @@ -265,6 +274,7 @@ void PPPMElectrode::init() // pre-compute Green's function denomiator expansion // pre-compute 1d charge distribution coefficients + compute_gf_denom(); if (differentiation_flag == 1) compute_sf_precoeff(); compute_rho_coeff(); @@ -308,8 +318,6 @@ void PPPMElectrode::setup() double zprd_slab = zprd * slab_volfactor; volume = xprd_wire * yprd_wire * zprd_slab; - boundcorr->setup(xprd_wire, yprd_wire, zprd_slab); - delxinv = nx_pppm / xprd_wire; delyinv = ny_pppm / yprd_wire; delzinv = nz_pppm / zprd_slab; @@ -323,7 +331,7 @@ void PPPMElectrode::setup() // fkx,fky,fkz for my FFT grid pts for (i = nxlo_fft; i <= nxhi_fft; i++) { - int per = i - nx_pppm * (2 * i / nx_pppm); // TODO int division intentional? + int per = i - nx_pppm * (2 * i / nx_pppm); fkx[i] = unitkx * per; } @@ -378,7 +386,7 @@ void PPPMElectrode::setup() called by fix balance b/c it changed sizes of processor sub-domains ------------------------------------------------------------------------- */ -void PPPMElectrode::setup_grid() +void PPPMElectrode::reset_grid() { // free all arrays previously allocated @@ -435,17 +443,16 @@ void PPPMElectrode::compute(int eflag, int vflag) // return if there are no charges - // if (qsqsum == 0.0) return; TODO move back in - start_compute(); - if (compute_vector_called) { - // electrolyte_density_brick is filled, so we can - // grab only electrode atoms + if (compute_vector_called && last_invert_source) { + // electrolyte_density_brick is filled, so we can grab only electrode atoms. + // Does not work for direct cg algorithm because electrode charges change after compute_vector. + // Therefore, only when last_invert_source true. // TODO: this is dangerous now that compute_vector's interface has been // changed since a compute could call an arbitrary source, needs tightening make_rho_in_brick(last_source_grpbit, density_brick, !last_invert_source); - gc->reverse_comm(GridComm::KSPACE, this, 1, sizeof(FFT_SCALAR), REVERSE_RHO, gc_buf1, gc_buf2, + gc->reverse_comm(Grid3d::KSPACE, this, REVERSE_RHO, 1, sizeof(FFT_SCALAR), gc_buf1, gc_buf2, MPI_FFT_SCALAR); for (int nz = nzlo_out; nz <= nzhi_out; nz++) for (int ny = nylo_out; ny <= nyhi_out; ny++) @@ -459,7 +466,7 @@ void PPPMElectrode::compute(int eflag, int vflag) // to fully sum contribution in their 3d bricks // remap from 3d decomposition to FFT decomposition - gc->reverse_comm(GridComm::KSPACE, this, 1, sizeof(FFT_SCALAR), REVERSE_RHO, gc_buf1, gc_buf2, + gc->reverse_comm(Grid3d::KSPACE, this, REVERSE_RHO, 1, sizeof(FFT_SCALAR), gc_buf1, gc_buf2, MPI_FFT_SCALAR); } @@ -471,28 +478,25 @@ void PPPMElectrode::compute(int eflag, int vflag) // also performs per-atom calculations via poisson_peratom() poisson(); - // cout << "###" << endl - //<< "POISSON ENERGY: " << energy * 0.5 * volume << endl - //<< "###" << endl; // all procs communicate E-field values // to fill ghost cells surrounding their 3d bricks if (differentiation_flag == 1) - gc->forward_comm(GridComm::KSPACE, this, 1, sizeof(FFT_SCALAR), FORWARD_AD, gc_buf1, gc_buf2, + gc->forward_comm(Grid3d::KSPACE, this, FORWARD_AD, 1, sizeof(FFT_SCALAR), gc_buf1, gc_buf2, MPI_FFT_SCALAR); else - gc->forward_comm(GridComm::KSPACE, this, 3, sizeof(FFT_SCALAR), FORWARD_IK, gc_buf1, gc_buf2, + gc->forward_comm(Grid3d::KSPACE, this, FORWARD_IK, 3, sizeof(FFT_SCALAR), gc_buf1, gc_buf2, MPI_FFT_SCALAR); // extra per-atom energy/virial communication if (evflag_atom) { if (differentiation_flag == 1 && vflag_atom) - gc->forward_comm(GridComm::KSPACE, this, 6, sizeof(FFT_SCALAR), FORWARD_AD_PERATOM, gc_buf1, + gc->forward_comm(Grid3d::KSPACE, this, FORWARD_AD_PERATOM, 6, sizeof(FFT_SCALAR), gc_buf1, gc_buf2, MPI_FFT_SCALAR); else if (differentiation_flag == 0) - gc->forward_comm(GridComm::KSPACE, this, 7, sizeof(FFT_SCALAR), FORWARD_IK_PERATOM, gc_buf1, + gc->forward_comm(Grid3d::KSPACE, this, FORWARD_IK_PERATOM, 7, sizeof(FFT_SCALAR), gc_buf1, gc_buf2, MPI_FFT_SCALAR); } @@ -552,7 +556,7 @@ void PPPMElectrode::compute(int eflag, int vflag) } } - boundcorr->compute_corr(qsum, slab_volfactor, eflag_atom, eflag_global, energy, eatom); + boundcorr->compute_corr(qsum, eflag_atom, eflag_global, energy, eatom); compute_vector_called = false; } @@ -590,7 +594,7 @@ void PPPMElectrode::compute_vector(double *vec, int sensor_grpbit, int source_gr make_rho_in_brick(source_grpbit, electrolyte_density_brick, invert_source); density_brick = electrolyte_density_brick; density_fft = electrolyte_density_fft; - gc->reverse_comm(GridComm::KSPACE, this, 1, sizeof(FFT_SCALAR), REVERSE_RHO, gc_buf1, gc_buf2, + gc->reverse_comm(Grid3d::KSPACE, this, REVERSE_RHO, 1, sizeof(FFT_SCALAR), gc_buf1, gc_buf2, MPI_FFT_SCALAR); brick2fft(); // switch back pointers @@ -618,7 +622,7 @@ void PPPMElectrode::compute_vector(double *vec, int sensor_grpbit, int source_gr u_brick[k][j][i] = work2[n]; n += 2; } - gc->forward_comm(GridComm::KSPACE, this, 1, sizeof(FFT_SCALAR), FORWARD_AD, gc_buf1, gc_buf2, + gc->forward_comm(Grid3d::KSPACE, this, FORWARD_AD, 1, sizeof(FFT_SCALAR), gc_buf1, gc_buf2, MPI_FFT_SCALAR); project_psi(vec, sensor_grpbit); compute_vector_called = true; @@ -665,11 +669,12 @@ void PPPMElectrode::project_psi(double *vec, int sensor_grpbit) void PPPMElectrode::compute_matrix(bigint *imat, double **matrix, bool timer_flag) { - // TODO replace compute with required setup - compute(1, 0); + compute(1, 0); // make sure density bricks etc. are set up - // fft green's function k -> r - std::vector greens_real((std::size_t) nz_pppm * ny_pppm * nx_pppm, 0.0); + // fft green's function k -> r (double) + double *greens_real; + memory->create(greens_real, nz_pppm * ny_pppm * nx_pppm, "pppm/electrode:greens_real"); + memset(greens_real, 0, (std::size_t)nz_pppm * (std::size_t)ny_pppm * (std::size_t)nx_pppm * sizeof(double)); for (int i = 0, n = 0; i < nfft; i++) { work2[n++] = greensfn[i]; work2[n++] = ZEROF; @@ -681,13 +686,14 @@ void PPPMElectrode::compute_matrix(bigint *imat, double **matrix, bool timer_fla greens_real[ny_pppm * nx_pppm * k + nx_pppm * j + i] = work2[n]; n += 2; } - MPI_Allreduce(MPI_IN_PLACE, &greens_real.front(), nz_pppm * ny_pppm * nx_pppm, MPI_DOUBLE, - MPI_SUM, world); + MPI_Allreduce(MPI_IN_PLACE, greens_real, nz_pppm * ny_pppm * nx_pppm, MPI_DOUBLE, MPI_SUM, world); int const nlocal = atom->nlocal; int nmat = std::count_if(&imat[0], &imat[nlocal], [](int x) { return x >= 0; }); MPI_Allreduce(MPI_IN_PLACE, &nmat, 1, MPI_INT, MPI_SUM, world); + + // gather x_ele double **x_ele; memory->create(x_ele, nmat, 3, "pppm/electrode:x_ele"); memset(&(x_ele[0][0]), 0, nmat * 3 * sizeof(double)); @@ -703,14 +709,14 @@ void PPPMElectrode::compute_matrix(bigint *imat, double **matrix, bool timer_fla one_step_multiplication(imat, greens_real, x_ele, matrix, nmat, timer_flag); else two_step_multiplication(imat, greens_real, x_ele, matrix, nmat, timer_flag); + memory->destroy(greens_real); memory->destroy(x_ele); } /* ----------------------------------------------------------------------*/ -void PPPMElectrode::one_step_multiplication(bigint *imat, const std::vector &greens_real, - double **x_ele, double **matrix, int const nmat, - bool timer_flag) +void PPPMElectrode::one_step_multiplication(bigint *imat, double *greens_real, double **x_ele, + double **matrix, int const nmat, bool timer_flag) { // map green's function in real space from mesh to particle positions // with matrix multiplication 'W^T G W' in one steps. Uses less memory than @@ -722,11 +728,19 @@ void PPPMElectrode::one_step_multiplication(bigint *imat, const std::vector>> rho1d_j( - nlocal, std::vector>(3, std::vector(order, 0))); + std::vector j_list; for (int j = 0; j < nlocal; j++) { int jpos = imat[j]; if (jpos < 0) continue; + j_list.push_back(j); + } + int const nj_local = j_list.size(); + + FFT_SCALAR ***rho1d_j; + memory->create(rho1d_j, nj_local, 3, order, "pppm/electrode:rho1d_j"); + + for (int jlist_pos = 0; jlist_pos < nj_local; jlist_pos++) { + int j = j_list[jlist_pos]; int njx = part2grid[j][0]; int njy = part2grid[j][1]; int njz = part2grid[j][2]; @@ -735,7 +749,7 @@ void PPPMElectrode::one_step_multiplication(bigint *imat, const std::vectorcreate(amesh, order6, "pppm/electrode:amesh"); for (int ipos = 0; ipos < nmat; ipos++) { double *_noalias xi_ele = x_ele[ipos]; // new calculation for nx, ny, nz because part2grid available for nlocal, @@ -754,44 +772,48 @@ void PPPMElectrode::one_step_multiplication(bigint *imat, const std::vectordestroy(amesh); + memory->destroy(rho1d_j); MPI_Barrier(world); if (timer_flag && (comm->me == 0)) utils::logmesg(lmp, fmt::format("Single step time: {:.4g} s\n", MPI_Wtime() - step1_time)); @@ -799,9 +821,38 @@ void PPPMElectrode::one_step_multiplication(bigint *imat, const std::vector &greens_real, - double **x_ele, double **matrix, int const nmat, - bool timer_flag) +void PPPMElectrode::build_amesh(const int dx, // = njx - nix + const int dy, // = njy - niy + const int dz, // = njz - niz + double *amesh, double *const greens_real) +{ + auto fmod = [](int x, int n) { // fast unsigned mod + int r = abs(x); + while (r >= n) r -= n; + return r; + }; + int ind_amesh = 0; + + for (int iz = 0; iz < order; iz++) + for (int jz = 0; jz < order; jz++) { + int const mz = fmod(dz + jz - iz, nz_pppm) * nx_pppm * ny_pppm; + for (int iy = 0; iy < order; iy++) + for (int jy = 0; jy < order; jy++) { + int const my = fmod(dy + jy - iy, ny_pppm) * nx_pppm; + for (int ix = 0; ix < order; ix++) + for (int jx = 0; jx < order; jx++) { + int const mx = fmod(dx + jx - ix, nx_pppm); + amesh[ind_amesh] = greens_real[mz + my + mx]; + ind_amesh++; + } + } + } +} + +/* ----------------------------------------------------------------------*/ + +void PPPMElectrode::two_step_multiplication(bigint *imat, double *greens_real, double **x_ele, + double **matrix, int const nmat, bool timer_flag) { // map green's function in real space from mesh to particle positions // with matrix multiplication 'W^T G W' in two steps. gw is result of @@ -813,7 +864,16 @@ void PPPMElectrode::two_step_multiplication(bigint *imat, const std::vector> gw(nmat, std::vector(nxyz, 0.)); + + double **gw; + memory->create(gw, nmat, nxyz, "pppm/electrode:gw"); + memset(&(gw[0][0]), 0, (std::size_t)nmat * (std::size_t)nxyz * sizeof(double)); + + auto fmod = [](int x, int n) { // fast unsigned mod + int r = abs(x); + while (r >= n) r -= n; + return r; + }; // loops over weights of electrode atoms and weights of complete grid // (nx,ny,nz) = global coords of grid pt to "lower left" of charge @@ -830,21 +890,21 @@ void PPPMElectrode::two_step_multiplication(bigint *imat, const std::vectorx; for (int i = 0; i < nlocal; i++) { @@ -894,14 +956,14 @@ void PPPMElectrode::two_step_multiplication(bigint *imat, const std::vectordestroy(gw); if (timer_flag && (comm->me == 0)) utils::logmesg(lmp, fmt::format("step 2 time: {:.4g} s\n", MPI_Wtime() - step2_time)); } /* ---------------------------------------------------------------------- allocate memory that depends on # of K-vectors and order -------------------------------------------------------------------------- -*/ +------------------------------------------------------------------------- */ void PPPMElectrode::allocate() { @@ -916,10 +978,123 @@ void PPPMElectrode::allocate() boundcorr = new BoundaryCorrection(lmp); } + // ---------------------------------------------------------------------- + // code from PPPM::allocate(), altered to use different Grid3d constructor + // ---------------------------------------------------------------------- + + // create ghost grid object for rho and electric field communication + // returns local owned and ghost grid bounds + // setup communication patterns and buffers + + gc = new Grid3d(lmp,world,nx_pppm,ny_pppm,nz_pppm, + nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, + nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out); + + gc->setup_comm(ngc_buf1,ngc_buf2); + + if (differentiation_flag) npergrid = 1; + else npergrid = 3; + + memory->create(gc_buf1,npergrid*ngc_buf1,"pppm:gc_buf1"); + memory->create(gc_buf2,npergrid*ngc_buf2,"pppm:gc_buf2"); + + // tally local grid sizes + // ngrid = count of owned+ghost grid cells on this proc + // nfft_brick = FFT points in 3d brick-decomposition on this proc + // same as count of owned grid cells + // nfft = FFT points in x-pencil FFT decomposition on this proc + // nfft_both = greater of nfft and nfft_brick + + ngrid = (nxhi_out-nxlo_out+1) * (nyhi_out-nylo_out+1) * + (nzhi_out-nzlo_out+1); + + nfft_brick = (nxhi_in-nxlo_in+1) * (nyhi_in-nylo_in+1) * + (nzhi_in-nzlo_in+1); + + nfft = (nxhi_fft-nxlo_fft+1) * (nyhi_fft-nylo_fft+1) * + (nzhi_fft-nzlo_fft+1); + + nfft_both = MAX(nfft,nfft_brick); + + // allocate distributed grid data + + memory->create3d_offset(density_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out, + nxlo_out,nxhi_out,"pppm:density_brick"); + + memory->create(density_fft,nfft_both,"pppm:density_fft"); + memory->create(greensfn,nfft_both,"pppm:greensfn"); + memory->create(work1,2*nfft_both,"pppm:work1"); + memory->create(work2,2*nfft_both,"pppm:work2"); + memory->create(vg,nfft_both,6,"pppm:vg"); + + if (triclinic == 0) { + memory->create1d_offset(fkx,nxlo_fft,nxhi_fft,"pppm:fkx"); + memory->create1d_offset(fky,nylo_fft,nyhi_fft,"pppm:fky"); + memory->create1d_offset(fkz,nzlo_fft,nzhi_fft,"pppm:fkz"); + } else { + memory->create(fkx,nfft_both,"pppm:fkx"); + memory->create(fky,nfft_both,"pppm:fky"); + memory->create(fkz,nfft_both,"pppm:fkz"); + } + + if (differentiation_flag == 1) { + memory->create3d_offset(u_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out, + nxlo_out,nxhi_out,"pppm:u_brick"); + + memory->create(sf_precoeff1,nfft_both,"pppm:sf_precoeff1"); + memory->create(sf_precoeff2,nfft_both,"pppm:sf_precoeff2"); + memory->create(sf_precoeff3,nfft_both,"pppm:sf_precoeff3"); + memory->create(sf_precoeff4,nfft_both,"pppm:sf_precoeff4"); + memory->create(sf_precoeff5,nfft_both,"pppm:sf_precoeff5"); + memory->create(sf_precoeff6,nfft_both,"pppm:sf_precoeff6"); + + } else { + memory->create3d_offset(vdx_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out, + nxlo_out,nxhi_out,"pppm:vdx_brick"); + memory->create3d_offset(vdy_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out, + nxlo_out,nxhi_out,"pppm:vdy_brick"); + memory->create3d_offset(vdz_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out, + nxlo_out,nxhi_out,"pppm:vdz_brick"); + } + + // summation coeffs + + order_allocated = order; + if (!stagger_flag) memory->create(gf_b,order,"pppm:gf_b"); + memory->create2d_offset(rho1d,3,-order/2,order/2,"pppm:rho1d"); + memory->create2d_offset(drho1d,3,-order/2,order/2,"pppm:drho1d"); + memory->create2d_offset(rho_coeff,order,(1-order)/2,order/2,"pppm:rho_coeff"); + memory->create2d_offset(drho_coeff,order,(1-order)/2,order/2, + "pppm:drho_coeff"); + + // create 2 FFTs and a Remap + // 1st FFT keeps data in FFT decomposition + // 2nd FFT returns data in 3d brick decomposition + // remap takes data from 3d brick to FFT decomposition + + int tmp; + + fft1 = new FFT3d(lmp,world,nx_pppm,ny_pppm,nz_pppm, + nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft, + nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft, + 0,0,&tmp,collective_flag); + + fft2 = new FFT3d(lmp,world,nx_pppm,ny_pppm,nz_pppm, + nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft, + nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, + 0,0,&tmp,collective_flag); + + remap = new Remap(lmp,world, + nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, + nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft, + 1,0,0,FFT_PRECISION,collective_flag); + + // ELECTRODE specific allocations + memory->create3d_offset(electrolyte_density_brick, nzlo_out, nzhi_out, nylo_out, nyhi_out, nxlo_out, nxhi_out, "pppm/electrode:electrolyte_density_brick"); memory->create(electrolyte_density_fft, nfft_both, "pppm/electrode:electrolyte_density_fft"); - PPPM::allocate(); + if (differentiation_flag != 1) memory->create3d_offset(u_brick, nzlo_out, nzhi_out, nylo_out, nyhi_out, nxlo_out, nxhi_out, "pppm:u_brick"); @@ -932,6 +1107,12 @@ void PPPMElectrode::allocate() void PPPMElectrode::deallocate() { + delete gc; + gc = nullptr; + memory->destroy(gc_buf1); + memory->destroy(gc_buf2); + + if (boundcorr != nullptr) delete boundcorr; memory->destroy3d_offset(electrolyte_density_brick, nzlo_out, nylo_out, nxlo_out); memory->destroy(electrolyte_density_fft); @@ -967,8 +1148,12 @@ void PPPMElectrode::deallocate() memory->destroy2d_offset(rho_coeff, (1 - order_allocated) / 2); memory->destroy2d_offset(drho_coeff, (1 - order_allocated) / 2); - memory->destroy(gc_buf1); - memory->destroy(gc_buf2); + delete fft1; + delete fft2; + delete remap; + fft1 = nullptr; + fft2 = nullptr; + remap = nullptr; } void PPPMElectrode::allocate_peratom() @@ -1243,10 +1428,8 @@ double PPPMElectrode::compute_qopt() set local subset of PPPM/FFT grid that I own n xyz lo/hi in = 3d brick that I own (inclusive) n xyz lo/hi out = 3d brick + ghost cells in 6 directions (inclusive) - n xyz lo/hi fft = FFT columns that I own (all of x dim, 2d decomp in -yz) -------------------------------------------------------------------------- -*/ + n xyz lo/hi fft = FFT columns that I own (all of x dim, 2d decomp in yz) +------------------------------------------------------------------------- */ void PPPMElectrode::set_grid_local() { @@ -1290,6 +1473,7 @@ void PPPMElectrode::set_grid_local() shift = OFFSET + 0.5; else shift = OFFSET; + if (order % 2) shiftone = 0.0; else diff --git a/src/ELECTRODE/pppm_electrode.h b/src/ELECTRODE/pppm_electrode.h index 4bfa05c65f..1eda1d78b8 100644 --- a/src/ELECTRODE/pppm_electrode.h +++ b/src/ELECTRODE/pppm_electrode.h @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -35,7 +35,7 @@ class PPPMElectrode : public PPPM, public ElectrodeKSpace { ~PPPMElectrode() override; void init() override; void setup() override; - void setup_grid() override; + void reset_grid() override; void compute(int, int) override; void compute_vector(double *, int, int, bool) override; @@ -93,10 +93,9 @@ class PPPMElectrode : public PPPM, public ElectrodeKSpace { void start_compute(); void make_rho_in_brick(int, FFT_SCALAR ***, bool); void project_psi(double *, int); - void one_step_multiplication(bigint *, const std::vector &, double **, double **, - int const, bool); - void two_step_multiplication(bigint *, const std::vector &, double **, double **, - int const, bool); + void one_step_multiplication(bigint *, double *, double **, double **, int const, bool); + void two_step_multiplication(bigint *, double *, double **, double **, int const, bool); + void build_amesh(int, int, int, double *, double *); bool compute_vector_called; }; diff --git a/src/ELECTRODE/slab_2d.cpp b/src/ELECTRODE/slab_2d.cpp index 15d23d698d..f38f22617d 100644 --- a/src/ELECTRODE/slab_2d.cpp +++ b/src/ELECTRODE/slab_2d.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -18,10 +18,12 @@ #include "slab_2d.h" #include "atom.h" -#include "comm.h" #include "domain.h" +#include "force.h" +#include "kspace.h" #include "math_const.h" -#include "memory.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; @@ -32,13 +34,14 @@ using namespace MathConst; ------------------------------------------------------------------------- */ Slab2d::Slab2d(LAMMPS *lmp) : BoundaryCorrection(lmp){}; -void Slab2d::compute_corr(double /*qsum*/, double /*slab_volfactor*/, int eflag_atom, - int eflag_global, double &energy, double *eatom) +void Slab2d::compute_corr(double /*qsum*/, int eflag_atom, int eflag_global, double &energy, + double *eatom) { double *q = atom->q; double **x = atom->x; double **f = atom->f; int nlocal = atom->nlocal; + double const g_ewald = force->kspace->g_ewald; bigint natoms = atom->natoms; std::vector z = std::vector(nlocal); @@ -53,7 +56,9 @@ void Slab2d::compute_corr(double /*qsum*/, double /*slab_volfactor*/, int eflag_ &displs.front(), MPI_DOUBLE, world); const double g_ewald_inv = 1.0 / g_ewald; - const double qscale = qqrd2e * scale; + double const scale = 1.0; + const double qscale = force->qqrd2e * scale; + double const area = domain->xprd * domain->yprd; const double ffact = qscale * MY_2PI / area; const double efact = qscale * MY_PIS / area; double e_keq0 = 0; @@ -70,7 +75,7 @@ void Slab2d::compute_corr(double /*qsum*/, double /*slab_volfactor*/, int eflag_ } // per-atom energy; see eq. (20) in metalwalls ewald doc - if (eflag_atom) eatom[i] -= efact * q[i] * pot_ij; // TODO check if 0.5 factor + if (eflag_atom) eatom[i] -= efact * q[i] * pot_ij; if (eflag_global) e_keq0 -= q[i] * pot_ij; } if (eflag_global) { @@ -105,6 +110,8 @@ void Slab2d::vector_corr(double *vec, int sensor_grpbit, int source_grpbit, bool &recvcounts.front(), &displs.front(), MPI_DOUBLE, world); MPI_Allgatherv(&q_local.front(), n_electrolyte_local, MPI_DOUBLE, &q_all.front(), &recvcounts.front(), &displs.front(), MPI_DOUBLE, world); + double const g_ewald = force->kspace->g_ewald; + double const area = domain->xprd * domain->yprd; double const prefac = 2 * MY_PIS / area; for (int i = 0; i < nlocal; i++) { if (!(mask[i] & sensor_grpbit)) continue; @@ -148,8 +155,10 @@ void Slab2d::matrix_corr(bigint *imat, double **matrix) MPI_Allgatherv(&nprd_local.front(), ngrouplocal, MPI_DOUBLE, &nprd_all.front(), &recvcounts.front(), &displs.front(), MPI_DOUBLE, world); + double const g_ewald = force->kspace->g_ewald; const double g_ewald_inv = 1.0 / g_ewald; const double g_ewald_sq = g_ewald * g_ewald; + double const area = domain->xprd * domain->yprd; const double prefac = 2.0 * MY_PIS / area; std::vector jmat = gather_jmat(imat); for (int i = 0; i < nlocal; i++) { diff --git a/src/ELECTRODE/slab_2d.h b/src/ELECTRODE/slab_2d.h index 8f27218e0f..544602cfab 100644 --- a/src/ELECTRODE/slab_2d.h +++ b/src/ELECTRODE/slab_2d.h @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -27,7 +27,7 @@ class Slab2d : public BoundaryCorrection { Slab2d(LAMMPS *); void vector_corr(double *, int, int, bool) override; void matrix_corr(bigint *, double **) override; - void compute_corr(double, double, int, int, double &, double *) override; + void compute_corr(double, int, int, double &, double *) override; void setup(double); }; diff --git a/src/ELECTRODE/slab_dipole.cpp b/src/ELECTRODE/slab_dipole.cpp index 3f7538c85e..d5f3eae7aa 100644 --- a/src/ELECTRODE/slab_dipole.cpp +++ b/src/ELECTRODE/slab_dipole.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -18,10 +18,13 @@ #include "slab_dipole.h" #include "atom.h" -#include "comm.h" #include "domain.h" +#include "force.h" +#include "kspace.h" #include "math_const.h" +#include + using namespace LAMMPS_NS; using namespace MathConst; @@ -37,13 +40,14 @@ using namespace MathConst; */ SlabDipole::SlabDipole(LAMMPS *lmp) : BoundaryCorrection(lmp){}; -void SlabDipole::compute_corr(double qsum, double slab_volfactor, int eflag_atom, - int eflag_global, double &energy, double *eatom) +void SlabDipole::compute_corr(double qsum, int eflag_atom, int eflag_global, double &energy, + double *eatom) { // compute local contribution to global dipole moment + double const volume = get_volume(); double *q = atom->q; double **x = atom->x; - double zprd_slab = domain->zprd*slab_volfactor; + double zprd_slab = domain->zprd * force->kspace->slab_volfactor; int nlocal = atom->nlocal; double dipole = 0.0; for (int i = 0; i < nlocal; i++) dipole += q[i] * x[i][2]; @@ -65,8 +69,10 @@ void SlabDipole::compute_corr(double qsum, double slab_volfactor, int eflag_atom // compute corrections double const e_slabcorr = MY_2PI * - (dipole_all * dipole_all - qsum * dipole_r2 - qsum * qsum * zprd_slab * zprd_slab / 12.0) / volume; - double const qscale = qqrd2e * scale; + (dipole_all * dipole_all - qsum * dipole_r2 - qsum * qsum * zprd_slab * zprd_slab / 12.0) / + volume; + double const scale = 1.0; + double const qscale = force->qqrd2e * scale; if (eflag_global) energy += qscale * e_slabcorr; // per-atom energy @@ -86,6 +92,7 @@ void SlabDipole::compute_corr(double qsum, double slab_volfactor, int eflag_atom void SlabDipole::vector_corr(double *vec, int sensor_grpbit, int source_grpbit, bool invert_source) { + double const volume = get_volume(); int const nlocal = atom->nlocal; double **x = atom->x; double *q = atom->q; @@ -103,6 +110,7 @@ void SlabDipole::vector_corr(double *vec, int sensor_grpbit, int source_grpbit, void SlabDipole::matrix_corr(bigint *imat, double **matrix) { + double const volume = get_volume(); int nlocal = atom->nlocal; double **x = atom->x; @@ -137,5 +145,4 @@ void SlabDipole::matrix_corr(bigint *imat, double **matrix) if (imat[i] != jmat[j]) matrix[jmat[j]][imat[i]] += aij; } } - // TODO add ELC corrections, needs sum over all kpoints but not (0,0) } diff --git a/src/ELECTRODE/slab_dipole.h b/src/ELECTRODE/slab_dipole.h index 7522038698..baa5fb5a4b 100644 --- a/src/ELECTRODE/slab_dipole.h +++ b/src/ELECTRODE/slab_dipole.h @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -27,7 +27,7 @@ class SlabDipole : public BoundaryCorrection { SlabDipole(LAMMPS *); void vector_corr(double *, int, int, bool); void matrix_corr(bigint *, double **); - void compute_corr(double, double, int, int, double &, double *); + void compute_corr(double, int, int, double &, double *); void setup(double); }; diff --git a/src/ELECTRODE/wire_dipole.cpp b/src/ELECTRODE/wire_dipole.cpp index c2b64ad69e..5a3e3d976a 100644 --- a/src/ELECTRODE/wire_dipole.cpp +++ b/src/ELECTRODE/wire_dipole.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -19,7 +19,7 @@ #include "atom.h" #include "comm.h" -#include "domain.h" +#include "force.h" #include "math_const.h" using namespace LAMMPS_NS; @@ -34,9 +34,10 @@ using namespace MathConst; */ WireDipole::WireDipole(LAMMPS *lmp) : BoundaryCorrection(lmp){}; -void WireDipole::compute_corr(double /*qsum*/, double /*slab_volfactor*/, int eflag_atom, - int eflag_global, double &energy, double *eatom) +void WireDipole::compute_corr(double /*qsum*/, int eflag_atom, int eflag_global, double &energy, + double *eatom) { + double const volume = get_volume(); double *q = atom->q; double **x = atom->x; int nlocal = atom->nlocal; @@ -72,7 +73,8 @@ void WireDipole::compute_corr(double /*qsum*/, double /*slab_volfactor*/, int ef // compute corrections const double e_wirecorr = MY_PI * (xdipole_all * xdipole_all + ydipole_all * ydipole_all) / volume; - const double qscale = qqrd2e * scale; + double const scale = 1.0; + const double qscale = force->qqrd2e * scale; if (eflag_global) energy += qscale * e_wirecorr; // per-atom energy @@ -94,6 +96,7 @@ void WireDipole::compute_corr(double /*qsum*/, double /*slab_volfactor*/, int ef void WireDipole::vector_corr(double *vec, int sensor_grpbit, int source_grpbit, bool invert_source) { + double const volume = get_volume(); int const nlocal = atom->nlocal; double **x = atom->x; double *q = atom->q; @@ -113,6 +116,7 @@ void WireDipole::vector_corr(double *vec, int sensor_grpbit, int source_grpbit, void WireDipole::matrix_corr(bigint *imat, double **matrix) { + double const volume = get_volume(); int nlocal = atom->nlocal; double **x = atom->x; diff --git a/src/ELECTRODE/wire_dipole.h b/src/ELECTRODE/wire_dipole.h index 0db1b2a5f8..649913cd13 100644 --- a/src/ELECTRODE/wire_dipole.h +++ b/src/ELECTRODE/wire_dipole.h @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -27,7 +27,7 @@ class WireDipole : public BoundaryCorrection { WireDipole(LAMMPS *); void vector_corr(double *, int, int, bool); void matrix_corr(bigint *, double **); - void compute_corr(double, double, int, int, double &, double *); + void compute_corr(double, int, int, double &, double *); void setup(double); }; diff --git a/src/EXTRA-COMPUTE/compute_ackland_atom.cpp b/src/EXTRA-COMPUTE/compute_ackland_atom.cpp index 46a7818fd5..d8a77b9c2f 100644 --- a/src/EXTRA-COMPUTE/compute_ackland_atom.cpp +++ b/src/EXTRA-COMPUTE/compute_ackland_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_ackland_atom.h b/src/EXTRA-COMPUTE/compute_ackland_atom.h index 5c4234e728..32f165c083 100644 --- a/src/EXTRA-COMPUTE/compute_ackland_atom.h +++ b/src/EXTRA-COMPUTE/compute_ackland_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_adf.cpp b/src/EXTRA-COMPUTE/compute_adf.cpp index c33edab502..fc74cb8037 100644 --- a/src/EXTRA-COMPUTE/compute_adf.cpp +++ b/src/EXTRA-COMPUTE/compute_adf.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_adf.h b/src/EXTRA-COMPUTE/compute_adf.h index e1d5fda90f..5f30995aa2 100644 --- a/src/EXTRA-COMPUTE/compute_adf.h +++ b/src/EXTRA-COMPUTE/compute_adf.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_ave_sphere_atom.cpp b/src/EXTRA-COMPUTE/compute_ave_sphere_atom.cpp index 010051029a..89011e7177 100644 --- a/src/EXTRA-COMPUTE/compute_ave_sphere_atom.cpp +++ b/src/EXTRA-COMPUTE/compute_ave_sphere_atom.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_ave_sphere_atom.h b/src/EXTRA-COMPUTE/compute_ave_sphere_atom.h index 76350997f9..6c9b9402af 100644 --- a/src/EXTRA-COMPUTE/compute_ave_sphere_atom.h +++ b/src/EXTRA-COMPUTE/compute_ave_sphere_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_basal_atom.cpp b/src/EXTRA-COMPUTE/compute_basal_atom.cpp index 7b2e7b0770..b149746fb4 100644 --- a/src/EXTRA-COMPUTE/compute_basal_atom.cpp +++ b/src/EXTRA-COMPUTE/compute_basal_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -31,7 +31,6 @@ #include "update.h" #include -#include using namespace LAMMPS_NS; diff --git a/src/EXTRA-COMPUTE/compute_basal_atom.h b/src/EXTRA-COMPUTE/compute_basal_atom.h index 75dabb22f9..57716b4057 100644 --- a/src/EXTRA-COMPUTE/compute_basal_atom.h +++ b/src/EXTRA-COMPUTE/compute_basal_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_born_matrix.cpp b/src/EXTRA-COMPUTE/compute_born_matrix.cpp index 7a1d765e40..4eecbbfa14 100644 --- a/src/EXTRA-COMPUTE/compute_born_matrix.cpp +++ b/src/EXTRA-COMPUTE/compute_born_matrix.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -33,10 +33,8 @@ #include "modify.h" #include "molecule.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "pair.h" -#include "universe.h" #include "update.h" #include diff --git a/src/EXTRA-COMPUTE/compute_born_matrix.h b/src/EXTRA-COMPUTE/compute_born_matrix.h index 27b88caaba..d3872cab7c 100644 --- a/src/EXTRA-COMPUTE/compute_born_matrix.h +++ b/src/EXTRA-COMPUTE/compute_born_matrix.h @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_cnp_atom.cpp b/src/EXTRA-COMPUTE/compute_cnp_atom.cpp index 1f74188c06..526874d7a4 100644 --- a/src/EXTRA-COMPUTE/compute_cnp_atom.cpp +++ b/src/EXTRA-COMPUTE/compute_cnp_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_cnp_atom.h b/src/EXTRA-COMPUTE/compute_cnp_atom.h index 0c723faac3..a174bdc67d 100644 --- a/src/EXTRA-COMPUTE/compute_cnp_atom.h +++ b/src/EXTRA-COMPUTE/compute_cnp_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_entropy_atom.cpp b/src/EXTRA-COMPUTE/compute_entropy_atom.cpp index b2fcee7ae4..379f31c7bb 100644 --- a/src/EXTRA-COMPUTE/compute_entropy_atom.cpp +++ b/src/EXTRA-COMPUTE/compute_entropy_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_entropy_atom.h b/src/EXTRA-COMPUTE/compute_entropy_atom.h index 992d4dbf76..89a6fde131 100644 --- a/src/EXTRA-COMPUTE/compute_entropy_atom.h +++ b/src/EXTRA-COMPUTE/compute_entropy_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_gyration_shape.cpp b/src/EXTRA-COMPUTE/compute_gyration_shape.cpp index 47c94ac48d..efda6779a8 100644 --- a/src/EXTRA-COMPUTE/compute_gyration_shape.cpp +++ b/src/EXTRA-COMPUTE/compute_gyration_shape.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_gyration_shape.h b/src/EXTRA-COMPUTE/compute_gyration_shape.h index 45208055ca..19e76def49 100644 --- a/src/EXTRA-COMPUTE/compute_gyration_shape.h +++ b/src/EXTRA-COMPUTE/compute_gyration_shape.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_gyration_shape_chunk.cpp b/src/EXTRA-COMPUTE/compute_gyration_shape_chunk.cpp index b6a3d6b789..2a4eb78fa2 100644 --- a/src/EXTRA-COMPUTE/compute_gyration_shape_chunk.cpp +++ b/src/EXTRA-COMPUTE/compute_gyration_shape_chunk.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_gyration_shape_chunk.h b/src/EXTRA-COMPUTE/compute_gyration_shape_chunk.h index ba38b615c5..dc222f9f58 100644 --- a/src/EXTRA-COMPUTE/compute_gyration_shape_chunk.h +++ b/src/EXTRA-COMPUTE/compute_gyration_shape_chunk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_hexorder_atom.cpp b/src/EXTRA-COMPUTE/compute_hexorder_atom.cpp index 4d7ce9643b..ef694ff7da 100644 --- a/src/EXTRA-COMPUTE/compute_hexorder_atom.cpp +++ b/src/EXTRA-COMPUTE/compute_hexorder_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_hexorder_atom.h b/src/EXTRA-COMPUTE/compute_hexorder_atom.h index 7728ab37d7..8f8af52475 100644 --- a/src/EXTRA-COMPUTE/compute_hexorder_atom.h +++ b/src/EXTRA-COMPUTE/compute_hexorder_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_hma.cpp b/src/EXTRA-COMPUTE/compute_hma.cpp index 12d8325957..0f7279a5f5 100644 --- a/src/EXTRA-COMPUTE/compute_hma.cpp +++ b/src/EXTRA-COMPUTE/compute_hma.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_hma.h b/src/EXTRA-COMPUTE/compute_hma.h index 12af0e809e..d8b8e55b96 100644 --- a/src/EXTRA-COMPUTE/compute_hma.h +++ b/src/EXTRA-COMPUTE/compute_hma.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_momentum.cpp b/src/EXTRA-COMPUTE/compute_momentum.cpp index 9e7ae3f74a..a5f664b820 100644 --- a/src/EXTRA-COMPUTE/compute_momentum.cpp +++ b/src/EXTRA-COMPUTE/compute_momentum.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_momentum.h b/src/EXTRA-COMPUTE/compute_momentum.h index fd8d07cffa..119f5f4a6c 100644 --- a/src/EXTRA-COMPUTE/compute_momentum.h +++ b/src/EXTRA-COMPUTE/compute_momentum.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_msd_nongauss.cpp b/src/EXTRA-COMPUTE/compute_msd_nongauss.cpp index 24920e50cf..f75ab69a01 100644 --- a/src/EXTRA-COMPUTE/compute_msd_nongauss.cpp +++ b/src/EXTRA-COMPUTE/compute_msd_nongauss.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_msd_nongauss.h b/src/EXTRA-COMPUTE/compute_msd_nongauss.h index d3faf0e555..cc8b9c4d33 100644 --- a/src/EXTRA-COMPUTE/compute_msd_nongauss.h +++ b/src/EXTRA-COMPUTE/compute_msd_nongauss.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp b/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp index 1e942627bb..eb93a31655 100644 --- a/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp +++ b/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -20,7 +20,6 @@ #include "error.h" #include "force.h" #include "memory.h" -#include "modify.h" #include "neigh_list.h" #include "neighbor.h" #include "pair.h" diff --git a/src/EXTRA-COMPUTE/compute_stress_cartesian.h b/src/EXTRA-COMPUTE/compute_stress_cartesian.h index d4505a1e8e..0954d9ca71 100644 --- a/src/EXTRA-COMPUTE/compute_stress_cartesian.h +++ b/src/EXTRA-COMPUTE/compute_stress_cartesian.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_stress_cylinder.cpp b/src/EXTRA-COMPUTE/compute_stress_cylinder.cpp index 6304744ba1..f445b258b1 100644 --- a/src/EXTRA-COMPUTE/compute_stress_cylinder.cpp +++ b/src/EXTRA-COMPUTE/compute_stress_cylinder.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -21,7 +21,6 @@ #include "math_const.h" #include "math_special.h" #include "memory.h" -#include "modify.h" #include "neigh_list.h" #include "neighbor.h" #include "pair.h" @@ -29,7 +28,6 @@ #include #include -#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/EXTRA-COMPUTE/compute_stress_cylinder.h b/src/EXTRA-COMPUTE/compute_stress_cylinder.h index 40f7f9f551..4104b3f733 100644 --- a/src/EXTRA-COMPUTE/compute_stress_cylinder.h +++ b/src/EXTRA-COMPUTE/compute_stress_cylinder.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp index 883321bf2b..60f2d76e06 100644 --- a/src/EXTRA-COMPUTE/compute_stress_mop.cpp +++ b/src/EXTRA-COMPUTE/compute_stress_mop.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.h b/src/EXTRA-COMPUTE/compute_stress_mop.h index 220fc329cc..5357d36371 100644 --- a/src/EXTRA-COMPUTE/compute_stress_mop.h +++ b/src/EXTRA-COMPUTE/compute_stress_mop.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp index fc01903aa1..709f109cb1 100644 --- a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp +++ b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_stress_mop_profile.h b/src/EXTRA-COMPUTE/compute_stress_mop_profile.h index ba5509d717..b58f762c12 100644 --- a/src/EXTRA-COMPUTE/compute_stress_mop_profile.h +++ b/src/EXTRA-COMPUTE/compute_stress_mop_profile.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_stress_spherical.cpp b/src/EXTRA-COMPUTE/compute_stress_spherical.cpp index c893d21f51..6a6ec4745f 100644 --- a/src/EXTRA-COMPUTE/compute_stress_spherical.cpp +++ b/src/EXTRA-COMPUTE/compute_stress_spherical.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -19,19 +19,15 @@ #include "domain.h" #include "error.h" #include "force.h" -#include "lattice.h" #include "math_const.h" #include "math_special.h" #include "memory.h" -#include "modify.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "pair.h" #include "update.h" #include -#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/EXTRA-COMPUTE/compute_stress_spherical.h b/src/EXTRA-COMPUTE/compute_stress_spherical.h index c4e626a40f..5845547e5f 100644 --- a/src/EXTRA-COMPUTE/compute_stress_spherical.h +++ b/src/EXTRA-COMPUTE/compute_stress_spherical.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_temp_rotate.cpp b/src/EXTRA-COMPUTE/compute_temp_rotate.cpp index 300333c26f..1bc42b1134 100644 --- a/src/EXTRA-COMPUTE/compute_temp_rotate.cpp +++ b/src/EXTRA-COMPUTE/compute_temp_rotate.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_temp_rotate.h b/src/EXTRA-COMPUTE/compute_temp_rotate.h index 76eec14c31..d023e1140e 100644 --- a/src/EXTRA-COMPUTE/compute_temp_rotate.h +++ b/src/EXTRA-COMPUTE/compute_temp_rotate.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_ti.cpp b/src/EXTRA-COMPUTE/compute_ti.cpp index d416fab1de..d405ba86e9 100644 --- a/src/EXTRA-COMPUTE/compute_ti.cpp +++ b/src/EXTRA-COMPUTE/compute_ti.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-COMPUTE/compute_ti.h b/src/EXTRA-COMPUTE/compute_ti.h index 15a1e78667..be9c460cc5 100644 --- a/src/EXTRA-COMPUTE/compute_ti.h +++ b/src/EXTRA-COMPUTE/compute_ti.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-DUMP/dump_dcd.cpp b/src/EXTRA-DUMP/dump_dcd.cpp index 3aca5e8a98..f7e7ab2737 100644 --- a/src/EXTRA-DUMP/dump_dcd.cpp +++ b/src/EXTRA-DUMP/dump_dcd.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-DUMP/dump_dcd.h b/src/EXTRA-DUMP/dump_dcd.h index 79999f8b8e..1d893e25d8 100644 --- a/src/EXTRA-DUMP/dump_dcd.h +++ b/src/EXTRA-DUMP/dump_dcd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-DUMP/dump_xtc.cpp b/src/EXTRA-DUMP/dump_xtc.cpp index 8e0bb4a0d7..6b0b97181b 100644 --- a/src/EXTRA-DUMP/dump_xtc.cpp +++ b/src/EXTRA-DUMP/dump_xtc.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-DUMP/dump_xtc.h b/src/EXTRA-DUMP/dump_xtc.h index 1ffb2ba6bf..74147be06b 100644 --- a/src/EXTRA-DUMP/dump_xtc.h +++ b/src/EXTRA-DUMP/dump_xtc.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-DUMP/dump_yaml.cpp b/src/EXTRA-DUMP/dump_yaml.cpp index be1c9768bf..3c35ec43ba 100644 --- a/src/EXTRA-DUMP/dump_yaml.cpp +++ b/src/EXTRA-DUMP/dump_yaml.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -20,6 +20,8 @@ #include "thermo.h" #include "update.h" +#include + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/EXTRA-DUMP/dump_yaml.h b/src/EXTRA-DUMP/dump_yaml.h index 60ab894de4..bb846cdd98 100644 --- a/src/EXTRA-DUMP/dump_yaml.h +++ b/src/EXTRA-DUMP/dump_yaml.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_addtorque.cpp b/src/EXTRA-FIX/fix_addtorque.cpp index 3a29a5abd7..aee2f20e45 100644 --- a/src/EXTRA-FIX/fix_addtorque.cpp +++ b/src/EXTRA-FIX/fix_addtorque.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_addtorque.h b/src/EXTRA-FIX/fix_addtorque.h index 827e47ab80..23365ca894 100644 --- a/src/EXTRA-FIX/fix_addtorque.h +++ b/src/EXTRA-FIX/fix_addtorque.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_ave_correlate_long.cpp b/src/EXTRA-FIX/fix_ave_correlate_long.cpp index 9ed8a1e466..a44d6414f7 100644 --- a/src/EXTRA-FIX/fix_ave_correlate_long.cpp +++ b/src/EXTRA-FIX/fix_ave_correlate_long.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -26,76 +26,86 @@ #include "arg_info.h" #include "citeme.h" +#include "comm.h" #include "compute.h" #include "error.h" #include "input.h" +#include "math_special.h" #include "memory.h" #include "modify.h" #include "update.h" #include "variable.h" -#include #include using namespace LAMMPS_NS; using namespace FixConst; +using MathSpecial::powint; -enum{AUTO,UPPER,LOWER,AUTOUPPER,AUTOLOWER,FULL}; +enum { AUTO, UPPER, LOWER, AUTOUPPER, AUTOLOWER, FULL }; static const char cite_fix_ave_correlate_long[] = -"fix ave/correlate/long command: doi:10.1063/1.3491098\n\n" -"@Article{Ramirez10,\n" -" author = {Jorge Rami{\'}rez and Sathish K. Sukumaran and Bart Vorselaars and Alexei E. Likhtman},\n" -" title = {Efficient on the Fly Calculation of Time Correlation Functions in Computer Simulations}," -" journal = {J.~Chem.\\ Phys.},\n" -" year = 2010,\n" -" volume = 133,\n" -" number = 15,\n" -" pages = {154103}\n" -"}\n\n"; + "fix ave/correlate/long command: doi:10.1063/1.3491098\n\n" + "@Article{Ramirez10,\n" + " author = {Jorge Rami{\'}rez and Sathish K. Sukumaran and Bart Vorselaars and Alexei E. " + "Likhtman},\n" + " title = {Efficient on the Fly Calculation of Time Correlation Functions in Computer " + "Simulations}," + " journal = {J.~Chem.\\ Phys.},\n" + " year = 2010,\n" + " volume = 133,\n" + " number = 15,\n" + " pages = {154103}\n" + "}\n\n"; /* ---------------------------------------------------------------------- */ -FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg): - Fix (lmp, narg, arg) +FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg), shift(nullptr), shift2(nullptr), correlation(nullptr), + accumulator(nullptr), accumulator2(nullptr), ncorrelation(nullptr), naccumulator(nullptr), + insertindex(nullptr), fp(nullptr), cvalues(nullptr) { if (lmp->citeme) lmp->citeme->add(cite_fix_ave_correlate_long); - // At least nevery nfrez and one value are needed - if (narg < 6) error->all(FLERR,"Illegal fix ave/correlate/long command"); + // At least nevery nfreq and one value are needed + if (narg < 6) utils::missing_cmd_args(FLERR, "fix ave/correlate/long", error); - MPI_Comm_rank(world,&me); - - nevery = utils::inumeric(FLERR,arg[3],false,lmp); - nfreq = utils::inumeric(FLERR,arg[4],false,lmp); + nevery = utils::inumeric(FLERR, arg[3], false, lmp); + nfreq = utils::inumeric(FLERR, arg[4], false, lmp); restart_global = 1; global_freq = nfreq; time_depend = 1; - // parse values until one isn't recognized + // expand args if any have wildcard character "*" - which = new int[narg-5]; - argindex = new int[narg-5]; - ids = new char*[narg-5]; - value2index = new int[narg-5]; - nvalues = 0; + int expand = 0; + char **earg; + int nargnew = utils::expand_args(FLERR, narg - 5, &arg[5], 0, earg, lmp); - int iarg = 5; - while (iarg < narg) { + if (earg != &arg[5]) expand = 1; + arg = earg; + // parse values + + int iarg = 0; + while (iarg < nargnew) { ArgInfo argi(arg[iarg]); + value_t val; + if (argi.get_type() == ArgInfo::NONE) break; if ((argi.get_type() == ArgInfo::UNKNOWN) || (argi.get_dim() > 1)) - error->all(FLERR,"Illegal fix ave/correlate/long command"); + error->all(FLERR, "Unknown fix ave/correlate/long data type: {}", arg[iarg]); - which[nvalues] = argi.get_type(); - argindex[nvalues] = argi.get_index1(); - ids[nvalues] = argi.copy_name(); + val.which = argi.get_type(); + val.argindex = argi.get_index1(); + val.id = argi.get_name(); + val.val.c = nullptr; - nvalues++; + values.push_back(val); iarg++; } + nvalues = values.size(); // optional args @@ -103,128 +113,136 @@ FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg): startstep = 0; fp = nullptr; overwrite = 0; - numcorrelators=20; + numcorrelators = 20; p = 16; m = 2; char *title1 = nullptr; char *title2 = nullptr; - while (iarg < narg) { - if (strcmp(arg[iarg],"type") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal fix ave/correlate/long command"); - if (strcmp(arg[iarg+1],"auto") == 0) type = AUTO; - else if (strcmp(arg[iarg+1],"upper") == 0) type = UPPER; - else if (strcmp(arg[iarg+1],"lower") == 0) type = LOWER; - else if (strcmp(arg[iarg+1],"auto/upper") == 0) type = AUTOUPPER; - else if (strcmp(arg[iarg+1],"auto/lower") == 0) type = AUTOLOWER; - else if (strcmp(arg[iarg+1],"full") == 0) type = FULL; - else error->all(FLERR,"Illegal fix ave/correlate/long command"); + while (iarg < nargnew) { + if (strcmp(arg[iarg], "type") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate/long type", error); + if (strcmp(arg[iarg + 1], "auto") == 0) + type = AUTO; + else if (strcmp(arg[iarg + 1], "upper") == 0) + type = UPPER; + else if (strcmp(arg[iarg + 1], "lower") == 0) + type = LOWER; + else if (strcmp(arg[iarg + 1], "auto/upper") == 0) + type = AUTOUPPER; + else if (strcmp(arg[iarg + 1], "auto/lower") == 0) + type = AUTOLOWER; + else if (strcmp(arg[iarg + 1], "full") == 0) + type = FULL; + else + error->all(FLERR, "Unknown fix ave/correlate/long type: {}"); iarg += 2; - } else if (strcmp(arg[iarg],"start") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal fix ave/correlate/long command"); - startstep = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + } else if (strcmp(arg[iarg], "start") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate/long start", error); + startstep = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"ncorr") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal fix ave/correlate/long command"); - numcorrelators = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + } else if (strcmp(arg[iarg], "ncorr") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate/long ncorr", error); + numcorrelators = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"nlen") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal fix ave/correlate/long command"); - p = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + } else if (strcmp(arg[iarg], "nlen") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate/long nlen", error); + p = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"ncount") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal fix ave/correlate/long command"); - m = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + } else if (strcmp(arg[iarg], "ncount") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate/long ncount", error); + m = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"file") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal fix ave/correlate/long command"); - if (me == 0) { - fp = fopen(arg[iarg+1],"w"); + } else if (strcmp(arg[iarg], "file") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate/long file", error); + if (comm->me == 0) { + fp = fopen(arg[iarg + 1], "w"); if (fp == nullptr) - error->one(FLERR,"Cannot open fix ave/correlate/long file {}: {}", - arg[iarg+1],utils::getsyserror()); + error->one(FLERR, "Cannot open fix ave/correlate/long file {}: {}", arg[iarg + 1], + utils::getsyserror()); } iarg += 2; - } else if (strcmp(arg[iarg],"overwrite") == 0) { + } else if (strcmp(arg[iarg], "overwrite") == 0) { overwrite = 1; iarg += 1; - } else if (strcmp(arg[iarg],"title1") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal fix ave/correlate/long command"); + } else if (strcmp(arg[iarg], "title1") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate/long title1", error); delete[] title1; - title1 = utils::strdup(arg[iarg+1]); + title1 = utils::strdup(arg[iarg + 1]); iarg += 2; - } else if (strcmp(arg[iarg],"title2") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal fix ave/correlate/long command"); + } else if (strcmp(arg[iarg], "title2") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate/long title2", error); delete[] title2; - title2 = utils::strdup(arg[iarg+1]); + title2 = utils::strdup(arg[iarg + 1]); iarg += 2; - } else error->all(FLERR,"Illegal fix ave/correlate/long command"); + } else + error->all(FLERR, "Unknown fix ave/correlate/long keyword: {}", arg[iarg]); } - if (p % m != 0) error->all(FLERR,"fix_correlator: p mod m must be 0"); - dmin = p/m; - length = numcorrelators*p; + if (p % m != 0) error->all(FLERR, "Fix ave/correlate/long: nlen must be divisible by ncount"); + dmin = p / m; + length = numcorrelators * p; npcorr = 0; kmax = 0; // setup and error check // for fix inputs, check that fix frequency is acceptable - if (nevery <= 0 || nfreq <= 0) - error->all(FLERR,"Illegal fix ave/correlate/long command"); - if (nfreq % nevery) - error->all(FLERR,"Illegal fix ave/correlate/long command"); + if (nevery <= 0) error->all(FLERR, "Illegal fix ave/correlate/long nevery value: {}", nevery); + if (nfreq <= 0) error->all(FLERR, "Illegal fix ave/correlate/long nfreq value: {}", nfreq); + if (nfreq % nevery) error->all(FLERR, "Inconsistent fix ave/correlate/long nevery/nfreq values"); - for (int i = 0; i < nvalues; i++) { - if (which[i] == ArgInfo::COMPUTE) { - int icompute = modify->find_compute(ids[i]); - if (icompute < 0) - error->all(FLERR,"Compute ID for fix ave/correlate/long does not exist"); - if (argindex[i] == 0 && modify->compute[icompute]->scalar_flag == 0) - error->all(FLERR,"Fix ave/correlate/long compute does not calculate a scalar"); - if (argindex[i] && modify->compute[icompute]->vector_flag == 0) - error->all(FLERR,"Fix ave/correlate/long compute does not calculate a vector"); - if (argindex[i] && argindex[i] > modify->compute[icompute]->size_vector) - error->all(FLERR,"Fix ave/correlate/long compute vector is accessed out-of-range"); + for (auto &val : values) { - } else if (which[i] == ArgInfo::FIX) { - int ifix = modify->find_fix(ids[i]); - if (ifix < 0) - error->all(FLERR,"Fix ID for fix ave/correlate/long does not exist"); - if (argindex[i] == 0 && modify->fix[ifix]->scalar_flag == 0) - error->all(FLERR,"Fix ave/correlate/long fix does not calculate a scalar"); - if (argindex[i] && modify->fix[ifix]->vector_flag == 0) - error->all(FLERR,"Fix ave/correlate/long fix does not calculate a vector"); - if (argindex[i] && argindex[i] > modify->fix[ifix]->size_vector) - error->all(FLERR,"Fix ave/correlate/long fix vector is accessed out-of-range"); - if (nevery % modify->fix[ifix]->global_freq) - error->all(FLERR,"Fix for fix ave/correlate/long not computed at compatible time"); + if (val.which == ArgInfo::COMPUTE) { + val.val.c = modify->get_compute_by_id(val.id); + if (!val.val.c) + error->all(FLERR, "Compute ID {} for fix ave/correlate/long does not exist", val.id); + if (val.argindex == 0 && val.val.c->scalar_flag == 0) + error->all(FLERR, "Fix ave/correlate/long compute {} does not calculate a scalar", val.id); + if (val.argindex && val.val.c->vector_flag == 0) + error->all(FLERR, "Fix ave/correlate/long compute {} does not calculate a vector", val.id); + if (val.argindex && val.argindex > val.val.c->size_vector) + error->all(FLERR, "Fix ave/correlate/long compute {} vector is accessed out-of-range", + val.id); - } else if (which[i] == ArgInfo::VARIABLE) { - int ivariable = input->variable->find(ids[i]); - if (ivariable < 0) - error->all(FLERR,"Variable name for fix ave/correlate/long does not exist"); - if (input->variable->equalstyle(ivariable) == 0) - error->all(FLERR,"Fix ave/correlate/long variable is not equal-style variable"); + } else if (val.which == ArgInfo::FIX) { + val.val.f = modify->get_fix_by_id(val.id); + if (!val.val.f) + error->all(FLERR, "Fix ID {} for fix ave/correlate/long does not exist", val.id); + if (val.argindex == 0 && val.val.f->scalar_flag == 0) + error->all(FLERR, "Fix ave/correlate/long fix {} does not calculate a scalar", val.id); + if (val.argindex && val.val.f->vector_flag == 0) + error->all(FLERR, "Fix ave/correlate/long fix {} does not calculate a vector", val.id); + if (val.argindex && val.argindex > val.val.f->size_vector) + error->all(FLERR, "Fix ave/correlate/long fix {} vector is accessed out-of-range", val.id); + if (nevery % val.val.f->global_freq) + error->all(FLERR, "Fix {} for fix ave/correlate/long not computed at compatible time", + val.id); + + } else if (val.which == ArgInfo::VARIABLE) { + val.val.v = input->variable->find(val.id.c_str()); + if (val.val.v < 0) + error->all(FLERR, "Variable name {} for fix ave/correlate/long does not exist", val.id); + if (val.argindex == 0 && input->variable->equalstyle(val.val.v) == 0) + error->all(FLERR, "Fix ave/correlate/long variable {} is not equal-style variable", val.id); + if (val.argindex && input->variable->vectorstyle(val.val.v) == 0) + error->all(FLERR, "Fix ave/correlate/long variable {} is not vector-style variable", + val.id); } } // npair = # of correlation pairs to calculate + if (type == AUTO) npair = nvalues; - if (type == UPPER || type == LOWER) npair = nvalues*(nvalues-1)/2; - if (type == AUTOUPPER || type == AUTOLOWER) npair = nvalues*(nvalues+1)/2; - if (type == FULL) npair = nvalues*nvalues; + if (type == UPPER || type == LOWER) npair = nvalues * (nvalues - 1) / 2; + if (type == AUTOUPPER || type == AUTOLOWER) npair = nvalues * (nvalues + 1) / 2; + if (type == FULL) npair = nvalues * nvalues; // print file comment lines - if (fp && me == 0) { + + if (fp && comm->me == 0) { + clearerr(fp); if (title1) fprintf(fp,"%s\n",title1); else fprintf(fp,"# Time-correlated data for fix %s\n",id); if (title2) fprintf(fp,"%s\n",title2); @@ -232,38 +250,49 @@ FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg): fprintf(fp,"# Time"); if (type == AUTO) for (int i = 0; i < nvalues; i++) - fprintf(fp," %s*%s",arg[5+i],arg[5+i]); + fprintf(fp," %s*%s",earg[i],earg[i]); else if (type == UPPER) for (int i = 0; i < nvalues; i++) for (int j = i+1; j < nvalues; j++) - fprintf(fp," %s*%s",arg[5+i],arg[5+j]); + fprintf(fp," %s*%s",earg[i],earg[j]); else if (type == LOWER) for (int i = 0; i < nvalues; i++) for (int j = 0; j < i-1; j++) - fprintf(fp," %s*%s",arg[5+i],arg[5+j]); + fprintf(fp," %s*%s",earg[i],earg[j]); else if (type == AUTOUPPER) for (int i = 0; i < nvalues; i++) for (int j = i; j < nvalues; j++) - fprintf(fp," %s*%s",arg[5+i],arg[5+j]); + fprintf(fp," %s*%s",earg[i],earg[j]); else if (type == AUTOLOWER) for (int i = 0; i < nvalues; i++) for (int j = 0; j < i; j++) - fprintf(fp," %s*%s",arg[5+i],arg[5+j]); + fprintf(fp," %s*%s",earg[i],earg[j]); else if (type == FULL) for (int i = 0; i < nvalues; i++) for (int j = 0; j < nvalues; j++) - fprintf(fp," %s*%s",arg[5+i],arg[5+j]); + fprintf(fp," %s*%s",earg[i],earg[j]); fprintf(fp,"\n"); } + if (ferror(fp)) + error->one(FLERR,"Error writing ave/correlate/long header: {}", utils::getsyserror()); + filepos = platform::ftell(fp); } delete[] title1; delete[] title2; + // if wildcard expansion occurred, free earg memory from expand_args() + // wait to do this until after file comment lines are printed + + if (expand) { + for (int i = 0; i < nargnew; i++) delete[] earg[i]; + memory->sfree(earg); + } + // allocate and initialize memory for calculated values and correlators - memory->create(values,nvalues,"correlator:values"); + memory->create(cvalues,nvalues,"correlator:values"); memory->create(shift,npair,numcorrelators,p,"correlator:shift"); memory->create(shift2,npair,numcorrelators,p,"correlator:shift2"); //NOT OPTMAL memory->create(correlation,npair,numcorrelators,p,"correlator:correlation"); @@ -276,10 +305,10 @@ FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg): memory->create(t,length,"correlator:t"); memory->create(f,npair,length,"correlator:f"); - for (int i=0;idestroy(values); + memory->destroy(cvalues); memory->destroy(shift); memory->destroy(shift2); memory->destroy(correlation); @@ -332,7 +354,7 @@ FixAveCorrelateLong::~FixAveCorrelateLong() memory->destroy(t); memory->destroy(f); - if (fp && me == 0) fclose(fp); + if (fp && comm->me == 0) fclose(fp); } /* ---------------------------------------------------------------------- */ @@ -350,24 +372,22 @@ void FixAveCorrelateLong::init() { // set current indices for all computes,fixes,variables - for (int i = 0; i < nvalues; i++) { - if (which[i] == ArgInfo::COMPUTE) { - int icompute = modify->find_compute(ids[i]); - if (icompute < 0) - error->all(FLERR,"Compute ID for fix ave/correlate/long does not exist"); - value2index[i] = icompute; + for (auto &val : values) { - } else if (which[i] == ArgInfo::FIX) { - int ifix = modify->find_fix(ids[i]); - if (ifix < 0) - error->all(FLERR,"Fix ID for fix ave/correlate/long does not exist"); - value2index[i] = ifix; + if (val.which == ArgInfo::COMPUTE) { + val.val.c = modify->get_compute_by_id(val.id); + if (!val.val.c) + error->all(FLERR, "Compute ID {} for fix ave/correlate/long does not exist", val.id); - } else if (which[i] == ArgInfo::VARIABLE) { - int ivariable = input->variable->find(ids[i]); - if (ivariable < 0) - error->all(FLERR,"Variable name for fix ave/correlate/long does not exist"); - value2index[i] = ivariable; + } else if (val.which == ArgInfo::FIX) { + val.val.f = modify->get_fix_by_id(val.id); + if (!val.val.f) + error->all(FLERR,"Fix ID {} for fix ave/correlate/long does not exist", val.id); + + } else if (val.which == ArgInfo::VARIABLE) { + val.val.v = input->variable->find(val.id.c_str()); + if (val.val.v < 0) + error->all(FLERR,"Variable name {} for fix ave/correlate/long does not exist", val.id); } } @@ -392,9 +412,6 @@ void FixAveCorrelateLong::setup(int /*vflag*/) void FixAveCorrelateLong::end_of_step() { - int i,m; - double scalar; - // skip if not step which requires doing something bigint ntimestep = update->ntimestep; @@ -406,43 +423,51 @@ void FixAveCorrelateLong::end_of_step() modify->clearstep_compute(); - for (i = 0; i < nvalues; i++) { - m = value2index[i]; - scalar = 0.0; + int i = 0; + for (auto &val : values) { + double scalar = 0.0; // invoke compute if not previously invoked - if (which[i] == ArgInfo::COMPUTE) { - Compute *compute = modify->compute[m]; + if (val.which == ArgInfo::COMPUTE) { - if (argindex[i] == 0) { - if (!(compute->invoked_flag & Compute::INVOKED_SCALAR)) { - compute->compute_scalar(); - compute->invoked_flag |= Compute::INVOKED_SCALAR; + if (val.argindex == 0) { + if (!(val.val.c->invoked_flag & Compute::INVOKED_SCALAR)) { + val.val.c->compute_scalar(); + val.val.c->invoked_flag |= Compute::INVOKED_SCALAR; } - scalar = compute->scalar; + scalar = val.val.c->scalar; } else { - if (!(compute->invoked_flag & Compute::INVOKED_VECTOR)) { - compute->compute_vector(); - compute->invoked_flag |= Compute::INVOKED_VECTOR; + if (!(val.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { + val.val.c->compute_vector(); + val.val.c->invoked_flag |= Compute::INVOKED_VECTOR; } - scalar = compute->vector[argindex[i]-1]; + scalar = val.val.c->vector[val.argindex-1]; } - // access fix fields, guaranteed to be ready + // access fix fields, guaranteed to be ready - } else if (which[i] == ArgInfo::FIX) { - if (argindex[i] == 0) - scalar = modify->fix[m]->compute_scalar(); + } else if (val.which == ArgInfo::FIX) { + if (val.argindex == 0) + scalar = val.val.f->compute_scalar(); else - scalar = modify->fix[m]->compute_vector(argindex[i]-1); + scalar = val.val.f->compute_vector(val.argindex-1); - // evaluate equal-style variable + // evaluate equal-style or vector-style variable - } else if (which[i] == ArgInfo::VARIABLE) - scalar = input->variable->compute_equal(m); + } else if (val.which == ArgInfo::VARIABLE) { + if (val.argindex == 0) + scalar = input->variable->compute_equal(val.val.v); + else { + double *varvec; + int nvec = input->variable->compute_vector(val.val.v,&varvec); + int index = val.argindex; + if (nvec < index) scalar = 0.0; + else scalar = varvec[index-1]; + } + } - values[i] = scalar; + cvalues[i++] = scalar; } // fistindex = index in values ring of earliest time sample @@ -456,19 +481,25 @@ void FixAveCorrelateLong::end_of_step() if (ntimestep % nfreq) return; // output result to file + evaluate(); - if (fp && me == 0) { + if (fp && comm->me == 0) { + clearerr(fp); if (overwrite) platform::fseek(fp,filepos); fmt::print(fp,"# Timestep: {}\n", ntimestep); - for (unsigned int i=0;idt*nevery); - for (int j=0;jone(FLERR,"Error writing out fix ave/correlate/long data: {}", utils::getsyserror()); + fflush(fp); + if (overwrite) { bigint fileend = platform::ftell(fp); if ((fileend > 0) && (platform::ftruncate(fp,fileend))) @@ -481,20 +512,20 @@ void FixAveCorrelateLong::evaluate() { unsigned int jm=0; // First correlator - for (unsigned int j=0;j 0) { t[jm] = j; - for (int i=0;i0) { - t[jm] = j * pow((double)m, k); + t[jm] = j * powint((double)m, k); for (int i=0;intimestep <= last_accumulated_step) return; if (type == AUTO) { - for (i=0; intimestep; @@ -565,38 +596,38 @@ void FixAveCorrelateLong::add(const int i, const double w, const int k) { // Add to accumulator and, if needed, add to next correlator accumulator[i][k] += w; - if (i==0) ++naccumulator[k]; + if (i == 0) ++naccumulator[k]; if (naccumulator[k]==m) { add(i,accumulator[i][k]/m, k+1); accumulator[i][k]=0; - if (i==npair-1) naccumulator[k]=0; + if (i == npair-1) naccumulator[k]=0; } // Calculate correlation function unsigned int ind1=insertindex[k]; - if (k==0) { // First correlator is different + if (k == 0) { // First correlator is different int ind2=ind1; - for (unsigned int j=0;j -1e10) { correlation[i][k][j]+= shift[i][k][ind1]*shift[i][k][ind2]; if (i==0) ++ncorrelation[k][j]; } --ind2; - if (ind2<0) ind2+=p; + if (ind2 < 0) ind2+=p; } } else { int ind2=ind1-dmin; for (unsigned int j=dmin;j -1e10) { correlation[i][k][j]+= shift[i][k][ind1]*shift[i][k][ind2]; - if (i==0) ++ncorrelation[k][j]; + if (i == 0) ++ncorrelation[k][j]; } --ind2; } } - if (i==npair-1) { + if (i == npair-1) { ++insertindex[k]; if (insertindex[k]==p) insertindex[k]=0; } @@ -606,8 +637,7 @@ void FixAveCorrelateLong::add(const int i, const double w, const int k) { /* ---------------------------------------------------------------------- Add 2 scalar values to the cross-correlator k of pair i ------------------------------------------------------------------------- */ -void FixAveCorrelateLong::add(const int i, const double wA, const double wB, - const int k) { +void FixAveCorrelateLong::add(const int i, const double wA, const double wB, const int k) { if (k == numcorrelators) return; if (k > kmax) kmax=k; @@ -616,21 +646,21 @@ void FixAveCorrelateLong::add(const int i, const double wA, const double wB, accumulator[i][k] += wA; accumulator2[i][k] += wB; - if (i==0) ++naccumulator[k]; - if (naccumulator[k]==m) { + if (i == 0) ++naccumulator[k]; + if (naccumulator[k] == m) { add(i,accumulator[i][k]/m, accumulator2[i][k]/m,k+1); accumulator[i][k]=0; accumulator2[i][k]=0; - if (i==npair-1) naccumulator[k]=0; + if (i == npair-1) naccumulator[k]=0; } unsigned int ind1=insertindex[k]; - if (k==0) { + if (k == 0) { int ind2=ind1; - for (unsigned int j=0;j -1e10) { correlation[i][k][j]+= shift[i][k][ind1]*shift2[i][k][ind2]; - if (i==0) ++ncorrelation[k][j]; + if (i == 0) ++ncorrelation[k][j]; } --ind2; if (ind2<0) ind2+=p; @@ -638,19 +668,19 @@ void FixAveCorrelateLong::add(const int i, const double wA, const double wB, } else { int ind2=ind1-dmin; - for (unsigned int j=dmin;j -1e10) { correlation[i][k][j]+= shift[i][k][ind1]*shift2[i][k][ind2]; - if (i==0) ++ncorrelation[k][j]; + if (i == 0) ++ncorrelation[k][j]; } --ind2; } } - if (i==npair-1) { + if (i == npair-1) { ++insertindex[k]; - if (insertindex[k]==p) insertindex[k]=0; + if (insertindex[k] == p) insertindex[k]=0; } } @@ -696,20 +726,20 @@ double FixAveCorrelateLong::memory_usage() { ------------------------------------------------------------------------- */ // Save everything except t and f void FixAveCorrelateLong::write_restart(FILE *fp) { - if (me == 0) { + if (comm->me == 0) { int nsize = 3*npair*numcorrelators*p + 2*npair*numcorrelators + numcorrelators*p + 2*numcorrelators + 6; int n=0; double *list; memory->create(list,nsize,"correlator:list"); - list[n++]=npair; - list[n++]=numcorrelators; - list[n++]=p; - list[n++]=m; + list[n++] = npair; + list[n++] = numcorrelators; + list[n++] = p; + list[n++] = m; list[n++] = last_accumulated_step; - for (int i=0;i (list[n++]); + int npairin = static_cast(list[n++]); int numcorrelatorsin = static_cast (list[n++]); - int pin = static_cast (list[n++]); - int min = static_cast (list[n++]); - last_accumulated_step = static_cast (list[n++]); + int pin = static_cast(list[n++]); + int min = static_cast(list[n++]); + last_accumulated_step = static_cast(list[n++]); - if ((npairin!=npair) || (numcorrelatorsin!=numcorrelators) - || (pin!=(int)p) || (min!=(int)m)) - error->all(FLERR,"Fix ave/correlate/long: restart and input data are different"); + if ((npairin!=npair) || (numcorrelatorsin!=numcorrelators) || (pin!=(int)p) || (min!=(int)m)) + error->all(FLERR, "Fix ave/correlate/long: restart and input data are different"); - for (int i=0;i(list[n++]); - naccumulator[i] = static_cast (list[n++]); - insertindex[i] = static_cast (list[n++]); + naccumulator[i] = static_cast(list[n++]); + insertindex[i] = static_cast(list[n++]); } } diff --git a/src/EXTRA-FIX/fix_ave_correlate_long.h b/src/EXTRA-FIX/fix_ave_correlate_long.h index 0c540aa727..43a2e322a3 100644 --- a/src/EXTRA-FIX/fix_ave_correlate_long.h +++ b/src/EXTRA-FIX/fix_ave_correlate_long.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -58,18 +58,27 @@ class FixAveCorrelateLong : public Fix { int length; // Length of result arrays int kmax; // Maximum correlator attained during simulation - int me, nvalues; - int nfreq; + struct value_t { + int which; // type of data: COMPUTE, FIX, VARIABLE + int argindex; // 1-based index if data is vector, else 0 + std::string id; // compute/fix/variable ID + union { + class Compute *c; + class Fix *f; + int v; + } val; + }; + std::vector values; + + int nvalues, nfreq; bigint nvalid, nvalid_last, last_accumulated_step; - int *which, *argindex, *value2index; - char **ids; FILE *fp; int type, startstep, overwrite; bigint filepos; int npair; // number of correlation pairs to calculate - double *values; + double *cvalues; void accumulate(); void evaluate(); diff --git a/src/EXTRA-FIX/fix_controller.cpp b/src/EXTRA-FIX/fix_controller.cpp index 71005e4427..18bc30c23d 100644 --- a/src/EXTRA-FIX/fix_controller.cpp +++ b/src/EXTRA-FIX/fix_controller.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_controller.h b/src/EXTRA-FIX/fix_controller.h index d6a97b6dc7..74ad8db5dc 100644 --- a/src/EXTRA-FIX/fix_controller.h +++ b/src/EXTRA-FIX/fix_controller.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_drag.cpp b/src/EXTRA-FIX/fix_drag.cpp index 64d37a4853..45143fb665 100644 --- a/src/EXTRA-FIX/fix_drag.cpp +++ b/src/EXTRA-FIX/fix_drag.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_drag.h b/src/EXTRA-FIX/fix_drag.h index 519e3f79d3..a9c558a485 100644 --- a/src/EXTRA-FIX/fix_drag.h +++ b/src/EXTRA-FIX/fix_drag.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_electron_stopping.cpp b/src/EXTRA-FIX/fix_electron_stopping.cpp index 1417ece8a9..4a9421be6c 100644 --- a/src/EXTRA-FIX/fix_electron_stopping.cpp +++ b/src/EXTRA-FIX/fix_electron_stopping.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_electron_stopping.h b/src/EXTRA-FIX/fix_electron_stopping.h index 883854c1cb..ed94dcc240 100644 --- a/src/EXTRA-FIX/fix_electron_stopping.h +++ b/src/EXTRA-FIX/fix_electron_stopping.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_electron_stopping_fit.cpp b/src/EXTRA-FIX/fix_electron_stopping_fit.cpp index 3907ee8408..2657ddc85f 100644 --- a/src/EXTRA-FIX/fix_electron_stopping_fit.cpp +++ b/src/EXTRA-FIX/fix_electron_stopping_fit.cpp @@ -2,7 +2,7 @@ /* --------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_electron_stopping_fit.h b/src/EXTRA-FIX/fix_electron_stopping_fit.h index f6d5a279fd..d2d9f4a796 100644 --- a/src/EXTRA-FIX/fix_electron_stopping_fit.h +++ b/src/EXTRA-FIX/fix_electron_stopping_fit.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_ffl.cpp b/src/EXTRA-FIX/fix_ffl.cpp index 0b7f58e349..0a06707fbd 100644 --- a/src/EXTRA-FIX/fix_ffl.cpp +++ b/src/EXTRA-FIX/fix_ffl.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_ffl.h b/src/EXTRA-FIX/fix_ffl.h index bd29254106..5edeeaa18d 100644 --- a/src/EXTRA-FIX/fix_ffl.h +++ b/src/EXTRA-FIX/fix_ffl.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_filter_corotate.cpp b/src/EXTRA-FIX/fix_filter_corotate.cpp index cd8406f810..c88969344a 100644 --- a/src/EXTRA-FIX/fix_filter_corotate.cpp +++ b/src/EXTRA-FIX/fix_filter_corotate.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_filter_corotate.h b/src/EXTRA-FIX/fix_filter_corotate.h index d7853aea88..9db2e5b750 100644 --- a/src/EXTRA-FIX/fix_filter_corotate.h +++ b/src/EXTRA-FIX/fix_filter_corotate.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_flow_gauss.cpp b/src/EXTRA-FIX/fix_flow_gauss.cpp index 36a4788479..4a71bfa87e 100644 --- a/src/EXTRA-FIX/fix_flow_gauss.cpp +++ b/src/EXTRA-FIX/fix_flow_gauss.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_flow_gauss.h b/src/EXTRA-FIX/fix_flow_gauss.h index d8482a67b0..1f1ae63a89 100644 --- a/src/EXTRA-FIX/fix_flow_gauss.h +++ b/src/EXTRA-FIX/fix_flow_gauss.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_gld.cpp b/src/EXTRA-FIX/fix_gld.cpp index ea16976e83..db043acd34 100644 --- a/src/EXTRA-FIX/fix_gld.cpp +++ b/src/EXTRA-FIX/fix_gld.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_gld.h b/src/EXTRA-FIX/fix_gld.h index 4f0a87fad3..96dde46abc 100644 --- a/src/EXTRA-FIX/fix_gld.h +++ b/src/EXTRA-FIX/fix_gld.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_gle.cpp b/src/EXTRA-FIX/fix_gle.cpp index 54e9073361..c5a6c974f6 100644 --- a/src/EXTRA-FIX/fix_gle.cpp +++ b/src/EXTRA-FIX/fix_gle.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_gle.h b/src/EXTRA-FIX/fix_gle.h index e29daf76e8..dade871fa5 100644 --- a/src/EXTRA-FIX/fix_gle.h +++ b/src/EXTRA-FIX/fix_gle.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_momentum_chunk.cpp b/src/EXTRA-FIX/fix_momentum_chunk.cpp index 653d3e1806..884e3b228a 100644 --- a/src/EXTRA-FIX/fix_momentum_chunk.cpp +++ b/src/EXTRA-FIX/fix_momentum_chunk.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_momentum_chunk.h b/src/EXTRA-FIX/fix_momentum_chunk.h index b8272f0062..e962d570ca 100644 --- a/src/EXTRA-FIX/fix_momentum_chunk.h +++ b/src/EXTRA-FIX/fix_momentum_chunk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_npt_cauchy.cpp b/src/EXTRA-FIX/fix_npt_cauchy.cpp index 2f629f6f1c..380964f058 100644 --- a/src/EXTRA-FIX/fix_npt_cauchy.cpp +++ b/src/EXTRA-FIX/fix_npt_cauchy.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_npt_cauchy.h b/src/EXTRA-FIX/fix_npt_cauchy.h index b17d039724..e7e6630208 100644 --- a/src/EXTRA-FIX/fix_npt_cauchy.h +++ b/src/EXTRA-FIX/fix_npt_cauchy.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_numdiff.cpp b/src/EXTRA-FIX/fix_numdiff.cpp index 472c7288ae..dd9361f0ae 100644 --- a/src/EXTRA-FIX/fix_numdiff.cpp +++ b/src/EXTRA-FIX/fix_numdiff.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_numdiff.h b/src/EXTRA-FIX/fix_numdiff.h index 83d69406c4..6b74d96f22 100644 --- a/src/EXTRA-FIX/fix_numdiff.h +++ b/src/EXTRA-FIX/fix_numdiff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_numdiff_virial.cpp b/src/EXTRA-FIX/fix_numdiff_virial.cpp index fa854ab3b1..7336be81dc 100644 --- a/src/EXTRA-FIX/fix_numdiff_virial.cpp +++ b/src/EXTRA-FIX/fix_numdiff_virial.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_numdiff_virial.h b/src/EXTRA-FIX/fix_numdiff_virial.h index 5b50bbe5ec..7951659c2f 100644 --- a/src/EXTRA-FIX/fix_numdiff_virial.h +++ b/src/EXTRA-FIX/fix_numdiff_virial.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_nvk.cpp b/src/EXTRA-FIX/fix_nvk.cpp index fdb3e30532..7a2dc974c3 100644 --- a/src/EXTRA-FIX/fix_nvk.cpp +++ b/src/EXTRA-FIX/fix_nvk.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_nvk.h b/src/EXTRA-FIX/fix_nvk.h index d970f72ee7..8cddc2eebe 100644 --- a/src/EXTRA-FIX/fix_nvk.h +++ b/src/EXTRA-FIX/fix_nvk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_oneway.cpp b/src/EXTRA-FIX/fix_oneway.cpp index 7a4a0a02e3..d514a081f1 100644 --- a/src/EXTRA-FIX/fix_oneway.cpp +++ b/src/EXTRA-FIX/fix_oneway.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_oneway.h b/src/EXTRA-FIX/fix_oneway.h index 2a4ecb37e1..43413b806f 100644 --- a/src/EXTRA-FIX/fix_oneway.h +++ b/src/EXTRA-FIX/fix_oneway.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_pafi.cpp b/src/EXTRA-FIX/fix_pafi.cpp index c16daf9336..596bfdf667 100644 --- a/src/EXTRA-FIX/fix_pafi.cpp +++ b/src/EXTRA-FIX/fix_pafi.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_pafi.h b/src/EXTRA-FIX/fix_pafi.h index 84040dd279..1ac8b00f18 100644 --- a/src/EXTRA-FIX/fix_pafi.h +++ b/src/EXTRA-FIX/fix_pafi.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_rhok.cpp b/src/EXTRA-FIX/fix_rhok.cpp index d90277819e..72a0775359 100644 --- a/src/EXTRA-FIX/fix_rhok.cpp +++ b/src/EXTRA-FIX/fix_rhok.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org 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 diff --git a/src/EXTRA-FIX/fix_rhok.h b/src/EXTRA-FIX/fix_rhok.h index 3ddabf1ebb..dcb32e84f1 100644 --- a/src/EXTRA-FIX/fix_rhok.h +++ b/src/EXTRA-FIX/fix_rhok.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org 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 diff --git a/src/EXTRA-FIX/fix_smd.cpp b/src/EXTRA-FIX/fix_smd.cpp index 47fb5a5053..e19a605e71 100644 --- a/src/EXTRA-FIX/fix_smd.cpp +++ b/src/EXTRA-FIX/fix_smd.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_smd.h b/src/EXTRA-FIX/fix_smd.h index cae1319dc1..481ec80239 100644 --- a/src/EXTRA-FIX/fix_smd.h +++ b/src/EXTRA-FIX/fix_smd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_spring_rg.cpp b/src/EXTRA-FIX/fix_spring_rg.cpp index b4ddaaeb15..46afa905b3 100644 --- a/src/EXTRA-FIX/fix_spring_rg.cpp +++ b/src/EXTRA-FIX/fix_spring_rg.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_spring_rg.h b/src/EXTRA-FIX/fix_spring_rg.h index 76bd78526e..5b7e919b15 100644 --- a/src/EXTRA-FIX/fix_spring_rg.h +++ b/src/EXTRA-FIX/fix_spring_rg.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_temp_csld.cpp b/src/EXTRA-FIX/fix_temp_csld.cpp index e83eca424e..cbcd2ca7df 100644 --- a/src/EXTRA-FIX/fix_temp_csld.cpp +++ b/src/EXTRA-FIX/fix_temp_csld.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_temp_csld.h b/src/EXTRA-FIX/fix_temp_csld.h index da2751fa5c..0efc01b187 100644 --- a/src/EXTRA-FIX/fix_temp_csld.h +++ b/src/EXTRA-FIX/fix_temp_csld.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_temp_csvr.cpp b/src/EXTRA-FIX/fix_temp_csvr.cpp index 0c4742018a..b908d1a4ed 100644 --- a/src/EXTRA-FIX/fix_temp_csvr.cpp +++ b/src/EXTRA-FIX/fix_temp_csvr.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_temp_csvr.h b/src/EXTRA-FIX/fix_temp_csvr.h index 6749bee872..1bfe21ea5c 100644 --- a/src/EXTRA-FIX/fix_temp_csvr.h +++ b/src/EXTRA-FIX/fix_temp_csvr.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_ti_spring.cpp b/src/EXTRA-FIX/fix_ti_spring.cpp index 36d9b8bd05..a395e366e7 100644 --- a/src/EXTRA-FIX/fix_ti_spring.cpp +++ b/src/EXTRA-FIX/fix_ti_spring.cpp @@ -2,7 +2,7 @@ /* ------------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_ti_spring.h b/src/EXTRA-FIX/fix_ti_spring.h index 990c650f94..502fa1dca1 100644 --- a/src/EXTRA-FIX/fix_ti_spring.h +++ b/src/EXTRA-FIX/fix_ti_spring.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_tmd.cpp b/src/EXTRA-FIX/fix_tmd.cpp index e86b9d82e4..e88007a29d 100644 --- a/src/EXTRA-FIX/fix_tmd.cpp +++ b/src/EXTRA-FIX/fix_tmd.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_tmd.h b/src/EXTRA-FIX/fix_tmd.h index fa3c2e6665..b2922ab030 100644 --- a/src/EXTRA-FIX/fix_tmd.h +++ b/src/EXTRA-FIX/fix_tmd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_ttm.cpp b/src/EXTRA-FIX/fix_ttm.cpp index facb207bfe..fe0e982e80 100644 --- a/src/EXTRA-FIX/fix_ttm.cpp +++ b/src/EXTRA-FIX/fix_ttm.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -164,6 +164,7 @@ FixTTM::FixTTM(LAMMPS *lmp, int narg, char **arg) : FixTTM::~FixTTM() { delete [] infile; + delete [] outfile; delete random; @@ -225,13 +226,6 @@ void FixTTM::init() if (domain->triclinic) error->all(FLERR,"Cannot use fix ttm with triclinic box"); - // to allow this, would have to reset grid bounds dynamically - // for RCB balancing would have to reassign grid pts to procs - // and create a new GridComm, and pass old GC data to new GC - - if (domain->box_change) - error->all(FLERR,"Cannot use fix ttm with changing box shape, size, or sub-domains"); - // set force prefactors for (int i = 1; i <= atom->ntypes; i++) { @@ -483,9 +477,9 @@ void FixTTM::read_electron_temperatures(const std::string &filename) auto values = reader.next_values(4); ++nread; - int ix = values.next_int(); - int iy = values.next_int(); - int iz = values.next_int(); + int ix = values.next_int() - 1; + int iy = values.next_int() - 1; + int iz = values.next_int() - 1; double T_tmp = values.next_double(); // check correctness of input data @@ -529,8 +523,8 @@ void FixTTM::write_electron_temperatures(const std::string &filename) FILE *fp = fopen(filename.c_str(),"w"); if (!fp) error->one(FLERR,"Fix ttm could not open output file {}: {}", filename,utils::getsyserror()); - fmt::print(fp,"# DATE: {} UNITS: {} COMMENT: Electron temperature " - "{}x{}x{} grid at step {}. Created by fix {}\n", utils::current_date(), + fmt::print(fp,"# DATE: {} UNITS: {} COMMENT: Electron temperature on " + "{}x{}x{} grid at step {} - created by fix {}\n", utils::current_date(), update->unit_style, nxgrid, nygrid, nzgrid, update->ntimestep, style); int ix,iy,iz; @@ -538,7 +532,7 @@ void FixTTM::write_electron_temperatures(const std::string &filename) for (iz = 0; iz < nzgrid; iz++) for (iy = 0; iy < nygrid; iy++) for (ix = 0; ix < nxgrid; ix++) - fprintf(fp,"%d %d %d %20.16g\n",ix,iy,iz,T_electron[iz][iy][ix]); + fprintf(fp,"%d %d %d %20.16g\n",ix+1,iy+1,iz+1,T_electron[iz][iy][ix]); fclose(fp); } diff --git a/src/EXTRA-FIX/fix_ttm.h b/src/EXTRA-FIX/fix_ttm.h index 57a3e0f2ac..f05c7a5e6a 100644 --- a/src/EXTRA-FIX/fix_ttm.h +++ b/src/EXTRA-FIX/fix_ttm.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_ttm_grid.cpp b/src/EXTRA-FIX/fix_ttm_grid.cpp index 5e6022af58..ec5ba2540e 100644 --- a/src/EXTRA-FIX/fix_ttm_grid.cpp +++ b/src/EXTRA-FIX/fix_ttm_grid.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -23,7 +23,7 @@ #include "comm.h" #include "domain.h" #include "error.h" -#include "gridcomm.h" +#include "grid3d.h" #include "memory.h" #include "neighbor.h" #include "random_mars.h" @@ -39,6 +39,9 @@ using namespace FixConst; static constexpr int MAXLINE = 256; static constexpr int CHUNK = 1024; + +// OFFSET avoids outside-of-box atoms being rounded to grid pts incorrectly + static constexpr int OFFSET = 16384; /* ---------------------------------------------------------------------- */ @@ -46,6 +49,13 @@ static constexpr int OFFSET = 16384; FixTTMGrid::FixTTMGrid(LAMMPS *lmp, int narg, char **arg) : FixTTM(lmp, narg, arg) { + pergrid_flag = 1; + pergrid_freq = 1; + restart_file = 1; + + if (outfile) error->all(FLERR,"Fix ttm/grid does not support outfile option - " + "use dump grid command or restart files instead"); + skin_original = neighbor->skin; } @@ -86,7 +96,8 @@ void FixTTMGrid::post_constructor() if (infile) { read_electron_temperatures(infile); - gc->forward_comm(GridComm::FIX,this,1,sizeof(double),0,gc_buf1,gc_buf2,MPI_DOUBLE); + grid->forward_comm(Grid3d::FIX,this,0,1,sizeof(double), + grid_buf1,grid_buf2,MPI_DOUBLE); } } @@ -97,7 +108,7 @@ void FixTTMGrid::init() FixTTM::init(); if (neighbor->skin > skin_original) - error->all(FLERR,"Cannot extend neighbor skin after fix ttm/griddefined"); + error->all(FLERR,"Cannot extend neighbor skin after fix ttm/grid defined"); } /* ---------------------------------------------------------------------- */ @@ -125,9 +136,9 @@ void FixTTMGrid::post_force(int /*vflag*/) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { - ix = static_cast ((x[i][0]-boxlo[0])*dxinv + shift) - OFFSET; - iy = static_cast ((x[i][1]-boxlo[1])*dyinv + shift) - OFFSET; - iz = static_cast ((x[i][2]-boxlo[2])*dzinv + shift) - OFFSET; + ix = static_cast ((x[i][0]-boxlo[0])*dxinv + OFFSET) - OFFSET; + iy = static_cast ((x[i][1]-boxlo[1])*dyinv + OFFSET) - OFFSET; + iz = static_cast ((x[i][2]-boxlo[2])*dzinv + OFFSET) - OFFSET; // flag if ix,iy,iz is not within my ghost cell range @@ -184,17 +195,17 @@ void FixTTMGrid::end_of_step() for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { - ix = static_cast ((x[i][0]-boxlo[0])*dxinv + shift) - OFFSET; - iy = static_cast ((x[i][1]-boxlo[1])*dyinv + shift) - OFFSET; - iz = static_cast ((x[i][2]-boxlo[2])*dzinv + shift) - OFFSET; + ix = static_cast ((x[i][0]-boxlo[0])*dxinv + OFFSET) - OFFSET; + iy = static_cast ((x[i][1]-boxlo[1])*dyinv + OFFSET) - OFFSET; + iz = static_cast ((x[i][2]-boxlo[2])*dzinv + OFFSET) - OFFSET; net_energy_transfer[iz][iy][ix] += (flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] + flangevin[i][2]*v[i][2]); } - gc->reverse_comm(GridComm::FIX,this,1,sizeof(double),0, - gc_buf1,gc_buf2,MPI_DOUBLE); + grid->reverse_comm(Grid3d::FIX,this,0,1,sizeof(double), + grid_buf1,grid_buf2,MPI_DOUBLE); // clang-format off @@ -246,29 +257,20 @@ void FixTTMGrid::end_of_step() // communicate new T_electron values to ghost grid points - gc->forward_comm(GridComm::FIX,this,1,sizeof(double),0,gc_buf1,gc_buf2,MPI_DOUBLE); + grid->forward_comm(Grid3d::FIX,this,0,1,sizeof(double), + grid_buf1,grid_buf2,MPI_DOUBLE); } - - // clang-format on - - // output of grid temperatures to file - - if (outfile && (update->ntimestep % outevery == 0)) - write_electron_temperatures(fmt::format("{}.{}", outfile, update->ntimestep)); } /* ---------------------------------------------------------------------- read electron temperatures on grid from a user-specified file - proc 0 reads one chunk at a time, broadcasts to other procs - each proc stores values for grid points it owns ------------------------------------------------------------------------- */ void FixTTMGrid::read_electron_temperatures(const std::string &filename) { - int ***T_initial_set; - memory->create3d_offset(T_initial_set, nzlo_in, nzhi_in, nylo_in, nyhi_in, nxlo_in, nxhi_in, - "ttm/grid:T_initial_set"); - memset(&T_initial_set[nzlo_in][nylo_in][nxlo_in], 0, ngridmine * sizeof(int)); + memory->create3d_offset(T_electron_read, nzlo_in, nzhi_in, nylo_in, nyhi_in, nxlo_in, nxhi_in, + "ttm/grid:T_electron_read"); + memset(&T_electron_read[nzlo_in][nylo_in][nxlo_in], 0, ngridown * sizeof(int)); // proc 0 opens file @@ -278,101 +280,279 @@ void FixTTMGrid::read_electron_temperatures(const std::string &filename) if (!fp) error->one(FLERR, "Cannot open grid file: {}: {}", filename, utils::getsyserror()); } - // read electron temperature values from file, one chunk at a time + // read the file + // Grid3d::read_file() calls back to read_grid_lines() with chunks of lines - auto buffer = new char[CHUNK * MAXLINE]; - bigint ntotal = (bigint) nxgrid * nygrid * nzgrid; - bigint nread = 0; - - while (nread < ntotal) { - int nchunk = MIN(ntotal - nread, CHUNK); - int eof = utils::read_lines_from_file(fp, nchunk, MAXLINE, buffer, comm->me, world); - if (eof) error->all(FLERR, "Unexpected end of data file"); - - // loop over lines of grid point values - // tokenize the line into ix,iy,iz grid index plus temperature value - // if I own grid point, store the value - - for (const auto &line : utils::split_lines(buffer)) { - try { - ValueTokenizer values(utils::trim_comment(line)); - if (values.count() == 0) { - ; // ignore comment only lines - } else if (values.count() == 4) { - ++nread; - - int ix = values.next_int(); - int iy = values.next_int(); - int iz = values.next_int(); - - if (ix < 0 || ix >= nxgrid || iy < 0 || iy >= nygrid || iz < 0 || iz >= nzgrid) - throw TokenizerException("Fix ttm/grid invalid grid index in input", ""); - - if (ix >= nxlo_in && ix <= nxhi_in && iy >= nylo_in && iy <= nyhi_in && iz >= nzlo_in && - iz <= nzhi_in) { - T_electron[iz][iy][ix] = values.next_double(); - T_initial_set[iz][iy][ix] = 1; - } - } else { - throw TokenizerException("Incorrect format in fix ttm electron grid file", ""); - } - } catch (std::exception &e) { - error->one(FLERR, e.what()); - } - } - } + grid->read_file(Grid3d::FIX,this,fp,CHUNK,MAXLINE); // close file if (comm->me == 0) fclose(fp); - // clean up - - delete[] buffer; - // check completeness of input data int flag = 0; for (int iz = nzlo_in; iz <= nzhi_in; iz++) for (int iy = nylo_in; iy <= nyhi_in; iy++) for (int ix = nxlo_in; ix <= nxhi_in; ix++) - if (T_initial_set[iz][iy][ix] == 0) flag = 1; + if (T_electron_read[iz][iy][ix] == 0) flag = 1; int flagall; MPI_Allreduce(&flag, &flagall, 1, MPI_INT, MPI_SUM, world); if (flagall) error->all(FLERR, "Fix ttm/grid infile did not set all temperatures"); - memory->destroy3d_offset(T_initial_set, nzlo_in, nylo_in, nxlo_in); + memory->destroy3d_offset(T_electron_read, nzlo_in, nylo_in, nxlo_in); } /* ---------------------------------------------------------------------- - write out current electron temperatures to user-specified file - only written by proc 0 + process a chunk of lines in buffer + each proc stores values for grid points it owns + called back to from Grid3d::read_file() ------------------------------------------------------------------------- */ -void FixTTMGrid::write_electron_temperatures(const std::string &filename) +int FixTTMGrid::unpack_read_grid(int /*nlines*/, char *buffer) { - if (comm->me == 0) { - FPout = fopen(filename.c_str(), "w"); - if (!FPout) error->one(FLERR, "Fix ttm/grid could not open output file"); + // loop over chunk of lines of grid point values + // skip comment lines + // tokenize the line into ix,iy,iz grid index plus temperature value + // if I own grid point, store the value - fmt::print(FPout, - "# DATE: {} UNITS: {} COMMENT: Electron temperature " - "{}x{}x{} grid at step {}. Created by fix {}\n", - utils::current_date(), update->unit_style, nxgrid, nygrid, nzgrid, update->ntimestep, - style); + int nread = 0; + + for (const auto &line : utils::split_lines(buffer)) { + try { + ValueTokenizer values(utils::trim_comment(line)); + if (values.count() == 0) { + ; // ignore comment only or blank lines + } else if (values.count() == 4) { + ++nread; + + int ix = values.next_int() - 1; + int iy = values.next_int() - 1; + int iz = values.next_int() - 1; + + if (ix < 0 || ix >= nxgrid || iy < 0 || iy >= nygrid || iz < 0 || iz >= nzgrid) + throw TokenizerException("Fix ttm/grid invalid grid index in input", ""); + + if (ix >= nxlo_in && ix <= nxhi_in && iy >= nylo_in && iy <= nyhi_in && iz >= nzlo_in && + iz <= nzhi_in) { + T_electron[iz][iy][ix] = values.next_double(); + T_electron_read[iz][iy][ix] = 1; + } + } else { + throw TokenizerException("Incorrect format in fix ttm electron grid file", ""); + } + } catch (std::exception &e) { + error->one(FLERR, e.what()); + } } - gc->gather(GridComm::FIX, this, 1, sizeof(double), 1, nullptr, MPI_DOUBLE); + return nread; +} - if (comm->me == 0) fclose(FPout); +/* ---------------------------------------------------------------------- + pack state of Fix into one write, but not per-grid values +------------------------------------------------------------------------- */ + +void FixTTMGrid::write_restart(FILE *fp) +{ + double rlist[4]; + + rlist[0] = nxgrid; + rlist[1] = nygrid; + rlist[2] = nzgrid; + rlist[3] = seed; + + if (comm->me == 0) { + int size = 4 * sizeof(double); + fwrite(&size,sizeof(int),1,fp); + fwrite(rlist,sizeof(double),4,fp); + } +} + +/* ---------------------------------------------------------------------- + use state info from restart file to restart the Fix +------------------------------------------------------------------------- */ + +void FixTTMGrid::restart(char *buf) +{ + auto rlist = (double *) buf; + + // check that restart grid size is same as current grid size + + int nxgrid_old = static_cast (rlist[0]); + int nygrid_old = static_cast (rlist[1]); + int nzgrid_old = static_cast (rlist[2]); + + if (nxgrid_old != nxgrid || nygrid_old != nygrid || nzgrid_old != nzgrid) + error->all(FLERR,"Must restart fix ttm with same grid size"); + + // change RN seed from initial seed, to avoid same Langevin factors + // just increment by 1, since for RanMars that is a new RN stream + + seed = static_cast (rlist[3]) + 1; + delete random; + random = new RanMars(lmp,seed+comm->me); +} + +/* ---------------------------------------------------------------------- + write electron temperatures on grid to file + identical format to infile option, so info can be read in when restarting + each proc contributes info for its portion of grid +------------------------------------------------------------------------- */ + +void FixTTMGrid::write_restart_file(const char *file) +{ + // proc 0 opens file and writes header + + if (comm->me == 0) { + auto outfile = std::string(file) + ".ttm"; + fpout = fopen(outfile.c_str(),"w"); + if (fpout == nullptr) + error->one(FLERR,"Cannot open fix ttm/grid restart file {}: {}",outfile,utils::getsyserror()); + + fmt::print(fpout,"# DATE: {} UNITS: {} COMMENT: " + "Electron temperature on {}x{}x{} grid at step {} - " + "created by fix {}\n", + utils::current_date(),update->unit_style, + nxgrid,nygrid,nzgrid,update->ntimestep,style); + } + + // write file + // Grid3d::write_file() calls back to pack_write_file() and unpack_write_file() + + grid->write_file(Grid3d::FIX,this,0,1,sizeof(double), MPI_DOUBLE); + + // close file + + if (comm->me == 0) fclose(fpout); +} + +/* ---------------------------------------------------------------------- + pack values from local grid into buf +------------------------------------------------------------------------- */ + +void FixTTMGrid::pack_write_grid(int /*which*/, void *vbuf) +{ + int ix, iy, iz; + + auto buf = (double *) vbuf; + + int m = 0; + for (iz = nzlo_in; iz <= nzhi_in; iz++) + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + buf[m++] = T_electron[iz][iy][ix]; +} + +/* ---------------------------------------------------------------------- + unpack values from buf and write them to restart file +------------------------------------------------------------------------- */ + +void FixTTMGrid::unpack_write_grid(int /*which*/, void *vbuf, int *bounds) +{ + int ix, iy, iz; + + int xlo = bounds[0]; + int xhi = bounds[1]; + int ylo = bounds[2]; + int yhi = bounds[3]; + int zlo = bounds[4]; + int zhi = bounds[5]; + + auto buf = (double *) vbuf; + double value; + + int m = 0; + for (iz = zlo; iz <= zhi; iz++) + for (iy = ylo; iy <= yhi; iy++) + for (ix = xlo; ix <= xhi; ix++) { + value = buf[m++]; + fprintf(fpout, "%d %d %d %20.16g\n", ix+1, iy+1, iz+1, value); + } +} + +/* ---------------------------------------------------------------------- + subset of grid assigned to each proc may have changed + called by load balancer when proc subdomains are adjusted +------------------------------------------------------------------------- */ + +void FixTTMGrid::reset_grid() +{ + // check if new grid partitioning is different on any proc + // if not, just return + + int tmp[12]; + double maxdist = 0.5 * neighbor->skin; + Grid3d *gridnew = new Grid3d(lmp, world, nxgrid, nygrid, nzgrid); + gridnew->set_distance(maxdist); + gridnew->set_stencil_grid(1,1); + gridnew->setup_grid(tmp[0],tmp[1],tmp[2],tmp[3],tmp[4],tmp[5], + tmp[6],tmp[7],tmp[8],tmp[9],tmp[10],tmp[11]); + + if (grid->identical(gridnew)) { + delete gridnew; + return; + } else delete gridnew; + + // delete grid data which doesn't need to persist from previous to new decomp + + memory->destroy(grid_buf1); + memory->destroy(grid_buf2); + memory->destroy3d_offset(T_electron_old, nzlo_out, nylo_out, nxlo_out); + memory->destroy3d_offset(net_energy_transfer, nzlo_out, nylo_out, nxlo_out); + + // make copy of ptrs to grid data which does need to persist + + grid_previous = grid; + T_electron_previous = T_electron; + nxlo_out_previous = nxlo_out; + nylo_out_previous = nylo_out; + nzlo_out_previous = nzlo_out; + + // allocate new per-grid data for new decomposition + + allocate_grid(); + + // perform remap from previous decomp to new decomp + + int nremap_buf1,nremap_buf2; + grid->setup_remap(grid_previous,nremap_buf1,nremap_buf2); + + double *remap_buf1,*remap_buf2; + memory->create(remap_buf1, nremap_buf1, "ttm/grid:remap_buf1"); + memory->create(remap_buf2, nremap_buf2, "ttm/grid:remap_buf2"); + + grid->remap(Grid3d::FIX,this,0,1,sizeof(double),remap_buf1,remap_buf2,MPI_DOUBLE); + + memory->destroy(remap_buf1); + memory->destroy(remap_buf2); + + // delete grid data and grid for previous decomposition + + memory->destroy3d_offset(T_electron_previous, + nzlo_out_previous, nylo_out_previous, + nxlo_out_previous); + delete grid_previous; + + // communicate temperatures to ghost cells on new grid + + grid->forward_comm(Grid3d::FIX,this,0,1,sizeof(double), + grid_buf1,grid_buf2,MPI_DOUBLE); + + // zero new net_energy_transfer + // in case compute_vector accesses it on timestep 0 + + outflag = 0; + memset(&net_energy_transfer[nzlo_out][nylo_out][nxlo_out],0, + ngridout*sizeof(double)); } /* ---------------------------------------------------------------------- pack own values to buf to send to another proc ------------------------------------------------------------------------- */ -void FixTTMGrid::pack_forward_grid(int /*flag*/, void *vbuf, int nlist, int *list) +void FixTTMGrid::pack_forward_grid(int /*which*/, void *vbuf, int nlist, int *list) { auto buf = (double *) vbuf; double *src = &T_electron[nzlo_out][nylo_out][nxlo_out]; @@ -384,7 +564,7 @@ void FixTTMGrid::pack_forward_grid(int /*flag*/, void *vbuf, int nlist, int *lis unpack another proc's own values from buf and set own ghost values ------------------------------------------------------------------------- */ -void FixTTMGrid::unpack_forward_grid(int /*flag*/, void *vbuf, int nlist, int *list) +void FixTTMGrid::unpack_forward_grid(int /*which*/, void *vbuf, int nlist, int *list) { auto buf = (double *) vbuf; double *dest = &T_electron[nzlo_out][nylo_out][nxlo_out]; @@ -396,7 +576,7 @@ void FixTTMGrid::unpack_forward_grid(int /*flag*/, void *vbuf, int nlist, int *l pack ghost values into buf to send to another proc ------------------------------------------------------------------------- */ -void FixTTMGrid::pack_reverse_grid(int /*flag*/, void *vbuf, int nlist, int *list) +void FixTTMGrid::pack_reverse_grid(int /*which*/, void *vbuf, int nlist, int *list) { auto buf = (double *) vbuf; double *src = &net_energy_transfer[nzlo_out][nylo_out][nxlo_out]; @@ -408,7 +588,7 @@ void FixTTMGrid::pack_reverse_grid(int /*flag*/, void *vbuf, int nlist, int *lis unpack another proc's ghost values from buf and add to own values ------------------------------------------------------------------------- */ -void FixTTMGrid::unpack_reverse_grid(int /*flag*/, void *vbuf, int nlist, int *list) +void FixTTMGrid::unpack_reverse_grid(int /*which*/, void *vbuf, int nlist, int *list) { auto buf = (double *) vbuf; double *dest = &net_energy_transfer[nzlo_out][nylo_out][nxlo_out]; @@ -416,65 +596,56 @@ void FixTTMGrid::unpack_reverse_grid(int /*flag*/, void *vbuf, int nlist, int *l for (int i = 0; i < nlist; i++) dest[list[i]] += buf[i]; } +/* ---------------------------------------------------------------------- + pack old grid values to buf to send to another proc +------------------------------------------------------------------------- */ + +void FixTTMGrid::pack_remap_grid(int /*which*/, void *vbuf, int nlist, int *list) +{ + auto buf = (double *) vbuf; + double *src = + &T_electron_previous[nzlo_out_previous][nylo_out_previous][nxlo_out_previous]; + + for (int i = 0; i < nlist; i++) buf[i] = src[list[i]]; +} + +/* ---------------------------------------------------------------------- + unpack another proc's own values from buf and set own ghost values +------------------------------------------------------------------------- */ + +void FixTTMGrid::unpack_remap_grid(int /*which*/, void *vbuf, int nlist, int *list) +{ + auto buf = (double *) vbuf; + double *dest = &T_electron[nzlo_out][nylo_out][nxlo_out]; + + for (int i = 0; i < nlist; i++) dest[list[i]] = buf[i]; +} + /* ---------------------------------------------------------------------- allocate 3d grid quantities ------------------------------------------------------------------------- */ void FixTTMGrid::allocate_grid() { - // partition global grid across procs - // n xyz lo/hi in = lower/upper bounds of global grid this proc owns - // indices range from 0 to N-1 inclusive in each dim + double maxdist = 0.5 * neighbor->skin; - comm->partition_grid(nxgrid, nygrid, nzgrid, 0.0, nxlo_in, nxhi_in, nylo_in, nyhi_in, nzlo_in, - nzhi_in); + grid = new Grid3d(lmp, world, nxgrid, nygrid, nzgrid); + grid->set_distance(maxdist); + grid->set_stencil_grid(1,1); + grid->setup_grid(nxlo_in, nxhi_in, nylo_in, nyhi_in, nzlo_in, nzhi_in, + nxlo_out, nxhi_out, nylo_out, nyhi_out, nzlo_out, nzhi_out); - // nlo,nhi = min/max index of global grid pt my owned atoms can be mapped to - // finite difference stencil requires extra grid pt around my owned grid pts - // max of these 2 quantities is the ghost cells needed in each dim - // nlo_out,nhi_out = nlo_in,nhi_in + ghost cells + ngridown = (nxhi_in - nxlo_in + 1) * (nyhi_in - nylo_in + 1) * + (nzhi_in - nzlo_in + 1); + ngridout = (nxhi_out - nxlo_out + 1) * (nyhi_out - nylo_out + 1) * + (nzhi_out - nzlo_out + 1); - double *boxlo = domain->boxlo; - double *sublo = domain->sublo; - double *subhi = domain->subhi; - double dxinv = nxgrid / domain->xprd; - double dyinv = nxgrid / domain->yprd; - double dzinv = nxgrid / domain->zprd; + // setup grid communication and allocate grid data structs - int nlo, nhi; - double cuthalf = 0.5 * neighbor->skin; + grid->setup_comm(ngrid_buf1, ngrid_buf2); - nlo = static_cast((sublo[0] - cuthalf - boxlo[0]) * dxinv + shift) - OFFSET; - nhi = static_cast((subhi[0] + cuthalf - boxlo[0]) * dxinv + shift) - OFFSET; - nxlo_out = MIN(nlo, nxlo_in - 1); - nxhi_out = MAX(nhi, nxhi_in + 1); - - nlo = static_cast((sublo[1] - cuthalf - boxlo[1]) * dyinv + shift) - OFFSET; - nhi = static_cast((subhi[1] + cuthalf - boxlo[1]) * dyinv + shift) - OFFSET; - nylo_out = MIN(nlo, nylo_in - 1); - nyhi_out = MAX(nhi, nyhi_in + 1); - - nlo = static_cast((sublo[2] - cuthalf - boxlo[2]) * dzinv + shift) - OFFSET; - nhi = static_cast((subhi[2] + cuthalf - boxlo[2]) * dzinv + shift) - OFFSET; - nzlo_out = MIN(nlo, nzlo_in - 1); - nzhi_out = MAX(nhi, nzhi_in + 1); - - bigint totalmine; - totalmine = - (bigint) (nxhi_out - nxlo_out + 1) * (nyhi_out - nylo_out + 1) * (nzhi_out - nzlo_out + 1); - if (totalmine > MAXSMALLINT) error->one(FLERR, "Too many owned+ghost grid points in fix ttm"); - ngridout = totalmine; - - totalmine = (bigint) (nxhi_in - nxlo_in + 1) * (nyhi_in - nylo_in + 1) * (nzhi_in - nzlo_in + 1); - ngridmine = totalmine; - - gc = new GridComm(lmp, world, nxgrid, nygrid, nzgrid, nxlo_in, nxhi_in, nylo_in, nyhi_in, nzlo_in, - nzhi_in, nxlo_out, nxhi_out, nylo_out, nyhi_out, nzlo_out, nzhi_out); - - gc->setup(ngc_buf1, ngc_buf2); - - memory->create(gc_buf1, ngc_buf1, "ttm/grid:gc_buf1"); - memory->create(gc_buf2, ngc_buf2, "ttm/grid:gc_buf2"); + memory->create(grid_buf1, ngrid_buf1, "ttm/grid:grid_buf1"); + memory->create(grid_buf2, ngrid_buf2, "ttm/grid:grid_buf2"); memory->create3d_offset(T_electron_old, nzlo_out, nzhi_out, nylo_out, nyhi_out, nxlo_out, nxhi_out, "ttm/grid:T_electron_old"); @@ -490,9 +661,9 @@ void FixTTMGrid::allocate_grid() void FixTTMGrid::deallocate_grid() { - delete gc; - memory->destroy(gc_buf1); - memory->destroy(gc_buf2); + delete grid; + memory->destroy(grid_buf1); + memory->destroy(grid_buf2); memory->destroy3d_offset(T_electron_old, nzlo_out, nylo_out, nxlo_out); memory->destroy3d_offset(T_electron, nzlo_out, nylo_out, nxlo_out); @@ -500,129 +671,66 @@ void FixTTMGrid::deallocate_grid() } /* ---------------------------------------------------------------------- - pack entire state of Fix into one write + return index of grid associated with name + this class can store M named grids, indexed 0 to M-1 + also set dim for 2d vs 3d grid + return -1 if grid name not found ------------------------------------------------------------------------- */ -void FixTTMGrid::write_restart(FILE *fp) +int FixTTMGrid::get_grid_by_name(const std::string &name, int &dim) { - int rsize = nxgrid * nygrid * nzgrid + 4; - double *rlist; - memory->create(rlist, rsize, "ttm/grid:rlist"); - - int n = 0; - rlist[n++] = nxgrid; - rlist[n++] = nygrid; - rlist[n++] = nzgrid; - rlist[n++] = seed; - - // gather rest of rlist on proc 0 as global grid values - - gc->gather(GridComm::FIX, this, 1, sizeof(double), 0, &rlist[4], MPI_DOUBLE); - - if (comm->me == 0) { - int size = rsize * sizeof(double); - fwrite(&size, sizeof(int), 1, fp); - fwrite(rlist, sizeof(double), rsize, fp); + if (name == "grid") { + dim = 3; + return 0; } - memory->destroy(rlist); + return -1; } /* ---------------------------------------------------------------------- - use state info from restart file to restart the Fix + return ptr to Grid data struct for grid with index + this class can store M named grids, indexed 0 to M-1 + return nullptr if index is invalid ------------------------------------------------------------------------- */ -void FixTTMGrid::restart(char *buf) +void *FixTTMGrid::get_grid_by_index(int index) { - int ix, iy, iz; + if (index == 0) return grid; - int n = 0; - auto rlist = (double *) buf; - - // check that restart grid size is same as current grid size - - int nxgrid_old = static_cast(rlist[n++]); - int nygrid_old = static_cast(rlist[n++]); - int nzgrid_old = static_cast(rlist[n++]); - - if (nxgrid_old != nxgrid || nygrid_old != nygrid || nzgrid_old != nzgrid) - error->all(FLERR, "Must restart fix ttm/grid with same grid size"); - - // change RN seed from initial seed, to avoid same Langevin factors - // just increment by 1, since for RanMars that is a new RN stream - - seed = static_cast(rlist[n++]) + 1; - delete random; - random = new RanMars(lmp, seed + comm->me); - - // extract this proc's local grid values from global grid in rlist - - int iglobal; - - for (iz = nzlo_in; iz <= nzhi_in; iz++) - for (iy = nylo_in; iy <= nyhi_in; iy++) - for (ix = nxlo_in; ix <= nxhi_in; ix++) { - iglobal = nygrid * nxgrid * iz + nxgrid * iy + ix; - T_electron[iz][iy][ix] = rlist[n + iglobal]; - } - - // communicate new T_electron values to ghost grid points - - gc->forward_comm(GridComm::FIX, this, 1, sizeof(double), 0, gc_buf1, gc_buf2, MPI_DOUBLE); + return nullptr; } /* ---------------------------------------------------------------------- - pack values from local grid into buf - used by which = 0 and 1 + return index of data associated with name in grid with index igrid + this class can store M named grids, indexed 0 to M-1 + each grid can store G named data sets, indexed 0 to G-1 + a data set name can be associated with multiple grids + set ncol for data set, 0 = vector, 1-N for array with N columns + vector = single value per grid pt, array = N values per grid pt + return -1 if data name not found ------------------------------------------------------------------------- */ -void FixTTMGrid::pack_gather_grid(int /*which*/, void *vbuf) +int FixTTMGrid::get_griddata_by_name(int igrid, const std::string &name, int &ncol) { - int ix, iy, iz; - - auto buf = (double *) vbuf; - - int m = 0; - for (iz = nzlo_in; iz <= nzhi_in; iz++) - for (iy = nylo_in; iy <= nyhi_in; iy++) - for (ix = nxlo_in; ix <= nxhi_in; ix++) buf[m++] = T_electron[iz][iy][ix]; -} - -/* ---------------------------------------------------------------------- - which = 0: unpack values from buf into global gbuf based on their indices - which = 1: print values from buf to FPout file -------------------------------------------------------------------------- */ - -void FixTTMGrid::unpack_gather_grid(int which, void *vbuf, void *vgbuf, int xlo, int xhi, int ylo, - int yhi, int zlo, int zhi) -{ - int ix, iy, iz; - - auto buf = (double *) vbuf; - auto gbuf = (double *) vgbuf; - - if (which == 0) { - int iglobal; - int ilocal = 0; - - for (iz = zlo; iz <= zhi; iz++) - for (iy = ylo; iy <= yhi; iy++) - for (ix = xlo; ix <= xhi; ix++) { - iglobal = nygrid * nxgrid * iz + nxgrid * iy + ix; - gbuf[iglobal] = buf[ilocal++]; - } - - } else if (which == 1) { - int ilocal = 0; - double value; - - for (iz = zlo; iz <= zhi; iz++) - for (iy = ylo; iy <= yhi; iy++) - for (ix = xlo; ix <= xhi; ix++) { - value = buf[ilocal++]; - fprintf(FPout, "%d %d %d %20.16g\n", ix, iy, iz, value); - } + if ((igrid == 0) && (name == "data")) { + ncol = 0; + return 0; } + + return -1; +} + +/* ---------------------------------------------------------------------- + return ptr to multidim data array associated with index + this class can store G named data sets, indexed 0 to M-1 + return nullptr if index is invalid +------------------------------------------------------------------------- */ + +void *FixTTMGrid::get_griddata_by_index(int index) +{ + if (index == 0) return T_electron; + + return nullptr; } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-FIX/fix_ttm_grid.h b/src/EXTRA-FIX/fix_ttm_grid.h index f6f467fce0..7d18ba2c1a 100644 --- a/src/EXTRA-FIX/fix_ttm_grid.h +++ b/src/EXTRA-FIX/fix_ttm_grid.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -32,37 +32,52 @@ class FixTTMGrid : public FixTTM { void init() override; void post_force(int) override; void end_of_step() override; + void write_restart(FILE *) override; + void restart(char *) override; + void write_restart_file(const char *) override; + double compute_vector(int) override; + double memory_usage() override; // grid communication + void reset_grid() override; + void pack_forward_grid(int, void *, int, int *) override; void unpack_forward_grid(int, void *, int, int *) override; void pack_reverse_grid(int, void *, int, int *) override; void unpack_reverse_grid(int, void *, int, int *) override; - void pack_gather_grid(int, void *) override; - void unpack_gather_grid(int, void *, void *, int, int, int, int, int, int) override; + void pack_remap_grid(int, void *, int, int *) override; + void unpack_remap_grid(int, void *, int, int *) override; + int unpack_read_grid(int, char *) override; + void pack_write_grid(int, void *) override; + void unpack_write_grid(int, void *, int *) override; - void write_restart(FILE *) override; - void restart(char *) override; - double compute_vector(int) override; - double memory_usage() override; + int get_grid_by_name(const std::string &, int &) override; + void *get_grid_by_index(int) override; + int get_griddata_by_name(int, const std::string &, int &) override; + void *get_griddata_by_index(int) override; private: - int ngridmine, ngridout; + int ngridown, ngridout; int nxlo_in, nxhi_in, nylo_in, nyhi_in, nzlo_in, nzhi_in; int nxlo_out, nxhi_out, nylo_out, nyhi_out, nzlo_out, nzhi_out; double delxinv, delyinv, delzinv; double skin_original; - FILE *FPout; + double shift; + FILE *fpout; - class GridComm *gc; - int ngc_buf1, ngc_buf2; - double *gc_buf1, *gc_buf2; + class Grid3d *grid; + class Grid3d *grid_previous; + double ***T_electron_previous; + int ngrid_buf1, ngrid_buf2; + double *grid_buf1, *grid_buf2; + + double ***T_electron_read; + int nxlo_out_previous,nylo_out_previous,nzlo_out_previous; void allocate_grid() override; void deallocate_grid() override; void read_electron_temperatures(const std::string &) override; - void write_electron_temperatures(const std::string &) override; }; } // namespace LAMMPS_NS diff --git a/src/EXTRA-FIX/fix_ttm_mod.cpp b/src/EXTRA-FIX/fix_ttm_mod.cpp index 1b82e5452b..65ccbda4c1 100644 --- a/src/EXTRA-FIX/fix_ttm_mod.cpp +++ b/src/EXTRA-FIX/fix_ttm_mod.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_ttm_mod.h b/src/EXTRA-FIX/fix_ttm_mod.h index d9967753fd..28c3209697 100644 --- a/src/EXTRA-FIX/fix_ttm_mod.h +++ b/src/EXTRA-FIX/fix_ttm_mod.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_viscosity.cpp b/src/EXTRA-FIX/fix_viscosity.cpp index 1d84d76124..a44050636d 100644 --- a/src/EXTRA-FIX/fix_viscosity.cpp +++ b/src/EXTRA-FIX/fix_viscosity.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_viscosity.h b/src/EXTRA-FIX/fix_viscosity.h index 9ff4ddf2de..3b73d4fce7 100644 --- a/src/EXTRA-FIX/fix_viscosity.h +++ b/src/EXTRA-FIX/fix_viscosity.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_viscous_sphere.cpp b/src/EXTRA-FIX/fix_viscous_sphere.cpp index 771b6f1c10..5b4dd72231 100644 --- a/src/EXTRA-FIX/fix_viscous_sphere.cpp +++ b/src/EXTRA-FIX/fix_viscous_sphere.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -14,11 +14,9 @@ #include "fix_viscous_sphere.h" #include "atom.h" -#include "comm.h" #include "error.h" #include "input.h" #include "memory.h" -#include "modify.h" #include "respa.h" #include "update.h" #include "variable.h" diff --git a/src/EXTRA-FIX/fix_viscous_sphere.h b/src/EXTRA-FIX/fix_viscous_sphere.h index e95ff3f74c..2d63c0ca92 100644 --- a/src/EXTRA-FIX/fix_viscous_sphere.h +++ b/src/EXTRA-FIX/fix_viscous_sphere.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_wall_ees.cpp b/src/EXTRA-FIX/fix_wall_ees.cpp index a6226930c4..bbddd919af 100644 --- a/src/EXTRA-FIX/fix_wall_ees.cpp +++ b/src/EXTRA-FIX/fix_wall_ees.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_wall_ees.h b/src/EXTRA-FIX/fix_wall_ees.h index c6935605c2..6db42a0d09 100644 --- a/src/EXTRA-FIX/fix_wall_ees.h +++ b/src/EXTRA-FIX/fix_wall_ees.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_wall_reflect_stochastic.cpp b/src/EXTRA-FIX/fix_wall_reflect_stochastic.cpp index 5f3ebfa959..7899c88473 100644 --- a/src/EXTRA-FIX/fix_wall_reflect_stochastic.cpp +++ b/src/EXTRA-FIX/fix_wall_reflect_stochastic.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_wall_reflect_stochastic.h b/src/EXTRA-FIX/fix_wall_reflect_stochastic.h index 6abe194077..dd62eb8313 100644 --- a/src/EXTRA-FIX/fix_wall_reflect_stochastic.h +++ b/src/EXTRA-FIX/fix_wall_reflect_stochastic.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_wall_region_ees.cpp b/src/EXTRA-FIX/fix_wall_region_ees.cpp index a9f6205373..f8cc6776ac 100644 --- a/src/EXTRA-FIX/fix_wall_region_ees.cpp +++ b/src/EXTRA-FIX/fix_wall_region_ees.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-FIX/fix_wall_region_ees.h b/src/EXTRA-FIX/fix_wall_region_ees.h index 75ffac174a..14cfe36786 100644 --- a/src/EXTRA-FIX/fix_wall_region_ees.h +++ b/src/EXTRA-FIX/fix_wall_region_ees.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/angle_cosine_delta.cpp b/src/EXTRA-MOLECULE/angle_cosine_delta.cpp index e13174d70d..099f1a3c79 100644 --- a/src/EXTRA-MOLECULE/angle_cosine_delta.cpp +++ b/src/EXTRA-MOLECULE/angle_cosine_delta.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/angle_cosine_delta.h b/src/EXTRA-MOLECULE/angle_cosine_delta.h index f9ec915fa8..b562862da3 100644 --- a/src/EXTRA-MOLECULE/angle_cosine_delta.h +++ b/src/EXTRA-MOLECULE/angle_cosine_delta.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/angle_cosine_periodic.cpp b/src/EXTRA-MOLECULE/angle_cosine_periodic.cpp index 4a7768722f..15d0575f6d 100644 --- a/src/EXTRA-MOLECULE/angle_cosine_periodic.cpp +++ b/src/EXTRA-MOLECULE/angle_cosine_periodic.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/angle_cosine_periodic.h b/src/EXTRA-MOLECULE/angle_cosine_periodic.h index 542147dffe..4e584b4543 100644 --- a/src/EXTRA-MOLECULE/angle_cosine_periodic.h +++ b/src/EXTRA-MOLECULE/angle_cosine_periodic.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/angle_cosine_shift.cpp b/src/EXTRA-MOLECULE/angle_cosine_shift.cpp index 1829537165..ce9b4c4133 100644 --- a/src/EXTRA-MOLECULE/angle_cosine_shift.cpp +++ b/src/EXTRA-MOLECULE/angle_cosine_shift.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/angle_cosine_shift.h b/src/EXTRA-MOLECULE/angle_cosine_shift.h index f52c532bba..fbf6437431 100644 --- a/src/EXTRA-MOLECULE/angle_cosine_shift.h +++ b/src/EXTRA-MOLECULE/angle_cosine_shift.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/angle_cosine_shift_exp.cpp b/src/EXTRA-MOLECULE/angle_cosine_shift_exp.cpp index 43ecc3c692..a411ea3199 100644 --- a/src/EXTRA-MOLECULE/angle_cosine_shift_exp.cpp +++ b/src/EXTRA-MOLECULE/angle_cosine_shift_exp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/angle_cosine_shift_exp.h b/src/EXTRA-MOLECULE/angle_cosine_shift_exp.h index f372d9bc30..c8a99ecdc3 100644 --- a/src/EXTRA-MOLECULE/angle_cosine_shift_exp.h +++ b/src/EXTRA-MOLECULE/angle_cosine_shift_exp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/angle_fourier.cpp b/src/EXTRA-MOLECULE/angle_fourier.cpp index a1248d41db..49b8bdb698 100644 --- a/src/EXTRA-MOLECULE/angle_fourier.cpp +++ b/src/EXTRA-MOLECULE/angle_fourier.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/angle_fourier.h b/src/EXTRA-MOLECULE/angle_fourier.h index 84859fc216..104a5984a6 100644 --- a/src/EXTRA-MOLECULE/angle_fourier.h +++ b/src/EXTRA-MOLECULE/angle_fourier.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/angle_fourier_simple.cpp b/src/EXTRA-MOLECULE/angle_fourier_simple.cpp index 4f76c68281..931b7c1f8f 100644 --- a/src/EXTRA-MOLECULE/angle_fourier_simple.cpp +++ b/src/EXTRA-MOLECULE/angle_fourier_simple.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/angle_fourier_simple.h b/src/EXTRA-MOLECULE/angle_fourier_simple.h index d66f32f13f..49fae85d79 100644 --- a/src/EXTRA-MOLECULE/angle_fourier_simple.h +++ b/src/EXTRA-MOLECULE/angle_fourier_simple.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/angle_gaussian.cpp b/src/EXTRA-MOLECULE/angle_gaussian.cpp index 54c2aa1880..7290cb70cc 100644 --- a/src/EXTRA-MOLECULE/angle_gaussian.cpp +++ b/src/EXTRA-MOLECULE/angle_gaussian.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -28,8 +28,8 @@ using namespace LAMMPS_NS; using namespace MathConst; -#define SMAL 0.001 -#define SMALL 1.0e-8 +static constexpr double SMALL = 0.001; +static constexpr double SMALLG = 2.0e-308; /* ---------------------------------------------------------------------- */ @@ -112,7 +112,7 @@ void AngleGaussian::compute(int eflag, int vflag) if (c < -1.0) c = -1.0; s = sqrt(1.0 - c * c); - if (s < SMAL) s = SMAL; + if (s < SMALL) s = SMALL; s = 1.0 / s; // force & energy @@ -123,13 +123,15 @@ void AngleGaussian::compute(int eflag, int vflag) for (int i = 0; i < nterms[type]; i++) { dtheta = theta - theta0[type][i]; prefactor = (alpha[type][i] / (width[type][i] * sqrt(MY_PI2))); - exponent = -2 * dtheta * dtheta / (width[type][i] * width[type][i]); + exponent = -2.0 * dtheta * dtheta / (width[type][i] * width[type][i]); g_i = prefactor * exp(exponent); sum_g_i += g_i; sum_numerator += g_i * dtheta / (width[type][i] * width[type][i]); } - if (sum_g_i < SMALL) sum_g_i = SMALL; + // avoid overflow + if (sum_g_i < sum_numerator * SMALLG) sum_g_i = sum_numerator * SMALLG; + if (eflag) eangle = -(force->boltz * angle_temperature[type]) * log(sum_g_i); // I should check about the sign of this expression @@ -198,14 +200,16 @@ void AngleGaussian::allocate() void AngleGaussian::coeff(int narg, char **arg) { - if (narg < 6) error->all(FLERR, "Incorrect args for angle coefficients"); + if (narg < 6) utils::missing_cmd_args(FLERR, "angle_coeff", error); int ilo, ihi; utils::bounds(FLERR, arg[0], 1, atom->nangletypes, ilo, ihi, error); double angle_temperature_one = utils::numeric(FLERR, arg[1], false, lmp); int n = utils::inumeric(FLERR, arg[2], false, lmp); - if (narg != 3 * n + 3) error->all(FLERR, "Incorrect args for angle coefficients"); + if (n < 1) error->all(FLERR, "Invalid angle style gaussian value for n: {}", n); + + if (narg != 3 * n + 3) utils::missing_cmd_args(FLERR, "angle_coeff", error); if (!allocated) allocate(); @@ -223,7 +227,9 @@ void AngleGaussian::coeff(int narg, char **arg) theta0[i] = new double[n]; for (int j = 0; j < n; j++) { alpha[i][j] = utils::numeric(FLERR, arg[3 + 3 * j], false, lmp); + if (alpha[i][j] <= 0.0) error->all(FLERR, "Invalid value for A_{}: {}", j, alpha[i][j]); width[i][j] = utils::numeric(FLERR, arg[4 + 3 * j], false, lmp); + if (width[i][j] <= 0.0) error->all(FLERR, "Invalid value for w_{}: {}", j, width[i][j]); theta0[i][j] = utils::numeric(FLERR, arg[5 + 3 * j], false, lmp) * MY_PI / 180.0; setflag[i] = 1; } diff --git a/src/EXTRA-MOLECULE/angle_gaussian.h b/src/EXTRA-MOLECULE/angle_gaussian.h index 367a810cf2..305565b032 100644 --- a/src/EXTRA-MOLECULE/angle_gaussian.h +++ b/src/EXTRA-MOLECULE/angle_gaussian.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/angle_quartic.cpp b/src/EXTRA-MOLECULE/angle_quartic.cpp index f88c628fb1..f28e209a77 100644 --- a/src/EXTRA-MOLECULE/angle_quartic.cpp +++ b/src/EXTRA-MOLECULE/angle_quartic.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/angle_quartic.h b/src/EXTRA-MOLECULE/angle_quartic.h index 1253ec2f0f..3f0396f27b 100644 --- a/src/EXTRA-MOLECULE/angle_quartic.h +++ b/src/EXTRA-MOLECULE/angle_quartic.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/bond_fene_nm.cpp b/src/EXTRA-MOLECULE/bond_fene_nm.cpp index 291c9bc465..5451479881 100644 --- a/src/EXTRA-MOLECULE/bond_fene_nm.cpp +++ b/src/EXTRA-MOLECULE/bond_fene_nm.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/bond_fene_nm.h b/src/EXTRA-MOLECULE/bond_fene_nm.h index d68c937aa8..07da20e425 100644 --- a/src/EXTRA-MOLECULE/bond_fene_nm.h +++ b/src/EXTRA-MOLECULE/bond_fene_nm.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/bond_gaussian.cpp b/src/EXTRA-MOLECULE/bond_gaussian.cpp index 76637dbd88..baca0b6e1a 100644 --- a/src/EXTRA-MOLECULE/bond_gaussian.cpp +++ b/src/EXTRA-MOLECULE/bond_gaussian.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -27,7 +27,7 @@ using namespace LAMMPS_NS; using namespace MathConst; -#define SMALL 1.0e-10 +static constexpr double SMALL = 2.0e-308; /* ---------------------------------------------------------------------- */ @@ -92,15 +92,16 @@ void BondGaussian::compute(int eflag, int vflag) for (int i = 0; i < nterms[type]; i++) { dr = r - r0[type][i]; prefactor = (alpha[type][i] / (width[type][i] * sqrt(MY_PI2))); - exponent = -2 * dr * dr / (width[type][i] * width[type][i]); + exponent = -2.0 * dr * dr / (width[type][i] * width[type][i]); g_i = prefactor * exp(exponent); sum_g_i += g_i; sum_numerator += g_i * dr / (width[type][i] * width[type][i]); } - // force & energy - if (sum_g_i < SMALL) sum_g_i = SMALL; + // avoid overflow + if (sum_g_i < sum_numerator * SMALL) sum_g_i = sum_numerator * SMALL; + // force & energy if (r > 0.0) fbond = -4.0 * (force->boltz * bond_temperature[type]) * (sum_numerator / sum_g_i) / r; else @@ -153,14 +154,15 @@ void BondGaussian::allocate() void BondGaussian::coeff(int narg, char **arg) { - if (narg < 6) error->all(FLERR, "Incorrect args for bond coefficients"); + if (narg < 6) utils::missing_cmd_args(FLERR, "bond_coeff", error); int ilo, ihi; utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error); double bond_temp_one = utils::numeric(FLERR, arg[1], false, lmp); int n = utils::inumeric(FLERR, arg[2], false, lmp); - if (narg != 3 * n + 3) error->all(FLERR, "Incorrect args for bond coefficients"); + if (n < 1) error->all(FLERR, "Invalid bond style gaussian value for n: {}", n); + if (narg != 3 * n + 3) utils::missing_cmd_args(FLERR, "bond_coeff", error); if (!allocated) allocate(); @@ -176,8 +178,11 @@ void BondGaussian::coeff(int narg, char **arg) r0[i] = new double[n]; for (int j = 0; j < n; j++) { alpha[i][j] = utils::numeric(FLERR, arg[3 + 3 * j], false, lmp); + if (alpha[i][j] <= 0.0) error->all(FLERR, "Invalid value for A_{}: {}", j, alpha[i][j]); width[i][j] = utils::numeric(FLERR, arg[4 + 3 * j], false, lmp); + if (width[i][j] <= 0.0) error->all(FLERR, "Invalid value for w_{}: {}", j, width[i][j]); r0[i][j] = utils::numeric(FLERR, arg[5 + 3 * j], false, lmp); + if (r0[i][j] <= 0.0) error->all(FLERR, "Invalid value for r0_{}: {}", j, r0[i][j]); setflag[i] = 1; } count++; diff --git a/src/EXTRA-MOLECULE/bond_gaussian.h b/src/EXTRA-MOLECULE/bond_gaussian.h index 17ae23fb5f..7af6f1f4d9 100644 --- a/src/EXTRA-MOLECULE/bond_gaussian.h +++ b/src/EXTRA-MOLECULE/bond_gaussian.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/bond_harmonic_shift.cpp b/src/EXTRA-MOLECULE/bond_harmonic_shift.cpp index da6046f23f..2f8bfbaa08 100644 --- a/src/EXTRA-MOLECULE/bond_harmonic_shift.cpp +++ b/src/EXTRA-MOLECULE/bond_harmonic_shift.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/bond_harmonic_shift.h b/src/EXTRA-MOLECULE/bond_harmonic_shift.h index 0b7d0ab6b8..2df13cee27 100644 --- a/src/EXTRA-MOLECULE/bond_harmonic_shift.h +++ b/src/EXTRA-MOLECULE/bond_harmonic_shift.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/bond_harmonic_shift_cut.cpp b/src/EXTRA-MOLECULE/bond_harmonic_shift_cut.cpp index f6420b0c4a..fedcb95ee8 100644 --- a/src/EXTRA-MOLECULE/bond_harmonic_shift_cut.cpp +++ b/src/EXTRA-MOLECULE/bond_harmonic_shift_cut.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/bond_harmonic_shift_cut.h b/src/EXTRA-MOLECULE/bond_harmonic_shift_cut.h index 74d97143f7..752ac010d9 100644 --- a/src/EXTRA-MOLECULE/bond_harmonic_shift_cut.h +++ b/src/EXTRA-MOLECULE/bond_harmonic_shift_cut.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/bond_nonlinear.cpp b/src/EXTRA-MOLECULE/bond_nonlinear.cpp index e1cac4743f..873c54e917 100644 --- a/src/EXTRA-MOLECULE/bond_nonlinear.cpp +++ b/src/EXTRA-MOLECULE/bond_nonlinear.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/bond_nonlinear.h b/src/EXTRA-MOLECULE/bond_nonlinear.h index ae2f6b6c6c..3023add89d 100644 --- a/src/EXTRA-MOLECULE/bond_nonlinear.h +++ b/src/EXTRA-MOLECULE/bond_nonlinear.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/dihedral_cosine_shift_exp.cpp b/src/EXTRA-MOLECULE/dihedral_cosine_shift_exp.cpp index 419cfe5d3f..7165cde1fd 100644 --- a/src/EXTRA-MOLECULE/dihedral_cosine_shift_exp.cpp +++ b/src/EXTRA-MOLECULE/dihedral_cosine_shift_exp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/dihedral_cosine_shift_exp.h b/src/EXTRA-MOLECULE/dihedral_cosine_shift_exp.h index f45eefdceb..06387d7ef6 100644 --- a/src/EXTRA-MOLECULE/dihedral_cosine_shift_exp.h +++ b/src/EXTRA-MOLECULE/dihedral_cosine_shift_exp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/dihedral_fourier.cpp b/src/EXTRA-MOLECULE/dihedral_fourier.cpp index afc309ee17..f9b4a0d13e 100644 --- a/src/EXTRA-MOLECULE/dihedral_fourier.cpp +++ b/src/EXTRA-MOLECULE/dihedral_fourier.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/dihedral_fourier.h b/src/EXTRA-MOLECULE/dihedral_fourier.h index 18116af25c..558879a543 100644 --- a/src/EXTRA-MOLECULE/dihedral_fourier.h +++ b/src/EXTRA-MOLECULE/dihedral_fourier.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/dihedral_helix.cpp b/src/EXTRA-MOLECULE/dihedral_helix.cpp index 4bbf8edcf4..059bef74a4 100644 --- a/src/EXTRA-MOLECULE/dihedral_helix.cpp +++ b/src/EXTRA-MOLECULE/dihedral_helix.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/dihedral_helix.h b/src/EXTRA-MOLECULE/dihedral_helix.h index 966696a427..436895c5c3 100644 --- a/src/EXTRA-MOLECULE/dihedral_helix.h +++ b/src/EXTRA-MOLECULE/dihedral_helix.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/dihedral_nharmonic.cpp b/src/EXTRA-MOLECULE/dihedral_nharmonic.cpp index 9e3caa1393..206ad4f3ad 100644 --- a/src/EXTRA-MOLECULE/dihedral_nharmonic.cpp +++ b/src/EXTRA-MOLECULE/dihedral_nharmonic.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -25,7 +25,6 @@ #include "force.h" #include "memory.h" #include "neighbor.h" -#include "domain.h" #include diff --git a/src/EXTRA-MOLECULE/dihedral_nharmonic.h b/src/EXTRA-MOLECULE/dihedral_nharmonic.h index 28dd2e084e..738e98f072 100644 --- a/src/EXTRA-MOLECULE/dihedral_nharmonic.h +++ b/src/EXTRA-MOLECULE/dihedral_nharmonic.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/dihedral_quadratic.cpp b/src/EXTRA-MOLECULE/dihedral_quadratic.cpp index 9b1ae5f9cb..cbe9e3e3a2 100644 --- a/src/EXTRA-MOLECULE/dihedral_quadratic.cpp +++ b/src/EXTRA-MOLECULE/dihedral_quadratic.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/dihedral_quadratic.h b/src/EXTRA-MOLECULE/dihedral_quadratic.h index 7ea7839c1f..90d8c3be6e 100644 --- a/src/EXTRA-MOLECULE/dihedral_quadratic.h +++ b/src/EXTRA-MOLECULE/dihedral_quadratic.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/dihedral_spherical.cpp b/src/EXTRA-MOLECULE/dihedral_spherical.cpp index 9918e92101..c577565792 100644 --- a/src/EXTRA-MOLECULE/dihedral_spherical.cpp +++ b/src/EXTRA-MOLECULE/dihedral_spherical.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/dihedral_spherical.h b/src/EXTRA-MOLECULE/dihedral_spherical.h index 993f12ceb3..3e86933443 100644 --- a/src/EXTRA-MOLECULE/dihedral_spherical.h +++ b/src/EXTRA-MOLECULE/dihedral_spherical.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/dihedral_table_cut.cpp b/src/EXTRA-MOLECULE/dihedral_table_cut.cpp index 4830516b1d..5a75cb5e34 100644 --- a/src/EXTRA-MOLECULE/dihedral_table_cut.cpp +++ b/src/EXTRA-MOLECULE/dihedral_table_cut.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/dihedral_table_cut.h b/src/EXTRA-MOLECULE/dihedral_table_cut.h index 5bdf0a6922..c53eee1e6c 100644 --- a/src/EXTRA-MOLECULE/dihedral_table_cut.h +++ b/src/EXTRA-MOLECULE/dihedral_table_cut.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/improper_cossq.cpp b/src/EXTRA-MOLECULE/improper_cossq.cpp index ea5bd1b43e..d08c2afebe 100644 --- a/src/EXTRA-MOLECULE/improper_cossq.cpp +++ b/src/EXTRA-MOLECULE/improper_cossq.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/improper_cossq.h b/src/EXTRA-MOLECULE/improper_cossq.h index 854aa3ed05..cc7e94ca5c 100644 --- a/src/EXTRA-MOLECULE/improper_cossq.h +++ b/src/EXTRA-MOLECULE/improper_cossq.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/improper_distance.cpp b/src/EXTRA-MOLECULE/improper_distance.cpp index 189440e318..b16e2cc674 100644 --- a/src/EXTRA-MOLECULE/improper_distance.cpp +++ b/src/EXTRA-MOLECULE/improper_distance.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/improper_distance.h b/src/EXTRA-MOLECULE/improper_distance.h index d814405906..b0bfaea6e6 100644 --- a/src/EXTRA-MOLECULE/improper_distance.h +++ b/src/EXTRA-MOLECULE/improper_distance.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/improper_fourier.cpp b/src/EXTRA-MOLECULE/improper_fourier.cpp index 56200fec8c..58f8677fd6 100644 --- a/src/EXTRA-MOLECULE/improper_fourier.cpp +++ b/src/EXTRA-MOLECULE/improper_fourier.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/improper_fourier.h b/src/EXTRA-MOLECULE/improper_fourier.h index f420c534a2..96354b6818 100644 --- a/src/EXTRA-MOLECULE/improper_fourier.h +++ b/src/EXTRA-MOLECULE/improper_fourier.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/improper_ring.cpp b/src/EXTRA-MOLECULE/improper_ring.cpp index 36de27804b..ce3f16a696 100644 --- a/src/EXTRA-MOLECULE/improper_ring.cpp +++ b/src/EXTRA-MOLECULE/improper_ring.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-MOLECULE/improper_ring.h b/src/EXTRA-MOLECULE/improper_ring.h index 3afb5a8d98..db8a681f75 100644 --- a/src/EXTRA-MOLECULE/improper_ring.h +++ b/src/EXTRA-MOLECULE/improper_ring.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_beck.cpp b/src/EXTRA-PAIR/pair_beck.cpp index 07c40c2ff0..1fdaf4bf73 100644 --- a/src/EXTRA-PAIR/pair_beck.cpp +++ b/src/EXTRA-PAIR/pair_beck.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_beck.h b/src/EXTRA-PAIR/pair_beck.h index cca5f53cde..46d8397821 100644 --- a/src/EXTRA-PAIR/pair_beck.h +++ b/src/EXTRA-PAIR/pair_beck.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_born_coul_dsf.cpp b/src/EXTRA-PAIR/pair_born_coul_dsf.cpp index 84bfed6908..c1be749d7b 100644 --- a/src/EXTRA-PAIR/pair_born_coul_dsf.cpp +++ b/src/EXTRA-PAIR/pair_born_coul_dsf.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_born_coul_dsf.h b/src/EXTRA-PAIR/pair_born_coul_dsf.h index 8a271dffbc..1215ae011e 100644 --- a/src/EXTRA-PAIR/pair_born_coul_dsf.h +++ b/src/EXTRA-PAIR/pair_born_coul_dsf.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_born_coul_wolf.cpp b/src/EXTRA-PAIR/pair_born_coul_wolf.cpp index 54eaed1dc2..e3ebe884e2 100644 --- a/src/EXTRA-PAIR/pair_born_coul_wolf.cpp +++ b/src/EXTRA-PAIR/pair_born_coul_wolf.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_born_coul_wolf.h b/src/EXTRA-PAIR/pair_born_coul_wolf.h index 6a1a3e52f3..629a9a6e86 100644 --- a/src/EXTRA-PAIR/pair_born_coul_wolf.h +++ b/src/EXTRA-PAIR/pair_born_coul_wolf.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_buck_mdf.cpp b/src/EXTRA-PAIR/pair_buck_mdf.cpp index cea3399ef1..30485ec71d 100644 --- a/src/EXTRA-PAIR/pair_buck_mdf.cpp +++ b/src/EXTRA-PAIR/pair_buck_mdf.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_buck_mdf.h b/src/EXTRA-PAIR/pair_buck_mdf.h index 6eddb8c0c3..431a3ae399 100644 --- a/src/EXTRA-PAIR/pair_buck_mdf.h +++ b/src/EXTRA-PAIR/pair_buck_mdf.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_cosine_squared.cpp b/src/EXTRA-PAIR/pair_cosine_squared.cpp index 1e61142c0b..fafe0400d5 100644 --- a/src/EXTRA-PAIR/pair_cosine_squared.cpp +++ b/src/EXTRA-PAIR/pair_cosine_squared.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_cosine_squared.h b/src/EXTRA-PAIR/pair_cosine_squared.h index 0ae26817bb..65fff657ef 100644 --- a/src/EXTRA-PAIR/pair_cosine_squared.h +++ b/src/EXTRA-PAIR/pair_cosine_squared.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_coul_cut_global.cpp b/src/EXTRA-PAIR/pair_coul_cut_global.cpp index 48f726c062..e724a48959 100644 --- a/src/EXTRA-PAIR/pair_coul_cut_global.cpp +++ b/src/EXTRA-PAIR/pair_coul_cut_global.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_coul_cut_global.h b/src/EXTRA-PAIR/pair_coul_cut_global.h index d35f7a2c2e..85ccc827dc 100644 --- a/src/EXTRA-PAIR/pair_coul_cut_global.h +++ b/src/EXTRA-PAIR/pair_coul_cut_global.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_coul_diel.cpp b/src/EXTRA-PAIR/pair_coul_diel.cpp index fb110eed84..9d7904ba07 100644 --- a/src/EXTRA-PAIR/pair_coul_diel.cpp +++ b/src/EXTRA-PAIR/pair_coul_diel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_coul_diel.h b/src/EXTRA-PAIR/pair_coul_diel.h index a7dbe6a6d7..5b061b38ec 100644 --- a/src/EXTRA-PAIR/pair_coul_diel.h +++ b/src/EXTRA-PAIR/pair_coul_diel.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_coul_exclude.cpp b/src/EXTRA-PAIR/pair_coul_exclude.cpp index efd612d1d6..8781f6abf0 100644 --- a/src/EXTRA-PAIR/pair_coul_exclude.cpp +++ b/src/EXTRA-PAIR/pair_coul_exclude.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_coul_exclude.h b/src/EXTRA-PAIR/pair_coul_exclude.h index 5d7db1edb0..269748beaf 100644 --- a/src/EXTRA-PAIR/pair_coul_exclude.h +++ b/src/EXTRA-PAIR/pair_coul_exclude.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_coul_slater_cut.cpp b/src/EXTRA-PAIR/pair_coul_slater_cut.cpp index eca5d5dd63..4b12e65e3f 100644 --- a/src/EXTRA-PAIR/pair_coul_slater_cut.cpp +++ b/src/EXTRA-PAIR/pair_coul_slater_cut.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_coul_slater_cut.h b/src/EXTRA-PAIR/pair_coul_slater_cut.h index b8aaa41e03..015dd5ee33 100644 --- a/src/EXTRA-PAIR/pair_coul_slater_cut.h +++ b/src/EXTRA-PAIR/pair_coul_slater_cut.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_coul_slater_long.cpp b/src/EXTRA-PAIR/pair_coul_slater_long.cpp index 6662ae3721..4109309345 100644 --- a/src/EXTRA-PAIR/pair_coul_slater_long.cpp +++ b/src/EXTRA-PAIR/pair_coul_slater_long.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_coul_slater_long.h b/src/EXTRA-PAIR/pair_coul_slater_long.h index 7650ce5a92..ef1742ece1 100644 --- a/src/EXTRA-PAIR/pair_coul_slater_long.h +++ b/src/EXTRA-PAIR/pair_coul_slater_long.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_e3b.cpp b/src/EXTRA-PAIR/pair_e3b.cpp index ab68b5c729..efd8c5e9af 100644 --- a/src/EXTRA-PAIR/pair_e3b.cpp +++ b/src/EXTRA-PAIR/pair_e3b.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_e3b.h b/src/EXTRA-PAIR/pair_e3b.h index e887919ba6..c61bb10798 100644 --- a/src/EXTRA-PAIR/pair_e3b.h +++ b/src/EXTRA-PAIR/pair_e3b.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_gauss.cpp b/src/EXTRA-PAIR/pair_gauss.cpp index 70b01dbbc0..1c2bb5f0d6 100644 --- a/src/EXTRA-PAIR/pair_gauss.cpp +++ b/src/EXTRA-PAIR/pair_gauss.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_gauss.h b/src/EXTRA-PAIR/pair_gauss.h index a20e810aa6..9bb69f14e2 100644 --- a/src/EXTRA-PAIR/pair_gauss.h +++ b/src/EXTRA-PAIR/pair_gauss.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_gauss_cut.cpp b/src/EXTRA-PAIR/pair_gauss_cut.cpp index 99d3675f7b..7e445d728e 100644 --- a/src/EXTRA-PAIR/pair_gauss_cut.cpp +++ b/src/EXTRA-PAIR/pair_gauss_cut.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_gauss_cut.h b/src/EXTRA-PAIR/pair_gauss_cut.h index a485c2637f..c3ed3cbbbf 100644 --- a/src/EXTRA-PAIR/pair_gauss_cut.h +++ b/src/EXTRA-PAIR/pair_gauss_cut.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_harmonic_cut.cpp b/src/EXTRA-PAIR/pair_harmonic_cut.cpp index 0cd9261aee..84e15b54bb 100644 --- a/src/EXTRA-PAIR/pair_harmonic_cut.cpp +++ b/src/EXTRA-PAIR/pair_harmonic_cut.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_harmonic_cut.h b/src/EXTRA-PAIR/pair_harmonic_cut.h index f044faedd0..a8d368cc8c 100644 --- a/src/EXTRA-PAIR/pair_harmonic_cut.h +++ b/src/EXTRA-PAIR/pair_harmonic_cut.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lennard_mdf.cpp b/src/EXTRA-PAIR/pair_lennard_mdf.cpp index 87f89c6780..b97f0ba342 100644 --- a/src/EXTRA-PAIR/pair_lennard_mdf.cpp +++ b/src/EXTRA-PAIR/pair_lennard_mdf.cpp @@ -3,7 +3,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lennard_mdf.h b/src/EXTRA-PAIR/pair_lennard_mdf.h index 9453def779..1d7e25da3a 100644 --- a/src/EXTRA-PAIR/pair_lennard_mdf.h +++ b/src/EXTRA-PAIR/pair_lennard_mdf.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj96_cut.cpp b/src/EXTRA-PAIR/pair_lj96_cut.cpp index 4b7c2912b0..1cc94e7827 100644 --- a/src/EXTRA-PAIR/pair_lj96_cut.cpp +++ b/src/EXTRA-PAIR/pair_lj96_cut.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj96_cut.h b/src/EXTRA-PAIR/pair_lj96_cut.h index 243e94bfed..658dbff35f 100644 --- a/src/EXTRA-PAIR/pair_lj96_cut.h +++ b/src/EXTRA-PAIR/pair_lj96_cut.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj_cubic.cpp b/src/EXTRA-PAIR/pair_lj_cubic.cpp index 31f1d71550..e5d45786ac 100644 --- a/src/EXTRA-PAIR/pair_lj_cubic.cpp +++ b/src/EXTRA-PAIR/pair_lj_cubic.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj_cubic.h b/src/EXTRA-PAIR/pair_lj_cubic.h index b1f6028589..9f0603ff6c 100644 --- a/src/EXTRA-PAIR/pair_lj_cubic.h +++ b/src/EXTRA-PAIR/pair_lj_cubic.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj_cubic_const.h b/src/EXTRA-PAIR/pair_lj_cubic_const.h index ce3e578ebc..869fc84116 100644 --- a/src/EXTRA-PAIR/pair_lj_cubic_const.h +++ b/src/EXTRA-PAIR/pair_lj_cubic_const.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj_cut_coul_debye.cpp b/src/EXTRA-PAIR/pair_lj_cut_coul_debye.cpp index 1c25b4b9c0..84bb909d41 100644 --- a/src/EXTRA-PAIR/pair_lj_cut_coul_debye.cpp +++ b/src/EXTRA-PAIR/pair_lj_cut_coul_debye.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj_cut_coul_debye.h b/src/EXTRA-PAIR/pair_lj_cut_coul_debye.h index 1845f0d5eb..72301f593e 100644 --- a/src/EXTRA-PAIR/pair_lj_cut_coul_debye.h +++ b/src/EXTRA-PAIR/pair_lj_cut_coul_debye.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj_cut_coul_dsf.cpp b/src/EXTRA-PAIR/pair_lj_cut_coul_dsf.cpp index 9782844c26..49e1468af1 100644 --- a/src/EXTRA-PAIR/pair_lj_cut_coul_dsf.cpp +++ b/src/EXTRA-PAIR/pair_lj_cut_coul_dsf.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj_cut_coul_dsf.h b/src/EXTRA-PAIR/pair_lj_cut_coul_dsf.h index 642d32f58a..14ac28097a 100644 --- a/src/EXTRA-PAIR/pair_lj_cut_coul_dsf.h +++ b/src/EXTRA-PAIR/pair_lj_cut_coul_dsf.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj_cut_coul_wolf.cpp b/src/EXTRA-PAIR/pair_lj_cut_coul_wolf.cpp index aa0875f11c..20f38891ad 100644 --- a/src/EXTRA-PAIR/pair_lj_cut_coul_wolf.cpp +++ b/src/EXTRA-PAIR/pair_lj_cut_coul_wolf.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj_cut_coul_wolf.h b/src/EXTRA-PAIR/pair_lj_cut_coul_wolf.h index 115d171f27..0fec0470dc 100644 --- a/src/EXTRA-PAIR/pair_lj_cut_coul_wolf.h +++ b/src/EXTRA-PAIR/pair_lj_cut_coul_wolf.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj_expand_coul_long.cpp b/src/EXTRA-PAIR/pair_lj_expand_coul_long.cpp index 3841b50d45..28b1ff5ea6 100644 --- a/src/EXTRA-PAIR/pair_lj_expand_coul_long.cpp +++ b/src/EXTRA-PAIR/pair_lj_expand_coul_long.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj_expand_coul_long.h b/src/EXTRA-PAIR/pair_lj_expand_coul_long.h index 7f8db4570c..567d9bc72b 100644 --- a/src/EXTRA-PAIR/pair_lj_expand_coul_long.h +++ b/src/EXTRA-PAIR/pair_lj_expand_coul_long.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj_gromacs.cpp b/src/EXTRA-PAIR/pair_lj_gromacs.cpp index c5b23d24d9..4f728b2fbb 100644 --- a/src/EXTRA-PAIR/pair_lj_gromacs.cpp +++ b/src/EXTRA-PAIR/pair_lj_gromacs.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj_gromacs.h b/src/EXTRA-PAIR/pair_lj_gromacs.h index 3a5b92788e..f210c8c145 100644 --- a/src/EXTRA-PAIR/pair_lj_gromacs.h +++ b/src/EXTRA-PAIR/pair_lj_gromacs.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj_gromacs_coul_gromacs.cpp b/src/EXTRA-PAIR/pair_lj_gromacs_coul_gromacs.cpp index 71911169cf..e20af2b81f 100644 --- a/src/EXTRA-PAIR/pair_lj_gromacs_coul_gromacs.cpp +++ b/src/EXTRA-PAIR/pair_lj_gromacs_coul_gromacs.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj_gromacs_coul_gromacs.h b/src/EXTRA-PAIR/pair_lj_gromacs_coul_gromacs.h index d6c002861b..5f2d4dd814 100644 --- a/src/EXTRA-PAIR/pair_lj_gromacs_coul_gromacs.h +++ b/src/EXTRA-PAIR/pair_lj_gromacs_coul_gromacs.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj_mdf.cpp b/src/EXTRA-PAIR/pair_lj_mdf.cpp index eb435e3c65..091c49152c 100644 --- a/src/EXTRA-PAIR/pair_lj_mdf.cpp +++ b/src/EXTRA-PAIR/pair_lj_mdf.cpp @@ -3,7 +3,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj_mdf.h b/src/EXTRA-PAIR/pair_lj_mdf.h index dbf35292a7..f723fe0875 100644 --- a/src/EXTRA-PAIR/pair_lj_mdf.h +++ b/src/EXTRA-PAIR/pair_lj_mdf.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj_relres.cpp b/src/EXTRA-PAIR/pair_lj_relres.cpp index 88621fe54a..85d0a04bf9 100644 --- a/src/EXTRA-PAIR/pair_lj_relres.cpp +++ b/src/EXTRA-PAIR/pair_lj_relres.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj_relres.h b/src/EXTRA-PAIR/pair_lj_relres.h index 9851b13ae6..572e42b032 100644 --- a/src/EXTRA-PAIR/pair_lj_relres.h +++ b/src/EXTRA-PAIR/pair_lj_relres.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj_smooth.cpp b/src/EXTRA-PAIR/pair_lj_smooth.cpp index 5346a39e62..5092951dd3 100644 --- a/src/EXTRA-PAIR/pair_lj_smooth.cpp +++ b/src/EXTRA-PAIR/pair_lj_smooth.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj_smooth.h b/src/EXTRA-PAIR/pair_lj_smooth.h index 0212ef812c..fde28a4179 100644 --- a/src/EXTRA-PAIR/pair_lj_smooth.h +++ b/src/EXTRA-PAIR/pair_lj_smooth.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj_smooth_linear.cpp b/src/EXTRA-PAIR/pair_lj_smooth_linear.cpp index 7454a2f90c..a1b847340f 100644 --- a/src/EXTRA-PAIR/pair_lj_smooth_linear.cpp +++ b/src/EXTRA-PAIR/pair_lj_smooth_linear.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_lj_smooth_linear.h b/src/EXTRA-PAIR/pair_lj_smooth_linear.h index 6948933496..b1e039e7b6 100644 --- a/src/EXTRA-PAIR/pair_lj_smooth_linear.h +++ b/src/EXTRA-PAIR/pair_lj_smooth_linear.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_mie_cut.cpp b/src/EXTRA-PAIR/pair_mie_cut.cpp index 8556bacb30..01e0104ae4 100644 --- a/src/EXTRA-PAIR/pair_mie_cut.cpp +++ b/src/EXTRA-PAIR/pair_mie_cut.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_mie_cut.h b/src/EXTRA-PAIR/pair_mie_cut.h index 68a712d738..39ea15d99b 100644 --- a/src/EXTRA-PAIR/pair_mie_cut.h +++ b/src/EXTRA-PAIR/pair_mie_cut.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_momb.cpp b/src/EXTRA-PAIR/pair_momb.cpp index d8b6e04d11..e6b03d623d 100644 --- a/src/EXTRA-PAIR/pair_momb.cpp +++ b/src/EXTRA-PAIR/pair_momb.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_momb.h b/src/EXTRA-PAIR/pair_momb.h index 0f6d535f6d..3a87b0a636 100644 --- a/src/EXTRA-PAIR/pair_momb.h +++ b/src/EXTRA-PAIR/pair_momb.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_morse_smooth_linear.cpp b/src/EXTRA-PAIR/pair_morse_smooth_linear.cpp index 59949a7aed..2cbcf29a66 100644 --- a/src/EXTRA-PAIR/pair_morse_smooth_linear.cpp +++ b/src/EXTRA-PAIR/pair_morse_smooth_linear.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_morse_smooth_linear.h b/src/EXTRA-PAIR/pair_morse_smooth_linear.h index b2c10f0e18..22bc2ddf96 100644 --- a/src/EXTRA-PAIR/pair_morse_smooth_linear.h +++ b/src/EXTRA-PAIR/pair_morse_smooth_linear.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_nm_cut.cpp b/src/EXTRA-PAIR/pair_nm_cut.cpp index 66762869ea..18b5810abc 100644 --- a/src/EXTRA-PAIR/pair_nm_cut.cpp +++ b/src/EXTRA-PAIR/pair_nm_cut.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -18,8 +18,6 @@ #include "pair_nm_cut.h" -#include -#include #include "atom.h" #include "comm.h" #include "force.h" @@ -28,6 +26,8 @@ #include "memory.h" #include "error.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/EXTRA-PAIR/pair_nm_cut.h b/src/EXTRA-PAIR/pair_nm_cut.h index 14078a81a4..ab91747252 100644 --- a/src/EXTRA-PAIR/pair_nm_cut.h +++ b/src/EXTRA-PAIR/pair_nm_cut.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_nm_cut_coul_cut.cpp b/src/EXTRA-PAIR/pair_nm_cut_coul_cut.cpp index d9cfbf1525..adc6d5a058 100644 --- a/src/EXTRA-PAIR/pair_nm_cut_coul_cut.cpp +++ b/src/EXTRA-PAIR/pair_nm_cut_coul_cut.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -223,8 +223,7 @@ void PairNMCutCoulCut::settings(int narg, char **arg) void PairNMCutCoulCut::coeff(int narg, char **arg) { - if (narg < 6 || narg > 8) - error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 6 || narg > 8) error->all(FLERR,"Incorrect args for pair coefficients"); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -238,8 +237,8 @@ void PairNMCutCoulCut::coeff(int narg, char **arg) double cut_lj_one = cut_lj_global; double cut_coul_one = cut_coul_global; - if (narg >= 7) cut_coul_one = cut_lj_one = utils::numeric(FLERR,arg[4],false,lmp); - if (narg == 8) cut_coul_one = utils::numeric(FLERR,arg[5],false,lmp); + if (narg >= 7) cut_coul_one = cut_lj_one = utils::numeric(FLERR,arg[6],false,lmp); + if (narg == 8) cut_coul_one = utils::numeric(FLERR,arg[7],false,lmp); int count = 0; for (int i = ilo; i <= ihi; i++) { diff --git a/src/EXTRA-PAIR/pair_nm_cut_coul_cut.h b/src/EXTRA-PAIR/pair_nm_cut_coul_cut.h index 9ae33df593..ff51920c63 100644 --- a/src/EXTRA-PAIR/pair_nm_cut_coul_cut.h +++ b/src/EXTRA-PAIR/pair_nm_cut_coul_cut.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_nm_cut_coul_long.cpp b/src/EXTRA-PAIR/pair_nm_cut_coul_long.cpp index 66f4e53ab2..13171c87dd 100644 --- a/src/EXTRA-PAIR/pair_nm_cut_coul_long.cpp +++ b/src/EXTRA-PAIR/pair_nm_cut_coul_long.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -277,7 +277,7 @@ void PairNMCutCoulLong::coeff(int narg, char **arg) double mm_one = utils::numeric(FLERR,arg[5],false,lmp); double cut_lj_one = cut_lj_global; - if (narg == 7) cut_lj_one = utils::numeric(FLERR,arg[4],false,lmp); + if (narg == 7) cut_lj_one = utils::numeric(FLERR,arg[6],false,lmp); int count = 0; for (int i = ilo; i <= ihi; i++) { diff --git a/src/EXTRA-PAIR/pair_nm_cut_coul_long.h b/src/EXTRA-PAIR/pair_nm_cut_coul_long.h index f9b7a434ba..1e1d61ff90 100644 --- a/src/EXTRA-PAIR/pair_nm_cut_coul_long.h +++ b/src/EXTRA-PAIR/pair_nm_cut_coul_long.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_nm_cut_split.cpp b/src/EXTRA-PAIR/pair_nm_cut_split.cpp index 45323b931c..183420972c 100644 --- a/src/EXTRA-PAIR/pair_nm_cut_split.cpp +++ b/src/EXTRA-PAIR/pair_nm_cut_split.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_nm_cut_split.h b/src/EXTRA-PAIR/pair_nm_cut_split.h index 4f548a5118..b2615b22b1 100644 --- a/src/EXTRA-PAIR/pair_nm_cut_split.h +++ b/src/EXTRA-PAIR/pair_nm_cut_split.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_ufm.cpp b/src/EXTRA-PAIR/pair_ufm.cpp index c2f7e25227..e45b0814b3 100644 --- a/src/EXTRA-PAIR/pair_ufm.cpp +++ b/src/EXTRA-PAIR/pair_ufm.cpp @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_ufm.h b/src/EXTRA-PAIR/pair_ufm.h index 24f9c9dd2f..e22700e06a 100644 --- a/src/EXTRA-PAIR/pair_ufm.h +++ b/src/EXTRA-PAIR/pair_ufm.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_wf_cut.cpp b/src/EXTRA-PAIR/pair_wf_cut.cpp index 3bfe46921f..d572521d90 100644 --- a/src/EXTRA-PAIR/pair_wf_cut.cpp +++ b/src/EXTRA-PAIR/pair_wf_cut.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/EXTRA-PAIR/pair_wf_cut.h b/src/EXTRA-PAIR/pair_wf_cut.h index 80059ab1d9..c09a5b67de 100644 --- a/src/EXTRA-PAIR/pair_wf_cut.h +++ b/src/EXTRA-PAIR/pair_wf_cut.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/compute_fep.cpp b/src/FEP/compute_fep.cpp index 7a813018ad..995e2f9f3d 100644 --- a/src/FEP/compute_fep.cpp +++ b/src/FEP/compute_fep.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -190,22 +190,34 @@ void ComputeFEP::init() Perturb *pert = &perturb[m]; pert->ivar = input->variable->find(pert->var); - if (pert->ivar < 0) error->all(FLERR, "Variable name for compute fep does not exist"); + if (pert->ivar < 0) + error->all(FLERR, "Variable name {} for compute fep does not exist", pert->var); if (!input->variable->equalstyle(pert->ivar)) - error->all(FLERR, "Variable for compute fep is of invalid style"); + error->all(FLERR, "Variable {} for compute fep is of invalid style", pert->var); if (force->pair == nullptr) error->all(FLERR, "compute fep pair requires pair interactions"); if (pert->which == PAIR) { pairflag = 1; + Pair *pair = nullptr; + if (lmp->suffix_enable) { + if (lmp->suffix) { + auto pstyle = fmt::format("{}/{}", pert->pstyle, lmp->suffix); + pair = force->pair_match(pstyle, 1); + } + if ((pair == nullptr) && lmp->suffix2) { + auto pstyle = fmt::format("{}/{}", pert->pstyle, lmp->suffix2); + pair = force->pair_match(pstyle, 1); + } + } - Pair *pair = force->pair_match(pert->pstyle, 1); + if (pair == nullptr) pair = force->pair_match(pert->pstyle, 1); if (pair == nullptr) - error->all(FLERR, - "compute fep pair style " - "does not exist"); + error->all(FLERR, "compute fep pair style {} does not exist", pert->pstyle); + void *ptr = pair->extract(pert->pparam, pert->pdim); - if (ptr == nullptr) error->all(FLERR, "compute fep pair style param not supported"); + if (ptr == nullptr) + error->all(FLERR, "compute fep pair style param {} not supported", pert->pparam); pert->array = (double **) ptr; diff --git a/src/FEP/compute_fep.h b/src/FEP/compute_fep.h index c586dae341..ef25cb2ccb 100644 --- a/src/FEP/compute_fep.h +++ b/src/FEP/compute_fep.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/compute_fep_ta.cpp b/src/FEP/compute_fep_ta.cpp index 9ab848f6db..786bf53bfa 100644 --- a/src/FEP/compute_fep_ta.cpp +++ b/src/FEP/compute_fep_ta.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -30,7 +30,6 @@ #include "kspace.h" #include "memory.h" #include "modify.h" -#include "neighbor.h" #include "pair.h" #include "timer.h" #include "update.h" diff --git a/src/FEP/compute_fep_ta.h b/src/FEP/compute_fep_ta.h index ccbabc6295..5b5891660e 100644 --- a/src/FEP/compute_fep_ta.h +++ b/src/FEP/compute_fep_ta.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/fix_adapt_fep.cpp b/src/FEP/fix_adapt_fep.cpp index 7d2831e179..2d2409d27f 100644 --- a/src/FEP/fix_adapt_fep.cpp +++ b/src/FEP/fix_adapt_fep.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/fix_adapt_fep.h b/src/FEP/fix_adapt_fep.h index 86b6a93733..a93349a780 100644 --- a/src/FEP/fix_adapt_fep.h +++ b/src/FEP/fix_adapt_fep.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/pair_coul_cut_soft.cpp b/src/FEP/pair_coul_cut_soft.cpp index 493ddbf3e8..df4d19fc41 100644 --- a/src/FEP/pair_coul_cut_soft.cpp +++ b/src/FEP/pair_coul_cut_soft.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/pair_coul_cut_soft.h b/src/FEP/pair_coul_cut_soft.h index e327074f21..1454e70d61 100644 --- a/src/FEP/pair_coul_cut_soft.h +++ b/src/FEP/pair_coul_cut_soft.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/pair_coul_long_soft.cpp b/src/FEP/pair_coul_long_soft.cpp index 03a0fbcbb6..1607f44b3d 100644 --- a/src/FEP/pair_coul_long_soft.cpp +++ b/src/FEP/pair_coul_long_soft.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/pair_coul_long_soft.h b/src/FEP/pair_coul_long_soft.h index c5469148ad..e81bfa1fce 100644 --- a/src/FEP/pair_coul_long_soft.h +++ b/src/FEP/pair_coul_long_soft.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/pair_lj_charmm_coul_long_soft.cpp b/src/FEP/pair_lj_charmm_coul_long_soft.cpp index 63e7be5490..bd37b88b38 100644 --- a/src/FEP/pair_lj_charmm_coul_long_soft.cpp +++ b/src/FEP/pair_lj_charmm_coul_long_soft.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/pair_lj_charmm_coul_long_soft.h b/src/FEP/pair_lj_charmm_coul_long_soft.h index e1fab23fbf..90424d4b2d 100644 --- a/src/FEP/pair_lj_charmm_coul_long_soft.h +++ b/src/FEP/pair_lj_charmm_coul_long_soft.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/pair_lj_class2_coul_cut_soft.cpp b/src/FEP/pair_lj_class2_coul_cut_soft.cpp index 2854062641..5dc8141190 100644 --- a/src/FEP/pair_lj_class2_coul_cut_soft.cpp +++ b/src/FEP/pair_lj_class2_coul_cut_soft.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/pair_lj_class2_coul_cut_soft.h b/src/FEP/pair_lj_class2_coul_cut_soft.h index db8b76d443..79b372a99d 100644 --- a/src/FEP/pair_lj_class2_coul_cut_soft.h +++ b/src/FEP/pair_lj_class2_coul_cut_soft.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/pair_lj_class2_coul_long_soft.cpp b/src/FEP/pair_lj_class2_coul_long_soft.cpp index db01dedea6..40aea52436 100644 --- a/src/FEP/pair_lj_class2_coul_long_soft.cpp +++ b/src/FEP/pair_lj_class2_coul_long_soft.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/pair_lj_class2_coul_long_soft.h b/src/FEP/pair_lj_class2_coul_long_soft.h index f125d02f27..a40b1c33af 100644 --- a/src/FEP/pair_lj_class2_coul_long_soft.h +++ b/src/FEP/pair_lj_class2_coul_long_soft.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/pair_lj_class2_soft.cpp b/src/FEP/pair_lj_class2_soft.cpp index e43c02a50d..79d2f19da6 100644 --- a/src/FEP/pair_lj_class2_soft.cpp +++ b/src/FEP/pair_lj_class2_soft.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/pair_lj_class2_soft.h b/src/FEP/pair_lj_class2_soft.h index 75fff9107a..df0207f52a 100644 --- a/src/FEP/pair_lj_class2_soft.h +++ b/src/FEP/pair_lj_class2_soft.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org 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 diff --git a/src/FEP/pair_lj_cut_coul_cut_soft.cpp b/src/FEP/pair_lj_cut_coul_cut_soft.cpp index b6b9063d0f..1405a18cf1 100644 --- a/src/FEP/pair_lj_cut_coul_cut_soft.cpp +++ b/src/FEP/pair_lj_cut_coul_cut_soft.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/pair_lj_cut_coul_cut_soft.h b/src/FEP/pair_lj_cut_coul_cut_soft.h index 0e621faf29..c04c018d81 100644 --- a/src/FEP/pair_lj_cut_coul_cut_soft.h +++ b/src/FEP/pair_lj_cut_coul_cut_soft.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/pair_lj_cut_coul_long_soft.cpp b/src/FEP/pair_lj_cut_coul_long_soft.cpp index 8090562c3e..458d4c3566 100644 --- a/src/FEP/pair_lj_cut_coul_long_soft.cpp +++ b/src/FEP/pair_lj_cut_coul_long_soft.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/pair_lj_cut_coul_long_soft.h b/src/FEP/pair_lj_cut_coul_long_soft.h index cc5c39dabe..cc070e2ead 100644 --- a/src/FEP/pair_lj_cut_coul_long_soft.h +++ b/src/FEP/pair_lj_cut_coul_long_soft.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/pair_lj_cut_soft.cpp b/src/FEP/pair_lj_cut_soft.cpp index 2f2b29af86..95c88132a0 100644 --- a/src/FEP/pair_lj_cut_soft.cpp +++ b/src/FEP/pair_lj_cut_soft.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/pair_lj_cut_soft.h b/src/FEP/pair_lj_cut_soft.h index 77e4fc09a2..b37774146e 100644 --- a/src/FEP/pair_lj_cut_soft.h +++ b/src/FEP/pair_lj_cut_soft.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/pair_lj_cut_tip4p_long_soft.cpp b/src/FEP/pair_lj_cut_tip4p_long_soft.cpp index 3cd374b1e4..bced5c17cc 100644 --- a/src/FEP/pair_lj_cut_tip4p_long_soft.cpp +++ b/src/FEP/pair_lj_cut_tip4p_long_soft.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -20,8 +20,6 @@ #include "pair_lj_cut_tip4p_long_soft.h" -#include -#include #include "angle.h" #include "atom.h" #include "bond.h" @@ -33,6 +31,8 @@ #include "memory.h" #include "error.h" +#include +#include using namespace LAMMPS_NS; @@ -460,9 +460,17 @@ void PairLJCutTIP4PLongSoft::init_style() // set alpha parameter - double theta = force->angle->equilibrium_angle(typeA); - double blen = force->bond->equilibrium_distance(typeB); + const double theta = force->angle->equilibrium_angle(typeA); + const double blen = force->bond->equilibrium_distance(typeB); alpha = qdist / (cos(0.5*theta) * blen); + + const double mincut = cut_coul + qdist + blen + neighbor->skin; + if (comm->get_comm_cutoff() < mincut) { + if (comm->me == 0) + error->warning(FLERR, "Increasing communication cutoff to {:.8} for TIP4P pair style", + mincut); + comm->cutghostuser = mincut; + } } /* ---------------------------------------------------------------------- diff --git a/src/FEP/pair_lj_cut_tip4p_long_soft.h b/src/FEP/pair_lj_cut_tip4p_long_soft.h index 47e6fc5959..3d54376a20 100644 --- a/src/FEP/pair_lj_cut_tip4p_long_soft.h +++ b/src/FEP/pair_lj_cut_tip4p_long_soft.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/pair_morse_soft.cpp b/src/FEP/pair_morse_soft.cpp index 56c63d758d..d9be7e136d 100644 --- a/src/FEP/pair_morse_soft.cpp +++ b/src/FEP/pair_morse_soft.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/pair_morse_soft.h b/src/FEP/pair_morse_soft.h index b471938231..0c12fbafde 100644 --- a/src/FEP/pair_morse_soft.h +++ b/src/FEP/pair_morse_soft.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/FEP/pair_tip4p_long_soft.cpp b/src/FEP/pair_tip4p_long_soft.cpp index 5a04e29a5a..4c357b32e0 100644 --- a/src/FEP/pair_tip4p_long_soft.cpp +++ b/src/FEP/pair_tip4p_long_soft.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -20,8 +20,6 @@ #include "pair_tip4p_long_soft.h" -#include -#include #include "angle.h" #include "atom.h" #include "bond.h" @@ -33,6 +31,8 @@ #include "memory.h" #include "error.h" +#include +#include using namespace LAMMPS_NS; @@ -417,9 +417,17 @@ void PairTIP4PLongSoft::init_style() // set alpha parameter - double theta = force->angle->equilibrium_angle(typeA); - double blen = force->bond->equilibrium_distance(typeB); + const double theta = force->angle->equilibrium_angle(typeA); + const double blen = force->bond->equilibrium_distance(typeB); alpha = qdist / (cos(0.5*theta) * blen); + + const double mincut = cut_coul + qdist + blen + neighbor->skin; + if (comm->get_comm_cutoff() < mincut) { + if (comm->me == 0) + error->warning(FLERR, "Increasing communication cutoff to {:.8} for TIP4P pair style", + mincut); + comm->cutghostuser = mincut; + } } /* ---------------------------------------------------------------------- diff --git a/src/FEP/pair_tip4p_long_soft.h b/src/FEP/pair_tip4p_long_soft.h index 06916d00f1..af30d77b05 100644 --- a/src/FEP/pair_tip4p_long_soft.h +++ b/src/FEP/pair_tip4p_long_soft.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/Install.sh b/src/GPU/Install.sh index 1768ec024f..d28e6260f8 100755 --- a/src/GPU/Install.sh +++ b/src/GPU/Install.sh @@ -176,7 +176,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*gpu.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*gpu.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/gpu\/Makefile.lammps @@ -191,7 +191,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*gpu.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*gpu.*$/d' ../Makefile.package.settings fi fi diff --git a/src/GPU/fix_gpu.cpp b/src/GPU/fix_gpu.cpp index 0de2ab51f8..97f22da0a7 100644 --- a/src/GPU/fix_gpu.cpp +++ b/src/GPU/fix_gpu.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -120,8 +120,8 @@ FixGPU::FixGPU(LAMMPS *lmp, int narg, char **arg) : // If ngpu is 0, autoset ngpu to the number of devices per node matching // best device - int ngpu = atoi(arg[3]); - if (ngpu < 0) error->all(FLERR,"Illegal package gpu command"); + int ngpu = utils::inumeric(FLERR, arg[3], false, lmp); + if (ngpu < 0) error->all(FLERR,"Illegal number of GPUs ({}) in package gpu command", ngpu); // Negative value indicate GPU package should find the best device ID int first_gpu_id = -1; @@ -136,7 +136,6 @@ FixGPU::FixGPU(LAMMPS *lmp, int narg, char **arg) : double binsize = 0.0; char *opencl_args = nullptr; int block_pair = -1; - int pair_only_flag = 0; int ocl_platform = -1; char *device_type_flags = nullptr; @@ -194,7 +193,7 @@ FixGPU::FixGPU(LAMMPS *lmp, int narg, char **arg) : iarg += 2; } else if (strcmp(arg[iarg],"pair/only") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal package gpu command"); - pair_only_flag = utils::logical(FLERR,arg[iarg+1],false,lmp); + lmp->pair_only_flag = utils::logical(FLERR,arg[iarg+1],false,lmp); iarg += 2; } else if (strcmp(arg[iarg],"ocl_args") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal package gpu command"); @@ -224,16 +223,6 @@ FixGPU::FixGPU(LAMMPS *lmp, int narg, char **arg) : if (force->newton_pair == 1 && _particle_split < 1) error->all(FLERR,"Cannot use newton pair on for split less than 1 for now"); - if (pair_only_flag) { - lmp->suffixp = lmp->suffix; - lmp->suffix = nullptr; - } else { - if (lmp->suffixp) { - lmp->suffix = lmp->suffixp; - lmp->suffixp = nullptr; - } - } - // pass params to GPU library // change binsize default (0.0) to -1.0 used by GPU lib diff --git a/src/GPU/fix_gpu.h b/src/GPU/fix_gpu.h index 9df789f6e5..4e5bc38f1e 100644 --- a/src/GPU/fix_gpu.h +++ b/src/GPU/fix_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/fix_nh_gpu.cpp b/src/GPU/fix_nh_gpu.cpp index 53999fe52c..9d4fbcc668 100644 --- a/src/GPU/fix_nh_gpu.cpp +++ b/src/GPU/fix_nh_gpu.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/fix_nh_gpu.h b/src/GPU/fix_nh_gpu.h index b7d61ca1e1..f3e35a2e61 100644 --- a/src/GPU/fix_nh_gpu.h +++ b/src/GPU/fix_nh_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/fix_npt_gpu.cpp b/src/GPU/fix_npt_gpu.cpp index 94907678e8..8f2d04d5ed 100644 --- a/src/GPU/fix_npt_gpu.cpp +++ b/src/GPU/fix_npt_gpu.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/fix_npt_gpu.h b/src/GPU/fix_npt_gpu.h index aa35396422..805c90e5a7 100644 --- a/src/GPU/fix_npt_gpu.h +++ b/src/GPU/fix_npt_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/fix_nve_asphere_gpu.cpp b/src/GPU/fix_nve_asphere_gpu.cpp index 1112641837..06d1d7a7ca 100644 --- a/src/GPU/fix_nve_asphere_gpu.cpp +++ b/src/GPU/fix_nve_asphere_gpu.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/fix_nve_asphere_gpu.h b/src/GPU/fix_nve_asphere_gpu.h index f8ea6b3a5b..3d38d31303 100644 --- a/src/GPU/fix_nve_asphere_gpu.h +++ b/src/GPU/fix_nve_asphere_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/fix_nve_gpu.cpp b/src/GPU/fix_nve_gpu.cpp index 9392953398..19d6f572a2 100644 --- a/src/GPU/fix_nve_gpu.cpp +++ b/src/GPU/fix_nve_gpu.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/fix_nve_gpu.h b/src/GPU/fix_nve_gpu.h index f41f4f3dd6..f6136f1fd5 100644 --- a/src/GPU/fix_nve_gpu.h +++ b/src/GPU/fix_nve_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/fix_nvt_gpu.cpp b/src/GPU/fix_nvt_gpu.cpp index c1d23090d5..6b1254e8da 100644 --- a/src/GPU/fix_nvt_gpu.cpp +++ b/src/GPU/fix_nvt_gpu.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/fix_nvt_gpu.h b/src/GPU/fix_nvt_gpu.h index 96cca54148..1a2817493d 100644 --- a/src/GPU/fix_nvt_gpu.h +++ b/src/GPU/fix_nvt_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/gpu_extra.h b/src/GPU/gpu_extra.h index 1ed9e8c45b..662bfb7b84 100644 --- a/src/GPU/gpu_extra.h +++ b/src/GPU/gpu_extra.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_beck_gpu.cpp b/src/GPU/pair_beck_gpu.cpp index 1c95becba7..3c21a99105 100644 --- a/src/GPU/pair_beck_gpu.cpp +++ b/src/GPU/pair_beck_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_beck_gpu.h b/src/GPU/pair_beck_gpu.h index b7ca8b2524..97587fdb7a 100644 --- a/src/GPU/pair_beck_gpu.h +++ b/src/GPU/pair_beck_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_born_coul_long_cs_gpu.cpp b/src/GPU/pair_born_coul_long_cs_gpu.cpp index 5b414a5b07..61618ede71 100644 --- a/src/GPU/pair_born_coul_long_cs_gpu.cpp +++ b/src/GPU/pair_born_coul_long_cs_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_born_coul_long_cs_gpu.h b/src/GPU/pair_born_coul_long_cs_gpu.h index 443cfb7439..bd9ee6be4e 100644 --- a/src/GPU/pair_born_coul_long_cs_gpu.h +++ b/src/GPU/pair_born_coul_long_cs_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_born_coul_long_gpu.cpp b/src/GPU/pair_born_coul_long_gpu.cpp index 1cafc55213..ba950aca44 100644 --- a/src/GPU/pair_born_coul_long_gpu.cpp +++ b/src/GPU/pair_born_coul_long_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_born_coul_long_gpu.h b/src/GPU/pair_born_coul_long_gpu.h index 09934474f3..013aad6d3a 100644 --- a/src/GPU/pair_born_coul_long_gpu.h +++ b/src/GPU/pair_born_coul_long_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp index 4493ec18cc..214a9575be 100644 --- a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp +++ b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_born_coul_wolf_cs_gpu.h b/src/GPU/pair_born_coul_wolf_cs_gpu.h index df45f9be24..cb11d0f35b 100644 --- a/src/GPU/pair_born_coul_wolf_cs_gpu.h +++ b/src/GPU/pair_born_coul_wolf_cs_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_born_coul_wolf_gpu.cpp b/src/GPU/pair_born_coul_wolf_gpu.cpp index 16dbd93812..02a671adc9 100644 --- a/src/GPU/pair_born_coul_wolf_gpu.cpp +++ b/src/GPU/pair_born_coul_wolf_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_born_coul_wolf_gpu.h b/src/GPU/pair_born_coul_wolf_gpu.h index 6e35a8aec0..650c9d8afc 100644 --- a/src/GPU/pair_born_coul_wolf_gpu.h +++ b/src/GPU/pair_born_coul_wolf_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_born_gpu.cpp b/src/GPU/pair_born_gpu.cpp index 3ff08858bb..905278cdb7 100644 --- a/src/GPU/pair_born_gpu.cpp +++ b/src/GPU/pair_born_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_born_gpu.h b/src/GPU/pair_born_gpu.h index 1e7760a57e..33a53effe8 100644 --- a/src/GPU/pair_born_gpu.h +++ b/src/GPU/pair_born_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_buck_coul_cut_gpu.cpp b/src/GPU/pair_buck_coul_cut_gpu.cpp index c972fbfc78..125ffbfbbd 100644 --- a/src/GPU/pair_buck_coul_cut_gpu.cpp +++ b/src/GPU/pair_buck_coul_cut_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_buck_coul_cut_gpu.h b/src/GPU/pair_buck_coul_cut_gpu.h index d55d336802..3394c15bfd 100644 --- a/src/GPU/pair_buck_coul_cut_gpu.h +++ b/src/GPU/pair_buck_coul_cut_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_buck_coul_long_gpu.cpp b/src/GPU/pair_buck_coul_long_gpu.cpp index 6de1e8480b..a0bb455ad2 100644 --- a/src/GPU/pair_buck_coul_long_gpu.cpp +++ b/src/GPU/pair_buck_coul_long_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_buck_coul_long_gpu.h b/src/GPU/pair_buck_coul_long_gpu.h index c52fb95797..da3d54f023 100644 --- a/src/GPU/pair_buck_coul_long_gpu.h +++ b/src/GPU/pair_buck_coul_long_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_buck_gpu.cpp b/src/GPU/pair_buck_gpu.cpp index da07af8eff..d6dcdf30bc 100644 --- a/src/GPU/pair_buck_gpu.cpp +++ b/src/GPU/pair_buck_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_buck_gpu.h b/src/GPU/pair_buck_gpu.h index 9241575abf..ce36cceee8 100644 --- a/src/GPU/pair_buck_gpu.h +++ b/src/GPU/pair_buck_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_colloid_gpu.cpp b/src/GPU/pair_colloid_gpu.cpp index a21094dd80..c0e85907bb 100644 --- a/src/GPU/pair_colloid_gpu.cpp +++ b/src/GPU/pair_colloid_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_colloid_gpu.h b/src/GPU/pair_colloid_gpu.h index ebe5b08670..08ed4cbe4d 100644 --- a/src/GPU/pair_colloid_gpu.h +++ b/src/GPU/pair_colloid_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_coul_cut_gpu.cpp b/src/GPU/pair_coul_cut_gpu.cpp index 188b0c85a9..d48ee1cb7b 100644 --- a/src/GPU/pair_coul_cut_gpu.cpp +++ b/src/GPU/pair_coul_cut_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_coul_cut_gpu.h b/src/GPU/pair_coul_cut_gpu.h index 992c16095f..f67b847a21 100644 --- a/src/GPU/pair_coul_cut_gpu.h +++ b/src/GPU/pair_coul_cut_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_coul_debye_gpu.cpp b/src/GPU/pair_coul_debye_gpu.cpp index 4b070f2b6e..ed9781c016 100644 --- a/src/GPU/pair_coul_debye_gpu.cpp +++ b/src/GPU/pair_coul_debye_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_coul_debye_gpu.h b/src/GPU/pair_coul_debye_gpu.h index d587d82ba2..9ed9144e7d 100644 --- a/src/GPU/pair_coul_debye_gpu.h +++ b/src/GPU/pair_coul_debye_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_coul_dsf_gpu.cpp b/src/GPU/pair_coul_dsf_gpu.cpp index d6453c6160..a4837ed8cb 100644 --- a/src/GPU/pair_coul_dsf_gpu.cpp +++ b/src/GPU/pair_coul_dsf_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_coul_dsf_gpu.h b/src/GPU/pair_coul_dsf_gpu.h index a7ddcf9254..17dc9ec336 100644 --- a/src/GPU/pair_coul_dsf_gpu.h +++ b/src/GPU/pair_coul_dsf_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_coul_long_cs_gpu.cpp b/src/GPU/pair_coul_long_cs_gpu.cpp index f4a12d051a..0e1a80a8a7 100644 --- a/src/GPU/pair_coul_long_cs_gpu.cpp +++ b/src/GPU/pair_coul_long_cs_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_coul_long_cs_gpu.h b/src/GPU/pair_coul_long_cs_gpu.h index 71180d61ab..338e00412d 100644 --- a/src/GPU/pair_coul_long_cs_gpu.h +++ b/src/GPU/pair_coul_long_cs_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_coul_long_gpu.cpp b/src/GPU/pair_coul_long_gpu.cpp index fefc2c768d..d8ce12ea85 100644 --- a/src/GPU/pair_coul_long_gpu.cpp +++ b/src/GPU/pair_coul_long_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_coul_long_gpu.h b/src/GPU/pair_coul_long_gpu.h index b0eb0e83b1..cd73e3daf6 100644 --- a/src/GPU/pair_coul_long_gpu.h +++ b/src/GPU/pair_coul_long_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_dpd_gpu.cpp b/src/GPU/pair_dpd_gpu.cpp index ffc05cc0d0..79fd3f1345 100644 --- a/src/GPU/pair_dpd_gpu.cpp +++ b/src/GPU/pair_dpd_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_dpd_gpu.h b/src/GPU/pair_dpd_gpu.h index 02819f35df..80e1ceb6f5 100644 --- a/src/GPU/pair_dpd_gpu.h +++ b/src/GPU/pair_dpd_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_dpd_tstat_gpu.cpp b/src/GPU/pair_dpd_tstat_gpu.cpp index c949c9a9aa..49dacf3f1e 100644 --- a/src/GPU/pair_dpd_tstat_gpu.cpp +++ b/src/GPU/pair_dpd_tstat_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_dpd_tstat_gpu.h b/src/GPU/pair_dpd_tstat_gpu.h index ff05dc740a..472600f07a 100644 --- a/src/GPU/pair_dpd_tstat_gpu.h +++ b/src/GPU/pair_dpd_tstat_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp index 65fc0fcdfb..71e41eb53e 100644 --- a/src/GPU/pair_eam_alloy_gpu.cpp +++ b/src/GPU/pair_eam_alloy_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_eam_alloy_gpu.h b/src/GPU/pair_eam_alloy_gpu.h index a0c562753a..1067854487 100644 --- a/src/GPU/pair_eam_alloy_gpu.h +++ b/src/GPU/pair_eam_alloy_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp index ed8ce0c78b..ff234cfa60 100644 --- a/src/GPU/pair_eam_fs_gpu.cpp +++ b/src/GPU/pair_eam_fs_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_eam_fs_gpu.h b/src/GPU/pair_eam_fs_gpu.h index 9f7952406b..052c9c1f4a 100644 --- a/src/GPU/pair_eam_fs_gpu.h +++ b/src/GPU/pair_eam_fs_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_eam_gpu.cpp b/src/GPU/pair_eam_gpu.cpp index 1ef3a0a3a8..17af6cfb22 100644 --- a/src/GPU/pair_eam_gpu.cpp +++ b/src/GPU/pair_eam_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_eam_gpu.h b/src/GPU/pair_eam_gpu.h index cf7a165e4a..8cf99ad6b2 100644 --- a/src/GPU/pair_eam_gpu.h +++ b/src/GPU/pair_eam_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_gauss_gpu.cpp b/src/GPU/pair_gauss_gpu.cpp index 3843616445..17b9e9a650 100644 --- a/src/GPU/pair_gauss_gpu.cpp +++ b/src/GPU/pair_gauss_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_gauss_gpu.h b/src/GPU/pair_gauss_gpu.h index 76f14f6e9d..a8be57405d 100644 --- a/src/GPU/pair_gauss_gpu.h +++ b/src/GPU/pair_gauss_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_gayberne_gpu.cpp b/src/GPU/pair_gayberne_gpu.cpp index 1d954bb66d..5f12b1eaf4 100644 --- a/src/GPU/pair_gayberne_gpu.cpp +++ b/src/GPU/pair_gayberne_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_gayberne_gpu.h b/src/GPU/pair_gayberne_gpu.h index 84defb9200..89d21b9046 100644 --- a/src/GPU/pair_gayberne_gpu.h +++ b/src/GPU/pair_gayberne_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj96_cut_gpu.cpp b/src/GPU/pair_lj96_cut_gpu.cpp index c0dc11f403..5b1dd47340 100644 --- a/src/GPU/pair_lj96_cut_gpu.cpp +++ b/src/GPU/pair_lj96_cut_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj96_cut_gpu.h b/src/GPU/pair_lj96_cut_gpu.h index 5f83dcb972..9e93c2096e 100644 --- a/src/GPU/pair_lj96_cut_gpu.h +++ b/src/GPU/pair_lj96_cut_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_charmm_coul_charmm_gpu.cpp b/src/GPU/pair_lj_charmm_coul_charmm_gpu.cpp index 7f15ad1c48..d894d6acf1 100644 --- a/src/GPU/pair_lj_charmm_coul_charmm_gpu.cpp +++ b/src/GPU/pair_lj_charmm_coul_charmm_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_charmm_coul_charmm_gpu.h b/src/GPU/pair_lj_charmm_coul_charmm_gpu.h index eaaeb9392d..64a1792de9 100644 --- a/src/GPU/pair_lj_charmm_coul_charmm_gpu.h +++ b/src/GPU/pair_lj_charmm_coul_charmm_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp index 9f0cac9f98..997922aa25 100644 --- a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_charmm_coul_long_gpu.h b/src/GPU/pair_lj_charmm_coul_long_gpu.h index 7eeb7dfd84..4101050560 100644 --- a/src/GPU/pair_lj_charmm_coul_long_gpu.h +++ b/src/GPU/pair_lj_charmm_coul_long_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_class2_coul_long_gpu.cpp b/src/GPU/pair_lj_class2_coul_long_gpu.cpp index 5efad208c0..c27abfd75f 100644 --- a/src/GPU/pair_lj_class2_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_class2_coul_long_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_class2_coul_long_gpu.h b/src/GPU/pair_lj_class2_coul_long_gpu.h index ffb168a877..8d80edbfd3 100644 --- a/src/GPU/pair_lj_class2_coul_long_gpu.h +++ b/src/GPU/pair_lj_class2_coul_long_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_class2_gpu.cpp b/src/GPU/pair_lj_class2_gpu.cpp index 73ad42f5a5..7d7edb773d 100644 --- a/src/GPU/pair_lj_class2_gpu.cpp +++ b/src/GPU/pair_lj_class2_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_class2_gpu.h b/src/GPU/pair_lj_class2_gpu.h index f7016d078e..37581a9ac3 100644 --- a/src/GPU/pair_lj_class2_gpu.h +++ b/src/GPU/pair_lj_class2_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_cubic_gpu.cpp b/src/GPU/pair_lj_cubic_gpu.cpp index 1f8c5a251d..4a1316a00a 100644 --- a/src/GPU/pair_lj_cubic_gpu.cpp +++ b/src/GPU/pair_lj_cubic_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_cubic_gpu.h b/src/GPU/pair_lj_cubic_gpu.h index 26489b9f05..e29d16aa31 100644 --- a/src/GPU/pair_lj_cubic_gpu.h +++ b/src/GPU/pair_lj_cubic_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp index 600afe2d5c..7bae62ff02 100644 --- a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_cut_coul_cut_gpu.h b/src/GPU/pair_lj_cut_coul_cut_gpu.h index c04cbb22cb..648c0c7bbf 100644 --- a/src/GPU/pair_lj_cut_coul_cut_gpu.h +++ b/src/GPU/pair_lj_cut_coul_cut_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp index 819245ca0b..9c598a7572 100644 --- a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_cut_coul_debye_gpu.h b/src/GPU/pair_lj_cut_coul_debye_gpu.h index 87428b17be..277ffe2367 100644 --- a/src/GPU/pair_lj_cut_coul_debye_gpu.h +++ b/src/GPU/pair_lj_cut_coul_debye_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp index 144777e4b6..90c8b556dc 100644 --- a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_cut_coul_dsf_gpu.h b/src/GPU/pair_lj_cut_coul_dsf_gpu.h index 8c6af561a2..a49c870ff0 100644 --- a/src/GPU/pair_lj_cut_coul_dsf_gpu.h +++ b/src/GPU/pair_lj_cut_coul_dsf_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_cut_coul_long_gpu.cpp b/src/GPU/pair_lj_cut_coul_long_gpu.cpp index 79b6dff9f5..b195ed9d74 100644 --- a/src/GPU/pair_lj_cut_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_long_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_cut_coul_long_gpu.h b/src/GPU/pair_lj_cut_coul_long_gpu.h index 6d16a7b7ac..72f8605e50 100644 --- a/src/GPU/pair_lj_cut_coul_long_gpu.h +++ b/src/GPU/pair_lj_cut_coul_long_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp index 0225127f29..c1aaa6323a 100644 --- a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_cut_coul_msm_gpu.h b/src/GPU/pair_lj_cut_coul_msm_gpu.h index afcc4620ef..a0ae841fbe 100644 --- a/src/GPU/pair_lj_cut_coul_msm_gpu.h +++ b/src/GPU/pair_lj_cut_coul_msm_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp index 2c47b76418..cac0582138 100644 --- a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_cut_dipole_cut_gpu.h b/src/GPU/pair_lj_cut_dipole_cut_gpu.h index 5fb980c3d8..7ef61f4d4a 100644 --- a/src/GPU/pair_lj_cut_dipole_cut_gpu.h +++ b/src/GPU/pair_lj_cut_dipole_cut_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp index 6db936447f..3215715fad 100644 --- a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_cut_dipole_long_gpu.h b/src/GPU/pair_lj_cut_dipole_long_gpu.h index c11440b7ab..8851f52daf 100644 --- a/src/GPU/pair_lj_cut_dipole_long_gpu.h +++ b/src/GPU/pair_lj_cut_dipole_long_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_cut_gpu.cpp b/src/GPU/pair_lj_cut_gpu.cpp index c629a5f3bb..422990e1cb 100644 --- a/src/GPU/pair_lj_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_cut_gpu.h b/src/GPU/pair_lj_cut_gpu.h index d8d0d8cf12..09061b0ff9 100644 --- a/src/GPU/pair_lj_cut_gpu.h +++ b/src/GPU/pair_lj_cut_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp index 938aeaea3f..0357732106 100644 --- a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -150,11 +150,9 @@ void PairLJCutTIP4PLongGPU::init_style() if (atom->map_style == Atom::MAP_HASH) error->all(FLERR, - "GPU-accelerated lj/cut/tip4p/long currently" - " requires 'array' style atom map (atom_modify map array)"); + "GPU-accelerated pair style lj/cut/tip4p/long currently" + " requires an 'array' style atom map (atom_modify map array)"); - //PairLJCutCoulLong::init_style(); - // Repeat cutsq calculation because done after call to init_style double maxcut = -1.0; double cut; for (int i = 1; i <= atom->ntypes; i++) { @@ -188,12 +186,11 @@ void PairLJCutTIP4PLongGPU::init_style() cut_coulsq = cut_coul * cut_coul; double cut_coulplus = cut_coul + qdist + blen; double cut_coulsqplus = cut_coulplus * cut_coulplus; - if (maxcut < cut_coulsqplus) { cell_size = cut_coulplus + neighbor->skin; } - if (comm->cutghostuser < cell_size) { + if (maxcut < cut_coulsqplus) cell_size = cut_coulplus + neighbor->skin; + if (comm->get_comm_cutoff() < cell_size) { if (comm->me == 0) - error->warning(FLERR, - "Increasing communication cutoff from {:.8} to {:.8} for TIP4P GPU style", - comm->cutghostuser, cell_size); + error->warning(FLERR, "Increasing communication cutoff to {:.8} for TIP4P GPU style", + cell_size); comm->cutghostuser = cell_size; } diff --git a/src/GPU/pair_lj_cut_tip4p_long_gpu.h b/src/GPU/pair_lj_cut_tip4p_long_gpu.h index 3d567943c9..42e73bf79d 100644 --- a/src/GPU/pair_lj_cut_tip4p_long_gpu.h +++ b/src/GPU/pair_lj_cut_tip4p_long_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_expand_coul_long_gpu.cpp b/src/GPU/pair_lj_expand_coul_long_gpu.cpp index e14ffef0ea..fa97ee013a 100644 --- a/src/GPU/pair_lj_expand_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_expand_coul_long_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_expand_coul_long_gpu.h b/src/GPU/pair_lj_expand_coul_long_gpu.h index 8712f8c98c..a52be0d64a 100644 --- a/src/GPU/pair_lj_expand_coul_long_gpu.h +++ b/src/GPU/pair_lj_expand_coul_long_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_expand_gpu.cpp b/src/GPU/pair_lj_expand_gpu.cpp index fd6888e81f..8d7dcf2c21 100644 --- a/src/GPU/pair_lj_expand_gpu.cpp +++ b/src/GPU/pair_lj_expand_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_expand_gpu.h b/src/GPU/pair_lj_expand_gpu.h index 18af19d952..0ff9f65e81 100644 --- a/src/GPU/pair_lj_expand_gpu.h +++ b/src/GPU/pair_lj_expand_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_gromacs_gpu.cpp b/src/GPU/pair_lj_gromacs_gpu.cpp index 7d47936f8c..424bce480c 100644 --- a/src/GPU/pair_lj_gromacs_gpu.cpp +++ b/src/GPU/pair_lj_gromacs_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_gromacs_gpu.h b/src/GPU/pair_lj_gromacs_gpu.h index 3b797c1f8d..c461a6ffc4 100644 --- a/src/GPU/pair_lj_gromacs_gpu.h +++ b/src/GPU/pair_lj_gromacs_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp index 84b9f70624..9bd5dc4749 100644 --- a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp +++ b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_sf_dipole_sf_gpu.h b/src/GPU/pair_lj_sf_dipole_sf_gpu.h index b89a54c1a9..c9ab6ac568 100644 --- a/src/GPU/pair_lj_sf_dipole_sf_gpu.h +++ b/src/GPU/pair_lj_sf_dipole_sf_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_smooth_gpu.cpp b/src/GPU/pair_lj_smooth_gpu.cpp index a78c6c395e..8ae295282e 100644 --- a/src/GPU/pair_lj_smooth_gpu.cpp +++ b/src/GPU/pair_lj_smooth_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_smooth_gpu.h b/src/GPU/pair_lj_smooth_gpu.h index 2c4a2625bf..7263a51ebf 100644 --- a/src/GPU/pair_lj_smooth_gpu.h +++ b/src/GPU/pair_lj_smooth_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_spica_coul_long_gpu.cpp b/src/GPU/pair_lj_spica_coul_long_gpu.cpp index a1f7838a59..0947ca06c8 100644 --- a/src/GPU/pair_lj_spica_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_spica_coul_long_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_spica_coul_long_gpu.h b/src/GPU/pair_lj_spica_coul_long_gpu.h index 3fd267fe5a..e9b898fd7b 100644 --- a/src/GPU/pair_lj_spica_coul_long_gpu.h +++ b/src/GPU/pair_lj_spica_coul_long_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_spica_gpu.cpp b/src/GPU/pair_lj_spica_gpu.cpp index 24f556a3b6..71756a8c26 100644 --- a/src/GPU/pair_lj_spica_gpu.cpp +++ b/src/GPU/pair_lj_spica_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_lj_spica_gpu.h b/src/GPU/pair_lj_spica_gpu.h index e8953d90da..0c9eafe39e 100644 --- a/src/GPU/pair_lj_spica_gpu.h +++ b/src/GPU/pair_lj_spica_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_mie_cut_gpu.cpp b/src/GPU/pair_mie_cut_gpu.cpp index 4d257feba1..075546588a 100644 --- a/src/GPU/pair_mie_cut_gpu.cpp +++ b/src/GPU/pair_mie_cut_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_mie_cut_gpu.h b/src/GPU/pair_mie_cut_gpu.h index c364b35abb..34c5402857 100644 --- a/src/GPU/pair_mie_cut_gpu.h +++ b/src/GPU/pair_mie_cut_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_morse_gpu.cpp b/src/GPU/pair_morse_gpu.cpp index 842bd29fa9..b0ac2cce14 100644 --- a/src/GPU/pair_morse_gpu.cpp +++ b/src/GPU/pair_morse_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_morse_gpu.h b/src/GPU/pair_morse_gpu.h index 6653cb13fb..7e9dd45179 100644 --- a/src/GPU/pair_morse_gpu.h +++ b/src/GPU/pair_morse_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_resquared_gpu.cpp b/src/GPU/pair_resquared_gpu.cpp index 2ee0da8f49..c0e700c5e6 100644 --- a/src/GPU/pair_resquared_gpu.cpp +++ b/src/GPU/pair_resquared_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_resquared_gpu.h b/src/GPU/pair_resquared_gpu.h index a4c924c935..6d79952c39 100644 --- a/src/GPU/pair_resquared_gpu.h +++ b/src/GPU/pair_resquared_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_soft_gpu.cpp b/src/GPU/pair_soft_gpu.cpp index dc970858e5..973e82c13a 100644 --- a/src/GPU/pair_soft_gpu.cpp +++ b/src/GPU/pair_soft_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_soft_gpu.h b/src/GPU/pair_soft_gpu.h index 12220dd4aa..6e5ea5c03a 100644 --- a/src/GPU/pair_soft_gpu.h +++ b/src/GPU/pair_soft_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_sw_gpu.cpp b/src/GPU/pair_sw_gpu.cpp index e79221fadd..67c52e0602 100644 --- a/src/GPU/pair_sw_gpu.cpp +++ b/src/GPU/pair_sw_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -219,9 +219,11 @@ void PairSWGPU::init_style() if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_GHOST); - if (comm->cutghostuser < (2.0 * cutmax + neighbor->skin)) { + if (comm->get_comm_cutoff() < (2.0 * cutmax + neighbor->skin)) { comm->cutghostuser = 2.0 * cutmax + neighbor->skin; - if (comm->me == 0) error->warning(FLERR, "Increasing communication cutoff for GPU style"); + if (comm->me == 0) + error->warning(FLERR, "Increasing communication cutoff to {:.8} for GPU pair style", + comm->cutghostuser); } } diff --git a/src/GPU/pair_sw_gpu.h b/src/GPU/pair_sw_gpu.h index 46feb1d179..db4c299653 100644 --- a/src/GPU/pair_sw_gpu.h +++ b/src/GPU/pair_sw_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_table_gpu.cpp b/src/GPU/pair_table_gpu.cpp index 8331e28010..6615710b8a 100644 --- a/src/GPU/pair_table_gpu.cpp +++ b/src/GPU/pair_table_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_table_gpu.h b/src/GPU/pair_table_gpu.h index d36f9ee194..3d4375cab6 100644 --- a/src/GPU/pair_table_gpu.h +++ b/src/GPU/pair_table_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_tersoff_gpu.cpp b/src/GPU/pair_tersoff_gpu.cpp index ad4275cfac..9f0c8fa883 100644 --- a/src/GPU/pair_tersoff_gpu.cpp +++ b/src/GPU/pair_tersoff_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -223,9 +223,11 @@ void PairTersoffGPU::init_style() if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_GHOST); - if (comm->cutghostuser < (2.0 * cutmax + neighbor->skin)) { + if (comm->get_comm_cutoff() < (2.0 * cutmax + neighbor->skin)) { comm->cutghostuser = 2.0 * cutmax + neighbor->skin; - if (comm->me == 0) error->warning(FLERR, "Increasing communication cutoff for GPU style"); + if (comm->me == 0) + error->warning(FLERR, "Increasing communication cutoff to {:.8} for GPU pair style", + comm->cutghostuser); } } diff --git a/src/GPU/pair_tersoff_gpu.h b/src/GPU/pair_tersoff_gpu.h index 0766c24b92..ebf4065f83 100644 --- a/src/GPU/pair_tersoff_gpu.h +++ b/src/GPU/pair_tersoff_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_tersoff_mod_gpu.cpp b/src/GPU/pair_tersoff_mod_gpu.cpp index 3c1220771a..15bfc9a85e 100644 --- a/src/GPU/pair_tersoff_mod_gpu.cpp +++ b/src/GPU/pair_tersoff_mod_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -221,9 +221,11 @@ void PairTersoffMODGPU::init_style() if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_GHOST); - if (comm->cutghostuser < (2.0 * cutmax + neighbor->skin)) { + if (comm->get_comm_cutoff() < (2.0 * cutmax + neighbor->skin)) { comm->cutghostuser = 2.0 * cutmax + neighbor->skin; - if (comm->me == 0) error->warning(FLERR, "Increasing communication cutoff for GPU style"); + if (comm->me == 0) + error->warning(FLERR, "Increasing communication cutoff to {:.8} for GPU pair style", + comm->cutghostuser); } } diff --git a/src/GPU/pair_tersoff_mod_gpu.h b/src/GPU/pair_tersoff_mod_gpu.h index a5d002d129..15f44dcbb1 100644 --- a/src/GPU/pair_tersoff_mod_gpu.h +++ b/src/GPU/pair_tersoff_mod_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_tersoff_zbl_gpu.cpp b/src/GPU/pair_tersoff_zbl_gpu.cpp index c7b605ae0d..68b0d9dfa7 100644 --- a/src/GPU/pair_tersoff_zbl_gpu.cpp +++ b/src/GPU/pair_tersoff_zbl_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -239,9 +239,11 @@ void PairTersoffZBLGPU::init_style() if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_GHOST); - if (comm->cutghostuser < (2.0 * cutmax + neighbor->skin)) { + if (comm->get_comm_cutoff() < (2.0 * cutmax + neighbor->skin)) { comm->cutghostuser = 2.0 * cutmax + neighbor->skin; - if (comm->me == 0) error->warning(FLERR, "Increasing communication cutoff for GPU style"); + if (comm->me == 0) + error->warning(FLERR, "Increasing communication cutoff to {:.8} for GPU pair style", + comm->cutghostuser); } } diff --git a/src/GPU/pair_tersoff_zbl_gpu.h b/src/GPU/pair_tersoff_zbl_gpu.h index 3dff093263..36bc335dbb 100644 --- a/src/GPU/pair_tersoff_zbl_gpu.h +++ b/src/GPU/pair_tersoff_zbl_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_ufm_gpu.cpp b/src/GPU/pair_ufm_gpu.cpp index 96f034b91d..099bfe1e63 100644 --- a/src/GPU/pair_ufm_gpu.cpp +++ b/src/GPU/pair_ufm_gpu.cpp @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_ufm_gpu.h b/src/GPU/pair_ufm_gpu.h index 030f719d6d..636f791343 100644 --- a/src/GPU/pair_ufm_gpu.h +++ b/src/GPU/pair_ufm_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_vashishta_gpu.cpp b/src/GPU/pair_vashishta_gpu.cpp index 5b517b613c..0fb0491ad3 100644 --- a/src/GPU/pair_vashishta_gpu.cpp +++ b/src/GPU/pair_vashishta_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -218,9 +218,11 @@ void PairVashishtaGPU::init_style() if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_GHOST); - if (comm->cutghostuser < (2.0 * cutmax + neighbor->skin)) { + if (comm->get_comm_cutoff() < (2.0 * cutmax + neighbor->skin)) { comm->cutghostuser = 2.0 * cutmax + neighbor->skin; - if (comm->me == 0) error->warning(FLERR, "Increasing communication cutoff for GPU style"); + if (comm->me == 0) + error->warning(FLERR, "Increasing communication cutoff to {:.8} for GPU pair style", + comm->cutghostuser); } } diff --git a/src/GPU/pair_vashishta_gpu.h b/src/GPU/pair_vashishta_gpu.h index a9fee5045b..8a67aac3d5 100644 --- a/src/GPU/pair_vashishta_gpu.h +++ b/src/GPU/pair_vashishta_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_yukawa_colloid_gpu.cpp b/src/GPU/pair_yukawa_colloid_gpu.cpp index 8a9938143d..8701a9ee80 100644 --- a/src/GPU/pair_yukawa_colloid_gpu.cpp +++ b/src/GPU/pair_yukawa_colloid_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_yukawa_colloid_gpu.h b/src/GPU/pair_yukawa_colloid_gpu.h index 78bad04566..aeb9dfb041 100644 --- a/src/GPU/pair_yukawa_colloid_gpu.h +++ b/src/GPU/pair_yukawa_colloid_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_yukawa_gpu.cpp b/src/GPU/pair_yukawa_gpu.cpp index 3a56d40c76..e2caef9515 100644 --- a/src/GPU/pair_yukawa_gpu.cpp +++ b/src/GPU/pair_yukawa_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_yukawa_gpu.h b/src/GPU/pair_yukawa_gpu.h index 61c4b0099c..0d3aab234f 100644 --- a/src/GPU/pair_yukawa_gpu.h +++ b/src/GPU/pair_yukawa_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_zbl_gpu.cpp b/src/GPU/pair_zbl_gpu.cpp index 68e4c05c53..cbb2c198f7 100644 --- a/src/GPU/pair_zbl_gpu.cpp +++ b/src/GPU/pair_zbl_gpu.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pair_zbl_gpu.h b/src/GPU/pair_zbl_gpu.h index d4812188a1..ef29f91f89 100644 --- a/src/GPU/pair_zbl_gpu.h +++ b/src/GPU/pair_zbl_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GPU/pppm_gpu.cpp b/src/GPU/pppm_gpu.cpp index d0fd3e66ea..a2a2b0eed8 100644 --- a/src/GPU/pppm_gpu.cpp +++ b/src/GPU/pppm_gpu.cpp @@ -1,8 +1,9 @@ + // clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -25,7 +26,7 @@ #include "fix.h" #include "force.h" #include "gpu_extra.h" -#include "gridcomm.h" +#include "grid3d.h" #include "math_const.h" #include "memory.h" #include "modify.h" @@ -252,12 +253,12 @@ void PPPMGPU::compute(int eflag, int vflag) // remap from 3d decomposition to FFT decomposition if (triclinic == 0) { - gc->reverse_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR), - REVERSE_RHO_GPU,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO_GPU,1,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); brick2fft_gpu(); } else { - gc->reverse_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR), - REVERSE_RHO,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); PPPM::brick2fft(); } @@ -271,21 +272,21 @@ void PPPMGPU::compute(int eflag, int vflag) // to fill ghost cells surrounding their 3d bricks if (differentiation_flag == 1) - gc->forward_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR), - FORWARD_AD,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_AD,1,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); else - gc->forward_comm(GridComm::KSPACE,this,3,sizeof(FFT_SCALAR), - FORWARD_IK,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK,3,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); // extra per-atom energy/virial communication if (evflag_atom) { if (differentiation_flag == 1 && vflag_atom) - gc->forward_comm(GridComm::KSPACE,this,6,sizeof(FFT_SCALAR), - FORWARD_AD_PERATOM,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_PERATOM,6,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); else if (differentiation_flag == 0) - gc->forward_comm(GridComm::KSPACE,this,7,sizeof(FFT_SCALAR), - FORWARD_IK_PERATOM,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_PERATOM,7,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); } poisson_time += platform::walltime()-t3; @@ -828,8 +829,8 @@ void PPPMGPU::compute_group_group(int groupbit_A, int groupbit_B, int AA_flag) density_brick = density_A_brick; density_fft = density_A_fft; - gc->reverse_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR), - REVERSE_RHO,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); brick2fft(); // group B @@ -837,8 +838,8 @@ void PPPMGPU::compute_group_group(int groupbit_A, int groupbit_B, int AA_flag) density_brick = density_B_brick; density_fft = density_B_fft; - gc->reverse_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR), - REVERSE_RHO,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); brick2fft(); // switch back pointers diff --git a/src/GPU/pppm_gpu.h b/src/GPU/pppm_gpu.h index 84ce88590e..e8237986e9 100644 --- a/src/GPU/pppm_gpu.h +++ b/src/GPU/pppm_gpu.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GRANULAR/compute_contact_atom.cpp b/src/GRANULAR/compute_contact_atom.cpp index b090fb8631..310fdb5a41 100644 --- a/src/GRANULAR/compute_contact_atom.cpp +++ b/src/GRANULAR/compute_contact_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -25,8 +25,6 @@ #include "neighbor.h" #include "update.h" -#include - using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/GRANULAR/compute_contact_atom.h b/src/GRANULAR/compute_contact_atom.h index 5262c1b29b..f453ba4119 100644 --- a/src/GRANULAR/compute_contact_atom.h +++ b/src/GRANULAR/compute_contact_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GRANULAR/compute_fabric.cpp b/src/GRANULAR/compute_fabric.cpp index 77168df90e..fb95a8b446 100644 --- a/src/GRANULAR/compute_fabric.cpp +++ b/src/GRANULAR/compute_fabric.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GRANULAR/compute_fabric.h b/src/GRANULAR/compute_fabric.h index 0cdc758a7f..f1402fab38 100644 --- a/src/GRANULAR/compute_fabric.h +++ b/src/GRANULAR/compute_fabric.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GRANULAR/fix_damping_cundall.cpp b/src/GRANULAR/fix_damping_cundall.cpp index 6f2234d68f..f5ef24c3cc 100644 --- a/src/GRANULAR/fix_damping_cundall.cpp +++ b/src/GRANULAR/fix_damping_cundall.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GRANULAR/fix_damping_cundall.h b/src/GRANULAR/fix_damping_cundall.h index 238d1370c1..53bb1867ca 100644 --- a/src/GRANULAR/fix_damping_cundall.h +++ b/src/GRANULAR/fix_damping_cundall.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GRANULAR/fix_freeze.cpp b/src/GRANULAR/fix_freeze.cpp index 576daaff9c..744c1a4986 100644 --- a/src/GRANULAR/fix_freeze.cpp +++ b/src/GRANULAR/fix_freeze.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GRANULAR/fix_freeze.h b/src/GRANULAR/fix_freeze.h index 24180051d7..f7a92cba5b 100644 --- a/src/GRANULAR/fix_freeze.h +++ b/src/GRANULAR/fix_freeze.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp index 00455096f8..86d66b3a0b 100644 --- a/src/GRANULAR/fix_pour.cpp +++ b/src/GRANULAR/fix_pour.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GRANULAR/fix_pour.h b/src/GRANULAR/fix_pour.h index 7fa48ee761..4a6e4abdae 100644 --- a/src/GRANULAR/fix_pour.h +++ b/src/GRANULAR/fix_pour.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index f59a7fa2e1..e49571d3ff 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GRANULAR/fix_wall_gran.h b/src/GRANULAR/fix_wall_gran.h index 8c69be6e16..37481c7718 100644 --- a/src/GRANULAR/fix_wall_gran.h +++ b/src/GRANULAR/fix_wall_gran.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GRANULAR/fix_wall_gran_region.cpp b/src/GRANULAR/fix_wall_gran_region.cpp index 6509c88a0b..f1bd55a7bc 100644 --- a/src/GRANULAR/fix_wall_gran_region.cpp +++ b/src/GRANULAR/fix_wall_gran_region.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GRANULAR/fix_wall_gran_region.h b/src/GRANULAR/fix_wall_gran_region.h index 18307e87e2..72e1080268 100644 --- a/src/GRANULAR/fix_wall_gran_region.h +++ b/src/GRANULAR/fix_wall_gran_region.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GRANULAR/pair_gran_hertz_history.cpp b/src/GRANULAR/pair_gran_hertz_history.cpp index 04fc0cf6f0..d79526087a 100644 --- a/src/GRANULAR/pair_gran_hertz_history.cpp +++ b/src/GRANULAR/pair_gran_hertz_history.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GRANULAR/pair_gran_hertz_history.h b/src/GRANULAR/pair_gran_hertz_history.h index 511312921d..a6e0653e37 100644 --- a/src/GRANULAR/pair_gran_hertz_history.h +++ b/src/GRANULAR/pair_gran_hertz_history.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GRANULAR/pair_gran_hooke.cpp b/src/GRANULAR/pair_gran_hooke.cpp index 12ce25f7b3..bb3e0fcd64 100644 --- a/src/GRANULAR/pair_gran_hooke.cpp +++ b/src/GRANULAR/pair_gran_hooke.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GRANULAR/pair_gran_hooke.h b/src/GRANULAR/pair_gran_hooke.h index 7f616d9c98..ff48a645ec 100644 --- a/src/GRANULAR/pair_gran_hooke.h +++ b/src/GRANULAR/pair_gran_hooke.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index c43c975177..e9506e8a03 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -27,7 +27,6 @@ #include "memory.h" #include "modify.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "update.h" diff --git a/src/GRANULAR/pair_gran_hooke_history.h b/src/GRANULAR/pair_gran_hooke_history.h index 35c4cf7606..54491147e8 100644 --- a/src/GRANULAR/pair_gran_hooke_history.h +++ b/src/GRANULAR/pair_gran_hooke_history.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index df46e27b95..946e902dc5 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -32,7 +32,6 @@ #include "memory.h" #include "modify.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "update.h" diff --git a/src/GRANULAR/pair_granular.h b/src/GRANULAR/pair_granular.h index 5c3edf30a2..209c84cfd4 100644 --- a/src/GRANULAR/pair_granular.h +++ b/src/GRANULAR/pair_granular.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/H5MD/Install.sh b/src/H5MD/Install.sh index 1070afaa96..ee442d80bc 100755 --- a/src/H5MD/Install.sh +++ b/src/H5MD/Install.sh @@ -45,7 +45,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*h5md.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*h5md.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/h5md\/Makefile.lammps @@ -60,7 +60,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*h5md.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*h5md.*$/d' ../Makefile.package.settings fi fi diff --git a/src/H5MD/dump_h5md.cpp b/src/H5MD/dump_h5md.cpp index 2bb5af3043..21c02bfc23 100644 --- a/src/H5MD/dump_h5md.cpp +++ b/src/H5MD/dump_h5md.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/H5MD/dump_h5md.h b/src/H5MD/dump_h5md.h index 7d766e0eec..1a3988aac4 100644 --- a/src/H5MD/dump_h5md.h +++ b/src/H5MD/dump_h5md.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/angle_charmm_intel.cpp b/src/INTEL/angle_charmm_intel.cpp index 48e179c997..1ea9c8348e 100644 --- a/src/INTEL/angle_charmm_intel.cpp +++ b/src/INTEL/angle_charmm_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/angle_charmm_intel.h b/src/INTEL/angle_charmm_intel.h index 0b503dccfe..35a9578b2d 100644 --- a/src/INTEL/angle_charmm_intel.h +++ b/src/INTEL/angle_charmm_intel.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/angle_harmonic_intel.cpp b/src/INTEL/angle_harmonic_intel.cpp index 57dc152fbf..8cdab1d43a 100644 --- a/src/INTEL/angle_harmonic_intel.cpp +++ b/src/INTEL/angle_harmonic_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/angle_harmonic_intel.h b/src/INTEL/angle_harmonic_intel.h index 25293298e4..786cb496db 100644 --- a/src/INTEL/angle_harmonic_intel.h +++ b/src/INTEL/angle_harmonic_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/bond_fene_intel.cpp b/src/INTEL/bond_fene_intel.cpp index 12579372e9..c679c0950f 100644 --- a/src/INTEL/bond_fene_intel.cpp +++ b/src/INTEL/bond_fene_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/bond_fene_intel.h b/src/INTEL/bond_fene_intel.h index 8c90e3a633..062f27b15b 100644 --- a/src/INTEL/bond_fene_intel.h +++ b/src/INTEL/bond_fene_intel.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/bond_harmonic_intel.cpp b/src/INTEL/bond_harmonic_intel.cpp index b3283f63bc..a60050bb6b 100644 --- a/src/INTEL/bond_harmonic_intel.cpp +++ b/src/INTEL/bond_harmonic_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/bond_harmonic_intel.h b/src/INTEL/bond_harmonic_intel.h index 048ece6fcb..5223355874 100644 --- a/src/INTEL/bond_harmonic_intel.h +++ b/src/INTEL/bond_harmonic_intel.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/dihedral_charmm_intel.cpp b/src/INTEL/dihedral_charmm_intel.cpp index 2b3f8e2208..7949680c7e 100644 --- a/src/INTEL/dihedral_charmm_intel.cpp +++ b/src/INTEL/dihedral_charmm_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/dihedral_charmm_intel.h b/src/INTEL/dihedral_charmm_intel.h index a4f9109aa1..8dea498f6f 100644 --- a/src/INTEL/dihedral_charmm_intel.h +++ b/src/INTEL/dihedral_charmm_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -67,7 +67,7 @@ class DihedralCharmmIntel : public DihedralCharmm { fc_packed3 *fc; flt_t *weight; - ForceConst() : ljp(nullptr), fc(nullptr), _npairtypes(0), _ndihderaltypes(0) {} + ForceConst() : ljp(nullptr), fc(nullptr), weight(nullptr), _npairtypes(0), _ndihderaltypes(0) {} ~ForceConst() { set_ntypes(0, 0, nullptr); } void set_ntypes(const int npairtypes, const int ndihderaltypes, Memory *memory); diff --git a/src/INTEL/dihedral_fourier_intel.cpp b/src/INTEL/dihedral_fourier_intel.cpp index 68e9fedd44..5448fdae98 100644 --- a/src/INTEL/dihedral_fourier_intel.cpp +++ b/src/INTEL/dihedral_fourier_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/dihedral_fourier_intel.h b/src/INTEL/dihedral_fourier_intel.h index 36ad7dcd31..5d8c4fec85 100644 --- a/src/INTEL/dihedral_fourier_intel.h +++ b/src/INTEL/dihedral_fourier_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/dihedral_harmonic_intel.cpp b/src/INTEL/dihedral_harmonic_intel.cpp index 831b3a94f4..8d91a3fd27 100644 --- a/src/INTEL/dihedral_harmonic_intel.cpp +++ b/src/INTEL/dihedral_harmonic_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/dihedral_harmonic_intel.h b/src/INTEL/dihedral_harmonic_intel.h index 406116f5a7..de609409a5 100644 --- a/src/INTEL/dihedral_harmonic_intel.h +++ b/src/INTEL/dihedral_harmonic_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/dihedral_opls_intel.cpp b/src/INTEL/dihedral_opls_intel.cpp index ff54923c34..82151a8585 100644 --- a/src/INTEL/dihedral_opls_intel.cpp +++ b/src/INTEL/dihedral_opls_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/dihedral_opls_intel.h b/src/INTEL/dihedral_opls_intel.h index 1be502739e..b8cd98a7b0 100644 --- a/src/INTEL/dihedral_opls_intel.h +++ b/src/INTEL/dihedral_opls_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/electrode_accel_intel.cpp b/src/INTEL/electrode_accel_intel.cpp index ef5553cf81..3b7da17b7c 100644 --- a/src/INTEL/electrode_accel_intel.cpp +++ b/src/INTEL/electrode_accel_intel.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/electrode_accel_intel.h b/src/INTEL/electrode_accel_intel.h index 6b2c456715..eba6bc0157 100644 --- a/src/INTEL/electrode_accel_intel.h +++ b/src/INTEL/electrode_accel_intel.h @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -23,8 +23,8 @@ namespace LAMMPS_NS { class ElectrodeAccelIntel : public ElectrodeAccelInterface { public: ElectrodeAccelIntel(class LAMMPS *lmp); - void intel_find_fix(); - void intel_pack_buffers(); + void intel_find_fix() override; + void intel_pack_buffers() override; private: class FixIntel *fix; diff --git a/src/INTEL/fix_electrode_conp_intel.h b/src/INTEL/fix_electrode_conp_intel.h index a9ea938dcc..920cdcb89a 100644 --- a/src/INTEL/fix_electrode_conp_intel.h +++ b/src/INTEL/fix_electrode_conp_intel.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -36,8 +36,7 @@ class FixElectrodeConpIntel : public FixElectrodeConp { FixElectrodeConpIntel(class LAMMPS *lmp, int narg, char **arg) : FixElectrodeConp(lmp, narg, arg) { intelflag = true; - delete accel_interface; - accel_interface = new ElectrodeAccelIntel(lmp); + accel_interface = std::unique_ptr(new ElectrodeAccelIntel(lmp)); } }; diff --git a/src/INTEL/fix_electrode_conq_intel.h b/src/INTEL/fix_electrode_conq_intel.h index 77ff4bf297..2bc04a72fc 100644 --- a/src/INTEL/fix_electrode_conq_intel.h +++ b/src/INTEL/fix_electrode_conq_intel.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -36,8 +36,7 @@ class FixElectrodeConqIntel : public FixElectrodeConq { FixElectrodeConqIntel(class LAMMPS *lmp, int narg, char **arg) : FixElectrodeConq(lmp, narg, arg) { intelflag = true; - delete accel_interface; - accel_interface = new ElectrodeAccelIntel(lmp); + accel_interface = std::unique_ptr(new ElectrodeAccelIntel(lmp)); } }; diff --git a/src/INTEL/fix_electrode_thermo_intel.h b/src/INTEL/fix_electrode_thermo_intel.h index d6e76af6c1..de6d5fa29c 100644 --- a/src/INTEL/fix_electrode_thermo_intel.h +++ b/src/INTEL/fix_electrode_thermo_intel.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -37,8 +37,7 @@ class FixElectrodeThermoIntel : public FixElectrodeThermo { FixElectrodeThermo(lmp, narg, arg) { intelflag = true; - delete accel_interface; - accel_interface = new ElectrodeAccelIntel(lmp); + accel_interface = std::unique_ptr(new ElectrodeAccelIntel(lmp)); } }; diff --git a/src/INTEL/fix_intel.cpp b/src/INTEL/fix_intel.cpp index 4f81293e1b..1ce0b41338 100644 --- a/src/INTEL/fix_intel.cpp +++ b/src/INTEL/fix_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/fix_intel.h b/src/INTEL/fix_intel.h index f7c0709171..9214fe3419 100644 --- a/src/INTEL/fix_intel.h +++ b/src/INTEL/fix_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/fix_nh_intel.cpp b/src/INTEL/fix_nh_intel.cpp index 2f10b63922..53389ff684 100644 --- a/src/INTEL/fix_nh_intel.cpp +++ b/src/INTEL/fix_nh_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/fix_nh_intel.h b/src/INTEL/fix_nh_intel.h index 2b68a06615..124a7ae7e9 100644 --- a/src/INTEL/fix_nh_intel.h +++ b/src/INTEL/fix_nh_intel.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/fix_npt_intel.cpp b/src/INTEL/fix_npt_intel.cpp index d014b34d62..d1cf5a1fd8 100644 --- a/src/INTEL/fix_npt_intel.cpp +++ b/src/INTEL/fix_npt_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/fix_npt_intel.h b/src/INTEL/fix_npt_intel.h index 376c7571ba..622f6c422c 100644 --- a/src/INTEL/fix_npt_intel.h +++ b/src/INTEL/fix_npt_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/fix_nve_asphere_intel.cpp b/src/INTEL/fix_nve_asphere_intel.cpp index 2917edd3e8..7e429901a4 100644 --- a/src/INTEL/fix_nve_asphere_intel.cpp +++ b/src/INTEL/fix_nve_asphere_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/fix_nve_asphere_intel.h b/src/INTEL/fix_nve_asphere_intel.h index 4bc5305302..b45669693a 100644 --- a/src/INTEL/fix_nve_asphere_intel.h +++ b/src/INTEL/fix_nve_asphere_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/fix_nve_intel.cpp b/src/INTEL/fix_nve_intel.cpp index 249e797713..a02ddf2419 100644 --- a/src/INTEL/fix_nve_intel.cpp +++ b/src/INTEL/fix_nve_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/fix_nve_intel.h b/src/INTEL/fix_nve_intel.h index d7c48db81f..bd3334741f 100644 --- a/src/INTEL/fix_nve_intel.h +++ b/src/INTEL/fix_nve_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/fix_nvt_intel.cpp b/src/INTEL/fix_nvt_intel.cpp index c54bd37bc6..c9e87499de 100644 --- a/src/INTEL/fix_nvt_intel.cpp +++ b/src/INTEL/fix_nvt_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/fix_nvt_intel.h b/src/INTEL/fix_nvt_intel.h index 4c840de9de..31ba688f0f 100644 --- a/src/INTEL/fix_nvt_intel.h +++ b/src/INTEL/fix_nvt_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/fix_nvt_sllod_intel.cpp b/src/INTEL/fix_nvt_sllod_intel.cpp index aa85d74310..b2036de8cb 100644 --- a/src/INTEL/fix_nvt_sllod_intel.cpp +++ b/src/INTEL/fix_nvt_sllod_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/fix_nvt_sllod_intel.h b/src/INTEL/fix_nvt_sllod_intel.h index dc7ee05977..7221a75fbc 100644 --- a/src/INTEL/fix_nvt_sllod_intel.h +++ b/src/INTEL/fix_nvt_sllod_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/improper_cvff_intel.cpp b/src/INTEL/improper_cvff_intel.cpp index ad0702f7b1..09b2d42167 100644 --- a/src/INTEL/improper_cvff_intel.cpp +++ b/src/INTEL/improper_cvff_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/improper_cvff_intel.h b/src/INTEL/improper_cvff_intel.h index b35fe639f3..234dc0f010 100644 --- a/src/INTEL/improper_cvff_intel.h +++ b/src/INTEL/improper_cvff_intel.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/improper_harmonic_intel.cpp b/src/INTEL/improper_harmonic_intel.cpp index d71c0bdf10..a9a152d5f0 100644 --- a/src/INTEL/improper_harmonic_intel.cpp +++ b/src/INTEL/improper_harmonic_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/improper_harmonic_intel.h b/src/INTEL/improper_harmonic_intel.h index d5f0db21a4..648288b97a 100644 --- a/src/INTEL/improper_harmonic_intel.h +++ b/src/INTEL/improper_harmonic_intel.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/intel_buffers.cpp b/src/INTEL/intel_buffers.cpp index 535fa5605e..07e59b1bcf 100644 --- a/src/INTEL/intel_buffers.cpp +++ b/src/INTEL/intel_buffers.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/INTEL/intel_buffers.h b/src/INTEL/intel_buffers.h index 9e855c4959..397c503c5c 100644 --- a/src/INTEL/intel_buffers.h +++ b/src/INTEL/intel_buffers.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/intel_intrinsics.h b/src/INTEL/intel_intrinsics.h index fef7be2968..1ff405edd2 100644 --- a/src/INTEL/intel_intrinsics.h +++ b/src/INTEL/intel_intrinsics.h @@ -2,7 +2,7 @@ /* *- c++ -*- ----------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/intel_preprocess.h b/src/INTEL/intel_preprocess.h index 7ff8f7d099..a3c961f436 100644 --- a/src/INTEL/intel_preprocess.h +++ b/src/INTEL/intel_preprocess.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -134,6 +134,9 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR, #undef INTEL_VECTOR_WIDTH #define INTEL_VECTOR_WIDTH 1 #define INTEL_COMPILE_WIDTH 1 +#if defined(__AVX512F__) && !defined(INTEL_VMASK) +#define INTEL_VMASK 1 +#endif #endif diff --git a/src/INTEL/intel_simd.h b/src/INTEL/intel_simd.h index d75b2b9175..37842621dc 100644 --- a/src/INTEL/intel_simd.h +++ b/src/INTEL/intel_simd.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/math_extra_intel.h b/src/INTEL/math_extra_intel.h index 0c081a4725..a8869f7384 100644 --- a/src/INTEL/math_extra_intel.h +++ b/src/INTEL/math_extra_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/nbin_intel.cpp b/src/INTEL/nbin_intel.cpp index 4dd4e45323..3e7acec1f9 100644 --- a/src/INTEL/nbin_intel.cpp +++ b/src/INTEL/nbin_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/nbin_intel.h b/src/INTEL/nbin_intel.h index 678189d08c..283363d861 100644 --- a/src/INTEL/nbin_intel.h +++ b/src/INTEL/nbin_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/npair_full_bin_ghost_intel.cpp b/src/INTEL/npair_full_bin_ghost_intel.cpp index e6ca266933..b7b9ee4aea 100644 --- a/src/INTEL/npair_full_bin_ghost_intel.cpp +++ b/src/INTEL/npair_full_bin_ghost_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/npair_full_bin_ghost_intel.h b/src/INTEL/npair_full_bin_ghost_intel.h index 6b70778f13..4ae5ddad5f 100644 --- a/src/INTEL/npair_full_bin_ghost_intel.h +++ b/src/INTEL/npair_full_bin_ghost_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/npair_full_bin_intel.cpp b/src/INTEL/npair_full_bin_intel.cpp index c0f3874eee..2f8af4c8af 100644 --- a/src/INTEL/npair_full_bin_intel.cpp +++ b/src/INTEL/npair_full_bin_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/npair_full_bin_intel.h b/src/INTEL/npair_full_bin_intel.h index 8649610b90..58ff21d22c 100644 --- a/src/INTEL/npair_full_bin_intel.h +++ b/src/INTEL/npair_full_bin_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/npair_half_bin_newton_intel.cpp b/src/INTEL/npair_half_bin_newton_intel.cpp index accef78573..24e8b01572 100644 --- a/src/INTEL/npair_half_bin_newton_intel.cpp +++ b/src/INTEL/npair_half_bin_newton_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/npair_half_bin_newton_intel.h b/src/INTEL/npair_half_bin_newton_intel.h index 0f7c86d993..092d4f2101 100644 --- a/src/INTEL/npair_half_bin_newton_intel.h +++ b/src/INTEL/npair_half_bin_newton_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/npair_half_bin_newton_tri_intel.cpp b/src/INTEL/npair_half_bin_newton_tri_intel.cpp index db517f6da4..a903ef8e9a 100644 --- a/src/INTEL/npair_half_bin_newton_tri_intel.cpp +++ b/src/INTEL/npair_half_bin_newton_tri_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/npair_half_bin_newton_tri_intel.h b/src/INTEL/npair_half_bin_newton_tri_intel.h index 8e486313ff..8ef65c12e5 100644 --- a/src/INTEL/npair_half_bin_newton_tri_intel.h +++ b/src/INTEL/npair_half_bin_newton_tri_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/npair_halffull_newtoff_intel.h b/src/INTEL/npair_halffull_newtoff_intel.h index fbf52d89d5..f77ddb74d6 100644 --- a/src/INTEL/npair_halffull_newtoff_intel.h +++ b/src/INTEL/npair_halffull_newtoff_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/npair_halffull_newtoff_trim_intel.h b/src/INTEL/npair_halffull_newtoff_trim_intel.h index 923a0c8c95..d8594ce3b8 100644 --- a/src/INTEL/npair_halffull_newtoff_trim_intel.h +++ b/src/INTEL/npair_halffull_newtoff_trim_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/npair_halffull_newton_intel.cpp b/src/INTEL/npair_halffull_newton_intel.cpp index 6755ffc799..cd05d5f97a 100644 --- a/src/INTEL/npair_halffull_newton_intel.cpp +++ b/src/INTEL/npair_halffull_newton_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/npair_halffull_newton_intel.h b/src/INTEL/npair_halffull_newton_intel.h index 8464c1385c..149983d08e 100644 --- a/src/INTEL/npair_halffull_newton_intel.h +++ b/src/INTEL/npair_halffull_newton_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/npair_halffull_newton_trim_intel.cpp b/src/INTEL/npair_halffull_newton_trim_intel.cpp index e0c01086da..e38375f750 100644 --- a/src/INTEL/npair_halffull_newton_trim_intel.cpp +++ b/src/INTEL/npair_halffull_newton_trim_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/npair_halffull_newton_trim_intel.h b/src/INTEL/npair_halffull_newton_trim_intel.h index 096cf3bd66..0ca551d682 100644 --- a/src/INTEL/npair_halffull_newton_trim_intel.h +++ b/src/INTEL/npair_halffull_newton_trim_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/npair_intel.cpp b/src/INTEL/npair_intel.cpp index cfbea387a0..b85873f677 100644 --- a/src/INTEL/npair_intel.cpp +++ b/src/INTEL/npair_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/npair_intel.h b/src/INTEL/npair_intel.h index 22560cbdcb..0d468a36b4 100644 --- a/src/INTEL/npair_intel.h +++ b/src/INTEL/npair_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/npair_skip_intel.cpp b/src/INTEL/npair_skip_intel.cpp index 6f34463ac8..b023955dd9 100644 --- a/src/INTEL/npair_skip_intel.cpp +++ b/src/INTEL/npair_skip_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/npair_skip_intel.h b/src/INTEL/npair_skip_intel.h index 4f1763146e..d38173895a 100644 --- a/src/INTEL/npair_skip_intel.h +++ b/src/INTEL/npair_skip_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/npair_trim_intel.cpp b/src/INTEL/npair_trim_intel.cpp index 61c20db547..d377419f1b 100644 --- a/src/INTEL/npair_trim_intel.cpp +++ b/src/INTEL/npair_trim_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/npair_trim_intel.h b/src/INTEL/npair_trim_intel.h index 6a68c19b26..2cb9f4a839 100644 --- a/src/INTEL/npair_trim_intel.h +++ b/src/INTEL/npair_trim_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pair_airebo_intel.cpp b/src/INTEL/pair_airebo_intel.cpp index 25e52d02d2..0b05447dd7 100644 --- a/src/INTEL/pair_airebo_intel.cpp +++ b/src/INTEL/pair_airebo_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -1968,7 +1968,7 @@ void ref_frebo_single_interaction(KernelArgsAIREBOT * ka, int i, flt_t Aij = ka->params.A[itype][jtype]; flt_t alphaij = ka->params.alpha[itype][jtype]; - flt_t exp_alphar = exp(-alphaij * rij); + flt_t exp_alphar = overloaded::exp(-alphaij * rij); flt_t VR_by_wij = (1.0 + (Qij / rij)) * Aij * exp_alphar; flt_t VR = wij * VR_by_wij; flt_t pre = wij * Aij * exp_alphar; @@ -2108,7 +2108,7 @@ void ref_lennard_jones_single_interaction(KernelArgsAIREBOT * ka, flt_t vdw, dvdw; if (morseflag) { - const flt_t exr = exp(-rij * ka->params.lj4[itype][jtype]); + const flt_t exr = overloaded::exp(-rij * ka->params.lj4[itype][jtype]); vdw = ka->params.lj1[itype][jtype] * exr * (ka->params.lj2[itype][jtype]*exr - 2); dvdw = ka->params.lj3[itype][jtype] * exr * diff --git a/src/INTEL/pair_airebo_intel.h b/src/INTEL/pair_airebo_intel.h index 16d77a8a06..8ca5b11439 100644 --- a/src/INTEL/pair_airebo_intel.h +++ b/src/INTEL/pair_airebo_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pair_airebo_morse_intel.cpp b/src/INTEL/pair_airebo_morse_intel.cpp index 8b9894dc02..f1c033aff2 100644 --- a/src/INTEL/pair_airebo_morse_intel.cpp +++ b/src/INTEL/pair_airebo_morse_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pair_airebo_morse_intel.h b/src/INTEL/pair_airebo_morse_intel.h index 1d75c632ea..7d3037ce30 100644 --- a/src/INTEL/pair_airebo_morse_intel.h +++ b/src/INTEL/pair_airebo_morse_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pair_buck_coul_cut_intel.cpp b/src/INTEL/pair_buck_coul_cut_intel.cpp index 62d6d02952..01a9f91bcf 100644 --- a/src/INTEL/pair_buck_coul_cut_intel.cpp +++ b/src/INTEL/pair_buck_coul_cut_intel.cpp @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -294,7 +294,7 @@ void PairBuckCoulCutIntel::eval(const int offload, const int vflag, if (rsq < c_cuti[jtype].cut_ljsq) { #endif flt_t r6inv = r2inv * r2inv * r2inv; - flt_t rexp = exp(-r * c_forcei[jtype].rhoinv); + flt_t rexp = std::exp(-r * c_forcei[jtype].rhoinv); forcebuck = r * rexp * c_forcei[jtype].buck1 - r6inv * c_forcei[jtype].buck2; if (EFLAG) diff --git a/src/INTEL/pair_buck_coul_cut_intel.h b/src/INTEL/pair_buck_coul_cut_intel.h index cd09604258..6635096b14 100644 --- a/src/INTEL/pair_buck_coul_cut_intel.h +++ b/src/INTEL/pair_buck_coul_cut_intel.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -15,7 +15,6 @@ Contributing author: Rodrigo Canales (RWTH Aachen University) ------------------------------------------------------------------------- */ - #ifdef PAIR_CLASS // clang-format off PairStyle(buck/coul/cut/intel,PairBuckCoulCutIntel); diff --git a/src/INTEL/pair_buck_coul_long_intel.cpp b/src/INTEL/pair_buck_coul_long_intel.cpp index 1425317a0a..ff57b571a4 100644 --- a/src/INTEL/pair_buck_coul_long_intel.cpp +++ b/src/INTEL/pair_buck_coul_long_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -336,7 +336,7 @@ void PairBuckCoulLongIntel::eval(const int offload, const int vflag, const flt_t INV_EWALD_P = 1.0 / 0.3275911; const flt_t grij = g_ewald * r; - const flt_t expm2 = exp(-grij * grij); + const flt_t expm2 = std::exp(-grij * grij); const flt_t t = INV_EWALD_P / (INV_EWALD_P + grij); const flt_t erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; const flt_t prefactor = qqrd2e * qtmp * q[j] / r; @@ -377,7 +377,7 @@ void PairBuckCoulLongIntel::eval(const int offload, const int vflag, if (rsq < c_forcei[jtype].cut_ljsq) { #endif flt_t r6inv = r2inv * r2inv * r2inv; - flt_t rexp = exp(-r * rho_invi[jtype]); + flt_t rexp = std::exp(-r * rho_invi[jtype]); forcebuck = r * rexp * c_forcei[jtype].buck1 - r6inv * c_forcei[jtype].buck2; if (EFLAG) evdwl = rexp * c_energyi[jtype].a - diff --git a/src/INTEL/pair_buck_coul_long_intel.h b/src/INTEL/pair_buck_coul_long_intel.h index 24005a5646..638fe7f18c 100644 --- a/src/INTEL/pair_buck_coul_long_intel.h +++ b/src/INTEL/pair_buck_coul_long_intel.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pair_buck_intel.cpp b/src/INTEL/pair_buck_intel.cpp index 46ea291420..2461361788 100644 --- a/src/INTEL/pair_buck_intel.cpp +++ b/src/INTEL/pair_buck_intel.cpp @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -262,7 +262,7 @@ void PairBuckIntel::eval(const int offload, const int vflag, if (rsq < c_forcei[jtype].cutsq) { #endif const flt_t r6inv = r2inv * r2inv * r2inv; - const flt_t rexp = exp(-r * c_forcei[jtype].rhoinv); + const flt_t rexp = std::exp(-r * c_forcei[jtype].rhoinv); forcebuck = r * rexp * c_forcei[jtype].buck1 - r6inv * c_forcei[jtype].buck2; diff --git a/src/INTEL/pair_buck_intel.h b/src/INTEL/pair_buck_intel.h index 655593a89d..643defe6dd 100644 --- a/src/INTEL/pair_buck_intel.h +++ b/src/INTEL/pair_buck_intel.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pair_dpd_intel.cpp b/src/INTEL/pair_dpd_intel.cpp index 763bd2fb57..5ed50e54ba 100644 --- a/src/INTEL/pair_dpd_intel.cpp +++ b/src/INTEL/pair_dpd_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/INTEL/pair_dpd_intel.h b/src/INTEL/pair_dpd_intel.h index 08b7d29e34..87cf39be41 100644 --- a/src/INTEL/pair_dpd_intel.h +++ b/src/INTEL/pair_dpd_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pair_eam_alloy_intel.cpp b/src/INTEL/pair_eam_alloy_intel.cpp index 40e802e730..f19534a574 100644 --- a/src/INTEL/pair_eam_alloy_intel.cpp +++ b/src/INTEL/pair_eam_alloy_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pair_eam_alloy_intel.h b/src/INTEL/pair_eam_alloy_intel.h index 3b2c640c6f..bc26322b16 100644 --- a/src/INTEL/pair_eam_alloy_intel.h +++ b/src/INTEL/pair_eam_alloy_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pair_eam_fs_intel.cpp b/src/INTEL/pair_eam_fs_intel.cpp index 7b235a05e8..dd2b146808 100644 --- a/src/INTEL/pair_eam_fs_intel.cpp +++ b/src/INTEL/pair_eam_fs_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pair_eam_fs_intel.h b/src/INTEL/pair_eam_fs_intel.h index f09274e02a..e265875204 100644 --- a/src/INTEL/pair_eam_fs_intel.h +++ b/src/INTEL/pair_eam_fs_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pair_eam_intel.cpp b/src/INTEL/pair_eam_intel.cpp index 0fff4f0632..ba5047a15a 100644 --- a/src/INTEL/pair_eam_intel.cpp +++ b/src/INTEL/pair_eam_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pair_eam_intel.h b/src/INTEL/pair_eam_intel.h index 3142b8a187..41b533bf95 100644 --- a/src/INTEL/pair_eam_intel.h +++ b/src/INTEL/pair_eam_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pair_gayberne_intel.cpp b/src/INTEL/pair_gayberne_intel.cpp index 1c2cdf0d49..5609479388 100644 --- a/src/INTEL/pair_gayberne_intel.cpp +++ b/src/INTEL/pair_gayberne_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/INTEL/pair_gayberne_intel.h b/src/INTEL/pair_gayberne_intel.h index 926cbda6fd..88870a2f59 100644 --- a/src/INTEL/pair_gayberne_intel.h +++ b/src/INTEL/pair_gayberne_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pair_lj_charmm_coul_charmm_intel.cpp b/src/INTEL/pair_lj_charmm_coul_charmm_intel.cpp index 9cc76a277c..e920257ef4 100644 --- a/src/INTEL/pair_lj_charmm_coul_charmm_intel.cpp +++ b/src/INTEL/pair_lj_charmm_coul_charmm_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/INTEL/pair_lj_charmm_coul_charmm_intel.h b/src/INTEL/pair_lj_charmm_coul_charmm_intel.h index 485cc15e09..cafb6b913c 100644 --- a/src/INTEL/pair_lj_charmm_coul_charmm_intel.h +++ b/src/INTEL/pair_lj_charmm_coul_charmm_intel.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pair_lj_charmm_coul_long_intel.cpp b/src/INTEL/pair_lj_charmm_coul_long_intel.cpp index e30c1dec32..0a93621bcd 100644 --- a/src/INTEL/pair_lj_charmm_coul_long_intel.cpp +++ b/src/INTEL/pair_lj_charmm_coul_long_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. @@ -341,7 +341,7 @@ void PairLJCharmmCoulLongIntel::eval(const int offload, const int vflag, const flt_t r = (flt_t)1.0 / sqrt(r2inv); const flt_t grij = g_ewald * r; - const flt_t expm2 = exp(-grij * grij); + const flt_t expm2 = std::exp(-grij * grij); const flt_t t = INV_EWALD_P / (INV_EWALD_P + grij); const flt_t erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; const flt_t prefactor = qqrd2e * qtmp * q[j] / r; diff --git a/src/INTEL/pair_lj_charmm_coul_long_intel.h b/src/INTEL/pair_lj_charmm_coul_long_intel.h index 85b2a4eb1a..acc58028a2 100644 --- a/src/INTEL/pair_lj_charmm_coul_long_intel.h +++ b/src/INTEL/pair_lj_charmm_coul_long_intel.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pair_lj_cut_coul_long_intel.cpp b/src/INTEL/pair_lj_cut_coul_long_intel.cpp index 17e6b6361d..89e556defa 100644 --- a/src/INTEL/pair_lj_cut_coul_long_intel.cpp +++ b/src/INTEL/pair_lj_cut_coul_long_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. @@ -334,7 +334,7 @@ void PairLJCutCoulLongIntel::eval(const int offload, const int vflag, const flt_t r = (flt_t)1.0 / sqrt(r2inv); const flt_t grij = g_ewald * r; - const flt_t expm2 = exp(-grij * grij); + const flt_t expm2 = std::exp(-grij * grij); const flt_t t = INV_EWALD_P / (INV_EWALD_P + grij); const flt_t erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; const flt_t prefactor = qqrd2e * qtmp * q[j] / r; diff --git a/src/INTEL/pair_lj_cut_coul_long_intel.h b/src/INTEL/pair_lj_cut_coul_long_intel.h index 0a8123d667..d816154554 100644 --- a/src/INTEL/pair_lj_cut_coul_long_intel.h +++ b/src/INTEL/pair_lj_cut_coul_long_intel.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pair_lj_cut_intel.cpp b/src/INTEL/pair_lj_cut_intel.cpp index c1d9a947f6..f2be6d5b6a 100644 --- a/src/INTEL/pair_lj_cut_intel.cpp +++ b/src/INTEL/pair_lj_cut_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/INTEL/pair_lj_cut_intel.h b/src/INTEL/pair_lj_cut_intel.h index 84f786a02a..54b58869a5 100644 --- a/src/INTEL/pair_lj_cut_intel.h +++ b/src/INTEL/pair_lj_cut_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pair_lj_long_coul_long_intel.cpp b/src/INTEL/pair_lj_long_coul_long_intel.cpp index 02527a681b..d29e435e91 100644 --- a/src/INTEL/pair_lj_long_coul_long_intel.cpp +++ b/src/INTEL/pair_lj_long_coul_long_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pair_lj_long_coul_long_intel.h b/src/INTEL/pair_lj_long_coul_long_intel.h index 870417c0db..dcbd536cd9 100644 --- a/src/INTEL/pair_lj_long_coul_long_intel.h +++ b/src/INTEL/pair_lj_long_coul_long_intel.h @@ -1,7 +1,7 @@ /* *- c++ -*- ----------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pair_rebo_intel.cpp b/src/INTEL/pair_rebo_intel.cpp index 75be02e06c..9333bd3a32 100644 --- a/src/INTEL/pair_rebo_intel.cpp +++ b/src/INTEL/pair_rebo_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pair_rebo_intel.h b/src/INTEL/pair_rebo_intel.h index 478a95e945..07856c05df 100644 --- a/src/INTEL/pair_rebo_intel.h +++ b/src/INTEL/pair_rebo_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pair_sw_intel.cpp b/src/INTEL/pair_sw_intel.cpp index 6e239afc7d..07d590ee2c 100644 --- a/src/INTEL/pair_sw_intel.cpp +++ b/src/INTEL/pair_sw_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -411,7 +411,7 @@ void PairSWIntel::eval(const int offload, const int vflag, } const flt_t rainvsq = rainv1 * rainv1 * r1; - flt_t expsrainv = exp(sigma * rainv1); + flt_t expsrainv = std::exp(sigma * rainv1); if (jj >= ejnumhalf) expsrainv = (flt_t)0.0; const flt_t fpair = (c1 * rp - c2 * rq + (c3 * rp - c4 * rq) * rainvsq) * expsrainv * rinvsq1; @@ -453,7 +453,7 @@ void PairSWIntel::eval(const int offload, const int vflag, flt_t gsrainv1 = sigma_gamma * rainv1; flt_t gsrainvsq1 = gsrainv1 * rainv1 / r1; - flt_t expgsrainv1 = exp(gsrainv1); + flt_t expgsrainv1 = std::exp(gsrainv1); for (int kk = 0; kk < ejnum; kk++) { int iktype, ijktype; @@ -479,7 +479,7 @@ void PairSWIntel::eval(const int offload, const int vflag, const flt_t rainv2 = (flt_t)1.0 / (r2 - cut); const flt_t gsrainv2 = sigma_gamma * rainv2; const flt_t gsrainvsq2 = gsrainv2 * rainv2 / r2; - const flt_t expgsrainv2 = exp(gsrainv2); + const flt_t expgsrainv2 = std::exp(gsrainv2); const flt_t rinv12 = (flt_t)1.0 / (r1 * r2); const flt_t cs = (delx * delr2[0] + dely * delr2[1] + diff --git a/src/INTEL/pair_sw_intel.h b/src/INTEL/pair_sw_intel.h index fe6f1c0c8d..e0425421bc 100644 --- a/src/INTEL/pair_sw_intel.h +++ b/src/INTEL/pair_sw_intel.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pair_tersoff_intel.cpp b/src/INTEL/pair_tersoff_intel.cpp index 42378c999c..758eca21ec 100644 --- a/src/INTEL/pair_tersoff_intel.cpp +++ b/src/INTEL/pair_tersoff_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pair_tersoff_intel.h b/src/INTEL/pair_tersoff_intel.h index a813acf196..14a0b7c520 100644 --- a/src/INTEL/pair_tersoff_intel.h +++ b/src/INTEL/pair_tersoff_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pppm_disp_intel.cpp b/src/INTEL/pppm_disp_intel.cpp index 7921dd157e..fdff23fe5e 100644 --- a/src/INTEL/pppm_disp_intel.cpp +++ b/src/INTEL/pppm_disp_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -23,7 +23,7 @@ #include "domain.h" #include "error.h" #include "force.h" -#include "gridcomm.h" +#include "grid3d.h" #include "math_const.h" #include "math_special.h" #include "memory.h" @@ -292,7 +292,7 @@ void PPPMDispIntel::compute(int eflag, int vflag) make_rho_c(fix->get_single_buffers()); } - gc->reverse_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR),REVERSE_RHO, + gc->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(FFT_SCALAR), gc_buf1,gc_buf2,MPI_FFT_SCALAR); brick2fft(nxlo_in, nylo_in, nzlo_in, nxhi_in, nyhi_in, nzhi_in, @@ -306,7 +306,7 @@ void PPPMDispIntel::compute(int eflag, int vflag) energy_1, greensfn, virial_1, vg,vg2, u_brick, v0_brick, v1_brick, v2_brick, v3_brick, v4_brick, v5_brick); - gc->forward_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR),FORWARD_AD, + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_AD,1,sizeof(FFT_SCALAR), gc_buf1,gc_buf2,MPI_FFT_SCALAR); if (fix->precision() == FixIntel::PREC_MODE_MIXED) { @@ -318,8 +318,8 @@ void PPPMDispIntel::compute(int eflag, int vflag) } if (vflag_atom) - gc->forward_comm(GridComm::KSPACE,this,6,sizeof(FFT_SCALAR), - FORWARD_AD_PERATOM,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_PERATOM,6,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); } else { poisson_ik(work1, work2, density_fft, fft1, fft2, @@ -331,7 +331,7 @@ void PPPMDispIntel::compute(int eflag, int vflag) u_brick, v0_brick, v1_brick, v2_brick, v3_brick, v4_brick, v5_brick); - gc->forward_comm(GridComm::KSPACE,this,3,sizeof(FFT_SCALAR),FORWARD_IK, + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK,3,sizeof(FFT_SCALAR), gc_buf1,gc_buf2,MPI_FFT_SCALAR); if (fix->precision() == FixIntel::PREC_MODE_MIXED) { @@ -343,8 +343,8 @@ void PPPMDispIntel::compute(int eflag, int vflag) } if (evflag_atom) - gc->forward_comm(GridComm::KSPACE,this,7,sizeof(FFT_SCALAR), - FORWARD_IK_PERATOM,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_PERATOM,7,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); } if (evflag_atom) fieldforce_c_peratom(); } @@ -376,7 +376,7 @@ void PPPMDispIntel::compute(int eflag, int vflag) make_rho_g(fix->get_single_buffers()); } - gc6->reverse_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR),REVERSE_RHO_G, + gc6->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO_G,1,sizeof(FFT_SCALAR), gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); brick2fft(nxlo_in_6, nylo_in_6, nzlo_in_6, nxhi_in_6, nyhi_in_6, nzhi_in_6, @@ -391,7 +391,7 @@ void PPPMDispIntel::compute(int eflag, int vflag) virial_6, vg_6, vg2_6, u_brick_g, v0_brick_g, v1_brick_g, v2_brick_g, v3_brick_g, v4_brick_g, v5_brick_g); - gc6->forward_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR),FORWARD_AD_G, + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_G,1,sizeof(FFT_SCALAR), gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); if (fix->precision() == FixIntel::PREC_MODE_MIXED) { @@ -403,8 +403,8 @@ void PPPMDispIntel::compute(int eflag, int vflag) } if (vflag_atom) - gc6->forward_comm(GridComm::KSPACE,this,7,sizeof(FFT_SCALAR), - FORWARD_AD_PERATOM_G,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_PERATOM_G,7,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); } else { poisson_ik(work1_6, work2_6, density_fft_g, fft1_6, fft2_6, @@ -416,7 +416,7 @@ void PPPMDispIntel::compute(int eflag, int vflag) vdz_brick_g, virial_6, vg_6, vg2_6, u_brick_g, v0_brick_g, v1_brick_g, v2_brick_g, v3_brick_g, v4_brick_g, v5_brick_g); - gc6->forward_comm(GridComm::KSPACE,this,3,sizeof(FFT_SCALAR),FORWARD_IK_G, + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_G,3,sizeof(FFT_SCALAR), gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); if (fix->precision() == FixIntel::PREC_MODE_MIXED) { @@ -428,8 +428,8 @@ void PPPMDispIntel::compute(int eflag, int vflag) } if (evflag_atom) - gc6->forward_comm(GridComm::KSPACE,this,6,sizeof(FFT_SCALAR), - FORWARD_IK_PERATOM_G,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_PERATOM_G,6,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); } if (evflag_atom) fieldforce_g_peratom(); @@ -461,7 +461,7 @@ void PPPMDispIntel::compute(int eflag, int vflag) make_rho_a(fix->get_single_buffers()); } - gc->reverse_comm(GridComm::KSPACE,this,7,sizeof(FFT_SCALAR),REVERSE_RHO_A, + gc->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO_A,7,sizeof(FFT_SCALAR), gc_buf1,gc_buf2,MPI_FFT_SCALAR); brick2fft_a(); @@ -487,7 +487,7 @@ void PPPMDispIntel::compute(int eflag, int vflag) v5_brick_a2, u_brick_a4, v0_brick_a4, v1_brick_a4, v2_brick_a4, v3_brick_a4, v4_brick_a4, v5_brick_a4); - gc6->forward_comm(GridComm::KSPACE,this,7,sizeof(FFT_SCALAR),FORWARD_AD_A, + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_A,7,sizeof(FFT_SCALAR), gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); if (fix->precision() == FixIntel::PREC_MODE_MIXED) { @@ -499,8 +499,8 @@ void PPPMDispIntel::compute(int eflag, int vflag) } if (evflag_atom) - gc6->forward_comm(GridComm::KSPACE,this,42,sizeof(FFT_SCALAR), - FORWARD_AD_PERATOM_A,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_PERATOM_A,42,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); } else { poisson_ik(work1_6, work2_6, density_fft_a3, fft1_6, fft2_6, @@ -530,7 +530,7 @@ void PPPMDispIntel::compute(int eflag, int vflag) u_brick_a4, v0_brick_a4, v1_brick_a4, v2_brick_a4, v3_brick_a4, v4_brick_a4, v5_brick_a4); - gc6->forward_comm(GridComm::KSPACE,this,18,sizeof(FFT_SCALAR),FORWARD_IK_A, + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_A,18,sizeof(FFT_SCALAR), gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); if (fix->precision() == FixIntel::PREC_MODE_MIXED) { @@ -542,8 +542,8 @@ void PPPMDispIntel::compute(int eflag, int vflag) } if (evflag_atom) - gc6->forward_comm(GridComm::KSPACE,this,49,sizeof(FFT_SCALAR), - FORWARD_IK_PERATOM_A,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_PERATOM_A,49,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); } if (evflag_atom) fieldforce_a_peratom(); @@ -576,7 +576,7 @@ void PPPMDispIntel::compute(int eflag, int vflag) make_rho_none(fix->get_single_buffers()); } - gc->reverse_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR),REVERSE_RHO_NONE, + gc->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO_NONE,1,sizeof(FFT_SCALAR), gc_buf1,gc_buf2,MPI_FFT_SCALAR); brick2fft_none(); @@ -592,8 +592,8 @@ void PPPMDispIntel::compute(int eflag, int vflag) n += 2; } - gc6->forward_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR), - FORWARD_AD_NONE,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_NONE,1,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); if (fix->precision() == FixIntel::PREC_MODE_MIXED) { fieldforce_none_ad(fix->get_mixed_buffers()); @@ -604,8 +604,7 @@ void PPPMDispIntel::compute(int eflag, int vflag) } if (vflag_atom) - gc6->forward_comm(GridComm::KSPACE,this,6,sizeof(FFT_SCALAR), - FORWARD_AD_PERATOM_NONE, + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_PERATOM_NONE,6,sizeof(FFT_SCALAR), gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); } else { @@ -622,8 +621,7 @@ void PPPMDispIntel::compute(int eflag, int vflag) n += 2; } - gc6->forward_comm(GridComm::KSPACE,this,3,sizeof(FFT_SCALAR), - FORWARD_IK_NONE, + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_NONE,3,sizeof(FFT_SCALAR), gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); if (fix->precision() == FixIntel::PREC_MODE_MIXED) { @@ -635,8 +633,7 @@ void PPPMDispIntel::compute(int eflag, int vflag) } if (evflag_atom) - gc6->forward_comm(GridComm::KSPACE,this,7,sizeof(FFT_SCALAR), - FORWARD_IK_PERATOM_NONE, + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_PERATOM_NONE,7,sizeof(FFT_SCALAR), gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); } diff --git a/src/INTEL/pppm_disp_intel.h b/src/INTEL/pppm_disp_intel.h index 7543688154..20c59c00e8 100644 --- a/src/INTEL/pppm_disp_intel.h +++ b/src/INTEL/pppm_disp_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/pppm_electrode_intel.cpp b/src/INTEL/pppm_electrode_intel.cpp index da0f2fad3b..7a15f1d8a6 100644 --- a/src/INTEL/pppm_electrode_intel.cpp +++ b/src/INTEL/pppm_electrode_intel.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -23,12 +23,13 @@ #include "angle.h" #include "atom.h" #include "bond.h" +#include "citeme.h" #include "comm.h" #include "domain.h" #include "error.h" #include "fft3d_wrap.h" #include "force.h" -#include "gridcomm.h" +#include "grid3d.h" #include "math_const.h" #include "math_special.h" #include "memory.h" @@ -65,10 +66,24 @@ enum : bool { ELECTRODE = true, ELECTROLYTE = false }; #define ONEF 1.0 #endif +static const char cite_pppm_electrode[] = + "kspace_style pppm/electrode command:\n\n" + "@article{Ahrens2021,\n" + "author = {Ahrens-Iwers, Ludwig J.V. and Mei{\\ss}ner, Robert H.},\n" + "doi = {10.1063/5.0063381},\n" + "title = {{Constant potential simulations on a mesh}},\n" + "journal = {Journal of Chemical Physics},\n" + "year = {2021}\n" + "volume = {155},\n" + "pages = {104104},\n" + "}\n"; + PPPMElectrodeIntel::PPPMElectrodeIntel(LAMMPS *lmp) : PPPMIntel(lmp), ElectrodeKSpace(), electrolyte_density_brick(nullptr), - electrolyte_density_fft(nullptr) + electrolyte_density_fft(nullptr), boundcorr(nullptr) { + if (lmp->citeme) lmp->citeme->add(cite_pppm_electrode); + group_group_enable = 0; electrolyte_density_brick = nullptr; electrolyte_density_fft = nullptr; @@ -83,7 +98,6 @@ PPPMElectrodeIntel::~PPPMElectrodeIntel() memory->destroy(electrolyte_density_fft); if ((differentiation_flag != 1) && !peratom_allocate_flag) memory->destroy3d_offset(u_brick, nzlo_out, nylo_out, nxlo_out); - delete boundcorr; } void PPPMElectrodeIntel::init() @@ -156,7 +170,6 @@ void PPPMElectrodeIntel::setup() prd[0] /= wire_volfactor; prd[1] /= wire_volfactor; - boundcorr->setup(xprd_wire, yprd_wire, zprd_slab); } void PPPMElectrodeIntel::compute(int eflag, int vflag) @@ -210,7 +223,7 @@ void PPPMElectrodeIntel::compute(int eflag, int vflag) make_rho_in_brick(fix->get_single_buffers(), last_source_grpbit, density_brick, !last_invert_source); } - gc->reverse_comm(GridComm::KSPACE, this, 1, sizeof(FFT_SCALAR), REVERSE_RHO, gc_buf1, gc_buf2, + gc->reverse_comm(Grid3d::KSPACE, this, REVERSE_RHO, 1, sizeof(FFT_SCALAR), gc_buf1, gc_buf2, MPI_FFT_SCALAR); for (int nz = nzlo_out; nz <= nzhi_out; nz++) for (int ny = nylo_out; ny <= nyhi_out; ny++) @@ -232,7 +245,7 @@ void PPPMElectrodeIntel::compute(int eflag, int vflag) // to fully sum contribution in their 3d bricks // remap from 3d decomposition to FFT decomposition - gc->reverse_comm(GridComm::KSPACE, this, 1, sizeof(FFT_SCALAR), REVERSE_RHO, gc_buf1, gc_buf2, + gc->reverse_comm(Grid3d::KSPACE, this, REVERSE_RHO, 1, sizeof(FFT_SCALAR), gc_buf1, gc_buf2, MPI_FFT_SCALAR); } @@ -252,27 +265,27 @@ void PPPMElectrodeIntel::compute(int eflag, int vflag) // to fill ghost cells surrounding their 3d bricks if (differentiation_flag == 1) - gc->forward_comm(GridComm::KSPACE, this, 1, sizeof(FFT_SCALAR), FORWARD_AD, gc_buf1, gc_buf2, + gc->forward_comm(Grid3d::KSPACE, this, FORWARD_AD, 1, sizeof(FFT_SCALAR), gc_buf1, gc_buf2, MPI_FFT_SCALAR); else - gc->forward_comm(GridComm::KSPACE, this, 3, sizeof(FFT_SCALAR), FORWARD_IK, gc_buf1, gc_buf2, + gc->forward_comm(Grid3d::KSPACE, this, FORWARD_IK, 3, sizeof(FFT_SCALAR), gc_buf1, gc_buf2, MPI_FFT_SCALAR); // extra per-atom energy/virial communication if (evflag_atom) { if (differentiation_flag == 1 && vflag_atom) - gc->forward_comm(GridComm::KSPACE, this, 6, sizeof(FFT_SCALAR), FORWARD_AD_PERATOM, gc_buf1, + gc->forward_comm(Grid3d::KSPACE, this, FORWARD_AD_PERATOM, 6, sizeof(FFT_SCALAR), gc_buf1, gc_buf2, MPI_FFT_SCALAR); else if (differentiation_flag == 0) - gc->forward_comm(GridComm::KSPACE, this, 7, sizeof(FFT_SCALAR), FORWARD_IK_PERATOM, gc_buf1, + gc->forward_comm(Grid3d::KSPACE, this, FORWARD_IK_PERATOM, 7, sizeof(FFT_SCALAR), gc_buf1, gc_buf2, MPI_FFT_SCALAR); } int tempslabflag = slabflag; slabflag = 0; // bypass compute_second's slabcorr() PPPMIntel::compute_second(eflag, vflag); slabflag = tempslabflag; - boundcorr->compute_corr(qsum, slab_volfactor, eflag_atom, eflag_global, energy, eatom); + boundcorr->compute_corr(qsum, eflag_atom, eflag_global, energy, eatom); compute_vector_called = false; } @@ -340,7 +353,7 @@ void PPPMElectrodeIntel::compute_vector(double *vec, int sensor_grpbit, int sour } density_brick = electrolyte_density_brick; density_fft = electrolyte_density_fft; - gc->reverse_comm(GridComm::KSPACE, this, 1, sizeof(FFT_SCALAR), REVERSE_RHO, gc_buf1, gc_buf2, + gc->reverse_comm(Grid3d::KSPACE, this, REVERSE_RHO, 1, sizeof(FFT_SCALAR), gc_buf1, gc_buf2, MPI_FFT_SCALAR); brick2fft(); // switch back pointers @@ -370,7 +383,7 @@ void PPPMElectrodeIntel::compute_vector(double *vec, int sensor_grpbit, int sour n += 2; } - gc->forward_comm(GridComm::KSPACE, this, 1, sizeof(FFT_SCALAR), FORWARD_AD, gc_buf1, gc_buf2, + gc->forward_comm(Grid3d::KSPACE, this, FORWARD_AD, 1, sizeof(FFT_SCALAR), gc_buf1, gc_buf2, MPI_FFT_SCALAR); switch (fix->precision()) { @@ -505,7 +518,9 @@ void PPPMElectrodeIntel::compute_matrix(bigint *imat, double **matrix, bool time compute(1, 0); // fft green's function k -> r - vector greens_real(nz_pppm * ny_pppm * nx_pppm, 0.); + double *greens_real; + memory->create(greens_real, nz_pppm * ny_pppm * nx_pppm, "pppm/electrode:greens_real"); + memset(greens_real, 0, nz_pppm * ny_pppm * nx_pppm * sizeof(double)); for (int i = 0, n = 0; i < nfft; i++) { work2[n++] = greensfn[i]; work2[n++] = ZEROF; @@ -517,8 +532,7 @@ void PPPMElectrodeIntel::compute_matrix(bigint *imat, double **matrix, bool time greens_real[ny_pppm * nx_pppm * k + nx_pppm * j + i] = work2[n]; n += 2; } - MPI_Allreduce(MPI_IN_PLACE, &greens_real.front(), nz_pppm * ny_pppm * nx_pppm, MPI_DOUBLE, - MPI_SUM, world); + MPI_Allreduce(MPI_IN_PLACE, greens_real, nz_pppm * ny_pppm * nx_pppm, MPI_DOUBLE, MPI_SUM, world); int const nlocal = atom->nlocal; int nmat = std::count_if(&imat[0], &imat[nlocal], [](int x) { return x >= 0; @@ -539,47 +553,50 @@ void PPPMElectrodeIntel::compute_matrix(bigint *imat, double **matrix, bool time one_step_multiplication(imat, greens_real, x_ele, matrix, nmat, timer_flag); else two_step_multiplication(imat, greens_real, x_ele, matrix, nmat, timer_flag); + memory->destroy(greens_real); memory->destroy(x_ele); } /* ----------------------------------------------------------------------*/ -void PPPMElectrodeIntel::one_step_multiplication(bigint *imat, vector greens_real, - double **x_ele, double **matrix, int const nmat, - bool timer_flag) +void PPPMElectrodeIntel::one_step_multiplication(bigint *imat, double *greens_real, double **x_ele, + double **matrix, int const nmat, bool timer_flag) { // map green's function in real space from mesh to particle positions // with matrix multiplication 'W^T G W' in one steps. Uses less memory than // two_step_multiplication // int const nlocal = atom->nlocal; - // double **x = atom->x; + double **x = atom->x; MPI_Barrier(world); double step1_time = MPI_Wtime(); // precalculate rho_1d for local electrode - vector>> rho1d_j(nlocal, - vector>(3, vector(order, 0))); - - _alignvar(FFT_SCALAR rho[3][INTEL_P3M_ALIGNED_MAXORDER], 64) = {0}; - + std::vector j_list; for (int j = 0; j < nlocal; j++) { int jpos = imat[j]; if (jpos < 0) continue; - double *_noalias xj = x_ele[jpos]; + j_list.push_back(j); + } + int const nj_local = j_list.size(); + + FFT_SCALAR ***rho1d_j; + memory->create(rho1d_j, nj_local, 3, order, "pppm/electrode:rho1d_j"); + + _alignvar(FFT_SCALAR rho[3][INTEL_P3M_ALIGNED_MAXORDER], 64) = {0}; + + for (int jlist_pos = 0; jlist_pos < nj_local; jlist_pos++) { + int j = j_list[jlist_pos]; int njx = part2grid[j][0]; int njy = part2grid[j][1]; int njz = part2grid[j][2]; - FFT_SCALAR djx = njx + shiftone - (xj[0] - boxlo[0]) * delxinv; - FFT_SCALAR djy = njy + shiftone - (xj[1] - boxlo[1]) * delyinv; - FFT_SCALAR djz = njz + shiftone - (xj[2] - boxlo[2]) * delzinv; + FFT_SCALAR const djx = njx + shiftone - (x[j][0] - boxlo[0]) * delxinv; + FFT_SCALAR const djy = njy + shiftone - (x[j][1] - boxlo[1]) * delyinv; + FFT_SCALAR const djz = njz + shiftone - (x[j][2] - boxlo[2]) * delzinv; if (_use_table) { - djx = djx * half_rho_scale + half_rho_scale_plus; - int idx = djx; - djy = djy * half_rho_scale + half_rho_scale_plus; - int idy = djy; - djz = djz * half_rho_scale + half_rho_scale_plus; - int idz = djz; + int idx = (int) (djx * half_rho_scale + half_rho_scale_plus); + int idy = (int) (djy * half_rho_scale + half_rho_scale_plus); + int idz = (int) (djz * half_rho_scale + half_rho_scale_plus); #if defined(LMP_SIMD_COMPILER) #pragma simd #endif @@ -607,7 +624,7 @@ void PPPMElectrodeIntel::one_step_multiplication(bigint *imat, vector gr } } for (int dim = 0; dim < 3; dim++) { - for (int oi = 0; oi < order; oi++) { rho1d_j[j][dim][oi] = (double) rho[dim][oi]; } + for (int oi = 0; oi < order; oi++) { rho1d_j[jlist_pos][dim][oi] = rho[dim][oi]; } } } @@ -615,6 +632,9 @@ void PPPMElectrodeIntel::one_step_multiplication(bigint *imat, vector gr // (nx,ny,nz) = global coords of grid pt to "lower left" of charge // (dx,dy,dz) = distance to "lower left" grid pt // (mx,my,mz) = global coords of moving stencil pt + int const order2 = INTEL_P3M_ALIGNED_MAXORDER * INTEL_P3M_ALIGNED_MAXORDER; + int const order6 = order2 * order2 * order2; + _alignvar(double amesh[order6], 64) = {0}; for (int ipos = 0; ipos < nmat; ipos++) { double *_noalias xi_ele = x_ele[ipos]; // new calculation for nx, ny, nz because part2grid available for nlocal, @@ -626,12 +646,9 @@ void PPPMElectrodeIntel::one_step_multiplication(bigint *imat, vector gr FFT_SCALAR diy = niy + shiftone - (xi_ele[1] - boxlo[1]) * delyinv; FFT_SCALAR diz = niz + shiftone - (xi_ele[2] - boxlo[2]) * delzinv; if (_use_table) { - dix = dix * half_rho_scale + half_rho_scale_plus; - int idx = dix; - diy = diy * half_rho_scale + half_rho_scale_plus; - int idy = diy; - diz = diz * half_rho_scale + half_rho_scale_plus; - int idz = diz; + int idx = (int) (dix * half_rho_scale + half_rho_scale_plus); + int idy = (int) (diy * half_rho_scale + half_rho_scale_plus); + int idz = (int) (diz * half_rho_scale + half_rho_scale_plus); #if defined(LMP_SIMD_COMPILER) #pragma simd #endif @@ -658,54 +675,85 @@ void PPPMElectrodeIntel::one_step_multiplication(bigint *imat, vector gr rho[2][k - nlower] = r3; } } - for (int j = 0; j < nlocal; j++) { + int njx = -1; + int njy = -1; + int njz = -1; // force initial build_amesh + for (int jlist_pos = 0; jlist_pos < nj_local; jlist_pos++) { + int j = j_list[jlist_pos]; int jpos = imat[j]; - if (jpos < 0) continue; + if ((ipos < jpos) == !((ipos - jpos) % 2)) continue; double aij = 0.; - int njx = part2grid[j][0]; - int njy = part2grid[j][1]; - int njz = part2grid[j][2]; - for (int ni = nlower; ni <= nupper; ni++) { - double iz0 = rho[2][ni - nlower]; - int miz = ni + niz; - for (int mi = nlower; mi <= nupper; mi++) { - double iy0 = iz0 * rho[1][mi - nlower]; - int miy = mi + niy; - for (int li = nlower; li <= nupper; li++) { - int mix = li + nix; - double const ix0 = iy0 * rho[0][li - nlower]; - for (int nj = nlower; nj <= nupper; nj++) { - double jz0 = rho1d_j[j][2][nj - nlower]; - int mjz = nj + njz; - int mz = abs(mjz - miz) % nz_pppm; - for (int mj = nlower; mj <= nupper; mj++) { - double jy0 = jz0 * rho1d_j[j][1][mj - nlower]; - int mjy = mj + njy; - int my = abs(mjy - miy) % ny_pppm; - for (int lj = nlower; lj <= nupper; lj++) { - int mjx = lj + njx; - int mx = abs(mjx - mix) % nx_pppm; - double const jx0 = jy0 * rho1d_j[j][0][lj - nlower]; - aij += ix0 * jx0 * greens_real[mz * nx_pppm * ny_pppm + my * nx_pppm + mx]; + if (njx != part2grid[j][0] || njy != part2grid[j][1] || njz != part2grid[j][2]) { + njx = part2grid[j][0]; + njy = part2grid[j][1]; + njz = part2grid[j][2]; + build_amesh(njx - nix, njy - niy, njz - niz, amesh, greens_real); + } + int ind_amesh = 0; + for (int ni = 0; ni < order; ni++) { + FFT_SCALAR const iz0 = rho[2][ni]; + for (int nj = 0; nj < order; nj++) { + FFT_SCALAR const jz0 = rho1d_j[jlist_pos][2][nj]; + for (int mi = 0; mi < order; mi++) { + FFT_SCALAR const iy0 = iz0 * rho[1][mi]; + for (int mj = 0; mj < order; mj++) { + FFT_SCALAR const jy0 = jz0 * rho1d_j[jlist_pos][1][mj]; + for (int li = 0; li < order; li++) { + FFT_SCALAR const ix0 = iy0 * rho[0][li]; + double aij_xscan = 0.; + for (int lj = 0; lj < order; lj++) { + aij_xscan += amesh[ind_amesh] * rho1d_j[jlist_pos][0][lj]; + ind_amesh++; } + aij += (double) ix0 * jy0 * aij_xscan; } } } } } matrix[ipos][jpos] += aij / volume; + if (ipos != jpos) matrix[jpos][ipos] += aij / volume; } } MPI_Barrier(world); + memory->destroy(rho1d_j); if (timer_flag && (comm->me == 0)) utils::logmesg(lmp, fmt::format("Single step time: {:.4g} s\n", MPI_Wtime() - step1_time)); } /* ----------------------------------------------------------------------*/ -void PPPMElectrodeIntel::two_step_multiplication(bigint *imat, vector greens_real, - double **x_ele, double **matrix, int const nmat, - bool timer_flag) +void PPPMElectrodeIntel::build_amesh(const int dx, // = njx - nix + const int dy, // = njy - niy + const int dz, // = njz - niz + double *amesh, double *const greens_real) +{ + auto fmod = [](int x, int n) { // fast unsigned mod + int r = abs(x); + while (r >= n) r -= n; + return r; + }; + int ind_amesh = 0; + + for (int iz = 0; iz < order; iz++) + for (int jz = 0; jz < order; jz++) { + int const mz = fmod(dz + jz - iz, nz_pppm) * nx_pppm * ny_pppm; + for (int iy = 0; iy < order; iy++) + for (int jy = 0; jy < order; jy++) { + int const my = fmod(dy + jy - iy, ny_pppm) * nx_pppm; + for (int ix = 0; ix < order; ix++) + for (int jx = 0; jx < order; jx++) { + int const mx = fmod(dx + jx - ix, nx_pppm); + amesh[ind_amesh] = greens_real[mz + my + mx]; + ind_amesh++; + } + } + } +} +/* ----------------------------------------------------------------------*/ + +void PPPMElectrodeIntel::two_step_multiplication(bigint *imat, double *greens_real, double **x_ele, + double **matrix, int const nmat, bool timer_flag) { // map green's function in real space from mesh to particle positions // with matrix multiplication 'W^T G W' in two steps. gw is result of @@ -1099,6 +1147,7 @@ void PPPMElectrodeIntel::allocate_peratom() void PPPMElectrodeIntel::deallocate() { + if (boundcorr != nullptr) delete boundcorr; // duplicated to always deallocate u_brick memory->destroy3d_offset(density_brick, nzlo_out, nylo_out, nxlo_out); memory->destroy3d_offset(u_brick, nzlo_out, nylo_out, nxlo_out); diff --git a/src/INTEL/pppm_electrode_intel.h b/src/INTEL/pppm_electrode_intel.h index 048b148496..8277aa9a82 100644 --- a/src/INTEL/pppm_electrode_intel.h +++ b/src/INTEL/pppm_electrode_intel.h @@ -1,7 +1,7 @@ /* *- c++ -*- ----------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -89,10 +89,9 @@ class PPPMElectrodeIntel : public PPPMIntel, public ElectrodeKSpace { project_psi(buffers, vec, sensor_grpbit); } - void one_step_multiplication(bigint *, std::vector, double **, double **, int const, - bool); - void two_step_multiplication(bigint *, std::vector, double **, double **, int const, - bool); + void one_step_multiplication(bigint *, double *, double **, double **, int const, bool); + void two_step_multiplication(bigint *, double *, double **, double **, int const, bool); + void build_amesh(int, int, int, double *, double *); bool compute_vector_called; }; diff --git a/src/INTEL/pppm_intel.cpp b/src/INTEL/pppm_intel.cpp index fc25d64847..2ceca54d29 100644 --- a/src/INTEL/pppm_intel.cpp +++ b/src/INTEL/pppm_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -26,7 +26,7 @@ #include "domain.h" #include "error.h" #include "force.h" -#include "gridcomm.h" +#include "grid3d.h" #include "math_const.h" #include "math_special.h" #include "memory.h" @@ -227,7 +227,7 @@ void PPPMIntel::compute_first(int eflag, int vflag) // to fully sum contribution in their 3d bricks // remap from 3d decomposition to FFT decomposition - gc->reverse_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR),REVERSE_RHO, + gc->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(FFT_SCALAR), gc_buf1,gc_buf2,MPI_FFT_SCALAR); brick2fft(); @@ -243,21 +243,21 @@ void PPPMIntel::compute_first(int eflag, int vflag) // to fill ghost cells surrounding their 3d bricks if (differentiation_flag == 1) - gc->forward_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR),FORWARD_AD, + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_AD,1,sizeof(FFT_SCALAR), gc_buf1,gc_buf2,MPI_FFT_SCALAR); else - gc->forward_comm(GridComm::KSPACE,this,3,sizeof(FFT_SCALAR),FORWARD_IK, + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK,3,sizeof(FFT_SCALAR), gc_buf1,gc_buf2,MPI_FFT_SCALAR); // extra per-atom energy/virial communication if (evflag_atom) { if (differentiation_flag == 1 && vflag_atom) - gc->forward_comm(GridComm::KSPACE,this,6,sizeof(FFT_SCALAR), - FORWARD_AD_PERATOM,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_PERATOM,6,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); else if (differentiation_flag == 0) - gc->forward_comm(GridComm::KSPACE,this,7,sizeof(FFT_SCALAR), - FORWARD_IK_PERATOM,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_PERATOM,7,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); } } diff --git a/src/INTEL/pppm_intel.h b/src/INTEL/pppm_intel.h index bddd9a95a1..a016cfd4fa 100644 --- a/src/INTEL/pppm_intel.h +++ b/src/INTEL/pppm_intel.h @@ -2,7 +2,7 @@ /* *- c++ -*- ----------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/verlet_lrt_intel.cpp b/src/INTEL/verlet_lrt_intel.cpp index 4102510c66..4459d69c8d 100644 --- a/src/INTEL/verlet_lrt_intel.cpp +++ b/src/INTEL/verlet_lrt_intel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTEL/verlet_lrt_intel.h b/src/INTEL/verlet_lrt_intel.h index c976656ae3..f2e5a0bb99 100644 --- a/src/INTEL/verlet_lrt_intel.h +++ b/src/INTEL/verlet_lrt_intel.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTERLAYER/interlayer_taper.h b/src/INTERLAYER/interlayer_taper.h index a496daca5d..abf898fb00 100644 --- a/src/INTERLAYER/interlayer_taper.h +++ b/src/INTERLAYER/interlayer_taper.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTERLAYER/pair_coul_shield.cpp b/src/INTERLAYER/pair_coul_shield.cpp index 68873a3350..e647e1ea91 100644 --- a/src/INTERLAYER/pair_coul_shield.cpp +++ b/src/INTERLAYER/pair_coul_shield.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTERLAYER/pair_coul_shield.h b/src/INTERLAYER/pair_coul_shield.h index 9bc3a37fce..e4e6f3e827 100644 --- a/src/INTERLAYER/pair_coul_shield.h +++ b/src/INTERLAYER/pair_coul_shield.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTERLAYER/pair_drip.cpp b/src/INTERLAYER/pair_drip.cpp index e7b340c516..90773b4034 100644 --- a/src/INTERLAYER/pair_drip.cpp +++ b/src/INTERLAYER/pair_drip.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -28,7 +28,6 @@ #include "force.h" #include "memory.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "potential_file_reader.h" diff --git a/src/INTERLAYER/pair_drip.h b/src/INTERLAYER/pair_drip.h index 3678149776..c59c1d5b0d 100644 --- a/src/INTERLAYER/pair_drip.h +++ b/src/INTERLAYER/pair_drip.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTERLAYER/pair_ilp_graphene_hbn.cpp b/src/INTERLAYER/pair_ilp_graphene_hbn.cpp index 17f2260af4..0ff2811339 100644 --- a/src/INTERLAYER/pair_ilp_graphene_hbn.cpp +++ b/src/INTERLAYER/pair_ilp_graphene_hbn.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTERLAYER/pair_ilp_graphene_hbn.h b/src/INTERLAYER/pair_ilp_graphene_hbn.h index de7bd3e02f..9987830b1d 100644 --- a/src/INTERLAYER/pair_ilp_graphene_hbn.h +++ b/src/INTERLAYER/pair_ilp_graphene_hbn.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTERLAYER/pair_ilp_tmd.cpp b/src/INTERLAYER/pair_ilp_tmd.cpp index 65163acb48..c024e23079 100644 --- a/src/INTERLAYER/pair_ilp_tmd.cpp +++ b/src/INTERLAYER/pair_ilp_tmd.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -22,15 +22,12 @@ #include "atom.h" #include "citeme.h" -#include "comm.h" #include "error.h" #include "force.h" #include "interlayer_taper.h" #include "memory.h" #include "my_page.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "neighbor.h" #include #include diff --git a/src/INTERLAYER/pair_ilp_tmd.h b/src/INTERLAYER/pair_ilp_tmd.h index 8d5446d49c..8381c2e830 100644 --- a/src/INTERLAYER/pair_ilp_tmd.h +++ b/src/INTERLAYER/pair_ilp_tmd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTERLAYER/pair_kolmogorov_crespi_full.cpp b/src/INTERLAYER/pair_kolmogorov_crespi_full.cpp index 0f9dd9ec47..b2eba787b1 100644 --- a/src/INTERLAYER/pair_kolmogorov_crespi_full.cpp +++ b/src/INTERLAYER/pair_kolmogorov_crespi_full.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTERLAYER/pair_kolmogorov_crespi_full.h b/src/INTERLAYER/pair_kolmogorov_crespi_full.h index 51fd3d8270..14b0a12d31 100644 --- a/src/INTERLAYER/pair_kolmogorov_crespi_full.h +++ b/src/INTERLAYER/pair_kolmogorov_crespi_full.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTERLAYER/pair_kolmogorov_crespi_z.cpp b/src/INTERLAYER/pair_kolmogorov_crespi_z.cpp index a2abdc9a1c..1c4600b68e 100644 --- a/src/INTERLAYER/pair_kolmogorov_crespi_z.cpp +++ b/src/INTERLAYER/pair_kolmogorov_crespi_z.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTERLAYER/pair_kolmogorov_crespi_z.h b/src/INTERLAYER/pair_kolmogorov_crespi_z.h index 2177b518e2..35335ca090 100644 --- a/src/INTERLAYER/pair_kolmogorov_crespi_z.h +++ b/src/INTERLAYER/pair_kolmogorov_crespi_z.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTERLAYER/pair_lebedeva_z.cpp b/src/INTERLAYER/pair_lebedeva_z.cpp index 0c2c285504..8e97e553fd 100644 --- a/src/INTERLAYER/pair_lebedeva_z.cpp +++ b/src/INTERLAYER/pair_lebedeva_z.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTERLAYER/pair_lebedeva_z.h b/src/INTERLAYER/pair_lebedeva_z.h index 4e4fa3f6e3..0f3a22094f 100644 --- a/src/INTERLAYER/pair_lebedeva_z.h +++ b/src/INTERLAYER/pair_lebedeva_z.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/INTERLAYER/pair_saip_metal.cpp b/src/INTERLAYER/pair_saip_metal.cpp index 4e768a9168..05fbfbf7f4 100644 --- a/src/INTERLAYER/pair_saip_metal.cpp +++ b/src/INTERLAYER/pair_saip_metal.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -26,8 +26,6 @@ #include "force.h" #include "interlayer_taper.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "neighbor.h" #include #include diff --git a/src/INTERLAYER/pair_saip_metal.h b/src/INTERLAYER/pair_saip_metal.h index cd02f16524..8b2ab3442f 100644 --- a/src/INTERLAYER/pair_saip_metal.h +++ b/src/INTERLAYER/pair_saip_metal.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KIM/Install.sh b/src/KIM/Install.sh index 7ddb9c8227..533f4f997a 100755 --- a/src/KIM/Install.sh +++ b/src/KIM/Install.sh @@ -44,7 +44,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*kim.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*kim.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/kim\/Makefile.lammps @@ -58,7 +58,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*kim.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*kim.*$/d' ../Makefile.package.settings fi fi diff --git a/src/KIM/fix_store_kim.cpp b/src/KIM/fix_store_kim.cpp index e57f759e87..415ba4c410 100644 --- a/src/KIM/fix_store_kim.cpp +++ b/src/KIM/fix_store_kim.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KIM/fix_store_kim.h b/src/KIM/fix_store_kim.h index bc41f54390..cd37563cbb 100644 --- a/src/KIM/fix_store_kim.h +++ b/src/KIM/fix_store_kim.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KIM/kim_command.cpp b/src/KIM/kim_command.cpp index b93b87fa7c..820e4dcba7 100644 --- a/src/KIM/kim_command.cpp +++ b/src/KIM/kim_command.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KIM/kim_command.h b/src/KIM/kim_command.h index 1347aaea5f..0fcd833859 100644 --- a/src/KIM/kim_command.h +++ b/src/KIM/kim_command.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KIM/kim_init.cpp b/src/KIM/kim_init.cpp index 7c3e4c2361..037fb2857e 100644 --- a/src/KIM/kim_init.cpp +++ b/src/KIM/kim_init.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KIM/kim_init.h b/src/KIM/kim_init.h index 9224f05ebe..73fa35491c 100644 --- a/src/KIM/kim_init.h +++ b/src/KIM/kim_init.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KIM/kim_interactions.cpp b/src/KIM/kim_interactions.cpp index 94c182026a..5a91109e53 100644 --- a/src/KIM/kim_interactions.cpp +++ b/src/KIM/kim_interactions.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KIM/kim_interactions.h b/src/KIM/kim_interactions.h index 34da625604..dc70f7aac0 100644 --- a/src/KIM/kim_interactions.h +++ b/src/KIM/kim_interactions.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KIM/kim_param.cpp b/src/KIM/kim_param.cpp index d4dfb0ead6..6473cb2ad0 100644 --- a/src/KIM/kim_param.cpp +++ b/src/KIM/kim_param.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -155,11 +155,9 @@ void KimParam::command(int narg, char **arg) std::string kim_param_get_set(arg[0]); - if ((kim_param_get_set != "get") && (kim_param_get_set != "set")) { - std::string msg("Incorrect arguments in 'kim param' command.\n"); - msg += "'kim param get/set' is mandatory"; - error->all(FLERR, msg); - } + if ((kim_param_get_set != "get") && (kim_param_get_set != "set")) + error->all(FLERR, "Incorrect arguments in 'kim param' command.\n" + "'kim param get/set' is mandatory"); int const ifix = modify->find_fix("KIM_MODEL_STORE"); if (ifix >= 0) { @@ -170,8 +168,7 @@ void KimParam::command(int narg, char **arg) fix_store->getptr("simulator_model")); if (simulatorModel) - error->all(FLERR, - "'kim param' can only be used with a KIM Portable Model"); + error->all(FLERR, "'kim param' can only be used with a KIM Portable Model"); } input->write_echo(fmt::format("#=== BEGIN kim param {} ===================" @@ -196,13 +193,10 @@ void KimParam::command(int narg, char **arg) } else error->all(FLERR, "Pair style is defined, but there is " "no match for kim style in lammps"); - } else { - auto msg = fmt::format("Illegal 'kim param {0}' command.\nTo {0} the new " - "parameter values, pair style must be assigned.\n" - "Must use 'kim interactions' or 'pair_style kim' " - "before 'kim param {0}'", kim_param_get_set); - error->all(FLERR, msg); - } + } else + error->all(FLERR, "Illegal 'kim param {0}' command.\nTo {0} the new parameter values, " + "pair style must be assigned.\nMust use 'kim interactions' or 'pair_style kim' " + "before 'kim param {0}'", kim_param_get_set); // Get the number of mutable parameters in the kim model int numberOfParameters(0); @@ -243,12 +237,9 @@ void KimParam::command(int narg, char **arg) if (paramname == str_name_str) break; } - if (param_index >= numberOfParameters) { - auto msg = fmt::format("Wrong argument in 'kim param get' command.\n" - "This Model does not have the requested '{}' " - "parameter", paramname); - error->all(FLERR, msg); - } + if (param_index >= numberOfParameters) + error->all(FLERR, "Wrong argument in 'kim param get' command.\n" + "This Model does not have the requested '{}' parameter", paramname); // Get the index_range for the requested parameter int nlbound(0); @@ -259,12 +250,9 @@ void KimParam::command(int narg, char **arg) // Check to see if the indices range contains // only integer numbers and/or range : - if (argtostr.find_first_not_of("0123456789:") != std::string::npos) { - auto msg = fmt::format("Illegal index_range.\nExpected integer " - "parameter(s) instead of '{}' in " - "index_range", argtostr); - error->all(FLERR, msg); - } + if (argtostr.find_first_not_of("0123456789:") != std::string::npos) + error->all(FLERR, "Illegal index_range.\nExpected integer parameter(s) instead " + "of '{}' in index_range", argtostr); std::string::size_type npos = argtostr.find(':'); if (npos != std::string::npos) { @@ -273,30 +261,20 @@ void KimParam::command(int narg, char **arg) nlbound = atoi(words[0].c_str()); nubound = atoi(words[1].c_str()); - if (nubound < 1 || nubound > extent || - nlbound < 1 || nlbound > nubound) { - auto msg = fmt::format("Illegal index_range '{}-{}' for '{}' " - "parameter with the extent of '{}'", - nlbound, nubound, paramname, extent); - error->all(FLERR, msg); - } + if ((nubound < 1) || (nubound > extent) || (nlbound < 1) || (nlbound > nubound)) + error->all(FLERR, "Illegal index_range '{}-{}' for '{}' parameter with the " + "extent of '{}'",nlbound, nubound, paramname, extent); } else { nlbound = atoi(argtostr.c_str()); - if (nlbound < 1 || nlbound > extent) { - auto msg = fmt::format("Illegal index '{}' for '{}' parameter " - "with the extent of '{}'", nlbound, - paramname, extent); - error->all(FLERR, msg); - } - + if (nlbound < 1 || nlbound > extent) + error->all(FLERR, "Illegal index '{}' for '{}' parameter with the extent of '{}'", + nlbound, paramname, extent); nubound = nlbound; } - } else { - std::string msg("Wrong number of arguments in 'kim param get' "); - msg += "command.\nIndex range after parameter name is mandatory"; - error->all(FLERR, msg); - } + } else + error->all(FLERR, "Wrong number of arguments in 'kim param get' command.\n" + "Index range after parameter name is mandatory"); int const nvars = nubound - nlbound + 1; std::vector varsname; @@ -304,15 +282,11 @@ void KimParam::command(int narg, char **arg) if (i < narg) { // Get the variable/variable_base name varname = std::string(arg[i++]); - if ((varname == "split") || - (varname == "list") || - (varname == "explicit")) - error->all(FLERR, "Illegal variable name in 'kim param get'"); - } else { - std::string msg("Wrong number of arguments in 'kim param get' "); - msg += "command.\nThe LAMMPS variable name is mandatory"; - error->all(FLERR, msg); - } + if ((varname == "split") || (varname == "list") || (varname == "explicit")) + error->all(FLERR, "Illegal variable name '{}' in 'kim param get'", varname); + } else + error->all(FLERR, "Wrong number of arguments in 'kim param get' command.\n" + "The LAMMPS variable name is mandatory"); // indicator flag for list request bool list_requested(false); @@ -337,28 +311,22 @@ void KimParam::command(int narg, char **arg) --i; for (int j = 0; j < nvars; ++j, ++i) { varsname[j] = std::string(arg[i]); - if (varsname[j] == "split" || varsname[j] == "list" || - varsname[j] == "explicit") - error->all(FLERR, "Illegal variable name in 'kim param get'"); + if (varsname[j] == "split" || varsname[j] == "list" || varsname[j] == "explicit") + error->all(FLERR, "Illegal variable name '{}' in 'kim param get'", varsname[j]); } if (i < narg) { formatarg = std::string(arg[i]); if (formatarg == "explicit") ++i; } } else { - auto msg = - fmt::format("Wrong number of arguments in 'kim param get' " - "command.\nThe LAMMPS '{}' variable names or " - "'{} split' is mandatory", nvars, varname); - error->all(FLERR, msg); + error->all(FLERR, "Wrong number of arguments in 'kim param get' command.\n" + "The LAMMPS '{}' variable names or '{} split' is mandatory", + nvars, varname); } - } else { - auto msg = - fmt::format("Wrong number of arguments in 'kim param get' " - "command.\nThe LAMMPS '{}' variable names or " - "'{} split/list' is mandatory", nvars, varname); - error->all(FLERR, msg); - } + } else + error->all(FLERR, "Wrong number of arguments in 'kim param get' command.\n" + "The LAMMPS '{}' variable names or '{} split/list' is mandatory", + nvars, varname); } else { varsname.resize(1); if (i < narg) { diff --git a/src/KIM/kim_param.h b/src/KIM/kim_param.h index 409100f730..d160d2f1b1 100644 --- a/src/KIM/kim_param.h +++ b/src/KIM/kim_param.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KIM/kim_property.cpp b/src/KIM/kim_property.cpp index 8145533107..7d060ad8b1 100644 --- a/src/KIM/kim_property.cpp +++ b/src/KIM/kim_property.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KIM/kim_property.h b/src/KIM/kim_property.h index 11522186d0..7cc857cf6d 100644 --- a/src/KIM/kim_property.h +++ b/src/KIM/kim_property.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp index 4851338367..ebb1790e6e 100644 --- a/src/KIM/kim_query.cpp +++ b/src/KIM/kim_query.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KIM/kim_query.h b/src/KIM/kim_query.h index 1dd72a7a72..0071b691d9 100644 --- a/src/KIM/kim_query.h +++ b/src/KIM/kim_query.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KIM/kim_units.cpp b/src/KIM/kim_units.cpp index 1377e3c4ee..7c57e3b71a 100644 --- a/src/KIM/kim_units.cpp +++ b/src/KIM/kim_units.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KIM/kim_units.h b/src/KIM/kim_units.h index e5e9c2809a..e85760ab82 100644 --- a/src/KIM/kim_units.h +++ b/src/KIM/kim_units.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index b6e6d175d0..6a5a792797 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -483,15 +483,13 @@ void PairKIM::coeff(int narg, char **arg) nlbound = atoi(words[0].c_str()); nubound = atoi(words[1].c_str()); - if (nubound < 1 || nubound > extent || - nlbound < 1 || nlbound > nubound) - error->all(FLERR,"Illegal index_range '{}-{}' for '{}' " - "parameter with the extent of '{}'", + if ((nubound < 1) || (nubound > extent) || (nlbound < 1) || (nlbound > nubound)) + error->all(FLERR,"Illegal index_range '{}-{}' for '{}' parameter with the extent of '{}'", nlbound, nubound, paramname, extent); } else { nlbound = atoi(argtostr.c_str()); - if (nlbound < 1 || nlbound > extent) + if ((nlbound < 1) || (nlbound > extent)) error->all(FLERR,"Illegal index '{}' for '{}' parameter with the extent of '{}'", nlbound, paramname, extent); @@ -1081,8 +1079,7 @@ void PairKIM::set_kim_model_has_flags() KIM_ComputeArguments_GetArgumentSupportStatus( pargs, computeArgumentName, &supportStatus); - if (KIM_ComputeArgumentName_Equal(computeArgumentName, - KIM_COMPUTE_ARGUMENT_NAME_partialEnergy)) + if (KIM_ComputeArgumentName_Equal(computeArgumentName, KIM_COMPUTE_ARGUMENT_NAME_partialEnergy)) kim_model_support_for_energy = supportStatus; else if (KIM_ComputeArgumentName_Equal( computeArgumentName, KIM_COMPUTE_ARGUMENT_NAME_partialForces)) @@ -1095,17 +1092,14 @@ void PairKIM::set_kim_model_has_flags() computeArgumentName, KIM_COMPUTE_ARGUMENT_NAME_partialParticleVirial)) kim_model_support_for_particleVirial = supportStatus; - else if (KIM_SupportStatus_Equal(supportStatus, - KIM_SUPPORT_STATUS_required)) { - std::string msg("KIM Model requires unsupported compute argument: "); - msg += KIM_ComputeArgumentName_ToString(computeArgumentName); - error->all(FLERR,msg); + else if (KIM_SupportStatus_Equal(supportStatus, KIM_SUPPORT_STATUS_required)) { + error->all(FLERR, "KIM Model requires unsupported compute argument: {}", + KIM_ComputeArgumentName_ToString(computeArgumentName)); } } if (comm->me == 0) { - if (KIM_SupportStatus_Equal(kim_model_support_for_energy, - KIM_SUPPORT_STATUS_notSupported)) + if (KIM_SupportStatus_Equal(kim_model_support_for_energy, KIM_SUPPORT_STATUS_notSupported)) error->warning(FLERR,"KIM Model does not provide 'partialEnergy'; Potential energy will be zero"); if (KIM_SupportStatus_Equal(kim_model_support_for_forces, diff --git a/src/KIM/pair_kim.h b/src/KIM/pair_kim.h index 10c9c11a0e..90adb863e2 100644 --- a/src/KIM/pair_kim.h +++ b/src/KIM/pair_kim.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh index cfdf0356f7..a5bf6437fc 100755 --- a/src/KOKKOS/Install.sh +++ b/src/KOKKOS/Install.sh @@ -64,8 +64,8 @@ action atom_vec_bond_kokkos.cpp atom_vec_bond.cpp action atom_vec_bond_kokkos.h atom_vec_bond.h action atom_vec_charge_kokkos.cpp action atom_vec_charge_kokkos.h -action atom_vec_spin_kokkos.cpp -action atom_vec_spin_kokkos.h +action atom_vec_spin_kokkos.cpp atom_vec_spin.cpp +action atom_vec_spin_kokkos.h atom_vec_spin.h action atom_vec_dpd_kokkos.cpp atom_vec_dpd.cpp action atom_vec_dpd_kokkos.h atom_vec_dpd.h action atom_vec_full_kokkos.cpp atom_vec_full.cpp @@ -117,6 +117,8 @@ action fix_acks2_reaxff_kokkos.cpp fix_acks2_reaxff.cpp action fix_acks2_reaxff_kokkos.h fix_acks2_reaxff.h action fix_deform_kokkos.cpp action fix_deform_kokkos.h +action fix_dt_reset_kokkos.cpp +action fix_dt_reset_kokkos.h action fix_enforce2d_kokkos.cpp action fix_enforce2d_kokkos.h action fix_eos_table_rx_kokkos.cpp fix_eos_table_rx.cpp @@ -165,12 +167,14 @@ action fix_wall_lj93_kokkos.cpp action fix_wall_lj93_kokkos.h action fix_wall_reflect_kokkos.cpp action fix_wall_reflect_kokkos.h +action fix_viscous_kokkos.cpp +action fix_viscous_kokkos.h action fix_dpd_energy_kokkos.cpp fix_dpd_energy.cpp action fix_dpd_energy_kokkos.h fix_dpd_energy.h action fix_rx_kokkos.cpp fix_rx.cpp action fix_rx_kokkos.h fix_rx.h -action gridcomm_kokkos.cpp fft3d.h -action gridcomm_kokkos.h fft3d.h +action grid3d_kokkos.cpp fft3d.h +action grid3d_kokkos.h fft3d.h action improper_class2_kokkos.cpp improper_class2.cpp action improper_class2_kokkos.h improper_class2.h action improper_harmonic_kokkos.cpp improper_harmonic.cpp @@ -190,6 +194,16 @@ action meam_funcs_kokkos.h meam_funcs.cpp action meam_impl_kokkos.h meam_impl.cpp action meam_setup_done_kokkos.h meam_setup_done.cpp action memory_kokkos.h +action mliap_data_kokkos.cpp mliap_data.cpp +action mliap_data_kokkos.h mliap_data.h +action mliap_descriptor_kokkos.h mliap_descriptor.h +action mliap_descriptor_so3_kokkos.cpp mliap_descriptor_so3.cpp +action mliap_descriptor_so3_kokkos.h mliap_descriptor_so3.h +action mliap_model_linear_kokkos.cpp mliap_model_linear.cpp +action mliap_model_linear_kokkos.h mliap_model_linear.h +action mliap_model_kokkos.h mliap_model.h +action mliap_so3_kokkos.cpp mliap_so3.cpp +action mliap_so3_kokkos.h mliap_so3.h action modify_kokkos.cpp action modify_kokkos.h action neigh_bond_kokkos.cpp @@ -298,6 +312,8 @@ action pair_lj_spica_kokkos.cpp pair_lj_spica.cpp action pair_lj_spica_kokkos.h pair_lj_spica.h action pair_meam_kokkos.cpp pair_meam.cpp action pair_meam_kokkos.h pair_meam.h +action pair_mliap_kokkos.cpp pair_mliap.cpp +action pair_mliap_kokkos.h pair_mliap.h action pair_morse_kokkos.cpp action pair_morse_kokkos.h action pair_multi_lucy_rx_kokkos.cpp pair_multi_lucy_rx.cpp @@ -362,7 +378,7 @@ if (test $1 = 1) then if (test -e ../Makefile.package.settings) then sed -i -e '/CXX\ =\ \$(CC)/d' ../Makefile.package.settings - sed -i -e '/^include.*kokkos.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*kokkos.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ CXX = $(CC) @@ -389,7 +405,7 @@ elif (test $1 = 0) then if (test -e ../Makefile.package.settings) then sed -i -e '/CXX\ =\ \$(CC)/d' ../Makefile.package.settings - sed -i -e '/^include.*kokkos.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*kokkos.*$/d' ../Makefile.package.settings fi fi diff --git a/src/KOKKOS/angle_charmm_kokkos.cpp b/src/KOKKOS/angle_charmm_kokkos.cpp index 74ced2a934..8b41a93451 100644 --- a/src/KOKKOS/angle_charmm_kokkos.cpp +++ b/src/KOKKOS/angle_charmm_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/angle_charmm_kokkos.h b/src/KOKKOS/angle_charmm_kokkos.h index e52cdb0bb2..197f9160a0 100644 --- a/src/KOKKOS/angle_charmm_kokkos.h +++ b/src/KOKKOS/angle_charmm_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/angle_class2_kokkos.cpp b/src/KOKKOS/angle_class2_kokkos.cpp index 2a386f6489..8f77ab4c94 100644 --- a/src/KOKKOS/angle_class2_kokkos.cpp +++ b/src/KOKKOS/angle_class2_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/angle_class2_kokkos.h b/src/KOKKOS/angle_class2_kokkos.h index 9fb737187f..81bed169bc 100644 --- a/src/KOKKOS/angle_class2_kokkos.h +++ b/src/KOKKOS/angle_class2_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/angle_cosine_kokkos.cpp b/src/KOKKOS/angle_cosine_kokkos.cpp index 8b3360988f..24d1b5caea 100644 --- a/src/KOKKOS/angle_cosine_kokkos.cpp +++ b/src/KOKKOS/angle_cosine_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/angle_cosine_kokkos.h b/src/KOKKOS/angle_cosine_kokkos.h index b4d074c05a..33b80f5a5f 100644 --- a/src/KOKKOS/angle_cosine_kokkos.h +++ b/src/KOKKOS/angle_cosine_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/angle_harmonic_kokkos.cpp b/src/KOKKOS/angle_harmonic_kokkos.cpp index 6342c2f46f..1d8ada4bd9 100644 --- a/src/KOKKOS/angle_harmonic_kokkos.cpp +++ b/src/KOKKOS/angle_harmonic_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/angle_harmonic_kokkos.h b/src/KOKKOS/angle_harmonic_kokkos.h index dc635a9be2..ce4b9d9976 100644 --- a/src/KOKKOS/angle_harmonic_kokkos.h +++ b/src/KOKKOS/angle_harmonic_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/atom_kokkos.cpp b/src/KOKKOS/atom_kokkos.cpp index 071ce7bc23..2de65e24fb 100644 --- a/src/KOKKOS/atom_kokkos.cpp +++ b/src/KOKKOS/atom_kokkos.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -104,23 +104,23 @@ AtomKokkos::~AtomKokkos() void AtomKokkos::sync(const ExecutionSpace space, unsigned int mask) { - if (space == Device && lmp->kokkos->auto_sync) ((AtomVecKokkos *) avec)->modified(Host, mask); + if (space == Device && lmp->kokkos->auto_sync) avecKK->modified(Host, mask); - ((AtomVecKokkos *) avec)->sync(space, mask); + avecKK->sync(space, mask); } /* ---------------------------------------------------------------------- */ void AtomKokkos::modified(const ExecutionSpace space, unsigned int mask) { - ((AtomVecKokkos *) avec)->modified(space, mask); + avecKK->modified(space, mask); - if (space == Device && lmp->kokkos->auto_sync) ((AtomVecKokkos *) avec)->sync(Host, mask); + if (space == Device && lmp->kokkos->auto_sync) avecKK->sync(Host, mask); } void AtomKokkos::sync_overlapping_device(const ExecutionSpace space, unsigned int mask) { - ((AtomVecKokkos *) avec)->sync_overlapping_device(space, mask); + avecKK->sync_overlapping_device(space, mask); } /* ---------------------------------------------------------------------- */ @@ -380,5 +380,8 @@ AtomVec *AtomKokkos::new_avec(const std::string &style, int trysuffix, int &sfla { AtomVec *avec = Atom::new_avec(style, trysuffix, sflag); if (!avec->kokkosable) error->all(FLERR, "KOKKOS package requires a kokkos enabled atom_style"); + + avecKK = dynamic_cast(avec); + return avec; } diff --git a/src/KOKKOS/atom_kokkos.h b/src/KOKKOS/atom_kokkos.h index 89cf6c1d6e..08bfaf20cd 100644 --- a/src/KOKKOS/atom_kokkos.h +++ b/src/KOKKOS/atom_kokkos.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -78,6 +78,8 @@ class AtomKokkos : public Atom { DAT::tdual_int_scalar k_error_flag; dual_hash_type k_map_hash; + class AtomVecKokkos* avecKK; + // map lookup function inlined for efficiency // return -1 if no map defined diff --git a/src/KOKKOS/atom_map_kokkos.cpp b/src/KOKKOS/atom_map_kokkos.cpp index a76941bd8f..f8cc5ab2c4 100644 --- a/src/KOKKOS/atom_map_kokkos.cpp +++ b/src/KOKKOS/atom_map_kokkos.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/atom_vec_angle_kokkos.cpp b/src/KOKKOS/atom_vec_angle_kokkos.cpp index 3746f62a81..23406415d0 100644 --- a/src/KOKKOS/atom_vec_angle_kokkos.cpp +++ b/src/KOKKOS/atom_vec_angle_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -27,27 +27,10 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -AtomVecAngleKokkos::AtomVecAngleKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) +AtomVecAngleKokkos::AtomVecAngleKokkos(LAMMPS *lmp) : AtomVec(lmp), +AtomVecKokkos(lmp), AtomVecAngle(lmp) { - molecular = Atom::MOLECULAR; - bonds_allow = angles_allow = 1; - mass_type = PER_TYPE; - comm_x_only = comm_f_only = 1; - size_forward = 3; - size_reverse = 3; - size_border = 7; - size_velocity = 3; - size_data_atom = 6; - size_data_vel = 4; - xcol_data = 4; - - atom->molecule_flag = 1; - - k_count = DAT::tdual_int_1d("atom::k_count",1); - atomKK = (AtomKokkos *) atom; - commKK = (CommKokkos *) comm; - buffer = nullptr; } /* ---------------------------------------------------------------------- @@ -172,52 +155,6 @@ void AtomVecAngleKokkos::grow_pointers() h_angle_atom3 = atomKK->k_angle_atom3.h_view; } -/* ---------------------------------------------------------------------- - copy atom I info to atom J -------------------------------------------------------------------------- */ - -void AtomVecAngleKokkos::copy(int i, int j, int delflag) -{ - int k; - - h_tag[j] = h_tag[i]; - h_type[j] = h_type[i]; - mask[j] = mask[i]; - h_image[j] = h_image[i]; - h_x(j,0) = h_x(i,0); - h_x(j,1) = h_x(i,1); - h_x(j,2) = h_x(i,2); - h_v(j,0) = h_v(i,0); - h_v(j,1) = h_v(i,1); - h_v(j,2) = h_v(i,2); - - h_molecule(j) = h_molecule(i); - - h_num_bond(j) = h_num_bond(i); - for (k = 0; k < h_num_bond(j); k++) { - h_bond_type(j,k) = h_bond_type(i,k); - h_bond_atom(j,k) = h_bond_atom(i,k); - } - - h_nspecial(j,0) = h_nspecial(i,0); - h_nspecial(j,1) = h_nspecial(i,1); - h_nspecial(j,2) = h_nspecial(i,2); - for (k = 0; k < h_nspecial(j,2); k++) - h_special(j,k) = h_special(i,k); - - h_num_angle(j) = h_num_angle(i); - for (k = 0; k < h_num_angle(j); k++) { - h_angle_type(j,k) = h_angle_type(i,k); - h_angle_atom1(j,k) = h_angle_atom1(i,k); - h_angle_atom2(j,k) = h_angle_atom2(i,k); - h_angle_atom3(j,k) = h_angle_atom3(i,k); - } - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag); -} - /* ---------------------------------------------------------------------- */ template @@ -508,171 +445,6 @@ void AtomVecAngleKokkos::unpack_comm_kokkos(const int &n, const int &first, /* ---------------------------------------------------------------------- */ -int AtomVecAngleKokkos::pack_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz; - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; - dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; - dz = pbc[2]*domain->zprd; - } - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - } - } - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecAngleKokkos::pack_comm_vel(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz,dvx,dvy,dvz; - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; - dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; - dz = pbc[2]*domain->zprd; - } - if (!deform_vremap) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } else { - dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; - dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; - dvz = pbc[2]*h_rate[2]; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - if (mask[i] & deform_groupbit) { - buf[m++] = h_v(j,0) + dvx; - buf[m++] = h_v(j,1) + dvy; - buf[m++] = h_v(j,2) + dvz; - } else { - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } - } - } - return m; -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecAngleKokkos::unpack_comm(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - } -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecAngleKokkos::unpack_comm_vel(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_v(i,0) = buf[m++]; - h_v(i,1) = buf[m++]; - h_v(i,2) = buf[m++]; - } -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecAngleKokkos::pack_reverse(int n, int first, double *buf) -{ - if (n > 0) - atomKK->sync(Host,F_MASK); - - int m = 0; - const int last = first + n; - for (int i = first; i < last; i++) { - buf[m++] = h_f(i,0); - buf[m++] = h_f(i,1); - buf[m++] = h_f(i,2); - } - return m; -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecAngleKokkos::unpack_reverse(int n, int *list, double *buf) -{ - if (n > 0) - atomKK->modified(Host,F_MASK); - - int m = 0; - for (int i = 0; i < n; i++) { - const int j = list[i]; - h_f(j,0) += buf[m++]; - h_f(j,1) += buf[m++]; - h_f(j,2) += buf[m++]; - } -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecAngleKokkos_PackBorder { typedef DeviceType device_type; @@ -774,149 +546,6 @@ int AtomVecAngleKokkos::pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, /* ---------------------------------------------------------------------- */ -int AtomVecAngleKokkos::pack_border(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz; - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = ubuf(h_molecule(j)).d; - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]; - dy = pbc[1]; - dz = pbc[2]; - } - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = ubuf(h_molecule(j)).d; - } - } - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); - - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecAngleKokkos::pack_border_vel(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz,dvx,dvy,dvz; - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = ubuf(h_molecule(j)).d; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]; - dy = pbc[1]; - dz = pbc[2]; - } - if (!deform_vremap) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = ubuf(h_molecule(j)).d; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } else { - dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; - dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; - dvz = pbc[2]*h_rate[2]; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = ubuf(h_molecule(j)).d; - if (mask[i] & deform_groupbit) { - buf[m++] = h_v(j,0) + dvx; - buf[m++] = h_v(j,1) + dvy; - buf[m++] = h_v(j,2) + dvz; - } else { - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } - } - } - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); - - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecAngleKokkos::pack_border_hybrid(int n, int *list, double *buf) -{ - int i,j,m; - - m = 0; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_molecule(j); - } - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecAngleKokkos_UnpackBorder { typedef DeviceType device_type; @@ -977,78 +606,6 @@ void AtomVecAngleKokkos::unpack_border_kokkos(const int &n, const int &first, /* ---------------------------------------------------------------------- */ -void AtomVecAngleKokkos::unpack_border(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - while (last > nmax) grow(0); - - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_tag(i) = (tagint) ubuf(buf[m++]).i; - h_type(i) = (int) ubuf(buf[m++]).i; - h_mask(i) = (int) ubuf(buf[m++]).i; - h_molecule(i) = (tagint) ubuf(buf[m++]).i; - } - - atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK); - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]-> - unpack_border(n,first,&buf[m]); -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecAngleKokkos::unpack_border_vel(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - while (last > nmax) grow(0); - - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_tag(i) = (tagint) ubuf(buf[m++]).i; - h_type(i) = (int) ubuf(buf[m++]).i; - h_mask(i) = (int) ubuf(buf[m++]).i; - h_molecule(i) = (tagint) ubuf(buf[m++]).i; - h_v(i,0) = buf[m++]; - h_v(i,1) = buf[m++]; - h_v(i,2) = buf[m++]; - } - - atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK|V_MASK); - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]-> - unpack_border(n,first,&buf[m]); -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecAngleKokkos::unpack_border_hybrid(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - for (i = first; i < last; i++) - h_molecule(i) = (tagint) ubuf(buf[m++]).i; - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecAngleKokkos_PackExchangeFunctor { typedef DeviceType device_type; @@ -1245,50 +802,6 @@ int AtomVecAngleKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_ /* ---------------------------------------------------------------------- */ -int AtomVecAngleKokkos::pack_exchange(int i, double *buf) -{ - int k; - int m = 1; - buf[m++] = h_x(i,0); - buf[m++] = h_x(i,1); - buf[m++] = h_x(i,2); - buf[m++] = h_v(i,0); - buf[m++] = h_v(i,1); - buf[m++] = h_v(i,2); - buf[m++] = ubuf(h_tag(i)).d; - buf[m++] = ubuf(h_type(i)).d; - buf[m++] = ubuf(h_mask(i)).d; - buf[m++] = ubuf(h_image(i)).d; - buf[m++] = ubuf(h_molecule(i)).d; - - buf[m++] = ubuf(h_num_bond(i)).d; - for (k = 0; k < h_num_bond(i); k++) { - buf[m++] = ubuf(h_bond_type(i,k)).d; - buf[m++] = ubuf(h_bond_atom(i,k)).d; - } - buf[m++] = ubuf(h_num_angle(i)).d; - for (k = 0; k < h_num_angle(i); k++) { - buf[m++] = ubuf(h_angle_type(i,k)).d; - buf[m++] = ubuf(h_angle_atom1(i,k)).d; - buf[m++] = ubuf(h_angle_atom2(i,k)).d; - buf[m++] = ubuf(h_angle_atom3(i,k)).d; - } - buf[m++] = ubuf(h_nspecial(i,0)).d; - buf[m++] = ubuf(h_nspecial(i,1)).d; - buf[m++] = ubuf(h_nspecial(i,2)).d; - for (k = 0; k < h_nspecial(i,2); k++) - buf[m++] = ubuf(h_special(i,k)).d; - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]); - - buf[0] = m; - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecAngleKokkos_UnpackExchangeFunctor { typedef DeviceType device_type; @@ -1416,361 +929,6 @@ int AtomVecAngleKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int n /* ---------------------------------------------------------------------- */ -int AtomVecAngleKokkos::unpack_exchange(double *buf) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) grow(0); - atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | MOLECULE_MASK | BOND_MASK | - ANGLE_MASK | SPECIAL_MASK); - - int k; - int m = 1; - h_x(nlocal,0) = buf[m++]; - h_x(nlocal,1) = buf[m++]; - h_x(nlocal,2) = buf[m++]; - h_v(nlocal,0) = buf[m++]; - h_v(nlocal,1) = buf[m++]; - h_v(nlocal,2) = buf[m++]; - h_tag(nlocal) = (tagint) ubuf(buf[m++]).i; - h_type(nlocal) = (int) ubuf(buf[m++]).i; - h_mask(nlocal) = (int) ubuf(buf[m++]).i; - h_image(nlocal) = (imageint) ubuf(buf[m++]).i; - h_molecule(nlocal) = (tagint) ubuf(buf[m++]).i; - - h_num_bond(nlocal) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_num_bond(nlocal); k++) { - h_bond_type(nlocal,k) = (int) ubuf(buf[m++]).i; - h_bond_atom(nlocal,k) = (tagint) ubuf(buf[m++]).i; - } - h_num_angle(nlocal) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_num_angle(nlocal); k++) { - h_angle_type(nlocal,k) = (int) ubuf(buf[m++]).i; - h_angle_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_angle_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_angle_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i; - } - h_nspecial(nlocal,0) = (int) ubuf(buf[m++]).i; - h_nspecial(nlocal,1) = (int) ubuf(buf[m++]).i; - h_nspecial(nlocal,2) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_nspecial(nlocal,2); k++) - h_special(nlocal,k) = (tagint) ubuf(buf[m++]).i; - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - m += modify->fix[atom->extra_grow[iextra]]-> - unpack_exchange(nlocal,&buf[m]); - - atom->nlocal++; - return m; -} - -/* ---------------------------------------------------------------------- - size of restart data for all atoms owned by this proc - include extra data stored by fixes -------------------------------------------------------------------------- */ - -int AtomVecAngleKokkos::size_restart() -{ - int i; - - int nlocal = atom->nlocal; - int n = 0; - for (i = 0; i < nlocal; i++) - n += 14 + 2*h_num_bond(i) + 4*h_num_angle(i); - - if (atom->nextra_restart) - for (int iextra = 0; iextra < atom->nextra_restart; iextra++) - for (i = 0; i < nlocal; i++) - n += modify->fix[atom->extra_restart[iextra]]->size_restart(i); - - return n; -} - -/* ---------------------------------------------------------------------- - pack atom I's data for restart file including extra quantities - xyz must be 1st 3 values, so that read_restart can test on them - molecular types may be negative, but write as positive -------------------------------------------------------------------------- */ - -int AtomVecAngleKokkos::pack_restart(int i, double *buf) -{ - atomKK->sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | MOLECULE_MASK | BOND_MASK | - ANGLE_MASK | SPECIAL_MASK); - - int m = 1; - buf[m++] = h_x(i,0); - buf[m++] = h_x(i,1); - buf[m++] = h_x(i,2); - buf[m++] = ubuf(h_tag(i)).d; - buf[m++] = ubuf(h_type(i)).d; - buf[m++] = ubuf(h_mask(i)).d; - buf[m++] = ubuf(h_image(i)).d; - buf[m++] = h_v(i,0); - buf[m++] = h_v(i,1); - buf[m++] = h_v(i,2); - - buf[m++] = ubuf(h_molecule(i)).d; - - buf[m++] = ubuf(h_num_bond(i)).d; - for (int k = 0; k < h_num_bond(i); k++) { - buf[m++] = ubuf(MAX(h_bond_type(i,k),-h_bond_type(i,k))).d; - buf[m++] = ubuf(h_bond_atom(i,k)).d; - } - - buf[m++] = ubuf(h_num_angle(i)).d; - for (int k = 0; k < h_num_angle(i); k++) { - buf[m++] = ubuf(MAX(h_angle_type(i,k),-h_angle_type(i,k))).d; - buf[m++] = ubuf(h_angle_atom1(i,k)).d; - buf[m++] = ubuf(h_angle_atom2(i,k)).d; - buf[m++] = ubuf(h_angle_atom3(i,k)).d; - } - - if (atom->nextra_restart) - for (int iextra = 0; iextra < atom->nextra_restart; iextra++) - m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]); - - buf[0] = m; - return m; -} - -/* ---------------------------------------------------------------------- - unpack data for one atom from restart file including extra quantities -------------------------------------------------------------------------- */ - -int AtomVecAngleKokkos::unpack_restart(double *buf) -{ - int k; - - int nlocal = atom->nlocal; - if (nlocal == nmax) { - grow(0); - if (atom->nextra_store) - memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra"); - } - atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | MOLECULE_MASK | BOND_MASK | - ANGLE_MASK | SPECIAL_MASK); - - int m = 1; - h_x(nlocal,0) = buf[m++]; - h_x(nlocal,1) = buf[m++]; - h_x(nlocal,2) = buf[m++]; - h_tag(nlocal) = (tagint) ubuf(buf[m++]).i; - h_type(nlocal) = (int) ubuf(buf[m++]).i; - h_mask(nlocal) = (int) ubuf(buf[m++]).i; - h_image(nlocal) = (imageint) ubuf(buf[m++]).i; - h_v(nlocal,0) = buf[m++]; - h_v(nlocal,1) = buf[m++]; - h_v(nlocal,2) = buf[m++]; - - h_molecule(nlocal) = (tagint) ubuf(buf[m++]).i; - - h_num_bond(nlocal) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_num_bond(nlocal); k++) { - h_bond_type(nlocal,k) = (int) ubuf(buf[m++]).i; - h_bond_atom(nlocal,k) = (tagint) ubuf(buf[m++]).i; - } - - h_num_angle(nlocal) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_num_angle(nlocal); k++) { - h_angle_type(nlocal,k) = (int) ubuf(buf[m++]).i; - h_angle_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_angle_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_angle_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i; - } - - h_nspecial(nlocal,0) = h_nspecial(nlocal,1) = h_nspecial(nlocal,2) = 0; - - double **extra = atom->extra; - if (atom->nextra_store) { - int size = static_cast (buf[0]) - m; - for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++]; - } - - atom->nlocal++; - return m; -} - -/* ---------------------------------------------------------------------- - create one atom of itype at coord - set other values to defaults -------------------------------------------------------------------------- */ - -void AtomVecAngleKokkos::create_atom(int itype, double *coord) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) { - atomKK->modified(Host,ALL_MASK); - grow(0); - } - atomKK->modified(Host,ALL_MASK); - - tag[nlocal] = 0; - type[nlocal] = itype; - h_x(nlocal,0) = coord[0]; - h_x(nlocal,1) = coord[1]; - h_x(nlocal,2) = coord[2]; - h_mask(nlocal) = 1; - h_image(nlocal) = ((imageint) IMGMAX << IMG2BITS) | - ((imageint) IMGMAX << IMGBITS) | IMGMAX; - h_v(nlocal,0) = 0.0; - h_v(nlocal,1) = 0.0; - h_v(nlocal,2) = 0.0; - - h_molecule(nlocal) = 0; - h_num_bond(nlocal) = 0; - h_num_angle(nlocal) = 0; - h_nspecial(nlocal,0) = h_nspecial(nlocal,1) = h_nspecial(nlocal,2) = 0; - - atom->nlocal++; -} - -/* ---------------------------------------------------------------------- - unpack one line from Atoms section of data file - initialize other atom quantities -------------------------------------------------------------------------- */ - -void AtomVecAngleKokkos::data_atom(double *coord, imageint imagetmp, - const std::vector &values, std::string &extract) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) grow(0); - atomKK->modified(Host,ALL_MASK); - - h_tag(nlocal) = utils::inumeric(FLERR,values[0],true,lmp); - h_molecule(nlocal) = utils::inumeric(FLERR,values[1],true,lmp); - h_type(nlocal) = utils::inumeric(FLERR,values[2],true,lmp); - extract = values[2]; - if (h_type(nlocal) <= 0 || h_type(nlocal) > atom->ntypes) - error->one(FLERR,"Invalid atom type in Atoms section of data file"); - - h_x(nlocal,0) = coord[0]; - h_x(nlocal,1) = coord[1]; - h_x(nlocal,2) = coord[2]; - - h_image(nlocal) = imagetmp; - - h_mask(nlocal) = 1; - h_v(nlocal,0) = 0.0; - h_v(nlocal,1) = 0.0; - h_v(nlocal,2) = 0.0; - h_num_bond(nlocal) = 0; - h_num_angle(nlocal) = 0; - - atom->nlocal++; -} - -/* ---------------------------------------------------------------------- - unpack hybrid quantities from one line in Atoms section of data file - initialize other atom quantities for this sub-style -------------------------------------------------------------------------- */ - -int AtomVecAngleKokkos::data_atom_hybrid(int nlocal, const std::vector &values, - int offset) -{ - h_molecule(nlocal) = utils::inumeric(FLERR,values[offset],true,lmp); - h_num_bond(nlocal) = 0; - h_num_angle(nlocal) = 0; - return 1; -} - -/* ---------------------------------------------------------------------- - pack atom info for data file including 3 image flags -------------------------------------------------------------------------- */ - -void AtomVecAngleKokkos::pack_data(double **buf) -{ - int nlocal = atom->nlocal; - for (int i = 0; i < nlocal; i++) { - buf[i][0] = h_tag(i); - buf[i][1] = h_molecule(i); - buf[i][2] = h_type(i); - buf[i][3] = h_x(i,0); - buf[i][4] = h_x(i,1); - buf[i][5] = h_x(i,2); - buf[i][6] = (h_image[i] & IMGMASK) - IMGMAX; - buf[i][7] = (h_image[i] >> IMGBITS & IMGMASK) - IMGMAX; - buf[i][8] = (h_image[i] >> IMG2BITS) - IMGMAX; - } -} - -/* ---------------------------------------------------------------------- - pack hybrid atom info for data file -------------------------------------------------------------------------- */ - -int AtomVecAngleKokkos::pack_data_hybrid(int i, double *buf) -{ - buf[0] = h_molecule(i); - return 1; -} - -/* ---------------------------------------------------------------------- - write atom info to data file including 3 image flags -------------------------------------------------------------------------- */ - -void AtomVecAngleKokkos::write_data(FILE *fp, int n, double **buf) -{ - for (int i = 0; i < n; i++) - fprintf(fp,"%d %d %d %-1.16e %-1.16e %-1.16e %d %d %d\n", - (int) buf[i][0],(int) buf[i][1], (int) buf[i][2], - buf[i][3],buf[i][4],buf[i][5], - (int) buf[i][6],(int) buf[i][7],(int) buf[i][8]); -} - -/* ---------------------------------------------------------------------- - write hybrid atom info to data file -------------------------------------------------------------------------- */ - -int AtomVecAngleKokkos::write_data_hybrid(FILE *fp, double *buf) -{ - fprintf(fp," " TAGINT_FORMAT, (tagint) (buf[0])); - return 1; -} - -/* ---------------------------------------------------------------------- - return # of bytes of allocated memory -------------------------------------------------------------------------- */ - -double AtomVecAngleKokkos::memory_usage() -{ - double bytes = 0; - - if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax); - if (atom->memcheck("type")) bytes += memory->usage(type,nmax); - if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax); - if (atom->memcheck("image")) bytes += memory->usage(image,nmax); - if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3); - if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3); - if (atom->memcheck("f")) bytes += memory->usage(f,nmax*commKK->nthreads,3); - - if (atom->memcheck("molecule")) bytes += memory->usage(molecule,nmax); - if (atom->memcheck("nspecial")) bytes += memory->usage(nspecial,nmax,3); - if (atom->memcheck("special")) - bytes += memory->usage(special,nmax,atom->maxspecial); - - if (atom->memcheck("num_bond")) bytes += memory->usage(num_bond,nmax); - if (atom->memcheck("bond_type")) - bytes += memory->usage(bond_type,nmax,atom->bond_per_atom); - if (atom->memcheck("bond_atom")) - bytes += memory->usage(bond_atom,nmax,atom->bond_per_atom); - - if (atom->memcheck("num_angle")) bytes += memory->usage(num_angle,nmax); - if (atom->memcheck("angle_type")) - bytes += memory->usage(angle_type,nmax,atom->angle_per_atom); - if (atom->memcheck("angle_atom1")) - bytes += memory->usage(angle_atom1,nmax,atom->angle_per_atom); - if (atom->memcheck("angle_atom2")) - bytes += memory->usage(angle_atom2,nmax,atom->angle_per_atom); - if (atom->memcheck("angle_atom3")) - bytes += memory->usage(angle_atom3,nmax,atom->angle_per_atom); - - return bytes; -} - -/* ---------------------------------------------------------------------- */ - void AtomVecAngleKokkos::sync(ExecutionSpace space, unsigned int mask) { if (space == Device) { @@ -1826,6 +984,8 @@ void AtomVecAngleKokkos::sync(ExecutionSpace space, unsigned int mask) } } +/* ---------------------------------------------------------------------- */ + void AtomVecAngleKokkos::sync_overlapping_device(ExecutionSpace space, unsigned int mask) { if (space == Device) { @@ -1973,4 +1133,3 @@ void AtomVecAngleKokkos::modified(ExecutionSpace space, unsigned int mask) } } } - diff --git a/src/KOKKOS/atom_vec_angle_kokkos.h b/src/KOKKOS/atom_vec_angle_kokkos.h index 193d4b7635..cb1331aa04 100644 --- a/src/KOKKOS/atom_vec_angle_kokkos.h +++ b/src/KOKKOS/atom_vec_angle_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,41 +24,15 @@ AtomStyle(angle/kk/host,AtomVecAngleKokkos); #define LMP_ATOM_VEC_ANGLE_KOKKOS_H #include "atom_vec_kokkos.h" +#include "atom_vec_angle.h" namespace LAMMPS_NS { -class AtomVecAngleKokkos : public AtomVecKokkos { +class AtomVecAngleKokkos : public AtomVecKokkos, public AtomVecAngle { public: AtomVecAngleKokkos(class LAMMPS *); void grow(int) override; - void copy(int, int, int) override; - int pack_comm(int, int *, double *, int, int *) override; - int pack_comm_vel(int, int *, double *, int, int *) override; - void unpack_comm(int, int, double *) override; - void unpack_comm_vel(int, int, double *) override; - int pack_reverse(int, int, double *) override; - void unpack_reverse(int, int *, double *) override; - int pack_border(int, int *, double *, int, int *) override; - int pack_border_vel(int, int *, double *, int, int *) override; - int pack_border_hybrid(int, int *, double *) override; - void unpack_border(int, int, double *) override; - void unpack_border_vel(int, int, double *) override; - int unpack_border_hybrid(int, int, double *) override; - int pack_exchange(int, double *) override; - int unpack_exchange(double *) override; - int size_restart() override; - int pack_restart(int, double *) override; - int unpack_restart(double *) override; - void create_atom(int, double *) override; - void data_atom(double *, imageint, const std::vector &, std::string &) override; - int data_atom_hybrid(int, const std::vector &, int) override; - void pack_data(double **) override; - int pack_data_hybrid(int, double *) override; - void write_data(FILE *, int, double **) override; - int write_data_hybrid(FILE *, double *) override; - double memory_usage() override; - void grow_pointers() override; int pack_comm_kokkos(const int &n, const DAT::tdual_int_2d &k_sendlist, const int & iswap, @@ -89,21 +63,9 @@ class AtomVecAngleKokkos : public AtomVecKokkos { void sync_overlapping_device(ExecutionSpace space, unsigned int mask) override; protected: - - tagint *tag; - int *type,*mask; - imageint *image; - double **x,**v,**f; - tagint *molecule; - int **nspecial; tagint **special; - int *num_bond; - int **bond_type; tagint **bond_atom; - - int *num_angle; - int **angle_type; tagint **angle_atom1,**angle_atom2,**angle_atom3; DAT::t_tagint_1d d_tag; @@ -142,13 +104,9 @@ class AtomVecAngleKokkos : public AtomVecKokkos { HAT::t_int_1d h_num_angle; HAT::t_int_2d h_angle_type; HAT::t_tagint_2d h_angle_atom1,h_angle_atom2,h_angle_atom3; - - DAT::tdual_int_1d k_count; - }; -} +} // namespace LAMMPS_NS #endif #endif - diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.cpp b/src/KOKKOS/atom_vec_atomic_kokkos.cpp index e291c10c39..632383154a 100644 --- a/src/KOKKOS/atom_vec_atomic_kokkos.cpp +++ b/src/KOKKOS/atom_vec_atomic_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -27,23 +27,10 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -AtomVecAtomicKokkos::AtomVecAtomicKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) +AtomVecAtomicKokkos::AtomVecAtomicKokkos(LAMMPS *lmp) : AtomVec(lmp), +AtomVecKokkos(lmp), AtomVecAtomic(lmp) { - molecular = Atom::ATOMIC; - mass_type = PER_TYPE; - comm_x_only = comm_f_only = 1; - size_forward = 3; - size_reverse = 3; - size_border = 6; - size_velocity = 3; - size_data_atom = 5; - size_data_vel = 4; - xcol_data = 3; - - k_count = DAT::tdual_int_1d("atom::k_count",1); - atomKK = (AtomKokkos *) atom; - commKK = (CommKokkos *) comm; } /* ---------------------------------------------------------------------- @@ -113,28 +100,6 @@ void AtomVecAtomicKokkos::grow_pointers() h_f = atomKK->k_f.h_view; } -/* ---------------------------------------------------------------------- - copy atom I info to atom J -------------------------------------------------------------------------- */ - -void AtomVecAtomicKokkos::copy(int i, int j, int delflag) -{ - h_tag[j] = h_tag[i]; - h_type[j] = h_type[i]; - mask[j] = mask[i]; - h_image[j] = h_image[i]; - h_x(j,0) = h_x(i,0); - h_x(j,1) = h_x(i,1); - h_x(j,2) = h_x(i,2); - h_v(j,0) = h_v(i,0); - h_v(j,1) = h_v(i,1); - h_v(j,2) = h_v(i,2); - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag); -} - /* ---------------------------------------------------------------------- */ template @@ -232,130 +197,6 @@ int AtomVecAtomicKokkos::pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, /* ---------------------------------------------------------------------- */ -int AtomVecAtomicKokkos::pack_border(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz; - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]; - dy = pbc[1]; - dz = pbc[2]; - } - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - } - } - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); - - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecAtomicKokkos::pack_border_vel(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz,dvx,dvy,dvz; - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]; - dy = pbc[1]; - dz = pbc[2]; - } - if (!deform_vremap) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } else { - dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; - dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; - dvz = pbc[2]*h_rate[2]; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - if (mask[i] & deform_groupbit) { - buf[m++] = h_v(j,0) + dvx; - buf[m++] = h_v(j,1) + dvy; - buf[m++] = h_v(j,2) + dvz; - } else { - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } - } - } - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); - - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecAtomicKokkos_UnpackBorder { typedef DeviceType device_type; @@ -408,63 +249,6 @@ void AtomVecAtomicKokkos::unpack_border_kokkos(const int &n, const int &first, /* ---------------------------------------------------------------------- */ -void AtomVecAtomicKokkos::unpack_border(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - while (last > nmax) grow(0); - - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_tag(i) = (tagint) ubuf(buf[m++]).i; - h_type(i) = (int) ubuf(buf[m++]).i; - h_mask(i) = (int) ubuf(buf[m++]).i; - } - - atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK); - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]-> - unpack_border(n,first,&buf[m]); -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecAtomicKokkos::unpack_border_vel(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - while (last > nmax) grow(0); - - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_tag(i) = (tagint) ubuf(buf[m++]).i; - h_type(i) = (int) ubuf(buf[m++]).i; - h_mask(i) = (int) ubuf(buf[m++]).i; - h_v(i,0) = buf[m++]; - h_v(i,1) = buf[m++]; - h_v(i,2) = buf[m++]; - } - - atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|V_MASK); - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]-> - unpack_border(n,first,&buf[m]); -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecAtomicKokkos_PackExchangeFunctor { typedef DeviceType device_type; @@ -568,30 +352,6 @@ int AtomVecAtomicKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat /* ---------------------------------------------------------------------- */ -int AtomVecAtomicKokkos::pack_exchange(int i, double *buf) -{ - int m = 1; - buf[m++] = h_x(i,0); - buf[m++] = h_x(i,1); - buf[m++] = h_x(i,2); - buf[m++] = h_v(i,0); - buf[m++] = h_v(i,1); - buf[m++] = h_v(i,2); - buf[m++] = ubuf(h_tag(i)).d; - buf[m++] = ubuf(h_type(i)).d; - buf[m++] = ubuf(h_mask(i)).d; - buf[m++] = ubuf(h_image(i)).d; - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]); - - buf[0] = m; - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecAtomicKokkos_UnpackExchangeFunctor { typedef DeviceType device_type; @@ -671,238 +431,6 @@ int AtomVecAtomicKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int /* ---------------------------------------------------------------------- */ -int AtomVecAtomicKokkos::unpack_exchange(double *buf) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) grow(0); - atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK); - - int m = 1; - h_x(nlocal,0) = buf[m++]; - h_x(nlocal,1) = buf[m++]; - h_x(nlocal,2) = buf[m++]; - h_v(nlocal,0) = buf[m++]; - h_v(nlocal,1) = buf[m++]; - h_v(nlocal,2) = buf[m++]; - h_tag(nlocal) = (tagint) ubuf(buf[m++]).i; - h_type(nlocal) = (int) ubuf(buf[m++]).i; - h_mask(nlocal) = (int) ubuf(buf[m++]).i; - h_image(nlocal) = (imageint) ubuf(buf[m++]).i; - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - m += modify->fix[atom->extra_grow[iextra]]-> - unpack_exchange(nlocal,&buf[m]); - - atom->nlocal++; - return m; -} - -/* ---------------------------------------------------------------------- - size of restart data for all atoms owned by this proc - include extra data stored by fixes -------------------------------------------------------------------------- */ - -int AtomVecAtomicKokkos::size_restart() -{ - int i; - - int nlocal = atom->nlocal; - int n = 11 * nlocal; - - if (atom->nextra_restart) - for (int iextra = 0; iextra < atom->nextra_restart; iextra++) - for (i = 0; i < nlocal; i++) - n += modify->fix[atom->extra_restart[iextra]]->size_restart(i); - - return n; -} - -/* ---------------------------------------------------------------------- - pack atom I's data for restart file including extra quantities - xyz must be 1st 3 values, so that read_restart can test on them - molecular types may be negative, but write as positive -------------------------------------------------------------------------- */ - -int AtomVecAtomicKokkos::pack_restart(int i, double *buf) -{ - atomKK->sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK ); - - int m = 1; - buf[m++] = h_x(i,0); - buf[m++] = h_x(i,1); - buf[m++] = h_x(i,2); - buf[m++] = ubuf(h_tag(i)).d; - buf[m++] = ubuf(h_type(i)).d; - buf[m++] = ubuf(h_mask(i)).d; - buf[m++] = ubuf(h_image(i)).d; - buf[m++] = h_v(i,0); - buf[m++] = h_v(i,1); - buf[m++] = h_v(i,2); - - if (atom->nextra_restart) - for (int iextra = 0; iextra < atom->nextra_restart; iextra++) - m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]); - - buf[0] = m; - return m; -} - -/* ---------------------------------------------------------------------- - unpack data for one atom from restart file including extra quantities -------------------------------------------------------------------------- */ - -int AtomVecAtomicKokkos::unpack_restart(double *buf) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) { - grow(0); - if (atom->nextra_store) - memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra"); - } - atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK ); - - int m = 1; - h_x(nlocal,0) = buf[m++]; - h_x(nlocal,1) = buf[m++]; - h_x(nlocal,2) = buf[m++]; - h_tag(nlocal) = (tagint) ubuf(buf[m++]).i; - h_type(nlocal) = (int) ubuf(buf[m++]).i; - h_mask(nlocal) = (int) ubuf(buf[m++]).i; - h_image(nlocal) = (imageint) ubuf(buf[m++]).i; - h_v(nlocal,0) = buf[m++]; - h_v(nlocal,1) = buf[m++]; - h_v(nlocal,2) = buf[m++]; - - double **extra = atom->extra; - if (atom->nextra_store) { - int size = static_cast (buf[0]) - m; - for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++]; - } - - atom->nlocal++; - return m; -} - -/* ---------------------------------------------------------------------- - create one atom of itype at coord - set other values to defaults -------------------------------------------------------------------------- */ - -void AtomVecAtomicKokkos::create_atom(int itype, double *coord) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) { - //if(nlocal>2) printf("typeA: %i %i\n",type[0],type[1]); - atomKK->modified(Host,ALL_MASK); - grow(0); - //if(nlocal>2) printf("typeB: %i %i\n",type[0],type[1]); - } - atomKK->modified(Host,ALL_MASK); - - tag[nlocal] = 0; - type[nlocal] = itype; - h_x(nlocal,0) = coord[0]; - h_x(nlocal,1) = coord[1]; - h_x(nlocal,2) = coord[2]; - h_mask[nlocal] = 1; - h_image[nlocal] = ((tagint) IMGMAX << IMG2BITS) | - ((tagint) IMGMAX << IMGBITS) | IMGMAX; - h_v(nlocal,0) = 0.0; - h_v(nlocal,1) = 0.0; - h_v(nlocal,2) = 0.0; - - atom->nlocal++; -} - -/* ---------------------------------------------------------------------- - unpack one line from Atoms section of data file - initialize other atom quantities -------------------------------------------------------------------------- */ - -void AtomVecAtomicKokkos::data_atom(double *coord, imageint imagetmp, - const std::vector &values, std::string &extract) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) grow(0); - - h_tag[nlocal] = utils::inumeric(FLERR,values[0],true,lmp); - h_type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); - extract = values[1]; - if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) - error->one(FLERR,"Invalid atom type in Atoms section of data file"); - - h_x(nlocal,0) = coord[0]; - h_x(nlocal,1) = coord[1]; - h_x(nlocal,2) = coord[2]; - - h_image[nlocal] = imagetmp; - - h_mask[nlocal] = 1; - h_v(nlocal,0) = 0.0; - h_v(nlocal,1) = 0.0; - h_v(nlocal,2) = 0.0; - - atomKK->modified(Host,ALL_MASK); - - atom->nlocal++; -} - -/* ---------------------------------------------------------------------- - pack atom info for data file including 3 image flags -------------------------------------------------------------------------- */ - -void AtomVecAtomicKokkos::pack_data(double **buf) -{ - int nlocal = atom->nlocal; - for (int i = 0; i < nlocal; i++) { - buf[i][0] = h_tag[i]; - buf[i][1] = h_type[i]; - buf[i][2] = h_x(i,0); - buf[i][3] = h_x(i,1); - buf[i][4] = h_x(i,2); - buf[i][5] = (h_image[i] & IMGMASK) - IMGMAX; - buf[i][6] = (h_image[i] >> IMGBITS & IMGMASK) - IMGMAX; - buf[i][7] = (h_image[i] >> IMG2BITS) - IMGMAX; - } -} - -/* ---------------------------------------------------------------------- - write atom info to data file including 3 image flags -------------------------------------------------------------------------- */ - -void AtomVecAtomicKokkos::write_data(FILE *fp, int n, double **buf) -{ - for (int i = 0; i < n; i++) - fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %d %d %d\n", - (int) buf[i][0],(int) buf[i][1],buf[i][2],buf[i][3],buf[i][4], - (int) buf[i][5],(int) buf[i][6],(int) buf[i][7]); -} - -/* ---------------------------------------------------------------------- - return # of bytes of allocated memory -------------------------------------------------------------------------- */ - -double AtomVecAtomicKokkos::memory_usage() -{ - double bytes = 0; - - if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax); - if (atom->memcheck("type")) bytes += memory->usage(type,nmax); - if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax); - if (atom->memcheck("image")) bytes += memory->usage(image,nmax); - if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3); - if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3); - if (atom->memcheck("f")) bytes += memory->usage(f,nmax*commKK->nthreads,3); - - return bytes; -} - -/* ---------------------------------------------------------------------- */ - void AtomVecAtomicKokkos::sync(ExecutionSpace space, unsigned int mask) { if (space == Device) { @@ -983,4 +511,3 @@ void AtomVecAtomicKokkos::modified(ExecutionSpace space, unsigned int mask) if (mask & IMAGE_MASK) atomKK->k_image.modify(); } } - diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.h b/src/KOKKOS/atom_vec_atomic_kokkos.h index 410a0f66e2..83c311483e 100644 --- a/src/KOKKOS/atom_vec_atomic_kokkos.h +++ b/src/KOKKOS/atom_vec_atomic_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale AtomicKokkos/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,31 +24,16 @@ AtomStyle(atomic/kk/host,AtomVecAtomicKokkos); #define LMP_ATOM_VEC_ATOMIC_KOKKOS_H #include "atom_vec_kokkos.h" +#include "atom_vec_atomic.h" #include "kokkos_type.h" namespace LAMMPS_NS { -class AtomVecAtomicKokkos : public AtomVecKokkos { +class AtomVecAtomicKokkos : public AtomVecKokkos, public AtomVecAtomic { public: AtomVecAtomicKokkos(class LAMMPS *); void grow(int) override; - void copy(int, int, int) override; - int pack_border(int, int *, double *, int, int *) override; - int pack_border_vel(int, int *, double *, int, int *) override; - void unpack_border(int, int, double *) override; - void unpack_border_vel(int, int, double *) override; - int pack_exchange(int, double *) override; - int unpack_exchange(double *) override; - int size_restart() override; - int pack_restart(int, double *) override; - int unpack_restart(double *) override; - void create_atom(int, double *) override; - void data_atom(double *, imageint, const std::vector &, std::string &) override; - void pack_data(double **) override; - void write_data(FILE *, int, double **) override; - double memory_usage() override; - void grow_pointers() override; int pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, DAT::tdual_xfloat_2d buf,int iswap, @@ -70,11 +55,6 @@ class AtomVecAtomicKokkos : public AtomVecKokkos { void sync_overlapping_device(ExecutionSpace space, unsigned int mask) override; protected: - tagint *tag; - imageint *image; - int *type,*mask; - double **x,**v,**f; - DAT::t_tagint_1d d_tag; HAT::t_tagint_1d h_tag; DAT::t_imageint_1d d_image; @@ -85,8 +65,6 @@ class AtomVecAtomicKokkos : public AtomVecKokkos { DAT::t_x_array d_x; DAT::t_v_array d_v; DAT::t_f_array d_f; - - DAT::tdual_int_1d k_count; }; } diff --git a/src/KOKKOS/atom_vec_bond_kokkos.cpp b/src/KOKKOS/atom_vec_bond_kokkos.cpp index bc5db852ae..17419c7338 100644 --- a/src/KOKKOS/atom_vec_bond_kokkos.cpp +++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -27,26 +27,10 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -AtomVecBondKokkos::AtomVecBondKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) +AtomVecBondKokkos::AtomVecBondKokkos(LAMMPS *lmp) : AtomVec(lmp), +AtomVecKokkos(lmp), AtomVecBond(lmp) { - molecular = Atom::MOLECULAR; - bonds_allow = 1; - mass_type = PER_TYPE; - comm_x_only = comm_f_only = 1; - size_forward = 3; - size_reverse = 3; - size_border = 7; - size_velocity = 3; - size_data_atom = 6; - size_data_vel = 4; - xcol_data = 4; - - atom->molecule_flag = 1; - - k_count = DAT::tdual_int_1d("atom::k_count",1); - atomKK = (AtomKokkos *) atom; - commKK = (CommKokkos *) comm; } /* ---------------------------------------------------------------------- @@ -142,43 +126,6 @@ void AtomVecBondKokkos::grow_pointers() h_bond_atom = atomKK->k_bond_atom.h_view; } -/* ---------------------------------------------------------------------- - copy atom I info to atom J -------------------------------------------------------------------------- */ - -void AtomVecBondKokkos::copy(int i, int j, int delflag) -{ - int k; - - h_tag[j] = h_tag[i]; - h_type[j] = h_type[i]; - mask[j] = mask[i]; - h_image[j] = h_image[i]; - h_x(j,0) = h_x(i,0); - h_x(j,1) = h_x(i,1); - h_x(j,2) = h_x(i,2); - h_v(j,0) = h_v(i,0); - h_v(j,1) = h_v(i,1); - h_v(j,2) = h_v(i,2); - - h_molecule(j) = h_molecule(i); - - h_num_bond(j) = h_num_bond(i); - for (k = 0; k < h_num_bond(j); k++) { - h_bond_type(j,k) = h_bond_type(i,k); - h_bond_atom(j,k) = h_bond_atom(i,k); - } - - h_nspecial(j,0) = h_nspecial(i,0); - h_nspecial(j,1) = h_nspecial(i,1); - h_nspecial(j,2) = h_nspecial(i,2); - for (k = 0; k < h_nspecial(j,2); k++) h_special(j,k) = h_special(i,k); - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag); -} - /* ---------------------------------------------------------------------- */ template @@ -282,149 +229,6 @@ int AtomVecBondKokkos::pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, /* ---------------------------------------------------------------------- */ -int AtomVecBondKokkos::pack_border(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz; - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = ubuf(h_molecule(j)).d; - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]; - dy = pbc[1]; - dz = pbc[2]; - } - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = ubuf(h_molecule(j)).d; - } - } - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); - - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecBondKokkos::pack_border_vel(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz,dvx,dvy,dvz; - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = ubuf(h_molecule(j)).d; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]; - dy = pbc[1]; - dz = pbc[2]; - } - if (!deform_vremap) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = ubuf(h_molecule(j)).d; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } else { - dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; - dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; - dvz = pbc[2]*h_rate[2]; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = ubuf(h_molecule(j)).d; - if (mask[i] & deform_groupbit) { - buf[m++] = h_v(j,0) + dvx; - buf[m++] = h_v(j,1) + dvy; - buf[m++] = h_v(j,2) + dvz; - } else { - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } - } - } - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); - - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecBondKokkos::pack_border_hybrid(int n, int *list, double *buf) -{ - int i,j,m; - - m = 0; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_molecule(j); - } - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecBondKokkos_UnpackBorder { typedef DeviceType device_type; @@ -485,78 +289,6 @@ void AtomVecBondKokkos::unpack_border_kokkos(const int &n, const int &first, /* ---------------------------------------------------------------------- */ -void AtomVecBondKokkos::unpack_border(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - while (last > nmax) grow(0); - - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_tag(i) = (tagint) ubuf(buf[m++]).i; - h_type(i) = (int) ubuf(buf[m++]).i; - h_mask(i) = (int) ubuf(buf[m++]).i; - h_molecule(i) = (tagint) ubuf(buf[m++]).i; - } - - atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK); - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]-> - unpack_border(n,first,&buf[m]); -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecBondKokkos::unpack_border_vel(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - while (last > nmax) grow(0); - - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_tag(i) = (tagint) ubuf(buf[m++]).i; - h_type(i) = (int) ubuf(buf[m++]).i; - h_mask(i) = (int) ubuf(buf[m++]).i; - h_molecule(i) = (tagint) ubuf(buf[m++]).i; - h_v(i,0) = buf[m++]; - h_v(i,1) = buf[m++]; - h_v(i,2) = buf[m++]; - } - - atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK|V_MASK); - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]-> - unpack_border(n,first,&buf[m]); -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecBondKokkos::unpack_border_hybrid(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - for (i = first; i < last; i++) - h_molecule(i) = (tagint) ubuf(buf[m++]).i; - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecBondKokkos_PackExchangeFunctor { typedef DeviceType device_type; @@ -721,43 +453,6 @@ int AtomVecBondKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2 /* ---------------------------------------------------------------------- */ -int AtomVecBondKokkos::pack_exchange(int i, double *buf) -{ - int k; - int m = 1; - buf[m++] = h_x(i,0); - buf[m++] = h_x(i,1); - buf[m++] = h_x(i,2); - buf[m++] = h_v(i,0); - buf[m++] = h_v(i,1); - buf[m++] = h_v(i,2); - buf[m++] = ubuf(h_tag(i)).d; - buf[m++] = ubuf(h_type(i)).d; - buf[m++] = ubuf(h_mask(i)).d; - buf[m++] = ubuf(h_image(i)).d; - buf[m++] = ubuf(h_molecule(i)).d; - - buf[m++] = ubuf(h_num_bond(i)).d; - for (k = 0; k < h_num_bond(i); k++) { - buf[m++] = ubuf(h_bond_type(i,k)).d; - buf[m++] = ubuf(h_bond_atom(i,k)).d; - } - buf[m++] = ubuf(h_nspecial(i,0)).d; - buf[m++] = ubuf(h_nspecial(i,1)).d; - buf[m++] = ubuf(h_nspecial(i,2)).d; - for (k = 0; k < h_nspecial(i,2); k++) - buf[m++] = ubuf(h_special(i,k)).d; - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]); - - buf[0] = m; - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecBondKokkos_UnpackExchangeFunctor { typedef DeviceType device_type; @@ -870,321 +565,6 @@ int AtomVecBondKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int nr /* ---------------------------------------------------------------------- */ -int AtomVecBondKokkos::unpack_exchange(double *buf) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) grow(0); - atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | MOLECULE_MASK | BOND_MASK | SPECIAL_MASK); - - int k; - int m = 1; - h_x(nlocal,0) = buf[m++]; - h_x(nlocal,1) = buf[m++]; - h_x(nlocal,2) = buf[m++]; - h_v(nlocal,0) = buf[m++]; - h_v(nlocal,1) = buf[m++]; - h_v(nlocal,2) = buf[m++]; - h_tag(nlocal) = (tagint) ubuf(buf[m++]).i; - h_type(nlocal) = (int) ubuf(buf[m++]).i; - h_mask(nlocal) = (int) ubuf(buf[m++]).i; - h_image(nlocal) = (imageint) ubuf(buf[m++]).i; - h_molecule(nlocal) = (tagint) ubuf(buf[m++]).i; - - h_num_bond(nlocal) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_num_bond(nlocal); k++) { - h_bond_type(nlocal,k) = (int) ubuf(buf[m++]).i; - h_bond_atom(nlocal,k) = (tagint) ubuf(buf[m++]).i; - } - - h_nspecial(nlocal,0) = (int) ubuf(buf[m++]).i; - h_nspecial(nlocal,1) = (int) ubuf(buf[m++]).i; - h_nspecial(nlocal,2) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_nspecial(nlocal,2); k++) - h_special(nlocal,k) = (tagint) ubuf(buf[m++]).i; - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - m += modify->fix[atom->extra_grow[iextra]]-> - unpack_exchange(nlocal,&buf[m]); - - atom->nlocal++; - return m; -} - -/* ---------------------------------------------------------------------- - size of restart data for all atoms owned by this proc - include extra data stored by fixes -------------------------------------------------------------------------- */ - -int AtomVecBondKokkos::size_restart() -{ - int i; - - int nlocal = atom->nlocal; - int n = 0; - for (i = 0; i < nlocal; i++) - n += 13 + 2*h_num_bond[i]; - - if (atom->nextra_restart) - for (int iextra = 0; iextra < atom->nextra_restart; iextra++) - for (i = 0; i < nlocal; i++) - n += modify->fix[atom->extra_restart[iextra]]->size_restart(i); - - return n; -} - -/* ---------------------------------------------------------------------- - pack atom I's data for restart file including extra quantities - xyz must be 1st 3 values, so that read_restart can test on them - molecular types may be negative, but write as positive -------------------------------------------------------------------------- */ - -int AtomVecBondKokkos::pack_restart(int i, double *buf) -{ - atomKK->sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | MOLECULE_MASK | BOND_MASK | SPECIAL_MASK); - int m = 1; - buf[m++] = h_x(i,0); - buf[m++] = h_x(i,1); - buf[m++] = h_x(i,2); - buf[m++] = ubuf(h_tag(i)).d; - buf[m++] = ubuf(h_type(i)).d; - buf[m++] = ubuf(h_mask(i)).d; - buf[m++] = ubuf(h_image(i)).d; - buf[m++] = h_v(i,0); - buf[m++] = h_v(i,1); - buf[m++] = h_v(i,2); - - buf[m++] = ubuf(h_molecule(i)).d; - - buf[m++] = ubuf(h_num_bond(i)).d; - for (int k = 0; k < h_num_bond(i); k++) { - buf[m++] = ubuf(MAX(h_bond_type(i,k),-h_bond_type(i,k))).d; - buf[m++] = ubuf(h_bond_atom(i,k)).d; - } - - if (atom->nextra_restart) - for (int iextra = 0; iextra < atom->nextra_restart; iextra++) - m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]); - - buf[0] = m; - return m; -} - -/* ---------------------------------------------------------------------- - unpack data for one atom from restart file including extra quantities -------------------------------------------------------------------------- */ - -int AtomVecBondKokkos::unpack_restart(double *buf) -{ - int k; - - int nlocal = atom->nlocal; - if (nlocal == nmax) { - grow(0); - if (atom->nextra_store) - memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra"); - } - atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | MOLECULE_MASK | BOND_MASK | SPECIAL_MASK); - int m = 1; - h_x(nlocal,0) = buf[m++]; - h_x(nlocal,1) = buf[m++]; - h_x(nlocal,2) = buf[m++]; - h_tag(nlocal) = (tagint) ubuf(buf[m++]).i; - h_type(nlocal) = (int) ubuf(buf[m++]).i; - h_mask(nlocal) = (int) ubuf(buf[m++]).i; - h_image(nlocal) = (imageint) ubuf(buf[m++]).i; - h_v(nlocal,0) = buf[m++]; - h_v(nlocal,1) = buf[m++]; - h_v(nlocal,2) = buf[m++]; - - h_molecule(nlocal) = (tagint) ubuf(buf[m++]).i; - - h_num_bond(nlocal) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_num_bond(nlocal); k++) { - h_bond_type(nlocal,k) = (int) ubuf(buf[m++]).i; - h_bond_atom(nlocal,k) = (tagint) ubuf(buf[m++]).i; - } - - h_nspecial(nlocal,0) = h_nspecial(nlocal,1) = h_nspecial(nlocal,2) = 0; - - double **extra = atom->extra; - if (atom->nextra_store) { - int size = static_cast (buf[0]) - m; - for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++]; - } - - atom->nlocal++; - return m; -} - -/* ---------------------------------------------------------------------- - create one atom of itype at coord - set other values to defaults -------------------------------------------------------------------------- */ - -void AtomVecBondKokkos::create_atom(int itype, double *coord) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) { - atomKK->modified(Host,ALL_MASK); - grow(0); - } - atomKK->modified(Host,ALL_MASK); - - tag[nlocal] = 0; - type[nlocal] = itype; - h_x(nlocal,0) = coord[0]; - h_x(nlocal,1) = coord[1]; - h_x(nlocal,2) = coord[2]; - h_mask(nlocal) = 1; - h_image(nlocal) = ((imageint) IMGMAX << IMG2BITS) | - ((imageint) IMGMAX << IMGBITS) | IMGMAX; - h_v(nlocal,0) = 0.0; - h_v(nlocal,1) = 0.0; - h_v(nlocal,2) = 0.0; - - h_molecule(nlocal) = 0; - h_num_bond(nlocal) = 0; - h_nspecial(nlocal,0) = h_nspecial(nlocal,1) = h_nspecial(nlocal,2) = 0; - - atom->nlocal++; -} - -/* ---------------------------------------------------------------------- - unpack one line from Atoms section of data file - initialize other atom quantities -------------------------------------------------------------------------- */ - -void AtomVecBondKokkos::data_atom(double *coord, imageint imagetmp, - const std::vector &values, std::string &extract) -{ - int nlocal = atomKK->nlocal; - if (nlocal == nmax) grow(0); - atomKK->modified(Host,ALL_MASK); - - h_tag(nlocal) = utils::inumeric(FLERR,values[0],true,lmp); - h_molecule(nlocal) = utils::inumeric(FLERR,values[1],true,lmp); - h_type(nlocal) = utils::inumeric(FLERR,values[2],true,lmp); - extract = values[2]; - if (h_type(nlocal) <= 0 || h_type(nlocal) > atom->ntypes) - error->one(FLERR,"Invalid atom type in Atoms section of data file"); - - h_x(nlocal,0) = coord[0]; - h_x(nlocal,1) = coord[1]; - h_x(nlocal,2) = coord[2]; - - h_image(nlocal) = imagetmp; - - h_mask(nlocal) = 1; - h_v(nlocal,0) = 0.0; - h_v(nlocal,1) = 0.0; - h_v(nlocal,2) = 0.0; - h_num_bond(nlocal) = 0; - - atomKK->nlocal++; -} - -/* ---------------------------------------------------------------------- - unpack hybrid quantities from one line in Atoms section of data file - initialize other atom quantities for this sub-style -------------------------------------------------------------------------- */ - -int AtomVecBondKokkos::data_atom_hybrid(int nlocal, const std::vector &values, - int offset) -{ - h_molecule(nlocal) = utils::inumeric(FLERR,values[offset],true,lmp); - h_num_bond(nlocal) = 0; - return 1; -} - -/* ---------------------------------------------------------------------- - pack atom info for data file including 3 image flags -------------------------------------------------------------------------- */ - -void AtomVecBondKokkos::pack_data(double **buf) -{ - int nlocal = atom->nlocal; - for (int i = 0; i < nlocal; i++) { - buf[i][0] = h_tag(i); - buf[i][1] = h_molecule(i); - buf[i][2] = h_type(i); - buf[i][3] = h_x(i,0); - buf[i][4] = h_x(i,1); - buf[i][5] = h_x(i,2); - buf[i][6] = (h_image[i] & IMGMASK) - IMGMAX; - buf[i][7] = (h_image[i] >> IMGBITS & IMGMASK) - IMGMAX; - buf[i][8] = (h_image[i] >> IMG2BITS) - IMGMAX; - } -} - -/* ---------------------------------------------------------------------- - pack hybrid atom info for data file -------------------------------------------------------------------------- */ - -int AtomVecBondKokkos::pack_data_hybrid(int i, double *buf) -{ - buf[0] = h_molecule(i); - return 1; -} - -/* ---------------------------------------------------------------------- - write atom info to data file including 3 image flags -------------------------------------------------------------------------- */ - -void AtomVecBondKokkos::write_data(FILE *fp, int n, double **buf) -{ - for (int i = 0; i < n; i++) - fprintf(fp,"%d %d %d %-1.16e %-1.16e %-1.16e %d %d %d\n", - (int) buf[i][0],(int) buf[i][1], (int) buf[i][2], - buf[i][3],buf[i][4],buf[i][5], - (int) buf[i][6],(int) buf[i][7],(int) buf[i][8]); -} - -/* ---------------------------------------------------------------------- - write hybrid atom info to data file -------------------------------------------------------------------------- */ - -int AtomVecBondKokkos::write_data_hybrid(FILE *fp, double *buf) -{ - fprintf(fp," " TAGINT_FORMAT, (tagint) (buf[0])); - return 1; -} - -/* ---------------------------------------------------------------------- - return # of bytes of allocated memory -------------------------------------------------------------------------- */ - -double AtomVecBondKokkos::memory_usage() -{ - double bytes = 0; - - if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax); - if (atom->memcheck("type")) bytes += memory->usage(type,nmax); - if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax); - if (atom->memcheck("image")) bytes += memory->usage(image,nmax); - if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3); - if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3); - if (atom->memcheck("f")) bytes += memory->usage(f,nmax*commKK->nthreads,3); - - if (atom->memcheck("molecule")) bytes += memory->usage(molecule,nmax); - if (atom->memcheck("nspecial")) bytes += memory->usage(nspecial,nmax,3); - if (atom->memcheck("special")) - bytes += memory->usage(special,nmax,atom->maxspecial); - - if (atom->memcheck("num_bond")) bytes += memory->usage(num_bond,nmax); - if (atom->memcheck("bond_type")) - bytes += memory->usage(bond_type,nmax,atom->bond_per_atom); - if (atom->memcheck("bond_atom")) - bytes += memory->usage(bond_atom,nmax,atom->bond_per_atom); - - return bytes; -} - -/* ---------------------------------------------------------------------- */ - void AtomVecBondKokkos::sync(ExecutionSpace space, unsigned int mask) { if (space == Device) { @@ -1337,4 +717,3 @@ void AtomVecBondKokkos::modified(ExecutionSpace space, unsigned int mask) } } } - diff --git a/src/KOKKOS/atom_vec_bond_kokkos.h b/src/KOKKOS/atom_vec_bond_kokkos.h index 573438ed41..82c50f7d0d 100644 --- a/src/KOKKOS/atom_vec_bond_kokkos.h +++ b/src/KOKKOS/atom_vec_bond_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,35 +24,15 @@ AtomStyle(bond/kk/host,AtomVecBondKokkos); #define LMP_ATOM_VEC_BOND_KOKKOS_H #include "atom_vec_kokkos.h" +#include "atom_vec_bond.h" namespace LAMMPS_NS { -class AtomVecBondKokkos : public AtomVecKokkos { +class AtomVecBondKokkos : public AtomVecKokkos, public AtomVecBond { public: AtomVecBondKokkos(class LAMMPS *); void grow(int) override; - void copy(int, int, int) override; - int pack_border(int, int *, double *, int, int *) override; - int pack_border_vel(int, int *, double *, int, int *) override; - int pack_border_hybrid(int, int *, double *) override; - void unpack_border(int, int, double *) override; - void unpack_border_vel(int, int, double *) override; - int unpack_border_hybrid(int, int, double *) override; - int pack_exchange(int, double *) override; - int unpack_exchange(double *) override; - int size_restart() override; - int pack_restart(int, double *) override; - int unpack_restart(double *) override; - void create_atom(int, double *) override; - void data_atom(double *, imageint, const std::vector &, std::string &) override; - int data_atom_hybrid(int, const std::vector &, int) override; - void pack_data(double **) override; - int pack_data_hybrid(int, double *) override; - void write_data(FILE *, int, double **) override; - int write_data_hybrid(FILE *, double *) override; - double memory_usage() override; - void grow_pointers() override; int pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, DAT::tdual_xfloat_2d buf,int iswap, @@ -73,18 +53,9 @@ class AtomVecBondKokkos : public AtomVecKokkos { void modified(ExecutionSpace space, unsigned int mask) override; void sync_overlapping_device(ExecutionSpace space, unsigned int mask) override; - protected: - - tagint *tag; - int *type,*mask; - imageint *image; - double **x,**v,**f; - + private: tagint *molecule; - int **nspecial; tagint **special; - int *num_bond; - int **bond_type; tagint **bond_atom; DAT::t_tagint_1d d_tag; @@ -112,9 +83,6 @@ class AtomVecBondKokkos : public AtomVecKokkos { HAT::t_int_1d h_num_bond; HAT::t_int_2d h_bond_type; HAT::t_tagint_2d h_bond_atom; - - DAT::tdual_int_1d k_count; - }; } diff --git a/src/KOKKOS/atom_vec_charge_kokkos.cpp b/src/KOKKOS/atom_vec_charge_kokkos.cpp index 0cf39938d9..66520652be 100644 --- a/src/KOKKOS/atom_vec_charge_kokkos.cpp +++ b/src/KOKKOS/atom_vec_charge_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -27,25 +27,9 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -AtomVecChargeKokkos::AtomVecChargeKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) +AtomVecChargeKokkos::AtomVecChargeKokkos(LAMMPS *lmp) : AtomVec(lmp), +AtomVecKokkos(lmp), AtomVecCharge(lmp) { - molecular = Atom::ATOMIC; - mass_type = PER_TYPE; - - comm_x_only = comm_f_only = 1; - size_forward = 3; - size_reverse = 3; - size_border = 7; - size_velocity = 3; - size_data_atom = 6; - size_data_vel = 4; - xcol_data = 4; - - atom->q_flag = 1; - - k_count = DAT::tdual_int_1d("atom::k_count",1); - atomKK = (AtomKokkos *) atom; - commKK = (CommKokkos *) comm; } @@ -123,30 +107,6 @@ void AtomVecChargeKokkos::grow_pointers() } -/* ---------------------------------------------------------------------- - copy atom I info to atom J -------------------------------------------------------------------------- */ - -void AtomVecChargeKokkos::copy(int i, int j, int delflag) -{ - h_tag[j] = h_tag[i]; - h_type[j] = h_type[i]; - mask[j] = mask[i]; - h_image[j] = h_image[i]; - h_x(j,0) = h_x(i,0); - h_x(j,1) = h_x(i,1); - h_x(j,2) = h_x(i,2); - h_v(j,0) = h_v(i,0); - h_v(j,1) = h_v(i,1); - h_v(j,2) = h_v(i,2); - - h_q[j] = h_q[i]; - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag); -} - /* ---------------------------------------------------------------------- */ template @@ -297,150 +257,6 @@ int AtomVecChargeKokkos::pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, return n*size_border; } -/* ---------------------------------------------------------------------- */ - -int AtomVecChargeKokkos::pack_border(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz; - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = h_q(j); - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]; - dy = pbc[1]; - dz = pbc[2]; - } - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = h_q(j); - } - } - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); - - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecChargeKokkos::pack_border_vel(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz,dvx,dvy,dvz; - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = h_q[j]; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]; - dy = pbc[1]; - dz = pbc[2]; - } - if (!deform_vremap) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = h_q[j]; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } else { - dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; - dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; - dvz = pbc[2]*h_rate[2]; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = h_q[j]; - if (mask[i] & deform_groupbit) { - buf[m++] = h_v(j,0) + dvx; - buf[m++] = h_v(j,1) + dvy; - buf[m++] = h_v(j,2) + dvz; - } else { - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } - } - } - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); - - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecChargeKokkos::pack_border_hybrid(int n, int *list, double *buf) -{ - int i,j,m; - - m = 0; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_q[j]; - } - return m; -} - - /* ---------------------------------------------------------------------- */ template @@ -500,78 +316,6 @@ void AtomVecChargeKokkos::unpack_border_kokkos(const int &n, const int &first, /* ---------------------------------------------------------------------- */ -void AtomVecChargeKokkos::unpack_border(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - while (last > nmax) grow(0); - - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_tag(i) = (tagint) ubuf(buf[m++]).i; - h_type(i) = (int) ubuf(buf[m++]).i; - h_mask(i) = (int) ubuf(buf[m++]).i; - h_q[i] = buf[m++]; - } - - atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|Q_MASK); - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]-> - unpack_border(n,first,&buf[m]); -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecChargeKokkos::unpack_border_vel(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - while (last > nmax) grow(0); - - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_tag(i) = (tagint) ubuf(buf[m++]).i; - h_type(i) = (int) ubuf(buf[m++]).i; - h_mask(i) = (int) ubuf(buf[m++]).i; - h_q[i] = buf[m++]; - h_v(i,0) = buf[m++]; - h_v(i,1) = buf[m++]; - h_v(i,2) = buf[m++]; - } - - atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|Q_MASK|V_MASK); - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]-> - unpack_border(n,first,&buf[m]); -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecChargeKokkos::unpack_border_hybrid(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - for (i = first; i < last; i++) - h_q[i] = buf[m++]; - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecChargeKokkos_PackExchangeFunctor { typedef DeviceType device_type; @@ -688,31 +432,6 @@ int AtomVecChargeKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat /* ---------------------------------------------------------------------- */ -int AtomVecChargeKokkos::pack_exchange(int i, double *buf) -{ - int m = 1; - buf[m++] = h_x(i,0); - buf[m++] = h_x(i,1); - buf[m++] = h_x(i,2); - buf[m++] = h_v(i,0); - buf[m++] = h_v(i,1); - buf[m++] = h_v(i,2); - buf[m++] = ubuf(h_tag(i)).d; - buf[m++] = ubuf(h_type(i)).d; - buf[m++] = ubuf(h_mask(i)).d; - buf[m++] = ubuf(h_image(i)).d; - buf[m++] = h_q[i]; - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]); - - buf[0] = m; - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecChargeKokkos_UnpackExchangeFunctor { typedef DeviceType device_type; @@ -797,281 +516,6 @@ int AtomVecChargeKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int /* ---------------------------------------------------------------------- */ -int AtomVecChargeKokkos::unpack_exchange(double *buf) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) grow(0); - atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | Q_MASK); - - int m = 1; - h_x(nlocal,0) = buf[m++]; - h_x(nlocal,1) = buf[m++]; - h_x(nlocal,2) = buf[m++]; - h_v(nlocal,0) = buf[m++]; - h_v(nlocal,1) = buf[m++]; - h_v(nlocal,2) = buf[m++]; - h_tag(nlocal) = (tagint) ubuf(buf[m++]).i; - h_type(nlocal) = (int) ubuf(buf[m++]).i; - h_mask(nlocal) = (int) ubuf(buf[m++]).i; - h_image(nlocal) = (imageint) ubuf(buf[m++]).i; - h_q[nlocal] = buf[m++]; - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - m += modify->fix[atom->extra_grow[iextra]]-> - unpack_exchange(nlocal,&buf[m]); - - atom->nlocal++; - return m; -} - -/* ---------------------------------------------------------------------- - size of restart data for all atoms owned by this proc - include extra data stored by fixes -------------------------------------------------------------------------- */ - -int AtomVecChargeKokkos::size_restart() -{ - int i; - - int nlocal = atom->nlocal; - int n = 12 * nlocal; - - if (atom->nextra_restart) - for (int iextra = 0; iextra < atom->nextra_restart; iextra++) - for (i = 0; i < nlocal; i++) - n += modify->fix[atom->extra_restart[iextra]]->size_restart(i); - - return n; -} - -/* ---------------------------------------------------------------------- - pack atom I's data for restart file including extra quantities - xyz must be 1st 3 values, so that read_restart can test on them - molecular types may be negative, but write as positive -------------------------------------------------------------------------- */ - -int AtomVecChargeKokkos::pack_restart(int i, double *buf) -{ - atomKK->sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | Q_MASK); - - int m = 1; - buf[m++] = h_x(i,0); - buf[m++] = h_x(i,1); - buf[m++] = h_x(i,2); - buf[m++] = ubuf(h_tag(i)).d; - buf[m++] = ubuf(h_type(i)).d; - buf[m++] = ubuf(h_mask(i)).d; - buf[m++] = ubuf(h_image(i)).d; - buf[m++] = h_v(i,0); - buf[m++] = h_v(i,1); - buf[m++] = h_v(i,2); - - buf[m++] = h_q[i]; - - if (atom->nextra_restart) - for (int iextra = 0; iextra < atom->nextra_restart; iextra++) - m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]); - - buf[0] = m; - return m; -} - -/* ---------------------------------------------------------------------- - unpack data for one atom from restart file including extra quantities -------------------------------------------------------------------------- */ - -int AtomVecChargeKokkos::unpack_restart(double *buf) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) { - grow(0); - if (atom->nextra_store) - memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra"); - } - - atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | Q_MASK); - - int m = 1; - h_x(nlocal,0) = buf[m++]; - h_x(nlocal,1) = buf[m++]; - h_x(nlocal,2) = buf[m++]; - h_tag(nlocal) = (tagint) ubuf(buf[m++]).i; - h_type(nlocal) = (int) ubuf(buf[m++]).i; - h_mask(nlocal) = (int) ubuf(buf[m++]).i; - h_image(nlocal) = (imageint) ubuf(buf[m++]).i; - h_v(nlocal,0) = buf[m++]; - h_v(nlocal,1) = buf[m++]; - h_v(nlocal,2) = buf[m++]; - - h_q[nlocal] = buf[m++]; - - double **extra = atom->extra; - if (atom->nextra_store) { - int size = static_cast (buf[0]) - m; - for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++]; - } - - atom->nlocal++; - return m; -} - -/* ---------------------------------------------------------------------- - create one atom of itype at coord - set other values to defaults -------------------------------------------------------------------------- */ - -void AtomVecChargeKokkos::create_atom(int itype, double *coord) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) { - atomKK->modified(Host,ALL_MASK); - grow(0); - } - atomKK->sync(Host,ALL_MASK); - atomKK->modified(Host,ALL_MASK); - - tag[nlocal] = 0; - type[nlocal] = itype; - h_x(nlocal,0) = coord[0]; - h_x(nlocal,1) = coord[1]; - h_x(nlocal,2) = coord[2]; - h_mask[nlocal] = 1; - h_image[nlocal] = ((imageint) IMGMAX << IMG2BITS) | - ((imageint) IMGMAX << IMGBITS) | IMGMAX; - h_v(nlocal,0) = 0.0; - h_v(nlocal,1) = 0.0; - h_v(nlocal,2) = 0.0; - - h_q[nlocal] = 0.0; - - atom->nlocal++; -} - -/* ---------------------------------------------------------------------- - unpack one line from Atoms section of data file - initialize other atom quantities -------------------------------------------------------------------------- */ - -void AtomVecChargeKokkos::data_atom(double *coord, imageint imagetmp, - const std::vector &values, std::string &extract) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) grow(0); - - h_tag[nlocal] = utils::inumeric(FLERR,values[0],true,lmp); - h_type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); - extract = values[1]; - if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) - error->one(FLERR,"Invalid atom type in Atoms section of data file"); - - h_q[nlocal] = utils::numeric(FLERR,values[2],true,lmp); - - h_x(nlocal,0) = coord[0]; - h_x(nlocal,1) = coord[1]; - h_x(nlocal,2) = coord[2]; - - h_image[nlocal] = imagetmp; - - h_mask[nlocal] = 1; - h_v(nlocal,0) = 0.0; - h_v(nlocal,1) = 0.0; - h_v(nlocal,2) = 0.0; - - atomKK->modified(Host,ALL_MASK); - - atom->nlocal++; -} -/* ---------------------------------------------------------------------- - unpack hybrid quantities from one line in Atoms section of data file - initialize other atom quantities for this sub-style -------------------------------------------------------------------------- */ - -int AtomVecChargeKokkos::data_atom_hybrid(int nlocal, const std::vector &values, - int offset) -{ - h_q[nlocal] = utils::numeric(FLERR,values[offset],true,lmp); - - return 1; -} -/* ---------------------------------------------------------------------- - pack atom info for data file including 3 image flags -------------------------------------------------------------------------- */ - -void AtomVecChargeKokkos::pack_data(double **buf) -{ - int nlocal = atom->nlocal; - for (int i = 0; i < nlocal; i++) { - buf[i][0] = h_tag[i]; - buf[i][1] = h_type[i]; - buf[i][2] = h_q[i]; - buf[i][3] = h_x(i,0); - buf[i][4] = h_x(i,1); - buf[i][5] = h_x(i,2); - buf[i][6] = (h_image[i] & IMGMASK) - IMGMAX; - buf[i][7] = (h_image[i] >> IMGBITS & IMGMASK) - IMGMAX; - buf[i][8] = (h_image[i] >> IMG2BITS) - IMGMAX; - } -} - -/* ---------------------------------------------------------------------- - pack hybrid atom info for data file -------------------------------------------------------------------------- */ - -int AtomVecChargeKokkos::pack_data_hybrid(int i, double *buf) -{ - buf[0] = h_q[i]; - return 1; -} - -/* ---------------------------------------------------------------------- - write atom info to data file including 3 image flags -------------------------------------------------------------------------- */ - -void AtomVecChargeKokkos::write_data(FILE *fp, int n, double **buf) -{ - for (int i = 0; i < n; i++) - fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n", - (int) buf[i][0],(int) buf[i][1],buf[i][2],buf[i][3],buf[i][4],buf[i][5], - (int) buf[i][6],(int) buf[i][7],(int) buf[i][8]); -} - -/* ---------------------------------------------------------------------- - write hybrid atom info to data file -------------------------------------------------------------------------- */ - -int AtomVecChargeKokkos::write_data_hybrid(FILE *fp, double *buf) -{ - fprintf(fp," %-1.16e",buf[0]); - return 1; -} - -/* ---------------------------------------------------------------------- - return # of bytes of allocated memory -------------------------------------------------------------------------- */ - -double AtomVecChargeKokkos::memory_usage() -{ - double bytes = 0; - - if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax); - if (atom->memcheck("type")) bytes += memory->usage(type,nmax); - if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax); - if (atom->memcheck("image")) bytes += memory->usage(image,nmax); - if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3); - if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3); - if (atom->memcheck("f")) bytes += memory->usage(f,nmax*commKK->nthreads,3); - - if (atom->memcheck("q")) bytes += memory->usage(q,nmax); - - return bytes; -} - -/* ---------------------------------------------------------------------- */ - void AtomVecChargeKokkos::sync(ExecutionSpace space, unsigned int mask) { if (space == Device) { @@ -1120,6 +564,8 @@ void AtomVecChargeKokkos::modified(ExecutionSpace space, unsigned int mask) } } +/* ---------------------------------------------------------------------- */ + void AtomVecChargeKokkos::sync_overlapping_device(ExecutionSpace space, unsigned int mask) { if (space == Device) { @@ -1158,4 +604,3 @@ void AtomVecChargeKokkos::sync_overlapping_device(ExecutionSpace space, unsigned perform_async_copy(atomKK->k_q,space); } } - diff --git a/src/KOKKOS/atom_vec_charge_kokkos.h b/src/KOKKOS/atom_vec_charge_kokkos.h index 10b482fca5..556d03fedd 100644 --- a/src/KOKKOS/atom_vec_charge_kokkos.h +++ b/src/KOKKOS/atom_vec_charge_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,36 +24,16 @@ AtomStyle(charge/kk/host,AtomVecChargeKokkos); #define LMP_ATOM_VEC_CHARGE_KOKKOS_H #include "atom_vec_kokkos.h" +#include "atom_vec_charge.h" #include "kokkos_type.h" namespace LAMMPS_NS { -class AtomVecChargeKokkos : public AtomVecKokkos { +class AtomVecChargeKokkos : public AtomVecKokkos, public AtomVecCharge { public: AtomVecChargeKokkos(class LAMMPS *); void grow(int) override; - void copy(int, int, int) override; - int pack_border(int, int *, double *, int, int *) override; - int pack_border_vel(int, int *, double *, int, int *) override; - int pack_border_hybrid(int, int *, double *) override; - void unpack_border(int, int, double *) override; - void unpack_border_vel(int, int, double *) override; - int unpack_border_hybrid(int, int, double *) override; - int pack_exchange(int, double *) override; - int unpack_exchange(double *) override; - int size_restart() override; - int pack_restart(int, double *) override; - int unpack_restart(double *) override; - void create_atom(int, double *) override; - void data_atom(double *, imageint, const std::vector &, std::string &) override; - int data_atom_hybrid(int , const std::vector &, int) override; - void pack_data(double **) override; - int pack_data_hybrid(int, double *) override; - void write_data(FILE *, int, double **) override; - int write_data_hybrid(FILE *, double *) override; - double memory_usage() override; - void grow_pointers() override; int pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, DAT::tdual_xfloat_2d buf,int iswap, @@ -75,11 +55,6 @@ class AtomVecChargeKokkos : public AtomVecKokkos { void sync_overlapping_device(ExecutionSpace space, unsigned int mask) override; protected: - tagint *tag; - int *type,*mask; - imageint *image; - double **x,**v,**f; - double *q; DAT::t_tagint_1d d_tag; @@ -98,12 +73,9 @@ class AtomVecChargeKokkos : public AtomVecKokkos { DAT::t_float_1d d_q; HAT::t_float_1d h_q; - - DAT::tdual_int_1d k_count; }; -} +} // namespace LAMMPS_NS #endif #endif - diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp index 9176de6a67..7bf54445e0 100644 --- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp +++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -27,27 +27,9 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -AtomVecDPDKokkos::AtomVecDPDKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) +AtomVecDPDKokkos::AtomVecDPDKokkos(LAMMPS *lmp) : AtomVec(lmp), +AtomVecKokkos(lmp), AtomVecDPD(lmp) { - molecular = Atom::ATOMIC; - mass_type = PER_TYPE; - - comm_x_only = comm_f_only = 0; - size_forward = 7; - size_reverse = 3; - size_border = 12; - size_velocity = 3; - size_data_atom = 6; - size_data_vel = 4; - xcol_data = 4; - - atom->rho_flag = 1; - atom->dpd_flag = 1; - - k_count = DAT::tdual_int_1d("atom::k_count",1); - atomKK = (AtomKokkos *) atom; - commKK = (CommKokkos *) comm; - no_comm_vel_flag = 1; } @@ -153,44 +135,6 @@ void AtomVecDPDKokkos::grow_pointers() h_duChem = atomKK->k_duChem.h_view; } -/* ---------------------------------------------------------------------- - copy atom I info to atom J -------------------------------------------------------------------------- */ - -void AtomVecDPDKokkos::copy(int i, int j, int delflag) -{ - atomKK->sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | DPDTHETA_MASK | - UCG_MASK | UCGNEW_MASK | - UCOND_MASK | UMECH_MASK | UCHEM_MASK | DVECTOR_MASK); - - h_tag[j] = h_tag[i]; - h_type[j] = h_type[i]; - mask[j] = mask[i]; - h_image[j] = h_image[i]; - h_x(j,0) = h_x(i,0); - h_x(j,1) = h_x(i,1); - h_x(j,2) = h_x(i,2); - h_v(j,0) = h_v(i,0); - h_v(j,1) = h_v(i,1); - h_v(j,2) = h_v(i,2); - h_dpdTheta[j] = h_dpdTheta[i]; - h_uCond[j] = h_uCond[i]; - h_uMech[j] = h_uMech[i]; - h_uChem[j] = h_uChem[i]; - h_uCG[j] = h_uCG[i]; - h_uCGnew[j] = h_uCGnew[i]; - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag); - - atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | DPDTHETA_MASK | - UCG_MASK | UCGNEW_MASK | - UCOND_MASK | UMECH_MASK | UCHEM_MASK | DVECTOR_MASK); -} - /* ---------------------------------------------------------------------- */ template @@ -547,209 +491,6 @@ void AtomVecDPDKokkos::unpack_comm_kokkos(const int &n, const int &first, /* ---------------------------------------------------------------------- */ -int AtomVecDPDKokkos::pack_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz; - - atomKK->sync(Host,X_MASK|DPDTHETA_MASK|UCOND_MASK|UMECH_MASK|UCHEM_MASK); - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = h_dpdTheta[j]; - buf[m++] = h_uCond[j]; - buf[m++] = h_uMech[j]; - buf[m++] = h_uChem[j]; - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; - dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; - dz = pbc[2]*domain->zprd; - } - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = h_dpdTheta[j]; - buf[m++] = h_uCond[j]; - buf[m++] = h_uMech[j]; - buf[m++] = h_uChem[j]; - } - } - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecDPDKokkos::pack_comm_vel(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz,dvx,dvy,dvz; - - atomKK->sync(Host,X_MASK|V_MASK|DPDTHETA_MASK|UCOND_MASK|UMECH_MASK|UCHEM_MASK); - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - buf[m++] = h_dpdTheta[j]; - buf[m++] = h_uCond[j]; - buf[m++] = h_uMech[j]; - buf[m++] = h_uChem[j]; - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; - dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; - dz = pbc[2]*domain->zprd; - } - if (!deform_vremap) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - buf[m++] = h_dpdTheta[j]; - buf[m++] = h_uCond[j]; - buf[m++] = h_uMech[j]; - buf[m++] = h_uChem[j]; - } - } else { - dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; - dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; - dvz = pbc[2]*h_rate[2]; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - if (mask[i] & deform_groupbit) { - buf[m++] = h_v(j,0) + dvx; - buf[m++] = h_v(j,1) + dvy; - buf[m++] = h_v(j,2) + dvz; - } else { - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - buf[m++] = h_dpdTheta(j); - buf[m++] = h_uCond(j); - buf[m++] = h_uMech(j); - buf[m++] = h_uChem(j); - } - } - } - return m; -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecDPDKokkos::unpack_comm(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_dpdTheta[i] = buf[m++]; - h_uCond[i] = buf[m++]; - h_uMech[i] = buf[m++]; - h_uChem[i] = buf[m++]; - } - - atomKK->modified(Host,X_MASK|DPDTHETA_MASK|UCOND_MASK|UMECH_MASK|UCHEM_MASK); -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecDPDKokkos::unpack_comm_vel(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_v(i,0) = buf[m++]; - h_v(i,1) = buf[m++]; - h_v(i,2) = buf[m++]; - h_dpdTheta[i] = buf[m++]; - h_uCond[i] = buf[m++]; - h_uMech[i] = buf[m++]; - h_uChem[i] = buf[m++]; - } - - atomKK->modified(Host,X_MASK|V_MASK|DPDTHETA_MASK|UCOND_MASK|UMECH_MASK|UCHEM_MASK); -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecDPDKokkos::pack_reverse(int n, int first, double *buf) -{ - if (n > 0) - atomKK->sync(Host,F_MASK); - - int m = 0; - const int last = first + n; - for (int i = first; i < last; i++) { - buf[m++] = h_f(i,0); - buf[m++] = h_f(i,1); - buf[m++] = h_f(i,2); - } - return m; -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecDPDKokkos::unpack_reverse(int n, int *list, double *buf) -{ - if (n > 0) { - atomKK->sync(Host,F_MASK); - atomKK->modified(Host,F_MASK); - } - - int m = 0; - for (int i = 0; i < n; i++) { - const int j = list[i]; - h_f(j,0) += buf[m++]; - h_f(j,1) += buf[m++]; - h_f(j,2) += buf[m++]; - } -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecDPDKokkos_PackBorder { typedef DeviceType device_type; @@ -871,206 +612,6 @@ int AtomVecDPDKokkos::pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, DA /* ---------------------------------------------------------------------- */ -int AtomVecDPDKokkos::pack_border(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz; - - atomKK->sync(Host,ALL_MASK); - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = h_dpdTheta(j); - buf[m++] = h_uCond(j); - buf[m++] = h_uMech(j); - buf[m++] = h_uChem(j); - buf[m++] = h_uCG(j); - buf[m++] = h_uCGnew(j); - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]; - dy = pbc[1]; - dz = pbc[2]; - } - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = h_dpdTheta(j); - buf[m++] = h_uCond(j); - buf[m++] = h_uMech(j); - buf[m++] = h_uChem(j); - buf[m++] = h_uCG(j); - buf[m++] = h_uCGnew(j); - } - } - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); - - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecDPDKokkos::pack_border_vel(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz,dvx,dvy,dvz; - - atomKK->sync(Host,ALL_MASK); - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - buf[m++] = h_dpdTheta(j); - buf[m++] = h_uCond(j); - buf[m++] = h_uMech(j); - buf[m++] = h_uChem(j); - buf[m++] = h_uCG(j); - buf[m++] = h_uCGnew(j); - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]; - dy = pbc[1]; - dz = pbc[2]; - } - if (!deform_vremap) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - buf[m++] = h_dpdTheta(j); - buf[m++] = h_uCond(j); - buf[m++] = h_uMech(j); - buf[m++] = h_uChem(j); - buf[m++] = h_uCG(j); - buf[m++] = h_uCGnew(j); - } - } else { - dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; - dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; - dvz = pbc[2]*h_rate[2]; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - if (mask[i] & deform_groupbit) { - buf[m++] = h_v(j,0) + dvx; - buf[m++] = h_v(j,1) + dvy; - buf[m++] = h_v(j,2) + dvz; - } else { - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - buf[m++] = h_dpdTheta(j); - buf[m++] = h_uCond(j); - buf[m++] = h_uMech(j); - buf[m++] = h_uChem(j); - buf[m++] = h_uCG(j); - buf[m++] = h_uCGnew(j); - } - } - } - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); - - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecDPDKokkos::pack_comm_hybrid(int n, int *list, double *buf) -{ - int i,j,m; - - atomKK->sync(Host,DPDTHETA_MASK | UCOND_MASK | - UMECH_MASK | UCHEM_MASK); - - m = 0; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_dpdTheta[j]; - buf[m++] = h_uCond[j]; - buf[m++] = h_uMech[j]; - buf[m++] = h_uChem[j]; - } - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecDPDKokkos::pack_border_hybrid(int n, int *list, double *buf) -{ - int i,j,m; - - atomKK->sync(Host,DPDTHETA_MASK | UCOND_MASK | - UMECH_MASK | UCHEM_MASK | UCG_MASK | UCGNEW_MASK); - - m = 0; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_dpdTheta[j]; - buf[m++] = h_uCond[j]; - buf[m++] = h_uMech[j]; - buf[m++] = h_uChem[j]; - buf[m++] = h_uCG[j]; - buf[m++] = h_uCGnew[j]; - } - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecDPDKokkos_UnpackBorder { typedef DeviceType device_type; @@ -1152,123 +693,6 @@ void AtomVecDPDKokkos::unpack_border_kokkos(const int &n, const int &first, /* ---------------------------------------------------------------------- */ -void AtomVecDPDKokkos::unpack_border(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - while (last > nmax) grow(0); - - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_tag(i) = (tagint) ubuf(buf[m++]).i; - h_type(i) = (int) ubuf(buf[m++]).i; - h_mask(i) = (int) ubuf(buf[m++]).i; - h_dpdTheta(i) = buf[m++]; - h_uCond(i) = buf[m++]; - h_uMech(i) = buf[m++]; - h_uChem(i) = buf[m++]; - h_uCG(i) = buf[m++]; - h_uCGnew(i) = buf[m++]; - } - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]-> - unpack_border(n,first,&buf[m]); - - atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK| - DPDTHETA_MASK|UCOND_MASK|UMECH_MASK|UCHEM_MASK| - UCG_MASK|UCGNEW_MASK|DVECTOR_MASK); -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecDPDKokkos::unpack_border_vel(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - while (last > nmax) grow(0); - - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_tag(i) = (tagint) ubuf(buf[m++]).i; - h_type(i) = (int) ubuf(buf[m++]).i; - h_mask(i) = (int) ubuf(buf[m++]).i; - h_v(i,0) = buf[m++]; - h_v(i,1) = buf[m++]; - h_v(i,2) = buf[m++]; - h_dpdTheta(i) = buf[m++]; - h_uCond(i) = buf[m++]; - h_uMech(i) = buf[m++]; - h_uChem(i) = buf[m++]; - h_uCG(i) = buf[m++]; - h_uCGnew(i) = buf[m++]; - } - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]-> - unpack_border(n,first,&buf[m]); - - atomKK->modified(Host,X_MASK|V_MASK|TAG_MASK|TYPE_MASK|MASK_MASK| - DPDTHETA_MASK|UCOND_MASK|UMECH_MASK|UCHEM_MASK| - UCG_MASK|UCGNEW_MASK|DVECTOR_MASK); -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecDPDKokkos::unpack_comm_hybrid(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - for (i = first; i < last; i++) { - h_dpdTheta(i) = buf[m++]; - h_uCond(i) = buf[m++]; - h_uMech(i) = buf[m++]; - h_uChem(i) = buf[m++]; - } - - atomKK->modified(Host,DPDTHETA_MASK | UCOND_MASK | - UMECH_MASK | UCHEM_MASK ); - - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecDPDKokkos::unpack_border_hybrid(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - for (i = first; i < last; i++) { - h_dpdTheta(i) = buf[m++]; - h_uCond(i) = buf[m++]; - h_uMech(i) = buf[m++]; - h_uChem(i) = buf[m++]; - h_uCG(i) = buf[m++]; - h_uCGnew(i) = buf[m++]; - } - - atomKK->modified(Host,DPDTHETA_MASK | UCOND_MASK | - UMECH_MASK | UCHEM_MASK | UCG_MASK | UCGNEW_MASK); - - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecDPDKokkos_PackExchangeFunctor { typedef DeviceType device_type; @@ -1401,41 +825,6 @@ int AtomVecDPDKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d /* ---------------------------------------------------------------------- */ -int AtomVecDPDKokkos::pack_exchange(int i, double *buf) -{ - atomKK->sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK| DPDTHETA_MASK | UCOND_MASK | - UMECH_MASK | UCHEM_MASK | UCG_MASK | UCGNEW_MASK | - DVECTOR_MASK); - - int m = 1; - buf[m++] = h_x(i,0); - buf[m++] = h_x(i,1); - buf[m++] = h_x(i,2); - buf[m++] = h_v(i,0); - buf[m++] = h_v(i,1); - buf[m++] = h_v(i,2); - buf[m++] = ubuf(h_tag(i)).d; - buf[m++] = ubuf(h_type(i)).d; - buf[m++] = ubuf(h_mask(i)).d; - buf[m++] = ubuf(h_image(i)).d; - buf[m++] = h_dpdTheta[i]; - buf[m++] = h_uCond[i]; - buf[m++] = h_uMech[i]; - buf[m++] = h_uChem[i]; - buf[m++] = h_uCG[i]; - buf[m++] = h_uCGnew[i]; - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]); - - buf[0] = m; - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecDPDKokkos_UnpackExchangeFunctor { typedef DeviceType device_type; @@ -1531,334 +920,6 @@ int AtomVecDPDKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int nre /* ---------------------------------------------------------------------- */ -int AtomVecDPDKokkos::unpack_exchange(double *buf) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) grow(0); - - int m = 1; - h_x(nlocal,0) = buf[m++]; - h_x(nlocal,1) = buf[m++]; - h_x(nlocal,2) = buf[m++]; - h_v(nlocal,0) = buf[m++]; - h_v(nlocal,1) = buf[m++]; - h_v(nlocal,2) = buf[m++]; - h_tag(nlocal) = (tagint) ubuf(buf[m++]).i; - h_type(nlocal) = (int) ubuf(buf[m++]).i; - h_mask(nlocal) = (int) ubuf(buf[m++]).i; - h_image(nlocal) = (imageint) ubuf(buf[m++]).i; - h_dpdTheta[nlocal] = buf[m++]; - h_uCond[nlocal] = buf[m++]; - h_uMech[nlocal] = buf[m++]; - h_uChem[nlocal] = buf[m++]; - h_uCG[nlocal] = buf[m++]; - h_uCGnew[nlocal] = buf[m++]; - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - m += modify->fix[atom->extra_grow[iextra]]-> - unpack_exchange(nlocal,&buf[m]); - - atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK| DPDTHETA_MASK | UCOND_MASK | - UMECH_MASK | UCHEM_MASK | UCG_MASK | UCGNEW_MASK | - DVECTOR_MASK); - - atom->nlocal++; - return m; -} - -/* ---------------------------------------------------------------------- - size of restart data for all atoms owned by this proc - include extra data stored by fixes -------------------------------------------------------------------------- */ - -int AtomVecDPDKokkos::size_restart() -{ - int i; - - int nlocal = atom->nlocal; - int n = 15 * nlocal; // 11 + dpdTheta + uCond + uMech + uChem - - if (atom->nextra_restart) - for (int iextra = 0; iextra < atom->nextra_restart; iextra++) - for (i = 0; i < nlocal; i++) - n += modify->fix[atom->extra_restart[iextra]]->size_restart(i); - - return n; -} - -/* ---------------------------------------------------------------------- - pack atom I's data for restart file including extra quantities - xyz must be 1st 3 values, so that read_restart can test on them - molecular types may be negative, but write as positive -------------------------------------------------------------------------- */ - -int AtomVecDPDKokkos::pack_restart(int i, double *buf) -{ - atomKK->sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | DPDTHETA_MASK | - UCOND_MASK | UMECH_MASK | UCHEM_MASK | DVECTOR_MASK); - - int m = 1; - buf[m++] = h_x(i,0); - buf[m++] = h_x(i,1); - buf[m++] = h_x(i,2); - buf[m++] = ubuf(h_tag(i)).d; - buf[m++] = ubuf(h_type(i)).d; - buf[m++] = ubuf(h_mask(i)).d; - buf[m++] = ubuf(h_image(i)).d; - buf[m++] = h_v(i,0); - buf[m++] = h_v(i,1); - buf[m++] = h_v(i,2); - buf[m++] = h_dpdTheta[i]; - buf[m++] = h_uCond[i]; - buf[m++] = h_uMech[i]; - buf[m++] = h_uChem[i]; - - if (atom->nextra_restart) - for (int iextra = 0; iextra < atom->nextra_restart; iextra++) - m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]); - - buf[0] = m; - return m; -} - -/* ---------------------------------------------------------------------- - unpack data for one atom from restart file including extra quantities -------------------------------------------------------------------------- */ - -int AtomVecDPDKokkos::unpack_restart(double *buf) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) { - grow(0); - if (atom->nextra_store) - memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra"); - } - - int m = 1; - h_x(nlocal,0) = buf[m++]; - h_x(nlocal,1) = buf[m++]; - h_x(nlocal,2) = buf[m++]; - h_tag(nlocal) = (tagint) ubuf(buf[m++]).i; - h_type(nlocal) = (int) ubuf(buf[m++]).i; - h_mask(nlocal) = (int) ubuf(buf[m++]).i; - h_image(nlocal) = (imageint) ubuf(buf[m++]).i; - h_v(nlocal,0) = buf[m++]; - h_v(nlocal,1) = buf[m++]; - h_v(nlocal,2) = buf[m++]; - h_dpdTheta[nlocal] = buf[m++]; - h_uCond[nlocal] = buf[m++]; - h_uMech[nlocal] = buf[m++]; - h_uChem[nlocal] = buf[m++]; - h_uCG[nlocal] = 0.0; - h_uCGnew[nlocal] = 0.0; - - double **extra = atom->extra; - if (atom->nextra_store) { - int size = static_cast (buf[0]) - m; - for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++]; - } - - atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | DPDTHETA_MASK | - UCG_MASK | UCGNEW_MASK | - UCOND_MASK | UMECH_MASK | UCHEM_MASK | DVECTOR_MASK); - - atom->nlocal++; - return m; -} - -/* ---------------------------------------------------------------------- - create one atom of itype at coord - set other values to defaults -------------------------------------------------------------------------- */ - -void AtomVecDPDKokkos::create_atom(int itype, double *coord) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) { - //if(nlocal>2) printf("typeA: %i %i\n",type[0],type[1]); - atomKK->modified(Host,ALL_MASK); - grow(0); - //if(nlocal>2) printf("typeB: %i %i\n",type[0],type[1]); - } - atomKK->modified(Host,ALL_MASK); - - tag[nlocal] = 0; - type[nlocal] = itype; - h_x(nlocal,0) = coord[0]; - h_x(nlocal,1) = coord[1]; - h_x(nlocal,2) = coord[2]; - h_mask[nlocal] = 1; - h_image[nlocal] = ((tagint) IMGMAX << IMG2BITS) | - ((tagint) IMGMAX << IMGBITS) | IMGMAX; - h_v(nlocal,0) = 0.0; - h_v(nlocal,1) = 0.0; - h_v(nlocal,2) = 0.0; - h_rho[nlocal] = 0.0; - h_dpdTheta[nlocal] = 0.0; - h_uCond[nlocal] = 0.0; - h_uMech[nlocal] = 0.0; - h_uChem[nlocal] = 0.0; - h_uCG[nlocal] = 0.0; - h_uCGnew[nlocal] = 0.0; - h_duChem[nlocal] = 0.0; - - //atomKK->modified(Host,TAG_MASK|TYPE_MASK|DPDTHETA_MASK|X_MASK|IMAGE_MASK| - // MASK_MASK|V_MASK|DPDRHO_MASK|UCOND_MASK|UMECH_MASK| - // UCHEM_MASK|UCG_MASK|UCGNEW_MASK); - - atom->nlocal++; -} - -/* ---------------------------------------------------------------------- - unpack one line from Atoms section of data file - initialize other atom quantities -------------------------------------------------------------------------- */ - -void AtomVecDPDKokkos::data_atom(double *coord, imageint imagetmp, - const std::vector &values, std::string &extract) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) grow(0); - - h_tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); - h_type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); - extract = values[1]; - if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) - error->one(FLERR,"Invalid atom type in Atoms section of data file"); - - h_dpdTheta[nlocal] = utils::numeric(FLERR,values[2],true,lmp); - if (h_dpdTheta[nlocal] <= 0) - error->one(FLERR,"Internal temperature in Atoms section of date file must be > zero"); - - h_x(nlocal,0) = coord[0]; - h_x(nlocal,1) = coord[1]; - h_x(nlocal,2) = coord[2]; - - h_image[nlocal] = imagetmp; - - h_mask[nlocal] = 1; - h_v(nlocal,0) = 0.0; - h_v(nlocal,1) = 0.0; - h_v(nlocal,2) = 0.0; - - h_rho[nlocal] = 0.0; - h_uCond[nlocal] = 0.0; - h_uMech[nlocal] = 0.0; - h_uChem[nlocal] = 0.0; - h_uCG[nlocal] = 0.0; - h_uCGnew[nlocal] = 0.0; - - atomKK->modified(Host,ALL_MASK); - - atom->nlocal++; -} - -/* ---------------------------------------------------------------------- - unpack hybrid quantities from one line in Atoms section of data file - initialize other atom quantities for this sub-style -------------------------------------------------------------------------- */ - -int AtomVecDPDKokkos::data_atom_hybrid(int nlocal, const std::vector &values, - int offset) -{ - h_dpdTheta(nlocal) = utils::numeric(FLERR,values[offset],true,lmp); - - atomKK->modified(Host,DPDTHETA_MASK); - - return 1; -} - -/* ---------------------------------------------------------------------- - pack atom info for data file including 3 image flags -------------------------------------------------------------------------- */ - -void AtomVecDPDKokkos::pack_data(double **buf) -{ - atomKK->sync(Host,TAG_MASK|TYPE_MASK|DPDTHETA_MASK|X_MASK|IMAGE_MASK); - - int nlocal = atom->nlocal; - for (int i = 0; i < nlocal; i++) { - buf[i][0] = ubuf(h_tag(i)).d; - buf[i][1] = ubuf(h_type(i)).d; - buf[i][2] = h_dpdTheta(i); - buf[i][3] = h_x(i,0); - buf[i][4] = h_x(i,1); - buf[i][5] = h_x(i,2); - buf[i][6] = (h_image[i] & IMGMASK) - IMGMAX; - buf[i][7] = (h_image[i] >> IMGBITS & IMGMASK) - IMGMAX; - buf[i][8] = (h_image[i] >> IMG2BITS) - IMGMAX; - } -} - -/* ---------------------------------------------------------------------- - pack hybrid atom info for data file -------------------------------------------------------------------------- */ - -int AtomVecDPDKokkos::pack_data_hybrid(int i, double *buf) -{ - atomKK->sync(Host,DPDTHETA_MASK); - - buf[0] = h_dpdTheta(i); - return 1; -} - -/* ---------------------------------------------------------------------- - write atom info to data file including 3 image flags -------------------------------------------------------------------------- */ - -void AtomVecDPDKokkos::write_data(FILE *fp, int n, double **buf) -{ - for (int i = 0; i < n; i++) - fprintf(fp,TAGINT_FORMAT " %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n", - (tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i, - buf[i][2],buf[i][3],buf[i][4],buf[i][5], - (int) ubuf(buf[i][6]).i,(int) ubuf(buf[i][7]).i, - (int) ubuf(buf[i][8]).i); -} - -/* ---------------------------------------------------------------------- - write hybrid atom info to data file -------------------------------------------------------------------------- */ - -int AtomVecDPDKokkos::write_data_hybrid(FILE *fp, double *buf) -{ - fprintf(fp," %-1.16e",buf[0]); - return 1; -} - -/* ---------------------------------------------------------------------- - return # of bytes of allocated memory -------------------------------------------------------------------------- */ - -double AtomVecDPDKokkos::memory_usage() -{ - double bytes = 0; - - if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax); - if (atom->memcheck("type")) bytes += memory->usage(type,nmax); - if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax); - if (atom->memcheck("image")) bytes += memory->usage(image,nmax); - if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3); - if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3); - if (atom->memcheck("f")) bytes += memory->usage(f,nmax*commKK->nthreads,3); - if (atom->memcheck("rho")) bytes += memory->usage(rho,nmax); - if (atom->memcheck("dpdTheta")) bytes += memory->usage(dpdTheta,nmax); - if (atom->memcheck("uCond")) bytes += memory->usage(uCond,nmax); - if (atom->memcheck("uMech")) bytes += memory->usage(uMech,nmax); - if (atom->memcheck("uChem")) bytes += memory->usage(uChem,nmax); - if (atom->memcheck("uCG")) bytes += memory->usage(uCG,nmax); - if (atom->memcheck("uCGnew")) bytes += memory->usage(uCGnew,nmax); - if (atom->memcheck("duChem")) bytes += memory->usage(duChem,nmax); - - return bytes; -} - -/* ---------------------------------------------------------------------- */ - void AtomVecDPDKokkos::sync(ExecutionSpace space, unsigned int mask) { if (space == Device) { @@ -2011,4 +1072,3 @@ void AtomVecDPDKokkos::modified(ExecutionSpace space, unsigned int mask) if (mask & DVECTOR_MASK) atomKK->k_dvector.modify(); } } - diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.h b/src/KOKKOS/atom_vec_dpd_kokkos.h index 338e0f6004..203bbb19a5 100644 --- a/src/KOKKOS/atom_vec_dpd_kokkos.h +++ b/src/KOKKOS/atom_vec_dpd_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale AtomicKokkos/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,44 +24,16 @@ AtomStyle(dpd/kk/host,AtomVecDPDKokkos); #define LMP_ATOM_VEC_DPD_KOKKOS_H #include "atom_vec_kokkos.h" +#include "atom_vec_dpd.h" #include "kokkos_type.h" namespace LAMMPS_NS { -class AtomVecDPDKokkos : public AtomVecKokkos { +class AtomVecDPDKokkos : public AtomVecKokkos, public AtomVecDPD { public: AtomVecDPDKokkos(class LAMMPS *); void grow(int) override; - void copy(int, int, int) override; - int pack_comm(int, int *, double *, int, int *) override; - int pack_comm_vel(int, int *, double *, int, int *) override; - int pack_comm_hybrid(int, int *, double *) override; - void unpack_comm(int, int, double *) override; - void unpack_comm_vel(int, int, double *) override; - int unpack_comm_hybrid(int, int, double *) override; - int pack_reverse(int, int, double *) override; - void unpack_reverse(int, int *, double *) override; - int pack_border(int, int *, double *, int, int *) override; - int pack_border_vel(int, int *, double *, int, int *) override; - int pack_border_hybrid(int, int *, double *) override; - void unpack_border(int, int, double *) override; - void unpack_border_vel(int, int, double *) override; - int unpack_border_hybrid(int, int, double *) override; - int pack_exchange(int, double *) override; - int unpack_exchange(double *) override; - int size_restart() override; - int pack_restart(int, double *) override; - int unpack_restart(double *) override; - void create_atom(int, double *) override; - void data_atom(double *, imageint, const std::vector &, std::string &) override; - int data_atom_hybrid(int, const std::vector &, int) override; - void pack_data(double **) override; - int pack_data_hybrid(int, double *) override; - void write_data(FILE *, int, double **) override; - int write_data_hybrid(FILE *, double *) override; - double memory_usage() override; - void grow_pointers() override; int pack_comm_kokkos(const int &n, const DAT::tdual_int_2d &k_sendlist, const int & iswap, @@ -90,18 +62,13 @@ class AtomVecDPDKokkos : public AtomVecKokkos { void sync(ExecutionSpace space, unsigned int mask) override; void modified(ExecutionSpace space, unsigned int mask) override; void sync_overlapping_device(ExecutionSpace space, unsigned int mask) override; - double *uCond,*uMech,*uChem,*uCG,*uCGnew,*rho,*dpdTheta; + double *duChem; protected: DAT::t_efloat_1d d_uCond, d_uMech, d_uChem, d_uCG, d_uCGnew,d_rho,d_dpdTheta,d_duChem; HAT::t_efloat_1d h_uCond, h_uMech, h_uChem, h_uCG, h_uCGnew,h_rho,h_dpdTheta,h_duChem; - tagint *tag; - imageint *image; - int *type,*mask; - double **x,**v,**f; - DAT::t_tagint_1d d_tag; HAT::t_tagint_1d h_tag; DAT::t_imageint_1d d_image; @@ -112,12 +79,9 @@ class AtomVecDPDKokkos : public AtomVecKokkos { DAT::t_x_array d_x; DAT::t_v_array d_v; DAT::t_f_array d_f; - - DAT::tdual_int_1d k_count; }; -} +} // namespace LAMMPS_NS #endif #endif - diff --git a/src/KOKKOS/atom_vec_full_kokkos.cpp b/src/KOKKOS/atom_vec_full_kokkos.cpp index 807953ef41..bce165240b 100644 --- a/src/KOKKOS/atom_vec_full_kokkos.cpp +++ b/src/KOKKOS/atom_vec_full_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -27,26 +27,10 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -AtomVecFullKokkos::AtomVecFullKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) +AtomVecFullKokkos::AtomVecFullKokkos(LAMMPS *lmp) : AtomVec(lmp), +AtomVecKokkos(lmp), AtomVecFull(lmp) { - molecular = Atom::MOLECULAR; - bonds_allow = angles_allow = dihedrals_allow = impropers_allow = 1; - mass_type = PER_TYPE; - comm_x_only = comm_f_only = 1; - size_forward = 3; - size_reverse = 3; - size_border = 8; - size_velocity = 3; - size_data_atom = 7; - size_data_vel = 4; - xcol_data = 5; - - atom->molecule_flag = atom->q_flag = 1; - - k_count = DAT::tdual_int_1d("atom::k_count",1); - atomKK = (AtomKokkos *) atom; - commKK = (CommKokkos *) comm; } /* ---------------------------------------------------------------------- @@ -241,71 +225,6 @@ void AtomVecFullKokkos::grow_pointers() h_improper_atom4 = atomKK->k_improper_atom4.h_view; } -/* ---------------------------------------------------------------------- - copy atom I info to atom J -------------------------------------------------------------------------- */ - -void AtomVecFullKokkos::copy(int i, int j, int delflag) -{ - int k; - - h_tag[j] = h_tag[i]; - h_type[j] = h_type[i]; - mask[j] = mask[i]; - h_image[j] = h_image[i]; - h_x(j,0) = h_x(i,0); - h_x(j,1) = h_x(i,1); - h_x(j,2) = h_x(i,2); - h_v(j,0) = h_v(i,0); - h_v(j,1) = h_v(i,1); - h_v(j,2) = h_v(i,2); - - h_q[j] = h_q[i]; - h_molecule(j) = h_molecule(i); - - h_num_bond(j) = h_num_bond(i); - for (k = 0; k < h_num_bond(j); k++) { - h_bond_type(j,k) = h_bond_type(i,k); - h_bond_atom(j,k) = h_bond_atom(i,k); - } - - h_nspecial(j,0) = h_nspecial(i,0); - h_nspecial(j,1) = h_nspecial(i,1); - h_nspecial(j,2) = h_nspecial(i,2); - for (k = 0; k < h_nspecial(j,2); k++) - h_special(j,k) = h_special(i,k); - - h_num_angle(j) = h_num_angle(i); - for (k = 0; k < h_num_angle(j); k++) { - h_angle_type(j,k) = h_angle_type(i,k); - h_angle_atom1(j,k) = h_angle_atom1(i,k); - h_angle_atom2(j,k) = h_angle_atom2(i,k); - h_angle_atom3(j,k) = h_angle_atom3(i,k); - } - - h_num_dihedral(j) = h_num_dihedral(i); - for (k = 0; k < h_num_dihedral(j); k++) { - h_dihedral_type(j,k) = h_dihedral_type(i,k); - h_dihedral_atom1(j,k) = h_dihedral_atom1(i,k); - h_dihedral_atom2(j,k) = h_dihedral_atom2(i,k); - h_dihedral_atom3(j,k) = h_dihedral_atom3(i,k); - h_dihedral_atom4(j,k) = h_dihedral_atom4(i,k); - } - - h_num_improper(j) = h_num_improper(i); - for (k = 0; k < h_num_improper(j); k++) { - h_improper_type(j,k) = h_improper_type(i,k); - h_improper_atom1(j,k) = h_improper_atom1(i,k); - h_improper_atom2(j,k) = h_improper_atom2(i,k); - h_improper_atom3(j,k) = h_improper_atom3(i,k); - h_improper_atom4(j,k) = h_improper_atom4(i,k); - } - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag); -} - /* ---------------------------------------------------------------------- */ template @@ -413,155 +332,6 @@ int AtomVecFullKokkos::pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, /* ---------------------------------------------------------------------- */ -int AtomVecFullKokkos::pack_border(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz; - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = h_q(j); - buf[m++] = ubuf(h_molecule(j)).d; - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]; - dy = pbc[1]; - dz = pbc[2]; - } - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = h_q(j); - buf[m++] = ubuf(h_molecule(j)).d; - } - } - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); - - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecFullKokkos::pack_border_vel(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz,dvx,dvy,dvz; - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = h_q(j); - buf[m++] = ubuf(h_molecule(j)).d; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]; - dy = pbc[1]; - dz = pbc[2]; - } - if (!deform_vremap) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = h_q(j); - buf[m++] = ubuf(h_molecule(j)).d; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } else { - dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; - dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; - dvz = pbc[2]*h_rate[2]; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = h_q(j); - buf[m++] = ubuf(h_molecule(j)).d; - if (mask[i] & deform_groupbit) { - buf[m++] = h_v(j,0) + dvx; - buf[m++] = h_v(j,1) + dvy; - buf[m++] = h_v(j,2) + dvz; - } else { - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } - } - } - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); - - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecFullKokkos::pack_border_hybrid(int n, int *list, double *buf) -{ - int i,j,m; - - m = 0; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_q(j); - buf[m++] = ubuf(h_molecule(j)).d; - } - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecFullKokkos_UnpackBorder { typedef DeviceType device_type; @@ -628,82 +398,6 @@ void AtomVecFullKokkos::unpack_border_kokkos(const int &n, const int &first, /* ---------------------------------------------------------------------- */ -void AtomVecFullKokkos::unpack_border(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - while (last > nmax) grow(0); - - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_tag(i) = (tagint) ubuf(buf[m++]).i; - h_type(i) = (int) ubuf(buf[m++]).i; - h_mask(i) = (int) ubuf(buf[m++]).i; - h_q(i) = buf[m++]; - h_molecule(i) = (tagint) ubuf(buf[m++]).i; - } - - atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|Q_MASK|MOLECULE_MASK); - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]-> - unpack_border(n,first,&buf[m]); -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecFullKokkos::unpack_border_vel(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - while (last > nmax) grow(0); - - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_tag(i) = (tagint) ubuf(buf[m++]).i; - h_type(i) = (int) ubuf(buf[m++]).i; - h_mask(i) = (int) ubuf(buf[m++]).i; - h_q(i) = buf[m++]; - h_molecule(i) = (tagint) ubuf(buf[m++]).i; - h_v(i,0) = buf[m++]; - h_v(i,1) = buf[m++]; - h_v(i,2) = buf[m++]; - } - - atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|Q_MASK|MOLECULE_MASK|V_MASK); - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]-> - unpack_border(n,first,&buf[m]); -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecFullKokkos::unpack_border_hybrid(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - for (i = first; i < last; i++) { - h_q(i) = buf[m++]; - h_molecule(i) = (tagint) ubuf(buf[m++]).i; - } - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecFullKokkos_PackExchangeFunctor { typedef DeviceType device_type; @@ -983,66 +677,6 @@ int AtomVecFullKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2 /* ---------------------------------------------------------------------- */ -int AtomVecFullKokkos::pack_exchange(int i, double *buf) -{ - int k; - int m = 1; - buf[m++] = h_x(i,0); - buf[m++] = h_x(i,1); - buf[m++] = h_x(i,2); - buf[m++] = h_v(i,0); - buf[m++] = h_v(i,1); - buf[m++] = h_v(i,2); - buf[m++] = ubuf(h_tag(i)).d; - buf[m++] = ubuf(h_type(i)).d; - buf[m++] = ubuf(h_mask(i)).d; - buf[m++] = ubuf(h_image(i)).d; - buf[m++] = h_q(i); - buf[m++] = ubuf(h_molecule(i)).d; - buf[m++] = ubuf(h_num_bond(i)).d; - for (k = 0; k < h_num_bond(i); k++) { - buf[m++] = ubuf(h_bond_type(i,k)).d; - buf[m++] = ubuf(h_bond_atom(i,k)).d; - } - buf[m++] = ubuf(h_num_angle(i)).d; - for (k = 0; k < h_num_angle(i); k++) { - buf[m++] = ubuf(h_angle_type(i,k)).d; - buf[m++] = ubuf(h_angle_atom1(i,k)).d; - buf[m++] = ubuf(h_angle_atom2(i,k)).d; - buf[m++] = ubuf(h_angle_atom3(i,k)).d; - } - buf[m++] = ubuf(h_num_dihedral(i)).d; - for (k = 0; k < h_num_dihedral(i); k++) { - buf[m++] = ubuf(h_dihedral_type(i,k)).d; - buf[m++] = ubuf(h_dihedral_atom1(i,k)).d; - buf[m++] = ubuf(h_dihedral_atom2(i,k)).d; - buf[m++] = ubuf(h_dihedral_atom3(i,k)).d; - buf[m++] = ubuf(h_dihedral_atom4(i,k)).d; - } - buf[m++] = ubuf(h_num_improper(i)).d; - for (k = 0; k < h_num_improper(i); k++) { - buf[m++] = ubuf(h_improper_type(i,k)).d; - buf[m++] = ubuf(h_improper_atom1(i,k)).d; - buf[m++] = ubuf(h_improper_atom2(i,k)).d; - buf[m++] = ubuf(h_improper_atom3(i,k)).d; - buf[m++] = ubuf(h_improper_atom4(i,k)).d; - } - buf[m++] = ubuf(h_nspecial(i,0)).d; - buf[m++] = ubuf(h_nspecial(i,1)).d; - buf[m++] = ubuf(h_nspecial(i,2)).d; - for (k = 0; k < h_nspecial(i,2); k++) - buf[m++] = ubuf(h_special(i,k)).d; - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]); - - buf[0] = m; - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecFullKokkos_UnpackExchangeFunctor { typedef DeviceType device_type; @@ -1211,457 +845,6 @@ int AtomVecFullKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int nr /* ---------------------------------------------------------------------- */ -int AtomVecFullKokkos::unpack_exchange(double *buf) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) grow(0); - atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | Q_MASK | MOLECULE_MASK | BOND_MASK | - ANGLE_MASK | DIHEDRAL_MASK | IMPROPER_MASK | SPECIAL_MASK); - - int k; - int m = 1; - h_x(nlocal,0) = buf[m++]; - h_x(nlocal,1) = buf[m++]; - h_x(nlocal,2) = buf[m++]; - h_v(nlocal,0) = buf[m++]; - h_v(nlocal,1) = buf[m++]; - h_v(nlocal,2) = buf[m++]; - h_tag(nlocal) = (tagint) ubuf(buf[m++]).i; - h_type(nlocal) = (int) ubuf(buf[m++]).i; - h_mask(nlocal) = (int) ubuf(buf[m++]).i; - h_image(nlocal) = (imageint) ubuf(buf[m++]).i; - h_q(nlocal) = buf[m++]; - h_molecule(nlocal) = (tagint) ubuf(buf[m++]).i; - - h_num_bond(nlocal) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_num_bond(nlocal); k++) { - h_bond_type(nlocal,k) = (int) ubuf(buf[m++]).i; - h_bond_atom(nlocal,k) = (tagint) ubuf(buf[m++]).i; - } - h_num_angle(nlocal) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_num_angle(nlocal); k++) { - h_angle_type(nlocal,k) = (int) ubuf(buf[m++]).i; - h_angle_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_angle_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_angle_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i; - } - h_num_dihedral(nlocal) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_num_dihedral(nlocal); k++) { - h_dihedral_type(nlocal,k) = (int) ubuf(buf[m++]).i; - h_dihedral_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_dihedral_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_dihedral_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_dihedral_atom4(nlocal,k) = (tagint) ubuf(buf[m++]).i; - } - h_num_improper(nlocal) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_num_improper(nlocal); k++) { - h_improper_type(nlocal,k) = (int) ubuf(buf[m++]).i; - h_improper_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_improper_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_improper_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_improper_atom4(nlocal,k) = (tagint) ubuf(buf[m++]).i; - } - h_nspecial(nlocal,0) = (int) ubuf(buf[m++]).i; - h_nspecial(nlocal,1) = (int) ubuf(buf[m++]).i; - h_nspecial(nlocal,2) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_nspecial(nlocal,2); k++) - h_special(nlocal,k) = (tagint) ubuf(buf[m++]).i; - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - m += modify->fix[atom->extra_grow[iextra]]-> - unpack_exchange(nlocal,&buf[m]); - - atom->nlocal++; - return m; -} - -/* ---------------------------------------------------------------------- - size of restart data for all atoms owned by this proc - include extra data stored by fixes -------------------------------------------------------------------------- */ - -int AtomVecFullKokkos::size_restart() -{ - int i; - - int nlocal = atom->nlocal; - int n = 0; - for (i = 0; i < nlocal; i++) - n += 17 + 2*num_bond[i] + 4*num_angle[i] + - 5*num_dihedral[i] + 5*num_improper[i]; - - if (atom->nextra_restart) - for (int iextra = 0; iextra < atom->nextra_restart; iextra++) - for (i = 0; i < nlocal; i++) - n += modify->fix[atom->extra_restart[iextra]]->size_restart(i); - - return n; -} - -/* ---------------------------------------------------------------------- - pack atom I's data for restart file including extra quantities - xyz must be 1st 3 values, so that read_restart can test on them - molecular types may be negative, but write as positive -------------------------------------------------------------------------- */ - -int AtomVecFullKokkos::pack_restart(int i, double *buf) -{ - atomKK->sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | Q_MASK | MOLECULE_MASK | BOND_MASK | - ANGLE_MASK | DIHEDRAL_MASK | IMPROPER_MASK | SPECIAL_MASK); - - int m = 1; - buf[m++] = h_x(i,0); - buf[m++] = h_x(i,1); - buf[m++] = h_x(i,2); - buf[m++] = ubuf(h_tag(i)).d; - buf[m++] = ubuf(h_type(i)).d; - buf[m++] = ubuf(h_mask(i)).d; - buf[m++] = ubuf(h_image(i)).d; - buf[m++] = h_v(i,0); - buf[m++] = h_v(i,1); - buf[m++] = h_v(i,2); - - buf[m++] = h_q(i); - buf[m++] = ubuf(h_molecule(i)).d; - - buf[m++] = ubuf(h_num_bond(i)).d; - for (int k = 0; k < h_num_bond(i); k++) { - buf[m++] = ubuf(MAX(h_bond_type(i,k),-h_bond_type(i,k))).d; - buf[m++] = ubuf(h_bond_atom(i,k)).d; - } - - buf[m++] = ubuf(h_num_angle(i)).d; - for (int k = 0; k < h_num_angle(i); k++) { - buf[m++] = ubuf(MAX(h_angle_type(i,k),-h_angle_type(i,k))).d; - buf[m++] = ubuf(h_angle_atom1(i,k)).d; - buf[m++] = ubuf(h_angle_atom2(i,k)).d; - buf[m++] = ubuf(h_angle_atom3(i,k)).d; - } - - buf[m++] = ubuf(h_num_dihedral(i)).d; - for (int k = 0; k < h_num_dihedral(i); k++) { - buf[m++] = ubuf(MAX(h_dihedral_type(i,k),-h_dihedral_type(i,k))).d; - buf[m++] = ubuf(h_dihedral_atom1(i,k)).d; - buf[m++] = ubuf(h_dihedral_atom2(i,k)).d; - buf[m++] = ubuf(h_dihedral_atom3(i,k)).d; - buf[m++] = ubuf(h_dihedral_atom4(i,k)).d; - } - - buf[m++] = ubuf(h_num_improper(i)).d; - for (int k = 0; k < h_num_improper(i); k++) { - buf[m++] = ubuf(MAX(h_improper_type(i,k),-h_improper_type(i,k))).d; - buf[m++] = ubuf(h_improper_atom1(i,k)).d; - buf[m++] = ubuf(h_improper_atom2(i,k)).d; - buf[m++] = ubuf(h_improper_atom3(i,k)).d; - buf[m++] = ubuf(h_improper_atom4(i,k)).d; - } - - if (atom->nextra_restart) - for (int iextra = 0; iextra < atom->nextra_restart; iextra++) - m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]); - - buf[0] = m; - return m; -} - -/* ---------------------------------------------------------------------- - unpack data for one atom from restart file including extra quantities -------------------------------------------------------------------------- */ - -int AtomVecFullKokkos::unpack_restart(double *buf) -{ - int k; - - int nlocal = atom->nlocal; - if (nlocal == nmax) { - grow(0); - if (atom->nextra_store) - memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra"); - } - atomKK->sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | Q_MASK | MOLECULE_MASK | BOND_MASK | - ANGLE_MASK | DIHEDRAL_MASK | IMPROPER_MASK | SPECIAL_MASK); - atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | Q_MASK | MOLECULE_MASK | BOND_MASK | - ANGLE_MASK | DIHEDRAL_MASK | IMPROPER_MASK | SPECIAL_MASK); - - int m = 1; - h_x(nlocal,0) = buf[m++]; - h_x(nlocal,1) = buf[m++]; - h_x(nlocal,2) = buf[m++]; - h_tag(nlocal) = (tagint) ubuf(buf[m++]).i; - h_type(nlocal) = (int) ubuf(buf[m++]).i; - h_mask(nlocal) = (int) ubuf(buf[m++]).i; - h_image(nlocal) = (imageint) ubuf(buf[m++]).i; - h_v(nlocal,0) = buf[m++]; - h_v(nlocal,1) = buf[m++]; - h_v(nlocal,2) = buf[m++]; - - h_q(nlocal) = buf[m++]; - h_molecule(nlocal) = (tagint) ubuf(buf[m++]).i; - - h_num_bond(nlocal) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_num_bond(nlocal); k++) { - h_bond_type(nlocal,k) = (int) ubuf(buf[m++]).i; - h_bond_atom(nlocal,k) = (tagint) ubuf(buf[m++]).i; - } - - h_num_angle(nlocal) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_num_angle(nlocal); k++) { - h_angle_type(nlocal,k) = (int) ubuf(buf[m++]).i; - h_angle_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_angle_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_angle_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i; - } - - h_num_dihedral(nlocal) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_num_dihedral(nlocal); k++) { - h_dihedral_type(nlocal,k) = (int) ubuf(buf[m++]).i; - h_dihedral_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_dihedral_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_dihedral_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_dihedral_atom4(nlocal,k) = (tagint) ubuf(buf[m++]).i; - } - - h_num_improper(nlocal) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_num_improper(nlocal); k++) { - h_improper_type(nlocal,k) = (int) ubuf(buf[m++]).i; - h_improper_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_improper_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_improper_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_improper_atom4(nlocal,k) = (tagint) ubuf(buf[m++]).i; - } - - h_nspecial(nlocal,0) = h_nspecial(nlocal,1) = h_nspecial(nlocal,2) = 0; - - double **extra = atom->extra; - if (atom->nextra_store) { - int size = static_cast (buf[0]) - m; - for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++]; - } - - atom->nlocal++; - return m; -} - -/* ---------------------------------------------------------------------- - create one atom of itype at coord - set other values to defaults -------------------------------------------------------------------------- */ - -void AtomVecFullKokkos::create_atom(int itype, double *coord) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) { - atomKK->modified(Host,ALL_MASK); - grow(0); - } - atomKK->sync(Host,ALL_MASK); - atomKK->modified(Host,ALL_MASK); - - tag[nlocal] = 0; - type[nlocal] = itype; - h_x(nlocal,0) = coord[0]; - h_x(nlocal,1) = coord[1]; - h_x(nlocal,2) = coord[2]; - h_mask(nlocal) = 1; - h_image(nlocal) = ((imageint) IMGMAX << IMG2BITS) | - ((imageint) IMGMAX << IMGBITS) | IMGMAX; - h_v(nlocal,0) = 0.0; - h_v(nlocal,1) = 0.0; - h_v(nlocal,2) = 0.0; - - h_q(nlocal) = 0.0; - h_molecule(nlocal) = 0; - h_num_bond(nlocal) = 0; - h_num_angle(nlocal) = 0; - h_num_dihedral(nlocal) = 0; - h_num_improper(nlocal) = 0; - h_nspecial(nlocal,0) = h_nspecial(nlocal,1) = h_nspecial(nlocal,2) = 0; - - atom->nlocal++; -} - -/* ---------------------------------------------------------------------- - unpack one line from Atoms section of data file - initialize other atom quantities -------------------------------------------------------------------------- */ - -void AtomVecFullKokkos::data_atom(double *coord, imageint imagetmp, - const std::vector &values, std::string &extract) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) grow(0); - atomKK->modified(Host,ALL_MASK); - - h_tag(nlocal) = utils::inumeric(FLERR,values[0],true,lmp); - h_molecule(nlocal) = utils::inumeric(FLERR,values[1],true,lmp); - h_type(nlocal) = utils::inumeric(FLERR,values[2],true,lmp); - extract = values[2]; - if (h_type(nlocal) <= 0 || h_type(nlocal) > atom->ntypes) - error->one(FLERR,"Invalid atom type in Atoms section of data file"); - - h_q(nlocal) = utils::numeric(FLERR,values[3],true,lmp); - - h_x(nlocal,0) = coord[0]; - h_x(nlocal,1) = coord[1]; - h_x(nlocal,2) = coord[2]; - - h_image(nlocal) = imagetmp; - - h_mask(nlocal) = 1; - h_v(nlocal,0) = 0.0; - h_v(nlocal,1) = 0.0; - h_v(nlocal,2) = 0.0; - h_num_bond(nlocal) = 0; - h_num_angle(nlocal) = 0; - h_num_dihedral(nlocal) = 0; - h_num_improper(nlocal) = 0; - - atom->nlocal++; -} - -/* ---------------------------------------------------------------------- - unpack hybrid quantities from one line in Atoms section of data file - initialize other atom quantities for this sub-style -------------------------------------------------------------------------- */ - -int AtomVecFullKokkos::data_atom_hybrid(int nlocal, const std::vector &values, - int offset) -{ - h_molecule(nlocal) = utils::inumeric(FLERR,values[offset],true,lmp); - h_q(nlocal) = utils::numeric(FLERR,values[offset+1],true,lmp); - h_num_bond(nlocal) = 0; - h_num_angle(nlocal) = 0; - h_num_dihedral(nlocal) = 0; - h_num_improper(nlocal) = 0; - return 2; -} - -/* ---------------------------------------------------------------------- - pack atom info for data file including 3 image flags -------------------------------------------------------------------------- */ - -void AtomVecFullKokkos::pack_data(double **buf) -{ - int nlocal = atom->nlocal; - for (int i = 0; i < nlocal; i++) { - buf[i][0] = h_tag(i); - buf[i][1] = h_molecule(i); - buf[i][2] = h_type(i); - buf[i][3] = h_q(i); - buf[i][4] = h_x(i,0); - buf[i][5] = h_x(i,1); - buf[i][6] = h_x(i,2); - buf[i][7] = (h_image[i] & IMGMASK) - IMGMAX; - buf[i][8] = (h_image[i] >> IMGBITS & IMGMASK) - IMGMAX; - buf[i][9] = (h_image[i] >> IMG2BITS) - IMGMAX; - } -} - -/* ---------------------------------------------------------------------- - pack hybrid atom info for data file -------------------------------------------------------------------------- */ - -int AtomVecFullKokkos::pack_data_hybrid(int i, double *buf) -{ - buf[0] = h_molecule(i); - buf[1] = h_q(i); - return 2; -} - -/* ---------------------------------------------------------------------- - write atom info to data file including 3 image flags -------------------------------------------------------------------------- */ - -void AtomVecFullKokkos::write_data(FILE *fp, int n, double **buf) -{ - for (int i = 0; i < n; i++) - fprintf(fp,"%d %d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n", - (int) buf[i][0],(int) buf[i][1], (int) buf[i][2], buf[i][3], - buf[i][4],buf[i][5],buf[i][6], - (int) buf[i][7],(int) buf[i][8],(int) buf[i][9]); -} - -/* ---------------------------------------------------------------------- - write hybrid atom info to data file -------------------------------------------------------------------------- */ - -int AtomVecFullKokkos::write_data_hybrid(FILE *fp, double *buf) -{ - fprintf(fp," " TAGINT_FORMAT " %-1.16e",(tagint) ubuf(buf[0]).i,buf[1]); - return 2; -} - -/* ---------------------------------------------------------------------- - return # of bytes of allocated memory -------------------------------------------------------------------------- */ - -double AtomVecFullKokkos::memory_usage() -{ - double bytes = 0; - - if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax); - if (atom->memcheck("type")) bytes += memory->usage(type,nmax); - if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax); - if (atom->memcheck("image")) bytes += memory->usage(image,nmax); - if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3); - if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3); - if (atom->memcheck("f")) bytes += memory->usage(f,nmax*commKK->nthreads,3); - - if (atom->memcheck("q")) bytes += memory->usage(q,nmax); - if (atom->memcheck("molecule")) bytes += memory->usage(molecule,nmax); - if (atom->memcheck("nspecial")) bytes += memory->usage(nspecial,nmax,3); - if (atom->memcheck("special")) - bytes += memory->usage(special,nmax,atom->maxspecial); - - if (atom->memcheck("num_bond")) bytes += memory->usage(num_bond,nmax); - if (atom->memcheck("bond_type")) - bytes += memory->usage(bond_type,nmax,atom->bond_per_atom); - if (atom->memcheck("bond_atom")) - bytes += memory->usage(bond_atom,nmax,atom->bond_per_atom); - - if (atom->memcheck("num_angle")) bytes += memory->usage(num_angle,nmax); - if (atom->memcheck("angle_type")) - bytes += memory->usage(angle_type,nmax,atom->angle_per_atom); - if (atom->memcheck("angle_atom1")) - bytes += memory->usage(angle_atom1,nmax,atom->angle_per_atom); - if (atom->memcheck("angle_atom2")) - bytes += memory->usage(angle_atom2,nmax,atom->angle_per_atom); - if (atom->memcheck("angle_atom3")) - bytes += memory->usage(angle_atom3,nmax,atom->angle_per_atom); - - if (atom->memcheck("num_dihedral")) bytes += memory->usage(num_dihedral,nmax); - if (atom->memcheck("dihedral_type")) - bytes += memory->usage(dihedral_type,nmax,atom->dihedral_per_atom); - if (atom->memcheck("dihedral_atom1")) - bytes += memory->usage(dihedral_atom1,nmax,atom->dihedral_per_atom); - if (atom->memcheck("dihedral_atom2")) - bytes += memory->usage(dihedral_atom2,nmax,atom->dihedral_per_atom); - if (atom->memcheck("dihedral_atom3")) - bytes += memory->usage(dihedral_atom3,nmax,atom->dihedral_per_atom); - if (atom->memcheck("dihedral_atom4")) - bytes += memory->usage(dihedral_atom4,nmax,atom->dihedral_per_atom); - if (atom->memcheck("num_improper")) bytes += memory->usage(num_improper,nmax); - if (atom->memcheck("improper_type")) - bytes += memory->usage(improper_type,nmax,atom->improper_per_atom); - if (atom->memcheck("improper_atom1")) - bytes += memory->usage(improper_atom1,nmax,atom->improper_per_atom); - if (atom->memcheck("improper_atom2")) - bytes += memory->usage(improper_atom2,nmax,atom->improper_per_atom); - if (atom->memcheck("improper_atom3")) - bytes += memory->usage(improper_atom3,nmax,atom->improper_per_atom); - if (atom->memcheck("improper_atom4")) - bytes += memory->usage(improper_atom4,nmax,atom->improper_per_atom); - - return bytes; -} - -/* ---------------------------------------------------------------------- */ - void AtomVecFullKokkos::sync(ExecutionSpace space, unsigned int mask) { if (space == Device) { @@ -1992,4 +1175,3 @@ void AtomVecFullKokkos::modified(ExecutionSpace space, unsigned int mask) } } } - diff --git a/src/KOKKOS/atom_vec_full_kokkos.h b/src/KOKKOS/atom_vec_full_kokkos.h index 9fc25b509e..3985f19dcb 100644 --- a/src/KOKKOS/atom_vec_full_kokkos.h +++ b/src/KOKKOS/atom_vec_full_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,35 +24,15 @@ AtomStyle(full/kk/host,AtomVecFullKokkos); #define LMP_ATOM_VEC_FULL_KOKKOS_H #include "atom_vec_kokkos.h" +#include "atom_vec_full.h" namespace LAMMPS_NS { -class AtomVecFullKokkos : public AtomVecKokkos { +class AtomVecFullKokkos : public AtomVecKokkos, public AtomVecFull { public: AtomVecFullKokkos(class LAMMPS *); void grow(int) override; - void copy(int, int, int) override; - int pack_border(int, int *, double *, int, int *) override; - int pack_border_vel(int, int *, double *, int, int *) override; - int pack_border_hybrid(int, int *, double *) override; - void unpack_border(int, int, double *) override; - void unpack_border_vel(int, int, double *) override; - int unpack_border_hybrid(int, int, double *) override; - int pack_exchange(int, double *) override; - int unpack_exchange(double *) override; - int size_restart() override; - int pack_restart(int, double *) override; - int unpack_restart(double *) override; - void create_atom(int, double *) override; - void data_atom(double *, imageint, const std::vector &, std::string &) override; - int data_atom_hybrid(int, const std::vector &, int) override; - void pack_data(double **) override; - int pack_data_hybrid(int, double *) override; - void write_data(FILE *, int, double **) override; - int write_data_hybrid(FILE *, double *) override; - double memory_usage() override; - void grow_pointers() override; int pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, DAT::tdual_xfloat_2d buf,int iswap, @@ -74,30 +54,12 @@ class AtomVecFullKokkos : public AtomVecKokkos { void sync_overlapping_device(ExecutionSpace space, unsigned int mask) override; protected: - - tagint *tag; - int *type,*mask; - imageint *image; - double **x,**v,**f; - double *q; - tagint *molecule; - int **nspecial; tagint **special; - int *num_bond; - int **bond_type; tagint **bond_atom; - - int *num_angle; - int **angle_type; tagint **angle_atom1,**angle_atom2,**angle_atom3; - - int *num_dihedral; - int **dihedral_type; tagint **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4; - int *num_improper; - int **improper_type; tagint **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4; DAT::t_tagint_1d d_tag; @@ -154,9 +116,6 @@ class AtomVecFullKokkos : public AtomVecKokkos { HAT::t_int_2d h_improper_type; HAT::t_tagint_2d h_improper_atom1,h_improper_atom2, h_improper_atom3,h_improper_atom4; - - HAT::tdual_int_1d k_count; - }; } diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp index d9c3aa89f7..c8bccc00c8 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -28,7 +28,9 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -AtomVecHybridKokkos::AtomVecHybridKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) { +AtomVecHybridKokkos::AtomVecHybridKokkos(LAMMPS *lmp) : AtomVec(lmp), +AtomVecKokkos(lmp), AtomVecHybrid(lmp) +{ no_comm_vel_flag = 1; no_border_vel_flag = 1; } @@ -37,218 +39,7 @@ AtomVecHybridKokkos::AtomVecHybridKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) { AtomVecHybridKokkos::~AtomVecHybridKokkos() { - for (int k = 0; k < nstyles; k++) delete styles[k]; - delete [] styles; - for (int k = 0; k < nstyles; k++) delete [] keywords[k]; - delete [] keywords; -} -/* ---------------------------------------------------------------------- - process sub-style args -------------------------------------------------------------------------- */ - -void AtomVecHybridKokkos::process_args(int narg, char **arg) -{ - // build list of all known atom styles - - build_styles(); - - // allocate list of sub-styles as big as possibly needed if no extra args - - styles = new AtomVec*[narg]; - keywords = new char*[narg]; - - // allocate each sub-style - // call process_args() with set of args that are not atom style names - // use known_style() to determine which args these are - - int i,jarg,dummy; - - int iarg = 0; - nstyles = 0; - while (iarg < narg) { - if (strcmp(arg[iarg],"hybrid") == 0) - error->all(FLERR,"Atom style hybrid cannot have hybrid as an argument"); - for (i = 0; i < nstyles; i++) - if (strcmp(arg[iarg],keywords[i]) == 0) - error->all(FLERR,"Atom style hybrid cannot use same atom style twice"); - styles[nstyles] = atom->new_avec(arg[iarg],1,dummy); - keywords[nstyles] = utils::strdup(arg[iarg]); - jarg = iarg + 1; - while (jarg < narg && !known_style(arg[jarg])) jarg++; - styles[nstyles]->process_args(jarg-iarg-1,&arg[iarg+1]); - iarg = jarg; - nstyles++; - } - - // free allstyles created by build_styles() - - for (int i = 0; i < nallstyles; i++) delete [] allstyles[i]; - delete [] allstyles; - - // hybrid settings are MAX or MIN of sub-style settings - // hybrid sizes are minimal values plus extra values for each sub-style - - molecular = Atom::ATOMIC; - comm_x_only = comm_f_only = 1; - - size_forward = 3; - size_reverse = 3; - size_border = 6; - size_data_atom = 5; - size_data_vel = 4; - xcol_data = 3; - - for (int k = 0; k < nstyles; k++) { - if ((styles[k]->molecular == Atom::MOLECULAR && molecular == Atom::TEMPLATE) || - (styles[k]->molecular == Atom::TEMPLATE && molecular == Atom::MOLECULAR)) - error->all(FLERR,"Cannot mix molecular and molecule template " - "atom styles"); - molecular = MAX(molecular,styles[k]->molecular); - - bonds_allow = MAX(bonds_allow,styles[k]->bonds_allow); - angles_allow = MAX(angles_allow,styles[k]->angles_allow); - dihedrals_allow = MAX(dihedrals_allow,styles[k]->dihedrals_allow); - impropers_allow = MAX(impropers_allow,styles[k]->impropers_allow); - mass_type = MAX(mass_type,styles[k]->mass_type); - dipole_type = MAX(dipole_type,styles[k]->dipole_type); - forceclearflag = MAX(forceclearflag,styles[k]->forceclearflag); - - if (styles[k]->molecular == Atom::TEMPLATE) onemols = styles[k]->onemols; - - comm_x_only = MIN(comm_x_only,styles[k]->comm_x_only); - comm_f_only = MIN(comm_f_only,styles[k]->comm_f_only); - size_forward += styles[k]->size_forward - 3; - size_reverse += styles[k]->size_reverse - 3; - size_border += styles[k]->size_border - 6; - size_data_atom += styles[k]->size_data_atom - 5; - size_data_vel += styles[k]->size_data_vel - 4; - } - - size_velocity = 3; - if (atom->omega_flag) size_velocity += 3; - if (atom->angmom_flag) size_velocity += 3; -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecHybridKokkos::init() -{ - AtomVec::init(); - for (int k = 0; k < nstyles; k++) styles[k]->init(); -} - -/* ---------------------------------------------------------------------- - grow atom arrays - n = 0 grows arrays by a chunk - n > 0 allocates arrays to size n -------------------------------------------------------------------------- */ - -void AtomVecHybridKokkos::grow(int n) -{ - if (n == 0) grow_nmax(); - else nmax = n; - atom->nmax = nmax; - if (nmax < 0 || nmax > MAXSMALLINT) - error->one(FLERR,"Per-processor system is too big"); - - // sub-styles perform all reallocation - // turn off nextra_grow so hybrid can do that once below - - int tmp = atom->nextra_grow; - atom->nextra_grow = 0; - for (int k = 0; k < nstyles; k++) styles[k]->grow(nmax); - atom->nextra_grow = tmp; - - // insure hybrid local ptrs and sub-style ptrs are up to date - // for sub-styles, do this in case - // multiple sub-style reallocs of same array occurred - - grow_pointers(); - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax); -} - -/* ---------------------------------------------------------------------- - reset local array ptrs -------------------------------------------------------------------------- */ - -void AtomVecHybridKokkos::grow_pointers() -{ - tag = atomKK->tag; - d_tag = atomKK->k_tag.d_view; - h_tag = atomKK->k_tag.h_view; - - type = atomKK->type; - d_type = atomKK->k_type.d_view; - h_type = atomKK->k_type.h_view; - - mask = atomKK->mask; - d_mask = atomKK->k_mask.d_view; - h_mask = atomKK->k_mask.h_view; - - image = atomKK->image; - d_image = atomKK->k_image.d_view; - h_image = atomKK->k_image.h_view; - - x = atomKK->x; - d_x = atomKK->k_x.d_view; - h_x = atomKK->k_x.h_view; - - v = atomKK->v; - d_v = atomKK->k_v.d_view; - h_v = atomKK->k_v.h_view; - - f = atomKK->f; - d_f = atomKK->k_f.d_view; - h_f = atomKK->k_f.h_view; - - v = atomKK->v; - d_v = atomKK->k_v.d_view; - h_v = atomKK->k_v.h_view; - - omega = atomKK->omega; - d_omega = atomKK->k_omega.d_view; - h_omega = atomKK->k_omega.h_view; - - angmom = atomKK->angmom; - d_angmom = atomKK->k_angmom.d_view; - h_angmom = atomKK->k_angmom.h_view; - - for (int k = 0; k < nstyles; k++) styles[k]->grow_pointers(); -} - -/* ---------------------------------------------------------------------- - copy atom I info to atom J for all sub-styles -------------------------------------------------------------------------- */ - -void AtomVecHybridKokkos::copy(int i, int j, int delflag) -{ - int tmp = atom->nextra_grow; - atom->nextra_grow = 0; - for (int k = 0; k < nstyles; k++) styles[k]->copy(i,j,delflag); - atom->nextra_grow = tmp; - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag); -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecHybridKokkos::clear_bonus() -{ - for (int k = 0; k < nstyles; k++) styles[k]->clear_bonus(); -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecHybridKokkos::force_clear(int n, size_t nbytes) -{ - for (int k = 0; k < nstyles; k++) - if (styles[k]->forceclearflag) styles[k]->force_clear(n,nbytes); } /* ---------------------------------------------------------------------- */ @@ -261,11 +52,13 @@ int AtomVecHybridKokkos::pack_comm_kokkos(const int &/*n*/, const DAT::tdual_int error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm"); return 0; } + void AtomVecHybridKokkos::unpack_comm_kokkos(const int &/*n*/, const int &/*nfirst*/, const DAT::tdual_xfloat_2d &/*buf*/) { error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm"); } + int AtomVecHybridKokkos::pack_comm_self(const int &/*n*/, const DAT::tdual_int_2d &/*list*/, const int & /*iswap*/, const int /*nfirst*/, const int &/*pbc_flag*/, const int pbc[]) @@ -273,6 +66,7 @@ int AtomVecHybridKokkos::pack_comm_self(const int &/*n*/, const DAT::tdual_int_2 error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm"); return 0; } + int AtomVecHybridKokkos::pack_border_kokkos(int /*n*/, DAT::tdual_int_2d /*k_sendlist*/, DAT::tdual_xfloat_2d /*buf*/,int /*iswap*/, int /*pbc_flag*/, int * /*pbc*/, ExecutionSpace /*space*/) @@ -280,12 +74,14 @@ int AtomVecHybridKokkos::pack_border_kokkos(int /*n*/, DAT::tdual_int_2d /*k_sen error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm"); return 0; } + void AtomVecHybridKokkos::unpack_border_kokkos(const int &/*n*/, const int &/*nfirst*/, const DAT::tdual_xfloat_2d &/*buf*/, ExecutionSpace /*space*/) { error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm"); } + int AtomVecHybridKokkos::pack_exchange_kokkos(const int &/*nsend*/,DAT::tdual_xfloat_2d &/*buf*/, DAT::tdual_int_1d /*k_sendlist*/, DAT::tdual_int_1d /*k_copylist*/, @@ -295,6 +91,7 @@ int AtomVecHybridKokkos::pack_exchange_kokkos(const int &/*nsend*/,DAT::tdual_xf error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm"); return 0; } + int AtomVecHybridKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d & /*k_buf*/, int /*nrecv*/, int /*nlocal*/, int /*dim*/, X_FLOAT /*lo*/, X_FLOAT /*hi*/, ExecutionSpace /*space*/) @@ -303,921 +100,25 @@ int AtomVecHybridKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d & /*k_buf*/ return 0; } -/* ---------------------------------------------------------------------- */ - -int AtomVecHybridKokkos::pack_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - atomKK->sync(Host,X_MASK); - - int i,j,k,m; - double dx,dy,dz; - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; - dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; - dz = pbc[2]*domain->zprd; - } - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - } - } - - // pack sub-style contributions as contiguous chunks - - for (k = 0; k < nstyles; k++) - m += styles[k]->pack_comm_hybrid(n,list,&buf[m]); - - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecHybridKokkos::pack_comm_vel(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - atomKK->sync(Host,X_MASK|V_MASK|OMEGA_MASK/*|ANGMOM_MASK*/); - - int i,j,k,m; - double dx,dy,dz,dvx,dvy,dvz; - int omega_flag = atom->omega_flag; - int angmom_flag = atom->angmom_flag; - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - if (omega_flag) { - buf[m++] = h_omega(j,0); - buf[m++] = h_omega(j,1); - buf[m++] = h_omega(j,2); - } - if (angmom_flag) { - buf[m++] = h_angmom(j,0); - buf[m++] = h_angmom(j,1); - buf[m++] = h_angmom(j,2); - } - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; - dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; - dz = pbc[2]*domain->zprd; - } - if (!deform_vremap) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - if (omega_flag) { - buf[m++] = h_omega(j,0); - buf[m++] = h_omega(j,1); - buf[m++] = h_omega(j,2); - } - if (angmom_flag) { - buf[m++] = h_angmom(j,0); - buf[m++] = h_angmom(j,1); - buf[m++] = h_angmom(j,2); - } - } - } else { - dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; - dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; - dvz = pbc[2]*h_rate[2]; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - if (h_mask[i] & deform_groupbit) { - buf[m++] = h_v(j,0) + dvx; - buf[m++] = h_v(j,1) + dvy; - buf[m++] = h_v(j,2) + dvz; - } else { - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - if (omega_flag) { - buf[m++] = h_omega(j,0); - buf[m++] = h_omega(j,1); - buf[m++] = h_omega(j,2); - } - if (angmom_flag) { - buf[m++] = h_angmom(j,0); - buf[m++] = h_angmom(j,1); - buf[m++] = h_angmom(j,2); - } - } - } - } - - // pack sub-style contributions as contiguous chunks - - for (k = 0; k < nstyles; k++) - m += styles[k]->pack_comm_hybrid(n,list,&buf[m]); - - return m; -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecHybridKokkos::unpack_comm(int n, int first, double *buf) -{ - int i,k,m,last; - - m = 0; - last = first + n; - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - } - - atomKK->modified(Host,X_MASK); - - // unpack sub-style contributions as contiguous chunks - - for (k = 0; k < nstyles; k++) - m += styles[k]->unpack_comm_hybrid(n,first,&buf[m]); -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecHybridKokkos::unpack_comm_vel(int n, int first, double *buf) -{ - int i,k,m,last; - int omega_flag = atom->omega_flag; - int angmom_flag = atom->angmom_flag; - - m = 0; - last = first + n; - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_v(i,0) = buf[m++]; - h_v(i,1) = buf[m++]; - h_v(i,2) = buf[m++]; - if (omega_flag) { - h_omega(i,0) = buf[m++]; - h_omega(i,1) = buf[m++]; - h_omega(i,2) = buf[m++]; - } - if (angmom_flag) { - h_angmom(i,0) = buf[m++]; - h_angmom(i,1) = buf[m++]; - h_angmom(i,2) = buf[m++]; - } - } - - atomKK->modified(Host,X_MASK|V_MASK|OMEGA_MASK/*|ANGMOM_MASK*/); - - // unpack sub-style contributions as contiguous chunks - - for (k = 0; k < nstyles; k++) - m += styles[k]->unpack_comm_hybrid(n,first,&buf[m]); -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecHybridKokkos::pack_reverse(int n, int first, double *buf) -{ - atomKK->sync(Host,F_MASK); - - int i,k,m,last; - - m = 0; - last = first + n; - for (i = first; i < last; i++) { - buf[m++] = h_f(i,0); - buf[m++] = h_f(i,1); - buf[m++] = h_f(i,2); - } - - // pack sub-style contributions as contiguous chunks - - for (k = 0; k < nstyles; k++) - m += styles[k]->pack_reverse_hybrid(n,first,&buf[m]); - - return m; -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecHybridKokkos::unpack_reverse(int n, int *list, double *buf) -{ - int i,j,k,m; - - m = 0; - for (i = 0; i < n; i++) { - j = list[i]; - h_f(j,0) += buf[m++]; - h_f(j,1) += buf[m++]; - h_f(j,2) += buf[m++]; - } - - atomKK->modified(Host,F_MASK); - - // unpack sub-style contributions as contiguous chunks - - for (k = 0; k < nstyles; k++) - m += styles[k]->unpack_reverse_hybrid(n,list,&buf[m]); -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecHybridKokkos::pack_border(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - atomKK->sync(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK); - - int i,j,k,m; - double dx,dy,dz; - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = ubuf(h_tag[j]).d; - buf[m++] = ubuf(h_type[j]).d; - buf[m++] = ubuf(h_mask[j]).d; - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]; - dy = pbc[1]; - dz = pbc[2]; - } - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag[j]).d; - buf[m++] = ubuf(h_type[j]).d; - buf[m++] = ubuf(h_mask[j]).d; - } - } - - // pack sub-style contributions as contiguous chunks - - for (k = 0; k < nstyles; k++) - m += styles[k]->pack_border_hybrid(n,list,&buf[m]); - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); - - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecHybridKokkos::pack_border_vel(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - atomKK->sync(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|V_MASK|OMEGA_MASK/*|ANGMOM_MASK*/); - int i,j,k,m; - double dx,dy,dz,dvx,dvy,dvz; - int omega_flag = atom->omega_flag; - int angmom_flag = atom->angmom_flag; - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = ubuf(h_tag[j]).d; - buf[m++] = ubuf(h_type[j]).d; - buf[m++] = ubuf(h_mask[j]).d; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - if (omega_flag) { - buf[m++] = h_omega(j,0); - buf[m++] = h_omega(j,1); - buf[m++] = h_omega(j,2); - } - if (angmom_flag) { - buf[m++] = h_angmom(j,0); - buf[m++] = h_angmom(j,1); - buf[m++] = h_angmom(j,2); - } - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]; - dy = pbc[1]; - dz = pbc[2]; - } - if (!deform_vremap) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag[j]).d; - buf[m++] = ubuf(h_type[j]).d; - buf[m++] = ubuf(h_mask[j]).d; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - if (omega_flag) { - buf[m++] = h_omega(j,0); - buf[m++] = h_omega(j,1); - buf[m++] = h_omega(j,2); - } - if (angmom_flag) { - buf[m++] = h_angmom(j,0); - buf[m++] = h_angmom(j,1); - buf[m++] = h_angmom(j,2); - } - } - } else { - dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; - dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; - dvz = pbc[2]*h_rate[2]; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag[j]).d; - buf[m++] = ubuf(h_type[j]).d; - buf[m++] = ubuf(h_mask[j]).d; - if (h_mask[i] & deform_groupbit) { - buf[m++] = h_v(j,0) + dvx; - buf[m++] = h_v(j,1) + dvy; - buf[m++] = h_v(j,2) + dvz; - } else { - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - if (omega_flag) { - buf[m++] = h_omega(j,0); - buf[m++] = h_omega(j,1); - buf[m++] = h_omega(j,2); - } - if (angmom_flag) { - buf[m++] = h_angmom(j,0); - buf[m++] = h_angmom(j,1); - buf[m++] = h_angmom(j,2); - } - } - } - } - - // pack sub-style contributions as contiguous chunks - - for (k = 0; k < nstyles; k++) - m += styles[k]->pack_border_hybrid(n,list,&buf[m]); - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); - - return m; -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecHybridKokkos::unpack_border(int n, int first, double *buf) -{ - int i,k,m,last; - - m = 0; - last = first + n; - while (last > nmax) grow(0); - - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_tag[i] = (tagint) ubuf(buf[m++]).i; - h_type[i] = (int) ubuf(buf[m++]).i; - h_mask[i] = (int) ubuf(buf[m++]).i; - } - - atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK); - - // unpack sub-style contributions as contiguous chunks - - for (k = 0; k < nstyles; k++) - m += styles[k]->unpack_border_hybrid(n,first,&buf[m]); - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]-> - unpack_border(n,first,&buf[m]); -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecHybridKokkos::unpack_border_vel(int n, int first, double *buf) -{ - int i,k,m,last; - int omega_flag = atom->omega_flag; - int angmom_flag = atom->angmom_flag; - - m = 0; - last = first + n; - while (last > nmax) grow(0); - - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_tag[i] = (tagint) ubuf(buf[m++]).i; - h_type[i] = (int) ubuf(buf[m++]).i; - h_mask[i] = (int) ubuf(buf[m++]).i; - h_v(i,0) = buf[m++]; - h_v(i,1) = buf[m++]; - h_v(i,2) = buf[m++]; - if (omega_flag) { - h_omega(i,0) = buf[m++]; - h_omega(i,1) = buf[m++]; - h_omega(i,2) = buf[m++]; - } - if (angmom_flag) { - h_angmom(i,0) = buf[m++]; - h_angmom(i,1) = buf[m++]; - h_angmom(i,2) = buf[m++]; - } - } - - atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|V_MASK|OMEGA_MASK/*|ANGMOM_MASK*/); - - // unpack sub-style contributions as contiguous chunks - - for (k = 0; k < nstyles; k++) - m += styles[k]->unpack_border_hybrid(n,first,&buf[m]); - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]-> - unpack_border(n,first,&buf[m]); -} - -/* ---------------------------------------------------------------------- - pack data for atom I for sending to another proc - pack each sub-style one after the other -------------------------------------------------------------------------- */ - -int AtomVecHybridKokkos::pack_exchange(int i, double *buf) -{ - int k,m; - - int tmp = atom->nextra_grow; - atom->nextra_grow = 0; - - m = 0; - for (k = 0; k < nstyles; k++) - m += styles[k]->pack_exchange(i,&buf[m]); - - atom->nextra_grow = tmp; - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]); - - buf[0] = m; - return m; -} - -/* ---------------------------------------------------------------------- - unpack data for single atom received from another proc - unpack each sub-style one after the other - grow() occurs here so arrays for all sub-styles are grown -------------------------------------------------------------------------- */ - -int AtomVecHybridKokkos::unpack_exchange(double *buf) -{ - int k,m; - - int nlocal = atom->nlocal; - if (nlocal == nmax) grow(0); - - int tmp = atom->nextra_grow; - atom->nextra_grow = 0; - - m = 0; - for (k = 0; k < nstyles; k++) { - m += styles[k]->unpack_exchange(&buf[m]); - atom->nlocal--; - } - - atom->nextra_grow = tmp; - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - m += modify->fix[atom->extra_grow[iextra]]-> - unpack_exchange(nlocal,&buf[m]); - - atom->nlocal++; - return m; -} - -/* ---------------------------------------------------------------------- - size of restart data for all atoms owned by this proc - include extra data stored by fixes -------------------------------------------------------------------------- */ - -int AtomVecHybridKokkos::size_restart() -{ - int tmp = atom->nextra_restart; - atom->nextra_restart = 0; - - int n = 0; - for (int k = 0; k < nstyles; k++) - n += styles[k]->size_restart(); - - atom->nextra_restart = tmp; - - int nlocal = atom->nlocal; - if (atom->nextra_restart) - for (int iextra = 0; iextra < atom->nextra_restart; iextra++) - for (int i = 0; i < nlocal; i++) - n += modify->fix[atom->extra_restart[iextra]]->size_restart(i); - - return n; -} - -/* ---------------------------------------------------------------------- - pack atom I's data for restart file including extra quantities - xyz must be 1st 3 values, so that read_restart can test on them - pack each sub-style one after the other -------------------------------------------------------------------------- */ - -int AtomVecHybridKokkos::pack_restart(int i, double *buf) -{ - int tmp = atom->nextra_restart; - atom->nextra_restart = 0; - - int m = 0; - for (int k = 0; k < nstyles; k++) - m += styles[k]->pack_restart(i,&buf[m]); - - atom->nextra_restart = tmp; - - if (atom->nextra_restart) - for (int iextra = 0; iextra < atom->nextra_restart; iextra++) - m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]); - - buf[0] = m; - return m; -} - -/* ---------------------------------------------------------------------- - unpack data for one atom from restart file including extra quantities - unpack each sub-style one after the other - grow() occurs here so arrays for all sub-styles are grown -------------------------------------------------------------------------- */ - -int AtomVecHybridKokkos::unpack_restart(double *buf) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) { - grow(0); - if (atom->nextra_store) - memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra"); - } - - int tmp = atom->nextra_store; - atom->nextra_store = 0; - - int m = 0; - for (int k = 0; k < nstyles; k++) { - m += styles[k]->unpack_restart(&buf[m]); - atom->nlocal--; - } - atom->nextra_store = tmp; - - double **extra = atom->extra; - if (atom->nextra_store) { - int size = static_cast (buf[0]) - m; - for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++]; - } - - atom->nlocal++; - return m; -} - -/* ---------------------------------------------------------------------- - create one atom of itype at coord - create each sub-style one after the other - grow() occurs here so arrays for all sub-styles are grown -------------------------------------------------------------------------- */ - -void AtomVecHybridKokkos::create_atom(int itype, double *coord) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) grow(0); - - for (int k = 0; k < nstyles; k++) { - styles[k]->create_atom(itype,coord); - atom->nlocal--; - } - atom->nlocal++; -} - -/* ---------------------------------------------------------------------- - unpack one line from Atoms section of data file - grow() occurs here so arrays for all sub-styles are grown -------------------------------------------------------------------------- */ - -void AtomVecHybridKokkos::data_atom(double *coord, imageint imagetmp, - const std::vector &values, std::string &extract) -{ - atomKK->sync(Host,X_MASK|TAG_MASK|TYPE_MASK|IMAGE_MASK|MASK_MASK|V_MASK|OMEGA_MASK/*|ANGMOM_MASK*/); - - int nlocal = atom->nlocal; - if (nlocal == nmax) grow(0); - - h_tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); - h_type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); - extract = values[1]; - if (h_type[nlocal] <= 0 || h_type[nlocal] > atom->ntypes) - error->one(FLERR,"Invalid atom h_type in Atoms section of data file"); - - h_x(nlocal,0) = coord[0]; - h_x(nlocal,1) = coord[1]; - h_x(nlocal,2) = coord[2]; - - h_image[nlocal] = imagetmp; - h_mask[nlocal] = 1; - - h_v(nlocal,0) = 0.0; - h_v(nlocal,1) = 0.0; - h_v(nlocal,2) = 0.0; - if (atom->omega_flag) { - h_omega(nlocal,0) = 0.0; - h_omega(nlocal,1) = 0.0; - h_omega(nlocal,2) = 0.0; - } - if (atom->angmom_flag) { - h_angmom(nlocal,0) = 0.0; - h_angmom(nlocal,1) = 0.0; - h_angmom(nlocal,2) = 0.0; - } - - atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|IMAGE_MASK|MASK_MASK|V_MASK|OMEGA_MASK/*|ANGMOM_MASK*/); - - // each sub-style parses sub-style specific values - - int m = 5; - for (int k = 0; k < nstyles; k++) - m += styles[k]->data_atom_hybrid(nlocal,values,m); - - atom->nlocal++; -} - -/* ---------------------------------------------------------------------- - unpack one line from Velocities section of data file -------------------------------------------------------------------------- */ - -void AtomVecHybridKokkos::data_vel(int m, const std::vector &values) -{ - atomKK->sync(Host,V_MASK); - - int ivalue = 1; - h_v(m,0) = utils::numeric(FLERR,values[ivalue++],true,lmp); - h_v(m,1) = utils::numeric(FLERR,values[ivalue++],true,lmp); - h_v(m,2) = utils::numeric(FLERR,values[ivalue++],true,lmp); - - atomKK->modified(Host,V_MASK); - - // each sub-style parses sub-style specific values - - for (int k = 0; k < nstyles; k++) - ivalue += styles[k]->data_vel_hybrid(m,values,ivalue); -} - -/* ---------------------------------------------------------------------- - pack atom info for data file including 3 image flags -------------------------------------------------------------------------- */ - -void AtomVecHybridKokkos::pack_data(double **buf) -{ - atomKK->sync(Host,TAG_MASK|TYPE_MASK|X_MASK); - - int k,m; - - int nlocal = atom->nlocal; - for (int i = 0; i < nlocal; i++) { - buf[i][0] = ubuf(h_tag[i]).d; - buf[i][1] = ubuf(h_type[i]).d; - buf[i][2] = h_x(i,0); - buf[i][3] = h_x(i,1); - buf[i][4] = h_x(i,2); - - m = 5; - for (k = 0; k < nstyles; k++) - m += styles[k]->pack_data_hybrid(i,&buf[i][m]); - - buf[i][m] = ubuf((h_image[i] & IMGMASK) - IMGMAX).d; - buf[i][m+1] = ubuf((h_image[i] >> IMGBITS & IMGMASK) - IMGMAX).d; - buf[i][m+2] = ubuf((h_image[i] >> IMG2BITS) - IMGMAX).d; - } -} - -/* ---------------------------------------------------------------------- - write atom info to data file including 3 h_image flags -------------------------------------------------------------------------- */ - -void AtomVecHybridKokkos::write_data(FILE *fp, int n, double **buf) -{ - int k,m; - - for (int i = 0; i < n; i++) { - fmt::print(fp,"{} {} {:.16e} {:.16e} {:.16e}", ubuf(buf[i][0]).i, ubuf(buf[i][1]).i, - buf[i][2], buf[i][3], buf[i][4]); - - m = 5; - for (k = 0; k < nstyles; k++) - m += styles[k]->write_data_hybrid(fp,&buf[i][m]); - - fmt::print(fp," {} {} {}\n", ubuf(buf[i][m]).i, ubuf(buf[i][m+1]).i, ubuf(buf[i][m+2]).i); - } -} - -/* ---------------------------------------------------------------------- - pack velocity info for data file -------------------------------------------------------------------------- */ - -void AtomVecHybridKokkos::pack_vel(double **buf) -{ - atomKK->sync(Host,V_MASK); - - int k,m; - - int nlocal = atom->nlocal; - for (int i = 0; i < nlocal; i++) { - buf[i][0] = ubuf(h_tag[i]).d; - buf[i][1] = h_v(i,0); - buf[i][2] = h_v(i,1); - buf[i][3] = h_v(i,2); - - m = 4; - for (k = 0; k < nstyles; k++) - m += styles[k]->pack_vel_hybrid(i,&buf[i][m]); - } -} - -/* ---------------------------------------------------------------------- - write velocity info to data file -------------------------------------------------------------------------- */ - -void AtomVecHybridKokkos::write_vel(FILE *fp, int n, double **buf) -{ - int k,m; - - for (int i = 0; i < n; i++) { - fmt::print(fp,"{} {} {} {}", (tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3]); - - m = 4; - for (k = 0; k < nstyles; k++) - m += styles[k]->write_vel_hybrid(fp,&buf[i][m]); - - fprintf(fp,"\n"); - } -} - -/* ---------------------------------------------------------------------- - assign an index to named atom property and return index - returned value encodes which sub-style and index returned by sub-style - return -1 if name is unknown to any sub-styles -------------------------------------------------------------------------- */ - -int AtomVecHybridKokkos::property_atom(const std::string &name) -{ - for (int k = 0; k < nstyles; k++) { - int index = styles[k]->property_atom(name); - if (index >= 0) return index*nstyles + k; - } - return -1; -} - -/* ---------------------------------------------------------------------- - pack per-atom data into buf for ComputePropertyAtom - index maps to data specific to this atom style -------------------------------------------------------------------------- */ - -void AtomVecHybridKokkos::pack_property_atom(int multiindex, double *buf, int nvalues, int groupbit) -{ - int k = multiindex % nstyles; - int index = multiindex/nstyles; - styles[k]->pack_property_atom(index,buf,nvalues,groupbit); -} - -/* ---------------------------------------------------------------------- - allstyles = list of all atom styles in this LAMMPS executable -------------------------------------------------------------------------- */ - -void AtomVecHybridKokkos::build_styles() -{ - nallstyles = 0; -#define ATOM_CLASS -#define AtomStyle(key,Class) nallstyles++; -#include "style_atom.h" -#undef AtomStyle -#undef ATOM_CLASS - - allstyles = new char*[nallstyles]; - - nallstyles = 0; -#define ATOM_CLASS -#define AtomStyle(key,Class) \ - allstyles[nallstyles] = utils::strdup(#key); \ - nallstyles++; -#include "style_atom.h" // IWYU pragma: keep -#undef AtomStyle -#undef ATOM_CLASS -} - -/* ---------------------------------------------------------------------- - allstyles = list of all known atom styles -------------------------------------------------------------------------- */ - -int AtomVecHybridKokkos::known_style(char *str) -{ - for (int i = 0; i < nallstyles; i++) - if (strcmp(str,allstyles[i]) == 0) return 1; - return 0; -} - -/* ---------------------------------------------------------------------- - return # of bytes of allocated memory -------------------------------------------------------------------------- */ - -double AtomVecHybridKokkos::memory_usage() -{ - double bytes = 0; - for (int k = 0; k < nstyles; k++) bytes += styles[k]->memory_usage(); - return bytes; -} +// TODO: move dynamic_cast into init /* ---------------------------------------------------------------------- */ void AtomVecHybridKokkos::sync(ExecutionSpace space, unsigned int h_mask) { - for (int k = 0; k < nstyles; k++) ((AtomVecKokkos*) styles[k])->sync(space,h_mask); + for (int k = 0; k < nstyles; k++) (dynamic_cast(styles[k]))->sync(space,h_mask); } /* ---------------------------------------------------------------------- */ void AtomVecHybridKokkos::sync_overlapping_device(ExecutionSpace space, unsigned int h_mask) { - for (int k = 0; k < nstyles; k++) ((AtomVecKokkos*) styles[k])->sync_overlapping_device(space,h_mask); + for (int k = 0; k < nstyles; k++) (dynamic_cast(styles[k]))->sync_overlapping_device(space,h_mask); } /* ---------------------------------------------------------------------- */ void AtomVecHybridKokkos::modified(ExecutionSpace space, unsigned int h_mask) { - for (int k = 0; k < nstyles; k++) ((AtomVecKokkos*) styles[k])->modified(space,h_mask); + for (int k = 0; k < nstyles; k++) (dynamic_cast(styles[k]))->modified(space,h_mask); } diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.h b/src/KOKKOS/atom_vec_hybrid_kokkos.h index f633460634..150682ef46 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.h +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -22,11 +22,12 @@ AtomStyle(hybrid/kk,AtomVecHybridKokkos); #define LMP_ATOM_VEC_HYBRID_KOKKOS_H #include "atom_vec_kokkos.h" +#include "atom_vec_hybrid.h" #include "kokkos_type.h" namespace LAMMPS_NS { -class AtomVecHybridKokkos : public AtomVecKokkos { +class AtomVecHybridKokkos : public AtomVecKokkos, public AtomVecHybrid { public: int nstyles; class AtomVec **styles; @@ -34,39 +35,6 @@ class AtomVecHybridKokkos : public AtomVecKokkos { AtomVecHybridKokkos(class LAMMPS *); ~AtomVecHybridKokkos() override; - void process_args(int, char **) override; - void init() override; - void grow(int) override; - void grow_pointers() override; - void copy(int, int, int) override; - void clear_bonus() override; - void force_clear(int, size_t) override; - int pack_comm(int, int *, double *, int, int *) override; - int pack_comm_vel(int, int *, double *, int, int *) override; - void unpack_comm(int, int, double *) override; - void unpack_comm_vel(int, int, double *) override; - int pack_reverse(int, int, double *) override; - void unpack_reverse(int, int *, double *) override; - int pack_border(int, int *, double *, int, int *) override; - int pack_border_vel(int, int *, double *, int, int *) override; - void unpack_border(int, int, double *) override; - void unpack_border_vel(int, int, double *) override; - int pack_exchange(int, double *) override; - int unpack_exchange(double *) override; - int size_restart() override; - int pack_restart(int, double *) override; - int unpack_restart(double *) override; - void create_atom(int, double *) override; - void data_atom(double *, imageint, const std::vector &, std::string &) override; - int data_atom_hybrid(int, const std::vector &, int) override {return 0;} - void data_vel(int, const std::vector &) override; - void pack_data(double **) override; - void write_data(FILE *, int, double **) override; - void pack_vel(double **) override; - void write_vel(FILE *, int, double **) override; - int property_atom(const std::string &) override; - void pack_property_atom(int, double *, int, int) override; - double memory_usage() override; int pack_comm_kokkos(const int &n, const DAT::tdual_int_2d &k_sendlist, const int & iswap, @@ -97,10 +65,6 @@ class AtomVecHybridKokkos : public AtomVecKokkos { void sync_overlapping_device(ExecutionSpace space, unsigned int mask) override; private: - tagint *tag; - int *type,*mask; - imageint *image; - double **x,**v,**f; double **omega,**angmom; DAT::t_tagint_1d d_tag; @@ -121,8 +85,6 @@ class AtomVecHybridKokkos : public AtomVecKokkos { DAT::t_v_array d_omega, d_angmom; HAT::t_v_array h_omega, h_angmom; - DAT::tdual_int_1d k_count; - int nallstyles; char **allstyles; @@ -130,8 +92,7 @@ class AtomVecHybridKokkos : public AtomVecKokkos { int known_style(char *); }; -} +} // namespace LAMMPS_NS #endif #endif - diff --git a/src/KOKKOS/atom_vec_kokkos.cpp b/src/KOKKOS/atom_vec_kokkos.cpp index 931cd8d8f4..cc02f1e617 100644 --- a/src/KOKKOS/atom_vec_kokkos.cpp +++ b/src/KOKKOS/atom_vec_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -32,22 +32,19 @@ AtomVecKokkos::AtomVecKokkos(LAMMPS *lmp) : AtomVec(lmp) no_comm_vel_flag = 0; no_border_vel_flag = 1; + + k_count = DAT::tdual_int_1d("atom::k_count",1); + atomKK = (AtomKokkos *) atom; + commKK = (CommKokkos *) comm; } -/* ---------------------------------------------------------------------- - roundup N so it is a multiple of DELTA - error if N exceeds 32-bit int, since will be used as arg to grow() - overload needed because Kokkos uses a smaller DELTA than in atom_vec.cpp - and an exponential instead of a linear growth -------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- */ -bigint AtomVecKokkos::roundup(bigint n) +AtomVecKokkos::~AtomVecKokkos() { - auto DELTA = LMP_KOKKOS_AV_DELTA; - if (n % DELTA) n = n/DELTA * DELTA + DELTA; - if (n > MAXSMALLINT) - error->one(FLERR,"Too many atoms created on one or more procs"); - return n; + // Kokkos already deallocated host memory + + ngrow = 0; } /* ---------------------------------------------------------------------- */ @@ -708,138 +705,6 @@ void AtomVecKokkos::unpack_comm_vel_kokkos(const int &n, const int &first, /* ---------------------------------------------------------------------- */ -int AtomVecKokkos::pack_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz; - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; - dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; - dz = pbc[2]*domain->zprd; - } - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - } - } - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecKokkos::pack_comm_vel(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz,dvx,dvy,dvz; - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; - dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; - dz = pbc[2]*domain->zprd; - } - if (!deform_vremap) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } else { - dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; - dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; - dvz = pbc[2]*h_rate[2]; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - if (atom->mask[i] & deform_groupbit) { - buf[m++] = h_v(j,0) + dvx; - buf[m++] = h_v(j,1) + dvy; - buf[m++] = h_v(j,2) + dvz; - } else { - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } - } - } - return m; -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecKokkos::unpack_comm(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - } -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecKokkos::unpack_comm_vel(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_v(i,0) = buf[m++]; - h_v(i,1) = buf[m++]; - h_v(i,2) = buf[m++]; - } -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecKokkos_PackReverse { typedef DeviceType device_type; @@ -977,84 +842,3 @@ void AtomVecKokkos::unpack_reverse_kokkos(const int &n, atomKK->modified(Device,F_MASK); } } - -/* ---------------------------------------------------------------------- */ - -int AtomVecKokkos::pack_reverse(int n, int first, double *buf) -{ - if (n > 0) - atomKK->sync(Host,F_MASK); - - int m = 0; - const int last = first + n; - for (int i = first; i < last; i++) { - buf[m++] = h_f(i,0); - buf[m++] = h_f(i,1); - buf[m++] = h_f(i,2); - } - - return m; -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecKokkos::unpack_reverse(int n, int *list, double *buf) -{ - int m = 0; - for (int i = 0; i < n; i++) { - const int j = list[i]; - h_f(j,0) += buf[m++]; - h_f(j,1) += buf[m++]; - h_f(j,2) += buf[m++]; - } - - if (n > 0) - atomKK->modified(Host,F_MASK); -} - -/* ---------------------------------------------------------------------- - * unpack one line from Velocities section of data file - * ------------------------------------------------------------------------- */ - -void AtomVecKokkos::data_vel(int m, const std::vector &values) -{ - double **v = atom->v; - int ivalue = 1; - v[m][0] = utils::numeric(FLERR,values[ivalue++],true,lmp); - v[m][1] = utils::numeric(FLERR,values[ivalue++],true,lmp); - v[m][2] = utils::numeric(FLERR,values[ivalue++],true,lmp); - - atomKK->modified(Host,V_MASK); -} - -/* ---------------------------------------------------------------------- - * pack velocity info for data file - * ------------------------------------------------------------------------- */ - -void AtomVecKokkos::pack_vel(double **buf) -{ - double **v = atom->v; - tagint *tag = atom->tag; - int nlocal = atom->nlocal; - - atomKK->sync(Host,V_MASK|TAG_MASK); - - for (int i = 0; i < nlocal; i++) { - buf[i][0] = ubuf(tag[i]).d; - buf[i][1] = v[i][0]; - buf[i][2] = v[i][1]; - buf[i][3] = v[i][2]; - } -} - -/* ---------------------------------------------------------------------- - * write velocity info to data file - * ------------------------------------------------------------------------- */ - -void AtomVecKokkos::write_vel(FILE *fp, int n, double **buf) -{ - for (int i = 0; i < n; i++) - fprintf(fp,TAGINT_FORMAT " %-1.16e %-1.16e %-1.16e\n", - (tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3]); -} - diff --git a/src/KOKKOS/atom_vec_kokkos.h b/src/KOKKOS/atom_vec_kokkos.h index 969b4f7474..b7047ad38b 100644 --- a/src/KOKKOS/atom_vec_kokkos.h +++ b/src/KOKKOS/atom_vec_kokkos.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -33,20 +33,10 @@ union d_ubuf { d_ubuf(int arg) : i(arg) {} }; -class AtomVecKokkos : public AtomVec { +class AtomVecKokkos : virtual public AtomVec { public: AtomVecKokkos(class LAMMPS *); - - bigint roundup(bigint) override; - int pack_comm(int, int *, double *, int, int *) override; - int pack_comm_vel(int, int *, double *, int, int *) override; - void unpack_comm(int, int, double *) override; - void unpack_comm_vel(int, int, double *) override; - int pack_reverse(int, int, double *) override; - void unpack_reverse(int, int *, double *) override; - void data_vel(int, const std::vector &) override; - void pack_vel(double **) override; - void write_vel(FILE *, int, double **) override; + ~AtomVecKokkos() override; virtual void sync(ExecutionSpace space, unsigned int mask) = 0; virtual void modified(ExecutionSpace space, unsigned int mask) = 0; @@ -130,7 +120,6 @@ class AtomVecKokkos : public AtomVec { int no_comm_vel_flag,no_border_vel_flag; protected: - HAT::t_x_array h_x; HAT::t_v_array h_v; HAT::t_f_array h_f; @@ -139,6 +128,8 @@ class AtomVecKokkos : public AtomVec { size_t buffer_size; void* buffer; + DAT::tdual_int_1d k_count; + #ifdef LMP_KOKKOS_GPU template Kokkos::Viewmolecule_flag = 1; - - k_count = DAT::tdual_int_1d("atom::k_count",1); - atomKK = (AtomKokkos *) atom; - commKK = (CommKokkos *) comm; } /* ---------------------------------------------------------------------- @@ -233,70 +217,6 @@ void AtomVecMolecularKokkos::grow_pointers() h_improper_atom4 = atomKK->k_improper_atom4.h_view; } -/* ---------------------------------------------------------------------- - copy atom I info to atom J -------------------------------------------------------------------------- */ - -void AtomVecMolecularKokkos::copy(int i, int j, int delflag) -{ - int k; - - h_tag[j] = h_tag[i]; - h_type[j] = h_type[i]; - mask[j] = mask[i]; - h_image[j] = h_image[i]; - h_x(j,0) = h_x(i,0); - h_x(j,1) = h_x(i,1); - h_x(j,2) = h_x(i,2); - h_v(j,0) = h_v(i,0); - h_v(j,1) = h_v(i,1); - h_v(j,2) = h_v(i,2); - - h_molecule(j) = h_molecule(i); - - h_num_bond(j) = h_num_bond(i); - for (k = 0; k < h_num_bond(j); k++) { - h_bond_type(j,k) = h_bond_type(i,k); - h_bond_atom(j,k) = h_bond_atom(i,k); - } - - h_nspecial(j,0) = h_nspecial(i,0); - h_nspecial(j,1) = h_nspecial(i,1); - h_nspecial(j,2) = h_nspecial(i,2); - for (k = 0; k < h_nspecial(j,2); k++) - h_special(j,k) = h_special(i,k); - - h_num_angle(j) = h_num_angle(i); - for (k = 0; k < h_num_angle(j); k++) { - h_angle_type(j,k) = h_angle_type(i,k); - h_angle_atom1(j,k) = h_angle_atom1(i,k); - h_angle_atom2(j,k) = h_angle_atom2(i,k); - h_angle_atom3(j,k) = h_angle_atom3(i,k); - } - - h_num_dihedral(j) = h_num_dihedral(i); - for (k = 0; k < h_num_dihedral(j); k++) { - h_dihedral_type(j,k) = h_dihedral_type(i,k); - h_dihedral_atom1(j,k) = h_dihedral_atom1(i,k); - h_dihedral_atom2(j,k) = h_dihedral_atom2(i,k); - h_dihedral_atom3(j,k) = h_dihedral_atom3(i,k); - h_dihedral_atom4(j,k) = h_dihedral_atom4(i,k); - } - - h_num_improper(j) = h_num_improper(i); - for (k = 0; k < h_num_improper(j); k++) { - h_improper_type(j,k) = h_improper_type(i,k); - h_improper_atom1(j,k) = h_improper_atom1(i,k); - h_improper_atom2(j,k) = h_improper_atom2(i,k); - h_improper_atom3(j,k) = h_improper_atom3(i,k); - h_improper_atom4(j,k) = h_improper_atom4(i,k); - } - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag); -} - /* ---------------------------------------------------------------------- */ template @@ -580,171 +500,6 @@ void AtomVecMolecularKokkos::unpack_comm_kokkos(const int &n, const int &first, /* ---------------------------------------------------------------------- */ -int AtomVecMolecularKokkos::pack_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz; - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; - dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; - dz = pbc[2]*domain->zprd; - } - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - } - } - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecMolecularKokkos::pack_comm_vel(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz,dvx,dvy,dvz; - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; - dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; - dz = pbc[2]*domain->zprd; - } - if (!deform_vremap) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } else { - dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; - dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; - dvz = pbc[2]*h_rate[2]; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - if (mask[i] & deform_groupbit) { - buf[m++] = h_v(j,0) + dvx; - buf[m++] = h_v(j,1) + dvy; - buf[m++] = h_v(j,2) + dvz; - } else { - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } - } - } - return m; -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecMolecularKokkos::unpack_comm(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - } -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecMolecularKokkos::unpack_comm_vel(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_v(i,0) = buf[m++]; - h_v(i,1) = buf[m++]; - h_v(i,2) = buf[m++]; - } -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecMolecularKokkos::pack_reverse(int n, int first, double *buf) -{ - if (n > 0) - atomKK->sync(Host,F_MASK); - - int m = 0; - const int last = first + n; - for (int i = first; i < last; i++) { - buf[m++] = h_f(i,0); - buf[m++] = h_f(i,1); - buf[m++] = h_f(i,2); - } - return m; -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecMolecularKokkos::unpack_reverse(int n, int *list, double *buf) -{ - if (n > 0) - atomKK->modified(Host,F_MASK); - - int m = 0; - for (int i = 0; i < n; i++) { - const int j = list[i]; - h_f(j,0) += buf[m++]; - h_f(j,1) += buf[m++]; - h_f(j,2) += buf[m++]; - } -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecMolecularKokkos_PackBorder { typedef DeviceType device_type; @@ -846,149 +601,6 @@ int AtomVecMolecularKokkos::pack_border_kokkos(int n, DAT::tdual_int_2d k_sendli /* ---------------------------------------------------------------------- */ -int AtomVecMolecularKokkos::pack_border(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz; - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = ubuf(h_molecule(j)).d; - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]; - dy = pbc[1]; - dz = pbc[2]; - } - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = ubuf(h_molecule(j)).d; - } - } - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); - - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecMolecularKokkos::pack_border_vel(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz,dvx,dvy,dvz; - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = ubuf(h_molecule(j)).d; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]; - dy = pbc[1]; - dz = pbc[2]; - } - if (!deform_vremap) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = ubuf(h_molecule(j)).d; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } else { - dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; - dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; - dvz = pbc[2]*h_rate[2]; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = ubuf(h_molecule(j)).d; - if (mask[i] & deform_groupbit) { - buf[m++] = h_v(j,0) + dvx; - buf[m++] = h_v(j,1) + dvy; - buf[m++] = h_v(j,2) + dvz; - } else { - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } - } - } - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); - - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecMolecularKokkos::pack_border_hybrid(int n, int *list, double *buf) -{ - int i,j,m; - - m = 0; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_molecule(j); - } - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecMolecularKokkos_UnpackBorder { typedef DeviceType device_type; @@ -1049,78 +661,6 @@ void AtomVecMolecularKokkos::unpack_border_kokkos(const int &n, const int &first /* ---------------------------------------------------------------------- */ -void AtomVecMolecularKokkos::unpack_border(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - while (last > nmax) grow(0); - - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_tag(i) = (tagint) ubuf(buf[m++]).i; - h_type(i) = (int) ubuf(buf[m++]).i; - h_mask(i) = (int) ubuf(buf[m++]).i; - h_molecule(i) = (tagint) ubuf(buf[m++]).i; - } - - atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK); - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]-> - unpack_border(n,first,&buf[m]); -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecMolecularKokkos::unpack_border_vel(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - while (last > nmax) grow(0); - - for (i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_tag(i) = (tagint) ubuf(buf[m++]).i; - h_type(i) = (int) ubuf(buf[m++]).i; - h_mask(i) = (int) ubuf(buf[m++]).i; - h_molecule(i) = (tagint) ubuf(buf[m++]).i; - h_v(i,0) = buf[m++]; - h_v(i,1) = buf[m++]; - h_v(i,2) = buf[m++]; - } - - atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK|V_MASK); - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]-> - unpack_border(n,first,&buf[m]); -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecMolecularKokkos::unpack_border_hybrid(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - for (i = first; i < last; i++) - h_molecule(i) = (tagint) ubuf(buf[m++]).i; - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecMolecularKokkos_PackExchangeFunctor { typedef DeviceType device_type; @@ -1393,66 +933,6 @@ int AtomVecMolecularKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfl /* ---------------------------------------------------------------------- */ -int AtomVecMolecularKokkos::pack_exchange(int i, double *buf) -{ - int k; - int m = 1; - buf[m++] = h_x(i,0); - buf[m++] = h_x(i,1); - buf[m++] = h_x(i,2); - buf[m++] = h_v(i,0); - buf[m++] = h_v(i,1); - buf[m++] = h_v(i,2); - buf[m++] = ubuf(h_tag(i)).d; - buf[m++] = ubuf(h_type(i)).d; - buf[m++] = ubuf(h_mask(i)).d; - buf[m++] = ubuf(h_image(i)).d; - buf[m++] = ubuf(h_molecule(i)).d; - - buf[m++] = ubuf(h_num_bond(i)).d; - for (k = 0; k < h_num_bond(i); k++) { - buf[m++] = ubuf(h_bond_type(i,k)).d; - buf[m++] = ubuf(h_bond_atom(i,k)).d; - } - buf[m++] = ubuf(h_num_angle(i)).d; - for (k = 0; k < h_num_angle(i); k++) { - buf[m++] = ubuf(h_angle_type(i,k)).d; - buf[m++] = ubuf(h_angle_atom1(i,k)).d; - buf[m++] = ubuf(h_angle_atom2(i,k)).d; - buf[m++] = ubuf(h_angle_atom3(i,k)).d; - } - buf[m++] = ubuf(h_num_dihedral(i)).d; - for (k = 0; k < h_num_dihedral(i); k++) { - buf[m++] = ubuf(h_dihedral_type(i,k)).d; - buf[m++] = ubuf(h_dihedral_atom1(i,k)).d; - buf[m++] = ubuf(h_dihedral_atom2(i,k)).d; - buf[m++] = ubuf(h_dihedral_atom3(i,k)).d; - buf[m++] = ubuf(h_dihedral_atom4(i,k)).d; - } - buf[m++] = ubuf(h_num_improper(i)).d; - for (k = 0; k < h_num_improper(i); k++) { - buf[m++] = ubuf(h_improper_type(i,k)).d; - buf[m++] = ubuf(h_improper_atom1(i,k)).d; - buf[m++] = ubuf(h_improper_atom2(i,k)).d; - buf[m++] = ubuf(h_improper_atom3(i,k)).d; - buf[m++] = ubuf(h_improper_atom4(i,k)).d; - } - buf[m++] = ubuf(h_nspecial(i,0)).d; - buf[m++] = ubuf(h_nspecial(i,1)).d; - buf[m++] = ubuf(h_nspecial(i,2)).d; - for (k = 0; k < h_nspecial(i,2); k++) - buf[m++] = ubuf(h_special(i,k)).d; - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]); - - buf[0] = m; - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecMolecularKokkos_UnpackExchangeFunctor { typedef DeviceType device_type; @@ -1619,444 +1099,6 @@ int AtomVecMolecularKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,i /* ---------------------------------------------------------------------- */ -int AtomVecMolecularKokkos::unpack_exchange(double *buf) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) grow(0); - atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | MOLECULE_MASK | BOND_MASK | - ANGLE_MASK | DIHEDRAL_MASK | IMPROPER_MASK | SPECIAL_MASK); - - int k; - int m = 1; - h_x(nlocal,0) = buf[m++]; - h_x(nlocal,1) = buf[m++]; - h_x(nlocal,2) = buf[m++]; - h_v(nlocal,0) = buf[m++]; - h_v(nlocal,1) = buf[m++]; - h_v(nlocal,2) = buf[m++]; - h_tag(nlocal) = (tagint) ubuf(buf[m++]).i; - h_type(nlocal) = (int) ubuf(buf[m++]).i; - h_mask(nlocal) = (int) ubuf(buf[m++]).i; - h_image(nlocal) = (imageint) ubuf(buf[m++]).i; - h_molecule(nlocal) = (tagint) ubuf(buf[m++]).i; - - h_num_bond(nlocal) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_num_bond(nlocal); k++) { - h_bond_type(nlocal,k) = (int) ubuf(buf[m++]).i; - h_bond_atom(nlocal,k) = (tagint) ubuf(buf[m++]).i; - } - h_num_angle(nlocal) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_num_angle(nlocal); k++) { - h_angle_type(nlocal,k) = (int) ubuf(buf[m++]).i; - h_angle_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_angle_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_angle_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i; - } - h_num_dihedral(nlocal) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_num_dihedral(nlocal); k++) { - h_dihedral_type(nlocal,k) = (int) ubuf(buf[m++]).i; - h_dihedral_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_dihedral_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_dihedral_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_dihedral_atom4(nlocal,k) = (tagint) ubuf(buf[m++]).i; - } - h_num_improper(nlocal) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_num_improper(nlocal); k++) { - h_improper_type(nlocal,k) = (int) ubuf(buf[m++]).i; - h_improper_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_improper_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_improper_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_improper_atom4(nlocal,k) = (tagint) ubuf(buf[m++]).i; - } - h_nspecial(nlocal,0) = (int) ubuf(buf[m++]).i; - h_nspecial(nlocal,1) = (int) ubuf(buf[m++]).i; - h_nspecial(nlocal,2) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_nspecial(nlocal,2); k++) - h_special(nlocal,k) = (tagint) ubuf(buf[m++]).i; - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - m += modify->fix[atom->extra_grow[iextra]]-> - unpack_exchange(nlocal,&buf[m]); - - atom->nlocal++; - return m; -} - -/* ---------------------------------------------------------------------- - size of restart data for all atoms owned by this proc - include extra data stored by fixes -------------------------------------------------------------------------- */ - -int AtomVecMolecularKokkos::size_restart() -{ - int i; - - int nlocal = atom->nlocal; - int n = 0; - for (i = 0; i < nlocal; i++) - n += 16 + 2*num_bond[i] + 4*num_angle[i] + - 5*num_dihedral[i] + 5*num_improper[i]; - - if (atom->nextra_restart) - for (int iextra = 0; iextra < atom->nextra_restart; iextra++) - for (i = 0; i < nlocal; i++) - n += modify->fix[atom->extra_restart[iextra]]->size_restart(i); - - return n; -} - -/* ---------------------------------------------------------------------- - pack atom I's data for restart file including extra quantities - xyz must be 1st 3 values, so that read_restart can test on them - molecular types may be negative, but write as positive -------------------------------------------------------------------------- */ - -int AtomVecMolecularKokkos::pack_restart(int i, double *buf) -{ - atomKK->sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | MOLECULE_MASK | BOND_MASK | - ANGLE_MASK | DIHEDRAL_MASK | IMPROPER_MASK | SPECIAL_MASK); - - int m = 1; - buf[m++] = h_x(i,0); - buf[m++] = h_x(i,1); - buf[m++] = h_x(i,2); - buf[m++] = ubuf(h_tag(i)).d; - buf[m++] = ubuf(h_type(i)).d; - buf[m++] = ubuf(h_mask(i)).d; - buf[m++] = ubuf(h_image(i)).d; - buf[m++] = h_v(i,0); - buf[m++] = h_v(i,1); - buf[m++] = h_v(i,2); - - buf[m++] = ubuf(h_molecule(i)).d; - - buf[m++] = ubuf(h_num_bond(i)).d; - for (int k = 0; k < h_num_bond(i); k++) { - buf[m++] = ubuf(MAX(h_bond_type(i,k),-h_bond_type(i,k))).d; - buf[m++] = ubuf(h_bond_atom(i,k)).d; - } - - buf[m++] = ubuf(h_num_angle(i)).d; - for (int k = 0; k < h_num_angle(i); k++) { - buf[m++] = ubuf(MAX(h_angle_type(i,k),-h_angle_type(i,k))).d; - buf[m++] = ubuf(h_angle_atom1(i,k)).d; - buf[m++] = ubuf(h_angle_atom2(i,k)).d; - buf[m++] = ubuf(h_angle_atom3(i,k)).d; - } - - buf[m++] = ubuf(h_num_dihedral(i)).d; - for (int k = 0; k < h_num_dihedral(i); k++) { - buf[m++] = ubuf(MAX(h_dihedral_type(i,k),-h_dihedral_type(i,k))).d; - buf[m++] = ubuf(h_dihedral_atom1(i,k)).d; - buf[m++] = ubuf(h_dihedral_atom2(i,k)).d; - buf[m++] = ubuf(h_dihedral_atom3(i,k)).d; - buf[m++] = ubuf(h_dihedral_atom4(i,k)).d; - } - - buf[m++] = ubuf(h_num_improper(i)).d; - for (int k = 0; k < h_num_improper(i); k++) { - buf[m++] = ubuf(MAX(h_improper_type(i,k),-h_improper_type(i,k))).d; - buf[m++] = ubuf(h_improper_atom1(i,k)).d; - buf[m++] = ubuf(h_improper_atom2(i,k)).d; - buf[m++] = ubuf(h_improper_atom3(i,k)).d; - buf[m++] = ubuf(h_improper_atom4(i,k)).d; - } - - if (atom->nextra_restart) - for (int iextra = 0; iextra < atom->nextra_restart; iextra++) - m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]); - - buf[0] = m; - return m; -} - -/* ---------------------------------------------------------------------- - unpack data for one atom from restart file including extra quantities -------------------------------------------------------------------------- */ - -int AtomVecMolecularKokkos::unpack_restart(double *buf) -{ - int k; - - int nlocal = atom->nlocal; - if (nlocal == nmax) { - grow(0); - if (atom->nextra_store) - memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra"); - } - - atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | MOLECULE_MASK | BOND_MASK | - ANGLE_MASK | DIHEDRAL_MASK | IMPROPER_MASK | SPECIAL_MASK); - - int m = 1; - h_x(nlocal,0) = buf[m++]; - h_x(nlocal,1) = buf[m++]; - h_x(nlocal,2) = buf[m++]; - h_tag(nlocal) = (tagint) ubuf(buf[m++]).i; - h_type(nlocal) = (int) ubuf(buf[m++]).i; - h_mask(nlocal) = (int) ubuf(buf[m++]).i; - h_image(nlocal) = (imageint) ubuf(buf[m++]).i; - h_v(nlocal,0) = buf[m++]; - h_v(nlocal,1) = buf[m++]; - h_v(nlocal,2) = buf[m++]; - - h_molecule(nlocal) = (tagint) ubuf(buf[m++]).i; - - h_num_bond(nlocal) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_num_bond(nlocal); k++) { - h_bond_type(nlocal,k) = (int) ubuf(buf[m++]).i; - h_bond_atom(nlocal,k) = (tagint) ubuf(buf[m++]).i; - } - - h_num_angle(nlocal) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_num_angle(nlocal); k++) { - h_angle_type(nlocal,k) = (int) ubuf(buf[m++]).i; - h_angle_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_angle_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_angle_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i; - } - - h_num_dihedral(nlocal) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_num_dihedral(nlocal); k++) { - h_dihedral_type(nlocal,k) = (int) ubuf(buf[m++]).i; - h_dihedral_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_dihedral_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_dihedral_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_dihedral_atom4(nlocal,k) = (tagint) ubuf(buf[m++]).i; - } - - h_num_improper(nlocal) = (int) ubuf(buf[m++]).i; - for (k = 0; k < h_num_improper(nlocal); k++) { - h_improper_type(nlocal,k) = (int) ubuf(buf[m++]).i; - h_improper_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_improper_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_improper_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i; - h_improper_atom4(nlocal,k) = (tagint) ubuf(buf[m++]).i; - } - - h_nspecial(nlocal,0) = h_nspecial(nlocal,1) = h_nspecial(nlocal,2) = 0; - - double **extra = atom->extra; - if (atom->nextra_store) { - int size = static_cast (buf[0]) - m; - for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++]; - } - - atom->nlocal++; - return m; -} - -/* ---------------------------------------------------------------------- - create one atom of itype at coord - set other values to defaults -------------------------------------------------------------------------- */ - -void AtomVecMolecularKokkos::create_atom(int itype, double *coord) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) { - atomKK->modified(Host,ALL_MASK); - grow(0); - } - atomKK->modified(Host,ALL_MASK); - - tag[nlocal] = 0; - type[nlocal] = itype; - h_x(nlocal,0) = coord[0]; - h_x(nlocal,1) = coord[1]; - h_x(nlocal,2) = coord[2]; - h_mask(nlocal) = 1; - h_image(nlocal) = ((imageint) IMGMAX << IMG2BITS) | - ((imageint) IMGMAX << IMGBITS) | IMGMAX; - h_v(nlocal,0) = 0.0; - h_v(nlocal,1) = 0.0; - h_v(nlocal,2) = 0.0; - - h_molecule(nlocal) = 0; - h_num_bond(nlocal) = 0; - h_num_angle(nlocal) = 0; - h_num_dihedral(nlocal) = 0; - h_num_improper(nlocal) = 0; - h_nspecial(nlocal,0) = h_nspecial(nlocal,1) = h_nspecial(nlocal,2) = 0; - - atom->nlocal++; -} - -/* ---------------------------------------------------------------------- - unpack one line from Atoms section of data file - initialize other atom quantities -------------------------------------------------------------------------- */ - -void AtomVecMolecularKokkos::data_atom(double *coord, imageint imagetmp, - const std::vector &values, std::string &extract) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) grow(0); - atomKK->modified(Host,ALL_MASK); - - h_tag(nlocal) = utils::inumeric(FLERR,values[0],true,lmp); - h_molecule(nlocal) = utils::inumeric(FLERR,values[1],true,lmp); - h_type(nlocal) = utils::inumeric(FLERR,values[2],true,lmp); - extract = values[2]; - if (h_type(nlocal) <= 0 || h_type(nlocal) > atom->ntypes) - error->one(FLERR,"Invalid atom type in Atoms section of data file"); - - h_x(nlocal,0) = coord[0]; - h_x(nlocal,1) = coord[1]; - h_x(nlocal,2) = coord[2]; - - h_image(nlocal) = imagetmp; - - h_mask(nlocal) = 1; - h_v(nlocal,0) = 0.0; - h_v(nlocal,1) = 0.0; - h_v(nlocal,2) = 0.0; - h_num_bond(nlocal) = 0; - h_num_angle(nlocal) = 0; - h_num_dihedral(nlocal) = 0; - h_num_improper(nlocal) = 0; - - atom->nlocal++; -} - -/* ---------------------------------------------------------------------- - unpack hybrid quantities from one line in Atoms section of data file - initialize other atom quantities for this sub-style -------------------------------------------------------------------------- */ - -int AtomVecMolecularKokkos::data_atom_hybrid(int nlocal, const std::vector &values, - int offset) -{ - h_molecule(nlocal) = utils::inumeric(FLERR,values[offset],true,lmp); - h_num_bond(nlocal) = 0; - h_num_angle(nlocal) = 0; - h_num_dihedral(nlocal) = 0; - h_num_improper(nlocal) = 0; - return 1; -} - -/* ---------------------------------------------------------------------- - pack atom info for data file including 3 image flags -------------------------------------------------------------------------- */ - -void AtomVecMolecularKokkos::pack_data(double **buf) -{ - int nlocal = atom->nlocal; - for (int i = 0; i < nlocal; i++) { - buf[i][0] = h_tag(i); - buf[i][1] = h_molecule(i); - buf[i][2] = h_type(i); - buf[i][3] = h_x(i,0); - buf[i][4] = h_x(i,1); - buf[i][5] = h_x(i,2); - buf[i][6] = (h_image[i] & IMGMASK) - IMGMAX; - buf[i][7] = (h_image[i] >> IMGBITS & IMGMASK) - IMGMAX; - buf[i][8] = (h_image[i] >> IMG2BITS) - IMGMAX; - } -} - -/* ---------------------------------------------------------------------- - pack hybrid atom info for data file -------------------------------------------------------------------------- */ - -int AtomVecMolecularKokkos::pack_data_hybrid(int i, double *buf) -{ - buf[0] = h_molecule(i); - return 1; -} - -/* ---------------------------------------------------------------------- - write atom info to data file including 3 image flags -------------------------------------------------------------------------- */ - -void AtomVecMolecularKokkos::write_data(FILE *fp, int n, double **buf) -{ - for (int i = 0; i < n; i++) - fprintf(fp,"%d %d %d %-1.16e %-1.16e %-1.16e %d %d %d\n", - (int) buf[i][0],(int) buf[i][1], (int) buf[i][2], - buf[i][3],buf[i][4],buf[i][5], - (int) buf[i][6],(int) buf[i][7],(int) buf[i][8]); -} - -/* ---------------------------------------------------------------------- - write hybrid atom info to data file -------------------------------------------------------------------------- */ - -int AtomVecMolecularKokkos::write_data_hybrid(FILE *fp, double *buf) -{ - fprintf(fp," " TAGINT_FORMAT, (tagint) (buf[0])); - return 1; -} - -/* ---------------------------------------------------------------------- - return # of bytes of allocated memory -------------------------------------------------------------------------- */ - -double AtomVecMolecularKokkos::memory_usage() -{ - double bytes = 0; - - if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax); - if (atom->memcheck("type")) bytes += memory->usage(type,nmax); - if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax); - if (atom->memcheck("image")) bytes += memory->usage(image,nmax); - if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3); - if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3); - if (atom->memcheck("f")) bytes += memory->usage(f,nmax*commKK->nthreads,3); - - if (atom->memcheck("molecule")) bytes += memory->usage(molecule,nmax); - if (atom->memcheck("nspecial")) bytes += memory->usage(nspecial,nmax,3); - if (atom->memcheck("special")) - bytes += memory->usage(special,nmax,atom->maxspecial); - - if (atom->memcheck("num_bond")) bytes += memory->usage(num_bond,nmax); - if (atom->memcheck("bond_type")) - bytes += memory->usage(bond_type,nmax,atom->bond_per_atom); - if (atom->memcheck("bond_atom")) - bytes += memory->usage(bond_atom,nmax,atom->bond_per_atom); - - if (atom->memcheck("num_angle")) bytes += memory->usage(num_angle,nmax); - if (atom->memcheck("angle_type")) - bytes += memory->usage(angle_type,nmax,atom->angle_per_atom); - if (atom->memcheck("angle_atom1")) - bytes += memory->usage(angle_atom1,nmax,atom->angle_per_atom); - if (atom->memcheck("angle_atom2")) - bytes += memory->usage(angle_atom2,nmax,atom->angle_per_atom); - if (atom->memcheck("angle_atom3")) - bytes += memory->usage(angle_atom3,nmax,atom->angle_per_atom); - - if (atom->memcheck("num_dihedral")) bytes += memory->usage(num_dihedral,nmax); - if (atom->memcheck("dihedral_type")) - bytes += memory->usage(dihedral_type,nmax,atom->dihedral_per_atom); - if (atom->memcheck("dihedral_atom1")) - bytes += memory->usage(dihedral_atom1,nmax,atom->dihedral_per_atom); - if (atom->memcheck("dihedral_atom2")) - bytes += memory->usage(dihedral_atom2,nmax,atom->dihedral_per_atom); - if (atom->memcheck("dihedral_atom3")) - bytes += memory->usage(dihedral_atom3,nmax,atom->dihedral_per_atom); - if (atom->memcheck("dihedral_atom4")) - bytes += memory->usage(dihedral_atom4,nmax,atom->dihedral_per_atom); - if (atom->memcheck("num_improper")) bytes += memory->usage(num_improper,nmax); - if (atom->memcheck("improper_type")) - bytes += memory->usage(improper_type,nmax,atom->improper_per_atom); - if (atom->memcheck("improper_atom1")) - bytes += memory->usage(improper_atom1,nmax,atom->improper_per_atom); - if (atom->memcheck("improper_atom2")) - bytes += memory->usage(improper_atom2,nmax,atom->improper_per_atom); - if (atom->memcheck("improper_atom3")) - bytes += memory->usage(improper_atom3,nmax,atom->improper_per_atom); - if (atom->memcheck("improper_atom4")) - bytes += memory->usage(improper_atom4,nmax,atom->improper_per_atom); - - return bytes; -} - -/* ---------------------------------------------------------------------- */ - void AtomVecMolecularKokkos::sync(ExecutionSpace space, unsigned int mask) { if (space == Device) { @@ -2377,4 +1419,3 @@ void AtomVecMolecularKokkos::modified(ExecutionSpace space, unsigned int mask) } } } - diff --git a/src/KOKKOS/atom_vec_molecular_kokkos.h b/src/KOKKOS/atom_vec_molecular_kokkos.h index cca7c3c6d9..6c011823fe 100644 --- a/src/KOKKOS/atom_vec_molecular_kokkos.h +++ b/src/KOKKOS/atom_vec_molecular_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,41 +24,15 @@ AtomStyle(molecular/kk/host,AtomVecMolecularKokkos); #define LMP_ATOM_VEC_MOLECULAR_KOKKOS_H #include "atom_vec_kokkos.h" +#include "atom_vec_molecular.h" namespace LAMMPS_NS { -class AtomVecMolecularKokkos : public AtomVecKokkos { +class AtomVecMolecularKokkos : public AtomVecKokkos, public AtomVecMolecular { public: AtomVecMolecularKokkos(class LAMMPS *); void grow(int) override; - void copy(int, int, int) override; - int pack_comm(int, int *, double *, int, int *) override; - int pack_comm_vel(int, int *, double *, int, int *) override; - void unpack_comm(int, int, double *) override; - void unpack_comm_vel(int, int, double *) override; - int pack_reverse(int, int, double *) override; - void unpack_reverse(int, int *, double *) override; - int pack_border(int, int *, double *, int, int *) override; - int pack_border_vel(int, int *, double *, int, int *) override; - int pack_border_hybrid(int, int *, double *) override; - void unpack_border(int, int, double *) override; - void unpack_border_vel(int, int, double *) override; - int unpack_border_hybrid(int, int, double *) override; - int pack_exchange(int, double *) override; - int unpack_exchange(double *) override; - int size_restart() override; - int pack_restart(int, double *) override; - int unpack_restart(double *) override; - void create_atom(int, double *) override; - void data_atom(double *, imageint, const std::vector &, std::string &) override; - int data_atom_hybrid(int, const std::vector &, int) override; - void pack_data(double **) override; - int pack_data_hybrid(int, double *) override; - void write_data(FILE *, int, double **) override; - int write_data_hybrid(FILE *, double *) override; - double memory_usage() override; - void grow_pointers() override; int pack_comm_kokkos(const int &n, const DAT::tdual_int_2d &k_sendlist, const int & iswap, @@ -89,28 +63,11 @@ class AtomVecMolecularKokkos : public AtomVecKokkos { void sync_overlapping_device(ExecutionSpace space, unsigned int mask) override; protected: - - tagint *tag; - int *type,*mask; - imageint *image; - double **x,**v,**f; - tagint *molecule; - int **nspecial; tagint **special; - int *num_bond; - int **bond_type; tagint **bond_atom; - - int *num_angle; - int **angle_type; tagint **angle_atom1,**angle_atom2,**angle_atom3; - - int *num_dihedral; - int **dihedral_type; tagint **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4; - int *num_improper; - int **improper_type; tagint **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4; DAT::t_tagint_1d d_tag; @@ -167,13 +124,9 @@ class AtomVecMolecularKokkos : public AtomVecKokkos { HAT::t_int_2d h_improper_type; HAT::t_tagint_2d h_improper_atom1,h_improper_atom2, h_improper_atom3,h_improper_atom4; - - HAT::tdual_int_1d k_count; - }; -} +} // namespace LAMMPS_NS #endif #endif - diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp index fa952beb5f..b197e7c831 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp +++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -33,55 +33,12 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -AtomVecSphereKokkos::AtomVecSphereKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) +AtomVecSphereKokkos::AtomVecSphereKokkos(LAMMPS *lmp) : AtomVec(lmp), +AtomVecKokkos(lmp), AtomVecSphere(lmp) { - molecular = Atom::ATOMIC; - - comm_x_only = 1; - comm_f_only = 0; - size_forward = 3; - size_reverse = 6; - size_border = 8; - size_velocity = 6; - size_data_atom = 7; - size_data_vel = 7; - xcol_data = 5; - - atom->sphere_flag = 1; - atom->radius_flag = atom->rmass_flag = atom->omega_flag = - atom->torque_flag = 1; - - k_count = DAT::tdual_int_1d("atom::k_count",1); - atomKK = (AtomKokkos *) atom; - commKK = (CommKokkos *) comm; - no_border_vel_flag = 0; } -/* ---------------------------------------------------------------------- */ - -void AtomVecSphereKokkos::init() -{ - AtomVec::init(); - - // set radvary if particle diameters are time-varying due to fix adapt - - radvary = 0; - comm_x_only = 1; - size_forward = 3; - - for (int i = 0; i < modify->nfix; i++) { - if (strcmp(modify->fix[i]->style,"adapt") == 0) { - FixAdapt *fix = (FixAdapt *) modify->fix[i]; - if (fix->diamflag) { - radvary = 1; - comm_x_only = 0; - size_forward = 5; - } - } - } -} - /* ---------------------------------------------------------------------- grow atom arrays n = 0 grows arrays by a chunk @@ -165,42 +122,6 @@ void AtomVecSphereKokkos::grow_pointers() h_torque = atomKK->k_torque.h_view; } -/* ---------------------------------------------------------------------- - copy atom I info to atom J -------------------------------------------------------------------------- */ - -void AtomVecSphereKokkos::copy(int i, int j, int delflag) -{ - atomKK->sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | RADIUS_MASK | - RMASS_MASK | OMEGA_MASK); - - h_tag[j] = h_tag[i]; - h_type[j] = h_type[i]; - h_mask[j] = h_mask[i]; - h_image[j] = h_image[i]; - h_x(j,0) = h_x(i,0); - h_x(j,1) = h_x(i,1); - h_x(j,2) = h_x(i,2); - h_v(j,0) = h_v(i,0); - h_v(j,1) = h_v(i,1); - h_v(j,2) = h_v(i,2); - - h_radius[j] = h_radius[i]; - h_rmass[j] = h_rmass[i]; - h_omega(j,0) = h_omega(i,0); - h_omega(j,1) = h_omega(i,1); - h_omega(j,2) = h_omega(i,2); - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag); - - atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | RADIUS_MASK | - RMASS_MASK | OMEGA_MASK); -} - /* ---------------------------------------------------------------------- */ template @@ -1035,397 +956,6 @@ void AtomVecSphereKokkos::unpack_comm_vel_kokkos( /* ---------------------------------------------------------------------- */ -int AtomVecSphereKokkos::pack_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz; - - if (radvary == 0) { - // Not sure if we need to call sync for X here - atomKK->sync(Host,X_MASK); - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; - dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; - dz = pbc[2]*domain->zprd; - } - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - } - } - } else { - atomKK->sync(Host,X_MASK|RADIUS_MASK|RMASS_MASK); - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = h_radius[j]; - buf[m++] = h_rmass[j]; - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; - dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; - dz = pbc[2]*domain->zprd; - } - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = h_radius[j]; - buf[m++] = h_rmass[j]; - } - } - } - - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecSphereKokkos::pack_comm_vel(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz,dvx,dvy,dvz; - - if (radvary == 0) { - atomKK->sync(Host,X_MASK|V_MASK|OMEGA_MASK); - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - buf[m++] = h_omega(j,0); - buf[m++] = h_omega(j,1); - buf[m++] = h_omega(j,2); - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; - dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; - dz = pbc[2]*domain->zprd; - } - if (!deform_vremap) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - buf[m++] = h_omega(j,0); - buf[m++] = h_omega(j,1); - buf[m++] = h_omega(j,2); - } - } else { - dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; - dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; - dvz = pbc[2]*h_rate[2]; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - if (mask[i] & deform_groupbit) { - buf[m++] = h_v(j,0) + dvx; - buf[m++] = h_v(j,1) + dvy; - buf[m++] = h_v(j,2) + dvz; - } else { - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - buf[m++] = h_omega(j,0); - buf[m++] = h_omega(j,1); - buf[m++] = h_omega(j,2); - } - } - } - } else { - atomKK->sync(Host,X_MASK|RADIUS_MASK|RMASS_MASK|V_MASK|OMEGA_MASK); - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = h_radius[j]; - buf[m++] = h_rmass[j]; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - buf[m++] = h_omega(j,0); - buf[m++] = h_omega(j,1); - buf[m++] = h_omega(j,2); - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; - dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; - dz = pbc[2]*domain->zprd; - } - if (!deform_vremap) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = h_radius[j]; - buf[m++] = h_rmass[j]; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - buf[m++] = h_omega(j,0); - buf[m++] = h_omega(j,1); - buf[m++] = h_omega(j,2); - } - } else { - dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; - dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; - dvz = pbc[2]*h_rate[2]; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = h_radius[j]; - buf[m++] = h_rmass[j]; - if (mask[i] & deform_groupbit) { - buf[m++] = h_v(j,0) + dvx; - buf[m++] = h_v(j,1) + dvy; - buf[m++] = h_v(j,2) + dvz; - } else { - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - buf[m++] = h_omega(j,0); - buf[m++] = h_omega(j,1); - buf[m++] = h_omega(j,2); - } - } - } - } - - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecSphereKokkos::pack_comm_hybrid(int n, int *list, double *buf) -{ - if (radvary == 0) return 0; - - atomKK->sync(Host,RADIUS_MASK|RMASS_MASK); - - int m = 0; - for (int i = 0; i < n; i++) { - const int j = list[i]; - buf[m++] = h_radius[j]; - buf[m++] = h_rmass[j]; - } - return m; -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecSphereKokkos::unpack_comm(int n, int first, double *buf) -{ - if (radvary == 0) { - int m = 0; - const int last = first + n; - for (int i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - } - atomKK->modified(Host,X_MASK); - } else { - int m = 0; - const int last = first + n; - for (int i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_radius[i] = buf[m++]; - h_rmass[i] = buf[m++]; - } - atomKK->modified(Host,X_MASK|RADIUS_MASK|RMASS_MASK); - } -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecSphereKokkos::unpack_comm_vel(int n, int first, double *buf) -{ - if (radvary == 0) { - int m = 0; - const int last = first + n; - for (int i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_v(i,0) = buf[m++]; - h_v(i,1) = buf[m++]; - h_v(i,2) = buf[m++]; - h_omega(i,0) = buf[m++]; - h_omega(i,1) = buf[m++]; - h_omega(i,2) = buf[m++]; - } - atomKK->modified(Host,X_MASK|V_MASK|OMEGA_MASK); - } else { - int m = 0; - const int last = first + n; - for (int i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_radius[i] = buf[m++]; - h_rmass[i] = buf[m++]; - h_v(i,0) = buf[m++]; - h_v(i,1) = buf[m++]; - h_v(i,2) = buf[m++]; - h_omega(i,0) = buf[m++]; - h_omega(i,1) = buf[m++]; - h_omega(i,2) = buf[m++]; - } - atomKK->modified(Host,X_MASK|RADIUS_MASK|RMASS_MASK|V_MASK|OMEGA_MASK); - } -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecSphereKokkos::unpack_comm_hybrid(int n, int first, double *buf) -{ - if (radvary == 0) return 0; - - int m = 0; - const int last = first + n; - for (int i = first; i < last; i++) { - h_radius[i] = buf[m++]; - h_rmass[i] = buf[m++]; - } - atomKK->modified(Host,RADIUS_MASK|RMASS_MASK); - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecSphereKokkos::pack_reverse(int n, int first, double *buf) -{ - if (n > 0) - atomKK->sync(Host,F_MASK|TORQUE_MASK); - - int m = 0; - const int last = first + n; - for (int i = first; i < last; i++) { - buf[m++] = h_f(i,0); - buf[m++] = h_f(i,1); - buf[m++] = h_f(i,2); - buf[m++] = h_torque(i,0); - buf[m++] = h_torque(i,1); - buf[m++] = h_torque(i,2); - } - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecSphereKokkos::pack_reverse_hybrid(int n, int first, double *buf) -{ - if (n > 0) - atomKK->sync(Host,TORQUE_MASK); - - int m = 0; - const int last = first + n; - for (int i = first; i < last; i++) { - buf[m++] = h_torque(i,0); - buf[m++] = h_torque(i,1); - buf[m++] = h_torque(i,2); - } - return m; -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecSphereKokkos::unpack_reverse(int n, int *list, double *buf) -{ - if (n > 0) { - atomKK->modified(Host,F_MASK|TORQUE_MASK); - } - - int m = 0; - for (int i = 0; i < n; i++) { - const int j = list[i]; - h_f(j,0) += buf[m++]; - h_f(j,1) += buf[m++]; - h_f(j,2) += buf[m++]; - h_torque(j,0) += buf[m++]; - h_torque(j,1) += buf[m++]; - h_torque(j,2) += buf[m++]; - } -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecSphereKokkos::unpack_reverse_hybrid(int n, int *list, double *buf) -{ - if (n > 0) { - atomKK->modified(Host,TORQUE_MASK); - } - - int m = 0; - for (int i = 0; i < n; i++) { - const int j = list[i]; - h_torque(j,0) += buf[m++]; - h_torque(j,1) += buf[m++]; - h_torque(j,2) += buf[m++]; - } - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecSphereKokkos_PackBorder { typedef DeviceType device_type; @@ -1541,60 +1071,6 @@ int AtomVecSphereKokkos::pack_border_kokkos( /* ---------------------------------------------------------------------- */ -int AtomVecSphereKokkos::pack_border( - int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz; - - atomKK->sync(Host,ALL_MASK); - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = ubuf(h_tag[j]).d; - buf[m++] = ubuf(h_type[j]).d; - buf[m++] = ubuf(h_mask[j]).d; - buf[m++] = h_radius[j]; - buf[m++] = h_rmass[j]; - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]; - dy = pbc[1]; - dz = pbc[2]; - } - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag[j]).d; - buf[m++] = ubuf(h_type[j]).d; - buf[m++] = ubuf(h_mask[j]).d; - buf[m++] = h_radius[j]; - buf[m++] = h_rmass[j]; - } - } - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); - - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecSphereKokkos_PackBorderVel { typedef DeviceType device_type; @@ -1769,115 +1245,6 @@ int AtomVecSphereKokkos::pack_border_vel_kokkos( /* ---------------------------------------------------------------------- */ -int AtomVecSphereKokkos::pack_border_vel(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz,dvx,dvy,dvz; - - atomKK->sync(Host,ALL_MASK); - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = ubuf(h_tag[j]).d; - buf[m++] = ubuf(h_type[j]).d; - buf[m++] = ubuf(h_mask[j]).d; - buf[m++] = h_radius[j]; - buf[m++] = h_rmass[j]; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - buf[m++] = h_omega(j,0); - buf[m++] = h_omega(j,1); - buf[m++] = h_omega(j,2); - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]; - dy = pbc[1]; - dz = pbc[2]; - } - if (!deform_vremap) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag[j]).d; - buf[m++] = ubuf(h_type[j]).d; - buf[m++] = ubuf(h_mask[j]).d; - buf[m++] = h_radius[j]; - buf[m++] = h_rmass[j]; - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - buf[m++] = h_omega(j,0); - buf[m++] = h_omega(j,1); - buf[m++] = h_omega(j,2); - } - } else { - dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; - dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; - dvz = pbc[2]*h_rate[2]; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag[j]).d; - buf[m++] = ubuf(h_type[j]).d; - buf[m++] = ubuf(h_mask[j]).d; - buf[m++] = h_radius[j]; - buf[m++] = h_rmass[j]; - if (mask[i] & deform_groupbit) { - buf[m++] = h_v(j,0) + dvx; - buf[m++] = h_v(j,1) + dvy; - buf[m++] = h_v(j,2) + dvz; - } else { - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - buf[m++] = h_omega(j,0); - buf[m++] = h_omega(j,1); - buf[m++] = h_omega(j,2); - } - } - } - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); - - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecSphereKokkos::pack_border_hybrid(int n, int *list, double *buf) -{ - atomKK->sync(Host,RADIUS_MASK|RMASS_MASK); - - int m = 0; - for (int i = 0; i < n; i++) { - const int j = list[i]; - buf[m++] = h_radius[j]; - buf[m++] = h_rmass[j]; - } - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecSphereKokkos_UnpackBorder { typedef DeviceType device_type; @@ -1945,34 +1312,6 @@ void AtomVecSphereKokkos::unpack_border_kokkos(const int &n, const int &first, RADIUS_MASK|RMASS_MASK); } -/* ---------------------------------------------------------------------- */ - -void AtomVecSphereKokkos::unpack_border(int n, int first, double *buf) -{ - int m = 0; - const int last = first + n; - while (last > nmax) grow(0); - - for (int i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_tag[i] = (tagint) ubuf(buf[m++]).i; - h_type[i] = (int) ubuf(buf[m++]).i; - h_mask[i] = (int) ubuf(buf[m++]).i; - h_radius[i] = buf[m++]; - h_rmass[i] = buf[m++]; - } - - atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|RADIUS_MASK|RMASS_MASK); - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]-> - unpack_border(n,first,&buf[m]); -} - - /* ---------------------------------------------------------------------- */ template @@ -2058,53 +1397,6 @@ void AtomVecSphereKokkos::unpack_border_vel_kokkos( /* ---------------------------------------------------------------------- */ -void AtomVecSphereKokkos::unpack_border_vel(int n, int first, double *buf) -{ - int m = 0; - const int last = first + n; - while (last > nmax) grow(0); - - for (int i = first; i < last; i++) { - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_tag[i] = (tagint) ubuf(buf[m++]).i; - h_type[i] = (int) ubuf(buf[m++]).i; - h_mask[i] = (int) ubuf(buf[m++]).i; - h_radius[i] = buf[m++]; - h_rmass[i] = buf[m++]; - h_v(i,0) = buf[m++]; - h_v(i,1) = buf[m++]; - h_v(i,2) = buf[m++]; - h_omega(i,0) = buf[m++]; - h_omega(i,1) = buf[m++]; - h_omega(i,2) = buf[m++]; - } - - atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|RADIUS_MASK|RMASS_MASK|V_MASK|OMEGA_MASK); - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]-> - unpack_border(n,first,&buf[m]); -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecSphereKokkos::unpack_border_hybrid(int n, int first, double *buf) -{ - int m = 0; - const int last = first + n; - for (int i = first; i < last; i++) { - h_radius[i] = buf[m++]; - h_rmass[i] = buf[m++]; - } - atomKK->modified(Host,RADIUS_MASK|RMASS_MASK); - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecSphereKokkos_PackExchangeFunctor { typedef DeviceType device_type; @@ -2233,44 +1525,6 @@ int AtomVecSphereKokkos::pack_exchange_kokkos( return nsend*16; } -/* ---------------------------------------------------------------------- - pack data for atom I for sending to another proc - xyz must be 1st 3 values, so comm::exchange() can test on them -------------------------------------------------------------------------- */ - -int AtomVecSphereKokkos::pack_exchange(int i, double *buf) -{ - atomKK->sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK| RADIUS_MASK | RMASS_MASK | - OMEGA_MASK); - - - int m = 1; - buf[m++] = h_x(i,0); - buf[m++] = h_x(i,1); - buf[m++] = h_x(i,2); - buf[m++] = h_v(i,0); - buf[m++] = h_v(i,1); - buf[m++] = h_v(i,2); - buf[m++] = ubuf(h_tag[i]).d; - buf[m++] = ubuf(h_type[i]).d; - buf[m++] = ubuf(h_mask[i]).d; - buf[m++] = ubuf(h_image[i]).d; - - buf[m++] = h_radius[i]; - buf[m++] = h_rmass[i]; - buf[m++] = h_omega(i,0); - buf[m++] = h_omega(i,1); - buf[m++] = h_omega(i,2); - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]); - - buf[0] = m; - return m; -} - /* ---------------------------------------------------------------------- */ template @@ -2366,437 +1620,6 @@ int AtomVecSphereKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int /* ---------------------------------------------------------------------- */ -int AtomVecSphereKokkos::unpack_exchange(double *buf) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) grow(0); - - int m = 1; - h_x(nlocal,0) = buf[m++]; - h_x(nlocal,1) = buf[m++]; - h_x(nlocal,2) = buf[m++]; - h_v(nlocal,0) = buf[m++]; - h_v(nlocal,1) = buf[m++]; - h_v(nlocal,2) = buf[m++]; - h_tag[nlocal] = (tagint) ubuf(buf[m++]).i; - h_type[nlocal] = (int) ubuf(buf[m++]).i; - h_mask[nlocal] = (int) ubuf(buf[m++]).i; - h_image[nlocal] = (imageint) ubuf(buf[m++]).i; - - h_radius[nlocal] = buf[m++]; - h_rmass[nlocal] = buf[m++]; - h_omega(nlocal,0) = buf[m++]; - h_omega(nlocal,1) = buf[m++]; - h_omega(nlocal,2) = buf[m++]; - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - m += modify->fix[atom->extra_grow[iextra]]-> - unpack_exchange(nlocal,&buf[m]); - - atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | RADIUS_MASK | RMASS_MASK | - OMEGA_MASK); - - atom->nlocal++; - return m; -} - -/* ---------------------------------------------------------------------- - size of restart data for all atoms owned by this proc - include extra data stored by fixes -------------------------------------------------------------------------- */ - -int AtomVecSphereKokkos::size_restart() -{ - int i; - - int nlocal = atom->nlocal; - int n = 16 * nlocal; - - if (atom->nextra_restart) - for (int iextra = 0; iextra < atom->nextra_restart; iextra++) - for (i = 0; i < nlocal; i++) - n += modify->fix[atom->extra_restart[iextra]]->size_restart(i); - - return n; -} - -/* ---------------------------------------------------------------------- - pack atom I's data for restart file including extra quantities - xyz must be 1st 3 values, so that read_restart can test on them - molecular types may be negative, but write as positive -------------------------------------------------------------------------- */ - -int AtomVecSphereKokkos::pack_restart(int i, double *buf) -{ - atomKK->sync(Host,X_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | V_MASK | - RADIUS_MASK | RMASS_MASK | OMEGA_MASK); - - int m = 1; - buf[m++] = h_x(i,0); - buf[m++] = h_x(i,1); - buf[m++] = h_x(i,2); - buf[m++] = ubuf(h_tag[i]).d; - buf[m++] = ubuf(h_type[i]).d; - buf[m++] = ubuf(h_mask[i]).d; - buf[m++] = ubuf(h_image[i]).d; - buf[m++] = h_v(i,0); - buf[m++] = h_v(i,1); - buf[m++] = h_v(i,2); - - buf[m++] = h_radius[i]; - buf[m++] = h_rmass[i]; - buf[m++] = h_omega(i,0); - buf[m++] = h_omega(i,1); - buf[m++] = h_omega(i,2); - - if (atom->nextra_restart) - for (int iextra = 0; iextra < atom->nextra_restart; iextra++) - m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]); - - buf[0] = m; - return m; -} - -/* ---------------------------------------------------------------------- - unpack data for one atom from restart file including extra quantities -------------------------------------------------------------------------- */ - -int AtomVecSphereKokkos::unpack_restart(double *buf) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) { - grow(0); - if (atom->nextra_store) - memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra"); - } - - int m = 1; - h_x(nlocal,0) = buf[m++]; - h_x(nlocal,1) = buf[m++]; - h_x(nlocal,2) = buf[m++]; - h_tag[nlocal] = (tagint) ubuf(buf[m++]).i; - h_type[nlocal] = (int) ubuf(buf[m++]).i; - h_mask[nlocal] = (int) ubuf(buf[m++]).i; - h_image[nlocal] = (imageint) ubuf(buf[m++]).i; - h_v(nlocal,0) = buf[m++]; - h_v(nlocal,1) = buf[m++]; - h_v(nlocal,2) = buf[m++]; - - h_radius[nlocal] = buf[m++]; - h_rmass[nlocal] = buf[m++]; - h_omega(nlocal,0) = buf[m++]; - h_omega(nlocal,1) = buf[m++]; - h_omega(nlocal,2) = buf[m++]; - - double **extra = atom->extra; - if (atom->nextra_store) { - int size = static_cast (buf[0]) - m; - for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++]; - } - - atomKK->modified(Host,X_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | V_MASK | - RADIUS_MASK | RMASS_MASK | OMEGA_MASK); - - atom->nlocal++; - return m; -} - -/* ---------------------------------------------------------------------- - create one atom of itype at coord - set other values to defaults -------------------------------------------------------------------------- */ - -void AtomVecSphereKokkos::create_atom(int itype, double *coord) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) { - grow(0); - } - - h_tag[nlocal] = 0; - h_type[nlocal] = itype; - h_x(nlocal,0) = coord[0]; - h_x(nlocal,1) = coord[1]; - h_x(nlocal,2) = coord[2]; - h_mask[nlocal] = 1; - h_image[nlocal] = ((imageint) IMGMAX << IMG2BITS) | - ((imageint) IMGMAX << IMGBITS) | IMGMAX; - h_v(nlocal,0) = 0.0; - h_v(nlocal,1) = 0.0; - h_v(nlocal,2) = 0.0; - - h_radius[nlocal] = 0.5; - h_rmass[nlocal] = 4.0*MY_PI/3.0 * h_radius[nlocal]*h_radius[nlocal]*h_radius[nlocal]; - h_omega(nlocal,0) = 0.0; - h_omega(nlocal,1) = 0.0; - h_omega(nlocal,2) = 0.0; - - atomKK->modified(Host,ALL_MASK); - - atom->nlocal++; -} - -/* ---------------------------------------------------------------------- - unpack one line from Atoms section of data file - initialize other atom quantities -------------------------------------------------------------------------- */ - -void AtomVecSphereKokkos::data_atom(double *coord, imageint imagetmp, - const std::vector &values, std::string &extract) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) grow(0); - - tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); - type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); - extract = values[1]; - if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) - error->one(FLERR,"Invalid atom type in Atoms section of data file"); - - radius[nlocal] = 0.5 * utils::numeric(FLERR,values[2],true,lmp); - if (radius[nlocal] < 0.0) - error->one(FLERR,"Invalid radius in Atoms section of data file"); - - double density = utils::numeric(FLERR,values[3],true,lmp); - if (density <= 0.0) - error->one(FLERR,"Invalid density in Atoms section of data file"); - - if (radius[nlocal] == 0.0) rmass[nlocal] = density; - else - rmass[nlocal] = 4.0*MY_PI/3.0 * - radius[nlocal]*radius[nlocal]*radius[nlocal] * density; - - x[nlocal][0] = coord[0]; - x[nlocal][1] = coord[1]; - x[nlocal][2] = coord[2]; - - image[nlocal] = imagetmp; - - mask[nlocal] = 1; - v[nlocal][0] = 0.0; - v[nlocal][1] = 0.0; - v[nlocal][2] = 0.0; - omega[nlocal][0] = 0.0; - omega[nlocal][1] = 0.0; - omega[nlocal][2] = 0.0; - - atomKK->modified(Host,ALL_MASK); - - atom->nlocal++; -} - -/* ---------------------------------------------------------------------- - unpack hybrid quantities from one line in Atoms section of data file - initialize other atom quantities for this sub-style -------------------------------------------------------------------------- */ - -int AtomVecSphereKokkos::data_atom_hybrid(int nlocal, const std::vector &values, - int offset) -{ - radius[nlocal] = 0.5 * utils::numeric(FLERR,values[offset],true,lmp); - if (radius[nlocal] < 0.0) - error->one(FLERR,"Invalid radius in Atoms section of data file"); - - double density = utils::numeric(FLERR,values[offset+1],true,lmp); - if (density <= 0.0) - error->one(FLERR,"Invalid density in Atoms section of data file"); - - if (radius[nlocal] == 0.0) rmass[nlocal] = density; - else - rmass[nlocal] = 4.0*MY_PI/3.0 * - radius[nlocal]*radius[nlocal]*radius[nlocal] * density; - - - atomKK->modified(Host,RADIUS_MASK|RMASS_MASK); - - return 2; -} - -/* ---------------------------------------------------------------------- - unpack one line from Velocities section of data file -------------------------------------------------------------------------- */ - -void AtomVecSphereKokkos::data_vel(int m, const std::vector &values) -{ - int ivalue = 1; - atomKK->sync(Host,V_MASK|OMEGA_MASK); - h_v(m,0) = utils::numeric(FLERR,values[ivalue++],true,lmp); - h_v(m,1) = utils::numeric(FLERR,values[ivalue++],true,lmp); - h_v(m,2) = utils::numeric(FLERR,values[ivalue++],true,lmp); - h_omega(m,0) = utils::numeric(FLERR,values[ivalue++],true,lmp); - h_omega(m,1) = utils::numeric(FLERR,values[ivalue++],true,lmp); - h_omega(m,2) = utils::numeric(FLERR,values[ivalue++],true,lmp); - atomKK->modified(Host,V_MASK|OMEGA_MASK); -} - -/* ---------------------------------------------------------------------- - unpack hybrid quantities from one line in Velocities section of data file -------------------------------------------------------------------------- */ - -int AtomVecSphereKokkos::data_vel_hybrid(int m, const std::vector &values, - int offset) -{ - atomKK->sync(Host,OMEGA_MASK); - omega[m][0] = utils::numeric(FLERR,values[offset],true,lmp); - omega[m][1] = utils::numeric(FLERR,values[offset+1],true,lmp); - omega[m][2] = utils::numeric(FLERR,values[offset+2],true,lmp); - atomKK->modified(Host,OMEGA_MASK); - return 3; -} - -/* ---------------------------------------------------------------------- - pack atom info for data file including 3 image flags -------------------------------------------------------------------------- */ - -void AtomVecSphereKokkos::pack_data(double **buf) -{ - atomKK->sync(Host,TAG_MASK|TYPE_MASK|RADIUS_MASK|RMASS_MASK|X_MASK|IMAGE_MASK); - - int nlocal = atom->nlocal; - for (int i = 0; i < nlocal; i++) { - buf[i][0] = ubuf(h_tag[i]).d; - buf[i][1] = ubuf(h_type[i]).d; - buf[i][2] = 2.0*h_radius[i]; - if (h_radius[i] == 0.0) buf[i][3] = h_rmass[i]; - else - buf[i][3] = h_rmass[i] / (4.0*MY_PI/3.0 * h_radius[i]*h_radius[i]*h_radius[i]); - buf[i][4] = h_x(i,0); - buf[i][5] = h_x(i,1); - buf[i][6] = h_x(i,2); - buf[i][7] = ubuf((h_image[i] & IMGMASK) - IMGMAX).d; - buf[i][8] = ubuf((h_image[i] >> IMGBITS & IMGMASK) - IMGMAX).d; - buf[i][9] = ubuf((h_image[i] >> IMG2BITS) - IMGMAX).d; - } -} - -/* ---------------------------------------------------------------------- - pack hybrid atom info for data file -------------------------------------------------------------------------- */ - -int AtomVecSphereKokkos::pack_data_hybrid(int i, double *buf) -{ - atomKK->sync(Host,RADIUS_MASK|RMASS_MASK); - - buf[0] = 2.0*h_radius[i]; - if (h_radius[i] == 0.0) buf[1] = h_rmass[i]; - else buf[1] = h_rmass[i] / (4.0*MY_PI/3.0 * h_radius[i]*h_radius[i]*h_radius[i]); - return 2; -} - -/* ---------------------------------------------------------------------- - write atom info to data file including 3 image flags -------------------------------------------------------------------------- */ - -void AtomVecSphereKokkos::write_data(FILE *fp, int n, double **buf) -{ - for (int i = 0; i < n; i++) - fprintf(fp,TAGINT_FORMAT - " %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n", - (tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i, - buf[i][2],buf[i][3], - buf[i][4],buf[i][5],buf[i][6], - (int) ubuf(buf[i][7]).i,(int) ubuf(buf[i][8]).i, - (int) ubuf(buf[i][9]).i); -} - -/* ---------------------------------------------------------------------- - write hybrid atom info to data file -------------------------------------------------------------------------- */ - -int AtomVecSphereKokkos::write_data_hybrid(FILE *fp, double *buf) -{ - fprintf(fp," %-1.16e %-1.16e",buf[0],buf[1]); - return 2; -} - -/* ---------------------------------------------------------------------- - pack velocity info for data file -------------------------------------------------------------------------- */ - -void AtomVecSphereKokkos::pack_vel(double **buf) -{ - atomKK->sync(Host,TAG_MASK|V_MASK|OMEGA_MASK); - - int nlocal = atom->nlocal; - for (int i = 0; i < nlocal; i++) { - buf[i][0] = ubuf(h_tag[i]).d; - buf[i][1] = h_v(i,0); - buf[i][2] = h_v(i,1); - buf[i][3] = h_v(i,2); - buf[i][4] = h_omega(i,0); - buf[i][5] = h_omega(i,1); - buf[i][6] = h_omega(i,2); - } -} - -/* ---------------------------------------------------------------------- - pack hybrid velocity info for data file -------------------------------------------------------------------------- */ - -int AtomVecSphereKokkos::pack_vel_hybrid(int i, double *buf) -{ - atomKK->sync(Host,OMEGA_MASK); - - buf[0] = h_omega(i,0); - buf[1] = h_omega(i,1); - buf[2] = h_omega(i,2); - return 3; -} - -/* ---------------------------------------------------------------------- - write velocity info to data file -------------------------------------------------------------------------- */ - -void AtomVecSphereKokkos::write_vel(FILE *fp, int n, double **buf) -{ - for (int i = 0; i < n; i++) - fprintf(fp,TAGINT_FORMAT - " %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e\n", - (tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3], - buf[i][4],buf[i][5],buf[i][6]); -} - -/* ---------------------------------------------------------------------- - write hybrid velocity info to data file -------------------------------------------------------------------------- */ - -int AtomVecSphereKokkos::write_vel_hybrid(FILE *fp, double *buf) -{ - fprintf(fp," %-1.16e %-1.16e %-1.16e",buf[0],buf[1],buf[2]); - return 3; -} - -/* ---------------------------------------------------------------------- - return # of bytes of allocated memory -------------------------------------------------------------------------- */ - -double AtomVecSphereKokkos::memory_usage() -{ - double bytes = 0; - - if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax); - if (atom->memcheck("type")) bytes += memory->usage(type,nmax); - if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax); - if (atom->memcheck("image")) bytes += memory->usage(image,nmax); - if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3); - if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3); - if (atom->memcheck("f")) bytes += memory->usage(f,nmax*comm->nthreads,3); - - if (atom->memcheck("radius")) bytes += memory->usage(radius,nmax); - if (atom->memcheck("rmass")) bytes += memory->usage(rmass,nmax); - if (atom->memcheck("omega")) bytes += memory->usage(omega,nmax,3); - if (atom->memcheck("torque")) - bytes += memory->usage(torque,nmax*comm->nthreads,3); - - return bytes; -} - -/* ---------------------------------------------------------------------- */ - void AtomVecSphereKokkos::sync(ExecutionSpace space, unsigned int mask) { if (space == Device) { diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.h b/src/KOKKOS/atom_vec_sphere_kokkos.h index fee46ff5cf..0783fd874e 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.h +++ b/src/KOKKOS/atom_vec_sphere_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,53 +24,17 @@ AtomStyle(sphere/kk/host,AtomVecSphereKokkos); #define LMP_ATOM_VEC_SPHERE_KOKKOS_H #include "atom_vec_kokkos.h" +#include "atom_vec_sphere.h" #include "kokkos_type.h" namespace LAMMPS_NS { -class AtomVecSphereKokkos : public AtomVecKokkos { +class AtomVecSphereKokkos : public AtomVecKokkos, public AtomVecSphere { public: AtomVecSphereKokkos(class LAMMPS *); - void init() override; void grow(int) override; void grow_pointers() override; - void copy(int, int, int) override; - int pack_comm(int, int *, double *, int, int *) override; - int pack_comm_vel(int, int *, double *, int, int *) override; - int pack_comm_hybrid(int, int *, double *) override; - void unpack_comm(int, int, double *) override; - void unpack_comm_vel(int, int, double *) override; - int unpack_comm_hybrid(int, int, double *) override; - int pack_reverse(int, int, double *) override; - int pack_reverse_hybrid(int, int, double *) override; - void unpack_reverse(int, int *, double *) override; - int unpack_reverse_hybrid(int, int *, double *) override; - int pack_border(int, int *, double *, int, int *) override; - int pack_border_vel(int, int *, double *, int, int *) override; - int pack_border_hybrid(int, int *, double *) override; - void unpack_border(int, int, double *) override; - void unpack_border_vel(int, int, double *) override; - int unpack_border_hybrid(int, int, double *) override; - int pack_exchange(int, double *) override; - int unpack_exchange(double *) override; - int size_restart() override; - int pack_restart(int, double *) override; - int unpack_restart(double *) override; - void create_atom(int, double *) override; - void data_atom(double *, imageint, const std::vector &, std::string &) override; - int data_atom_hybrid(int, const std::vector &, int) override; - void data_vel(int, const std::vector &) override; - int data_vel_hybrid(int, const std::vector &, int) override; - void pack_data(double **) override; - int pack_data_hybrid(int, double *) override; - void write_data(FILE *, int, double **) override; - int write_data_hybrid(FILE *, double *) override; - void pack_vel(double **) override; - int pack_vel_hybrid(int, double *) override; - void write_vel(FILE *, int, double **) override; - int write_vel_hybrid(FILE *, double *) override; - double memory_usage() override; int pack_comm_kokkos(const int &n, const DAT::tdual_int_2d &k_sendlist, const int & iswap, @@ -113,13 +77,7 @@ class AtomVecSphereKokkos : public AtomVecKokkos { void sync_overlapping_device(ExecutionSpace space, unsigned int mask) override; private: - tagint *tag; - int *type,*mask; - imageint *image; - double **x,**v,**f; - double *radius,*rmass; - double **omega,**torque; - int radvary; + double **torque; DAT::t_tagint_1d d_tag; HAT::t_tagint_1d h_tag; @@ -139,12 +97,9 @@ class AtomVecSphereKokkos : public AtomVecKokkos { HAT::t_v_array h_omega; DAT::t_f_array d_torque; HAT::t_f_array h_torque; - - DAT::tdual_int_1d k_count; }; -} +} // namespace LAMMPS_NS #endif #endif - diff --git a/src/KOKKOS/atom_vec_spin_kokkos.cpp b/src/KOKKOS/atom_vec_spin_kokkos.cpp index 3d22cbd183..655f2ec8c1 100644 --- a/src/KOKKOS/atom_vec_spin_kokkos.cpp +++ b/src/KOKKOS/atom_vec_spin_kokkos.cpp @@ -3,7 +3,7 @@ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -41,26 +41,10 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -AtomVecSpinKokkos::AtomVecSpinKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) +AtomVecSpinKokkos::AtomVecSpinKokkos(LAMMPS *lmp) : AtomVec(lmp), +AtomVecKokkos(lmp), AtomVecSpin(lmp) { - molecular = 0; - mass_type = 1; - forceclearflag = 1; - comm_x_only = comm_f_only = 0; - size_forward = 7; - size_reverse = 9; - size_border = 10; - size_velocity = 3; - size_data_atom = 9; - size_data_vel = 4; - xcol_data = 4; - - atom->sp_flag = 1; - - k_count = DAT::tdual_int_1d("atom::k_count",1); - atomKK = (AtomKokkos *) atom; - commKK = (CommKokkos *) comm; } /* ---------------------------------------------------------------------- @@ -147,33 +131,6 @@ void AtomVecSpinKokkos::grow_pointers() h_fm_long = atomKK->k_fm_long.h_view; } -/* ---------------------------------------------------------------------- - copy atom I info to atom J -------------------------------------------------------------------------- */ - -void AtomVecSpinKokkos::copy(int i, int j, int delflag) -{ - h_tag[j] = h_tag[i]; - h_type[j] = h_type[i]; - mask[j] = mask[i]; - h_image[j] = h_image[i]; - h_x(j,0) = h_x(i,0); - h_x(j,1) = h_x(i,1); - h_x(j,2) = h_x(i,2); - h_v(j,0) = h_v(i,0); - h_v(j,1) = h_v(i,1); - h_v(j,2) = h_v(i,2); - - h_sp(j,0) = h_sp(i,0); - h_sp(j,1) = h_sp(i,1); - h_sp(j,2) = h_sp(i,2); - h_sp(j,3) = h_sp(i,3); - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag); -} - /* ---------------------------------------------------------------------- */ template @@ -347,167 +304,6 @@ int AtomVecSpinKokkos::pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, D /* ---------------------------------------------------------------------- */ -int AtomVecSpinKokkos::pack_border(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz; - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = h_sp(j,0); - buf[m++] = h_sp(j,1); - buf[m++] = h_sp(j,2); - buf[m++] = h_sp(j,3); - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]; - dy = pbc[1]; - dz = pbc[2]; - } - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = h_sp(j,0); - buf[m++] = h_sp(j,1); - buf[m++] = h_sp(j,2); - buf[m++] = h_sp(j,3); - } - } - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); - - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecSpinKokkos::pack_border_vel(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - double dx,dy,dz,dvx,dvy,dvz; - - m = 0; - if (pbc_flag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0); - buf[m++] = h_x(j,1); - buf[m++] = h_x(j,2); - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = h_sp(j,0); - buf[m++] = h_sp(j,1); - buf[m++] = h_sp(j,2); - buf[m++] = h_sp(j,3); - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } else { - if (domain->triclinic == 0) { - dx = pbc[0]*domain->xprd; - dy = pbc[1]*domain->yprd; - dz = pbc[2]*domain->zprd; - } else { - dx = pbc[0]; - dy = pbc[1]; - dz = pbc[2]; - } - if (!deform_vremap) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = h_sp(j,0); - buf[m++] = h_sp(j,1); - buf[m++] = h_sp(j,2); - buf[m++] = h_sp(j,3); - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } else { - dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; - dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; - dvz = pbc[2]*h_rate[2]; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_x(j,0) + dx; - buf[m++] = h_x(j,1) + dy; - buf[m++] = h_x(j,2) + dz; - buf[m++] = ubuf(h_tag(j)).d; - buf[m++] = ubuf(h_type(j)).d; - buf[m++] = ubuf(h_mask(j)).d; - buf[m++] = h_sp(j,0); - buf[m++] = h_sp(j,1); - buf[m++] = h_sp(j,2); - buf[m++] = h_sp(j,3); - if (mask[i] & deform_groupbit) { - buf[m++] = h_v(j,0) + dvx; - buf[m++] = h_v(j,1) + dvy; - buf[m++] = h_v(j,2) + dvz; - } else { - buf[m++] = h_v(j,0); - buf[m++] = h_v(j,1); - buf[m++] = h_v(j,2); - } - } - } - } - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); - - return m; -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecSpinKokkos::pack_border_hybrid(int n, int *list, double *buf) -{ - int i,j,m; - - m = 0; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = h_sp(j,0); - buf[m++] = h_sp(j,1); - buf[m++] = h_sp(j,2); - buf[m++] = h_sp(j,3); - } - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecSpinKokkos_UnpackBorder { typedef DeviceType device_type; @@ -568,87 +364,6 @@ void AtomVecSpinKokkos::unpack_border_kokkos(const int &n, const int &first, /* ---------------------------------------------------------------------- */ -void AtomVecSpinKokkos::unpack_border(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - - for (i = first; i < last; i++) { - if (i == nmax) { - grow(0); - } - atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|SP_MASK); - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_tag(i) = (tagint) ubuf(buf[m++]).i; - h_type(i) = (int) ubuf(buf[m++]).i; - h_mask(i) = (int) ubuf(buf[m++]).i; - h_sp(i,0) = buf[m++]; - h_sp(i,1) = buf[m++]; - h_sp(i,2) = buf[m++]; - h_sp(i,3) = buf[m++]; - } - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]-> - unpack_border(n,first,&buf[m]); -} - -/* ---------------------------------------------------------------------- */ - -void AtomVecSpinKokkos::unpack_border_vel(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - for (i = first; i < last; i++) { - if (i == nmax) grow(0); - atomKK->modified(Host,X_MASK|V_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|SP_MASK); - h_x(i,0) = buf[m++]; - h_x(i,1) = buf[m++]; - h_x(i,2) = buf[m++]; - h_tag(i) = (tagint) ubuf(buf[m++]).i; - h_type(i) = (int) ubuf(buf[m++]).i; - h_mask(i) = (int) ubuf(buf[m++]).i; - h_sp(i,0) = buf[m++]; - h_sp(i,1) = buf[m++]; - h_sp(i,2) = buf[m++]; - h_sp(i,3) = buf[m++]; - h_v(i,0) = buf[m++]; - h_v(i,1) = buf[m++]; - h_v(i,2) = buf[m++]; - } - - if (atom->nextra_border) - for (int iextra = 0; iextra < atom->nextra_border; iextra++) - m += modify->fix[atom->extra_border[iextra]]-> - unpack_border(n,first,&buf[m]); -} - -/* ---------------------------------------------------------------------- */ - -int AtomVecSpinKokkos::unpack_border_hybrid(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - for (i = first; i < last; i++) { - h_sp(i,0) = buf[m++]; - h_sp(i,1) = buf[m++]; - h_sp(i,2) = buf[m++]; - h_sp(i,3) = buf[m++]; - } - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecSpinKokkos_PackExchangeFunctor { typedef DeviceType device_type; @@ -771,34 +486,6 @@ int AtomVecSpinKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2 /* ---------------------------------------------------------------------- */ -int AtomVecSpinKokkos::pack_exchange(int i, double *buf) -{ - int m = 1; - buf[m++] = h_x(i,0); - buf[m++] = h_x(i,1); - buf[m++] = h_x(i,2); - buf[m++] = h_v(i,0); - buf[m++] = h_v(i,1); - buf[m++] = h_v(i,2); - buf[m++] = ubuf(h_tag(i)).d; - buf[m++] = ubuf(h_type(i)).d; - buf[m++] = ubuf(h_mask(i)).d; - buf[m++] = ubuf(h_image(i)).d; - buf[m++] = h_sp(i,0); - buf[m++] = h_sp(i,1); - buf[m++] = h_sp(i,2); - buf[m++] = h_sp(i,3); - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]); - - buf[0] = m; - return m; -} - -/* ---------------------------------------------------------------------- */ - template struct AtomVecSpinKokkos_UnpackExchangeFunctor { typedef DeviceType device_type; @@ -886,321 +573,6 @@ int AtomVecSpinKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int nr /* ---------------------------------------------------------------------- */ -int AtomVecSpinKokkos::unpack_exchange(double *buf) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) grow(0); - atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | SP_MASK); - - int m = 1; - h_x(nlocal,0) = buf[m++]; - h_x(nlocal,1) = buf[m++]; - h_x(nlocal,2) = buf[m++]; - h_v(nlocal,0) = buf[m++]; - h_v(nlocal,1) = buf[m++]; - h_v(nlocal,2) = buf[m++]; - h_tag(nlocal) = (tagint) ubuf(buf[m++]).i; - h_type(nlocal) = (int) ubuf(buf[m++]).i; - h_mask(nlocal) = (int) ubuf(buf[m++]).i; - h_image(nlocal) = (imageint) ubuf(buf[m++]).i; - h_sp(nlocal,0) = buf[m++]; - h_sp(nlocal,1) = buf[m++]; - h_sp(nlocal,2) = buf[m++]; - h_sp(nlocal,3) = buf[m++]; - - if (atom->nextra_grow) - for (int iextra = 0; iextra < atom->nextra_grow; iextra++) - m += modify->fix[atom->extra_grow[iextra]]-> - unpack_exchange(nlocal,&buf[m]); - - atom->nlocal++; - return m; -} - -/* ---------------------------------------------------------------------- - size of restart data for all atoms owned by this proc - include extra data stored by fixes -------------------------------------------------------------------------- */ - -int AtomVecSpinKokkos::size_restart() -{ - int i; - - int nlocal = atom->nlocal; - int n = 15 * nlocal; - - if (atom->nextra_restart) - for (int iextra = 0; iextra < atom->nextra_restart; iextra++) - for (i = 0; i < nlocal; i++) - n += modify->fix[atom->extra_restart[iextra]]->size_restart(i); - - return n; -} - -/* ---------------------------------------------------------------------- - pack atom I's data for restart file including extra quantities - xyz must be 1st 3 values, so that read_restart can test on them - molecular types may be negative, but write as positive -------------------------------------------------------------------------- */ - -int AtomVecSpinKokkos::pack_restart(int i, double *buf) -{ - atomKK->sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | SP_MASK); - - int m = 1; - buf[m++] = h_x(i,0); - buf[m++] = h_x(i,1); - buf[m++] = h_x(i,2); - buf[m++] = ubuf(h_tag(i)).d; - buf[m++] = ubuf(h_type(i)).d; - buf[m++] = ubuf(h_mask(i)).d; - buf[m++] = ubuf(h_image(i)).d; - buf[m++] = h_v(i,0); - buf[m++] = h_v(i,1); - buf[m++] = h_v(i,2); - - buf[m++] = h_sp(i,0); - buf[m++] = h_sp(i,1); - buf[m++] = h_sp(i,2); - buf[m++] = h_sp(i,3); - - if (atom->nextra_restart) - for (int iextra = 0; iextra < atom->nextra_restart; iextra++) - m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]); - - buf[0] = m; - return m; -} - -/* ---------------------------------------------------------------------- - unpack data for one atom from restart file including extra quantities -------------------------------------------------------------------------- */ - -int AtomVecSpinKokkos::unpack_restart(double *buf) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) { - grow(0); - if (atom->nextra_store) - memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra"); - } - - atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | - MASK_MASK | IMAGE_MASK | SP_MASK); - - int m = 1; - h_x(nlocal,0) = buf[m++]; - h_x(nlocal,1) = buf[m++]; - h_x(nlocal,2) = buf[m++]; - h_tag(nlocal) = (tagint) ubuf(buf[m++]).i; - h_type(nlocal) = (int) ubuf(buf[m++]).i; - h_mask(nlocal) = (int) ubuf(buf[m++]).i; - h_image(nlocal) = (imageint) ubuf(buf[m++]).i; - h_v(nlocal,0) = buf[m++]; - h_v(nlocal,1) = buf[m++]; - h_v(nlocal,2) = buf[m++]; - - h_sp(nlocal,0) = buf[m++]; - h_sp(nlocal,1) = buf[m++]; - h_sp(nlocal,2) = buf[m++]; - h_sp(nlocal,3) = buf[m++]; - - double **extra = atom->extra; - if (atom->nextra_store) { - int size = static_cast (buf[0]) - m; - for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++]; - } - - atom->nlocal++; - return m; -} - -/* ---------------------------------------------------------------------- - create one atom of itype at coord - set other values to defaults -------------------------------------------------------------------------- */ - -void AtomVecSpinKokkos::create_atom(int itype, double *coord) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) { - atomKK->modified(Host,ALL_MASK); - grow(0); - } - atomKK->sync(Host,ALL_MASK); - atomKK->modified(Host,ALL_MASK); - - h_tag[nlocal] = 0; - h_type[nlocal] = itype; - h_x(nlocal,0) = coord[0]; - h_x(nlocal,1) = coord[1]; - h_x(nlocal,2) = coord[2]; - h_mask[nlocal] = 1; - h_image[nlocal] = ((imageint) IMGMAX << IMG2BITS) | - ((imageint) IMGMAX << IMGBITS) | IMGMAX; - h_v(nlocal,0) = 0.0; - h_v(nlocal,1) = 0.0; - h_v(nlocal,2) = 0.0; - - h_sp(nlocal,0) = 0.0; - h_sp(nlocal,1) = 0.0; - h_sp(nlocal,2) = 0.0; - h_sp(nlocal,3) = 0.0; - - atom->nlocal++; -} - -/* ---------------------------------------------------------------------- - unpack one line from Atoms section of data file - initialize other atom quantities -------------------------------------------------------------------------- */ - -void AtomVecSpinKokkos::data_atom(double *coord, imageint imagetmp, - const std::vector &values, std::string &extract) -{ - int nlocal = atom->nlocal; - if (nlocal == nmax) grow(0); - - h_tag[nlocal] = utils::inumeric(FLERR,values[0],true,lmp); - h_type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); - extract = values[1]; - if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) - error->one(FLERR,"Invalid atom type in Atoms section of data file"); - - h_sp(nlocal,3) = utils::numeric(FLERR,values[2],true,lmp); - h_sp(nlocal,0) = utils::numeric(FLERR,values[6],true,lmp); - h_sp(nlocal,1) = utils::numeric(FLERR,values[7],true,lmp); - h_sp(nlocal,2) = utils::numeric(FLERR,values[8],true,lmp); - double inorm = 1.0/sqrt(sp[nlocal][0]*sp[nlocal][0] + - sp[nlocal][1]*sp[nlocal][1] + - sp[nlocal][2]*sp[nlocal][2]); - h_sp(nlocal,0) *= inorm; - h_sp(nlocal,1) *= inorm; - h_sp(nlocal,2) *= inorm; - - h_x(nlocal,0) = coord[0]; - h_x(nlocal,1) = coord[1]; - h_x(nlocal,2) = coord[2]; - - h_image[nlocal] = imagetmp; - - h_mask[nlocal] = 1; - h_v(nlocal,0) = 0.0; - h_v(nlocal,1) = 0.0; - h_v(nlocal,2) = 0.0; - - atomKK->modified(Host,ALL_MASK); - - atom->nlocal++; -} - -/* ---------------------------------------------------------------------- - unpack hybrid quantities from one line in Atoms section of data file - initialize other atom quantities for this sub-style -------------------------------------------------------------------------- */ - -int AtomVecSpinKokkos::data_atom_hybrid(int nlocal, const std::vector &values, - int offset) -{ - h_sp(nlocal,3) = utils::numeric(FLERR,values[offset],true,lmp); - h_sp(nlocal,0) = utils::numeric(FLERR,values[offset+1],true,lmp); - h_sp(nlocal,1) = utils::numeric(FLERR,values[offset+2],true,lmp); - h_sp(nlocal,2) = utils::numeric(FLERR,values[offset+3],true,lmp); - double inorm = 1.0/sqrt(sp[nlocal][0]*sp[nlocal][0] + - sp[nlocal][1]*sp[nlocal][1] + - sp[nlocal][2]*sp[nlocal][2]); - sp[nlocal][0] *= inorm; - sp[nlocal][1] *= inorm; - sp[nlocal][2] *= inorm; - - return 4; -} - -/* ---------------------------------------------------------------------- - pack atom info for data file including 3 image flags -------------------------------------------------------------------------- */ - -void AtomVecSpinKokkos::pack_data(double **buf) -{ - int nlocal = atom->nlocal; - for (int i = 0; i < nlocal; i++) { - buf[i][0] = h_tag[i]; - buf[i][1] = h_type[i]; - buf[i][2] = h_sp(i,0); - buf[i][3] = h_x(i,0); - buf[i][4] = h_x(i,1); - buf[i][5] = h_x(i,2); - buf[i][2] = h_sp(i,1); - buf[i][2] = h_sp(i,2); - buf[i][2] = h_sp(i,3); - buf[i][6] = (h_image[i] & IMGMASK) - IMGMAX; - buf[i][7] = (h_image[i] >> IMGBITS & IMGMASK) - IMGMAX; - buf[i][8] = (h_image[i] >> IMG2BITS) - IMGMAX; - } -} - -/* ---------------------------------------------------------------------- - pack hybrid atom info for data file -------------------------------------------------------------------------- */ - -int AtomVecSpinKokkos::pack_data_hybrid(int i, double *buf) -{ - buf[0] = h_sp(i,3); - buf[1] = h_sp(i,0); - buf[2] = h_sp(i,1); - buf[3] = h_sp(i,2); - return 4; -} - -/* ---------------------------------------------------------------------- - write atom info to data file including 3 image flags -------------------------------------------------------------------------- */ - -void AtomVecSpinKokkos::write_data(FILE *fp, int n, double **buf) -{ - for (int i = 0; i < n; i++) - fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n", - (int) buf[i][0],(int) buf[i][1],buf[i][2],buf[i][3],buf[i][4], - buf[i][5],(int) buf[i][6],(int) buf[i][7],(int) buf[i][8]); -} - -/* ---------------------------------------------------------------------- - write hybrid atom info to data file -------------------------------------------------------------------------- */ - -int AtomVecSpinKokkos::write_data_hybrid(FILE *fp, double *buf) -{ - fprintf(fp," %-1.16e %-1.16e %-1.16e %-1.16e",buf[0],buf[1],buf[2],buf[3]); - return 4; -} - -/* ---------------------------------------------------------------------- - return # of bytes of allocated memory -------------------------------------------------------------------------- */ - -double AtomVecSpinKokkos::memory_usage() -{ - bigint bytes = 0; - - if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax); - if (atom->memcheck("type")) bytes += memory->usage(type,nmax); - if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax); - if (atom->memcheck("image")) bytes += memory->usage(image,nmax); - if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3); - if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3); - if (atom->memcheck("f")) bytes += memory->usage(f,nmax*commKK->nthreads,3); - - if (atom->memcheck("sp")) bytes += memory->usage(sp,nmax,4); - if (atom->memcheck("fm")) bytes += memory->usage(fm,nmax*comm->nthreads,3); - if (atom->memcheck("fm_long")) bytes += memory->usage(fm_long,nmax*comm->nthreads,3); - - return bytes; -} - -/* ---------------------------------------------------------------------- */ - void AtomVecSpinKokkos::sync(ExecutionSpace space, unsigned int mask) { if (space == Device) { @@ -1303,14 +675,3 @@ void AtomVecSpinKokkos::sync_overlapping_device(ExecutionSpace space, unsigned i perform_async_copy(atomKK->k_fm_long,space); } } - -/* ---------------------------------------------------------------------- - clear all forces (mech and mag) -------------------------------------------------------------------------- */ - -void AtomVecSpinKokkos::force_clear(int n, size_t nbytes) -{ - memset(&f[n][0],0,3*nbytes); - memset(&fm[n][0],0,3*nbytes); - memset(&fm_long[n][0],0,3*nbytes); -} diff --git a/src/KOKKOS/atom_vec_spin_kokkos.h b/src/KOKKOS/atom_vec_spin_kokkos.h index 3f48ad323a..68834d4ef2 100644 --- a/src/KOKKOS/atom_vec_spin_kokkos.h +++ b/src/KOKKOS/atom_vec_spin_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,39 +24,15 @@ AtomStyle(spin/kk/host,AtomVecSpinKokkos); #define LMP_ATOM_VEC_SPIN_KOKKOS_H #include "atom_vec_kokkos.h" +#include "atom_vec_spin.h" #include "kokkos_type.h" namespace LAMMPS_NS { -class AtomVecSpinKokkos : public AtomVecKokkos { +class AtomVecSpinKokkos : public AtomVecKokkos, public AtomVecSpin { public: AtomVecSpinKokkos(class LAMMPS *); void grow(int) override; - void copy(int, int, int) override; - int pack_border(int, int *, double *, int, int *) override; - int pack_border_vel(int, int *, double *, int, int *) override; - int pack_border_hybrid(int, int *, double *) override; - void unpack_border(int, int, double *) override; - void unpack_border_vel(int, int, double *) override; - int unpack_border_hybrid(int, int, double *) override; - int pack_exchange(int, double *) override; - int unpack_exchange(double *) override; - int size_restart() override; - int pack_restart(int, double *) override; - int unpack_restart(double *) override; - void create_atom(int, double *) override; - void data_atom(double *, imageint, const std::vector &, std::string &) override; - int data_atom_hybrid(int, const std::vector &, int) override; - void pack_data(double **) override; - int pack_data_hybrid(int, double *) override; - void write_data(FILE *, int, double **) override; - int write_data_hybrid(FILE *, double *) override; - double memory_usage() override; - - // clear magnetic and mechanic forces - - void force_clear(int, size_t) override; - void grow_pointers() override; // input lists to be checked int pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, @@ -79,17 +55,6 @@ class AtomVecSpinKokkos : public AtomVecKokkos { void sync_overlapping_device(ExecutionSpace space, unsigned int mask) override; protected: - tagint *tag; - int *type,*mask; - imageint *image; - double **x,**v,**f; // lattice quantities - - // spin quantities - double **sp; // sp[i][0-2] direction of the spin i - // sp[i][3] atomic magnetic moment of the spin i - double **fm; // fm[i][0-2] direction of magnetic precession - double **fm_long; // storage of long-range spin prec. components - DAT::t_tagint_1d d_tag; HAT::t_tagint_1d h_tag; @@ -110,12 +75,9 @@ class AtomVecSpinKokkos : public AtomVecKokkos { HAT::t_sp_array h_sp; HAT::t_fm_array h_fm; HAT::t_fm_long_array h_fm_long; - - DAT::tdual_int_1d k_count; }; -} +} // namespace LAMMPS_NS #endif #endif - diff --git a/src/KOKKOS/bond_class2_kokkos.cpp b/src/KOKKOS/bond_class2_kokkos.cpp index b4e87b4119..eeecc385b0 100644 --- a/src/KOKKOS/bond_class2_kokkos.cpp +++ b/src/KOKKOS/bond_class2_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/bond_class2_kokkos.h b/src/KOKKOS/bond_class2_kokkos.h index b6017c1c94..0eb3c4d39a 100644 --- a/src/KOKKOS/bond_class2_kokkos.h +++ b/src/KOKKOS/bond_class2_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/bond_fene_kokkos.cpp b/src/KOKKOS/bond_fene_kokkos.cpp index e988262901..0a294bde36 100644 --- a/src/KOKKOS/bond_fene_kokkos.cpp +++ b/src/KOKKOS/bond_fene_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/bond_fene_kokkos.h b/src/KOKKOS/bond_fene_kokkos.h index 845ebd98da..e2ba64a114 100644 --- a/src/KOKKOS/bond_fene_kokkos.h +++ b/src/KOKKOS/bond_fene_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/bond_harmonic_kokkos.cpp b/src/KOKKOS/bond_harmonic_kokkos.cpp index 9b99ab0f4c..7dcdf24c66 100644 --- a/src/KOKKOS/bond_harmonic_kokkos.cpp +++ b/src/KOKKOS/bond_harmonic_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/bond_harmonic_kokkos.h b/src/KOKKOS/bond_harmonic_kokkos.h index 2f0e68933b..837e669b98 100644 --- a/src/KOKKOS/bond_harmonic_kokkos.h +++ b/src/KOKKOS/bond_harmonic_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp index 527ac2c174..6fad33a918 100644 --- a/src/KOKKOS/comm_kokkos.cpp +++ b/src/KOKKOS/comm_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -146,7 +146,9 @@ void CommKokkos::init() if (!comm_f_only) // not all Kokkos atom_vec styles have reverse pack/unpack routines yet reverse_comm_classic = true; - if (ghost_velocity && ((AtomVecKokkos*)atom->avec)->no_comm_vel_flag) // not all Kokkos atom_vec styles have comm vel pack/unpack routines yet + atomKK->avecKK = dynamic_cast(atom->avec); + + if (ghost_velocity && atomKK->avecKK->no_comm_vel_flag) // not all Kokkos atom_vec styles have comm vel pack/unpack routines yet forward_comm_classic = true; } @@ -186,7 +188,6 @@ void CommKokkos::forward_comm_device(int) { int n; MPI_Request request; - AtomVecKokkos *avec = (AtomVecKokkos *) atom->avec; double *buf; // exchange data with another proc @@ -200,7 +201,7 @@ void CommKokkos::forward_comm_device(int) k_swap.sync(); k_swap2.sync(); k_pbc.sync(); - n = avec->pack_comm_self_fused(totalsend,k_sendlist,k_sendnum_scan, + n = atomKK->avecKK->pack_comm_self_fused(totalsend,k_sendlist,k_sendnum_scan, k_firstrecv,k_pbc_flag,k_pbc,k_g2l); } else { @@ -213,7 +214,7 @@ void CommKokkos::forward_comm_device(int) MPI_Irecv(buf,size_forward_recv[iswap],MPI_DOUBLE, recvproc[iswap],0,world,&request); } - n = avec->pack_comm_kokkos(sendnum[iswap],k_sendlist, + n = atomKK->avecKK->pack_comm_kokkos(sendnum[iswap],k_sendlist, iswap,k_buf_send,pbc_flag[iswap],pbc[iswap]); DeviceType().fence(); if (n) { @@ -232,7 +233,7 @@ void CommKokkos::forward_comm_device(int) size_forward_recv[iswap],MPI_DOUBLE, recvproc[iswap],0,world,&request); } - n = avec->pack_comm_vel_kokkos(sendnum[iswap],k_sendlist,iswap, + n = atomKK->avecKK->pack_comm_vel_kokkos(sendnum[iswap],k_sendlist,iswap, k_buf_send,pbc_flag[iswap],pbc[iswap]); DeviceType().fence(); if (n) { @@ -240,34 +241,34 @@ void CommKokkos::forward_comm_device(int) MPI_DOUBLE,sendproc[iswap],0,world); } if (size_forward_recv[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); - avec->unpack_comm_vel_kokkos(recvnum[iswap],firstrecv[iswap],k_buf_recv); + atomKK->avecKK->unpack_comm_vel_kokkos(recvnum[iswap],firstrecv[iswap],k_buf_recv); DeviceType().fence(); } else { if (size_forward_recv[iswap]) MPI_Irecv(k_buf_recv.view().data(), size_forward_recv[iswap],MPI_DOUBLE, recvproc[iswap],0,world,&request); - n = avec->pack_comm_kokkos(sendnum[iswap],k_sendlist,iswap, + n = atomKK->avecKK->pack_comm_kokkos(sendnum[iswap],k_sendlist,iswap, k_buf_send,pbc_flag[iswap],pbc[iswap]); DeviceType().fence(); if (n) MPI_Send(k_buf_send.view().data(),n, MPI_DOUBLE,sendproc[iswap],0,world); if (size_forward_recv[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); - avec->unpack_comm_kokkos(recvnum[iswap],firstrecv[iswap],k_buf_recv); + atomKK->avecKK->unpack_comm_kokkos(recvnum[iswap],firstrecv[iswap],k_buf_recv); DeviceType().fence(); } } else { if (!ghost_velocity) { if (sendnum[iswap]) - n = avec->pack_comm_self(sendnum[iswap],k_sendlist,iswap, + n = atomKK->avecKK->pack_comm_self(sendnum[iswap],k_sendlist,iswap, firstrecv[iswap],pbc_flag[iswap],pbc[iswap]); DeviceType().fence(); } else { - n = avec->pack_comm_vel_kokkos(sendnum[iswap],k_sendlist,iswap, + n = atomKK->avecKK->pack_comm_vel_kokkos(sendnum[iswap],k_sendlist,iswap, k_buf_send,pbc_flag[iswap],pbc[iswap]); DeviceType().fence(); - avec->unpack_comm_vel_kokkos(recvnum[iswap],firstrecv[iswap],k_buf_send); + atomKK->avecKK->unpack_comm_vel_kokkos(recvnum[iswap],firstrecv[iswap],k_buf_send); DeviceType().fence(); } } @@ -310,7 +311,6 @@ void CommKokkos::reverse_comm_device() { int n; MPI_Request request; - AtomVecKokkos *avec = (AtomVecKokkos *) atom->avec; double *buf; // exchange data with another proc @@ -343,19 +343,19 @@ void CommKokkos::reverse_comm_device() MPI_Irecv(k_buf_recv.view().data(), size_reverse_recv[iswap],MPI_DOUBLE, sendproc[iswap],0,world,&request); - n = avec->pack_reverse_kokkos(recvnum[iswap],firstrecv[iswap],k_buf_send); + n = atomKK->avecKK->pack_reverse_kokkos(recvnum[iswap],firstrecv[iswap],k_buf_send); DeviceType().fence(); if (n) MPI_Send(k_buf_send.view().data(),n, MPI_DOUBLE,recvproc[iswap],0,world); if (size_reverse_recv[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); } - avec->unpack_reverse_kokkos(sendnum[iswap],k_sendlist,iswap, + atomKK->avecKK->unpack_reverse_kokkos(sendnum[iswap],k_sendlist,iswap, k_buf_recv); DeviceType().fence(); } else { if (sendnum[iswap]) - n = avec->unpack_reverse_self(sendnum[iswap],k_sendlist,iswap, + n = atomKK->avecKK->unpack_reverse_self(sendnum[iswap],k_sendlist,iswap, firstrecv[iswap]); } } @@ -717,7 +717,6 @@ void CommKokkos::exchange_device() double **x; double *sublo,*subhi; MPI_Request request; - AtomVecKokkos *avec = (AtomVecKokkos *) atom->avec; // clear global->local map for owned and ghost atoms // b/c atoms migrate to new procs in exchange() and @@ -800,7 +799,7 @@ void CommKokkos::exchange_device() nsend = k_count.h_view(); if (nsend > maxsend) grow_send_kokkos(nsend,1); nsend = - avec->pack_exchange_kokkos(k_count.h_view(),k_buf_send, + atomKK->avecKK->pack_exchange_kokkos(k_count.h_view(),k_buf_send, k_exchange_sendlist,k_exchange_copylist, ExecutionSpaceFromDevice::space, dim,lo,hi); @@ -809,8 +808,8 @@ void CommKokkos::exchange_device() while (i < nlocal) { if (x[i][dim] < lo || x[i][dim] >= hi) { if (nsend > maxsend) grow_send_kokkos(nsend,1); - nsend += avec->pack_exchange(i,&buf_send[nsend]); - avec->copy(nlocal-1,i,1); + nsend += atomKK->avecKK->pack_exchange(i,&buf_send[nsend]); + atomKK->avecKK->copy(nlocal-1,i,1); nlocal--; } else i++; } @@ -825,7 +824,7 @@ void CommKokkos::exchange_device() if (procgrid[dim] == 1) { nrecv = nsend; if (nrecv) { - atom->nlocal=avec-> + atom->nlocal=atomKK->avecKK-> unpack_exchange_kokkos(k_buf_send,nrecv,atom->nlocal,dim,lo,hi, ExecutionSpaceFromDevice::space); DeviceType().fence(); @@ -858,7 +857,7 @@ void CommKokkos::exchange_device() } if (nrecv) { - atom->nlocal = avec-> + atom->nlocal = atomKK->avecKK-> unpack_exchange_kokkos(k_buf_recv,nrecv,atom->nlocal,dim,lo,hi, ExecutionSpaceFromDevice::space); DeviceType().fence(); @@ -896,7 +895,7 @@ void CommKokkos::borders() static int print = 1; if (mode != Comm::SINGLE || bordergroup || - (ghost_velocity && ((AtomVecKokkos*)atom->avec)->no_border_vel_flag)) { + (ghost_velocity && atomKK->avecKK->no_border_vel_flag)) { if (print && comm->me==0) { error->warning(FLERR,"Required border comm not yet implemented in Kokkos communication, " "switching to classic exchange/border communication"); @@ -982,7 +981,6 @@ void CommKokkos::borders_device() { double **x; double *mlo,*mhi; MPI_Request request; - AtomVecKokkos *avec = (AtomVecKokkos *) atom->avec; ExecutionSpace exec_space = ExecutionSpaceFromDevice::space; atomKK->sync(exec_space,ALL_MASK); @@ -1122,13 +1120,13 @@ void CommKokkos::borders_device() { if (nsend*size_border > maxsend) grow_send_kokkos(nsend*size_border,0); if (ghost_velocity) { - n = avec-> + n = atomKK->avecKK-> pack_border_vel_kokkos(nsend,k_sendlist,k_buf_send,iswap, pbc_flag[iswap],pbc[iswap],exec_space); DeviceType().fence(); } else { - n = avec-> + n = atomKK->avecKK-> pack_border_kokkos(nsend,k_sendlist,k_buf_send,iswap, pbc_flag[iswap],pbc[iswap],exec_space); DeviceType().fence(); @@ -1157,21 +1155,21 @@ void CommKokkos::borders_device() { if (ghost_velocity) { if (sendproc[iswap] != me) { - avec->unpack_border_vel_kokkos(nrecv,atom->nlocal+atom->nghost, + atomKK->avecKK->unpack_border_vel_kokkos(nrecv,atom->nlocal+atom->nghost, k_buf_recv,exec_space); DeviceType().fence(); } else { - avec->unpack_border_vel_kokkos(nrecv,atom->nlocal+atom->nghost, + atomKK->avecKK->unpack_border_vel_kokkos(nrecv,atom->nlocal+atom->nghost, k_buf_send,exec_space); DeviceType().fence(); } } else { if (sendproc[iswap] != me) { - avec->unpack_border_kokkos(nrecv,atom->nlocal+atom->nghost, + atomKK->avecKK->unpack_border_kokkos(nrecv,atom->nlocal+atom->nghost, k_buf_recv,exec_space); DeviceType().fence(); } else { - avec->unpack_border_kokkos(nrecv,atom->nlocal+atom->nghost, + atomKK->avecKK->unpack_border_kokkos(nrecv,atom->nlocal+atom->nghost, k_buf_send,exec_space); DeviceType().fence(); } @@ -1299,7 +1297,7 @@ void CommKokkos::grow_recv(int n) void CommKokkos::grow_send_kokkos(int n, int flag, ExecutionSpace space) { maxsend = static_cast (BUFFACTOR * n); - int maxsend_border = (maxsend+BUFEXTRA+5)/atom->avec->size_border + 2; + int maxsend_border = (maxsend+BUFEXTRA+5)/atomKK->avecKK->size_border + 2; if (flag) { if (space == Device) k_buf_send.modify(); @@ -1308,9 +1306,9 @@ void CommKokkos::grow_send_kokkos(int n, int flag, ExecutionSpace space) if (ghost_velocity) k_buf_send.resize(maxsend_border, - atom->avec->size_border + atom->avec->size_velocity); + atomKK->avecKK->size_border + atomKK->avecKK->size_velocity); else - k_buf_send.resize(maxsend_border,atom->avec->size_border); + k_buf_send.resize(maxsend_border,atomKK->avecKK->size_border); buf_send = k_buf_send.view().data(); } else { @@ -1318,10 +1316,10 @@ void CommKokkos::grow_send_kokkos(int n, int flag, ExecutionSpace space) k_buf_send = DAT:: tdual_xfloat_2d("comm:k_buf_send", maxsend_border, - atom->avec->size_border + atom->avec->size_velocity); + atomKK->avecKK->size_border + atomKK->avecKK->size_velocity); else k_buf_send = DAT:: - tdual_xfloat_2d("comm:k_buf_send",maxsend_border,atom->avec->size_border); + tdual_xfloat_2d("comm:k_buf_send",maxsend_border,atomKK->avecKK->size_border); buf_send = k_buf_send.view().data(); } } @@ -1333,9 +1331,9 @@ void CommKokkos::grow_send_kokkos(int n, int flag, ExecutionSpace space) void CommKokkos::grow_recv_kokkos(int n, ExecutionSpace /*space*/) { maxrecv = static_cast (BUFFACTOR * n); - int maxrecv_border = (maxrecv+BUFEXTRA+5)/atom->avec->size_border + 2; + int maxrecv_border = (maxrecv+BUFEXTRA+5)/atomKK->avecKK->size_border + 2; k_buf_recv = DAT:: - tdual_xfloat_2d("comm:k_buf_recv",maxrecv_border,atom->avec->size_border); + tdual_xfloat_2d("comm:k_buf_recv",maxrecv_border,atomKK->avecKK->size_border); buf_recv = k_buf_recv.view().data(); } diff --git a/src/KOKKOS/comm_kokkos.h b/src/KOKKOS/comm_kokkos.h index 80736c1f92..f7cf06d191 100644 --- a/src/KOKKOS/comm_kokkos.h +++ b/src/KOKKOS/comm_kokkos.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/comm_tiled_kokkos.cpp b/src/KOKKOS/comm_tiled_kokkos.cpp index 1a0603b25e..990b613630 100644 --- a/src/KOKKOS/comm_tiled_kokkos.cpp +++ b/src/KOKKOS/comm_tiled_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -30,7 +30,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -CommTiledKokkos::CommTiledKokkos(LAMMPS *lmp) : CommTiled(lmp) {} +CommTiledKokkos::CommTiledKokkos(LAMMPS *_lmp) : CommTiled(_lmp) {} /* ---------------------------------------------------------------------- */ //IMPORTANT: we *MUST* pass "*oldcomm" to the Comm initializer here, as @@ -39,7 +39,7 @@ CommTiledKokkos::CommTiledKokkos(LAMMPS *lmp) : CommTiled(lmp) {} // The call to Comm::copy_arrays() then converts the shallow copy // into a deep copy of the class with the new layout. -CommTiledKokkos::CommTiledKokkos(LAMMPS *lmp, Comm *oldcomm) : CommTiled(lmp,oldcomm) {} +CommTiledKokkos::CommTiledKokkos(LAMMPS *_lmp, Comm *oldcomm) : CommTiled(_lmp,oldcomm) {} /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/comm_tiled_kokkos.h b/src/KOKKOS/comm_tiled_kokkos.h index 61c1d5ea16..833dc38294 100644 --- a/src/KOKKOS/comm_tiled_kokkos.h +++ b/src/KOKKOS/comm_tiled_kokkos.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/compute_ave_sphere_atom_kokkos.cpp b/src/KOKKOS/compute_ave_sphere_atom_kokkos.cpp index 7873bd0d92..8049dafee7 100644 --- a/src/KOKKOS/compute_ave_sphere_atom_kokkos.cpp +++ b/src/KOKKOS/compute_ave_sphere_atom_kokkos.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/compute_ave_sphere_atom_kokkos.h b/src/KOKKOS/compute_ave_sphere_atom_kokkos.h index a2ba6bff63..81cb6a3373 100644 --- a/src/KOKKOS/compute_ave_sphere_atom_kokkos.h +++ b/src/KOKKOS/compute_ave_sphere_atom_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/compute_coord_atom_kokkos.cpp b/src/KOKKOS/compute_coord_atom_kokkos.cpp index e877400028..713f4f7361 100644 --- a/src/KOKKOS/compute_coord_atom_kokkos.cpp +++ b/src/KOKKOS/compute_coord_atom_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/compute_coord_atom_kokkos.h b/src/KOKKOS/compute_coord_atom_kokkos.h index 46a297cdf3..315288d3bf 100644 --- a/src/KOKKOS/compute_coord_atom_kokkos.h +++ b/src/KOKKOS/compute_coord_atom_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/compute_orientorder_atom_kokkos.cpp b/src/KOKKOS/compute_orientorder_atom_kokkos.cpp index 29683f1ca4..fa4dccb0ac 100644 --- a/src/KOKKOS/compute_orientorder_atom_kokkos.cpp +++ b/src/KOKKOS/compute_orientorder_atom_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/compute_orientorder_atom_kokkos.h b/src/KOKKOS/compute_orientorder_atom_kokkos.h index ef1f874a12..c490b62c30 100644 --- a/src/KOKKOS/compute_orientorder_atom_kokkos.h +++ b/src/KOKKOS/compute_orientorder_atom_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/compute_temp_deform_kokkos.cpp b/src/KOKKOS/compute_temp_deform_kokkos.cpp index eb8a75f04c..55db344d6a 100644 --- a/src/KOKKOS/compute_temp_deform_kokkos.cpp +++ b/src/KOKKOS/compute_temp_deform_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/compute_temp_deform_kokkos.h b/src/KOKKOS/compute_temp_deform_kokkos.h index 7df399df34..17f0f6e0ab 100644 --- a/src/KOKKOS/compute_temp_deform_kokkos.h +++ b/src/KOKKOS/compute_temp_deform_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/compute_temp_kokkos.cpp b/src/KOKKOS/compute_temp_kokkos.cpp index e9198dc9db..3bee2a220f 100644 --- a/src/KOKKOS/compute_temp_kokkos.cpp +++ b/src/KOKKOS/compute_temp_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/compute_temp_kokkos.h b/src/KOKKOS/compute_temp_kokkos.h index c54ee05b45..0bc56f13ba 100644 --- a/src/KOKKOS/compute_temp_kokkos.h +++ b/src/KOKKOS/compute_temp_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/dihedral_charmm_kokkos.cpp b/src/KOKKOS/dihedral_charmm_kokkos.cpp index 70a40b2d98..8c2b442856 100644 --- a/src/KOKKOS/dihedral_charmm_kokkos.cpp +++ b/src/KOKKOS/dihedral_charmm_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/dihedral_charmm_kokkos.h b/src/KOKKOS/dihedral_charmm_kokkos.h index 34d09d28ed..96a9d2ffc1 100644 --- a/src/KOKKOS/dihedral_charmm_kokkos.h +++ b/src/KOKKOS/dihedral_charmm_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/dihedral_class2_kokkos.cpp b/src/KOKKOS/dihedral_class2_kokkos.cpp index 2ecaf3003e..2d6032600b 100644 --- a/src/KOKKOS/dihedral_class2_kokkos.cpp +++ b/src/KOKKOS/dihedral_class2_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/dihedral_class2_kokkos.h b/src/KOKKOS/dihedral_class2_kokkos.h index 600c5c05f3..6e1dceb0cf 100644 --- a/src/KOKKOS/dihedral_class2_kokkos.h +++ b/src/KOKKOS/dihedral_class2_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/dihedral_harmonic_kokkos.cpp b/src/KOKKOS/dihedral_harmonic_kokkos.cpp index 9beb16f17f..96287946ea 100644 --- a/src/KOKKOS/dihedral_harmonic_kokkos.cpp +++ b/src/KOKKOS/dihedral_harmonic_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/dihedral_harmonic_kokkos.h b/src/KOKKOS/dihedral_harmonic_kokkos.h index 5c329fc1a3..e73f19afd1 100644 --- a/src/KOKKOS/dihedral_harmonic_kokkos.h +++ b/src/KOKKOS/dihedral_harmonic_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/dihedral_opls_kokkos.cpp b/src/KOKKOS/dihedral_opls_kokkos.cpp index e4a4008c23..670faa9e84 100644 --- a/src/KOKKOS/dihedral_opls_kokkos.cpp +++ b/src/KOKKOS/dihedral_opls_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/dihedral_opls_kokkos.h b/src/KOKKOS/dihedral_opls_kokkos.h index fdad649d6a..886f4abcae 100644 --- a/src/KOKKOS/dihedral_opls_kokkos.h +++ b/src/KOKKOS/dihedral_opls_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/domain_kokkos.cpp b/src/KOKKOS/domain_kokkos.cpp index 8408957ff9..379aa20ec8 100644 --- a/src/KOKKOS/domain_kokkos.cpp +++ b/src/KOKKOS/domain_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/domain_kokkos.h b/src/KOKKOS/domain_kokkos.h index 28319c4197..1693424d34 100644 --- a/src/KOKKOS/domain_kokkos.h +++ b/src/KOKKOS/domain_kokkos.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/dynamical_matrix_kokkos.cpp b/src/KOKKOS/dynamical_matrix_kokkos.cpp index 0075324ac4..48fe02258b 100644 --- a/src/KOKKOS/dynamical_matrix_kokkos.cpp +++ b/src/KOKKOS/dynamical_matrix_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/dynamical_matrix_kokkos.h b/src/KOKKOS/dynamical_matrix_kokkos.h index 861ff80f4f..e69a5ae548 100644 --- a/src/KOKKOS/dynamical_matrix_kokkos.h +++ b/src/KOKKOS/dynamical_matrix_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fft3d_kokkos.cpp b/src/KOKKOS/fft3d_kokkos.cpp index f2dd9df7da..82e4140f77 100644 --- a/src/KOKKOS/fft3d_kokkos.cpp +++ b/src/KOKKOS/fft3d_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fft3d_kokkos.h b/src/KOKKOS/fft3d_kokkos.h index f4bc3fe58a..a0489f69bb 100644 --- a/src/KOKKOS/fft3d_kokkos.h +++ b/src/KOKKOS/fft3d_kokkos.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fftdata_kokkos.h b/src/KOKKOS/fftdata_kokkos.h index 388ecbb963..8f7bf7d234 100644 --- a/src/KOKKOS/fftdata_kokkos.h +++ b/src/KOKKOS/fftdata_kokkos.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_acks2_reaxff_kokkos.cpp b/src/KOKKOS/fix_acks2_reaxff_kokkos.cpp index 8fa352c03d..e40cfc99f7 100644 --- a/src/KOKKOS/fix_acks2_reaxff_kokkos.cpp +++ b/src/KOKKOS/fix_acks2_reaxff_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_acks2_reaxff_kokkos.h b/src/KOKKOS/fix_acks2_reaxff_kokkos.h index e81479d3ba..664f4dcb81 100644 --- a/src/KOKKOS/fix_acks2_reaxff_kokkos.h +++ b/src/KOKKOS/fix_acks2_reaxff_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_deform_kokkos.cpp b/src/KOKKOS/fix_deform_kokkos.cpp index 104ac41188..cdfbeb1a60 100644 --- a/src/KOKKOS/fix_deform_kokkos.cpp +++ b/src/KOKKOS/fix_deform_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_deform_kokkos.h b/src/KOKKOS/fix_deform_kokkos.h index 298260a8fa..32140c8766 100644 --- a/src/KOKKOS/fix_deform_kokkos.h +++ b/src/KOKKOS/fix_deform_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_dpd_energy_kokkos.cpp b/src/KOKKOS/fix_dpd_energy_kokkos.cpp index d45af7df71..4106aed711 100644 --- a/src/KOKKOS/fix_dpd_energy_kokkos.cpp +++ b/src/KOKKOS/fix_dpd_energy_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_dpd_energy_kokkos.h b/src/KOKKOS/fix_dpd_energy_kokkos.h index 9e52eab9cc..a8f7ec2530 100644 --- a/src/KOKKOS/fix_dpd_energy_kokkos.h +++ b/src/KOKKOS/fix_dpd_energy_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_dt_reset_kokkos.cpp b/src/KOKKOS/fix_dt_reset_kokkos.cpp new file mode 100644 index 0000000000..f3435e711e --- /dev/null +++ b/src/KOKKOS/fix_dt_reset_kokkos.cpp @@ -0,0 +1,195 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "fix_dt_reset_kokkos.h" + +#include "atom_kokkos.h" +#include "atom_masks.h" +#include "error.h" +#include "force.h" +#include "input.h" +#include "integrate.h" +#include "kokkos_base.h" +#include "memory_kokkos.h" +#include "modify.h" +#include "output.h" +#include "pair.h" +#include "update.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +#define BIG 1.0e20 + +/* ---------------------------------------------------------------------- */ + +template +FixDtResetKokkos::FixDtResetKokkos(LAMMPS *lmp, int narg, char **arg) : + FixDtReset(lmp, narg, arg) +{ + kokkosable = 1; + atomKK = (AtomKokkos *) atom; + execution_space = ExecutionSpaceFromDevice::space; + datamask_read = EMPTY_MASK; + datamask_modify = EMPTY_MASK; +} + +/* ---------------------------------------------------------------------- */ + +template +void FixDtResetKokkos::init() +{ + FixDtReset::init(); + + k_emax = Kokkos::DualView("FixDtResetKokkos:gamma", 1); + + k_emax.h_view(0) = emax; + + + k_emax.template modify(); + k_emax.template sync(); + + if (utils::strmatch(update->integrate_style,"^respa")) + error->all(FLERR,"Cannot (yet) use respa with Kokkos"); +} + +/* ---------------------------------------------------------------------- */ + +template +void FixDtResetKokkos::end_of_step() +{ + atomKK->sync(execution_space, V_MASK | F_MASK | MASK_MASK | TYPE_MASK | RMASS_MASK); + + v = atomKK->k_v.view(); + f = atomKK->k_f.view(); + mask = atomKK->k_mask.view(); + type = atomKK->k_type.view(); + if (atomKK->rmass) + rmass = atomKK->k_rmass.view(); + else + mass = atomKK->k_mass.view(); + + int nlocal = atom->nlocal; + + double dt; + + copymode = 1; + if (atomKK->rmass) + Kokkos::parallel_reduce(Kokkos::RangePolicy(0,nlocal), *this, Kokkos::Min(dt)); + else + Kokkos::parallel_reduce(Kokkos::RangePolicy(0,nlocal), *this, Kokkos::Min(dt)); + copymode = 0; + + MPI_Allreduce(MPI_IN_PLACE, &dt, 1, MPI_DOUBLE, MPI_MIN, world); + + atomKK->modified(execution_space, F_MASK); + + if (minbound) dt = MAX(dt, tmin); + if (maxbound) dt = MIN(dt, tmax); + + // if timestep didn't change, just return + // else reset update->dt and other classes that depend on it + // rRESPA, pair style, fixes + + if (dt == update->dt) return; + + laststep = update->ntimestep; + + // calls to other classes that need to know timestep size changed + // similar logic is in Input::timestep() + + update->update_time(); + update->dt = dt; + update->dt_default = 0; + if (force->pair) force->pair->reset_dt(); + for (int i = 0; i < modify->nfix; i++) modify->fix[i]->reset_dt(); + output->reset_dt(); + +} + +/* ---------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void FixDtResetKokkos::operator()(TagFixDtResetMass, const int &i, double &k_dt) const { + + double dtv, dtf, dte, dtsq; + double vsq, fsq, massinv; + double delx, dely, delz, delr; + + double emax = k_emax.d_view(0); + + if (mask[i] & groupbit) { + + massinv = 1.0 / mass[type[i]]; + vsq = v(i,0) * v(i,0) + v(i,1) * v(i,1) + v(i,2) * v(i,2); + fsq = f(i,0) * f(i,0) + f(i,1) * f(i,1) + f(i,2) * f(i,2); + dtv = dtf = dte = BIG; + if (vsq > 0.0) dtv = xmax / sqrt(vsq); + if (fsq > 0.0) dtf = sqrt(2.0 * xmax / (ftm2v * sqrt(fsq) * massinv)); + k_dt = MIN(dtv, dtf); + if ((emax > 0.0) && (fsq * vsq > 0.0)) { + dte = emax / sqrt(fsq * vsq) / sqrt(ftm2v * mvv2e); + k_dt = MIN(dt, dte); + } + dtsq = k_dt * k_dt; + delx = k_dt * v(i,0) + 0.5 * dtsq * massinv * f(i,0) * ftm2v; + dely = k_dt * v(i,1) + 0.5 * dtsq * massinv * f(i,1) * ftm2v; + delz = k_dt * v(i,2) + 0.5 * dtsq * massinv * f(i,2) * ftm2v; + delr = sqrt(delx * delx + dely * dely + delz * delz); + if (delr > xmax) k_dt *= xmax / delr; + } + } + +/* ---------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void FixDtResetKokkos::operator()(TagFixDtResetRMass, const int &i, double &k_dt) const { + + double dtv, dtf, dte, dtsq; + double vsq, fsq, massinv; + double delx, dely, delz, delr; + + double emax = k_emax.d_view(0); + + if (mask[i] & groupbit) { + + massinv = 1.0 / rmass[i]; + vsq = v(i,0) * v(i,0) + v(i,1) * v(i,1) + v(i,2) * v(i,2); + fsq = f(i,0) * f(i,0) + f(i,1) * f(i,1) + f(i,2) * f(i,2); + dtv = dtf = dte = BIG; + if (vsq > 0.0) dtv = xmax / sqrt(vsq); + if (fsq > 0.0) dtf = sqrt(2.0 * xmax / (ftm2v * sqrt(fsq) * massinv)); + k_dt = MIN(dtv, dtf); + if ((emax > 0.0) && (fsq * vsq > 0.0)) { + dte = emax / sqrt(fsq * vsq) / sqrt(ftm2v * mvv2e); + k_dt = MIN(dt, dte); + } + dtsq = k_dt * k_dt; + delx = k_dt * v(i,0) + 0.5 * dtsq * massinv * f(i,0) * ftm2v; + dely = k_dt * v(i,1) + 0.5 * dtsq * massinv * f(i,1) * ftm2v; + delz = k_dt * v(i,2) + 0.5 * dtsq * massinv * f(i,2) * ftm2v; + delr = sqrt(delx * delx + dely * dely + delz * delz); + if (delr > xmax) k_dt *= xmax / delr; + } +} + +namespace LAMMPS_NS { +template class FixDtResetKokkos; +#ifdef LMP_KOKKOS_GPU +template class FixDtResetKokkos; +#endif +} + diff --git a/src/KOKKOS/fix_dt_reset_kokkos.h b/src/KOKKOS/fix_dt_reset_kokkos.h new file mode 100644 index 0000000000..a269b58137 --- /dev/null +++ b/src/KOKKOS/fix_dt_reset_kokkos.h @@ -0,0 +1,66 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS +// clang-format off +FixStyle(dt/reset/kk,FixDtResetKokkos); +FixStyle(dt/reset/kk/device,FixDtResetKokkos); +FixStyle(dt/reset/kk/host,FixDtResetKokkos); +// clang-format on +#else + +// clang-format off +#ifndef LMP_FIX_DT_RESET_KOKKOS_H +#define LMP_FIX_DT_RESET_KOKKOS_H + +#include "fix_dt_reset.h" +#include "kokkos_type.h" + +namespace LAMMPS_NS { + +struct TagFixDtResetMass{}; +struct TagFixDtResetRMass{}; + +template +class FixDtResetKokkos : public FixDtReset { + public: + typedef DeviceType device_type; + typedef ArrayTypes AT; + + FixDtResetKokkos(class LAMMPS *, int, char **); +// ~FixDtResetKokkos() override; + void init() override; + void end_of_step() override; + + KOKKOS_INLINE_FUNCTION + void operator()(TagFixDtResetMass, const int&, double&) const; + KOKKOS_INLINE_FUNCTION + void operator()(TagFixDtResetRMass, const int&, double&) const; + + private: + typename AT::t_v_array v; + typename AT::t_f_array f; + typename AT::t_int_1d_randomread mask; + typename AT::t_int_1d_randomread type; + typename ArrayTypes::t_float_1d_randomread rmass; + typename ArrayTypes::t_float_1d_randomread mass; + + + Kokkos::DualView k_emax; +}; + +} + +#endif +#endif + diff --git a/src/KOKKOS/fix_enforce2d_kokkos.cpp b/src/KOKKOS/fix_enforce2d_kokkos.cpp index ea2ebf3f47..11402e4568 100644 --- a/src/KOKKOS/fix_enforce2d_kokkos.cpp +++ b/src/KOKKOS/fix_enforce2d_kokkos.cpp @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_enforce2d_kokkos.h b/src/KOKKOS/fix_enforce2d_kokkos.h index 33967f19f3..cd6903f6c9 100644 --- a/src/KOKKOS/fix_enforce2d_kokkos.h +++ b/src/KOKKOS/fix_enforce2d_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_eos_table_rx_kokkos.cpp b/src/KOKKOS/fix_eos_table_rx_kokkos.cpp index 68247f6918..309eaeeebf 100644 --- a/src/KOKKOS/fix_eos_table_rx_kokkos.cpp +++ b/src/KOKKOS/fix_eos_table_rx_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_eos_table_rx_kokkos.h b/src/KOKKOS/fix_eos_table_rx_kokkos.h index 84db3f0eb9..6a50b21b68 100644 --- a/src/KOKKOS/fix_eos_table_rx_kokkos.h +++ b/src/KOKKOS/fix_eos_table_rx_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_freeze_kokkos.cpp b/src/KOKKOS/fix_freeze_kokkos.cpp index 9a486a3fcc..44d3fb5b1b 100644 --- a/src/KOKKOS/fix_freeze_kokkos.cpp +++ b/src/KOKKOS/fix_freeze_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_freeze_kokkos.h b/src/KOKKOS/fix_freeze_kokkos.h index 28438d5f91..0a134030fb 100644 --- a/src/KOKKOS/fix_freeze_kokkos.h +++ b/src/KOKKOS/fix_freeze_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_gravity_kokkos.cpp b/src/KOKKOS/fix_gravity_kokkos.cpp index 63ac87a786..42a16eda78 100644 --- a/src/KOKKOS/fix_gravity_kokkos.cpp +++ b/src/KOKKOS/fix_gravity_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_gravity_kokkos.h b/src/KOKKOS/fix_gravity_kokkos.h index 779da5a8b0..8df695a8df 100644 --- a/src/KOKKOS/fix_gravity_kokkos.h +++ b/src/KOKKOS/fix_gravity_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_langevin_kokkos.cpp b/src/KOKKOS/fix_langevin_kokkos.cpp index 1e2930626e..b7305644c9 100644 --- a/src/KOKKOS/fix_langevin_kokkos.cpp +++ b/src/KOKKOS/fix_langevin_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_langevin_kokkos.h b/src/KOKKOS/fix_langevin_kokkos.h index c570cb26cb..43f809d548 100644 --- a/src/KOKKOS/fix_langevin_kokkos.h +++ b/src/KOKKOS/fix_langevin_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_minimize_kokkos.cpp b/src/KOKKOS/fix_minimize_kokkos.cpp index f78e55f10a..07c78e86a3 100644 --- a/src/KOKKOS/fix_minimize_kokkos.cpp +++ b/src/KOKKOS/fix_minimize_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_minimize_kokkos.h b/src/KOKKOS/fix_minimize_kokkos.h index af0f9c20f7..e84cbd1ec2 100644 --- a/src/KOKKOS/fix_minimize_kokkos.h +++ b/src/KOKKOS/fix_minimize_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_momentum_kokkos.cpp b/src/KOKKOS/fix_momentum_kokkos.cpp index a92c5f46ac..b9220a417f 100644 --- a/src/KOKKOS/fix_momentum_kokkos.cpp +++ b/src/KOKKOS/fix_momentum_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_momentum_kokkos.h b/src/KOKKOS/fix_momentum_kokkos.h index bb68c52d97..3bb46035fe 100644 --- a/src/KOKKOS/fix_momentum_kokkos.h +++ b/src/KOKKOS/fix_momentum_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_neigh_history_kokkos.cpp b/src/KOKKOS/fix_neigh_history_kokkos.cpp index 4837148ee0..390976dd79 100644 --- a/src/KOKKOS/fix_neigh_history_kokkos.cpp +++ b/src/KOKKOS/fix_neigh_history_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -20,6 +20,7 @@ #include "modify.h" #include "neigh_list_kokkos.h" #include "pair_kokkos.h" +#include "atom_masks.h" using namespace LAMMPS_NS; @@ -170,6 +171,7 @@ template void FixNeighHistoryKokkos::post_neighbor() { tag = atomKK->k_tag.view(); + atomKK->sync(execution_space,TAG_MASK); k_firstflag.sync(); k_firstvalue.sync(); diff --git a/src/KOKKOS/fix_neigh_history_kokkos.h b/src/KOKKOS/fix_neigh_history_kokkos.h index e27d92bee8..7885160eeb 100644 --- a/src/KOKKOS/fix_neigh_history_kokkos.h +++ b/src/KOKKOS/fix_neigh_history_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_nh_kokkos.cpp b/src/KOKKOS/fix_nh_kokkos.cpp index 722f52557e..939b88889c 100644 --- a/src/KOKKOS/fix_nh_kokkos.cpp +++ b/src/KOKKOS/fix_nh_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_nh_kokkos.h b/src/KOKKOS/fix_nh_kokkos.h index d004815a8e..c6669d60d0 100644 --- a/src/KOKKOS/fix_nh_kokkos.h +++ b/src/KOKKOS/fix_nh_kokkos.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_nph_kokkos.cpp b/src/KOKKOS/fix_nph_kokkos.cpp index 81a79473b7..89e7ff0776 100644 --- a/src/KOKKOS/fix_nph_kokkos.cpp +++ b/src/KOKKOS/fix_nph_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_nph_kokkos.h b/src/KOKKOS/fix_nph_kokkos.h index e276ab0f43..2d144c97ac 100644 --- a/src/KOKKOS/fix_nph_kokkos.h +++ b/src/KOKKOS/fix_nph_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_npt_kokkos.cpp b/src/KOKKOS/fix_npt_kokkos.cpp index 127c9f3453..d646490661 100644 --- a/src/KOKKOS/fix_npt_kokkos.cpp +++ b/src/KOKKOS/fix_npt_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_npt_kokkos.h b/src/KOKKOS/fix_npt_kokkos.h index b2b26c0742..3c6ab00c39 100644 --- a/src/KOKKOS/fix_npt_kokkos.h +++ b/src/KOKKOS/fix_npt_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_nve_kokkos.cpp b/src/KOKKOS/fix_nve_kokkos.cpp index 5ceb86f6a4..5dcb611d41 100644 --- a/src/KOKKOS/fix_nve_kokkos.cpp +++ b/src/KOKKOS/fix_nve_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_nve_kokkos.h b/src/KOKKOS/fix_nve_kokkos.h index cb0e982aeb..215aacb4a0 100644 --- a/src/KOKKOS/fix_nve_kokkos.h +++ b/src/KOKKOS/fix_nve_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_nve_sphere_kokkos.cpp b/src/KOKKOS/fix_nve_sphere_kokkos.cpp index 12b170acee..a1e8e76cd8 100644 --- a/src/KOKKOS/fix_nve_sphere_kokkos.cpp +++ b/src/KOKKOS/fix_nve_sphere_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_nve_sphere_kokkos.h b/src/KOKKOS/fix_nve_sphere_kokkos.h index 2f85fea1b9..551e64eb5c 100644 --- a/src/KOKKOS/fix_nve_sphere_kokkos.h +++ b/src/KOKKOS/fix_nve_sphere_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_nvt_kokkos.cpp b/src/KOKKOS/fix_nvt_kokkos.cpp index 92fec733fa..d98ba5c163 100644 --- a/src/KOKKOS/fix_nvt_kokkos.cpp +++ b/src/KOKKOS/fix_nvt_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_nvt_kokkos.h b/src/KOKKOS/fix_nvt_kokkos.h index ef6957bf72..56febf9dbc 100644 --- a/src/KOKKOS/fix_nvt_kokkos.h +++ b/src/KOKKOS/fix_nvt_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_nvt_sllod_kokkos.cpp b/src/KOKKOS/fix_nvt_sllod_kokkos.cpp index 8f3d830507..d9fca7e0e9 100644 --- a/src/KOKKOS/fix_nvt_sllod_kokkos.cpp +++ b/src/KOKKOS/fix_nvt_sllod_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + LAMMPS development team: developers@lammps.org, Sandia National Laboratories Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_nvt_sllod_kokkos.h b/src/KOKKOS/fix_nvt_sllod_kokkos.h index 1ae9a19729..2fc0dd3afd 100644 --- a/src/KOKKOS/fix_nvt_sllod_kokkos.h +++ b/src/KOKKOS/fix_nvt_sllod_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_property_atom_kokkos.cpp b/src/KOKKOS/fix_property_atom_kokkos.cpp index 97931f5d67..2c515510ee 100644 --- a/src/KOKKOS/fix_property_atom_kokkos.cpp +++ b/src/KOKKOS/fix_property_atom_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_property_atom_kokkos.h b/src/KOKKOS/fix_property_atom_kokkos.h index 42de42093b..90eddc98e0 100644 --- a/src/KOKKOS/fix_property_atom_kokkos.h +++ b/src/KOKKOS/fix_property_atom_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_qeq_reaxff_kokkos.cpp b/src/KOKKOS/fix_qeq_reaxff_kokkos.cpp index 43fd832700..40828013ed 100644 --- a/src/KOKKOS/fix_qeq_reaxff_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reaxff_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_qeq_reaxff_kokkos.h b/src/KOKKOS/fix_qeq_reaxff_kokkos.h index bd38522811..9db491c6d6 100644 --- a/src/KOKKOS/fix_qeq_reaxff_kokkos.h +++ b/src/KOKKOS/fix_qeq_reaxff_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_reaxff_bonds_kokkos.cpp b/src/KOKKOS/fix_reaxff_bonds_kokkos.cpp index 36830f9a00..7d9e3745ec 100644 --- a/src/KOKKOS/fix_reaxff_bonds_kokkos.cpp +++ b/src/KOKKOS/fix_reaxff_bonds_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_reaxff_bonds_kokkos.h b/src/KOKKOS/fix_reaxff_bonds_kokkos.h index fda20f7344..29c8d457fd 100644 --- a/src/KOKKOS/fix_reaxff_bonds_kokkos.h +++ b/src/KOKKOS/fix_reaxff_bonds_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_reaxff_species_kokkos.cpp b/src/KOKKOS/fix_reaxff_species_kokkos.cpp index 3bc854d3a0..960ba07a86 100644 --- a/src/KOKKOS/fix_reaxff_species_kokkos.cpp +++ b/src/KOKKOS/fix_reaxff_species_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_reaxff_species_kokkos.h b/src/KOKKOS/fix_reaxff_species_kokkos.h index 2dae02822e..1848825a19 100644 --- a/src/KOKKOS/fix_reaxff_species_kokkos.h +++ b/src/KOKKOS/fix_reaxff_species_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_rx_kokkos.cpp b/src/KOKKOS/fix_rx_kokkos.cpp index c4254043f6..963fb32a1a 100644 --- a/src/KOKKOS/fix_rx_kokkos.cpp +++ b/src/KOKKOS/fix_rx_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_rx_kokkos.h b/src/KOKKOS/fix_rx_kokkos.h index 28c27cacd5..fba67de7bd 100644 --- a/src/KOKKOS/fix_rx_kokkos.h +++ b/src/KOKKOS/fix_rx_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_setforce_kokkos.cpp b/src/KOKKOS/fix_setforce_kokkos.cpp index 3b8165670e..4b1c31bec0 100644 --- a/src/KOKKOS/fix_setforce_kokkos.cpp +++ b/src/KOKKOS/fix_setforce_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_setforce_kokkos.h b/src/KOKKOS/fix_setforce_kokkos.h index dc468aa415..4ed2cc5f0e 100644 --- a/src/KOKKOS/fix_setforce_kokkos.h +++ b/src/KOKKOS/fix_setforce_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_shake_kokkos.cpp b/src/KOKKOS/fix_shake_kokkos.cpp index d622da94ec..109b1c69b5 100644 --- a/src/KOKKOS/fix_shake_kokkos.cpp +++ b/src/KOKKOS/fix_shake_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -60,6 +60,8 @@ FixShakeKokkos::FixShakeKokkos(LAMMPS *lmp, int narg, char **arg) : datamask_read = EMPTY_MASK; datamask_modify = EMPTY_MASK; + memory->destroy(xshake); + shake_flag_tmp = shake_flag; shake_atom_tmp = shake_atom; shake_type_tmp = shake_type; diff --git a/src/KOKKOS/fix_shake_kokkos.h b/src/KOKKOS/fix_shake_kokkos.h index df5256422f..ad8a69e616 100644 --- a/src/KOKKOS/fix_shake_kokkos.h +++ b/src/KOKKOS/fix_shake_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_shardlow_kokkos.cpp b/src/KOKKOS/fix_shardlow_kokkos.cpp index 035a2ffbb8..77b90f6739 100644 --- a/src/KOKKOS/fix_shardlow_kokkos.cpp +++ b/src/KOKKOS/fix_shardlow_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_shardlow_kokkos.h b/src/KOKKOS/fix_shardlow_kokkos.h index 7d3ace56c8..ab4f0fe578 100644 --- a/src/KOKKOS/fix_shardlow_kokkos.h +++ b/src/KOKKOS/fix_shardlow_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_viscous_kokkos.cpp b/src/KOKKOS/fix_viscous_kokkos.cpp new file mode 100644 index 0000000000..80ddff2fce --- /dev/null +++ b/src/KOKKOS/fix_viscous_kokkos.cpp @@ -0,0 +1,106 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "fix_viscous_kokkos.h" + +#include "atom_kokkos.h" +#include "update.h" +#include "modify.h" +#include "input.h" +#include "memory_kokkos.h" +#include "error.h" +#include "atom_masks.h" +#include "kokkos_base.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +/* ---------------------------------------------------------------------- */ + +template +FixViscousKokkos::FixViscousKokkos(LAMMPS *lmp, int narg, char **arg) : + FixViscous(lmp, narg, arg) +{ + kokkosable = 1; + atomKK = (AtomKokkos *) atom; + execution_space = ExecutionSpaceFromDevice::space; + datamask_read = EMPTY_MASK; + datamask_modify = EMPTY_MASK; +} + +/* ---------------------------------------------------------------------- */ + +template +FixViscousKokkos::~FixViscousKokkos() +{ + if (copymode) return; +} + +/* ---------------------------------------------------------------------- */ + +template +void FixViscousKokkos::init() +{ + FixViscous::init(); + + k_gamma = Kokkos::DualView("FixViscousKokkos:gamma",atom->ntypes+1); + + for (int i = 1; i <= atom->ntypes; i++) k_gamma.h_view(i) = gamma[i]; + + k_gamma.template modify(); + k_gamma.template sync(); + + if (utils::strmatch(update->integrate_style,"^respa")) + error->all(FLERR,"Cannot (yet) use respa with Kokkos"); +} + +/* ---------------------------------------------------------------------- */ + +template +void FixViscousKokkos::post_force(int /*vflag*/) +{ + atomKK->sync(execution_space, V_MASK | F_MASK | MASK_MASK | TYPE_MASK); + + v = atomKK->k_v.view(); + f = atomKK->k_f.view(); + mask = atomKK->k_mask.view(); + type = atomKK->k_type.view(); + + int nlocal = atom->nlocal; + + copymode = 1; + Kokkos::parallel_for(Kokkos::RangePolicy(0,nlocal),*this); + copymode = 0; + + atomKK->modified(execution_space, F_MASK); +} + +template +KOKKOS_INLINE_FUNCTION +void FixViscousKokkos::operator()(TagFixViscous, const int &i) const { + if (mask[i] & groupbit) { + double drag = k_gamma.d_view(type[i]); + f(i,0) -= drag*v(i,0); + f(i,1) -= drag*v(i,1); + f(i,2) -= drag*v(i,2); + } +} + +namespace LAMMPS_NS { +template class FixViscousKokkos; +#ifdef LMP_KOKKOS_GPU +template class FixViscousKokkos; +#endif +} + diff --git a/src/KOKKOS/fix_viscous_kokkos.h b/src/KOKKOS/fix_viscous_kokkos.h new file mode 100644 index 0000000000..2594c0cf85 --- /dev/null +++ b/src/KOKKOS/fix_viscous_kokkos.h @@ -0,0 +1,60 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS +// clang-format off +FixStyle(viscous/kk,FixViscousKokkos); +FixStyle(viscous/kk/device,FixViscousKokkos); +FixStyle(viscous/kk/host,FixViscousKokkos); +// clang-format on +#else + +// clang-format off +#ifndef LMP_FIX_VISCOUS_KOKKOS_H +#define LMP_FIX_VISCOUS_KOKKOS_H + +#include "fix_viscous.h" +#include "kokkos_type.h" + +namespace LAMMPS_NS { + +struct TagFixViscous{}; + +template +class FixViscousKokkos : public FixViscous { + public: + typedef DeviceType device_type; + typedef ArrayTypes AT; + + FixViscousKokkos(class LAMMPS *, int, char **); + ~FixViscousKokkos() override; + void init() override; + void post_force(int) override; + + KOKKOS_INLINE_FUNCTION + void operator()(TagFixViscous, const int&) const; + + private: + typename AT::t_v_array v; + typename AT::t_f_array f; + typename AT::t_int_1d_randomread mask; + typename AT::t_int_1d_randomread type; + + Kokkos::DualView k_gamma; +}; + +} + +#endif +#endif + diff --git a/src/KOKKOS/fix_wall_lj93_kokkos.cpp b/src/KOKKOS/fix_wall_lj93_kokkos.cpp index f34a79430b..03bf6cf8ea 100644 --- a/src/KOKKOS/fix_wall_lj93_kokkos.cpp +++ b/src/KOKKOS/fix_wall_lj93_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_wall_lj93_kokkos.h b/src/KOKKOS/fix_wall_lj93_kokkos.h index d507f571a5..2bc78f3781 100644 --- a/src/KOKKOS/fix_wall_lj93_kokkos.h +++ b/src/KOKKOS/fix_wall_lj93_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_wall_reflect_kokkos.cpp b/src/KOKKOS/fix_wall_reflect_kokkos.cpp index 15aca43b57..32b9ee61b1 100644 --- a/src/KOKKOS/fix_wall_reflect_kokkos.cpp +++ b/src/KOKKOS/fix_wall_reflect_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/fix_wall_reflect_kokkos.h b/src/KOKKOS/fix_wall_reflect_kokkos.h index b6aba1fa02..ca8476b3b5 100644 --- a/src/KOKKOS/fix_wall_reflect_kokkos.h +++ b/src/KOKKOS/fix_wall_reflect_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/gridcomm_kokkos.cpp b/src/KOKKOS/grid3d_kokkos.cpp similarity index 78% rename from src/KOKKOS/gridcomm_kokkos.cpp rename to src/KOKKOS/grid3d_kokkos.cpp index 4a0985219b..01aee810be 100644 --- a/src/KOKKOS/gridcomm_kokkos.cpp +++ b/src/KOKKOS/grid3d_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -12,9 +12,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "gridcomm_kokkos.h" +#include "grid3d_kokkos.h" #include "comm.h" +#include "error.h" #include "irregular.h" #include "kokkos.h" #include "kokkos_base_fft.h" @@ -23,74 +24,62 @@ using namespace LAMMPS_NS; -enum{REGULAR,TILED}; - #define DELTA 16 /* ---------------------------------------------------------------------- - NOTES - tiled implementation only currently works for RCB, not general tiled - b/c RCB tree is used to find neighboring tiles + NOTES: if o indices for ghosts are < 0 or hi indices are >= N, then grid is treated as periodic in that dimension, - communication is done across the periodic boundaries + comm is done across the periodic boundaries + tiled implementations only work for RCB, not general tilings + b/c RCB tree is used to find neighboring tiles ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - constructor called by all classes except MSM - gcomm = world communicator - gn xyz = size of global grid - i xyz lohi = portion of global grid this proc owns, 0 <= index < N - o xyz lohi = owned grid portion + ghost grid cells needed in all directions - if o indices are < 0 or hi indices are >= N, - then grid is treated as periodic in that dimension, - communication is done across the periodic boundaries + constructor to create a 3d distributed grid + Grid3d assigns owned/ghost cells to each proc via setup_grid() + it MUST be called after constructor + gcomm = caller's communicator + gnx,gny,gnz = global grid size ------------------------------------------------------------------------- */ template -GridCommKokkos::GridCommKokkos(LAMMPS *lmp, MPI_Comm gcomm, - int gnx, int gny, int gnz, - int ixlo, int ixhi, int iylo, int iyhi, int izlo, int izhi, - int oxlo, int oxhi, int oylo, int oyhi, int ozlo, int ozhi) - : GridComm(lmp, gcomm, - gnx, gny, gnz, - ixlo,ixhi, iylo, iyhi, izlo, izhi, - oxlo, oxhi, oylo, oyhi, ozlo, ozhi) +Grid3dKokkos::Grid3dKokkos(LAMMPS *lmp, MPI_Comm gcomm,int gnx, int gny, int gnz) : + Grid3d(lmp, gcomm, gnx, gny, gnz) { + } /* ---------------------------------------------------------------------- - constructor called by MSM - gcomm = world communicator or sub-communicator for a hierarchical grid - flag = 1 if e xyz lohi values = larger grid stored by caller in gcomm = world - flag = 2 if e xyz lohi values = 6 neighbor procs in gcomm - gn xyz = size of global grid - i xyz lohi = portion of global grid this proc owns, 0 <= index < N - o xyz lohi = owned grid portion + ghost grid cells needed in all directions - e xyz lohi for flag = 1: extent of larger grid stored by caller - e xyz lohi for flag = 2: 6 neighbor procs + alternate constructor to create a 3d distributed grid + caller assigns owned/ghost cells to each proc + setup_grid() must NOT be called + used by MSM and PPPM/Electrode b/c their definition of ghost cells is complex + gcomm = caller's communicator + gnx,gny,gnz = global grid size + i xyz lo/hi = extent of owned grid cells on this proc + o xyz lo/hi = extent of owned+ghost grid cells on this proc + owned and ghost indices are inclusive + owned indices range from 0 to N-1 + ghost indices can extend < 0 or >= N ------------------------------------------------------------------------- */ template -GridCommKokkos::GridCommKokkos(LAMMPS *lmp, MPI_Comm gcomm, int /*flag*/, - int gnx, int gny, int gnz, +Grid3dKokkos::Grid3dKokkos(LAMMPS *lmp, MPI_Comm gcomm, int gnx, int gny, int gnz, int ixlo, int ixhi, int iylo, int iyhi, int izlo, int izhi, - int oxlo, int oxhi, int oylo, int oyhi, int ozlo, int ozhi, - int /*exlo*/, int /*exhi*/, int /*eylo*/, int /*eyhi*/, int /*ezlo*/, int /*ezhi*/) - : GridComm(lmp, gcomm, - gnx, gny, gnz, - ixlo,ixhi, iylo, iyhi, izlo, izhi, + int oxlo, int oxhi, int oylo, int oyhi, int ozlo, int ozhi) + : Grid3d(lmp, gcomm, gnx, gny, gnz, + ixlo, ixhi, iylo, iyhi, izlo, izhi, oxlo, oxhi, oylo, oyhi, ozlo, ozhi) { + } /* ---------------------------------------------------------------------- */ template -GridCommKokkos::~GridCommKokkos() +Grid3dKokkos::~Grid3dKokkos() { - // regular comm data struct - for (int i = 0; i < nswap; i++) { swap[i].packlist = nullptr; swap[i].unpacklist = nullptr; @@ -108,11 +97,14 @@ GridCommKokkos::~GridCommKokkos() copy[i].packlist = nullptr; copy[i].unpacklist = nullptr; } - } /* ---------------------------------------------------------------------- - setup comm for a regular grid of procs + grow list of swaps by DELTA +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + setup owned/ghost comm for brick comm each proc has 6 neighbors comm pattern = series of swaps with one of those 6 procs can be multiple swaps with same proc if ghost extent is large @@ -121,7 +113,7 @@ GridCommKokkos::~GridCommKokkos() ------------------------------------------------------------------------- */ template -void GridCommKokkos::setup_regular(int &nbuf1, int &nbuf2) +void Grid3dKokkos::setup_comm_brick(int &nbuf1, int &nbuf2) { int nsent,sendfirst,sendlast,recvfirst,recvlast; int sendplanes,recvplanes; @@ -414,7 +406,7 @@ void GridCommKokkos::setup_regular(int &nbuf1, int &nbuf2) } /* ---------------------------------------------------------------------- - setup comm for RCB tiled proc domains + setup owned/ghost comm for tiled comm each proc has arbitrary # of neighbors that overlap its ghost extent identify which procs will send me ghost cells, and vice versa may not be symmetric if both procs do not need same layers of ghosts @@ -423,29 +415,14 @@ void GridCommKokkos::setup_regular(int &nbuf1, int &nbuf2) ------------------------------------------------------------------------- */ template -void GridCommKokkos::setup_tiled(int &nbuf1, int &nbuf2) +void Grid3dKokkos::setup_comm_tiled(int &nbuf1, int &nbuf2) { int i,m; double xlo,xhi,ylo,yhi,zlo,zhi; int ghostbox[6],pbc[3]; - // setup RCB tree of cut info for grid - // access CommTiled to get cut dimension - // cut = this proc's inlo in that dim - // dim is -1 for proc 0, but never accessed - - rcbinfo = (RCBinfo *) - memory->smalloc(nprocs*sizeof(RCBinfo),"GridComm:rcbinfo"); - RCBinfo rcbone; - rcbone.dim = comm->rcbcutdim; - if (rcbone.dim <= 0) rcbone.cut = inxlo; - else if (rcbone.dim == 1) rcbone.cut = inylo; - else if (rcbone.dim == 2) rcbone.cut = inzlo; - MPI_Allgather(&rcbone,sizeof(RCBinfo),MPI_CHAR, - rcbinfo,sizeof(RCBinfo),MPI_CHAR,gridcomm); - - // find overlaps of my extended ghost box with all other procs - // accounts for crossings of periodic boundaries + // find overlaps of my extended ghost box with all owned boxes + // accounts for ghost box overlapping periodic boundaries // noverlap = # of overlaps, including self // overlap = vector of overlap info using Overlap data struct @@ -458,27 +435,28 @@ void GridCommKokkos::setup_tiled(int &nbuf1, int &nbuf2) pbc[0] = pbc[1] = pbc[2] = 0; - memory->create(overlap_procs,nprocs,"GridComm:overlap_procs"); - noverlap = maxoverlap = 0; - overlap = nullptr; - - ghost_box_drop(ghostbox,pbc); + Overlap *overlap; + int noverlap = compute_overlap(1,ghostbox,pbc,overlap); // send each proc an overlap message // content: me, index of my overlap, box that overlaps with its owned cells - // ncopy = # of overlaps with myself, across a periodic boundary + // ncopy = # of overlaps with myself across a periodic boundary + // skip copy to self when non-PBC int *proclist; - memory->create(proclist,noverlap,"GridComm:proclist"); + memory->create(proclist,noverlap,"grid3d:proclist"); srequest = (Request *) - memory->smalloc(noverlap*sizeof(Request),"GridComm:srequest"); + memory->smalloc(noverlap*sizeof(Request),"grid3d:srequest"); int nsend_request = 0; ncopy = 0; for (m = 0; m < noverlap; m++) { - if (overlap[m].proc == me) ncopy++; - else { + if (overlap[m].proc == me) { + if (overlap[m].pbc[0] == 0 && overlap[m].pbc[1] == 0 && + overlap[m].pbc[2] == 0) continue; + ncopy++; + } else { proclist[nsend_request] = overlap[m].proc; srequest[nsend_request].sender = me; srequest[nsend_request].index = m; @@ -488,24 +466,22 @@ void GridCommKokkos::setup_tiled(int &nbuf1, int &nbuf2) } } - Irregular *irregular = new Irregular(lmp); + auto irregular = new Irregular(lmp); int nrecv_request = irregular->create_data(nsend_request,proclist,1); - Request *rrequest = - (Request *) memory->smalloc(nrecv_request*sizeof(Request),"GridComm:rrequest"); + auto rrequest = (Request *) memory->smalloc(nrecv_request*sizeof(Request),"grid3d:rrequest"); irregular->exchange_data((char *) srequest,sizeof(Request),(char *) rrequest); irregular->destroy_data(); // compute overlaps between received ghost boxes and my owned box // overlap box used to setup my Send data struct and respond to requests - send = (Send *) memory->smalloc(nrecv_request*sizeof(Send),"GridComm:send"); + send = (Send *) memory->smalloc(nrecv_request*sizeof(Send),"grid3d:send"); - k_send_packlist = DAT::tdual_int_2d("GridComm:send_packlist",nrecv_request,k_send_packlist.extent(1)); + k_send_packlist = DAT::tdual_int_2d("grid3d:send_packlist",nrecv_request,k_send_packlist.extent(1)); - sresponse = (Response *) - memory->smalloc(nrecv_request*sizeof(Response),"GridComm:sresponse"); + sresponse = (Response *) memory->smalloc(nrecv_request*sizeof(Response),"grid3d:sresponse"); memory->destroy(proclist); - memory->create(proclist,nrecv_request,"GridComm:proclist"); + memory->create(proclist,nrecv_request,"grid3d:proclist"); for (m = 0; m < nrecv_request; m++) { send[m].proc = rrequest[m].sender; @@ -534,8 +510,7 @@ void GridCommKokkos::setup_tiled(int &nbuf1, int &nbuf2) int nsend_response = nrecv_request; int nrecv_response = irregular->create_data(nsend_response,proclist,1); - Response *rresponse = - (Response *) memory->smalloc(nrecv_response*sizeof(Response),"GridComm:rresponse"); + auto rresponse = (Response *) memory->smalloc(nrecv_response*sizeof(Response),"grid3d:rresponse"); irregular->exchange_data((char *) sresponse,sizeof(Response),(char *) rresponse); irregular->destroy_data(); delete irregular; @@ -544,9 +519,9 @@ void GridCommKokkos::setup_tiled(int &nbuf1, int &nbuf2) // box used to setup my Recv data struct after unwrapping via PBC // adjacent = 0 if any box of ghost cells does not adjoin my owned cells - recv = (Recv *) memory->smalloc(nrecv_response*sizeof(Recv),"GridComm:recv"); + recv = (Recv *) memory->smalloc(nrecv_response*sizeof(Recv),"grid3d:recv"); - k_recv_unpacklist = DAT::tdual_int_2d("GridComm:recv_unpacklist",nrecv_response,k_recv_unpacklist.extent(1)); + k_recv_unpacklist = DAT::tdual_int_2d("grid3d:recv_unpacklist",nrecv_response,k_recv_unpacklist.extent(1)); adjacent = 1; @@ -569,15 +544,18 @@ void GridCommKokkos::setup_tiled(int &nbuf1, int &nbuf2) nrecv = nrecv_response; // create Copy data struct from overlaps with self + // skip copy to self when non-PBC - copy = (Copy *) memory->smalloc(ncopy*sizeof(Copy),"GridComm:copy"); + copy = (Copy *) memory->smalloc(ncopy*sizeof(Copy),"grid3d:copy"); - k_copy_packlist = DAT::tdual_int_2d("GridComm:copy_packlist",ncopy,k_copy_packlist.extent(1)); - k_copy_unpacklist = DAT::tdual_int_2d("GridComm:copy_unpacklist",ncopy,k_copy_unpacklist.extent(1)); + k_copy_packlist = DAT::tdual_int_2d("grid3d:copy_packlist",ncopy,k_copy_packlist.extent(1)); + k_copy_unpacklist = DAT::tdual_int_2d("grid3d:copy_unpacklist",ncopy,k_copy_unpacklist.extent(1)); ncopy = 0; for (m = 0; m < noverlap; m++) { if (overlap[m].proc != me) continue; + if (overlap[m].pbc[0] == 0 && overlap[m].pbc[1] == 0 && + overlap[m].pbc[2] == 0) continue; xlo = overlap[m].box[0]; xhi = overlap[m].box[1]; ylo = overlap[m].box[2]; @@ -616,10 +594,8 @@ void GridCommKokkos::setup_tiled(int &nbuf1, int &nbuf2) // clean-up - memory->sfree(rcbinfo); + clean_overlap(); memory->destroy(proclist); - memory->destroy(overlap_procs); - memory->sfree(overlap); memory->sfree(srequest); memory->sfree(rrequest); memory->sfree(sresponse); @@ -650,28 +626,36 @@ void GridCommKokkos::setup_tiled(int &nbuf1, int &nbuf2) nbuf2 = MAX(nbufs,nbufr); } +// ---------------------------------------------------------------------- +// forward/reverse comm of owned/ghost grid data via callbacks +// ---------------------------------------------------------------------- + /* ---------------------------------------------------------------------- forward comm of my owned cells to other's ghost cells ------------------------------------------------------------------------- */ template -void GridCommKokkos::forward_comm_kspace(KSpace *kspace, int nper, int which, - FFT_DAT::tdual_FFT_SCALAR_1d &k_buf1, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf2, MPI_Datatype datatype) +void Grid3dKokkos::forward_comm(int caller, void *ptr, int which, int nper, int nbyte, + FFT_DAT::tdual_FFT_SCALAR_1d& k_buf1, FFT_DAT::tdual_FFT_SCALAR_1d& k_buf2, + MPI_Datatype datatype) { - if (layout == REGULAR) - forward_comm_kspace_regular(kspace,nper,which,k_buf1,k_buf2,datatype); + if (caller == KSPACE) { + if (layout != Comm::LAYOUT_TILED) + forward_comm_kspace_brick((KSpace *) ptr,which,nper,k_buf1,k_buf2,datatype); else - forward_comm_kspace_tiled(kspace,nper,which,k_buf1,k_buf2,datatype); + forward_comm_kspace_tiled((KSpace *) ptr,which,nper,k_buf1,k_buf2,datatype); + } else + error->all(FLERR,"Kokkos grid comm only supports Kspace"); } /* ---------------------------------------------------------------------- - forward comm on regular grid of procs via list of swaps with 6 neighbor procs + forward comm for brick decomp via list of swaps with 6 neighbor procs ------------------------------------------------------------------------- */ template -void GridCommKokkos:: -forward_comm_kspace_regular(KSpace *kspace, int nper, int which, - FFT_DAT::tdual_FFT_SCALAR_1d &k_buf1, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf2, MPI_Datatype datatype) +void Grid3dKokkos:: +forward_comm_kspace_brick(KSpace *kspace, int which, int nper, + FFT_DAT::tdual_FFT_SCALAR_1d &k_buf1, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf2, MPI_Datatype datatype) { int m; MPI_Request request; @@ -719,12 +703,12 @@ forward_comm_kspace_regular(KSpace *kspace, int nper, int which, } /* ---------------------------------------------------------------------- - forward comm on tiled grid decomp via Send/Recv lists of each neighbor proc + forward comm for tiled decomp via Send/Recv lists of each neighbor proc ------------------------------------------------------------------------- */ template -void GridCommKokkos:: -forward_comm_kspace_tiled(KSpace *kspace, int nper, int which, +void Grid3dKokkos:: +forward_comm_kspace_tiled(KSpace *kspace, int which, int nper, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf1, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf2, MPI_Datatype datatype) { int i,m,offset; @@ -791,23 +775,27 @@ forward_comm_kspace_tiled(KSpace *kspace, int nper, int which, ------------------------------------------------------------------------- */ template -void GridCommKokkos::reverse_comm_kspace(KSpace *kspace, int nper, int which, - FFT_DAT::tdual_FFT_SCALAR_1d &k_buf1, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf2, MPI_Datatype datatype) +void Grid3dKokkos::reverse_comm(int caller, void *ptr, int which, int nper, int nbyte, + FFT_DAT::tdual_FFT_SCALAR_1d& k_buf1, FFT_DAT::tdual_FFT_SCALAR_1d& k_buf2, + MPI_Datatype datatype) { - if (layout == REGULAR) - reverse_comm_kspace_regular(kspace,nper,which,k_buf1,k_buf2,datatype); - else - reverse_comm_kspace_tiled(kspace,nper,which,k_buf1,k_buf2,datatype); + if (caller == KSPACE) { + if (layout != Comm::LAYOUT_TILED) + reverse_comm_kspace_brick((KSpace *) ptr,which,nper,k_buf1,k_buf2,datatype); + else + reverse_comm_kspace_tiled((KSpace *) ptr,which,nper,k_buf1,k_buf2,datatype); + } else + error->all(FLERR,"Kokkos grid comm only supports Kspace"); } /* ---------------------------------------------------------------------- - reverse comm on regular grid of procs via list of swaps with 6 neighbor procs + reverse comm for brick decomp via list of swaps with 6 neighbor procs ------------------------------------------------------------------------- */ template -void GridCommKokkos:: -reverse_comm_kspace_regular(KSpace *kspace, int nper, int which, - FFT_DAT::tdual_FFT_SCALAR_1d &k_buf1, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf2, MPI_Datatype datatype) +void Grid3dKokkos:: +reverse_comm_kspace_brick(KSpace *kspace, int which, int nper, + FFT_DAT::tdual_FFT_SCALAR_1d &k_buf1, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf2, MPI_Datatype datatype) { int m; MPI_Request request; @@ -856,12 +844,12 @@ reverse_comm_kspace_regular(KSpace *kspace, int nper, int which, } /* ---------------------------------------------------------------------- - reverse comm on tiled grid decomp via Send/Recv lists of each neighbor proc + reverse comm for tiled decomp via Send/Recv lists of each neighbor proc ------------------------------------------------------------------------- */ template -void GridCommKokkos:: -reverse_comm_kspace_tiled(KSpace *kspace, int nper, int which, +void Grid3dKokkos:: +reverse_comm_kspace_tiled(KSpace *kspace, int which, int nper, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf1, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf2, MPI_Datatype datatype) { int i,m,offset; @@ -908,7 +896,6 @@ reverse_comm_kspace_tiled(KSpace *kspace, int nper, int which, } // unpack all received data - for (i = 0; i < nsend; i++) { MPI_Waitany(nsend,requests,&m,MPI_STATUS_IGNORE); @@ -924,24 +911,23 @@ reverse_comm_kspace_tiled(KSpace *kspace, int nper, int which, } } +// ---------------------------------------------------------------------- +// miscellaneous methods +// ---------------------------------------------------------------------- + /* ---------------------------------------------------------------------- - create swap stencil for grid own/ghost communication - swaps covers all 3 dimensions and both directions - swaps cover multiple iterations in a direction if need grid pts - from further away than nearest-neighbor proc - same swap list used by forward and reverse communication + grow list of swaps by DELTA ------------------------------------------------------------------------- */ template -void GridCommKokkos::grow_swap() +void Grid3dKokkos::grow_swap() { maxswap += DELTA; - swap = (Swap *) - memory->srealloc(swap,maxswap*sizeof(Swap),"GridComm:swap"); + swap = (Swap *) memory->srealloc(swap,maxswap*sizeof(Swap),"grid3d:swap"); if (!k_swap_packlist.d_view.data()) { - k_swap_packlist = DAT::tdual_int_2d("GridComm:swap_packlist",maxswap,k_swap_packlist.extent(1)); - k_swap_unpacklist = DAT::tdual_int_2d("GridComm:swap_unpacklist",maxswap,k_swap_unpacklist.extent(1)); + k_swap_packlist = DAT::tdual_int_2d("grid3d:swap_packlist",maxswap,k_swap_packlist.extent(1)); + k_swap_unpacklist = DAT::tdual_int_2d("grid3d:swap_unpacklist",maxswap,k_swap_unpacklist.extent(1)); } else { k_swap_packlist.resize(maxswap,k_swap_packlist.extent(1)); k_swap_unpacklist.resize(maxswap,k_swap_unpacklist.extent(1)); @@ -950,12 +936,12 @@ void GridCommKokkos::grow_swap() /* ---------------------------------------------------------------------- create 1d list of offsets into 3d array section (xlo:xhi,ylo:yhi,zlo:zhi) - assume 3d array is allocated as + assume caller's 3d array is allocated as (fullxlo:fullxhi,fullylo:fullyhi,fullzlo:fullzhi) ------------------------------------------------------------------------- */ template -int GridCommKokkos::indices(DAT::tdual_int_2d &k_list, int index, +int Grid3dKokkos::indices(DAT::tdual_int_2d &k_list, int index, int xlo, int xhi, int ylo, int yhi, int zlo, int zhi) { int nmax = (xhi-xlo+1) * (yhi-ylo+1) * (zhi-zlo+1); @@ -983,9 +969,9 @@ int GridCommKokkos::indices(DAT::tdual_int_2d &k_list, int index, } namespace LAMMPS_NS { -template class GridCommKokkos; +template class Grid3dKokkos; #ifdef LMP_KOKKOS_GPU -template class GridCommKokkos; +template class Grid3dKokkos; #endif } diff --git a/src/KOKKOS/gridcomm_kokkos.h b/src/KOKKOS/grid3d_kokkos.h similarity index 64% rename from src/KOKKOS/gridcomm_kokkos.h rename to src/KOKKOS/grid3d_kokkos.h index e067dd27e5..19751d83c9 100644 --- a/src/KOKKOS/gridcomm_kokkos.h +++ b/src/KOKKOS/grid3d_kokkos.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -12,33 +12,31 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#ifndef LMP_GRIDCOMM_KOKKOS_H -#define LMP_GRIDCOMM_KOKKOS_H +#ifndef LMP_GRID3D_KOKKOS_H +#define LMP_GRID3D_KOKKOS_H -#include "gridcomm.h" +#include "grid3d.h" #include "kokkos_type.h" #include "fftdata_kokkos.h" namespace LAMMPS_NS { template -class GridCommKokkos : public GridComm { +class Grid3dKokkos : public Grid3d { public: + enum { KSPACE = 0, PAIR = 1, FIX = 2 }; // calling classes typedef DeviceType device_type; typedef ArrayTypes AT; typedef FFTArrayTypes FFT_AT; - GridCommKokkos(class LAMMPS *, MPI_Comm, int, int, int, - int, int, int, int, int, int, - int, int, int, int, int, int); - GridCommKokkos(class LAMMPS *, MPI_Comm, int, int, int, int, - int, int, int, int, int, int, - int, int, int, int, int, int, - int, int, int, int, int, int); - ~GridCommKokkos() override; - void forward_comm_kspace(class KSpace *, int, int, - FFT_DAT::tdual_FFT_SCALAR_1d &, FFT_DAT::tdual_FFT_SCALAR_1d &, MPI_Datatype); - void reverse_comm_kspace(class KSpace *, int, int, - FFT_DAT::tdual_FFT_SCALAR_1d &, FFT_DAT::tdual_FFT_SCALAR_1d &, MPI_Datatype); + Grid3dKokkos(class LAMMPS *, MPI_Comm, int, int, int); + Grid3dKokkos(class LAMMPS *, MPI_Comm, int, int, int, + int, int, int, int, int, int, int, int, int, int, int, int); + ~Grid3dKokkos() override; + + void forward_comm(int, void *, int, int, int, + FFT_DAT::tdual_FFT_SCALAR_1d &, FFT_DAT::tdual_FFT_SCALAR_1d &, MPI_Datatype); + void reverse_comm(int, void *, int, int, int, + FFT_DAT::tdual_FFT_SCALAR_1d &, FFT_DAT::tdual_FFT_SCALAR_1d &, MPI_Datatype); private: DAT::tdual_int_2d k_swap_packlist; @@ -55,14 +53,14 @@ class GridCommKokkos : public GridComm { // internal methods // ------------------------------------------- - void setup_regular(int &, int &) override; - void setup_tiled(int &, int &) override; + void setup_comm_brick(int &, int &) override; + void setup_comm_tiled(int &, int &) override; - void forward_comm_kspace_regular(class KSpace *, int, int, + void forward_comm_kspace_brick(class KSpace *, int, int, FFT_DAT::tdual_FFT_SCALAR_1d &, FFT_DAT::tdual_FFT_SCALAR_1d &, MPI_Datatype); void forward_comm_kspace_tiled(class KSpace *, int, int, FFT_DAT::tdual_FFT_SCALAR_1d &, FFT_DAT::tdual_FFT_SCALAR_1d &, MPI_Datatype); - void reverse_comm_kspace_regular(class KSpace *, int, int, + void reverse_comm_kspace_brick(class KSpace *, int, int, FFT_DAT::tdual_FFT_SCALAR_1d &, FFT_DAT::tdual_FFT_SCALAR_1d &, MPI_Datatype); void reverse_comm_kspace_tiled(class KSpace *, int, int, FFT_DAT::tdual_FFT_SCALAR_1d &, FFT_DAT::tdual_FFT_SCALAR_1d &, MPI_Datatype); @@ -72,6 +70,6 @@ class GridCommKokkos : public GridComm { int indices(DAT::tdual_int_2d &, int, int, int, int, int, int, int); }; -} +} // namespace LAMMPS_NS #endif diff --git a/src/KOKKOS/improper_class2_kokkos.cpp b/src/KOKKOS/improper_class2_kokkos.cpp index c2da884558..f1ed6fdbc0 100644 --- a/src/KOKKOS/improper_class2_kokkos.cpp +++ b/src/KOKKOS/improper_class2_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/improper_class2_kokkos.h b/src/KOKKOS/improper_class2_kokkos.h index b0500c606d..da939b69b0 100644 --- a/src/KOKKOS/improper_class2_kokkos.h +++ b/src/KOKKOS/improper_class2_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/improper_harmonic_kokkos.cpp b/src/KOKKOS/improper_harmonic_kokkos.cpp index 77f24a7cf7..1d217461d0 100644 --- a/src/KOKKOS/improper_harmonic_kokkos.cpp +++ b/src/KOKKOS/improper_harmonic_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/improper_harmonic_kokkos.h b/src/KOKKOS/improper_harmonic_kokkos.h index ae4cc26fe0..8bd206aaf0 100644 --- a/src/KOKKOS/improper_harmonic_kokkos.h +++ b/src/KOKKOS/improper_harmonic_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/kissfft_kokkos.h b/src/KOKKOS/kissfft_kokkos.h index 48180828a3..265677a21c 100644 --- a/src/KOKKOS/kissfft_kokkos.h +++ b/src/KOKKOS/kissfft_kokkos.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index 7e637788ec..d735419ab3 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -121,11 +121,12 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) } else if (strcmp(arg[iarg],"g") == 0 || strcmp(arg[iarg],"gpus") == 0) { -#ifndef LMP_KOKKOS_GPU - error->all(FLERR,"GPUs are requested but Kokkos has not been compiled using a GPU-enabled backend"); -#endif if (iarg+2 > narg) error->all(FLERR,"Invalid Kokkos command-line args"); ngpus = utils::inumeric(FLERR, arg[iarg+1], false, lmp); +#ifndef LMP_KOKKOS_GPU + if (ngpus > 0) + error->all(FLERR,"GPUs are requested but Kokkos has not been compiled using a GPU-enabled backend"); +#endif int skip_gpu = 9999; if (iarg+2 < narg && isdigit(arg[iarg+2][0])) { @@ -143,28 +144,36 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) set_flag = 1; } if ((str = getenv("MPT_LRANK"))) { - int local_rank = atoi(str); - device = local_rank % ngpus; - if (device >= skip_gpu) device++; - set_flag = 1; + if (ngpus > 0) { + int local_rank = atoi(str); + device = local_rank % ngpus; + if (device >= skip_gpu) device++; + set_flag = 1; + } } if ((str = getenv("MV2_COMM_WORLD_LOCAL_RANK"))) { - int local_rank = atoi(str); - device = local_rank % ngpus; - if (device >= skip_gpu) device++; - set_flag = 1; + if (ngpus > 0) { + int local_rank = atoi(str); + device = local_rank % ngpus; + if (device >= skip_gpu) device++; + set_flag = 1; + } } if ((str = getenv("OMPI_COMM_WORLD_LOCAL_RANK"))) { - int local_rank = atoi(str); - device = local_rank % ngpus; - if (device >= skip_gpu) device++; - set_flag = 1; + if (ngpus > 0) { + int local_rank = atoi(str); + device = local_rank % ngpus; + if (device >= skip_gpu) device++; + set_flag = 1; + } } if ((str = getenv("PMI_LOCAL_RANK"))) { - int local_rank = atoi(str); - device = local_rank % ngpus; - if (device >= skip_gpu) device++; - set_flag = 1; + if (ngpus > 0) { + int local_rank = atoi(str); + device = local_rank % ngpus; + if (device >= skip_gpu) device++; + set_flag = 1; + } } if (ngpus > 1 && !set_flag) @@ -207,7 +216,8 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) init_ngpus = ngpus; } - if (me == 0) utils::logmesg(lmp, " will use up to {} GPU(s) per node\n", ngpus); + if ((me == 0) && (ngpus > 0)) + utils::logmesg(lmp, " will use up to {} GPU(s) per node\n", ngpus); #ifdef LMP_KOKKOS_GPU if (ngpus <= 0) @@ -364,7 +374,6 @@ void KokkosLMP::finalize() void KokkosLMP::accelerator(int narg, char **arg) { - int pair_only_flag = 0; int iarg = 0; while (iarg < narg) { if (strcmp(arg[iarg],"neigh") == 0) { @@ -483,7 +492,7 @@ void KokkosLMP::accelerator(int narg, char **arg) iarg += 2; } else if (strcmp(arg[iarg],"pair/only") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal package kokkos command"); - pair_only_flag = utils::logical(FLERR,arg[iarg+1],false,lmp); + lmp->pair_only_flag = utils::logical(FLERR,arg[iarg+1],false,lmp); iarg += 2; } else if (strcmp(arg[iarg],"neigh/thread") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal package kokkos command"); @@ -499,24 +508,12 @@ void KokkosLMP::accelerator(int narg, char **arg) #ifdef LMP_KOKKOS_GPU - if (pair_only_flag) { - lmp->suffixp = lmp->suffix; - lmp->suffix = utils::strdup("kk/host"); - } else { - // restore settings to regular suffix use, if previously, pair/only was used - if (lmp->suffixp) { - delete[] lmp->suffix; - lmp->suffix = lmp->suffixp; - lmp->suffixp = nullptr; - } - } - int nmpi = 0; MPI_Comm_size(world,&nmpi); // if "gpu/aware off" or "pair/only on", and "comm device", change to "comm no" - if ((!gpu_aware_flag && nmpi > 1) || pair_only_flag) { + if ((!gpu_aware_flag && nmpi > 1) || lmp->pair_only_flag) { if (exchange_comm_classic == 0 && exchange_comm_on_host == 0) { exchange_comm_classic = 1; exchange_comm_changed = 1; @@ -545,7 +542,7 @@ void KokkosLMP::accelerator(int narg, char **arg) // if "gpu/aware on" and "pair/only off", and comm flags were changed previously, change them back - if (gpu_aware_flag && !pair_only_flag) { + if (gpu_aware_flag && !lmp->pair_only_flag) { if (exchange_comm_changed) { exchange_comm_classic = 0; exchange_comm_changed = 0; diff --git a/src/KOKKOS/kokkos.h b/src/KOKKOS/kokkos.h index 1cecd69c5f..b6a9d57345 100644 --- a/src/KOKKOS/kokkos.h +++ b/src/KOKKOS/kokkos.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/kokkos_base.h b/src/KOKKOS/kokkos_base.h index c593f0ae60..6ab9b76c1c 100644 --- a/src/KOKKOS/kokkos_base.h +++ b/src/KOKKOS/kokkos_base.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/kokkos_base_fft.h b/src/KOKKOS/kokkos_base_fft.h index 669b60bc0b..55805acfd1 100644 --- a/src/KOKKOS/kokkos_base_fft.h +++ b/src/KOKKOS/kokkos_base_fft.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h index f7aeb3d1cd..7fa07b85c5 100644 --- a/src/KOKKOS/kokkos_type.h +++ b/src/KOKKOS/kokkos_type.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -709,6 +709,15 @@ typedef tdual_float_2d::t_dev_um t_float_2d_um; typedef tdual_float_2d::t_dev_const_um t_float_2d_const_um; typedef tdual_float_2d::t_dev_const_randomread t_float_2d_randomread; +//3d float array n +typedef Kokkos::DualView tdual_float_3d; +typedef tdual_float_3d::t_dev t_float_3d; +typedef tdual_float_3d::t_dev_const t_float_3d_const; +typedef tdual_float_3d::t_dev_um t_float_3d_um; +typedef tdual_float_3d::t_dev_const_um t_float_3d_const_um; +typedef tdual_float_3d::t_dev_const_randomread t_float_3d_randomread; + + //Position Types //1d X_FLOAT array n typedef Kokkos::DualView tdual_xfloat_1d; diff --git a/src/KOKKOS/math_special_kokkos.h b/src/KOKKOS/math_special_kokkos.h index 35a8bf56c5..d8af28d33a 100644 --- a/src/KOKKOS/math_special_kokkos.h +++ b/src/KOKKOS/math_special_kokkos.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/meam_dens_final_kokkos.h b/src/KOKKOS/meam_dens_final_kokkos.h index a3b95e837d..bcc7b558dc 100644 --- a/src/KOKKOS/meam_dens_final_kokkos.h +++ b/src/KOKKOS/meam_dens_final_kokkos.h @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/meam_dens_init_kokkos.h b/src/KOKKOS/meam_dens_init_kokkos.h index 4342cc1ba1..31ac046dcf 100644 --- a/src/KOKKOS/meam_dens_init_kokkos.h +++ b/src/KOKKOS/meam_dens_init_kokkos.h @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/meam_funcs_kokkos.h b/src/KOKKOS/meam_funcs_kokkos.h index 6cb4a1014e..b9c5cab021 100644 --- a/src/KOKKOS/meam_funcs_kokkos.h +++ b/src/KOKKOS/meam_funcs_kokkos.h @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/meam_impl_kokkos.h b/src/KOKKOS/meam_impl_kokkos.h index be69f247be..bdd8728356 100644 --- a/src/KOKKOS/meam_impl_kokkos.h +++ b/src/KOKKOS/meam_impl_kokkos.h @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/meam_kokkos.h b/src/KOKKOS/meam_kokkos.h index 1f289d6a4f..cc75023810 100644 --- a/src/KOKKOS/meam_kokkos.h +++ b/src/KOKKOS/meam_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/meam_setup_done_kokkos.h b/src/KOKKOS/meam_setup_done_kokkos.h index 8b705217b0..fa3cf7e085 100644 --- a/src/KOKKOS/meam_setup_done_kokkos.h +++ b/src/KOKKOS/meam_setup_done_kokkos.h @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/memory_kokkos.h b/src/KOKKOS/memory_kokkos.h index b421bcc825..9d894a344a 100644 --- a/src/KOKKOS/memory_kokkos.h +++ b/src/KOKKOS/memory_kokkos.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -175,7 +175,7 @@ TYPE create_kokkos(TYPE &data, typename TYPE::value_type **&array, array = (typename TYPE::value_type **) smalloc(nbytes,name); for (int i = 0; i < n1; i++) { - if (n2==0) + if (n2 == 0) array[i] = nullptr; else array[i] = &data.h_view(i,0); @@ -194,7 +194,7 @@ template array = (typename TYPE::value_type **) smalloc(nbytes,name); for (int i = 0; i < n1; i++) { - if (n2==0) + if (n2 == 0) array[i] = nullptr; else array[i] = &h_data(i,0); @@ -202,6 +202,67 @@ template return data; } +template + TYPE create_kokkos(TYPE &data, HTYPE &h_data, int n1, int n2, int n3, + const char *name) +{ + data = TYPE(std::string(name),n1,n2,n3); + h_data = Kokkos::create_mirror_view(data); + return data; +} + +template +TYPE create_kokkos(TYPE &data, typename TYPE::value_type ***&array, + int n1, int n2, int n3, const char *name) +{ + data = TYPE(std::string(name),n1,n2); + bigint nbytes = ((bigint) sizeof(typename TYPE::value_type **)) * n1; + array = (typename TYPE::value_type ***) smalloc(nbytes,name); + + for (int i = 0; i < n1; i++) { + if (n2 == 0) { + array[i] = nullptr; + } else { + nbytes = ((bigint) sizeof(typename TYPE::value_type *)) * n2; + array[i] = (typename TYPE::value_type **) smalloc(nbytes,name); + for (int j = 0; j < n2; j++) { + if (n3 == 0) + array[i][j] = nullptr; + else + array[i][j] = &data.h_view(i,j,0); + } + } + } + return data; +} + +template + TYPE create_kokkos(TYPE &data, HTYPE &h_data, + typename TYPE::value_type ***&array, int n1, int n2, int n3, + const char *name) +{ + data = TYPE(std::string(name),n1,n2); + h_data = Kokkos::create_mirror_view(data); + bigint nbytes = ((bigint) sizeof(typename TYPE::value_type **)) * n1; + array = (typename TYPE::value_type ***) smalloc(nbytes,name); + + for (int i = 0; i < n1; i++) { + if (n2 == 0) { + array[i] = nullptr; + } else { + nbytes = ((bigint) sizeof(typename TYPE::value_type *)) * n2; + array[i] = (typename TYPE::value_type **) smalloc(nbytes,name); + for (int j = 0; j < n2; j++) { + if (n3 == 0) + array[i][j] = nullptr; + else + array[i][j] = &data.h_view(i,j,0); + } + } + } + return data; +} + /* ---------------------------------------------------------------------- grow or shrink 1st dim of a 2d array last dim must stay the same @@ -217,7 +278,7 @@ TYPE grow_kokkos(TYPE &data, typename TYPE::value_type **&array, array = (typename TYPE::value_type**) srealloc(array,nbytes,name); for (int i = 0; i < n1; i++) - if (n2==0) + if (n2 == 0) array[i] = nullptr; else array[i] = &data.h_view(i,0); @@ -234,7 +295,7 @@ TYPE create_kokkos(TYPE &data, typename TYPE::value_type **&array, array = (typename TYPE::value_type **) smalloc(nbytes,name); for (int i = 0; i < n1; i++) - if (data.h_view.extent(1)==0) + if (data.h_view.extent(1) == 0) array[i] = nullptr; else array[i] = &data.h_view(i,0); @@ -254,7 +315,7 @@ TYPE grow_kokkos(TYPE &data, typename TYPE::value_type **&array, array = (typename TYPE::value_type **) srealloc(array,nbytes,name); for (int i = 0; i < n1; i++) - if (data.h_view.extent(1)==0) + if (data.h_view.extent(1) == 0) array[i] = nullptr; else array[i] = &data.h_view(i,0); @@ -275,6 +336,22 @@ void destroy_kokkos(TYPE data, typename TYPE::value_type** &array) array = nullptr; } +/* ---------------------------------------------------------------------- + destroy a 3d array +------------------------------------------------------------------------- */ + +template +void destroy_kokkos(TYPE data, typename TYPE::value_type*** &array) +{ + if (array == nullptr) return; + int n1 = data.extent(0); + for (int i = 0; i < n1; ++i) + sfree(array[i]); + data = TYPE(); + sfree(array); + array = nullptr; +} + /* ---------------------------------------------------------------------- reallocate Kokkos views without initialization deallocate first to reduce memory use diff --git a/src/KOKKOS/min_cg_kokkos.cpp b/src/KOKKOS/min_cg_kokkos.cpp index 53c4031f9b..d9a7088c3b 100644 --- a/src/KOKKOS/min_cg_kokkos.cpp +++ b/src/KOKKOS/min_cg_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/min_cg_kokkos.h b/src/KOKKOS/min_cg_kokkos.h index 4eded98003..40b97b4ab4 100644 --- a/src/KOKKOS/min_cg_kokkos.h +++ b/src/KOKKOS/min_cg_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/min_kokkos.cpp b/src/KOKKOS/min_kokkos.cpp index a590409c49..a492146731 100644 --- a/src/KOKKOS/min_kokkos.cpp +++ b/src/KOKKOS/min_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/min_kokkos.h b/src/KOKKOS/min_kokkos.h index bf539aea3c..7c88707d8c 100644 --- a/src/KOKKOS/min_kokkos.h +++ b/src/KOKKOS/min_kokkos.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/min_linesearch_kokkos.cpp b/src/KOKKOS/min_linesearch_kokkos.cpp index 76ea522fa8..920e06f70c 100644 --- a/src/KOKKOS/min_linesearch_kokkos.cpp +++ b/src/KOKKOS/min_linesearch_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -376,11 +376,15 @@ double MinLineSearchKokkos::alpha_step(double alpha, int resetflag) }); } + atomKK->modified(Device,X_MASK); + // step forward along h if (alpha > 0.0) { if (nextra_global) modify->min_step(alpha,hextra); + atomKK->sync(Device,X_MASK); // positions can be modified by fix box/relax + // local variables for lambda capture auto l_xvec = xvec; diff --git a/src/KOKKOS/min_linesearch_kokkos.h b/src/KOKKOS/min_linesearch_kokkos.h index 67cfe9bcd1..bf0b886b0c 100644 --- a/src/KOKKOS/min_linesearch_kokkos.h +++ b/src/KOKKOS/min_linesearch_kokkos.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/mliap_data_kokkos.cpp b/src/KOKKOS/mliap_data_kokkos.cpp new file mode 100644 index 0000000000..f9453301c7 --- /dev/null +++ b/src/KOKKOS/mliap_data_kokkos.cpp @@ -0,0 +1,341 @@ +// clang-format off +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + 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: Matt Bettencourt (NVIDIA) +------------------------------------------------------------------------- */ + +#include "mliap_data_kokkos.h" + +#include "atom_kokkos.h" +#include "kokkos_type.h" +#include "pair_mliap_kokkos.h" +#include "atom_masks.h" +#include "mliap_descriptor.h" +#include "lammps.h" +#include "kokkos.h" + +/* ---------------------------------------------------------------------- */ + +namespace LAMMPS_NS { +template +MLIAPDataKokkos::MLIAPDataKokkos(LAMMPS *lmp_in, int gradgradflag_in, int *map_in, + class MLIAPModel* model_in, + class MLIAPDescriptor* descriptor_in, + class PairMLIAPKokkos* pairmliap_in) : + MLIAPData(lmp_in, gradgradflag_in, map_in, model_in, descriptor_in, pairmliap_in), + k_pairmliap(pairmliap_in), + lmp(lmp_in) +{ + execution_space = ExecutionSpaceFromDevice::space; +} + +/* ---------------------------------------------------------------------- */ + +template +MLIAPDataKokkos::~MLIAPDataKokkos() { + memoryKK->destroy_kokkos(k_gradforce,gradforce); + memoryKK->destroy_kokkos(k_betas,betas); + memoryKK->destroy_kokkos(k_descriptors,descriptors); + memoryKK->destroy_kokkos(k_eatoms,eatoms); + memoryKK->destroy_kokkos(k_gamma_row_index,gamma_row_index); + memoryKK->destroy_kokkos(k_gamma_col_index,gamma_col_index); + memoryKK->destroy_kokkos(k_gamma,gamma); + memoryKK->destroy_kokkos(k_iatoms,iatoms); + memoryKK->destroy_kokkos(k_ielems,ielems); + memoryKK->destroy_kokkos(k_numneighs,numneighs); + memoryKK->destroy_kokkos(k_jatoms,jatoms); + memoryKK->destroy_kokkos(k_jelems,jelems); + memoryKK->destroy_kokkos(k_ij); + memoryKK->destroy_kokkos(k_rij,rij); + memoryKK->destroy_kokkos(k_graddesc,graddesc); +} + +/* ---------------------------------------------------------------------- */ + +template +void MLIAPDataKokkos::generate_neighdata(class NeighList *list_in, int eflag_in, int vflag_in) { + + list = list_in; + + // grow nmax gradforce array if necessary + + if (atom->nmax > nmax) { + nmax = atom->nmax; + memoryKK->destroy_kokkos(k_gradforce,gradforce); + memoryKK->create_kokkos(k_gradforce, gradforce, nmax, size_gradforce, "mliap_data:gradforce"); + } + + // clear gradforce array + + auto d_gradforce = k_gradforce.template view(); + Kokkos::deep_copy(d_gradforce, 0.); + + // grow arrays if necessary + + nlistatoms = list->inum; + if (nlistatoms_max < nlistatoms) { + memoryKK->destroy_kokkos(k_betas,betas); + memoryKK->create_kokkos(k_betas, betas, nlistatoms, ndescriptors, "mliap_data:betas"); + memoryKK->destroy_kokkos(k_descriptors,descriptors); + memoryKK->create_kokkos(k_descriptors, descriptors, nlistatoms, ndescriptors, "mliap_data:descriptors"); + memoryKK->destroy_kokkos(k_eatoms,eatoms); + memoryKK->create_kokkos(k_eatoms, eatoms, nlistatoms, "mliap_data:eatoms"); + nlistatoms_max = nlistatoms; + } + + // grow gamma arrays if necessary + + if (gradgradflag == 1) { + if (natomgamma_max < nlistatoms) { + memoryKK->destroy_kokkos(k_gamma_row_index,gamma_row_index); + memoryKK->create_kokkos(k_gamma_row_index, gamma_row_index, nlistatoms, gamma_nnz, "mliap_data:gamma_row_index"); + memoryKK->destroy_kokkos(k_gamma_col_index,gamma_col_index); + memoryKK->create_kokkos(k_gamma_col_index, gamma_col_index, nlistatoms, gamma_nnz, "mliap_data:gamma_col_index"); + memoryKK->destroy_kokkos(k_gamma,gamma); + memoryKK->create_kokkos(k_gamma, gamma, nlistatoms, gamma_nnz, "mliap_data:"); + natomgamma_max = nlistatoms; + } + } + atomKK->sync(execution_space,X_MASK | V_MASK | F_MASK | TYPE_MASK); + k_pairmliap->x = atomKK->k_x.view(); + k_pairmliap->v = atomKK->k_v.view(); + k_pairmliap->f = atomKK->k_f.view(); + + grow_neigharrays(); + + // Use the ielems memory for prefix scan and set it at the end to the i type + + auto d_iatoms = k_iatoms.template view(); + auto d_ielems = k_ielems.template view(); + auto d_ij = k_ij.template view(); + auto d_numneighs = k_numneighs.template view(); + auto d_jatoms = k_jatoms.template view(); + auto d_jelems= k_jelems.template view(); + auto d_rij= k_rij.template view(); + + NeighListKokkos* k_list = static_cast*>(list); + auto d_numneigh = k_list->d_numneigh; + auto d_neighbors = k_list->d_neighbors; + auto d_ilist = k_list->d_ilist; + auto d_cutsq=k_pairmliap->k_cutsq.template view(); + + AtomKokkos *atomKK = (AtomKokkos *) atom; + auto x = atomKK->k_x.view(); + auto type = atomKK->k_type.view(); + auto map=k_pairmliap->k_map.template view(); + + Kokkos::parallel_scan(nlistatoms, KOKKOS_LAMBDA (int ii, int &update, const bool final) { + if (final) + d_ij(ii) = update; + update += d_numneighs(ii); + }); + + Kokkos::parallel_for(nlistatoms, KOKKOS_LAMBDA (int ii) { + int ij = d_ij(ii); + const int i = d_ilist[ii]; + const double xtmp = x(i, 0); + const double ytmp = x(i, 1); + const double ztmp = x(i, 2); + const int itype = type(i); + const int ielem = map(itype); + const int jnum = d_numneigh(i); + for (int jj = 0; jj < jnum; jj++) { + int j = d_neighbors(i,jj); + j &= NEIGHMASK; + const double delx = x(j,0) - xtmp; + const double dely = x(j,1) - ytmp; + const double delz = x(j,2) - ztmp; + const double rsq = delx*delx + dely*dely + delz*delz; + int jtype = type(j); + const int jelem = map(jtype); + if (rsq < d_cutsq(itype,jtype)) { + d_jatoms(ij) = j; + d_jelems(ij) = jelem; + d_rij(ij, 0) = delx; + d_rij(ij, 1) = dely; + d_rij(ij, 2) = delz; + ij++; + } + } + d_iatoms[ii] = i; + d_ielems[ii] = ielem; + }); + + modified(execution_space, NUMNEIGHS_MASK | IATOMS_MASK | IELEMS_MASK | JATOMS_MASK | JELEMS_MASK | RIJ_MASK | IJ_MASK ); + eflag = eflag_in; + vflag = vflag_in; +} + +/* ---------------------------------------------------------------------- */ + +template +void MLIAPDataKokkos::grow_neigharrays() { + AtomKokkos *atomKK = (AtomKokkos *) atom; + + // grow neighbor arrays if necessary + + if (natomneigh_max < nlistatoms) { + natomneigh_max = nlistatoms; + + memoryKK->destroy_kokkos(k_iatoms,iatoms); + memoryKK->create_kokkos(k_iatoms, iatoms, natomneigh_max, "mliap_data:iatoms"); + memoryKK->destroy_kokkos(k_ielems,ielems); + memoryKK->create_kokkos(k_ielems, ielems, natomneigh_max, "mliap_data:ielems"); + memoryKK->destroy_kokkos(k_ij); + memoryKK->create_kokkos(k_ij, natomneigh_max, "mliap_data:ij"); + memoryKK->destroy_kokkos(k_numneighs,numneighs); + memoryKK->create_kokkos(k_numneighs, numneighs, natomneigh_max, "mliap_data:numneighs"); + } + + NeighListKokkos* k_list = static_cast*>(list); + auto d_numneigh = k_list->d_numneigh; + auto d_neighbors = k_list->d_neighbors; + auto d_ilist = k_list->d_ilist; + + auto x = atomKK->k_x.view(); + auto type = atomKK->k_type.view(); + auto d_cutsq=k_pairmliap->k_cutsq.template view(); + auto d_numneighs = k_numneighs.template view(); + Kokkos::parallel_reduce(nlistatoms, KOKKOS_LAMBDA (int ii, int &contrib) { + const int i = d_ilist[ii]; + int count=0; + const double xtmp = x(i, 0); + const double ytmp = x(i, 1); + const double ztmp = x(i, 2); + const int itype = type(i); + const int jnum = d_numneigh(i); + for (int jj = 0; jj < jnum; jj++) { + int j = d_neighbors(i,jj); + j &= NEIGHMASK; + const double delx = x(j,0) - xtmp; + const double dely = x(j,1) - ytmp; + const double delz = x(j,2) - ztmp; + const double rsq = delx*delx + dely*dely + delz*delz; + int jtype = type(j); + if (rsq < d_cutsq(itype,jtype)) + count++; + } + d_numneighs(ii) = count; + contrib += count; + }, nij_total); + modified(execution_space, NUMNEIGHS_MASK); + + if (nneigh_max < nij_total) { + memoryKK->destroy_kokkos(k_jatoms,jatoms); + memoryKK->create_kokkos(k_jatoms, jatoms, nij_total, "mliap_data:jatoms"); + memoryKK->destroy_kokkos(k_jelems,jelems); + memoryKK->create_kokkos(k_jelems, jelems, nij_total, "mliap_data:jelems"); + memoryKK->destroy_kokkos(k_rij,rij); + memoryKK->create_kokkos(k_rij, rij, nij_total, 3, "mliap_data:rij"); + + if (gradgradflag == 0){ + memoryKK->destroy_kokkos(k_graddesc,graddesc); + memoryKK->create_kokkos(k_graddesc, graddesc, nij_total, ndescriptors,3, "mliap_data:graddesc"); + } + nneigh_max = nij_total; + } +} + +/* ---------------------------------------------------------------------- */ + +template +void MLIAPDataKokkos::modified(ExecutionSpace space, unsigned int mask, bool ignore_auto_sync) { + if (space == Device) { + if (mask & IATOMS_MASK ) k_iatoms .modify(); + if (mask & IELEMS_MASK ) k_ielems .modify(); + if (mask & JATOMS_MASK ) k_jatoms .modify(); + if (mask & JELEMS_MASK ) k_jelems .modify(); + if (mask & IJ_MASK ) k_ij .modify(); + if (mask & BETAS_MASK ) k_betas .modify(); + if (mask & DESCRIPTORS_MASK ) k_descriptors .modify(); + if (mask & EATOMS_MASK ) k_eatoms .modify(); + if (mask & RIJ_MASK ) k_rij .modify(); + if (mask & GRADFORCE_MASK ) k_gradforce .modify(); + if (mask & GRADDESC_MASK ) k_graddesc .modify(); + if (mask & NUMNEIGHS_MASK ) k_numneighs .modify(); + if (mask & GAMMA_MASK_MASK ) k_gamma .modify(); + if (mask & GAMMA_ROW_MASK ) k_gamma_row_index.modify(); + if (mask & GAMMA_COL_MASK ) k_gamma_col_index.modify(); + + if (lmp->kokkos->auto_sync && !ignore_auto_sync) sync(Host, mask, true); + } else { + if (mask & IATOMS_MASK ) k_iatoms .modify(); + if (mask & IELEMS_MASK ) k_ielems .modify(); + if (mask & JATOMS_MASK ) k_jatoms .modify(); + if (mask & JELEMS_MASK ) k_jelems .modify(); + if (mask & IJ_MASK ) k_ij .modify(); + if (mask & BETAS_MASK ) k_betas .modify(); + if (mask & DESCRIPTORS_MASK ) k_descriptors .modify(); + if (mask & EATOMS_MASK ) k_eatoms .modify(); + if (mask & RIJ_MASK ) k_rij .modify(); + if (mask & GRADFORCE_MASK ) k_gradforce .modify(); + if (mask & GRADDESC_MASK ) k_graddesc .modify(); + if (mask & NUMNEIGHS_MASK ) k_numneighs .modify(); + if (mask & GAMMA_MASK_MASK ) k_gamma .modify(); + if (mask & GAMMA_ROW_MASK ) k_gamma_row_index.modify(); + if (mask & GAMMA_COL_MASK ) k_gamma_col_index.modify(); + if (lmp->kokkos->auto_sync && !ignore_auto_sync) sync(Device, mask, true); + } +} + +/* ---------------------------------------------------------------------- */ + +template +void MLIAPDataKokkos::sync(ExecutionSpace space, unsigned int mask, bool ignore_auto_sync) { + + if (space == Device) { + if (lmp->kokkos->auto_sync && !ignore_auto_sync) modified(Host, mask, true); + if (mask & IATOMS_MASK ) k_iatoms .sync(); + if (mask & IELEMS_MASK ) k_ielems .sync(); + if (mask & JATOMS_MASK ) k_jatoms .sync(); + if (mask & JELEMS_MASK ) k_jelems .sync(); + if (mask & IJ_MASK ) k_ij .sync(); + if (mask & BETAS_MASK ) k_betas .sync(); + if (mask & DESCRIPTORS_MASK ) k_descriptors .sync(); + if (mask & EATOMS_MASK ) k_eatoms .sync(); + if (mask & RIJ_MASK ) k_rij .sync(); + if (mask & GRADFORCE_MASK ) k_gradforce .sync(); + if (mask & GRADDESC_MASK ) k_graddesc .sync(); + if (mask & NUMNEIGHS_MASK ) k_numneighs .sync(); + if (mask & GAMMA_MASK_MASK ) k_gamma .sync(); + if (mask & GAMMA_ROW_MASK ) k_gamma_row_index.sync(); + if (mask & GAMMA_COL_MASK ) k_gamma_col_index.sync(); + } else { + if (lmp->kokkos->auto_sync && !ignore_auto_sync) modified(Device, mask, true); + if (mask & IATOMS_MASK ) k_iatoms .sync(); + if (mask & IELEMS_MASK ) k_ielems .sync(); + if (mask & JATOMS_MASK ) k_jatoms .sync(); + if (mask & JELEMS_MASK ) k_jelems .sync(); + if (mask & IJ_MASK ) k_ij .sync(); + if (mask & BETAS_MASK ) k_betas .sync(); + if (mask & DESCRIPTORS_MASK ) k_descriptors .sync(); + if (mask & EATOMS_MASK ) k_eatoms .sync(); + if (mask & RIJ_MASK ) k_rij .sync(); + if (mask & GRADFORCE_MASK ) k_gradforce .sync(); + if (mask & GRADDESC_MASK ) k_graddesc .sync(); + if (mask & NUMNEIGHS_MASK ) k_numneighs .sync(); + if (mask & GAMMA_MASK_MASK ) k_gamma .sync(); + if (mask & GAMMA_ROW_MASK ) k_gamma_row_index.sync(); + if (mask & GAMMA_COL_MASK ) k_gamma_col_index.sync(); + } +} + +/* ---------------------------------------------------------------------- */ + +template class MLIAPDataKokkos; +#ifdef LMP_KOKKOS_GPU +template class MLIAPDataKokkos; +#endif +}// namespace diff --git a/src/KOKKOS/mliap_data_kokkos.h b/src/KOKKOS/mliap_data_kokkos.h new file mode 100644 index 0000000000..ba81e2a226 --- /dev/null +++ b/src/KOKKOS/mliap_data_kokkos.h @@ -0,0 +1,87 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + 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: Matt Bettencourt (NVIDIA) +------------------------------------------------------------------------- */ + +#ifndef LMP_MLIAP_DATA_KOKKOS_H +#define LMP_MLIAP_DATA_KOKKOS_H + +#include "mliap_data.h" + +#include "kokkos_type.h" +#include "memory_kokkos.h" +#include "pair_mliap_kokkos.h" +#include "pointers.h" + +namespace LAMMPS_NS { +// clang-format off +enum { + IATOMS_MASK = 0x00000001, + IELEMS_MASK = 0x00000002, + JATOMS_MASK = 0x00000004, + JELEMS_MASK = 0x00000008, + IJ_MASK = 0x00000010, + BETAS_MASK = 0x00000020, + DESCRIPTORS_MASK = 0x00000040, + EATOMS_MASK = 0x00000080, + RIJ_MASK = 0x00000100, + GRADFORCE_MASK = 0x00000200, + GRADDESC_MASK = 0x00000400, + NUMNEIGHS_MASK = 0x00000800, + GAMMA_MASK_MASK = 0x00001000, + GAMMA_ROW_MASK = 0x00002000, + GAMMA_COL_MASK = 0x00004000, +}; +// clang-format on + +template class MLIAPDataKokkos : public MLIAPData { + public: + MLIAPDataKokkos(class LAMMPS *, int, int *, class MLIAPModel *, class MLIAPDescriptor *, + class PairMLIAPKokkos * = nullptr); + ~MLIAPDataKokkos() override; + ExecutionSpace execution_space; + + void generate_neighdata(class NeighList *, int = 0, int = 0) override; + void grow_neigharrays() override; + + void modified(ExecutionSpace space, unsigned int mask, bool ignore_auto_sync = false); + + void sync(ExecutionSpace space, unsigned int mask, bool ignore_auto_sync = false); + + PairMLIAPKokkos *k_pairmliap; + + DAT::tdual_int_1d k_iatoms; // index of each atom + DAT::tdual_int_1d k_ielems; // element of each atom + DAT::tdual_int_1d k_jatoms; // index of each neighbor + DAT::tdual_int_1d k_jelems; // element of each neighbor + DAT::tdual_int_1d k_ij; // Start location for each particle + DAT::tdual_float_2d k_betas; // betas for all atoms in list + DAT::tdual_float_2d k_descriptors; // descriptors for all atoms in list + DAT::tdual_float_1d k_eatoms; // energies for all atoms in list + DAT::tdual_float_2d k_rij; // distance vector of each neighbor + DAT::tdual_float_2d k_gradforce; + DAT::tdual_float_3d k_graddesc; // descriptor gradient w.r.t. each neighbor + DAT::tdual_int_1d k_numneighs; // neighbors count for each atom + DAT::tdual_float_2d k_gamma; // gamma element + DAT::tdual_int_2d k_gamma_row_index; // row (parameter) index + DAT::tdual_int_2d k_gamma_col_index; // column (descriptor) index + + int nij_total; + + protected: + class LAMMPS *lmp; +}; +} // namespace LAMMPS_NS +#endif diff --git a/src/KOKKOS/mliap_descriptor_kokkos.h b/src/KOKKOS/mliap_descriptor_kokkos.h new file mode 100644 index 0000000000..cb02a81648 --- /dev/null +++ b/src/KOKKOS/mliap_descriptor_kokkos.h @@ -0,0 +1,54 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + 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: Matt Bettencourt (NVIDIA) +------------------------------------------------------------------------- */ + +#ifndef LMP_MLIAP_DESCRIPTOR_KOKKOS_H +#define LMP_MLIAP_DESCRIPTOR_KOKKOS_H + +#include "kokkos_type.h" +#include "memory_kokkos.h" +#include "mliap_descriptor.h" +#include "pointers.h" + +namespace LAMMPS_NS { +template class MLIAPDescriptorKokkos : virtual protected Pointers { + public: + MLIAPDescriptorKokkos(LAMMPS *lmp, MLIAPDescriptor *descriptor_in) : + Pointers(lmp), descriptor(descriptor_in) + { + memoryKK->destroy_kokkos(k_wjelem); + } + + void init_data() + { + int num_elems = descriptor->nelements; + memoryKK->destroy_kokkos(k_wjelem); + memoryKK->create_kokkos(k_wjelem, num_elems, "MLIAPDescriptorKokkos::k_wjelem"); + for (int i = 0; i < num_elems; ++i) k_wjelem.h_view(i) = descriptor->wjelem[i]; + k_wjelem.modify(); + k_wjelem.sync(); + } + + virtual ~MLIAPDescriptorKokkos() + { + memoryKK->destroy_kokkos(k_wjelem); + } + + MLIAPDescriptor *descriptor; + DAT::tdual_float_1d k_wjelem; +}; +} // namespace LAMMPS_NS +#endif diff --git a/src/KOKKOS/mliap_descriptor_so3_kokkos.cpp b/src/KOKKOS/mliap_descriptor_so3_kokkos.cpp new file mode 100644 index 0000000000..177ddff80e --- /dev/null +++ b/src/KOKKOS/mliap_descriptor_so3_kokkos.cpp @@ -0,0 +1,275 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + 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: Matt Bettencourt (NVIDIA) + ------------------------------------------------------------------------- */ + +#include "mliap_descriptor_so3_kokkos.h" + +#include "atom_kokkos.h" +#include "comm.h" +#include "error.h" +#include "memory.h" +#include "mliap_data_kokkos.h" +#include "mliap_so3_kokkos.h" +#include "pair_mliap.h" +#include "tokenizer.h" + +#include + +using namespace LAMMPS_NS; + +#define MAXLINE 1024 +#define MAXWORD 3 + +/* ---------------------------------------------------------------------- */ +template +MLIAPDescriptorSO3Kokkos::MLIAPDescriptorSO3Kokkos(LAMMPS *lmp, char *paramfilename) + // TODO: why take self as param, shouldn't be needed + : Pointers(lmp), MLIAPDescriptorSO3(lmp, paramfilename), MLIAPDescriptorKokkos(lmp, this) +{ + // TODO: the MLIAP_SO3 object likely needs a kokkos-ified version + so3ptr_kokkos = new MLIAP_SO3Kokkos(lmp, rcutfac, lmax, nmax, alpha); +} + +/* ---------------------------------------------------------------------- */ + +template +MLIAPDescriptorSO3Kokkos::~MLIAPDescriptorSO3Kokkos() +{ +} + +/* ---------------------------------------------------------------------- */ + +template +void MLIAPDescriptorSO3Kokkos::compute_descriptors(class MLIAPData *data_) +{ + auto data = static_cast*>(data_); + so3ptr_kokkos->spectrum(data->nlistatoms, data->k_numneighs, data->k_jelems, this->k_wjelem, data->k_rij, data->k_ij, + nmax, lmax, rcutfac, alpha, data->nij_total, data->ndescriptors); + + Kokkos::deep_copy(data->k_descriptors.template view(), so3ptr_kokkos->m_plist_r); + Kokkos::deep_copy(data->k_descriptors.h_view, so3ptr_kokkos->m_plist_r); +} + +/* ---------------------------------------------------------------------- */ + +template +void MLIAPDescriptorSO3Kokkos::compute_forces(class MLIAPData *data_) +{ + auto data = static_cast*>(data_); + int npairs = data->nij_total; + auto d_numneighs = data->k_numneighs.template view(); + so3ptr_kokkos->spectrum_dxdr(data->nlistatoms, data->k_numneighs, data->k_jelems, this->k_wjelem, data->k_rij, data->k_ij, + nmax, lmax, rcutfac, alpha, npairs, data->ndescriptors); + + auto d_f = atomKK->k_f.view(); + auto d_iatoms = data->k_iatoms.template view(); + auto d_jatoms = data->k_jatoms.template view(); + auto d_betas = data->k_betas.template view(); + auto d_rij = data->k_rij.template view(); + auto d_ij = data->k_ij.template view(); + auto ndescriptors = data->ndescriptors; + auto d_dplist_r = so3ptr_kokkos->k_dplist_r; + auto vflag=data->vflag; + int vflag_either=data->k_pairmliap->vflag_either, vflag_global=data->pairmliap->vflag_global, vflag_atom=data->pairmliap->vflag_atom; + auto d_vatom = data->k_pairmliap->k_vatom.template view(); + Kokkos::View virial("virial"); + data->k_pairmliap->k_vatom.template modify(); + data->k_pairmliap->k_vatom.template sync(); + Kokkos::parallel_for(data->nlistatoms, KOKKOS_LAMBDA(int ii) { + double fij[3]; + const int i = d_iatoms(ii); + + // ensure rij, inside, wj, and rcutij are of size jnum + + const int jnum = d_numneighs(ii); + int ij = d_ij(ii); // use precomputed ij to break loop dependency + for (int jj = 0; jj < jnum; jj++) { + int j = d_jatoms(ij); + + for (int ir = 0; ir < 3; ir++) { + fij[ir] = 0.0; + for (int icoeff = 0; icoeff < ndescriptors; icoeff++) { + fij[ir] += d_betas(ii, icoeff) * + d_dplist_r(ij,icoeff, ir); + } + } + + Kokkos::atomic_add(&d_f(i, 0),fij[0]); + Kokkos::atomic_add(&d_f(i, 1),fij[1]); + Kokkos::atomic_add(&d_f(i, 2),fij[2]); + Kokkos::atomic_add(&d_f(j, 0),-fij[0]); + Kokkos::atomic_add(&d_f(j, 1),-fij[1]); + Kokkos::atomic_add(&d_f(j, 2),-fij[2]); + + if (vflag) { + v_tally(vflag_either, vflag_global, vflag_atom, i, j, ij, fij, d_rij, virial, d_vatom); + } + ij++; + } + }); + + if (vflag) { + if (vflag_global) { + Kokkos::View h_virial("h_virial"); + Kokkos::deep_copy(h_virial,virial); + for (int i=0;i<6;++i) + data->k_pairmliap->virial[i]+=h_virial[i]; + } + if (vflag_atom) { + data->k_pairmliap->k_vatom.template modify(); + data->k_pairmliap->k_vatom.template sync(); + } + } +} + +/* ---------------------------------------------------------------------- + add virial contribution into global and per-atom accumulators +------------------------------------------------------------------------- */ +template +template +KOKKOS_INLINE_FUNCTION +void MLIAPDescriptorSO3Kokkos::v_tally(int vflag_either, int vflag_global, int vflag_atom, int i, int j, int ij, + double *fij, ViewType rij, Kokkos::View virial, ViewType vatom) +{ + double v[6]; + if (vflag_either) { + v[0] = -rij(ij,0)*fij[0]; + v[1] = -rij(ij,1)*fij[1]; + v[2] = -rij(ij,2)*fij[2]; + v[3] = -rij(ij,0)*fij[1]; + v[4] = -rij(ij,0)*fij[2]; + v[5] = -rij(ij,1)*fij[2]; + if (vflag_global) { + Kokkos::atomic_add(&virial[0], v[0]); + Kokkos::atomic_add(&virial[1], v[1]); + Kokkos::atomic_add(&virial[2], v[2]); + Kokkos::atomic_add(&virial[3], v[3]); + Kokkos::atomic_add(&virial[4], v[4]); + Kokkos::atomic_add(&virial[5], v[5]); + } + if (vflag_atom) { + Kokkos::atomic_add(&vatom(i,0), 0.5*v[0]); + Kokkos::atomic_add(&vatom(i,1), 0.5*v[1]); + Kokkos::atomic_add(&vatom(i,2), 0.5*v[2]); + Kokkos::atomic_add(&vatom(i,3), 0.5*v[3]); + Kokkos::atomic_add(&vatom(i,4), 0.5*v[4]); + Kokkos::atomic_add(&vatom(i,5), 0.5*v[5]); + + Kokkos::atomic_add(&vatom(j,0), 0.5*v[0]); + Kokkos::atomic_add(&vatom(j,1), 0.5*v[1]); + Kokkos::atomic_add(&vatom(j,2), 0.5*v[2]); + Kokkos::atomic_add(&vatom(j,3), 0.5*v[3]); + Kokkos::atomic_add(&vatom(j,4), 0.5*v[4]); + Kokkos::atomic_add(&vatom(j,5), 0.5*v[5]); + } + } +} +/* ---------------------------------------------------------------------- */ + +template +void MLIAPDescriptorSO3Kokkos::compute_force_gradients(class MLIAPData *data_) +{ + error->all(FLERR,"This has not been tested in cuda/kokkos"); + + auto data = static_cast*>(data_); + int npairs = data->nij_total; + so3ptr_kokkos->spectrum_dxdr(data->nlistatoms, data->k_numneighs, data->k_jelems, this->k_wjelem, data->k_rij, data->k_ij, + nmax, lmax, rcutfac, alpha, npairs, data->ndescriptors); + auto d_dplist_r = so3ptr_kokkos->k_dplist_r; + auto d_gradforce = data->k_gradforce.template view(); + auto d_gamma = data->k_gamma.template view(); + auto d_gamma_row_index = data->k_gamma_row_index.template view(); + auto d_gamma_col_index = data->k_gamma_col_index.template view(); + auto d_jatoms = data->k_jatoms.template view(); + auto d_ij = data->k_ij.template view(); + auto d_numneighs = data->k_numneighs.template view(); + auto d_iatoms = data->k_iatoms.template view(); + + auto yoffset = data->yoffset, zoffset = data->zoffset, gamma_nnz = data->gamma_nnz; + + Kokkos::parallel_for (data->nlistatoms, KOKKOS_LAMBDA (int ii) { + const int i = d_iatoms(ii); + + // insure rij, inside, wj, and rcutij are of size jnum + + const int jnum = d_numneighs(ii); + int ij = d_ij(ii); + for (int jj = 0; jj < jnum; jj++) { + int j = d_jatoms(ij); + + for (int inz = 0; inz < gamma_nnz; inz++) { + const int l = d_gamma_row_index(ii, inz); + const int k = d_gamma_col_index(ii, inz); + + Kokkos::atomic_add(&d_gradforce(i, l), + + d_gamma(ii, inz) * d_dplist_r(ij, k, 0)); + Kokkos::atomic_add(&d_gradforce(i, l + yoffset), + + d_gamma(ii, inz) * d_dplist_r(ij, k, 1)); + Kokkos::atomic_add(&d_gradforce(i, l + zoffset), + + d_gamma(ii, inz) * d_dplist_r(ij, k, 2)); + Kokkos::atomic_add(&d_gradforce(j, l), - + d_gamma(ii, inz) * d_dplist_r(ij, k, 0)); + Kokkos::atomic_add(&d_gradforce(j, l + yoffset), - + d_gamma(ii, inz) * d_dplist_r(ij, k, 1)); + Kokkos::atomic_add(&d_gradforce(j, l + zoffset), - + d_gamma(ii, inz) * d_dplist_r(ij, k, 2)); + } + ij++; + } + }); +} + +/* ---------------------------------------------------------------------- */ + +template +void MLIAPDescriptorSO3Kokkos::compute_descriptor_gradients(class MLIAPData *data_) +{ + auto data = static_cast*>(data_); + bigint npairs = data->nij_total; + so3ptr_kokkos->spectrum_dxdr(data->nlistatoms, data->k_numneighs, data->k_jelems, this->k_wjelem, data->k_rij, data->k_ij, + nmax, lmax, rcutfac, alpha, npairs, data->ndescriptors); + auto graddesc = data->k_graddesc.template view(); + Kokkos::deep_copy(graddesc, so3ptr_kokkos->k_dplist_r); + Kokkos::deep_copy(data->k_graddesc.h_view, graddesc); +} + +/* ---------------------------------------------------------------------- */ + +template +void MLIAPDescriptorSO3Kokkos::init() +{ + so3ptr_kokkos->init(); + MLIAPDescriptorKokkos::init_data(); +} + +/* ---------------------------------------------------------------------- */ + +template +double MLIAPDescriptorSO3Kokkos::memory_usage() +{ + double bytes = MLIAPDescriptor::memory_usage(); + bytes += so3ptr_kokkos->memory_usage(); + + return bytes; +} + +namespace LAMMPS_NS { +template class MLIAPDescriptorSO3Kokkos; +#ifdef LMP_KOKKOS_GPU +template class MLIAPDescriptorSO3Kokkos; +#endif +} diff --git a/src/KOKKOS/mliap_descriptor_so3_kokkos.h b/src/KOKKOS/mliap_descriptor_so3_kokkos.h new file mode 100644 index 0000000000..aea4540632 --- /dev/null +++ b/src/KOKKOS/mliap_descriptor_so3_kokkos.h @@ -0,0 +1,51 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + 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: Matt Bettencourt (NVIDIA) + ------------------------------------------------------------------------- */ + +#ifndef LMP_MLIAP_DESCRIPTOR_SO3_KOKKOS_H +#define LMP_MLIAP_DESCRIPTOR_SO3_KOKKOS_H + +#include "mliap_descriptor_kokkos.h" +#include "mliap_descriptor_so3.h" +#include "mliap_so3_kokkos.h" + +namespace LAMMPS_NS { +template +class MLIAPDescriptorSO3Kokkos : + public MLIAPDescriptorSO3, + public MLIAPDescriptorKokkos { + public: + MLIAPDescriptorSO3Kokkos(LAMMPS *, char *); + ~MLIAPDescriptorSO3Kokkos() override; + + void compute_descriptors(class MLIAPData *) override; + void compute_forces(class MLIAPData *) override; + void compute_force_gradients(class MLIAPData *) override; + void compute_descriptor_gradients(class MLIAPData *) override; + void init() override; + double memory_usage() override; + + protected: + template + KOKKOS_FUNCTION static void v_tally(int vflag_either, int vflag_global, int vflag_atom, int i, + int j, int ij, double *fij, ViewType rij, + Kokkos::View virial, ViewType vatom); + class MLIAP_SO3Kokkos *so3ptr_kokkos; + + // inherited from non-Kokkos class +}; +} // namespace LAMMPS_NS +#endif diff --git a/src/KOKKOS/mliap_model_kokkos.h b/src/KOKKOS/mliap_model_kokkos.h new file mode 100644 index 0000000000..792bad4e48 --- /dev/null +++ b/src/KOKKOS/mliap_model_kokkos.h @@ -0,0 +1,54 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + 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: Matt Bettencourt (NVIDIA) + ------------------------------------------------------------------------- */ + +#ifndef LMP_MLIAP_MODEL_KOKKOS_H +#define LMP_MLIAP_MODEL_KOKKOS_H + +#include "kokkos_type.h" +#include "memory_kokkos.h" +#include "pointers.h" + +namespace LAMMPS_NS { + +template class MLIAPModelKokkos : protected Pointers { + public: + MLIAPModelKokkos(LAMMPS *lmp, MLIAPModel *model_in) : Pointers(lmp), model(model_in) {} + virtual ~MLIAPModelKokkos() + { + memoryKK->destroy_kokkos(k_coeffelem); + model->coeffelem = nullptr; + } + + void set_k_coeffelem() + { + double **tmp = nullptr; + memoryKK->destroy_kokkos(k_coeffelem); + memoryKK->create_kokkos(k_coeffelem, tmp, model->nelements, model->nparams, + "MLIAPModelKokkos::coeffelem"); + for (int i = 0; i < model->nelements; ++i) + for (int j = 0; j < model->nparams; ++j) tmp[i][j] = model->coeffelem[i][j]; + delete model->coeffelem; + model->coeffelem = tmp; + k_coeffelem.modify(); + k_coeffelem.sync(); + } + + MLIAPModel *model; + DAT::tdual_float_2d k_coeffelem; +}; +} // namespace LAMMPS_NS +#endif diff --git a/src/KOKKOS/mliap_model_linear_kokkos.cpp b/src/KOKKOS/mliap_model_linear_kokkos.cpp new file mode 100644 index 0000000000..14166ab3cd --- /dev/null +++ b/src/KOKKOS/mliap_model_linear_kokkos.cpp @@ -0,0 +1,99 @@ +// clang-format off +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + 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: Matt Bettencourt (NVIDIA) + ------------------------------------------------------------------------- */ + +#include "mliap_model_linear_kokkos.h" + +#include "mliap_data_kokkos.h" +#include "error.h" + +using namespace LAMMPS_NS; + +template +MLIAPModelLinearKokkos::MLIAPModelLinearKokkos(LAMMPS *lmp, char *args) : + MLIAPModelLinear(lmp,args), + MLIAPModelKokkos(lmp, this) +{ + if (args) MLIAPModelKokkos::set_k_coeffelem(); +} + +/* ---------------------------------------------------------------------- */ + +template +void MLIAPModelLinearKokkos::compute_gradients(class MLIAPData *data) +{ + MLIAPDataKokkos *k_data = (MLIAPDataKokkos*)(data); + + // read but never changes + auto d_coeffelem = this->k_coeffelem.template view(); + + // read + auto d_ielems = k_data->k_ielems.template view(); + auto d_descriptors = k_data->k_descriptors.template view(); + + // written + auto d_betas = k_data->k_betas.template view(); + auto d_eatoms = k_data->k_eatoms.template view(); + + const auto eflag = data->eflag; + const int ndescriptors=data->ndescriptors; + + Kokkos::parallel_reduce(data->nlistatoms, KOKKOS_LAMBDA (int ii, double &update) { + const int ielem = d_ielems(ii); + + for (int icoeff = 0; icoeff < ndescriptors; icoeff++) + d_betas(ii,icoeff) = d_coeffelem(ielem,icoeff+1); + + // add in contributions to global and per-atom energy + // this is optional and has no effect on force calculation + if (eflag) { + // energy of atom I + double etmp = d_coeffelem(ielem,0); + + // E_i = beta.B_i + for (int icoeff = 0; icoeff < ndescriptors; icoeff++) + etmp += d_coeffelem(ielem,icoeff+1)*d_descriptors(ii, icoeff); + update += etmp; + d_eatoms(ii) = etmp; + } + }, data->energy); +} + +/* ---------------------------------------------------------------------- */ + +template +void MLIAPModelLinearKokkos::compute_gradgrads(class MLIAPData *data) +{ + MLIAPModelLinear::compute_gradgrads(data); +} + +/* ---------------------------------------------------------------------- */ + +template +void MLIAPModelLinearKokkos::compute_force_gradients(class MLIAPData *data) +{ + MLIAPModelLinear::compute_force_gradients(data); +} + +/* ---------------------------------------------------------------------- */ + +namespace LAMMPS_NS { +template class MLIAPModelLinearKokkos; +#ifdef LMP_KOKKOS_GPU +template class MLIAPModelLinearKokkos; +#endif +} diff --git a/src/KOKKOS/mliap_model_linear_kokkos.h b/src/KOKKOS/mliap_model_linear_kokkos.h new file mode 100644 index 0000000000..829e3c4039 --- /dev/null +++ b/src/KOKKOS/mliap_model_linear_kokkos.h @@ -0,0 +1,37 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + 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: Matt Bettencourt (NVIDIA) + ------------------------------------------------------------------------- */ + +#ifndef LMP_MLIAP_MODEL_LINEAR_KOKKOS_H +#define LMP_MLIAP_MODEL_LINEAR_KOKKOS_H + +#include "mliap_model_linear.h" + +#include "mliap_model_kokkos.h" + +namespace LAMMPS_NS { + +template +class MLIAPModelLinearKokkos : public MLIAPModelLinear, public MLIAPModelKokkos { + public: + MLIAPModelLinearKokkos(LAMMPS *, char * = nullptr); + + void compute_gradients(class MLIAPData *) override; + void compute_gradgrads(class MLIAPData *) override; + void compute_force_gradients(class MLIAPData *) override; +}; +} // namespace LAMMPS_NS +#endif diff --git a/src/KOKKOS/mliap_so3_kokkos.cpp b/src/KOKKOS/mliap_so3_kokkos.cpp new file mode 100644 index 0000000000..128e0f0a0c --- /dev/null +++ b/src/KOKKOS/mliap_so3_kokkos.cpp @@ -0,0 +1,1194 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + 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: Matt Bettencourt (NVIDIA) + ------------------------------------------------------------------------- */ + +#include "mliap_so3_kokkos.h" + +#include "error.h" +#include "math_const.h" +#include "math_special_kokkos.h" +#include "memory.h" +#include "memory_kokkos.h" +#include "mliap_so3_math.h" + +#include + +using namespace SO3Math; +using namespace LAMMPS_NS; +using namespace MathConst; +using namespace MathSpecialKokkos; + +#define SMALL 1.0e-8 + +/* ---------------------------------------------------------------------- */ + +template +MLIAP_SO3Kokkos::MLIAP_SO3Kokkos(LAMMPS *lmp, double vrcut, int vlmax, int vnmax, double valpha) : Pointers(lmp) +{ + m_rcut = vrcut; + m_alpha = valpha; + m_lmax = vlmax; + m_nmax = vnmax; + compute_ncoeff(); + + m_Nmax = (m_nmax + m_lmax + 1) * 10; + m_numYlms = (m_lmax + 1) * (m_lmax + 1); + + m_init_arrays = 0; + m_dfac_l1 = m_dfac_l2 = 0; + m_pfac_l1 = m_pfac_l2 = 0; + m_idxu_count = m_idxy_count = 0; + alloc_init = alloc_arrays = 0.0; +} + +/* ---------------------------------------------------------------------- */ + +template +MLIAP_SO3Kokkos::~MLIAP_SO3Kokkos() +{ + memoryKK->destroy_kokkos(m_ellpl1); + memoryKK->destroy_kokkos(m_ellm1); + memoryKK->destroy_kokkos(m_pfac); + memoryKK->destroy_kokkos(m_Ylms); + memoryKK->destroy_kokkos(m_dfac0); + memoryKK->destroy_kokkos(m_dfac1); + memoryKK->destroy_kokkos(m_dfac2); + memoryKK->destroy_kokkos(m_dfac3); + memoryKK->destroy_kokkos(m_dfac4); + memoryKK->destroy_kokkos(m_dfac5); + memoryKK->destroy_kokkos(m_w); + memoryKK->destroy_kokkos(m_g_array); + + memoryKK->destroy_kokkos(m_rootpq); + memoryKK->destroy_kokkos(m_idxu_block); + memoryKK->destroy_kokkos(m_idxylm); + + memoryKK->destroy_kokkos(m_rip_array); + memoryKK->destroy_kokkos(m_rip_darray); + + memoryKK->destroy_kokkos(m_sbes_array); + memoryKK->destroy_kokkos(m_sbes_darray); + + memoryKK->destroy_kokkos(m_plist_r); + + memoryKK->destroy_kokkos(m_ulist_r); + memoryKK->destroy_kokkos(m_ulist_i); + + memoryKK->destroy_kokkos(m_dYlm_r); + memoryKK->destroy_kokkos(m_dYlm_i); + + memoryKK->destroy_kokkos(k_dplist_r); + + memoryKK->destroy_kokkos(m_dclist); + + memoryKK->destroy_kokkos(m_clisttot_r); + memoryKK->destroy_kokkos(m_clisttot_i); + + t_numneighs = int_1d(); + t_jelems = int_1d(); + t_wjelem = float_1d(); + t_rij = float_2d(); + t_ij = int_1d(); +} + +/* ---------------------------------------------------------------------- */ + +template +void MLIAP_SO3Kokkos::compute_ncoeff() +{ + ncoeff = m_nmax * (m_nmax + 1) * (m_lmax + 1) / 2; +} + +/* ---------------------------------------------------------------------- */ + +template +void MLIAP_SO3Kokkos::init() +{ + int totali; + + totali = m_lmax + 1; + memoryKK->destroy_kokkos(m_ellpl1); + memoryKK->create_kokkos(m_ellpl1, totali, "MLIAP_SO3Kokkos:m_ellpl1"); + memoryKK->destroy_kokkos(m_ellm1); + memoryKK->create_kokkos(m_ellm1, totali, "MLIAP_SO3Kokkos:m_ellm1"); + alloc_init = 2.0 * totali * sizeof(double); + using range=Kokkos::RangePolicy; + auto ellpl1 = m_ellpl1, ellm1 = m_ellm1; + + Kokkos::parallel_for(range(0,m_lmax), KOKKOS_LAMBDA (int ll) { + int l=ll+1; + ellpl1[l] = get_sum(0, l + 2, 1, 2); + ellm1[l] = get_sum(0, l, 1, 2); + }); + + double pfac1 = 1.0 / 4.0 / MY_PI; + m_pfac_l1 = m_lmax + 2; + m_pfac_l2 = (m_lmax + 2) * (m_lmax + 2) + 1; + totali = m_pfac_l1 * m_pfac_l2; + memoryKK->destroy_kokkos(m_pfac); + memoryKK->create_kokkos(m_pfac, totali, "MLIAP_SO3Kokkos:m_pfac"); + memoryKK->destroy_kokkos(m_Ylms); + memoryKK->create_kokkos(m_Ylms, totali, "MLIAP_SO3Kokkos:m_Ylms"); + alloc_init += 2 * totali * sizeof(double); + + auto pfac = m_pfac, Ylms = m_Ylms; + auto pfac_l2 = m_pfac_l2, lmax = m_lmax; + // Serial but just to make sure run with device memory + Kokkos::parallel_for(range(0,1), KOKKOS_LAMBDA (int ) { + int i=0; + for (int l = 0; l < lmax + 2; l++) + for (int m = -l; m < l + 1; m++) { + pfac[l * pfac_l2 + m] = sqrt((2.0 * l + 1.0) * pfac1) * powsign(m); + Ylms[i] = pfac[l * pfac_l2 + m]; + i += 1; + } + }); + + m_dfac_l1 = m_lmax + 1; + m_dfac_l2 = m_numYlms + 1; + totali = m_dfac_l1 * m_dfac_l2; + memoryKK->destroy_kokkos(m_dfac0); + memoryKK->create_kokkos(m_dfac0, totali, "MLIAP_SO3Kokkos:m_dfac0"); + memoryKK->destroy_kokkos(m_dfac1); + memoryKK->create_kokkos(m_dfac1, totali, "MLIAP_SO3Kokkos:m_dfac1"); + memoryKK->destroy_kokkos(m_dfac2); + memoryKK->create_kokkos(m_dfac2, totali, "MLIAP_SO3Kokkos:m_dfac2"); + memoryKK->destroy_kokkos(m_dfac3); + memoryKK->create_kokkos(m_dfac3, totali, "MLIAP_SO3Kokkos:m_dfac3"); + memoryKK->destroy_kokkos(m_dfac4); + memoryKK->create_kokkos(m_dfac4, totali, "MLIAP_SO3Kokkos:m_dfac4"); + memoryKK->destroy_kokkos(m_dfac5); + memoryKK->create_kokkos(m_dfac5, totali, "MLIAP_SO3Kokkos:m_dfac5"); + alloc_init += 6.0 * totali * sizeof(double); + + auto dfac0 = m_dfac0,dfac1 = m_dfac1,dfac2 = m_dfac2,dfac3 = m_dfac3,dfac4 = m_dfac4,dfac5 = m_dfac5; + auto dfac_l2 = m_dfac_l2; + + Kokkos::parallel_for(range(0,m_lmax), KOKKOS_LAMBDA (int ll) { + int l = ll+1; + for (int m = -l; m < l + 1; m++) { + dfac0[l * dfac_l2 + m] = + -sqrt(((l + 1.0) * (l + 1.0) - m * m) / (2.0 * l + 1.0) / (2.0 * l + 3.0)) * l; + dfac1[l * dfac_l2 + m] = + sqrt((l * l - m * m) / (2.0 * l - 1.0) / (2.0 * l + 1.0)) * (l + 1.0); + dfac2[l * dfac_l2 + m] = + -sqrt((l + m + 1.0) * (l + m + 2.0) / 2.0 / (2.0 * l + 1.0) / (2.0 * l + 3.0)) * l; + dfac3[l * dfac_l2 + m] = + sqrt((l - m - 1.0) * (l - m) / 2.0 / (2.0 * l - 1.0) / (2.0 * l + 1.0)) * (l + 1.0); + dfac4[l * dfac_l2 + m] = + -sqrt((l - m + 1.0) * (l - m + 2.0) / 2.0 / (2.0 * l + 1.0) / (2.0 * l + 3.0)) * l; + dfac5[l * dfac_l2 + m] = + sqrt((l + m - 1.0) * (l + m) / 2.0 / (2.0 * l - 1.0) / (2.0 * l + 1.0)) * (l + 1.0); + } + }); + + totali = m_nmax * m_nmax; + memoryKK->destroy_kokkos(m_w); + memoryKK->create_kokkos(m_w, totali, "MLIAP_SO3Kokkos:w"); + alloc_init += totali * sizeof(double); + + totali = m_nmax * m_Nmax; + memoryKK->destroy_kokkos(m_g_array); + memoryKK->create_kokkos(m_g_array, totali, "MLIAP_SO3Kokkos:g_array"); + alloc_init += totali * sizeof(double); + + { + Kokkos::View w("w", m_nmax * m_nmax), g_array("g_array", m_nmax * m_Nmax); + compute_W(m_nmax, w.data()); + init_garray(m_nmax, m_lmax, m_rcut, m_alpha, w.data(), m_nmax, g_array.data(), m_Nmax); + Kokkos::deep_copy(m_w,w); + Kokkos::deep_copy(m_g_array,g_array); + } + + int twolmax; + twolmax = 2 * (m_lmax + 1); + int m_ldim = twolmax + 1; + totali = m_ldim * m_ldim; + memoryKK->destroy_kokkos(m_rootpq); + memoryKK->create_kokkos(m_rootpq, totali, "MLIAP_SO3Kokkos:rootpq"); + alloc_init += totali * sizeof(double); + + auto rootpq=m_rootpq; + auto ldim=m_ldim; + Kokkos::parallel_for(range(1,m_ldim), KOKKOS_LAMBDA (int p) { + for (int q = 1; q < ldim; q++) + rootpq[p * ldim + q] = sqrt(static_cast(p) / q); + }); + + memoryKK->destroy_kokkos(m_idxu_block); + memoryKK->create_kokkos(m_idxu_block, m_ldim, "MLIAP_SO3Kokkos:idxu_bloc"); + alloc_init += totali * sizeof(double); + + totali = square(m_lmax + 2); + memoryKK->destroy_kokkos(m_idxylm); + memoryKK->create_kokkos(m_idxylm, totali, "MLIAP_SO3Kokkos:idxylm"); + alloc_init += totali * sizeof(double); + + Kokkos::View idxu_block("idxu_block",m_ldim); + Kokkos::View idxylm("idxylm",totali); + m_idxu_count = m_idxy_count = 0; + for (int l = 0; l < m_ldim; l++) { + idxu_block[l] = m_idxu_count; + for (int mb = 0; mb < l + 1; mb++) + for (int ma = 0; ma < l + 1; ma++) { + if (l % 2 == 0 && ma == l / 2) { + idxylm[m_idxy_count] = m_idxu_count; + m_idxy_count += 1; + } + m_idxu_count += 1; + } + } + Kokkos::deep_copy(m_idxu_block,idxu_block); + Kokkos::deep_copy(m_idxylm,idxylm); +} + +/* ---------------------------------------------------------------------- */ + +template +void MLIAP_SO3Kokkos::init_arrays(int nlocal, int ncoefs) +{ + + { + // sum up the temp memory space per particle + int sum_of_temps=0; + //ulist_r and i + sum_of_temps += m_idxu_count*2; + //m_dYlm_r + sum_of_temps += m_numYlms * 3 * 2; + //m_clisttot_r + sum_of_temps += m_nmax * m_numYlms * 2; + // k_dclist + sum_of_temps += m_nmax * m_numYlms * 3 * 2; + m_chunk_size = m_temp_memory_size/(sum_of_temps * sizeof(double)); + } + + int totali = nlocal * ncoefs; + if ( nlocal > (int)m_plist_r.extent(0)) { + memoryKK->destroy_kokkos(m_plist_r); + memoryKK->create_kokkos(m_plist_r, nlocal, ncoefs, "MLIAP_SO3Kokkos:m_plist_r"); + alloc_arrays = totali * sizeof(double); + } + + int num_of_temp = std::min(nlocal, m_chunk_size); + if ((int)m_ulist_r.extent(0) < num_of_temp ) { + totali = m_idxu_count; + memoryKK->destroy_kokkos(m_ulist_r); + memoryKK->create_kokkos(m_ulist_r, num_of_temp, totali, "MLIAP_SO3Kokkos:m_ulist_r"); + memoryKK->destroy_kokkos(m_ulist_i); + memoryKK->create_kokkos(m_ulist_i, num_of_temp, totali, "MLIAP_SO3Kokkos:m_ulist_i"); + alloc_arrays += 2.0 * totali * num_of_temp * sizeof(double); + + totali = m_numYlms * 3; + memoryKK->destroy_kokkos(m_dYlm_r); + memoryKK->create_kokkos(m_dYlm_r, num_of_temp, m_numYlms, 3, "MLIAP_SO3Kokkos:m_dYlm_r"); + memoryKK->destroy_kokkos(m_dYlm_i); + memoryKK->create_kokkos(m_dYlm_i, num_of_temp, m_numYlms, 3, "MLIAP_SO3Kokkos:m_dYlm_i"); + alloc_arrays += 2.0 * m_numYlms * 3 * num_of_temp * sizeof(double); + + memoryKK->destroy_kokkos(m_dclist); + memoryKK->create_kokkos(m_dclist, num_of_temp, m_nmax, m_numYlms, 3, "MLIAP_SO3Kokkos:k_dclist_r"); + alloc_arrays += m_nmax * m_numYlms * 3 * num_of_temp* sizeof(double); + + memoryKK->destroy_kokkos(m_clisttot_r); + memoryKK->create_kokkos(m_clisttot_r, num_of_temp, m_nmax, m_numYlms, "MLIAP_SO3Kokkos:m_clisttot_r"); + memoryKK->destroy_kokkos(m_clisttot_i); + memoryKK->create_kokkos(m_clisttot_i, num_of_temp, m_nmax, m_numYlms, "MLIAP_SO3Kokkos:m_clisttot_i"); + alloc_arrays += 2.0 * m_nmax * m_numYlms * num_of_temp * sizeof(double); + m_init_arrays = 1; + } +} + +/* ---------------------------------------------------------------------- */ + +template +double MLIAP_SO3Kokkos::memory_usage() +{ + return alloc_init + alloc_arrays; +} + +/* ---------------------------------------------------------------------- */ + +template +void MLIAP_SO3Kokkos::compute_W(int nmax, double *arr) +{ + int alpha, beta, temp1, temp2; + + for (alpha = 1; alpha < nmax + 1; alpha++) { + temp1 = (2 * alpha + 5) * (2 * alpha + 6) * (2 * alpha + 7); + for (beta = 1; beta < alpha + 1; beta++) { + temp2 = (2 * beta + 5) * (2 * beta + 6) * (2 * beta + 7); + arr[(alpha - 1) * nmax + beta - 1] = + sqrt(temp1 * temp2) / (5 + alpha + beta) / (6 + alpha + beta) / (7 + alpha + beta); + arr[(beta - 1) * nmax + alpha - 1] = arr[(alpha - 1) * nmax + beta - 1]; + } + } + + int i, j, k, n = nmax; + auto outeig = new double[n]; + auto outeigvec = new double[n * n]; + auto arrinv = new double[n * n]; + + auto sqrtD = new double[n * n]; + auto tempM = new double[n * n]; + + auto temparr = new double *[n]; + auto tempvl = new double *[n]; + auto tempout = new double[n]; + + int info; + + info = invert_matrix(n, arr, arrinv); + if (info != 0) error->all(FLERR, "Invert matrix Error in W calculation!"); + + for (i = 0; i < n; i++) { + temparr[i] = new double[n]; + tempvl[i] = new double[n]; + for (j = 0; j < n; j++) temparr[i][j] = arrinv[i * n + j]; + } + + jacobin(n, temparr, tempout, tempvl); + + for (i = 0; i < n; i++) + for (j = 0; j < n; j++) outeigvec[i * n + j] = tempvl[i][j]; + + for (i = 0; i < n; i++) + for (j = 0; j < n; j++) + if (i == j) + sqrtD[i * n + j] = sqrt(tempout[i]); + else + sqrtD[i * n + j] = 0.0; + + double dtemp; + for (i = 0; i < n; i++) + for (j = 0; j < n; j++) { + dtemp = 0; + for (k = 0; k < n; k++) dtemp += outeigvec[i * n + k] * sqrtD[k * n + j]; + + tempM[i * n + j] = dtemp; + } + + info = invert_matrix(n, outeigvec, arrinv); + if (info != 0) error->all(FLERR, "Invert matrix Error in W calculation!"); + + for (i = 0; i < n; i++) + for (j = 0; j < n; j++) { + dtemp = 0; + for (k = 0; k < n; k++) dtemp += tempM[i * n + k] * arrinv[k * n + j]; + + arr[i * n + j] = dtemp; + } + + delete[] outeig; + delete[] outeigvec; + delete[] arrinv; + + delete[] sqrtD; + delete[] tempM; + + for (i = 0; i < n; i++) { + delete[] temparr[i]; + delete[] tempvl[i]; + } + delete[] temparr; + delete[] tempvl; + delete[] tempout; +} + +/* ---------------------------------------------------------------------- */ +template +template +KOKKOS_INLINE_FUNCTION +void MLIAP_SO3Kokkos::compute_pi(int nmax, int lmax, ViewType clisttot_r, ViewType clisttot_i, int /*lcl2*/, + float_2d plist_r, int indpl) const +{ + int n1, n2, j, l, m, i = 0; + double norm; + for (n1 = 0; n1 < nmax; n1++) + for (n2 = 0; n2 < n1 + 1; n2++) { + j = 0; + for (l = 0; l < lmax + 1; l++) { + norm = 2.0 * sqrt(2.0) * MY_PI / sqrt(2.0 * l + 1.0); + + for (m = -l; m < l + 1; m++) { + + plist_r(indpl, i) += (clisttot_r(n1, j) * clisttot_r(n2, j) + + clisttot_i(n1, j) * clisttot_i(n2, j)) * + norm; + j += 1; + } + i += 1; + } + } +} + +/* ---------------------------------------------------------------------- */ + +template +double MLIAP_SO3Kokkos::phi(double r, int alpha, double rcut) +{ + return powint((rcut - r), (alpha + 2)) / + sqrt(2 * powint(rcut, (2 * alpha + 7)) / (2 * alpha + 5) / (2 * alpha + 6) / (2 * alpha + 7)); +} + +/* ---------------------------------------------------------------------- */ + +template +double MLIAP_SO3Kokkos::compute_g(double r, int n, int nmax, double rcut, double *w, int lw1) +{ + double Sum; + Sum = 0.0; + int alpha; + + for (alpha = 1; alpha < nmax + 1; alpha++) + Sum += w[(n - 1) * lw1 + alpha - 1] * phi(r, alpha, rcut); + + return Sum; +} + +/* ---------------------------------------------------------------------- */ +template +KOKKOS_INLINE_FUNCTION +double MLIAP_SO3Kokkos::Cosine(double Rij, double Rc) const +{ + + return 0.5 * (cos(MY_PI * Rij / Rc) + 1.0); +} + +/* ---------------------------------------------------------------------- */ +template +KOKKOS_INLINE_FUNCTION +double MLIAP_SO3Kokkos::CosinePrime(double Rij, double Rc) const +{ + + return -0.5 * MY_PI / Rc * sin(MY_PI * Rij / Rc); +} + +/* ---------------------------------------------------------------------- */ +template +KOKKOS_INLINE_FUNCTION +double MLIAP_SO3Kokkos::compute_sfac(double r, double rcut) const +{ + if (r > rcut) + return 0.0; + else + return Cosine(r, rcut); +} + +/* ---------------------------------------------------------------------- */ +template +KOKKOS_INLINE_FUNCTION +double MLIAP_SO3Kokkos::compute_dsfac(double r, double rcut) const +{ + if (r > rcut) + return 0.0; + else + return CosinePrime(r, rcut); +} + +/* ---------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +int MLIAP_SO3Kokkos::get_sum(int istart, int iend, int id, int imult) +{ + int ires = 0; + int i; + + for (i = istart; i < iend; i = i + id) ires += i * imult; + + return ires; +} + +/* ---------------------------------------------------------------------- */ + +template +template +KOKKOS_INLINE_FUNCTION +void MLIAP_SO3Kokkos::compute_uarray_recursive(double x, double y, double z, double r, int twol, + UlistView ulist_r, UlistView ulist_i, int_1d idxu_block, + float_1d rootpqarray) const +{ + int l, llu, llup, mb, ma, mbpar, mapar; + double rootpq; + int ldim = twol + 1; + + double theta, phi, atheta, btheta; + + double aphi_r, aphi_i, a_r, a_i, b_r, b_i; + + theta = acos(z / r); + phi = atan2(y, x); + + atheta = cos(theta / 2); + btheta = sin(theta / 2); + + aphi_r = cos(phi / 2); + aphi_i = sin(phi / 2); + + a_r = atheta * aphi_r; + a_i = atheta * aphi_i; + b_r = btheta * aphi_r; + b_i = btheta * aphi_i; + + ulist_r[0] = 1.0; + ulist_i[0] = 0.0; + + for (l = 1; l < ldim; l++) { + + llu = idxu_block[l]; + llup = idxu_block[l - 1]; + mb = 0; + + while (2 * mb <= l) { + + ulist_r[llu] = 0.0; + ulist_i[llu] = 0.0; + for (ma = 0; ma < l; ma++) { + + rootpq = rootpqarray[(l - ma) * ldim + l - mb]; + + ulist_r[llu] += rootpq * (a_r * ulist_r[llup] + a_i * ulist_i[llup]); + ulist_i[llu] += rootpq * (a_r * ulist_i[llup] - a_i * ulist_r[llup]); + + rootpq = rootpqarray[(ma + 1) * ldim + l - mb]; + + ulist_r[llu + 1] += -rootpq * (b_r * ulist_r[llup] + b_i * ulist_i[llup]); + ulist_i[llu + 1] += -rootpq * (b_r * ulist_i[llup] - b_i * ulist_r[llup]); + + llu += 1; + llup += 1; + } + + llu += 1; + mb += 1; + } + + llu = idxu_block[l]; + llup = llu + (l + 1) * (l + 1) - 1; + mbpar = 1; + mb = 0; + + while (2 * mb <= l) { + mapar = mbpar; + for (ma = 0; ma < l + 1; ma++) { + if (mapar == 1) { + + ulist_r[llup] = ulist_r[llu]; + ulist_i[llup] = -ulist_i[llu]; + + } else { + + ulist_r[llup] = -ulist_r[llu]; + ulist_i[llup] = ulist_i[llu]; + } + mapar = -mapar; + llu += 1; + llup -= 1; + } + mbpar = -mbpar; + mb += 1; + } + } +} + +/* ---------------------------------------------------------------------- */ + +template +void MLIAP_SO3Kokkos::init_garray(int nmax, int lmax, double rcut, double alpha, double *w, int lw1, + double *g_array, int lg2) +{ + int i, n, Nmax = (nmax + lmax + 1) * 10; + double x, xi; + + for (i = 1; i < Nmax + 1; i++) { + // roots of Chebyshev polynomial of degree N + x = cos((2 * i - 1) * MY_PI / 2 / Nmax); + // transform the interval [-1,1] to [0, rcut] + xi = rcut / 2 * (x + 1); + for (n = 1; n < nmax + 1; n++) + // r**2*g(n)(r)*e^(-alpha*r**2) + g_array[(n - 1) * lg2 + i - 1] = rcut / 2 * MY_PI / Nmax * sqrt(1 - x * x) * xi * xi * + compute_g(xi, n, nmax, rcut, w, lw1) * exp(-alpha * xi * xi); + } +} + +/* ---------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void MLIAP_SO3Kokkos::operator() (const MLIAPSO3GetSBESArrayTag&, int ii) const{ + int ipair = t_ij(ii); + for (int neighbor = 0; neighbor < t_numneighs[ii]; neighbor++) { + double x = t_rij(ipair, 0); + double y = t_rij(ipair, 1); + double z = t_rij(ipair, 2); + ipair++; + + double ri = sqrt(x * x + y * y + z * z); + + if (ri < SMALL) continue; + + const double pfac1 = t_alpha * t_rcut; + const double pfac4 = t_rcut / 2.0; + const double pfac3 = MY_PI / 2.0 / m_Nmax; + double pfac2 = pfac1 * ri; + const int findex = m_Nmax * (m_lmax + 1); + const int gindex = (ipair - 1) * findex; + const int mindex = m_lmax + 1; + + for (int i = 1; i < m_Nmax + 1; i++) { + const bigint i1mindex = (bigint) (i - 1) * mindex; + + x = cos((2 * i - 1) * pfac3); + double xi = pfac4 * (x + 1); + double rb = pfac2 * (x + 1); + + double sa = sinh(rb) / rb; + double sb = (cosh(rb) - sa) / rb; + + m_sbes_array[gindex + i1mindex + 0] = sa; + m_sbes_array[gindex + i1mindex + 1] = sb; + + int j; + for (j = 2; j < t_lmax + 1; j++) + m_sbes_array[gindex + i1mindex + j] = m_sbes_array[gindex + i1mindex + j - 2] - + (2 * j - 1) / rb * m_sbes_array[gindex + i1mindex + j - 1]; + + double exts = m_sbes_array[gindex + i1mindex + j - 2] - + (2 * j - 1) / rb * m_sbes_array[gindex + i1mindex + j - 1]; + + m_sbes_darray[gindex + i1mindex + 0] = sb; + + for (j = 1; j < t_lmax; j++) + m_sbes_darray[gindex + i1mindex + j] = xi * + (j * m_sbes_array[gindex + i1mindex + j - 1] + + (j + 1) * m_sbes_array[gindex + i1mindex + j + 1]) / + (2 * j + 1); + + m_sbes_darray[gindex + i1mindex + j] = + xi * (j * m_sbes_array[gindex + i1mindex + j - 1] + (j + 1) * exts) / (2 * j + 1); + m_sbes_darray[gindex + i1mindex + 0] = xi * sb; + } + } +} + +/* ---------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void MLIAP_SO3Kokkos::operator() (const MLIAPSO3GetRipArrayTag&, int ii) const{ + int ipair = t_ij(ii); + for (int neighbor = 0; neighbor < t_numneighs[ii]; neighbor++) { + + double x = t_rij(ipair, 0); + double y = t_rij(ipair, 1); + double z = t_rij(ipair, 2); + ipair++; + + double ri = sqrt(x * x + y * y + z * z); + if (ri < SMALL) continue; + + double expfac = 4 * MY_PI * exp(-t_alpha * ri * ri); + for (int n = 1; n < t_nmax + 1; n++) + for (int l = 0; l < t_lmax + 1; l++) { + double integral = 0.0, integrald = 0.0; + for (int i = 0; i < m_Nmax; i++) { + integral += m_g_array[(n - 1) * m_Nmax + i] * + m_sbes_array[(ipair - 1) * m_Nmax * (m_lmax + 1) + (bigint) i * (m_lmax + 1) + l]; + integrald += m_g_array[(n - 1) * m_Nmax + i] * + m_sbes_darray[(ipair - 1) * m_Nmax * (m_lmax + 1) + (bigint) i * (m_lmax + 1) + l]; + } + + m_rip_array[(ipair - 1) * m_nmax * (m_lmax + 1) + (bigint) (n - 1) * (m_lmax + 1) + l] = + integral * expfac; + m_rip_darray[(ipair - 1) * m_nmax * (m_lmax + 1) + (bigint) (n - 1) * (m_lmax + 1) + l] = + integrald * expfac; + } + } +} + +/* ---------------------------------------------------------------------- */ + +template +void MLIAP_SO3Kokkos::spectrum(int nlocal, DAT::tdual_int_1d numneighs, DAT::tdual_int_1d jelems, DAT::tdual_float_1d wjelem, + DAT::tdual_float_2d rij, DAT::tdual_int_1d k_ij, + int nmax, int lmax, double rcut, double alpha, int totaln, int ncoefs) +{ + init_arrays(nlocal, ncoefs); + + bigint totali; + + totali = totaln * m_Nmax * (m_lmax + 1); + if ( totali > (int)m_sbes_array.extent(0)) { + memoryKK->realloc_kokkos(m_sbes_array, "MLIAP_SO3Kokkos:m_sbes_array", totali); + memoryKK->realloc_kokkos(m_sbes_darray, "MLIAP_SO3Kokkos:m_sbes_darray", totali); + alloc_arrays += 2.0 * totali * sizeof(double); + } + + totali = totaln * m_nmax * (m_lmax + 1); + if ( totali > (int)m_rip_array.extent(0)) { + memoryKK->realloc_kokkos(m_rip_array, "MLIAP_SO3Kokkos:m_rip_array", totali); + memoryKK->realloc_kokkos(m_rip_darray, "MLIAP_SO3Kokkos:m_rip_darray", totali); + alloc_arrays += 2.0 * totali * sizeof(double); + } + + totali = totaln * ncoefs * 3; + if ( totali > (int)k_dplist_r.extent(0)) { + memoryKK->realloc_kokkos(k_dplist_r, "MLIAP_SO3Kokkos:m_dplist_r", (int)totaln, ncoefs, 3); + alloc_arrays += 2.0 * totali * sizeof(double); + } + + t_numneighs = numneighs.template view(); + t_jelems = jelems.template view(); + t_wjelem = wjelem.template view(); + t_rij = rij.template view(); + t_ij = k_ij.template view(); + t_nmax = nmax; + t_lmax = lmax; + t_rcut = rcut; + t_alpha = alpha; + + { + Kokkos::RangePolicy range(0,nlocal); + Kokkos::parallel_for(range, *this); + } + + { + Kokkos::RangePolicy range(0,nlocal); + Kokkos::parallel_for(range, *this); + } + + Kokkos::deep_copy(m_plist_r,0.); + for (int start=0; start < nlocal; start += m_chunk_size) { + int end=std::min(nlocal, start+m_chunk_size); + Kokkos::deep_copy(m_clisttot_r, 0); + Kokkos::deep_copy(m_clisttot_i, 0); + { + Kokkos::RangePolicy range(start,end); + Kokkos::parallel_for(range, *this); + } + } +} + +/* ---------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void MLIAP_SO3Kokkos::operator() (const MLIAP_SO3Kokkos::MLIAPSO3SpectrumTag&, int ii) const { + int ii_chunk = ii%m_chunk_size; + auto ulist_r = Kokkos::subview(m_ulist_r,ii_chunk,Kokkos::ALL); + auto ulist_i = Kokkos::subview(m_ulist_i,ii_chunk,Kokkos::ALL); + auto clisttot_r=Kokkos::subview(m_clisttot_r,ii_chunk,Kokkos::ALL, Kokkos::ALL); + auto clisttot_i=Kokkos::subview(m_clisttot_i,ii_chunk,Kokkos::ALL, Kokkos::ALL); + + const int twolmax = 2 * (t_lmax + 1); + const int findex = m_nmax * (m_lmax + 1); + int ipair = t_ij(ii); + for (int neighbor = 0; neighbor < t_numneighs[ii]; neighbor++) { + const int jelem = t_jelems[ipair]; + int weight = t_wjelem[jelem]; + + double x = t_rij(ipair, 0); + double y = t_rij(ipair, 1); + double z = t_rij(ipair, 2); + ipair++; + + double r = sqrt(x * x + y * y + z * z); + + if (r < SMALL) continue; + for (int ti = 0; ti < m_idxu_count; ti++) { + ulist_r[ti] = 0.0; + ulist_i[ti] = 0.0; + } + + compute_uarray_recursive(x, y, z, r, twolmax, ulist_r, ulist_i, m_idxu_block, m_rootpq); + + double sfac_weight = compute_sfac(r, t_rcut)*double(weight); + + int gindex = (ipair - 1) * findex; + for (int n = 1; n < t_nmax + 1; n++) { + int i = 0; + for (int l = 0; l < t_lmax + 1; l++) { + double r_int = m_rip_array[gindex + (bigint) (n - 1) * (m_lmax + 1) + l]; + + for (int m = -l; m < l + 1; m++) { + + double Ylm_r = (ulist_r[m_idxylm[i]]) * m_pfac[l * m_pfac_l2 + m]; + clisttot_r((n - 1), i) += r_int * Ylm_r * sfac_weight; + double Ylm_i = (ulist_i[m_idxylm[i]]) * m_pfac[l * m_pfac_l2 + m]; + clisttot_i((n - 1), i) += r_int * Ylm_i * sfac_weight; + i += 1; + } + } + } + } + compute_pi(t_nmax, t_lmax, clisttot_r, clisttot_i, m_numYlms, m_plist_r, ii); +} + +/* ---------------------------------------------------------------------- */ + +template +void MLIAP_SO3Kokkos::spectrum_dxdr(int nlocal, DAT::tdual_int_1d numneighs, DAT::tdual_int_1d jelems, DAT::tdual_float_1d wjelem, + DAT::tdual_float_2d rij, DAT::tdual_int_1d k_ij, + int nmax, int lmax, double rcut, double alpha, bigint totaln, + int ncoefs) +{ + bigint totali; + + if ( nlocal > (int)m_clisttot_r.extent(0)){ + memoryKK->destroy_kokkos(m_clisttot_r); + memoryKK->create_kokkos(m_clisttot_r, nlocal, m_nmax, m_numYlms, "MLIAP_SO3Kokkos:m_clisttot_r"); + memoryKK->destroy_kokkos(m_clisttot_i); + memoryKK->create_kokkos(m_clisttot_i, nlocal, m_nmax, m_numYlms, "MLIAP_SO3Kokkos:m_clisttot_i"); + int num_of_temp = std::min(nlocal, m_chunk_size); + int delta=num_of_temp-m_ulist_r.extent(0); + if (delta > 0 ){ + memoryKK->destroy_kokkos(m_ulist_r); + memoryKK->create_kokkos(m_ulist_r, num_of_temp, m_idxu_count, "MLIAP_SO3Kokkos:m_ulist_r"); + memoryKK->destroy_kokkos(m_ulist_i); + memoryKK->create_kokkos(m_ulist_i, num_of_temp, m_idxu_count, "MLIAP_SO3Kokkos:m_ulist_i"); + alloc_arrays += 2.0 * m_idxu_count * delta * sizeof(double); + memoryKK->destroy_kokkos(m_dYlm_r); + memoryKK->create_kokkos(m_dYlm_r, num_of_temp, m_numYlms, 3, "MLIAP_SO3Kokkos:m_dYlm_r"); + memoryKK->destroy_kokkos(m_dYlm_i); + memoryKK->create_kokkos(m_dYlm_i, num_of_temp, m_numYlms, 3, "MLIAP_SO3Kokkos:m_dYlm_i"); + alloc_arrays += 2.0 * m_numYlms * 3 * delta * sizeof(double); + } + } + + totali = totaln * m_Nmax * (m_lmax + 1); + if ( totali > (int)m_sbes_array.extent(0)) { + memoryKK->destroy_kokkos(m_sbes_array); + memoryKK->create_kokkos(m_sbes_array, totali, "MLIAP_SO3Kokkos:m_sbes_array"); + memoryKK->destroy_kokkos(m_sbes_darray); + memoryKK->create_kokkos(m_sbes_darray, totali, "MLIAP_SO3Kokkos:m_sbes_darray"); + + totali = totaln * m_nmax * (m_lmax + 1); + memoryKK->destroy_kokkos(m_rip_array); + memoryKK->create_kokkos(m_rip_array, totali, "MLIAP_SO3Kokkos:m_rip_array"); + memoryKK->destroy_kokkos(m_rip_darray); + memoryKK->create_kokkos(m_rip_darray, totali, "MLIAP_SO3Kokkos:m_rip_darray"); + + memoryKK->destroy_kokkos(k_dplist_r); + memoryKK->create_kokkos(k_dplist_r, (int)totaln, ncoefs, 3, "MLIAP_SO3Kokkos:m_dplist_r"); + } + + t_numneighs=numneighs.template view(); + t_jelems=jelems.template view(); + t_wjelem=wjelem.template view(); + t_rij=rij.template view(); + t_ij = k_ij.template view(); + t_nmax=nmax; + t_lmax=lmax; + t_rcut=rcut; + t_alpha=alpha; + + { + Kokkos::RangePolicy range(0,nlocal); + Kokkos::parallel_for(range, *this); + } + + { + Kokkos::RangePolicy range(0,nlocal); + Kokkos::parallel_for(range, *this); + } + + Kokkos::deep_copy(k_dplist_r, 0.0); + for (int start=0; start < nlocal; start += m_chunk_size) { + int end=std::min(nlocal, start+m_chunk_size); + Kokkos::deep_copy(m_clisttot_r, 0); + Kokkos::deep_copy(m_clisttot_i, 0); + { + Kokkos::RangePolicy range(start,end); + Kokkos::parallel_for(range, *this); + } + } +} + +/* ---------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void MLIAP_SO3Kokkos::operator() (const MLIAP_SO3Kokkos::MLIAPSO3SpectrumDXDRTag&, int ii) const { + //TO-DO Need to move m_ulist_r, m_ulist_i into local shared memory + int ii_chunk = ii%m_chunk_size; + auto ulist_r = Kokkos::subview(m_ulist_r,ii_chunk,Kokkos::ALL); + auto ulist_i = Kokkos::subview(m_ulist_i,ii_chunk,Kokkos::ALL); + auto clisttot_r=Kokkos::subview(m_clisttot_r,ii_chunk,Kokkos::ALL, Kokkos::ALL); + auto clisttot_i=Kokkos::subview(m_clisttot_i,ii_chunk,Kokkos::ALL, Kokkos::ALL); + auto dYlm_r = Kokkos::subview(m_dYlm_r,ii_chunk,Kokkos::ALL,Kokkos::ALL); + auto dYlm_i = Kokkos::subview(m_dYlm_i,ii_chunk,Kokkos::ALL,Kokkos::ALL); + auto dclist = Kokkos::subview(m_dclist,ii_chunk,Kokkos::ALL,Kokkos::ALL,Kokkos::ALL); + int twolmax = 2 * (t_lmax + 1); + int findex = m_nmax * (m_lmax + 1); + int ipair = t_ij(ii); + for (int neighbor = 0; neighbor < t_numneighs[ii]; neighbor++) { + + const int jelem = t_jelems[ipair]; + int weight = t_wjelem[jelem]; + + double x = t_rij(ipair, 0); + double y = t_rij(ipair, 1); + double z = t_rij(ipair, 2); + ipair++; + + double r = sqrt(x * x + y * y + z * z); + + if (r < SMALL) continue; + + for (bigint ti = 0; ti < m_idxu_count; ti++) { + ulist_r[ti] = 0.0; + ulist_i[ti] = 0.0; + } + + compute_uarray_recursive(x, y, z, r, twolmax, ulist_r, ulist_i, m_idxu_block, m_rootpq); + + double sfac_weight = compute_sfac(r, t_rcut)*double(weight); + bigint gindex = (ipair - 1) * findex; + for (int n = 0; n < t_nmax; n++) { + int i = 0; + for (int l = 0; l < t_lmax + 1; l++) { + double r_int = m_rip_array[gindex + n * (m_lmax + 1) + l]; + + for (int m = -l; m < l + 1; m++) { + double Ylm_r = (ulist_r[m_idxylm[i]]) * m_pfac[l * m_pfac_l2 + m]; + clisttot_r(n, i) += r_int * Ylm_r * sfac_weight; + double Ylm_i = (ulist_i[m_idxylm[i]]) * m_pfac[l * m_pfac_l2 + m]; + clisttot_i(n, i) += r_int * Ylm_i * sfac_weight; + i += 1; + } + } + } + + } + + ipair = t_ij(ii); + for (int neighbor = 0; neighbor < t_numneighs[ii]; neighbor++) { + const int jelem = t_jelems[ipair]; + int weight = t_wjelem[jelem]; + + double x = t_rij(ipair, 0); + double y = t_rij(ipair, 1); + double z = t_rij(ipair, 2); + ipair++; + auto dplist_r=Kokkos::subview(k_dplist_r,ipair-1,Kokkos::ALL, Kokkos::ALL); + + double r = sqrt(x * x + y * y + z * z); + if (r < SMALL) continue; + + for (int ti = 0; ti < m_idxu_count; ti++) { + ulist_r[ti] = 0.0; + ulist_i[ti] = 0.0; + } + + compute_uarray_recursive(x, y, z, r, twolmax, ulist_r, ulist_i, m_idxu_block, m_rootpq); + + ///////// compute_carray_wD //////// + { + double rvec[3]; + rvec[0] = x; + rvec[1] = y; + rvec[2] = z; + + for (int i=0;i; +#ifdef LMP_KOKKOS_GPU +template class MLIAP_SO3Kokkos; +#endif +} diff --git a/src/KOKKOS/mliap_so3_kokkos.h b/src/KOKKOS/mliap_so3_kokkos.h new file mode 100644 index 0000000000..164fb3b24d --- /dev/null +++ b/src/KOKKOS/mliap_so3_kokkos.h @@ -0,0 +1,142 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + 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: Matt Bettencourt (NVIDIA) + ------------------------------------------------------------------------- */ + +#ifndef LMP_MLIAP_SO3_KOKKOS_H +#define LMP_MLIAP_SO3_KOKKOS_H + +#include "kokkos_type.h" +#include "pointers.h" + +namespace LAMMPS_NS { + +template class MLIAP_SO3Kokkos : protected Pointers { + public: + MLIAP_SO3Kokkos(LAMMPS *, double vrcut, int vlmax, int vnmax, double valpha); + MLIAP_SO3Kokkos(LAMMPS *_lmp) : Pointers(_lmp){}; + ~MLIAP_SO3Kokkos() override; + + void init(); + double memory_usage(); + + using MemoryDeviceType = typename KKDevice::value; + using float_1d = Kokkos::View; + using float_2d = Kokkos::View; + using float_3d = Kokkos::View; + using float_4d = Kokkos::View; + using int_1d = Kokkos::View; + + int ncoeff; + float_2d m_plist_r; + float_3d k_dplist_r; + + private: + double alloc_init, alloc_arrays; + int_1d m_ellpl1, m_ellm1; + float_1d m_pfac, m_Ylms; + int m_pfac_l1, m_pfac_l2; + float_1d m_dfac0, m_dfac1, m_dfac2, m_dfac3, m_dfac4, m_dfac5; + int m_dfac_l1, m_dfac_l2; + double m_rcut, m_alpha; + int m_lmax, m_nmax, m_Nmax; + float_1d m_g_array, m_w; + float_1d m_rootpq; + int_1d m_idxu_block, m_idxylm; + int m_idxu_count, m_idxy_count; + int m_numYlms; + + float_3d m_clisttot_r, m_clisttot_i; + float_1d m_rip_array, m_rip_darray; + float_1d m_sbes_array, m_sbes_darray; + int m_init_arrays; + + float_2d m_ulist_r, m_ulist_i; + + float_3d m_dYlm_r, m_dYlm_i; + float_4d m_dclist; + + // arguments for operators. + int_1d t_numneighs; + int_1d t_jelems; + float_1d t_wjelem; + float_2d t_rij; + int t_nmax; + int t_lmax; + double t_rcut; + double t_alpha; + int_1d t_ij; + + static constexpr bigint m_temp_memory_size = 512 * 1024 * 1024; + int m_chunk_size; + + public: + void spectrum(int nlocal, DAT::tdual_int_1d numneighs, DAT::tdual_int_1d jelems, + DAT::tdual_float_1d wjelem, DAT::tdual_float_2d rij, DAT::tdual_int_1d k_ij, + int nmax, int lmax, double rcut, double alpha, int totaln, int ncoefs); + struct MLIAPSO3SpectrumTag {}; + KOKKOS_FUNCTION + void operator()(const MLIAPSO3SpectrumTag &, int ii) const; + + void spectrum_dxdr(int nlocal, DAT::tdual_int_1d numneighs, DAT::tdual_int_1d jelems, + DAT::tdual_float_1d wjelem, DAT::tdual_float_2d rij, DAT::tdual_int_1d k_ij, + int nmax, int lmax, double rcut, double alpha, bigint npairs, int ncoefs); + struct MLIAPSO3SpectrumDXDRTag {}; + KOKKOS_FUNCTION + void operator()(const MLIAPSO3SpectrumDXDRTag &, int ii) const; + + KOKKOS_FUNCTION + double Cosine(double Rij, double Rc) const; + KOKKOS_FUNCTION + double CosinePrime(double Rij, double Rc) const; + KOKKOS_FUNCTION + double compute_sfac(double r, double rcut) const; + KOKKOS_FUNCTION + double compute_dsfac(double r, double rcut) const; + + struct MLIAPSO3GetSBESArrayTag {}; + KOKKOS_FUNCTION + void operator()(const MLIAPSO3GetSBESArrayTag &, int ii) const; + + struct MLIAPSO3GetRipArrayTag {}; + KOKKOS_FUNCTION + void operator()(const MLIAPSO3GetRipArrayTag &, int ii) const; + + void init_arrays(int nlocal, int ncoefs); + void init_garray(int nmax, int lmax, double rcut, double alpha, double *w, int lw1, + double *g_array, int lg2); + + template + KOKKOS_FUNCTION void compute_uarray_recursive(double x, double y, double z, double r, int twol, + UlistView ulist_r, UlistView ulist_i, + int_1d idxu_block, float_1d rootpqarray) const; + void compute_ncoeff(); + + KOKKOS_FUNCTION + static int get_sum(int istart, int iend, int id, int imult); + + double compute_g(double r, int n, int nmax, double rcut, double *w, int lw1); + double phi(double r, int alpha, double rcut); + + template + KOKKOS_FUNCTION void compute_pi(int nmax, int lmax, ViewType clisttot_r, ViewType clisttot_i, + int lcl2, float_2d plist_r, int indpl) const; + + void compute_W(int nmax, double *arr); +}; + +} // namespace LAMMPS_NS + +#endif diff --git a/src/KOKKOS/modify_kokkos.cpp b/src/KOKKOS/modify_kokkos.cpp index 5545351f53..9d8c16603e 100644 --- a/src/KOKKOS/modify_kokkos.cpp +++ b/src/KOKKOS/modify_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/modify_kokkos.h b/src/KOKKOS/modify_kokkos.h index b6993552be..5edf5cd662 100644 --- a/src/KOKKOS/modify_kokkos.h +++ b/src/KOKKOS/modify_kokkos.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/nbin_kokkos.cpp b/src/KOKKOS/nbin_kokkos.cpp index 64d67285b6..ed9b670b42 100644 --- a/src/KOKKOS/nbin_kokkos.cpp +++ b/src/KOKKOS/nbin_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/nbin_kokkos.h b/src/KOKKOS/nbin_kokkos.h index 6000900062..c7535bb919 100644 --- a/src/KOKKOS/nbin_kokkos.h +++ b/src/KOKKOS/nbin_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/nbin_ssa_kokkos.cpp b/src/KOKKOS/nbin_ssa_kokkos.cpp index 3395386edb..27930e6fad 100644 --- a/src/KOKKOS/nbin_ssa_kokkos.cpp +++ b/src/KOKKOS/nbin_ssa_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/nbin_ssa_kokkos.h b/src/KOKKOS/nbin_ssa_kokkos.h index 2d10b74de4..8ce7cd2e0a 100644 --- a/src/KOKKOS/nbin_ssa_kokkos.h +++ b/src/KOKKOS/nbin_ssa_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/neigh_bond_kokkos.cpp b/src/KOKKOS/neigh_bond_kokkos.cpp index c3d5eb1725..5a250b6d23 100644 --- a/src/KOKKOS/neigh_bond_kokkos.cpp +++ b/src/KOKKOS/neigh_bond_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/neigh_bond_kokkos.h b/src/KOKKOS/neigh_bond_kokkos.h index 67439e59e2..e4be1aeee3 100644 --- a/src/KOKKOS/neigh_bond_kokkos.h +++ b/src/KOKKOS/neigh_bond_kokkos.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/neigh_list_kokkos.cpp b/src/KOKKOS/neigh_list_kokkos.cpp index 2337b1ef3d..0d231d7205 100644 --- a/src/KOKKOS/neigh_list_kokkos.cpp +++ b/src/KOKKOS/neigh_list_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/neigh_list_kokkos.h b/src/KOKKOS/neigh_list_kokkos.h index d06a3e76cf..589f9db5d7 100644 --- a/src/KOKKOS/neigh_list_kokkos.h +++ b/src/KOKKOS/neigh_list_kokkos.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/neighbor_kokkos.cpp b/src/KOKKOS/neighbor_kokkos.cpp index 207ff7501b..b64fb91434 100644 --- a/src/KOKKOS/neighbor_kokkos.cpp +++ b/src/KOKKOS/neighbor_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/neighbor_kokkos.h b/src/KOKKOS/neighbor_kokkos.h index 8361461420..2f470cbdb4 100644 --- a/src/KOKKOS/neighbor_kokkos.h +++ b/src/KOKKOS/neighbor_kokkos.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/npair_copy_kokkos.cpp b/src/KOKKOS/npair_copy_kokkos.cpp index 55c1d52596..6485319883 100644 --- a/src/KOKKOS/npair_copy_kokkos.cpp +++ b/src/KOKKOS/npair_copy_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/npair_copy_kokkos.h b/src/KOKKOS/npair_copy_kokkos.h index 7ba54d4007..ff3abf67c2 100644 --- a/src/KOKKOS/npair_copy_kokkos.h +++ b/src/KOKKOS/npair_copy_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/npair_halffull_kokkos.cpp b/src/KOKKOS/npair_halffull_kokkos.cpp index 3005f0e463..ec17cec844 100644 --- a/src/KOKKOS/npair_halffull_kokkos.cpp +++ b/src/KOKKOS/npair_halffull_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/npair_halffull_kokkos.h b/src/KOKKOS/npair_halffull_kokkos.h index ce2321f6fd..c5a09f0b62 100644 --- a/src/KOKKOS/npair_halffull_kokkos.h +++ b/src/KOKKOS/npair_halffull_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/npair_kokkos.cpp b/src/KOKKOS/npair_kokkos.cpp index a1f8fcbf48..aae8592b7a 100644 --- a/src/KOKKOS/npair_kokkos.cpp +++ b/src/KOKKOS/npair_kokkos.cpp @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/npair_kokkos.h b/src/KOKKOS/npair_kokkos.h index 16b77648b4..ce63c30c4b 100644 --- a/src/KOKKOS/npair_kokkos.h +++ b/src/KOKKOS/npair_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/npair_skip_kokkos.cpp b/src/KOKKOS/npair_skip_kokkos.cpp index fb9b0730c5..4492a3794a 100644 --- a/src/KOKKOS/npair_skip_kokkos.cpp +++ b/src/KOKKOS/npair_skip_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/npair_skip_kokkos.h b/src/KOKKOS/npair_skip_kokkos.h index c2aac9052b..fd1217bef4 100644 --- a/src/KOKKOS/npair_skip_kokkos.h +++ b/src/KOKKOS/npair_skip_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/npair_ssa_kokkos.cpp b/src/KOKKOS/npair_ssa_kokkos.cpp index 7c7f0280fd..9f809adaae 100644 --- a/src/KOKKOS/npair_ssa_kokkos.cpp +++ b/src/KOKKOS/npair_ssa_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/npair_ssa_kokkos.h b/src/KOKKOS/npair_ssa_kokkos.h index ccee73f1ce..6fd5231ffe 100644 --- a/src/KOKKOS/npair_ssa_kokkos.h +++ b/src/KOKKOS/npair_ssa_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/npair_trim_kokkos.cpp b/src/KOKKOS/npair_trim_kokkos.cpp index bd2761f40c..97931bf250 100644 --- a/src/KOKKOS/npair_trim_kokkos.cpp +++ b/src/KOKKOS/npair_trim_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Trimright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/npair_trim_kokkos.h b/src/KOKKOS/npair_trim_kokkos.h index 67b60f7337..69ced14d4a 100644 --- a/src/KOKKOS/npair_trim_kokkos.h +++ b/src/KOKKOS/npair_trim_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Trimright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pack_kokkos.h b/src/KOKKOS/pack_kokkos.h index 244af8f796..fe90d294a6 100644 --- a/src/KOKKOS/pack_kokkos.h +++ b/src/KOKKOS/pack_kokkos.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- SPARTA - Stochastic PArallel Rarefied-gas Time-accurate Analyzer http://sparta.sandia.gov - Steve Plimpton, sjplimp@sandia.gov, Michael Gallis, magalli@sandia.gov + LAMMPS development team: developers@lammps.org, Michael Gallis, magalli@sandia.gov Sandia National Laboratories Copyright (2014) Sandia Corporation. Under the terms of Contract diff --git a/src/KOKKOS/pair_adp_kokkos.cpp b/src/KOKKOS/pair_adp_kokkos.cpp index 93806a8dc5..3873f1e31b 100644 --- a/src/KOKKOS/pair_adp_kokkos.cpp +++ b/src/KOKKOS/pair_adp_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -111,7 +111,6 @@ void PairADPKokkos::compute(int eflag_in, int vflag_in) x = atomKK->k_x.view(); f = atomKK->k_f.view(); type = atomKK->k_type.view(); - tag = atomKK->k_tag.view(); nlocal = atom->nlocal; nall = atom->nlocal + atom->nghost; newton_pair = force->newton_pair; diff --git a/src/KOKKOS/pair_adp_kokkos.h b/src/KOKKOS/pair_adp_kokkos.h index ce163f6120..5714bdb699 100644 --- a/src/KOKKOS/pair_adp_kokkos.h +++ b/src/KOKKOS/pair_adp_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -120,7 +120,6 @@ class PairADPKokkos : public PairADP, public KokkosBase typename AT::t_x_array x; typename AT::t_f_array f; typename AT::t_int_1d type; - typename AT::t_tagint_1d tag; DAT::tdual_efloat_1d k_eatom; DAT::tdual_virial_array k_vatom; diff --git a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp index 9b19cbcc7a..39bdc255f5 100644 --- a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_buck_coul_cut_kokkos.h b/src/KOKKOS/pair_buck_coul_cut_kokkos.h index ecba0c1e1b..b91348d557 100644 --- a/src/KOKKOS/pair_buck_coul_cut_kokkos.h +++ b/src/KOKKOS/pair_buck_coul_cut_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp index 5200db8356..34e42be775 100644 --- a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_buck_coul_long_kokkos.h b/src/KOKKOS/pair_buck_coul_long_kokkos.h index e7b7ded20d..b776a84e3c 100644 --- a/src/KOKKOS/pair_buck_coul_long_kokkos.h +++ b/src/KOKKOS/pair_buck_coul_long_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_buck_kokkos.cpp b/src/KOKKOS/pair_buck_kokkos.cpp index 8e0156331b..8e69536b38 100644 --- a/src/KOKKOS/pair_buck_kokkos.cpp +++ b/src/KOKKOS/pair_buck_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -98,7 +98,6 @@ void PairBuckKokkos::compute(int eflag_in, int vflag_in) c_x = atomKK->k_x.view(); f = atomKK->k_f.view(); type = atomKK->k_type.view(); - tag = atomKK->k_tag.view(); nlocal = atom->nlocal; nall = atom->nlocal + atom->nghost; newton_pair = force->newton_pair; diff --git a/src/KOKKOS/pair_buck_kokkos.h b/src/KOKKOS/pair_buck_kokkos.h index f68be6fa6f..364716453b 100644 --- a/src/KOKKOS/pair_buck_kokkos.h +++ b/src/KOKKOS/pair_buck_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -74,7 +74,6 @@ class PairBuckKokkos : public PairBuck { typename AT::t_x_array c_x; typename AT::t_f_array f; typename AT::t_int_1d_randomread type; - typename AT::t_tagint_1d tag; DAT::tdual_efloat_1d k_eatom; DAT::tdual_virial_array k_vatom; diff --git a/src/KOKKOS/pair_coul_cut_kokkos.cpp b/src/KOKKOS/pair_coul_cut_kokkos.cpp index 77dfd6b607..d2739f53ce 100644 --- a/src/KOKKOS/pair_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_coul_cut_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_coul_cut_kokkos.h b/src/KOKKOS/pair_coul_cut_kokkos.h index 3c447539cc..6626889660 100644 --- a/src/KOKKOS/pair_coul_cut_kokkos.h +++ b/src/KOKKOS/pair_coul_cut_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_coul_debye_kokkos.cpp b/src/KOKKOS/pair_coul_debye_kokkos.cpp index 3f17f0bb64..9930a4f3f1 100644 --- a/src/KOKKOS/pair_coul_debye_kokkos.cpp +++ b/src/KOKKOS/pair_coul_debye_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_coul_debye_kokkos.h b/src/KOKKOS/pair_coul_debye_kokkos.h index 382f6f9a16..b6bed9d557 100644 --- a/src/KOKKOS/pair_coul_debye_kokkos.h +++ b/src/KOKKOS/pair_coul_debye_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_coul_dsf_kokkos.cpp index 097fa36419..6b0818251d 100644 --- a/src/KOKKOS/pair_coul_dsf_kokkos.cpp +++ b/src/KOKKOS/pair_coul_dsf_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_coul_dsf_kokkos.h b/src/KOKKOS/pair_coul_dsf_kokkos.h index 8dcbbaddcc..1740b6a296 100644 --- a/src/KOKKOS/pair_coul_dsf_kokkos.h +++ b/src/KOKKOS/pair_coul_dsf_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_coul_long_kokkos.cpp b/src/KOKKOS/pair_coul_long_kokkos.cpp index 7f749a1e8a..ac52e95bad 100644 --- a/src/KOKKOS/pair_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_coul_long_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_coul_long_kokkos.h b/src/KOKKOS/pair_coul_long_kokkos.h index afc7b14cc0..fcb1402028 100644 --- a/src/KOKKOS/pair_coul_long_kokkos.h +++ b/src/KOKKOS/pair_coul_long_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_coul_wolf_kokkos.cpp b/src/KOKKOS/pair_coul_wolf_kokkos.cpp index 48491b4894..2bac3cfb9a 100644 --- a/src/KOKKOS/pair_coul_wolf_kokkos.cpp +++ b/src/KOKKOS/pair_coul_wolf_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_coul_wolf_kokkos.h b/src/KOKKOS/pair_coul_wolf_kokkos.h index 0c25cbe2a2..320716c9e7 100644 --- a/src/KOKKOS/pair_coul_wolf_kokkos.h +++ b/src/KOKKOS/pair_coul_wolf_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_dpd_ext_kokkos.cpp b/src/KOKKOS/pair_dpd_ext_kokkos.cpp index 81a1b0b0a3..42fcff0596 100644 --- a/src/KOKKOS/pair_dpd_ext_kokkos.cpp +++ b/src/KOKKOS/pair_dpd_ext_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_dpd_ext_kokkos.h b/src/KOKKOS/pair_dpd_ext_kokkos.h index b952513de1..8df218f82c 100644 --- a/src/KOKKOS/pair_dpd_ext_kokkos.h +++ b/src/KOKKOS/pair_dpd_ext_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_dpd_ext_tstat_kokkos.cpp b/src/KOKKOS/pair_dpd_ext_tstat_kokkos.cpp index 76b7658ac9..a6c5da37fa 100644 --- a/src/KOKKOS/pair_dpd_ext_tstat_kokkos.cpp +++ b/src/KOKKOS/pair_dpd_ext_tstat_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_dpd_ext_tstat_kokkos.h b/src/KOKKOS/pair_dpd_ext_tstat_kokkos.h index 4fce2f7305..99490894d3 100644 --- a/src/KOKKOS/pair_dpd_ext_tstat_kokkos.h +++ b/src/KOKKOS/pair_dpd_ext_tstat_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp index dc22938dc8..2cd7503ba5 100644 --- a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp +++ b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.h b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.h index 5913e3ce2d..29f74c72ec 100644 --- a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.h +++ b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_dpd_kokkos.cpp b/src/KOKKOS/pair_dpd_kokkos.cpp index 2b2c4594ac..bee4fa0be1 100644 --- a/src/KOKKOS/pair_dpd_kokkos.cpp +++ b/src/KOKKOS/pair_dpd_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_dpd_kokkos.h b/src/KOKKOS/pair_dpd_kokkos.h index f8d97556ce..4fce75db80 100644 --- a/src/KOKKOS/pair_dpd_kokkos.h +++ b/src/KOKKOS/pair_dpd_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_dpd_tstat_kokkos.cpp b/src/KOKKOS/pair_dpd_tstat_kokkos.cpp index d9a37c825a..9f835fde56 100644 --- a/src/KOKKOS/pair_dpd_tstat_kokkos.cpp +++ b/src/KOKKOS/pair_dpd_tstat_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_dpd_tstat_kokkos.h b/src/KOKKOS/pair_dpd_tstat_kokkos.h index 1654340850..6a655e6892 100644 --- a/src/KOKKOS/pair_dpd_tstat_kokkos.h +++ b/src/KOKKOS/pair_dpd_tstat_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp index dc85b84fa0..0be0dffd93 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp +++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -110,7 +110,6 @@ void PairEAMAlloyKokkos::compute(int eflag_in, int vflag_in) x = atomKK->k_x.view(); f = atomKK->k_f.view(); type = atomKK->k_type.view(); - tag = atomKK->k_tag.view(); nlocal = atom->nlocal; nall = atom->nlocal + atom->nghost; newton_pair = force->newton_pair; diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.h b/src/KOKKOS/pair_eam_alloy_kokkos.h index 06530abec9..c6cb73ca5d 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.h +++ b/src/KOKKOS/pair_eam_alloy_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -119,7 +119,6 @@ class PairEAMAlloyKokkos : public PairEAM, public KokkosBase { typename AT::t_x_array x; typename AT::t_f_array f; typename AT::t_int_1d type; - typename AT::t_tagint_1d tag; DAT::tdual_efloat_1d k_eatom; DAT::tdual_virial_array k_vatom; diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp index 5d1060a01b..bf0f398e60 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.cpp +++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -110,7 +110,6 @@ void PairEAMFSKokkos::compute(int eflag_in, int vflag_in) x = atomKK->k_x.view(); f = atomKK->k_f.view(); type = atomKK->k_type.view(); - tag = atomKK->k_tag.view(); nlocal = atom->nlocal; nall = atom->nlocal + atom->nghost; newton_pair = force->newton_pair; diff --git a/src/KOKKOS/pair_eam_fs_kokkos.h b/src/KOKKOS/pair_eam_fs_kokkos.h index 9fd05e8e8f..06a395cba7 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.h +++ b/src/KOKKOS/pair_eam_fs_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -119,7 +119,6 @@ class PairEAMFSKokkos : public PairEAM, public KokkosBase { typename AT::t_x_array x; typename AT::t_f_array f; typename AT::t_int_1d type; - typename AT::t_tagint_1d tag; DAT::tdual_efloat_1d k_eatom; DAT::tdual_virial_array k_vatom; diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp index 26b3ec6880..6e1cd1feea 100644 --- a/src/KOKKOS/pair_eam_kokkos.cpp +++ b/src/KOKKOS/pair_eam_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -105,7 +105,6 @@ void PairEAMKokkos::compute(int eflag_in, int vflag_in) x = atomKK->k_x.view(); f = atomKK->k_f.view(); type = atomKK->k_type.view(); - tag = atomKK->k_tag.view(); nlocal = atom->nlocal; nall = atom->nlocal + atom->nghost; newton_pair = force->newton_pair; diff --git a/src/KOKKOS/pair_eam_kokkos.h b/src/KOKKOS/pair_eam_kokkos.h index 4bc7a55196..006dceb1f2 100644 --- a/src/KOKKOS/pair_eam_kokkos.h +++ b/src/KOKKOS/pair_eam_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -115,7 +115,6 @@ class PairEAMKokkos : public PairEAM, public KokkosBase { typename AT::t_x_array x; typename AT::t_f_array f; typename AT::t_int_1d type; - typename AT::t_tagint_1d tag; DAT::tdual_efloat_1d k_eatom; DAT::tdual_virial_array k_vatom; diff --git a/src/KOKKOS/pair_exp6_rx_kokkos.cpp b/src/KOKKOS/pair_exp6_rx_kokkos.cpp index 534551e7e6..f8e51bc4cc 100644 --- a/src/KOKKOS/pair_exp6_rx_kokkos.cpp +++ b/src/KOKKOS/pair_exp6_rx_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_exp6_rx_kokkos.h b/src/KOKKOS/pair_exp6_rx_kokkos.h index 149c092faa..920010120a 100644 --- a/src/KOKKOS/pair_exp6_rx_kokkos.h +++ b/src/KOKKOS/pair_exp6_rx_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp index 1456bab0bc..2cfbbf0ee7 100644 --- a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp +++ b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -134,7 +134,6 @@ void PairGranHookeHistoryKokkos::compute(int eflag_in, int vflag_in) torque = atomKK->k_torque.view(); type = atomKK->k_type.view(); mask = atomKK->k_mask.view(); - tag = atomKK->k_tag.view(); rmass = atomKK->k_rmass.view(); radius = atomKK->k_radius.view(); nlocal = atom->nlocal; diff --git a/src/KOKKOS/pair_gran_hooke_history_kokkos.h b/src/KOKKOS/pair_gran_hooke_history_kokkos.h index 88514e2233..ef068e970a 100644 --- a/src/KOKKOS/pair_gran_hooke_history_kokkos.h +++ b/src/KOKKOS/pair_gran_hooke_history_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -86,7 +86,6 @@ class PairGranHookeHistoryKokkos : public PairGranHookeHistory { DAT::tdual_virial_array k_vatom; typename AT::t_efloat_1d d_eatom; typename AT::t_virial_array d_vatom; - typename AT::t_tagint_1d tag; typename AT::t_neighbors_2d d_neighbors; typename AT::t_int_1d_randomread d_ilist; diff --git a/src/KOKKOS/pair_hybrid_kokkos.cpp b/src/KOKKOS/pair_hybrid_kokkos.cpp index e000a7199c..2be290658c 100644 --- a/src/KOKKOS/pair_hybrid_kokkos.cpp +++ b/src/KOKKOS/pair_hybrid_kokkos.cpp @@ -3,7 +3,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_hybrid_kokkos.h b/src/KOKKOS/pair_hybrid_kokkos.h index 440b6983e6..c50224cddd 100644 --- a/src/KOKKOS/pair_hybrid_kokkos.h +++ b/src/KOKKOS/pair_hybrid_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp index 7b0e79075d..cfdb9b7c63 100644 --- a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp +++ b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_hybrid_overlay_kokkos.h b/src/KOKKOS/pair_hybrid_overlay_kokkos.h index 3b4327679a..b60e5c32fa 100644 --- a/src/KOKKOS/pair_hybrid_overlay_kokkos.h +++ b/src/KOKKOS/pair_hybrid_overlay_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h index d9c11c2ea4..0ff244f67d 100644 --- a/src/KOKKOS/pair_kokkos.h +++ b/src/KOKKOS/pair_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp index 37697a91fb..d9edbbbf6b 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.h b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.h index 2fb861c4d1..ae27ee68ab 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.h +++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp index 4414116f1a..41a6214938 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.h b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.h index 46b527257e..912ad573c6 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.h +++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp index 6f3449afd1..6d6a94dcda 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.h b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.h index fc0af13845..4ae8a12944 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.h +++ b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp index fc6b1758b5..8abcd374a1 100644 --- a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.h b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.h index c55c487dd7..5ca276c28e 100644 --- a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.h +++ b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp index afa0ac6925..6fd9804b0b 100644 --- a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.h b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.h index 0a10f9ffcd..599cc2a83c 100644 --- a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.h +++ b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_lj_class2_kokkos.cpp b/src/KOKKOS/pair_lj_class2_kokkos.cpp index a29a2d46cc..d37a190b6c 100644 --- a/src/KOKKOS/pair_lj_class2_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -99,7 +99,6 @@ void PairLJClass2Kokkos::compute(int eflag_in, int vflag_in) c_x = atomKK->k_x.view(); f = atomKK->k_f.view(); type = atomKK->k_type.view(); - tag = atomKK->k_tag.view(); nlocal = atom->nlocal; nall = atom->nlocal + atom->nghost; newton_pair = force->newton_pair; diff --git a/src/KOKKOS/pair_lj_class2_kokkos.h b/src/KOKKOS/pair_lj_class2_kokkos.h index d5952655e9..0936399ca8 100644 --- a/src/KOKKOS/pair_lj_class2_kokkos.h +++ b/src/KOKKOS/pair_lj_class2_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -80,7 +80,6 @@ class PairLJClass2Kokkos : public PairLJClass2 { typename AT::t_x_array c_x; typename AT::t_f_array f; typename AT::t_int_1d_randomread type; - typename AT::t_tagint_1d tag; DAT::tdual_efloat_1d k_eatom; DAT::tdual_virial_array k_vatom; diff --git a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp index 18c537ce9b..0df93fb73f 100644 --- a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h index 4704bacd4c..87464b37dc 100644 --- a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h +++ b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp index fc4febf575..a9991c03f3 100644 --- a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.h b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.h index 8695930f68..ea0b401959 100644 --- a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.h +++ b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp index f24ddcc90f..113e97c0c9 100644 --- a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.h b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.h index b390537e08..e420bd22a9 100644 --- a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.h +++ b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp index 5c0584cd8c..ba0904fa95 100644 --- a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.h b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.h index 6ed46984e2..bcb97a59cd 100644 --- a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.h +++ b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_lj_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_kokkos.cpp index eeb9f44c81..c6353cc083 100644 --- a/src/KOKKOS/pair_lj_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -94,7 +94,6 @@ void PairLJCutKokkos::compute(int eflag_in, int vflag_in) c_x = atomKK->k_x.view(); f = atomKK->k_f.view(); type = atomKK->k_type.view(); - tag = atomKK->k_tag.view(); nlocal = atom->nlocal; nall = atom->nlocal + atom->nghost; newton_pair = force->newton_pair; diff --git a/src/KOKKOS/pair_lj_cut_kokkos.h b/src/KOKKOS/pair_lj_cut_kokkos.h index 17f1032855..106f1a9048 100644 --- a/src/KOKKOS/pair_lj_cut_kokkos.h +++ b/src/KOKKOS/pair_lj_cut_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -80,7 +80,6 @@ class PairLJCutKokkos : public PairLJCut { DAT::tdual_virial_array k_vatom; typename AT::t_efloat_1d d_eatom; typename AT::t_virial_array d_vatom; - typename AT::t_tagint_1d tag; int newton_pair; double special_lj[4]; diff --git a/src/KOKKOS/pair_lj_expand_kokkos.cpp b/src/KOKKOS/pair_lj_expand_kokkos.cpp index ca5d7c5233..ecdb3a7b22 100644 --- a/src/KOKKOS/pair_lj_expand_kokkos.cpp +++ b/src/KOKKOS/pair_lj_expand_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -98,7 +98,6 @@ void PairLJExpandKokkos::compute(int eflag_in, int vflag_in) c_x = atomKK->k_x.view(); f = atomKK->k_f.view(); type = atomKK->k_type.view(); - tag = atomKK->k_tag.view(); nlocal = atom->nlocal; nall = atom->nlocal + atom->nghost; newton_pair = force->newton_pair; diff --git a/src/KOKKOS/pair_lj_expand_kokkos.h b/src/KOKKOS/pair_lj_expand_kokkos.h index ab62ff1df2..0df0a6f8f8 100644 --- a/src/KOKKOS/pair_lj_expand_kokkos.h +++ b/src/KOKKOS/pair_lj_expand_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -80,7 +80,6 @@ class PairLJExpandKokkos : public PairLJExpand { typename AT::t_x_array c_x; typename AT::t_f_array f; typename AT::t_int_1d_randomread type; - typename AT::t_tagint_1d tag; DAT::tdual_efloat_1d k_eatom; DAT::tdual_virial_array k_vatom; diff --git a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp index b956c50758..6b4aae7945 100644 --- a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp +++ b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.h b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.h index 33d2bfce97..359c4a1229 100644 --- a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.h +++ b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp index 79ee36f8c7..5f209037b7 100644 --- a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp +++ b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_lj_gromacs_kokkos.h b/src/KOKKOS/pair_lj_gromacs_kokkos.h index 94d5524b6b..95c600a415 100644 --- a/src/KOKKOS/pair_lj_gromacs_kokkos.h +++ b/src/KOKKOS/pair_lj_gromacs_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_lj_spica_kokkos.cpp b/src/KOKKOS/pair_lj_spica_kokkos.cpp index 60640c8715..345c18bd30 100644 --- a/src/KOKKOS/pair_lj_spica_kokkos.cpp +++ b/src/KOKKOS/pair_lj_spica_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -98,7 +98,6 @@ void PairLJSPICAKokkos::compute(int eflag_in, int vflag_in) c_x = atomKK->k_x.view(); f = atomKK->k_f.view(); type = atomKK->k_type.view(); - tag = atomKK->k_tag.view(); nlocal = atom->nlocal; nall = atom->nlocal + atom->nghost; newton_pair = force->newton_pair; diff --git a/src/KOKKOS/pair_lj_spica_kokkos.h b/src/KOKKOS/pair_lj_spica_kokkos.h index ba6c996df4..b330af4bfd 100644 --- a/src/KOKKOS/pair_lj_spica_kokkos.h +++ b/src/KOKKOS/pair_lj_spica_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -80,7 +80,6 @@ class PairLJSPICAKokkos : public PairLJSPICA { typename AT::t_x_array c_x; typename AT::t_f_array f; typename AT::t_int_1d_randomread type; - typename AT::t_tagint_1d tag; DAT::tdual_efloat_1d k_eatom; DAT::tdual_virial_array k_vatom; diff --git a/src/KOKKOS/pair_meam_kokkos.cpp b/src/KOKKOS/pair_meam_kokkos.cpp index 86b4a2ed51..90e714cefe 100644 --- a/src/KOKKOS/pair_meam_kokkos.cpp +++ b/src/KOKKOS/pair_meam_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -408,7 +408,7 @@ void PairMEAMKokkos::operator()(TagPairMEAMUnpackForwardComm, const template int PairMEAMKokkos::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { meam_inst_kk->k_rho0.sync_host(); meam_inst_kk->k_rho1.sync_host(); diff --git a/src/KOKKOS/pair_meam_kokkos.h b/src/KOKKOS/pair_meam_kokkos.h index a213c1e9b1..c5fe82fa79 100644 --- a/src/KOKKOS/pair_meam_kokkos.h +++ b/src/KOKKOS/pair_meam_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_mliap_kokkos.cpp b/src/KOKKOS/pair_mliap_kokkos.cpp new file mode 100644 index 0000000000..5f00c7473a --- /dev/null +++ b/src/KOKKOS/pair_mliap_kokkos.cpp @@ -0,0 +1,288 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + 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: Matt Bettencourt (NVIDIA) +------------------------------------------------------------------------- */ + +#include "pair_mliap_kokkos.h" +#include "memory_kokkos.h" +#include "atom_kokkos.h" +#include "atom_masks.h" +#include "mliap_data_kokkos.h" +#include "mliap_descriptor_so3_kokkos.h" +#include "mliap_model_linear_kokkos.h" +#include "error.h" +#include "neigh_request.h" +#include "lammps.h" +#include "kokkos.h" +#include "pointers.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +template +PairMLIAPKokkos::PairMLIAPKokkos(class LAMMPS* l) : PairMLIAP(l) +{ + kokkosable = 1; + execution_space = ExecutionSpaceFromDevice::space; + datamask_modify = 0; +} + +/* ---------------------------------------------------------------------- */ + +template +PairMLIAPKokkos::~PairMLIAPKokkos() +{ + memoryKK->destroy_kokkos(k_map, map); + memoryKK->destroy_kokkos(k_cutsq, cutsq); + memoryKK->destroy_kokkos(k_setflag, setflag); + memoryKK->destroy_kokkos(k_eatom,eatom); + memoryKK->destroy_kokkos(k_vatom,vatom); + allocated = 0; +} + +/* ---------------------------------------------------------------------- */ + +template +void PairMLIAPKokkos::compute(int eflag, int vflag) +{ + atomKK->sync(Host,F_MASK | ENERGY_MASK | VIRIAL_MASK); + atomKK->sync(execution_space,X_MASK | TYPE_MASK ); + MLIAPDataKokkos *k_data = (MLIAPDataKokkos*)(data); + + int is_kokkos_model = (dynamic_cast*>(model)) != nullptr; + int is_kokkos_descriptor = (dynamic_cast*>(descriptor)) != nullptr; + auto model_space = is_kokkos_model ? execution_space : Host; + auto descriptor_space = is_kokkos_descriptor? execution_space : Host; + + // consistency checks + if (data->ndescriptors != model->ndescriptors) + error->all(FLERR, "Incompatible model and descriptor descriptor count"); + + if (data->nelements != model->nelements) + error->all(FLERR, "Incompatible model and descriptor element count"); + + ev_init(eflag, vflag); + if (eflag_atom && (int)k_eatom.h_view.extent(0) < maxeatom) { + memoryKK->destroy_kokkos(k_eatom,eatom); + memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom"); + } + + if (vflag_atom && (int)k_vatom.h_view.extent(0) < maxeatom) { + memoryKK->destroy_kokkos(k_vatom,vatom); + memoryKK->create_kokkos(k_vatom,vatom,maxeatom,6,"pair:eatom"); + } + + data->generate_neighdata(list, eflag, vflag); + + // compute descriptors, if needed + if (model->nonlinearflag || eflag) { + k_data->sync(descriptor_space, NUMNEIGHS_MASK | IATOMS_MASK | IELEMS_MASK | JATOMS_MASK | JELEMS_MASK | RIJ_MASK ); + descriptor->compute_descriptors(data); + if (!is_kokkos_descriptor) + k_data->modified(descriptor_space, DESCRIPTORS_MASK); + } + + // compute E_i and beta_i = dE_i/dB_i for all i in list + k_data->sync(model_space, IELEMS_MASK | DESCRIPTORS_MASK); + model->compute_gradients(data); + k_data->modified(model_space, BETAS_MASK); + if (eflag_atom) + k_data->modified(model_space, EATOMS_MASK); + e_tally(data); + + // calculate force contributions beta_i*dB_i/dR_j + k_data->sync(descriptor_space, NUMNEIGHS_MASK | IATOMS_MASK | IELEMS_MASK | BETAS_MASK | JATOMS_MASK | JELEMS_MASK | RIJ_MASK ); + descriptor->compute_forces(data); + + if (evflag) { + atomKK->modified(descriptor_space,F_MASK | ENERGY_MASK | VIRIAL_MASK); + atomKK->sync(execution_space,F_MASK | ENERGY_MASK | VIRIAL_MASK); + } else { + atomKK->modified(descriptor_space,F_MASK); + atomKK->sync(execution_space,F_MASK); + } + + // calculate stress + if (vflag_fdotr) { + pair_virial_fdotr_compute(this); + } +} + +/* ---------------------------------------------------------------------- */ + +template +void PairMLIAPKokkos::allocate() +{ + int n = atom->ntypes; + memoryKK->destroy_kokkos(k_map, map); + memoryKK->destroy_kokkos(k_cutsq, cutsq); + memoryKK->destroy_kokkos(k_setflag, setflag); + memoryKK->create_kokkos(k_map, map, n+1, "pair_mliap:map"); + memoryKK->create_kokkos(k_cutsq, cutsq, n+1, n+1, "pair_mliap:cutsq"); + memoryKK->create_kokkos(k_setflag, setflag, n+1, n+1, "pair_mliap:setflag"); + + // this is for the base class so it doesn't double delete + allocated = 1; +} + +/* ---------------------------------------------------------------------- */ + +template +void PairMLIAPKokkos::settings(int narg, char ** arg) +{ + PairMLIAP::settings(narg, arg); + int iarg=0; + while (iarg < narg) { + if (strcmp(arg[iarg],"model") == 0) { + if (strcmp(arg[iarg+1],"linear") == 0) { + if (iarg+3 > narg) error->all(FLERR,"Illegal pair_style mliap command"); + delete model; + model = new MLIAPModelLinearKokkos(lmp,arg[iarg+2]); + iarg += 3; + } else + iarg += 2; + } else if (strcmp(arg[iarg],"descriptor") == 0) { + if (strcmp(arg[iarg+1],"so3") == 0) { + if (iarg+3 > narg) error->all(FLERR,"Illegal pair_style mliap command"); + delete descriptor; + descriptor = new MLIAPDescriptorSO3Kokkos(lmp,arg[iarg+2]); + iarg += 3; + } else + iarg ++; + } else + iarg++; + } +} + +/* ---------------------------------------------------------------------- */ + +template +void PairMLIAPKokkos::coeff(int narg, char **arg) { + if (narg < 3) error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) { + PairMLIAP::allocate(); + allocate(); + } + + char* type1 = arg[0]; + char* type2 = arg[1]; + char** elemtypes = &arg[2]; + + // insure I,J args are * * + + if (strcmp(type1,"*") != 0 || strcmp(type2,"*") != 0) + error->all(FLERR,"Incorrect args for pair coefficients"); + + // read args that map atom types to elements + // map[i] = which element the Ith atom type is, -1 if not mapped + // map[0] is not used + + for (int i = 1; i <= atom->ntypes; i++) { + char* elemname = elemtypes[i-1]; + int jelem; + for (jelem = 0; jelem < descriptor->nelements; jelem++) + if (strcmp(elemname,descriptor->elements[jelem]) == 0) + break; + + if (jelem < descriptor->nelements) + map[i] = jelem; + else if (strcmp(elemname,"NULL") == 0) map[i] = -1; + else error->all(FLERR,"Incorrect args for pair coefficients"); + } + k_map.modify(); + k_map.sync(); + + auto h_cutsq=k_cutsq.template view(); + for (int itype=1; itype <= atom->ntypes; ++itype) + for (int jtype=1; jtype <= atom->ntypes; ++jtype) + h_cutsq(itype,jtype) = descriptor->cutsq[map[itype]][map[jtype]]; + k_cutsq.modify(); + k_cutsq.sync(); + + // clear setflag since coeff() called once with I,J = * * + + int n = atom->ntypes; + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + // set setflag i,j for type pairs where both are mapped to elements + + int count = 0; + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + if (map[i] >= 0 && map[j] >= 0) { + setflag[i][j] = 1; + count++; + } + k_setflag.modify(); + k_setflag.sync(); + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + + // set up model, descriptor, and mliap data structures + model->init(); + descriptor->init(); + int gradgradflag = -1; + delete data; + data = new MLIAPDataKokkos(lmp, gradgradflag, map, model, descriptor, this); + data->init(); +} + +/* ---------------------------------------------------------------------- + add energies to eng_vdwl and per-atom energy +------------------------------------------------------------------------- */ + +template +void PairMLIAPKokkos::e_tally(MLIAPData* data) +{ + if (eflag_global) eng_vdwl += data->energy; + if (eflag_atom) { + MLIAPDataKokkos *k_data = static_cast*>(data); + k_data->sync(execution_space, IATOMS_MASK | EATOMS_MASK); + auto d_iatoms = k_data->k_iatoms.template view(); + auto d_eatoms = k_data->k_eatoms.template view(); + auto d_eatom = k_eatom.template view(); + Kokkos::parallel_for(data->nlistatoms, KOKKOS_LAMBDA (int ii) { + d_eatom(d_iatoms(ii)) = d_eatoms(ii); + }); + k_eatom.modify(); + // This sync has to be here for the hybrid pair type + k_eatom.sync(); + } +} + +/* ---------------------------------------------------------------------- */ + +template +void PairMLIAPKokkos::init_style() +{ + + PairMLIAP::init_style(); + auto request = neighbor->find_request(this); + request->set_kokkos_host(std::is_same::value && + !std::is_same::value); + request->set_kokkos_device(std::is_same::value); +} + +/* ---------------------------------------------------------------------- */ + +namespace LAMMPS_NS { +template class PairMLIAPKokkos; +#ifdef LMP_KOKKOS_GPU +template class PairMLIAPKokkos; +#endif +} diff --git a/src/KOKKOS/pair_mliap_kokkos.h b/src/KOKKOS/pair_mliap_kokkos.h new file mode 100644 index 0000000000..1acac6bf24 --- /dev/null +++ b/src/KOKKOS/pair_mliap_kokkos.h @@ -0,0 +1,67 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + 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: Matt Bettencourt (NVIDIA) +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(mliap/kk,PairMLIAPKokkos); +PairStyle(mliap/kk/device,PairMLIAPKokkos); +PairStyle(mliap/kk/host,PairMLIAPKokkos); +// clang-format off +#else + +#ifndef LMP_PAIR_MLIAP_KOKKOS_H +#define LMP_PAIR_MLIAP_KOKKOS_H + +#include "pair_mliap.h" +#include "pair_kokkos.h" +#include "kokkos_type.h" + +namespace LAMMPS_NS { + +template +class PairMLIAPKokkos : public PairMLIAP { +public: + typedef DeviceType device_type; + typedef ArrayTypes AT; + + PairMLIAPKokkos(class LAMMPS*); + ~PairMLIAPKokkos(); + void settings(int narg, char ** arg); + void init_style(); + + void compute(int, int); + void e_tally(MLIAPData* data); + + void allocate(); + + void coeff(int narg, char **arg); + typename AT::t_x_array_randomread x; + typename AT::t_x_array_randomread v; + typename AT::t_f_array f; + DAT::tdual_int_1d k_map; + DAT::tdual_double_2d k_cutsq; + DAT::tdual_int_2d k_setflag; + DAT::tdual_efloat_1d k_eatom; + DAT::tdual_double_2d k_vatom; + + + friend void pair_virial_fdotr_compute(PairMLIAPKokkos*); +}; + +} +#endif +#endif diff --git a/src/KOKKOS/pair_morse_kokkos.cpp b/src/KOKKOS/pair_morse_kokkos.cpp index a6b346673b..50df64e3ca 100644 --- a/src/KOKKOS/pair_morse_kokkos.cpp +++ b/src/KOKKOS/pair_morse_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -101,7 +101,6 @@ void PairMorseKokkos::compute(int eflag_in, int vflag_in) c_x = atomKK->k_x.view(); f = atomKK->k_f.view(); type = atomKK->k_type.view(); - tag = atomKK->k_tag.view(); nlocal = atom->nlocal; nall = atom->nlocal + atom->nghost; newton_pair = force->newton_pair; diff --git a/src/KOKKOS/pair_morse_kokkos.h b/src/KOKKOS/pair_morse_kokkos.h index 2a1205a65d..d06cf2deb1 100644 --- a/src/KOKKOS/pair_morse_kokkos.h +++ b/src/KOKKOS/pair_morse_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -80,7 +80,6 @@ class PairMorseKokkos : public PairMorse { DAT::tdual_virial_array k_vatom; typename ArrayTypes::t_efloat_1d d_eatom; typename ArrayTypes::t_virial_array d_vatom; - typename ArrayTypes::t_tagint_1d tag; int newton_pair; double special_lj[4]; diff --git a/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp b/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp index 96b6e75307..9ca86c3e95 100644 --- a/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp +++ b/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_multi_lucy_rx_kokkos.h b/src/KOKKOS/pair_multi_lucy_rx_kokkos.h index a6ef904417..c335ed526f 100644 --- a/src/KOKKOS/pair_multi_lucy_rx_kokkos.h +++ b/src/KOKKOS/pair_multi_lucy_rx_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_pace_kokkos.cpp b/src/KOKKOS/pair_pace_kokkos.cpp index 8cd62e5a14..dd5b97fe32 100644 --- a/src/KOKKOS/pair_pace_kokkos.cpp +++ b/src/KOKKOS/pair_pace_kokkos.cpp @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract aE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_pace_kokkos.h b/src/KOKKOS/pair_pace_kokkos.h index 6cab23b8dc..cc2a3cb674 100644 --- a/src/KOKKOS/pair_pace_kokkos.h +++ b/src/KOKKOS/pair_pace_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_reaxff_kokkos.cpp b/src/KOKKOS/pair_reaxff_kokkos.cpp index bb6ee0c1f1..0bfcef90cf 100644 --- a/src/KOKKOS/pair_reaxff_kokkos.cpp +++ b/src/KOKKOS/pair_reaxff_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -63,7 +63,7 @@ PairReaxFFKokkos::PairReaxFFKokkos(LAMMPS *lmp) : PairReaxFF(lmp) kokkosable = 1; atomKK = (AtomKokkos *) atom; execution_space = ExecutionSpaceFromDevice::space; - datamask_read = X_MASK | Q_MASK | F_MASK | TYPE_MASK | ENERGY_MASK | VIRIAL_MASK; + datamask_read = X_MASK | Q_MASK | F_MASK | TAG_MASK | TYPE_MASK | ENERGY_MASK | VIRIAL_MASK; datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK; k_resize_bo = DAT::tdual_int_scalar("pair:resize_bo"); @@ -3238,7 +3238,9 @@ void PairReaxFFKokkos::operator()(TagPairReaxComputeTorsionPreproces const F_FLOAT inv_sin_ijk_rnd = 1.0 / sin_ijk_rnd; const F_FLOAT inv_sin_jil_rnd = 1.0 / sin_jil_rnd; +#ifdef LMP_KOKKOS_GPU #pragma unroll +#endif for (int d = 0; d < 3; d++) { // dcos_omega_di F_FLOAT dcos_omega_dk = ((htra-arg*hnra) * inv_rik) * delik[d] - dellk[d]; diff --git a/src/KOKKOS/pair_reaxff_kokkos.h b/src/KOKKOS/pair_reaxff_kokkos.h index 836a2de731..5edf439641 100644 --- a/src/KOKKOS/pair_reaxff_kokkos.h +++ b/src/KOKKOS/pair_reaxff_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_snap_kokkos.cpp b/src/KOKKOS/pair_snap_kokkos.cpp index 954a086412..e227486d38 100644 --- a/src/KOKKOS/pair_snap_kokkos.cpp +++ b/src/KOKKOS/pair_snap_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_snap_kokkos.h b/src/KOKKOS/pair_snap_kokkos.h index 2937359822..fba95a679e 100644 --- a/src/KOKKOS/pair_snap_kokkos.h +++ b/src/KOKKOS/pair_snap_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index d36497964e..45bacb4c97 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_sw_kokkos.cpp b/src/KOKKOS/pair_sw_kokkos.cpp index a3d8d11380..679d022437 100644 --- a/src/KOKKOS/pair_sw_kokkos.cpp +++ b/src/KOKKOS/pair_sw_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_sw_kokkos.h b/src/KOKKOS/pair_sw_kokkos.h index 06e4341b68..80235d2844 100644 --- a/src/KOKKOS/pair_sw_kokkos.h +++ b/src/KOKKOS/pair_sw_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_table_kokkos.cpp b/src/KOKKOS/pair_table_kokkos.cpp index 59b2c0516f..b1514c8c6f 100644 --- a/src/KOKKOS/pair_table_kokkos.cpp +++ b/src/KOKKOS/pair_table_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_table_kokkos.h b/src/KOKKOS/pair_table_kokkos.h index ef34b83731..80226d3770 100644 --- a/src/KOKKOS/pair_table_kokkos.h +++ b/src/KOKKOS/pair_table_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_table_rx_kokkos.cpp b/src/KOKKOS/pair_table_rx_kokkos.cpp index 0d3f88d10d..b7a1f05ceb 100644 --- a/src/KOKKOS/pair_table_rx_kokkos.cpp +++ b/src/KOKKOS/pair_table_rx_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_table_rx_kokkos.h b/src/KOKKOS/pair_table_rx_kokkos.h index fb4c653841..5db19fa38a 100644 --- a/src/KOKKOS/pair_table_rx_kokkos.h +++ b/src/KOKKOS/pair_table_rx_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_tersoff_kokkos.cpp b/src/KOKKOS/pair_tersoff_kokkos.cpp index cde22ce63c..cae17102a8 100644 --- a/src/KOKKOS/pair_tersoff_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -70,7 +70,7 @@ PairTersoffKokkos::PairTersoffKokkos(LAMMPS *lmp) : PairTersoff(lmp) kokkosable = 1; atomKK = (AtomKokkos *) atom; execution_space = ExecutionSpaceFromDevice::space; - datamask_read = X_MASK | F_MASK | TYPE_MASK | ENERGY_MASK | VIRIAL_MASK; + datamask_read = X_MASK | F_MASK | TAG_MASK | TYPE_MASK | ENERGY_MASK | VIRIAL_MASK; datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK; } diff --git a/src/KOKKOS/pair_tersoff_kokkos.h b/src/KOKKOS/pair_tersoff_kokkos.h index 6679920bbe..522fdd4ee8 100644 --- a/src/KOKKOS/pair_tersoff_kokkos.h +++ b/src/KOKKOS/pair_tersoff_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp index 711bf41e2b..06ef0dcceb 100644 --- a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -60,7 +60,7 @@ PairTersoffMODKokkos::PairTersoffMODKokkos(LAMMPS *lmp) : PairTersof kokkosable = 1; atomKK = (AtomKokkos *) atom; execution_space = ExecutionSpaceFromDevice::space; - datamask_read = X_MASK | F_MASK | TYPE_MASK | ENERGY_MASK | VIRIAL_MASK; + datamask_read = X_MASK | F_MASK | TAG_MASK | TYPE_MASK | ENERGY_MASK | VIRIAL_MASK; datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK; } diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.h b/src/KOKKOS/pair_tersoff_mod_kokkos.h index 6bcbc66386..b5b573fb4d 100644 --- a/src/KOKKOS/pair_tersoff_mod_kokkos.h +++ b/src/KOKKOS/pair_tersoff_mod_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp index c628ee5ddf..accbe9a863 100644 --- a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -62,7 +62,7 @@ PairTersoffZBLKokkos::PairTersoffZBLKokkos(LAMMPS *lmp) : PairTersof kokkosable = 1; atomKK = (AtomKokkos *) atom; execution_space = ExecutionSpaceFromDevice::space; - datamask_read = X_MASK | F_MASK | TYPE_MASK | ENERGY_MASK | VIRIAL_MASK; + datamask_read = X_MASK | F_MASK | TAG_MASK | TYPE_MASK | ENERGY_MASK | VIRIAL_MASK; datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK; if (strcmp(update->unit_style,"metal") == 0) { diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.h b/src/KOKKOS/pair_tersoff_zbl_kokkos.h index 6cf7f8175a..862bae52fb 100644 --- a/src/KOKKOS/pair_tersoff_zbl_kokkos.h +++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_vashishta_kokkos.cpp b/src/KOKKOS/pair_vashishta_kokkos.cpp index 432cfbcf20..aa8cb550c7 100644 --- a/src/KOKKOS/pair_vashishta_kokkos.cpp +++ b/src/KOKKOS/pair_vashishta_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_vashishta_kokkos.h b/src/KOKKOS/pair_vashishta_kokkos.h index ec0e4e2e7e..4cd12b3e07 100644 --- a/src/KOKKOS/pair_vashishta_kokkos.h +++ b/src/KOKKOS/pair_vashishta_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_yukawa_kokkos.cpp b/src/KOKKOS/pair_yukawa_kokkos.cpp index 486c5598e5..7bdb9a9617 100644 --- a/src/KOKKOS/pair_yukawa_kokkos.cpp +++ b/src/KOKKOS/pair_yukawa_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -173,7 +173,6 @@ void PairYukawaKokkos::compute(int eflag_in, int vflag_in) c_x = atomKK->k_x.view(); f = atomKK->k_f.view(); type = atomKK->k_type.view(); - tag = atomKK->k_tag.view(); nlocal = atom->nlocal; nall = atom->nlocal + atom->nghost; newton_pair = force->newton_pair; diff --git a/src/KOKKOS/pair_yukawa_kokkos.h b/src/KOKKOS/pair_yukawa_kokkos.h index 481f4dabb2..e04f65264b 100644 --- a/src/KOKKOS/pair_yukawa_kokkos.h +++ b/src/KOKKOS/pair_yukawa_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -83,7 +83,6 @@ class PairYukawaKokkos : public PairYukawa { DAT::tdual_virial_array k_vatom; typename AT::t_efloat_1d d_eatom; typename AT::t_virial_array d_vatom; - typename AT::t_tagint_1d tag; int newton_pair; double special_lj[4]; diff --git a/src/KOKKOS/pair_zbl_kokkos.cpp b/src/KOKKOS/pair_zbl_kokkos.cpp index e881196e5e..4303687939 100644 --- a/src/KOKKOS/pair_zbl_kokkos.cpp +++ b/src/KOKKOS/pair_zbl_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pair_zbl_kokkos.h b/src/KOKKOS/pair_zbl_kokkos.h index 376ad8f600..bd33cdb5e0 100644 --- a/src/KOKKOS/pair_zbl_kokkos.h +++ b/src/KOKKOS/pair_zbl_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index ec32bebbcc..46146959a3 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,7 @@ #include "error.h" #include "fft3d_kokkos.h" #include "force.h" -#include "gridcomm_kokkos.h" +#include "grid3d_kokkos.h" #include "kokkos.h" #include "math_const.h" #include "math_special_kokkos.h" @@ -66,39 +66,9 @@ PPPMKokkos::PPPMKokkos(LAMMPS *lmp) : PPPM(lmp) datamask_read = X_MASK | F_MASK | TYPE_MASK | Q_MASK; datamask_modify = F_MASK; - pppmflag = 1; group_group_enable = 0; triclinic_support = 1; - nfactors = 3; - //factors = new int[nfactors]; - factors[0] = 2; - factors[1] = 3; - factors[2] = 5; - - MPI_Comm_rank(world,&me); - MPI_Comm_size(world,&nprocs); - - //density_brick = d_vdx_brick = d_vdy_brick = d_vdz_brick = nullptr; - //d_density_fft = nullptr; - //d_u_brick = nullptr; - //d_v0_brick = d_v1_brick = d_v2_brick = d_v3_brick = d_v4_brick = d_v5_brick = nullptr; - //greensfn = nullptr; - //d_work1 = d_work2 = nullptr; - //vg = nullptr; - //d_fkx = d_fky = d_fkz = nullptr; - - - //gf_b = nullptr; - //rho1d = rho_coeff = drho1d = drho_coeff = nullptr; - - fft1 = fft2 = nullptr; - remap = nullptr; - gc = nullptr; - - nmax = 0; - //part2grid = nullptr; - peratom_allocate_flag = 0; // define acons coefficients for estimation of kspace errors @@ -136,13 +106,24 @@ PPPMKokkos::PPPMKokkos(LAMMPS *lmp) : PPPM(lmp) acons(7,6) = 4887769399.0 / 37838389248.0; k_flag = DAT::tdual_int_scalar("PPPM:flag"); + + // same name but different than base class + + gc = nullptr; + fft1 = nullptr; + fft2 = nullptr; + remap = nullptr; } template void PPPMKokkos::settings(int narg, char **arg) { - if (narg < 1) error->all(FLERR,"Illegal kspace_style pppm/kk command"); + if (narg < 1) error->all(FLERR,"Illegal kspace_style {} command", force->kspace_style); + accuracy_relative = fabs(utils::numeric(FLERR,arg[0],false,lmp)); + if (accuracy_relative > 1.0) + error->all(FLERR, "Invalid relative accuracy {:g} for kspace_style {}", + accuracy_relative, force->kspace_style); } /* ---------------------------------------------------------------------- @@ -154,16 +135,11 @@ PPPMKokkos::~PPPMKokkos() { if (copymode) return; - //delete [] factors; deallocate(); if (peratom_allocate_flag) deallocate_peratom(); - //memory->destroy(part2grid); - //memory->destroy(acons); memoryKK->destroy_kokkos(k_eatom,eatom); memoryKK->destroy_kokkos(k_vatom,vatom); - eatom = nullptr; - vatom = nullptr; } /* ---------------------------------------------------------------------- @@ -173,10 +149,7 @@ PPPMKokkos::~PPPMKokkos() template void PPPMKokkos::init() { - if (me == 0) { - if (screen) fprintf(screen,"PPPM initialization ...\n"); - if (logfile) fprintf(logfile,"PPPM initialization ...\n"); - } + if (me == 0) utils::logmesg(lmp,"PPPM initialization ...\n"); // error check @@ -185,12 +158,12 @@ void PPPMKokkos::init() triclinic_check(); if (domain->triclinic && slabflag) - error->all(FLERR,"Cannot (yet) use PPPM with triclinic box and " - "slab correction"); - if (domain->dimension == 2) error->all(FLERR, - "Cannot use PPPM with 2d simulation"); + error->all(FLERR,"Cannot (yet) use PPPM with triclinic box and slab correction"); + if (domain->dimension == 2) + error->all(FLERR,"Cannot use PPPM with 2d simulation"); - if (!atomKK->q_flag) error->all(FLERR,"Kspace style requires atom attribute q"); + if (!atom->q_flag) + error->all(FLERR,"Kspace style requires atom attribute q"); if (slabflag == 0 && domain->nonperiodic > 0) error->all(FLERR,"Cannot use non-periodic boundaries with PPPM"); @@ -213,7 +186,7 @@ void PPPMKokkos::init() pair_check(); int itmp = 0; - double *p_cutoff = (double *) force->pair->extract("cut_coul",itmp); + auto p_cutoff = (double *) force->pair->extract("cut_coul",itmp); if (p_cutoff == nullptr) error->all(FLERR,"KSpace style is incompatible with Pair style"); cutoff = *p_cutoff; @@ -231,7 +204,7 @@ void PPPMKokkos::init() scale = 1.0; qqrd2e = force->qqrd2e; qsum_qsq(); - natoms_original = atomKK->natoms; + natoms_original = atom->natoms; // set accuracy (force units) from accuracy_relative or accuracy_absolute @@ -249,7 +222,6 @@ void PPPMKokkos::init() // or overlap is allowed, then done // else reduce order and try again - GridCommKokkos *gctmp = nullptr; int iteration = 0; while (order >= minorder) { @@ -261,23 +233,28 @@ void PPPMKokkos::init() set_grid_local(); if (overlap_allowed) break; - gctmp = new GridCommKokkos(lmp,world,nx_pppm,ny_pppm,nz_pppm, - nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, - nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out); + gc = new Grid3dKokkos(lmp,world,nx_pppm,ny_pppm,nz_pppm); + gc->set_distance(0.5*neighbor->skin + qdist); + gc->set_stencil_atom(-nlower,nupper); + gc->set_shift_atom(shiftatom_lo,shiftatom_hi); + gc->set_zfactor(slab_volfactor); + + gc->setup_grid(nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, + nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out); + int tmp1,tmp2; - gctmp->setup(tmp1,tmp2); - if (!gctmp->ghost_adjacent()) break; - delete gctmp; + gc->setup_comm(tmp1,tmp2); + if (gc->ghost_adjacent()) break; + delete gc; order--; iteration++; } if (order < minorder) error->all(FLERR,"PPPM order < minimum allowed order"); - if (!overlap_allowed && gctmp->ghost_adjacent()) - error->all(FLERR,"PPPM grid stencil extends " - "beyond nearest neighbor processor"); - if (gctmp) delete gctmp; + if (!overlap_allowed && !gc->ghost_adjacent()) + error->all(FLERR,"PPPM grid stencil extends beyond nearest neighbor processor"); + if (gc) delete gc; // adjust g_ewald @@ -287,6 +264,20 @@ void PPPMKokkos::init() double estimated_accuracy = final_accuracy(); + // allocate K-space dependent memory + // don't invoke allocate peratom() or group(), will be allocated when needed + + allocate(); + + // pre-compute Green's function denomiator expansion + // pre-compute 1d charge distribution coefficients + + compute_gf_denom(); + compute_rho_coeff(); + + k_rho_coeff.template modify(); + k_rho_coeff.template sync(); + // print stats int ngrid_max,nfft_both_max; @@ -306,21 +297,6 @@ void PPPMKokkos::init() ngrid_max,nfft_both_max); utils::logmesg(lmp,mesg); } - - // allocate K-space dependent memory - // don't invoke allocate peratom(), will be allocated when needed - - allocate(); - - // pre-compute Green's function denomiator expansion - // pre-compute 1d charge distribution coefficients - - compute_gf_denom(); - compute_rho_coeff(); - - k_rho_coeff.template modify(); - k_rho_coeff.template sync(); - } /* ---------------------------------------------------------------------- @@ -551,7 +527,7 @@ void PPPMKokkos::operator()(TagPPPM_setup_triclinic2, const int &n) ------------------------------------------------------------------------- */ template -void PPPMKokkos::setup_grid() +void PPPMKokkos::reset_grid() { // free all arrays previously allocated @@ -569,8 +545,7 @@ void PPPMKokkos::setup_grid() allocate(); if (!overlap_allowed && !gc->ghost_adjacent()) - error->all(FLERR,"PPPM grid stencil extends " - "beyond nearest neighbor processor"); + error->all(FLERR,"PPPM grid stencil extends beyond nearest neighbor processor"); // pre-compute Green's function denomiator expansion // pre-compute 1d charge distribution coefficients @@ -623,9 +598,9 @@ void PPPMKokkos::compute(int eflag, int vflag) // if atom count has changed, update qsum and qsqsum - if (atomKK->natoms != natoms_original) { + if (atom->natoms != natoms_original) { qsum_qsq(); - natoms_original = atomKK->natoms; + natoms_original = atom->natoms; } // return if there are no charges @@ -647,10 +622,8 @@ void PPPMKokkos::compute(int eflag, int vflag) // extend size of per-atom arrays if necessary - if (atomKK->nmax > nmax) { - //memory->destroy(part2grid); + if (atom->nmax > nmax) { nmax = atomKK->nmax; - //memory->create(part2grid,nmax,3,"pppm:part2grid"); d_part2grid = typename AT::t_int_1d_3("pppm:part2grid",nmax); d_rho1d = typename FFT_AT::t_FFT_SCALAR_2d_3("pppm:rho1d",nmax,order/2+order/2+1); } @@ -665,8 +638,8 @@ void PPPMKokkos::compute(int eflag, int vflag) // to fully sum contribution in their 3d bricks // remap from 3d decomposition to FFT decomposition - gc->reverse_comm_kspace(this,1,REVERSE_RHO, - k_gc_buf1,k_gc_buf2,MPI_FFT_SCALAR); + gc->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(FFT_SCALAR), + k_gc_buf1,k_gc_buf2,MPI_FFT_SCALAR); brick2fft(); // compute potential gradient on my FFT grid and @@ -679,14 +652,14 @@ void PPPMKokkos::compute(int eflag, int vflag) // all procs communicate E-field values // to fill ghost cells surrounding their 3d bricks - gc->forward_comm_kspace(this,3,FORWARD_IK, - k_gc_buf1,k_gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK,3,sizeof(FFT_SCALAR), + k_gc_buf1,k_gc_buf2,MPI_FFT_SCALAR); // extra per-atom energy/virial communication if (evflag_atom) - gc->forward_comm_kspace(this,7,FORWARD_IK_PERATOM, - k_gc_buf1,k_gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_PERATOM,7,sizeof(FFT_SCALAR), + k_gc_buf1,k_gc_buf2,MPI_FFT_SCALAR); // calculate the force on my particles @@ -721,18 +694,16 @@ void PPPMKokkos::compute(int eflag, int vflag) // per-atom energy/virial // energy includes self-energy correction - // notal accounts for TIP4P tallying d_eatom/vatom for ghost atoms + // ntotal accounts for TIP4P tallying eatom/vatom for ghost atoms if (evflag_atom) { int nlocal = atomKK->nlocal; int ntotal = nlocal; - //if (tip4pflag) ntotal += atomKK->nghost; if (eflag_atom) { copymode = 1; Kokkos::parallel_for(Kokkos::RangePolicy(0,nlocal),*this); copymode = 0; - //for (i = nlocal; i < ntotal; i++) d_eatom[i] *= 0.5*qscale; } if (vflag_atom) { @@ -748,7 +719,7 @@ void PPPMKokkos::compute(int eflag, int vflag) // convert atoms back from lamda to box coords - if (triclinic) domain->lamda2x(atomKK->nlocal); + if (triclinic) domain->lamda2x(atom->nlocal); if (eflag_atom) { k_eatom.template modify(); @@ -785,6 +756,46 @@ void PPPMKokkos::operator()(TagPPPM_self2, const int &i) const template void PPPMKokkos::allocate() { + // create ghost grid object for rho and electric field communication + // returns local owned and ghost grid bounds + // setup communication patterns and buffers + + gc = new Grid3dKokkos(lmp,world,nx_pppm,ny_pppm,nz_pppm); + gc->set_distance(0.5*neighbor->skin + qdist); + gc->set_stencil_atom(-nlower,nupper); + gc->set_shift_atom(shiftatom_lo,shiftatom_hi); + gc->set_zfactor(slab_volfactor); + + gc->setup_grid(nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, + nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out); + + gc->setup_comm(ngc_buf1,ngc_buf2); + + npergrid = 3; + + k_gc_buf1 = FFT_DAT::tdual_FFT_SCALAR_1d("pppm:gc_buf1",npergrid*ngc_buf1); + k_gc_buf2 = FFT_DAT::tdual_FFT_SCALAR_1d("pppm:gc_buf2",npergrid*ngc_buf2); + + // tally local grid sizes + // ngrid = count of owned+ghost grid cells on this proc + // nfft_brick = FFT points in 3d brick-decomposition on this proc + // same as count of owned grid cells + // nfft = FFT points in x-pencil FFT decomposition on this proc + // nfft_both = greater of nfft and nfft_brick + + ngrid = (nxhi_out-nxlo_out+1) * (nyhi_out-nylo_out+1) * + (nzhi_out-nzlo_out+1); + + nfft_brick = (nxhi_in-nxlo_in+1) * (nyhi_in-nylo_in+1) * + (nzhi_in-nzlo_in+1); + + nfft = (nxhi_fft-nxlo_fft+1) * (nyhi_fft-nylo_fft+1) * + (nzhi_fft-nzlo_fft+1); + + nfft_both = MAX(nfft,nfft_brick); + + // allocate distributed grid data + d_density_brick = typename FFT_AT::t_FFT_SCALAR_3d("pppm:density_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1); memoryKK->create_kokkos(k_density_fft,density_fft,nfft_both,"pppm:d_density_fft"); @@ -843,20 +854,6 @@ void PPPMKokkos::allocate() nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft, 1,0,0,FFT_PRECISION,collective_flag,gpu_aware_flag); - - // create ghost grid object for rho and electric field communication - // also create 2 bufs for ghost grid cell comm, passed to GridComm methods - - gc = new GridCommKokkos(lmp,world,nx_pppm,ny_pppm,nz_pppm, - nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, - nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out); - - gc->setup(ngc_buf1,ngc_buf2); - - npergrid = 3; - - k_gc_buf1 = FFT_DAT::tdual_FFT_SCALAR_1d("pppm:gc_buf1",npergrid*ngc_buf1); - k_gc_buf2 = FFT_DAT::tdual_FFT_SCALAR_1d("pppm:gc_buf2",npergrid*ngc_buf2); } /* ---------------------------------------------------------------------- @@ -866,23 +863,22 @@ void PPPMKokkos::allocate() template void PPPMKokkos::deallocate() { + delete gc; + gc = nullptr; + memory->destroy(gc_buf1); + memory->destroy(gc_buf2); + memoryKK->destroy_kokkos(d_density_fft,density_fft); - density_fft = nullptr; memoryKK->destroy_kokkos(d_greensfn,greensfn); - greensfn = nullptr; memoryKK->destroy_kokkos(d_work1,work1); - work1 = nullptr; memoryKK->destroy_kokkos(d_work2,work2); - work2 = nullptr; delete fft1; fft1 = nullptr; delete fft2; - fft2 = nullptr; + fft1 = nullptr; delete remap; remap = nullptr; - delete gc; - gc = nullptr; } /* ---------------------------------------------------------------------- @@ -905,7 +901,7 @@ void PPPMKokkos::allocate_peratom() // use same GC ghost grid object for peratom grid communication - // but need to reallocate a larger gc_buf1 and gc_buf2 + // but need to reallocate a larger gc_buf1 and gc_buf2 npergrid = 7; @@ -951,7 +947,7 @@ void PPPMKokkos::set_grid_global() if (accuracy <= 0.0) error->all(FLERR,"KSpace accuracy must be > 0"); if (q2 == 0.0) - error->all(FLERR,"Must use 'kspace_modify gewald' for uncharged system"); + error->all(FLERR,"Must use kspace_modify gewald for uncharged system"); g_ewald = accuracy*sqrt(natoms*cutoff*xprd*yprd*zprd) / (2.0*q2); if (g_ewald >= 1.0) g_ewald = (1.35 - 0.15*log(accuracy))/cutoff; else g_ewald = sqrt(-log(g_ewald)) / cutoff; @@ -1020,7 +1016,7 @@ void PPPMKokkos::set_grid_global() tmp[0] = nx_pppm; tmp[1] = ny_pppm; tmp[2] = nz_pppm; - KSpace::x2lamdaT(&tmp[0],&tmp[0]); + x2lamdaT(&tmp[0],&tmp[0]); h_x = 1.0/tmp[0]; h_y = 1.0/tmp[1]; h_z = 1.0/tmp[2]; @@ -1064,7 +1060,7 @@ double PPPMKokkos::compute_df_kspace() double yprd = domain->yprd; double zprd = domain->zprd; double zprd_slab = zprd*slab_volfactor; - bigint natoms = atomKK->natoms; + bigint natoms = atom->natoms; double df_kspace = 0.0; double lprx = estimate_ik_error(h_x,xprd,natoms); double lpry = estimate_ik_error(h_y,yprd,natoms); @@ -1104,10 +1100,7 @@ void PPPMKokkos::adjust_gewald() g_ewald -= dx; if (fabs(newton_raphson_f()) < SMALL) return; } - - char str[128]; - sprintf(str, "Could not compute g_ewald"); - error->all(FLERR, str); + error->all(FLERR, "Could not compute g_ewald"); } /* ---------------------------------------------------------------------- @@ -1120,7 +1113,7 @@ double PPPMKokkos::newton_raphson_f() double xprd = domain->xprd; double yprd = domain->yprd; double zprd = domain->zprd; - bigint natoms = atomKK->natoms; + bigint natoms = atom->natoms; double df_rspace = 2.0*q2*exp(-g_ewald*g_ewald*cutoff*cutoff) / sqrt(natoms*cutoff*xprd*yprd*zprd); @@ -1161,7 +1154,7 @@ double PPPMKokkos::final_accuracy() double xprd = domain->xprd; double yprd = domain->yprd; double zprd = domain->zprd; - bigint natoms = atomKK->natoms; + bigint natoms = atom->natoms; if (natoms == 0) natoms = 1; // avoid division by zero double df_kspace = compute_df_kspace(); @@ -1175,10 +1168,10 @@ double PPPMKokkos::final_accuracy() } /* ---------------------------------------------------------------------- - set local subset of PPPM/FFT grid that I own - n xyz lo/hi in = 3d brick that I own (inclusive) - n xyz lo/hi out = 3d brick + ghost cells in 6 directions (inclusive) - n xyz lo/hi fft = FFT columns that I own (all of x dim, 2d decomp in yz) + set params which determine which owned and ghost cells this proc owns + Grid3d uses these params to partition grid + also partition FFT grid + n xyz lo/hi fft = FFT columns that I own (all of x dim, 2d decomp in yz) ------------------------------------------------------------------------- */ template @@ -1470,8 +1463,6 @@ void PPPMKokkos::make_rho() { // clear 3d density array - //memset(&(density_brick(nzlo_out,nylo_out,nxlo_out)),0, - // ngrid*sizeof(FFT_SCALAR)); numz_out = nzhi_out-nzlo_out + 1; numy_out = nyhi_out-nylo_out + 1; numx_out = nxhi_out-nxlo_out + 1; @@ -1484,7 +1475,7 @@ void PPPMKokkos::make_rho() // loop over my charges, add their contribution to nearby grid points // (nx,ny,nz) = global coords of grid pt to "lower left" of charge // (dx,dy,dz) = distance to "lower left" grid pt - // (mx,my,mz) = global coords of moving stencil pt + // (mx,my,mz) = global indices of moving stencil pt nlocal = atomKK->nlocal; @@ -2929,7 +2920,7 @@ double PPPMKokkos::memory_usage() if (peratom_allocate_flag) bytes += (double)6 * nbrick * sizeof(FFT_SCALAR); - // two GridComm bufs + // two Grid3d bufs bytes += (double)(ngc_buf1 + ngc_buf2) * npergrid * sizeof(FFT_SCALAR); diff --git a/src/KOKKOS/pppm_kokkos.h b/src/KOKKOS/pppm_kokkos.h index 701fe5c4d3..1bdb03335e 100644 --- a/src/KOKKOS/pppm_kokkos.h +++ b/src/KOKKOS/pppm_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -23,7 +23,7 @@ KSpaceStyle(pppm/kk/host,PPPMKokkos); #ifndef LMP_PPPM_KOKKOS_H #define LMP_PPPM_KOKKOS_H -#include "gridcomm_kokkos.h" +#include "grid3d_kokkos.h" #include "remap_kokkos.h" #include "fft3d_kokkos.h" #include "kokkos_base_fft.h" @@ -124,7 +124,7 @@ class PPPMKokkos : public PPPM, public KokkosBaseFFT { ~PPPMKokkos() override; void init() override; void setup() override; - void setup_grid() override; + void reset_grid() override; void settings(int, char **) override; void compute(int, int) override; int timing_1d(int, double &) override; @@ -353,8 +353,6 @@ class PPPMKokkos : public PPPM, public KokkosBaseFFT { typename ArrayTypes::t_efloat_1d d_eatom; typename ArrayTypes::t_virial_array d_vatom; - int factors[3]; - typename FFT_AT::t_FFT_SCALAR_3d d_density_brick; typename FFT_AT::t_FFT_SCALAR_3d d_vdx_brick,d_vdy_brick,d_vdz_brick; typename FFT_AT::t_FFT_SCALAR_3d d_u_brick; @@ -387,7 +385,7 @@ class PPPMKokkos : public PPPM, public KokkosBaseFFT { FFT3dKokkos *fft1,*fft2; RemapKokkos *remap; - GridCommKokkos *gc; + Grid3dKokkos *gc; FFT_DAT::tdual_FFT_SCALAR_1d k_gc_buf1,k_gc_buf2; int ngc_buf1,ngc_buf2,npergrid; diff --git a/src/KOKKOS/rand_pool_wrap_kokkos.cpp b/src/KOKKOS/rand_pool_wrap_kokkos.cpp index aead3788ec..efdd932987 100644 --- a/src/KOKKOS/rand_pool_wrap_kokkos.cpp +++ b/src/KOKKOS/rand_pool_wrap_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/rand_pool_wrap_kokkos.h b/src/KOKKOS/rand_pool_wrap_kokkos.h index 8d3275370e..f79a6a1caa 100644 --- a/src/KOKKOS/rand_pool_wrap_kokkos.h +++ b/src/KOKKOS/rand_pool_wrap_kokkos.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/region_block_kokkos.cpp b/src/KOKKOS/region_block_kokkos.cpp index fd76fa94b6..cfee46e916 100644 --- a/src/KOKKOS/region_block_kokkos.cpp +++ b/src/KOKKOS/region_block_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/region_block_kokkos.h b/src/KOKKOS/region_block_kokkos.h index 06335c8f8e..017e4e5ee4 100644 --- a/src/KOKKOS/region_block_kokkos.h +++ b/src/KOKKOS/region_block_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/remap_kokkos.cpp b/src/KOKKOS/remap_kokkos.cpp index f3bd241b41..efc6742a25 100644 --- a/src/KOKKOS/remap_kokkos.cpp +++ b/src/KOKKOS/remap_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/remap_kokkos.h b/src/KOKKOS/remap_kokkos.h index a2d3e274b6..a62c14f00b 100644 --- a/src/KOKKOS/remap_kokkos.h +++ b/src/KOKKOS/remap_kokkos.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/sna_kokkos.h b/src/KOKKOS/sna_kokkos.h index 2efd9133ac..78a3dfa669 100644 --- a/src/KOKKOS/sna_kokkos.h +++ b/src/KOKKOS/sna_kokkos.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/sna_kokkos_impl.h b/src/KOKKOS/sna_kokkos_impl.h index 2769d132cb..fd58f1c4f3 100644 --- a/src/KOKKOS/sna_kokkos_impl.h +++ b/src/KOKKOS/sna_kokkos_impl.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/third_order_kokkos.cpp b/src/KOKKOS/third_order_kokkos.cpp index 5216b7910c..933b3f66b9 100644 --- a/src/KOKKOS/third_order_kokkos.cpp +++ b/src/KOKKOS/third_order_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/third_order_kokkos.h b/src/KOKKOS/third_order_kokkos.h index 5cdf39efd0..c3b001d495 100644 --- a/src/KOKKOS/third_order_kokkos.h +++ b/src/KOKKOS/third_order_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/transpose_helper_kokkos.h b/src/KOKKOS/transpose_helper_kokkos.h index 676b6da530..3b84873b6b 100644 --- a/src/KOKKOS/transpose_helper_kokkos.h +++ b/src/KOKKOS/transpose_helper_kokkos.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp index 573a6118b9..e3fc6fe925 100644 --- a/src/KOKKOS/verlet_kokkos.cpp +++ b/src/KOKKOS/verlet_kokkos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KOKKOS/verlet_kokkos.h b/src/KOKKOS/verlet_kokkos.h index a45de20f7f..067df54f4f 100644 --- a/src/KOKKOS/verlet_kokkos.h +++ b/src/KOKKOS/verlet_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/ewald.cpp b/src/KSPACE/ewald.cpp index 2dba85d6a6..b61a1d36c6 100644 --- a/src/KSPACE/ewald.cpp +++ b/src/KSPACE/ewald.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -66,11 +66,16 @@ Ewald::Ewald(LAMMPS *lmp) : KSpace(lmp), kcount = 0; } +/* ---------------------------------------------------------------------- */ + void Ewald::settings(int narg, char **arg) { - if (narg != 1) error->all(FLERR,"Illegal kspace_style ewald command"); + if (narg != 1) error->all(FLERR,"Illegal kspace_style {} command", force->kspace_style); accuracy_relative = fabs(utils::numeric(FLERR,arg[0],false,lmp)); + if (accuracy_relative > 1.0) + error->all(FLERR, "Invalid relative accuracy {:g} for kspace_style {}", + accuracy_relative, force->kspace_style); } /* ---------------------------------------------------------------------- diff --git a/src/KSPACE/ewald.h b/src/KSPACE/ewald.h index 59da5a742c..fa69df74af 100644 --- a/src/KSPACE/ewald.h +++ b/src/KSPACE/ewald.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/ewald_const.h b/src/KSPACE/ewald_const.h index 3562b93644..f529fb911a 100644 --- a/src/KSPACE/ewald_const.h +++ b/src/KSPACE/ewald_const.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/ewald_dipole.cpp b/src/KSPACE/ewald_dipole.cpp index 2aeacd3609..7a3a1da8ff 100644 --- a/src/KSPACE/ewald_dipole.cpp +++ b/src/KSPACE/ewald_dipole.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/ewald_dipole.h b/src/KSPACE/ewald_dipole.h index a65aca2095..b3d22ee4b4 100644 --- a/src/KSPACE/ewald_dipole.h +++ b/src/KSPACE/ewald_dipole.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/ewald_dipole_spin.cpp b/src/KSPACE/ewald_dipole_spin.cpp index cd5f2209c9..c679e164f7 100644 --- a/src/KSPACE/ewald_dipole_spin.cpp +++ b/src/KSPACE/ewald_dipole_spin.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/ewald_dipole_spin.h b/src/KSPACE/ewald_dipole_spin.h index c6c2063650..b5f97b4af4 100644 --- a/src/KSPACE/ewald_dipole_spin.h +++ b/src/KSPACE/ewald_dipole_spin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/ewald_disp.cpp b/src/KSPACE/ewald_disp.cpp index 1374905a26..c075360061 100644 --- a/src/KSPACE/ewald_disp.cpp +++ b/src/KSPACE/ewald_disp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -111,13 +111,17 @@ EwaldDisp::EwaldDisp(LAMMPS *lmp) : KSpace(lmp), M2 = 0; } +/* ---------------------------------------------------------------------- */ + void EwaldDisp::settings(int narg, char **arg) { - if (narg!=1) error->all(FLERR,"Illegal kspace_style ewald/n command"); + if (narg!=1) error->all(FLERR,"Illegal kspace_style {} command", force->kspace_style); accuracy_relative = fabs(utils::numeric(FLERR,arg[0],false,lmp)); + if (accuracy_relative > 1.0) + error->all(FLERR, "Invalid relative accuracy {:g} for kspace_style {}", + accuracy_relative, force->kspace_style); } - /* ---------------------------------------------------------------------- */ EwaldDisp::~EwaldDisp() @@ -1209,7 +1213,7 @@ void EwaldDisp::compute_virial_dipole() double *ke, c[EWALD_NFUNCS] = { 8.0*MY_PI*qscale/volume, 2.0*MY_PI*MY_PIS/(12.0*volume), 2.0*MY_PI*MY_PIS/(192.0*volume), 8.0*MY_PI*mumurd2e/volume}; - int i, kx, ky, lbytes = (2*nbox+1)*sizeof(cvector), *type = atom->type; + int i, kx, ky, lbytes = (2*nbox+1)*sizeof(cvector); int func[EWALD_NFUNCS]; memcpy(func, function, EWALD_NFUNCS*sizeof(int)); @@ -1273,7 +1277,6 @@ void EwaldDisp::compute_virial_dipole() vatomj[n] -= mysum[n]; z = (cvector *) ((char *) z+lbytes); - ++type; if (vflag_atom) vatomj += 6; } diff --git a/src/KSPACE/ewald_disp.h b/src/KSPACE/ewald_disp.h index 05017e1c76..3c8cc59005 100644 --- a/src/KSPACE/ewald_disp.h +++ b/src/KSPACE/ewald_disp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/fft3d.cpp b/src/KSPACE/fft3d.cpp index 7a338eddd4..a9956f4397 100644 --- a/src/KSPACE/fft3d.cpp +++ b/src/KSPACE/fft3d.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/fft3d.h b/src/KSPACE/fft3d.h index 3d15be9e2b..f4ddeebc4d 100644 --- a/src/KSPACE/fft3d.h +++ b/src/KSPACE/fft3d.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/fft3d_wrap.cpp b/src/KSPACE/fft3d_wrap.cpp index 56a59755a1..478cf6fc9d 100644 --- a/src/KSPACE/fft3d_wrap.cpp +++ b/src/KSPACE/fft3d_wrap.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/fft3d_wrap.h b/src/KSPACE/fft3d_wrap.h index 708d6354d2..f72cfd4622 100644 --- a/src/KSPACE/fft3d_wrap.h +++ b/src/KSPACE/fft3d_wrap.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/fix_tune_kspace.cpp b/src/KSPACE/fix_tune_kspace.cpp index 34fe89c651..7b68deeeb9 100644 --- a/src/KSPACE/fix_tune_kspace.cpp +++ b/src/KSPACE/fix_tune_kspace.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -278,9 +278,13 @@ void FixTuneKspace::update_kspace_style(const std::string &new_kspace_style, force->init(); // set up grid - force->kspace->setup_grid(); - // Re-init neighbor list. Probably only needed when redefining the pair style. Should happen after pair->init() to get pair style neighbor list request registered + force->kspace->reset_grid(); + + // re-init neighbor list + // probably only needed when redefining the pair style + // should happen after pair->init() to get pair style + // neighbor list request registered neighbor->init(); diff --git a/src/KSPACE/fix_tune_kspace.h b/src/KSPACE/fix_tune_kspace.h index 5bfacbac91..75ac318226 100644 --- a/src/KSPACE/fix_tune_kspace.h +++ b/src/KSPACE/fix_tune_kspace.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/kissfft.h b/src/KSPACE/kissfft.h index cfc672902e..89906076c1 100644 --- a/src/KSPACE/kissfft.h +++ b/src/KSPACE/kissfft.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ diff --git a/src/KSPACE/msm.cpp b/src/KSPACE/msm.cpp index b518d8efe1..d9c328fbfc 100644 --- a/src/KSPACE/msm.cpp +++ b/src/KSPACE/msm.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -23,8 +23,9 @@ #include "domain.h" #include "error.h" #include "force.h" -#include "gridcomm.h" +#include "grid3d.h" #include "math_const.h" +#include "math_extra.h" #include "memory.h" #include "neighbor.h" #include "pair.h" @@ -80,8 +81,12 @@ MSM::MSM(LAMMPS *lmp) void MSM::settings(int narg, char **arg) { - if (narg < 1) error->all(FLERR,"Illegal kspace_style msm command"); + if (narg < 1) error->all(FLERR,"Illegal kspace_style {} command", force->kspace_style); + accuracy_relative = fabs(utils::numeric(FLERR,arg[0],false,lmp)); + if (accuracy_relative > 1.0) + error->all(FLERR, "Invalid relative accuracy {:g} for kspace_style {}", + accuracy_relative, force->kspace_style); } /* ---------------------------------------------------------------------- @@ -124,9 +129,8 @@ void MSM::init() triclinic_check(); if (domain->dimension == 2) error->all(FLERR,"Cannot (yet) use MSM with 2d simulation"); - if (comm->style != 0) - error->universe_all(FLERR,"MSM can only currently be used with " - "comm_style brick"); + if (comm->style != Comm::BRICK) + error->universe_all(FLERR,"MSM can only currently be used with comm_style brick"); if (!atom->q_flag) error->all(FLERR,"Kspace style requires atom attribute q"); @@ -326,7 +330,7 @@ void MSM::setup() if (triclinic) { double tmp[3]; - kspacebbox(a,&tmp[0]); + MathExtra::tribbox(domain->h,a,&tmp[0]); ax = tmp[0]; ay = tmp[1]; az = tmp[2]; @@ -444,8 +448,8 @@ void MSM::compute(int eflag, int vflag) // to fully sum contribution in their 3d grid current_level = 0; - gcall->reverse_comm(GridComm::KSPACE,this,1,sizeof(double), - REVERSE_RHO,gcall_buf1,gcall_buf2,MPI_DOUBLE); + gcall->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(double), + gcall_buf1,gcall_buf2,MPI_DOUBLE); // forward communicate charge density values to fill ghost grid points // compute direct sum interaction and then restrict to coarser grid @@ -453,8 +457,8 @@ void MSM::compute(int eflag, int vflag) for (int n=0; n<=levels-2; n++) { if (!active_flag[n]) continue; current_level = n; - gc[n]->forward_comm(GridComm::KSPACE,this,1,sizeof(double), - FORWARD_RHO,gc_buf1[n],gc_buf2[n],MPI_DOUBLE); + gc[n]->forward_comm(Grid3d::KSPACE,this,FORWARD_RHO,1,sizeof(double), + gc_buf1[n],gc_buf2[n],MPI_DOUBLE); direct(n); restriction(n); } @@ -466,16 +470,16 @@ void MSM::compute(int eflag, int vflag) if (domain->nonperiodic) { current_level = levels-1; gc[levels-1]-> - forward_comm(GridComm::KSPACE,this,1,sizeof(double), - FORWARD_RHO,gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE); + forward_comm(Grid3d::KSPACE,this,FORWARD_RHO,1,sizeof(double), + gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE); direct_top(levels-1); gc[levels-1]-> - reverse_comm(GridComm::KSPACE,this,1,sizeof(double), - REVERSE_AD,gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE); + reverse_comm(Grid3d::KSPACE,this,REVERSE_AD,1,sizeof(double), + gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE); if (vflag_atom) gc[levels-1]-> - reverse_comm(GridComm::KSPACE,this,6,sizeof(double), - REVERSE_AD_PERATOM,gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE); + reverse_comm(Grid3d::KSPACE,this,REVERSE_AD_PERATOM,6,sizeof(double), + gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE); } else { // Here using MPI_Allreduce is cheaper than using commgrid @@ -485,8 +489,8 @@ void MSM::compute(int eflag, int vflag) current_level = levels-1; if (vflag_atom) gc[levels-1]-> - reverse_comm(GridComm::KSPACE,this,6,sizeof(double), - REVERSE_AD_PERATOM,gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE); + reverse_comm(Grid3d::KSPACE,this,REVERSE_AD_PERATOM,6,sizeof(double), + gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE); } } @@ -498,28 +502,28 @@ void MSM::compute(int eflag, int vflag) prolongation(n); current_level = n; - gc[n]->reverse_comm(GridComm::KSPACE,this,1,sizeof(double), - REVERSE_AD,gc_buf1[n],gc_buf2[n],MPI_DOUBLE); + gc[n]->reverse_comm(Grid3d::KSPACE,this,REVERSE_AD,1,sizeof(double), + gc_buf1[n],gc_buf2[n],MPI_DOUBLE); // extra per-atom virial communication if (vflag_atom) - gc[n]->reverse_comm(GridComm::KSPACE,this,6,sizeof(double), - REVERSE_AD_PERATOM,gc_buf1[n],gc_buf2[n],MPI_DOUBLE); + gc[n]->reverse_comm(Grid3d::KSPACE,this,REVERSE_AD_PERATOM,6,sizeof(double), + gc_buf1[n],gc_buf2[n],MPI_DOUBLE); } // all procs communicate E-field values // to fill ghost cells surrounding their 3d bricks current_level = 0; - gcall->forward_comm(GridComm::KSPACE,this,1,sizeof(double), - FORWARD_AD,gcall_buf1,gcall_buf2,MPI_DOUBLE); + gcall->forward_comm(Grid3d::KSPACE,this,FORWARD_AD,1,sizeof(double), + gcall_buf1,gcall_buf2,MPI_DOUBLE); // extra per-atom energy/virial communication if (vflag_atom) - gcall->forward_comm(GridComm::KSPACE,this,6,sizeof(double), - FORWARD_AD_PERATOM,gcall_buf1,gcall_buf2,MPI_DOUBLE); + gcall->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_PERATOM,6,sizeof(double), + gcall_buf1,gcall_buf2,MPI_DOUBLE); // calculate the force on my particles (interpolation) @@ -593,17 +597,19 @@ void MSM::allocate() memory->create2d_offset(phi1d,3,-order,order,"msm:phi1d"); memory->create2d_offset(dphi1d,3,-order,order,"msm:dphi1d"); - // commgrid using all processors for finest grid level + // one Grid3d for finest grid level, using world comm and all procs + // use set_caller_grid() b/c MSM allocates local grid > out_all values - gcall = new GridComm(lmp,world,1,nx_msm[0],ny_msm[0],nz_msm[0], - nxlo_in[0],nxhi_in[0],nylo_in[0], - nyhi_in[0],nzlo_in[0],nzhi_in[0], - nxlo_out_all,nxhi_out_all,nylo_out_all, - nyhi_out_all,nzlo_out_all,nzhi_out_all, - nxlo_out[0],nxhi_out[0],nylo_out[0], - nyhi_out[0],nzlo_out[0],nzhi_out[0]); + gcall = new Grid3d(lmp,world,nx_msm[0],ny_msm[0],nz_msm[0], + nxlo_in[0],nxhi_in[0],nylo_in[0], + nyhi_in[0],nzlo_in[0],nzhi_in[0], + nxlo_out_all,nxhi_out_all,nylo_out_all, + nyhi_out_all,nzlo_out_all,nzhi_out_all); - gcall->setup(ngcall_buf1,ngcall_buf2); + gcall->set_caller_grid(nxlo_out[0],nxhi_out[0],nylo_out[0], + nyhi_out[0],nzlo_out[0],nzhi_out[0]); + + gcall->setup_comm(ngcall_buf1,ngcall_buf2); npergrid = 1; memory->destroy(gcall_buf1); memory->destroy(gcall_buf2); @@ -612,7 +618,7 @@ void MSM::allocate() // allocate memory for each grid level - for (int n=0; ndestroy3d_offset(qgrid[n],nzlo_out[n],nylo_out[n],nxlo_out[n]); memory->create3d_offset(qgrid[n],nzlo_out[n],nzhi_out[n], nylo_out[n],nyhi_out[n],nxlo_out[n],nxhi_out[n],"msm:qgrid"); @@ -621,26 +627,27 @@ void MSM::allocate() memory->create3d_offset(egrid[n],nzlo_out[n],nzhi_out[n], nylo_out[n],nyhi_out[n],nxlo_out[n],nxhi_out[n],"msm:egrid"); - // create commgrid object for rho and electric field communication + // one Grid3d per level, using level-specific comm for coarser grids + // use set_proc_neigh() b/c MSM excludes non-participating procs from owned/ghost comm if (active_flag[n]) { delete gc[n]; + + gc[n] = new Grid3d(lmp,world_levels[n],nx_msm[n],ny_msm[n],nz_msm[n], + nxlo_in[n],nxhi_in[n],nylo_in[n],nyhi_in[n],nzlo_in[n],nzhi_in[n], + nxlo_out[n],nxhi_out[n],nylo_out[n],nyhi_out[n],nzlo_out[n],nzhi_out[n]); + int **procneigh = procneigh_levels[n]; + gc[n]->set_proc_neighs(procneigh[0][0],procneigh[0][1],procneigh[1][0], + procneigh[1][1],procneigh[2][0],procneigh[2][1]); - gc[n] = new GridComm(lmp,world_levels[n],2,nx_msm[n],ny_msm[n],nz_msm[n], - nxlo_in[n],nxhi_in[n],nylo_in[n],nyhi_in[n], - nzlo_in[n],nzhi_in[n], - nxlo_out[n],nxhi_out[n],nylo_out[n],nyhi_out[n], - nzlo_out[n],nzhi_out[n], - procneigh[0][0],procneigh[0][1],procneigh[1][0], - procneigh[1][1],procneigh[2][0],procneigh[2][1]); - - gc[n]->setup(ngc_buf1[n],ngc_buf2[n]); + gc[n]->setup_comm(ngc_buf1[n],ngc_buf2[n]); npergrid = 1; memory->destroy(gc_buf1[n]); memory->destroy(gc_buf2[n]); memory->create(gc_buf1[n],npergrid*ngc_buf1[n],"msm:gc_buf1"); memory->create(gc_buf2[n],npergrid*ngc_buf2[n],"msm:gc_buf2"); + } else { delete gc[n]; memory->destroy(gc_buf1[n]); @@ -743,7 +750,7 @@ void MSM::allocate_levels() { ngrid = new int[levels]; - gc = new GridComm*[levels]; + gc = new Grid3d*[levels]; gc_buf1 = new double*[levels]; gc_buf2 = new double*[levels]; ngc_buf1 = new int[levels]; @@ -1159,19 +1166,25 @@ void MSM::set_grid_local() { // loop over grid levels - for (int n=0; ndestroy3d_offset(qgrid[n],nzlo_out[n],nylo_out[n],nxlo_out[n]); memory->destroy3d_offset(egrid[n],nzlo_out[n],nylo_out[n],nxlo_out[n]); - // partition global grid across procs - // n xyz lo/hi in[] = lower/upper bounds of global grid this proc owns - // indices range from 0 to N-1 inclusive in each dim + // use Grid3d to partition each grid into owned cells on each proc + // assignment of ghost cells is done below + // Grid3d is called later in allocate() with owned+ghost bounds - comm->partition_grid(nx_msm[n],ny_msm[n],nz_msm[n],0.0, - nxlo_in[n],nxhi_in[n],nylo_in[n],nyhi_in[n], - nzlo_in[n],nzhi_in[n]); + gcall = new Grid3d(lmp,world,nx_msm[n],ny_msm[n],nz_msm[n]); + gcall->setup_grid(nxlo_in[n],nxhi_in[n],nylo_in[n], + nyhi_in[n],nzlo_in[n],nzhi_in[n], + nxlo_out[n],nxhi_out[n],nylo_out[n], + nyhi_out[n],nzlo_out[n],nzhi_out[n]); + delete gcall; + + // nlower/nupper = stencil size for mapping particles to grid nlower = -(order-1)/2; nupper = order/2; @@ -1194,22 +1207,22 @@ void MSM::set_grid_local() double yprd = prd[1]; double zprd = prd[2]; - // shift values for particle <-> grid mapping - // add/subtract OFFSET to avoid int(-0.75) = 0 when want it to be -1 - // nlo_out,nhi_out = lower/upper limits of the 3d sub-brick of // global MSM grid that my particles can contribute charge to + // add/subtract OFFSET to avoid int(-0.75) = 0 when want it to be -1 // effectively nlo_in,nhi_in + ghost cells // nlo,nhi = global coords of grid pt to "lower left" of smallest/largest // position a particle in my box can be at // dist[3] = particle position bound = subbox + skin/2.0 // nlo_out,nhi_out = nlo,nhi + stencil size for particle mapping + // for n = 0, use a smaller ghost region for interpolation + // for n > 0, larger ghost region needed for direct sum and restriction/prolongation double dist[3]; double cuthalf = 0.0; - if (n == 0) cuthalf = 0.5*neighbor->skin; // only applies to finest grid + if (n == 0) cuthalf = 0.5*neighbor->skin; // only applies to finest grid dist[0] = dist[1] = dist[2] = cuthalf; - if (triclinic) kspacebbox(cuthalf,&dist[0]); + if (triclinic) MathExtra::tribbox(domain->h,cuthalf,&dist[0]); int nlo,nhi; @@ -1217,12 +1230,12 @@ void MSM::set_grid_local() nx_msm[n]/xprd + OFFSET) - OFFSET; nhi = static_cast ((subhi[0]+dist[0]-boxlo[0]) * nx_msm[n]/xprd + OFFSET) - OFFSET; + if (n == 0) { - // use a smaller ghost region for interpolation nxlo_out_all = nlo + nlower; nxhi_out_all = nhi + nupper; } - // a larger ghost region is needed for the direct sum and for restriction/prolongation + nxlo_out[n] = nlo + MIN(-order,nxlo_direct); nxhi_out[n] = nhi + MAX(order,nxhi_direct); @@ -1234,6 +1247,7 @@ void MSM::set_grid_local() nylo_out_all = nlo + nlower; nyhi_out_all = nhi + nupper; } + nylo_out[n] = nlo + MIN(-order,nylo_direct); nyhi_out[n] = nhi + MAX(order,nyhi_direct); @@ -1245,8 +1259,10 @@ void MSM::set_grid_local() nzlo_out_all = nlo + nlower; nzhi_out_all = nhi + nupper; } - // a hemisphere is used for direct sum interactions, - // so no ghosting is needed for direct sum in the -z direction + + // hemisphere is used for direct sum interactions + // so no ghosting is needed for direct sum in the -z direction + nzlo_out[n] = nlo - order; nzhi_out[n] = nhi + MAX(order,nzhi_direct); @@ -1254,7 +1270,6 @@ void MSM::set_grid_local() // skip reset of lo/hi for procs who do not own any grid cells if (domain->nonperiodic) { - if (!domain->xperiodic && nxlo_in[n] <= nxhi_in[n]) { if (nxlo_in[n] == 0) nxlo_in[n] = alpha[n]; nxlo_out[n] = MAX(nxlo_out[n],alpha[n]); @@ -1379,7 +1394,7 @@ void MSM::set_proc_grid(int n) called by fix balance b/c it changed sizes of processor sub-domains ------------------------------------------------------------------------- */ -void MSM::setup_grid() +void MSM::reset_grid() { // free all arrays previously allocated // pre-compute volume-dependent coeffs @@ -3394,7 +3409,7 @@ double MSM::memory_usage() // NOTE: Stan, fill in other memory allocations here - // all GridComm bufs + // all Grid3d bufs bytes += (double)(ngcall_buf1 + ngcall_buf2) * npergrid * sizeof(double); diff --git a/src/KSPACE/msm.h b/src/KSPACE/msm.h index c39988b13b..bf41710a31 100644 --- a/src/KSPACE/msm.h +++ b/src/KSPACE/msm.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -81,8 +81,8 @@ class MSM : public KSpace { int myloc[3]; // which proc I am in each dim int ***procneigh_levels; // my 6 neighboring procs, 0/1 = left/right - class GridComm *gcall; // GridComm class for finest level grid - class GridComm **gc; // GridComm classes for each hierarchical level + class Grid3d *gcall; // GridComm class for finest level grid + class Grid3d **gc; // GridComm classes for each hierarchical level double *gcall_buf1, *gcall_buf2; double **gc_buf1, **gc_buf2; @@ -100,7 +100,7 @@ class MSM : public KSpace { void set_grid_global(); void set_proc_grid(int); void set_grid_local(); - void setup_grid() override; + void reset_grid() override; double estimate_1d_error(double, double); double estimate_3d_error(); double estimate_total_error(); diff --git a/src/KSPACE/msm_cg.cpp b/src/KSPACE/msm_cg.cpp index 3073e9c9dc..4a8daedf10 100644 --- a/src/KSPACE/msm_cg.cpp +++ b/src/KSPACE/msm_cg.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -19,7 +19,7 @@ #include "msm_cg.h" #include "atom.h" -#include "gridcomm.h" +#include "grid3d.h" #include "domain.h" #include "error.h" #include "force.h" @@ -52,7 +52,7 @@ MSMCG::MSMCG(LAMMPS *lmp) : MSM(lmp), void MSMCG::settings(int narg, char **arg) { if ((narg < 1) || (narg > 2)) - error->all(FLERR,"Illegal kspace_style msm/cg command"); + error->all(FLERR,"Illegal kspace_style {} command", force->kspace_style); // first argument is processed in parent class @@ -160,8 +160,8 @@ void MSMCG::compute(int eflag, int vflag) // to fully sum contribution in their 3d grid current_level = 0; - gcall->reverse_comm(GridComm::KSPACE,this,1,sizeof(double), - REVERSE_RHO,gcall_buf1,gcall_buf2,MPI_DOUBLE); + gcall->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(double), + gcall_buf1,gcall_buf2,MPI_DOUBLE); // forward communicate charge density values to fill ghost grid points // compute direct sum interaction and then restrict to coarser grid @@ -169,8 +169,8 @@ void MSMCG::compute(int eflag, int vflag) for (n=0; n<=levels-2; n++) { if (!active_flag[n]) continue; current_level = n; - gc[n]->forward_comm(GridComm::KSPACE,this,1,sizeof(double), - FORWARD_RHO,gc_buf1[n],gc_buf2[n],MPI_DOUBLE); + gc[n]->forward_comm(Grid3d::KSPACE,this,FORWARD_RHO,1,sizeof(double), + gc_buf1[n],gc_buf2[n],MPI_DOUBLE); direct(n); restriction(n); } @@ -182,16 +182,16 @@ void MSMCG::compute(int eflag, int vflag) if (domain->nonperiodic) { current_level = levels-1; gc[levels-1]-> - forward_comm(GridComm::KSPACE,this,1,sizeof(double), - FORWARD_RHO,gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE); + forward_comm(Grid3d::KSPACE,this,FORWARD_RHO,1,sizeof(double), + gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE); direct_top(levels-1); gc[levels-1]-> - reverse_comm(GridComm::KSPACE,this,1,sizeof(double), - REVERSE_AD,gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE); + reverse_comm(Grid3d::KSPACE,this,REVERSE_AD,1,sizeof(double), + gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE); if (vflag_atom) gc[levels-1]-> - reverse_comm(GridComm::KSPACE,this,6,sizeof(double), - REVERSE_AD_PERATOM,gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE); + reverse_comm(Grid3d::KSPACE,this,REVERSE_AD_PERATOM,6,sizeof(double), + gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE); } else { // Here using MPI_Allreduce is cheaper than using commgrid @@ -201,8 +201,8 @@ void MSMCG::compute(int eflag, int vflag) current_level = levels-1; if (vflag_atom) gc[levels-1]-> - reverse_comm(GridComm::KSPACE,this,6,sizeof(double), - REVERSE_AD_PERATOM,gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE); + reverse_comm(Grid3d::KSPACE,this,REVERSE_AD_PERATOM,6,sizeof(double), + gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE); } } @@ -214,28 +214,28 @@ void MSMCG::compute(int eflag, int vflag) prolongation(n); current_level = n; - gc[n]->reverse_comm(GridComm::KSPACE,this,1,sizeof(double), - REVERSE_AD,gc_buf1[n],gc_buf2[n],MPI_DOUBLE); + gc[n]->reverse_comm(Grid3d::KSPACE,this,REVERSE_AD,1,sizeof(double), + gc_buf1[n],gc_buf2[n],MPI_DOUBLE); // extra per-atom virial communication if (vflag_atom) - gc[n]->reverse_comm(GridComm::KSPACE,this,6,sizeof(double), - REVERSE_AD_PERATOM,gc_buf1[n],gc_buf2[n],MPI_DOUBLE); + gc[n]->reverse_comm(Grid3d::KSPACE,this,REVERSE_AD_PERATOM,6,sizeof(double), + gc_buf1[n],gc_buf2[n],MPI_DOUBLE); } // all procs communicate E-field values // to fill ghost cells surrounding their 3d bricks current_level = 0; - gcall->forward_comm(GridComm::KSPACE,this,1,sizeof(double), - FORWARD_AD,gcall_buf1,gcall_buf2,MPI_DOUBLE); + gcall->forward_comm(Grid3d::KSPACE,this,FORWARD_AD,1,sizeof(double), + gcall_buf1,gcall_buf2,MPI_DOUBLE); // extra per-atom energy/virial communication if (vflag_atom) - gcall->forward_comm(GridComm::KSPACE,this,6,sizeof(double), - FORWARD_AD_PERATOM,gcall_buf1,gcall_buf2,MPI_DOUBLE); + gcall->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_PERATOM,6,sizeof(double), + gcall_buf1,gcall_buf2,MPI_DOUBLE); // calculate the force on my particles (interpolation) diff --git a/src/KSPACE/msm_cg.h b/src/KSPACE/msm_cg.h index ad5c4f2a67..b2db9755f1 100644 --- a/src/KSPACE/msm_cg.h +++ b/src/KSPACE/msm_cg.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_born_coul_long.cpp b/src/KSPACE/pair_born_coul_long.cpp index 8298fe792c..cc56ada7e2 100644 --- a/src/KSPACE/pair_born_coul_long.cpp +++ b/src/KSPACE/pair_born_coul_long.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_born_coul_long.h b/src/KSPACE/pair_born_coul_long.h index 9d6b821d0a..e76526457e 100644 --- a/src/KSPACE/pair_born_coul_long.h +++ b/src/KSPACE/pair_born_coul_long.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_born_coul_msm.cpp b/src/KSPACE/pair_born_coul_msm.cpp index df6342f627..d039ccb62c 100644 --- a/src/KSPACE/pair_born_coul_msm.cpp +++ b/src/KSPACE/pair_born_coul_msm.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_born_coul_msm.h b/src/KSPACE/pair_born_coul_msm.h index 2eebbb26ad..7b65919047 100644 --- a/src/KSPACE/pair_born_coul_msm.h +++ b/src/KSPACE/pair_born_coul_msm.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_buck_coul_long.cpp b/src/KSPACE/pair_buck_coul_long.cpp index 50e5c9052c..0b2cb45b23 100644 --- a/src/KSPACE/pair_buck_coul_long.cpp +++ b/src/KSPACE/pair_buck_coul_long.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_buck_coul_long.h b/src/KSPACE/pair_buck_coul_long.h index ae6b71a441..03efff198b 100644 --- a/src/KSPACE/pair_buck_coul_long.h +++ b/src/KSPACE/pair_buck_coul_long.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_buck_coul_msm.cpp b/src/KSPACE/pair_buck_coul_msm.cpp index f20ecb6285..bef9baa8ad 100644 --- a/src/KSPACE/pair_buck_coul_msm.cpp +++ b/src/KSPACE/pair_buck_coul_msm.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_buck_coul_msm.h b/src/KSPACE/pair_buck_coul_msm.h index 77ce4e205c..37cf71072e 100644 --- a/src/KSPACE/pair_buck_coul_msm.h +++ b/src/KSPACE/pair_buck_coul_msm.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_buck_long_coul_long.cpp b/src/KSPACE/pair_buck_long_coul_long.cpp index b4beaa9766..820b76b96f 100644 --- a/src/KSPACE/pair_buck_long_coul_long.cpp +++ b/src/KSPACE/pair_buck_long_coul_long.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_buck_long_coul_long.h b/src/KSPACE/pair_buck_long_coul_long.h index 7a2474c0f7..e4cd9ded45 100644 --- a/src/KSPACE/pair_buck_long_coul_long.h +++ b/src/KSPACE/pair_buck_long_coul_long.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_coul_long.cpp b/src/KSPACE/pair_coul_long.cpp index 6b991beec7..7d3df59584 100644 --- a/src/KSPACE/pair_coul_long.cpp +++ b/src/KSPACE/pair_coul_long.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_coul_long.h b/src/KSPACE/pair_coul_long.h index 8629e80efb..8fcec92aff 100644 --- a/src/KSPACE/pair_coul_long.h +++ b/src/KSPACE/pair_coul_long.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_coul_msm.cpp b/src/KSPACE/pair_coul_msm.cpp index 11c4579c6f..1800107679 100644 --- a/src/KSPACE/pair_coul_msm.cpp +++ b/src/KSPACE/pair_coul_msm.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_coul_msm.h b/src/KSPACE/pair_coul_msm.h index ad0d1427d2..c8bc9ef326 100644 --- a/src/KSPACE/pair_coul_msm.h +++ b/src/KSPACE/pair_coul_msm.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_coul_streitz.cpp b/src/KSPACE/pair_coul_streitz.cpp index d0ad285f31..67d3466d6a 100644 --- a/src/KSPACE/pair_coul_streitz.cpp +++ b/src/KSPACE/pair_coul_streitz.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_coul_streitz.h b/src/KSPACE/pair_coul_streitz.h index eb1032aadd..059ec3f6ae 100644 --- a/src/KSPACE/pair_coul_streitz.h +++ b/src/KSPACE/pair_coul_streitz.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_lj_charmm_coul_long.cpp b/src/KSPACE/pair_lj_charmm_coul_long.cpp index d1ca3117e9..3d88d914cb 100644 --- a/src/KSPACE/pair_lj_charmm_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmm_coul_long.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_lj_charmm_coul_long.h b/src/KSPACE/pair_lj_charmm_coul_long.h index c67cfb8c36..ed40e2afca 100644 --- a/src/KSPACE/pair_lj_charmm_coul_long.h +++ b/src/KSPACE/pair_lj_charmm_coul_long.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_lj_charmm_coul_msm.cpp b/src/KSPACE/pair_lj_charmm_coul_msm.cpp index c0e7878f62..7f54b198d8 100644 --- a/src/KSPACE/pair_lj_charmm_coul_msm.cpp +++ b/src/KSPACE/pair_lj_charmm_coul_msm.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_lj_charmm_coul_msm.h b/src/KSPACE/pair_lj_charmm_coul_msm.h index b3409035e2..d0b325953c 100644 --- a/src/KSPACE/pair_lj_charmm_coul_msm.h +++ b/src/KSPACE/pair_lj_charmm_coul_msm.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp index 02dd4ac541..98fb162872 100644 --- a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.h b/src/KSPACE/pair_lj_charmmfsw_coul_long.h index b077b84a56..092fc81945 100644 --- a/src/KSPACE/pair_lj_charmmfsw_coul_long.h +++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_lj_cut_coul_long.cpp b/src/KSPACE/pair_lj_cut_coul_long.cpp index da9a783dec..cd4c89bef6 100644 --- a/src/KSPACE/pair_lj_cut_coul_long.cpp +++ b/src/KSPACE/pair_lj_cut_coul_long.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_lj_cut_coul_long.h b/src/KSPACE/pair_lj_cut_coul_long.h index 6800f05fb6..7aec4c79ee 100644 --- a/src/KSPACE/pair_lj_cut_coul_long.h +++ b/src/KSPACE/pair_lj_cut_coul_long.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_lj_cut_coul_msm.cpp b/src/KSPACE/pair_lj_cut_coul_msm.cpp index 8ed150f266..dda3ed0d1a 100644 --- a/src/KSPACE/pair_lj_cut_coul_msm.cpp +++ b/src/KSPACE/pair_lj_cut_coul_msm.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_lj_cut_coul_msm.h b/src/KSPACE/pair_lj_cut_coul_msm.h index 4d3b326085..49fc514e6e 100644 --- a/src/KSPACE/pair_lj_cut_coul_msm.h +++ b/src/KSPACE/pair_lj_cut_coul_msm.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_lj_cut_tip4p_long.cpp b/src/KSPACE/pair_lj_cut_tip4p_long.cpp index d0e4b74309..817b335b3a 100644 --- a/src/KSPACE/pair_lj_cut_tip4p_long.cpp +++ b/src/KSPACE/pair_lj_cut_tip4p_long.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -19,8 +19,6 @@ #include "pair_lj_cut_tip4p_long.h" -#include -#include #include "angle.h" #include "atom.h" #include "bond.h" @@ -32,6 +30,8 @@ #include "memory.h" #include "error.h" +#include +#include using namespace LAMMPS_NS; @@ -474,9 +474,17 @@ void PairLJCutTIP4PLong::init_style() // set alpha parameter - double theta = force->angle->equilibrium_angle(typeA); - double blen = force->bond->equilibrium_distance(typeB); + const double theta = force->angle->equilibrium_angle(typeA); + const double blen = force->bond->equilibrium_distance(typeB); alpha = qdist / (cos(0.5*theta) * blen); + + const double mincut = cut_coul + qdist + blen + neighbor->skin; + if (comm->get_comm_cutoff() < mincut) { + if (comm->me == 0) + error->warning(FLERR, "Increasing communication cutoff to {:.8} for TIP4P pair style", + mincut); + comm->cutghostuser = mincut; + } } /* ---------------------------------------------------------------------- diff --git a/src/KSPACE/pair_lj_cut_tip4p_long.h b/src/KSPACE/pair_lj_cut_tip4p_long.h index bf5deab14e..3a07ce31d3 100644 --- a/src/KSPACE/pair_lj_cut_tip4p_long.h +++ b/src/KSPACE/pair_lj_cut_tip4p_long.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_lj_long_coul_long.cpp b/src/KSPACE/pair_lj_long_coul_long.cpp index c1bba53d75..5f77009d6c 100644 --- a/src/KSPACE/pair_lj_long_coul_long.cpp +++ b/src/KSPACE/pair_lj_long_coul_long.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_lj_long_coul_long.h b/src/KSPACE/pair_lj_long_coul_long.h index dab24d0c53..e513f730db 100644 --- a/src/KSPACE/pair_lj_long_coul_long.h +++ b/src/KSPACE/pair_lj_long_coul_long.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_lj_long_tip4p_long.cpp b/src/KSPACE/pair_lj_long_tip4p_long.cpp index cf947f2e19..8c331922f6 100644 --- a/src/KSPACE/pair_lj_long_tip4p_long.cpp +++ b/src/KSPACE/pair_lj_long_tip4p_long.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -19,8 +19,6 @@ #include "pair_lj_long_tip4p_long.h" -#include -#include #include "angle.h" #include "atom.h" #include "bond.h" @@ -32,6 +30,8 @@ #include "memory.h" #include "error.h" +#include +#include using namespace LAMMPS_NS; @@ -1489,9 +1489,17 @@ void PairLJLongTIP4PLong::init_style() // set alpha parameter - double theta = force->angle->equilibrium_angle(typeA); - double blen = force->bond->equilibrium_distance(typeB); + const double theta = force->angle->equilibrium_angle(typeA); + const double blen = force->bond->equilibrium_distance(typeB); alpha = qdist / (cos(0.5*theta) * blen); + + const double mincut = cut_coul + qdist + blen + neighbor->skin; + if (comm->get_comm_cutoff() < mincut) { + if (comm->me == 0) + error->warning(FLERR, "Increasing communication cutoff to {:.8} for TIP4P pair style", + mincut); + comm->cutghostuser = mincut; + } } /* ---------------------------------------------------------------------- diff --git a/src/KSPACE/pair_lj_long_tip4p_long.h b/src/KSPACE/pair_lj_long_tip4p_long.h index a7f1fac4d6..ba87117302 100644 --- a/src/KSPACE/pair_lj_long_tip4p_long.h +++ b/src/KSPACE/pair_lj_long_tip4p_long.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pair_tip4p_long.cpp b/src/KSPACE/pair_tip4p_long.cpp index 16cf04dea1..83eeccca9c 100644 --- a/src/KSPACE/pair_tip4p_long.cpp +++ b/src/KSPACE/pair_tip4p_long.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -431,9 +431,17 @@ void PairTIP4PLong::init_style() // set alpha parameter - double theta = force->angle->equilibrium_angle(typeA); - double blen = force->bond->equilibrium_distance(typeB); + const double theta = force->angle->equilibrium_angle(typeA); + const double blen = force->bond->equilibrium_distance(typeB); alpha = qdist / (cos(0.5*theta) * blen); + + const double mincut = cut_coul + qdist + blen + neighbor->skin; + if (comm->get_comm_cutoff() < mincut) { + if (comm->me == 0) + error->warning(FLERR, "Increasing communication cutoff to {:.8} for TIP4P pair style", + mincut); + comm->cutghostuser = mincut; + } } /* ---------------------------------------------------------------------- diff --git a/src/KSPACE/pair_tip4p_long.h b/src/KSPACE/pair_tip4p_long.h index b64a08bf3d..a0f2915743 100644 --- a/src/KSPACE/pair_tip4p_long.h +++ b/src/KSPACE/pair_tip4p_long.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp index b50c1f358c..3b1971de92 100644 --- a/src/KSPACE/pppm.cpp +++ b/src/KSPACE/pppm.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -29,8 +29,9 @@ #include "error.h" #include "fft3d_wrap.h" #include "force.h" -#include "gridcomm.h" +#include "grid3d.h" #include "math_const.h" +#include "math_extra.h" #include "math_special.h" #include "memory.h" #include "neighbor.h" @@ -161,8 +162,12 @@ PPPM::PPPM(LAMMPS *lmp) : KSpace(lmp), void PPPM::settings(int narg, char **arg) { - if (narg < 1) error->all(FLERR,"Illegal kspace_style pppm command"); + if (narg < 1) error->all(FLERR,"Illegal kspace_style {} command", force->kspace_style); + accuracy_relative = fabs(utils::numeric(FLERR,arg[0],false,lmp)); + if (accuracy_relative > 1.0) + error->all(FLERR, "Invalid relative accuracy {:g} for kspace_style {}", + accuracy_relative, force->kspace_style); } /* ---------------------------------------------------------------------- @@ -291,7 +296,7 @@ void PPPM::init() // or overlap is allowed, then done // else reduce order and try again - GridComm *gctmp = nullptr; + gc = nullptr; int iteration = 0; while (order >= minorder) { @@ -304,23 +309,28 @@ void PPPM::init() set_grid_local(); if (overlap_allowed) break; - gctmp = new GridComm(lmp,world,nx_pppm,ny_pppm,nz_pppm, - nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, - nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out); + gc = new Grid3d(lmp,world,nx_pppm,ny_pppm,nz_pppm); + gc->set_distance(0.5*neighbor->skin + qdist); + gc->set_stencil_atom(-nlower,nupper); + gc->set_shift_atom(shiftatom_lo,shiftatom_hi); + gc->set_zfactor(slab_volfactor); + + gc->setup_grid(nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, + nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out); int tmp1,tmp2; - gctmp->setup(tmp1,tmp2); - if (gctmp->ghost_adjacent()) break; - delete gctmp; + gc->setup_comm(tmp1,tmp2); + if (gc->ghost_adjacent()) break; + delete gc; order--; iteration++; } if (order < minorder) error->all(FLERR,"PPPM order < minimum allowed order"); - if (!overlap_allowed && !gctmp->ghost_adjacent()) + if (!overlap_allowed && !gc->ghost_adjacent()) error->all(FLERR,"PPPM grid stencil extends beyond nearest neighbor processor"); - if (gctmp) delete gctmp; + if (gc) delete gc; // adjust g_ewald @@ -330,6 +340,18 @@ void PPPM::init() double estimated_accuracy = final_accuracy(); + // allocate K-space dependent memory + // don't invoke allocate peratom() or group(), will be allocated when needed + + allocate(); + + // pre-compute Green's function denomiator expansion + // pre-compute 1d charge distribution coefficients + + compute_gf_denom(); + if (differentiation_flag == 1) compute_sf_precoeff(); + compute_rho_coeff(); + // print stats int ngrid_max,nfft_both_max; @@ -349,18 +371,6 @@ void PPPM::init() ngrid_max,nfft_both_max); utils::logmesg(lmp,mesg); } - - // allocate K-space dependent memory - // don't invoke allocate peratom() or group(), will be allocated when needed - - allocate(); - - // pre-compute Green's function denomiator expansion - // pre-compute 1d charge distribution coefficients - - compute_gf_denom(); - if (differentiation_flag == 1) compute_sf_precoeff(); - compute_rho_coeff(); } /* ---------------------------------------------------------------------- @@ -549,7 +559,7 @@ void PPPM::setup_triclinic() called by fix balance b/c it changed sizes of processor sub-domains ------------------------------------------------------------------------- */ -void PPPM::setup_grid() +void PPPM::reset_grid() { // free all arrays previously allocated @@ -634,8 +644,8 @@ void PPPM::compute(int eflag, int vflag) // to fully sum contribution in their 3d bricks // remap from 3d decomposition to FFT decomposition - gc->reverse_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR), - REVERSE_RHO,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); brick2fft(); // compute potential gradient on my FFT grid and @@ -649,21 +659,21 @@ void PPPM::compute(int eflag, int vflag) // to fill ghost cells surrounding their 3d bricks if (differentiation_flag == 1) - gc->forward_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR), - FORWARD_AD,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_AD,1,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); else - gc->forward_comm(GridComm::KSPACE,this,3,sizeof(FFT_SCALAR), - FORWARD_IK,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK,3,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); // extra per-atom energy/virial communication if (evflag_atom) { if (differentiation_flag == 1 && vflag_atom) - gc->forward_comm(GridComm::KSPACE,this,6,sizeof(FFT_SCALAR), - FORWARD_AD_PERATOM,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_PERATOM,6,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); else if (differentiation_flag == 0) - gc->forward_comm(GridComm::KSPACE,this,7,sizeof(FFT_SCALAR), - FORWARD_IK_PERATOM,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_PERATOM,7,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); } // calculate the force on my particles @@ -738,6 +748,47 @@ void PPPM::compute(int eflag, int vflag) void PPPM::allocate() { + // create ghost grid object for rho and electric field communication + // returns local owned and ghost grid bounds + // setup communication patterns and buffers + + gc = new Grid3d(lmp,world,nx_pppm,ny_pppm,nz_pppm); + gc->set_distance(0.5*neighbor->skin + qdist); + gc->set_stencil_atom(-nlower,nupper); + gc->set_shift_atom(shiftatom_lo,shiftatom_hi); + gc->set_zfactor(slab_volfactor); + + gc->setup_grid(nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, + nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out); + + gc->setup_comm(ngc_buf1,ngc_buf2); + + if (differentiation_flag) npergrid = 1; + else npergrid = 3; + + memory->create(gc_buf1,npergrid*ngc_buf1,"pppm:gc_buf1"); + memory->create(gc_buf2,npergrid*ngc_buf2,"pppm:gc_buf2"); + + // tally local grid sizes + // ngrid = count of owned+ghost grid cells on this proc + // nfft_brick = FFT points in 3d brick-decomposition on this proc + // same as count of owned grid cells + // nfft = FFT points in x-pencil FFT decomposition on this proc + // nfft_both = greater of nfft and nfft_brick + + ngrid = (nxhi_out-nxlo_out+1) * (nyhi_out-nylo_out+1) * + (nzhi_out-nzlo_out+1); + + nfft_brick = (nxhi_in-nxlo_in+1) * (nyhi_in-nylo_in+1) * + (nzhi_in-nzlo_in+1); + + nfft = (nxhi_fft-nxlo_fft+1) * (nyhi_fft-nylo_fft+1) * + (nzhi_fft-nzlo_fft+1); + + nfft_both = MAX(nfft,nfft_brick); + + // allocate distributed grid data + memory->create3d_offset(density_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out, nxlo_out,nxhi_out,"pppm:density_brick"); @@ -808,21 +859,6 @@ void PPPM::allocate() nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft, 1,0,0,FFT_PRECISION,collective_flag); - - // create ghost grid object for rho and electric field communication - // also create 2 bufs for ghost grid cell comm, passed to GridComm methods - - gc = new GridComm(lmp,world,nx_pppm,ny_pppm,nz_pppm, - nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, - nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out); - - gc->setup(ngc_buf1,ngc_buf2); - - if (differentiation_flag) npergrid = 1; - else npergrid = 3; - - memory->create(gc_buf1,npergrid*ngc_buf1,"pppm:gc_buf1"); - memory->create(gc_buf2,npergrid*ngc_buf2,"pppm:gc_buf2"); } /* ---------------------------------------------------------------------- @@ -831,6 +867,10 @@ void PPPM::allocate() void PPPM::deallocate() { + delete gc; + memory->destroy(gc_buf1); + memory->destroy(gc_buf2); + memory->destroy3d_offset(density_brick,nzlo_out,nylo_out,nxlo_out); if (differentiation_flag == 1) { @@ -873,9 +913,6 @@ void PPPM::deallocate() delete fft1; delete fft2; delete remap; - delete gc; - memory->destroy(gc_buf1); - memory->destroy(gc_buf2); } /* ---------------------------------------------------------------------- @@ -1308,115 +1345,46 @@ double PPPM::final_accuracy() } /* ---------------------------------------------------------------------- - set local subset of PPPM/FFT grid that I own - n xyz lo/hi in = 3d brick that I own (inclusive) - n xyz lo/hi out = 3d brick + ghost cells in 6 directions (inclusive) - n xyz lo/hi fft = FFT columns that I own (all of x dim, 2d decomp in yz) + set params which determine which owned and ghost cells this proc owns + Grid3d uses these params to partition grid + also partition FFT grid + n xyz lo/hi fft = FFT columns that I own (all of x dim, 2d decomp in yz) ------------------------------------------------------------------------- */ void PPPM::set_grid_local() { - // partition global grid across procs - // n xyz lo/hi in = lower/upper bounds of global grid this proc owns - // indices range from 0 to N-1 inclusive in each dim + // shift values for particle <-> grid mapping depend on stencil order + // add/subtract OFFSET to avoid int(-0.75) = 0 when want it to be -1 + // used in particle_map() and make_rho() and fieldforce() - comm->partition_grid(nx_pppm,ny_pppm,nz_pppm,slab_volfactor, - nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in); + if (order % 2) shift = OFFSET + 0.5; + else shift = OFFSET; - // nlower,nupper = stencil size for mapping particles to PPPM grid + if (order % 2) shiftone = 0.0; + else shiftone = 0.5; + + // nlower/nupper = stencil size for mapping particles to grid nlower = -(order-1)/2; nupper = order/2; - // shift values for particle <-> grid mapping - // add/subtract OFFSET to avoid int(-0.75) = 0 when want it to be -1 + // shiftatom lo/hi are passed to Grid3d to determine ghost cell extents + // shiftatom_lo = min shift on lo side + // shiftatom_hi = max shift on hi side + // for PPPMStagger, stagger value (0.0 or 0.5) also affects this - if (order % 2) shift = OFFSET + 0.5; - else shift = OFFSET; - if (order % 2) shiftone = 0.0; - else shiftone = 0.5; - - // nlo_out,nhi_out = lower/upper limits of the 3d sub-brick of - // global PPPM grid that my particles can contribute charge to - // effectively nlo_in,nhi_in + ghost cells - // nlo,nhi = index of global grid pt to "lower left" of smallest/largest - // position a particle in my box can be at - // dist[3] = max particle position outside subbox = skin/2.0 + qdist - // qdist = offset due to TIP4P fictitious charge - // convert to triclinic if necessary - // nlo_out,nhi_out = nlo,nhi + stencil size for particle mapping - // for slab PPPM, assign z grid as if it were not extended - - double *prd,*sublo,*subhi; - - if (triclinic == 0) { - prd = domain->prd; - boxlo = domain->boxlo; - sublo = domain->sublo; - subhi = domain->subhi; - } else { - prd = domain->prd_lamda; - boxlo = domain->boxlo_lamda; - sublo = domain->sublo_lamda; - subhi = domain->subhi_lamda; - } - - double xprd = prd[0]; - double yprd = prd[1]; - double zprd = prd[2]; - double zprd_slab = zprd*slab_volfactor; - - double dist[3] = {0.0,0.0,0.0}; - double cuthalf = 0.5*neighbor->skin + qdist; - if (triclinic == 0) dist[0] = dist[1] = dist[2] = cuthalf; - else kspacebbox(cuthalf,&dist[0]); - - int nlo,nhi; - nlo = nhi = 0; - - nlo = static_cast ((sublo[0]-dist[0]-boxlo[0]) * - nx_pppm/xprd + shift) - OFFSET; - nhi = static_cast ((subhi[0]+dist[0]-boxlo[0]) * - nx_pppm/xprd + shift) - OFFSET; - nxlo_out = nlo + nlower; - nxhi_out = nhi + nupper; - - nlo = static_cast ((sublo[1]-dist[1]-boxlo[1]) * - ny_pppm/yprd + shift) - OFFSET; - nhi = static_cast ((subhi[1]+dist[1]-boxlo[1]) * - ny_pppm/yprd + shift) - OFFSET; - nylo_out = nlo + nlower; - nyhi_out = nhi + nupper; - - nlo = static_cast ((sublo[2]-dist[2]-boxlo[2]) * - nz_pppm/zprd_slab + shift) - OFFSET; - nhi = static_cast ((subhi[2]+dist[2]-boxlo[2]) * - nz_pppm/zprd_slab + shift) - OFFSET; - nzlo_out = nlo + nlower; - nzhi_out = nhi + nupper; - - if (stagger_flag) { - nxhi_out++; - nyhi_out++; - nzhi_out++; - } - - // for slab PPPM, change the grid boundary for processors at +z end - // to include the empty volume between periodically repeating slabs - // for slab PPPM, want charge data communicated from -z proc to +z proc, - // but not vice versa, also want field data communicated from +z proc to - // -z proc, but not vice versa - // this is accomplished by nzhi_in = nzhi_out on +z end (no ghost cells) - // also insure no other procs use ghost cells beyond +z limit - // differnet logic for non-tiled vs tiled decomposition - - if (slabflag == 1) { - if (comm->layout != Comm::LAYOUT_TILED) { - if (comm->myloc[2] == comm->procgrid[2]-1) nzhi_in = nzhi_out = nz_pppm - 1; - } else { - if (comm->mysplit[2][1] == 1.0) nzhi_in = nzhi_out = nz_pppm - 1; - } - nzhi_out = MIN(nzhi_out,nz_pppm-1); + if ((order % 2) && !stagger_flag) { + shiftatom_lo = 0.5; + shiftatom_hi = 0.5; + } else if ((order % 2) && stagger_flag) { + shiftatom_lo = 0.5; + shiftatom_hi = 0.5 + 0.5; + } else if ((order % 2 == 0) && !stagger_flag) { + shiftatom_lo = 0.0; + shiftatom_hi = 0.0; + } else if ((order % 2 == 0) && stagger_flag) { + shiftatom_lo = 0.0; + shiftatom_hi = 0.0 + 0.5; } // x-pencil decomposition of FFT mesh @@ -1444,22 +1412,6 @@ void PPPM::set_grid_local() nyhi_fft = (me_y+1)*ny_pppm/npey_fft - 1; nzlo_fft = me_z*nz_pppm/npez_fft; nzhi_fft = (me_z+1)*nz_pppm/npez_fft - 1; - - // ngrid = count of PPPM grid pts owned by this proc, including ghosts - - ngrid = (nxhi_out-nxlo_out+1) * (nyhi_out-nylo_out+1) * - (nzhi_out-nzlo_out+1); - - // count of FFT grids pts owned by this proc, without ghosts - // nfft = FFT points in x-pencil FFT decomposition on this proc - // nfft_brick = FFT points in 3d brick-decomposition on this proc - // nfft_both = greater of 2 values - - nfft = (nxhi_fft-nxlo_fft+1) * (nyhi_fft-nylo_fft+1) * - (nzhi_fft-nzlo_fft+1); - int nfft_brick = (nxhi_in-nxlo_in+1) * (nyhi_in-nylo_in+1) * - (nzhi_in-nzlo_in+1); - nfft_both = MAX(nfft,nfft_brick); } /* ---------------------------------------------------------------------- @@ -1907,7 +1859,7 @@ void PPPM::make_rho() // loop over my charges, add their contribution to nearby grid points // (nx,ny,nz) = global coords of grid pt to "lower left" of charge // (dx,dy,dz) = distance to "lower left" grid pt - // (mx,my,mz) = global coords of moving stencil pt + // (mx,my,mz) = global indices of moving stencil pt double *q = atom->q; double **x = atom->x; @@ -3055,7 +3007,7 @@ double PPPM::memory_usage() bytes += (double)2 * nfft_both * sizeof(FFT_SCALAR);; } - // two GridComm bufs + // two Grid3d bufs bytes += (double)(ngc_buf1 + ngc_buf2) * npergrid * sizeof(FFT_SCALAR); @@ -3115,8 +3067,8 @@ void PPPM::compute_group_group(int groupbit_A, int groupbit_B, int AA_flag) density_brick = density_A_brick; density_fft = density_A_fft; - gc->reverse_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR), - REVERSE_RHO,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); brick2fft(); // group B @@ -3124,8 +3076,8 @@ void PPPM::compute_group_group(int groupbit_A, int groupbit_B, int AA_flag) density_brick = density_B_brick; density_fft = density_B_fft; - gc->reverse_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR), - REVERSE_RHO,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); brick2fft(); // switch back pointers diff --git a/src/KSPACE/pppm.h b/src/KSPACE/pppm.h index cac5338ed7..9d85399272 100644 --- a/src/KSPACE/pppm.h +++ b/src/KSPACE/pppm.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -21,7 +21,7 @@ KSpaceStyle(pppm,PPPM); #define LMP_PPPM_H #include "kspace.h" -#include "lmpfftsettings.h" +#include "lmpfftsettings.h" // IWYU pragma: export namespace LAMMPS_NS { @@ -32,7 +32,7 @@ class PPPM : public KSpace { void settings(int, char **) override; void init() override; void setup() override; - void setup_grid() override; + void reset_grid() override; void compute(int, int) override; int timing_1d(int, double &) override; int timing_3d(int, double &) override; @@ -48,7 +48,7 @@ class PPPM : public KSpace { double volume; double delxinv, delyinv, delzinv, delvolinv; double h_x, h_y, h_z; - double shift, shiftone; + double shift, shiftone, shiftatom_lo, shiftatom_hi; int peratom_allocate_flag; int nxlo_in, nylo_in, nzlo_in, nxhi_in, nyhi_in, nzhi_in; @@ -56,7 +56,7 @@ class PPPM : public KSpace { int nxlo_ghost, nxhi_ghost, nylo_ghost, nyhi_ghost, nzlo_ghost, nzhi_ghost; int nxlo_fft, nylo_fft, nzlo_fft, nxhi_fft, nyhi_fft, nzhi_fft; int nlower, nupper; - int ngrid, nfft, nfft_both; + int ngrid, nfft_brick, nfft, nfft_both; FFT_SCALAR ***density_brick; FFT_SCALAR ***vdx_brick, ***vdy_brick, ***vdz_brick; @@ -80,7 +80,7 @@ class PPPM : public KSpace { class FFT3d *fft1, *fft2; class Remap *remap; - class GridComm *gc; + class Grid3d *gc; FFT_SCALAR *gc_buf1, *gc_buf2; int ngc_buf1, ngc_buf2, npergrid; diff --git a/src/KSPACE/pppm_cg.cpp b/src/KSPACE/pppm_cg.cpp index 6697c69985..845abe0078 100644 --- a/src/KSPACE/pppm_cg.cpp +++ b/src/KSPACE/pppm_cg.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -21,7 +21,8 @@ #include "atom.h" #include "domain.h" #include "error.h" -#include "gridcomm.h" +#include "force.h" +#include "grid3d.h" #include "math_const.h" #include "memory.h" #include "neighbor.h" @@ -59,7 +60,7 @@ PPPMCG::PPPMCG(LAMMPS *lmp) : PPPM(lmp), void PPPMCG::settings(int narg, char **arg) { if ((narg < 1) || (narg > 2)) - error->all(FLERR,"Illegal kspace_style pppm/cg command"); + error->all(FLERR,"Illegal kspace_style {} command", force->kspace_style); // first argument is processed in parent class @@ -177,8 +178,8 @@ void PPPMCG::compute(int eflag, int vflag) // to fully sum contribution in their 3d bricks // remap from 3d decomposition to FFT decomposition - gc->reverse_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR), - REVERSE_RHO,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); brick2fft(); // compute potential gradient on my FFT grid and @@ -192,21 +193,21 @@ void PPPMCG::compute(int eflag, int vflag) // to fill ghost cells surrounding their 3d bricks if (differentiation_flag == 1) - gc->forward_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR), - FORWARD_AD,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_AD,1,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); else - gc->forward_comm(GridComm::KSPACE,this,3,sizeof(FFT_SCALAR), - FORWARD_IK,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK,3,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); // extra per-atom energy/virial communication if (evflag_atom) { if (differentiation_flag == 1 && vflag_atom) - gc->forward_comm(GridComm::KSPACE,this,6,sizeof(FFT_SCALAR), - FORWARD_AD_PERATOM,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_PERATOM,6,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); else if (differentiation_flag == 0) - gc->forward_comm(GridComm::KSPACE,this,7,sizeof(FFT_SCALAR), - FORWARD_IK_PERATOM,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_PERATOM,7,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); } // calculate the force on my particles diff --git a/src/KSPACE/pppm_cg.h b/src/KSPACE/pppm_cg.h index 3f1c293415..e36b13defb 100644 --- a/src/KSPACE/pppm_cg.h +++ b/src/KSPACE/pppm_cg.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pppm_dipole.cpp b/src/KSPACE/pppm_dipole.cpp index aef14b0189..a01ffea1dc 100644 --- a/src/KSPACE/pppm_dipole.cpp +++ b/src/KSPACE/pppm_dipole.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,10 +24,11 @@ #include "error.h" #include "fft3d_wrap.h" #include "force.h" -#include "gridcomm.h" +#include "grid3d.h" #include "math_const.h" #include "math_special.h" #include "memory.h" +#include "neighbor.h" #include "pair.h" #include "remap_wrap.h" #include "update.h" @@ -116,14 +117,13 @@ void PPPMDipole::init() if (domain->dimension == 2) error->all(FLERR,"Cannot use PPPMDipole with 2d simulation"); - if (comm->style != 0) - error->universe_all(FLERR,"PPPMDipole can only currently be used with " - "comm_style brick"); + if (comm->style != Comm::BRICK) + error->universe_all(FLERR,"PPPMDipole can only currently be used with comm_style brick"); if (!atom->mu) error->all(FLERR,"Kspace style requires atom attribute mu"); - if (atom->mu && differentiation_flag == 1) error->all(FLERR,"Cannot (yet) use kspace_modify diff" - " ad with dipoles"); + if (atom->mu && differentiation_flag == 1) + error->all(FLERR,"Cannot (yet) use kspace_modify diff ad with dipoles"); if (dipoleflag && strcmp(update->unit_style,"electron") == 0) error->all(FLERR,"Cannot (yet) use 'electron' units with dipoles"); @@ -137,8 +137,7 @@ void PPPMDipole::init() } if (order < 2 || order > MAXORDER) - error->all(FLERR,"PPPMDipole order cannot be < 2 or > {}", - MAXORDER); + error->all(FLERR,"PPPMDipole order cannot be < 2 or > {}", MAXORDER); // compute two charge force @@ -188,7 +187,7 @@ void PPPMDipole::init() // or overlap is allowed, then done // else reduce order and try again - GridComm *gctmp = nullptr; + gc_dipole = nullptr; int iteration = 0; while (order >= minorder) { @@ -201,23 +200,28 @@ void PPPMDipole::init() set_grid_local(); if (overlap_allowed) break; - gctmp = new GridComm(lmp,world,nx_pppm,ny_pppm,nz_pppm, - nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, - nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out); + gc_dipole = new Grid3d(lmp,world,nx_pppm,ny_pppm,nz_pppm); + gc_dipole->set_distance(0.5*neighbor->skin + qdist); + gc_dipole->set_stencil_atom(-nlower,nupper); + gc_dipole->set_shift_atom(shiftatom_lo,shiftatom_hi); + gc_dipole->set_zfactor(slab_volfactor); + + gc_dipole->setup_grid(nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, + nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out); int tmp1,tmp2; - gctmp->setup(tmp1,tmp2); - if (gctmp->ghost_adjacent()) break; - delete gctmp; + gc_dipole->setup_comm(tmp1,tmp2); + if (gc_dipole->ghost_adjacent()) break; + delete gc_dipole; order--; iteration++; } if (order < minorder) error->all(FLERR,"PPPMDipole order < minimum allowed order"); - if (!overlap_allowed && !gctmp->ghost_adjacent()) + if (!overlap_allowed && !gc_dipole->ghost_adjacent()) error->all(FLERR,"PPPMDipole grid stencil extends beyond nearest neighbor processor"); - if (gctmp) delete gctmp; + if (gc_dipole) delete gc_dipole; // adjust g_ewald @@ -227,6 +231,17 @@ void PPPMDipole::init() double estimated_accuracy = final_accuracy_dipole(); + // allocate K-space dependent memory + // don't invoke allocate peratom(), will be allocated when needed + + allocate(); + + // pre-compute Green's function denomiator expansion + // pre-compute 1d charge distribution coefficients + + compute_gf_denom(); + compute_rho_coeff(); + // print stats int ngrid_max,nfft_both_max; @@ -246,17 +261,6 @@ void PPPMDipole::init() ngrid_max,nfft_both_max); utils::logmesg(lmp,mesg); } - - // allocate K-space dependent memory - // don't invoke allocate peratom(), will be allocated when needed - - allocate(); - - // pre-compute Green's function denomiator expansion - // pre-compute 1d charge distribution coefficients - - compute_gf_denom(); - compute_rho_coeff(); } /* ---------------------------------------------------------------------- @@ -356,7 +360,7 @@ void PPPMDipole::setup() called by fix balance b/c it changed sizes of processor sub-domains ------------------------------------------------------------------------- */ -void PPPMDipole::setup_grid() +void PPPMDipole::reset_grid() { // free all arrays previously allocated @@ -441,8 +445,8 @@ void PPPMDipole::compute(int eflag, int vflag) // to fully sum contribution in their 3d bricks // remap from 3d decomposition to FFT decomposition - gc_dipole->reverse_comm(GridComm::KSPACE,this,3,sizeof(FFT_SCALAR), - REVERSE_MU,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc_dipole->reverse_comm(Grid3d::KSPACE,this,REVERSE_MU,3,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); brick2fft_dipole(); // compute potential gradient on my FFT grid and @@ -455,14 +459,14 @@ void PPPMDipole::compute(int eflag, int vflag) // all procs communicate E-field values // to fill ghost cells surrounding their 3d bricks - gc_dipole->forward_comm(GridComm::KSPACE,this,9,sizeof(FFT_SCALAR), - FORWARD_MU,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc_dipole->forward_comm(Grid3d::KSPACE,this,FORWARD_MU,9,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); // extra per-atom energy/virial communication if (evflag_atom) - gc_dipole->forward_comm(GridComm::KSPACE,this,18,sizeof(FFT_SCALAR), - FORWARD_MU_PERATOM,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc_dipole->forward_comm(Grid3d::KSPACE,this,FORWARD_MU_PERATOM,18,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); // calculate the force on my particles @@ -528,6 +532,46 @@ void PPPMDipole::compute(int eflag, int vflag) void PPPMDipole::allocate() { + // create ghost grid object for rho and electric field communication + // returns local owned and ghost grid bounds + // setup communication patterns and buffers + + gc_dipole = new Grid3d(lmp,world,nx_pppm,ny_pppm,nz_pppm); + gc_dipole->set_distance(0.5*neighbor->skin + qdist); + gc_dipole->set_stencil_atom(-nlower,nupper); + gc_dipole->set_shift_atom(shiftatom_lo,shiftatom_hi); + gc_dipole->set_zfactor(slab_volfactor); + + gc_dipole->setup_grid(nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, + nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out); + + gc_dipole->setup_comm(ngc_buf1,ngc_buf2); + + npergrid = 9; + + memory->create(gc_buf1,npergrid*ngc_buf1,"pppm:gc_buf1"); + memory->create(gc_buf2,npergrid*ngc_buf2,"pppm:gc_buf2"); + + // tally local grid sizes + // ngrid = count of owned+ghost grid cells on this proc + // nfft_brick = FFT points in 3d brick-decomposition on this proc + // same as count of owned grid cells + // nfft = FFT points in x-pencil FFT decomposition on this proc + // nfft_both = greater of nfft and nfft_brick + + ngrid = (nxhi_out-nxlo_out+1) * (nyhi_out-nylo_out+1) * + (nzhi_out-nzlo_out+1); + + nfft_brick = (nxhi_in-nxlo_in+1) * (nyhi_in-nylo_in+1) * + (nzhi_in-nzlo_in+1); + + nfft = (nxhi_fft-nxlo_fft+1) * (nyhi_fft-nylo_fft+1) * + (nzhi_fft-nzlo_fft+1); + + nfft_both = MAX(nfft,nfft_brick); + + // allocate distributed grid data + memory->create3d_offset(densityx_brick_dipole,nzlo_out,nzhi_out,nylo_out,nyhi_out, nxlo_out,nxhi_out,"pppm_dipole:densityx_brick_dipole"); memory->create3d_offset(densityy_brick_dipole,nzlo_out,nzhi_out,nylo_out,nyhi_out, @@ -601,20 +645,6 @@ void PPPMDipole::allocate() nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft, 1,0,0,FFT_PRECISION,collective_flag); - - // create ghost grid object for rho and electric field communication - // also create 2 bufs for ghost grid cell comm, passed to GridComm methods - - gc_dipole = new GridComm(lmp,world,nx_pppm,ny_pppm,nz_pppm, - nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, - nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out); - - gc_dipole->setup(ngc_buf1,ngc_buf2); - - npergrid = 9; - - memory->create(gc_buf1,npergrid*ngc_buf1,"pppm:gc_buf1"); - memory->create(gc_buf2,npergrid*ngc_buf2,"pppm:gc_buf2"); } /* ---------------------------------------------------------------------- @@ -623,6 +653,11 @@ void PPPMDipole::allocate() void PPPMDipole::deallocate() { + delete gc_dipole; + memory->destroy(gc_buf1); + memory->destroy(gc_buf2); + gc_buf1 = gc_buf2 = nullptr; + memory->destroy3d_offset(densityx_brick_dipole,nzlo_out,nylo_out,nxlo_out); memory->destroy3d_offset(densityy_brick_dipole,nzlo_out,nylo_out,nxlo_out); memory->destroy3d_offset(densityz_brick_dipole,nzlo_out,nylo_out,nxlo_out); @@ -645,7 +680,12 @@ void PPPMDipole::deallocate() memory->destroy(work3); memory->destroy(work4); - delete gc_dipole; + delete fft1; + delete fft2; + delete remap; + + fft1 = fft2 = nullptr; + remap = nullptr; } /* ---------------------------------------------------------------------- @@ -2519,7 +2559,7 @@ double PPPMDipole::memory_usage() if (peratom_allocate_flag) bytes += (double)21 * nbrick * sizeof(FFT_SCALAR); - // two GridComm bufs + // two Grid3d bufs bytes += (double)(ngc_buf1 + ngc_buf2) * npergrid * sizeof(FFT_SCALAR); diff --git a/src/KSPACE/pppm_dipole.h b/src/KSPACE/pppm_dipole.h index 4415d4014e..edc969b0f3 100644 --- a/src/KSPACE/pppm_dipole.h +++ b/src/KSPACE/pppm_dipole.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -30,7 +30,7 @@ class PPPMDipole : public PPPM { ~PPPMDipole() override; void init() override; void setup() override; - void setup_grid() override; + void reset_grid() override; void compute(int, int) override; int timing_1d(int, double &) override; int timing_3d(int, double &) override; @@ -70,7 +70,7 @@ class PPPMDipole : public PPPM { FFT_SCALAR *work3, *work4; FFT_SCALAR *densityx_fft_dipole, *densityy_fft_dipole, *densityz_fft_dipole; - class GridComm *gc_dipole; + class Grid3d *gc_dipole; int only_dipole_flag; double musum, musqsum, mu2; diff --git a/src/KSPACE/pppm_dipole_spin.cpp b/src/KSPACE/pppm_dipole_spin.cpp index 148da52770..e96378180a 100644 --- a/src/KSPACE/pppm_dipole_spin.cpp +++ b/src/KSPACE/pppm_dipole_spin.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -23,9 +23,10 @@ #include "domain.h" #include "error.h" #include "force.h" -#include "gridcomm.h" +#include "grid3d.h" #include "math_const.h" #include "memory.h" +#include "neighbor.h" #include "pair.h" #include "update.h" @@ -101,14 +102,13 @@ void PPPMDipoleSpin::init() if (domain->dimension == 2) error->all(FLERR, "Cannot use PPPMDipoleSpin with 2d simulation"); - if (comm->style != 0) - error->universe_all(FLERR,"PPPMDipoleSpin can only currently be used with " - "comm_style brick"); + if (comm->style != Comm::BRICK) + error->universe_all(FLERR,"PPPMDipoleSpin can only currently be used with comm_style brick"); if (!atom->sp) error->all(FLERR,"Kspace style requires atom attribute sp"); - if (atom->sp && differentiation_flag == 1) error->all(FLERR,"Cannot (yet) use" - " kspace_modify diff ad with spins"); + if (atom->sp && differentiation_flag == 1) + error->all(FLERR,"Cannot (yet) use kspace_modify diff ad with spins"); if (spinflag && strcmp(update->unit_style,"metal") != 0) error->all(FLERR,"'metal' units have to be used with spins"); @@ -122,8 +122,7 @@ void PPPMDipoleSpin::init() } if (order < 2 || order > MAXORDER) - error->all(FLERR,"PPPMDipoleSpin order cannot be < 2 or > {}", - MAXORDER); + error->all(FLERR,"PPPMDipoleSpin order cannot be < 2 or > {}",MAXORDER); // compute two charge force @@ -173,7 +172,7 @@ void PPPMDipoleSpin::init() // or overlap is allowed, then done // else reduce order and try again - GridComm *gctmp = nullptr; + gc_dipole = nullptr; int iteration = 0; while (order >= minorder) { @@ -186,23 +185,28 @@ void PPPMDipoleSpin::init() set_grid_local(); if (overlap_allowed) break; - gctmp = new GridComm(lmp,world,nx_pppm,ny_pppm,nz_pppm, - nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, - nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out); + gc_dipole = new Grid3d(lmp,world,nx_pppm,ny_pppm,nz_pppm); + gc_dipole->set_distance(0.5*neighbor->skin + qdist); + gc_dipole->set_stencil_atom(-nlower,nupper); + gc_dipole->set_shift_atom(shiftatom_lo,shiftatom_hi); + gc_dipole->set_zfactor(slab_volfactor); + + gc_dipole->setup_grid(nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, + nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out); int tmp1,tmp2; - gctmp->setup(tmp1,tmp2); - if (gctmp->ghost_adjacent()) break; - delete gctmp; + gc_dipole->setup_comm(tmp1,tmp2); + if (gc_dipole->ghost_adjacent()) break; + delete gc_dipole; order--; iteration++; } if (order < minorder) error->all(FLERR,"PPPMDipoleSpin order < minimum allowed order"); - if (!overlap_allowed && !gctmp->ghost_adjacent()) + if (!overlap_allowed && !gc_dipole->ghost_adjacent()) error->all(FLERR,"PPPMDipoleSpin grid stencil extends beyond nearest neighbor processor"); - if (gctmp) delete gctmp; + if (gc_dipole) delete gc_dipole; // adjust g_ewald @@ -298,8 +302,8 @@ void PPPMDipoleSpin::compute(int eflag, int vflag) // to fully sum contribution in their 3d bricks // remap from 3d decomposition to FFT decomposition - gc_dipole->reverse_comm(GridComm::KSPACE,this,3,sizeof(FFT_SCALAR), - REVERSE_MU,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc_dipole->reverse_comm(Grid3d::KSPACE,this,REVERSE_MU,3,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); brick2fft_dipole(); // compute potential gradient on my FFT grid and @@ -312,14 +316,14 @@ void PPPMDipoleSpin::compute(int eflag, int vflag) // all procs communicate E-field values // to fill ghost cells surrounding their 3d bricks - gc_dipole->forward_comm(GridComm::KSPACE,this,9,sizeof(FFT_SCALAR), - FORWARD_MU,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc_dipole->forward_comm(Grid3d::KSPACE,this,FORWARD_MU,9,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); // extra per-atom energy/virial communication if (evflag_atom) - gc->forward_comm(GridComm::KSPACE,this,18,sizeof(FFT_SCALAR), - FORWARD_MU_PERATOM,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_MU_PERATOM,18,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); // calculate the force on my particles diff --git a/src/KSPACE/pppm_dipole_spin.h b/src/KSPACE/pppm_dipole_spin.h index f70d157b8d..9c81dea268 100644 --- a/src/KSPACE/pppm_dipole_spin.h +++ b/src/KSPACE/pppm_dipole_spin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp index f0f17ed927..f6b95c46c1 100644 --- a/src/KSPACE/pppm_disp.cpp +++ b/src/KSPACE/pppm_disp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -27,7 +27,7 @@ #include "error.h" #include "fft3d_wrap.h" #include "force.h" -#include "gridcomm.h" +#include "grid3d.h" #include "math_const.h" #include "memory.h" #include "neighbor.h" @@ -228,8 +228,12 @@ PPPMDisp::PPPMDisp(LAMMPS *lmp) : KSpace(lmp), void PPPMDisp::settings(int narg, char **arg) { - if (narg < 1) error->all(FLERR,"Illegal kspace_style pppm/disp command"); + if (narg < 1) error->all(FLERR,"Illegal kspace_style {} command", force->kspace_style); + accuracy_relative = fabs(utils::numeric(FLERR,arg[0],false,lmp)); + if (accuracy_relative > 1.0) + error->all(FLERR, "Invalid relative accuracy {:g} for kspace_style {}", + accuracy_relative, force->kspace_style); } /* ---------------------------------------------------------------------- @@ -266,9 +270,8 @@ void PPPMDisp::init() if (domain->dimension == 2) error->all(FLERR,"Cannot use PPPMDisp with 2d simulation"); - if (comm->style != 0) - error->universe_all(FLERR,"PPPMDisp can only currently be used with " - "comm_style brick"); + if (comm->style != Comm::BRICK) + error->universe_all(FLERR,"PPPMDisp can only currently be used with comm_style brick"); if (slabflag == 0 && domain->nonperiodic > 0) error->all(FLERR,"Cannot use non-periodic boundaries with PPPMDisp"); @@ -279,8 +282,7 @@ void PPPMDisp::init() } if (order > MAXORDER || order_6 > MAXORDER) - error->all(FLERR,"PPPMDisp coulomb or dispersion order cannot" - " be greater than {}",MAXORDER); + error->all(FLERR,"PPPMDisp coulomb or dispersion order cannot be greater than {}",MAXORDER); // compute two charge force @@ -328,8 +330,7 @@ void PPPMDisp::init() else error->all(FLERR,"Unsupported mixing rule in kspace_style pppm/disp"); break; default: - error->all(FLERR,std::string("Unsupported order in kspace_style " - "pppm/disp, pair_style ") + error->all(FLERR,std::string("Unsupported order in kspace_style pppm/disp, pair_style ") + force->pair_style); } function[k] = 1; @@ -392,8 +393,8 @@ void PPPMDisp::init() alpha = qdist / (cos(0.5*theta) * blen); } - //if g_ewald and g_ewald_6 have not been specified, set some initial value - // to avoid problems when calculating the energies! + // if g_ewald and g_ewald_6 have not been specified, + // set some initial value, to avoid problems when calculating the energies! if (!gewaldflag) g_ewald = 1; if (!gewaldflag_6) g_ewald_6 = 1; @@ -410,10 +411,13 @@ void PPPMDisp::init() if (accuracy_absolute >= 0.0) accuracy = accuracy_absolute; else accuracy = accuracy_relative * two_charge_force; + double acc; + double acc_6,acc_real_6,acc_kspace_6; + int iteration = 0; if (function[0]) { - GridComm *gctmp = nullptr; + gc = nullptr; while (order >= minorder) { if (iteration && me == 0) @@ -423,77 +427,55 @@ void PPPMDisp::init() // set grid for dispersion interaction and coulomb interactions - set_grid(); + set_grid_global(); if (nx_pppm >= OFFSET || ny_pppm >= OFFSET || nz_pppm >= OFFSET) - error->all(FLERR,"PPPMDisp Coulomb grid is too large"); + error->all(FLERR,"PPPMDisp Coulomb grid is too large"); - set_fft_parameters(nx_pppm,ny_pppm,nz_pppm, - nxlo_fft,nylo_fft,nzlo_fft, - nxhi_fft,nyhi_fft,nzhi_fft, - nxlo_in,nylo_in,nzlo_in, - nxhi_in,nyhi_in,nzhi_in, - nxlo_out,nylo_out,nzlo_out, - nxhi_out,nyhi_out,nzhi_out, - nlower,nupper, - ngrid,nfft,nfft_both, - shift,shiftone,order); + set_grid_local(order,nx_pppm,ny_pppm,nz_pppm, + shift,shiftone,shiftatom_lo,shiftatom_hi, + nlower,nupper, + nxlo_fft,nylo_fft,nzlo_fft, + nxhi_fft,nyhi_fft,nzhi_fft); if (overlap_allowed) break; - gctmp = new GridComm(lmp,world,nx_pppm,ny_pppm,nz_pppm, - nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, - nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out); + gc = new Grid3d(lmp,world,nx_pppm,ny_pppm,nz_pppm); + gc->set_distance(0.5*neighbor->skin + qdist); + gc->set_stencil_atom(-nlower,nupper); + gc->set_shift_atom(shiftatom_lo,shiftatom_lo); + gc->set_zfactor(slab_volfactor); + + gc->setup_grid(nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, + nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out); int tmp1,tmp2; - gctmp->setup(tmp1,tmp2); - if (gctmp->ghost_adjacent()) break; - delete gctmp; + gc->setup_comm(tmp1,tmp2); + if (gc->ghost_adjacent()) break; + delete gc; order--; } if (order < minorder) error->all(FLERR,"Coulomb PPPMDisp order has been reduced below minorder"); - if (!overlap_allowed && !gctmp->ghost_adjacent()) + if (!overlap_allowed && !gc->ghost_adjacent()) error->all(FLERR,"PPPMDisp grid stencil extends beyond nearest neighbor processor"); - if (gctmp) delete gctmp; + if (gc) delete gc; // adjust g_ewald if (!gewaldflag) adjust_gewald(); - // calculate the final accuracy + // calculate the final Coulomb accuracy - double acc = final_accuracy(); - - // print stats - - int ngrid_max,nfft_both_max; - MPI_Allreduce(&ngrid,&ngrid_max,1,MPI_INT,MPI_MAX,world); - MPI_Allreduce(&nfft_both,&nfft_both_max,1,MPI_INT,MPI_MAX,world); - - if (me == 0) { - std::string mesg = fmt::format(" Coulomb G vector (1/distance)= {:.16g}\n", - g_ewald); - mesg += fmt::format(" Coulomb grid = {} {} {}\n", - nx_pppm,ny_pppm,nz_pppm); - mesg += fmt::format(" Coulomb stencil order = {}\n",order); - mesg += fmt::format(" Coulomb estimated absolute RMS force accuracy " - "= {:.8g}\n",acc); - mesg += fmt::format(" Coulomb estimated relative force accuracy = {:.8g}\n", - acc/two_charge_force); - mesg += " using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"; - mesg += fmt::format(" 3d grid and FFT values/proc = {} {}\n", - ngrid_max,nfft_both_max); - utils::logmesg(lmp,mesg); - } + acc = final_accuracy(); } iteration = 0; if (function[1] + function[2] + function[3]) { - GridComm *gctmp = nullptr; + gc6 = nullptr; while (order_6 >= minorder) { if (iteration && me == 0) @@ -501,34 +483,32 @@ void PPPMDisp::init() "b/c stencil extends beyond neighbor processor"); iteration++; - set_grid_6(); + set_grid_global_6(); if (nx_pppm_6 >= OFFSET || ny_pppm_6 >= OFFSET || nz_pppm_6 >= OFFSET) - error->all(FLERR,"PPPMDisp Dispersion grid is too large"); + error->all(FLERR,"PPPMDisp Dispersion grid is too large"); - set_fft_parameters(nx_pppm_6,ny_pppm_6,nz_pppm_6, - nxlo_fft_6,nylo_fft_6,nzlo_fft_6, - nxhi_fft_6,nyhi_fft_6,nzhi_fft_6, - nxlo_in_6,nylo_in_6,nzlo_in_6, - nxhi_in_6,nyhi_in_6,nzhi_in_6, - nxlo_out_6,nylo_out_6,nzlo_out_6, - nxhi_out_6,nyhi_out_6,nzhi_out_6, - nlower_6,nupper_6, - ngrid_6,nfft_6,nfft_both_6, - shift_6,shiftone_6,order_6); + set_grid_local(order_6,nx_pppm_6,ny_pppm_6,nz_pppm_6, + shift_6,shiftone_6,shiftatom_lo_6,shiftatom_hi_6, + nlower_6,nupper_6, + nxlo_fft_6,nylo_fft_6,nzlo_fft_6, + nxhi_fft_6,nyhi_fft_6,nzhi_fft_6); if (overlap_allowed) break; - gctmp = new GridComm(lmp,world,nx_pppm_6,ny_pppm_6,nz_pppm_6, - nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6, - nzlo_in_6,nzhi_in_6, - nxlo_out_6,nxhi_out_6,nylo_out_6,nyhi_out_6, - nzlo_out_6,nzhi_out_6); + gc6 = new Grid3d(lmp,world,nx_pppm_6,ny_pppm_6,nz_pppm_6); + gc6->set_distance(0.5*neighbor->skin + qdist); + gc6->set_stencil_atom(-nlower_6,nupper_6); + gc6->set_shift_atom(shiftatom_lo_6,shiftatom_hi_6); + gc6->set_zfactor(slab_volfactor); + + gc6->setup_grid(nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6, + nxlo_out_6,nxhi_out_6,nylo_out_6,nyhi_out_6,nzlo_out_6,nzhi_out_6); int tmp1,tmp2; - gctmp->setup(tmp1,tmp2); - if (gctmp->ghost_adjacent()) break; - delete gctmp; + gc6->setup_comm(tmp1,tmp2); + if (gc6->ghost_adjacent()) break; + delete gc6; order_6--; } @@ -536,41 +516,17 @@ void PPPMDisp::init() if (order_6 < minorder) error->all(FLERR,"Dispersion PPPMDisp order has been " "reduced below minorder"); - if (!overlap_allowed && !gctmp->ghost_adjacent()) + if (!overlap_allowed && !gc6->ghost_adjacent()) error->all(FLERR,"Dispersion PPPMDisp grid stencil extends beyond nearest neighbor proc"); - if (gctmp) delete gctmp; + if (gc6) delete gc6; // adjust g_ewald_6 - if (!gewaldflag_6 && accuracy_kspace_6 == accuracy_real_6) - adjust_gewald_6(); + if (!gewaldflag_6 && accuracy_kspace_6 == accuracy_real_6) adjust_gewald_6(); - // calculate the final accuracy + // calculate the final displerson accuracy - double acc,acc_real,acc_kspace; - final_accuracy_6(acc,acc_real,acc_kspace); - - // print stats - - int ngrid_6_max,nfft_both_6_max; - MPI_Allreduce(&ngrid_6,&ngrid_6_max,1,MPI_INT,MPI_MAX,world); - MPI_Allreduce(&nfft_both_6,&nfft_both_6_max,1,MPI_INT,MPI_MAX,world); - - if (me == 0) { - std::string mesg = fmt::format(" Dispersion G vector (1/distance)= " - "{:.16}\n",g_ewald_6); - mesg += fmt::format(" Dispersion grid = {} {} {}\n", - nx_pppm_6,ny_pppm_6,nz_pppm_6); - mesg += fmt::format(" Dispersion stencil order = {}\n",order_6); - mesg += fmt::format(" Dispersion estimated absolute RMS force accuracy " - "= {:.8}\n",acc); - mesg += fmt::format(" Dispersion estimated relative force accuracy " - "= {:.8}\n",acc/two_charge_force); - mesg += " using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"; - mesg += fmt::format(" 3d grid and FFT values/proc = {} {}\n", - ngrid_6_max,nfft_both_6_max); - utils::logmesg(lmp,mesg); - } + final_accuracy_6(acc_6,acc_real_6,acc_kspace_6); } // allocate K-space dependent memory @@ -600,6 +556,54 @@ void PPPMDisp::init() sf_precoeff1_6,sf_precoeff2_6,sf_precoeff3_6, sf_precoeff4_6,sf_precoeff5_6,sf_precoeff6_6); } + + // print Coulomb stats + + if (function[0]) { + int ngrid_max,nfft_both_max; + MPI_Allreduce(&ngrid,&ngrid_max,1,MPI_INT,MPI_MAX,world); + MPI_Allreduce(&nfft_both,&nfft_both_max,1,MPI_INT,MPI_MAX,world); + + if (me == 0) { + std::string mesg = fmt::format(" Coulomb G vector (1/distance)= {:.16g}\n", + g_ewald); + mesg += fmt::format(" Coulomb grid = {} {} {}\n", + nx_pppm,ny_pppm,nz_pppm); + mesg += fmt::format(" Coulomb stencil order = {}\n",order); + mesg += fmt::format(" Coulomb estimated absolute RMS force accuracy " + "= {:.8g}\n",acc); + mesg += fmt::format(" Coulomb estimated relative force accuracy = {:.8g}\n", + acc/two_charge_force); + mesg += " using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"; + mesg += fmt::format(" 3d grid and FFT values/proc = {} {}\n", + ngrid_max,nfft_both_max); + utils::logmesg(lmp,mesg); + } + } + + // print dipserion stats + + if (function[1] + function[2] + function[3]) { + int ngrid_6_max,nfft_both_6_max; + MPI_Allreduce(&ngrid_6,&ngrid_6_max,1,MPI_INT,MPI_MAX,world); + MPI_Allreduce(&nfft_both_6,&nfft_both_6_max,1,MPI_INT,MPI_MAX,world); + + if (me == 0) { + std::string mesg = fmt::format(" Dispersion G vector (1/distance)= " + "{:.16}\n",g_ewald_6); + mesg += fmt::format(" Dispersion grid = {} {} {}\n", + nx_pppm_6,ny_pppm_6,nz_pppm_6); + mesg += fmt::format(" Dispersion stencil order = {}\n",order_6); + mesg += fmt::format(" Dispersion estimated absolute RMS force accuracy " + "= {:.8}\n",acc_6); + mesg += fmt::format(" Dispersion estimated relative force accuracy " + "= {:.8}\n",acc_6/two_charge_force); + mesg += " using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"; + mesg += fmt::format(" 3d grid and FFT values/proc = {} {}\n", + ngrid_6_max,nfft_both_6_max); + utils::logmesg(lmp,mesg); + } + } } /* ---------------------------------------------------------------------- @@ -794,7 +798,7 @@ void PPPMDisp::setup() called by fix balance b/c it changed sizes of processor sub-domains ------------------------------------------------------------------------- */ -void PPPMDisp::setup_grid() +void PPPMDisp::reset_grid() { // free all arrays previously allocated @@ -804,28 +808,18 @@ void PPPMDisp::setup_grid() // reset portion of global grid that each proc owns if (function[0]) - set_fft_parameters(nx_pppm,ny_pppm,nz_pppm, - nxlo_fft,nylo_fft,nzlo_fft, - nxhi_fft,nyhi_fft,nzhi_fft, - nxlo_in,nylo_in,nzlo_in, - nxhi_in,nyhi_in,nzhi_in, - nxlo_out,nylo_out,nzlo_out, - nxhi_out,nyhi_out,nzhi_out, - nlower,nupper, - ngrid,nfft,nfft_both, - shift,shiftone,order); + set_grid_local(order,nx_pppm,ny_pppm,nz_pppm, + shift,shiftone,shiftatom_lo,shiftatom_hi, + nlower,nupper, + nxlo_fft,nylo_fft,nzlo_fft, + nxhi_fft,nyhi_fft,nzhi_fft); if (function[1] + function[2] + function[3]) - set_fft_parameters(nx_pppm_6,ny_pppm_6,nz_pppm_6, - nxlo_fft_6,nylo_fft_6,nzlo_fft_6, - nxhi_fft_6,nyhi_fft_6,nzhi_fft_6, - nxlo_in_6,nylo_in_6,nzlo_in_6, - nxhi_in_6,nyhi_in_6,nzhi_in_6, - nxlo_out_6,nylo_out_6,nzlo_out_6, - nxhi_out_6,nyhi_out_6,nzhi_out_6, - nlower_6,nupper_6, - ngrid_6,nfft_6,nfft_both_6, - shift_6,shiftone_6,order_6); + set_grid_local(order_6,nx_pppm_6,ny_pppm_6,nz_pppm_6, + shift_6,shiftone_6,shiftatom_lo_6,shiftatom_hi_6, + nlower_6,nupper_6, + nxlo_fft_6,nylo_fft_6,nzlo_fft_6, + nxhi_fft_6,nyhi_fft_6,nzhi_fft_6); // reallocate K-space dependent memory // check if grid communication is now overlapping if not allowed @@ -926,8 +920,8 @@ void PPPMDisp::compute(int eflag, int vflag) make_rho_c(); - gc->reverse_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR), - REVERSE_RHO,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); brick2fft(nxlo_in,nylo_in,nzlo_in,nxhi_in,nyhi_in,nzhi_in, density_brick,density_fft,work1,remap); @@ -941,14 +935,14 @@ void PPPMDisp::compute(int eflag, int vflag) virial_1,vg,vg2, u_brick,v0_brick,v1_brick,v2_brick,v3_brick,v4_brick,v5_brick); - gc->forward_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR), - FORWARD_AD,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_AD,1,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); fieldforce_c_ad(); if (vflag_atom) - gc->forward_comm(GridComm::KSPACE,this,6,sizeof(FFT_SCALAR), - FORWARD_AD_PERATOM,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_PERATOM,6,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); } else { poisson_ik(work1,work2,density_fft,fft1,fft2, @@ -960,14 +954,14 @@ void PPPMDisp::compute(int eflag, int vflag) vdx_brick,vdy_brick,vdz_brick,virial_1,vg,vg2, u_brick,v0_brick,v1_brick,v2_brick,v3_brick,v4_brick,v5_brick); - gc->forward_comm(GridComm::KSPACE,this,3,sizeof(FFT_SCALAR), - FORWARD_IK,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK,3,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); fieldforce_c_ik(); if (evflag_atom) - gc->forward_comm(GridComm::KSPACE,this,7,sizeof(FFT_SCALAR), - FORWARD_IK_PERATOM,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_PERATOM,7,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); } if (evflag_atom) fieldforce_c_peratom(); @@ -984,8 +978,8 @@ void PPPMDisp::compute(int eflag, int vflag) make_rho_g(); - gc6->reverse_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR), - REVERSE_RHO_GEOM,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO_GEOM,1,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); brick2fft(nxlo_in_6,nylo_in_6,nzlo_in_6,nxhi_in_6,nyhi_in_6,nzhi_in_6, density_brick_g,density_fft_g,work1_6,remap_6); @@ -1000,14 +994,14 @@ void PPPMDisp::compute(int eflag, int vflag) u_brick_g,v0_brick_g,v1_brick_g,v2_brick_g, v3_brick_g,v4_brick_g,v5_brick_g); - gc6->forward_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR), - FORWARD_AD_GEOM,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_GEOM,1,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); fieldforce_g_ad(); if (vflag_atom) - gc6->forward_comm(GridComm::KSPACE,this,6,sizeof(FFT_SCALAR), - FORWARD_AD_PERATOM_GEOM,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_PERATOM_GEOM,6,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); } else { poisson_ik(work1_6,work2_6,density_fft_g,fft1_6,fft2_6, @@ -1020,14 +1014,14 @@ void PPPMDisp::compute(int eflag, int vflag) u_brick_g,v0_brick_g,v1_brick_g,v2_brick_g, v3_brick_g,v4_brick_g,v5_brick_g); - gc6->forward_comm(GridComm::KSPACE,this,3,sizeof(FFT_SCALAR), - FORWARD_IK_GEOM,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_GEOM,3,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); fieldforce_g_ik(); if (evflag_atom) - gc6->forward_comm(GridComm::KSPACE,this,7,sizeof(FFT_SCALAR), - FORWARD_IK_PERATOM_GEOM,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_PERATOM_GEOM,7,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); } if (evflag_atom) fieldforce_g_peratom(); @@ -1044,8 +1038,8 @@ void PPPMDisp::compute(int eflag, int vflag) make_rho_a(); - gc6->reverse_comm(GridComm::KSPACE,this,7,sizeof(FFT_SCALAR), - REVERSE_RHO_ARITH,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO_ARITH,7,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); brick2fft_a(); @@ -1074,14 +1068,14 @@ void PPPMDisp::compute(int eflag, int vflag) u_brick_a4,v0_brick_a4,v1_brick_a4,v2_brick_a4, v3_brick_a4,v4_brick_a4,v5_brick_a4); - gc6->forward_comm(GridComm::KSPACE,this,7,sizeof(FFT_SCALAR), - FORWARD_AD_ARITH,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_ARITH,7,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); fieldforce_a_ad(); if (evflag_atom) - gc6->forward_comm(GridComm::KSPACE,this,42,sizeof(FFT_SCALAR), - FORWARD_AD_PERATOM_ARITH,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_PERATOM_ARITH,42,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); } else { poisson_ik(work1_6,work2_6,density_fft_a3,fft1_6,fft2_6, @@ -1115,14 +1109,14 @@ void PPPMDisp::compute(int eflag, int vflag) u_brick_a4,v0_brick_a4,v1_brick_a4,v2_brick_a4, v3_brick_a4,v4_brick_a4,v5_brick_a4); - gc6->forward_comm(GridComm::KSPACE,this,21,sizeof(FFT_SCALAR), - FORWARD_IK_ARITH,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_ARITH,21,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); fieldforce_a_ik(); if (evflag_atom) - gc6->forward_comm(GridComm::KSPACE,this,49,sizeof(FFT_SCALAR), - FORWARD_IK_PERATOM_ARITH,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_PERATOM_ARITH,49,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); } if (evflag_atom) fieldforce_a_peratom(); @@ -1139,8 +1133,8 @@ void PPPMDisp::compute(int eflag, int vflag) make_rho_none(); - gc6->reverse_comm(GridComm::KSPACE,this,nsplit_alloc,sizeof(FFT_SCALAR), - REVERSE_RHO_NONE,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO_NONE,nsplit_alloc,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); brick2fft_none(); @@ -1154,14 +1148,14 @@ void PPPMDisp::compute(int eflag, int vflag) n += 2; } - gc6->forward_comm(GridComm::KSPACE,this,1*nsplit_alloc,sizeof(FFT_SCALAR), - FORWARD_AD_NONE,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_NONE,1*nsplit_alloc,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); fieldforce_none_ad(); if (vflag_atom) - gc6->forward_comm(GridComm::KSPACE,this,6*nsplit_alloc,sizeof(FFT_SCALAR), - FORWARD_AD_PERATOM_NONE,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_PERATOM_NONE,6*nsplit_alloc,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); } else { int n = 0; @@ -1174,14 +1168,14 @@ void PPPMDisp::compute(int eflag, int vflag) n += 2; } - gc6->forward_comm(GridComm::KSPACE,this,3*nsplit_alloc,sizeof(FFT_SCALAR), - FORWARD_IK_NONE,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_NONE,3*nsplit_alloc,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); fieldforce_none_ik(); if (evflag_atom) - gc6->forward_comm(GridComm::KSPACE,this,7*nsplit_alloc,sizeof(FFT_SCALAR), - FORWARD_IK_PERATOM_NONE,gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); + gc6->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_PERATOM_NONE,7*nsplit_alloc,sizeof(FFT_SCALAR), + gc6_buf1,gc6_buf2,MPI_FFT_SCALAR); } if (evflag_atom) fieldforce_none_peratom(); @@ -1685,7 +1679,53 @@ int PPPMDisp::check_convergence(double** A, double** Q, double** A0, void _noopt PPPMDisp::allocate() { + // -------------------------------------- + // Coulomb grids + // -------------------------------------- + if (function[0]) { + + // create ghost grid object for rho and electric field communication + // returns local owned and ghost grid bounds + // setup communication patterns and buffers + + gc = new Grid3d(lmp,world,nx_pppm,ny_pppm,nz_pppm); + gc->set_distance(0.5*neighbor->skin + qdist); + gc->set_stencil_atom(-nlower,nupper); + gc->set_shift_atom(shiftatom_lo,shiftatom_hi); + gc->set_zfactor(slab_volfactor); + + gc->setup_grid(nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, + nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out); + + gc->setup_comm(ngc_buf1,ngc_buf2); + + if (differentiation_flag) npergrid = 1; + else npergrid = 3; + + memory->create(gc_buf1,npergrid*ngc_buf1,"pppm/disp:gc_buf1"); + memory->create(gc_buf2,npergrid*ngc_buf2,"pppm/disp:gc_buf2"); + + // tally local grid sizes + // ngrid = count of owned+ghost grid cells on this proc + // nfft_brick = FFT points in 3d brick-decomposition on this proc + // same as count of owned grid cells + // nfft = FFT points in x-pencil FFT decomposition on this proc + // nfft_both = greater of nfft and nfft_brick + + ngrid = (nxhi_out-nxlo_out+1) * (nyhi_out-nylo_out+1) * + (nzhi_out-nzlo_out+1); + + nfft_brick = (nxhi_in-nxlo_in+1) * (nyhi_in-nylo_in+1) * + (nzhi_in-nzlo_in+1); + + nfft = (nxhi_fft-nxlo_fft+1) * (nyhi_fft-nylo_fft+1) * + (nzhi_fft-nzlo_fft+1); + + nfft_both = MAX(nfft,nfft_brick); + + // allocate distributed grid data + memory->create(work1,2*nfft_both,"pppm/disp:work1"); memory->create(work2,2*nfft_both,"pppm/disp:work2"); @@ -1710,6 +1750,8 @@ void _noopt PPPMDisp::allocate() memory->create3d_offset(density_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out, nxlo_out,nxhi_out,"pppm/disp:density_brick"); + memory->create(density_fft,nfft_both,"pppm/disp:density_fft"); + if (differentiation_flag == 1) { memory->create3d_offset(u_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out, nxlo_out,nxhi_out,"pppm/disp:u_brick"); @@ -1728,7 +1770,11 @@ void _noopt PPPMDisp::allocate() memory->create3d_offset(vdz_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out, nxlo_out,nxhi_out,"pppm/disp:vdz_brick"); } - memory->create(density_fft,nfft_both,"pppm/disp:density_fft"); + + // create 2 FFTs and a Remap + // 1st FFT keeps data in FFT decomposition + // 2nd FFT returns data in 3d brick decomposition + // remap takes data from 3d brick to FFT decomposition int tmp; @@ -1746,23 +1792,91 @@ void _noopt PPPMDisp::allocate() nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft, 1,0,0,FFT_PRECISION,collective_flag); - - // create ghost grid object for rho and electric field communication - // also create 2 bufs for ghost grid cell comm, passed to GridComm methods - - gc = new GridComm(lmp,world,nx_pppm,ny_pppm,nz_pppm, - nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in, - nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out); - - gc->setup(ngc_buf1,ngc_buf2); - - if (differentiation_flag) npergrid = 1; - else npergrid = 3; - - memory->create(gc_buf1,npergrid*ngc_buf1,"pppm:gc_buf1"); - memory->create(gc_buf2,npergrid*ngc_buf2,"pppm:gc_buf2"); } + // -------------------------------------- + // allocations common to all dispersion options + // -------------------------------------- + + if (function[1] + function[2] + function[3]) { + + // create ghost grid object for dispersion communication + // returns local owned and ghost grid bounds + // setup communication patterns and buffers + + gc6 = new Grid3d(lmp,world,nx_pppm_6,ny_pppm_6,nz_pppm_6); + gc6->set_distance(0.5*neighbor->skin + qdist); + gc6->set_stencil_atom(-nlower_6,nupper_6); + gc6->set_shift_atom(shiftatom_lo_6,shiftatom_hi_6); + gc6->set_zfactor(slab_volfactor); + + gc6->setup_grid(nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6, + nxlo_out_6,nxhi_out_6,nylo_out_6,nyhi_out_6,nzlo_out_6,nzhi_out_6); + + gc6->setup_comm(ngc6_buf1,ngc6_buf2); + + if (function[1]) { + if (differentiation_flag) npergrid6 = 1; + else npergrid6 = 3; + } else if (function[2]) { + if (differentiation_flag) npergrid6 = 7; + else npergrid6 = 21; + } else if (function[3]) { + if (differentiation_flag) npergrid6 = 1*nsplit_alloc; + else npergrid6 = 3*nsplit_alloc; + } + + memory->create(gc6_buf1,npergrid6*ngc6_buf1,"pppm:gc_buf1"); + memory->create(gc6_buf2,npergrid6*ngc6_buf2,"pppm:gc_buf2"); + + // tally local grid sizes + // ngrid = count of owned+ghost grid cells on this proc + // nfft_brick = FFT points in 3d brick-decomposition on this proc + // same as count of owned grid cells + // nfft = FFT points in x-pencil FFT decomposition on this proc + // nfft_both = greater of nfft and nfft_brick + + ngrid_6 = (nxhi_out_6-nxlo_out_6+1) * (nyhi_out_6-nylo_out_6+1) * + (nzhi_out_6-nzlo_out_6+1); + + nfft_brick_6 = (nxhi_in_6-nxlo_in_6+1) * (nyhi_in_6-nylo_in_6+1) * + (nzhi_in_6-nzlo_in_6+1); + + nfft_6 = (nxhi_fft_6-nxlo_fft_6+1) * (nyhi_fft_6-nylo_fft_6+1) * + (nzhi_fft_6-nzlo_fft_6+1); + + nfft_both_6 = MAX(nfft_6,nfft_brick_6); + + // create 2 FFTs and a Remap + // 1st FFT keeps data in FFT decomposition + // 2nd FFT returns data in 3d brick decomposition + // remap takes data from 3d brick to FFT decomposition + + int tmp; + + fft1_6 = + new FFT3d(lmp,world,nx_pppm_6,ny_pppm_6,nz_pppm_6, + nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6, + nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6, + 0,0,&tmp,collective_flag); + + fft2_6 = + new FFT3d(lmp,world,nx_pppm_6,ny_pppm_6,nz_pppm_6, + nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6, + nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6, + 0,0,&tmp,collective_flag); + + remap_6 = + new Remap(lmp,world, + nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6, + nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6, + 1,0,0,FFT_PRECISION,collective_flag); + } + + // -------------------------------------- + // dispersion grids with geometric mixing + // -------------------------------------- + if (function[1]) { memory->create(work1_6,2*nfft_both_6,"pppm/disp:work1_6"); memory->create(work2_6,2*nfft_both_6,"pppm/disp:work2_6"); @@ -1789,6 +1903,8 @@ void _noopt PPPMDisp::allocate() memory->create3d_offset(density_brick_g,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6, nxlo_out_6,nxhi_out_6,"pppm/disp:density_brick_g"); + memory->create(density_fft_g,nfft_both_6,"pppm/disp:density_fft_g"); + if (differentiation_flag == 1) { memory->create3d_offset(u_brick_g,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6, nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_g"); @@ -1808,45 +1924,12 @@ void _noopt PPPMDisp::allocate() memory->create3d_offset(vdz_brick_g,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6, nxlo_out_6,nxhi_out_6,"pppm/disp:vdz_brick_g"); } - memory->create(density_fft_g,nfft_both_6,"pppm/disp:density_fft_g"); - - int tmp; - - fft1_6 = - new FFT3d(lmp,world,nx_pppm_6,ny_pppm_6,nz_pppm_6, - nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6, - nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6, - 0,0,&tmp,collective_flag); - - fft2_6 = - new FFT3d(lmp,world,nx_pppm_6,ny_pppm_6,nz_pppm_6, - nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6, - nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6, - 0,0,&tmp,collective_flag); - - remap_6 = - new Remap(lmp,world, - nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6, - nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6, - 1,0,0,FFT_PRECISION,collective_flag); - - // create ghost grid object for rho and electric field communication - // also create 2 bufs for ghost grid cell comm, passed to GridComm methods - - gc6 = - new GridComm(lmp,world,nx_pppm_6,ny_pppm_6,nz_pppm_6, - nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6, - nxlo_out_6,nxhi_out_6,nylo_out_6,nyhi_out_6,nzlo_out_6,nzhi_out_6); - - gc6->setup(ngc6_buf1,ngc6_buf2); - - if (differentiation_flag) npergrid6 = 1; - else npergrid6 = 3; - - memory->create(gc6_buf1,npergrid6*ngc6_buf1,"pppm:gc_buf1"); - memory->create(gc6_buf2,npergrid6*ngc6_buf2,"pppm:gc_buf2"); } + // -------------------------------------- + // dispersion grids with arithmetic mixing + // -------------------------------------- + if (function[2]) { memory->create(work1_6,2*nfft_both_6,"pppm/disp:work1_6"); memory->create(work2_6,2*nfft_both_6,"pppm/disp:work2_6"); @@ -1975,41 +2058,12 @@ void _noopt PPPMDisp::allocate() memory->create3d_offset(vdz_brick_a6,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6, nxlo_out_6,nxhi_out_6,"pppm/disp:vdz_brick_a6"); } - - int tmp; - - fft1_6 = new FFT3d(lmp,world,nx_pppm_6,ny_pppm_6,nz_pppm_6, - nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6, - nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6, - 0,0,&tmp,collective_flag); - - fft2_6 = new FFT3d(lmp,world,nx_pppm_6,ny_pppm_6,nz_pppm_6, - nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6, - nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6, - 0,0,&tmp,collective_flag); - - remap_6 = new Remap(lmp,world, - nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6, - nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6, - 1,0,0,FFT_PRECISION,collective_flag); - - // create ghost grid object for rho and electric field communication - // also create 2 bufs for ghost grid cell comm, passed to GridComm methods - - gc6 = - new GridComm(lmp,world,nx_pppm_6,ny_pppm_6,nz_pppm_6, - nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6, - nxlo_out_6,nxhi_out_6,nylo_out_6,nyhi_out_6,nzlo_out_6,nzhi_out_6); - - gc6->setup(ngc6_buf1,ngc6_buf2); - - if (differentiation_flag) npergrid6 = 7; - else npergrid6 = 21; - - memory->create(gc6_buf1,npergrid6*ngc6_buf1,"pppm:gc_buf1"); - memory->create(gc6_buf2,npergrid6*ngc6_buf2,"pppm:gc_buf2"); } + // -------------------------------------- + // dispersion grids with no mixing + // -------------------------------------- + if (function[3]) { memory->create(work1_6,2*nfft_both_6,"pppm/disp:work1_6"); memory->create(work2_6,2*nfft_both_6,"pppm/disp:work2_6"); @@ -2037,6 +2091,9 @@ void _noopt PPPMDisp::allocate() memory->create4d_offset(density_brick_none,nsplit_alloc, nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6, nxlo_out_6,nxhi_out_6,"pppm/disp:density_brick_none"); + memory->create(density_fft_none,nsplit_alloc,nfft_both_6, + "pppm/disp:density_fft_none"); + if (differentiation_flag == 1) { memory->create4d_offset(u_brick_none,nsplit_alloc, nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6, @@ -2060,41 +2117,6 @@ void _noopt PPPMDisp::allocate() nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6, nxlo_out_6,nxhi_out_6,"pppm/disp:vdz_brick_none"); } - memory->create(density_fft_none,nsplit_alloc,nfft_both_6, - "pppm/disp:density_fft_none"); - - int tmp; - - fft1_6 = new FFT3d(lmp,world,nx_pppm_6,ny_pppm_6,nz_pppm_6, - nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6, - nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6, - 0,0,&tmp,collective_flag); - - fft2_6 = new FFT3d(lmp,world,nx_pppm_6,ny_pppm_6,nz_pppm_6, - nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6, - nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6, - 0,0,&tmp,collective_flag); - - remap_6 = new Remap(lmp,world, - nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6, - nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6, - 1,0,0,FFT_PRECISION,collective_flag); - - // create ghost grid object for rho and electric field communication - // also create 2 bufs for ghost grid cell comm, passed to GridComm methods - - gc6 = - new GridComm(lmp,world,nx_pppm_6,ny_pppm_6,nz_pppm_6, - nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6, - nxlo_out_6,nxhi_out_6,nylo_out_6,nyhi_out_6,nzlo_out_6,nzhi_out_6); - - gc6->setup(ngc6_buf1,ngc6_buf2); - - if (differentiation_flag) npergrid6 = 1*nsplit_alloc; - else npergrid6 = 3*nsplit_alloc; - - memory->create(gc6_buf1,npergrid6*ngc6_buf1,"pppm:gc6_buf1"); - memory->create(gc6_buf2,npergrid6*ngc6_buf2,"pppm:gc6_buf2"); } } @@ -2107,6 +2129,10 @@ void PPPMDisp::allocate_peratom() { peratom_allocate_flag = 1; + // -------------------------------------- + // Coulomb grids + // -------------------------------------- + if (function[0]) { if (differentiation_flag != 1) memory->create3d_offset(u_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out, @@ -2136,6 +2162,10 @@ void PPPMDisp::allocate_peratom() memory->create(gc_buf2,npergrid*ngc_buf2,"pppm:gc_buf2"); } + // -------------------------------------- + // dispersion grids with geometric mixing + // -------------------------------------- + if (function[1]) { if (differentiation_flag != 1 ) memory->create3d_offset(u_brick_g,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6, @@ -2165,6 +2195,10 @@ void PPPMDisp::allocate_peratom() memory->create(gc6_buf2,npergrid6*ngc6_buf2,"pppm:gc6_buf2"); } + // -------------------------------------- + // dispersion grids with arithmetic mixing + // -------------------------------------- + if (function[2]) { if (differentiation_flag != 1) { memory->create3d_offset(u_brick_a0,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6, @@ -2286,6 +2320,10 @@ void PPPMDisp::allocate_peratom() memory->create(gc6_buf2,npergrid6*ngc6_buf2,"pppm:gc6_buf2"); } + // -------------------------------------- + // dispersion grids with no mixing + // -------------------------------------- + if (function[3]) { if (differentiation_flag != 1) memory->create4d_offset(u_brick_none,nsplit_alloc, @@ -2602,11 +2640,10 @@ void PPPMDisp::deallocate_peratom() } /* ---------------------------------------------------------------------- - set size of FFT grid (nx,ny,nz_pppm) and g_ewald - for Coulomb interactions + set global grid and g_ewald for Coulomb interactions ------------------------------------------------------------------------- */ -void PPPMDisp::set_grid() +void PPPMDisp::set_grid_global() { double q2 = qsqsum * force->qqrd2e; @@ -2678,152 +2715,74 @@ void PPPMDisp::set_grid() } /* ---------------------------------------------------------------------- - set the FFT parameters + set params which determine which owned and ghost cells this proc owns + for Coulomb or dipsersion interactions + Grid3d uses these params to partition grids + also partition FFT grids + n xyz lo/hi fft = FFT columns that I own (all of x dim, 2d decomp in yz) ------------------------------------------------------------------------- */ -void PPPMDisp::set_fft_parameters(int& nx_p, int& ny_p, int& nz_p, - int& nxlo_f, int& nylo_f, int& nzlo_f, - int& nxhi_f, int& nyhi_f, int& nzhi_f, - int& nxlo_i, int& nylo_i, int& nzlo_i, - int& nxhi_i, int& nyhi_i, int& nzhi_i, - int& nxlo_o, int& nylo_o, int& nzlo_o, - int& nxhi_o, int& nyhi_o, int& nzhi_o, - int& nlow, int& nupp, - int& ng, int& nf, int& nfb, - double& sft, double& sftone, int& ord) +void PPPMDisp::set_grid_local(int order_either, + int nx_either, int ny_either, int nz_either, + double &shift_either, double &shiftone_either, + double &shiftatom_lo_either,double &shiftatom_hi_either, + int &nlower_either, int &nupper_either, + int &nxlo_fft_either, int &nylo_fft_either, int &nzlo_fft_either, + int &nxhi_fft_either, int &nyhi_fft_either, int &nzhi_fft_either) { - // partition global grid across procs - // n xyz lo/hi i = lower/upper bounds of global grid this proc owns - // indices range from 0 to N-1 inclusive in each dim - - comm->partition_grid(nx_p,ny_p,nz_p,slab_volfactor, - nxlo_i,nxhi_i,nylo_i,nyhi_i,nzlo_i,nzhi_i); - - // nlow,nupp = stencil size for mapping particles to PPPM grid - - nlow = -(ord-1)/2; - nupp = ord/2; - - // sft values for particle <-> grid mapping + // shift values for particle <-> grid mapping depend on stencil order // add/subtract OFFSET to avoid int(-0.75) = 0 when want it to be -1 + // used in particle_map() and make_rho() and fieldforce() - if (ord % 2) sft = OFFSET + 0.5; - else sft = OFFSET; - if (ord % 2) sftone = 0.0; - else sftone = 0.5; + if (order_either % 2) shift_either = OFFSET + 0.5; + else shift_either = OFFSET; - // nlo_out,nhi_out = lower/upper limits of the 3d sub-brick of - // global PPPM grid that my particles can contribute charge to - // effectively nlo_in,nhi_in + ghost cells - // nlo,nhi = global coords of grid pt to "lower left" of smallest/largest - // position a particle in my box can be at - // dist[3] = particle position bound = subbox + skin/2.0 + qdist - // qdist = offset due to TIP4P fictitious charge - // convert to triclinic if necessary - // nlo_out,nhi_out = nlo,nhi + stencil size for particle mapping - // for slab PPPM, assign z grid as if it were not extended + if (order_either % 2) shiftone_either = 0.0; + else shiftone_either = 0.5; - double *prd,*sublo,*subhi; + // nlower/nupper = stencil size for mapping particles to grid - if (triclinic == 0) { - prd = domain->prd; - boxlo = domain->boxlo; - sublo = domain->sublo; - subhi = domain->subhi; - } else { - prd = domain->prd_lamda; - boxlo = domain->boxlo_lamda; - sublo = domain->sublo_lamda; - subhi = domain->subhi_lamda; + nlower_either = -(order_either-1)/2; + nupper_either = order_either/2; + + // shiftatom lo/hi are passed to Grid3d to determine ghost cell extents + // shiftatom_lo = min shift on lo side + // shiftatom_hi = max shift on hi side + // for PPPMStagger, stagger value (0.0 or 0.5) also affects this + + if (order % 2) { + shiftatom_lo_either = 0.5; + shiftatom_hi_either = 0.5; + } else if (order % 2 == 0) { + shiftatom_lo_either = 0.0; + shiftatom_hi_either = 0.0; } - double xprd = prd[0]; - double yprd = prd[1]; - double zprd = prd[2]; - double zprd_slab = zprd*slab_volfactor; - - double dist[3]; - double cuthalf = 0.5*neighbor->skin + qdist; - if (triclinic == 0) dist[0] = dist[1] = dist[2] = cuthalf; - else { - dist[0] = cuthalf/domain->prd[0]; - dist[1] = cuthalf/domain->prd[1]; - dist[2] = cuthalf/domain->prd[2]; - } - - int nlo,nhi; - - nlo = static_cast ((sublo[0]-dist[0]-boxlo[0]) * - nx_p/xprd + sft) - OFFSET; - nhi = static_cast ((subhi[0]+dist[0]-boxlo[0]) * - nx_p/xprd + sft) - OFFSET; - nxlo_o = nlo + nlow; - nxhi_o = nhi + nupp; - - nlo = static_cast ((sublo[1]-dist[1]-boxlo[1]) * - ny_p/yprd + sft) - OFFSET; - nhi = static_cast ((subhi[1]+dist[1]-boxlo[1]) * - ny_p/yprd + sft) - OFFSET; - nylo_o = nlo + nlow; - nyhi_o = nhi + nupp; - - nlo = static_cast ((sublo[2]-dist[2]-boxlo[2]) * - nz_p/zprd_slab + sft) - OFFSET; - nhi = static_cast ((subhi[2]+dist[2]-boxlo[2]) * - nz_p/zprd_slab + sft) - OFFSET; - nzlo_o = nlo + nlow; - nzhi_o = nhi + nupp; - - // for slab PPPM, change the grid boundary for processors at +z end - // to include the empty volume between periodically repeating slabs - // for slab PPPM, want charge data communicated from -z proc to +z proc, - // but not vice versa, also want field data communicated from +z proc to - // -z proc, but not vice versa - // this is accomplished by nzhi_i = nzhi_o on +z end (no ghost cells) - - if (slabflag && (comm->myloc[2] == comm->procgrid[2]-1)) { - nzhi_i = nz_p - 1; - nzhi_o = nz_p - 1; - } - - // decomposition of FFT mesh + // x-pencil decomposition of Coulomb FFT mesh // global indices range from 0 to N-1 - // proc owns entire x-dimension, clump of columns in y,z dimensions + // each proc owns entire x-dimension, clumps of columns in y,z dimensions // npey_fft,npez_fft = # of procs in y,z dims // if nprocs is small enough, proc can own 1 or more entire xy planes, // else proc owns 2d sub-blocks of yz plane // me_y,me_z = which proc (0-npe_fft-1) I am in y,z dimensions // nlo_fft,nhi_fft = lower/upper limit of the section - // of the global FFT mesh that I own + // of the global FFT mesh that I own in x-pencil decomposition int npey_fft,npez_fft; - if (nz_p >= nprocs) { + if (nz_either >= nprocs) { npey_fft = 1; npez_fft = nprocs; - } else procs2grid2d(nprocs,ny_p,nz_p,&npey_fft,&npez_fft); + } else procs2grid2d(nprocs,ny_either,nz_either,&npey_fft,&npez_fft); int me_y = me % npey_fft; int me_z = me / npey_fft; - nxlo_f = 0; - nxhi_f = nx_p - 1; - nylo_f = me_y*ny_p/npey_fft; - nyhi_f = (me_y+1)*ny_p/npey_fft - 1; - nzlo_f = me_z*nz_p/npez_fft; - nzhi_f = (me_z+1)*nz_p/npez_fft - 1; - - // PPPM grid for this proc, including ghosts - - ng = (nxhi_o-nxlo_o+1) * (nyhi_o-nylo_o+1) * (nzhi_o-nzlo_o+1); - - // FFT arrays on this proc, without ghosts - // nf = nfft = FFT points in FFT decomposition on this proc - // nfft_brick = FFT points in 3d brick-decomposition on this proc - // nfb = nfft_both = greater of 2 values - - nf = (nxhi_f-nxlo_f+1) * (nyhi_f-nylo_f+1) * (nzhi_f-nzlo_f+1); - int nfft_brick = (nxhi_i-nxlo_i+1) * (nyhi_i-nylo_i+1) * (nzhi_i-nzlo_i+1); - nfb = MAX(nf,nfft_brick); + nxlo_fft_either = 0; + nxhi_fft_either = nx_either - 1; + nylo_fft_either = me_y*ny_either/npey_fft; + nyhi_fft_either = (me_y+1)*ny_either/npey_fft - 1; + nzlo_fft_either = me_z*nz_either/npez_fft; + nzhi_fft_either = (me_z+1)*nz_either/npez_fft - 1; } /* ---------------------------------------------------------------------- @@ -3365,17 +3324,15 @@ double PPPMDisp::compute_qopt_6_ad() } /* ---------------------------------------------------------------------- - set size of FFT grid and g_ewald_6 - for Dispersion interactions + set global grid and g_ewald_6 for dispersion interactions ------------------------------------------------------------------------- */ -void PPPMDisp::set_grid_6() +void PPPMDisp::set_grid_global_6() { - // calculate csum - if (!csumflag) calc_csum(); if (!gewaldflag_6) set_init_g6(); if (!gridflag_6) set_n_pppm_6(); + while (!factorable(nx_pppm_6)) nx_pppm_6++; while (!factorable(ny_pppm_6)) ny_pppm_6++; while (!factorable(nz_pppm_6)) nz_pppm_6++; @@ -8310,7 +8267,7 @@ double PPPMDisp::memory_usage() bytes += (double)nfft_both_6 * (mixing + 2) * sizeof(FFT_SCALAR); } - // four GridComm bufs + // four Grid3d bufs bytes += (double)(ngc_buf1 + ngc_buf2) * npergrid * sizeof(FFT_SCALAR); bytes += (double)(ngc6_buf1 + ngc6_buf2) * npergrid6 * sizeof(FFT_SCALAR); diff --git a/src/KSPACE/pppm_disp.h b/src/KSPACE/pppm_disp.h index 1f254e772d..a222e041d9 100644 --- a/src/KSPACE/pppm_disp.h +++ b/src/KSPACE/pppm_disp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -34,7 +34,7 @@ class PPPMDisp : public KSpace { ~PPPMDisp() override; void init() override; void setup() override; - void setup_grid() override; + void reset_grid() override; void settings(int, char **) override; void compute(int, int) override; int timing_1d(int, double &) override; @@ -64,19 +64,19 @@ class PPPMDisp : public KSpace { double delxinv, delyinv, delzinv, delvolinv; double delxinv_6, delyinv_6, delzinv_6, delvolinv_6; - double shift, shiftone; + double shift, shiftone, shiftatom_lo, shiftatom_hi; int nxlo_in, nylo_in, nzlo_in, nxhi_in, nyhi_in, nzhi_in; int nxlo_out, nylo_out, nzlo_out, nxhi_out, nyhi_out, nzhi_out; int nxlo_fft, nylo_fft, nzlo_fft, nxhi_fft, nyhi_fft, nzhi_fft; int nlower, nupper; - int ngrid, nfft, nfft_both; + int ngrid, nfft_brick, nfft, nfft_both; - double shift_6, shiftone_6; + double shift_6, shiftone_6, shiftatom_lo_6, shiftatom_hi_6; int nxlo_in_6, nylo_in_6, nzlo_in_6, nxhi_in_6, nyhi_in_6, nzhi_in_6; int nxlo_out_6, nylo_out_6, nzlo_out_6, nxhi_out_6, nyhi_out_6, nzhi_out_6; int nxlo_fft_6, nylo_fft_6, nzlo_fft_6, nxhi_fft_6, nyhi_fft_6, nzhi_fft_6; int nlower_6, nupper_6; - int ngrid_6, nfft_6, nfft_both_6; + int ngrid_6, nfft_brick_6, nfft_6, nfft_both_6; // the following variables are needed for every structure factor @@ -149,7 +149,8 @@ class PPPMDisp : public KSpace { FFT_SCALAR ****v0_brick_none, ****v1_brick_none, ****v2_brick_none, ****v3_brick_none, ****v4_brick_none, ****v5_brick_none; - //// needed for each interaction type + // needed for each interaction type + double *greensfn; double **vg; double **vg2; @@ -178,7 +179,7 @@ class PPPMDisp : public KSpace { class FFT3d *fft1, *fft2; class FFT3d *fft1_6, *fft2_6; class Remap *remap, *remap_6; - class GridComm *gc, *gc6; + class Grid3d *gc, *gc6; FFT_SCALAR *gc_buf1, *gc_buf2, *gc6_buf1, *gc6_buf2; int ngc_buf1, ngc_buf2, npergrid; @@ -190,7 +191,9 @@ class PPPMDisp : public KSpace { int triclinic; // domain settings, orthog or triclinic double *boxlo; + // TIP4P settings + int typeH, typeO; // atom types of TIP4P water H and O atoms double qdist; // distance from O site to negative charge double alpha; // geometric factor @@ -202,15 +205,16 @@ class PPPMDisp : public KSpace { void mmult(double **, double **, double **, int); int check_convergence(double **, double **, double **, double **, double **, double **, int); - void set_grid(); - void set_grid_6(); + void set_grid_global(); + void set_grid_global_6(); + void set_grid_local(int, int, int, int, double &, double &, double &, double &, + int &, int &, int &, int &, int &, int &, int &, int &); void set_init_g6(); - void set_fft_parameters(int &, int &, int &, int &, int &, int &, int &, int &, int &, int &, - int &, int &, int &, int &, int &, int &, int &, int &, int &, int &, - int &, int &, int &, int &, int &, int &, double &, double &, int &); void set_n_pppm_6(); + void adjust_gewald(); void adjust_gewald_6(); + double f(); double derivf(); double f_6(); @@ -218,6 +222,7 @@ class PPPMDisp : public KSpace { double final_accuracy(); void final_accuracy_6(double &, double &, double &); double lj_rspace_error(); + double compute_qopt(); double compute_qopt_6(); double compute_qopt_ik(); @@ -231,6 +236,7 @@ class PPPMDisp : public KSpace { virtual void allocate_peratom(); virtual void deallocate(); virtual void deallocate_peratom(); + int factorable(int); double rms(double, double, bigint, double, double **); double diffpr(double, double, double, double, double **); diff --git a/src/KSPACE/pppm_disp_tip4p.cpp b/src/KSPACE/pppm_disp_tip4p.cpp index 92b811984c..c5ed2f26d6 100644 --- a/src/KSPACE/pppm_disp_tip4p.cpp +++ b/src/KSPACE/pppm_disp_tip4p.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pppm_disp_tip4p.h b/src/KSPACE/pppm_disp_tip4p.h index e9d5babe0f..9cb9d112e2 100644 --- a/src/KSPACE/pppm_disp_tip4p.h +++ b/src/KSPACE/pppm_disp_tip4p.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pppm_stagger.cpp b/src/KSPACE/pppm_stagger.cpp index 35aec73169..d6f3c9cac6 100644 --- a/src/KSPACE/pppm_stagger.cpp +++ b/src/KSPACE/pppm_stagger.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -17,17 +17,17 @@ ------------------------------------------------------------------------- */ #include "pppm_stagger.h" -#include -#include -#include -#include "atom.h" -#include "gridcomm.h" -#include "domain.h" -#include "memory.h" -#include "error.h" +#include "atom.h" +#include "domain.h" +#include "error.h" +#include "grid3d.h" #include "math_const.h" #include "math_special.h" +#include "memory.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; @@ -145,7 +145,7 @@ void PPPMStagger::compute(int eflag, int vflag) nstagger = 2; stagger = 0.0; - for (int n=0; nreverse_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR), - REVERSE_RHO,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); brick2fft(); // compute potential gradient on my FFT grid and @@ -172,21 +172,21 @@ void PPPMStagger::compute(int eflag, int vflag) // to fill ghost cells surrounding their 3d bricks if (differentiation_flag == 1) - gc->forward_comm(GridComm::KSPACE,this,1,sizeof(FFT_SCALAR), - FORWARD_AD,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_AD,1,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); else - gc->forward_comm(GridComm::KSPACE,this,3,sizeof(FFT_SCALAR), - FORWARD_IK,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK,3,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); // extra per-atom energy/virial communication if (evflag_atom) { if (differentiation_flag == 1 && vflag_atom) - gc->forward_comm(GridComm::KSPACE,this,6,sizeof(FFT_SCALAR), - FORWARD_AD_PERATOM,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_PERATOM,6,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); else if (differentiation_flag == 0) - gc->forward_comm(GridComm::KSPACE,this,7,sizeof(FFT_SCALAR), - FORWARD_IK_PERATOM,gc_buf1,gc_buf2,MPI_FFT_SCALAR); + gc->forward_comm(Grid3d::KSPACE,this,FORWARD_IK_PERATOM,7,sizeof(FFT_SCALAR), + gc_buf1,gc_buf2,MPI_FFT_SCALAR); } // calculate the force on my particles @@ -197,7 +197,7 @@ void PPPMStagger::compute(int eflag, int vflag) if (evflag_atom) fieldforce_peratom(); - stagger += 1.0/float(nstagger); + stagger += 1.0/nstagger; } // update qsum and qsqsum, if atom count has changed and energy needed diff --git a/src/KSPACE/pppm_stagger.h b/src/KSPACE/pppm_stagger.h index 92e05d39b1..f434c19caf 100644 --- a/src/KSPACE/pppm_stagger.h +++ b/src/KSPACE/pppm_stagger.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/pppm_tip4p.cpp b/src/KSPACE/pppm_tip4p.cpp index 490c092004..730b604d7a 100644 --- a/src/KSPACE/pppm_tip4p.cpp +++ b/src/KSPACE/pppm_tip4p.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -17,14 +17,15 @@ ------------------------------------------------------------------------- */ #include "pppm_tip4p.h" -#include -#include + #include "atom.h" #include "domain.h" #include "force.h" #include "error.h" #include "math_const.h" +#include + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pppm_tip4p.h b/src/KSPACE/pppm_tip4p.h index 0e6b2cc91b..6af532c409 100644 --- a/src/KSPACE/pppm_tip4p.h +++ b/src/KSPACE/pppm_tip4p.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/remap.cpp b/src/KSPACE/remap.cpp index c3e8fafdac..2b2883e560 100644 --- a/src/KSPACE/remap.cpp +++ b/src/KSPACE/remap.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/remap.h b/src/KSPACE/remap.h index 0e0663be35..59d47ede53 100644 --- a/src/KSPACE/remap.h +++ b/src/KSPACE/remap.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/remap_wrap.cpp b/src/KSPACE/remap_wrap.cpp index 10e14d5618..ca98748011 100644 --- a/src/KSPACE/remap_wrap.cpp +++ b/src/KSPACE/remap_wrap.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/KSPACE/remap_wrap.h b/src/KSPACE/remap_wrap.h index dc59ad7402..fc34bc2df1 100644 --- a/src/KSPACE/remap_wrap.h +++ b/src/KSPACE/remap_wrap.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/LATBOLTZ/fix_lb_fluid.cpp b/src/LATBOLTZ/fix_lb_fluid.cpp index 049d9ce44e..f692d28084 100644 --- a/src/LATBOLTZ/fix_lb_fluid.cpp +++ b/src/LATBOLTZ/fix_lb_fluid.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -181,9 +181,9 @@ FixLbFluid::FixLbFluid(LAMMPS *lmp, int narg, char **arg) : // we require continuous time stepping time_depend = 1; - if (narg < 6) error->all(FLERR, "Illegal fix lb/fluid command"); + if (narg < 6) utils::missing_cmd_args(FLERR, "fix lb/fluid",error); - if (comm->style != 0) + if (comm->style != Comm::BRICK) error->universe_all(FLERR, "Fix lb/fluid can only currently be used with comm_style brick"); MPI_Comm_rank(world, &me); @@ -2483,7 +2483,8 @@ void FixLbFluid::write_restartfile() // we only take 1/2 force here. We can use fnew as it will be overwritten in initial_integrate. // This ensures total momentum is conserved after a restart. - double etacov[numvel]; + std::vector etacov; + etacov.resize(numvel); for (int i = 0; i < subNbx; i++) for (int j = 0; j < subNby; j++) for (int k = 0; k < subNbz; k++) { diff --git a/src/LATBOLTZ/fix_lb_fluid.h b/src/LATBOLTZ/fix_lb_fluid.h index a7843d4db2..19cd2c6dc3 100644 --- a/src/LATBOLTZ/fix_lb_fluid.h +++ b/src/LATBOLTZ/fix_lb_fluid.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ----------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/LATBOLTZ/fix_lb_momentum.cpp b/src/LATBOLTZ/fix_lb_momentum.cpp index b1683e90ac..96f48a8500 100644 --- a/src/LATBOLTZ/fix_lb_momentum.cpp +++ b/src/LATBOLTZ/fix_lb_momentum.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/LATBOLTZ/fix_lb_momentum.h b/src/LATBOLTZ/fix_lb_momentum.h index 51eaed4df5..37edcae7c6 100644 --- a/src/LATBOLTZ/fix_lb_momentum.h +++ b/src/LATBOLTZ/fix_lb_momentum.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/LATBOLTZ/fix_lb_viscous.cpp b/src/LATBOLTZ/fix_lb_viscous.cpp index 1656501613..ae05493187 100644 --- a/src/LATBOLTZ/fix_lb_viscous.cpp +++ b/src/LATBOLTZ/fix_lb_viscous.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/LATBOLTZ/fix_lb_viscous.h b/src/LATBOLTZ/fix_lb_viscous.h index d4891369af..a239c5cb9f 100644 --- a/src/LATBOLTZ/fix_lb_viscous.h +++ b/src/LATBOLTZ/fix_lb_viscous.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/LATBOLTZ/latboltz_const.h b/src/LATBOLTZ/latboltz_const.h index 618e3616df..65f717cf48 100644 --- a/src/LATBOLTZ/latboltz_const.h +++ b/src/LATBOLTZ/latboltz_const.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ----------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/LATTE/Install.sh b/src/LATTE/Install.sh index 73f8bc24cb..4d895ca434 100755 --- a/src/LATTE/Install.sh +++ b/src/LATTE/Install.sh @@ -47,7 +47,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*latte.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*latte.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/latte\/Makefile.lammps @@ -61,7 +61,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*latte.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*latte.*$/d' ../Makefile.package.settings fi fi diff --git a/src/LATTE/fix_latte.cpp b/src/LATTE/fix_latte.cpp index f97162cd40..d2bde641bf 100644 --- a/src/LATTE/fix_latte.cpp +++ b/src/LATTE/fix_latte.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/LATTE/fix_latte.h b/src/LATTE/fix_latte.h index 18730e7f5e..c3af3c4e3f 100644 --- a/src/LATTE/fix_latte.h +++ b/src/LATTE/fix_latte.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -47,7 +47,7 @@ class FixLatte : public Fix { int coulomb, pbcflag, pe_peratom, virial_global, virial_peratom, neighflag; int exclude, excludebit; int eflag_caller; - char *id_pe,*id_exclude; + char *id_pe, *id_exclude; int *exclusion_group_ptr; int setupflag, newsystem; bigint natoms_last; diff --git a/src/MACHDYN/Install.sh b/src/MACHDYN/Install.sh index bf18c332f3..604f53f8b1 100755 --- a/src/MACHDYN/Install.sh +++ b/src/MACHDYN/Install.sh @@ -45,7 +45,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*machdyn.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*machdyn.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/machdyn\/Makefile.lammps @@ -59,7 +59,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*machdyn.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*machdyn.*$/d' ../Makefile.package.settings fi fi diff --git a/src/MACHDYN/atom_vec_smd.cpp b/src/MACHDYN/atom_vec_smd.cpp index cfceadfbd4..d1bae9ecb7 100644 --- a/src/MACHDYN/atom_vec_smd.cpp +++ b/src/MACHDYN/atom_vec_smd.cpp @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -26,6 +26,8 @@ #include "atom.h" +#include + using namespace LAMMPS_NS; #define NMAT_FULL 9 diff --git a/src/MACHDYN/atom_vec_smd.h b/src/MACHDYN/atom_vec_smd.h index bde5b4595d..6ca7f08b4d 100644 --- a/src/MACHDYN/atom_vec_smd.h +++ b/src/MACHDYN/atom_vec_smd.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -35,7 +35,7 @@ AtomStyle(smd,AtomVecSMD); namespace LAMMPS_NS { -class AtomVecSMD : public AtomVec { +class AtomVecSMD : virtual public AtomVec { public: AtomVecSMD(class LAMMPS *); diff --git a/src/MACHDYN/compute_smd_contact_radius.cpp b/src/MACHDYN/compute_smd_contact_radius.cpp index 7a10b563f8..4f835e62a2 100644 --- a/src/MACHDYN/compute_smd_contact_radius.cpp +++ b/src/MACHDYN/compute_smd_contact_radius.cpp @@ -14,7 +14,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_contact_radius.h b/src/MACHDYN/compute_smd_contact_radius.h index 3891bc8800..8a528c1379 100644 --- a/src/MACHDYN/compute_smd_contact_radius.h +++ b/src/MACHDYN/compute_smd_contact_radius.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_damage.cpp b/src/MACHDYN/compute_smd_damage.cpp index f3b52ccfce..3ddee2731c 100644 --- a/src/MACHDYN/compute_smd_damage.cpp +++ b/src/MACHDYN/compute_smd_damage.cpp @@ -14,7 +14,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_damage.h b/src/MACHDYN/compute_smd_damage.h index 0200c2a3e3..616d789861 100644 --- a/src/MACHDYN/compute_smd_damage.h +++ b/src/MACHDYN/compute_smd_damage.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_hourglass_error.cpp b/src/MACHDYN/compute_smd_hourglass_error.cpp index 1e36c9d182..68c4778fef 100644 --- a/src/MACHDYN/compute_smd_hourglass_error.cpp +++ b/src/MACHDYN/compute_smd_hourglass_error.cpp @@ -14,7 +14,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_hourglass_error.h b/src/MACHDYN/compute_smd_hourglass_error.h index 8654028636..58df57cc6d 100644 --- a/src/MACHDYN/compute_smd_hourglass_error.h +++ b/src/MACHDYN/compute_smd_hourglass_error.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_internal_energy.cpp b/src/MACHDYN/compute_smd_internal_energy.cpp index 0d17588b13..136e50bd96 100644 --- a/src/MACHDYN/compute_smd_internal_energy.cpp +++ b/src/MACHDYN/compute_smd_internal_energy.cpp @@ -14,7 +14,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_internal_energy.h b/src/MACHDYN/compute_smd_internal_energy.h index 774e8f16e3..ded28192b7 100644 --- a/src/MACHDYN/compute_smd_internal_energy.h +++ b/src/MACHDYN/compute_smd_internal_energy.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_plastic_strain.cpp b/src/MACHDYN/compute_smd_plastic_strain.cpp index 3f5fbdf090..bb985a8c01 100644 --- a/src/MACHDYN/compute_smd_plastic_strain.cpp +++ b/src/MACHDYN/compute_smd_plastic_strain.cpp @@ -14,7 +14,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_plastic_strain.h b/src/MACHDYN/compute_smd_plastic_strain.h index 2315b2fcfe..aca1b2f972 100644 --- a/src/MACHDYN/compute_smd_plastic_strain.h +++ b/src/MACHDYN/compute_smd_plastic_strain.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_plastic_strain_rate.cpp b/src/MACHDYN/compute_smd_plastic_strain_rate.cpp index d215b0e321..9ad37f29b2 100644 --- a/src/MACHDYN/compute_smd_plastic_strain_rate.cpp +++ b/src/MACHDYN/compute_smd_plastic_strain_rate.cpp @@ -14,7 +14,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_plastic_strain_rate.h b/src/MACHDYN/compute_smd_plastic_strain_rate.h index 29fb8b5669..3bc580df1b 100644 --- a/src/MACHDYN/compute_smd_plastic_strain_rate.h +++ b/src/MACHDYN/compute_smd_plastic_strain_rate.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_rho.cpp b/src/MACHDYN/compute_smd_rho.cpp index f05c7c6e83..6cbf7f0d9e 100644 --- a/src/MACHDYN/compute_smd_rho.cpp +++ b/src/MACHDYN/compute_smd_rho.cpp @@ -13,7 +13,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_rho.h b/src/MACHDYN/compute_smd_rho.h index b4d41f1ee7..c6ab65e35a 100644 --- a/src/MACHDYN/compute_smd_rho.h +++ b/src/MACHDYN/compute_smd_rho.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_tlsph_defgrad.cpp b/src/MACHDYN/compute_smd_tlsph_defgrad.cpp index e8c78821dc..cbfd404460 100644 --- a/src/MACHDYN/compute_smd_tlsph_defgrad.cpp +++ b/src/MACHDYN/compute_smd_tlsph_defgrad.cpp @@ -13,7 +13,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_tlsph_defgrad.h b/src/MACHDYN/compute_smd_tlsph_defgrad.h index 61ce69bc9d..c210d4f3e2 100644 --- a/src/MACHDYN/compute_smd_tlsph_defgrad.h +++ b/src/MACHDYN/compute_smd_tlsph_defgrad.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_tlsph_dt.cpp b/src/MACHDYN/compute_smd_tlsph_dt.cpp index 44311fc4ce..334553a7c9 100644 --- a/src/MACHDYN/compute_smd_tlsph_dt.cpp +++ b/src/MACHDYN/compute_smd_tlsph_dt.cpp @@ -13,7 +13,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_tlsph_dt.h b/src/MACHDYN/compute_smd_tlsph_dt.h index 7a4154da9a..9b26678f8a 100644 --- a/src/MACHDYN/compute_smd_tlsph_dt.h +++ b/src/MACHDYN/compute_smd_tlsph_dt.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_tlsph_num_neighs.cpp b/src/MACHDYN/compute_smd_tlsph_num_neighs.cpp index 230a5946f8..85de6125c6 100644 --- a/src/MACHDYN/compute_smd_tlsph_num_neighs.cpp +++ b/src/MACHDYN/compute_smd_tlsph_num_neighs.cpp @@ -14,7 +14,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_tlsph_num_neighs.h b/src/MACHDYN/compute_smd_tlsph_num_neighs.h index 5c0a1295e1..08b1e3aef0 100644 --- a/src/MACHDYN/compute_smd_tlsph_num_neighs.h +++ b/src/MACHDYN/compute_smd_tlsph_num_neighs.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_tlsph_shape.cpp b/src/MACHDYN/compute_smd_tlsph_shape.cpp index 5e69c6650b..8c1c420fba 100644 --- a/src/MACHDYN/compute_smd_tlsph_shape.cpp +++ b/src/MACHDYN/compute_smd_tlsph_shape.cpp @@ -13,7 +13,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_tlsph_shape.h b/src/MACHDYN/compute_smd_tlsph_shape.h index e8d9080326..a311b57459 100644 --- a/src/MACHDYN/compute_smd_tlsph_shape.h +++ b/src/MACHDYN/compute_smd_tlsph_shape.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_tlsph_strain.cpp b/src/MACHDYN/compute_smd_tlsph_strain.cpp index bb71792442..84987a9891 100644 --- a/src/MACHDYN/compute_smd_tlsph_strain.cpp +++ b/src/MACHDYN/compute_smd_tlsph_strain.cpp @@ -14,7 +14,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_tlsph_strain.h b/src/MACHDYN/compute_smd_tlsph_strain.h index f1e3f43855..a76fea70b3 100644 --- a/src/MACHDYN/compute_smd_tlsph_strain.h +++ b/src/MACHDYN/compute_smd_tlsph_strain.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_tlsph_strain_rate.cpp b/src/MACHDYN/compute_smd_tlsph_strain_rate.cpp index d6da2d2288..72f92d54de 100644 --- a/src/MACHDYN/compute_smd_tlsph_strain_rate.cpp +++ b/src/MACHDYN/compute_smd_tlsph_strain_rate.cpp @@ -14,7 +14,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_tlsph_strain_rate.h b/src/MACHDYN/compute_smd_tlsph_strain_rate.h index 73a16d3ac3..a275d802c4 100644 --- a/src/MACHDYN/compute_smd_tlsph_strain_rate.h +++ b/src/MACHDYN/compute_smd_tlsph_strain_rate.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_tlsph_stress.cpp b/src/MACHDYN/compute_smd_tlsph_stress.cpp index 724fff5b88..4e48003755 100644 --- a/src/MACHDYN/compute_smd_tlsph_stress.cpp +++ b/src/MACHDYN/compute_smd_tlsph_stress.cpp @@ -13,7 +13,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_tlsph_stress.h b/src/MACHDYN/compute_smd_tlsph_stress.h index 8be9ff44c9..f16a5282c4 100644 --- a/src/MACHDYN/compute_smd_tlsph_stress.h +++ b/src/MACHDYN/compute_smd_tlsph_stress.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_triangle_vertices.cpp b/src/MACHDYN/compute_smd_triangle_vertices.cpp index 89a2a24b89..e66f36c48e 100644 --- a/src/MACHDYN/compute_smd_triangle_vertices.cpp +++ b/src/MACHDYN/compute_smd_triangle_vertices.cpp @@ -14,7 +14,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_triangle_vertices.h b/src/MACHDYN/compute_smd_triangle_vertices.h index b7fa2e4fc2..d11b7b52ba 100644 --- a/src/MACHDYN/compute_smd_triangle_vertices.h +++ b/src/MACHDYN/compute_smd_triangle_vertices.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_ulsph_effm.cpp b/src/MACHDYN/compute_smd_ulsph_effm.cpp index 35b0fe851d..e457b91e22 100644 --- a/src/MACHDYN/compute_smd_ulsph_effm.cpp +++ b/src/MACHDYN/compute_smd_ulsph_effm.cpp @@ -13,7 +13,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_ulsph_effm.h b/src/MACHDYN/compute_smd_ulsph_effm.h index 5a653b48cd..844532ae4d 100644 --- a/src/MACHDYN/compute_smd_ulsph_effm.h +++ b/src/MACHDYN/compute_smd_ulsph_effm.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_ulsph_num_neighs.cpp b/src/MACHDYN/compute_smd_ulsph_num_neighs.cpp index 7c181a6a82..f123729227 100644 --- a/src/MACHDYN/compute_smd_ulsph_num_neighs.cpp +++ b/src/MACHDYN/compute_smd_ulsph_num_neighs.cpp @@ -14,7 +14,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_ulsph_num_neighs.h b/src/MACHDYN/compute_smd_ulsph_num_neighs.h index 0d333e64c2..8d1d1555c5 100644 --- a/src/MACHDYN/compute_smd_ulsph_num_neighs.h +++ b/src/MACHDYN/compute_smd_ulsph_num_neighs.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_ulsph_strain.cpp b/src/MACHDYN/compute_smd_ulsph_strain.cpp index eed26821b0..ea278832cf 100644 --- a/src/MACHDYN/compute_smd_ulsph_strain.cpp +++ b/src/MACHDYN/compute_smd_ulsph_strain.cpp @@ -14,7 +14,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_ulsph_strain.h b/src/MACHDYN/compute_smd_ulsph_strain.h index b958c036fd..78f6046fc0 100644 --- a/src/MACHDYN/compute_smd_ulsph_strain.h +++ b/src/MACHDYN/compute_smd_ulsph_strain.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_ulsph_strain_rate.cpp b/src/MACHDYN/compute_smd_ulsph_strain_rate.cpp index b690bfab88..0913f789f9 100644 --- a/src/MACHDYN/compute_smd_ulsph_strain_rate.cpp +++ b/src/MACHDYN/compute_smd_ulsph_strain_rate.cpp @@ -13,7 +13,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_ulsph_strain_rate.h b/src/MACHDYN/compute_smd_ulsph_strain_rate.h index 2d3e5e3157..8251c5523c 100644 --- a/src/MACHDYN/compute_smd_ulsph_strain_rate.h +++ b/src/MACHDYN/compute_smd_ulsph_strain_rate.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_ulsph_stress.cpp b/src/MACHDYN/compute_smd_ulsph_stress.cpp index 22f563f918..4a98dd4ad6 100644 --- a/src/MACHDYN/compute_smd_ulsph_stress.cpp +++ b/src/MACHDYN/compute_smd_ulsph_stress.cpp @@ -13,7 +13,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_ulsph_stress.h b/src/MACHDYN/compute_smd_ulsph_stress.h index dc553beec8..83df0e16a3 100644 --- a/src/MACHDYN/compute_smd_ulsph_stress.h +++ b/src/MACHDYN/compute_smd_ulsph_stress.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_vol.cpp b/src/MACHDYN/compute_smd_vol.cpp index 2fdc4e34d2..cc7dbe441f 100644 --- a/src/MACHDYN/compute_smd_vol.cpp +++ b/src/MACHDYN/compute_smd_vol.cpp @@ -13,7 +13,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/compute_smd_vol.h b/src/MACHDYN/compute_smd_vol.h index e368633fba..5e3b5278b4 100644 --- a/src/MACHDYN/compute_smd_vol.h +++ b/src/MACHDYN/compute_smd_vol.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/fix_smd_adjust_dt.cpp b/src/MACHDYN/fix_smd_adjust_dt.cpp index 0890527640..d2728f1042 100644 --- a/src/MACHDYN/fix_smd_adjust_dt.cpp +++ b/src/MACHDYN/fix_smd_adjust_dt.cpp @@ -13,7 +13,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -43,8 +43,7 @@ using namespace FixConst; FixSMDTlsphDtReset::FixSMDTlsphDtReset(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) { - if (narg != 4) - error->all(FLERR, "Illegal fix smd/adjust_dt command"); + if (narg != 4) error->all(FLERR, "Illegal fix smd/adjust_dt command"); // set time_depend, else elapsed time accumulation can be messed up @@ -57,7 +56,7 @@ FixSMDTlsphDtReset::FixSMDTlsphDtReset(LAMMPS *lmp, int narg, char **arg) : extvector = 0; restart_global = 1; // this fix stores global (i.e., not per-atom) info: elaspsed time - safety_factor = atof(arg[3]); + safety_factor = utils::numeric(FLERR,arg[3],false,lmp); // initializations t_elapsed = 0.0; diff --git a/src/MACHDYN/fix_smd_adjust_dt.h b/src/MACHDYN/fix_smd_adjust_dt.h index afcac02e64..087c5a147e 100644 --- a/src/MACHDYN/fix_smd_adjust_dt.h +++ b/src/MACHDYN/fix_smd_adjust_dt.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/fix_smd_integrate_tlsph.cpp b/src/MACHDYN/fix_smd_integrate_tlsph.cpp index cb020d330d..f138a3c387 100644 --- a/src/MACHDYN/fix_smd_integrate_tlsph.cpp +++ b/src/MACHDYN/fix_smd_integrate_tlsph.cpp @@ -13,7 +13,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/fix_smd_integrate_tlsph.h b/src/MACHDYN/fix_smd_integrate_tlsph.h index d39f36f72a..70e49a5b41 100644 --- a/src/MACHDYN/fix_smd_integrate_tlsph.h +++ b/src/MACHDYN/fix_smd_integrate_tlsph.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/fix_smd_integrate_ulsph.cpp b/src/MACHDYN/fix_smd_integrate_ulsph.cpp index 2a082078a6..8ef5c65b67 100644 --- a/src/MACHDYN/fix_smd_integrate_ulsph.cpp +++ b/src/MACHDYN/fix_smd_integrate_ulsph.cpp @@ -13,7 +13,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/fix_smd_integrate_ulsph.h b/src/MACHDYN/fix_smd_integrate_ulsph.h index cbba1f5135..8c02959f66 100644 --- a/src/MACHDYN/fix_smd_integrate_ulsph.h +++ b/src/MACHDYN/fix_smd_integrate_ulsph.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/fix_smd_move_triangulated_surface.cpp b/src/MACHDYN/fix_smd_move_triangulated_surface.cpp index b0cf2e6740..441bc59a79 100644 --- a/src/MACHDYN/fix_smd_move_triangulated_surface.cpp +++ b/src/MACHDYN/fix_smd_move_triangulated_surface.cpp @@ -13,7 +13,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/fix_smd_move_triangulated_surface.h b/src/MACHDYN/fix_smd_move_triangulated_surface.h index 4ffc3dcc0f..2d2ab9226b 100644 --- a/src/MACHDYN/fix_smd_move_triangulated_surface.h +++ b/src/MACHDYN/fix_smd_move_triangulated_surface.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/fix_smd_setvel.cpp b/src/MACHDYN/fix_smd_setvel.cpp index 1b5578c7e0..7351edd0f9 100644 --- a/src/MACHDYN/fix_smd_setvel.cpp +++ b/src/MACHDYN/fix_smd_setvel.cpp @@ -13,7 +13,7 @@ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/fix_smd_setvel.h b/src/MACHDYN/fix_smd_setvel.h index df5f16a09f..c2b2f46d4f 100644 --- a/src/MACHDYN/fix_smd_setvel.h +++ b/src/MACHDYN/fix_smd_setvel.h @@ -12,7 +12,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/fix_smd_tlsph_reference_configuration.cpp b/src/MACHDYN/fix_smd_tlsph_reference_configuration.cpp index df23726b38..b236952e60 100644 --- a/src/MACHDYN/fix_smd_tlsph_reference_configuration.cpp +++ b/src/MACHDYN/fix_smd_tlsph_reference_configuration.cpp @@ -15,7 +15,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/fix_smd_tlsph_reference_configuration.h b/src/MACHDYN/fix_smd_tlsph_reference_configuration.h index 45ec11b6b5..09d42b103b 100644 --- a/src/MACHDYN/fix_smd_tlsph_reference_configuration.h +++ b/src/MACHDYN/fix_smd_tlsph_reference_configuration.h @@ -14,7 +14,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/fix_smd_wall_surface.cpp b/src/MACHDYN/fix_smd_wall_surface.cpp index 01c102d762..0715990076 100644 --- a/src/MACHDYN/fix_smd_wall_surface.cpp +++ b/src/MACHDYN/fix_smd_wall_surface.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/fix_smd_wall_surface.h b/src/MACHDYN/fix_smd_wall_surface.h index 07d0436417..fc7478c52b 100644 --- a/src/MACHDYN/fix_smd_wall_surface.h +++ b/src/MACHDYN/fix_smd_wall_surface.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/pair_smd_hertz.cpp b/src/MACHDYN/pair_smd_hertz.cpp index d115e71cdf..bf526f5e4e 100644 --- a/src/MACHDYN/pair_smd_hertz.cpp +++ b/src/MACHDYN/pair_smd_hertz.cpp @@ -13,7 +13,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -263,7 +263,7 @@ void PairHertz::coeff(int narg, char **arg) { utils::bounds(FLERR,arg[0], 1, atom->ntypes, ilo, ihi, error); utils::bounds(FLERR,arg[1], 1, atom->ntypes, jlo, jhi, error); - double bulkmodulus_one = atof(arg[2]); + double bulkmodulus_one = utils::numeric(FLERR,arg[2],false,lmp); // set short-range force constant double kn_one = 0.0; diff --git a/src/MACHDYN/pair_smd_hertz.h b/src/MACHDYN/pair_smd_hertz.h index 75bcfa9dca..e57faa48f5 100644 --- a/src/MACHDYN/pair_smd_hertz.h +++ b/src/MACHDYN/pair_smd_hertz.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/pair_smd_tlsph.cpp b/src/MACHDYN/pair_smd_tlsph.cpp index 6c8f286fe5..845fed3352 100644 --- a/src/MACHDYN/pair_smd_tlsph.cpp +++ b/src/MACHDYN/pair_smd_tlsph.cpp @@ -13,7 +13,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/pair_smd_tlsph.h b/src/MACHDYN/pair_smd_tlsph.h index 6b4cb229a5..f0ff56f1c1 100644 --- a/src/MACHDYN/pair_smd_tlsph.h +++ b/src/MACHDYN/pair_smd_tlsph.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/pair_smd_triangulated_surface.cpp b/src/MACHDYN/pair_smd_triangulated_surface.cpp index a1d1cd4572..e1ebc2562d 100644 --- a/src/MACHDYN/pair_smd_triangulated_surface.cpp +++ b/src/MACHDYN/pair_smd_triangulated_surface.cpp @@ -13,7 +13,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -345,7 +345,7 @@ void PairTriSurf::coeff(int narg, char **arg) { utils::bounds(FLERR,arg[0], 1,atom->ntypes, ilo, ihi, error); utils::bounds(FLERR,arg[1], 1,atom->ntypes, jlo, jhi, error); - double bulkmodulus_one = atof(arg[2]); + double bulkmodulus_one = utils::numeric(FLERR,arg[2],false,lmp); // set short-range force constant double kn_one = 0.0; diff --git a/src/MACHDYN/pair_smd_triangulated_surface.h b/src/MACHDYN/pair_smd_triangulated_surface.h index 0c07d81a3a..ae7e8198be 100644 --- a/src/MACHDYN/pair_smd_triangulated_surface.h +++ b/src/MACHDYN/pair_smd_triangulated_surface.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/pair_smd_ulsph.cpp b/src/MACHDYN/pair_smd_ulsph.cpp index d19f45900f..716940c1b2 100644 --- a/src/MACHDYN/pair_smd_ulsph.cpp +++ b/src/MACHDYN/pair_smd_ulsph.cpp @@ -13,7 +13,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/pair_smd_ulsph.h b/src/MACHDYN/pair_smd_ulsph.h index 0cd6eefb83..49264a3a3b 100644 --- a/src/MACHDYN/pair_smd_ulsph.h +++ b/src/MACHDYN/pair_smd_ulsph.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/smd_material_models.cpp b/src/MACHDYN/smd_material_models.cpp index d0c1038f79..e8b894e87f 100644 --- a/src/MACHDYN/smd_material_models.cpp +++ b/src/MACHDYN/smd_material_models.cpp @@ -13,7 +13,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MACHDYN/smd_material_models.h b/src/MACHDYN/smd_material_models.h index 769b2aa375..8b7cfe2c66 100644 --- a/src/MACHDYN/smd_material_models.h +++ b/src/MACHDYN/smd_material_models.h @@ -12,7 +12,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/fix_manifoldforce.cpp b/src/MANIFOLD/fix_manifoldforce.cpp index 9e56b624d7..c72a399e85 100644 --- a/src/MANIFOLD/fix_manifoldforce.cpp +++ b/src/MANIFOLD/fix_manifoldforce.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/fix_manifoldforce.h b/src/MANIFOLD/fix_manifoldforce.h index 5756428cd7..89044a806d 100644 --- a/src/MANIFOLD/fix_manifoldforce.h +++ b/src/MANIFOLD/fix_manifoldforce.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/fix_nve_manifold_rattle.cpp b/src/MANIFOLD/fix_nve_manifold_rattle.cpp index 1ccf7c2e04..b1efea951f 100644 --- a/src/MANIFOLD/fix_nve_manifold_rattle.cpp +++ b/src/MANIFOLD/fix_nve_manifold_rattle.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/fix_nve_manifold_rattle.h b/src/MANIFOLD/fix_nve_manifold_rattle.h index 2772b12f99..3eae9c4bc3 100644 --- a/src/MANIFOLD/fix_nve_manifold_rattle.h +++ b/src/MANIFOLD/fix_nve_manifold_rattle.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/fix_nvt_manifold_rattle.cpp b/src/MANIFOLD/fix_nvt_manifold_rattle.cpp index a7b2c5ed37..d8b91fdda1 100644 --- a/src/MANIFOLD/fix_nvt_manifold_rattle.cpp +++ b/src/MANIFOLD/fix_nvt_manifold_rattle.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/fix_nvt_manifold_rattle.h b/src/MANIFOLD/fix_nvt_manifold_rattle.h index 4fd9e96ae6..aadab93afb 100644 --- a/src/MANIFOLD/fix_nvt_manifold_rattle.h +++ b/src/MANIFOLD/fix_nvt_manifold_rattle.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold.h b/src/MANIFOLD/manifold.h index ab4319fd80..63665b97d7 100644 --- a/src/MANIFOLD/manifold.h +++ b/src/MANIFOLD/manifold.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_cylinder.cpp b/src/MANIFOLD/manifold_cylinder.cpp index edd3ecf974..570c979fde 100644 --- a/src/MANIFOLD/manifold_cylinder.cpp +++ b/src/MANIFOLD/manifold_cylinder.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_cylinder.h b/src/MANIFOLD/manifold_cylinder.h index cff6dab4ce..1ab9b9fef0 100644 --- a/src/MANIFOLD/manifold_cylinder.h +++ b/src/MANIFOLD/manifold_cylinder.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_cylinder_dent.cpp b/src/MANIFOLD/manifold_cylinder_dent.cpp index a559b7bd75..498cf89cb0 100644 --- a/src/MANIFOLD/manifold_cylinder_dent.cpp +++ b/src/MANIFOLD/manifold_cylinder_dent.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_cylinder_dent.h b/src/MANIFOLD/manifold_cylinder_dent.h index 4f0251455c..7de1fd0ac1 100644 --- a/src/MANIFOLD/manifold_cylinder_dent.h +++ b/src/MANIFOLD/manifold_cylinder_dent.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_dumbbell.cpp b/src/MANIFOLD/manifold_dumbbell.cpp index 15a3713528..89c6521e72 100644 --- a/src/MANIFOLD/manifold_dumbbell.cpp +++ b/src/MANIFOLD/manifold_dumbbell.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_dumbbell.h b/src/MANIFOLD/manifold_dumbbell.h index 69ccbda875..ee97552e24 100644 --- a/src/MANIFOLD/manifold_dumbbell.h +++ b/src/MANIFOLD/manifold_dumbbell.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_ellipsoid.cpp b/src/MANIFOLD/manifold_ellipsoid.cpp index d42324b4a2..b18fb1b4ec 100644 --- a/src/MANIFOLD/manifold_ellipsoid.cpp +++ b/src/MANIFOLD/manifold_ellipsoid.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_ellipsoid.h b/src/MANIFOLD/manifold_ellipsoid.h index 791b409074..efeeba7ed8 100644 --- a/src/MANIFOLD/manifold_ellipsoid.h +++ b/src/MANIFOLD/manifold_ellipsoid.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_factory.cpp b/src/MANIFOLD/manifold_factory.cpp index 9524791916..7113dc4080 100644 --- a/src/MANIFOLD/manifold_factory.cpp +++ b/src/MANIFOLD/manifold_factory.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_factory.h b/src/MANIFOLD/manifold_factory.h index b242b8ec36..b3a573cbc3 100644 --- a/src/MANIFOLD/manifold_factory.h +++ b/src/MANIFOLD/manifold_factory.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_gaussian_bump.cpp b/src/MANIFOLD/manifold_gaussian_bump.cpp index 1483ff7489..2130f9f0a8 100644 --- a/src/MANIFOLD/manifold_gaussian_bump.cpp +++ b/src/MANIFOLD/manifold_gaussian_bump.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_gaussian_bump.h b/src/MANIFOLD/manifold_gaussian_bump.h index 854a94f1a1..1310db9baa 100644 --- a/src/MANIFOLD/manifold_gaussian_bump.h +++ b/src/MANIFOLD/manifold_gaussian_bump.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_plane.cpp b/src/MANIFOLD/manifold_plane.cpp index 2c1ef91444..10c5aaf0f0 100644 --- a/src/MANIFOLD/manifold_plane.cpp +++ b/src/MANIFOLD/manifold_plane.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_plane.h b/src/MANIFOLD/manifold_plane.h index fc4dfa0514..10e6521259 100644 --- a/src/MANIFOLD/manifold_plane.h +++ b/src/MANIFOLD/manifold_plane.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_plane_wiggle.cpp b/src/MANIFOLD/manifold_plane_wiggle.cpp index be9a49dced..3eb2927248 100644 --- a/src/MANIFOLD/manifold_plane_wiggle.cpp +++ b/src/MANIFOLD/manifold_plane_wiggle.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_plane_wiggle.h b/src/MANIFOLD/manifold_plane_wiggle.h index 4d1ab2845d..e1cd1143c4 100644 --- a/src/MANIFOLD/manifold_plane_wiggle.h +++ b/src/MANIFOLD/manifold_plane_wiggle.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_sphere.h b/src/MANIFOLD/manifold_sphere.h index e8ba801476..3a2f3562a7 100644 --- a/src/MANIFOLD/manifold_sphere.h +++ b/src/MANIFOLD/manifold_sphere.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_spine.cpp b/src/MANIFOLD/manifold_spine.cpp index ddfaac1a62..bc36315b26 100644 --- a/src/MANIFOLD/manifold_spine.cpp +++ b/src/MANIFOLD/manifold_spine.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_spine.h b/src/MANIFOLD/manifold_spine.h index 2ea9f5b051..c2239221a9 100644 --- a/src/MANIFOLD/manifold_spine.h +++ b/src/MANIFOLD/manifold_spine.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_supersphere.h b/src/MANIFOLD/manifold_supersphere.h index 11c0a3fd1e..d71e9b68f7 100644 --- a/src/MANIFOLD/manifold_supersphere.h +++ b/src/MANIFOLD/manifold_supersphere.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_thylakoid.cpp b/src/MANIFOLD/manifold_thylakoid.cpp index a6cded49aa..3f674d8bda 100644 --- a/src/MANIFOLD/manifold_thylakoid.cpp +++ b/src/MANIFOLD/manifold_thylakoid.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_thylakoid.h b/src/MANIFOLD/manifold_thylakoid.h index 5c30ccbdba..72ffb870ca 100644 --- a/src/MANIFOLD/manifold_thylakoid.h +++ b/src/MANIFOLD/manifold_thylakoid.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_thylakoid_shared.cpp b/src/MANIFOLD/manifold_thylakoid_shared.cpp index 5efc20a298..6d2f8004bd 100644 --- a/src/MANIFOLD/manifold_thylakoid_shared.cpp +++ b/src/MANIFOLD/manifold_thylakoid_shared.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_thylakoid_shared.h b/src/MANIFOLD/manifold_thylakoid_shared.h index 67909802b0..17a6b37732 100644 --- a/src/MANIFOLD/manifold_thylakoid_shared.h +++ b/src/MANIFOLD/manifold_thylakoid_shared.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_torus.cpp b/src/MANIFOLD/manifold_torus.cpp index f09ffc4a96..c5c5bab674 100644 --- a/src/MANIFOLD/manifold_torus.cpp +++ b/src/MANIFOLD/manifold_torus.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANIFOLD/manifold_torus.h b/src/MANIFOLD/manifold_torus.h index 8155d79b27..53b4d391a7 100644 --- a/src/MANIFOLD/manifold_torus.h +++ b/src/MANIFOLD/manifold_torus.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp index 23a4d49566..6edd2fbbb0 100644 --- a/src/MANYBODY/fix_qeq_comb.cpp +++ b/src/MANYBODY/fix_qeq_comb.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/fix_qeq_comb.h b/src/MANYBODY/fix_qeq_comb.h index 1b98d21d12..ed17587988 100644 --- a/src/MANYBODY/fix_qeq_comb.h +++ b/src/MANYBODY/fix_qeq_comb.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp index ef34721389..5e7373b4df 100644 --- a/src/MANYBODY/pair_adp.cpp +++ b/src/MANYBODY/pair_adp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_adp.h b/src/MANYBODY/pair_adp.h index a82028687c..d68df368a7 100644 --- a/src/MANYBODY/pair_adp.h +++ b/src/MANYBODY/pair_adp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index fa3f407fc1..a78904051d 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_airebo.h b/src/MANYBODY/pair_airebo.h index 67309ee833..2eb85a7fb1 100644 --- a/src/MANYBODY/pair_airebo.h +++ b/src/MANYBODY/pair_airebo.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_airebo_morse.cpp b/src/MANYBODY/pair_airebo_morse.cpp index 01d2516415..18ae7fb1db 100644 --- a/src/MANYBODY/pair_airebo_morse.cpp +++ b/src/MANYBODY/pair_airebo_morse.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_airebo_morse.h b/src/MANYBODY/pair_airebo_morse.h index ed2deb0225..536ee2b16a 100644 --- a/src/MANYBODY/pair_airebo_morse.h +++ b/src/MANYBODY/pair_airebo_morse.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp index 9e125c3403..663e448a3c 100644 --- a/src/MANYBODY/pair_atm.cpp +++ b/src/MANYBODY/pair_atm.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_atm.h b/src/MANYBODY/pair_atm.h index 7ce4fac12f..bbfee0f9bc 100644 --- a/src/MANYBODY/pair_atm.h +++ b/src/MANYBODY/pair_atm.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index b1d128db24..f8c119c436 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -40,7 +40,6 @@ #include "atom.h" #include "comm.h" -#include "domain.h" #include "error.h" #include "force.h" #include "math_special.h" diff --git a/src/MANYBODY/pair_bop.h b/src/MANYBODY/pair_bop.h index 483675021b..b210d1cc07 100644 --- a/src/MANYBODY/pair_bop.h +++ b/src/MANYBODY/pair_bop.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp index ddaf378445..126544ddc5 100644 --- a/src/MANYBODY/pair_comb.cpp +++ b/src/MANYBODY/pair_comb.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_comb.h b/src/MANYBODY/pair_comb.h index 3b6cf221e4..c0fc8c6164 100644 --- a/src/MANYBODY/pair_comb.h +++ b/src/MANYBODY/pair_comb.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp index e5ea235363..ac1ac0ea62 100644 --- a/src/MANYBODY/pair_comb3.cpp +++ b/src/MANYBODY/pair_comb3.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_comb3.h b/src/MANYBODY/pair_comb3.h index 6aed74edc0..23c13f1b92 100644 --- a/src/MANYBODY/pair_comb3.h +++ b/src/MANYBODY/pair_comb3.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp index b14d47f7f0..ee824d291b 100644 --- a/src/MANYBODY/pair_eam.cpp +++ b/src/MANYBODY/pair_eam.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_eam.h b/src/MANYBODY/pair_eam.h index 11ab969d18..67bbde570d 100644 --- a/src/MANYBODY/pair_eam.h +++ b/src/MANYBODY/pair_eam.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_eam_alloy.cpp b/src/MANYBODY/pair_eam_alloy.cpp index 96f1728037..ed1d241c73 100644 --- a/src/MANYBODY/pair_eam_alloy.cpp +++ b/src/MANYBODY/pair_eam_alloy.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_eam_alloy.h b/src/MANYBODY/pair_eam_alloy.h index f39f989151..875209f2b9 100644 --- a/src/MANYBODY/pair_eam_alloy.h +++ b/src/MANYBODY/pair_eam_alloy.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_eam_cd.cpp b/src/MANYBODY/pair_eam_cd.cpp index e575a6643b..1746435fad 100644 --- a/src/MANYBODY/pair_eam_cd.cpp +++ b/src/MANYBODY/pair_eam_cd.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_eam_cd.h b/src/MANYBODY/pair_eam_cd.h index f7967d7fb6..5ffcc4c0e2 100644 --- a/src/MANYBODY/pair_eam_cd.h +++ b/src/MANYBODY/pair_eam_cd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_eam_fs.cpp b/src/MANYBODY/pair_eam_fs.cpp index 01e25de75a..019e117f5f 100644 --- a/src/MANYBODY/pair_eam_fs.cpp +++ b/src/MANYBODY/pair_eam_fs.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_eam_fs.h b/src/MANYBODY/pair_eam_fs.h index 17e0ae8f13..d189d718ee 100644 --- a/src/MANYBODY/pair_eam_fs.h +++ b/src/MANYBODY/pair_eam_fs.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_eam_he.cpp b/src/MANYBODY/pair_eam_he.cpp index a5a18a43a5..bfbdbad5de 100644 --- a/src/MANYBODY/pair_eam_he.cpp +++ b/src/MANYBODY/pair_eam_he.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_eam_he.h b/src/MANYBODY/pair_eam_he.h index c6c0553f81..94d7a9cfff 100644 --- a/src/MANYBODY/pair_eam_he.h +++ b/src/MANYBODY/pair_eam_he.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_edip.cpp b/src/MANYBODY/pair_edip.cpp index 87ccf9b18a..974dc9ab84 100644 --- a/src/MANYBODY/pair_edip.cpp +++ b/src/MANYBODY/pair_edip.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_edip.h b/src/MANYBODY/pair_edip.h index 9ced9fa4de..77f87e055a 100644 --- a/src/MANYBODY/pair_edip.h +++ b/src/MANYBODY/pair_edip.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_edip_multi.cpp b/src/MANYBODY/pair_edip_multi.cpp index e51e92893d..00be0ad829 100644 --- a/src/MANYBODY/pair_edip_multi.cpp +++ b/src/MANYBODY/pair_edip_multi.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_edip_multi.h b/src/MANYBODY/pair_edip_multi.h index c30d91bd38..737732f68d 100644 --- a/src/MANYBODY/pair_edip_multi.h +++ b/src/MANYBODY/pair_edip_multi.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp index 5a97e23b40..a4fd4e6c9f 100644 --- a/src/MANYBODY/pair_eim.cpp +++ b/src/MANYBODY/pair_eim.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_eim.h b/src/MANYBODY/pair_eim.h index cb30257b2e..a538b7eb35 100644 --- a/src/MANYBODY/pair_eim.h +++ b/src/MANYBODY/pair_eim.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_extep.cpp b/src/MANYBODY/pair_extep.cpp index f8446e16eb..6a3b302fc1 100644 --- a/src/MANYBODY/pair_extep.cpp +++ b/src/MANYBODY/pair_extep.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -32,7 +32,6 @@ #include #include -#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MANYBODY/pair_extep.h b/src/MANYBODY/pair_extep.h index 282b190e6e..7b3a86c2f2 100644 --- a/src/MANYBODY/pair_extep.h +++ b/src/MANYBODY/pair_extep.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp index ba315bdf70..be2a1e41f3 100644 --- a/src/MANYBODY/pair_gw.cpp +++ b/src/MANYBODY/pair_gw.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_gw.h b/src/MANYBODY/pair_gw.h index ca788226ed..15ddaa21a8 100644 --- a/src/MANYBODY/pair_gw.h +++ b/src/MANYBODY/pair_gw.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_gw_zbl.cpp b/src/MANYBODY/pair_gw_zbl.cpp index cb998abbb5..5e61778c68 100644 --- a/src/MANYBODY/pair_gw_zbl.cpp +++ b/src/MANYBODY/pair_gw_zbl.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_gw_zbl.h b/src/MANYBODY/pair_gw_zbl.h index b8209a2a4f..53826982a0 100644 --- a/src/MANYBODY/pair_gw_zbl.h +++ b/src/MANYBODY/pair_gw_zbl.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp index a5e15479e3..65191ae85e 100644 --- a/src/MANYBODY/pair_lcbop.cpp +++ b/src/MANYBODY/pair_lcbop.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_lcbop.h b/src/MANYBODY/pair_lcbop.h index e000beba96..5c80bb5aea 100644 --- a/src/MANYBODY/pair_lcbop.h +++ b/src/MANYBODY/pair_lcbop.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_local_density.cpp b/src/MANYBODY/pair_local_density.cpp index 789b1ddad9..46b14b96ff 100644 --- a/src/MANYBODY/pair_local_density.cpp +++ b/src/MANYBODY/pair_local_density.cpp @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_local_density.h b/src/MANYBODY/pair_local_density.h index dd466e622d..aa24d66751 100644 --- a/src/MANYBODY/pair_local_density.h +++ b/src/MANYBODY/pair_local_density.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_meam_spline.cpp b/src/MANYBODY/pair_meam_spline.cpp index ab4f39bf15..1c17f434f2 100644 --- a/src/MANYBODY/pair_meam_spline.cpp +++ b/src/MANYBODY/pair_meam_spline.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_meam_spline.h b/src/MANYBODY/pair_meam_spline.h index 5d692b98f2..3fec521109 100644 --- a/src/MANYBODY/pair_meam_spline.h +++ b/src/MANYBODY/pair_meam_spline.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_meam_sw_spline.cpp b/src/MANYBODY/pair_meam_sw_spline.cpp index c744e8f002..3e3e813c5b 100644 --- a/src/MANYBODY/pair_meam_sw_spline.cpp +++ b/src/MANYBODY/pair_meam_sw_spline.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_meam_sw_spline.h b/src/MANYBODY/pair_meam_sw_spline.h index b2f5fd7f67..9123f8c560 100644 --- a/src/MANYBODY/pair_meam_sw_spline.h +++ b/src/MANYBODY/pair_meam_sw_spline.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp index 3b25ac00a3..f0497d437c 100644 --- a/src/MANYBODY/pair_nb3b_harmonic.cpp +++ b/src/MANYBODY/pair_nb3b_harmonic.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_nb3b_harmonic.h b/src/MANYBODY/pair_nb3b_harmonic.h index c570a0186b..c92b65950f 100644 --- a/src/MANYBODY/pair_nb3b_harmonic.h +++ b/src/MANYBODY/pair_nb3b_harmonic.h @@ -1,7 +1,7 @@ /* -*- c++ -*- --------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp index cb7b3fe361..03ef6cb49f 100644 --- a/src/MANYBODY/pair_polymorphic.cpp +++ b/src/MANYBODY/pair_polymorphic.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -554,7 +554,8 @@ void PairPolymorphic::read_file(char *file) int ntypes = values.next_int(); if (ntypes != nelements) - error->one(FLERR,"Incorrect number of elements in potential file"); + error->one(FLERR,"Incorrect number of elements (expected: {} found: {}) in potential file", + nelements, ntypes); eta = values.next_int(); @@ -572,7 +573,7 @@ void PairPolymorphic::read_file(char *file) for (j = 0; j < nelements; j++) { if (name == elements[j]) break; } - if (j == nelements) error->one(FLERR,"Element not defined in potential file"); + if (j == nelements) error->one(FLERR, "Element {} in potential file not used", name); match[i] = j; } diff --git a/src/MANYBODY/pair_polymorphic.h b/src/MANYBODY/pair_polymorphic.h index 3c818955ec..00062a5358 100644 --- a/src/MANYBODY/pair_polymorphic.h +++ b/src/MANYBODY/pair_polymorphic.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_rebo.cpp b/src/MANYBODY/pair_rebo.cpp index 0c53f4a538..a12c6eb2fc 100644 --- a/src/MANYBODY/pair_rebo.cpp +++ b/src/MANYBODY/pair_rebo.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_rebo.h b/src/MANYBODY/pair_rebo.h index 430969c413..6de6df4851 100644 --- a/src/MANYBODY/pair_rebo.h +++ b/src/MANYBODY/pair_rebo.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index ce1f8193fd..540fd8772c 100644 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -46,6 +46,7 @@ PairSW::PairSW(LAMMPS *lmp) : Pair(lmp) centroidstressflag = CENTROID_NOTAVAIL; unit_convert_flag = utils::get_supported_conversions(utils::ENERGY); skip_threebody_flag = false; + params_mapped = 0; params = nullptr; @@ -225,12 +226,12 @@ void PairSW::compute(int eflag, int vflag) void PairSW::allocate() { allocated = 1; - int n = atom->ntypes; + int np1 = atom->ntypes + 1; - memory->create(setflag,n+1,n+1,"pair:setflag"); - memory->create(cutsq,n+1,n+1,"pair:cutsq"); - memory->create(neighshort,maxshort,"pair:neighshort"); - map = new int[n+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]; } /* ---------------------------------------------------------------------- @@ -262,12 +263,49 @@ void PairSW::coeff(int narg, char **arg) { if (!allocated) allocate(); - map_element2type(narg-3,arg+3); + // read potential file and set up element maps only once + if (one_coeff || !params_mapped) { + // make certain that the setflag array is always fully initialized + // the sw/intel pair style depends on it + if (!one_coeff) { + for (int i = 0; i <= atom->ntypes; i++) { + for (int j = 0; j <= atom->ntypes; j++) { + setflag[i][j] = 0; + } + } + } - // read potential file and initialize potential parameters + map_element2type(narg-3, arg+3, (one_coeff != 0)); - read_file(arg[2]); - setup_params(); + // read potential file and initialize potential parameters + + read_file(arg[2]); + setup_params(); + params_mapped = 1; + } + + if (!one_coeff) { + int ilo, ihi, jlo, jhi; + utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error); + utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + if (((map[i] >= 0) && (strcmp(arg[i+2], elements[map[i]]) != 0)) || + ((map[i] < 0) && (strcmp(arg[i+2], "NULL") != 0))) + error->all(FLERR, "Must use consistent type to element mappings with threebody off"); + if (map[i] < 0) error->all(FLERR, "Must not set pair_coeff mapped to NULL element"); + for (int j = MAX(jlo, i); j <= jhi; j++) { + if (((map[j] >= 0) && (strcmp(arg[j+2], elements[map[j]]) != 0)) || + ((map[j] < 0) && (strcmp(arg[j+2], "NULL") != 0))) + error->all(FLERR, "Must use consistent type to element mappings with threebody off"); + if (map[j] < 0) error->all(FLERR, "Must not set pair_coeff mapped to NULL element"); + setflag[i][j] = 1; + count++; + } + } + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + } } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_sw.h b/src/MANYBODY/pair_sw.h index bcc7227554..da25871040 100644 --- a/src/MANYBODY/pair_sw.h +++ b/src/MANYBODY/pair_sw.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -54,6 +54,7 @@ class PairSW : public Pair { int maxshort; // size of short neighbor list array int *neighshort; // short neighbor list array int skip_threebody_flag; // whether to run threebody loop + int params_mapped; // whether parameters have been read and mapped to elements void settings(int, char **) override; virtual void allocate(); diff --git a/src/MANYBODY/pair_sw_angle_table.cpp b/src/MANYBODY/pair_sw_angle_table.cpp index 5b9339780f..21f1967c0d 100644 --- a/src/MANYBODY/pair_sw_angle_table.cpp +++ b/src/MANYBODY/pair_sw_angle_table.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_sw_angle_table.h b/src/MANYBODY/pair_sw_angle_table.h index 04404210bd..18fd530f78 100644 --- a/src/MANYBODY/pair_sw_angle_table.h +++ b/src/MANYBODY/pair_sw_angle_table.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_sw_mod.cpp b/src/MANYBODY/pair_sw_mod.cpp index e6d17b0733..d7fdbcea4c 100644 --- a/src/MANYBODY/pair_sw_mod.cpp +++ b/src/MANYBODY/pair_sw_mod.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_sw_mod.h b/src/MANYBODY/pair_sw_mod.h index 0a5b1cdb4d..d7b007ff22 100644 --- a/src/MANYBODY/pair_sw_mod.h +++ b/src/MANYBODY/pair_sw_mod.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp index 8b4a51ae95..f38ba00861 100644 --- a/src/MANYBODY/pair_tersoff.cpp +++ b/src/MANYBODY/pair_tersoff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_tersoff.h b/src/MANYBODY/pair_tersoff.h index 88b529ff82..ad94e0bc7e 100644 --- a/src/MANYBODY/pair_tersoff.h +++ b/src/MANYBODY/pair_tersoff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_tersoff_mod.cpp b/src/MANYBODY/pair_tersoff_mod.cpp index f2edf81ba5..010ff8df87 100644 --- a/src/MANYBODY/pair_tersoff_mod.cpp +++ b/src/MANYBODY/pair_tersoff_mod.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_tersoff_mod.h b/src/MANYBODY/pair_tersoff_mod.h index b866226992..d3e5412e09 100644 --- a/src/MANYBODY/pair_tersoff_mod.h +++ b/src/MANYBODY/pair_tersoff_mod.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_tersoff_mod_c.cpp b/src/MANYBODY/pair_tersoff_mod_c.cpp index b0cffbd8e2..bdec854c41 100644 --- a/src/MANYBODY/pair_tersoff_mod_c.cpp +++ b/src/MANYBODY/pair_tersoff_mod_c.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_tersoff_mod_c.h b/src/MANYBODY/pair_tersoff_mod_c.h index 162d262e2c..aff1883bbd 100644 --- a/src/MANYBODY/pair_tersoff_mod_c.h +++ b/src/MANYBODY/pair_tersoff_mod_c.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_tersoff_table.cpp b/src/MANYBODY/pair_tersoff_table.cpp index 421d2c1e14..325542f97e 100644 --- a/src/MANYBODY/pair_tersoff_table.cpp +++ b/src/MANYBODY/pair_tersoff_table.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_tersoff_table.h b/src/MANYBODY/pair_tersoff_table.h index cb4dd7ce18..53f0e4d9a1 100644 --- a/src/MANYBODY/pair_tersoff_table.h +++ b/src/MANYBODY/pair_tersoff_table.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_tersoff_zbl.cpp b/src/MANYBODY/pair_tersoff_zbl.cpp index 3478268161..daf2718cb1 100644 --- a/src/MANYBODY/pair_tersoff_zbl.cpp +++ b/src/MANYBODY/pair_tersoff_zbl.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_tersoff_zbl.h b/src/MANYBODY/pair_tersoff_zbl.h index 7515311464..00ad932593 100644 --- a/src/MANYBODY/pair_tersoff_zbl.h +++ b/src/MANYBODY/pair_tersoff_zbl.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_threebody_table.cpp b/src/MANYBODY/pair_threebody_table.cpp index 044f69a8da..57f7021816 100644 --- a/src/MANYBODY/pair_threebody_table.cpp +++ b/src/MANYBODY/pair_threebody_table.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -445,7 +445,7 @@ void PairThreebodyTable::read_table(Table *tb, char *file, char *keyword, bool s char *line = reader.find_section_start(keyword); - if (!line) { error->one(FLERR, "Did not find keyword in table file"); } + 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 @@ -703,25 +703,25 @@ void PairThreebodyTable::uf_lookup(Param *pm, double r12, double r13, double the // 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; } + 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; } + if (r13 == (pm->mltable->rmin - 0.5 * dr)) nr13 = 0; nr13 -= nr12; ntheta = (theta - 0.00000001) / dtheta; - if (theta == 180.0) { ntheta = 79; } + if (theta >= 180.0) ntheta = (pm->mltable->ninput * 2) - 1; itable = 0; - for (i = 0; i < nr12; i++) { itable += (pm->mltable->ninput - i); } + 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; } + 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; } + if (r13 == (pm->mltable->rmin - 0.5 * dr)) nr13 = 0; ntheta = (theta - 0.00000001) / dtheta; - if (theta == 180.0) { ntheta = 79; } + if (theta >= 180.0) ntheta = (pm->mltable->ninput * 2) - 1; itable = nr12 * (pm->mltable->ninput); itable += nr13; itable *= (pm->mltable->ninput * 2); diff --git a/src/MANYBODY/pair_threebody_table.h b/src/MANYBODY/pair_threebody_table.h index 218bfeebd8..12eb27be43 100644 --- a/src/MANYBODY/pair_threebody_table.h +++ b/src/MANYBODY/pair_threebody_table.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp index 30855fa6da..531f15d263 100644 --- a/src/MANYBODY/pair_vashishta.cpp +++ b/src/MANYBODY/pair_vashishta.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_vashishta.h b/src/MANYBODY/pair_vashishta.h index 0b85266294..54fce7ad09 100644 --- a/src/MANYBODY/pair_vashishta.h +++ b/src/MANYBODY/pair_vashishta.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_vashishta_table.cpp b/src/MANYBODY/pair_vashishta_table.cpp index 8a46af69da..57452e9d66 100644 --- a/src/MANYBODY/pair_vashishta_table.cpp +++ b/src/MANYBODY/pair_vashishta_table.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MANYBODY/pair_vashishta_table.h b/src/MANYBODY/pair_vashishta_table.h index 460304ad91..7d8f149b71 100644 --- a/src/MANYBODY/pair_vashishta_table.h +++ b/src/MANYBODY/pair_vashishta_table.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MC/Install.sh b/src/MC/Install.sh new file mode 100755 index 0000000000..ccf6767c4d --- /dev/null +++ b/src/MC/Install.sh @@ -0,0 +1,63 @@ +# Install/unInstall package files in LAMMPS +# mode = 0/1/2 for uninstall/install/update + +# this is default Install.sh for all packages +# if package has an auxiliary library or a file with a dependency, +# then package dir has its own customized Install.sh + +mode=$1 + +# enforce using portable C locale +LC_ALL=C +export LC_ALL + +# arg1 = file, arg2 = file it depends on + +action () { + if (test $mode = 0) then + rm -f ../$1 + elif (! cmp -s $1 ../$1) then + if (test -z "$2" || test -e ../$2) then + cp $1 .. + if (test $mode = 2) then + echo " updating src/$1" + fi + fi + elif (test -n "$2") then + if (test ! -e ../$2) then + rm -f ../$1 + fi + fi +} + +# all package files with no dependencies + +for file in *.cpp *.h; do + test -f ${file} && action $file +done + + +action fix_atom_swap.cpp +action fix_atom_swap.h +action fix_bond_break.cpp +action fix_bond_break.h +action fix_bond_create_angle.cpp +action fix_bond_create_angle.h +action fix_bond_create.cpp +action fix_bond_create.h +action fix_bond_swap.cpp +action fix_bond_swap.h +action fix_charge_regulation.cpp +action fix_charge_regulation.h +action fix_gcmc.cpp +action fix_gcmc.h +action fix_mol_swap.cpp +action fix_mol_swap.h +action fix_sgcmc.cpp pair_eam.cpp +action fix_sgcmc.h pair_eam.h +action fix_tfmc.cpp +action fix_tfmc.h +action fix_widom.cpp +action fix_widom.h +action pair_dsmc.cpp +action pair_dsmc.h diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp index a231a94990..1a39481a47 100644 --- a/src/MC/fix_atom_swap.cpp +++ b/src/MC/fix_atom_swap.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MC/fix_atom_swap.h b/src/MC/fix_atom_swap.h index 4eda3cfcf6..05c95d13be 100644 --- a/src/MC/fix_atom_swap.h +++ b/src/MC/fix_atom_swap.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp index 7bd70e93ec..5261fc11a6 100644 --- a/src/MC/fix_bond_break.cpp +++ b/src/MC/fix_bond_break.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MC/fix_bond_break.h b/src/MC/fix_bond_break.h index 630b6cac90..cb6fa5267b 100644 --- a/src/MC/fix_bond_break.h +++ b/src/MC/fix_bond_break.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp index 6651dd9d13..b773de0392 100644 --- a/src/MC/fix_bond_create.cpp +++ b/src/MC/fix_bond_create.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MC/fix_bond_create.h b/src/MC/fix_bond_create.h index 9fc77cc427..6002c90aa1 100644 --- a/src/MC/fix_bond_create.h +++ b/src/MC/fix_bond_create.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MC/fix_bond_create_angle.cpp b/src/MC/fix_bond_create_angle.cpp index f3014a4b07..067dc1641e 100644 --- a/src/MC/fix_bond_create_angle.cpp +++ b/src/MC/fix_bond_create_angle.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MC/fix_bond_create_angle.h b/src/MC/fix_bond_create_angle.h index ae3d6afa97..2e0b01c87f 100644 --- a/src/MC/fix_bond_create_angle.h +++ b/src/MC/fix_bond_create_angle.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp index a1f1c2b307..5d601a0ed2 100644 --- a/src/MC/fix_bond_swap.cpp +++ b/src/MC/fix_bond_swap.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MC/fix_bond_swap.h b/src/MC/fix_bond_swap.h index 0c27fa6991..dba5ed3a79 100644 --- a/src/MC/fix_bond_swap.h +++ b/src/MC/fix_bond_swap.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MC/fix_charge_regulation.cpp b/src/MC/fix_charge_regulation.cpp index c1bcba007f..22ce38089f 100644 --- a/src/MC/fix_charge_regulation.cpp +++ b/src/MC/fix_charge_regulation.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MC/fix_charge_regulation.h b/src/MC/fix_charge_regulation.h index 21634ec95a..c81af6f3bc 100644 --- a/src/MC/fix_charge_regulation.h +++ b/src/MC/fix_charge_regulation.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index ef1ad324b0..063eeee7e8 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MC/fix_gcmc.h b/src/MC/fix_gcmc.h index 685451aaa1..e2425cb95e 100644 --- a/src/MC/fix_gcmc.h +++ b/src/MC/fix_gcmc.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MC/fix_mol_swap.cpp b/src/MC/fix_mol_swap.cpp index c23ceb7d36..9fa22542b9 100644 --- a/src/MC/fix_mol_swap.cpp +++ b/src/MC/fix_mol_swap.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -33,6 +33,7 @@ #include "update.h" #include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MC/fix_mol_swap.h b/src/MC/fix_mol_swap.h index cf9f34c112..dac4798ca5 100644 --- a/src/MC/fix_mol_swap.h +++ b/src/MC/fix_mol_swap.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MC/fix_sgcmc.cpp b/src/MC/fix_sgcmc.cpp new file mode 100644 index 0000000000..7dd50a2792 --- /dev/null +++ b/src/MC/fix_sgcmc.cpp @@ -0,0 +1,1019 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + 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. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + * Parallel Monte-Carlo code for the semi-grandcanonical ensemble (SGC) + * and the variance-constrained semi-grandcanonical ensemble (VC-SGC). + * + * See Sadigh et al., Phys. Rev. B 85, 184203 (2012) for a + * description of the algorithm. + * + * Code author: Alexander Stukowski (stukowski@mm.tu-darmstadt.de) + * + * Updates for integrtion into LAMMPS: Aidan Thompson, SNL and Axel Kohlmeyer, Temple U +------------------------------------------------------------------------- */ + +#include "fix_sgcmc.h" + +#include "angle.h" +#include "atom.h" +#include "bond.h" +#include "comm.h" +#include "compute.h" +#include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "improper.h" +#include "integrate.h" +#include "kspace.h" +#include "modify.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "pair.h" +#include "universe.h" +#include "update.h" + +#include "pair_eam.h" +#include "random_park.h" + +#include +#include +#include + +using namespace LAMMPS_NS; +using namespace FixConst; + +/********************************************************************* + * Constructs the fix object and parses the input parameters + * that control the Monte Carlo routine. + *********************************************************************/ +FixSemiGrandCanonicalMC::FixSemiGrandCanonicalMC(LAMMPS *_lmp, int narg, char **arg) : + Fix(_lmp, narg, arg), random(nullptr), localRandom(nullptr), neighborList(nullptr), + pairEAM(nullptr), compute_pe(nullptr) +{ + scalar_flag = 0; + vector_flag = 1; + extvector = 0; + global_freq = 1; + + // Specifies the number of output fields this fix produces for thermo output. + // It calculates the + // - Number of accepted trial moves + // - Number of rejected trial moves + // - Atom counts for each species. + size_vector = 2 + atom->ntypes; + + // Let LAMMPS know the number of data values per atom to transfer in MPI communication. + comm_forward = 4; + comm_reverse = 3; + + samplingWindowUserSize = 0; + samplingWindowPosition = 5; + nAcceptedSwaps = 0; + nRejectedSwaps = 0; + kappa = 0; + serialMode = false; + + if (domain->triclinic) + error->all(FLERR, "Fix sgcmc does not support non-orthogonal simulation boxes."); + + if (narg < 6) utils::missing_cmd_args(FLERR, "fix sgcmc", error); + + // Parse the number of MD timesteps to do between MC. + nevery_mdsteps = utils::inumeric(FLERR, arg[3], false, lmp); + if (nevery_mdsteps <= 0) error->all(FLERR, "Invalid number of MD timesteps {}", nevery_mdsteps); + if (comm->me == 0) utils::logmesg(lmp, " SGC - Number of MD timesteps: {}\n", nevery_mdsteps); + + // Parse the fraction of atoms swaps attempted during each cycle. + swap_fraction = utils::numeric(FLERR, arg[4], false, lmp); + if ((swap_fraction < 0.0) || (swap_fraction > 1.0)) + error->all(FLERR, "Invalid fraction {} of swap atoms", swap_fraction); + if (comm->me == 0) utils::logmesg(lmp, " SGC - Fraction of swap atoms: {}\n", swap_fraction); + + // Parse temperature for MC. + double temperature = utils::numeric(FLERR, arg[5], false, lmp); + if (temperature <= 0) error->all(FLERR, "Temperature {} invalid", temperature); + if (comm->me == 0) utils::logmesg(lmp, " SGC - Temperature: {}\n", temperature); + beta = 1.0 / (force->boltz * temperature); + + // Parse chemical potentials. + int iarg = 6; + deltamu.resize(atom->ntypes + 1); + deltamu[0] = 0.0; + deltamu[1] = 0.0; + if (atom->ntypes < 2) + error->all(FLERR, "Fix sgcmc can only be used in simulations with at least two atom types."); + for (int i = 2; i <= atom->ntypes; i++, iarg++) { + if (iarg >= narg) error->all(FLERR, "Too few chemical potentials specified"); + deltamu[i] = utils::numeric(FLERR, arg[iarg], false, lmp); + if (comm->me == 0) + utils::logmesg(lmp, " SGC - Chemical potential of species {}: {}\n", i, deltamu[i]); + } + + // Default values for optional parameters (where applicable). + numSamplingWindowMoves = 8; + seed = 324234; + + // Parse extra/optional parameters + while (iarg < narg) { + + if (strcmp(arg[iarg], "randseed") == 0) { + // Random number seed. + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix sgcmc randseed", error); + seed = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + if (seed <= 0) error->all(FLERR, "Random number seed {} must be positive", seed); + if (comm->me == 0) utils::logmesg(lmp, " SGC - Random number seed: {}\n", seed); + iarg += 2; + + } else if (strcmp(arg[iarg], "window_moves") == 0) { + // Parse number of window moves. + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix sgcmc window_moves", error); + numSamplingWindowMoves = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + if (numSamplingWindowMoves <= 0) + error->all(FLERR, "Invalid number {} of sampling window moves", numSamplingWindowMoves); + if (comm->me == 0) + utils::logmesg(lmp, " SGC - Number of sampling window moves: {}\n", + numSamplingWindowMoves); + iarg += 2; + + } else if (strcmp(arg[iarg], "window_size") == 0) { + // Parse sampling window size parameter. + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix sgcmc window_moves", error); + samplingWindowUserSize = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + if ((samplingWindowUserSize < 0.5) || (samplingWindowUserSize > 1.0)) + error->all(FLERR, "Sampling window size {} is out of range.", samplingWindowUserSize); + if (comm->me == 0) + utils::logmesg(lmp, " SGC - Sampling window size: {}\n", samplingWindowUserSize); + iarg += 2; + + } else if (strcmp(arg[iarg], "variance") == 0) { + // Parse parameters for variance constraint ensemble. + if (iarg + 1 + atom->ntypes > narg) + utils::missing_cmd_args(FLERR, "fix sgcmc variance", error); + iarg++; + + kappa = utils::numeric(FLERR, arg[iarg], false, lmp); + if (kappa < 0) error->all(FLERR, "Variance constraint parameter must not be negative."); + if (comm->me == 0) utils::logmesg(lmp, " SGC - Kappa: {}\n", kappa); + iarg++; + + targetConcentration.resize(atom->ntypes + 1); + targetConcentration[0] = 1.0; + targetConcentration[1] = 1.0; + for (int i = 2; i <= atom->ntypes; i++, iarg++) { + targetConcentration[i] = utils::numeric(FLERR, arg[iarg], false, lmp); + targetConcentration[1] -= targetConcentration[i]; + } + for (int i = 1; i <= atom->ntypes; i++, iarg++) { + if ((targetConcentration[i] < 0.0) || (targetConcentration[i] > 1.0)) + error->all(FLERR, "Target concentration {} for species {} is out of range", + targetConcentration[i], i); + if (comm->me == 0) + utils::logmesg(lmp, " SGC - Target concentration of species {}: {}\n", i, + targetConcentration[i]); + } + + } else if (strcmp(arg[iarg], "serial") == 0) { + // Switch off second rejection. + serialMode = true; + if (comm->me == 0) + utils::logmesg(lmp, " SGC - Using serial MC version without second rejection.\n"); + iarg++; + + if (comm->nprocs != 1) + error->all(FLERR, "Cannot use serial mode Monte Carlo in a parallel simulation."); + } else { + error->all(FLERR, "Unknown fix sgcmc keyword: {}", arg[iarg]); + } + } + + // Initialize random number generators. + random = new RanPark(lmp, seed); + localRandom = new RanPark(lmp, seed + universe->me); +} + +/********************************************************************* + * Destructor. Cleans up the random number generators. + *********************************************************************/ +FixSemiGrandCanonicalMC::~FixSemiGrandCanonicalMC() +{ + delete random; + delete localRandom; +} + +// clang-format off + +/********************************************************************* + * The return value of this method specifies at which points the + * fix is invoked during the simulation. + *********************************************************************/ +int FixSemiGrandCanonicalMC::setmask() +{ + // We want the MC routine to be called in between the MD steps. + // We need the electron densities for each atom, so after the + // EAM potential has computed them in the force routine is a good + // time to invoke the MC routine. + int mask = 0; + mask |= POST_FORCE; + mask |= POST_FORCE_RESPA; + return mask; +} + +/********************************************************************* + * This gets called by the system before the simulation starts. + *********************************************************************/ +void FixSemiGrandCanonicalMC::init() +{ + // Make sure the user has defined only one Monte-Carlo fix. + int count = 0; + for (int i = 0; i < modify->nfix; i++) + if (strcmp(modify->fix[i]->style,"sgcmc") == 0) count++; + if (count > 1) error->all(FLERR, "More than one fix sgcmc defined."); + + // Save a pointer to the EAM potential. + pairEAM = dynamic_cast(force->pair); + if (!pairEAM) { + if (comm->me == 0) + utils::logmesg(lmp, " SGC - Using naive total energy calculation for MC -> SLOW!\n"); + + if (comm->nprocs > 1) + error->all(FLERR, "Can not run fix vcsgc with naive total energy calculation and more than one MPI process."); + + // Create a compute that will provide the total energy of the system. + // This is needed by computeTotalEnergy(). + char* id_pe = (char*)"thermo_pe"; + int ipe = modify->find_compute(id_pe); + compute_pe = modify->compute[ipe]; + } + interactionRadius = force->pair->cutforce; + if (comm->me == 0) utils::logmesg(lmp, " SGC - Interaction radius: {}\n", interactionRadius); + + // This fix needs a full neighbor list. + neighbor->add_request(this, NeighConst::REQ_FULL); + + // Count local number of atoms from each species. + const int *type = atom->type; + const int *mask = atom->mask; + std::vector localSpeciesCounts(atom->ntypes+1, 0); + for (int i = 0; i < atom->nlocal; i++, ++type) { + if (mask[i] & groupbit) + localSpeciesCounts[*type]++; + } + + // MPI sum to get global concentrations. + speciesCounts.resize(atom->ntypes+1); + MPI_Allreduce(&localSpeciesCounts.front(), &speciesCounts.front(), localSpeciesCounts.size(), + MPI_INT, MPI_SUM, world); +} + +/********************************************************************* + * Assigns the requested neighbor list to the fix. + *********************************************************************/ +void FixSemiGrandCanonicalMC::init_list(int /*id*/, NeighList *ptr) +{ + neighborList = ptr; +} + +/********************************************************************* + * Called after the EAM force calculation during each timestep. + * This method triggers the MC routine from time to time. + *********************************************************************/ +void FixSemiGrandCanonicalMC::post_force(int /*vflag*/) +{ + if ((update->ntimestep % nevery_mdsteps) == 0) + doMC(); +} + +/********************************************************************* + * This routine does one full MC step. + *********************************************************************/ +void FixSemiGrandCanonicalMC::doMC() +{ + // Allocate array memory. + changedAtoms.resize(atom->nmax); + + // During the last MD timestep the EAM potential routine has computed the + // electron densities for all atoms that belong to this processor. + // They are stored in the rho array of the PairEAM class. + // But computing the energy change caused by flipping one atom of this processor + // might require the electron densities of atoms that belong to other processors. + // So we first need to fetch those electron densities for our ghost atoms now. + fetchGhostAtomElectronDensities(); + + const int *mask = atom->mask; + + // Reset counters. + int nAcceptedSwapsLocal = 0; + int nRejectedSwapsLocal = 0; + + int oldSpecies, newSpecies; + std::vector deltaN(atom->ntypes+1, 0); //< Local change in number of atoms of each species. + std::vector deltaNGlobal(atom->ntypes+1, 0); //< Global change in number of atoms of each species. + + for (int i = 0; i < numSamplingWindowMoves; i++) { + + // Reset flag array that keeps track of changed per-atom quantities. + std::fill(changedAtoms.begin(), changedAtoms.end(), false); + + // Position the sampling window within the node's boundaries. + // By default the size of the sampling window is the size of the processor bounds minus two cutoff radii. + // This ensures that changing atoms in the sampling windows of two adjacent processors cannot affect + // the same atoms in the region between the two sampling windows. + // For debugging purposes the sampling window can be chosen larger than the default size. Then it is + // considered an 'oversize' window and we have to exchange atom information after each and + // and every swap step, which is very slow. + bool oversizeWindow = placeSamplingWindow(); + + /// The number of times we want to swap an atom. + int nDice = (int)(swap_fraction * numFixAtomsLocal / numSamplingWindowMoves); + + // This number must be synchronized with the other nodes. We take the largest + // of all nodes and skip trial moves later. + int largestnDice; + MPI_Allreduce(&nDice, &largestnDice, 1, MPI_INT, MPI_MAX, world); + + // The probability to do one swap step. + double diceProbability = (double)nDice / (double)largestnDice; + + // Inner MC loop that swaps atom types. + for (int j = 0; j < largestnDice; j++) { + + double deltaE = 0; + std::fill(deltaN.begin(), deltaN.end(), 0); + int selectedAtom = -1, selectedAtomNL = -1; + + // As already said above, we have to do swap steps only with a certain probability + // to keep nodes in sync. + if (localRandom->uniform() <= diceProbability) { + + // Choose a random atom from the pool of atoms that are inside the sampling window. + int index = (int)(localRandom->uniform() * (double)samplingWindowAtoms.size()); + selectedAtomNL = samplingWindowAtoms[index]; + + // Get the real atom index. + selectedAtom = neighborList->ilist[selectedAtomNL]; + oldSpecies = atom->type[selectedAtom]; + + // Choose the new type for the swapping atom by random. + if (atom->ntypes > 2) { + // Use a random number to choose the new species if there are three or more atom types. + newSpecies = (int)(localRandom->uniform() * (atom->ntypes-1)) + 1; + if (newSpecies >= oldSpecies) newSpecies++; + } + else { + // If there are only two atom types, then the decision is clear. + newSpecies = (oldSpecies == 1) ? 2 : 1; + } + deltaN[oldSpecies] = -1; + deltaN[newSpecies] = +1; + + // Compute the energy difference that swapping this atom would cost or gain. + if (pairEAM) { + deltaE = computeEnergyChangeEAM(selectedAtom, selectedAtomNL, oldSpecies, newSpecies); + } else { + // Generic case: + deltaE = computeEnergyChangeGeneric(selectedAtom, oldSpecies, newSpecies); + } + + // Perform inner MC acceptance test. + double dm = 0.0; + if (serialMode && kappa != 0.0) { + for (int i = 2; i <= atom->ntypes; i++) + dm += (deltamu[i] + kappa / atom->natoms * (2.0 * speciesCounts[i] + deltaN[i])) * deltaN[i]; + } + else { + for (int i = 2; i <= atom->ntypes; i++) + dm += deltamu[i] * deltaN[i]; + } + double deltaB = -(deltaE + dm) * beta; + if (deltaB < 0.0) { + if (deltaB < log(localRandom->uniform())) { + std::fill(deltaN.begin(), deltaN.end(), 0); + selectedAtom = -1; + deltaE = 0; + } + } + } + + if (kappa != 0.0 && serialMode == false) { + + // What follows is the second rejection test for the variance-constrained + // semi-grandcanonical method. + + // MPI sum of total change in number of particles. + MPI_Allreduce(&deltaN.front(), &deltaNGlobal.front(), deltaN.size(), MPI_INT, MPI_SUM, world); + + // Perform outer MC acceptance test. + // This is done in sync by all processors. + double A = 0.0; + for (int i = 1; i <= atom->ntypes; i++) { + A += deltaNGlobal[i] * deltaNGlobal[i]; + A += 2.0 * deltaNGlobal[i] * (speciesCounts[i] - (int)(targetConcentration[i] * atom->natoms)); + } + double deltaB = -(kappa / atom->natoms) * A; + if (deltaB < 0.0) { + if (deltaB < log(random->uniform())) { + std::fill(deltaN.begin(), deltaN.end(), 0); + std::fill(deltaNGlobal.begin(), deltaNGlobal.end(), 0); + selectedAtom = -1; + } + } + + // Update global species counters. + for (int i = 1; i <= atom->ntypes; i++) + speciesCounts[i] += deltaNGlobal[i]; + } + else if (serialMode) { + // Update the local species counters. + for (int i = 1; i <= atom->ntypes; i++) + speciesCounts[i] += deltaN[i]; + } + + // Make accepted atom swap permanent. + if (selectedAtom >= 0) { + if (pairEAM) + flipAtomEAM(selectedAtom, selectedAtomNL, oldSpecies, newSpecies); + else + flipAtomGeneric(selectedAtom, oldSpecies, newSpecies); + nAcceptedSwapsLocal++; + } + else { + nRejectedSwapsLocal++; + } + + if (oversizeWindow) { + // In case of an oversized sampling window we have to exchange the atom types and all other + // per-atom quantities after each and every swap step. This is very slow and should only be used + // for debugging purposes. + communicateRhoAndTypes(); + } + } + + // Finally the changed electron densities and atom types must be exchanged before + // the sampling window is moved. + if (!oversizeWindow) + communicateRhoAndTypes(); + } + + // MPI sum total number of accepted/rejected swaps. + MPI_Allreduce(&nAcceptedSwapsLocal, &nAcceptedSwaps, 1, MPI_INT, MPI_SUM, world); + MPI_Allreduce(&nRejectedSwapsLocal, &nRejectedSwaps, 1, MPI_INT, MPI_SUM, world); + + // For (parallelized) semi-grandcanonical MC we have to determine the current concentrations now. + // For the serial version and variance-constrained MC it has already been done in the loop. + if (kappa == 0.0 && serialMode == false) { + const int *type = atom->type; + std::vector localSpeciesCounts(atom->ntypes+1, 0); + for (int i = 0; i < atom->nlocal; i++, ++type) { + if (mask[i] & groupbit) + localSpeciesCounts[*type]++; + } + MPI_Allreduce(&localSpeciesCounts.front(), &speciesCounts.front(), localSpeciesCounts.size(), MPI_INT, MPI_SUM, world); + } +} + +/********************************************************************* + * Fetches the electron densities for the local ghost atoms + * from the neighbor nodes. + *********************************************************************/ +void FixSemiGrandCanonicalMC::fetchGhostAtomElectronDensities() +{ + if (pairEAM) { + // Transfer original EAM rho values. + communicationStage = 1; + comm->forward_comm(this); + } +} + +/********************************************************************* + * Transfers the locally changed electron densities and atom + * types to the neighbors. + *********************************************************************/ +void FixSemiGrandCanonicalMC::communicateRhoAndTypes() +{ + // Electron densities can have changed for real atoms as well as ghost atoms during the last MC step. + // So we have to perform a forward and a reverse communication to keep everything in sync. + // In the array changedAtoms we kept track of which rhos have been changed by the MC. This helps us + // here to not overwrite values when doing the bidirectional exchange. + + if (pairEAM) { + // Transfer changed electron densities of ghost atoms to the real atoms. + communicationStage = 2; + comm->reverse_comm(this); + } + + // Transfer changed atom types and electron densities of the real atoms to the ghost atoms. + communicationStage = 3; + comm->forward_comm(this); +} + +/********************************************************************* + * This is for MPI communication with neighbor nodes. + *********************************************************************/ +int FixSemiGrandCanonicalMC::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, + int * /*pbc*/) +{ + int m = 0; + if (communicationStage == 1) { + // Send electron densities of local atoms to neighbors. + for (int i = 0; i < n; i++) buf[m++] = pairEAM->rho[list[i]]; + } else if (communicationStage == 3) { + if (pairEAM) { + // Send types and rhos of real atoms to the ghost atoms of the neighbor proc. + for (int i = 0; i < n; i++) { + buf[m++] = atom->type[list[i]]; + buf[m++] = pairEAM->rho[list[i]]; + } + } else { + // Generic potential case: + for (int i = 0; i < n; i++) { + buf[m++] = atom->type[list[i]]; + } + } + } + return m; +} + +/********************************************************************* + * This is for MPI communication with neighbor nodes. + *********************************************************************/ +void FixSemiGrandCanonicalMC::unpack_forward_comm(int n, int first, double* buf) +{ + if (communicationStage == 1) { + // Receive electron densities of ghost atoms from neighbors. + int last = first + n; + for (int i = first; i < last; i++) pairEAM->rho[i] = *buf++; + } else if (communicationStage == 3) { + int last = first + n; + if (pairEAM) { + // Receive types and rhos of real atoms of the neighbor proc and assign them + // to the local ghost atoms. + for (int i = first; i < last; i++, buf += 2) { + atom->type[i] = (int)buf[0]; + // We have to make sure that rhos changed locally do not get overridden by the rhos + // sent by the neighbor procs. + if (!changedAtoms[i]) + pairEAM->rho[i] = buf[1]; + } + } else { + // Generic potential case: + for (int i = first; i < last; i++, buf += 1) { + atom->type[i] = (int)buf[0]; + } + } + } +} + +/********************************************************************* + * This is for MPI communication with neighbor nodes. + *********************************************************************/ +int FixSemiGrandCanonicalMC::pack_reverse_comm(int n, int first, double* buf) +{ + int m = 0; + + // Send changed electron densities of ghost atoms to the real atoms of neighbor procs. + int last = first + n; + for (int i = first; i < last; i++) buf[m++] = pairEAM->rho[i]; + return m; +} + +/********************************************************************* + * This is for MPI communication with neighbor nodes. + *********************************************************************/ +void FixSemiGrandCanonicalMC::unpack_reverse_comm(int n, int *list, double* buf) +{ + // Received changed electron densities of ghost atoms of neighbor procs and assign them to our + // real atoms. + for (int i = 0; i < n; i++, buf++) { + // We have to make sure that rhos changed locally do not get overridden by the rhos + // sent by the neighbor procs. + if (!changedAtoms[list[i]]) + pairEAM->rho[list[i]] = *buf; + } +} + +/********************************************************************* + * Positions the sampling window inside the node's bounding box. + *********************************************************************/ +bool FixSemiGrandCanonicalMC::placeSamplingWindow() +{ + // By default the size of the sampling window is the size of the processor bounds minus two cutoff radii. + // This ensures that changing atoms in the sampling windows of two adjacent processors cannot affect + // the same atoms in the region between the two sampling windows. + // For debugging purposes the sampling window can be chosen larger than the default size. Then it is + // considered an 'oversize' window. + bool oversizeWindow = false; + + // Align the sampling window to one of the 8 corners of the processor cell. + double samplingWindowLo[3]; + double samplingWindowHi[3]; + double margin[3]; + for (int i = 0; i < 3; i++) { + + margin[i] = interactionRadius * 2.0; + if (samplingWindowUserSize > 0.0) { + margin[i] = (domain->subhi[i] - domain->sublo[i]) * (1.0 - samplingWindowUserSize); + if (margin[i] < interactionRadius * 2.0) + oversizeWindow = true; + } + + double shift = (double)((samplingWindowPosition >> i) & 1) * margin[i]; + samplingWindowLo[i] = domain->sublo[i] + shift; + samplingWindowHi[i] = domain->subhi[i] + shift - margin[i]; + + // Check if processor cells are large enough. + // Node bounds must be at least four times as large as the atom interaction radius. + // Sampling window must be at least half as wise as the processor cell to cover the cell completely. + if (samplingWindowHi[i] - samplingWindowLo[i] + 1e-6 < (domain->subhi[i] - domain->sublo[i]) * 0.5) { + error->one(FLERR, "Per-node simulation cell is too small for fix sgcmc. Processor cell size must be at least 4 times cutoff radius."); + } + } + // Increase counter by one. + // Since we are only using the lower 3 bits of the integer value the alignment will + // be the same after 8 iterations. + samplingWindowPosition += 1; + + // Compile a list of atoms that are inside the sampling window. + samplingWindowAtoms.resize(0); + samplingWindowAtoms.reserve(atom->nlocal); + numSamplingWindowAtoms = 0; + numFixAtomsLocal = 0; + + const int *mask = atom->mask; + for (int ii = 0; ii < neighborList->inum; ii++) { + int i = neighborList->ilist[ii]; + if (mask[i] & groupbit) { + numFixAtomsLocal++; + const double* x = atom->x[i]; + // Is atom inside window region? + if (x[0] >= samplingWindowLo[0] && x[0] < samplingWindowHi[0] && + x[1] >= samplingWindowLo[1] && x[1] < samplingWindowHi[1] && + x[2] >= samplingWindowLo[2] && x[2] < samplingWindowHi[2]) { + // Atoms within a distance of two times the interaction radius from the cell border + // are less often inside the sampling window than atoms in the center of the node cell, + // which are always inside the window. + // We therefore have to increase their probability here to make them chosen + // as often as the core atoms. + int multiplicity = 1; + for (int k=0; k < 3; k++) { + if (x[k] < domain->sublo[k] + margin[k] || + x[k] > domain->subhi[k] - margin[k]) + multiplicity *= 2; + } + + for (int m = 0; m < multiplicity; m++) + samplingWindowAtoms.push_back(ii); + + numSamplingWindowAtoms++; + } + } + } + + return oversizeWindow; +} + +/********************************************************************* + * Calculates the change in energy that swapping the given + * atom would produce. This routine is for the standard EAM potential. + * + * Parameters: + * + * flipAtom [in] + * This specifies the atom to be swapped. It's an index into the local list of atoms. + * + * flipAtomNL [in] + * This specifies the atom to be swapped. It's an index into the neighbor list. + * + * oldSpecies [in] + * The current species of the atom before the routine is called. + * + * newSpecies [in] + * The new species of the atom. The atom's type is not changed by this routine. It only computes the induced energy change. + * + * Return value: + * The expected change in total potential energy. + *********************************************************************/ +double FixSemiGrandCanonicalMC::computeEnergyChangeEAM(int flipAtom, int flipAtomNL, int oldSpecies, int newSpecies) +{ + double p; + int m; + double const* rho = pairEAM->rho; + double* coeff; + double new_total_rho_i = 0.0; + double deltaE = 0.0; + + // Calculate change of electron density at the surrounding + // sites induced by the swapped atom. Then calculate the change of embedding energy for each neighbor atom. + // Also recalculate the total electron density at the site of the swapped atom. + + double xi = atom->x[flipAtom][0]; + double yi = atom->x[flipAtom][1]; + double zi = atom->x[flipAtom][2]; + + // Loop over all neighbors of the selected atom. + int* jlist = neighborList->firstneigh[flipAtomNL]; + int jnum = neighborList->numneigh[flipAtomNL]; + for (int jj = 0; jj < jnum; jj++) { + int j = jlist[jj]; + + double delx = xi - atom->x[j][0]; + double dely = yi - atom->x[j][1]; + double delz = zi - atom->x[j][2]; + double rsq = delx*delx + dely*dely + delz*delz; + if (rsq >= pairEAM->cutforcesq) continue; + + int jtype = atom->type[j]; + double r = sqrt(rsq); + + p = r * pairEAM->rdr + 1.0; + m = static_cast(p); + m = MIN(m, pairEAM->nr - 1); + p -= m; + p = MIN(p, 1.0); + + // Calculate change of pair energy ij. + coeff = pairEAM->z2r_spline[pairEAM->type2z2r[oldSpecies][jtype]][m]; + double oldz2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; + coeff = pairEAM->z2r_spline[pairEAM->type2z2r[newSpecies][jtype]][m]; + double newz2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; + deltaE += (newz2 - oldz2) / r; + + // Calculate change of electron density at site j. + coeff = pairEAM->rhor_spline[pairEAM->type2rhor[oldSpecies][jtype]][m]; + double oldrho_contr = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; + coeff = pairEAM->rhor_spline[pairEAM->type2rhor[newSpecies][jtype]][m]; + double newrho_contr = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; + double delta_rho = newrho_contr - oldrho_contr; + + // Sum total rho at site of swapped atom. + coeff = pairEAM->rhor_spline[pairEAM->type2rhor[jtype][newSpecies]][m]; + new_total_rho_i += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; + + // Calculate old embedding energy of atom j. + p = rho[j] * pairEAM->rdrho + 1.0; + m = static_cast(p); + m = MAX(1, MIN(m, pairEAM->nrho - 1)); + p -= m; + p = MIN(p, 1.0); + coeff = pairEAM->frho_spline[pairEAM->type2frho[jtype]][m]; + double oldF = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; + + // Calculate new embedding energy of atom j. + p = (rho[j] + delta_rho) * pairEAM->rdrho + 1.0; + m = static_cast(p); + m = MAX(1, MIN(m, pairEAM->nrho - 1)); + p -= m; + p = MIN(p, 1.0); + coeff = pairEAM->frho_spline[pairEAM->type2frho[jtype]][m]; + double newF = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; + + deltaE += newF - oldF; + } + + // Compute the change in embedding energy of the changing atom. + p = rho[flipAtom] * pairEAM->rdrho + 1.0; + m = static_cast(p); + m = MAX(1, MIN(m, pairEAM->nrho - 1)); + p -= m; + p = MIN(p, 1.0); + coeff = pairEAM->frho_spline[pairEAM->type2frho[oldSpecies]][m]; + double oldF = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; + + p = new_total_rho_i * pairEAM->rdrho + 1.0; + m = static_cast(p); + m = MAX(1, MIN(m, pairEAM->nrho - 1)); + p -= m; + p = MIN(p, 1.0); + coeff = pairEAM->frho_spline[pairEAM->type2frho[newSpecies]][m]; + double newF = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; + + deltaE += newF - oldF; + + return deltaE; +} + +/********************************************************************* + * Calculates the change in energy that swapping the given atom would produce. + * This routine is for the general case of an arbitrary potential and + * IS VERY SLOW! It computes the total energies of the system for the unmodified state + * and for the modified state and then returns the difference of both values. + * This routine should only be used for debugging purposes. + * + * Parameters: + * + * flipAtom [in] + * This specifies the atom to be swapped. It's an index into the local list of atoms. + * + * oldSpecies [in] + * The current species of the atom before the routine is called. + * + * newSpecies [in] + * The new species of the atom. The atom's type is not changed by this method. It only computes the induced energy change. + * + * Return value: + * The expected change in total potential energy. + *********************************************************************/ +double FixSemiGrandCanonicalMC::computeEnergyChangeGeneric(int flipAtom, int oldSpecies, int newSpecies) +{ + // This routine is called even when no trial move is being performed during the + // the current iteration to keep the parallel processors in sync. If no trial + // move is performed then the energy is calculated twice for the same state of the system. + if (flipAtom >= 0) { + // Change system. Perform trial move. + atom->type[flipAtom] = newSpecies; + } + // Transfer changed atom types of the real atoms to the ghost atoms. + communicationStage = 3; + comm->forward_comm(this); + + // Calculate new total energy. + double newEnergy = computeTotalEnergy(); + + // Undo trial move. Restore old system state. + if (flipAtom >= 0) { + atom->type[flipAtom] = oldSpecies; + } + // Transfer changed atom types of the real atoms to the ghost atoms. + communicationStage = 3; + comm->forward_comm(this); + + // Calculate old total energy. + double oldEnergy = computeTotalEnergy(); + + // Restore the correct electron densities and forces. + update->integrate->setup_minimal(0); + fetchGhostAtomElectronDensities(); + + return newEnergy - oldEnergy; +} + +/********************************************************************* + * Lets LAMMPS calculate the total potential energy of the system. + *********************************************************************/ +double FixSemiGrandCanonicalMC::computeTotalEnergy() +{ + int eflag = 1; + int vflag = 0; + + if (force->pair) force->pair->compute(eflag,vflag); + + if (atom->molecular) { + if (force->bond) force->bond->compute(eflag,vflag); + if (force->angle) force->angle->compute(eflag,vflag); + if (force->dihedral) force->dihedral->compute(eflag,vflag); + if (force->improper) force->improper->compute(eflag,vflag); + } + + if (force->kspace) force->kspace->compute(eflag,vflag); + + update->eflag_global = update->ntimestep; + return compute_pe->compute_scalar(); +} + +/********************************************************************* + * Flips the type of one atom and changes the electron densities + * of nearby atoms accordingly. + * This routine is for the case of a standard EAM potential. + * + * Parameters: + * + * flipAtom [in] + * This specifies the atom to be swapped. It's an index into the local list of atoms. + * + * flipAtomNL [in] + * This specifies the atom to be swapped. It's an index into the neighbor list. + * + * oldSpecies [in] + * The current species of the atom before the routine is called. + * + * newSpecies [in] + * The new type to be assigned to the atom. + *********************************************************************/ +void FixSemiGrandCanonicalMC::flipAtomEAM(int flipAtom, int flipAtomNL, int oldSpecies, int newSpecies) +{ + double p; + int m; + double* rho = pairEAM->rho; + double* coeff; + double new_total_rho_i = 0.0; + + // Change atom's type and mark it for exchange. + atom->type[flipAtom] = newSpecies; + changedAtoms[flipAtom] = true; + + // Rescale particle velocity vector to conserve kinetic energy. + double vScaleFactor = sqrt(atom->mass[oldSpecies] / atom->mass[newSpecies]); + atom->v[flipAtom][0] *= vScaleFactor; + atom->v[flipAtom][1] *= vScaleFactor; + atom->v[flipAtom][2] *= vScaleFactor; + + double xi = atom->x[flipAtom][0]; + double yi = atom->x[flipAtom][1]; + double zi = atom->x[flipAtom][2]; + + // Loop over all neighbors of the selected atom. + int* jlist = neighborList->firstneigh[flipAtomNL]; + int jnum = neighborList->numneigh[flipAtomNL]; + for (int jj = 0; jj < jnum; jj++) { + int j = jlist[jj]; + + double delx = xi - atom->x[j][0]; + double dely = yi - atom->x[j][1]; + double delz = zi - atom->x[j][2]; + double rsq = delx*delx + dely*dely + delz*delz; + if (rsq >= pairEAM->cutforcesq) continue; + + int jtype = atom->type[j]; + double r = sqrt(rsq); + p = r * pairEAM->rdr + 1.0; + m = static_cast(p); + m = MIN(m, pairEAM->nr - 1); + p -= m; + p = MIN(p, 1.0); + + // Calculate change of electron density at site j. + coeff = pairEAM->rhor_spline[pairEAM->type2rhor[oldSpecies][jtype]][m]; + double oldrho_contr = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; + coeff = pairEAM->rhor_spline[pairEAM->type2rhor[newSpecies][jtype]][m]; + double newrho_contr = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; + double delta_rho = newrho_contr - oldrho_contr; + + rho[j] += delta_rho; + + // Sum total rho at site of swapped atom. + coeff = pairEAM->rhor_spline[pairEAM->type2rhor[jtype][newSpecies]][m]; + new_total_rho_i += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; + + // Set the flag for this atom to indicate that its rho has changed and needs + // to be transfered at end of MC step. + changedAtoms[j] = true; + } + + // Store newly calculated electron density at swapped atom site. + rho[flipAtom] = new_total_rho_i; +} + +/********************************************************************* + * Flips the type of one atom. + * This routine is for the generic case. + * + * Parameters: + * + * flipAtom [in] + * This specifies the atom to be swapped. It's an index into the local list of atoms. + * + * oldSpecies [in] + * The current species of the atom before the routine is called. + * + * newSpecies [in] + * The new type to be assigned to the atom. + *********************************************************************/ +void FixSemiGrandCanonicalMC::flipAtomGeneric(int flipAtom, int oldSpecies, int newSpecies) +{ + atom->type[flipAtom] = newSpecies; + + // Rescale particle velocity vector to conserve kinetic energy. + double vScaleFactor = sqrt(atom->mass[oldSpecies] / atom->mass[newSpecies]); + atom->v[flipAtom][0] *= vScaleFactor; + atom->v[flipAtom][1] *= vScaleFactor; + atom->v[flipAtom][2] *= vScaleFactor; + + changedAtoms[flipAtom] = true; +} + +/********************************************************************* + * Lets the fix report one of its internal state variables to LAMMPS. + *********************************************************************/ +double FixSemiGrandCanonicalMC::compute_vector(int index) +{ + if (index == 0) return nAcceptedSwaps; + if (index == 1) return nRejectedSwaps; + index -= 1; + int totalAtoms = 0; + for (int i = 0; i < (int)speciesCounts.size(); i++) + totalAtoms += speciesCounts[i]; + if (index <= atom->ntypes) + return (double)speciesCounts[index] / (totalAtoms > 0 ? totalAtoms : 1); + return 0.0; +} + +/********************************************************************* + * Reports the memory usage of this fix to LAMMPS. + *********************************************************************/ +double FixSemiGrandCanonicalMC::memory_usage() +{ + return (changedAtoms.size() * sizeof(bool)) + + (samplingWindowAtoms.size() * sizeof(int)); +} + diff --git a/src/MC/fix_sgcmc.h b/src/MC/fix_sgcmc.h new file mode 100644 index 0000000000..9ad3f65214 --- /dev/null +++ b/src/MC/fix_sgcmc.h @@ -0,0 +1,188 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + 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. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + * Parallel Monte-Carlo code for the semi-grandcanonical ensemble (SGC) + * and the variance-constrained semi-grandcanonical ensemble (VC-SGC). + * + * See Sadigh et al., Phys. Rev. B 85, 184203 (2012) for a + * description of the algorithm. + * + * Code author: Alexander Stukowski (stukowski@mm.tu-darmstadt.de) +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS +// clang-format off +FixStyle(sgcmc,FixSemiGrandCanonicalMC); +// clang-format on +#else + +#ifndef FIX_SGCMC_H +#define FIX_SGCMC_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixSemiGrandCanonicalMC : public Fix { + public: + FixSemiGrandCanonicalMC(class LAMMPS *, int, char **); + + ~FixSemiGrandCanonicalMC() override; + + int setmask() override; + void init() override; + void init_list(int id, class NeighList *ptr) override; + void post_force(int vflag) override; + double compute_vector(int index) override; + + int pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) override; + void unpack_forward_comm(int n, int first, double *buf) override; + int pack_reverse_comm(int n, int first, double *buf) override; + void unpack_reverse_comm(int n, int *list, double *buf) override; + + double memory_usage() override; + + /******************** Monte-Carlo routines ************************/ + + // This routine does one full MC step. + void doMC(); + + // Fetches the electron densities for the local ghost atoms from the neighbor nodes. + void fetchGhostAtomElectronDensities(); + + // Positions the sampling window inside the node's bounding box. + bool placeSamplingWindow(); + + // Calculates the change in energy that swapping the given atom would produce. + // This routine is for the case of a standard EAM potential. + double computeEnergyChangeEAM(int flipAtom, int flipAtomNL, int oldSpecies, int newSpecies); + + // Calculates the change in energy that swapping the given atom would produce. + // This routine is for the general case of an arbitrary potential and + // IS VERY SLOW! It computes the total energies of the system for the unmodified state + // and for the modified state and then returns the difference of both values. + // This routine should only be used for debugging purposes. + double computeEnergyChangeGeneric(int flipAtom, int oldSpecies, int newSpecies); + + // Lets LAMMPS calculate the total potential energy of the system. + double computeTotalEnergy(); + + // Flips the type of one atom and changes the electron densities of nearby atoms accordingly. + // This routine is for the case of a standard EAM potential. + void flipAtomEAM(int flipAtom, int flipAtomNL, int oldSpecies, int newSpecies); + + // Flips the type of one atom. + // This routine is for the generic case. + void flipAtomGeneric(int flipAtom, int oldSpecies, int newSpecies); + + // Transfers the locally changed electron densities and atom types to the neighbors. + void communicateRhoAndTypes(); + + private: + // The number of MD steps between each MC cycle. + int nevery_mdsteps; + + // The number of times the sampling window should be repositioned during one MC cycle. + int numSamplingWindowMoves; + + // The fraction of atoms that should be swapped per MC step. + double swap_fraction; + + // The maximum interaction radius of all potentials. + double interactionRadius; + + // The inverse MC temperature. + double beta; + + // Chemical potential differences for all species. The differences are relative to the chemical + // potential of the first species. Note that this array is based on index 1 (not 0 as normal C arrays). + // This means the first two elements of this vector are always zero. + std::vector deltamu; + + // Enables serial implementation without second rejection in the VCSGC ensemble. + bool serialMode; + + // The MC variance constraint parameter. + double kappa; + + // The target concentration values for each species. The concentration of first species is + // implicitely defined as one minues all other concentrations. Please note that this vector + // is based on index 1. The first element at index 0 is not used. + std::vector targetConcentration; + + // The master seed value for the random number generators on all nodes. + int seed; + + // The random number generator that is in sync with all other nodes. + class RanPark *random; + + // The local random number generator for this proc only. + class RanPark *localRandom; + + // The total number of atoms of the different species in the whole system. + // Divide this by the total number of atoms to get the global concentration. + // Since LAMMPS atom types start at index 1 this array is also based on index 1. + // The first array element at index 0 is not used. + std::vector speciesCounts; + + // The full neighbor list used by this fix. + class NeighList *neighborList; + + // The user-defined size of the sampling window. It is specified as a fraction + // of the processor's cell boundaries. + // If this parameter is 0 then the default sampling window size is used. + double samplingWindowUserSize; + + // This counter is increased each time the sampling window is repositioned. + // The lowest 3 bits of this integer value specify the alignment of the sampling window in + // the processor cell. That means that after 8 iterations the 8 corners have been sampled + // and it starts at the first corner again. + int samplingWindowPosition; + + // Array with indices of all atoms that are within the sampling window. + // Note 1: that an atom can be more than once in this array if its multiplicity is greater than on. + // Note 2: Indices are into the I array of the neighbor list and not into the atoms array. + std::vector samplingWindowAtoms; + + // The number of atoms inside the sampling window. Counting each atom only once. + int numSamplingWindowAtoms; + + // The number of local atoms that are in the fix group. + int numFixAtomsLocal; + + // Pointer to the EAM potential class. + // This is required to access the Rho arrays calculated by the potential class and its potential tables. + class PairEAM *pairEAM; + + // This array contains a boolean value per atom (real and ghosts) that indicates whether + // the electron density or another property at that site has been affected by one of the accepted MC swaps. + std::vector changedAtoms; + + // This counter indicates the current MPI communication stage to let the + // pack/unpack routines know which data is being transmitted. + int communicationStage; + + // The total number of accepted swaps during the last MC step. + int nAcceptedSwaps; + + // The total number of rejected swaps during the last MC step. + int nRejectedSwaps; + + // A compute used to compute the total potential energy of the system. + class Compute *compute_pe; +}; +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/MC/fix_tfmc.cpp b/src/MC/fix_tfmc.cpp index 84371b9f2b..614ca56a53 100644 --- a/src/MC/fix_tfmc.cpp +++ b/src/MC/fix_tfmc.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MC/fix_tfmc.h b/src/MC/fix_tfmc.h index 3fb4177e9e..331acbad4e 100644 --- a/src/MC/fix_tfmc.h +++ b/src/MC/fix_tfmc.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MC/fix_widom.cpp b/src/MC/fix_widom.cpp index 72c02203e3..6f0afdc6ba 100644 --- a/src/MC/fix_widom.cpp +++ b/src/MC/fix_widom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MC/fix_widom.h b/src/MC/fix_widom.h index cf9a54fe02..3d01c1599f 100644 --- a/src/MC/fix_widom.h +++ b/src/MC/fix_widom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MC/pair_dsmc.cpp b/src/MC/pair_dsmc.cpp index 8a0918e2e0..4773ac7653 100644 --- a/src/MC/pair_dsmc.cpp +++ b/src/MC/pair_dsmc.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MC/pair_dsmc.h b/src/MC/pair_dsmc.h index 71dd93e0f5..4f2d6545b1 100644 --- a/src/MC/pair_dsmc.h +++ b/src/MC/pair_dsmc.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MDI/Install.sh b/src/MDI/Install.sh index bc19162a17..804e66be5e 100755 --- a/src/MDI/Install.sh +++ b/src/MDI/Install.sh @@ -49,7 +49,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*mdi.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*mdi.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/mdi\/Makefile.lammps @@ -65,7 +65,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*mdi.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*mdi.*$/d' ../Makefile.package.settings fi fi diff --git a/src/MDI/fix_mdi_engine.cpp b/src/MDI/fix_mdi_engine.cpp index e68b9b54b4..0c70678add 100644 --- a/src/MDI/fix_mdi_engine.cpp +++ b/src/MDI/fix_mdi_engine.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MDI/fix_mdi_engine.h b/src/MDI/fix_mdi_engine.h index 7dd8a724f2..42755abdb1 100644 --- a/src/MDI/fix_mdi_engine.h +++ b/src/MDI/fix_mdi_engine.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MDI/fix_mdi_qm.cpp b/src/MDI/fix_mdi_qm.cpp index 18b0a8f8c2..fc4ae832da 100644 --- a/src/MDI/fix_mdi_qm.cpp +++ b/src/MDI/fix_mdi_qm.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -301,7 +301,7 @@ void FixMDIQM::setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixMDIQM::post_force(int vflag) +void FixMDIQM::post_force(int /*vflag*/) { int index, ierr; diff --git a/src/MDI/fix_mdi_qm.h b/src/MDI/fix_mdi_qm.h index e06de83d4a..19343ed4af 100644 --- a/src/MDI/fix_mdi_qm.h +++ b/src/MDI/fix_mdi_qm.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MDI/library_mdi.cpp b/src/MDI/library_mdi.cpp index 10f2531b24..2216704e5a 100644 --- a/src/MDI/library_mdi.cpp +++ b/src/MDI/library_mdi.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MDI/library_mdi.h b/src/MDI/library_mdi.h index 575d181f2f..ef4f889563 100644 --- a/src/MDI/library_mdi.h +++ b/src/MDI/library_mdi.h @@ -1,7 +1,7 @@ /* -*- c -*- ------------------------------------------------------------ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MDI/mdi_command.cpp b/src/MDI/mdi_command.cpp index 52f02a8e8f..28a7e96b96 100644 --- a/src/MDI/mdi_command.cpp +++ b/src/MDI/mdi_command.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MDI/mdi_command.h b/src/MDI/mdi_command.h index 1bd2c7df6c..88e1901ab1 100644 --- a/src/MDI/mdi_command.h +++ b/src/MDI/mdi_command.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MDI/mdi_engine.cpp b/src/MDI/mdi_engine.cpp index 69f7442a65..d866c0fea9 100644 --- a/src/MDI/mdi_engine.cpp +++ b/src/MDI/mdi_engine.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -941,7 +941,7 @@ void MDIEngine::evaluate() output->thermo->compute(1); } else { - if (!comm->style) { + if (comm->style == Comm::BRICK) { if (domain->triclinic) domain->x2lamda(atom->nlocal); domain->pbc(); domain->reset_box(); diff --git a/src/MDI/mdi_engine.h b/src/MDI/mdi_engine.h index 56db28c73d..78cf5d7dac 100644 --- a/src/MDI/mdi_engine.h +++ b/src/MDI/mdi_engine.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MDI/mdi_plugin.cpp b/src/MDI/mdi_plugin.cpp index 8d2384dcb7..08dfd0ad1f 100644 --- a/src/MDI/mdi_plugin.cpp +++ b/src/MDI/mdi_plugin.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MDI/mdi_plugin.h b/src/MDI/mdi_plugin.h index c28f1997f7..fb640a3019 100644 --- a/src/MDI/mdi_plugin.h +++ b/src/MDI/mdi_plugin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MEAM/meam.h b/src/MEAM/meam.h index 5e22fda07e..9ec7de3426 100644 --- a/src/MEAM/meam.h +++ b/src/MEAM/meam.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MEAM/meam_dens_final.cpp b/src/MEAM/meam_dens_final.cpp index e4df007230..cf964a4724 100644 --- a/src/MEAM/meam_dens_final.cpp +++ b/src/MEAM/meam_dens_final.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MEAM/meam_dens_init.cpp b/src/MEAM/meam_dens_init.cpp index f6de79de53..b60e1a7a17 100644 --- a/src/MEAM/meam_dens_init.cpp +++ b/src/MEAM/meam_dens_init.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MEAM/meam_force.cpp b/src/MEAM/meam_force.cpp index 88b6140f80..acc3d5672a 100644 --- a/src/MEAM/meam_force.cpp +++ b/src/MEAM/meam_force.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MEAM/meam_funcs.cpp b/src/MEAM/meam_funcs.cpp index 0f6036e6f1..f3a6e99772 100644 --- a/src/MEAM/meam_funcs.cpp +++ b/src/MEAM/meam_funcs.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MEAM/meam_impl.cpp b/src/MEAM/meam_impl.cpp index d0d81cee88..bbfb83e94a 100644 --- a/src/MEAM/meam_impl.cpp +++ b/src/MEAM/meam_impl.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MEAM/meam_setup_done.cpp b/src/MEAM/meam_setup_done.cpp index dd9cc39ea2..93f2552465 100644 --- a/src/MEAM/meam_setup_done.cpp +++ b/src/MEAM/meam_setup_done.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MEAM/meam_setup_global.cpp b/src/MEAM/meam_setup_global.cpp index 28dcd73ce4..545a2ad3f4 100644 --- a/src/MEAM/meam_setup_global.cpp +++ b/src/MEAM/meam_setup_global.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MEAM/meam_setup_param.cpp b/src/MEAM/meam_setup_param.cpp index 5612936c20..32634004c2 100644 --- a/src/MEAM/meam_setup_param.cpp +++ b/src/MEAM/meam_setup_param.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MEAM/pair_meam.cpp b/src/MEAM/pair_meam.cpp index b0f11ba0c1..f1a628076e 100644 --- a/src/MEAM/pair_meam.cpp +++ b/src/MEAM/pair_meam.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MEAM/pair_meam.h b/src/MEAM/pair_meam.h index 304e7eb41f..16ba38fcb2 100644 --- a/src/MEAM/pair_meam.h +++ b/src/MEAM/pair_meam.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MESONT/Install.sh b/src/MESONT/Install.sh index 6e51bfae64..09e6c03dde 100644 --- a/src/MESONT/Install.sh +++ b/src/MESONT/Install.sh @@ -47,7 +47,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*mesont.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*mesont.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/mesont\/Makefile.lammps @@ -61,7 +61,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*mesont.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*mesont.*$/d' ../Makefile.package.settings fi fi diff --git a/src/MESONT/angle_mesocnt.cpp b/src/MESONT/angle_mesocnt.cpp index c2f27a0584..06ec135e3c 100644 --- a/src/MESONT/angle_mesocnt.cpp +++ b/src/MESONT/angle_mesocnt.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MESONT/angle_mesocnt.h b/src/MESONT/angle_mesocnt.h index 06e15c730d..50e06c68ce 100644 --- a/src/MESONT/angle_mesocnt.h +++ b/src/MESONT/angle_mesocnt.h @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MESONT/atom_vec_mesont.cpp b/src/MESONT/atom_vec_mesont.cpp index e3d03ff3e1..23cb4b8146 100644 --- a/src/MESONT/atom_vec_mesont.cpp +++ b/src/MESONT/atom_vec_mesont.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MESONT/atom_vec_mesont.h b/src/MESONT/atom_vec_mesont.h index 25f2a9d243..44f3f97084 100644 --- a/src/MESONT/atom_vec_mesont.h +++ b/src/MESONT/atom_vec_mesont.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -26,7 +26,7 @@ AtomStyle(mesont,AtomVecMesoNT); namespace LAMMPS_NS { -class AtomVecMesoNT : public AtomVec { +class AtomVecMesoNT : virtual public AtomVec { public: AtomVecMesoNT(class LAMMPS *); }; diff --git a/src/MESONT/bond_mesocnt.cpp b/src/MESONT/bond_mesocnt.cpp index b0b5f67234..1623c4b1fc 100644 --- a/src/MESONT/bond_mesocnt.cpp +++ b/src/MESONT/bond_mesocnt.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MESONT/bond_mesocnt.h b/src/MESONT/bond_mesocnt.h index 7a4ae81128..1fe1431770 100644 --- a/src/MESONT/bond_mesocnt.h +++ b/src/MESONT/bond_mesocnt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MESONT/compute_mesont.cpp b/src/MESONT/compute_mesont.cpp index 3c31cdc84d..a2831e5d7a 100644 --- a/src/MESONT/compute_mesont.cpp +++ b/src/MESONT/compute_mesont.cpp @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MESONT/compute_mesont.h b/src/MESONT/compute_mesont.h index b8b08f1b78..893d61a990 100644 --- a/src/MESONT/compute_mesont.h +++ b/src/MESONT/compute_mesont.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MESONT/export_mesont.h b/src/MESONT/export_mesont.h index 2438dd98dc..92ce1acf95 100644 --- a/src/MESONT/export_mesont.h +++ b/src/MESONT/export_mesont.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MESONT/pair_mesocnt.cpp b/src/MESONT/pair_mesocnt.cpp index 39427db5a4..badb7657b1 100644 --- a/src/MESONT/pair_mesocnt.cpp +++ b/src/MESONT/pair_mesocnt.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MESONT/pair_mesocnt.h b/src/MESONT/pair_mesocnt.h index 941caba34f..d7517e9f31 100644 --- a/src/MESONT/pair_mesocnt.h +++ b/src/MESONT/pair_mesocnt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MESONT/pair_mesocnt_viscous.cpp b/src/MESONT/pair_mesocnt_viscous.cpp index 4bf4c7c9d6..10ce8b8344 100644 --- a/src/MESONT/pair_mesocnt_viscous.cpp +++ b/src/MESONT/pair_mesocnt_viscous.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MESONT/pair_mesocnt_viscous.h b/src/MESONT/pair_mesocnt_viscous.h index 611e67602a..bfa765cf94 100644 --- a/src/MESONT/pair_mesocnt_viscous.h +++ b/src/MESONT/pair_mesocnt_viscous.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MESONT/pair_mesont_tpm.cpp b/src/MESONT/pair_mesont_tpm.cpp index 0c1ef1939a..39582f3e6a 100644 --- a/src/MESONT/pair_mesont_tpm.cpp +++ b/src/MESONT/pair_mesont_tpm.cpp @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MESONT/pair_mesont_tpm.h b/src/MESONT/pair_mesont_tpm.h index 86cd245d20..a83e124b56 100644 --- a/src/MESONT/pair_mesont_tpm.h +++ b/src/MESONT/pair_mesont_tpm.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/mgpt_bgmul_7.c.h b/src/MGPT/mgpt_bgmul_7.c.h index ababcdab84..c7e3a475a0 100644 --- a/src/MGPT/mgpt_bgmul_7.c.h +++ b/src/MGPT/mgpt_bgmul_7.c.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/mgpt_linalg.cpp b/src/MGPT/mgpt_linalg.cpp index d0ea59d447..1af2826897 100644 --- a/src/MGPT/mgpt_linalg.cpp +++ b/src/MGPT/mgpt_linalg.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/mgpt_linalg.h b/src/MGPT/mgpt_linalg.h index 5b93885f4e..9f76361523 100644 --- a/src/MGPT/mgpt_linalg.h +++ b/src/MGPT/mgpt_linalg.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/mgpt_mmul3_538.c.h b/src/MGPT/mgpt_mmul3_538.c.h index 7e701933a0..31256a27a1 100644 --- a/src/MGPT/mgpt_mmul3_538.c.h +++ b/src/MGPT/mgpt_mmul3_538.c.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/mgpt_mmul3_748.c.h b/src/MGPT/mgpt_mmul3_748.c.h index 24e3fc9082..82d8e57081 100644 --- a/src/MGPT/mgpt_mmul3_748.c.h +++ b/src/MGPT/mgpt_mmul3_748.c.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/mgpt_mmul3d_526.c.h b/src/MGPT/mgpt_mmul3d_526.c.h index ea3f28b2ff..eb4e717641 100644 --- a/src/MGPT/mgpt_mmul3d_526.c.h +++ b/src/MGPT/mgpt_mmul3d_526.c.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/mgpt_mmul3d_744.c.h b/src/MGPT/mgpt_mmul3d_744.c.h index 91877e9c32..f0c90fa20b 100644 --- a/src/MGPT/mgpt_mmul3d_744.c.h +++ b/src/MGPT/mgpt_mmul3d_744.c.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/mgpt_mmul_bg_552.c.h b/src/MGPT/mgpt_mmul_bg_552.c.h index 5597d34d73..87e4f4e557 100644 --- a/src/MGPT/mgpt_mmul_bg_552.c.h +++ b/src/MGPT/mgpt_mmul_bg_552.c.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/mgpt_mmul_bg_722.c.h b/src/MGPT/mgpt_mmul_bg_722.c.h index 1a18fb70f5..63520a1968 100644 --- a/src/MGPT/mgpt_mmul_bg_722.c.h +++ b/src/MGPT/mgpt_mmul_bg_722.c.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h b/src/MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h index 6cec7f7d28..c60f88efd5 100644 --- a/src/MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h +++ b/src/MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h b/src/MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h index ccbbca5884..fea6024801 100644 --- a/src/MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h +++ b/src/MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/mgpt_readpot.cpp b/src/MGPT/mgpt_readpot.cpp index dd196142f5..ab25a9e190 100644 --- a/src/MGPT/mgpt_readpot.cpp +++ b/src/MGPT/mgpt_readpot.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/mgpt_readpot.h b/src/MGPT/mgpt_readpot.h index 89b59aa243..0a80f55557 100644 --- a/src/MGPT/mgpt_readpot.h +++ b/src/MGPT/mgpt_readpot.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/mgpt_splinetab.cpp b/src/MGPT/mgpt_splinetab.cpp index fd6d4541c2..5bc81c0018 100644 --- a/src/MGPT/mgpt_splinetab.cpp +++ b/src/MGPT/mgpt_splinetab.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/mgpt_splinetab.h b/src/MGPT/mgpt_splinetab.h index 81049338a1..6b393df7a8 100644 --- a/src/MGPT/mgpt_splinetab.h +++ b/src/MGPT/mgpt_splinetab.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/mgpt_ttr_5022.c.h b/src/MGPT/mgpt_ttr_5022.c.h index a3f365788d..314e1387c4 100644 --- a/src/MGPT/mgpt_ttr_5022.c.h +++ b/src/MGPT/mgpt_ttr_5022.c.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/mgpt_ttr_5042.c.h b/src/MGPT/mgpt_ttr_5042.c.h index 0cdb8b5be1..f7f44ff9b1 100644 --- a/src/MGPT/mgpt_ttr_5042.c.h +++ b/src/MGPT/mgpt_ttr_5042.c.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/mgpt_ttr_5123.c.h b/src/MGPT/mgpt_ttr_5123.c.h index 1124ca35d6..95bcbe1579 100644 --- a/src/MGPT/mgpt_ttr_5123.c.h +++ b/src/MGPT/mgpt_ttr_5123.c.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/mgpt_ttr_5141.c.h b/src/MGPT/mgpt_ttr_5141.c.h index 5200a9a2b1..33d9efd265 100644 --- a/src/MGPT/mgpt_ttr_5141.c.h +++ b/src/MGPT/mgpt_ttr_5141.c.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/mgpt_ttr_7022.c.h b/src/MGPT/mgpt_ttr_7022.c.h index 75ed1283cd..a895e5e4f7 100644 --- a/src/MGPT/mgpt_ttr_7022.c.h +++ b/src/MGPT/mgpt_ttr_7022.c.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/mgpt_ttr_7042.c.h b/src/MGPT/mgpt_ttr_7042.c.h index 8a6ee14fdc..0957a0e459 100644 --- a/src/MGPT/mgpt_ttr_7042.c.h +++ b/src/MGPT/mgpt_ttr_7042.c.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/mgpt_ttr_7123.c.h b/src/MGPT/mgpt_ttr_7123.c.h index 68fe692ade..9072739f65 100644 --- a/src/MGPT/mgpt_ttr_7123.c.h +++ b/src/MGPT/mgpt_ttr_7123.c.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/mgpt_ttr_7141.c.h b/src/MGPT/mgpt_ttr_7141.c.h index 9e72d0bd1f..707fcf5217 100644 --- a/src/MGPT/mgpt_ttr_7141.c.h +++ b/src/MGPT/mgpt_ttr_7141.c.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/pair_mgpt.cpp b/src/MGPT/pair_mgpt.cpp index 8d6831c58f..5c4b889f8a 100644 --- a/src/MGPT/pair_mgpt.cpp +++ b/src/MGPT/pair_mgpt.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MGPT/pair_mgpt.h b/src/MGPT/pair_mgpt.h index 355a17522b..409643c059 100644 --- a/src/MGPT/pair_mgpt.h +++ b/src/MGPT/pair_mgpt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MISC/bond_special.cpp b/src/MISC/bond_special.cpp index c7009742e0..d0c6652672 100644 --- a/src/MISC/bond_special.cpp +++ b/src/MISC/bond_special.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MISC/bond_special.h b/src/MISC/bond_special.h index b7c4d2eebe..f0e2c28646 100644 --- a/src/MISC/bond_special.h +++ b/src/MISC/bond_special.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MISC/compute_viscosity_cos.cpp b/src/MISC/compute_viscosity_cos.cpp index e4ed1e5392..274c4f294e 100644 --- a/src/MISC/compute_viscosity_cos.cpp +++ b/src/MISC/compute_viscosity_cos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MISC/compute_viscosity_cos.h b/src/MISC/compute_viscosity_cos.h index 8453de6f01..467c444aaf 100644 --- a/src/MISC/compute_viscosity_cos.h +++ b/src/MISC/compute_viscosity_cos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MISC/fix_accelerate_cos.cpp b/src/MISC/fix_accelerate_cos.cpp index 72a148a27e..4bb5a21e79 100644 --- a/src/MISC/fix_accelerate_cos.cpp +++ b/src/MISC/fix_accelerate_cos.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MISC/fix_accelerate_cos.h b/src/MISC/fix_accelerate_cos.h index 343f815f9d..dbabfcf660 100644 --- a/src/MISC/fix_accelerate_cos.h +++ b/src/MISC/fix_accelerate_cos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MISC/fix_imd.cpp b/src/MISC/fix_imd.cpp index 4a4a077cb4..d979766a5d 100644 --- a/src/MISC/fix_imd.cpp +++ b/src/MISC/fix_imd.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MISC/fix_imd.h b/src/MISC/fix_imd.h index 314b629ac1..2312540e66 100644 --- a/src/MISC/fix_imd.h +++ b/src/MISC/fix_imd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MISC/fix_ipi.cpp b/src/MISC/fix_ipi.cpp index 65e431146e..8f39c2f2d8 100644 --- a/src/MISC/fix_ipi.cpp +++ b/src/MISC/fix_ipi.cpp @@ -1,8 +1,7 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -47,12 +46,12 @@ using namespace FixConst; // socket interface #ifndef _WIN32 -#include -#include -#include -#include -#include #include +#include +#include +#include +#include +#include #else #ifndef WIN32_LEAN_AND_MEAN #define WIN32_LEAN_AND_MEAN @@ -65,8 +64,7 @@ using namespace FixConst; /* Utility functions to simplify the interface with POSIX sockets */ -static void open_socket(int &sockfd, int inet, int port, char* host, - Error *error) +static void open_socket(int &sockfd, int inet, int port, char *host, Error *error) /* Opens a socket. Args: @@ -83,9 +81,9 @@ static void open_socket(int &sockfd, int inet, int port, char* host, int ai_err; #ifdef _WIN32 - error->one(FLERR,"i-PI socket implementation requires UNIX environment"); + error->one(FLERR, "i-PI socket implementation requires UNIX environment"); #else - if (inet>0) { // creates an internet socket + if (inet > 0) { // creates an internet socket // fetches information on the host struct addrinfo hints, *res; @@ -96,40 +94,39 @@ static void open_socket(int &sockfd, int inet, int port, char* host, hints.ai_flags = AI_PASSIVE; ai_err = getaddrinfo(host, std::to_string(port).c_str(), &hints, &res); - if (ai_err!=0) - error->one(FLERR,"Error fetching host data. Wrong host name?"); + if (ai_err != 0) error->one(FLERR, "Error fetching host data. Wrong host name?"); // creates socket sockfd = socket(res->ai_family, res->ai_socktype, res->ai_protocol); - if (sockfd < 0) - error->one(FLERR,"Error opening socket"); + if (sockfd < 0) error->one(FLERR, "Error opening socket"); // makes connection if (connect(sockfd, res->ai_addr, res->ai_addrlen) < 0) - error->one(FLERR,"Error opening INET socket: wrong port or server unreachable"); + error->one(FLERR, "Error opening INET socket: wrong port or server unreachable"); freeaddrinfo(res); - } else { // creates a unix socket + } else { // creates a unix socket struct sockaddr_un serv_addr; // fills up details of the socket address memset(&serv_addr, 0, sizeof(serv_addr)); serv_addr.sun_family = AF_UNIX; strcpy(serv_addr.sun_path, "/tmp/ipi_"); - strcpy(serv_addr.sun_path+9, host); + strcpy(serv_addr.sun_path + 9, host); // creates the socket sockfd = socket(AF_UNIX, SOCK_STREAM, 0); // connects if (connect(sockfd, (struct sockaddr *) &serv_addr, sizeof(serv_addr)) < 0) - error->one(FLERR,"Error opening UNIX socket: server may not be running " + error->one(FLERR, + "Error opening UNIX socket: server may not be running " "or the path to the socket unavailable"); } #endif } -static void writebuffer(int sockfd, const char *data, int len, Error* error) +static void writebuffer(int sockfd, const char *data, int len, Error *error) /* Writes to a socket. Args: @@ -140,14 +137,11 @@ static void writebuffer(int sockfd, const char *data, int len, Error* error) { int n; - n = write(sockfd,data,len); - if (n < 0) - error->one(FLERR,"Error writing to socket: broken connection"); + n = write(sockfd, data, len); + if (n < 0) error->one(FLERR, "Error writing to socket: broken connection"); } - - -static void readbuffer(int sockfd, char *data, int len, Error* error) +static void readbuffer(int sockfd, char *data, int len, Error *error) /* Reads from a socket. Args: @@ -158,44 +152,52 @@ static void readbuffer(int sockfd, char *data, int len, Error* error) { int n, nr; - n = nr = read(sockfd,data,len); + n = nr = read(sockfd, data, len); - while (nr>0 && n 0 && n < len) { + nr = read(sockfd, &data[n], len - n); + n += nr; } - if (n == 0) - error->one(FLERR,"Error reading from socket: broken connection"); + if (n == 0) error->one(FLERR, "Error reading from socket: broken connection"); } /* ---------------------------------------------------------------------- */ -FixIPI::FixIPI(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg), irregular(nullptr) +FixIPI::FixIPI(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), irregular(nullptr) { - /* format for fix: - * fix num group_id ipi host port [unix] - */ - if (strcmp(style,"ipi") != 0 && narg < 5) - error->all(FLERR,"Illegal fix ipi command"); + if (narg < 5) utils::missing_cmd_args(FLERR, "fix ipi", error); - if (atom->tag_enable == 0) - error->all(FLERR,"Cannot use fix ipi without atom IDs"); + if (atom->tag_enable == 0) error->all(FLERR, "Cannot use fix ipi without atom IDs"); + if (atom->tag_consecutive() == 0) error->all(FLERR, "Fix ipi requires consecutive atom IDs"); + if (strcmp(update->unit_style, "lj") == 0) error->all(FLERR, "Fix ipi does not support lj units"); - if (atom->tag_consecutive() == 0) - error->all(FLERR,"Fix ipi requires consecutive atom IDs"); - - if (strcmp(arg[1],"all") != 0) - error->warning(FLERR,"Fix ipi always uses group all"); + if ((strcmp(arg[1], "all") != 0) && (comm->me == 0)) + error->warning(FLERR, "Not using group 'all' with fix ipi can result in undefined behavior"); host = strdup(arg[3]); - port = utils::inumeric(FLERR,arg[4],false,lmp); + port = utils::inumeric(FLERR, arg[4], false, lmp); - inet = ((narg > 5) && (strcmp(arg[5],"unix") == 0) ) ? 0 : 1; - master = (comm->me==0) ? 1 : 0; - // check if forces should be reinitialized and set flag - reset_flag = ((narg > 6 && (strcmp(arg[5],"reset") == 0 )) || ((narg > 5) && (strcmp(arg[5],"reset") == 0)) ) ? 1 : 0; + master = (comm->me == 0) ? 1 : 0; + inet = 1; + reset_flag = 0; + + int iarg = 5; + while (iarg < narg) { + if (strcmp(arg[iarg], "unix") == 0) { + inet = 0; + ++iarg; + } else if (strcmp(arg[iarg], "reset") == 0) { + reset_flag = 1; + ++iarg; + } else { + error->all(FLERR, "Unknown fix ipi keyword: {}", arg[iarg]); + } + } + + // sanity check + if (inet && ((port <= 1024) || (port > 65536))) + error->all(FLERR, "Invalid port for fix ipi: {}", port); hasdata = bsize = 0; @@ -223,7 +225,6 @@ FixIPI::~FixIPI() delete irregular; } - /* ---------------------------------------------------------------------- */ int FixIPI::setmask() @@ -240,9 +241,11 @@ void FixIPI::init() { //only opens socket on master process if (master) { - if (!socketflag) open_socket(ipisock, inet, port, host, error); - } else ipisock=0; - //! should check for success in socket opening -- but the current open_socket routine dies brutally if unsuccessful + if (!socketflag) open_socket(ipisock, inet, port, host, error); + } else + ipisock = 0; + // TODO: should check for success in socket opening, + // but the current open_socket routine dies brutally if unsuccessful // tell lammps we have assigned a socket socketflag = 1; @@ -252,11 +255,13 @@ void FixIPI::init() kspace_flag = (force->kspace) ? 1 : 0; - // makes sure that neighbor lists are re-built at each step (cannot make assumptions when cycling over beads!) + // makes sure that neighbor lists are re-built at each step + // (cannot make assumptions when cycling over beads!) neighbor->delay = 0; neighbor->every = 1; } +// clang-format off void FixIPI::initial_integrate(int /*vflag*/) { /* This is called at the beginning of the integration loop, @@ -374,9 +379,9 @@ void FixIPI::initial_integrate(int /*vflag*/) // kspace->setup() is in some cases not enough since, e.g., g_ewald needs // to be reestimated due to changes in box dimensions. force->init(); - // setup_grid() is necessary for pppm since init() is not calling - // setup() nor setup_grid() upon calling init(). - if (force->kspace->pppmflag) force->kspace->setup_grid(); + // reset_grid() is necessary for pppm since init() is not calling + // setup() nor reset_grid() upon calling init(). + if (force->kspace->pppmflag) force->kspace->reset_grid(); // other kspace styles might need too another setup()? } else if (!reset_flag && kspace_flag) { // original version diff --git a/src/MISC/fix_ipi.h b/src/MISC/fix_ipi.h index 07d1c729a9..de954c8578 100644 --- a/src/MISC/fix_ipi.h +++ b/src/MISC/fix_ipi.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MISC/fix_srp.cpp b/src/MISC/fix_srp.cpp index e82e98448f..58bf39f8fe 100644 --- a/src/MISC/fix_srp.cpp +++ b/src/MISC/fix_srp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MISC/fix_srp.h b/src/MISC/fix_srp.h index 48f1f77a86..fad82a48ad 100644 --- a/src/MISC/fix_srp.h +++ b/src/MISC/fix_srp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MISC/fix_srp_react.cpp b/src/MISC/fix_srp_react.cpp index 7ead11314b..6e8446d4f4 100644 --- a/src/MISC/fix_srp_react.cpp +++ b/src/MISC/fix_srp_react.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MISC/fix_srp_react.h b/src/MISC/fix_srp_react.h index e892631416..cc1b16c5c8 100644 --- a/src/MISC/fix_srp_react.h +++ b/src/MISC/fix_srp_react.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MISC/pair_agni.cpp b/src/MISC/pair_agni.cpp index 3c309d578b..539c0ca00f 100644 --- a/src/MISC/pair_agni.cpp +++ b/src/MISC/pair_agni.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MISC/pair_agni.h b/src/MISC/pair_agni.h index 9f416ec292..2d2bacf63f 100644 --- a/src/MISC/pair_agni.h +++ b/src/MISC/pair_agni.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MISC/pair_list.cpp b/src/MISC/pair_list.cpp index f6a27538ab..25e53149f6 100644 --- a/src/MISC/pair_list.cpp +++ b/src/MISC/pair_list.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -172,7 +172,8 @@ void PairList::compute(int eflag, int vflag) const double dexp = exp(-par.param.morse.alpha * dr); fpair = 2.0 * par.param.morse.d0 * par.param.morse.alpha * (dexp * dexp - dexp) / r; - if (eflag_either) epair = par.param.morse.d0 * (dexp * dexp - 2.0 * dexp + 1.0) - par.offset; + if (eflag_either) + epair = par.param.morse.d0 * (dexp * dexp - 2.0 * dexp + 1.0) - par.offset; } else if (par.style == LJ126) { @@ -186,7 +187,7 @@ void PairList::compute(int eflag, int vflag) } else if (par.style == QUARTIC) { const double r = sqrt(rsq); - double dr = r - sqrt(par.cutsq); + double dr = r - par.param.quartic.r0; double ra = dr - par.param.quartic.b1; double rb = dr - par.param.quartic.b2; double r2 = dr * dr; @@ -303,10 +304,9 @@ void PairList::settings(int narg, char **arg) case QUARTIC: oneparam.param.quartic.k = values.next_double(); + oneparam.param.quartic.r0 = values.next_double(); oneparam.param.quartic.b1 = values.next_double(); oneparam.param.quartic.b2 = values.next_double(); - if (!values.has_next()) - throw FileReaderException("Must specify individual cutoff for quartic interaction"); ++nquartic; break; diff --git a/src/MISC/pair_list.h b/src/MISC/pair_list.h index dab8ba3fc9..258db61c0e 100644 --- a/src/MISC/pair_list.h +++ b/src/MISC/pair_list.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -50,10 +50,9 @@ class PairList : public Pair { double epsilon, sigma; }; struct quartic_p { - double k, b1, b2; + double k, r0, b1, b2; }; - union param_u { harm_p harm; morse_p morse; diff --git a/src/MISC/pair_srp.cpp b/src/MISC/pair_srp.cpp index 1c95caadc2..ddcfb92e9c 100644 --- a/src/MISC/pair_srp.cpp +++ b/src/MISC/pair_srp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MISC/pair_srp.h b/src/MISC/pair_srp.h index da04ba2ab1..3fb1563728 100644 --- a/src/MISC/pair_srp.h +++ b/src/MISC/pair_srp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MISC/pair_srp_react.cpp b/src/MISC/pair_srp_react.cpp index 4a3f260fe0..f8cbafaca9 100644 --- a/src/MISC/pair_srp_react.cpp +++ b/src/MISC/pair_srp_react.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -34,14 +34,11 @@ There is an example script for this package in examples/PACKAGES/srp_react/. #include "error.h" #include "fix_srp_react.h" #include "force.h" -#include "memory.h" #include "modify.h" -#include "neigh_list.h" #include "neighbor.h" #include "output.h" #include "thermo.h" -#include #include using namespace LAMMPS_NS; diff --git a/src/MISC/pair_srp_react.h b/src/MISC/pair_srp_react.h index a6e4cebb6f..3333f5bac4 100644 --- a/src/MISC/pair_srp_react.h +++ b/src/MISC/pair_srp_react.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MISC/pair_tracker.cpp b/src/MISC/pair_tracker.cpp index e24e8f3265..1a9fb1f7c7 100644 --- a/src/MISC/pair_tracker.cpp +++ b/src/MISC/pair_tracker.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -27,8 +27,8 @@ #include "neighbor.h" #include "tokenizer.h" #include "update.h" -#include "utils.h" +#include #include using namespace LAMMPS_NS; diff --git a/src/MISC/pair_tracker.h b/src/MISC/pair_tracker.h index e483590883..47128b8073 100644 --- a/src/MISC/pair_tracker.h +++ b/src/MISC/pair_tracker.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-HDNNP/Install.sh b/src/ML-HDNNP/Install.sh index 74e5f1b91e..f343f38851 100644 --- a/src/ML-HDNNP/Install.sh +++ b/src/ML-HDNNP/Install.sh @@ -46,7 +46,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*hdnnp.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*hdnnp.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/hdnnp\/Makefile.lammps @@ -60,7 +60,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*hdnnp.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*hdnnp.*$/d' ../Makefile.package.settings fi fi diff --git a/src/ML-HDNNP/pair_hdnnp.cpp b/src/ML-HDNNP/pair_hdnnp.cpp index 6873f76779..35b0dd0ae8 100644 --- a/src/ML-HDNNP/pair_hdnnp.cpp +++ b/src/ML-HDNNP/pair_hdnnp.cpp @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-HDNNP/pair_hdnnp.h b/src/ML-HDNNP/pair_hdnnp.h index e186e29785..feea0ab6f3 100644 --- a/src/ML-HDNNP/pair_hdnnp.h +++ b/src/ML-HDNNP/pair_hdnnp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-IAP/Install.sh b/src/ML-IAP/Install.sh index 27c9b19b01..18812c6026 100755 --- a/src/ML-IAP/Install.sh +++ b/src/ML-IAP/Install.sh @@ -52,7 +52,7 @@ if (test $1 = 1) then sed -i -e 's|^PKG_INC =[ \t]*|&-DMLIAP_PYTHON |' ../Makefile.package fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*python.*mliap_python.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*python.*mliap_python.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/python\/Makefile.mliap_python @@ -68,7 +68,7 @@ elif (test $1 = 0) then fi rm -f ../mliap_model_python_couple.cpp ../mliap_model_python_couple.h \ ../mliap_unified_couple.cpp ../mliap_unified_couple.h - sed -i -e '/^include.*python.*mliap_python.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*python.*mliap_python.*$/d' ../Makefile.package.settings elif (test $1 = 2) then if (type cythonize > /dev/null 2>&1 && test -e ../python_impl.cpp) then @@ -77,12 +77,12 @@ elif (test $1 = 2) then fi rm -f ../mliap_model_python_couple.cpp ../mliap_model_python_couple.h \ ../mliap_unified_couple.cpp ../mliap_unified_couple.h - sed -i -e '/^include.*python.*mliap_python.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*python.*mliap_python.*$/d' ../Makefile.package.settings if (test -e ../Makefile.package) then sed -i -e 's|^PKG_INC =[ \t]*|&-DMLIAP_PYTHON |' ../Makefile.package fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*python.*mliap_python.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*python.*mliap_python.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/python\/Makefile.mliap_python diff --git a/src/ML-IAP/compute_mliap.cpp b/src/ML-IAP/compute_mliap.cpp index f7f5e5bb15..161613fae6 100644 --- a/src/ML-IAP/compute_mliap.cpp +++ b/src/ML-IAP/compute_mliap.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -98,9 +98,7 @@ ComputeMLIAP::ComputeMLIAP(LAMMPS *lmp, int narg, char **arg) : descriptorflag = 1; } else if (strcmp(arg[iarg],"gradgradflag") == 0) { if (iarg+1 > narg) error->all(FLERR,"Illegal compute mliap command"); - gradgradflag = atoi(arg[iarg+1]); - if (gradgradflag != 0 && gradgradflag != 1) - error->all(FLERR,"Illegal compute mliap command"); + gradgradflag = utils::logical(FLERR, arg[iarg+1], false, lmp); iarg += 2; } else error->all(FLERR,"Illegal compute mliap command"); diff --git a/src/ML-IAP/compute_mliap.h b/src/ML-IAP/compute_mliap.h index 05e0b33d2f..6e4774020e 100644 --- a/src/ML-IAP/compute_mliap.h +++ b/src/ML-IAP/compute_mliap.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-IAP/mliap_data.cpp b/src/ML-IAP/mliap_data.cpp index dd729ff330..974a125a2f 100644 --- a/src/ML-IAP/mliap_data.cpp +++ b/src/ML-IAP/mliap_data.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-IAP/mliap_data.h b/src/ML-IAP/mliap_data.h index 562dcd63cb..562eb3e850 100644 --- a/src/ML-IAP/mliap_data.h +++ b/src/ML-IAP/mliap_data.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -26,8 +26,8 @@ class MLIAPData : protected Pointers { ~MLIAPData() override; void init(); - void generate_neighdata(class NeighList *, int = 0, int = 0); - void grow_neigharrays(); + virtual void generate_neighdata(class NeighList *, int = 0, int = 0); + virtual void grow_neigharrays(); double memory_usage(); int size_array_rows, size_array_cols; @@ -77,7 +77,7 @@ class MLIAPData : protected Pointers { int vflag; // indicates if virial is needed class PairMLIAP *pairmliap; // access to pair tally functions - private: + protected: class MLIAPModel *model; class MLIAPDescriptor *descriptor; diff --git a/src/ML-IAP/mliap_descriptor.cpp b/src/ML-IAP/mliap_descriptor.cpp index ce8abf4e56..34f81c3902 100644 --- a/src/ML-IAP/mliap_descriptor.cpp +++ b/src/ML-IAP/mliap_descriptor.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-IAP/mliap_descriptor.h b/src/ML-IAP/mliap_descriptor.h index 6db872ccaf..7f05c6804a 100644 --- a/src/ML-IAP/mliap_descriptor.h +++ b/src/ML-IAP/mliap_descriptor.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -18,7 +18,7 @@ namespace LAMMPS_NS { -class MLIAPDescriptor : protected Pointers { +class MLIAPDescriptor : virtual protected Pointers { public: MLIAPDescriptor(LAMMPS *); ~MLIAPDescriptor() override; diff --git a/src/ML-IAP/mliap_descriptor_snap.cpp b/src/ML-IAP/mliap_descriptor_snap.cpp index fc65ca5207..b8f9aa087b 100644 --- a/src/ML-IAP/mliap_descriptor_snap.cpp +++ b/src/ML-IAP/mliap_descriptor_snap.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -36,7 +36,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -MLIAPDescriptorSNAP::MLIAPDescriptorSNAP(LAMMPS *_lmp, char *paramfilename) : MLIAPDescriptor(_lmp) +MLIAPDescriptorSNAP::MLIAPDescriptorSNAP(LAMMPS *_lmp, char *paramfilename) : Pointers(_lmp), MLIAPDescriptor(_lmp) { radelem = nullptr; wjelem = nullptr; diff --git a/src/ML-IAP/mliap_descriptor_snap.h b/src/ML-IAP/mliap_descriptor_snap.h index 2939252629..2459173152 100644 --- a/src/ML-IAP/mliap_descriptor_snap.h +++ b/src/ML-IAP/mliap_descriptor_snap.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-IAP/mliap_descriptor_so3.cpp b/src/ML-IAP/mliap_descriptor_so3.cpp index 9d3a8052ea..96a589eadd 100644 --- a/src/ML-IAP/mliap_descriptor_so3.cpp +++ b/src/ML-IAP/mliap_descriptor_so3.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -10,6 +10,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ + /* ---------------------------------------------------------------------- Contributing authors: Byungkyun Kang (University of Nevada, Las Vegas) ------------------------------------------------------------------------- */ @@ -34,7 +35,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -MLIAPDescriptorSO3::MLIAPDescriptorSO3(LAMMPS *lmp, char *paramfilename) : MLIAPDescriptor(lmp) +MLIAPDescriptorSO3::MLIAPDescriptorSO3(LAMMPS *lmp, char *paramfilename) : Pointers(lmp), MLIAPDescriptor(lmp) { radelem = nullptr; wjelem = nullptr; diff --git a/src/ML-IAP/mliap_descriptor_so3.h b/src/ML-IAP/mliap_descriptor_so3.h index df10837121..94785f63e5 100644 --- a/src/ML-IAP/mliap_descriptor_so3.h +++ b/src/ML-IAP/mliap_descriptor_so3.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -18,7 +18,7 @@ namespace LAMMPS_NS { -class MLIAPDescriptorSO3 : public MLIAPDescriptor { +class MLIAPDescriptorSO3 : public MLIAPDescriptor, virtual protected Pointers { public: MLIAPDescriptorSO3(LAMMPS *, char *); diff --git a/src/ML-IAP/mliap_model.cpp b/src/ML-IAP/mliap_model.cpp index d998cc4973..a93090d364 100644 --- a/src/ML-IAP/mliap_model.cpp +++ b/src/ML-IAP/mliap_model.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-IAP/mliap_model.h b/src/ML-IAP/mliap_model.h index bc38b8b58d..0f7a8e8e4f 100644 --- a/src/ML-IAP/mliap_model.h +++ b/src/ML-IAP/mliap_model.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -14,7 +14,7 @@ #ifndef LMP_MLIAP_MODEL_H #define LMP_MLIAP_MODEL_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/ML-IAP/mliap_model_linear.cpp b/src/ML-IAP/mliap_model_linear.cpp index 066a19816f..4d8500ae43 100644 --- a/src/ML-IAP/mliap_model_linear.cpp +++ b/src/ML-IAP/mliap_model_linear.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -57,22 +57,17 @@ void MLIAPModelLinear::compute_gradients(MLIAPData* data) for (int ii = 0; ii < data->nlistatoms; ii++) { const int ielem = data->ielems[ii]; - double* coeffi = coeffelem[ielem]; + double const* coeffi = coeffelem[ielem]; for (int icoeff = 0; icoeff < data->ndescriptors; icoeff++) data->betas[ii][icoeff] = coeffi[icoeff+1]; // add in contributions to global and per-atom energy // this is optional and has no effect on force calculation - if (data->eflag) { - // energy of atom I - - double* coeffi = coeffelem[ielem]; double etmp = coeffi[0]; // E_i = beta.B_i - for (int icoeff = 0; icoeff < data->ndescriptors; icoeff++) etmp += coeffi[icoeff+1]*data->descriptors[ii][icoeff]; diff --git a/src/ML-IAP/mliap_model_linear.h b/src/ML-IAP/mliap_model_linear.h index cd22ca8d7d..27ad5f009d 100644 --- a/src/ML-IAP/mliap_model_linear.h +++ b/src/ML-IAP/mliap_model_linear.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-IAP/mliap_model_nn.cpp b/src/ML-IAP/mliap_model_nn.cpp index c64fae2a1f..6c039f9a07 100644 --- a/src/ML-IAP/mliap_model_nn.cpp +++ b/src/ML-IAP/mliap_model_nn.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-IAP/mliap_model_nn.h b/src/ML-IAP/mliap_model_nn.h index f2e43bccc8..db9933ec4e 100644 --- a/src/ML-IAP/mliap_model_nn.h +++ b/src/ML-IAP/mliap_model_nn.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-IAP/mliap_model_python.cpp b/src/ML-IAP/mliap_model_python.cpp index 50347cd4f5..774d14098d 100644 --- a/src/ML-IAP/mliap_model_python.cpp +++ b/src/ML-IAP/mliap_model_python.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -26,7 +26,6 @@ #include "mliap_model_python_couple.h" #include "pair_mliap.h" #include "python_compat.h" -#include "utils.h" #include @@ -125,7 +124,7 @@ void MLIAPModelPython::connect_param_counts() } PyGILState_Release(gstate); model_loaded = 1; - utils::logmesg(lmp, "Loading python model complete.\n"); + if (comm->me == 0) utils::logmesg(lmp, "Loading python model complete.\n"); } /* ---------------------------------------------------------------------- diff --git a/src/ML-IAP/mliap_model_python.h b/src/ML-IAP/mliap_model_python.h index 915e79e53c..e7aee37345 100644 --- a/src/ML-IAP/mliap_model_python.h +++ b/src/ML-IAP/mliap_model_python.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-IAP/mliap_model_quadratic.cpp b/src/ML-IAP/mliap_model_quadratic.cpp index 10507adc91..e6ad3955cb 100644 --- a/src/ML-IAP/mliap_model_quadratic.cpp +++ b/src/ML-IAP/mliap_model_quadratic.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-IAP/mliap_model_quadratic.h b/src/ML-IAP/mliap_model_quadratic.h index 36eab165e4..477bdc2082 100644 --- a/src/ML-IAP/mliap_model_quadratic.h +++ b/src/ML-IAP/mliap_model_quadratic.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-IAP/mliap_so3.cpp b/src/ML-IAP/mliap_so3.cpp index 29e436279b..916b8cfcf5 100644 --- a/src/ML-IAP/mliap_so3.cpp +++ b/src/ML-IAP/mliap_so3.cpp @@ -1,18 +1,18 @@ /* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org - 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. + 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. + See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing authors: Byungkyun Kang (University of Nevada, Las Vegas) + Contributing authors: Byungkyun Kang (University of Nevada, Las Vegas) ------------------------------------------------------------------------- */ #include "mliap_so3.h" @@ -84,7 +84,6 @@ MLIAP_SO3::MLIAP_SO3(LAMMPS *lmp, double vrcut, int vlmax, int vnmax, double val m_dYlm_i = nullptr; m_dplist_r = nullptr; - m_dplist_i = nullptr; m_dclist_r = nullptr; m_dclist_i = nullptr; @@ -145,7 +144,6 @@ MLIAP_SO3::~MLIAP_SO3() memory->destroy(m_dYlm_i); memory->destroy(m_dplist_r); - memory->destroy(m_dplist_i); memory->destroy(m_dclist_r); memory->destroy(m_dclist_i); @@ -846,8 +844,6 @@ void MLIAP_SO3::spectrum(int nlocal, int *numneighs, int *jelems, double *wjelem totali = totaln * ncoefs * 3; memory->destroy(m_dplist_r); memory->create(m_dplist_r, totali, "MLIAP_SO3:m_dplist_r"); - memory->destroy(m_dplist_i); - memory->create(m_dplist_i, totali, "MLIAP_SO3:m_dplist_i"); alloc_arrays += 2.0 * totali * sizeof(double); get_sbes_array(nlocal, numneighs, rij, lmax, rcut, alpha); @@ -977,14 +973,11 @@ void MLIAP_SO3::spectrum_dxdr(int nlocal, int *numneighs, int *jelems, double *w totali = totaln * ncoefs * 3; memory->destroy(m_dplist_r); memory->create(m_dplist_r, totali, "MLIAP_SO3:m_dplist_r"); - memory->destroy(m_dplist_i); - memory->create(m_dplist_i, totali, "MLIAP_SO3:m_dplist_i"); totali = npairs * ncoefs * 3; for (int i = 0; i < totali; i++) { m_dplist_r[i] = 0.0; - m_dplist_i[i] = 0.0; } numps = nmax * (nmax + 1) * (lmax + 1) / 2; diff --git a/src/ML-IAP/mliap_so3.h b/src/ML-IAP/mliap_so3.h index 27d4f406e4..caf6adff76 100644 --- a/src/ML-IAP/mliap_so3.h +++ b/src/ML-IAP/mliap_so3.h @@ -14,7 +14,6 @@ class MLIAP_SO3 : protected Pointers { ~MLIAP_SO3() override; void init(); - double memory_usage(); int ncoeff; @@ -46,7 +45,7 @@ class MLIAP_SO3 : protected Pointers { double *m_ulist_r, *m_ulist_i; double *m_Ylms_r, *m_Ylms_i, *m_dYlm_r, *m_dYlm_i; - double *m_dplist_i, *m_dclist_r, *m_dclist_i, *m_tempdp_r; + double *m_dclist_r, *m_dclist_i, *m_tempdp_r; public: void spectrum(int nlocal, int *numneighs, int *jelems, double *wjelem, double **rij, int nmax, diff --git a/src/ML-IAP/mliap_so3_math.h b/src/ML-IAP/mliap_so3_math.h index 1e26b4d223..21f7261496 100644 --- a/src/ML-IAP/mliap_so3_math.h +++ b/src/ML-IAP/mliap_so3_math.h @@ -9,6 +9,7 @@ #define LMP_MLIAP_SO3_MATH_H #include "math_eigen_impl.h" +#include namespace SO3Math { @@ -22,7 +23,7 @@ void LUPSolve(int n, double *A, double *B, int *P); using namespace MathEigen; typedef Jacobi Jacobi_v2; -int SO3Math::jacobin(int n, double const *const *mat, double *eval, double **evec) +inline int SO3Math::jacobin(int n, double const *const *mat, double *eval, double **evec) { int *midx = new int[n]; double **M = new double *[n]; @@ -48,7 +49,7 @@ int SO3Math::jacobin(int n, double const *const *mat, double *eval, double **eve return ierror; } -int SO3Math::invert_matrix(int n, double *A, double *Ainv) +inline int SO3Math::invert_matrix(int n, double *A, double *Ainv) { int i, j; @@ -85,7 +86,7 @@ int SO3Math::invert_matrix(int n, double *A, double *Ainv) return rv; } -int SO3Math::LUPdecompose(int n, double dtol, double *A, int *P) +inline int SO3Math::LUPdecompose(int n, double dtol, double *A, int *P) { int i, j, k, maxi; double maxA, Atemp; @@ -148,7 +149,7 @@ int SO3Math::LUPdecompose(int n, double dtol, double *A, int *P) return 0; } -void SO3Math::LUPSolve(int n, double *A, double *B, int *P) +inline void SO3Math::LUPSolve(int n, double *A, double *B, int *P) { int i, j; double dtemp; diff --git a/src/ML-IAP/mliap_unified.cpp b/src/ML-IAP/mliap_unified.cpp index 9d3b591002..a3727976de 100644 --- a/src/ML-IAP/mliap_unified.cpp +++ b/src/ML-IAP/mliap_unified.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -33,7 +33,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -MLIAPDummyDescriptor::MLIAPDummyDescriptor(LAMMPS *_lmp) : MLIAPDescriptor(_lmp) {} +MLIAPDummyDescriptor::MLIAPDummyDescriptor(LAMMPS *_lmp) : Pointers(_lmp), MLIAPDescriptor(_lmp) {} MLIAPDummyDescriptor::~MLIAPDummyDescriptor() { diff --git a/src/ML-IAP/mliap_unified.h b/src/ML-IAP/mliap_unified.h index adc900d8c1..1ee8dfd60d 100644 --- a/src/ML-IAP/mliap_unified.h +++ b/src/ML-IAP/mliap_unified.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -22,7 +22,7 @@ namespace LAMMPS_NS { -class MLIAPDummyDescriptor : public MLIAPDescriptor { +class MLIAPDummyDescriptor : public MLIAPDescriptor, virtual protected Pointers { public: MLIAPDummyDescriptor(LAMMPS *); ~MLIAPDummyDescriptor() override; diff --git a/src/ML-IAP/pair_mliap.cpp b/src/ML-IAP/pair_mliap.cpp index 865019ba55..a79a8c0627 100644 --- a/src/ML-IAP/pair_mliap.cpp +++ b/src/ML-IAP/pair_mliap.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -30,12 +30,10 @@ #endif #include "atom.h" -#include "comm.h" #include "error.h" #include "force.h" #include "memory.h" #include "neighbor.h" -#include "neigh_request.h" #include #include @@ -135,10 +133,10 @@ void PairMLIAP::settings(int narg, char ** arg) // set flags for required keywords - int modelflag = 0; - int descriptorflag = 0; delete model; + model = nullptr; delete descriptor; + descriptor = nullptr; // process keywords @@ -147,7 +145,7 @@ void PairMLIAP::settings(int narg, char ** arg) while (iarg < narg) { if (strcmp(arg[iarg],"model") == 0) { if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "pair_style mliap model", error); - if (modelflag) error->all(FLERR,"Illegal multiple pair_style mliap model definition"); + if (model != nullptr) error->all(FLERR,"Illegal multiple pair_style mliap model definition"); if (strcmp(arg[iarg+1],"linear") == 0) { if (iarg+3 > narg) utils::missing_cmd_args(FLERR, "pair_style mliap model linear", error); model = new MLIAPModelLinear(lmp,arg[iarg+2]); @@ -169,10 +167,9 @@ void PairMLIAP::settings(int narg, char ** arg) error->all(FLERR,"Using pair_style mliap model mliappy requires ML-IAP with python support"); #endif } else error->all(FLERR,"Unknown pair_style mliap model keyword: {}", arg[iarg]); - modelflag = 1; } else if (strcmp(arg[iarg],"descriptor") == 0) { if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "pair_style mliap descriptor", error); - if (descriptorflag) error->all(FLERR,"Illegal multiple pair_style mliap descriptor definition"); + if (descriptor != nullptr) error->all(FLERR,"Illegal multiple pair_style mliap descriptor definition"); if (strcmp(arg[iarg+1],"sna") == 0) { if (iarg+3 > narg) utils::missing_cmd_args(FLERR, "pair_style mliap descriptor sna", error); descriptor = new MLIAPDescriptorSNAP(lmp,arg[iarg+2]); @@ -183,11 +180,10 @@ void PairMLIAP::settings(int narg, char ** arg) iarg += 3; } else error->all(FLERR,"Illegal pair_style mliap command"); - descriptorflag = 1; } else if (strcmp(arg[iarg], "unified") == 0) { #ifdef MLIAP_PYTHON - if (modelflag) error->all(FLERR,"Illegal multiple pair_style mliap model definitions"); - if (descriptorflag) error->all(FLERR,"Illegal multiple pair_style mliap descriptor definitions"); + if (model != nullptr) error->all(FLERR,"Illegal multiple pair_style mliap model definitions"); + if (descriptor != nullptr) error->all(FLERR,"Illegal multiple pair_style mliap descriptor definitions"); if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "pair_style mliap unified", error); MLIAPBuildUnified_t build = build_unified(arg[iarg+1], data, lmp); if (iarg+3 > narg) { @@ -199,8 +195,6 @@ void PairMLIAP::settings(int narg, char ** arg) iarg += 3; model = build.model; descriptor = build.descriptor; - modelflag = 1; - descriptorflag = 1; #else error->all(FLERR,"Using pair_style mliap unified requires ML-IAP with python support"); #endif @@ -208,7 +202,7 @@ void PairMLIAP::settings(int narg, char ** arg) error->all(FLERR,"Unknown pair_style mliap keyword: {}", arg[iarg]); } - if (modelflag == 0 || descriptorflag == 0) + if (model == nullptr || descriptor == nullptr) error->all(FLERR,"Incomplete pair_style mliap setup: need model and descriptor, or unified"); } diff --git a/src/ML-IAP/pair_mliap.h b/src/ML-IAP/pair_mliap.h index 902b005041..a8327b11c6 100644 --- a/src/ML-IAP/pair_mliap.h +++ b/src/ML-IAP/pair_mliap.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-PACE/Install.sh b/src/ML-PACE/Install.sh index c099ddd2c4..c0a0958424 100644 --- a/src/ML-PACE/Install.sh +++ b/src/ML-PACE/Install.sh @@ -44,7 +44,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*pace.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*pace.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/pace\/Makefile.lammps @@ -58,7 +58,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*pace.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*pace.*$/d' ../Makefile.package.settings fi fi diff --git a/src/ML-PACE/pair_pace.cpp b/src/ML-PACE/pair_pace.cpp index 2520f5c0a4..57f12597d1 100644 --- a/src/ML-PACE/pair_pace.cpp +++ b/src/ML-PACE/pair_pace.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-PACE/pair_pace.h b/src/ML-PACE/pair_pace.h index 1f0cffeb3f..94649ecaab 100644 --- a/src/ML-PACE/pair_pace.h +++ b/src/ML-PACE/pair_pace.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/ML-PACE/pair_pace_extrapolation.cpp b/src/ML-PACE/pair_pace_extrapolation.cpp index b9a673eb25..ec185e75df 100644 --- a/src/ML-PACE/pair_pace_extrapolation.cpp +++ b/src/ML-PACE/pair_pace_extrapolation.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -96,6 +96,7 @@ PairPACEExtrapolation::PairPACEExtrapolation(LAMMPS *lmp) : Pair(lmp) aceimpl = new ACEALImpl; scale = nullptr; + flag_compute_extrapolation_grade = 0; extrapolation_grade_gamma = nullptr; } @@ -382,10 +383,10 @@ void PairPACEExtrapolation::coeff(int narg, char **arg) aceimpl->ace->load_active_set(active_set_inv_filename); bool is_linear_extrapolation_grade = aceimpl->ace->get_is_linear_extrapolation_grade(); if (comm->me == 0) { - if (is_linear_extrapolation_grade) - utils::logmesg(lmp, "LINEAR ASI is loaded\n"); - else - utils::logmesg(lmp, "FULL ASI is loaded\n"); + if (is_linear_extrapolation_grade) + utils::logmesg(lmp, "LINEAR ASI is loaded\n"); + else + utils::logmesg(lmp, "FULL ASI is loaded\n"); } // clear setflag since coeff() called once with I,J = * * diff --git a/src/ML-PACE/pair_pace_extrapolation.h b/src/ML-PACE/pair_pace_extrapolation.h index 6e4eb53965..c5d9da23db 100644 --- a/src/ML-PACE/pair_pace_extrapolation.h +++ b/src/ML-PACE/pair_pace_extrapolation.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. @@ -51,7 +51,6 @@ class PairPACEExtrapolation : public Pair { void allocate(); std::vector element_names; // list of elements (used by dump pace/extrapolation) - int nelements; // # of unique elements double *extrapolation_grade_gamma; //per-atom gamma value int flag_compute_extrapolation_grade; diff --git a/src/ML-POD/Install.sh b/src/ML-POD/Install.sh new file mode 100755 index 0000000000..a62887e1b3 --- /dev/null +++ b/src/ML-POD/Install.sh @@ -0,0 +1,59 @@ +# Install/unInstall package files in LAMMPS +# mode = 0/1/2 for uninstall/install/update + +mode=$1 + +# enforce using portable C locale +LC_ALL=C +export LC_ALL + +# arg1 = file, arg2 = file it depends on + +action () { + if (test $mode = 0) then + rm -f ../$1 + elif (! cmp -s $1 ../$1) then + if (test -z "$2" || test -e ../$2) then + cp $1 .. + if (test $mode = 2) then + echo " updating src/$1" + fi + fi + elif (test -n "$2") then + if (test ! -e ../$2) then + rm -f ../$1 + fi + fi +} + +# all package files with no dependencies + +for file in *.cpp *.h; do + test -f ${file} && action $file +done + +if (test $1 = 1) then + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*mlpod[^ \t]* //g' ../Makefile.package + sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/mlpod |' ../Makefile.package + sed -i -e 's|^PKG_LIB =[ \t]*|&-lmlpod |' ../Makefile.package + sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(mlpod_SYSPATH) |' ../Makefile.package + sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(mlpod_SYSLIB) |' ../Makefile.package + fi + if (test -e ../Makefile.package.settings) then + sed -i -e '/^[ \t]*include.*mlpod.*$/d' ../Makefile.package.settings + # multiline form needed for BSD sed on Macs + sed -i -e '4 i \ +include ..\/..\/lib\/mlpod\/Makefile.lammps +' ../Makefile.package.settings + fi + +elif (test $1 = 0) then + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*mlpod[^ \t]* //g' ../Makefile.package + fi + if (test -e ../Makefile.package.settings) then + sed -i -e '/^[ \t]*include.*mlpod.*$/d' ../Makefile.package.settings + fi +fi + diff --git a/src/ML-POD/fitpod_command.cpp b/src/ML-POD/fitpod_command.cpp new file mode 100644 index 0000000000..97ef93ab91 --- /dev/null +++ b/src/ML-POD/fitpod_command.cpp @@ -0,0 +1,1817 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + 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 authors: Ngoc Cuong Nguyen (MIT) and Andrew Rohskopf (SNL) +------------------------------------------------------------------------- */ + +#include "fitpod_command.h" + +#include "mlpod.h" + +#include "comm.h" +#include "error.h" +#include "math_special.h" +#include "memory.h" +#include "tokenizer.h" + +#include +#include +#include +#include + +using namespace LAMMPS_NS; +using MathSpecial::powint; + +#define MAXLINE 1024 + +static constexpr double SMALL = 1.0e-10; + +FitPOD::FitPOD(LAMMPS *_lmp) : Command(_lmp), podptr(nullptr) +{ +} + +void FitPOD::command(int narg, char **arg) +{ + if (narg < 2) utils::missing_cmd_args(FLERR, "fitpod", error); + + std::string pod_file = std::string(arg[0]); // pod input file + std::string data_file = std::string(arg[1]); // data input file + std::string coeff_file; // coefficient input file + + if (narg > 2) + coeff_file = std::string(arg[2]); // coefficient input file + else + coeff_file = ""; + + podptr = new MLPOD(lmp, pod_file, coeff_file); + read_data_files(data_file, podptr->pod.species); + + if ((int) traindata.data_path.size() > 1) + allocate_memory(traindata); + else if ((int) testdata.data_path.size() > 1) + allocate_memory(testdata); + + // get POD coefficients from an input file + + if (coeff_file != "") podArrayCopy(desc.c, podptr->pod.coeff, podptr->pod.nd); + + // compute POD coefficients using least-squares method + + least_squares_fit(traindata); + + // calculate errors for the training data set + + if ((traindata.training_analysis) && ((int) traindata.data_path.size() > 1) ) + error_analysis(traindata, desc.c); + + // calculate errors for the test data set + + if ((testdata.test_analysis) && ((int) testdata.data_path.size() > 1) && (testdata.data_path != traindata.data_path)) + error_analysis(testdata, desc.c); + + // calculate energy and force for the training data set + + if ((traindata.training_calculation) && ((int) traindata.data_path.size() > 1) ) + energyforce_calculation(traindata, desc.c); + + // calculate energy and force for the test data set + + if ((testdata.test_calculation) && ((int) testdata.data_path.size() > 1) && (testdata.data_path != traindata.data_path) ) + energyforce_calculation(testdata, desc.c); + + // deallocate training data + + if ((int) traindata.data_path.size() > 1){ + memory->destroy(traindata.lattice); + memory->destroy(traindata.energy); + memory->destroy(traindata.stress); + memory->destroy(traindata.position); + memory->destroy(traindata.force); + memory->destroy(traindata.atomtype); + } + + // deallocate testing data + + if ((int) testdata.data_path.size() > 1 && (testdata.data_path != traindata.data_path)){ + memory->destroy(testdata.lattice); + memory->destroy(testdata.energy); + memory->destroy(testdata.stress); + memory->destroy(testdata.position); + memory->destroy(testdata.force); + memory->destroy(testdata.atomtype); + } + + // deallocate descriptors + + memory->destroy(desc.gd); + memory->destroy(desc.gdd); + memory->destroy(desc.A); + memory->destroy(desc.b); + memory->destroy(desc.c); + memory->destroy(desc.tmpint); + + // deallocate neighbor data + + memory->destroy(nb.alist); + memory->destroy(nb.pairnum); + memory->destroy(nb.pairnum_cumsum); + memory->destroy(nb.pairlist); + memory->destroy(nb.y); + delete podptr; +} + +/* ---------------------------------------------------------------------- */ + +int FitPOD::read_data_file(double *fitting_weights, std::string &file_format, + std::string &file_extension, std::string &test_path, + std::string &training_path, std::string &filenametag, + const std::string &data_file) +{ + int precision = 8; + + std::string datafilename = data_file; + FILE *fpdata; + if (comm->me == 0) { + + fpdata = utils::open_potential(datafilename,lmp,nullptr); + if (fpdata == nullptr) + error->one(FLERR,"Cannot open training data file {}: ", datafilename, utils::getsyserror()); + } + + // loop through lines of training data file and parse keywords + + char line[MAXLINE],*ptr; + int eof = 0; + while (true) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fpdata); + if (ptr == nullptr) { + eof = 1; + fclose(fpdata); + } + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + + // words = ptrs to all words in line + // strip single and double quotes from words + + std::vector words; + try { + words = Tokenizer(utils::trim_comment(line),"\"' \t\n\r\f").as_vector(); + } catch (TokenizerException &) { + // ignore + } + + if (words.size() == 0) continue; + + auto keywd = words[0]; + + if (words.size() != 2) + error->one(FLERR,"Improper POD file.", utils::getsyserror()); + + // settings for fitting weights + + if (keywd == "fitting_weight_energy") fitting_weights[0] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "fitting_weight_force") fitting_weights[1] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "fitting_weight_stress") fitting_weights[2] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "error_analysis_for_training_data_set") fitting_weights[3] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "error_analysis_for_test_data_set") fitting_weights[4] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "energy_force_calculation_for_training_data_set") fitting_weights[5] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "energy_force_calculation_for_test_data_set") fitting_weights[6] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "fraction_training_data_set") fitting_weights[7] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "fraction_test_data_set") fitting_weights[8] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "randomize_training_data_set") fitting_weights[9] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "randomize_test_data_set") fitting_weights[10] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "fitting_regularization_parameter") fitting_weights[11] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "precision_for_pod_coefficients") precision = utils::inumeric(FLERR,words[1],false,lmp); + + // other settings + + if (keywd == "file_format") file_format = words[1]; + if (keywd == "file_extension") file_extension = words[1]; + if (keywd == "path_to_training_data_set") training_path = words[1]; + if (keywd == "path_to_test_data_set") test_path = words[1]; + if (keywd == "basename_for_output_files") filenametag = words[1]; + } + + if (comm->me == 0) { + utils::logmesg(lmp, "**************** Begin of Data File ****************\n"); + utils::logmesg(lmp, "file format: {}\n", file_format); + utils::logmesg(lmp, "file extension: {}\n", file_extension); + utils::logmesg(lmp, "path to training data set: {}\n", training_path); + utils::logmesg(lmp, "path to test data set: {}\n", test_path); + utils::logmesg(lmp, "training fraction: {}\n", fitting_weights[7]); + utils::logmesg(lmp, "test fraction: {}\n", fitting_weights[8]); + utils::logmesg(lmp, "randomize training data set: {}\n", fitting_weights[9]); + utils::logmesg(lmp, "randomize test data set: {}\n", fitting_weights[10]); + utils::logmesg(lmp, "error analysis for training data set: {}\n", fitting_weights[3]); + utils::logmesg(lmp, "error analysis for test data set: {}\n", fitting_weights[4]); + utils::logmesg(lmp, "energy/force calculation for training data set: {}\n", fitting_weights[5]); + utils::logmesg(lmp, "energy/force calculation for test data set: {}\n", fitting_weights[6]); + utils::logmesg(lmp, "fitting weight for energy: {}\n", fitting_weights[0]); + utils::logmesg(lmp, "fitting weight for force: {}\n", fitting_weights[1]); + utils::logmesg(lmp, "fitting weight for stress: {}\n", fitting_weights[2]); + utils::logmesg(lmp, "fitting regularization parameter: {}\n", fitting_weights[11]); + utils::logmesg(lmp, "**************** End of Data File ****************\n"); + } + + return precision; +} + +void FitPOD::get_exyz_files(std::vector& files, const std::string &datapath, + const std::string &extension) +{ + auto allfiles = platform::list_directory(datapath); + std::sort(allfiles.begin(), allfiles.end()); + for (const auto &fname : allfiles) { + if (utils::strmatch(fname, fmt::format(".*\\.{}$", extension))) + files.push_back(datapath + platform::filepathsep + fname); + } +} + +int FitPOD::get_number_atom_exyz(std::vector& num_atom, int& num_atom_sum, std::string file) +{ + std::string filename = std::move(file); + FILE *fp; + if (comm->me == 0) { + fp = utils::open_potential(filename,lmp,nullptr); + if (fp == nullptr) + error->one(FLERR,"Cannot open POD coefficient file {}: ", filename, utils::getsyserror()); + } + + char line[MAXLINE],*ptr; + int eof = 0; + int num_configs = 0; + num_atom_sum = 0; + + // loop over all lines of this xyz file and extract number of atoms and number of configs + + while (true) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fp); + if (ptr == nullptr) { + eof = 1; + fclose(fp); + } + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + + // words = ptrs to all words in line + // strip single and double quotes from words + + std::vector words; + try { + words = Tokenizer(utils::trim_comment(line),"\"' \t\n\r\f").as_vector(); + } catch (TokenizerException &) { + // ignore + } + + if (words.size() == 0) continue; + + int natom; + if (words.size() == 1) { + natom = utils::inumeric(FLERR,words[0],false,lmp); + num_atom.push_back(natom); + num_configs += 1; + num_atom_sum += natom; + } + } + return num_configs; +} + +int FitPOD::get_number_atoms(std::vector& num_atom, std::vector &num_atom_sum, std::vector& num_config, std::vector training_files) +{ + int nfiles = training_files.size(); // number of files + int d, n; + + for (int i=0; i species) +{ + + std::string filename = std::move(file); + FILE *fp; + if (comm->me == 0) { + fp = utils::open_potential(filename,lmp,nullptr); + if (fp == nullptr) + error->one(FLERR,"Cannot open POD coefficient file {}: ", filename, utils::getsyserror()); + } + + char line[MAXLINE],*ptr; + int eof = 0; + int cfi = 0; + int nat = 0; + int ns = species.size(); + + // loop over all lines of this xyz file and extract training data + + while (true) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fp); + if (ptr == nullptr) { + eof = 1; + fclose(fp); + } + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + + // words = ptrs to all words in line + // strip single and double quotes from words + + std::vector words; + try { + words = Tokenizer(utils::trim_comment(line),"\"' \t\n\r\f").as_vector(); + } catch (TokenizerException &) { + // ignore + } + + if (words.size() == 0) continue; + + ValueTokenizer text(utils::trim_comment(line),"\"' \t\n\r\f"); + if (text.contains("attice")) { + + // find the word containing "lattice" + + auto it = std::find_if(words.begin(), words.end(), [](const std::string& str) { return str.find("attice") != std::string::npos; }); + + // get index of element from iterator + + int index = std::distance(words.begin(), it); + + if (words[index].find("=") != std::string::npos) { + + // lattice numbers start at index + 1 + + for (int k = 0; k < 9; k++) { + lattice[k + 9*cfi] = utils::numeric(FLERR,words[index+1+k],false,lmp); + } + } else { + + // lattice numbers start at index + 2 + + for (int k = 0; k < 9; k++) { + lattice[k + 9*cfi] = utils::numeric(FLERR,words[index+2+k],false,lmp); + } + } + + // find the word containing "energy" + + it = std::find_if(words.begin(), words.end(), [](const std::string& str) { return str.find("nergy") != std::string::npos; }); + + // get index of element from iterator + + index = std::distance(words.begin(), it); + + if (words[index].find("=") != std::string::npos) { + + // energy is after "=" inside this string + + std::size_t found = words[index].find("="); + energy[cfi] = utils::numeric(FLERR,words[index].substr(found+1),false,lmp); + } else { + + // energy is at index + 2 + + energy[cfi] = utils::numeric(FLERR,words[index+2],false,lmp); + + } + + // find the word containing "stress" + + it = std::find_if(words.begin(), words.end(), [](const std::string& str) { return str.find("tress") != std::string::npos; }); + + // get index of element from iterator + + index = std::distance(words.begin(), it); + + if (words[index].find("=") != std::string::npos) { + + // stress numbers start at index + 1 + + for (int k = 0; k < 9; k++) { + stress[k + 9*cfi] = utils::numeric(FLERR,words[index+1+k],false,lmp); + } + } else { + + // lattice numbers start at index + 2 + + for (int k = 0; k < 9; k++) { + stress[k + 9*cfi] = utils::numeric(FLERR,words[index+2+k],false,lmp); + } + } + + cfi += 1; + + } + + // loop over atoms + + else if (words.size() > 1) { + + for (int ii = 0; ii < ns; ii++) + if (species[ii] == words[0]) + atomtype[nat] = ii+1; + + for (int k = 0; k < 6; k++) { + if (k <= 2) pos[k + 3*nat] = utils::numeric(FLERR,words[1+k],false,lmp); + if (k > 2 ) forces[k-3 + 3*nat] = utils::numeric(FLERR,words[1+k],false,lmp); + } + nat += 1; + } + } +} + +void FitPOD::get_data(datastruct &data, const std::vector& species) +{ + get_exyz_files(data.data_files, data.data_path, data.file_extension); + data.num_atom_sum = get_number_atoms(data.num_atom, data.num_atom_each_file, data.num_config, data.data_files); + data.num_config_sum = data.num_atom.size(); + size_t maxname = 9; + for (const auto &fname : data.data_files) maxname = MAX(maxname,fname.size()); + maxname -= data.data_path.size()+1; + const std::string sepline(maxname+46, '-'); + if (comm->me == 0) + utils::logmesg(lmp, "{}\n {:^{}} | number of configurations | number of atoms\n{}\n", + sepline, "data file", maxname, sepline); + int i = 0; + for (const auto &fname : data.data_files) { + std::string filename = fname.substr(data.data_path.size()+1); + data.filenames.push_back(filename); + if (comm->me == 0) + utils::logmesg(lmp, " {:<{}} | {:>10} | {:>8}\n", + filename, maxname, data.num_config[i], data.num_atom_each_file[i]); + ++i; + } + if (comm->me == 0) { + utils::logmesg(lmp, "{}\n", sepline); + utils::logmesg(lmp, "number of files: {}\n", data.data_files.size()); + utils::logmesg(lmp, "number of configurations in all files: {}\n", data.num_config_sum); + utils::logmesg(lmp, "number of atoms in all files: {}\n", data.num_atom_sum); + } + + if (data.data_files.size() < 1) error->all(FLERR, "Cannot fit potential without data files"); + + int n = data.num_config_sum; + memory->create(data.lattice, 9*n, "fitpod:lattice"); + memory->create(data.stress, 9*n, "fitpod:stress"); + memory->create(data.energy, n, "fitpod:energy"); + n = data.num_atom_sum; + memory->create(data.position, 3*n, "fitpod:position"); + memory->create(data.force, 3*n, "fitpod:force"); + memory->create(data.atomtype, n, "fitpod:atomtype"); + + int nfiles = data.data_files.size(); // number of files + int nconfigs = 0; + int natoms = 0; + for (int i=0; ime == 0) { + utils::logmesg(lmp, "minimum number of atoms: {}\n", data.num_atom_min); + utils::logmesg(lmp, "maximum number of atoms: {}\n", data.num_atom_max); + } +} + +std::vector FitPOD::linspace(int start_in, int end_in, int num_in) +{ + + std::vector linspaced; + + double start = static_cast(start_in); + double end = static_cast(end_in); + double num = static_cast(num_in); + + int elm; + + if (num == 0) { return linspaced; } + if (num == 1) + { + elm = (int) std::round(start); + linspaced.push_back(elm); + return linspaced; + } + + double delta = (end - start) / (num - 1); + + for(int i=0; i < num-1; ++i) + { + elm = (int) std::round(start + delta * i); + linspaced.push_back(elm); + } + + elm = (int) std::round(end); + linspaced.push_back(elm); + + return linspaced; +} + +std::vector FitPOD::shuffle(int start_in, int end_in, int num_in) +{ + int sz = end_in - start_in + 1; + std::vector myvector(sz); + + for (int i = 0; i shuffle_vec(num_in); + for (int i = 0; i FitPOD::select(int n, double fraction, int randomize) +{ + std::vector selected; + + int m = (int) std::round(n*fraction); + m = MAX(m, 1); + + selected = (randomize==1) ? shuffle(1, n, m) : linspace(1, n, m); + + return selected; +} + +void FitPOD::select_data(datastruct &newdata, const datastruct &data) +{ + double fraction = data.fraction; + int randomize = data.randomize; + + if (comm->me == 0) { + if (randomize==1) + utils::logmesg(lmp, "Select {} fraction of the data set at random using shuffle\n", data.fraction); + else + utils::logmesg(lmp, "Select {} fraction of the data set deterministically using linspace\n", data.fraction); + } + + int nfiles = data.data_files.size(); // number of files + std::vector> selected(nfiles); + + newdata.num_config.resize(nfiles); + newdata.num_config_cumsum.resize(nfiles+1); + newdata.num_atom_each_file.resize(nfiles); + + for (int file = 0; file < nfiles; file++) { + int nconfigs = data.num_config[file]; + selected[file] = select(nconfigs, fraction, randomize); + int ns = (int) selected[file].size(); // number of selected configurations + + newdata.num_config[file] = ns; + int num_atom_sum = 0; + for (int ii=0; ii < ns; ii++) { // loop over each selected configuration in a file + int ci = data.num_config_cumsum[file] + selected[file][ii] - 1; + int natom = data.num_atom[ci]; + newdata.num_atom.push_back(natom); + num_atom_sum += natom; + } + newdata.num_atom_each_file[file] = num_atom_sum; + } + int len = newdata.num_atom.size(); + newdata.num_atom_min = podArrayMin(&newdata.num_atom[0], len); + newdata.num_atom_max = podArrayMax(&newdata.num_atom[0], len); + newdata.num_atom_cumsum.resize(len+1); + podCumsum(&newdata.num_atom_cumsum[0], &newdata.num_atom[0], len+1); + newdata.num_atom_sum = newdata.num_atom_cumsum[len]; + podCumsum(&newdata.num_config_cumsum[0], &newdata.num_config[0], nfiles+1); + newdata.num_config_sum = newdata.num_atom.size(); + + int n = data.num_config_sum; + memory->create(newdata.lattice, 9*n, "fitpod:newdata_lattice"); + memory->create(newdata.stress, 9*n, "fitpod:newdata_stress"); + memory->create(newdata.energy, n, "fitpod:newdata_energy"); + n = data.num_atom_sum; + memory->create(newdata.position, 3*n, "fitpod:newdata_position"); + memory->create(newdata.force, 3*n, "fitpod:newdata_force"); + memory->create(newdata.atomtype, n, "fitpod:newdata_atomtype"); + + int cn = 0; + int dim = 3; + for (int file = 0; file < nfiles; file++) { + int ns = (int) selected[file].size(); // number of selected configurations + for (int ii=0; ii < ns; ii++) { // loop over each selected configuration in a file + int ci = data.num_config_cumsum[file] + selected[file][ii] - 1; + int natom = data.num_atom[ci]; + int natom_cumsum = data.num_atom_cumsum[ci]; + + int natomnew = newdata.num_atom[cn]; + int natomnew_cumsum = newdata.num_atom_cumsum[cn]; + + if (natom != natomnew) + error->all(FLERR,"number of atoms in the new data set must be the same as that in the old data set."); + + int *atomtype = &data.atomtype[natom_cumsum]; + double *position = &data.position[dim*natom_cumsum]; + double *force = &data.force[dim*natom_cumsum]; + + newdata.energy[cn] = data.energy[ci]; + for (int j=0; j<9; j++) { + newdata.stress[j+9*cn] = data.stress[j+9*ci]; + newdata.lattice[j+9*cn] = data.lattice[j+9*ci]; + } + + for (int na=0; name == 0) + utils::logmesg(lmp, "{:-<{}}\n {:^{}} | # configs (selected) | # atoms (selected) " + "| # configs (original) | # atoms (original)\n{:-<{}}\n", + "", maxname+90, "data_file", maxname, "", maxname+90); + for (int i=0; i< (int) newdata.data_files.size(); i++) { + std::string filename = newdata.data_files[i].substr(newdata.data_path.size()+1,newdata.data_files[i].size()); + newdata.filenames.emplace_back(filename.c_str()); + if (comm->me == 0) + utils::logmesg(lmp, " {:<{}} | {:>8} | {:>8} | {:>8} | {:>8}\n", + newdata.filenames[i], maxname, newdata.num_config[i], newdata.num_atom_each_file[i], + data.num_config[i], data.num_atom_each_file[i]); + } + if (comm->me == 0) { + utils::logmesg(lmp, "{:-<{}}\nnumber of files: {}\n", "", maxname+90, newdata.data_files.size()); + utils::logmesg(lmp, "number of configurations in all files (selected and original): {} and {}\n", newdata.num_config_sum, data.num_config_sum); + utils::logmesg(lmp, "number of atoms in all files (selected and original: {} and {}\n", newdata.num_atom_sum, data.num_atom_sum); + } +} + +void FitPOD::read_data_files(const std::string& data_file, const std::vector& species) +{ + datastruct data; + + // read data input file to datastruct + + data.precision = read_data_file(data.fitting_weights, data.file_format, data.file_extension, + testdata.data_path, data.data_path, data.filenametag, data_file); + + data.training_analysis = (int) data.fitting_weights[3]; + data.test_analysis = (int) data.fitting_weights[4]; + data.training_calculation = (int) data.fitting_weights[5]; + data.test_calculation = (int) data.fitting_weights[6]; + data.fraction = data.fitting_weights[7]; + data.randomize = (int) data.fitting_weights[9]; + + data.copydatainfo(traindata); + + if (data.fraction >= 1.0) { + if (comm->me == 0) + utils::logmesg(lmp, "**************** Begin of Training Data Set ****************\n"); + if (traindata.data_path.size() > 1) + get_data(traindata, species); + else + error->all(FLERR,"data set is not found"); + if (comm->me == 0) + utils::logmesg(lmp, "**************** End of Training Data Set ****************\n"); + } else { + if (comm->me == 0) + utils::logmesg(lmp, "**************** Begin of Training Data Set ****************\n"); + if (data.data_path.size() > 1) + get_data(data, species); + else + error->all(FLERR,"data set is not found"); + if (comm->me == 0) + utils::logmesg(lmp, "**************** End of Training Data Set ****************\n"); + + if (comm->me == 0) + utils::logmesg(lmp, "**************** Begin of Select Training Data Set ****************\n"); + select_data(traindata, data); + if (comm->me == 0) + utils::logmesg(lmp, "**************** End of Select Training Data Set ****************\n"); + + memory->destroy(data.lattice); + memory->destroy(data.energy); + memory->destroy(data.stress); + memory->destroy(data.position); + memory->destroy(data.force); + memory->destroy(data.atomtype); + } + + if (((int) testdata.data_path.size() > 1) && (testdata.data_path != traindata.data_path)) { + testdata.training = 0; + testdata.file_format = traindata.file_format; + testdata.file_extension = traindata.file_extension; + testdata.training_analysis = traindata.training_analysis; + testdata.test_analysis = traindata.test_analysis; + testdata.training_calculation = traindata.training_calculation; + testdata.test_calculation = traindata.test_calculation; + testdata.fraction = traindata.fitting_weights[8]; + testdata.randomize = (int) traindata.fitting_weights[10]; + if (comm->me == 0) + utils::logmesg(lmp, "**************** Begin of Test Data Set ****************\n"); + get_data(testdata, species); + if (comm->me == 0) + utils::logmesg(lmp, "**************** End of Test Data Set ****************\n"); + } + else { + testdata.data_path = traindata.data_path; + } +} + +int FitPOD::latticecoords(double *y, int *alist, double *x, double *a1, double *a2, double *a3, double rcut, int *pbc, int nx) +{ + int m=0, n=0, p=0; + if (pbc[0] == 1) m = (int) ceil(rcut/a1[0]); + if (pbc[1] == 1) n = (int) ceil(rcut/a2[1]); + if (pbc[2] == 1) p = (int) ceil(rcut/a3[2]); + + // index for the center lattice + + int ind = m + (2*m+1)*(n) + (2*m+1)*(2*n+1)*(p); + + // number of lattices + + int nl = (2*m+1)*(2*n+1)*(2*p+1); + + for (int j=0; j<3*nx; j++) + y[j] = x[j]; + int q = nx; + + for (int i = 0; i < (2*p+1); i++) + for (int j = 0; j < (2*n+1); j++) + for (int k = 0; k < (2*m+1); k++) { + int ii = k + (2*m+1)*j + (2*m+1)*(2*n+1)*i; + if (ii != ind) { + double x0 = a1[0]*(k - m) + a2[0]*(j - n) + a3[0]*(i - p); + double x1 = a1[1]*(k - m) + a2[1]*(j - n) + a3[1]*(i - p); + double x2 = a1[2]*(k - m) + a2[2]*(j - n) + a3[2]*(i - p); + for (int jj=0; jj SMALL) && (rijsq <= rcutsq)) { + inc += 1; + neighlist[k] = j; + k += 1; + } + } + numneigh[i] = inc; + } + return k; +} + +int FitPOD::podfullneighborlist(double *y, int *alist, int *neighlist, int *numneigh, int *numneighsum, + double *x, double *a1, double *a2, double *a3, double rcut, int *pbc, int nx) +{ + double rcutsq = rcut*rcut; + int dim = 3, nl = 0, nn = 0; + + // number of lattices + + nl = latticecoords(y, alist, x, a1, a2, a3, rcut, pbc, nx); + int N = nx*nl; + + // total number of neighbors + + nn = podneighborlist(neighlist, numneigh, y, rcutsq, nx, N, dim); + + podCumsum(numneighsum, numneigh, nx+1); + + return nn; +} + +void FitPOD::allocate_memory(const datastruct &data) +{ + int nd = podptr->pod.nd; + memory->create(desc.gd, nd, "fitpod:desc_gd"); + memory->create(desc.A, nd*nd, "fitpod:desc_A"); + memory->create(desc.b, nd, "fitpod:desc_b"); + memory->create(desc.c, nd, "fitpod:desc_c"); + podArraySetValue(desc.A, 0.0, nd*nd); + podArraySetValue(desc.b, 0.0, nd); + podArraySetValue(desc.c, 0.0, nd); + + int dim = 3; + int natom_max = data.num_atom_max; + int nd1 = podptr->pod.nd1; + int nd2 = podptr->pod.nd2; + int nd3 = podptr->pod.nd3; + int nd4 = podptr->pod.nd4; + int nelements = podptr->pod.nelements; + int nbesselpars = podptr->pod.nbesselpars; + int nrbf2 = podptr->pod.nbf2; + int nabf3 = podptr->pod.nabf3; + int nrbf3 = podptr->pod.nrbf3; + int *pdegree2 = podptr->pod.twobody; + int *pdegree3 = podptr->pod.threebody; + int *pbc = podptr->pod.pbc; + double rcut = podptr->pod.rcut; + + int Nj=0, Nij=0; + int m=0, n=0, p=0, nl=0, ny=0, na=0, np=0; + + for (int ci=0; ci<(int) data.num_atom.size(); ci++) + { + int natom = data.num_atom[ci]; + double *lattice = &data.lattice[9*ci]; + double *a1 = &lattice[0]; + double *a2 = &lattice[3]; + double *a3 = &lattice[6]; + if (pbc[0] == 1) m = (int) ceil(rcut/a1[0]); + if (pbc[1] == 1) n = (int) ceil(rcut/a2[1]); + if (pbc[2] == 1) p = (int) ceil(rcut/a3[2]); + + // number of lattices + + nl = (2*m+1)*(2*n+1)*(2*p+1); + ny = MAX(ny,dim*natom*nl); + na = MAX(na, natom*nl); + np = MAX(np, natom*natom*nl); + } + + memory->create(nb.y, ny, "fitpod:nb_y"); + memory->create(nb.alist, na, "fitpod:nb_alist"); + memory->create(nb.pairnum, natom_max, "fitpod:nb_pairnum"); + memory->create(nb.pairnum_cumsum, natom_max+1, "fitpod:nb_pairnum_cumsum"); + memory->create(nb.pairlist, np, "fitpod:nb_pairlist"); + + nb.natom_max = natom_max; + nb.sze = nelements*nelements; + nb.sza = na; + nb.szy = ny; + nb.szp = np; + + if (comm->me == 0) + utils::logmesg(lmp,"**************** Begin of Memory Allocation ****************\n"); + + int szd = 0, szi=0, szsnap=0; + for (int ci=0; ci<(int) data.num_atom.size(); ci++) + { + int natom = data.num_atom[ci]; + int natom_cumsum = data.num_atom_cumsum[ci]; + double *x = &data.position[dim*natom_cumsum]; + double *lattice = &data.lattice[9*ci]; + double *a1 = &lattice[0]; + double *a2 = &lattice[3]; + double *a3 = &lattice[6]; + + Nij = podfullneighborlist(nb.y, nb.alist, nb.pairlist, nb.pairnum, nb.pairnum_cumsum, x, a1, a2, a3, rcut, pbc, natom); + + int ns2 = pdegree2[0]*nbesselpars + pdegree2[1]; + int ns3 = pdegree3[0]*nbesselpars + pdegree3[1]; + + int szd1 = 3*Nij+ (1+dim)*Nij*MAX(nrbf2+ns2,nrbf3+ns3) + (nabf3+1)*7; + int szi1 = 6*Nij + 2*natom+1 + (Nj-1)*Nj; + szd = MAX(szd, szd1); + szi = MAX(szi, szi1); + + if (podptr->sna.twojmax>0) { + szd1 = 0; + szd1 += Nij*dim; // rij + szd1 += MAX(2*podptr->sna.idxu_max*Nij, 2*podptr->sna.idxz_max*podptr->sna.ndoubles*natom); // (Ur, Ui) and (Zr, Zi) + szd1 += 2*podptr->sna.idxu_max*dim*Nij; // dUr, dUi + szd1 += MAX(podptr->sna.idxb_max*podptr->sna.ntriples*dim*Nij, 2*podptr->sna.idxu_max*podptr->sna.nelements*natom); // dblist and (Utotr, Utoti) + szsnap = MAX(szsnap, szd1); + } + } + + szd = MAX(szsnap, szd); + szd = MAX(natom_max*(nd1+nd2+nd3+nd4) + szd, dim*natom_max*(nd-nd1-nd2-nd3-nd4)); + szd = dim*natom_max*(nd1+nd2+nd3+nd4) + szd; + + // gdd includes linear descriptors derivatives, quadratic descriptors derivatives and temporary memory + + memory->create(desc.gdd, szd, "fitpod:desc_gdd"); + memory->create(desc.tmpint, szi, "fitpod:desc_tmpint"); + desc.szd = szd; + desc.szi = szi; + + if (comm->me == 0) { + utils::logmesg(lmp, "maximum number of atoms in periodic domain: {}\n", natom_max); + utils::logmesg(lmp, "maximum number of atoms in extended domain: {}\n", nb.sza); + utils::logmesg(lmp, "maximum number of neighbors in extended domain: {}\n", nb.szp); + utils::logmesg(lmp, "size of double memory: {}\n", szd); + utils::logmesg(lmp, "size of int memory: {}\n", szi); + utils::logmesg(lmp, "size of descriptor matrix: {} x {}\n", nd, nd); + utils::logmesg(lmp, "**************** End of Memory Allocation ****************\n"); + } +} + +void FitPOD::linear_descriptors(const datastruct &data, int ci) +{ + int dim = 3; + int nd1 = podptr->pod.nd1; + int nd2 = podptr->pod.nd2; + int nd3 = podptr->pod.nd3; + int nd4 = podptr->pod.nd4; + int nd1234 = nd1+nd2+nd3+nd4; + int *pbc = podptr->pod.pbc; + double rcut = podptr->pod.rcut; + + int natom = data.num_atom[ci]; + int natom_cumsum = data.num_atom_cumsum[ci]; + int *atomtype = &data.atomtype[natom_cumsum]; + double *position = &data.position[dim*natom_cumsum]; + double *lattice = &data.lattice[9*ci]; + double *a1 = &lattice[0]; + double *a2 = &lattice[3]; + double *a3 = &lattice[6]; + + // neighbor list + int Nij = podfullneighborlist(nb.y, nb.alist, nb.pairlist, nb.pairnum, nb.pairnum_cumsum, + position, a1, a2, a3, rcut, pbc, natom); + + int *tmpint = &desc.tmpint[0]; + double *tmpmem = &desc.gdd[dim*natom*nd1234+natom*nd1234]; + podptr->linear_descriptors(desc.gd, desc.gdd, nb.y, tmpmem, atomtype, nb.alist, + nb.pairlist, nb.pairnum, nb.pairnum_cumsum, tmpint, natom, Nij); + +} + +void FitPOD::quadratic_descriptors(const datastruct &data, int ci) +{ + int dim = 3; + int natom = data.num_atom[ci]; + int nd1 = podptr->pod.nd1; + int nd2 = podptr->pod.nd2; + int nd3 = podptr->pod.nd3; + int nd4 = podptr->pod.nd4; + int nd22 = podptr->pod.nd22; + int nd23 = podptr->pod.nd23; + int nd24 = podptr->pod.nd24; + int nd33 = podptr->pod.nd33; + int nd34 = podptr->pod.nd34; + int nd44 = podptr->pod.nd44; + int nd123 = nd1+nd2+nd3; + int nd1234 = nd1+nd2+nd3+nd4; + + double *fatom2 = &desc.gdd[dim*natom*(nd1)]; + double *fatom3 = &desc.gdd[dim*natom*(nd1+nd2)]; + double *fatom4 = &desc.gdd[dim*natom*(nd123)]; + + // global descriptors for four-body quadratic22 potential + + if (nd22 > 0) { + int nq2 = podptr->pod.quadratic22[0]*podptr->pod.nc2; + podptr->quadratic_descriptors(&desc.gd[nd1234], &desc.gdd[dim*natom*nd1234], + &desc.gd[nd1], fatom2, nq2, dim*natom); + } + + // global descriptors for four-body quadratic23 potential + + if (nd23 > 0) { + int nq2 = podptr->pod.quadratic23[0]*podptr->pod.nc2; + int nq3 = podptr->pod.quadratic23[1]*podptr->pod.nc3; + podptr->quadratic_descriptors(&desc.gd[nd1234+nd22], &desc.gdd[dim*natom*(nd1234+nd22)], + &desc.gd[nd1], &desc.gd[nd1+nd2], fatom2, fatom3, nq2, nq3, dim*natom); + } + + // global descriptors for five-body quadratic24 potential + + if (nd24 > 0) { + int nq2 = podptr->pod.quadratic24[0]*podptr->pod.nc2; + int nq4 = podptr->pod.quadratic24[1]*podptr->pod.nc4; + podptr->quadratic_descriptors(&desc.gd[nd1234+nd22+nd23], &desc.gdd[dim*natom*(nd1234+nd22+nd23)], + &desc.gd[nd1], &desc.gd[nd1+nd2+nd3], fatom2, fatom4, nq2, nq4, dim*natom); + } + + // global descriptors for five-body quadratic33 potential + + if (nd33 > 0) { + int nq3 = podptr->pod.quadratic33[0]*podptr->pod.nc3; + podptr->quadratic_descriptors(&desc.gd[nd1234+nd22+nd23+nd24], &desc.gdd[dim*natom*(nd1234+nd22+nd23+nd24)], + &desc.gd[nd1+nd2], fatom3, nq3, dim*natom); + } + + // global descriptors for six-body quadratic34 potential + + if (nd34 > 0) { + int nq3 = podptr->pod.quadratic34[0]*podptr->pod.nc3; + int nq4 = podptr->pod.quadratic34[1]*podptr->pod.nc4; + podptr->quadratic_descriptors(&desc.gd[nd1234+nd22+nd23+nd24+nd33], &desc.gdd[dim*natom*(nd1234+nd22+nd23+nd24+nd33)], + &desc.gd[nd1+nd2], &desc.gd[nd1+nd2+nd3], fatom3, fatom4, nq3, nq4, dim*natom); + } + + // global descriptors for seven-body quadratic44 potential + + if (nd44 > 0) { + int nq4 = podptr->pod.quadratic44[0]*podptr->pod.nc4; + podptr->quadratic_descriptors(&desc.gd[nd1234+nd22+nd23+nd24+nd33+nd34], &desc.gdd[dim*natom*(nd1234+nd22+nd23+nd24+nd33+nd34)], + &desc.gd[nd1+nd2+nd3], fatom4, nq4, dim*natom); + } + + // normalize quadratic descriptors + + for (int i=0; i<(nd22+nd23+nd24+nd33+nd34+nd44); i++) + desc.gd[nd1234+i] = desc.gd[nd1234+i]/(natom); + + for (int i=0; ipod.nd1; + int nd2 = podptr->pod.nd2; + int nd3 = podptr->pod.nd3; + int nd4 = podptr->pod.nd4; + int nd22 = podptr->pod.nd22; + int nd23 = podptr->pod.nd23; + int nd24 = podptr->pod.nd24; + int nd33 = podptr->pod.nd33; + int nd34 = podptr->pod.nd34; + int nd44 = podptr->pod.nd44; + int nd234 = podptr->pod.nd234; + int nd333 = podptr->pod.nd333; + int nd444 = podptr->pod.nd444; + int nd123 = nd1+nd2+nd3; + int nd1234 = nd1+nd2+nd3+nd4; + + // global descriptors for seven-body cubic234 potential + if (nd234 > 0) { + int nq2 = podptr->pod.cubic234[0]*podptr->pod.nc2; + int nq3 = podptr->pod.cubic234[1]*podptr->pod.nc3; + int nq4 = podptr->pod.cubic234[2]*podptr->pod.nc4; + int np3 = nd1234+nd22+nd23+nd24+nd33+nd34+nd44; + double *eatom2 = &desc.gd[nd1]; + double *eatom3 = &desc.gd[nd1+nd2]; + double *eatom4 = &desc.gd[nd123]; + double *fatom2 = &desc.gdd[dim*natom*(nd1)]; + double *fatom3 = &desc.gdd[dim*natom*(nd1+nd2)]; + double *fatom4 = &desc.gdd[dim*natom*(nd123)]; + podptr->cubic_descriptors(&desc.gd[np3], &desc.gdd[dim*natom*np3], + eatom2, eatom3, eatom4, fatom2, fatom3, fatom4, nq2, nq3, nq4, dim*natom); + } + + // global descriptors for seven-body cubic333 potential + + if (nd333 > 0) { + int nq3 = podptr->pod.cubic333[0]*podptr->pod.nc3; + int np3 = nd1234+nd22+nd23+nd24+nd33+nd34+nd44+nd234; + double *eatom3 = &desc.gd[nd1+nd2]; + double *fatom3 = &desc.gdd[dim*natom*(nd1+nd2)]; + podptr->cubic_descriptors(&desc.gd[np3], &desc.gdd[dim*natom*np3], + eatom3, fatom3, nq3, dim*natom); + } + + // global descriptors for ten-body cubic444 potential + + if (nd444 > 0) { + int nq4 = podptr->pod.cubic444[0]*podptr->pod.nc4; + int np4 = nd1234+nd22+nd23+nd24+nd33+nd34+nd44+nd234+nd333; + double *eatom4 = &desc.gd[nd123]; + double *fatom4 = &desc.gdd[dim*natom*(nd123)]; + podptr->cubic_descriptors(&desc.gd[np4], &desc.gdd[dim*natom*(np4)], + eatom4, fatom4, nq4, dim*natom); + } + + // normalize cubic descriptors + int nd = podptr->pod.nd; + for (int i=(nd1234+nd22+nd23+nd24+nd33+nd34+nd44); ipod.nd; + int nforce = dim*natom; + + // compute energy weight and force weight + + double normconst = 1.0; + if (data.normalizeenergy==1) normconst = 1.0/natom; + double we = data.fitting_weights[0]; + double wf = data.fitting_weights[1]; + double we2 = (we*we)*(normconst*normconst); + double wf2 = (wf*wf); + + // get energy and force from the training data set + + double energy = data.energy[ci]; + double *force = &data.force[dim*natom_cumsum]; + + // least-square matrix for all descriptors: A = A + (we*we)*(gd^T * gd) + + podKron(desc.A, desc.gd, desc.gd, we2, nd, nd); + + // least-square matrix for all descriptors derivatives: A = A + (wf*wf) * (gdd^T * gdd) + + char cht = 'T'; + char chn = 'N'; + double one = 1.0; + int inc1 = 1; + DGEMM(&cht, &chn, &nd, &nd, &nforce, &wf2, desc.gdd, &nforce, desc.gdd, &nforce, &one, desc.A, &nd); + + // least-square vector for all descriptors: b = b + (we*we*energy)*gd + + double wee = we2*energy; + for (int i = 0; i< nd; i++) + desc.b[i] += wee*desc.gd[i]; + + // least-square vector for all descriptors derivatives: b = b + (wf*wf) * (gdd^T * f) + + DGEMV(&cht, &nforce, &nd, &wf2, desc.gdd, &nforce, force, &inc1, &one, desc.b, &inc1); + +} + +void FitPOD::least_squares_fit(const datastruct &data) +{ + if (comm->me == 0) + utils::logmesg(lmp, "**************** Begin of Least-Squares Fitting ****************\n"); + + // loop over each configuration in the training data set + + for (int ci=0; ci < (int) data.num_atom.size(); ci++) { + + if ((ci % 100)==0) { + if (comm->me == 0) + utils::logmesg(lmp, "Configuration: # {}\n", ci+1); + } + + if ((ci % comm->nprocs) == comm->me) { + + // compute linear POD descriptors + + linear_descriptors(data, ci); + + // compute quadratic POD descriptors + + quadratic_descriptors(data, ci); + + // compute cubic POD descriptors + + cubic_descriptors(data, ci); + + // assemble the least-squares linear system + + least_squares_matrix(data, ci); + } + } + + int nd = podptr->pod.nd; + + MPI_Allreduce(MPI_IN_PLACE, desc.b, nd, MPI_DOUBLE, MPI_SUM, world); + MPI_Allreduce(MPI_IN_PLACE, desc.A, nd*nd, MPI_DOUBLE, MPI_SUM, world); + + if (comm->me == 0) { + + // symmetrize A + + for (int i = 0; i fabs(desc.b[i])) ? maxb : fabs(desc.b[i]); + + maxb = 1.0/maxb; + for (int i = 0; ime == 0) { // save coefficients into a text file + std::string filename = data.filenametag + "_coefficients" + ".pod"; + FILE *fp = fopen(filename.c_str(), "w"); + + fmt::print(fp, "POD_coefficients: {}\n", nd); + for (int count = 0; count < nd; count++) { + fmt::print(fp, "{:<10.{}f}\n", desc.c[count], data.precision); + } + fclose(fp); + utils::logmesg(lmp, "**************** End of Least-Squares Fitting ****************\n"); + } +} + +double FitPOD::energyforce_calculation(double *force, double *coeff, const datastruct &data, int ci) +{ + int dim = 3; + int *pbc = podptr->pod.pbc; + double rcut = podptr->pod.rcut; + int nd1234 = podptr->pod.nd1 + podptr->pod.nd2 + podptr->pod.nd3 + podptr->pod.nd4; + + int natom = data.num_atom[ci]; + int natom_cumsum2 = data.num_atom_cumsum[ci]; + int *atomtype = &data.atomtype[natom_cumsum2]; + double *position = &data.position[dim*natom_cumsum2]; + double *lattice = &data.lattice[9*ci]; + double *a1 = &lattice[0]; + double *a2 = &lattice[3]; + double *a3 = &lattice[6]; + + // neighbor list + + int Nij = podfullneighborlist(nb.y, nb.alist, nb.pairlist, nb.pairnum, nb.pairnum_cumsum, + position, a1, a2, a3, rcut, pbc, natom); + + double *tmpmem = &desc.gdd[0]; + int *tmpint = &desc.tmpint[0]; + double *rij = &tmpmem[0]; // 3*Nij + int *ai = &tmpint[0]; // Nij + int *aj = &tmpint[Nij]; // Nij + int *ti = &tmpint[2*Nij]; // Nij + int *tj = &tmpint[3*Nij]; // Nij + int *idxi = &tmpint[4*Nij]; // Nij + podptr->podNeighPairs(rij, nb.y, idxi, ai, aj, ti, tj, nb.pairnum_cumsum, atomtype, nb.pairlist, nb.alist, natom); + + double *effectivecoeff = &tmpmem[3*Nij]; // 3*Nij + podArraySetValue(effectivecoeff, 0.0, nd1234); + + double energy = podptr->energyforce_calculation(force, coeff, effectivecoeff, desc.gd, rij, + &tmpmem[3*Nij+nd1234], nb.pairnum_cumsum, atomtype, idxi, ai, aj, ti, tj, natom, Nij); + + return energy; +} + +void FitPOD::print_analysis(const datastruct &data, double *outarray, double *errors) +{ + int nfiles = data.data_files.size(); // number of files + int lm = 10; + for (int i = 0; i < nfiles; i++) + lm = MAX(lm, (int) data.filenames[i].size()); + lm = lm + 2; + + std::string filename_errors = fmt::format("{}_{}_errors.pod", data.filenametag, data.training ? "training" : "test"); + std::string filename_analysis = fmt::format("{}_{}_analysis.pod", data.filenametag, data.training ? "training" : "test"); + + FILE *fp_errors = nullptr; + FILE *fp_analysis = nullptr; + fp_errors = fopen(filename_errors.c_str(), "w"); + fp_analysis = fopen(filename_analysis.c_str(), "w"); + + std::string mystr = fmt::format("**************** Begin of Error Analysis for the {} Data Set ****************\n", + data.training ? "Training" : "Test"); + + utils::logmesg(lmp, mystr); + fmt::print(fp_errors, mystr); + + std::string sa(lm+80,'-'); + sa += '\n'; + std::string sb = fmt::format(" {:^{}} | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force\n", + "File", lm); + utils::logmesg(lmp, sa + sb + sa); + fmt::print(fp_errors, sa + sb + sa); + + int ci=0, m=8, nc=0, nf=0; + for (int file = 0; file < nfiles; file++) { + fmt::print(fp_analysis, "# {}\n", data.filenames[file]); + fmt::print(fp_analysis, " config # atoms energy DFT energy energy error " + " force DFT force force error\n"); + + int nforceall = 0; + int nconfigs = data.num_config[file]; + nc += nconfigs; + for (int ii=0; ii < nconfigs; ii++) { // loop over each configuration in a file + fmt::print(fp_analysis, "{:6} {:8} ", outarray[m*ci], outarray[1 + m*ci]); + for(int count = 2; count < m; count ++) + fmt::print(fp_analysis, "{:<15.10} ", outarray[count + m*ci]); + fmt::print(fp_analysis, "\n"); + + nforceall += 3*data.num_atom[ci]; + ci += 1; + } + nf += nforceall; + + int q = file+1; + auto s = fmt::format("{:<{}} {:>10} {:>11} {:<10.6f} {:<10.6f} {:<10.6f} {:<10.6f}\n", + data.filenames[file], lm, nconfigs, nforceall/3, + errors[0 + 4*q], errors[1 + 4*q], errors[2 + 4*q], errors[3 + 4*q]); + utils::logmesg(lmp, s); + fmt::print(fp_errors, s); + } + utils::logmesg(lmp, sa); + fmt::print(fp_errors, sa); + + auto s = fmt::format("{:<{}} {:>10} {:>11} {:<10.6f} {:<10.6f} {:<10.6f} {:<10.6f}\n", + "All files", lm, nc, nf/3, errors[0], errors[1], errors[2], errors[3]); + utils::logmesg(lmp, s + sa); + fmt::print(fp_errors, "{}", s + sa); + + mystr = fmt::format("**************** End of Error Analysis for the {} Data Set ****************\n", + data.training ? "Training" : "Test"); + + utils::logmesg(lmp, mystr); + fmt::print(fp_errors, mystr); + + fclose(fp_errors); + fclose(fp_analysis); +} + +void FitPOD::error_analysis(const datastruct &data, double *coeff) +{ + int dim = 3; + double energy; + std::vector force(dim*data.num_atom_max); + + int nfiles = data.data_files.size(); // number of files + int num_configs = data.num_atom.size(); // number of configurations in all files + + int m = 8; + std::vector outarray(m*num_configs); + for (int i=0; i ssrarray(num_configs); + for (int i=0; i errors(4*(nfiles+1)); + for (int i=0; i<4*(nfiles+1); i++) + errors[i] = 0.0; + + int nd1 = podptr->pod.nd1; + int nd2 = podptr->pod.nd2; + int nd3 = podptr->pod.nd3; + int nd4 = podptr->pod.nd4; + int nd22 = podptr->pod.nd22; + int nd23 = podptr->pod.nd23; + int nd24 = podptr->pod.nd24; + int nd33 = podptr->pod.nd33; + int nd34 = podptr->pod.nd34; + int nd44 = podptr->pod.nd44; + int nd1234 = nd1+nd2+nd3+nd4; + int nd = podptr->pod.nd; + + std::vector newcoeff(nd); + for (int j=0; jme == 0) + utils::logmesg(lmp, "**************** Begin of Error Calculation ****************\n"); + + int ci = 0; // configuration counter + for (int file = 0; file < nfiles; file++) { // loop over each file in the training data set + + int nconfigs = data.num_config[file]; + for (int ii=0; ii < nconfigs; ii++) { // loop over each configuration in a file + + if ((ci % 100)==0) { + if (comm->me == 0) + utils::logmesg(lmp, "Configuration: # {}\n", ci+1); + } + + if ((ci % comm->nprocs) == comm->me) { + int natom = data.num_atom[ci]; + int nforce = dim*natom; + + for (int j=nd1234; j<(nd1234+nd22+nd23+nd24+nd33+nd34+nd44); j++) + newcoeff[j] = coeff[j]/(natom); + + for (int j=(nd1234+nd22+nd23+nd24+nd33+nd34+nd44); jme == 0) { + utils::logmesg(lmp, "**************** End of Error Calculation ****************\n"); + print_analysis(data, outarray.data(), errors.data()); + } +} + +void FitPOD::energyforce_calculation(const datastruct &data, double *coeff) +{ + int dim = 3; + double energy; + std::vector force(1+dim*data.num_atom_max); + + int nfiles = data.data_files.size(); // number of files + + if (comm->me == 0) + utils::logmesg(lmp, "**************** Begin of Energy/Force Calculation ****************\n"); + + int ci = 0; // configuration counter + for (int file = 0; file < nfiles; file++) { // loop over each file in the data set + + int nconfigs = data.num_config[file]; + for (int ii=0; ii < nconfigs; ii++) { // loop over each configuration in a file + if ((ci % 100)==0) { + if (comm->me == 0) utils::logmesg(lmp, "Configuration: # {}\n", ci+1); + } + + int natom = data.num_atom[ci]; + int nforce = dim*natom; + + if ((ci % comm->nprocs) == comm->me) { + energy = energyforce_calculation(force.data()+1, coeff, data, ci); + + // save energy and force into a binary file + + force[0] = energy; + std::string filename = "energyforce_config" + std::to_string(ci+1) + ".bin"; + + FILE *fp = fopen(filename.c_str(), "wb"); + + fwrite( reinterpret_cast( force.data() ), sizeof(double) * (1 + nforce), 1, fp); + + fclose(fp); + } + ci += 1; + } + } + if (comm->me == 0) + utils::logmesg(lmp, "**************** End of Energy/Force Calculation ****************\n"); +} + +void FitPOD::print_matrix(const char *desc, int m, int n, double **a, int /*lda*/ ) +{ + int i, j; + printf( "\n %s\n", desc ); + + for( i = 0; i < m; i++ ) + { + for( j = 0; j < n; j++ ) printf( " %6.12f", a[j][i] ); + printf( "\n" ); + } +} + +void FitPOD::print_matrix(const char *desc, int m, int n, double *a, int lda ) +{ + int i, j; + printf( "\n %s\n", desc ); + + for( i = 0; i < m; i++ ) + { + for( j = 0; j < n; j++ ) printf( " %6.12f", a[i+j*lda] ); + printf( "\n" ); + } +} + +void FitPOD::print_matrix(const char *desc, int m, int n, int *a, int lda) +{ + int i, j; + printf( "\n %s\n", desc ); + + for( i = 0; i < m; i++ ) + { + for( j = 0; j < n; j++ ) printf( " %d", a[i+j*lda] ); + printf( "\n" ); + } +} + +void FitPOD::podArrayFill(int* output, int start, int length) +{ + for (int j = 0; j < length; ++j) + output[j] = start + j; +} + +double FitPOD::podArraySum(double *a, int n) +{ + double e = a[0]; + for (int i=1; ib) + b = a[i]; + return b; +} + +int FitPOD::podArrayMin(int *a, int n) +{ + int b = a[0]; + for (int i=1; ib) + b = a[i]; + return b; +} + +void FitPOD::podKron(double *C, double *A, double *B, double alpha, int M1, int M2) +{ + int M = M1*M2; + for (int idx=0; idx data_files; + std::vector filenames; + std::string filenametag = "pod"; + + std::vector num_atom; + std::vector num_atom_cumsum; + std::vector num_atom_each_file; + std::vector num_config; + std::vector num_config_cumsum; + int num_atom_sum; + int num_atom_min; + int num_atom_max; + int num_config_sum; + + double *lattice; + double *energy; + double *stress; + double *position; + double *force; + int *atomtype; + + int training = 1; + int normalizeenergy = 1; + int training_analysis = 1; + int test_analysis = 1; + int training_calculation = 0; + int test_calculation = 0; + int randomize = 1; + int precision = 8; + double fraction = 1.0; + + double fitting_weights[12] = {100.0, 1.0, 0.0, 1, 1, 0, 0, 1, 1, 1, 1, 1e-10}; + + void copydatainfo(datastruct &data) const + { + data.data_path = data_path; + data.file_format = file_format; + data.file_extension = file_extension; + data.data_files = data_files; + data.filenametag = filenametag; + data.filenames = filenames; + data.training_analysis = training_analysis; + data.test_analysis = test_analysis; + data.training_calculation = training_calculation; + data.test_calculation = test_calculation; + data.fraction = fraction; + data.randomize = randomize; + data.precision = precision; + data.training = training; + data.normalizeenergy = normalizeenergy; + for (int i = 0; i < 12; i++) data.fitting_weights[i] = fitting_weights[i]; + } + }; + + struct neighborstruct { + int *alist; + int *pairnum; + int *pairnum_cumsum; + int *pairlist; + double *y; + + int natom; + int nalist; + int natom_max; + int sze; + int sza; + int szy; + int szp; + }; + + struct descriptorstruct { + double *gd; // global descriptors + double *gdd; // derivatives of global descriptors and peratom descriptors + double *A; // least-square matrix for all descriptors + double *b; // least-square vector for all descriptors + double *c; // coefficents of descriptors + int *tmpint; + int szd; + int szi; + }; + + datastruct traindata; + datastruct testdata; + descriptorstruct desc; + neighborstruct nb; + class MLPOD *podptr; + + // functions for collecting/collating arrays + + void print_matrix(const char *desc, int m, int n, int *a, int lda); + void print_matrix(const char *desc, int m, int n, double *a, int lda); + void print_matrix(const char *desc, int m, int n, double **a, int lda); + void podCumsum(int *output, int *input, int length); + double podArrayNorm(double *a, int n); + double podArrayErrorNorm(double *a, double *b, int n); + void podArraySetValue(double *y, double a, int n); + void podArrayCopy(double *y, double *x, int n); + void podArrayFill(int *output, int start, int length); + double podArrayMin(double *a, int n); + double podArrayMax(double *a, int n); + double podArraySum(double *a, int n); + int podArrayMin(int *a, int n); + int podArrayMax(int *a, int n); + void podKron(double *C, double *A, double *B, double alpha, int M1, int M2); + void rotation_matrix(double *Rmat, double alpha, double beta, double gamma); + void triclinic_lattice_conversion(double *a, double *b, double *c, double *A, double *B, + double *C); + void matrix33_multiplication(double *xrot, double *Rmat, double *x, int natom); + void matrix33_inverse(double *invA, double *A1, double *A2, double *A3); + + // functions for reading input files and fitting + + int read_data_file(double *fitting_weights, std::string &file_format, std::string &file_extension, + std::string &test_path, std::string &training_path, std::string &filenametag, + const std::string &data_file); + void get_exyz_files(std::vector &, const std::string &, const std::string &); + int get_number_atom_exyz(std::vector &num_atom, int &num_atom_sum, std::string file); + int get_number_atoms(std::vector &num_atom, std::vector &num_atom_sum, + std::vector &num_config, std::vector training_files); + void read_exyz_file(double *lattice, double *stress, double *energy, double *pos, double *forces, + int *atomtype, std::string file, std::vector species); + void get_data(datastruct &data, const std::vector& species); + std::vector linspace(int start_in, int end_in, int num_in); + std::vector shuffle(int start_in, int end_in, int num_in); + std::vector select(int n, double fraction, int randomize); + void select_data(datastruct &newdata, const datastruct &data); + void read_data_files(const std::string& data_file, const std::vector& species); + int latticecoords(double *y, int *alist, double *x, double *a1, double *a2, double *a3, + double rcut, int *pbc, int nx); + int podneighborlist(int *neighlist, int *numneigh, double *r, double rcutsq, int nx, int N, + int dim); + int podfullneighborlist(double *y, int *alist, int *neighlist, int *numneigh, int *numneighsum, + double *x, double *a1, double *a2, double *a3, double rcut, int *pbc, + int nx); + void allocate_memory(const datastruct &data); + void linear_descriptors(const datastruct &data, int ci); + void quadratic_descriptors(const datastruct &data, int ci); + void cubic_descriptors(const datastruct &data, int ci); + void least_squares_matrix(const datastruct &data, int ci); + void least_squares_fit(const datastruct &data); + void print_analysis(const datastruct &data, double *outarray, double *errors); + void error_analysis(const datastruct &data, double *coeff); + double energyforce_calculation(double *force, double *coeff, const datastruct &data, int ci); + void energyforce_calculation(const datastruct &data, double *coeff); +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/ML-POD/mlpod.cpp b/src/ML-POD/mlpod.cpp new file mode 100644 index 0000000000..ef729e3ce6 --- /dev/null +++ b/src/ML-POD/mlpod.cpp @@ -0,0 +1,3698 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + 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 authors: Ngoc Cuong Nguyen (MIT) and Andrew Rohskopf (SNL) +------------------------------------------------------------------------- */ + +// POD header file + +#include "mlpod.h" + +// LAMMPS header files + +#include "comm.h" +#include "error.h" +#include "math_const.h" +#include "math_special.h" +#include "memory.h" +#include "tokenizer.h" + +#include + +using namespace LAMMPS_NS; +using MathConst::MY_PI; +using MathSpecial::cube; +using MathSpecial::powint; + +#define MAXLINE 1024 + +MLPOD::podstruct::podstruct() : + twobody{5, 10, 10}, threebody{4, 8, 8, 5}, fourbody{0, 0, 0, 0}, pbc(nullptr), + elemindex(nullptr), quadratic22{0, 0}, quadratic23{0, 0}, quadratic24{0, 0}, quadratic33{0, 0}, + quadratic34{0, 0}, quadratic44{0, 0}, cubic234{0, 0, 0}, cubic333{0, 0, 0}, cubic444{0, 0, 0}, + besselparams(nullptr), coeff(nullptr), Phi2(nullptr), Phi3(nullptr), Phi4(nullptr), + Lambda2(nullptr), Lambda3(nullptr), Lambda4(nullptr) +{ +} + +MLPOD::podstruct::~podstruct() +{ + delete[] pbc; + delete[] elemindex; + delete[] besselparams; +} + +MLPOD::MLPOD(LAMMPS *_lmp, const std::string &pod_file, const std::string &coeff_file) : + Pointers(_lmp) +{ + // read pod input file to podstruct + + read_pod(pod_file); + + // read pod coefficient file to podstruct + + if (coeff_file != "") read_coeff_file(coeff_file); + + if (pod.snaptwojmax > 0) InitSnap(); +} + +MLPOD::~MLPOD() +{ + // deallocate pod arrays + + memory->destroy(pod.coeff); + if (pod.ns2 > 0) { + memory->destroy(pod.Phi2); + memory->destroy(pod.Lambda2); + } + if (pod.ns3 > 0) { + memory->destroy(pod.Phi3); + memory->destroy(pod.Lambda3); + } + if (pod.ns4 > 0) { + memory->destroy(pod.Phi4); + memory->destroy(pod.Lambda4); + } + + // deallocate snap arrays if used + + if (pod.snaptwojmax > 0) { + memory->destroy(sna.map); + memory->destroy(sna.idx_max); + memory->destroy(sna.idxz); + memory->destroy(sna.idxb); + memory->destroy(sna.idxb_block); + memory->destroy(sna.idxu_block); + memory->destroy(sna.idxz_block); + memory->destroy(sna.idxcg_block); + memory->destroy(sna.rootpqarray); + memory->destroy(sna.cglist); + memory->destroy(sna.fac); + memory->destroy(sna.bzero); + memory->destroy(sna.wjelem); + memory->destroy(sna.radelem); + memory->destroy(sna.rcutsq); + } +} + +// clang-format off + +void MLPOD::podMatMul(double *c, double *a, double *b, int r1, int c1, int c2) +{ + int i, j, k; + + for(j = 0; j < c2; j++) + for(i = 0; i < r1; i++) + c[i + r1*j] = 0.0; + + for(j = 0; j < c2; j++) + for(i = 0; i < r1; i++) + for(k = 0; k < c1; k++) + c[i + r1*j] += a[i + r1*k] * b[k + c1*j]; +} + +void MLPOD::podArrayFill(int* output, int start, int length) +{ + for (int j = 0; j < length; ++j) + output[j] = start + j; +} + +void MLPOD::podArraySetValue(double *y, double a, int n) +{ + for (int i=0; icreate(xij, N, "pod:xij"); + memory->create(S, N*ns, "pod:S"); + memory->create(Q, N*ns, "pod:Q"); + memory->create(A, ns*ns, "pod:A"); + memory->create(b, ns, "pod:ns"); + + for (int i=0; i= max(1,3*N-1) + int info = 1; // = 0: successful exit + std::vector work(lwork); + DSYEV(&chv, &chu, &ns, A, &ns, b, work.data(), &lwork, &info); + + // order eigenvalues and eigenvectors from largest to smallest + + for (int j=0; jdestroy(xij); + memory->destroy(S); + memory->destroy(A); + memory->destroy(b); + memory->destroy(Q); +} + +void MLPOD::read_pod(const std::string &pod_file) +{ + pod.nbesselpars = 3; + delete[] pod.besselparams; + pod.besselparams = new double[3]; + delete[] pod.pbc; + pod.pbc = new int[3]; + + pod.besselparams[0] = 0.0; + pod.besselparams[1] = 2.0; + pod.besselparams[2] = 4.0; + + pod.nelements = 0; + pod.onebody = 1; + pod.besseldegree = 3; + pod.inversedegree = 6; + pod.quadraticpod = 0; + pod.rin = 0.5; + pod.rcut = 4.6; + + pod.snaptwojmax = 0; + pod.snapchemflag = 0; + pod.snaprfac0 = 0.99363; + + sna.twojmax = 0; + sna.ntypes = 0; + + std::string podfilename = pod_file; + FILE *fppod; + if (comm->me == 0) { + + fppod = utils::open_potential(podfilename,lmp,nullptr); + if (fppod == nullptr) + error->one(FLERR,"Cannot open POD coefficient file {}: ", + podfilename, utils::getsyserror()); + } + + // loop through lines of POD file and parse keywords + + char line[MAXLINE],*ptr; + int eof = 0; + while (true) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fppod); + if (ptr == nullptr) { + eof = 1; + fclose(fppod); + } + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + + // words = ptrs to all words in line + // strip single and double quotes from words + + std::vector words; + try { + words = Tokenizer(utils::trim_comment(line),"\"' \t\n\r\f").as_vector(); + } catch (TokenizerException &) { + // ignore + } + + if (words.size() == 0) continue; + + auto keywd = words[0]; + + if (keywd == "species") { + pod.nelements = words.size()-1; + for (int ielem = 1; ielem <= pod.nelements; ielem++) { + pod.species.push_back(words[ielem]); + } + } + + if (keywd == "pbc") { + if (words.size() != 4) + error->one(FLERR,"Improper POD file.", utils::getsyserror()); + pod.pbc[0] = utils::inumeric(FLERR,words[1],false,lmp); + pod.pbc[1] = utils::inumeric(FLERR,words[2],false,lmp); + pod.pbc[2] = utils::inumeric(FLERR,words[3],false,lmp); + } + + if ((keywd != "#") && (keywd != "species") && (keywd != "pbc")) { + + if (words.size() != 2) + error->one(FLERR,"Improper POD file.", utils::getsyserror()); + + if (keywd == "rin") pod.rin = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "rcut") pod.rcut = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "bessel_scaling_parameter1") + pod.besselparams[0] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "bessel_scaling_parameter2") + pod.besselparams[1] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "bessel_scaling_parameter3") + pod.besselparams[2] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "bessel_polynomial_degree") + pod.besseldegree = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "inverse_polynomial_degree") + pod.inversedegree = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "onebody") pod.onebody = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "twobody_bessel_polynomial_degree") + pod.twobody[0] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "twobody_inverse_polynomial_degree") + pod.twobody[1] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "twobody_number_radial_basis_functions") + pod.twobody[2] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "threebody_bessel_polynomial_degree") + pod.threebody[0] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "threebody_inverse_polynomial_degree") + pod.threebody[1] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "threebody_number_radial_basis_functions") + pod.threebody[2] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "threebody_number_angular_basis_functions") + pod.threebody[3] = utils::inumeric(FLERR,words[1],false,lmp)-1; + if (keywd == "fourbody_bessel_polynomial_degree") + pod.fourbody[0] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "fourbody_inverse_polynomial_degree") + pod.fourbody[1] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "fourbody_number_radial_basis_functions") + pod.fourbody[2] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "fourbody_snap_twojmax") + pod.snaptwojmax = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "fourbody_snap_chemflag") + pod.snapchemflag = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "fourbody_snap_rfac0") + pod.snaprfac0 = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "fourbody_snap_neighbor_weight1") + pod.snapelementweight[0] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "fourbody_snap_neighbor_weight2") + pod.snapelementweight[1] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "fourbody_snap_neighbor_weight3") + pod.snapelementweight[2] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "fourbody_snap_neighbor_weight4") + pod.snapelementweight[3] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "fourbody_snap_neighbor_weight5") + pod.snapelementweight[4] = utils::numeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic_pod_potential") + pod.quadraticpod = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic22_number_twobody_basis_functions") + pod.quadratic22[0] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic22_number_twobody_basis_functions") + pod.quadratic22[1] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic23_number_twobody_basis_functions") + pod.quadratic23[0] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic23_number_threebody_basis_functions") + pod.quadratic23[1] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic24_number_twobody_basis_functions") + pod.quadratic24[0] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic24_number_fourbody_basis_functions") + pod.quadratic24[1] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic33_number_threebody_basis_functions") + pod.quadratic33[0] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic33_number_threebody_basis_functions") + pod.quadratic33[1] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic34_number_threebody_basis_functions") + pod.quadratic34[0] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic34_number_fourbody_basis_functions") + pod.quadratic34[1] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic44_number_fourbody_basis_functions") + pod.quadratic44[0] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "quadratic44_number_fourbody_basis_functions") + pod.quadratic44[1] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "cubic234_number_twobody_basis_functions") + pod.cubic234[0] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "cubic234_number_threebody_basis_functions") + pod.cubic234[1] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "cubic234_number_fourbody_basis_functions") + pod.cubic234[2] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "cubic333_number_threebody_basis_functions") + pod.cubic333[0] = utils::inumeric(FLERR,words[1],false,lmp); + if (keywd == "cubic444_number_fourbody_basis_functions") + pod.cubic444[0] = utils::inumeric(FLERR,words[1],false,lmp); + } + } + + pod.twobody[0] = pod.besseldegree; + pod.twobody[1] = pod.inversedegree; + pod.threebody[0] = pod.besseldegree; + pod.threebody[1] = pod.inversedegree; + + // number of snapshots + + pod.ns2 = pod.nbesselpars*pod.twobody[0] + pod.twobody[1]; + pod.ns3 = pod.nbesselpars*pod.threebody[0] + pod.threebody[1]; + pod.ns4 = pod.nbesselpars*pod.fourbody[0] + pod.fourbody[1]; + + for (int i = 0; i < pod.nbesselpars; i++) + if (fabs(pod.besselparams[i]) < 1e-3) pod.besselparams[i] = 1e-3; + + // allocate memory for eigenvectors and eigenvalues + + if (pod.ns2 > 0) { + memory->create(pod.Phi2, pod.ns2*pod.ns2, "pod:pod_Phi2"); + memory->create(pod.Lambda2, pod.ns2, "pod:pod_Lambda2"); + } + if (pod.ns3 > 0) { + memory->create(pod.Phi3, pod.ns3*pod.ns3, "pod:pod_Phi3"); + memory->create(pod.Lambda3, pod.ns3, "pod:pod_Lambda3"); + } + if (pod.ns4 > 0) { + memory->create(pod.Phi4, pod.ns4*pod.ns4, "pod:pod_Phi4"); + memory->create(pod.Lambda4, pod.ns4, "pod:pod_Lambda4"); + } + + if (pod.ns2 > 0) { + podeigenvaluedecomposition(pod.Phi2, pod.Lambda2, pod.besselparams, pod.rin, pod.rcut, + pod.twobody[0], pod.twobody[1], pod.nbesselpars, 2000); + +// /* Print eigenvalues */ +// print_matrix( "Eigenvalues for two-body potential:", 1, pod.ns2, pod.Lambda2, 1 ); +// +// /* Print eigenvectors */ +// print_matrix( "Eigenvectors for two-body potential:", pod.ns2, pod.ns2, pod.Phi2, pod.ns2); + } + if (pod.ns3 > 0) { + podeigenvaluedecomposition(pod.Phi3, pod.Lambda3, pod.besselparams, pod.rin, pod.rcut, + pod.threebody[0], pod.threebody[1], pod.nbesselpars, 2000); + } + if (pod.ns4 > 0) { + podeigenvaluedecomposition(pod.Phi4, pod.Lambda4, pod.besselparams, pod.rin, pod.rcut, + pod.fourbody[0], pod.fourbody[1], pod.nbesselpars, 2000); + } + + // number of chemical combinations + + pod.nc2 = pod.nelements*(pod.nelements+1)/2; + pod.nc3 = pod.nelements*pod.nelements*(pod.nelements+1)/2; + pod.nc4 = pod.snapchemflag ? pod.nelements*pod.nelements*pod.nelements*pod.nelements : pod.nelements; + + // number of basis functions and descriptors for one-body potential + + if (pod.onebody==1) { + pod.nbf1 = 1; + pod.nd1 = pod.nelements; + } else { + pod.nbf1 = 0; + pod.nd1 = 0; + } + + // number of basis functions and descriptors for two-body potential + + pod.nbf2 = pod.twobody[2]; + pod.nd2 = pod.nbf2*pod.nc2; + + // number of basis functions and descriptors for three-body potential + + pod.nrbf3 = pod.threebody[2]; + pod.nabf3 = pod.threebody[3]; + pod.nbf3 = pod.nrbf3*(1 + pod.nabf3); + pod.nd3 = pod.nbf3*pod.nc3; + + // number of basis functions and descriptors for four-body potential + + int twojmax = pod.snaptwojmax; + int idxb_count = 0; + if (twojmax > 0) { + for(int j1 = 0; j1 <= twojmax; j1++) + for(int j2 = 0; j2 <= j1; j2++) + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) + if (j >= j1) idxb_count++; + } + pod.nbf4 = idxb_count; + pod.nd4 = pod.nbf4*pod.nc4; + + if (pod.quadraticpod==1) { + pod.quadratic23[0] = pod.nbf2; + pod.quadratic23[1] = pod.nbf3; + } + + pod.quadratic22[0] = MIN(pod.quadratic22[0], pod.nbf2); + pod.quadratic22[1] = MIN(pod.quadratic22[1], pod.nbf2); + pod.quadratic23[0] = MIN(pod.quadratic23[0], pod.nbf2); + pod.quadratic23[1] = MIN(pod.quadratic23[1], pod.nbf3); + pod.quadratic24[0] = MIN(pod.quadratic24[0], pod.nbf2); + pod.quadratic24[1] = MIN(pod.quadratic24[1], pod.nbf4); + pod.quadratic33[0] = MIN(pod.quadratic33[0], pod.nbf3); + pod.quadratic33[1] = MIN(pod.quadratic33[1], pod.nbf3); + pod.quadratic34[0] = MIN(pod.quadratic34[0], pod.nbf3); + pod.quadratic34[1] = MIN(pod.quadratic34[1], pod.nbf4); + pod.quadratic44[0] = MIN(pod.quadratic44[0], pod.nbf4); + pod.quadratic44[1] = MIN(pod.quadratic44[1], pod.nbf4); + + pod.cubic234[0] = MIN(pod.cubic234[0], pod.nbf2); + pod.cubic234[1] = MIN(pod.cubic234[1], pod.nbf3); + pod.cubic234[2] = MIN(pod.cubic234[2], pod.nbf4); + pod.cubic333[0] = MIN(pod.cubic333[0], pod.nbf3); + pod.cubic333[1] = MIN(pod.cubic333[0], pod.nbf3); + pod.cubic333[2] = MIN(pod.cubic333[0], pod.nbf3); + pod.cubic444[0] = MIN(pod.cubic444[0], pod.nbf4); + pod.cubic444[1] = MIN(pod.cubic444[0], pod.nbf4); + pod.cubic444[2] = MIN(pod.cubic444[0], pod.nbf4); + + // number of descriptors for quadratic POD potentials + + pod.nd22 = pod.quadratic22[0]*pod.quadratic22[1]*pod.nc2*pod.nc2; + pod.nd23 = pod.quadratic23[0]*pod.quadratic23[1]*pod.nc2*pod.nc3; + pod.nd24 = pod.quadratic24[0]*pod.quadratic24[1]*pod.nc2*pod.nc4; + pod.nd33 = pod.quadratic33[0]*pod.quadratic33[1]*pod.nc3*pod.nc3; + pod.nd34 = pod.quadratic34[0]*pod.quadratic34[1]*pod.nc3*pod.nc4; + pod.nd44 = pod.quadratic44[0]*pod.quadratic44[1]*pod.nc4*pod.nc4; + + int nq; + nq = pod.quadratic22[0]*pod.nc2; pod.nd22 = nq*(nq+1)/2; + nq = pod.quadratic33[0]*pod.nc3; pod.nd33 = nq*(nq+1)/2; + nq = pod.quadratic44[0]*pod.nc4; pod.nd44 = nq*(nq+1)/2; + + // number of descriptors for cubic POD potentials + + pod.nd234 = pod.cubic234[0]*pod.cubic234[1]*pod.cubic234[2]*pod.nc2*pod.nc3*pod.nc4; + nq = pod.cubic333[0]*pod.nc3; pod.nd333 = nq*(nq+1)*(nq+2)/6; + nq = pod.cubic444[0]*pod.nc4; pod.nd444 = nq*(nq+1)*(nq+2)/6; + + // total number of descriptors for all POD potentials + + pod.nd = pod.nd1 + pod.nd2 + pod.nd3 + pod.nd4 + pod.nd22 + pod.nd23 + pod.nd24 + + pod.nd33 + pod.nd34 + pod.nd44 + pod.nd234 + pod.nd333 + pod.nd444; + pod.nd1234 = pod.nd1 + pod.nd2 + pod.nd3 + pod.nd4; + + int nelements = pod.nelements; + delete[] pod.elemindex; + pod.elemindex = new int[nelements*nelements]; + + int k = 1; + for (int i=0; i < nelements; i++) { + for (int j=i; j < nelements; j++) { + pod.elemindex[i + nelements*j] = k; + pod.elemindex[j + nelements*i] = k; + k += 1; + } + } + + if (comm->me == 0) { + utils::logmesg(lmp, "**************** Begin of POD Potentials ****************\n"); + utils::logmesg(lmp, "species: "); + for (int i=0; ime == 0) { + + fpcoeff = utils::open_potential(coefffilename,lmp,nullptr); + if (fpcoeff == nullptr) + error->one(FLERR,"Cannot open POD coefficient file {}: ", + coefffilename, utils::getsyserror()); + } + + // check format for first line of file + + char line[MAXLINE],*ptr; + int eof = 0; + int nwords = 0; + while (nwords == 0) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fpcoeff); + if (ptr == nullptr) { + eof = 1; + fclose(fpcoeff); + } + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + + // strip comment, skip line if blank + + nwords = utils::count_words(utils::trim_comment(line)); + } + + if (nwords != 2) + error->all(FLERR,"Incorrect format in POD coefficient file"); + + // strip single and double quotes from words + + int ncoeffall; + std::string tmp_str; + try { + ValueTokenizer words(utils::trim_comment(line),"\"' \t\n\r\f"); + tmp_str = words.next_string(); + ncoeffall = words.next_int(); + } catch (TokenizerException &e) { + error->all(FLERR,"Incorrect format in POD coefficient file: {}", e.what()); + } + + // loop over single block of coefficients and insert values in pod.coeff + + memory->create(pod.coeff, ncoeffall, "pod:pod_coeff"); + + for (int icoeff = 0; icoeff < ncoeffall; icoeff++) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fpcoeff); + if (ptr == nullptr) { + eof = 1; + fclose(fpcoeff); + } + } + + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) + error->all(FLERR,"Incorrect format in POD coefficient file"); + MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world); + + try { + ValueTokenizer coeff(utils::trim_comment(line)); + if (coeff.count() != 1) + error->all(FLERR,"Incorrect format in POD coefficient file"); + + pod.coeff[icoeff] = coeff.next_double(); + } catch (TokenizerException &e) { + error->all(FLERR,"Incorrect format in POD coefficient file: {}", e.what()); + } + } + if (comm->me == 0) { + if (!eof) fclose(fpcoeff); + } +} + +/*********************************************************************************************************/ + +void MLPOD::linear_descriptors(double *gd, double *efatom, double *y, double *tmpmem, + int *atomtype, int *alist, int *pairlist, int * /*pairnum*/, + int *pairnumsum, int *tmpint, int natom, int Nij) +{ + int dim = 3; + int nelements = pod.nelements; + int nbesselpars = pod.nbesselpars; + int nrbf2 = pod.nbf2; + int nabf3 = pod.nabf3; + int nrbf3 = pod.nrbf3; + int nd1 = pod.nd1; + int nd2 = pod.nd2; + int nd3 = pod.nd3; + int nd4 = pod.nd4; + int nd1234 = nd1+nd2+nd3+nd4; + int *pdegree2 = pod.twobody; + int *elemindex = pod.elemindex; + double rin = pod.rin; + double rcut = pod.rcut; + double *Phi2 = pod.Phi2; + double *besselparams = pod.besselparams; + + double *fatom1 = &efatom[0]; + double *fatom2 = &efatom[dim*natom*(nd1)]; + double *fatom3 = &efatom[dim*natom*(nd1+nd2)]; + double *fatom4 = &efatom[dim*natom*(nd1+nd2+nd3)]; + double *eatom1 = &efatom[dim*natom*(nd1+nd2+nd3+nd4)]; + double *eatom2 = &efatom[dim*natom*(nd1+nd2+nd3+nd4)+natom*nd1]; + double *eatom3 = &efatom[dim*natom*(nd1+nd2+nd3+nd4)+natom*(nd1+nd2)]; + double *eatom4 = &efatom[dim*natom*(nd1+nd2+nd3+nd4)+natom*(nd1+nd2+nd3)]; + + podArraySetValue(fatom1, 0.0, (1+dim)*natom*(nd1+nd2+nd3+nd4)); + + double *rij = &tmpmem[0]; // 3*Nij + int *ai = &tmpint[0]; // Nij + int *aj = &tmpint[Nij]; // Nij + int *ti = &tmpint[2*Nij]; // Nij + int *tj = &tmpint[3*Nij]; // Nij + podNeighPairs(rij, y, ai, aj, ti, tj, pairlist, pairnumsum, atomtype, + alist, natom, dim); + + // peratom descriptors for one-body, two-body, and three-body linear potentials + + poddesc(eatom1, fatom1, eatom2, fatom2, eatom3, fatom3, rij, Phi2, besselparams, + &tmpmem[3*Nij], rin, rcut, pairnumsum, atomtype, ai, aj, ti, tj, elemindex, pdegree2, + nbesselpars, nrbf2, nrbf3, nabf3, nelements, Nij, natom); + + if (pod.snaptwojmax > 0) + snapdesc(eatom4, fatom4, rij, &tmpmem[3*Nij], atomtype, ai, aj, ti, tj, natom, Nij); + + // global descriptors for one-body, two-body, three-body, and four-bodt linear potentials + + podArraySetValue(tmpmem, 1.0, natom); + + char cht = 'T'; + double one = 1.0, zero = 0.0; + int inc1 = 1; + DGEMV(&cht, &natom, &nd1234, &one, eatom1, &natom, tmpmem, &inc1, &zero, gd, &inc1); +} + +void MLPOD::quadratic_descriptors(double* d23, double *dd23, double* d2, double *d3, double* dd2, double *dd3, + int M2, int M3, int N) +{ + for (int m3 = 0; m3 0) energy += quadratic_coefficients(c2, d2, coeff22, pod.quadratic22, nc2); + + // calculate energy for quadratic23 potential + + if (nd23 > 0) energy += quadratic_coefficients(c2, c3, d2, d3, coeff23, pod.quadratic23, nc2, nc3); + + // calculate energy for quadratic24 potential + + if (nd24 > 0) energy += quadratic_coefficients(c2, c4, d2, d4, coeff24, pod.quadratic24, nc2, nc4); + + // calculate energy for quadratic33 potential + + if (nd33 > 0) energy += quadratic_coefficients(c3, d3, coeff33, pod.quadratic33, nc3); + + // calculate energy for quadratic34 potential + + if (nd34 > 0) energy += quadratic_coefficients(c3, c4, d3, d4, coeff34, pod.quadratic34, nc3, nc4); + + // calculate energy for quadratic44 potential + + if (nd44 > 0) energy += quadratic_coefficients(c4, d4, coeff44, pod.quadratic44, nc4); + + // calculate energy for cubic234 potential + + if (nd234 > 0) energy += cubic_coefficients(c2, c3, c4, d2, d3, d4, coeff234, pod.cubic234, nc2, nc3, nc4); + + // calculate energy for cubic333 potential + + if (nd333 > 0) energy += cubic_coefficients(c3, d3, coeff333, pod.cubic333, nc3); + + // calculate energy for cubic444 potential + + if (nd444 > 0) energy += cubic_coefficients(c4, d4, coeff444, pod.cubic444, nc4); + + // calculate effective POD coefficients + + for (int i=0; i< nd1234; i++) c1[i] += coeff[i]; + + // calculate force = gdd * c1 + + char chn = 'N'; + double one = 1.0, zero = 0.0; + int inc1 = 1; + DGEMV(&chn, &nforce, &nd1234, &one, gdd, &nforce, c1, &inc1, &zero, force, &inc1); + + return energy; +} + +double MLPOD::energyforce_calculation(double *force, double *gd, double *gdd, double *coeff, double *y, + int *atomtype, int *alist, int *pairlist, int *pairnum, int *pairnumsum, int *tmpint, int natom, int Nij) +{ + int dim = 3; + int nd1234 = pod.nd1+pod.nd2+pod.nd3+pod.nd4; + double *tmpmem = &gdd[dim*natom*nd1234+natom*nd1234]; + + // calculate POD and SNAP descriptors and their derivatives + + linear_descriptors(gd, gdd, y, tmpmem, atomtype, alist, + pairlist, pairnum, pairnumsum, tmpint, natom, Nij); + + // calculate energy and force + + double energy = 0.0; + energy = calculate_energyforce(force, gd, gdd, coeff, &gdd[dim*natom*nd1234], natom); + + return energy; +} + +void MLPOD::podNeighPairs(double *xij, double *x, int *ai, int *aj, int *ti, int *tj, + int *pairlist, int *pairnumsum, int *atomtype, int *alist, int inum, int dim) +{ + for (int ii=0; ii j) + ik = lk + s; + k = aj[ik]; // atom k + typek = tj[ik] - 1; + xik1 = yij[0+dim*ik]; // xk - xi + xik2 = yij[1+dim*ik]; // xk - xi + xik3 = yij[2+dim*ik]; // xk - xi + riksq = xik1*xik1 + xik2*xik2 + xik3*xik3; + rik = sqrt(riksq); + + xdot = xij1*xik1 + xij2*xik2 + xij3*xik3; + costhe = xdot/(rij*rik); + costhe = costhe > 1.0 ? 1.0 : costhe; + costhe = costhe < -1.0 ? -1.0 : costhe; + xdot = costhe*(rij*rik); + + sinthe = sqrt(1.0 - costhe*costhe); + sinthe = sinthe > 1e-12 ? sinthe : 1e-12; + theta = acos(costhe); + dtheta = -1.0/sinthe; + + tm1 = 1.0/(rij*rijsq*rik); + tm2 = 1.0/(rij*riksq*rik); + dct1 = (xik1*rijsq - xij1*xdot)*tm1; + dct2 = (xik2*rijsq - xij2*xdot)*tm1; + dct3 = (xik3*rijsq - xij3*xdot)*tm1; + dct4 = (xij1*riksq - xik1*xdot)*tm2; + dct5 = (xij2*riksq - xik2*xdot)*tm2; + dct6 = (xij3*riksq - xik3*xdot)*tm2; + + for (int p=0; p = j1) idxb_count++; + + int idxb_max = idxb_count; + idx_max[2] = idxb_max; + + idxb_count = 0; + for(int j1 = 0; j1 <= twojmax; j1++) + for(int j2 = 0; j2 <= j1; j2++) + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) + if (j >= j1) { + idxb[idxb_count*3 + 0] = j1; + idxb[idxb_count*3 + 1] = j2; + idxb[idxb_count*3 + 2] = j; + idxb_count++; + } + + idxb_count = 0; + for(int j1 = 0; j1 <= twojmax; j1++) + for(int j2 = 0; j2 <= j1; j2++) + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) { + if (j >= j1) { + idxb_block[j + j2*jdim + j1*jdim*jdim] = idxb_count; + idxb_count++; + } + } + + // index list for zlist + + int idxz_count = 0; + + for(int j1 = 0; j1 <= twojmax; j1++) + for(int j2 = 0; j2 <= j1; j2++) + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) + for (int mb = 0; 2*mb <= j; mb++) + for (int ma = 0; ma <= j; ma++) + idxz_count++; + + int idxz_max = idxz_count; + idx_max[3] = idxz_max; + + idxz_count = 0; + for(int j1 = 0; j1 <= twojmax; j1++) + for(int j2 = 0; j2 <= j1; j2++) + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) { + idxz_block[j + j2*jdim + j1*jdim*jdim] = idxz_count; + + for (int mb = 0; 2*mb <= j; mb++) + for (int ma = 0; ma <= j; ma++) { + + idxz[idxz_count*10 + 0] = j1; + idxz[idxz_count*10 + 1] = j2; + idxz[idxz_count*10 + 2] = j; + idxz[idxz_count*10 + 3] = MAX(0, (2 * ma - j - j2 + j1) / 2); + idxz[idxz_count*10 + 4] = (2 * ma - j - (2 * idxz[idxz_count*10 + 3] - j1) + j2) / 2; + idxz[idxz_count*10 + 5] = MIN(j1, (2 * ma - j + j2 + j1) / 2) - idxz[idxz_count*10 + 3] + 1; + idxz[idxz_count*10 + 6] = MAX(0, (2 * mb - j - j2 + j1) / 2); + idxz[idxz_count*10 + 7] = (2 * mb - j - (2 * idxz[idxz_count*10 + 6] - j1) + j2) / 2; + idxz[idxz_count*10 + 8] = MIN(j1, (2 * mb - j + j2 + j1) / 2) - idxz[idxz_count*10 + 6] + 1; + + const int jju = idxu_block[j] + (j+1)*mb + ma; + idxz[idxz_count*10 + 9] = jju; + + idxz_count++; + } + } +}; + +void snapInitRootpqArray(double *rootpqarray, int twojmax) +{ + int jdim = twojmax + 1; + for (int p = 1; p <= twojmax; p++) + for (int q = 1; q <= twojmax; q++) + rootpqarray[p*jdim + q] = sqrt(((double) p)/q); +}; + +double snapDeltacg(double *factorial, int j1, int j2, int j) +{ + double sfaccg = factorial[(j1 + j2 + j) / 2 + 1]; + return sqrt(factorial[(j1 + j2 - j) / 2] * + factorial[(j1 - j2 + j) / 2] * + factorial[(-j1 + j2 + j) / 2] / sfaccg); +}; + +void snapInitClebschGordan(double *cglist, double *factorial, int twojmax) +{ + double sum,dcg,sfaccg; + int m, aa2, bb2, cc2; + int ifac; + + int idxcg_count = 0; + for(int j1 = 0; j1 <= twojmax; j1++) + for(int j2 = 0; j2 <= j1; j2++) + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) { + for (int m1 = 0; m1 <= j1; m1++) { + aa2 = 2 * m1 - j1; + + for (int m2 = 0; m2 <= j2; m2++) { + + bb2 = 2 * m2 - j2; + m = (aa2 + bb2 + j) / 2; + + if(m < 0 || m > j) { + cglist[idxcg_count] = 0.0; + idxcg_count++; + continue; + } + + sum = 0.0; + + for (int z = MAX(0, MAX(-(j - j2 + aa2) + / 2, -(j - j1 - bb2) / 2)); + z <= MIN((j1 + j2 - j) / 2, + MIN((j1 - aa2) / 2, (j2 + bb2) / 2)); + z++) { + ifac = z % 2 ? -1 : 1; + sum += ifac / + (factorial[z] * + factorial[(j1 + j2 - j) / 2 - z] * + factorial[(j1 - aa2) / 2 - z] * + factorial[(j2 + bb2) / 2 - z] * + factorial[(j - j2 + aa2) / 2 + z] * + factorial[(j - j1 - bb2) / 2 + z]); + } + + cc2 = 2 * m - j; + dcg = snapDeltacg(factorial, j1, j2, j); + sfaccg = sqrt(factorial[(j1 + aa2) / 2] * + factorial[(j1 - aa2) / 2] * + factorial[(j2 + bb2) / 2] * + factorial[(j2 - bb2) / 2] * + factorial[(j + cc2) / 2] * + factorial[(j - cc2) / 2] * + (j + 1)); + + cglist[idxcg_count] = sum * dcg * sfaccg; + idxcg_count++; + } + } + } +} + +void snapInitSna(double *rootpqarray, double *cglist, double *factorial, int *idx_max, int *idxz, + int *idxz_block, int *idxb, int *idxb_block, int *idxu_block, int *idxcg_block, int twojmax) +{ + snapBuildIndexList(idx_max, idxz, idxz_block, idxb, + idxb_block, idxu_block, idxcg_block, twojmax); + + snapInitRootpqArray(rootpqarray, twojmax); + snapInitClebschGordan(cglist, factorial, twojmax); +} + +void MLPOD::snapSetup(int twojmax, int ntypes) +{ + sna.twojmax = twojmax; + sna.ntypes = ntypes; + + int jdim = twojmax + 1; + int jdimpq = twojmax + 2; + + memory->create(sna.map, ntypes+1, "pod:sna_map"); + memory->create(sna.idxcg_block, jdim*jdim*jdim, "pod:sna_idxcg_block"); + memory->create(sna.idxz_block, jdim*jdim*jdim, "pod:sna_idxz_block"); + memory->create(sna.idxb_block, jdim*jdim*jdim, "pod:sna_idxb_block"); + memory->create(sna.idxu_block, jdim, "pod:sna_idxu_block"); + memory->create(sna.idx_max, 5, "pod:sna_idx_max"); + + int idxb_count = 0; + for(int j1 = 0; j1 <= twojmax; j1++) + for(int j2 = 0; j2 <= j1; j2++) + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) + if (j >= j1) idxb_count++; + + int idxz_count = 0; + for(int j1 = 0; j1 <= twojmax; j1++) + for(int j2 = 0; j2 <= j1; j2++) + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) + for (int mb = 0; 2*mb <= j; mb++) + for (int ma = 0; ma <= j; ma++) + idxz_count++; + + int idxcg_count = 0; + for(int j1 = 0; j1 <= twojmax; j1++) + for(int j2 = 0; j2 <= j1; j2++) + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) { + for (int m1 = 0; m1 <= j1; m1++) + for (int m2 = 0; m2 <= j2; m2++) + idxcg_count++; + } + + memory->create(sna.idxz, idxz_count*10, "pod:sna_idxz"); + memory->create(sna.idxb, idxb_count*3, "pod:sna_idxb"); + memory->create(sna.rcutsq, (ntypes+1)*(ntypes+1), "pod:sna_rcutsq"); + memory->create(sna.radelem, ntypes+1, "pod:sna_radelem"); + memory->create(sna.wjelem, ntypes+1, "pod:sna_wjelem"); + memory->create(sna.rootpqarray, jdimpq*jdimpq, "pod:sna_rootpqarray"); + memory->create(sna.cglist, idxcg_count, "pod:sna_cglist"); + memory->create(sna.bzero, jdim, "pod:sna_bzero"); + memory->create(sna.fac, 168, "pod:sna_fac"); + + for (int i=0; i rcutij) { + sfac = 0.0; + dsfac = 0.0; + } + else { + double rcutfac0 = MY_PI / (rcutij - rmin0); + sfac = 0.5 * (cos((r - rmin0) * rcutfac0) + 1.0); + dsfac = -0.5 * sin((r - rmin0) * rcutfac0) * rcutfac0; + } + } + sfac *= wjelem[tj[ij]]; + dsfac *= wjelem[tj[ij]]; + + double r0inv, dr0invdr; + double a_r, a_i, b_r, b_i; + double da_r[3], da_i[3], db_r[3], db_i[3]; + double dz0[3], dr0inv[3]; + double rootpq; + int jdim = twojmax + 1; + + r0inv = 1.0 / sqrt(r * r + z0 * z0); + a_r = r0inv * z0; + a_i = -r0inv * z; + b_r = r0inv * y; + b_i = -r0inv * x; + + dr0invdr = -cube(r0inv) * (r + z0 * dz0dr); + + dr0inv[0] = dr0invdr * ux; + dr0inv[1] = dr0invdr * uy; + dr0inv[2] = dr0invdr * uz; + + dz0[0] = dz0dr * ux; + dz0[1] = dz0dr * uy; + dz0[2] = dz0dr * uz; + + for (int k = 0; k < 3; k++) { + da_r[k] = dz0[k] * r0inv + z0 * dr0inv[k]; + da_i[k] = -z * dr0inv[k]; + } + da_i[2] += -r0inv; + + for (int k = 0; k < 3; k++) { + db_r[k] = y * dr0inv[k]; + db_i[k] = -x * dr0inv[k]; + } + db_i[0] += -r0inv; + db_r[1] += r0inv; + + Sr[ij+0*ijnum] = 1.0; + Si[ij+0*ijnum] = 0.0; + Srx[ij+0*ijnum] = 0.0; + Six[ij+0*ijnum] = 0.0; + Sry[ij+0*ijnum] = 0.0; + Siy[ij+0*ijnum] = 0.0; + Srz[ij+0*ijnum] = 0.0; + Siz[ij+0*ijnum] = 0.0; + for (int j = 1; j <= twojmax; j++) { + int jju = idxu_block[j]; + int jjup = idxu_block[j-1]; + + // fill in left side of matrix layer from previous layer + + for (int mb = 0; 2*mb <= j; mb++) { + Sr[ij+jju*ijnum] = 0.0; + Si[ij+jju*ijnum] = 0.0; + Srx[ij+jju*ijnum] = 0.0; + Six[ij+jju*ijnum] = 0.0; + Sry[ij+jju*ijnum] = 0.0; + Siy[ij+jju*ijnum] = 0.0; + Srz[ij+jju*ijnum] = 0.0; + Siz[ij+jju*ijnum] = 0.0; + for (int ma = 0; ma < j; ma++) { + rootpq = rootpqarray[(j - ma)*jdim + (j - mb)]; + int njju = ij+jju*ijnum; + int njju1 = ij+(jju+1)*ijnum; + int njjup = ij+jjup*ijnum; + double u_r = Sr[njjup]; + double u_i = Si[njjup]; + double ux_r = Srx[njjup]; + double ux_i = Six[njjup]; + double uy_r = Sry[njjup]; + double uy_i = Siy[njjup]; + double uz_r = Srz[njjup]; + double uz_i = Siz[njjup]; + + Sr[njju] += rootpq * (a_r * u_r + a_i * u_i); + Si[njju] += rootpq * (a_r * u_i - a_i * u_r); + Srx[njju] += rootpq * (da_r[0] * u_r + da_i[0] * u_i + a_r * ux_r + a_i * ux_i); + Six[njju] += rootpq * (da_r[0] * u_i - da_i[0] * u_r + a_r * ux_i - a_i * ux_r); + Sry[njju] += rootpq * (da_r[1] * u_r + da_i[1] * u_i + a_r * uy_r + a_i * uy_i); + Siy[njju] += rootpq * (da_r[1] * u_i - da_i[1] * u_r + a_r * uy_i - a_i * uy_r); + Srz[njju] += rootpq * (da_r[2] * u_r + da_i[2] * u_i + a_r * uz_r + a_i * uz_i); + Siz[njju] += rootpq * (da_r[2] * u_i - da_i[2] * u_r + a_r * uz_i - a_i * uz_r); + + rootpq = rootpqarray[(ma + 1)*jdim + (j - mb)]; + Sr[njju1] = -rootpq * (b_r * u_r + b_i * u_i); + Si[njju1] = -rootpq * (b_r * u_i - b_i * u_r); + Srx[njju1] = -rootpq * (db_r[0] * u_r + db_i[0] * u_i + b_r * ux_r + b_i * ux_i); + Six[njju1] = -rootpq * (db_r[0] * u_i - db_i[0] * u_r + b_r * ux_i - b_i * ux_r); + Sry[njju1] = -rootpq * (db_r[1] * u_r + db_i[1] * u_i + b_r * uy_r + b_i * uy_i); + Siy[njju1] = -rootpq * (db_r[1] * u_i - db_i[1] * u_r + b_r * uy_i - b_i * uy_r); + Srz[njju1] = -rootpq * (db_r[2] * u_r + db_i[2] * u_i + b_r * uz_r + b_i * uz_i); + Siz[njju1] = -rootpq * (db_r[2] * u_i - db_i[2] * u_r + b_r * uz_i - b_i * uz_r); + jju++; + jjup++; + } + jju++; + } + + jju = idxu_block[j]; + jjup = jju+(j+1)*(j+1)-1; + int mbpar = 1; + for (int mb = 0; 2*mb <= j; mb++) { + int mapar = mbpar; + for (int ma = 0; ma <= j; ma++) { + int njju = ij+jju*ijnum; + int njjup = ij+jjup*ijnum; + if (mapar == 1) { + Sr[njjup] = Sr[njju]; + Si[njjup] = -Si[njju]; + if (j%2==1 && mb==(j/2)) { + Srx[njjup] = Srx[njju]; + Six[njjup] = -Six[njju]; + Sry[njjup] = Sry[njju]; + Siy[njjup] = -Siy[njju]; + Srz[njjup] = Srz[njju]; + Siz[njjup] = -Siz[njju]; + } + } else { + Sr[njjup] = -Sr[njju]; + Si[njjup] = Si[njju]; + if (j%2==1 && mb==(j/2)) { + Srx[njjup] = -Srx[njju]; + Six[njjup] = Six[njju]; + Sry[njjup] = -Sry[njju]; + Siy[njjup] = Siy[njju]; + Srz[njjup] = -Srz[njju]; + Siz[njjup] = Siz[njju]; + } + } + mapar = -mapar; + jju++; + jjup--; + } + mbpar = -mbpar; + } + } + + for (int j = 0; j <= twojmax; j++) { + int jju = idxu_block[j]; + for (int mb = 0; 2*mb <= j; mb++) + for (int ma = 0; ma <= j; ma++) { + int ijk = ij+jju*ijnum; + Srx[ijk] = dsfac * Sr[ijk] * ux + sfac * Srx[ijk]; + Six[ijk] = dsfac * Si[ijk] * ux + sfac * Six[ijk]; + Sry[ijk] = dsfac * Sr[ijk] * uy + sfac * Sry[ijk]; + Siy[ijk] = dsfac * Si[ijk] * uy + sfac * Siy[ijk]; + Srz[ijk] = dsfac * Sr[ijk] * uz + sfac * Srz[ijk]; + Siz[ijk] = dsfac * Si[ijk] * uz + sfac * Siz[ijk]; + jju++; + } + } + + for (int k=0; k 1e-20) { + rij[ninside*3 + 0] = delx; + rij[ninside*3 + 1] = dely; + rij[ninside*3 + 2] = delz; + idxi[ninside] = ii; + ai[ninside] = gi; + aj[ninside] = gj; + ti[ninside] = itype; + tj[ninside] = atomtype[gj]; + ninside++; + pairnumsum[ii+1] += 1; + } + } + } + + pairnumsum[0] = 0; + for (int ii=0; ii j) + ik = lk + s; + typek = tj[ik] - 1; + xik1 = yij[0+dim*ik]; // xk - xi + xik2 = yij[1+dim*ik]; // xk - xi + xik3 = yij[2+dim*ik]; // xk - xi s + riksq = xik1*xik1 + xik2*xik2 + xik3*xik3; + rik = sqrt(riksq); + + xdot = xij1*xik1 + xij2*xik2 + xij3*xik3; + costhe = xdot/(rij*rik); + costhe = costhe > 1.0 ? 1.0 : costhe; + costhe = costhe < -1.0 ? -1.0 : costhe; + theta = acos(costhe); + + for (int p=0; p rcutij) { + sfac = 0.0; + } + else { + double rcutfac0 = MY_PI / (rcutij - rmin0); + sfac = 0.5 * (cos((r - rmin0) * rcutfac0) + 1.0); + } + } + sfac *= wjelem[tj[ij]]; + + double r0inv; + double a_r, a_i, b_r, b_i; + double rootpq; + int jdim = twojmax + 1; + + r0inv = 1.0 / sqrt(r * r + z0 * z0); + a_r = r0inv * z0; + a_i = -r0inv * z; + b_r = r0inv * y; + b_i = -r0inv * x; + + Sr[ij+0*ijnum] = 1.0; + Si[ij+0*ijnum] = 0.0; + for (int j = 1; j <= twojmax; j++) { + int jju = idxu_block[j]; + int jjup = idxu_block[j-1]; + + // fill in left side of matrix layer from previous layer + + for (int mb = 0; 2*mb <= j; mb++) { + Sr[ij+jju*ijnum] = 0.0; + Si[ij+jju*ijnum] = 0.0; + for (int ma = 0; ma < j; ma++) { + rootpq = rootpqarray[(j - ma)*jdim + (j - mb)]; + int njju = ij+jju*ijnum; + int njju1 = ij+(jju+1)*ijnum; + int njjup = ij+jjup*ijnum; + double u_r = Sr[njjup]; + double u_i = Si[njjup]; + + Sr[njju] += rootpq * (a_r * u_r + a_i * u_i); + Si[njju] += rootpq * (a_r * u_i - a_i * u_r); + + rootpq = rootpqarray[(ma + 1)*jdim + (j - mb)]; + Sr[njju1] = -rootpq * (b_r * u_r + b_i * u_i); + Si[njju1] = -rootpq * (b_r * u_i - b_i * u_r); + jju++; + jjup++; + } + jju++; + } + + jju = idxu_block[j]; + jjup = jju+(j+1)*(j+1)-1; + int mbpar = 1; + for (int mb = 0; 2*mb <= j; mb++) { + int mapar = mbpar; + for (int ma = 0; ma <= j; ma++) { + int njju = ij+jju*ijnum; + int njjup = ij+jjup*ijnum; + if (mapar == 1) { + Sr[njjup] = Sr[njju]; + Si[njjup] = -Si[njju]; + } else { + Sr[njjup] = -Sr[njju]; + Si[njjup] = Si[njju]; + } + mapar = -mapar; + jju++; + jjup--; + } + mbpar = -mbpar; + } + } + + for (int k=0; k 0) + snapdesc_ij(eatom4, rij, tmpmem, atomtype, idxi, ti, tj, natom, Nij); + + // global descriptors for one-body, two-body, three-body, and four-bodt linear potentials + + podArraySetValue(tmpmem, 1.0, natom); + + char cht = 'T'; + double one = 1.0; + int inc1 = 1; + DGEMV(&cht, &natom, &nd1234, &one, eatom1, &natom, tmpmem, &inc1, &one, gd, &inc1); +} + +double MLPOD::calculate_energy(double *effectivecoeff, double *gd, double *coeff) +{ + int nd1 = pod.nd1; + int nd2 = pod.nd2; + int nd3 = pod.nd3; + int nd4 = pod.nd4; + int nd1234 = nd1+nd2+nd3+nd4; + int nd22 = pod.nd22; + int nd23 = pod.nd23; + int nd24 = pod.nd24; + int nd33 = pod.nd33; + int nd34 = pod.nd34; + int nd44 = pod.nd44; + int nd234 = pod.nd234; + int nd333 = pod.nd333; + int nd444 = pod.nd444; + int nc2 = pod.nc2; + int nc3 = pod.nc3; + int nc4 = pod.nc4; + + // two-body, three-body, and four-body descriptors + + double *d2 = &gd[nd1]; + double *d3 = &gd[nd1+nd2]; + double *d4 = &gd[nd1+nd2+nd3]; + + // quadratic and cubic POD coefficients + + double *coeff22 = &coeff[nd1234]; + double *coeff23 = &coeff[nd1234+nd22]; + double *coeff24 = &coeff[nd1234+nd22+nd23]; + double *coeff33 = &coeff[nd1234+nd22+nd23+nd24]; + double *coeff34 = &coeff[nd1234+nd22+nd23+nd24+nd33]; + double *coeff44 = &coeff[nd1234+nd22+nd23+nd24+nd33+nd34]; + double *coeff234 = &coeff[nd1234+nd22+nd23+nd24+nd33+nd34+nd44]; + double *coeff333 = &coeff[nd1234+nd22+nd23+nd24+nd33+nd34+nd44+nd234]; + double *coeff444 = &coeff[nd1234+nd22+nd23+nd24+nd33+nd34+nd44+nd234+nd333]; + + // calculate energy for linear potentials + + double energy = 0.0; + for (int i=0; i< nd1234; i++) { + effectivecoeff[i] = 0.0; + energy += coeff[i]*gd[i]; + } + + // effective POD coefficients for calculating force + + double *c2 = &effectivecoeff[nd1]; + double *c3 = &effectivecoeff[nd1+nd2]; + double *c4 = &effectivecoeff[nd1+nd2+nd3]; + + // calculate energy for quadratic22 potential + + if (nd22 > 0) energy += quadratic_coefficients(c2, d2, coeff22, pod.quadratic22, nc2); + + // calculate energy for quadratic23 potential + + if (nd23 > 0) energy += quadratic_coefficients(c2, c3, d2, d3, coeff23, pod.quadratic23, nc2, nc3); + + // calculate energy for quadratic24 potential + + if (nd24 > 0) energy += quadratic_coefficients(c2, c4, d2, d4, coeff24, pod.quadratic24, nc2, nc4); + + // calculate energy for quadratic33 potential + + if (nd33 > 0) energy += quadratic_coefficients(c3, d3, coeff33, pod.quadratic33, nc3); + + // calculate energy for quadratic34 potential + + if (nd34 > 0) energy += quadratic_coefficients(c3, c4, d3, d4, coeff34, pod.quadratic34, nc3, nc4); + + // calculate energy for quadratic44 potential + + if (nd44 > 0) energy += quadratic_coefficients(c4, d4, coeff44, pod.quadratic44, nc4); + + // calculate energy for cubic234 potential + + if (nd234 > 0) energy += cubic_coefficients(c2, c3, c4, d2, d3, d4, coeff234, pod.cubic234, nc2, nc3, nc4); + + // calculate energy for cubic333 potential + + if (nd333 > 0) energy += cubic_coefficients(c3, d3, coeff333, pod.cubic333, nc3); + + // calculate energy for cubic444 potential + + if (nd444 > 0) energy += cubic_coefficients(c4, d4, coeff444, pod.cubic444, nc4); + + // calculate effective POD coefficients + + for (int i=0; i< nd1234; i++) effectivecoeff[i] += coeff[i]; + + return energy; +} + +double MLPOD::calculate_energy(double *energycoeff, double *forcecoeff, double *gd, + double *gdall, double *coeff) +{ + int nd1 = pod.nd1; + int nd2 = pod.nd2; + int nd3 = pod.nd3; + int nd4 = pod.nd4; + int nd1234 = nd1+nd2+nd3+nd4; + int nd22 = pod.nd22; + int nd23 = pod.nd23; + int nd24 = pod.nd24; + int nd33 = pod.nd33; + int nd34 = pod.nd34; + int nd44 = pod.nd44; + int nd234 = pod.nd234; + int nd333 = pod.nd333; + int nd444 = pod.nd444; + int nc2 = pod.nc2; + int nc3 = pod.nc3; + int nc4 = pod.nc4; + + // quadratic and cubic POD coefficients + + double *coeff22 = &coeff[nd1234]; + double *coeff23 = &coeff[nd1234+nd22]; + double *coeff24 = &coeff[nd1234+nd22+nd23]; + double *coeff33 = &coeff[nd1234+nd22+nd23+nd24]; + double *coeff34 = &coeff[nd1234+nd22+nd23+nd24+nd33]; + double *coeff44 = &coeff[nd1234+nd22+nd23+nd24+nd33+nd34]; + double *coeff234 = &coeff[nd1234+nd22+nd23+nd24+nd33+nd34+nd44]; + double *coeff333 = &coeff[nd1234+nd22+nd23+nd24+nd33+nd34+nd44+nd234]; + double *coeff444 = &coeff[nd1234+nd22+nd23+nd24+nd33+nd34+nd44+nd234+nd333]; + + // sum global descriptors over all MPI ranks + + MPI_Allreduce(gd, gdall, nd1234, MPI_DOUBLE, MPI_SUM, world); + + for (int i=0; i< nd1234; i++) { + energycoeff[i] = 0.0; + forcecoeff[i] = 0.0; + } + + // effective POD coefficients for calculating force + + double *c2 = &forcecoeff[nd1]; + double *c3 = &forcecoeff[nd1+nd2]; + double *c4 = &forcecoeff[nd1+nd2+nd3]; + + // effective POD coefficients for calculating energy + + double *ce2 = &energycoeff[nd1]; + double *ce3 = &energycoeff[nd1+nd2]; + double *ce4 = &energycoeff[nd1+nd2+nd3]; + + // two-body, three-body, and four-body descriptors + + double *d2 = &gdall[nd1]; + double *d3 = &gdall[nd1+nd2]; + double *d4 = &gdall[nd1+nd2+nd3]; + + // calculate energy for quadratic22 potential + + if (nd22 > 0) quadratic_coefficients(ce2, c2, d2, coeff22, pod.quadratic22, nc2); + + // calculate energy for quadratic23 potential + + if (nd23 > 0) quadratic_coefficients(ce2, ce3, c2, c3, d2, d3, coeff23, pod.quadratic23, nc2, nc3); + + // calculate energy for quadratic24 potential + + if (nd24 > 0) quadratic_coefficients(ce2, ce4, c2, c4, d2, d4, coeff24, pod.quadratic24, nc2, nc4); + + // calculate energy for quadratic33 potential + + if (nd33 > 0) quadratic_coefficients(ce3, c3, d3, coeff33, pod.quadratic33, nc3); + + // calculate energy for quadratic34 potential + + if (nd34 > 0) quadratic_coefficients(ce3, ce4, c3, c4, d3, d4, coeff34, pod.quadratic34, nc3, nc4); + + // calculate energy for quadratic44 potential + + if (nd44 > 0) quadratic_coefficients(ce4, c4, d4, coeff44, pod.quadratic44, nc4); + + // calculate energy for cubic234 potential + + if (nd234 > 0) cubic_coefficients(ce2, ce3, ce4, c2, c3, c4, d2, d3, d4, coeff234, pod.cubic234, nc2, nc3, nc4); + + // calculate energy for cubic333 potential + + if (nd333 > 0) cubic_coefficients(ce3, c3, d3, coeff333, pod.cubic333, nc3); + + // calculate energy for cubic444 potential + + if (nd444 > 0) cubic_coefficients(ce4, c4, d4, coeff444, pod.cubic444, nc4); + + // calculate effective POD coefficients + + for (int i=0; i< nd1234; i++) { + energycoeff[i] += coeff[i]; + forcecoeff[i] += coeff[i]; + } + + // calculate energy + + double energy = 0.0; + for (int i=0; i< nd1234; i++) + energy += energycoeff[i]*gd[i]; + + return energy; +} + +void MLPOD::pod2body_force(double *force, double *fij, double *coeff2, int *ai, int *aj, int *ti, + int *tj, int *elemindex, int nelements, int nbf, int /*natom*/, int N) +{ + int nelements2 = nelements*(nelements+1)/2; + for (int n=0; n j) + ik = lk + s; + k = aj[ik]; // atom k + typek = tj[ik] - 1; + xik1 = yij[0+dim*ik]; // xk - xi + xik2 = yij[1+dim*ik]; // xk - xi + xik3 = yij[2+dim*ik]; // xk - xi s + riksq = xik1*xik1 + xik2*xik2 + xik3*xik3; + rik = sqrt(riksq); + + xdot = xij1*xik1 + xij2*xik2 + xij3*xik3; + costhe = xdot/(rij*rik); + costhe = costhe > 1.0 ? 1.0 : costhe; + costhe = costhe < -1.0 ? -1.0 : costhe; + xdot = costhe*(rij*rik); + + sinthe = sqrt(1.0 - costhe*costhe); + sinthe = sinthe > 1e-12 ? sinthe : 1e-12; + theta = acos(costhe); + dtheta = -1.0/sinthe; + + tm1 = 1.0/(rij*rijsq*rik); + tm2 = 1.0/(rij*riksq*rik); + dct1 = (xik1*rijsq - xij1*xdot)*tm1; + dct2 = (xik2*rijsq - xij2*xdot)*tm1; + dct3 = (xik3*rijsq - xij3*xdot)*tm1; + dct4 = (xij1*riksq - xik1*xdot)*tm2; + dct5 = (xij2*riksq - xik2*xdot)*tm2; + dct6 = (xij3*riksq - xik3*xdot)*tm2; + + for (int p=0; p 0) + pod4body_force(force, rij, coeff4, tmpmem, atomtype, idxi, ai, aj, ti, tj, natom, Nij); +} + +double MLPOD::energyforce_calculation(double *force, double *podcoeff, double *effectivecoeff, double *gd, double *rij, + double *tmpmem, int *pairnumsum, int *atomtype, int *idxi, int *ai, int *aj, int *ti, int *tj, int natom, int Nij) +{ + int nd1234 = pod.nd1+pod.nd2+pod.nd3+pod.nd4; + double *eatom = &tmpmem[0]; + + podArraySetValue(gd, 0.0, nd1234); + linear_descriptors_ij(gd, eatom, rij, &tmpmem[natom*nd1234], pairnumsum, atomtype, idxi, ti, tj, natom, Nij); + + // Need to do MPI_Allreduce on gd for parallel + + double energy = calculate_energy(effectivecoeff, gd, podcoeff); + + podArraySetValue(force, 0.0, 3*natom); + + calculate_force(force, effectivecoeff, rij, tmpmem, pairnumsum, atomtype, idxi, ai, aj, ti, tj, natom, Nij); + + return energy; +} + + +void MLPOD::pod2body_force(double **force, double *fij, double *coeff2, int *ai, int *aj, int *ti, + int *tj, int *elemindex, int nelements, int nbf, int /*natom*/, int N) +{ + int nelements2 = nelements*(nelements+1)/2; + for (int n=0; n j) + ik = lk + s; + k = aj[ik]; // atom k + typek = tj[ik] - 1; + xik1 = yij[0+dim*ik]; // xk - xi + xik2 = yij[1+dim*ik]; // xk - xi + xik3 = yij[2+dim*ik]; // xk - xi s + riksq = xik1*xik1 + xik2*xik2 + xik3*xik3; + rik = sqrt(riksq); + + xdot = xij1*xik1 + xij2*xik2 + xij3*xik3; + costhe = xdot/(rij*rik); + costhe = costhe > 1.0 ? 1.0 : costhe; + costhe = costhe < -1.0 ? -1.0 : costhe; + xdot = costhe*(rij*rik); + + sinthe = pow(1.0 - costhe*costhe, 0.5); + sinthe = sinthe > 1e-12 ? sinthe : 1e-12; + theta = acos(costhe); + dtheta = -1.0/sinthe; + + tm1 = 1.0/(rij*rijsq*rik); + tm2 = 1.0/(rij*riksq*rik); + dct1 = (xik1*rijsq - xij1*xdot)*tm1; + dct2 = (xik2*rijsq - xij2*xdot)*tm1; + dct3 = (xik3*rijsq - xij3*xdot)*tm1; + dct4 = (xij1*riksq - xik1*xdot)*tm2; + dct5 = (xij2*riksq - xik2*xdot)*tm2; + dct6 = (xij3*riksq - xik3*xdot)*tm2; + + for (int p=0; p 0) + pod4body_force(force, rij, coeff4, tmpmem, atomtype, idxi, ai, aj, ti, tj, natom, Nij); +} diff --git a/src/ML-POD/mlpod.h b/src/ML-POD/mlpod.h new file mode 100644 index 0000000000..54e75988be --- /dev/null +++ b/src/ML-POD/mlpod.h @@ -0,0 +1,308 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_MLPOD_H +#define LMP_MLPOD_H + +#include "pointers.h" + +#define DDOT ddot_ +#define DGEMV dgemv_ +#define DGEMM dgemm_ +#define DGETRF dgetrf_ +#define DGETRI dgetri_ +#define DSYEV dsyev_ +#define DPOSV dposv_ + +extern "C" { +double DDOT(int *, double *, int *, double *, int *); +void DGEMV(char *, int *, int *, double *, double *, int *, double *, int *, double *, double *, + int *); +void DGEMM(char *, char *, int *, int *, int *, double *, double *, int *, double *, int *, + double *, double *, int *); +void DGETRF(int *, int *, double *, int *, int *, int *); +void DGETRI(int *, double *, int *, int *, double *, int *, int *); +void DSYEV(char *, char *, int *, double *, int *, double *, double *, int *, int *); +void DPOSV(char *, int *, int *, double *, int *, double *, int *, int *); +} + +namespace LAMMPS_NS { + +class MLPOD : protected Pointers { + + private: + // functions for reading input files + + void read_pod(const std::string &pod_file); + void read_coeff_file(const std::string &coeff_file); + + // functions for calculating/collating POD descriptors/coefficients for energies + + void podradialbasis(double *rbf, double *drbf, double *xij, double *besselparams, double rin, + double rmax, int besseldegree, int inversedegree, int nbesselpars, int N); + void pod1body(double *eatom, double *fatom, int *atomtype, int nelements, int natom); + void podtally2b(double *eatom, double *fatom, double *eij, double *fij, int *ai, int *aj, int *ti, + int *tj, int *elemindex, int nelements, int nbf, int natom, int N); + void pod3body(double *eatom, double *fatom, double *rij, double *e2ij, double *f2ij, + double *tmpmem, int *elemindex, int *pairnumsum, int *ai, int *aj, int *ti, int *tj, + int nrbf, int nabf, int nelements, int natom, int Nij); + void poddesc(double *eatom1, double *fatom1, double *eatom2, double *fatom2, double *eatom3, + double *fatom3, double *rij, double *Phi, double *besselparams, double *tmpmem, + double rin, double rcut, int *pairnumsum, int *atomtype, int *ai, int *aj, int *ti, + int *tj, int *elemindex, int *pdegree, int nbesselpars, int nrbf2, int nrbf3, + int nabf, int nelements, int Nij, int natom); + double quadratic_coefficients(double *c2, double *c3, double *d2, double *d3, double *coeff23, + int *quadratic, int nc2, int nc3); + double quadratic_coefficients(double *c3, double *d3, double *coeff33, int *quadratic, int nc3); + double cubic_coefficients(double *c2, double *c3, double *c4, double *d2, double *d3, double *d4, + double *coeff234, int *cubic, int nc2, int nc3, int nc4); + double cubic_coefficients(double *c3, double *d3, double *coeff333, int *cubic, int nc3); + double quadratic_coefficients(double *ce2, double *ce3, double *c2, double *c3, double *d2, + double *d3, double *coeff23, int *quadratic, int nc2, int nc3); + double quadratic_coefficients(double *ce3, double *c3, double *d3, double *coeff33, + int *quadratic, int nc3); + double cubic_coefficients(double *ce2, double *ce3, double *ce4, double *c2, double *c3, + double *c4, double *d2, double *d3, double *d4, double *coeff234, + int *cubic, int nc2, int nc3, int nc4); + double cubic_coefficients(double *ce3, double *c3, double *d3, double *coeff333, int *cubic, + int nc3); + + // functions for calculating/collating SNAP descriptors/coefficients for energies + + void snapSetup(int twojmax, int ntypes); + void InitSnap(); + void snapComputeUlist(double *Sr, double *Si, double *dSr, double *dSi, double *rootpqarray, + double *rij, double *wjelem, double *radelem, double rmin0, double rfac0, + double rcutfac, int *idxu_block, int *ti, int *tj, int twojmax, + int idxu_max, int ijnum, int switch_flag); + void snapZeroUarraytot2(double *Stotr, double *Stoti, double wself, int *idxu_block, int *type, + int *map, int *ai, int wselfall_flag, int chemflag, int idxu_max, + int nelements, int twojmax, int inum); + void snapAddUarraytot(double *Stotr, double *Stoti, double *Sr, double *Si, int *map, int *ai, + int *tj, int idxu_max, int inum, int ijnum, int chemflag); + void snapComputeZi2(double *zlist_r, double *zlist_i, double *Stotr, double *Stoti, + double *cglist, int *idxz, int *idxu_block, int *idxcg_block, int twojmax, + int idxu_max, int idxz_max, int nelements, int bnorm_flag, int inum); + void snapComputeBi1(double *blist, double *zlist_r, double *zlist_i, double *Stotr, double *Stoti, + int *idxb, int *idxu_block, int *idxz_block, int twojmax, int idxb_max, + int idxu_max, int idxz_max, int nelements, int inum); + void snapComputeDbidrj(double *dblist, double *zlist_r, double *zlist_i, double *dulist_r, + double *dulist_i, int *idxb, int *idxu_block, int *idxz_block, int *map, + int *ai, int *tj, int twojmax, int idxb_max, int idxu_max, int idxz_max, + int nelements, int bnorm_flag, int chemflag, int inum, int ijnum); + void snapdesc(double *blist, double *bd, double *rij, double *tmpmem, int *atomtype, int *ai, + int *aj, int *ti, int *tj, int natom, int Nij); + + // functions for calculating/collating POD descriptors/coefficients for forces + + void podradialbasis(double *rbf, double *xij, double *besselparams, double rin, double rmax, + int besseldegree, int inversedegree, int nbesselpars, int N); + void pod1body(double *eatom, int *atomtype, int nelements, int natom); + void podtally2b(double *eatom, double *eij, int *ai, int *ti, int *tj, int *elemindex, + int nelements, int nbf, int natom, int N); + void pod3body(double *eatom, double *yij, double *e2ij, double *tmpmem, int *elemindex, + int *pairnumsum, int *ai, int *ti, int *tj, int nrbf, int nabf, int nelements, + int natom, int Nij); + void poddesc_ij(double *eatom1, double *eatom2, double *eatom3, double *rij, double *Phi, + double *besselparams, double *tmpmem, double rin, double rcut, int *pairnumsum, + int *atomtype, int *ai, int *ti, int *tj, int *elemindex, int *pdegree, + int nbesselpars, int nrbf2, int nrbf3, int nabf, int nelements, int Nij, + int natom); + void snapComputeUij(double *Sr, double *Si, double *rootpqarray, double *rij, double *wjelem, + double *radelem, double rmin0, double rfac0, double rcutfac, int *idxu_block, + int *ti, int *tj, int twojmax, int idxu_max, int ijnum, int switch_flag); + void snapdesc_ij(double *blist, double *rij, double *tmpmem, int *atomtype, int *ai, int *ti, + int *tj, int natom, int Nij); + void pod2body_force(double *force, double *fij, double *coeff2, int *ai, int *aj, int *ti, + int *tj, int *elemindex, int nelements, int nbf, int natom, int Nij); + void pod3body_force(double *force, double *yij, double *e2ij, double *f2ij, double *coeff3, + double *tmpmem, int *elemindex, int *pairnumsum, int *ai, int *aj, int *ti, + int *tj, int nrbf, int nabf, int nelements, int natom, int Nij); + void snapTallyForce(double *force, double *dbdr, double *coeff4, int *ai, int *aj, int *ti, + int ijnum, int ncoeff, int ntype); + void pod4body_force(double *force, double *rij, double *coeff4, double *tmpmem, int *atomtype, + int *idxi, int *ai, int *aj, int *ti, int *tj, int natom, int Nij); + void pod2body_force(double **force, double *fij, double *coeff2, int *ai, int *aj, int *ti, + int *tj, int *elemindex, int nelements, int nbf, int natom, int Nij); + void pod3body_force(double **force, double *yij, double *e2ij, double *f2ij, double *coeff3, + double *tmpmem, int *elemindex, int *pairnumsum, int *ai, int *aj, int *ti, + int *tj, int nrbf, int nabf, int nelements, int natom, int Nij); + void snapTallyForce(double **force, double *dbdr, double *coeff4, int *ai, int *aj, int *ti, + int ijnum, int ncoeff, int ntype); + void pod4body_force(double **force, double *rij, double *coeff4, double *tmpmem, int *atomtype, + int *idxi, int *ai, int *aj, int *ti, int *tj, int natom, int Nij); + + // eigenproblem functions + + void podeigenvaluedecomposition(double *Phi, double *Lambda, double *besselparams, double rin, + double rcut, int besseldegree, int inversedegree, int nbesselpars, + int N); + + public: + MLPOD(LAMMPS *, const std::string &pod_file, const std::string &coeff_file); + + MLPOD(LAMMPS *lmp) : Pointers(lmp){}; + ~MLPOD() override; + + struct podstruct { + podstruct(); + virtual ~podstruct(); + + std::vector species; + int twobody[3]; + int threebody[4]; + int fourbody[4]; + int *pbc; + int *elemindex; + + int quadratic22[2]; + int quadratic23[2]; + int quadratic24[2]; + int quadratic33[2]; + int quadratic34[2]; + int quadratic44[2]; + int cubic234[3]; + int cubic333[3]; + int cubic444[3]; + int nelements; + int onebody; + int besseldegree; + int inversedegree; + + int quadraticpod; + + double rin; + double rcut; + double *besselparams; + double *coeff; + double *Phi2, *Phi3, *Phi4, *Lambda2, *Lambda3, *Lambda4; + + // variables declaring number of snapshots, descriptors, and combinations + + int nbesselpars = 3; + int ns2, ns3, + ns4; // number of snapshots for radial basis functions for linear POD potentials + int nc2, nc3, nc4; // number of chemical combinations for linear POD potentials + int nbf1, nbf2, nbf3, nbf4; // number of basis functions for linear POD potentials + int nd1, nd2, nd3, nd4; // number of descriptors for linear POD potentials + int nd22, nd23, nd24, nd33, nd34, nd44; // number of descriptors for quadratic POD potentials + int nd234, nd333, nd444; // number of descriptors for cubic POD potentials + int nrbf3, nabf3, nrbf4, nabf4; + int nd, nd1234; + + int snaptwojmax; // also used to tell if SNAP is used when allocating/deallocating + int snapchemflag; + double snaprfac0; + double snapelementradius[10]; + double snapelementweight[10]; + }; + + struct snastruct { + int twojmax; + int ncoeff; + int idxb_max; + int idxu_max; + int idxz_max; + int idxcg_max; + int ntypes; + int nelements; + int ndoubles; // number of multi-element pairs + int ntriples; // number of multi-element triplets + int bnormflag; + int chemflag; + int switchflag; + int bzeroflag; + int wselfallflag; + + double wself; + double rmin0; + double rfac0; + double rcutfac; + double rcutmax; + + int *map; // map types to [0,nelements) + int *idx_max; + int *idxz; + int *idxz_block; + int *idxb; + int *idxb_block; + int *idxu_block; + int *idxcg_block; + + double *rcutsq; + double *radelem; + double *wjelem; + double *bzero; + double *fac; + double *rootpqarray; + double *cglist; + }; + + podstruct pod; + snastruct sna; + + // functions for collecting/collating arrays + + void podMatMul(double *c, double *a, double *b, int r1, int c1, int c2); + void podArraySetValue(double *y, double a, int n); + void podArrayCopy(double *y, double *x, int n); + void podArrayFill(int *output, int start, int length); + + // functions for calculating energy and force descriptors + + void podNeighPairs(double *xij, double *x, int *ai, int *aj, int *ti, int *tj, int *pairlist, + int *pairnumsum, int *atomtype, int *alist, int inum, int dim); + void linear_descriptors(double *gd, double *efatom, double *y, double *tmpmem, int *atomtype, + int *alist, int *pairlist, int *pairnum, int *pairnumsum, int *tmpint, + int natom, int Nij); + void quadratic_descriptors(double *d23, double *dd23, double *d2, double *d3, double *dd2, + double *dd3, int M2, int M3, int N); + void quadratic_descriptors(double *d33, double *dd33, double *d3, double *dd3, int M3, int N); + void cubic_descriptors(double *d234, double *dd234, double *d2, double *d3, double *d4, + double *dd2, double *dd3, double *dd4, int M2, int M3, int M4, int N); + void cubic_descriptors(double *d333, double *Dd333, double *d3, double *Dd3, int M3, int N); + double calculate_energyforce(double *force, double *gd, double *gdd, double *coeff, double *tmp, + int natom); + double energyforce_calculation(double *f, double *gd, double *gdd, double *coeff, double *y, + int *atomtype, int *alist, int *pairlist, int *pairnum, + int *pairnumsum, int *tmpint, int natom, int Nij); + + // functions for calculating energies and forces + + void podNeighPairs(double *rij, double *x, int *idxi, int *ai, int *aj, int *ti, int *tj, + int *pairnumsum, int *atomtype, int *jlist, int *alist, int inum); + int lammpsNeighPairs(double *rij, double **x, double rcutsq, int *idxi, int *ai, int *aj, int *ti, + int *tj, int *pairnumsum, int *atomtype, int *numneigh, int *ilist, + int **jlist, int inum); + void linear_descriptors_ij(double *gd, double *eatom, double *rij, double *tmpmem, + int *pairnumsum, int *atomtype, int *ai, int *ti, int *tj, int natom, + int Nij); + double calculate_energy(double *effectivecoeff, double *gd, double *coeff); + double calculate_energy(double *energycoeff, double *forcecoeff, double *gd, double *gdall, + double *coeff); + void calculate_force(double *force, double *effectivecoeff, double *rij, double *tmpmem, + int *pairnumsum, int *atomtype, int *idxi, int *ai, int *aj, int *ti, + int *tj, int natom, int Nij); + void calculate_force(double **force, double *effectivecoeff, double *rij, double *tmpmem, + int *pairnumsum, int *atomtype, int *idxi, int *ai, int *aj, int *ti, + int *tj, int natom, int Nij); + double energyforce_calculation(double *force, double *podcoeff, double *effectivecoeff, + double *gd, double *rij, double *tmpmem, int *pairnumsum, + int *atomtype, int *idxi, int *ai, int *aj, int *ti, int *tj, + int natom, int Nij); + +}; + +} // namespace LAMMPS_NS + +#endif diff --git a/src/ML-POD/pair_pod.cpp b/src/ML-POD/pair_pod.cpp new file mode 100644 index 0000000000..d106b11a18 --- /dev/null +++ b/src/ML-POD/pair_pod.cpp @@ -0,0 +1,330 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + 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 authors: Ngoc Cuong Nguyen (MIT) and Andrew Rohskopf (SNL) +------------------------------------------------------------------------- */ + +#include "pair_pod.h" + +#include "mlpod.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairPOD::PairPOD(LAMMPS *lmp) : + Pair(lmp), gd(nullptr), gdall(nullptr), podcoeff(nullptr), newpodcoeff(nullptr), + energycoeff(nullptr), forcecoeff(nullptr), podptr(nullptr), tmpmem(nullptr), typeai(nullptr), + numneighsum(nullptr), rij(nullptr), idxi(nullptr), ai(nullptr), aj(nullptr), ti(nullptr), + tj(nullptr) +{ + single_enable = 0; + restartinfo = 0; + one_coeff = 1; + manybody_flag = 1; + centroidstressflag = CENTROID_NOTAVAIL; + peratom_warn = true; + + dim = 3; + nablockmax = 0; + nij = 0; + nijmax = 0; + szd = 0; +} + +/* ---------------------------------------------------------------------- */ + +PairPOD::~PairPOD() +{ + free_tempmemory(); + memory->destroy(podcoeff); + memory->destroy(newpodcoeff); + memory->destroy(gd); + memory->destroy(gdall); + memory->destroy(energycoeff); + memory->destroy(forcecoeff); + + delete podptr; + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + } +} + +void PairPOD::compute(int eflag, int vflag) +{ + ev_init(eflag, vflag); + + // we must enforce using F dot r, since we have no energy or stress tally calls. + vflag_fdotr = 1; + + if (peratom_warn && (vflag_atom || eflag_atom)) { + peratom_warn = false; + if (comm->me == 0) + error->warning(FLERR, "Pair style pod does not support per-atom energies or stresses"); + } + + double **x = atom->x; + double **f = atom->f; + int **firstneigh = list->firstneigh; + int *numneigh = list->numneigh; + int *type = atom->type; + int *ilist = list->ilist; + int inum = list->inum; + + // initialize global descriptors to zero + + int nd1234 = podptr->pod.nd1234; + podptr->podArraySetValue(gd, 0.0, nd1234); + + for (int ii = 0; ii < inum; ii++) { + int i = ilist[ii]; + int jnum = numneigh[i]; + + // allocate temporary memory + + if (nijmax < jnum) { + nijmax = MAX(nijmax, jnum); + nablockmax = 1; + free_tempmemory(); + estimate_tempmemory(); + allocate_tempmemory(); + } + + // get neighbor pairs for atom i + + lammpsNeighPairs(x, firstneigh, type, map, numneigh, i); + + // compute global POD descriptors for atom i + + podptr->linear_descriptors_ij(gd, tmpmem, rij, &tmpmem[nd1234], numneighsum, typeai, idxi, ti, + tj, 1, nij); + } + + int nd22 = podptr->pod.nd22; + int nd23 = podptr->pod.nd23; + int nd24 = podptr->pod.nd24; + int nd33 = podptr->pod.nd33; + int nd34 = podptr->pod.nd34; + int nd44 = podptr->pod.nd44; + int nd = podptr->pod.nd; + bigint natom = atom->natoms; + + for (int j = nd1234; j < (nd1234 + nd22 + nd23 + nd24 + nd33 + nd34 + nd44); j++) + newpodcoeff[j] = podcoeff[j] / (natom); + + for (int j = (nd1234 + nd22 + nd23 + nd24 + nd33 + nd34 + nd44); j < nd; j++) + newpodcoeff[j] = podcoeff[j] / (natom * natom); + + // compute energy and effective coefficients + eng_vdwl = podptr->calculate_energy(energycoeff, forcecoeff, gd, gdall, newpodcoeff); + + for (int ii = 0; ii < inum; ii++) { + int i = ilist[ii]; + + // get neighbor pairs for atom i + + lammpsNeighPairs(x, firstneigh, type, map, numneigh, i); + + // compute atomic force for atom i + + podptr->calculate_force(f, forcecoeff, rij, tmpmem, numneighsum, typeai, idxi, ai, aj, ti, tj, + 1, nij); + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairPOD::settings(int narg, char ** /* arg */) +{ + if (narg > 0) error->all(FLERR, "Pair style pod accepts no arguments"); +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairPOD::coeff(int narg, char **arg) +{ + const int np1 = atom->ntypes + 1; + memory->destroy(setflag); + memory->destroy(cutsq); + memory->create(setflag, np1, np1, "pair:setflag"); + memory->create(cutsq, np1, np1, "pair:cutsq"); + delete[] map; + map = new int[np1]; + allocated = 1; + + if (narg < 4) utils::missing_cmd_args(FLERR, "pair_coeff", error); + map_element2type(narg - 4, arg + 4); + + std::string pod_file = std::string(arg[2]); // pod input file + std::string coeff_file = std::string(arg[3]); // coefficient input file + + delete podptr; + podptr = new MLPOD(lmp, pod_file, coeff_file); + + if (coeff_file != "") { + memory->destroy(podcoeff); + memory->destroy(newpodcoeff); + memory->destroy(energycoeff); + memory->destroy(forcecoeff); + memory->destroy(gd); + memory->destroy(gdall); + memory->create(podcoeff, podptr->pod.nd, "pair:podcoeff"); + memory->create(newpodcoeff, podptr->pod.nd, "pair:newpodcoeff"); + memory->create(energycoeff, podptr->pod.nd1234, "pair:energycoeff"); + memory->create(forcecoeff, podptr->pod.nd1234, "pair:forcecoeff"); + memory->create(gd, podptr->pod.nd1234, "pair:gd"); + memory->create(gdall, podptr->pod.nd1234, "pair:gdall"); + podptr->podArrayCopy(podcoeff, podptr->pod.coeff, podptr->pod.nd); + podptr->podArrayCopy(newpodcoeff, podptr->pod.coeff, podptr->pod.nd); + } + + for (int ii = 0; ii < np1; ii++) + for (int jj = 0; jj < np1; jj++) cutsq[ii][jj] = podptr->pod.rcut * podptr->pod.rcut; +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairPOD::init_style() +{ + if (force->newton_pair == 0) error->all(FLERR, "Pair style pod requires newton pair on"); + + // need a full neighbor list + + neighbor->add_request(this, NeighConst::REQ_FULL); + + // reset flag to print warning about per-atom energies or stresses + peratom_warn = true; +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairPOD::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set"); + return podptr->pod.rcut; +} + +/* ---------------------------------------------------------------------- + memory usage +------------------------------------------------------------------------- */ + +double PairPOD::memory_usage() +{ + double bytes = Pair::memory_usage(); + return bytes; +} + +void PairPOD::free_tempmemory() +{ + memory->destroy(rij); + memory->destroy(idxi); + memory->destroy(ai); + memory->destroy(aj); + memory->destroy(ti); + memory->destroy(tj); + memory->destroy(numneighsum); + memory->destroy(typeai); + memory->destroy(tmpmem); +} + +void PairPOD::allocate_tempmemory() +{ + memory->create(rij, dim * nijmax, "pair:rij"); + memory->create(idxi, nijmax, "pair:idxi"); + memory->create(ai, nijmax, "pair:ai"); + memory->create(aj, nijmax, "pair:aj"); + memory->create(ti, nijmax, "pair:ti"); + memory->create(tj, nijmax, "pair:tj"); + memory->create(numneighsum, nablockmax + 1, "pair:numneighsum"); + memory->create(typeai, nablockmax, "pair:typeai"); + memory->create(tmpmem, szd, "pair:tmpmem"); +} + +void PairPOD::estimate_tempmemory() +{ + int nrbf2 = podptr->pod.nbf2; + int nabf3 = podptr->pod.nabf3; + int nrbf3 = podptr->pod.nrbf3; + int ns2 = podptr->pod.ns2; + int ns3 = podptr->pod.ns3; + + szd = dim * nijmax + (1 + dim) * nijmax * MAX(nrbf2 + ns2, nrbf3 + ns3) + (nabf3 + 1) * 7; + int szsnap = 0; + if (podptr->sna.twojmax > 0) { + szsnap += nijmax * dim; + szsnap += MAX(2 * podptr->sna.idxu_max * nijmax, + 2 * podptr->sna.idxz_max * podptr->sna.ndoubles * + nablockmax); // (Ur, Ui) and (Zr, Zi) + szsnap += 2 * podptr->sna.idxu_max * dim * nijmax; // dUr, dUi + szsnap += MAX(podptr->sna.idxb_max * podptr->sna.ntriples * dim * nijmax, + 2 * podptr->sna.idxu_max * podptr->sna.nelements * + nablockmax); // dblist and (Utotr, Utoti) + } + + szd = MAX(szsnap, szd); + szd = nablockmax * (podptr->pod.nd1234) + szd; +} + +void PairPOD::lammpsNeighPairs(double **x, int **firstneigh, int *atomtypes, int *map, + int *numneigh, int gi) +{ + + double rcutsq = podptr->pod.rcut * podptr->pod.rcut; + + nij = 0; + int itype = map[atomtypes[gi]] + 1; + int m = numneigh[gi]; + typeai[0] = itype; + for (int l = 0; l < m; l++) { // loop over each atom around atom i + int gj = firstneigh[gi][l]; // atom j + double delx = x[gj][0] - x[gi][0]; // xj - xi + double dely = x[gj][1] - x[gi][1]; // xj - xi + double delz = x[gj][2] - x[gi][2]; // xj - xi + double rsq = delx * delx + dely * dely + delz * delz; + if (rsq < rcutsq && rsq > 1e-20) { + rij[nij * 3 + 0] = delx; + rij[nij * 3 + 1] = dely; + rij[nij * 3 + 2] = delz; + idxi[nij] = 0; + ai[nij] = gi; + aj[nij] = gj; + ti[nij] = itype; + tj[nij] = map[atomtypes[gj]] + 1; + nij++; + } + } + + numneighsum[0] = 0; + numneighsum[1] = nij; +} diff --git a/src/ML-POD/pair_pod.h b/src/ML-POD/pair_pod.h new file mode 100644 index 0000000000..62b6e99f3b --- /dev/null +++ b/src/ML-POD/pair_pod.h @@ -0,0 +1,81 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/ Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + 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(pod,PairPOD); +// clang-format on +#else + +#ifndef LMP_PAIR_POD_H +#define LMP_PAIR_POD_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairPOD : public Pair { + public: + PairPOD(class LAMMPS *); + ~PairPOD() override; + void compute(int, int) override; + + void settings(int, char **) override; + void coeff(int, char **) override; + void init_style() override; + double init_one(int, int) override; + double memory_usage() override; + + int dim; // typically 3 + + double *gd; // global linear descriptors + double *gdall; // global linear descriptors summed over all MPI ranks + double *podcoeff; // POD coefficients + double *newpodcoeff; // normalized POD coefficients + double *energycoeff; // energy coefficients + double *forcecoeff; // force coefficients + + void estimate_tempmemory(); + void free_tempmemory(); + void allocate_tempmemory(); + + void lammpsNeighPairs(double **x, int **firstneigh, int *atomtype, int *map, int *numneigh, + int i); + + protected: + int nablockmax; // maximum number of atoms per computation block + int nij; // number of atom pairs + int nijmax; // maximum number of atom pairs + int szd; // size of tmpmem + + class MLPOD *podptr; + + // temporary arrays for computation blocks + + double *tmpmem; // temporary memory + int *typeai; // types of atoms I only + int *numneighsum; // cumulative sum for an array of numbers of neighbors + double *rij; // (xj - xi) for all pairs (I, J) + int *idxi; // storing linear indices for all pairs (I, J) + int *ai; // IDs of atoms I for all pairs (I, J) + int *aj; // IDs of atoms J for all pairs (I, J) + int *ti; // types of atoms I for all pairs (I, J) + int *tj; // types of atoms J for all pairs (I, J) + + bool peratom_warn; // print warning about missing per-atom energies or stresses +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/ML-QUIP/Install.sh b/src/ML-QUIP/Install.sh index 20174e664a..03f93c14b8 100755 --- a/src/ML-QUIP/Install.sh +++ b/src/ML-QUIP/Install.sh @@ -44,7 +44,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*quip.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*quip.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/quip\/Makefile.lammps\ @@ -58,7 +58,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*quip.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*quip.*$/d' ../Makefile.package.settings fi fi diff --git a/src/ML-QUIP/pair_quip.cpp b/src/ML-QUIP/pair_quip.cpp index f2879af6c4..aae008f1b2 100644 --- a/src/ML-QUIP/pair_quip.cpp +++ b/src/ML-QUIP/pair_quip.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-QUIP/pair_quip.h b/src/ML-QUIP/pair_quip.h index 49a381f5d0..3c0cdabf3b 100644 --- a/src/ML-QUIP/pair_quip.h +++ b/src/ML-QUIP/pair_quip.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-RANN/pair_rann.cpp b/src/ML-RANN/pair_rann.cpp index 8eb95f6dfb..f2948cbb43 100644 --- a/src/ML-RANN/pair_rann.cpp +++ b/src/ML-RANN/pair_rann.cpp @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-RANN/pair_rann.h b/src/ML-RANN/pair_rann.h index bd16187a13..faf628eacb 100644 --- a/src/ML-RANN/pair_rann.h +++ b/src/ML-RANN/pair_rann.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-RANN/rann_activation.h b/src/ML-RANN/rann_activation.h index e35056efa6..b4af460319 100644 --- a/src/ML-RANN/rann_activation.h +++ b/src/ML-RANN/rann_activation.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-RANN/rann_activation_linear.h b/src/ML-RANN/rann_activation_linear.h index 5fd30e086c..24ba1935ed 100644 --- a/src/ML-RANN/rann_activation_linear.h +++ b/src/ML-RANN/rann_activation_linear.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-RANN/rann_activation_sig_i.h b/src/ML-RANN/rann_activation_sig_i.h index 01384b2061..8c4d829db8 100644 --- a/src/ML-RANN/rann_activation_sig_i.h +++ b/src/ML-RANN/rann_activation_sig_i.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-RANN/rann_fingerprint.cpp b/src/ML-RANN/rann_fingerprint.cpp index 1b6e15466c..7f3305216e 100644 --- a/src/ML-RANN/rann_fingerprint.cpp +++ b/src/ML-RANN/rann_fingerprint.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-RANN/rann_fingerprint.h b/src/ML-RANN/rann_fingerprint.h index eb23ea04fb..516a40061c 100644 --- a/src/ML-RANN/rann_fingerprint.h +++ b/src/ML-RANN/rann_fingerprint.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-RANN/rann_fingerprint_bond.cpp b/src/ML-RANN/rann_fingerprint_bond.cpp index 48c73757e7..acc3318ba0 100644 --- a/src/ML-RANN/rann_fingerprint_bond.cpp +++ b/src/ML-RANN/rann_fingerprint_bond.cpp @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-RANN/rann_fingerprint_bond.h b/src/ML-RANN/rann_fingerprint_bond.h index 2d845f4e6f..99c9250b3f 100644 --- a/src/ML-RANN/rann_fingerprint_bond.h +++ b/src/ML-RANN/rann_fingerprint_bond.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-RANN/rann_fingerprint_bondscreened.cpp b/src/ML-RANN/rann_fingerprint_bondscreened.cpp index 6f65ca6454..8dcc2e4389 100644 --- a/src/ML-RANN/rann_fingerprint_bondscreened.cpp +++ b/src/ML-RANN/rann_fingerprint_bondscreened.cpp @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-RANN/rann_fingerprint_bondscreened.h b/src/ML-RANN/rann_fingerprint_bondscreened.h index 104c2b0bb8..d6acb1ebbd 100644 --- a/src/ML-RANN/rann_fingerprint_bondscreened.h +++ b/src/ML-RANN/rann_fingerprint_bondscreened.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-RANN/rann_fingerprint_bondscreenedspin.cpp b/src/ML-RANN/rann_fingerprint_bondscreenedspin.cpp index 1dcf8872d2..cbd3b2a6dc 100644 --- a/src/ML-RANN/rann_fingerprint_bondscreenedspin.cpp +++ b/src/ML-RANN/rann_fingerprint_bondscreenedspin.cpp @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-RANN/rann_fingerprint_bondscreenedspin.h b/src/ML-RANN/rann_fingerprint_bondscreenedspin.h index 227938a668..07735a4639 100644 --- a/src/ML-RANN/rann_fingerprint_bondscreenedspin.h +++ b/src/ML-RANN/rann_fingerprint_bondscreenedspin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-RANN/rann_fingerprint_bondspin.cpp b/src/ML-RANN/rann_fingerprint_bondspin.cpp index 76c4c016ac..1ccdf8ff62 100644 --- a/src/ML-RANN/rann_fingerprint_bondspin.cpp +++ b/src/ML-RANN/rann_fingerprint_bondspin.cpp @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-RANN/rann_fingerprint_bondspin.h b/src/ML-RANN/rann_fingerprint_bondspin.h index daa873a494..28e170bdbe 100644 --- a/src/ML-RANN/rann_fingerprint_bondspin.h +++ b/src/ML-RANN/rann_fingerprint_bondspin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-RANN/rann_fingerprint_radial.cpp b/src/ML-RANN/rann_fingerprint_radial.cpp index f5b381f1f1..e6936c5ee7 100644 --- a/src/ML-RANN/rann_fingerprint_radial.cpp +++ b/src/ML-RANN/rann_fingerprint_radial.cpp @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-RANN/rann_fingerprint_radial.h b/src/ML-RANN/rann_fingerprint_radial.h index c2cdd01c07..296a73681d 100644 --- a/src/ML-RANN/rann_fingerprint_radial.h +++ b/src/ML-RANN/rann_fingerprint_radial.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-RANN/rann_fingerprint_radialscreened.cpp b/src/ML-RANN/rann_fingerprint_radialscreened.cpp index b8af308389..959078dae7 100644 --- a/src/ML-RANN/rann_fingerprint_radialscreened.cpp +++ b/src/ML-RANN/rann_fingerprint_radialscreened.cpp @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-RANN/rann_fingerprint_radialscreened.h b/src/ML-RANN/rann_fingerprint_radialscreened.h index 885b15dee1..fd83540f08 100644 --- a/src/ML-RANN/rann_fingerprint_radialscreened.h +++ b/src/ML-RANN/rann_fingerprint_radialscreened.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-RANN/rann_fingerprint_radialscreenedspin.cpp b/src/ML-RANN/rann_fingerprint_radialscreenedspin.cpp index de28610c8b..97487b3466 100644 --- a/src/ML-RANN/rann_fingerprint_radialscreenedspin.cpp +++ b/src/ML-RANN/rann_fingerprint_radialscreenedspin.cpp @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-RANN/rann_fingerprint_radialscreenedspin.h b/src/ML-RANN/rann_fingerprint_radialscreenedspin.h index 38f6ae5c6d..2ae2a1d1c3 100644 --- a/src/ML-RANN/rann_fingerprint_radialscreenedspin.h +++ b/src/ML-RANN/rann_fingerprint_radialscreenedspin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-RANN/rann_fingerprint_radialspin.cpp b/src/ML-RANN/rann_fingerprint_radialspin.cpp index e7a4ef449e..2e98e5ff3c 100644 --- a/src/ML-RANN/rann_fingerprint_radialspin.cpp +++ b/src/ML-RANN/rann_fingerprint_radialspin.cpp @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-RANN/rann_fingerprint_radialspin.h b/src/ML-RANN/rann_fingerprint_radialspin.h index 778c479481..50b5b0be56 100644 --- a/src/ML-RANN/rann_fingerprint_radialspin.h +++ b/src/ML-RANN/rann_fingerprint_radialspin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-SNAP/compute_grid.cpp b/src/ML-SNAP/compute_grid.cpp index bedd8a04f4..d70344e1fb 100644 --- a/src/ML-SNAP/compute_grid.cpp +++ b/src/ML-SNAP/compute_grid.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -13,14 +13,10 @@ #include "compute_grid.h" -#include "atom.h" #include "comm.h" #include "domain.h" #include "error.h" -#include "force.h" #include "memory.h" -#include "modify.h" -#include "update.h" #include diff --git a/src/ML-SNAP/compute_grid.h b/src/ML-SNAP/compute_grid.h index 84b3bc4e98..a5c2fbea57 100644 --- a/src/ML-SNAP/compute_grid.h +++ b/src/ML-SNAP/compute_grid.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-SNAP/compute_grid_local.cpp b/src/ML-SNAP/compute_grid_local.cpp index 0fa9440a02..36c4d25305 100644 --- a/src/ML-SNAP/compute_grid_local.cpp +++ b/src/ML-SNAP/compute_grid_local.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -13,14 +13,10 @@ #include "compute_grid_local.h" -#include "atom.h" #include "comm.h" #include "domain.h" #include "error.h" -#include "force.h" #include "memory.h" -#include "modify.h" -#include "update.h" #include diff --git a/src/ML-SNAP/compute_grid_local.h b/src/ML-SNAP/compute_grid_local.h index 5bc6f2082a..471488853c 100644 --- a/src/ML-SNAP/compute_grid_local.h +++ b/src/ML-SNAP/compute_grid_local.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-SNAP/compute_sna_atom.cpp b/src/ML-SNAP/compute_sna_atom.cpp index 1d2190d50d..1ff01aaa4d 100644 --- a/src/ML-SNAP/compute_sna_atom.cpp +++ b/src/ML-SNAP/compute_sna_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-SNAP/compute_sna_atom.h b/src/ML-SNAP/compute_sna_atom.h index 059062670f..29a84c8dcf 100644 --- a/src/ML-SNAP/compute_sna_atom.h +++ b/src/ML-SNAP/compute_sna_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-SNAP/compute_sna_grid.cpp b/src/ML-SNAP/compute_sna_grid.cpp index dbce35ae08..2e2f0cbb66 100644 --- a/src/ML-SNAP/compute_sna_grid.cpp +++ b/src/ML-SNAP/compute_sna_grid.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -16,13 +16,11 @@ #include "atom.h" #include "comm.h" #include "error.h" -#include "force.h" #include "memory.h" #include "modify.h" #include "sna.h" #include "update.h" -#include #include using namespace LAMMPS_NS; diff --git a/src/ML-SNAP/compute_sna_grid.h b/src/ML-SNAP/compute_sna_grid.h index 839003dc2e..3a5a373826 100644 --- a/src/ML-SNAP/compute_sna_grid.h +++ b/src/ML-SNAP/compute_sna_grid.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-SNAP/compute_sna_grid_local.cpp b/src/ML-SNAP/compute_sna_grid_local.cpp index 4970584a12..09c989bffb 100644 --- a/src/ML-SNAP/compute_sna_grid_local.cpp +++ b/src/ML-SNAP/compute_sna_grid_local.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -16,13 +16,11 @@ #include "atom.h" #include "comm.h" #include "error.h" -#include "force.h" #include "memory.h" #include "modify.h" #include "sna.h" #include "update.h" -#include #include using namespace LAMMPS_NS; diff --git a/src/ML-SNAP/compute_sna_grid_local.h b/src/ML-SNAP/compute_sna_grid_local.h index 60f93b92b0..0475212e13 100644 --- a/src/ML-SNAP/compute_sna_grid_local.h +++ b/src/ML-SNAP/compute_sna_grid_local.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-SNAP/compute_snad_atom.cpp b/src/ML-SNAP/compute_snad_atom.cpp index 12839629a9..1b4c2f83db 100644 --- a/src/ML-SNAP/compute_snad_atom.cpp +++ b/src/ML-SNAP/compute_snad_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-SNAP/compute_snad_atom.h b/src/ML-SNAP/compute_snad_atom.h index ac27e10769..24a48528b1 100644 --- a/src/ML-SNAP/compute_snad_atom.h +++ b/src/ML-SNAP/compute_snad_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-SNAP/compute_snap.cpp b/src/ML-SNAP/compute_snap.cpp index 11b17ebcb2..788f1d2675 100644 --- a/src/ML-SNAP/compute_snap.cpp +++ b/src/ML-SNAP/compute_snap.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-SNAP/compute_snap.h b/src/ML-SNAP/compute_snap.h index 0a9af58519..2b8b972bbc 100644 --- a/src/ML-SNAP/compute_snap.h +++ b/src/ML-SNAP/compute_snap.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-SNAP/compute_snav_atom.cpp b/src/ML-SNAP/compute_snav_atom.cpp index 949dda8e5c..32c328e481 100644 --- a/src/ML-SNAP/compute_snav_atom.cpp +++ b/src/ML-SNAP/compute_snav_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-SNAP/compute_snav_atom.h b/src/ML-SNAP/compute_snav_atom.h index 2eac0b7b28..b46abadf26 100644 --- a/src/ML-SNAP/compute_snav_atom.h +++ b/src/ML-SNAP/compute_snav_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-SNAP/pair_snap.cpp b/src/ML-SNAP/pair_snap.cpp index 7c6e0a8b5d..7e0d75cde4 100644 --- a/src/ML-SNAP/pair_snap.cpp +++ b/src/ML-SNAP/pair_snap.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-SNAP/pair_snap.h b/src/ML-SNAP/pair_snap.h index 60de13f268..2ac4da881c 100644 --- a/src/ML-SNAP/pair_snap.h +++ b/src/ML-SNAP/pair_snap.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-SNAP/sna.cpp b/src/ML-SNAP/sna.cpp index 123c16e2ac..d9833f5422 100644 --- a/src/ML-SNAP/sna.cpp +++ b/src/ML-SNAP/sna.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ML-SNAP/sna.h b/src/ML-SNAP/sna.h index 0ba749028e..3390bed5a2 100644 --- a/src/ML-SNAP/sna.h +++ b/src/ML-SNAP/sna.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOFFF/angle_class2_p6.cpp b/src/MOFFF/angle_class2_p6.cpp index e72f9f34fc..bfa6a068f5 100644 --- a/src/MOFFF/angle_class2_p6.cpp +++ b/src/MOFFF/angle_class2_p6.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOFFF/angle_class2_p6.h b/src/MOFFF/angle_class2_p6.h index eb1a11e22c..13c164e9be 100644 --- a/src/MOFFF/angle_class2_p6.h +++ b/src/MOFFF/angle_class2_p6.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOFFF/angle_cosine_buck6d.cpp b/src/MOFFF/angle_cosine_buck6d.cpp index 6fc4fbd123..fc2a78eae1 100644 --- a/src/MOFFF/angle_cosine_buck6d.cpp +++ b/src/MOFFF/angle_cosine_buck6d.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOFFF/angle_cosine_buck6d.h b/src/MOFFF/angle_cosine_buck6d.h index 9d14e2d556..4821d4c1c9 100644 --- a/src/MOFFF/angle_cosine_buck6d.h +++ b/src/MOFFF/angle_cosine_buck6d.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOFFF/improper_inversion_harmonic.cpp b/src/MOFFF/improper_inversion_harmonic.cpp index 12494c805a..50ec3b0737 100644 --- a/src/MOFFF/improper_inversion_harmonic.cpp +++ b/src/MOFFF/improper_inversion_harmonic.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOFFF/improper_inversion_harmonic.h b/src/MOFFF/improper_inversion_harmonic.h index e3bf1a0bc5..2ad1bceba1 100644 --- a/src/MOFFF/improper_inversion_harmonic.h +++ b/src/MOFFF/improper_inversion_harmonic.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOFFF/pair_buck6d_coul_gauss_dsf.cpp b/src/MOFFF/pair_buck6d_coul_gauss_dsf.cpp index 6f7d50ebdd..71a6e7facf 100644 --- a/src/MOFFF/pair_buck6d_coul_gauss_dsf.cpp +++ b/src/MOFFF/pair_buck6d_coul_gauss_dsf.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOFFF/pair_buck6d_coul_gauss_dsf.h b/src/MOFFF/pair_buck6d_coul_gauss_dsf.h index bbedaadf2e..70da8db40e 100644 --- a/src/MOFFF/pair_buck6d_coul_gauss_dsf.h +++ b/src/MOFFF/pair_buck6d_coul_gauss_dsf.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOFFF/pair_buck6d_coul_gauss_long.cpp b/src/MOFFF/pair_buck6d_coul_gauss_long.cpp index 946aeb4635..cd4431276e 100644 --- a/src/MOFFF/pair_buck6d_coul_gauss_long.cpp +++ b/src/MOFFF/pair_buck6d_coul_gauss_long.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOFFF/pair_buck6d_coul_gauss_long.h b/src/MOFFF/pair_buck6d_coul_gauss_long.h index 621269b862..d861649550 100644 --- a/src/MOFFF/pair_buck6d_coul_gauss_long.h +++ b/src/MOFFF/pair_buck6d_coul_gauss_long.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/angle_charmm.cpp b/src/MOLECULE/angle_charmm.cpp index 5690c1738b..1b66260c55 100644 --- a/src/MOLECULE/angle_charmm.cpp +++ b/src/MOLECULE/angle_charmm.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/angle_charmm.h b/src/MOLECULE/angle_charmm.h index dcfcbd001a..2a77ac7864 100644 --- a/src/MOLECULE/angle_charmm.h +++ b/src/MOLECULE/angle_charmm.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/angle_cosine.cpp b/src/MOLECULE/angle_cosine.cpp index 7ef81ef808..86d67f94aa 100644 --- a/src/MOLECULE/angle_cosine.cpp +++ b/src/MOLECULE/angle_cosine.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -23,6 +23,7 @@ #include "neighbor.h" #include +#include using namespace LAMMPS_NS; using MathConst::MY_PI; diff --git a/src/MOLECULE/angle_cosine.h b/src/MOLECULE/angle_cosine.h index cbfbf47e91..7c493dadb2 100644 --- a/src/MOLECULE/angle_cosine.h +++ b/src/MOLECULE/angle_cosine.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/angle_cosine_squared.cpp b/src/MOLECULE/angle_cosine_squared.cpp index 39238463df..c6a9f50e66 100644 --- a/src/MOLECULE/angle_cosine_squared.cpp +++ b/src/MOLECULE/angle_cosine_squared.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/angle_cosine_squared.h b/src/MOLECULE/angle_cosine_squared.h index a4529d550b..48cd50ce02 100644 --- a/src/MOLECULE/angle_cosine_squared.h +++ b/src/MOLECULE/angle_cosine_squared.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/angle_harmonic.cpp b/src/MOLECULE/angle_harmonic.cpp index aa24fa27b4..4d0683b9bc 100644 --- a/src/MOLECULE/angle_harmonic.cpp +++ b/src/MOLECULE/angle_harmonic.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -23,6 +23,7 @@ #include "neighbor.h" #include +#include using namespace LAMMPS_NS; using MathConst::DEG2RAD; diff --git a/src/MOLECULE/angle_harmonic.h b/src/MOLECULE/angle_harmonic.h index a27f26c53d..c50df2ab4e 100644 --- a/src/MOLECULE/angle_harmonic.h +++ b/src/MOLECULE/angle_harmonic.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp index c3959dc898..03027700a6 100644 --- a/src/MOLECULE/angle_table.cpp +++ b/src/MOLECULE/angle_table.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -405,6 +405,9 @@ void AngleTable::read_table(Table *tb, char *file, char *keyword) reader.skip_line(); for (int i = 0; i < tb->ninput; i++) { line = reader.next_line(); + if (!line) + error->one(FLERR, "Data missing when parsing angle table '{}' line {} of {}.", keyword, i + 1, + tb->ninput); try { ValueTokenizer values(line); values.next_int(); diff --git a/src/MOLECULE/angle_table.h b/src/MOLECULE/angle_table.h index 1917908015..2e991d9d71 100644 --- a/src/MOLECULE/angle_table.h +++ b/src/MOLECULE/angle_table.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/atom_vec_angle.cpp b/src/MOLECULE/atom_vec_angle.cpp index 366e1d1a9e..9342f38617 100644 --- a/src/MOLECULE/atom_vec_angle.cpp +++ b/src/MOLECULE/atom_vec_angle.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/atom_vec_angle.h b/src/MOLECULE/atom_vec_angle.h index f7b9bc453a..76ef120176 100644 --- a/src/MOLECULE/atom_vec_angle.h +++ b/src/MOLECULE/atom_vec_angle.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,7 @@ AtomStyle(angle,AtomVecAngle); namespace LAMMPS_NS { -class AtomVecAngle : public AtomVec { +class AtomVecAngle : virtual public AtomVec { public: AtomVecAngle(class LAMMPS *); ~AtomVecAngle() override; @@ -35,7 +35,7 @@ class AtomVecAngle : public AtomVec { void unpack_restart_init(int) override; void data_atom_post(int) override; - private: + protected: int *num_bond, *num_angle; int **bond_type, **angle_type; int **nspecial; diff --git a/src/MOLECULE/atom_vec_bond.cpp b/src/MOLECULE/atom_vec_bond.cpp index 29a1a0f4e4..98f0eff6fa 100644 --- a/src/MOLECULE/atom_vec_bond.cpp +++ b/src/MOLECULE/atom_vec_bond.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/atom_vec_bond.h b/src/MOLECULE/atom_vec_bond.h index 98320dcab4..7c99829484 100644 --- a/src/MOLECULE/atom_vec_bond.h +++ b/src/MOLECULE/atom_vec_bond.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,7 @@ AtomStyle(bond,AtomVecBond); namespace LAMMPS_NS { -class AtomVecBond : public AtomVec { +class AtomVecBond : virtual public AtomVec { public: AtomVecBond(class LAMMPS *); ~AtomVecBond() override; @@ -35,7 +35,7 @@ class AtomVecBond : public AtomVec { void unpack_restart_init(int) override; void data_atom_post(int) override; - private: + protected: int *num_bond; int **bond_type; int **nspecial; diff --git a/src/MOLECULE/atom_vec_full.cpp b/src/MOLECULE/atom_vec_full.cpp index a78f3616a4..e84abcd119 100644 --- a/src/MOLECULE/atom_vec_full.cpp +++ b/src/MOLECULE/atom_vec_full.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/atom_vec_full.h b/src/MOLECULE/atom_vec_full.h index 6acdb6faa9..ed3be02812 100644 --- a/src/MOLECULE/atom_vec_full.h +++ b/src/MOLECULE/atom_vec_full.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,7 @@ AtomStyle(full,AtomVecFull); namespace LAMMPS_NS { -class AtomVecFull : public AtomVec { +class AtomVecFull : virtual public AtomVec { public: AtomVecFull(class LAMMPS *); ~AtomVecFull() override; @@ -35,7 +35,7 @@ class AtomVecFull : public AtomVec { void unpack_restart_init(int) override; void data_atom_post(int) override; - private: + protected: int *num_bond, *num_angle, *num_dihedral, *num_improper; int **bond_type, **angle_type, **dihedral_type, **improper_type; int **nspecial; diff --git a/src/MOLECULE/atom_vec_molecular.cpp b/src/MOLECULE/atom_vec_molecular.cpp index 72f094d7c2..a818215e23 100644 --- a/src/MOLECULE/atom_vec_molecular.cpp +++ b/src/MOLECULE/atom_vec_molecular.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/atom_vec_molecular.h b/src/MOLECULE/atom_vec_molecular.h index 64e346e61f..50434d0ae0 100644 --- a/src/MOLECULE/atom_vec_molecular.h +++ b/src/MOLECULE/atom_vec_molecular.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,7 @@ AtomStyle(molecular,AtomVecMolecular); namespace LAMMPS_NS { -class AtomVecMolecular : public AtomVec { +class AtomVecMolecular : virtual public AtomVec { public: AtomVecMolecular(class LAMMPS *); ~AtomVecMolecular() override; @@ -35,7 +35,7 @@ class AtomVecMolecular : public AtomVec { void unpack_restart_init(int) override; void data_atom_post(int) override; - private: + protected: int *num_bond, *num_angle, *num_dihedral, *num_improper; int **bond_type, **angle_type, **dihedral_type, **improper_type; int **nspecial; diff --git a/src/MOLECULE/atom_vec_template.cpp b/src/MOLECULE/atom_vec_template.cpp index 8202ea77f3..2678f44327 100644 --- a/src/MOLECULE/atom_vec_template.cpp +++ b/src/MOLECULE/atom_vec_template.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/atom_vec_template.h b/src/MOLECULE/atom_vec_template.h index 7653e12cc9..9a13ee2029 100644 --- a/src/MOLECULE/atom_vec_template.h +++ b/src/MOLECULE/atom_vec_template.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,7 @@ AtomStyle(template,AtomVecTemplate); namespace LAMMPS_NS { -class AtomVecTemplate : public AtomVec { +class AtomVecTemplate : virtual public AtomVec { public: AtomVecTemplate(class LAMMPS *); diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp index 2950d48ca6..0f279fccb6 100644 --- a/src/MOLECULE/bond_fene.cpp +++ b/src/MOLECULE/bond_fene.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/bond_fene.h b/src/MOLECULE/bond_fene.h index d205a0ef0f..eb9e981a32 100644 --- a/src/MOLECULE/bond_fene.h +++ b/src/MOLECULE/bond_fene.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/bond_fene_expand.cpp b/src/MOLECULE/bond_fene_expand.cpp index 288a0bc320..c7821b1826 100644 --- a/src/MOLECULE/bond_fene_expand.cpp +++ b/src/MOLECULE/bond_fene_expand.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/bond_fene_expand.h b/src/MOLECULE/bond_fene_expand.h index 7e88da422c..cdce710ea1 100644 --- a/src/MOLECULE/bond_fene_expand.h +++ b/src/MOLECULE/bond_fene_expand.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/bond_gromos.cpp b/src/MOLECULE/bond_gromos.cpp index 4572d2c900..9a7b6d4d6e 100644 --- a/src/MOLECULE/bond_gromos.cpp +++ b/src/MOLECULE/bond_gromos.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/bond_gromos.h b/src/MOLECULE/bond_gromos.h index 498e859769..be6a33257c 100644 --- a/src/MOLECULE/bond_gromos.h +++ b/src/MOLECULE/bond_gromos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/bond_harmonic.cpp b/src/MOLECULE/bond_harmonic.cpp index a55aa0f976..a1e926abea 100644 --- a/src/MOLECULE/bond_harmonic.cpp +++ b/src/MOLECULE/bond_harmonic.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/bond_harmonic.h b/src/MOLECULE/bond_harmonic.h index e089388d30..ec14287c39 100644 --- a/src/MOLECULE/bond_harmonic.h +++ b/src/MOLECULE/bond_harmonic.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/bond_morse.cpp b/src/MOLECULE/bond_morse.cpp index 3dd6ed52eb..e9555698da 100644 --- a/src/MOLECULE/bond_morse.cpp +++ b/src/MOLECULE/bond_morse.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/bond_morse.h b/src/MOLECULE/bond_morse.h index 8682a6bb13..5515ea023e 100644 --- a/src/MOLECULE/bond_morse.h +++ b/src/MOLECULE/bond_morse.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/bond_quartic.cpp b/src/MOLECULE/bond_quartic.cpp index 88effd6a05..60f310ecb7 100644 --- a/src/MOLECULE/bond_quartic.cpp +++ b/src/MOLECULE/bond_quartic.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/bond_quartic.h b/src/MOLECULE/bond_quartic.h index fdc9cc8707..af84cefdbf 100644 --- a/src/MOLECULE/bond_quartic.h +++ b/src/MOLECULE/bond_quartic.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp index 7af08a4a08..5978d63561 100644 --- a/src/MOLECULE/bond_table.cpp +++ b/src/MOLECULE/bond_table.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -330,6 +330,9 @@ void BondTable::read_table(Table *tb, char *file, char *keyword) reader.skip_line(); for (int i = 0; i < tb->ninput; i++) { line = reader.next_line(); + if (!line) + error->one(FLERR, "Data missing when parsing bond table '{}' line {} of {}.", keyword, i + 1, + tb->ninput); try { ValueTokenizer values(line); values.next_int(); diff --git a/src/MOLECULE/bond_table.h b/src/MOLECULE/bond_table.h index 054c3e94bd..18d517719c 100644 --- a/src/MOLECULE/bond_table.h +++ b/src/MOLECULE/bond_table.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp index bd783316cd..d863c873d4 100644 --- a/src/MOLECULE/dihedral_charmm.cpp +++ b/src/MOLECULE/dihedral_charmm.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/dihedral_charmm.h b/src/MOLECULE/dihedral_charmm.h index 1c59ed17e3..71e857d5f0 100644 --- a/src/MOLECULE/dihedral_charmm.h +++ b/src/MOLECULE/dihedral_charmm.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/dihedral_charmmfsw.cpp b/src/MOLECULE/dihedral_charmmfsw.cpp index cd94283842..8e6d9b54c4 100644 --- a/src/MOLECULE/dihedral_charmmfsw.cpp +++ b/src/MOLECULE/dihedral_charmmfsw.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/dihedral_charmmfsw.h b/src/MOLECULE/dihedral_charmmfsw.h index 2775575362..3930034356 100644 --- a/src/MOLECULE/dihedral_charmmfsw.h +++ b/src/MOLECULE/dihedral_charmmfsw.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/dihedral_harmonic.cpp b/src/MOLECULE/dihedral_harmonic.cpp index 3a4d1c9df0..b7dfa17575 100644 --- a/src/MOLECULE/dihedral_harmonic.cpp +++ b/src/MOLECULE/dihedral_harmonic.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/dihedral_harmonic.h b/src/MOLECULE/dihedral_harmonic.h index 8535a2019b..ad8d6c6b11 100644 --- a/src/MOLECULE/dihedral_harmonic.h +++ b/src/MOLECULE/dihedral_harmonic.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/dihedral_multi_harmonic.cpp b/src/MOLECULE/dihedral_multi_harmonic.cpp index b33a3c2320..11213b59cd 100644 --- a/src/MOLECULE/dihedral_multi_harmonic.cpp +++ b/src/MOLECULE/dihedral_multi_harmonic.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/dihedral_multi_harmonic.h b/src/MOLECULE/dihedral_multi_harmonic.h index cbadaaf472..4780028181 100644 --- a/src/MOLECULE/dihedral_multi_harmonic.h +++ b/src/MOLECULE/dihedral_multi_harmonic.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/dihedral_opls.cpp b/src/MOLECULE/dihedral_opls.cpp index 7c60cba923..af34cd24db 100644 --- a/src/MOLECULE/dihedral_opls.cpp +++ b/src/MOLECULE/dihedral_opls.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/dihedral_opls.h b/src/MOLECULE/dihedral_opls.h index b35d033cda..c6286b3b6f 100644 --- a/src/MOLECULE/dihedral_opls.h +++ b/src/MOLECULE/dihedral_opls.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/dihedral_table.cpp b/src/MOLECULE/dihedral_table.cpp index 1a9bc923a7..070d0a6972 100644 --- a/src/MOLECULE/dihedral_table.cpp +++ b/src/MOLECULE/dihedral_table.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -1021,6 +1021,9 @@ void DihedralTable::read_table(Table *tb, char *file, char *keyword) for (int i = 0; i < tb->ninput; i++) { line = reader.next_line(); + if (!line) + error->one(FLERR, "Data missing when parsing dihedral table '{}' line {} of {}.", + keyword, i + 1, tb->ninput); try { ValueTokenizer values(line); if (tb->f_unspecified) { diff --git a/src/MOLECULE/dihedral_table.h b/src/MOLECULE/dihedral_table.h index e55579a528..30178903d3 100644 --- a/src/MOLECULE/dihedral_table.h +++ b/src/MOLECULE/dihedral_table.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp index a0137ab40c..f74c05ef06 100644 --- a/src/MOLECULE/fix_cmap.cpp +++ b/src/MOLECULE/fix_cmap.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/fix_cmap.h b/src/MOLECULE/fix_cmap.h index d07122d0d0..fce76aa540 100644 --- a/src/MOLECULE/fix_cmap.h +++ b/src/MOLECULE/fix_cmap.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/improper_cvff.cpp b/src/MOLECULE/improper_cvff.cpp index 31871ca6c8..afe3bd9d73 100644 --- a/src/MOLECULE/improper_cvff.cpp +++ b/src/MOLECULE/improper_cvff.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/improper_cvff.h b/src/MOLECULE/improper_cvff.h index bcb6c5c486..ff550fe9e8 100644 --- a/src/MOLECULE/improper_cvff.h +++ b/src/MOLECULE/improper_cvff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/improper_harmonic.cpp b/src/MOLECULE/improper_harmonic.cpp index efcba09ef0..d2cd505e68 100644 --- a/src/MOLECULE/improper_harmonic.cpp +++ b/src/MOLECULE/improper_harmonic.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/improper_harmonic.h b/src/MOLECULE/improper_harmonic.h index 7b80389037..89ebe49dec 100644 --- a/src/MOLECULE/improper_harmonic.h +++ b/src/MOLECULE/improper_harmonic.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/improper_umbrella.cpp b/src/MOLECULE/improper_umbrella.cpp index aad5f06c67..fdf9870083 100644 --- a/src/MOLECULE/improper_umbrella.cpp +++ b/src/MOLECULE/improper_umbrella.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/improper_umbrella.h b/src/MOLECULE/improper_umbrella.h index fa54899807..9441810861 100644 --- a/src/MOLECULE/improper_umbrella.h +++ b/src/MOLECULE/improper_umbrella.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.cpp b/src/MOLECULE/pair_hbond_dreiding_lj.cpp index bdca9446a0..496e368452 100644 --- a/src/MOLECULE/pair_hbond_dreiding_lj.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_lj.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.h b/src/MOLECULE/pair_hbond_dreiding_lj.h index 5bd8c56412..91a906c5cb 100644 --- a/src/MOLECULE/pair_hbond_dreiding_lj.h +++ b/src/MOLECULE/pair_hbond_dreiding_lj.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.cpp b/src/MOLECULE/pair_hbond_dreiding_morse.cpp index 1530283f4d..7ec2db073d 100644 --- a/src/MOLECULE/pair_hbond_dreiding_morse.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_morse.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.h b/src/MOLECULE/pair_hbond_dreiding_morse.h index 98c5ae0899..8d4646451e 100644 --- a/src/MOLECULE/pair_hbond_dreiding_morse.h +++ b/src/MOLECULE/pair_hbond_dreiding_morse.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp index c1dd0ec48c..237b843ec5 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm.h b/src/MOLECULE/pair_lj_charmm_coul_charmm.h index 941929055c..1f92cf40f6 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm.h +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp index 4614c65fe7..0b5962c151 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.h b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.h index b358f6e1bc..5f363ae750 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.h +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp index 1259dba07b..5063c402c6 100644 --- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp +++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.h b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.h index 03f576ea37..139ccf8ee2 100644 --- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.h +++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp index b024afd575..19b4d6585f 100644 --- a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp +++ b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -502,9 +502,17 @@ void PairLJCutTIP4PCut::init_style() // set alpha parameter - double theta = force->angle->equilibrium_angle(typeA); - double blen = force->bond->equilibrium_distance(typeB); + const double theta = force->angle->equilibrium_angle(typeA); + const double blen = force->bond->equilibrium_distance(typeB); alpha = qdist / (cos(0.5*theta) * blen); + + const double mincut = cut_coul + qdist + blen + neighbor->skin; + if (comm->get_comm_cutoff() < mincut) { + if (comm->me == 0) + error->warning(FLERR, "Increasing communication cutoff to {:.8} for TIP4P pair style", + mincut); + comm->cutghostuser = mincut; + } } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/pair_lj_cut_tip4p_cut.h b/src/MOLECULE/pair_lj_cut_tip4p_cut.h index 03418a3ce5..75769274a8 100644 --- a/src/MOLECULE/pair_lj_cut_tip4p_cut.h +++ b/src/MOLECULE/pair_lj_cut_tip4p_cut.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLECULE/pair_tip4p_cut.cpp b/src/MOLECULE/pair_tip4p_cut.cpp index 1d46df3e13..25c9b82468 100644 --- a/src/MOLECULE/pair_tip4p_cut.cpp +++ b/src/MOLECULE/pair_tip4p_cut.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -431,9 +431,17 @@ void PairTIP4PCut::init_style() // set alpha parameter - double theta = force->angle->equilibrium_angle(typeA); - double blen = force->bond->equilibrium_distance(typeB); + const double theta = force->angle->equilibrium_angle(typeA); + const double blen = force->bond->equilibrium_distance(typeB); alpha = qdist / (cos(0.5*theta) * blen); + + const double mincut = cut_coul + qdist + blen + neighbor->skin; + if (comm->get_comm_cutoff() < mincut) { + if (comm->me == 0) + error->warning(FLERR, "Increasing communication cutoff to {:.8} for TIP4P pair style", + mincut); + comm->cutghostuser = mincut; + } } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/pair_tip4p_cut.h b/src/MOLECULE/pair_tip4p_cut.h index acf922fc94..85f9e4a72b 100644 --- a/src/MOLECULE/pair_tip4p_cut.h +++ b/src/MOLECULE/pair_tip4p_cut.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLFILE/Install.sh b/src/MOLFILE/Install.sh index 85885f66b9..3ae4357ade 100755 --- a/src/MOLFILE/Install.sh +++ b/src/MOLFILE/Install.sh @@ -44,7 +44,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*molfile.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*molfile.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/molfile\/Makefile.lammps @@ -58,7 +58,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*molfile.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*molfile.*$/d' ../Makefile.package.settings fi fi diff --git a/src/MOLFILE/dump_molfile.cpp b/src/MOLFILE/dump_molfile.cpp index 9d2c7bbadb..539eee37d7 100644 --- a/src/MOLFILE/dump_molfile.cpp +++ b/src/MOLFILE/dump_molfile.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLFILE/dump_molfile.h b/src/MOLFILE/dump_molfile.h index 80f20a78f4..8ac8623e94 100644 --- a/src/MOLFILE/dump_molfile.h +++ b/src/MOLFILE/dump_molfile.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLFILE/molfile_interface.cpp b/src/MOLFILE/molfile_interface.cpp index e6114e1b68..8f5ac8545e 100644 --- a/src/MOLFILE/molfile_interface.cpp +++ b/src/MOLFILE/molfile_interface.cpp @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLFILE/molfile_interface.h b/src/MOLFILE/molfile_interface.h index 151618286b..940b612cc6 100644 --- a/src/MOLFILE/molfile_interface.h +++ b/src/MOLFILE/molfile_interface.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLFILE/reader_molfile.cpp b/src/MOLFILE/reader_molfile.cpp index 7b12678329..49ed347e84 100644 --- a/src/MOLFILE/reader_molfile.cpp +++ b/src/MOLFILE/reader_molfile.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MOLFILE/reader_molfile.h b/src/MOLFILE/reader_molfile.h index df193c43e7..03906cbc9e 100644 --- a/src/MOLFILE/reader_molfile.h +++ b/src/MOLFILE/reader_molfile.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MPIIO/dump_atom_mpiio.cpp b/src/MPIIO/dump_atom_mpiio.cpp index 87ef2b0342..28f2981c15 100644 --- a/src/MPIIO/dump_atom_mpiio.cpp +++ b/src/MPIIO/dump_atom_mpiio.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MPIIO/dump_atom_mpiio.h b/src/MPIIO/dump_atom_mpiio.h index 8946034b8b..efa2211168 100644 --- a/src/MPIIO/dump_atom_mpiio.h +++ b/src/MPIIO/dump_atom_mpiio.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MPIIO/dump_cfg_mpiio.cpp b/src/MPIIO/dump_cfg_mpiio.cpp index a20ba624d6..4325010f71 100644 --- a/src/MPIIO/dump_cfg_mpiio.cpp +++ b/src/MPIIO/dump_cfg_mpiio.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MPIIO/dump_cfg_mpiio.h b/src/MPIIO/dump_cfg_mpiio.h index 289e5baf72..7c52d46c4e 100644 --- a/src/MPIIO/dump_cfg_mpiio.h +++ b/src/MPIIO/dump_cfg_mpiio.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MPIIO/dump_custom_mpiio.cpp b/src/MPIIO/dump_custom_mpiio.cpp index a5b2a681d3..0465c8cdad 100644 --- a/src/MPIIO/dump_custom_mpiio.cpp +++ b/src/MPIIO/dump_custom_mpiio.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MPIIO/dump_custom_mpiio.h b/src/MPIIO/dump_custom_mpiio.h index 79169f5a2c..3df72cb6e0 100644 --- a/src/MPIIO/dump_custom_mpiio.h +++ b/src/MPIIO/dump_custom_mpiio.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MPIIO/dump_xyz_mpiio.cpp b/src/MPIIO/dump_xyz_mpiio.cpp index 3225e397cc..c24ff80510 100644 --- a/src/MPIIO/dump_xyz_mpiio.cpp +++ b/src/MPIIO/dump_xyz_mpiio.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MPIIO/dump_xyz_mpiio.h b/src/MPIIO/dump_xyz_mpiio.h index dcbb15c82a..f1e41fabcd 100644 --- a/src/MPIIO/dump_xyz_mpiio.h +++ b/src/MPIIO/dump_xyz_mpiio.h @@ -1,7 +1,7 @@ /* -*- c++ -*- --------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MPIIO/restart_mpiio.cpp b/src/MPIIO/restart_mpiio.cpp index 57ade6c39e..0d40c2162c 100644 --- a/src/MPIIO/restart_mpiio.cpp +++ b/src/MPIIO/restart_mpiio.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MPIIO/restart_mpiio.h b/src/MPIIO/restart_mpiio.h index 6bf34841f4..f9a7540ab1 100644 --- a/src/MPIIO/restart_mpiio.h +++ b/src/MPIIO/restart_mpiio.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MSCG/Install.sh b/src/MSCG/Install.sh index 353403c7da..67f0f837ce 100755 --- a/src/MSCG/Install.sh +++ b/src/MSCG/Install.sh @@ -43,7 +43,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*mscg.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*mscg.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/mscg\/Makefile.lammps @@ -57,7 +57,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*mscg.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*mscg.*$/d' ../Makefile.package.settings fi fi diff --git a/src/MSCG/fix_mscg.cpp b/src/MSCG/fix_mscg.cpp index 1aa644b976..171258d6e7 100644 --- a/src/MSCG/fix_mscg.cpp +++ b/src/MSCG/fix_mscg.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/MSCG/fix_mscg.h b/src/MSCG/fix_mscg.h index ae1109e14d..71362e0648 100644 --- a/src/MSCG/fix_mscg.h +++ b/src/MSCG/fix_mscg.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/Makefile b/src/Makefile index 923cc535fd..6f3ece5376 100644 --- a/src/Makefile +++ b/src/Makefile @@ -55,7 +55,7 @@ PACKAGE = \ awpmd \ bocs \ body \ - bpm \ + bpm \ brownian \ cg-dna \ cg-spica \ @@ -99,6 +99,7 @@ PACKAGE = \ misc \ ml-hdnnp \ ml-pace \ + ml-pod \ ml-quip \ ml-rann \ ml-snap \ @@ -228,6 +229,7 @@ PACKLIB = \ molfile \ netcdf \ ml-pace \ + ml-pod \ plumed \ qmmm \ ml-quip \ @@ -238,7 +240,7 @@ PACKLIB = \ PACKSYS = compress latboltz mpiio python -PACKINT = atc awpmd colvars electrode gpu kokkos mesont poems +PACKINT = atc awpmd colvars electrode gpu kokkos mesont ml-pod poems PACKEXT = \ adios \ diff --git a/src/NETCDF/Install.sh b/src/NETCDF/Install.sh index 4d21f0f894..8c70d84fd8 100755 --- a/src/NETCDF/Install.sh +++ b/src/NETCDF/Install.sh @@ -42,7 +42,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*netcdf.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*netcdf.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/netcdf\/Makefile.lammps @@ -57,7 +57,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*netcdf.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*netcdf.*$/d' ../Makefile.package.settings fi fi diff --git a/src/NETCDF/dump_netcdf.cpp b/src/NETCDF/dump_netcdf.cpp index 13dc869021..6fecf7f41b 100644 --- a/src/NETCDF/dump_netcdf.cpp +++ b/src/NETCDF/dump_netcdf.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/NETCDF/dump_netcdf.h b/src/NETCDF/dump_netcdf.h index 3d27ffcb50..20c60ef104 100644 --- a/src/NETCDF/dump_netcdf.h +++ b/src/NETCDF/dump_netcdf.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/NETCDF/dump_netcdf_mpiio.cpp b/src/NETCDF/dump_netcdf_mpiio.cpp index dbf95953d7..6f7a3e0323 100644 --- a/src/NETCDF/dump_netcdf_mpiio.cpp +++ b/src/NETCDF/dump_netcdf_mpiio.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/NETCDF/dump_netcdf_mpiio.h b/src/NETCDF/dump_netcdf_mpiio.h index 937850fcac..5948dc272b 100644 --- a/src/NETCDF/dump_netcdf_mpiio.h +++ b/src/NETCDF/dump_netcdf_mpiio.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/NETCDF/netcdf_units.cpp b/src/NETCDF/netcdf_units.cpp index 0ee0ebbde0..e5a8417f45 100644 --- a/src/NETCDF/netcdf_units.cpp +++ b/src/NETCDF/netcdf_units.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/NETCDF/netcdf_units.h b/src/NETCDF/netcdf_units.h index 85f9b05888..c5a3bf9113 100644 --- a/src/NETCDF/netcdf_units.h +++ b/src/NETCDF/netcdf_units.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_charmm_omp.cpp b/src/OPENMP/angle_charmm_omp.cpp index 2994cfad13..9eb91bcb27 100644 --- a/src/OPENMP/angle_charmm_omp.cpp +++ b/src/OPENMP/angle_charmm_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_charmm_omp.h b/src/OPENMP/angle_charmm_omp.h index f478dfdc89..99aa11a1e4 100644 --- a/src/OPENMP/angle_charmm_omp.h +++ b/src/OPENMP/angle_charmm_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_class2_omp.cpp b/src/OPENMP/angle_class2_omp.cpp index 239b373004..300f8f2b3c 100644 --- a/src/OPENMP/angle_class2_omp.cpp +++ b/src/OPENMP/angle_class2_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_class2_omp.h b/src/OPENMP/angle_class2_omp.h index a9753c2e6b..bb3ff7336a 100644 --- a/src/OPENMP/angle_class2_omp.h +++ b/src/OPENMP/angle_class2_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_cosine_delta_omp.cpp b/src/OPENMP/angle_cosine_delta_omp.cpp index 48330a5087..98b6a7ac56 100644 --- a/src/OPENMP/angle_cosine_delta_omp.cpp +++ b/src/OPENMP/angle_cosine_delta_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_cosine_delta_omp.h b/src/OPENMP/angle_cosine_delta_omp.h index e5e70a24f9..43ad8d673a 100644 --- a/src/OPENMP/angle_cosine_delta_omp.h +++ b/src/OPENMP/angle_cosine_delta_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_cosine_omp.cpp b/src/OPENMP/angle_cosine_omp.cpp index cd5a9fab58..1985633c38 100644 --- a/src/OPENMP/angle_cosine_omp.cpp +++ b/src/OPENMP/angle_cosine_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_cosine_omp.h b/src/OPENMP/angle_cosine_omp.h index 25d07fc565..bdf337a85a 100644 --- a/src/OPENMP/angle_cosine_omp.h +++ b/src/OPENMP/angle_cosine_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_cosine_periodic_omp.cpp b/src/OPENMP/angle_cosine_periodic_omp.cpp index a97a9d7e89..43b3a54a47 100644 --- a/src/OPENMP/angle_cosine_periodic_omp.cpp +++ b/src/OPENMP/angle_cosine_periodic_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_cosine_periodic_omp.h b/src/OPENMP/angle_cosine_periodic_omp.h index 45a02cf2c4..86a6948831 100644 --- a/src/OPENMP/angle_cosine_periodic_omp.h +++ b/src/OPENMP/angle_cosine_periodic_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_cosine_shift_exp_omp.cpp b/src/OPENMP/angle_cosine_shift_exp_omp.cpp index 1f9b150a57..5831f59fab 100644 --- a/src/OPENMP/angle_cosine_shift_exp_omp.cpp +++ b/src/OPENMP/angle_cosine_shift_exp_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_cosine_shift_exp_omp.h b/src/OPENMP/angle_cosine_shift_exp_omp.h index b394e7e529..ad6f4ded41 100644 --- a/src/OPENMP/angle_cosine_shift_exp_omp.h +++ b/src/OPENMP/angle_cosine_shift_exp_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_cosine_shift_omp.cpp b/src/OPENMP/angle_cosine_shift_omp.cpp index 08649f01e2..020f7583ff 100644 --- a/src/OPENMP/angle_cosine_shift_omp.cpp +++ b/src/OPENMP/angle_cosine_shift_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_cosine_shift_omp.h b/src/OPENMP/angle_cosine_shift_omp.h index 073f5288f3..e61380102e 100644 --- a/src/OPENMP/angle_cosine_shift_omp.h +++ b/src/OPENMP/angle_cosine_shift_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_cosine_squared_omp.cpp b/src/OPENMP/angle_cosine_squared_omp.cpp index 6755426b71..9d98455fe4 100644 --- a/src/OPENMP/angle_cosine_squared_omp.cpp +++ b/src/OPENMP/angle_cosine_squared_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_cosine_squared_omp.h b/src/OPENMP/angle_cosine_squared_omp.h index 50b22fe5e4..702056266c 100644 --- a/src/OPENMP/angle_cosine_squared_omp.h +++ b/src/OPENMP/angle_cosine_squared_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_dipole_omp.cpp b/src/OPENMP/angle_dipole_omp.cpp index 4ff307f77f..3a8099ac73 100644 --- a/src/OPENMP/angle_dipole_omp.cpp +++ b/src/OPENMP/angle_dipole_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_dipole_omp.h b/src/OPENMP/angle_dipole_omp.h index ddd7aac6ea..7324b70c63 100644 --- a/src/OPENMP/angle_dipole_omp.h +++ b/src/OPENMP/angle_dipole_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_fourier_omp.cpp b/src/OPENMP/angle_fourier_omp.cpp index b1e4cf1f0a..0c85264342 100644 --- a/src/OPENMP/angle_fourier_omp.cpp +++ b/src/OPENMP/angle_fourier_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_fourier_omp.h b/src/OPENMP/angle_fourier_omp.h index 9a5964df49..39c23b45d8 100644 --- a/src/OPENMP/angle_fourier_omp.h +++ b/src/OPENMP/angle_fourier_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_fourier_simple_omp.cpp b/src/OPENMP/angle_fourier_simple_omp.cpp index b76e9c875e..a8f234918b 100644 --- a/src/OPENMP/angle_fourier_simple_omp.cpp +++ b/src/OPENMP/angle_fourier_simple_omp.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_fourier_simple_omp.h b/src/OPENMP/angle_fourier_simple_omp.h index db96dbfb86..06a3f67896 100644 --- a/src/OPENMP/angle_fourier_simple_omp.h +++ b/src/OPENMP/angle_fourier_simple_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_harmonic_omp.cpp b/src/OPENMP/angle_harmonic_omp.cpp index a67f784624..e83146a3ad 100644 --- a/src/OPENMP/angle_harmonic_omp.cpp +++ b/src/OPENMP/angle_harmonic_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_harmonic_omp.h b/src/OPENMP/angle_harmonic_omp.h index 8c6cc39f7a..8c25cf419f 100644 --- a/src/OPENMP/angle_harmonic_omp.h +++ b/src/OPENMP/angle_harmonic_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_quartic_omp.cpp b/src/OPENMP/angle_quartic_omp.cpp index 6592584c99..bb9a9837d2 100644 --- a/src/OPENMP/angle_quartic_omp.cpp +++ b/src/OPENMP/angle_quartic_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_quartic_omp.h b/src/OPENMP/angle_quartic_omp.h index 7953891d55..c85b8d1a11 100644 --- a/src/OPENMP/angle_quartic_omp.h +++ b/src/OPENMP/angle_quartic_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_spica_omp.cpp b/src/OPENMP/angle_spica_omp.cpp index f6198eab50..728e2ff435 100644 --- a/src/OPENMP/angle_spica_omp.cpp +++ b/src/OPENMP/angle_spica_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_spica_omp.h b/src/OPENMP/angle_spica_omp.h index a6186c3f5e..a9094b3ae1 100644 --- a/src/OPENMP/angle_spica_omp.h +++ b/src/OPENMP/angle_spica_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_table_omp.cpp b/src/OPENMP/angle_table_omp.cpp index d796ac23e3..d75bd8a694 100644 --- a/src/OPENMP/angle_table_omp.cpp +++ b/src/OPENMP/angle_table_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/angle_table_omp.h b/src/OPENMP/angle_table_omp.h index 585e40a934..e2c2fad4c5 100644 --- a/src/OPENMP/angle_table_omp.h +++ b/src/OPENMP/angle_table_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/bond_class2_omp.cpp b/src/OPENMP/bond_class2_omp.cpp index 9b7ed7169f..90a9f4676f 100644 --- a/src/OPENMP/bond_class2_omp.cpp +++ b/src/OPENMP/bond_class2_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/bond_class2_omp.h b/src/OPENMP/bond_class2_omp.h index 24a1ccebbc..b415de0809 100644 --- a/src/OPENMP/bond_class2_omp.h +++ b/src/OPENMP/bond_class2_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/bond_fene_expand_omp.cpp b/src/OPENMP/bond_fene_expand_omp.cpp index 30c6f154b7..11bbe94078 100644 --- a/src/OPENMP/bond_fene_expand_omp.cpp +++ b/src/OPENMP/bond_fene_expand_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/bond_fene_expand_omp.h b/src/OPENMP/bond_fene_expand_omp.h index 8995b2a00e..c576a02b41 100644 --- a/src/OPENMP/bond_fene_expand_omp.h +++ b/src/OPENMP/bond_fene_expand_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/bond_fene_omp.cpp b/src/OPENMP/bond_fene_omp.cpp index ef1343ec90..d7ae32b1ed 100644 --- a/src/OPENMP/bond_fene_omp.cpp +++ b/src/OPENMP/bond_fene_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/bond_fene_omp.h b/src/OPENMP/bond_fene_omp.h index 0029cc7db5..9108c6adf4 100644 --- a/src/OPENMP/bond_fene_omp.h +++ b/src/OPENMP/bond_fene_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/bond_gromos_omp.cpp b/src/OPENMP/bond_gromos_omp.cpp index 6089290386..895f38b3aa 100644 --- a/src/OPENMP/bond_gromos_omp.cpp +++ b/src/OPENMP/bond_gromos_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/bond_gromos_omp.h b/src/OPENMP/bond_gromos_omp.h index c9ff442fa6..3018112765 100644 --- a/src/OPENMP/bond_gromos_omp.h +++ b/src/OPENMP/bond_gromos_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/bond_harmonic_omp.cpp b/src/OPENMP/bond_harmonic_omp.cpp index cc9bbea5da..57a6eb6475 100644 --- a/src/OPENMP/bond_harmonic_omp.cpp +++ b/src/OPENMP/bond_harmonic_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/bond_harmonic_omp.h b/src/OPENMP/bond_harmonic_omp.h index a607d810b8..d6247e087c 100644 --- a/src/OPENMP/bond_harmonic_omp.h +++ b/src/OPENMP/bond_harmonic_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/bond_harmonic_shift_cut_omp.cpp b/src/OPENMP/bond_harmonic_shift_cut_omp.cpp index 702eae64d0..97761f1701 100644 --- a/src/OPENMP/bond_harmonic_shift_cut_omp.cpp +++ b/src/OPENMP/bond_harmonic_shift_cut_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/bond_harmonic_shift_cut_omp.h b/src/OPENMP/bond_harmonic_shift_cut_omp.h index 976013cad4..1146e51e60 100644 --- a/src/OPENMP/bond_harmonic_shift_cut_omp.h +++ b/src/OPENMP/bond_harmonic_shift_cut_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/bond_harmonic_shift_omp.cpp b/src/OPENMP/bond_harmonic_shift_omp.cpp index 375de2eff7..a65284fe5e 100644 --- a/src/OPENMP/bond_harmonic_shift_omp.cpp +++ b/src/OPENMP/bond_harmonic_shift_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/bond_harmonic_shift_omp.h b/src/OPENMP/bond_harmonic_shift_omp.h index cfbdc7d9f6..609a1b8cee 100644 --- a/src/OPENMP/bond_harmonic_shift_omp.h +++ b/src/OPENMP/bond_harmonic_shift_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/bond_morse_omp.cpp b/src/OPENMP/bond_morse_omp.cpp index b1938b926f..2a1e96cba2 100644 --- a/src/OPENMP/bond_morse_omp.cpp +++ b/src/OPENMP/bond_morse_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/bond_morse_omp.h b/src/OPENMP/bond_morse_omp.h index 592328fc0c..8d6877690a 100644 --- a/src/OPENMP/bond_morse_omp.h +++ b/src/OPENMP/bond_morse_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/bond_nonlinear_omp.cpp b/src/OPENMP/bond_nonlinear_omp.cpp index 209c7d4719..43af3c7a53 100644 --- a/src/OPENMP/bond_nonlinear_omp.cpp +++ b/src/OPENMP/bond_nonlinear_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/bond_nonlinear_omp.h b/src/OPENMP/bond_nonlinear_omp.h index 8799b159c6..be2fce5787 100644 --- a/src/OPENMP/bond_nonlinear_omp.h +++ b/src/OPENMP/bond_nonlinear_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/bond_quartic_omp.cpp b/src/OPENMP/bond_quartic_omp.cpp index 427293dd3e..5b13d6f014 100644 --- a/src/OPENMP/bond_quartic_omp.cpp +++ b/src/OPENMP/bond_quartic_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/bond_quartic_omp.h b/src/OPENMP/bond_quartic_omp.h index dd010537de..d7481f880c 100644 --- a/src/OPENMP/bond_quartic_omp.h +++ b/src/OPENMP/bond_quartic_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/bond_table_omp.cpp b/src/OPENMP/bond_table_omp.cpp index 011ba5cc49..bd4d2dde93 100644 --- a/src/OPENMP/bond_table_omp.cpp +++ b/src/OPENMP/bond_table_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/bond_table_omp.h b/src/OPENMP/bond_table_omp.h index 886fb0c9d7..49628276a6 100644 --- a/src/OPENMP/bond_table_omp.h +++ b/src/OPENMP/bond_table_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/dihedral_charmm_omp.cpp b/src/OPENMP/dihedral_charmm_omp.cpp index 72d6a93a64..a50f6099d0 100644 --- a/src/OPENMP/dihedral_charmm_omp.cpp +++ b/src/OPENMP/dihedral_charmm_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/dihedral_charmm_omp.h b/src/OPENMP/dihedral_charmm_omp.h index 40c5f10e43..7efc9975fd 100644 --- a/src/OPENMP/dihedral_charmm_omp.h +++ b/src/OPENMP/dihedral_charmm_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/dihedral_class2_omp.cpp b/src/OPENMP/dihedral_class2_omp.cpp index e2bcfaa990..8ec39ceee8 100644 --- a/src/OPENMP/dihedral_class2_omp.cpp +++ b/src/OPENMP/dihedral_class2_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/dihedral_class2_omp.h b/src/OPENMP/dihedral_class2_omp.h index 4465792da4..f3e53eb64c 100644 --- a/src/OPENMP/dihedral_class2_omp.h +++ b/src/OPENMP/dihedral_class2_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/dihedral_cosine_shift_exp_omp.cpp b/src/OPENMP/dihedral_cosine_shift_exp_omp.cpp index 45ca6ee84f..106db995c4 100644 --- a/src/OPENMP/dihedral_cosine_shift_exp_omp.cpp +++ b/src/OPENMP/dihedral_cosine_shift_exp_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/dihedral_cosine_shift_exp_omp.h b/src/OPENMP/dihedral_cosine_shift_exp_omp.h index 2259e1fcfc..c72c77c7cd 100644 --- a/src/OPENMP/dihedral_cosine_shift_exp_omp.h +++ b/src/OPENMP/dihedral_cosine_shift_exp_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/dihedral_fourier_omp.cpp b/src/OPENMP/dihedral_fourier_omp.cpp index 594cd3e922..aae1eec559 100644 --- a/src/OPENMP/dihedral_fourier_omp.cpp +++ b/src/OPENMP/dihedral_fourier_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/dihedral_fourier_omp.h b/src/OPENMP/dihedral_fourier_omp.h index 01e11122b0..906789b3f0 100644 --- a/src/OPENMP/dihedral_fourier_omp.h +++ b/src/OPENMP/dihedral_fourier_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/dihedral_harmonic_omp.cpp b/src/OPENMP/dihedral_harmonic_omp.cpp index dd93cfd126..8737c61cdd 100644 --- a/src/OPENMP/dihedral_harmonic_omp.cpp +++ b/src/OPENMP/dihedral_harmonic_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/dihedral_harmonic_omp.h b/src/OPENMP/dihedral_harmonic_omp.h index c664eccadb..60ea5227ea 100644 --- a/src/OPENMP/dihedral_harmonic_omp.h +++ b/src/OPENMP/dihedral_harmonic_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/dihedral_helix_omp.cpp b/src/OPENMP/dihedral_helix_omp.cpp index d33f7fb4d0..d778285974 100644 --- a/src/OPENMP/dihedral_helix_omp.cpp +++ b/src/OPENMP/dihedral_helix_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/dihedral_helix_omp.h b/src/OPENMP/dihedral_helix_omp.h index 9528ccdb42..d71f6884b6 100644 --- a/src/OPENMP/dihedral_helix_omp.h +++ b/src/OPENMP/dihedral_helix_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/dihedral_multi_harmonic_omp.cpp b/src/OPENMP/dihedral_multi_harmonic_omp.cpp index d8de18e3c3..d3f4447d08 100644 --- a/src/OPENMP/dihedral_multi_harmonic_omp.cpp +++ b/src/OPENMP/dihedral_multi_harmonic_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/dihedral_multi_harmonic_omp.h b/src/OPENMP/dihedral_multi_harmonic_omp.h index b0f7b9183b..fe86774ef6 100644 --- a/src/OPENMP/dihedral_multi_harmonic_omp.h +++ b/src/OPENMP/dihedral_multi_harmonic_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/dihedral_nharmonic_omp.cpp b/src/OPENMP/dihedral_nharmonic_omp.cpp index 11c0839529..f9a3f1328d 100644 --- a/src/OPENMP/dihedral_nharmonic_omp.cpp +++ b/src/OPENMP/dihedral_nharmonic_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/dihedral_nharmonic_omp.h b/src/OPENMP/dihedral_nharmonic_omp.h index c19dff9c0b..429d37e9e8 100644 --- a/src/OPENMP/dihedral_nharmonic_omp.h +++ b/src/OPENMP/dihedral_nharmonic_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/dihedral_opls_omp.cpp b/src/OPENMP/dihedral_opls_omp.cpp index b3b5ea9178..fbdc408c4d 100644 --- a/src/OPENMP/dihedral_opls_omp.cpp +++ b/src/OPENMP/dihedral_opls_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/dihedral_opls_omp.h b/src/OPENMP/dihedral_opls_omp.h index d71f2a8b43..a1d3bf05ea 100644 --- a/src/OPENMP/dihedral_opls_omp.h +++ b/src/OPENMP/dihedral_opls_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/dihedral_quadratic_omp.cpp b/src/OPENMP/dihedral_quadratic_omp.cpp index 2c08dd4505..43d97da5f2 100644 --- a/src/OPENMP/dihedral_quadratic_omp.cpp +++ b/src/OPENMP/dihedral_quadratic_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/dihedral_quadratic_omp.h b/src/OPENMP/dihedral_quadratic_omp.h index 00054f7de0..182cc37b80 100644 --- a/src/OPENMP/dihedral_quadratic_omp.h +++ b/src/OPENMP/dihedral_quadratic_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/dihedral_table_omp.cpp b/src/OPENMP/dihedral_table_omp.cpp index 6e5ba8ec73..1eb4aaa0e6 100644 --- a/src/OPENMP/dihedral_table_omp.cpp +++ b/src/OPENMP/dihedral_table_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/dihedral_table_omp.h b/src/OPENMP/dihedral_table_omp.h index 1e2d0e63ef..46bc2e3f24 100644 --- a/src/OPENMP/dihedral_table_omp.h +++ b/src/OPENMP/dihedral_table_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/domain_omp.cpp b/src/OPENMP/domain_omp.cpp index acc4be204f..32eebe45e9 100644 --- a/src/OPENMP/domain_omp.cpp +++ b/src/OPENMP/domain_omp.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/ewald_omp.cpp b/src/OPENMP/ewald_omp.cpp index 5f47b03096..ee2963659a 100644 --- a/src/OPENMP/ewald_omp.cpp +++ b/src/OPENMP/ewald_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/ewald_omp.h b/src/OPENMP/ewald_omp.h index a938360e2f..a27a143459 100644 --- a/src/OPENMP/ewald_omp.h +++ b/src/OPENMP/ewald_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_gravity_omp.cpp b/src/OPENMP/fix_gravity_omp.cpp index 72d2fdc59b..c81245bb1e 100644 --- a/src/OPENMP/fix_gravity_omp.cpp +++ b/src/OPENMP/fix_gravity_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_gravity_omp.h b/src/OPENMP/fix_gravity_omp.h index 688e92d466..b401c29b1e 100644 --- a/src/OPENMP/fix_gravity_omp.h +++ b/src/OPENMP/fix_gravity_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_neigh_history_omp.cpp b/src/OPENMP/fix_neigh_history_omp.cpp index ec101709c9..90f0b6dced 100644 --- a/src/OPENMP/fix_neigh_history_omp.cpp +++ b/src/OPENMP/fix_neigh_history_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_neigh_history_omp.h b/src/OPENMP/fix_neigh_history_omp.h index f2ba38850b..324215624a 100644 --- a/src/OPENMP/fix_neigh_history_omp.h +++ b/src/OPENMP/fix_neigh_history_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_nh_asphere_omp.cpp b/src/OPENMP/fix_nh_asphere_omp.cpp index 4b93706f32..9023d03b76 100644 --- a/src/OPENMP/fix_nh_asphere_omp.cpp +++ b/src/OPENMP/fix_nh_asphere_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_nh_asphere_omp.h b/src/OPENMP/fix_nh_asphere_omp.h index 55eee148c6..659480d991 100644 --- a/src/OPENMP/fix_nh_asphere_omp.h +++ b/src/OPENMP/fix_nh_asphere_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_nh_omp.cpp b/src/OPENMP/fix_nh_omp.cpp index 29186af629..aada50949e 100644 --- a/src/OPENMP/fix_nh_omp.cpp +++ b/src/OPENMP/fix_nh_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_nh_omp.h b/src/OPENMP/fix_nh_omp.h index cd6db0736f..9dc0935c68 100644 --- a/src/OPENMP/fix_nh_omp.h +++ b/src/OPENMP/fix_nh_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_nh_sphere_omp.cpp b/src/OPENMP/fix_nh_sphere_omp.cpp index 788db2b6ee..93a674cbce 100644 --- a/src/OPENMP/fix_nh_sphere_omp.cpp +++ b/src/OPENMP/fix_nh_sphere_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_nh_sphere_omp.h b/src/OPENMP/fix_nh_sphere_omp.h index 3d799f9c2d..436a3031ff 100644 --- a/src/OPENMP/fix_nh_sphere_omp.h +++ b/src/OPENMP/fix_nh_sphere_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_nph_asphere_omp.cpp b/src/OPENMP/fix_nph_asphere_omp.cpp index c7a28e84f4..8785f16416 100644 --- a/src/OPENMP/fix_nph_asphere_omp.cpp +++ b/src/OPENMP/fix_nph_asphere_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_nph_asphere_omp.h b/src/OPENMP/fix_nph_asphere_omp.h index 28604b3bc0..5bc2408ebb 100644 --- a/src/OPENMP/fix_nph_asphere_omp.h +++ b/src/OPENMP/fix_nph_asphere_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_nph_omp.cpp b/src/OPENMP/fix_nph_omp.cpp index 861d8f32ef..8fea8341d4 100644 --- a/src/OPENMP/fix_nph_omp.cpp +++ b/src/OPENMP/fix_nph_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_nph_omp.h b/src/OPENMP/fix_nph_omp.h index 3590f969e7..2a6f2ff37d 100644 --- a/src/OPENMP/fix_nph_omp.h +++ b/src/OPENMP/fix_nph_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_nph_sphere_omp.cpp b/src/OPENMP/fix_nph_sphere_omp.cpp index 8f8aa32b09..dd0d7555aa 100644 --- a/src/OPENMP/fix_nph_sphere_omp.cpp +++ b/src/OPENMP/fix_nph_sphere_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_nph_sphere_omp.h b/src/OPENMP/fix_nph_sphere_omp.h index 45576b533f..02bd33a7a9 100644 --- a/src/OPENMP/fix_nph_sphere_omp.h +++ b/src/OPENMP/fix_nph_sphere_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_npt_asphere_omp.cpp b/src/OPENMP/fix_npt_asphere_omp.cpp index 23b4111988..319738daf9 100644 --- a/src/OPENMP/fix_npt_asphere_omp.cpp +++ b/src/OPENMP/fix_npt_asphere_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_npt_asphere_omp.h b/src/OPENMP/fix_npt_asphere_omp.h index d989a87da8..da79c3b32c 100644 --- a/src/OPENMP/fix_npt_asphere_omp.h +++ b/src/OPENMP/fix_npt_asphere_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_npt_omp.cpp b/src/OPENMP/fix_npt_omp.cpp index 4d618f8d6f..ab9b8b0139 100644 --- a/src/OPENMP/fix_npt_omp.cpp +++ b/src/OPENMP/fix_npt_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_npt_omp.h b/src/OPENMP/fix_npt_omp.h index 68c3d58d71..089410f7a1 100644 --- a/src/OPENMP/fix_npt_omp.h +++ b/src/OPENMP/fix_npt_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_npt_sphere_omp.cpp b/src/OPENMP/fix_npt_sphere_omp.cpp index b82747013c..f6770a7174 100644 --- a/src/OPENMP/fix_npt_sphere_omp.cpp +++ b/src/OPENMP/fix_npt_sphere_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_npt_sphere_omp.h b/src/OPENMP/fix_npt_sphere_omp.h index 28cf26da0a..b5477f6355 100644 --- a/src/OPENMP/fix_npt_sphere_omp.h +++ b/src/OPENMP/fix_npt_sphere_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_nve_omp.cpp b/src/OPENMP/fix_nve_omp.cpp index 6562e90270..125d73023e 100644 --- a/src/OPENMP/fix_nve_omp.cpp +++ b/src/OPENMP/fix_nve_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_nve_omp.h b/src/OPENMP/fix_nve_omp.h index fa5300d741..2aaca44c51 100644 --- a/src/OPENMP/fix_nve_omp.h +++ b/src/OPENMP/fix_nve_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_nve_sphere_omp.cpp b/src/OPENMP/fix_nve_sphere_omp.cpp index ca7367bce0..be3fc8d147 100644 --- a/src/OPENMP/fix_nve_sphere_omp.cpp +++ b/src/OPENMP/fix_nve_sphere_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_nve_sphere_omp.h b/src/OPENMP/fix_nve_sphere_omp.h index 647668c440..507ba10cd8 100644 --- a/src/OPENMP/fix_nve_sphere_omp.h +++ b/src/OPENMP/fix_nve_sphere_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_nvt_asphere_omp.cpp b/src/OPENMP/fix_nvt_asphere_omp.cpp index 5ab29323bb..35c73840ec 100644 --- a/src/OPENMP/fix_nvt_asphere_omp.cpp +++ b/src/OPENMP/fix_nvt_asphere_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_nvt_asphere_omp.h b/src/OPENMP/fix_nvt_asphere_omp.h index e63a669d3f..cf0042b937 100644 --- a/src/OPENMP/fix_nvt_asphere_omp.h +++ b/src/OPENMP/fix_nvt_asphere_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_nvt_omp.cpp b/src/OPENMP/fix_nvt_omp.cpp index fdcea48e15..2ad5bf0183 100644 --- a/src/OPENMP/fix_nvt_omp.cpp +++ b/src/OPENMP/fix_nvt_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_nvt_omp.h b/src/OPENMP/fix_nvt_omp.h index b89cba9e73..a8c37ae280 100644 --- a/src/OPENMP/fix_nvt_omp.h +++ b/src/OPENMP/fix_nvt_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_nvt_sllod_omp.cpp b/src/OPENMP/fix_nvt_sllod_omp.cpp index d1d8910af1..b72748be70 100644 --- a/src/OPENMP/fix_nvt_sllod_omp.cpp +++ b/src/OPENMP/fix_nvt_sllod_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + LAMMPS development team: developers@lammps.org, Sandia National Laboratories Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_nvt_sllod_omp.h b/src/OPENMP/fix_nvt_sllod_omp.h index c78564aba8..fb5b57455f 100644 --- a/src/OPENMP/fix_nvt_sllod_omp.h +++ b/src/OPENMP/fix_nvt_sllod_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - www.cs.sandia.gov/~sjplimp/lammps.html - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_nvt_sphere_omp.cpp b/src/OPENMP/fix_nvt_sphere_omp.cpp index a3130c6ec4..20d729a972 100644 --- a/src/OPENMP/fix_nvt_sphere_omp.cpp +++ b/src/OPENMP/fix_nvt_sphere_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_nvt_sphere_omp.h b/src/OPENMP/fix_nvt_sphere_omp.h index 4b12d9093b..e5c7263b79 100644 --- a/src/OPENMP/fix_nvt_sphere_omp.h +++ b/src/OPENMP/fix_nvt_sphere_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_omp.cpp b/src/OPENMP/fix_omp.cpp index 4f5e990fcc..3a249bad82 100644 --- a/src/OPENMP/fix_omp.cpp +++ b/src/OPENMP/fix_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -25,7 +25,6 @@ #include "error.h" #include "force.h" #include "neighbor.h" -#include "neigh_request.h" #include "universe.h" #include "update.h" diff --git a/src/OPENMP/fix_omp.h b/src/OPENMP/fix_omp.h index b6e0e516f4..746c847602 100644 --- a/src/OPENMP/fix_omp.h +++ b/src/OPENMP/fix_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_qeq_comb_omp.cpp b/src/OPENMP/fix_qeq_comb_omp.cpp index a0d622401c..a2fcf85367 100644 --- a/src/OPENMP/fix_qeq_comb_omp.cpp +++ b/src/OPENMP/fix_qeq_comb_omp.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_qeq_comb_omp.h b/src/OPENMP/fix_qeq_comb_omp.h index 2f7188b5e9..390fa84d80 100644 --- a/src/OPENMP/fix_qeq_comb_omp.h +++ b/src/OPENMP/fix_qeq_comb_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ diff --git a/src/OPENMP/fix_qeq_reaxff_omp.cpp b/src/OPENMP/fix_qeq_reaxff_omp.cpp index 27a4ed037b..094c12b114 100644 --- a/src/OPENMP/fix_qeq_reaxff_omp.cpp +++ b/src/OPENMP/fix_qeq_reaxff_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_qeq_reaxff_omp.h b/src/OPENMP/fix_qeq_reaxff_omp.h index 20bcbdda29..2dcd1a1be8 100644 --- a/src/OPENMP/fix_qeq_reaxff_omp.h +++ b/src/OPENMP/fix_qeq_reaxff_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_rigid_nh_omp.cpp b/src/OPENMP/fix_rigid_nh_omp.cpp index ce13bf3c37..2f1b81fd5b 100644 --- a/src/OPENMP/fix_rigid_nh_omp.cpp +++ b/src/OPENMP/fix_rigid_nh_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_rigid_nh_omp.h b/src/OPENMP/fix_rigid_nh_omp.h index 03ec6766a4..6b70841058 100644 --- a/src/OPENMP/fix_rigid_nh_omp.h +++ b/src/OPENMP/fix_rigid_nh_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_rigid_nph_omp.cpp b/src/OPENMP/fix_rigid_nph_omp.cpp index 7bbf0fad81..d57ccd5f5c 100644 --- a/src/OPENMP/fix_rigid_nph_omp.cpp +++ b/src/OPENMP/fix_rigid_nph_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_rigid_nph_omp.h b/src/OPENMP/fix_rigid_nph_omp.h index b02134df21..069e9a1724 100644 --- a/src/OPENMP/fix_rigid_nph_omp.h +++ b/src/OPENMP/fix_rigid_nph_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_rigid_npt_omp.cpp b/src/OPENMP/fix_rigid_npt_omp.cpp index c661d68482..c231f798cd 100644 --- a/src/OPENMP/fix_rigid_npt_omp.cpp +++ b/src/OPENMP/fix_rigid_npt_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_rigid_npt_omp.h b/src/OPENMP/fix_rigid_npt_omp.h index 8d329d097d..63f8cbf8db 100644 --- a/src/OPENMP/fix_rigid_npt_omp.h +++ b/src/OPENMP/fix_rigid_npt_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_rigid_nve_omp.cpp b/src/OPENMP/fix_rigid_nve_omp.cpp index 2073a3c924..2efbb4de23 100644 --- a/src/OPENMP/fix_rigid_nve_omp.cpp +++ b/src/OPENMP/fix_rigid_nve_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_rigid_nve_omp.h b/src/OPENMP/fix_rigid_nve_omp.h index a9c1dfeaf4..53bf525ec1 100644 --- a/src/OPENMP/fix_rigid_nve_omp.h +++ b/src/OPENMP/fix_rigid_nve_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_rigid_nvt_omp.cpp b/src/OPENMP/fix_rigid_nvt_omp.cpp index 141b6e57d3..aaad0cf0fd 100644 --- a/src/OPENMP/fix_rigid_nvt_omp.cpp +++ b/src/OPENMP/fix_rigid_nvt_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_rigid_nvt_omp.h b/src/OPENMP/fix_rigid_nvt_omp.h index f3ee9bcbbc..075fccf5b3 100644 --- a/src/OPENMP/fix_rigid_nvt_omp.h +++ b/src/OPENMP/fix_rigid_nvt_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_rigid_omp.cpp b/src/OPENMP/fix_rigid_omp.cpp index b5d73fe18a..de381415a0 100644 --- a/src/OPENMP/fix_rigid_omp.cpp +++ b/src/OPENMP/fix_rigid_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_rigid_omp.h b/src/OPENMP/fix_rigid_omp.h index 657ae681ec..679dff7508 100644 --- a/src/OPENMP/fix_rigid_omp.h +++ b/src/OPENMP/fix_rigid_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_rigid_small_omp.cpp b/src/OPENMP/fix_rigid_small_omp.cpp index 62235b84a7..e11b98b7e1 100644 --- a/src/OPENMP/fix_rigid_small_omp.cpp +++ b/src/OPENMP/fix_rigid_small_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/fix_rigid_small_omp.h b/src/OPENMP/fix_rigid_small_omp.h index 335a070296..3d8bca1a6d 100644 --- a/src/OPENMP/fix_rigid_small_omp.h +++ b/src/OPENMP/fix_rigid_small_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/improper_class2_omp.cpp b/src/OPENMP/improper_class2_omp.cpp index 9474b696f5..b7387ea75a 100644 --- a/src/OPENMP/improper_class2_omp.cpp +++ b/src/OPENMP/improper_class2_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/improper_class2_omp.h b/src/OPENMP/improper_class2_omp.h index efb1f67c4c..7c04ff4aa0 100644 --- a/src/OPENMP/improper_class2_omp.h +++ b/src/OPENMP/improper_class2_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/improper_cossq_omp.cpp b/src/OPENMP/improper_cossq_omp.cpp index acb6cd0d46..3bfc86bcab 100644 --- a/src/OPENMP/improper_cossq_omp.cpp +++ b/src/OPENMP/improper_cossq_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/improper_cossq_omp.h b/src/OPENMP/improper_cossq_omp.h index 515ee0d076..0a609d4a01 100644 --- a/src/OPENMP/improper_cossq_omp.h +++ b/src/OPENMP/improper_cossq_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/improper_cvff_omp.cpp b/src/OPENMP/improper_cvff_omp.cpp index 47b9b930e1..310806d872 100644 --- a/src/OPENMP/improper_cvff_omp.cpp +++ b/src/OPENMP/improper_cvff_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/improper_cvff_omp.h b/src/OPENMP/improper_cvff_omp.h index 04faba38ac..07917e808e 100644 --- a/src/OPENMP/improper_cvff_omp.h +++ b/src/OPENMP/improper_cvff_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/improper_fourier_omp.cpp b/src/OPENMP/improper_fourier_omp.cpp index ef92e49e67..b70e3fb0ac 100644 --- a/src/OPENMP/improper_fourier_omp.cpp +++ b/src/OPENMP/improper_fourier_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/improper_fourier_omp.h b/src/OPENMP/improper_fourier_omp.h index e9b63b68dc..36e9840625 100644 --- a/src/OPENMP/improper_fourier_omp.h +++ b/src/OPENMP/improper_fourier_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/improper_harmonic_omp.cpp b/src/OPENMP/improper_harmonic_omp.cpp index 9d341febff..d17fe9407d 100644 --- a/src/OPENMP/improper_harmonic_omp.cpp +++ b/src/OPENMP/improper_harmonic_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/improper_harmonic_omp.h b/src/OPENMP/improper_harmonic_omp.h index 4caf47d56e..b50c348cb9 100644 --- a/src/OPENMP/improper_harmonic_omp.h +++ b/src/OPENMP/improper_harmonic_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/improper_ring_omp.cpp b/src/OPENMP/improper_ring_omp.cpp index 1be36ac71c..899727c685 100644 --- a/src/OPENMP/improper_ring_omp.cpp +++ b/src/OPENMP/improper_ring_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/improper_ring_omp.h b/src/OPENMP/improper_ring_omp.h index 7adce7014c..eb0efb61e9 100644 --- a/src/OPENMP/improper_ring_omp.h +++ b/src/OPENMP/improper_ring_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/improper_umbrella_omp.cpp b/src/OPENMP/improper_umbrella_omp.cpp index a07ac6a73f..e5d03863df 100644 --- a/src/OPENMP/improper_umbrella_omp.cpp +++ b/src/OPENMP/improper_umbrella_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/improper_umbrella_omp.h b/src/OPENMP/improper_umbrella_omp.h index 81f1a05787..c8ded8edc4 100644 --- a/src/OPENMP/improper_umbrella_omp.h +++ b/src/OPENMP/improper_umbrella_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/msm_cg_omp.cpp b/src/OPENMP/msm_cg_omp.cpp index c45e75f9a5..66cb32fdf5 100644 --- a/src/OPENMP/msm_cg_omp.cpp +++ b/src/OPENMP/msm_cg_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -23,7 +23,7 @@ #include "domain.h" #include "error.h" #include "force.h" -#include "gridcomm.h" +#include "grid3d.h" #include "memory.h" #include "neighbor.h" #include "thr_omp.h" @@ -59,7 +59,7 @@ MSMCGOMP::MSMCGOMP(LAMMPS *lmp) : MSMOMP(lmp), void MSMCGOMP::settings(int narg, char **arg) { if ((narg < 1) || (narg > 2)) - error->all(FLERR,"Illegal kspace_style msm/cg/omp command"); + error->all(FLERR,"Illegal kspace_style {} command", force->kspace_style); MSMOMP::settings(narg,arg); @@ -166,7 +166,7 @@ void MSMCGOMP::compute(int eflag, int vflag) // to fully sum contribution in their 3d grid current_level = 0; - gcall->reverse_comm(GridComm::KSPACE,this,1,sizeof(double),REVERSE_RHO, + gcall->reverse_comm(Grid3d::KSPACE,this,REVERSE_RHO,1,sizeof(double), gcall_buf1,gcall_buf2,MPI_DOUBLE); // forward communicate charge density values to fill ghost grid points @@ -175,7 +175,7 @@ void MSMCGOMP::compute(int eflag, int vflag) for (int n=0; n<=levels-2; n++) { if (!active_flag[n]) continue; current_level = n; - gc[n]->forward_comm(GridComm::KSPACE,this,1,sizeof(double),FORWARD_RHO, + gc[n]->forward_comm(Grid3d::KSPACE,this,FORWARD_RHO,1,sizeof(double), gc_buf1[n],gc_buf2[n],MPI_DOUBLE); direct(n); restriction(n); @@ -188,15 +188,15 @@ void MSMCGOMP::compute(int eflag, int vflag) if (domain->nonperiodic) { current_level = levels-1; gc[levels-1]-> - forward_comm(GridComm::KSPACE,this,1,sizeof(double),FORWARD_RHO, + forward_comm(Grid3d::KSPACE,this,FORWARD_RHO,1,sizeof(double), gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE); direct_top(levels-1); gc[levels-1]-> - reverse_comm(GridComm::KSPACE,this,1,sizeof(double),REVERSE_AD, + reverse_comm(Grid3d::KSPACE,this,REVERSE_AD,1,sizeof(double), gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE); if (vflag_atom) gc[levels-1]-> - reverse_comm(GridComm::KSPACE,this,6,sizeof(double),REVERSE_AD_PERATOM, + reverse_comm(Grid3d::KSPACE,this,REVERSE_AD_PERATOM,6,sizeof(double), gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE); } else { @@ -207,7 +207,7 @@ void MSMCGOMP::compute(int eflag, int vflag) current_level = levels-1; if (vflag_atom) gc[levels-1]-> - reverse_comm(GridComm::KSPACE,this,6,sizeof(double),REVERSE_AD_PERATOM, + reverse_comm(Grid3d::KSPACE,this,REVERSE_AD_PERATOM,6,sizeof(double), gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE); } } @@ -220,27 +220,27 @@ void MSMCGOMP::compute(int eflag, int vflag) prolongation(n); current_level = n; - gc[n]->reverse_comm(GridComm::KSPACE,this,1,sizeof(double),REVERSE_AD, + gc[n]->reverse_comm(Grid3d::KSPACE,this,REVERSE_AD,1,sizeof(double), gc_buf1[n],gc_buf2[n],MPI_DOUBLE); // extra per-atom virial communication if (vflag_atom) - gc[n]->reverse_comm(GridComm::KSPACE,this,6,sizeof(double), - REVERSE_AD_PERATOM,gc_buf1[n],gc_buf2[n],MPI_DOUBLE); + gc[n]->reverse_comm(Grid3d::KSPACE,this,REVERSE_AD_PERATOM,6,sizeof(double), + gc_buf1[n],gc_buf2[n],MPI_DOUBLE); } // all procs communicate E-field values // to fill ghost cells surrounding their 3d bricks current_level = 0; - gcall->forward_comm(GridComm::KSPACE,this,1,sizeof(double),FORWARD_AD, + gcall->forward_comm(Grid3d::KSPACE,this,FORWARD_AD,1,sizeof(double), gcall_buf1,gcall_buf2,MPI_DOUBLE); // extra per-atom energy/virial communication if (vflag_atom) - gcall->forward_comm(GridComm::KSPACE,this,6,sizeof(double),FORWARD_AD_PERATOM, + gcall->forward_comm(Grid3d::KSPACE,this,FORWARD_AD_PERATOM,6,sizeof(double), gcall_buf1,gcall_buf2,MPI_DOUBLE); // calculate the force on my particles (interpolation) diff --git a/src/OPENMP/msm_cg_omp.h b/src/OPENMP/msm_cg_omp.h index 910b40c678..7e88049679 100644 --- a/src/OPENMP/msm_cg_omp.h +++ b/src/OPENMP/msm_cg_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/msm_omp.cpp b/src/OPENMP/msm_omp.cpp index f4b298cc10..0a7a08a17a 100644 --- a/src/OPENMP/msm_omp.cpp +++ b/src/OPENMP/msm_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/msm_omp.h b/src/OPENMP/msm_omp.h index 2bad9d0db8..a982ba0535 100644 --- a/src/OPENMP/msm_omp.h +++ b/src/OPENMP/msm_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_full_bin_atomonly_omp.cpp b/src/OPENMP/npair_full_bin_atomonly_omp.cpp index b821ee85f7..0a37cca287 100644 --- a/src/OPENMP/npair_full_bin_atomonly_omp.cpp +++ b/src/OPENMP/npair_full_bin_atomonly_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_full_bin_atomonly_omp.h b/src/OPENMP/npair_full_bin_atomonly_omp.h index 1ccb6a84d0..50b1aa753c 100644 --- a/src/OPENMP/npair_full_bin_atomonly_omp.h +++ b/src/OPENMP/npair_full_bin_atomonly_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_full_bin_ghost_omp.cpp b/src/OPENMP/npair_full_bin_ghost_omp.cpp index f014170546..5723a418f5 100644 --- a/src/OPENMP/npair_full_bin_ghost_omp.cpp +++ b/src/OPENMP/npair_full_bin_ghost_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_full_bin_ghost_omp.h b/src/OPENMP/npair_full_bin_ghost_omp.h index cfc83a37a7..6de134dcf8 100644 --- a/src/OPENMP/npair_full_bin_ghost_omp.h +++ b/src/OPENMP/npair_full_bin_ghost_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_full_bin_omp.cpp b/src/OPENMP/npair_full_bin_omp.cpp index 106f430776..94668002a9 100644 --- a/src/OPENMP/npair_full_bin_omp.cpp +++ b/src/OPENMP/npair_full_bin_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_full_bin_omp.h b/src/OPENMP/npair_full_bin_omp.h index 8a1ef7ae1a..333025a1fb 100644 --- a/src/OPENMP/npair_full_bin_omp.h +++ b/src/OPENMP/npair_full_bin_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_full_multi_old_omp.cpp b/src/OPENMP/npair_full_multi_old_omp.cpp index 6480c55d59..f0ed6360ab 100644 --- a/src/OPENMP/npair_full_multi_old_omp.cpp +++ b/src/OPENMP/npair_full_multi_old_omp.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_full_multi_old_omp.h b/src/OPENMP/npair_full_multi_old_omp.h index ee8bf9024b..5d9f4c2f88 100644 --- a/src/OPENMP/npair_full_multi_old_omp.h +++ b/src/OPENMP/npair_full_multi_old_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_full_multi_omp.cpp b/src/OPENMP/npair_full_multi_omp.cpp index d3ff25c643..1e39838381 100644 --- a/src/OPENMP/npair_full_multi_omp.cpp +++ b/src/OPENMP/npair_full_multi_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_full_multi_omp.h b/src/OPENMP/npair_full_multi_omp.h index 6272a94c2a..0d71bf7bc6 100644 --- a/src/OPENMP/npair_full_multi_omp.h +++ b/src/OPENMP/npair_full_multi_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_full_nsq_ghost_omp.cpp b/src/OPENMP/npair_full_nsq_ghost_omp.cpp index ba268bf193..05f402a99d 100644 --- a/src/OPENMP/npair_full_nsq_ghost_omp.cpp +++ b/src/OPENMP/npair_full_nsq_ghost_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_full_nsq_ghost_omp.h b/src/OPENMP/npair_full_nsq_ghost_omp.h index c68e90b7a7..448354d4ba 100644 --- a/src/OPENMP/npair_full_nsq_ghost_omp.h +++ b/src/OPENMP/npair_full_nsq_ghost_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_full_nsq_omp.cpp b/src/OPENMP/npair_full_nsq_omp.cpp index 1c44629ba5..6349906771 100644 --- a/src/OPENMP/npair_full_nsq_omp.cpp +++ b/src/OPENMP/npair_full_nsq_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_full_nsq_omp.h b/src/OPENMP/npair_full_nsq_omp.h index 684a81be8e..53e913a18c 100644 --- a/src/OPENMP/npair_full_nsq_omp.h +++ b/src/OPENMP/npair_full_nsq_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_bin_atomonly_newton_omp.cpp b/src/OPENMP/npair_half_bin_atomonly_newton_omp.cpp index 2add88d358..1bc1199628 100644 --- a/src/OPENMP/npair_half_bin_atomonly_newton_omp.cpp +++ b/src/OPENMP/npair_half_bin_atomonly_newton_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_bin_atomonly_newton_omp.h b/src/OPENMP/npair_half_bin_atomonly_newton_omp.h index a74af6cd9a..dcec3aeee2 100644 --- a/src/OPENMP/npair_half_bin_atomonly_newton_omp.h +++ b/src/OPENMP/npair_half_bin_atomonly_newton_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_bin_newtoff_ghost_omp.cpp b/src/OPENMP/npair_half_bin_newtoff_ghost_omp.cpp index ff90dd26ed..2255033204 100644 --- a/src/OPENMP/npair_half_bin_newtoff_ghost_omp.cpp +++ b/src/OPENMP/npair_half_bin_newtoff_ghost_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_bin_newtoff_ghost_omp.h b/src/OPENMP/npair_half_bin_newtoff_ghost_omp.h index 264b8bba73..0258320f88 100644 --- a/src/OPENMP/npair_half_bin_newtoff_ghost_omp.h +++ b/src/OPENMP/npair_half_bin_newtoff_ghost_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_bin_newtoff_omp.cpp b/src/OPENMP/npair_half_bin_newtoff_omp.cpp index 796d5bf24e..36997d9bcb 100644 --- a/src/OPENMP/npair_half_bin_newtoff_omp.cpp +++ b/src/OPENMP/npair_half_bin_newtoff_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_bin_newtoff_omp.h b/src/OPENMP/npair_half_bin_newtoff_omp.h index d8520e58ab..e5d3034667 100644 --- a/src/OPENMP/npair_half_bin_newtoff_omp.h +++ b/src/OPENMP/npair_half_bin_newtoff_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_bin_newton_omp.cpp b/src/OPENMP/npair_half_bin_newton_omp.cpp index d2e6ef9743..1663a2f14c 100644 --- a/src/OPENMP/npair_half_bin_newton_omp.cpp +++ b/src/OPENMP/npair_half_bin_newton_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_bin_newton_omp.h b/src/OPENMP/npair_half_bin_newton_omp.h index 4f2567b4a6..68064cdf45 100644 --- a/src/OPENMP/npair_half_bin_newton_omp.h +++ b/src/OPENMP/npair_half_bin_newton_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_bin_newton_tri_omp.cpp b/src/OPENMP/npair_half_bin_newton_tri_omp.cpp index 9e44fd6f87..e754456ef1 100644 --- a/src/OPENMP/npair_half_bin_newton_tri_omp.cpp +++ b/src/OPENMP/npair_half_bin_newton_tri_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_bin_newton_tri_omp.h b/src/OPENMP/npair_half_bin_newton_tri_omp.h index a6605b6b25..90d5af5db1 100644 --- a/src/OPENMP/npair_half_bin_newton_tri_omp.h +++ b/src/OPENMP/npair_half_bin_newton_tri_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_multi_newtoff_omp.cpp b/src/OPENMP/npair_half_multi_newtoff_omp.cpp index d4a63cb9e8..1b65653f76 100644 --- a/src/OPENMP/npair_half_multi_newtoff_omp.cpp +++ b/src/OPENMP/npair_half_multi_newtoff_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_multi_newtoff_omp.h b/src/OPENMP/npair_half_multi_newtoff_omp.h index 46e3556b5b..658f41f926 100644 --- a/src/OPENMP/npair_half_multi_newtoff_omp.h +++ b/src/OPENMP/npair_half_multi_newtoff_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_multi_newton_omp.cpp b/src/OPENMP/npair_half_multi_newton_omp.cpp index 9ad740a043..8add1d3703 100644 --- a/src/OPENMP/npair_half_multi_newton_omp.cpp +++ b/src/OPENMP/npair_half_multi_newton_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_multi_newton_omp.h b/src/OPENMP/npair_half_multi_newton_omp.h index cd0b033de0..44bee84653 100644 --- a/src/OPENMP/npair_half_multi_newton_omp.h +++ b/src/OPENMP/npair_half_multi_newton_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_multi_newton_tri_omp.cpp b/src/OPENMP/npair_half_multi_newton_tri_omp.cpp index 71f1605366..a152d011a7 100644 --- a/src/OPENMP/npair_half_multi_newton_tri_omp.cpp +++ b/src/OPENMP/npair_half_multi_newton_tri_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_multi_newton_tri_omp.h b/src/OPENMP/npair_half_multi_newton_tri_omp.h index 431b24a557..21731f4f0b 100644 --- a/src/OPENMP/npair_half_multi_newton_tri_omp.h +++ b/src/OPENMP/npair_half_multi_newton_tri_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_multi_old_newtoff_omp.cpp b/src/OPENMP/npair_half_multi_old_newtoff_omp.cpp index 79120c905c..ac5e9dae04 100644 --- a/src/OPENMP/npair_half_multi_old_newtoff_omp.cpp +++ b/src/OPENMP/npair_half_multi_old_newtoff_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_multi_old_newtoff_omp.h b/src/OPENMP/npair_half_multi_old_newtoff_omp.h index 587997cf8e..26484d6c5b 100644 --- a/src/OPENMP/npair_half_multi_old_newtoff_omp.h +++ b/src/OPENMP/npair_half_multi_old_newtoff_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_multi_old_newton_omp.cpp b/src/OPENMP/npair_half_multi_old_newton_omp.cpp index 8588796a15..baa9dd0724 100644 --- a/src/OPENMP/npair_half_multi_old_newton_omp.cpp +++ b/src/OPENMP/npair_half_multi_old_newton_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_multi_old_newton_omp.h b/src/OPENMP/npair_half_multi_old_newton_omp.h index 7c78d50946..8182b49bd7 100644 --- a/src/OPENMP/npair_half_multi_old_newton_omp.h +++ b/src/OPENMP/npair_half_multi_old_newton_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_multi_old_newton_tri_omp.cpp b/src/OPENMP/npair_half_multi_old_newton_tri_omp.cpp index 78430df20e..e4895ff1a9 100644 --- a/src/OPENMP/npair_half_multi_old_newton_tri_omp.cpp +++ b/src/OPENMP/npair_half_multi_old_newton_tri_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_multi_old_newton_tri_omp.h b/src/OPENMP/npair_half_multi_old_newton_tri_omp.h index 7ddb75efc3..5efb007dc1 100644 --- a/src/OPENMP/npair_half_multi_old_newton_tri_omp.h +++ b/src/OPENMP/npair_half_multi_old_newton_tri_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_nsq_newtoff_ghost_omp.cpp b/src/OPENMP/npair_half_nsq_newtoff_ghost_omp.cpp index 7776f62cda..388e51e1af 100644 --- a/src/OPENMP/npair_half_nsq_newtoff_ghost_omp.cpp +++ b/src/OPENMP/npair_half_nsq_newtoff_ghost_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_nsq_newtoff_ghost_omp.h b/src/OPENMP/npair_half_nsq_newtoff_ghost_omp.h index 0234c420dc..4df15104c3 100644 --- a/src/OPENMP/npair_half_nsq_newtoff_ghost_omp.h +++ b/src/OPENMP/npair_half_nsq_newtoff_ghost_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_nsq_newtoff_omp.cpp b/src/OPENMP/npair_half_nsq_newtoff_omp.cpp index 12883967d5..002ea37e6b 100644 --- a/src/OPENMP/npair_half_nsq_newtoff_omp.cpp +++ b/src/OPENMP/npair_half_nsq_newtoff_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_nsq_newtoff_omp.h b/src/OPENMP/npair_half_nsq_newtoff_omp.h index 364c9deb9a..47a03750f7 100644 --- a/src/OPENMP/npair_half_nsq_newtoff_omp.h +++ b/src/OPENMP/npair_half_nsq_newtoff_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_nsq_newton_omp.cpp b/src/OPENMP/npair_half_nsq_newton_omp.cpp index 92c62d4a09..cb08cb7f7a 100644 --- a/src/OPENMP/npair_half_nsq_newton_omp.cpp +++ b/src/OPENMP/npair_half_nsq_newton_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_nsq_newton_omp.h b/src/OPENMP/npair_half_nsq_newton_omp.h index f34558d98a..00e975d389 100644 --- a/src/OPENMP/npair_half_nsq_newton_omp.h +++ b/src/OPENMP/npair_half_nsq_newton_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_respa_bin_newtoff_omp.cpp b/src/OPENMP/npair_half_respa_bin_newtoff_omp.cpp index ced2fac83d..c6be04419d 100644 --- a/src/OPENMP/npair_half_respa_bin_newtoff_omp.cpp +++ b/src/OPENMP/npair_half_respa_bin_newtoff_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_respa_bin_newtoff_omp.h b/src/OPENMP/npair_half_respa_bin_newtoff_omp.h index 3a488b68b8..8ad6209d21 100644 --- a/src/OPENMP/npair_half_respa_bin_newtoff_omp.h +++ b/src/OPENMP/npair_half_respa_bin_newtoff_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_respa_bin_newton_omp.cpp b/src/OPENMP/npair_half_respa_bin_newton_omp.cpp index 372f0e0715..51fc7a2ed8 100644 --- a/src/OPENMP/npair_half_respa_bin_newton_omp.cpp +++ b/src/OPENMP/npair_half_respa_bin_newton_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_respa_bin_newton_omp.h b/src/OPENMP/npair_half_respa_bin_newton_omp.h index 5c7d397453..695d0ce627 100644 --- a/src/OPENMP/npair_half_respa_bin_newton_omp.h +++ b/src/OPENMP/npair_half_respa_bin_newton_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_respa_bin_newton_tri_omp.cpp b/src/OPENMP/npair_half_respa_bin_newton_tri_omp.cpp index 59305ec667..c998f71290 100644 --- a/src/OPENMP/npair_half_respa_bin_newton_tri_omp.cpp +++ b/src/OPENMP/npair_half_respa_bin_newton_tri_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_respa_bin_newton_tri_omp.h b/src/OPENMP/npair_half_respa_bin_newton_tri_omp.h index 9120239d2d..df45372960 100644 --- a/src/OPENMP/npair_half_respa_bin_newton_tri_omp.h +++ b/src/OPENMP/npair_half_respa_bin_newton_tri_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_respa_nsq_newtoff_omp.cpp b/src/OPENMP/npair_half_respa_nsq_newtoff_omp.cpp index 8f99a66b6b..1167a7601b 100644 --- a/src/OPENMP/npair_half_respa_nsq_newtoff_omp.cpp +++ b/src/OPENMP/npair_half_respa_nsq_newtoff_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_respa_nsq_newtoff_omp.h b/src/OPENMP/npair_half_respa_nsq_newtoff_omp.h index b8439f2988..abd28fd51b 100644 --- a/src/OPENMP/npair_half_respa_nsq_newtoff_omp.h +++ b/src/OPENMP/npair_half_respa_nsq_newtoff_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_respa_nsq_newton_omp.cpp b/src/OPENMP/npair_half_respa_nsq_newton_omp.cpp index a2b055355a..6604861f74 100644 --- a/src/OPENMP/npair_half_respa_nsq_newton_omp.cpp +++ b/src/OPENMP/npair_half_respa_nsq_newton_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_respa_nsq_newton_omp.h b/src/OPENMP/npair_half_respa_nsq_newton_omp.h index 6e334ea2dc..d949ef7e93 100644 --- a/src/OPENMP/npair_half_respa_nsq_newton_omp.h +++ b/src/OPENMP/npair_half_respa_nsq_newton_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_size_bin_newtoff_omp.cpp b/src/OPENMP/npair_half_size_bin_newtoff_omp.cpp index 07082868f6..c205b67539 100644 --- a/src/OPENMP/npair_half_size_bin_newtoff_omp.cpp +++ b/src/OPENMP/npair_half_size_bin_newtoff_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_size_bin_newtoff_omp.h b/src/OPENMP/npair_half_size_bin_newtoff_omp.h index 7853c5ca00..a91836b152 100644 --- a/src/OPENMP/npair_half_size_bin_newtoff_omp.h +++ b/src/OPENMP/npair_half_size_bin_newtoff_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_size_bin_newton_omp.cpp b/src/OPENMP/npair_half_size_bin_newton_omp.cpp index 42a74f13aa..628057d41d 100644 --- a/src/OPENMP/npair_half_size_bin_newton_omp.cpp +++ b/src/OPENMP/npair_half_size_bin_newton_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_size_bin_newton_omp.h b/src/OPENMP/npair_half_size_bin_newton_omp.h index 708ae2a18a..efc554bb3c 100644 --- a/src/OPENMP/npair_half_size_bin_newton_omp.h +++ b/src/OPENMP/npair_half_size_bin_newton_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_size_bin_newton_tri_omp.cpp b/src/OPENMP/npair_half_size_bin_newton_tri_omp.cpp index 5a77de0796..c320296442 100644 --- a/src/OPENMP/npair_half_size_bin_newton_tri_omp.cpp +++ b/src/OPENMP/npair_half_size_bin_newton_tri_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_size_bin_newton_tri_omp.h b/src/OPENMP/npair_half_size_bin_newton_tri_omp.h index ec2b2db476..65b46395ca 100644 --- a/src/OPENMP/npair_half_size_bin_newton_tri_omp.h +++ b/src/OPENMP/npair_half_size_bin_newton_tri_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_size_multi_newtoff_omp.cpp b/src/OPENMP/npair_half_size_multi_newtoff_omp.cpp index d58d250209..73564a150c 100644 --- a/src/OPENMP/npair_half_size_multi_newtoff_omp.cpp +++ b/src/OPENMP/npair_half_size_multi_newtoff_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_size_multi_newtoff_omp.h b/src/OPENMP/npair_half_size_multi_newtoff_omp.h index 59c175382d..2e58d9ea38 100644 --- a/src/OPENMP/npair_half_size_multi_newtoff_omp.h +++ b/src/OPENMP/npair_half_size_multi_newtoff_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_size_multi_newton_omp.cpp b/src/OPENMP/npair_half_size_multi_newton_omp.cpp index 3190131442..0ed843ea0b 100644 --- a/src/OPENMP/npair_half_size_multi_newton_omp.cpp +++ b/src/OPENMP/npair_half_size_multi_newton_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_size_multi_newton_omp.h b/src/OPENMP/npair_half_size_multi_newton_omp.h index b235fd2d28..99f9174913 100644 --- a/src/OPENMP/npair_half_size_multi_newton_omp.h +++ b/src/OPENMP/npair_half_size_multi_newton_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_size_multi_newton_tri_omp.cpp b/src/OPENMP/npair_half_size_multi_newton_tri_omp.cpp index 717e023f4a..9a0ead482b 100644 --- a/src/OPENMP/npair_half_size_multi_newton_tri_omp.cpp +++ b/src/OPENMP/npair_half_size_multi_newton_tri_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_size_multi_newton_tri_omp.h b/src/OPENMP/npair_half_size_multi_newton_tri_omp.h index 117acb2a04..d4f6eacc27 100644 --- a/src/OPENMP/npair_half_size_multi_newton_tri_omp.h +++ b/src/OPENMP/npair_half_size_multi_newton_tri_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_size_multi_old_newtoff_omp.cpp b/src/OPENMP/npair_half_size_multi_old_newtoff_omp.cpp index 37dbe9cc53..c368e71095 100644 --- a/src/OPENMP/npair_half_size_multi_old_newtoff_omp.cpp +++ b/src/OPENMP/npair_half_size_multi_old_newtoff_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_size_multi_old_newtoff_omp.h b/src/OPENMP/npair_half_size_multi_old_newtoff_omp.h index 7dc8028643..05eb0a5269 100644 --- a/src/OPENMP/npair_half_size_multi_old_newtoff_omp.h +++ b/src/OPENMP/npair_half_size_multi_old_newtoff_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_size_multi_old_newton_omp.cpp b/src/OPENMP/npair_half_size_multi_old_newton_omp.cpp index 789ed33e6b..187efe04d1 100644 --- a/src/OPENMP/npair_half_size_multi_old_newton_omp.cpp +++ b/src/OPENMP/npair_half_size_multi_old_newton_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_size_multi_old_newton_omp.h b/src/OPENMP/npair_half_size_multi_old_newton_omp.h index 5644b34dbe..70ae082dbb 100644 --- a/src/OPENMP/npair_half_size_multi_old_newton_omp.h +++ b/src/OPENMP/npair_half_size_multi_old_newton_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_size_multi_old_newton_tri_omp.cpp b/src/OPENMP/npair_half_size_multi_old_newton_tri_omp.cpp index 8302d9fab2..c74b191f66 100644 --- a/src/OPENMP/npair_half_size_multi_old_newton_tri_omp.cpp +++ b/src/OPENMP/npair_half_size_multi_old_newton_tri_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_size_multi_old_newton_tri_omp.h b/src/OPENMP/npair_half_size_multi_old_newton_tri_omp.h index 124e72c8e6..3c1765b668 100644 --- a/src/OPENMP/npair_half_size_multi_old_newton_tri_omp.h +++ b/src/OPENMP/npair_half_size_multi_old_newton_tri_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_size_nsq_newtoff_omp.cpp b/src/OPENMP/npair_half_size_nsq_newtoff_omp.cpp index 7f4b22e729..020551bd8e 100644 --- a/src/OPENMP/npair_half_size_nsq_newtoff_omp.cpp +++ b/src/OPENMP/npair_half_size_nsq_newtoff_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_size_nsq_newtoff_omp.h b/src/OPENMP/npair_half_size_nsq_newtoff_omp.h index ee022b0cf5..93f038eed4 100644 --- a/src/OPENMP/npair_half_size_nsq_newtoff_omp.h +++ b/src/OPENMP/npair_half_size_nsq_newtoff_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_size_nsq_newton_omp.cpp b/src/OPENMP/npair_half_size_nsq_newton_omp.cpp index 9262b869af..35dc42ec5b 100644 --- a/src/OPENMP/npair_half_size_nsq_newton_omp.cpp +++ b/src/OPENMP/npair_half_size_nsq_newton_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_half_size_nsq_newton_omp.h b/src/OPENMP/npair_half_size_nsq_newton_omp.h index 5929a8ec49..9a7e912007 100644 --- a/src/OPENMP/npair_half_size_nsq_newton_omp.h +++ b/src/OPENMP/npair_half_size_nsq_newton_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_halffull_newtoff_omp.cpp b/src/OPENMP/npair_halffull_newtoff_omp.cpp index 9abbbae48f..379ae149f8 100644 --- a/src/OPENMP/npair_halffull_newtoff_omp.cpp +++ b/src/OPENMP/npair_halffull_newtoff_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_halffull_newtoff_omp.h b/src/OPENMP/npair_halffull_newtoff_omp.h index a9b89814a4..f0ff24dcf9 100644 --- a/src/OPENMP/npair_halffull_newtoff_omp.h +++ b/src/OPENMP/npair_halffull_newtoff_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_halffull_newtoff_trim_omp.cpp b/src/OPENMP/npair_halffull_newtoff_trim_omp.cpp index 20d497d53e..d35b3b2ee8 100644 --- a/src/OPENMP/npair_halffull_newtoff_trim_omp.cpp +++ b/src/OPENMP/npair_halffull_newtoff_trim_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_halffull_newtoff_trim_omp.h b/src/OPENMP/npair_halffull_newtoff_trim_omp.h index 6d701b5cb6..19e1c55eeb 100644 --- a/src/OPENMP/npair_halffull_newtoff_trim_omp.h +++ b/src/OPENMP/npair_halffull_newtoff_trim_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_halffull_newton_omp.cpp b/src/OPENMP/npair_halffull_newton_omp.cpp index 66b4e4b3b6..abd5f7eacb 100644 --- a/src/OPENMP/npair_halffull_newton_omp.cpp +++ b/src/OPENMP/npair_halffull_newton_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_halffull_newton_omp.h b/src/OPENMP/npair_halffull_newton_omp.h index 9a6339b934..3ce9fd9ebe 100644 --- a/src/OPENMP/npair_halffull_newton_omp.h +++ b/src/OPENMP/npair_halffull_newton_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_halffull_newton_trim_omp.cpp b/src/OPENMP/npair_halffull_newton_trim_omp.cpp index cefca47a5e..1446175013 100644 --- a/src/OPENMP/npair_halffull_newton_trim_omp.cpp +++ b/src/OPENMP/npair_halffull_newton_trim_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_halffull_newton_trim_omp.h b/src/OPENMP/npair_halffull_newton_trim_omp.h index a774a68c2b..4cb84f1b3a 100644 --- a/src/OPENMP/npair_halffull_newton_trim_omp.h +++ b/src/OPENMP/npair_halffull_newton_trim_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_omp.h b/src/OPENMP/npair_omp.h index b9ac9b2cc6..318fddfd54 100644 --- a/src/OPENMP/npair_omp.h +++ b/src/OPENMP/npair_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_skip_omp.h b/src/OPENMP/npair_skip_omp.h index 7f5daa6791..ce61968c17 100644 --- a/src/OPENMP/npair_skip_omp.h +++ b/src/OPENMP/npair_skip_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_trim_omp.cpp b/src/OPENMP/npair_trim_omp.cpp index 4b3b835f8c..d7ac0ddb40 100644 --- a/src/OPENMP/npair_trim_omp.cpp +++ b/src/OPENMP/npair_trim_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/npair_trim_omp.h b/src/OPENMP/npair_trim_omp.h index 48cd9eb6a0..eea8b4fd0d 100644 --- a/src/OPENMP/npair_trim_omp.h +++ b/src/OPENMP/npair_trim_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_adp_omp.cpp b/src/OPENMP/pair_adp_omp.cpp index 93a0fa1215..f04518eebb 100644 --- a/src/OPENMP/pair_adp_omp.cpp +++ b/src/OPENMP/pair_adp_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_adp_omp.h b/src/OPENMP/pair_adp_omp.h index f1df192f0e..aa724a7b5c 100644 --- a/src/OPENMP/pair_adp_omp.h +++ b/src/OPENMP/pair_adp_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_agni_omp.cpp b/src/OPENMP/pair_agni_omp.cpp index 4719d7e4a4..9d025a1b0a 100644 --- a/src/OPENMP/pair_agni_omp.cpp +++ b/src/OPENMP/pair_agni_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_agni_omp.h b/src/OPENMP/pair_agni_omp.h index 9288b982cf..a9fcf13890 100644 --- a/src/OPENMP/pair_agni_omp.h +++ b/src/OPENMP/pair_agni_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_airebo_morse_omp.cpp b/src/OPENMP/pair_airebo_morse_omp.cpp index 965f895add..03468a629f 100644 --- a/src/OPENMP/pair_airebo_morse_omp.cpp +++ b/src/OPENMP/pair_airebo_morse_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_airebo_morse_omp.h b/src/OPENMP/pair_airebo_morse_omp.h index b7212b1b1c..dae7723b8a 100644 --- a/src/OPENMP/pair_airebo_morse_omp.h +++ b/src/OPENMP/pair_airebo_morse_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_airebo_omp.cpp b/src/OPENMP/pair_airebo_omp.cpp index 6e7491787a..f5cd8ffd9d 100644 --- a/src/OPENMP/pair_airebo_omp.cpp +++ b/src/OPENMP/pair_airebo_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_airebo_omp.h b/src/OPENMP/pair_airebo_omp.h index 5f94c6d13a..2e821940cf 100644 --- a/src/OPENMP/pair_airebo_omp.h +++ b/src/OPENMP/pair_airebo_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ diff --git a/src/OPENMP/pair_beck_omp.cpp b/src/OPENMP/pair_beck_omp.cpp index dae9decc0e..107c348c4c 100644 --- a/src/OPENMP/pair_beck_omp.cpp +++ b/src/OPENMP/pair_beck_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_beck_omp.h b/src/OPENMP/pair_beck_omp.h index 55bf4db335..6855ad0db0 100644 --- a/src/OPENMP/pair_beck_omp.h +++ b/src/OPENMP/pair_beck_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_born_coul_long_omp.cpp b/src/OPENMP/pair_born_coul_long_omp.cpp index 9d52b6cc8c..0f51a3a5cc 100644 --- a/src/OPENMP/pair_born_coul_long_omp.cpp +++ b/src/OPENMP/pair_born_coul_long_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_born_coul_long_omp.h b/src/OPENMP/pair_born_coul_long_omp.h index e61353cbcd..d320eb18e2 100644 --- a/src/OPENMP/pair_born_coul_long_omp.h +++ b/src/OPENMP/pair_born_coul_long_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_born_coul_msm_omp.cpp b/src/OPENMP/pair_born_coul_msm_omp.cpp index ec6cb989c3..d168a2865f 100644 --- a/src/OPENMP/pair_born_coul_msm_omp.cpp +++ b/src/OPENMP/pair_born_coul_msm_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_born_coul_msm_omp.h b/src/OPENMP/pair_born_coul_msm_omp.h index 34f81b2eac..90bbbc4e35 100644 --- a/src/OPENMP/pair_born_coul_msm_omp.h +++ b/src/OPENMP/pair_born_coul_msm_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_born_coul_wolf_omp.cpp b/src/OPENMP/pair_born_coul_wolf_omp.cpp index af6771fd9c..1f57a8578f 100644 --- a/src/OPENMP/pair_born_coul_wolf_omp.cpp +++ b/src/OPENMP/pair_born_coul_wolf_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_born_coul_wolf_omp.h b/src/OPENMP/pair_born_coul_wolf_omp.h index afcfe41fe6..6c7c183edb 100644 --- a/src/OPENMP/pair_born_coul_wolf_omp.h +++ b/src/OPENMP/pair_born_coul_wolf_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_born_omp.cpp b/src/OPENMP/pair_born_omp.cpp index 673136b00b..8a449cb656 100644 --- a/src/OPENMP/pair_born_omp.cpp +++ b/src/OPENMP/pair_born_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_born_omp.h b/src/OPENMP/pair_born_omp.h index dfa262f300..d49f355cab 100644 --- a/src/OPENMP/pair_born_omp.h +++ b/src/OPENMP/pair_born_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_brownian_omp.cpp b/src/OPENMP/pair_brownian_omp.cpp index b34b854d74..45288f13dd 100644 --- a/src/OPENMP/pair_brownian_omp.cpp +++ b/src/OPENMP/pair_brownian_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. @@ -197,7 +197,6 @@ void PairBrownianOMP::eval(int iifrom, int iito, ThrData * const thr) double prethermostat; double xl[3],a_sq,a_sh,a_pu,Fbmag; double p1[3],p2[3],p3[3]; - int overlaps = 0; // scale factor for Brownian moments @@ -252,10 +251,6 @@ void PairBrownianOMP::eval(int iifrom, int iito, ThrData * const thr) h_sep = r - 2.0*radi; - // check for overlaps - - if (h_sep < 0.0) overlaps++; - // if less than minimum gap, use minimum gap instead if (r < cut_inner[itype][jtype]) diff --git a/src/OPENMP/pair_brownian_omp.h b/src/OPENMP/pair_brownian_omp.h index 53abf600a4..b0b452dff8 100644 --- a/src/OPENMP/pair_brownian_omp.h +++ b/src/OPENMP/pair_brownian_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_brownian_poly_omp.cpp b/src/OPENMP/pair_brownian_poly_omp.cpp index 1ccd753fbe..91a496979d 100644 --- a/src/OPENMP/pair_brownian_poly_omp.cpp +++ b/src/OPENMP/pair_brownian_poly_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. @@ -187,7 +187,6 @@ void PairBrownianPolyOMP::eval(int iifrom, int iito, ThrData * const thr) RanMars &rng = *random_thr[thr->get_tid()]; double vxmu2f = force->vxmu2f; - int overlaps = 0; double randr; double prethermostat; double xl[3],a_sq,a_sh,a_pu,Fbmag; @@ -248,10 +247,6 @@ void PairBrownianPolyOMP::eval(int iifrom, int iito, ThrData * const thr) h_sep = r - radi-radj; - // check for overlaps - - if (h_sep < 0.0) overlaps++; - // if less than minimum gap, use minimum gap instead if (r < cut_inner[itype][jtype]) diff --git a/src/OPENMP/pair_brownian_poly_omp.h b/src/OPENMP/pair_brownian_poly_omp.h index 9ff184fb78..adf1419ae3 100644 --- a/src/OPENMP/pair_brownian_poly_omp.h +++ b/src/OPENMP/pair_brownian_poly_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_buck_coul_cut_omp.cpp b/src/OPENMP/pair_buck_coul_cut_omp.cpp index 4f086932db..18d2a20c76 100644 --- a/src/OPENMP/pair_buck_coul_cut_omp.cpp +++ b/src/OPENMP/pair_buck_coul_cut_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_buck_coul_cut_omp.h b/src/OPENMP/pair_buck_coul_cut_omp.h index 5e714853d8..ee454cfc72 100644 --- a/src/OPENMP/pair_buck_coul_cut_omp.h +++ b/src/OPENMP/pair_buck_coul_cut_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_buck_coul_long_omp.cpp b/src/OPENMP/pair_buck_coul_long_omp.cpp index 0b4f26bf52..da4b0bb5b0 100644 --- a/src/OPENMP/pair_buck_coul_long_omp.cpp +++ b/src/OPENMP/pair_buck_coul_long_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_buck_coul_long_omp.h b/src/OPENMP/pair_buck_coul_long_omp.h index 2bca674344..aba5902ea0 100644 --- a/src/OPENMP/pair_buck_coul_long_omp.h +++ b/src/OPENMP/pair_buck_coul_long_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_buck_coul_msm_omp.cpp b/src/OPENMP/pair_buck_coul_msm_omp.cpp index e859a0e284..b4ecaf7663 100644 --- a/src/OPENMP/pair_buck_coul_msm_omp.cpp +++ b/src/OPENMP/pair_buck_coul_msm_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_buck_coul_msm_omp.h b/src/OPENMP/pair_buck_coul_msm_omp.h index a04f7a3f95..75b33b72fe 100644 --- a/src/OPENMP/pair_buck_coul_msm_omp.h +++ b/src/OPENMP/pair_buck_coul_msm_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_buck_long_coul_long_omp.cpp b/src/OPENMP/pair_buck_long_coul_long_omp.cpp index 372c993a8d..bb1bdd9f2a 100644 --- a/src/OPENMP/pair_buck_long_coul_long_omp.cpp +++ b/src/OPENMP/pair_buck_long_coul_long_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_buck_long_coul_long_omp.h b/src/OPENMP/pair_buck_long_coul_long_omp.h index 98425350ad..ecbc913f8d 100644 --- a/src/OPENMP/pair_buck_long_coul_long_omp.h +++ b/src/OPENMP/pair_buck_long_coul_long_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_buck_omp.cpp b/src/OPENMP/pair_buck_omp.cpp index 285e2fadde..2426d5c872 100644 --- a/src/OPENMP/pair_buck_omp.cpp +++ b/src/OPENMP/pair_buck_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_buck_omp.h b/src/OPENMP/pair_buck_omp.h index bea2608044..07ab0522ac 100644 --- a/src/OPENMP/pair_buck_omp.h +++ b/src/OPENMP/pair_buck_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_colloid_omp.cpp b/src/OPENMP/pair_colloid_omp.cpp index 64a7d06322..b6ec22dd51 100644 --- a/src/OPENMP/pair_colloid_omp.cpp +++ b/src/OPENMP/pair_colloid_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_colloid_omp.h b/src/OPENMP/pair_colloid_omp.h index f433c57723..618bdf2734 100644 --- a/src/OPENMP/pair_colloid_omp.h +++ b/src/OPENMP/pair_colloid_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_comb_omp.cpp b/src/OPENMP/pair_comb_omp.cpp index b3306d678c..aceff6e111 100644 --- a/src/OPENMP/pair_comb_omp.cpp +++ b/src/OPENMP/pair_comb_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_comb_omp.h b/src/OPENMP/pair_comb_omp.h index 0eedff3b5f..d15c84b745 100644 --- a/src/OPENMP/pair_comb_omp.h +++ b/src/OPENMP/pair_comb_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ diff --git a/src/OPENMP/pair_coul_cut_global_omp.cpp b/src/OPENMP/pair_coul_cut_global_omp.cpp index 7305f9c025..c4236295a1 100644 --- a/src/OPENMP/pair_coul_cut_global_omp.cpp +++ b/src/OPENMP/pair_coul_cut_global_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_coul_cut_global_omp.h b/src/OPENMP/pair_coul_cut_global_omp.h index f71d6afe21..7befef833e 100644 --- a/src/OPENMP/pair_coul_cut_global_omp.h +++ b/src/OPENMP/pair_coul_cut_global_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_coul_cut_omp.cpp b/src/OPENMP/pair_coul_cut_omp.cpp index 884fe532be..a406695375 100644 --- a/src/OPENMP/pair_coul_cut_omp.cpp +++ b/src/OPENMP/pair_coul_cut_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_coul_cut_omp.h b/src/OPENMP/pair_coul_cut_omp.h index 218ff4cfc2..9b89265186 100644 --- a/src/OPENMP/pair_coul_cut_omp.h +++ b/src/OPENMP/pair_coul_cut_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_coul_cut_soft_omp.cpp b/src/OPENMP/pair_coul_cut_soft_omp.cpp index 6b16d71442..47dc63fb08 100644 --- a/src/OPENMP/pair_coul_cut_soft_omp.cpp +++ b/src/OPENMP/pair_coul_cut_soft_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_coul_cut_soft_omp.h b/src/OPENMP/pair_coul_cut_soft_omp.h index b2ecc64b80..0f652fcdc5 100644 --- a/src/OPENMP/pair_coul_cut_soft_omp.h +++ b/src/OPENMP/pair_coul_cut_soft_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_coul_debye_omp.cpp b/src/OPENMP/pair_coul_debye_omp.cpp index 622a84da95..7e609a12ab 100644 --- a/src/OPENMP/pair_coul_debye_omp.cpp +++ b/src/OPENMP/pair_coul_debye_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_coul_debye_omp.h b/src/OPENMP/pair_coul_debye_omp.h index e1b67a7d26..bca15e01cd 100644 --- a/src/OPENMP/pair_coul_debye_omp.h +++ b/src/OPENMP/pair_coul_debye_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_coul_diel_omp.cpp b/src/OPENMP/pair_coul_diel_omp.cpp index 4de5b69f7e..36de394a2a 100644 --- a/src/OPENMP/pair_coul_diel_omp.cpp +++ b/src/OPENMP/pair_coul_diel_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_coul_diel_omp.h b/src/OPENMP/pair_coul_diel_omp.h index 4c7c386e86..dd91715e6b 100644 --- a/src/OPENMP/pair_coul_diel_omp.h +++ b/src/OPENMP/pair_coul_diel_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_coul_dsf_omp.cpp b/src/OPENMP/pair_coul_dsf_omp.cpp index e36c12172f..4609288d24 100644 --- a/src/OPENMP/pair_coul_dsf_omp.cpp +++ b/src/OPENMP/pair_coul_dsf_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_coul_dsf_omp.h b/src/OPENMP/pair_coul_dsf_omp.h index d0aa45c11c..47f8071d61 100644 --- a/src/OPENMP/pair_coul_dsf_omp.h +++ b/src/OPENMP/pair_coul_dsf_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_coul_long_omp.cpp b/src/OPENMP/pair_coul_long_omp.cpp index a54dc8c966..b8c7423e76 100644 --- a/src/OPENMP/pair_coul_long_omp.cpp +++ b/src/OPENMP/pair_coul_long_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_coul_long_omp.h b/src/OPENMP/pair_coul_long_omp.h index cbe876f3d4..55c6acf559 100644 --- a/src/OPENMP/pair_coul_long_omp.h +++ b/src/OPENMP/pair_coul_long_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_coul_long_soft_omp.cpp b/src/OPENMP/pair_coul_long_soft_omp.cpp index b7d9cfc2fa..3670a219b6 100644 --- a/src/OPENMP/pair_coul_long_soft_omp.cpp +++ b/src/OPENMP/pair_coul_long_soft_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_coul_long_soft_omp.h b/src/OPENMP/pair_coul_long_soft_omp.h index 6cee02c424..dd3671d7ef 100644 --- a/src/OPENMP/pair_coul_long_soft_omp.h +++ b/src/OPENMP/pair_coul_long_soft_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_coul_msm_omp.cpp b/src/OPENMP/pair_coul_msm_omp.cpp index bf18009117..b2327e1e9e 100644 --- a/src/OPENMP/pair_coul_msm_omp.cpp +++ b/src/OPENMP/pair_coul_msm_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_coul_msm_omp.h b/src/OPENMP/pair_coul_msm_omp.h index 65ac5d320b..80c295af91 100644 --- a/src/OPENMP/pair_coul_msm_omp.h +++ b/src/OPENMP/pair_coul_msm_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_coul_wolf_omp.cpp b/src/OPENMP/pair_coul_wolf_omp.cpp index 520fe790b7..229e6b7991 100644 --- a/src/OPENMP/pair_coul_wolf_omp.cpp +++ b/src/OPENMP/pair_coul_wolf_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_coul_wolf_omp.h b/src/OPENMP/pair_coul_wolf_omp.h index 47aadd7443..663745bf73 100644 --- a/src/OPENMP/pair_coul_wolf_omp.h +++ b/src/OPENMP/pair_coul_wolf_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_dpd_ext_omp.cpp b/src/OPENMP/pair_dpd_ext_omp.cpp new file mode 100644 index 0000000000..e84c1360da --- /dev/null +++ b/src/OPENMP/pair_dpd_ext_omp.cpp @@ -0,0 +1,273 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + This software is distributed under the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#include "pair_dpd_ext_omp.h" + +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neigh_list.h" +#include "update.h" +#include "random_mars.h" +#include "suffix.h" + +#include + +#include "omp_compat.h" +using namespace LAMMPS_NS; + +#define EPSILON 1.0e-10 + +/* ---------------------------------------------------------------------- */ + +PairDPDExtOMP::PairDPDExtOMP(LAMMPS *lmp) : + PairDPDExt(lmp), ThrOMP(lmp, THR_PAIR) +{ + suffix_flag |= Suffix::OMP; + respa_enable = 0; + random_thr = nullptr; + nthreads = 0; +} + +/* ---------------------------------------------------------------------- */ + +PairDPDExtOMP::~PairDPDExtOMP() +{ + if (random_thr) { + for (int i=1; i < nthreads; ++i) + delete random_thr[i]; + + delete[] random_thr; + random_thr = nullptr; + } +} + +/* ---------------------------------------------------------------------- */ + +void PairDPDExtOMP::compute(int eflag, int vflag) +{ + ev_init(eflag,vflag); + + const int nall = atom->nlocal + atom->nghost; + const int inum = list->inum; + + // number of threads has changed. reallocate pool of pRNGs + if (nthreads != comm->nthreads) { + if (random_thr) { + for (int i=1; i < nthreads; ++i) + delete random_thr[i]; + + delete[] random_thr; + } + + nthreads = comm->nthreads; + random_thr = new RanMars*[nthreads]; + for (int i=1; i < nthreads; ++i) + random_thr[i] = nullptr; + + // to ensure full compatibility with the serial DPD style + // we use the serial random number generator instance for thread 0 + random_thr[0] = random; + } + +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag,vflag) +#endif + { + int ifrom, ito, tid; + + loop_setup_thr(ifrom, ito, tid, inum, nthreads); + ThrData *thr = fix->get_thr(tid); + thr->timer(Timer::START); + ev_setup_thr(eflag, vflag, nall, eatom, vatom, nullptr, thr); + + // generate a random number generator instance for + // all threads != 0. make sure we use unique seeds. + if ((tid > 0) && (random_thr[tid] == nullptr)) + random_thr[tid] = new RanMars(Pair::lmp, seed + comm->me + + comm->nprocs*tid); + + if (evflag) { + if (eflag) { + if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr); + else eval<1,1,0>(ifrom, ito, thr); + } else { + if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr); + else eval<1,0,0>(ifrom, ito, thr); + } + } else { + if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr); + else eval<0,0,0>(ifrom, ito, thr); + } + + thr->timer(Timer::PAIR); + reduce_thr(this, eflag, vflag, thr); + } // end of omp parallel region +} + +template +void PairDPDExtOMP::eval(int iifrom, int iito, ThrData * const thr) +{ + int i,j,ii,jj,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpairx,fpairy,fpairz,fpair; + double vxtmp,vytmp,vztmp,delvx,delvy,delvz; + double rsq,r,rinv,dot,wd,wdPar,wdPerp,randnum,randnumx,randnumy,randnumz,factor_dpd; + double P[3][3]; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + + const auto * _noalias const x = (dbl3_t *) atom->x[0]; + const auto * _noalias const v = (dbl3_t *) atom->v[0]; + auto * _noalias const f = (dbl3_t *) thr->get_f()[0]; + const int * _noalias const type = atom->type; + const int nlocal = atom->nlocal; + const double *special_lj = force->special_lj; + const double dtinvsqrt = 1.0/sqrt(update->dt); + double fxtmp,fytmp,fztmp; + RanMars &rng = *random_thr[thr->get_tid()]; + + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = iifrom; ii < iito; ++ii) { + + i = ilist[ii]; + xtmp = x[i].x; + ytmp = x[i].y; + ztmp = x[i].z; + vxtmp = v[i].x; + vytmp = v[i].y; + vztmp = v[i].z; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + fxtmp=fytmp=fztmp=0.0; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_dpd = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j].x; + dely = ytmp - x[j].y; + delz = ztmp - x[j].z; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r = sqrt(rsq); + if (r < EPSILON) continue; // r can be 0.0 in DPD systems + rinv = 1.0/r; + delvx = vxtmp - v[j].x; + delvy = vytmp - v[j].y; + delvz = vztmp - v[j].z; + dot = delx*delvx + dely*delvy + delz*delvz; + + P[0][0] = 1.0 - delx*delx*rinv*rinv; + P[0][1] = - delx*dely*rinv*rinv; + P[0][2] = - delx*delz*rinv*rinv; + + P[1][0] = P[0][1]; + P[1][1] = 1.0 - dely*dely*rinv*rinv; + P[1][2] = - dely*delz*rinv*rinv; + + P[2][0] = P[0][2]; + P[2][1] = P[1][2]; + P[2][2] = 1.0 - delz*delz*rinv*rinv; + + wd = 1.0 - r/cut[itype][jtype]; + wdPar = pow(wd,ws[itype][jtype]); + wdPerp = pow(wd,wsT[itype][jtype]); + + randnum = rng.gaussian(); + randnumx = rng.gaussian(); + randnumy = rng.gaussian(); + randnumz = rng.gaussian(); + + // conservative force + fpair = a0[itype][jtype]*wd; + + // drag force - parallel + fpair -= gamma[itype][jtype]*wdPar*wdPar*dot*rinv; + + // random force - parallel + fpair += sigma[itype][jtype]*wdPar*randnum*dtinvsqrt; + + fpairx = fpair*rinv*delx; + fpairy = fpair*rinv*dely; + fpairz = fpair*rinv*delz; + + // drag force - perpendicular + fpairx -= gammaT[itype][jtype]*wdPerp*wdPerp* + (P[0][0]*delvx + P[0][1]*delvy + P[0][2]*delvz); + fpairy -= gammaT[itype][jtype]*wdPerp*wdPerp* + (P[1][0]*delvx + P[1][1]*delvy + P[1][2]*delvz); + fpairz -= gammaT[itype][jtype]*wdPerp*wdPerp* + (P[2][0]*delvx + P[2][1]*delvy + P[2][2]*delvz); + + // random force - perpendicular + fpairx += sigmaT[itype][jtype]*wdPerp* + (P[0][0]*randnumx + P[0][1]*randnumy + P[0][2]*randnumz)*dtinvsqrt; + fpairy += sigmaT[itype][jtype]*wdPerp* + (P[1][0]*randnumx + P[1][1]*randnumy + P[1][2]*randnumz)*dtinvsqrt; + fpairz += sigmaT[itype][jtype]*wdPerp* + (P[2][0]*randnumx + P[2][1]*randnumy + P[2][2]*randnumz)*dtinvsqrt; + + fpairx *= factor_dpd; + fpairy *= factor_dpd; + fpairz *= factor_dpd; + + fxtmp += fpairx; + fytmp += fpairy; + fztmp += fpairz; + if (NEWTON_PAIR || j < nlocal) { + f[j].x -= fpairx; + f[j].y -= fpairy; + f[j].z -= fpairz; + } + + if (EFLAG) { + // unshifted eng of conservative term: + // evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]); + // eng shifted to 0.0 at cutoff + evdwl = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd*wd; + evdwl *= factor_dpd; + } + + if (EVFLAG) ev_tally_xyz_thr(this, i,j,nlocal,NEWTON_PAIR,evdwl,0.0, + fpairx,fpairy,fpairz,delx,dely,delz,thr); + } + } + f[i].x += fxtmp; + f[i].y += fytmp; + f[i].z += fztmp; + } +} + +/* ---------------------------------------------------------------------- */ + +double PairDPDExtOMP::memory_usage() +{ + double bytes = memory_usage_thr(); + bytes += PairDPDExt::memory_usage(); + bytes += (double)comm->nthreads * sizeof(RanMars*); + bytes += (double)comm->nthreads * sizeof(RanMars); + + return bytes; +} diff --git a/src/OPENMP/pair_dpd_ext_omp.h b/src/OPENMP/pair_dpd_ext_omp.h new file mode 100644 index 0000000000..4ea82bbef5 --- /dev/null +++ b/src/OPENMP/pair_dpd_ext_omp.h @@ -0,0 +1,51 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(dpd/ext/omp,PairDPDExtOMP); +// clang-format on +#else + +#ifndef LMP_PAIR_DPD_EXT_OMP_H +#define LMP_PAIR_DPD_EXT_OMP_H + +#include "pair_dpd_ext.h" +#include "thr_omp.h" + +namespace LAMMPS_NS { + +class PairDPDExtOMP : public PairDPDExt, public ThrOMP { + + public: + PairDPDExtOMP(class LAMMPS *); + ~PairDPDExtOMP() override; + + void compute(int, int) override; + double memory_usage() override; + + protected: + class RanMars **random_thr; + int nthreads; + + private: + template + void eval(int ifrom, int ito, ThrData *const thr); +}; +} // namespace LAMMPS_NS +#endif +#endif diff --git a/src/OPENMP/pair_dpd_ext_tstat_omp.cpp b/src/OPENMP/pair_dpd_ext_tstat_omp.cpp new file mode 100644 index 0000000000..fa4c80abaa --- /dev/null +++ b/src/OPENMP/pair_dpd_ext_tstat_omp.cpp @@ -0,0 +1,275 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + This software is distributed under the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#include "pair_dpd_ext_tstat_omp.h" + +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neigh_list.h" +#include "update.h" +#include "random_mars.h" +#include "suffix.h" + +#include + +#include "omp_compat.h" +using namespace LAMMPS_NS; + +#define EPSILON 1.0e-10 + +/* ---------------------------------------------------------------------- */ + +PairDPDExtTstatOMP::PairDPDExtTstatOMP(LAMMPS *lmp) : + PairDPDExtTstat(lmp), ThrOMP(lmp, THR_PAIR) +{ + suffix_flag |= Suffix::OMP; + respa_enable = 0; + random_thr = nullptr; + nthreads = 0; +} + +/* ---------------------------------------------------------------------- */ + +PairDPDExtTstatOMP::~PairDPDExtTstatOMP() +{ + if (random_thr) { + for (int i=1; i < nthreads; ++i) + delete random_thr[i]; + + delete[] random_thr; + random_thr = nullptr; + } +} + +/* ---------------------------------------------------------------------- */ + +void PairDPDExtTstatOMP::compute(int eflag, int vflag) +{ + ev_init(eflag,vflag); + + const int nall = atom->nlocal + atom->nghost; + const int inum = list->inum; + + // number of threads has changed. reallocate pool of pRNGs + if (nthreads != comm->nthreads) { + if (random_thr) { + for (int i=1; i < nthreads; ++i) + delete random_thr[i]; + + delete[] random_thr; + } + + nthreads = comm->nthreads; + random_thr = new RanMars*[nthreads]; + for (int i=1; i < nthreads; ++i) + random_thr[i] = nullptr; + + // to ensure full compatibility with the serial DPD style + // we use the serial random number generator instance for thread 0 + random_thr[0] = random; + } + + // adjust sigma if target T is changing + + if (t_start != t_stop) { + double delta = update->ntimestep - update->beginstep; + if (delta != 0.0) delta /= update->endstep - update->beginstep; + temperature = t_start + delta * (t_stop-t_start); + double boltz = force->boltz; + for (int i = 1; i <= atom->ntypes; i++) { + for (int j = i; j <= atom->ntypes; j++) { + sigma[i][j] = sigma[j][i] = sqrt(2.0*boltz*temperature*gamma[i][j]); + sigmaT[i][j] = sigmaT[j][i] = sqrt(2.0*boltz*temperature*gammaT[i][j]); + } + } + } + +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag,vflag) +#endif + { + int ifrom, ito, tid; + + loop_setup_thr(ifrom, ito, tid, inum, nthreads); + ThrData *thr = fix->get_thr(tid); + thr->timer(Timer::START); + ev_setup_thr(eflag, vflag, nall, eatom, vatom, nullptr, thr); + + // generate a random number generator instance for + // all threads != 0. make sure we use unique seeds. + if ((tid > 0) && (random_thr[tid] == nullptr)) + random_thr[tid] = new RanMars(Pair::lmp, seed + comm->me + + comm->nprocs*tid); + + if (evflag) { + if (eflag) { + if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr); + else eval<1,1,0>(ifrom, ito, thr); + } else { + if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr); + else eval<1,0,0>(ifrom, ito, thr); + } + } else { + if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr); + else eval<0,0,0>(ifrom, ito, thr); + } + + thr->timer(Timer::PAIR); + reduce_thr(this, eflag, vflag, thr); + } // end of omp parallel region +} + +template +void PairDPDExtTstatOMP::eval(int iifrom, int iito, ThrData * const thr) +{ + int i,j,ii,jj,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,fpairx,fpairy,fpairz,fpair; + double vxtmp,vytmp,vztmp,delvx,delvy,delvz; + double rsq,r,rinv,dot,wd,wdPar,wdPerp,randnum,randnumx,randnumy,randnumz,factor_dpd; + double P[3][3]; + int *ilist,*jlist,*numneigh,**firstneigh; + + const auto * _noalias const x = (dbl3_t *) atom->x[0]; + const auto * _noalias const v = (dbl3_t *) atom->v[0]; + auto * _noalias const f = (dbl3_t *) thr->get_f()[0]; + const int * _noalias const type = atom->type; + const int nlocal = atom->nlocal; + const double *special_lj = force->special_lj; + const double dtinvsqrt = 1.0/sqrt(update->dt); + double fxtmp,fytmp,fztmp; + RanMars &rng = *random_thr[thr->get_tid()]; + + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = iifrom; ii < iito; ++ii) { + + i = ilist[ii]; + xtmp = x[i].x; + ytmp = x[i].y; + ztmp = x[i].z; + vxtmp = v[i].x; + vytmp = v[i].y; + vztmp = v[i].z; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + fxtmp=fytmp=fztmp=0.0; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_dpd = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j].x; + dely = ytmp - x[j].y; + delz = ztmp - x[j].z; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r = sqrt(rsq); + if (r < EPSILON) continue; // r can be 0.0 in DPD systems + rinv = 1.0/r; + delvx = vxtmp - v[j].x; + delvy = vytmp - v[j].y; + delvz = vztmp - v[j].z; + dot = delx*delvx + dely*delvy + delz*delvz; + + P[0][0] = 1.0 - delx*delx*rinv*rinv; + P[0][1] = - delx*dely*rinv*rinv; + P[0][2] = - delx*delz*rinv*rinv; + + P[1][0] = P[0][1]; + P[1][1] = 1.0 - dely*dely*rinv*rinv; + P[1][2] = - dely*delz*rinv*rinv; + + P[2][0] = P[0][2]; + P[2][1] = P[1][2]; + P[2][2] = 1.0 - delz*delz*rinv*rinv; + + wd = 1.0 - r/cut[itype][jtype]; + wdPar = pow(wd,ws[itype][jtype]); + wdPerp = pow(wd,wsT[itype][jtype]); + + randnum = rng.gaussian(); + randnumx = rng.gaussian(); + randnumy = rng.gaussian(); + randnumz = rng.gaussian(); + + // drag force - parallel + fpair = -gamma[itype][jtype]*wdPar*wdPar*dot*rinv; + + // random force - parallel + fpair += sigma[itype][jtype]*wdPar*randnum*dtinvsqrt; + + fpairx = fpair*rinv*delx; + fpairy = fpair*rinv*dely; + fpairz = fpair*rinv*delz; + + // drag force - perpendicular + fpairx -= gammaT[itype][jtype]*wdPerp*wdPerp* + (P[0][0]*delvx + P[0][1]*delvy + P[0][2]*delvz); + fpairy -= gammaT[itype][jtype]*wdPerp*wdPerp* + (P[1][0]*delvx + P[1][1]*delvy + P[1][2]*delvz); + fpairz -= gammaT[itype][jtype]*wdPerp*wdPerp* + (P[2][0]*delvx + P[2][1]*delvy + P[2][2]*delvz); + + // random force - perpendicular + fpairx += sigmaT[itype][jtype]*wdPerp* + (P[0][0]*randnumx + P[0][1]*randnumy + P[0][2]*randnumz)*dtinvsqrt; + fpairy += sigmaT[itype][jtype]*wdPerp* + (P[1][0]*randnumx + P[1][1]*randnumy + P[1][2]*randnumz)*dtinvsqrt; + fpairz += sigmaT[itype][jtype]*wdPerp* + (P[2][0]*randnumx + P[2][1]*randnumy + P[2][2]*randnumz)*dtinvsqrt; + + fpairx *= factor_dpd; + fpairy *= factor_dpd; + fpairz *= factor_dpd; + + fxtmp += fpairx; + fytmp += fpairy; + fztmp += fpairz; + if (NEWTON_PAIR || j < nlocal) { + f[j].x -= fpairx; + f[j].y -= fpairy; + f[j].z -= fpairz; + } + + if (EVFLAG) ev_tally_xyz_thr(this, i,j,nlocal,NEWTON_PAIR,0.0,0.0, + fpairx,fpairy,fpairz,delx,dely,delz,thr); + } + } + f[i].x += fxtmp; + f[i].y += fytmp; + f[i].z += fztmp; + } +} + +/* ---------------------------------------------------------------------- */ + +double PairDPDExtTstatOMP::memory_usage() +{ + double bytes = memory_usage_thr(); + bytes += PairDPDExtTstat::memory_usage(); + bytes += (double)comm->nthreads * sizeof(RanMars*); + bytes += (double)comm->nthreads * sizeof(RanMars); + + return bytes; +} diff --git a/src/OPENMP/pair_dpd_ext_tstat_omp.h b/src/OPENMP/pair_dpd_ext_tstat_omp.h new file mode 100644 index 0000000000..ef6d0494be --- /dev/null +++ b/src/OPENMP/pair_dpd_ext_tstat_omp.h @@ -0,0 +1,51 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(dpd/ext/tstat/omp,PairDPDExtTstatOMP); +// clang-format on +#else + +#ifndef LMP_PAIR_DPD_EXT_TSTAT_OMP_H +#define LMP_PAIR_DPD_EXT_TSTAT_OMP_H + +#include "pair_dpd_ext_tstat.h" +#include "thr_omp.h" + +namespace LAMMPS_NS { + +class PairDPDExtTstatOMP : public PairDPDExtTstat, public ThrOMP { + + public: + PairDPDExtTstatOMP(class LAMMPS *); + ~PairDPDExtTstatOMP() override; + + void compute(int, int) override; + double memory_usage() override; + + protected: + class RanMars **random_thr; + int nthreads; + + private: + template + void eval(int ifrom, int ito, ThrData *const thr); +}; +} // namespace LAMMPS_NS +#endif +#endif diff --git a/src/OPENMP/pair_dpd_omp.cpp b/src/OPENMP/pair_dpd_omp.cpp index 8d47a6d8b6..2babd4b24b 100644 --- a/src/OPENMP/pair_dpd_omp.cpp +++ b/src/OPENMP/pair_dpd_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_dpd_omp.h b/src/OPENMP/pair_dpd_omp.h index 4b004ad81e..85d0e6d527 100644 --- a/src/OPENMP/pair_dpd_omp.h +++ b/src/OPENMP/pair_dpd_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_dpd_tstat_omp.cpp b/src/OPENMP/pair_dpd_tstat_omp.cpp index 7909a1b8c1..ccd452ea9a 100644 --- a/src/OPENMP/pair_dpd_tstat_omp.cpp +++ b/src/OPENMP/pair_dpd_tstat_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_dpd_tstat_omp.h b/src/OPENMP/pair_dpd_tstat_omp.h index b9cbe902f7..6a658ace36 100644 --- a/src/OPENMP/pair_dpd_tstat_omp.h +++ b/src/OPENMP/pair_dpd_tstat_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_eam_alloy_omp.cpp b/src/OPENMP/pair_eam_alloy_omp.cpp index 5425be8356..033640598e 100644 --- a/src/OPENMP/pair_eam_alloy_omp.cpp +++ b/src/OPENMP/pair_eam_alloy_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_eam_alloy_omp.h b/src/OPENMP/pair_eam_alloy_omp.h index 38e32ddedf..7ce3d08447 100644 --- a/src/OPENMP/pair_eam_alloy_omp.h +++ b/src/OPENMP/pair_eam_alloy_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_eam_fs_omp.cpp b/src/OPENMP/pair_eam_fs_omp.cpp index 9c99345a3b..0ad43853dd 100644 --- a/src/OPENMP/pair_eam_fs_omp.cpp +++ b/src/OPENMP/pair_eam_fs_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_eam_fs_omp.h b/src/OPENMP/pair_eam_fs_omp.h index c68de71623..4f73f00b28 100644 --- a/src/OPENMP/pair_eam_fs_omp.h +++ b/src/OPENMP/pair_eam_fs_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_eam_omp.cpp b/src/OPENMP/pair_eam_omp.cpp index b3c963c3df..e99fbedbb7 100644 --- a/src/OPENMP/pair_eam_omp.cpp +++ b/src/OPENMP/pair_eam_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_eam_omp.h b/src/OPENMP/pair_eam_omp.h index 3401241808..1be24fc18a 100644 --- a/src/OPENMP/pair_eam_omp.h +++ b/src/OPENMP/pair_eam_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_edip_omp.cpp b/src/OPENMP/pair_edip_omp.cpp index 15619c277a..7c31f0db78 100644 --- a/src/OPENMP/pair_edip_omp.cpp +++ b/src/OPENMP/pair_edip_omp.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_edip_omp.h b/src/OPENMP/pair_edip_omp.h index e9afe243ab..25c682e7a9 100644 --- a/src/OPENMP/pair_edip_omp.h +++ b/src/OPENMP/pair_edip_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ diff --git a/src/OPENMP/pair_eim_omp.cpp b/src/OPENMP/pair_eim_omp.cpp index aa6d2532f5..3e2fc39730 100644 --- a/src/OPENMP/pair_eim_omp.cpp +++ b/src/OPENMP/pair_eim_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_eim_omp.h b/src/OPENMP/pair_eim_omp.h index 708c15243f..ab187ec222 100644 --- a/src/OPENMP/pair_eim_omp.h +++ b/src/OPENMP/pair_eim_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_gauss_cut_omp.cpp b/src/OPENMP/pair_gauss_cut_omp.cpp index 2460d66334..f138c48ef9 100644 --- a/src/OPENMP/pair_gauss_cut_omp.cpp +++ b/src/OPENMP/pair_gauss_cut_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_gauss_cut_omp.h b/src/OPENMP/pair_gauss_cut_omp.h index 3ed1603222..7fd0bef317 100644 --- a/src/OPENMP/pair_gauss_cut_omp.h +++ b/src/OPENMP/pair_gauss_cut_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_gauss_omp.cpp b/src/OPENMP/pair_gauss_omp.cpp index 3cdbb360e7..12c197e768 100644 --- a/src/OPENMP/pair_gauss_omp.cpp +++ b/src/OPENMP/pair_gauss_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_gauss_omp.h b/src/OPENMP/pair_gauss_omp.h index 4cda138e48..09f602fc9a 100644 --- a/src/OPENMP/pair_gauss_omp.h +++ b/src/OPENMP/pair_gauss_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_gayberne_omp.cpp b/src/OPENMP/pair_gayberne_omp.cpp index e756e580a7..7d53140ef6 100644 --- a/src/OPENMP/pair_gayberne_omp.cpp +++ b/src/OPENMP/pair_gayberne_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_gayberne_omp.h b/src/OPENMP/pair_gayberne_omp.h index 3038f0faf6..7356743903 100644 --- a/src/OPENMP/pair_gayberne_omp.h +++ b/src/OPENMP/pair_gayberne_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_gran_hertz_history_omp.cpp b/src/OPENMP/pair_gran_hertz_history_omp.cpp index 66be06020f..99439bec88 100644 --- a/src/OPENMP/pair_gran_hertz_history_omp.cpp +++ b/src/OPENMP/pair_gran_hertz_history_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_gran_hertz_history_omp.h b/src/OPENMP/pair_gran_hertz_history_omp.h index 393104d0d8..a03a4a892a 100644 --- a/src/OPENMP/pair_gran_hertz_history_omp.h +++ b/src/OPENMP/pair_gran_hertz_history_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_gran_hooke_history_omp.cpp b/src/OPENMP/pair_gran_hooke_history_omp.cpp index 8dad7f463a..98987ed62f 100644 --- a/src/OPENMP/pair_gran_hooke_history_omp.cpp +++ b/src/OPENMP/pair_gran_hooke_history_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_gran_hooke_history_omp.h b/src/OPENMP/pair_gran_hooke_history_omp.h index c07a847fab..c2650cfe1f 100644 --- a/src/OPENMP/pair_gran_hooke_history_omp.h +++ b/src/OPENMP/pair_gran_hooke_history_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_gran_hooke_omp.cpp b/src/OPENMP/pair_gran_hooke_omp.cpp index bfe91b63da..ac98610eca 100644 --- a/src/OPENMP/pair_gran_hooke_omp.cpp +++ b/src/OPENMP/pair_gran_hooke_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_gran_hooke_omp.h b/src/OPENMP/pair_gran_hooke_omp.h index 153290a780..fc66fa807f 100644 --- a/src/OPENMP/pair_gran_hooke_omp.h +++ b/src/OPENMP/pair_gran_hooke_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_harmonic_cut_omp.cpp b/src/OPENMP/pair_harmonic_cut_omp.cpp index d7540d7c11..530c9d8a40 100644 --- a/src/OPENMP/pair_harmonic_cut_omp.cpp +++ b/src/OPENMP/pair_harmonic_cut_omp.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_harmonic_cut_omp.h b/src/OPENMP/pair_harmonic_cut_omp.h index 9e84e508c0..213ed7517d 100644 --- a/src/OPENMP/pair_harmonic_cut_omp.h +++ b/src/OPENMP/pair_harmonic_cut_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_hbond_dreiding_lj_omp.cpp b/src/OPENMP/pair_hbond_dreiding_lj_omp.cpp index 66f1a85c39..e7ba4d72c6 100644 --- a/src/OPENMP/pair_hbond_dreiding_lj_omp.cpp +++ b/src/OPENMP/pair_hbond_dreiding_lj_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_hbond_dreiding_lj_omp.h b/src/OPENMP/pair_hbond_dreiding_lj_omp.h index 7b51c071b9..792a9a6f8c 100644 --- a/src/OPENMP/pair_hbond_dreiding_lj_omp.h +++ b/src/OPENMP/pair_hbond_dreiding_lj_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_hbond_dreiding_morse_omp.cpp b/src/OPENMP/pair_hbond_dreiding_morse_omp.cpp index f7cecda03a..99e2d2c5b1 100644 --- a/src/OPENMP/pair_hbond_dreiding_morse_omp.cpp +++ b/src/OPENMP/pair_hbond_dreiding_morse_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_hbond_dreiding_morse_omp.h b/src/OPENMP/pair_hbond_dreiding_morse_omp.h index c5ebd9bc47..016154b762 100644 --- a/src/OPENMP/pair_hbond_dreiding_morse_omp.h +++ b/src/OPENMP/pair_hbond_dreiding_morse_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj96_cut_omp.cpp b/src/OPENMP/pair_lj96_cut_omp.cpp index 7ffa4f6a97..f51ee48307 100644 --- a/src/OPENMP/pair_lj96_cut_omp.cpp +++ b/src/OPENMP/pair_lj96_cut_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj96_cut_omp.h b/src/OPENMP/pair_lj96_cut_omp.h index 59c6606cdb..706b13be0a 100644 --- a/src/OPENMP/pair_lj96_cut_omp.h +++ b/src/OPENMP/pair_lj96_cut_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp b/src/OPENMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp index 5addcd167a..38e76424ff 100644 --- a/src/OPENMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp +++ b/src/OPENMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_charmm_coul_charmm_implicit_omp.h b/src/OPENMP/pair_lj_charmm_coul_charmm_implicit_omp.h index d6c08e2e97..ae514fcc7e 100644 --- a/src/OPENMP/pair_lj_charmm_coul_charmm_implicit_omp.h +++ b/src/OPENMP/pair_lj_charmm_coul_charmm_implicit_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_charmm_coul_charmm_omp.cpp b/src/OPENMP/pair_lj_charmm_coul_charmm_omp.cpp index 7a14e76ea2..6afae058ad 100644 --- a/src/OPENMP/pair_lj_charmm_coul_charmm_omp.cpp +++ b/src/OPENMP/pair_lj_charmm_coul_charmm_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_charmm_coul_charmm_omp.h b/src/OPENMP/pair_lj_charmm_coul_charmm_omp.h index f020cba462..bfbf1c259a 100644 --- a/src/OPENMP/pair_lj_charmm_coul_charmm_omp.h +++ b/src/OPENMP/pair_lj_charmm_coul_charmm_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_charmm_coul_long_omp.cpp b/src/OPENMP/pair_lj_charmm_coul_long_omp.cpp index 64cfb69882..bee2f73443 100644 --- a/src/OPENMP/pair_lj_charmm_coul_long_omp.cpp +++ b/src/OPENMP/pair_lj_charmm_coul_long_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_charmm_coul_long_omp.h b/src/OPENMP/pair_lj_charmm_coul_long_omp.h index 5dae557380..c01a843660 100644 --- a/src/OPENMP/pair_lj_charmm_coul_long_omp.h +++ b/src/OPENMP/pair_lj_charmm_coul_long_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_charmm_coul_long_soft_omp.cpp b/src/OPENMP/pair_lj_charmm_coul_long_soft_omp.cpp index 9e127120a9..0852b92db3 100644 --- a/src/OPENMP/pair_lj_charmm_coul_long_soft_omp.cpp +++ b/src/OPENMP/pair_lj_charmm_coul_long_soft_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_charmm_coul_long_soft_omp.h b/src/OPENMP/pair_lj_charmm_coul_long_soft_omp.h index d4087d4e4f..bab6a20b51 100644 --- a/src/OPENMP/pair_lj_charmm_coul_long_soft_omp.h +++ b/src/OPENMP/pair_lj_charmm_coul_long_soft_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_charmm_coul_msm_omp.cpp b/src/OPENMP/pair_lj_charmm_coul_msm_omp.cpp index 6bbb4040e3..ea953b7be6 100644 --- a/src/OPENMP/pair_lj_charmm_coul_msm_omp.cpp +++ b/src/OPENMP/pair_lj_charmm_coul_msm_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_charmm_coul_msm_omp.h b/src/OPENMP/pair_lj_charmm_coul_msm_omp.h index 42acac59aa..6573df4b2f 100644 --- a/src/OPENMP/pair_lj_charmm_coul_msm_omp.h +++ b/src/OPENMP/pair_lj_charmm_coul_msm_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_class2_coul_cut_omp.cpp b/src/OPENMP/pair_lj_class2_coul_cut_omp.cpp index e9086f27e3..e13bdbbdb5 100644 --- a/src/OPENMP/pair_lj_class2_coul_cut_omp.cpp +++ b/src/OPENMP/pair_lj_class2_coul_cut_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_class2_coul_cut_omp.h b/src/OPENMP/pair_lj_class2_coul_cut_omp.h index 10d1574436..c0bfecc63a 100644 --- a/src/OPENMP/pair_lj_class2_coul_cut_omp.h +++ b/src/OPENMP/pair_lj_class2_coul_cut_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_class2_coul_long_omp.cpp b/src/OPENMP/pair_lj_class2_coul_long_omp.cpp index eaa6ac4366..0791cce8f3 100644 --- a/src/OPENMP/pair_lj_class2_coul_long_omp.cpp +++ b/src/OPENMP/pair_lj_class2_coul_long_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_class2_coul_long_omp.h b/src/OPENMP/pair_lj_class2_coul_long_omp.h index a6e297aea6..a0fbf1ca16 100644 --- a/src/OPENMP/pair_lj_class2_coul_long_omp.h +++ b/src/OPENMP/pair_lj_class2_coul_long_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_class2_omp.cpp b/src/OPENMP/pair_lj_class2_omp.cpp index 4cc9801357..0f269fb1f6 100644 --- a/src/OPENMP/pair_lj_class2_omp.cpp +++ b/src/OPENMP/pair_lj_class2_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_class2_omp.h b/src/OPENMP/pair_lj_class2_omp.h index e9864c5985..95c68b9a4d 100644 --- a/src/OPENMP/pair_lj_class2_omp.h +++ b/src/OPENMP/pair_lj_class2_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_cubic_omp.cpp b/src/OPENMP/pair_lj_cubic_omp.cpp index d89e6cb711..907a514de1 100644 --- a/src/OPENMP/pair_lj_cubic_omp.cpp +++ b/src/OPENMP/pair_lj_cubic_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_cubic_omp.h b/src/OPENMP/pair_lj_cubic_omp.h index a01c6ce5f1..10168e3010 100644 --- a/src/OPENMP/pair_lj_cubic_omp.h +++ b/src/OPENMP/pair_lj_cubic_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_cut_coul_cut_dielectric_omp.cpp b/src/OPENMP/pair_lj_cut_coul_cut_dielectric_omp.cpp index 5f88dbbd29..6546b60830 100644 --- a/src/OPENMP/pair_lj_cut_coul_cut_dielectric_omp.cpp +++ b/src/OPENMP/pair_lj_cut_coul_cut_dielectric_omp.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_cut_coul_cut_dielectric_omp.h b/src/OPENMP/pair_lj_cut_coul_cut_dielectric_omp.h index e663d81440..24ba2e9b42 100644 --- a/src/OPENMP/pair_lj_cut_coul_cut_dielectric_omp.h +++ b/src/OPENMP/pair_lj_cut_coul_cut_dielectric_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -32,8 +32,7 @@ class PairLJCutCoulCutDielectricOMP : public PairLJCutCoulCutDielectric, public void compute(int, int) override; protected: - template - void eval(int ifrom, int ito, ThrData *const thr); + template void eval(int ifrom, int ito, ThrData *const thr); }; } // namespace LAMMPS_NS diff --git a/src/OPENMP/pair_lj_cut_coul_cut_omp.cpp b/src/OPENMP/pair_lj_cut_coul_cut_omp.cpp index 0df235b626..939b840697 100644 --- a/src/OPENMP/pair_lj_cut_coul_cut_omp.cpp +++ b/src/OPENMP/pair_lj_cut_coul_cut_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_cut_coul_cut_omp.h b/src/OPENMP/pair_lj_cut_coul_cut_omp.h index 2b2af00741..eac0ce53eb 100644 --- a/src/OPENMP/pair_lj_cut_coul_cut_omp.h +++ b/src/OPENMP/pair_lj_cut_coul_cut_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_cut_coul_cut_soft_omp.cpp b/src/OPENMP/pair_lj_cut_coul_cut_soft_omp.cpp index b1afa96bf5..cc90837509 100644 --- a/src/OPENMP/pair_lj_cut_coul_cut_soft_omp.cpp +++ b/src/OPENMP/pair_lj_cut_coul_cut_soft_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_cut_coul_cut_soft_omp.h b/src/OPENMP/pair_lj_cut_coul_cut_soft_omp.h index 8482937910..2cd32ee994 100644 --- a/src/OPENMP/pair_lj_cut_coul_cut_soft_omp.h +++ b/src/OPENMP/pair_lj_cut_coul_cut_soft_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_cut_coul_debye_dielectric_omp.cpp b/src/OPENMP/pair_lj_cut_coul_debye_dielectric_omp.cpp index e02221f90c..79f76c8343 100644 --- a/src/OPENMP/pair_lj_cut_coul_debye_dielectric_omp.cpp +++ b/src/OPENMP/pair_lj_cut_coul_debye_dielectric_omp.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_cut_coul_debye_dielectric_omp.h b/src/OPENMP/pair_lj_cut_coul_debye_dielectric_omp.h index 9aa8bb8291..e4e64aa62b 100644 --- a/src/OPENMP/pair_lj_cut_coul_debye_dielectric_omp.h +++ b/src/OPENMP/pair_lj_cut_coul_debye_dielectric_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -32,8 +32,7 @@ class PairLJCutCoulDebyeDielectricOMP : public PairLJCutCoulDebyeDielectric, pub void compute(int, int) override; protected: - template - void eval(int ifrom, int ito, ThrData *const thr); + template void eval(int ifrom, int ito, ThrData *const thr); }; } // namespace LAMMPS_NS diff --git a/src/OPENMP/pair_lj_cut_coul_debye_omp.cpp b/src/OPENMP/pair_lj_cut_coul_debye_omp.cpp index 7797d938b7..9c8bf29d6e 100644 --- a/src/OPENMP/pair_lj_cut_coul_debye_omp.cpp +++ b/src/OPENMP/pair_lj_cut_coul_debye_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_cut_coul_debye_omp.h b/src/OPENMP/pair_lj_cut_coul_debye_omp.h index fdaf692bae..d46781f9e6 100644 --- a/src/OPENMP/pair_lj_cut_coul_debye_omp.h +++ b/src/OPENMP/pair_lj_cut_coul_debye_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_cut_coul_dsf_omp.cpp b/src/OPENMP/pair_lj_cut_coul_dsf_omp.cpp index e305c1caf9..f82dfa8d33 100644 --- a/src/OPENMP/pair_lj_cut_coul_dsf_omp.cpp +++ b/src/OPENMP/pair_lj_cut_coul_dsf_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_cut_coul_dsf_omp.h b/src/OPENMP/pair_lj_cut_coul_dsf_omp.h index c7d5baf921..5ba538255d 100644 --- a/src/OPENMP/pair_lj_cut_coul_dsf_omp.h +++ b/src/OPENMP/pair_lj_cut_coul_dsf_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_cut_coul_long_dielectric_omp.cpp b/src/OPENMP/pair_lj_cut_coul_long_dielectric_omp.cpp index 13c48c2812..c0f4693c58 100644 --- a/src/OPENMP/pair_lj_cut_coul_long_dielectric_omp.cpp +++ b/src/OPENMP/pair_lj_cut_coul_long_dielectric_omp.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_cut_coul_long_dielectric_omp.h b/src/OPENMP/pair_lj_cut_coul_long_dielectric_omp.h index 1c928a4244..361eda6a13 100644 --- a/src/OPENMP/pair_lj_cut_coul_long_dielectric_omp.h +++ b/src/OPENMP/pair_lj_cut_coul_long_dielectric_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -33,8 +33,7 @@ class PairLJCutCoulLongDielectricOMP : public PairLJCutCoulLongDielectric, publi void compute(int, int) override; protected: - template - void eval(int ifrom, int ito, ThrData *const thr); + template void eval(int ifrom, int ito, ThrData *const thr); }; } // namespace LAMMPS_NS diff --git a/src/OPENMP/pair_lj_cut_coul_long_omp.cpp b/src/OPENMP/pair_lj_cut_coul_long_omp.cpp index af551017b2..49ad3a508c 100644 --- a/src/OPENMP/pair_lj_cut_coul_long_omp.cpp +++ b/src/OPENMP/pair_lj_cut_coul_long_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_cut_coul_long_omp.h b/src/OPENMP/pair_lj_cut_coul_long_omp.h index ca7c30dede..3c900e5bb6 100644 --- a/src/OPENMP/pair_lj_cut_coul_long_omp.h +++ b/src/OPENMP/pair_lj_cut_coul_long_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_cut_coul_long_soft_omp.cpp b/src/OPENMP/pair_lj_cut_coul_long_soft_omp.cpp index 3ceb40b262..c8f3635b4f 100644 --- a/src/OPENMP/pair_lj_cut_coul_long_soft_omp.cpp +++ b/src/OPENMP/pair_lj_cut_coul_long_soft_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_cut_coul_long_soft_omp.h b/src/OPENMP/pair_lj_cut_coul_long_soft_omp.h index 00c6b031a4..7da647cca6 100644 --- a/src/OPENMP/pair_lj_cut_coul_long_soft_omp.h +++ b/src/OPENMP/pair_lj_cut_coul_long_soft_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_cut_coul_msm_omp.cpp b/src/OPENMP/pair_lj_cut_coul_msm_omp.cpp index d573a349c1..dcf2696b9f 100644 --- a/src/OPENMP/pair_lj_cut_coul_msm_omp.cpp +++ b/src/OPENMP/pair_lj_cut_coul_msm_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_cut_coul_msm_omp.h b/src/OPENMP/pair_lj_cut_coul_msm_omp.h index fa07edc79e..3088684fee 100644 --- a/src/OPENMP/pair_lj_cut_coul_msm_omp.h +++ b/src/OPENMP/pair_lj_cut_coul_msm_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_cut_coul_wolf_omp.cpp b/src/OPENMP/pair_lj_cut_coul_wolf_omp.cpp index 55c2bc6c11..4d21cb3d4c 100644 --- a/src/OPENMP/pair_lj_cut_coul_wolf_omp.cpp +++ b/src/OPENMP/pair_lj_cut_coul_wolf_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_cut_coul_wolf_omp.h b/src/OPENMP/pair_lj_cut_coul_wolf_omp.h index b0fd2b3258..72dbeef5b9 100644 --- a/src/OPENMP/pair_lj_cut_coul_wolf_omp.h +++ b/src/OPENMP/pair_lj_cut_coul_wolf_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_cut_dipole_cut_omp.cpp b/src/OPENMP/pair_lj_cut_dipole_cut_omp.cpp index 1cecb1c7c4..4c2b5ef297 100644 --- a/src/OPENMP/pair_lj_cut_dipole_cut_omp.cpp +++ b/src/OPENMP/pair_lj_cut_dipole_cut_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_cut_dipole_cut_omp.h b/src/OPENMP/pair_lj_cut_dipole_cut_omp.h index 117b17a0ac..44e7609271 100644 --- a/src/OPENMP/pair_lj_cut_dipole_cut_omp.h +++ b/src/OPENMP/pair_lj_cut_dipole_cut_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_cut_omp.cpp b/src/OPENMP/pair_lj_cut_omp.cpp index 96ecd959e2..654b91b7ba 100644 --- a/src/OPENMP/pair_lj_cut_omp.cpp +++ b/src/OPENMP/pair_lj_cut_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_cut_omp.h b/src/OPENMP/pair_lj_cut_omp.h index 604b5f2c81..554db4ebde 100644 --- a/src/OPENMP/pair_lj_cut_omp.h +++ b/src/OPENMP/pair_lj_cut_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_cut_soft_omp.cpp b/src/OPENMP/pair_lj_cut_soft_omp.cpp index c9b1a4bc42..c3470c288c 100644 --- a/src/OPENMP/pair_lj_cut_soft_omp.cpp +++ b/src/OPENMP/pair_lj_cut_soft_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_cut_soft_omp.h b/src/OPENMP/pair_lj_cut_soft_omp.h index 70a72f8986..e6222e708d 100644 --- a/src/OPENMP/pair_lj_cut_soft_omp.h +++ b/src/OPENMP/pair_lj_cut_soft_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_cut_thole_long_omp.cpp b/src/OPENMP/pair_lj_cut_thole_long_omp.cpp index 1034e8e0e5..1ad97a4416 100644 --- a/src/OPENMP/pair_lj_cut_thole_long_omp.cpp +++ b/src/OPENMP/pair_lj_cut_thole_long_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_cut_thole_long_omp.h b/src/OPENMP/pair_lj_cut_thole_long_omp.h index 4ef1321eeb..d842f0bae6 100644 --- a/src/OPENMP/pair_lj_cut_thole_long_omp.h +++ b/src/OPENMP/pair_lj_cut_thole_long_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_cut_tip4p_cut_omp.cpp b/src/OPENMP/pair_lj_cut_tip4p_cut_omp.cpp index be6f77f7f5..04e94ded0e 100644 --- a/src/OPENMP/pair_lj_cut_tip4p_cut_omp.cpp +++ b/src/OPENMP/pair_lj_cut_tip4p_cut_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_cut_tip4p_cut_omp.h b/src/OPENMP/pair_lj_cut_tip4p_cut_omp.h index 2516413af3..0667f4884f 100644 --- a/src/OPENMP/pair_lj_cut_tip4p_cut_omp.h +++ b/src/OPENMP/pair_lj_cut_tip4p_cut_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_cut_tip4p_long_omp.cpp b/src/OPENMP/pair_lj_cut_tip4p_long_omp.cpp index b6948f0c8b..b346154df0 100644 --- a/src/OPENMP/pair_lj_cut_tip4p_long_omp.cpp +++ b/src/OPENMP/pair_lj_cut_tip4p_long_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_cut_tip4p_long_omp.h b/src/OPENMP/pair_lj_cut_tip4p_long_omp.h index 54e93a4791..c7fae14215 100644 --- a/src/OPENMP/pair_lj_cut_tip4p_long_omp.h +++ b/src/OPENMP/pair_lj_cut_tip4p_long_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_cut_tip4p_long_soft_omp.cpp b/src/OPENMP/pair_lj_cut_tip4p_long_soft_omp.cpp index 49e76992f7..c19828bf04 100644 --- a/src/OPENMP/pair_lj_cut_tip4p_long_soft_omp.cpp +++ b/src/OPENMP/pair_lj_cut_tip4p_long_soft_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_cut_tip4p_long_soft_omp.h b/src/OPENMP/pair_lj_cut_tip4p_long_soft_omp.h index 0ea785b067..406e961b23 100644 --- a/src/OPENMP/pair_lj_cut_tip4p_long_soft_omp.h +++ b/src/OPENMP/pair_lj_cut_tip4p_long_soft_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_expand_omp.cpp b/src/OPENMP/pair_lj_expand_omp.cpp index 35d23aadc4..3fd6e7ea7c 100644 --- a/src/OPENMP/pair_lj_expand_omp.cpp +++ b/src/OPENMP/pair_lj_expand_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_expand_omp.h b/src/OPENMP/pair_lj_expand_omp.h index ddfc09b789..2e3e47fe78 100644 --- a/src/OPENMP/pair_lj_expand_omp.h +++ b/src/OPENMP/pair_lj_expand_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_gromacs_coul_gromacs_omp.cpp b/src/OPENMP/pair_lj_gromacs_coul_gromacs_omp.cpp index 096f60b1ec..d0c533dc99 100644 --- a/src/OPENMP/pair_lj_gromacs_coul_gromacs_omp.cpp +++ b/src/OPENMP/pair_lj_gromacs_coul_gromacs_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_gromacs_coul_gromacs_omp.h b/src/OPENMP/pair_lj_gromacs_coul_gromacs_omp.h index 7ee77daf77..d4be49d222 100644 --- a/src/OPENMP/pair_lj_gromacs_coul_gromacs_omp.h +++ b/src/OPENMP/pair_lj_gromacs_coul_gromacs_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_gromacs_omp.cpp b/src/OPENMP/pair_lj_gromacs_omp.cpp index f450d83705..2d26330be2 100644 --- a/src/OPENMP/pair_lj_gromacs_omp.cpp +++ b/src/OPENMP/pair_lj_gromacs_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_gromacs_omp.h b/src/OPENMP/pair_lj_gromacs_omp.h index 54e837864c..69650c1402 100644 --- a/src/OPENMP/pair_lj_gromacs_omp.h +++ b/src/OPENMP/pair_lj_gromacs_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_long_coul_long_omp.cpp b/src/OPENMP/pair_lj_long_coul_long_omp.cpp index e0707a87e0..e1f9e5fea4 100644 --- a/src/OPENMP/pair_lj_long_coul_long_omp.cpp +++ b/src/OPENMP/pair_lj_long_coul_long_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_long_coul_long_omp.h b/src/OPENMP/pair_lj_long_coul_long_omp.h index 24b38ceeb6..fa1dcfa6ac 100644 --- a/src/OPENMP/pair_lj_long_coul_long_omp.h +++ b/src/OPENMP/pair_lj_long_coul_long_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_long_tip4p_long_omp.cpp b/src/OPENMP/pair_lj_long_tip4p_long_omp.cpp index b0fdf3a393..b452960386 100644 --- a/src/OPENMP/pair_lj_long_tip4p_long_omp.cpp +++ b/src/OPENMP/pair_lj_long_tip4p_long_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_long_tip4p_long_omp.h b/src/OPENMP/pair_lj_long_tip4p_long_omp.h index dae649ff6a..624afbc38b 100644 --- a/src/OPENMP/pair_lj_long_tip4p_long_omp.h +++ b/src/OPENMP/pair_lj_long_tip4p_long_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_relres_omp.cpp b/src/OPENMP/pair_lj_relres_omp.cpp index 159b22bbb1..64384a4c41 100644 --- a/src/OPENMP/pair_lj_relres_omp.cpp +++ b/src/OPENMP/pair_lj_relres_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_relres_omp.h b/src/OPENMP/pair_lj_relres_omp.h index 9a4a587e14..290bb11bba 100644 --- a/src/OPENMP/pair_lj_relres_omp.h +++ b/src/OPENMP/pair_lj_relres_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_sf_dipole_sf_omp.cpp b/src/OPENMP/pair_lj_sf_dipole_sf_omp.cpp index 36ac61a14c..c01782b3c7 100644 --- a/src/OPENMP/pair_lj_sf_dipole_sf_omp.cpp +++ b/src/OPENMP/pair_lj_sf_dipole_sf_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_sf_dipole_sf_omp.h b/src/OPENMP/pair_lj_sf_dipole_sf_omp.h index 6f85cbd6ee..7edee62e9d 100644 --- a/src/OPENMP/pair_lj_sf_dipole_sf_omp.h +++ b/src/OPENMP/pair_lj_sf_dipole_sf_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_smooth_linear_omp.cpp b/src/OPENMP/pair_lj_smooth_linear_omp.cpp index 49768a8641..1f43e22a32 100644 --- a/src/OPENMP/pair_lj_smooth_linear_omp.cpp +++ b/src/OPENMP/pair_lj_smooth_linear_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_smooth_linear_omp.h b/src/OPENMP/pair_lj_smooth_linear_omp.h index b0ed2d6a12..0a6d18deb7 100644 --- a/src/OPENMP/pair_lj_smooth_linear_omp.h +++ b/src/OPENMP/pair_lj_smooth_linear_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_smooth_omp.cpp b/src/OPENMP/pair_lj_smooth_omp.cpp index f142fb7930..052525573b 100644 --- a/src/OPENMP/pair_lj_smooth_omp.cpp +++ b/src/OPENMP/pair_lj_smooth_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_smooth_omp.h b/src/OPENMP/pair_lj_smooth_omp.h index de8601b79c..66faa2cebd 100644 --- a/src/OPENMP/pair_lj_smooth_omp.h +++ b/src/OPENMP/pair_lj_smooth_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_spica_coul_long_omp.cpp b/src/OPENMP/pair_lj_spica_coul_long_omp.cpp index a0c90d872c..41a35c1faf 100644 --- a/src/OPENMP/pair_lj_spica_coul_long_omp.cpp +++ b/src/OPENMP/pair_lj_spica_coul_long_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_spica_coul_long_omp.h b/src/OPENMP/pair_lj_spica_coul_long_omp.h index 0cc7c588cd..e7057c3b85 100644 --- a/src/OPENMP/pair_lj_spica_coul_long_omp.h +++ b/src/OPENMP/pair_lj_spica_coul_long_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_spica_coul_msm_omp.cpp b/src/OPENMP/pair_lj_spica_coul_msm_omp.cpp index b353361abe..1267705a31 100644 --- a/src/OPENMP/pair_lj_spica_coul_msm_omp.cpp +++ b/src/OPENMP/pair_lj_spica_coul_msm_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_spica_coul_msm_omp.h b/src/OPENMP/pair_lj_spica_coul_msm_omp.h index b84bf35db8..fde6183b4d 100644 --- a/src/OPENMP/pair_lj_spica_coul_msm_omp.h +++ b/src/OPENMP/pair_lj_spica_coul_msm_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lj_spica_omp.cpp b/src/OPENMP/pair_lj_spica_omp.cpp index 054c5b7d44..7b9502673b 100644 --- a/src/OPENMP/pair_lj_spica_omp.cpp +++ b/src/OPENMP/pair_lj_spica_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_lj_spica_omp.h b/src/OPENMP/pair_lj_spica_omp.h index 34a5b357dd..149024abb1 100644 --- a/src/OPENMP/pair_lj_spica_omp.h +++ b/src/OPENMP/pair_lj_spica_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lubricate_omp.cpp b/src/OPENMP/pair_lubricate_omp.cpp index 2bab66e5ab..2145744a5b 100644 --- a/src/OPENMP/pair_lubricate_omp.cpp +++ b/src/OPENMP/pair_lubricate_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. @@ -162,8 +162,6 @@ void PairLubricateOMP::eval(int iifrom, int iito, ThrData * const thr) const int * const type = atom->type; const int nlocal = atom->nlocal; - int overlaps = 0; - ilist = list->ilist; numneigh = list->numneigh; firstneigh = list->firstneigh; @@ -317,10 +315,6 @@ void PairLubricateOMP::eval(int iifrom, int iito, ThrData * const thr) h_sep = r - 2.0*radi; - // check for overlaps - - if (h_sep < 0.0) overlaps++; - // if less than the minimum gap use the minimum gap instead if (r < cut_inner[itype][jtype]) diff --git a/src/OPENMP/pair_lubricate_omp.h b/src/OPENMP/pair_lubricate_omp.h index 4c5d25f67d..0aac79ab63 100644 --- a/src/OPENMP/pair_lubricate_omp.h +++ b/src/OPENMP/pair_lubricate_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_lubricate_poly_omp.cpp b/src/OPENMP/pair_lubricate_poly_omp.cpp index 55f63f92e5..5b98ec7b14 100644 --- a/src/OPENMP/pair_lubricate_poly_omp.cpp +++ b/src/OPENMP/pair_lubricate_poly_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. @@ -163,8 +163,6 @@ void PairLubricatePolyOMP::eval(int iifrom, int iito, ThrData * const thr) const int * const type = atom->type; const int nlocal = atom->nlocal; - int overlaps = 0; - ilist = list->ilist; numneigh = list->numneigh; firstneigh = list->firstneigh; @@ -322,10 +320,6 @@ void PairLubricatePolyOMP::eval(int iifrom, int iito, ThrData * const thr) h_sep = r - radi-radj; - // check for overlaps - - if (h_sep < 0.0) overlaps++; - // if less than the minimum gap use the minimum gap instead if (r < cut_inner[itype][jtype]) diff --git a/src/OPENMP/pair_lubricate_poly_omp.h b/src/OPENMP/pair_lubricate_poly_omp.h index d88a0f5630..ce01c8f5f4 100644 --- a/src/OPENMP/pair_lubricate_poly_omp.h +++ b/src/OPENMP/pair_lubricate_poly_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_meam_spline_omp.cpp b/src/OPENMP/pair_meam_spline_omp.cpp index d704b9c19c..5f26b58dd4 100644 --- a/src/OPENMP/pair_meam_spline_omp.cpp +++ b/src/OPENMP/pair_meam_spline_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_meam_spline_omp.h b/src/OPENMP/pair_meam_spline_omp.h index 5e7dc49f67..030447012b 100644 --- a/src/OPENMP/pair_meam_spline_omp.h +++ b/src/OPENMP/pair_meam_spline_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_morse_omp.cpp b/src/OPENMP/pair_morse_omp.cpp index 76026e7598..80e2806f34 100644 --- a/src/OPENMP/pair_morse_omp.cpp +++ b/src/OPENMP/pair_morse_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_morse_omp.h b/src/OPENMP/pair_morse_omp.h index a781ed327b..39e921a9ae 100644 --- a/src/OPENMP/pair_morse_omp.h +++ b/src/OPENMP/pair_morse_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_morse_smooth_linear_omp.cpp b/src/OPENMP/pair_morse_smooth_linear_omp.cpp index 448a094993..9ebd5ef3e4 100644 --- a/src/OPENMP/pair_morse_smooth_linear_omp.cpp +++ b/src/OPENMP/pair_morse_smooth_linear_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_morse_smooth_linear_omp.h b/src/OPENMP/pair_morse_smooth_linear_omp.h index 40aa62ee9e..bc8ec3ba83 100644 --- a/src/OPENMP/pair_morse_smooth_linear_omp.h +++ b/src/OPENMP/pair_morse_smooth_linear_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_nm_cut_coul_cut_omp.cpp b/src/OPENMP/pair_nm_cut_coul_cut_omp.cpp index 0dc2d7f094..4bff792ac1 100644 --- a/src/OPENMP/pair_nm_cut_coul_cut_omp.cpp +++ b/src/OPENMP/pair_nm_cut_coul_cut_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_nm_cut_coul_cut_omp.h b/src/OPENMP/pair_nm_cut_coul_cut_omp.h index 7a07dfda0d..615066a0c3 100644 --- a/src/OPENMP/pair_nm_cut_coul_cut_omp.h +++ b/src/OPENMP/pair_nm_cut_coul_cut_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_nm_cut_coul_long_omp.cpp b/src/OPENMP/pair_nm_cut_coul_long_omp.cpp index 9f09258ce8..6694a1237b 100644 --- a/src/OPENMP/pair_nm_cut_coul_long_omp.cpp +++ b/src/OPENMP/pair_nm_cut_coul_long_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_nm_cut_coul_long_omp.h b/src/OPENMP/pair_nm_cut_coul_long_omp.h index 0d59763ee5..b873560c4e 100644 --- a/src/OPENMP/pair_nm_cut_coul_long_omp.h +++ b/src/OPENMP/pair_nm_cut_coul_long_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_nm_cut_omp.cpp b/src/OPENMP/pair_nm_cut_omp.cpp index 6fe77934f1..da35f59a92 100644 --- a/src/OPENMP/pair_nm_cut_omp.cpp +++ b/src/OPENMP/pair_nm_cut_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_nm_cut_omp.h b/src/OPENMP/pair_nm_cut_omp.h index f9c93489c8..2f2c12589a 100644 --- a/src/OPENMP/pair_nm_cut_omp.h +++ b/src/OPENMP/pair_nm_cut_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_peri_lps_omp.cpp b/src/OPENMP/pair_peri_lps_omp.cpp index 2b299a5dd3..c34f3ac236 100644 --- a/src/OPENMP/pair_peri_lps_omp.cpp +++ b/src/OPENMP/pair_peri_lps_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_peri_lps_omp.h b/src/OPENMP/pair_peri_lps_omp.h index 5a2e32256c..65ff1d55f8 100644 --- a/src/OPENMP/pair_peri_lps_omp.h +++ b/src/OPENMP/pair_peri_lps_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_peri_pmb_omp.cpp b/src/OPENMP/pair_peri_pmb_omp.cpp index 25f36f2d22..0b903272fa 100644 --- a/src/OPENMP/pair_peri_pmb_omp.cpp +++ b/src/OPENMP/pair_peri_pmb_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_peri_pmb_omp.h b/src/OPENMP/pair_peri_pmb_omp.h index 4e48a30b5b..ea525d2206 100644 --- a/src/OPENMP/pair_peri_pmb_omp.h +++ b/src/OPENMP/pair_peri_pmb_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_reaxff_omp.cpp b/src/OPENMP/pair_reaxff_omp.cpp index c860514f6e..7ac46b6078 100644 --- a/src/OPENMP/pair_reaxff_omp.cpp +++ b/src/OPENMP/pair_reaxff_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_reaxff_omp.h b/src/OPENMP/pair_reaxff_omp.h index e8497d8321..9ae63a2e3b 100644 --- a/src/OPENMP/pair_reaxff_omp.h +++ b/src/OPENMP/pair_reaxff_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_rebo_omp.cpp b/src/OPENMP/pair_rebo_omp.cpp index b3f964f0f1..cb43d193cd 100644 --- a/src/OPENMP/pair_rebo_omp.cpp +++ b/src/OPENMP/pair_rebo_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_rebo_omp.h b/src/OPENMP/pair_rebo_omp.h index 55cfcfa647..561417b916 100644 --- a/src/OPENMP/pair_rebo_omp.h +++ b/src/OPENMP/pair_rebo_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_resquared_omp.cpp b/src/OPENMP/pair_resquared_omp.cpp index a02427f09f..edc54f7bbc 100644 --- a/src/OPENMP/pair_resquared_omp.cpp +++ b/src/OPENMP/pair_resquared_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_resquared_omp.h b/src/OPENMP/pair_resquared_omp.h index 515e3dc8ec..7aa13b0684 100644 --- a/src/OPENMP/pair_resquared_omp.h +++ b/src/OPENMP/pair_resquared_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_soft_omp.cpp b/src/OPENMP/pair_soft_omp.cpp index 277810a60e..0be8c80dcf 100644 --- a/src/OPENMP/pair_soft_omp.cpp +++ b/src/OPENMP/pair_soft_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_soft_omp.h b/src/OPENMP/pair_soft_omp.h index d8a4d885f2..5dc9d483f7 100644 --- a/src/OPENMP/pair_soft_omp.h +++ b/src/OPENMP/pair_soft_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_sw_mod_omp.cpp b/src/OPENMP/pair_sw_mod_omp.cpp index d87abc1d2c..3a620a16ae 100644 --- a/src/OPENMP/pair_sw_mod_omp.cpp +++ b/src/OPENMP/pair_sw_mod_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_sw_mod_omp.h b/src/OPENMP/pair_sw_mod_omp.h index 1b7fd31ee9..1c5a1465a9 100644 --- a/src/OPENMP/pair_sw_mod_omp.h +++ b/src/OPENMP/pair_sw_mod_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_sw_omp.cpp b/src/OPENMP/pair_sw_omp.cpp index 4f579a9e90..ede5b1a5ea 100644 --- a/src/OPENMP/pair_sw_omp.cpp +++ b/src/OPENMP/pair_sw_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_sw_omp.h b/src/OPENMP/pair_sw_omp.h index 84c35ae0e3..a841189e09 100644 --- a/src/OPENMP/pair_sw_omp.h +++ b/src/OPENMP/pair_sw_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_table_omp.cpp b/src/OPENMP/pair_table_omp.cpp index d60dfb58f1..ca58e9e4d6 100644 --- a/src/OPENMP/pair_table_omp.cpp +++ b/src/OPENMP/pair_table_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_table_omp.h b/src/OPENMP/pair_table_omp.h index 8ccb8d7e87..5ab519a4a8 100644 --- a/src/OPENMP/pair_table_omp.h +++ b/src/OPENMP/pair_table_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_tersoff_mod_c_omp.cpp b/src/OPENMP/pair_tersoff_mod_c_omp.cpp index bfd55f3b0e..38b18f78b5 100644 --- a/src/OPENMP/pair_tersoff_mod_c_omp.cpp +++ b/src/OPENMP/pair_tersoff_mod_c_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_tersoff_mod_c_omp.h b/src/OPENMP/pair_tersoff_mod_c_omp.h index c50d74b67a..0a0637e5b0 100644 --- a/src/OPENMP/pair_tersoff_mod_c_omp.h +++ b/src/OPENMP/pair_tersoff_mod_c_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ diff --git a/src/OPENMP/pair_tersoff_mod_omp.cpp b/src/OPENMP/pair_tersoff_mod_omp.cpp index d7c64002c5..ae7b0b5f0e 100644 --- a/src/OPENMP/pair_tersoff_mod_omp.cpp +++ b/src/OPENMP/pair_tersoff_mod_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_tersoff_mod_omp.h b/src/OPENMP/pair_tersoff_mod_omp.h index fd90a1bb57..23bf8a5b38 100644 --- a/src/OPENMP/pair_tersoff_mod_omp.h +++ b/src/OPENMP/pair_tersoff_mod_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ diff --git a/src/OPENMP/pair_tersoff_omp.cpp b/src/OPENMP/pair_tersoff_omp.cpp index 50c002a01b..32987ba83a 100644 --- a/src/OPENMP/pair_tersoff_omp.cpp +++ b/src/OPENMP/pair_tersoff_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_tersoff_omp.h b/src/OPENMP/pair_tersoff_omp.h index 22d7ea7597..95c0d27362 100644 --- a/src/OPENMP/pair_tersoff_omp.h +++ b/src/OPENMP/pair_tersoff_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ diff --git a/src/OPENMP/pair_tersoff_table_omp.cpp b/src/OPENMP/pair_tersoff_table_omp.cpp index 010a3f5610..5c44aa3329 100644 --- a/src/OPENMP/pair_tersoff_table_omp.cpp +++ b/src/OPENMP/pair_tersoff_table_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_tersoff_table_omp.h b/src/OPENMP/pair_tersoff_table_omp.h index 1426334ee0..0c66403390 100644 --- a/src/OPENMP/pair_tersoff_table_omp.h +++ b/src/OPENMP/pair_tersoff_table_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ diff --git a/src/OPENMP/pair_tersoff_zbl_omp.cpp b/src/OPENMP/pair_tersoff_zbl_omp.cpp index 4b3034a204..cefa89665a 100644 --- a/src/OPENMP/pair_tersoff_zbl_omp.cpp +++ b/src/OPENMP/pair_tersoff_zbl_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_tersoff_zbl_omp.h b/src/OPENMP/pair_tersoff_zbl_omp.h index cad15b2caa..57bf40a69d 100644 --- a/src/OPENMP/pair_tersoff_zbl_omp.h +++ b/src/OPENMP/pair_tersoff_zbl_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ diff --git a/src/OPENMP/pair_tip4p_cut_omp.cpp b/src/OPENMP/pair_tip4p_cut_omp.cpp index 91d0063a01..497743daff 100644 --- a/src/OPENMP/pair_tip4p_cut_omp.cpp +++ b/src/OPENMP/pair_tip4p_cut_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_tip4p_cut_omp.h b/src/OPENMP/pair_tip4p_cut_omp.h index 56cde26914..4f579598bf 100644 --- a/src/OPENMP/pair_tip4p_cut_omp.h +++ b/src/OPENMP/pair_tip4p_cut_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_tip4p_long_omp.cpp b/src/OPENMP/pair_tip4p_long_omp.cpp index 21d4484e99..8c0648cc4a 100644 --- a/src/OPENMP/pair_tip4p_long_omp.cpp +++ b/src/OPENMP/pair_tip4p_long_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_tip4p_long_omp.h b/src/OPENMP/pair_tip4p_long_omp.h index 37eaae6c25..d517052d97 100644 --- a/src/OPENMP/pair_tip4p_long_omp.h +++ b/src/OPENMP/pair_tip4p_long_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_tip4p_long_soft_omp.cpp b/src/OPENMP/pair_tip4p_long_soft_omp.cpp index e2d8023d4b..4a7d6bdfe2 100644 --- a/src/OPENMP/pair_tip4p_long_soft_omp.cpp +++ b/src/OPENMP/pair_tip4p_long_soft_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_tip4p_long_soft_omp.h b/src/OPENMP/pair_tip4p_long_soft_omp.h index be2840484f..6fbbf4d2a6 100644 --- a/src/OPENMP/pair_tip4p_long_soft_omp.h +++ b/src/OPENMP/pair_tip4p_long_soft_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_ufm_omp.cpp b/src/OPENMP/pair_ufm_omp.cpp index aa7a7ed3ea..63113d3b7b 100644 --- a/src/OPENMP/pair_ufm_omp.cpp +++ b/src/OPENMP/pair_ufm_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_ufm_omp.h b/src/OPENMP/pair_ufm_omp.h index 27f68613f2..35afe91f68 100644 --- a/src/OPENMP/pair_ufm_omp.h +++ b/src/OPENMP/pair_ufm_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_vashishta_omp.cpp b/src/OPENMP/pair_vashishta_omp.cpp index e867e58a6d..1241ea310a 100644 --- a/src/OPENMP/pair_vashishta_omp.cpp +++ b/src/OPENMP/pair_vashishta_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_vashishta_omp.h b/src/OPENMP/pair_vashishta_omp.h index a161bc7c8b..cf4395cd7b 100644 --- a/src/OPENMP/pair_vashishta_omp.h +++ b/src/OPENMP/pair_vashishta_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_vashishta_table_omp.cpp b/src/OPENMP/pair_vashishta_table_omp.cpp index eb9e80b7a3..0ba9be8116 100644 --- a/src/OPENMP/pair_vashishta_table_omp.cpp +++ b/src/OPENMP/pair_vashishta_table_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_vashishta_table_omp.h b/src/OPENMP/pair_vashishta_table_omp.h index 2bc731a04a..448f67f9e6 100644 --- a/src/OPENMP/pair_vashishta_table_omp.h +++ b/src/OPENMP/pair_vashishta_table_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_yukawa_colloid_omp.cpp b/src/OPENMP/pair_yukawa_colloid_omp.cpp index f879eeddf9..01cbcb6dfc 100644 --- a/src/OPENMP/pair_yukawa_colloid_omp.cpp +++ b/src/OPENMP/pair_yukawa_colloid_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_yukawa_colloid_omp.h b/src/OPENMP/pair_yukawa_colloid_omp.h index 5dddc26eb9..dc780f1ec1 100644 --- a/src/OPENMP/pair_yukawa_colloid_omp.h +++ b/src/OPENMP/pair_yukawa_colloid_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_yukawa_omp.cpp b/src/OPENMP/pair_yukawa_omp.cpp index efaa42fb50..92640549d4 100644 --- a/src/OPENMP/pair_yukawa_omp.cpp +++ b/src/OPENMP/pair_yukawa_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_yukawa_omp.h b/src/OPENMP/pair_yukawa_omp.h index c905359fa3..45cedfe7c9 100644 --- a/src/OPENMP/pair_yukawa_omp.h +++ b/src/OPENMP/pair_yukawa_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pair_zbl_omp.cpp b/src/OPENMP/pair_zbl_omp.cpp index a1083e0658..5bf1b3000f 100644 --- a/src/OPENMP/pair_zbl_omp.cpp +++ b/src/OPENMP/pair_zbl_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org This software is distributed under the GNU General Public License. diff --git a/src/OPENMP/pair_zbl_omp.h b/src/OPENMP/pair_zbl_omp.h index 3b482a7f5d..9a74ac7e7c 100644 --- a/src/OPENMP/pair_zbl_omp.h +++ b/src/OPENMP/pair_zbl_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pppm_cg_omp.cpp b/src/OPENMP/pppm_cg_omp.cpp index 5dd78770f5..4c751a16f7 100644 --- a/src/OPENMP/pppm_cg_omp.cpp +++ b/src/OPENMP/pppm_cg_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pppm_cg_omp.h b/src/OPENMP/pppm_cg_omp.h index 6ecceed759..2576b41bd7 100644 --- a/src/OPENMP/pppm_cg_omp.h +++ b/src/OPENMP/pppm_cg_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pppm_disp_omp.cpp b/src/OPENMP/pppm_disp_omp.cpp index e4937002a6..24bf2d9564 100644 --- a/src/OPENMP/pppm_disp_omp.cpp +++ b/src/OPENMP/pppm_disp_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pppm_disp_omp.h b/src/OPENMP/pppm_disp_omp.h index 731cdbfcbd..bdc48f5c9f 100644 --- a/src/OPENMP/pppm_disp_omp.h +++ b/src/OPENMP/pppm_disp_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pppm_disp_tip4p_omp.cpp b/src/OPENMP/pppm_disp_tip4p_omp.cpp index 56f3f14c2c..ab6342a047 100644 --- a/src/OPENMP/pppm_disp_tip4p_omp.cpp +++ b/src/OPENMP/pppm_disp_tip4p_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pppm_disp_tip4p_omp.h b/src/OPENMP/pppm_disp_tip4p_omp.h index ec432e3122..44912fe7ca 100644 --- a/src/OPENMP/pppm_disp_tip4p_omp.h +++ b/src/OPENMP/pppm_disp_tip4p_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pppm_omp.cpp b/src/OPENMP/pppm_omp.cpp index 221f0be836..86e65da101 100644 --- a/src/OPENMP/pppm_omp.cpp +++ b/src/OPENMP/pppm_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pppm_omp.h b/src/OPENMP/pppm_omp.h index 8da1f26bfd..67f2366ce6 100644 --- a/src/OPENMP/pppm_omp.h +++ b/src/OPENMP/pppm_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pppm_tip4p_omp.cpp b/src/OPENMP/pppm_tip4p_omp.cpp index b9902df398..66ce44b5ef 100644 --- a/src/OPENMP/pppm_tip4p_omp.cpp +++ b/src/OPENMP/pppm_tip4p_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/pppm_tip4p_omp.h b/src/OPENMP/pppm_tip4p_omp.h index 68662e5975..578f6312a6 100644 --- a/src/OPENMP/pppm_tip4p_omp.h +++ b/src/OPENMP/pppm_tip4p_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/reaxff_hydrogen_bonds_omp.cpp b/src/OPENMP/reaxff_hydrogen_bonds_omp.cpp index e8db77389f..6e1db5ffe7 100644 --- a/src/OPENMP/reaxff_hydrogen_bonds_omp.cpp +++ b/src/OPENMP/reaxff_hydrogen_bonds_omp.cpp @@ -56,7 +56,6 @@ namespace ReaxFF { int start_j, end_j, hb_start_j, hb_end_j; int hblist[MAX_BONDS]; int itr, top; - int num_hb_intrs = 0; double r_jk, theta, cos_theta, sin_xhz4, cos_xhz1, sin_theta2; double e_hb, e_hb_thr = 0.0, exp_hb2, exp_hb3, CEhb1, CEhb2, CEhb3; rvec dcos_theta_di, dcos_theta_dj, dcos_theta_dk; @@ -140,7 +139,6 @@ namespace ReaxFF { type_i = system->my_atoms[i].type; if (type_i < 0) continue; hbp = &(system->reax_param.hbp[type_i][type_j][type_k]); - ++num_hb_intrs; Calculate_Theta(pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk, &theta, &cos_theta); diff --git a/src/OPENMP/reaxff_omp.h b/src/OPENMP/reaxff_omp.h index a8fda4d247..2166494762 100644 --- a/src/OPENMP/reaxff_omp.h +++ b/src/OPENMP/reaxff_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/respa_omp.cpp b/src/OPENMP/respa_omp.cpp index cecde2ff02..254b6671e7 100644 --- a/src/OPENMP/respa_omp.cpp +++ b/src/OPENMP/respa_omp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/respa_omp.h b/src/OPENMP/respa_omp.h index b6f256604f..14eaf3cc2b 100644 --- a/src/OPENMP/respa_omp.h +++ b/src/OPENMP/respa_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/thr_data.cpp b/src/OPENMP/thr_data.cpp index f85b2b685f..6d4747ef62 100644 --- a/src/OPENMP/thr_data.cpp +++ b/src/OPENMP/thr_data.cpp @@ -1,7 +1,7 @@ /* ------------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/thr_data.h b/src/OPENMP/thr_data.h index f054738b56..d5a290be99 100644 --- a/src/OPENMP/thr_data.h +++ b/src/OPENMP/thr_data.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/thr_omp.cpp b/src/OPENMP/thr_omp.cpp index ed19f5a7a2..7bcb75130f 100644 --- a/src/OPENMP/thr_omp.cpp +++ b/src/OPENMP/thr_omp.cpp @@ -2,7 +2,7 @@ /* ------------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPENMP/thr_omp.h b/src/OPENMP/thr_omp.h index b1ecf93a88..b28c7c8049 100644 --- a/src/OPENMP/thr_omp.h +++ b/src/OPENMP/thr_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPT/pair_eam_alloy_opt.cpp b/src/OPT/pair_eam_alloy_opt.cpp index ce9b345e10..a78d597a9c 100644 --- a/src/OPT/pair_eam_alloy_opt.cpp +++ b/src/OPT/pair_eam_alloy_opt.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPT/pair_eam_alloy_opt.h b/src/OPT/pair_eam_alloy_opt.h index b83ddc235b..d5f4d7f465 100644 --- a/src/OPT/pair_eam_alloy_opt.h +++ b/src/OPT/pair_eam_alloy_opt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPT/pair_eam_fs_opt.cpp b/src/OPT/pair_eam_fs_opt.cpp index 3cc2f65f1d..13f7ca7cdf 100644 --- a/src/OPT/pair_eam_fs_opt.cpp +++ b/src/OPT/pair_eam_fs_opt.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPT/pair_eam_fs_opt.h b/src/OPT/pair_eam_fs_opt.h index 89cb54531c..e8d2c387d4 100644 --- a/src/OPT/pair_eam_fs_opt.h +++ b/src/OPT/pair_eam_fs_opt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPT/pair_eam_opt.cpp b/src/OPT/pair_eam_opt.cpp index 24ebdd8b4c..7c003b2dd1 100644 --- a/src/OPT/pair_eam_opt.cpp +++ b/src/OPT/pair_eam_opt.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPT/pair_eam_opt.h b/src/OPT/pair_eam_opt.h index 496439a3dc..419e57f132 100644 --- a/src/OPT/pair_eam_opt.h +++ b/src/OPT/pair_eam_opt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPT/pair_ilp_graphene_hbn_opt.cpp b/src/OPT/pair_ilp_graphene_hbn_opt.cpp index 953340ff5d..586c44be08 100644 --- a/src/OPT/pair_ilp_graphene_hbn_opt.cpp +++ b/src/OPT/pair_ilp_graphene_hbn_opt.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -23,17 +23,15 @@ #include "atom.h" #include "citeme.h" -#include "comm.h" #include "error.h" #include "force.h" #include "interlayer_taper.h" #include "memory.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include -#include +#include using namespace LAMMPS_NS; using namespace InterLayer; diff --git a/src/OPT/pair_ilp_graphene_hbn_opt.h b/src/OPT/pair_ilp_graphene_hbn_opt.h index f56c011e6a..0721014e00 100644 --- a/src/OPT/pair_ilp_graphene_hbn_opt.h +++ b/src/OPT/pair_ilp_graphene_hbn_opt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPT/pair_ilp_tmd_opt.cpp b/src/OPT/pair_ilp_tmd_opt.cpp index 5b70caae5c..834f2a0c9f 100644 --- a/src/OPT/pair_ilp_tmd_opt.cpp +++ b/src/OPT/pair_ilp_tmd_opt.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -33,17 +33,10 @@ #include "pair_ilp_tmd_opt.h" #include "atom.h" -#include "citeme.h" #include "comm.h" -#include "error.h" -#include "force.h" #include "interlayer_taper.h" #include "memory.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "neighbor.h" -#include #include using namespace LAMMPS_NS; diff --git a/src/OPT/pair_ilp_tmd_opt.h b/src/OPT/pair_ilp_tmd_opt.h index d39780fdfa..f6c999da3a 100644 --- a/src/OPT/pair_ilp_tmd_opt.h +++ b/src/OPT/pair_ilp_tmd_opt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPT/pair_lj_charmm_coul_long_opt.cpp b/src/OPT/pair_lj_charmm_coul_long_opt.cpp index bfc904b853..f5d38148a6 100644 --- a/src/OPT/pair_lj_charmm_coul_long_opt.cpp +++ b/src/OPT/pair_lj_charmm_coul_long_opt.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPT/pair_lj_charmm_coul_long_opt.h b/src/OPT/pair_lj_charmm_coul_long_opt.h index 0a652cfb93..dcae7413ad 100644 --- a/src/OPT/pair_lj_charmm_coul_long_opt.h +++ b/src/OPT/pair_lj_charmm_coul_long_opt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPT/pair_lj_cut_coul_long_opt.cpp b/src/OPT/pair_lj_cut_coul_long_opt.cpp index de6f562900..7ae43658d9 100644 --- a/src/OPT/pair_lj_cut_coul_long_opt.cpp +++ b/src/OPT/pair_lj_cut_coul_long_opt.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPT/pair_lj_cut_coul_long_opt.h b/src/OPT/pair_lj_cut_coul_long_opt.h index e86f0fac05..c718979b03 100644 --- a/src/OPT/pair_lj_cut_coul_long_opt.h +++ b/src/OPT/pair_lj_cut_coul_long_opt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPT/pair_lj_cut_opt.cpp b/src/OPT/pair_lj_cut_opt.cpp index 9fbddd492a..1544949a0e 100644 --- a/src/OPT/pair_lj_cut_opt.cpp +++ b/src/OPT/pair_lj_cut_opt.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPT/pair_lj_cut_opt.h b/src/OPT/pair_lj_cut_opt.h index fb34efd99a..d27a8eea3d 100644 --- a/src/OPT/pair_lj_cut_opt.h +++ b/src/OPT/pair_lj_cut_opt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPT/pair_lj_cut_tip4p_long_opt.cpp b/src/OPT/pair_lj_cut_tip4p_long_opt.cpp index 9f02547d7e..5e484fd866 100644 --- a/src/OPT/pair_lj_cut_tip4p_long_opt.cpp +++ b/src/OPT/pair_lj_cut_tip4p_long_opt.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPT/pair_lj_cut_tip4p_long_opt.h b/src/OPT/pair_lj_cut_tip4p_long_opt.h index 613aa28532..145096c3c5 100644 --- a/src/OPT/pair_lj_cut_tip4p_long_opt.h +++ b/src/OPT/pair_lj_cut_tip4p_long_opt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPT/pair_lj_long_coul_long_opt.cpp b/src/OPT/pair_lj_long_coul_long_opt.cpp index 5b8a1009f1..a7aa232882 100644 --- a/src/OPT/pair_lj_long_coul_long_opt.cpp +++ b/src/OPT/pair_lj_long_coul_long_opt.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPT/pair_lj_long_coul_long_opt.h b/src/OPT/pair_lj_long_coul_long_opt.h index 2ffcff23db..9aa3c0c4cc 100644 --- a/src/OPT/pair_lj_long_coul_long_opt.h +++ b/src/OPT/pair_lj_long_coul_long_opt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPT/pair_morse_opt.cpp b/src/OPT/pair_morse_opt.cpp index 2c256073a2..54457fb95a 100644 --- a/src/OPT/pair_morse_opt.cpp +++ b/src/OPT/pair_morse_opt.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPT/pair_morse_opt.h b/src/OPT/pair_morse_opt.h index 6afb8da4f5..b992a09afa 100644 --- a/src/OPT/pair_morse_opt.h +++ b/src/OPT/pair_morse_opt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPT/pair_saip_metal_opt.cpp b/src/OPT/pair_saip_metal_opt.cpp index 71275bf4df..e64b3a189e 100644 --- a/src/OPT/pair_saip_metal_opt.cpp +++ b/src/OPT/pair_saip_metal_opt.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -34,17 +34,10 @@ #include "pair_saip_metal_opt.h" #include "atom.h" -#include "citeme.h" #include "comm.h" -#include "error.h" -#include "force.h" #include "interlayer_taper.h" #include "memory.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "neighbor.h" -#include #include using namespace LAMMPS_NS; diff --git a/src/OPT/pair_saip_metal_opt.h b/src/OPT/pair_saip_metal_opt.h index 94ed6262d1..6be11573ee 100644 --- a/src/OPT/pair_saip_metal_opt.h +++ b/src/OPT/pair_saip_metal_opt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPT/pair_ufm_opt.cpp b/src/OPT/pair_ufm_opt.cpp index 6809420f8a..b133e69ddd 100644 --- a/src/OPT/pair_ufm_opt.cpp +++ b/src/OPT/pair_ufm_opt.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/OPT/pair_ufm_opt.h b/src/OPT/pair_ufm_opt.h index 06fd07dd02..41fee7bc51 100644 --- a/src/OPT/pair_ufm_opt.h +++ b/src/OPT/pair_ufm_opt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ORIENT/fix_orient_bcc.cpp b/src/ORIENT/fix_orient_bcc.cpp index a97123a33d..3e4c408e78 100644 --- a/src/ORIENT/fix_orient_bcc.cpp +++ b/src/ORIENT/fix_orient_bcc.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ORIENT/fix_orient_bcc.h b/src/ORIENT/fix_orient_bcc.h index ead626141f..7f08e60a7e 100644 --- a/src/ORIENT/fix_orient_bcc.h +++ b/src/ORIENT/fix_orient_bcc.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ORIENT/fix_orient_eco.cpp b/src/ORIENT/fix_orient_eco.cpp index b34ce8e33a..4efdacd090 100644 --- a/src/ORIENT/fix_orient_eco.cpp +++ b/src/ORIENT/fix_orient_eco.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratdir_veces - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ORIENT/fix_orient_eco.h b/src/ORIENT/fix_orient_eco.h index ca9fa31d7d..ec6f537a6a 100644 --- a/src/ORIENT/fix_orient_eco.h +++ b/src/ORIENT/fix_orient_eco.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ORIENT/fix_orient_fcc.cpp b/src/ORIENT/fix_orient_fcc.cpp index 57a6e5ffd8..5f0c62a5d6 100644 --- a/src/ORIENT/fix_orient_fcc.cpp +++ b/src/ORIENT/fix_orient_fcc.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ORIENT/fix_orient_fcc.h b/src/ORIENT/fix_orient_fcc.h index 5d50a8e300..428ac4aad4 100644 --- a/src/ORIENT/fix_orient_fcc.h +++ b/src/ORIENT/fix_orient_fcc.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp index 20eeef3042..f0cbd6eb04 100644 --- a/src/PERI/atom_vec_peri.cpp +++ b/src/PERI/atom_vec_peri.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PERI/atom_vec_peri.h b/src/PERI/atom_vec_peri.h index 8faaf0931e..4e05a1728b 100644 --- a/src/PERI/atom_vec_peri.h +++ b/src/PERI/atom_vec_peri.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,7 @@ AtomStyle(peri,AtomVecPeri); namespace LAMMPS_NS { -class AtomVecPeri : public AtomVec { +class AtomVecPeri : virtual public AtomVec { public: AtomVecPeri(class LAMMPS *); diff --git a/src/PERI/compute_damage_atom.cpp b/src/PERI/compute_damage_atom.cpp index 1e08e534c6..c41a34eabe 100644 --- a/src/PERI/compute_damage_atom.cpp +++ b/src/PERI/compute_damage_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PERI/compute_damage_atom.h b/src/PERI/compute_damage_atom.h index f51ed30782..7e34595026 100644 --- a/src/PERI/compute_damage_atom.h +++ b/src/PERI/compute_damage_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PERI/compute_dilatation_atom.cpp b/src/PERI/compute_dilatation_atom.cpp index 9d44602756..a5dcf3f803 100644 --- a/src/PERI/compute_dilatation_atom.cpp +++ b/src/PERI/compute_dilatation_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PERI/compute_dilatation_atom.h b/src/PERI/compute_dilatation_atom.h index 50f4404b06..8ad185bb99 100644 --- a/src/PERI/compute_dilatation_atom.h +++ b/src/PERI/compute_dilatation_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PERI/compute_plasticity_atom.cpp b/src/PERI/compute_plasticity_atom.cpp index 425f6379e0..95c64db481 100644 --- a/src/PERI/compute_plasticity_atom.cpp +++ b/src/PERI/compute_plasticity_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PERI/compute_plasticity_atom.h b/src/PERI/compute_plasticity_atom.h index 53abe86332..75cbb2275a 100644 --- a/src/PERI/compute_plasticity_atom.h +++ b/src/PERI/compute_plasticity_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PERI/fix_peri_neigh.cpp b/src/PERI/fix_peri_neigh.cpp index 51b8adf741..3d965b7280 100644 --- a/src/PERI/fix_peri_neigh.cpp +++ b/src/PERI/fix_peri_neigh.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -27,7 +27,6 @@ #include "comm.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "pair.h" #include "lattice.h" #include "memory.h" diff --git a/src/PERI/fix_peri_neigh.h b/src/PERI/fix_peri_neigh.h index 348e6393cb..b6bd606212 100644 --- a/src/PERI/fix_peri_neigh.h +++ b/src/PERI/fix_peri_neigh.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PERI/pair_peri.cpp b/src/PERI/pair_peri.cpp index f80de4c7b5..6606f36c6f 100644 --- a/src/PERI/pair_peri.cpp +++ b/src/PERI/pair_peri.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PERI/pair_peri.h b/src/PERI/pair_peri.h index 14c93aa14a..8a9fbe8dcd 100644 --- a/src/PERI/pair_peri.h +++ b/src/PERI/pair_peri.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PERI/pair_peri_eps.cpp b/src/PERI/pair_peri_eps.cpp index 19d73b0aed..77d8c078c4 100644 --- a/src/PERI/pair_peri_eps.cpp +++ b/src/PERI/pair_peri_eps.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PERI/pair_peri_eps.h b/src/PERI/pair_peri_eps.h index 260d1ceb97..60a6a8a3e6 100644 --- a/src/PERI/pair_peri_eps.h +++ b/src/PERI/pair_peri_eps.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp index e63125fe1a..2e11b8c76f 100644 --- a/src/PERI/pair_peri_lps.cpp +++ b/src/PERI/pair_peri_lps.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PERI/pair_peri_lps.h b/src/PERI/pair_peri_lps.h index 29e5f0fbfb..758e3234d2 100644 --- a/src/PERI/pair_peri_lps.h +++ b/src/PERI/pair_peri_lps.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp index 8743600d6e..1bed10a877 100644 --- a/src/PERI/pair_peri_pmb.cpp +++ b/src/PERI/pair_peri_pmb.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PERI/pair_peri_pmb.h b/src/PERI/pair_peri_pmb.h index f8756c2448..047bc3a5f0 100644 --- a/src/PERI/pair_peri_pmb.h +++ b/src/PERI/pair_peri_pmb.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp index a7df5f4659..7e43678919 100644 --- a/src/PERI/pair_peri_ves.cpp +++ b/src/PERI/pair_peri_ves.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PERI/pair_peri_ves.h b/src/PERI/pair_peri_ves.h index 9210dcfdb5..2c6680f9e7 100644 --- a/src/PERI/pair_peri_ves.h +++ b/src/PERI/pair_peri_ves.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PHONON/dynamical_matrix.cpp b/src/PHONON/dynamical_matrix.cpp index 8f667f51f2..8e4f8557a2 100644 --- a/src/PHONON/dynamical_matrix.cpp +++ b/src/PHONON/dynamical_matrix.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PHONON/fix_phonon.cpp b/src/PHONON/fix_phonon.cpp index 3b4f182a16..b08f005d87 100644 --- a/src/PHONON/fix_phonon.cpp +++ b/src/PHONON/fix_phonon.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PHONON/fix_phonon.h b/src/PHONON/fix_phonon.h index 7c790c5efb..c1489e5bcb 100644 --- a/src/PHONON/fix_phonon.h +++ b/src/PHONON/fix_phonon.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - www.cs.sandia.gov/~sjplimp/lammps.html - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PHONON/third_order.cpp b/src/PHONON/third_order.cpp index bbd6818b95..4a8948de77 100644 --- a/src/PHONON/third_order.cpp +++ b/src/PHONON/third_order.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -34,7 +34,6 @@ #include "memory.h" #include "modify.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "pair.h" #include "timer.h" diff --git a/src/PLUGIN/Install.sh b/src/PLUGIN/Install.sh index 0df642193e..86de36d7df 100755 --- a/src/PLUGIN/Install.sh +++ b/src/PLUGIN/Install.sh @@ -44,7 +44,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*plugin.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*plugin.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/plugin\/Makefile.lammps @@ -58,7 +58,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*plugin.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*plugin.*$/d' ../Makefile.package.settings fi fi diff --git a/src/PLUGIN/plugin.cpp b/src/PLUGIN/plugin.cpp index 1ca241d20a..f4a0903be4 100644 --- a/src/PLUGIN/plugin.cpp +++ b/src/PLUGIN/plugin.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -21,7 +21,6 @@ #include "force.h" #include "input.h" #include "modify.h" -#include "region.h" #include #include diff --git a/src/PLUGIN/plugin.h b/src/PLUGIN/plugin.h index 8cfabc9ef2..4d8d6c29f8 100644 --- a/src/PLUGIN/plugin.h +++ b/src/PLUGIN/plugin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PLUMED/Install.sh b/src/PLUMED/Install.sh index f879d42feb..500a55ec77 100755 --- a/src/PLUMED/Install.sh +++ b/src/PLUMED/Install.sh @@ -45,7 +45,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*plumed.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*plumed.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/plumed\/Makefile.lammps @@ -59,7 +59,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*plumed.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*plumed.*$/d' ../Makefile.package.settings fi fi diff --git a/src/PLUMED/fix_plumed.cpp b/src/PLUMED/fix_plumed.cpp index 85bf2df3bc..f06d5474f6 100644 --- a/src/PLUMED/fix_plumed.cpp +++ b/src/PLUMED/fix_plumed.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PLUMED/fix_plumed.h b/src/PLUMED/fix_plumed.h index f4dce376b8..b1cdc9db46 100644 --- a/src/PLUMED/fix_plumed.h +++ b/src/PLUMED/fix_plumed.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/POEMS/Install.sh b/src/POEMS/Install.sh index be407d76f0..37f8404738 100755 --- a/src/POEMS/Install.sh +++ b/src/POEMS/Install.sh @@ -44,7 +44,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*poems.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*poems.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/poems\/Makefile.lammps @@ -58,7 +58,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*poems.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*poems.*$/d' ../Makefile.package.settings fi fi diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp index 312208f4d9..f289a939e6 100644 --- a/src/POEMS/fix_poems.cpp +++ b/src/POEMS/fix_poems.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/POEMS/fix_poems.h b/src/POEMS/fix_poems.h index c57832a7f3..99af171636 100644 --- a/src/POEMS/fix_poems.h +++ b/src/POEMS/fix_poems.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PTM/compute_ptm_atom.cpp b/src/PTM/compute_ptm_atom.cpp index 676144eb42..e66bc1a17d 100644 --- a/src/PTM/compute_ptm_atom.cpp +++ b/src/PTM/compute_ptm_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PTM/compute_ptm_atom.h b/src/PTM/compute_ptm_atom.h index 61101f6efa..94dab27009 100644 --- a/src/PTM/compute_ptm_atom.h +++ b/src/PTM/compute_ptm_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PYTHON/Install.sh b/src/PYTHON/Install.sh index 8c394d43ad..b23cf574f8 100755 --- a/src/PYTHON/Install.sh +++ b/src/PYTHON/Install.sh @@ -50,7 +50,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*python.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*python.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/python\/Makefile.lammps @@ -65,7 +65,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*python.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*python.*$/d' ../Makefile.package.settings fi fi diff --git a/src/PYTHON/fix_python_invoke.cpp b/src/PYTHON/fix_python_invoke.cpp index 78ffe99ad3..786c48568d 100644 --- a/src/PYTHON/fix_python_invoke.cpp +++ b/src/PYTHON/fix_python_invoke.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PYTHON/fix_python_invoke.h b/src/PYTHON/fix_python_invoke.h index 0a50f6859d..12f463501f 100644 --- a/src/PYTHON/fix_python_invoke.h +++ b/src/PYTHON/fix_python_invoke.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PYTHON/fix_python_move.cpp b/src/PYTHON/fix_python_move.cpp index cdfce4a969..caa1557503 100644 --- a/src/PYTHON/fix_python_move.cpp +++ b/src/PYTHON/fix_python_move.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PYTHON/fix_python_move.h b/src/PYTHON/fix_python_move.h index d975dc79c5..85a9a37b00 100644 --- a/src/PYTHON/fix_python_move.h +++ b/src/PYTHON/fix_python_move.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp index 9bf7066a0d..695954604c 100644 --- a/src/PYTHON/pair_python.cpp +++ b/src/PYTHON/pair_python.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PYTHON/pair_python.h b/src/PYTHON/pair_python.h index 13c732aaf4..6651bcd153 100644 --- a/src/PYTHON/pair_python.h +++ b/src/PYTHON/pair_python.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PYTHON/python_compat.h b/src/PYTHON/python_compat.h index 98aec37d37..775435ffd8 100644 --- a/src/PYTHON/python_compat.h +++ b/src/PYTHON/python_compat.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp index aba8e88e10..9177381a35 100644 --- a/src/PYTHON/python_impl.cpp +++ b/src/PYTHON/python_impl.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -112,37 +112,42 @@ PythonImpl::~PythonImpl() void PythonImpl::command(int narg, char **arg) { - if (narg < 2) error->all(FLERR, "Invalid python command"); + if (narg < 2) utils::missing_cmd_args(FLERR, "python", error); // if invoke is only keyword, invoke the previously defined function if (narg == 2 && strcmp(arg[1], "invoke") == 0) { int ifunc = find(arg[0]); - if (ifunc < 0) error->all(FLERR, "Python invoke of undefined function"); + if (ifunc < 0) error->all(FLERR, "Python invoke of unknown function: {}", arg[0]); char *str = nullptr; if (pfuncs[ifunc].noutput) { str = input->variable->pythonstyle(pfuncs[ifunc].ovarname, pfuncs[ifunc].name); - if (!str) error->all(FLERR, "Python variable does not match Python function"); + if (!str) + error->all(FLERR, + "Python variable {} does not match variable {} " + "registered with Python function {}", + arg[0], pfuncs[ifunc].ovarname, pfuncs[ifunc].name); } invoke_function(ifunc, str); return; } - // if source is only keyword, execute the python code + // if source is only keyword, execute the python code in file - if (narg == 3 && strcmp(arg[1], "source") == 0) { - int err; + if ((narg > 1) && (strcmp(arg[0], "source") == 0)) { + int err = -1; - FILE *fp = fopen(arg[2], "r"); - if (fp == nullptr) + if ((narg > 2) && (strcmp(arg[1], "here") == 0)) { err = execute_string(arg[2]); - else - err = execute_file(arg[2]); - - if (fp) fclose(fp); - if (err) error->all(FLERR, "Could not process Python source command"); + } else { + if (platform::file_is_readable(arg[1])) + err = execute_file(arg[1]); + else + error->all(FLERR, "Could not open python source file {} for processing", arg[1]); + } + if (err) error->all(FLERR, "Failure in python source command"); return; } @@ -162,48 +167,51 @@ void PythonImpl::command(int narg, char **arg) int iarg = 1; while (iarg < narg) { if (strcmp(arg[iarg], "input") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Invalid python command"); + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "python input", error); ninput = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); - if (ninput < 0) error->all(FLERR, "Invalid python command"); + if (ninput < 0) error->all(FLERR, "Invalid number of python input arguments: {}", ninput); iarg += 2; delete[] istr; istr = new char *[ninput]; - if (iarg + ninput > narg) error->all(FLERR, "Invalid python command"); + if (iarg + ninput > narg) utils::missing_cmd_args(FLERR, "python input", error); for (int i = 0; i < ninput; i++) istr[i] = arg[iarg + i]; iarg += ninput; } else if (strcmp(arg[iarg], "return") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Invalid python command"); + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "python return", error); noutput = 1; ostr = arg[iarg + 1]; iarg += 2; } else if (strcmp(arg[iarg], "format") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Invalid python command"); + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "python format", error); format = utils::strdup(arg[iarg + 1]); iarg += 2; } else if (strcmp(arg[iarg], "length") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Invalid python command"); + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "python length", error); length_longstr = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); - if (length_longstr <= 0) error->all(FLERR, "Invalid python command"); + if (length_longstr <= 0) error->all(FLERR, "Invalid python return value length"); iarg += 2; } else if (strcmp(arg[iarg], "file") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Invalid python command"); + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "python file", error); delete[] pyfile; pyfile = utils::strdup(arg[iarg + 1]); iarg += 2; } else if (strcmp(arg[iarg], "here") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Invalid python command"); + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "python here", error); herestr = arg[iarg + 1]; iarg += 2; } else if (strcmp(arg[iarg], "exists") == 0) { existflag = 1; iarg++; } else - error->all(FLERR, "Invalid python command"); + error->all(FLERR, "Unknown python command keyword: {}", arg[iarg]); } - if (pyfile && herestr) error->all(FLERR, "Invalid python command"); - if (pyfile && existflag) error->all(FLERR, "Invalid python command"); - if (herestr && existflag) error->all(FLERR, "Invalid python command"); + if (pyfile && herestr) + error->all(FLERR, "Must not use python 'file' and 'here' keywords at the same time"); + if (pyfile && existflag) + error->all(FLERR, "Must not use python 'file' and 'exists' keywords at the same time"); + if (herestr && existflag) + error->all(FLERR, "Must not use python 'here' and 'exists' keywords at the same time"); // create or overwrite entry in pfuncs vector with name = arg[0] @@ -221,23 +229,21 @@ void PythonImpl::command(int narg, char **arg) if (fp == nullptr) { PyUtils::Print_Errors(); - error->all(FLERR, "Could not open Python file"); + error->all(FLERR, "Could not open Python file: {}", pyfile); } int err = PyRun_SimpleFile(fp, pyfile); - if (err) { PyUtils::Print_Errors(); - error->all(FLERR, "Could not process Python file"); + error->all(FLERR, "Could not process Python file: {}", pyfile); } - fclose(fp); + } else if (herestr) { int err = PyRun_SimpleString(herestr); - if (err) { PyUtils::Print_Errors(); - error->all(FLERR, "Could not process Python string"); + error->all(FLERR, "Could not process Python string: {}", herestr); } } @@ -280,14 +286,17 @@ void PythonImpl::invoke_function(int ifunc, char *result) int ninput = pfuncs[ifunc].ninput; PyObject *pArgs = PyTuple_New(ninput); - if (!pArgs) { error->all(FLERR, "Could not create Python function arguments"); } + if (!pArgs) + error->all(FLERR, "Could not prepare arguments for Python function {}", pfuncs[ifunc].name); for (int i = 0; i < ninput; i++) { int itype = pfuncs[ifunc].itype[i]; if (itype == INT) { if (pfuncs[ifunc].ivarflag[i]) { str = input->variable->retrieve(pfuncs[ifunc].svalue[i]); - if (!str) { error->all(FLERR, "Could not evaluate Python function input variable"); } + if (!str) + error->all(FLERR, "Could not evaluate Python function {} input variable: {}", + pfuncs[ifunc].name, pfuncs[ifunc].svalue[i]); pValue = PY_INT_FROM_LONG(atoi(str)); } else { pValue = PY_INT_FROM_LONG(pfuncs[ifunc].ivalue[i]); @@ -295,7 +304,9 @@ void PythonImpl::invoke_function(int ifunc, char *result) } else if (itype == DOUBLE) { if (pfuncs[ifunc].ivarflag[i]) { str = input->variable->retrieve(pfuncs[ifunc].svalue[i]); - if (!str) { error->all(FLERR, "Could not evaluate Python function input variable"); } + if (!str) + error->all(FLERR, "Could not evaluate Python function {} input variable: {}", + pfuncs[ifunc].name, pfuncs[ifunc].svalue[i]); pValue = PyFloat_FromDouble(atof(str)); } else { pValue = PyFloat_FromDouble(pfuncs[ifunc].dvalue[i]); @@ -303,7 +314,9 @@ void PythonImpl::invoke_function(int ifunc, char *result) } else if (itype == STRING) { if (pfuncs[ifunc].ivarflag[i]) { str = input->variable->retrieve(pfuncs[ifunc].svalue[i]); - if (!str) { error->all(FLERR, "Could not evaluate Python function input variable"); } + if (!str) + error->all(FLERR, "Could not evaluate Python function {} input variable: {}", + pfuncs[ifunc].name, pfuncs[ifunc].svalue[i]); pValue = PY_STRING_FROM_STRING(str); } else { pValue = PY_STRING_FROM_STRING(pfuncs[ifunc].svalue[i]); @@ -311,7 +324,7 @@ void PythonImpl::invoke_function(int ifunc, char *result) } else if (itype == PTR) { pValue = PY_VOID_POINTER(lmp); } else { - error->all(FLERR, "Unsupported variable type"); + error->all(FLERR, "Unsupported variable type: {}", itype); } PyTuple_SetItem(pArgs, i, pValue); } @@ -324,7 +337,7 @@ void PythonImpl::invoke_function(int ifunc, char *result) if (!pValue) { PyUtils::Print_Errors(); - error->one(FLERR, "Python function evaluation failed"); + error->one(FLERR, "Python evaluation of function {} failed", pfuncs[ifunc].name); } // function returned a value @@ -365,9 +378,9 @@ int PythonImpl::variable_match(const char *name, const char *varname, int numeri { int ifunc = find(name); if (ifunc < 0) return -1; - if (pfuncs[ifunc].noutput == 0) return -1; - if (strcmp(pfuncs[ifunc].ovarname, varname) != 0) return -1; - if (numeric && pfuncs[ifunc].otype == STRING) return -1; + if (pfuncs[ifunc].noutput == 0) return -2; + if (strcmp(pfuncs[ifunc].ovarname, varname) != 0) return -3; + if (numeric && pfuncs[ifunc].otype == STRING) return -4; return ifunc; } @@ -400,9 +413,10 @@ int PythonImpl::create_entry(char *name, int ninput, int noutput, int length_lon pfuncs[ifunc].noutput = noutput; if (!format && ninput + noutput) - error->all(FLERR, "Invalid python command"); + error->all(FLERR, "Missing python format keyword"); else if (format && ((int) strlen(format) != ninput + noutput)) - error->all(FLERR, "Invalid python command"); + error->all(FLERR, "Input/output arguments ({}) and format characters ({}) are inconsistent", + (ninput + noutput), strlen(format)); // process inputs as values or variables @@ -448,7 +462,7 @@ int PythonImpl::create_entry(char *name, int ninput, int noutput, int length_lon if (strcmp(istr[i], "SELF") != 0) error->all(FLERR, "Invalid python command"); } else - error->all(FLERR, "Invalid python command"); + error->all(FLERR, "Invalid python format character: {}", type); } // process output as value or variable @@ -465,7 +479,7 @@ int PythonImpl::create_entry(char *name, int ninput, int noutput, int length_lon else if (type == 's') pfuncs[ifunc].otype = STRING; else - error->all(FLERR, "Invalid python command"); + error->all(FLERR, "Invalid python return format character: {}", type); if (length_longstr) { if (pfuncs[ifunc].otype != STRING) @@ -486,7 +500,9 @@ int PythonImpl::create_entry(char *name, int ninput, int noutput, int length_lon int PythonImpl::execute_string(char *cmd) { PyUtils::GIL lock; - return PyRun_SimpleString(cmd); + int err = PyRun_SimpleString(cmd); + if (err) PyUtils::Print_Errors(); + return err; } /* ---------------------------------------------------------------------- */ @@ -498,6 +514,7 @@ int PythonImpl::execute_file(char *fname) PyUtils::GIL lock; int err = PyRun_SimpleFile(fp, fname); + if (err) PyUtils::Print_Errors(); if (fp) fclose(fp); return err; diff --git a/src/PYTHON/python_impl.h b/src/PYTHON/python_impl.h index 37f084156e..667980f8aa 100644 --- a/src/PYTHON/python_impl.h +++ b/src/PYTHON/python_impl.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/PYTHON/python_utils.h b/src/PYTHON/python_utils.h index bc801447a2..cc6b006e5f 100644 --- a/src/PYTHON/python_utils.h +++ b/src/PYTHON/python_utils.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/Purge.list b/src/Purge.list index 5b838be535..4d0533dfae 100644 --- a/src/Purge.list +++ b/src/Purge.list @@ -75,6 +75,9 @@ pair_lj_sdk_omp.cpp pair_lj_sdk_coul_msm_omp.h pair_lj_sdk_coul_long_omp.cpp angle_sdk_omp.h +# renamed on 13 Jun 2022 +fix_mdi_aimd.cpp +fix_mdi_aimd.h # removed on 8 April 2022 fix_client_md.cpp fix_client_md.h diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp index aec84947a1..c8112ca24d 100644 --- a/src/QEQ/fix_qeq.cpp +++ b/src/QEQ/fix_qeq.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -60,7 +60,7 @@ FixQEq::FixQEq(LAMMPS *lmp, int narg, char **arg) : b_t(nullptr), p(nullptr), q(nullptr), r(nullptr), d(nullptr), qf(nullptr), q1(nullptr), q2(nullptr), qv(nullptr) { - if (narg < 8) error->all(FLERR,"Illegal fix qeq command"); + if (narg < 8) utils::missing_cmd_args(FLERR, "fix " + std::string(style), error); scalar_flag = 1; extscalar = 0; diff --git a/src/QEQ/fix_qeq.h b/src/QEQ/fix_qeq.h index d381a61ba8..0d21d643fc 100644 --- a/src/QEQ/fix_qeq.h +++ b/src/QEQ/fix_qeq.h @@ -1,7 +1,7 @@ /* -*- c++ -*- --------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/QEQ/fix_qeq_dynamic.cpp b/src/QEQ/fix_qeq_dynamic.cpp index 257394ebb9..3bc0650ef1 100644 --- a/src/QEQ/fix_qeq_dynamic.cpp +++ b/src/QEQ/fix_qeq_dynamic.cpp @@ -1,8 +1,7 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -34,8 +33,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -FixQEqDynamic::FixQEqDynamic(LAMMPS *lmp, int narg, char **arg) : - FixQEq(lmp, narg, arg) +FixQEqDynamic::FixQEqDynamic(LAMMPS *lmp, int narg, char **arg) : FixQEq(lmp, narg, arg) { qdamp = 0.10; qstep = 0.02; @@ -43,19 +41,20 @@ FixQEqDynamic::FixQEqDynamic(LAMMPS *lmp, int narg, char **arg) : int iarg = 8; while (iarg < narg) { - if (strcmp(arg[iarg],"qdamp") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix qeq/dynamic command"); - qdamp = atof(arg[iarg+1]); + if (strcmp(arg[iarg], "qdamp") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix qeq/dynamic qdamp", error); + qdamp = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"qstep") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix qeq/dynamic command"); - qstep = atof(arg[iarg+1]); + } else if (strcmp(arg[iarg], "qstep") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix qeq/dynamic qstep", error); + qstep = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"warn") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix qeq/dynamic command"); - maxwarn = utils::logical(FLERR,arg[iarg+1],false,lmp); + } else if (strcmp(arg[iarg], "warn") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix qeq/dynamic warn", error); + maxwarn = utils::logical(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else error->all(FLERR,"Illegal fix qeq/dynamic command"); + } else + error->all(FLERR, "Unknown fix qeq/dynamic keyword: {}", arg[iarg]); } } @@ -69,16 +68,17 @@ void FixQEqDynamic::init() if (tolerance < 1e-4) if (comm->me == 0) - error->warning(FLERR,"Fix qeq/dynamic tolerance may be too small for damped dynamics"); + error->warning(FLERR, "Fix qeq/dynamic tolerance {} may be too small for damped dynamics", + tolerance); } /* ---------------------------------------------------------------------- */ void FixQEqDynamic::pre_force(int /*vflag*/) { - int i,ii,iloop,inum,*ilist; - double qmass,dtq2; - double enegchkall,enegmaxall; + int i, ii, iloop, inum, *ilist; + double qmass, dtq2; + double enegchkall, enegmaxall; double *q = atom->q; int *mask = atom->mask; @@ -94,20 +94,20 @@ void FixQEqDynamic::pre_force(int /*vflag*/) inum = list->inum; ilist = list->ilist; - qmass = 0.016; - dtq2 = 0.5*qstep*qstep/qmass; + qmass = 0.016; + dtq2 = 0.5 * qstep * qstep / qmass; for (ii = 0; ii < inum; ii++) { i = ilist[ii]; q1[i] = q2[i] = qf[i] = 0.0; } - for (iloop = 0; iloop < maxiter; iloop ++) { + for (iloop = 0; iloop < maxiter; iloop++) { for (ii = 0; ii < inum; ii++) { i = ilist[ii]; if (mask[i] & groupbit) { - q1[i] += qf[i]*dtq2 - qdamp*q1[i]; - q[i] += q1[i]; + q1[i] += qf[i] * dtq2 - qdamp * q1[i]; + q[i] += q1[i]; } } @@ -119,34 +119,32 @@ void FixQEqDynamic::pre_force(int /*vflag*/) enegchk = enegmax = 0.0; - for (ii = 0; ii < inum ; ii++) { + for (ii = 0; ii < inum; ii++) { i = ilist[ii]; if (mask[i] & groupbit) { - q2[i] = enegtot-qf[i]; - enegmax = MAX(enegmax,fabs(q2[i])); + q2[i] = enegtot - qf[i]; + enegmax = MAX(enegmax, fabs(q2[i])); enegchk += fabs(q2[i]); qf[i] = q2[i]; } } - MPI_Allreduce(&enegchk,&enegchkall,1,MPI_DOUBLE,MPI_SUM,world); - enegchk = enegchkall/ngroup; - MPI_Allreduce(&enegmax,&enegmaxall,1,MPI_DOUBLE,MPI_MAX,world); + MPI_Allreduce(&enegchk, &enegchkall, 1, MPI_DOUBLE, MPI_SUM, world); + enegchk = enegchkall / ngroup; + MPI_Allreduce(&enegmax, &enegmaxall, 1, MPI_DOUBLE, MPI_MAX, world); enegmax = enegmaxall; - if ((enegchk <= tolerance) && (enegmax <= 100.0*tolerance)) break; + if ((enegchk <= tolerance) && (enegmax <= 100.0 * tolerance)) break; for (ii = 0; ii < inum; ii++) { i = ilist[ii]; - if (mask[i] & groupbit) - q1[i] += qf[i]*dtq2 - qdamp*q1[i]; + if (mask[i] & groupbit) q1[i] += qf[i] * dtq2 - qdamp * q1[i]; } } matvecs = iloop; if ((comm->me == 0) && maxwarn && (iloop >= maxiter)) - error->warning(FLERR,"Charges did not converge at step {}: {}", - update->ntimestep,enegchk); + error->warning(FLERR, "Charges did not converge at step {}: {}", update->ntimestep, enegchk); if (force->kspace) force->kspace->qsum_qsq(); } @@ -172,8 +170,7 @@ double FixQEqDynamic::compute_eneg() for (ii = 0; ii < inum; ii++) { i = ilist[ii]; - if (mask[i] & groupbit) - qf[i] = 0.0; + if (mask[i] & groupbit) qf[i] = 0.0; } // communicating charge force to all nodes, first forward then reverse @@ -198,12 +195,12 @@ double FixQEqDynamic::compute_eneg() delr[0] = x[i][0] - x[j][0]; delr[1] = x[i][1] - x[j][1]; delr[2] = x[i][2] - x[j][2]; - rsq = delr[0]*delr[0] + delr[1]*delr[1] + delr[2]*delr[2]; + rsq = delr[0] * delr[0] + delr[1] * delr[1] + delr[2] * delr[2]; if (rsq > cutoff_sq) continue; r = sqrt(rsq); - rinv = 1.0/r; + rinv = 1.0 / r; qf[i] += q[j] * rinv; qf[j] += q[i] * rinv; } @@ -218,20 +215,17 @@ double FixQEqDynamic::compute_eneg() eneg = enegtot = 0.0; for (ii = 0; ii < inum; ii++) { i = ilist[ii]; - if (mask[i] & groupbit) - eneg += qf[i]; + if (mask[i] & groupbit) eneg += qf[i]; } - MPI_Allreduce(&eneg,&enegtot,1,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(&eneg, &enegtot, 1, MPI_DOUBLE, MPI_SUM, world); return enegtot; - } /* ---------------------------------------------------------------------- */ -int FixQEqDynamic::pack_forward_comm(int n, int *list, double *buf, - int /*pbc_flag*/, int * /*pbc*/) +int FixQEqDynamic::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { - int m=0; + int m = 0; if (pack_flag == 1) for (m = 0; m < n; m++) buf[m] = atom->q[list[m]]; diff --git a/src/QEQ/fix_qeq_dynamic.h b/src/QEQ/fix_qeq_dynamic.h index 771a4365c9..29dc3825f6 100644 --- a/src/QEQ/fix_qeq_dynamic.h +++ b/src/QEQ/fix_qeq_dynamic.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/QEQ/fix_qeq_fire.cpp b/src/QEQ/fix_qeq_fire.cpp index 429fcc79d6..34ef51d947 100644 --- a/src/QEQ/fix_qeq_fire.cpp +++ b/src/QEQ/fix_qeq_fire.cpp @@ -1,8 +1,7 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -45,7 +44,7 @@ using namespace FixConst; /* ---------------------------------------------------------------------- */ FixQEqFire::FixQEqFire(LAMMPS *lmp, int narg, char **arg) : - FixQEq(lmp, narg, arg), comb(nullptr), comb3(nullptr) + FixQEq(lmp, narg, arg), comb(nullptr), comb3(nullptr) { qdamp = 0.20; qstep = 0.20; @@ -53,19 +52,20 @@ FixQEqFire::FixQEqFire(LAMMPS *lmp, int narg, char **arg) : int iarg = 8; while (iarg < narg) { - if (strcmp(arg[iarg],"qdamp") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix qeq/fire command"); - qdamp = atof(arg[iarg+1]); + if (strcmp(arg[iarg], "qdamp") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix qeq/fire qdamp", error); + qdamp = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"qstep") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix qeq/fire command"); - qstep = atof(arg[iarg+1]); + } else if (strcmp(arg[iarg], "qstep") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix qeq/fire qstep", error); + qstep = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"warn") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix qeq/fire command"); - maxwarn = utils::logical(FLERR,arg[iarg+1],false,lmp); + } else if (strcmp(arg[iarg], "warn") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix qeq/fire warn", error); + maxwarn = utils::logical(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else error->all(FLERR,"Illegal fix qeq/fire command"); + } else + error->all(FLERR, "Unknown fix qeq/fire keyword: {}", arg[iarg]); } } @@ -79,10 +79,11 @@ void FixQEqFire::init() if (tolerance < 1e-4) if (comm->me == 0) - error->warning(FLERR,"Fix qeq/fire tolerance may be too small for damped fires"); + error->warning(FLERR, "Fix qeq/fire tolerance {} may be too small for damped fires", + tolerance); - comb3 = dynamic_cast(force->pair_match("^comb3",0)); - if (!comb3) comb = dynamic_cast(force->pair_match("^comb",0)); + comb3 = dynamic_cast(force->pair_match("^comb3", 0)); + if (!comb3) comb = dynamic_cast(force->pair_match("^comb", 0)); } /* ---------------------------------------------------------------------- */ @@ -90,13 +91,13 @@ void FixQEqFire::init() void FixQEqFire::pre_force(int /*vflag*/) { int inum, *ilist; - int i,ii,iloop; + int i, ii, iloop; double *q = atom->q; - double vmax,vdotf,vdotfall,vdotv,vdotvall,fdotf,fdotfall; - double scale1,scale2; - double dtvone,dtv; - double enegtot,enegchk; + double vmax, vdotf, vdotfall, vdotv, vdotvall, fdotf, fdotfall; + double scale1, scale2; + double dtvone, dtv; + double enegtot, enegchk; double alpha = qdamp; double dt, dtmax; double enegchkall; @@ -118,15 +119,15 @@ void FixQEqFire::pre_force(int /*vflag*/) dt = qstep; dtmax = TMAX * dt; - for (iloop = 0; iloop < maxiter; iloop ++) { + for (iloop = 0; iloop < maxiter; iloop++) { pack_flag = 1; comm->forward_comm(this); if (comb) { - comb->yasu_char(qf,igroup); + comb->yasu_char(qf, igroup); enegtot = comb->enegtot / ngroup; } else if (comb3) { - comb3->combqeq(qf,igroup); + comb3->combqeq(qf, igroup); enegtot = comb3->enegtot / ngroup; } else { enegtot = compute_eneg(); @@ -135,7 +136,7 @@ void FixQEqFire::pre_force(int /*vflag*/) for (ii = 0; ii < inum; ii++) { i = ilist[ii]; - qf[i] -= enegtot; // Enforce adiabatic + qf[i] -= enegtot; // Enforce adiabatic } // FIRE minimization algorithm @@ -143,30 +144,32 @@ void FixQEqFire::pre_force(int /*vflag*/) vdotf = 0.0; for (ii = 0; ii < inum; ii++) { i = ilist[ii]; - vdotf += (qv[i]*qf[i]); + vdotf += (qv[i] * qf[i]); } - MPI_Allreduce(&vdotf,&vdotfall,1,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(&vdotf, &vdotfall, 1, MPI_DOUBLE, MPI_SUM, world); if (vdotfall > 0.0) { vdotv = fdotf = 0.0; for (ii = 0; ii < inum; ii++) { i = ilist[ii]; - vdotv += qv[i]*qv[i]; - fdotf += qf[i]*qf[i]; + vdotv += qv[i] * qv[i]; + fdotf += qf[i] * qf[i]; } - MPI_Allreduce(&vdotv,&vdotvall,1,MPI_DOUBLE,MPI_SUM,world); - MPI_Allreduce(&fdotf,&fdotfall,1,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(&vdotv, &vdotvall, 1, MPI_DOUBLE, MPI_SUM, world); + MPI_Allreduce(&fdotf, &fdotfall, 1, MPI_DOUBLE, MPI_SUM, world); scale1 = 1.0 - alpha; - if (fdotfall == 0.0) scale2 = 0.0; - else scale2 = alpha * sqrt(vdotvall/fdotfall); + if (fdotfall == 0.0) + scale2 = 0.0; + else + scale2 = alpha * sqrt(vdotvall / fdotfall); for (ii = 0; ii < inum; ii++) { i = ilist[ii]; - qv[i] = scale1*qv[i] + scale2*qf[i]; + qv[i] = scale1 * qv[i] + scale2 * qf[i]; } if (ntimestep - last_negative > DELAYSTEP) { - dt = MIN(dt*DT_GROW,dtmax); + dt = MIN(dt * DT_GROW, dtmax); alpha *= ALPHA_SHRINK; } } else { @@ -184,10 +187,10 @@ void FixQEqFire::pre_force(int /*vflag*/) double dmax = 0.1; for (ii = 0; ii < inum; ii++) { i = ilist[ii]; - vmax = MAX(fabs(qv[i]),0); - if (dtvone*vmax > dmax) dtvone = dmax/vmax; + vmax = MAX(fabs(qv[i]), 0); + if (dtvone * vmax > dmax) dtvone = dmax / vmax; } - MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,world); + MPI_Allreduce(&dtvone, &dtv, 1, MPI_DOUBLE, MPI_MIN, world); //dtv = dt; // Euler integration step @@ -198,7 +201,7 @@ void FixQEqFire::pre_force(int /*vflag*/) qv[i] += dtv * qf[i]; enegchk += fabs(qf[i]); } - MPI_Allreduce(&enegchk,&enegchkall,1,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(&enegchk, &enegchkall, 1, MPI_DOUBLE, MPI_SUM, world); enegchk = enegchkall / ngroup; if (enegchk < tolerance) break; @@ -206,8 +209,7 @@ void FixQEqFire::pre_force(int /*vflag*/) matvecs = iloop; if ((comm->me == 0) && maxwarn && (iloop >= maxiter)) - error->warning(FLERR,"Charges did not converge at step {}: {}", - update->ntimestep,enegchk); + error->warning(FLERR, "Charges did not converge at step {}: {}", update->ntimestep, enegchk); if (force->kspace) force->kspace->qsum_qsq(); } @@ -233,8 +235,7 @@ double FixQEqFire::compute_eneg() for (ii = 0; ii < inum; ii++) { i = ilist[ii]; - if (mask[i] & groupbit) - qf[i] = 0.0; + if (mask[i] & groupbit) qf[i] = 0.0; } // communicating charge force to all nodes, first forward then reverse @@ -259,12 +260,12 @@ double FixQEqFire::compute_eneg() delr[0] = x[i][0] - x[j][0]; delr[1] = x[i][1] - x[j][1]; delr[2] = x[i][2] - x[j][2]; - rsq = delr[0]*delr[0] + delr[1]*delr[1] + delr[2]*delr[2]; + rsq = delr[0] * delr[0] + delr[1] * delr[1] + delr[2] * delr[2]; if (rsq > cutoff_sq) continue; r = sqrt(rsq); - rinv = 1.0/r; + rinv = 1.0 / r; qf[i] += q[j] * rinv; qf[j] += q[i] * rinv; } @@ -279,18 +280,15 @@ double FixQEqFire::compute_eneg() eneg = enegtot = 0.0; for (ii = 0; ii < inum; ii++) { i = ilist[ii]; - if (mask[i] & groupbit) - eneg += qf[i]; + if (mask[i] & groupbit) eneg += qf[i]; } - MPI_Allreduce(&eneg,&enegtot,1,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(&eneg, &enegtot, 1, MPI_DOUBLE, MPI_SUM, world); return enegtot; - } /* ---------------------------------------------------------------------- */ -int FixQEqFire::pack_forward_comm(int n, int *list, double *buf, - int /*pbc_flag*/, int * /*pbc*/) +int FixQEqFire::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { int m = 0; diff --git a/src/QEQ/fix_qeq_fire.h b/src/QEQ/fix_qeq_fire.h index 0af318bfa8..cc63618815 100644 --- a/src/QEQ/fix_qeq_fire.h +++ b/src/QEQ/fix_qeq_fire.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/QEQ/fix_qeq_point.cpp b/src/QEQ/fix_qeq_point.cpp index 9af903b0db..3eb150559c 100644 --- a/src/QEQ/fix_qeq_point.cpp +++ b/src/QEQ/fix_qeq_point.cpp @@ -1,8 +1,7 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -35,13 +34,15 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -FixQEqPoint::FixQEqPoint(LAMMPS *lmp, int narg, char **arg) : - FixQEq(lmp, narg, arg) { +FixQEqPoint::FixQEqPoint(LAMMPS *lmp, int narg, char **arg) : FixQEq(lmp, narg, arg) +{ if (narg == 10) { - if (strcmp(arg[8],"warn") == 0) { - maxwarn = utils::logical(FLERR,arg[9],false,lmp); - } else error->all(FLERR,"Illegal fix qeq/point command"); - } else if (narg > 8) error->all(FLERR,"Illegal fix qeq/point command"); + if (strcmp(arg[8], "warn") == 0) { + maxwarn = utils::logical(FLERR, arg[9], false, lmp); + } else + error->all(FLERR, "Illegal fix qeq/point command"); + } else if (narg > 8) + error->all(FLERR, "Illegal fix qeq/point command"); } /* ---------------------------------------------------------------------- */ @@ -53,9 +54,11 @@ void FixQEqPoint::init() neighbor->add_request(this, NeighConst::REQ_FULL); int ntypes = atom->ntypes; - memory->create(shld,ntypes+1,ntypes+1,"qeq:shielding"); + memory->create(shld, ntypes + 1, ntypes + 1, "qeq:shielding"); } +// clang-format off + /* ---------------------------------------------------------------------- */ void FixQEqPoint::pre_force(int /*vflag*/) diff --git a/src/QEQ/fix_qeq_point.h b/src/QEQ/fix_qeq_point.h index 849ecbf7ca..c94d446353 100644 --- a/src/QEQ/fix_qeq_point.h +++ b/src/QEQ/fix_qeq_point.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/QEQ/fix_qeq_shielded.cpp b/src/QEQ/fix_qeq_shielded.cpp index afd2bd6ba3..6987732048 100644 --- a/src/QEQ/fix_qeq_shielded.cpp +++ b/src/QEQ/fix_qeq_shielded.cpp @@ -1,8 +1,7 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -36,13 +35,15 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -FixQEqShielded::FixQEqShielded(LAMMPS *lmp, int narg, char **arg) : - FixQEq(lmp, narg, arg) { +FixQEqShielded::FixQEqShielded(LAMMPS *lmp, int narg, char **arg) : FixQEq(lmp, narg, arg) +{ if (narg == 10) { - if (strcmp(arg[8],"warn") == 0) { - maxwarn = utils::logical(FLERR,arg[9],false,lmp); - } else error->all(FLERR,"Illegal fix qeq/shielded command"); - } else if (narg > 8) error->all(FLERR,"Illegal fix qeq/shielded command"); + if (strcmp(arg[8], "warn") == 0) { + maxwarn = utils::logical(FLERR, arg[9], false, lmp); + } else + error->all(FLERR, "Illegal fix qeq/shielded command"); + } else if (narg > 8) + error->all(FLERR, "Illegal fix qeq/shielded command"); if (reax_flag) extract_reax(); } @@ -55,14 +56,13 @@ void FixQEqShielded::init() neighbor->add_request(this, NeighConst::REQ_FULL); int ntypes = atom->ntypes; - memory->create(shld,ntypes+1,ntypes+1,"qeq:shielding"); + memory->create(shld, ntypes + 1, ntypes + 1, "qeq:shielding"); init_shielding(); int i; for (i = 1; i <= ntypes; i++) { - if (gamma[i] == 0.0) - error->all(FLERR,"Invalid param file for fix qeq/shielded"); + if (gamma[i] == 0.0) error->all(FLERR, "Invalid param file for fix qeq/shielded"); } } @@ -70,17 +70,17 @@ void FixQEqShielded::init() void FixQEqShielded::extract_reax() { - Pair *pair = force->pair_match("^reax..",0); - if (pair == nullptr) error->all(FLERR,"No pair reaxff for fix qeq/shielded"); + Pair *pair = force->pair_match("^reax..", 0); + if (pair == nullptr) error->all(FLERR, "No pair reaxff for fix qeq/shielded"); int tmp; - chi = (double *) pair->extract("chi",tmp); - eta = (double *) pair->extract("eta",tmp); - gamma = (double *) pair->extract("gamma",tmp); + chi = (double *) pair->extract("chi", tmp); + eta = (double *) pair->extract("eta", tmp); + gamma = (double *) pair->extract("gamma", tmp); if (chi == nullptr || eta == nullptr || gamma == nullptr) error->all(FLERR, "Fix qeq/shielded could not extract params from pair reaxff"); } - +// clang-format off /* ---------------------------------------------------------------------- */ void FixQEqShielded::init_shielding() diff --git a/src/QEQ/fix_qeq_shielded.h b/src/QEQ/fix_qeq_shielded.h index a29ca0041e..cdbf0fa443 100644 --- a/src/QEQ/fix_qeq_shielded.h +++ b/src/QEQ/fix_qeq_shielded.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/QEQ/fix_qeq_slater.cpp b/src/QEQ/fix_qeq_slater.cpp index 2ac9db880e..e80bad04b9 100644 --- a/src/QEQ/fix_qeq_slater.cpp +++ b/src/QEQ/fix_qeq_slater.cpp @@ -1,8 +1,7 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -38,23 +37,23 @@ using namespace FixConst; /* ---------------------------------------------------------------------- */ -FixQEqSlater::FixQEqSlater(LAMMPS *lmp, int narg, char **arg) : - FixQEq(lmp, narg, arg) +FixQEqSlater::FixQEqSlater(LAMMPS *lmp, int narg, char **arg) : FixQEq(lmp, narg, arg) { alpha = 0.20; // optional arg int iarg = 8; while (iarg < narg) { - if (strcmp(arg[iarg],"alpha") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix qeq/slater command"); - alpha = atof(arg[iarg+1]); + if (strcmp(arg[iarg], "alpha") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix qeq/slater alpha", error); + alpha = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"warn") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix qeq/slater command"); - maxwarn = utils::logical(FLERR,arg[iarg+1],false,lmp); + } else if (strcmp(arg[iarg], "warn") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix qeq/slater warn", error); + maxwarn = utils::logical(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else error->all(FLERR,"Illegal fix qeq/slater command"); + } else + error->all(FLERR, "Unknown fix qeq/slater keyword: {}", arg[iarg]); } if (streitz_flag) extract_streitz(); @@ -70,8 +69,7 @@ void FixQEqSlater::init() int ntypes = atom->ntypes; for (int i = 1; i <= ntypes; i++) { - if (zeta[i] == 0.0) - error->all(FLERR,"Invalid param file for fix qeq/slater"); + if (zeta[i] == 0.0) error->all(FLERR, "Invalid parameter file values for fix qeq/slater"); } } @@ -79,21 +77,19 @@ void FixQEqSlater::init() void FixQEqSlater::extract_streitz() { - Pair *pair = force->pair_match("coul/streitz",1); - if (pair == nullptr) error->all(FLERR,"No pair coul/streitz for fix qeq/slater"); + Pair *pair = force->pair_match("coul/streitz", 1); + if (pair == nullptr) error->all(FLERR, "No pair style coul/streitz for fix qeq/slater"); int tmp; - chi = (double *) pair->extract("chi",tmp); - eta = (double *) pair->extract("eta",tmp); - gamma = (double *) pair->extract("gamma",tmp); - zeta = (double *) pair->extract("zeta",tmp); - zcore = (double *) pair->extract("zcore",tmp); - if (chi == nullptr || eta == nullptr || gamma == nullptr - || zeta == nullptr || zcore == nullptr) - error->all(FLERR, - "Fix qeq/slater could not extract params from pair coul/streitz"); - + chi = (double *) pair->extract("chi", tmp); + eta = (double *) pair->extract("eta", tmp); + gamma = (double *) pair->extract("gamma", tmp); + zeta = (double *) pair->extract("zeta", tmp); + zcore = (double *) pair->extract("zcore", tmp); + if (chi == nullptr || eta == nullptr || gamma == nullptr || zeta == nullptr || zcore == nullptr) + error->all(FLERR, "Fix qeq/slater could not extract parameters from pair coul/streitz"); } +// clang-format off /* ---------------------------------------------------------------------- */ void FixQEqSlater::pre_force(int /*vflag*/) diff --git a/src/QEQ/fix_qeq_slater.h b/src/QEQ/fix_qeq_slater.h index a1898e30e7..1f8127db24 100644 --- a/src/QEQ/fix_qeq_slater.h +++ b/src/QEQ/fix_qeq_slater.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/QMMM/Install.sh b/src/QMMM/Install.sh index 4bede66d80..0c9643b84e 100755 --- a/src/QMMM/Install.sh +++ b/src/QMMM/Install.sh @@ -47,7 +47,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*qmmm.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*qmmm.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/qmmm\/Makefile.lammps @@ -62,7 +62,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*qmmm.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*qmmm.*$/d' ../Makefile.package.settings fi fi diff --git a/src/QMMM/fix_qmmm.cpp b/src/QMMM/fix_qmmm.cpp index ee297aa5d0..a72b6229c4 100644 --- a/src/QMMM/fix_qmmm.cpp +++ b/src/QMMM/fix_qmmm.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/QMMM/fix_qmmm.h b/src/QMMM/fix_qmmm.h index 7c16c59fb9..7a103794e6 100644 --- a/src/QMMM/fix_qmmm.h +++ b/src/QMMM/fix_qmmm.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/QTB/fix_qbmsst.cpp b/src/QTB/fix_qbmsst.cpp index 8ce7b616b1..b5fb5ca77c 100644 --- a/src/QTB/fix_qbmsst.cpp +++ b/src/QTB/fix_qbmsst.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -45,7 +45,7 @@ using namespace MathConst; FixQBMSST::FixQBMSST(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) { - if (narg < 5) error->all(FLERR,"Illegal fix qbmsst command"); + if (narg < 5) utils::missing_cmd_args(FLERR,"fix qbmsst",error); if (strcmp(arg[3],"x") == 0) { direction = 0; @@ -57,11 +57,10 @@ FixQBMSST::FixQBMSST(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) direction = 2; box_change |= BOX_CHANGE_Z; } else { - error->all(FLERR,"Illegal fix qbmsst command"); + error->all(FLERR,"Unknown fix qbmsst direction keyword: {}", arg[3]); } - velocity = atof(arg[4]); - if (velocity < 0) - error->all(FLERR,"Illegal fix qbmsst command"); + velocity = utils::numeric(FLERR,arg[4],false,lmp); + if (velocity < 0) error->all(FLERR,"Illegal fix qbmsst velocity value {}", velocity); // default parameters diff --git a/src/QTB/fix_qbmsst.h b/src/QTB/fix_qbmsst.h index c3830b0c35..ecfa5abf8e 100644 --- a/src/QTB/fix_qbmsst.h +++ b/src/QTB/fix_qbmsst.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/QTB/fix_qtb.cpp b/src/QTB/fix_qtb.cpp index 217e386953..2f7ce4130a 100644 --- a/src/QTB/fix_qtb.cpp +++ b/src/QTB/fix_qtb.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/QTB/fix_qtb.h b/src/QTB/fix_qtb.h index 1ee939a68e..2c2da97b0e 100644 --- a/src/QTB/fix_qtb.h +++ b/src/QTB/fix_qtb.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp index a76d11630c..87d83da1ae 100644 --- a/src/REACTION/fix_bond_react.cpp +++ b/src/REACTION/fix_bond_react.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories -Steve Plimpton, sjplimp@sandia.gov +LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -22,6 +22,7 @@ Contributing Author: Jacob Gissinger (jacob.r.gissinger@gmail.com) #include "atom_vec.h" #include "citeme.h" #include "comm.h" +#include "compute.h" #include "domain.h" #include "error.h" #include "fix_bond_history.h" @@ -34,11 +35,10 @@ Contributing Author: Jacob Gissinger (jacob.r.gissinger@gmail.com) #include "modify.h" #include "molecule.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "pair.h" #include "random_mars.h" -#include "reset_mol_ids.h" +#include "reset_atoms_mol.h" #include "respa.h" #include "update.h" #include "variable.h" @@ -51,6 +51,7 @@ Contributing Author: Jacob Gissinger (jacob.r.gissinger@gmail.com) #include #include +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -80,7 +81,7 @@ static const char cite_fix_bond_react[] = #define DELTA 16 #define MAXGUESS 20 // max # of guesses allowed by superimpose algorithm #define MAXCONARGS 14 // max # of arguments for any type of constraint + rxnID -#define NUMVARVALS 4 // max # of keyword values that have variables as input +#define NUMVARVALS 5 // max # of keyword values that have variables as input // various statuses of superimpose algorithm: // ACCEPT: site successfully matched to pre-reacted template @@ -98,7 +99,7 @@ enum{DISTANCE,ANGLE,DIHEDRAL,ARRHENIUS,RMSD,CUSTOM}; enum{ATOM,FRAG}; // keyword values that accept variables as input -enum{NEVERY,RMIN,RMAX,PROB}; +enum{NEVERY,RMIN,RMAX,PROB,NRATE}; // flag for one-proc vs shared reaction sites enum{LOCAL,GLOBAL}; @@ -118,11 +119,8 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : fix3 = nullptr; reset_mol_ids = nullptr; - if (narg < 8) error->all(FLERR,"Illegal fix bond/react command: " - "too few arguments"); + if (narg < 8) utils::missing_cmd_args(FLERR,"fix bond/react", error); - MPI_Comm_rank(world,&me); - MPI_Comm_size(world,&nprocs); newton_bond = force->newton_bond; restart_global = 1; @@ -138,10 +136,15 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : status = PROCEED; // reaction functions used by 'custom' constraint - nrxnfunction = 2; + nrxnfunction = 3; rxnfunclist.resize(nrxnfunction); + peratomflag.resize(nrxnfunction); rxnfunclist[0] = "rxnsum"; + peratomflag[0] = 1; rxnfunclist[1] = "rxnave"; + peratomflag[1] = 1; + rxnfunclist[2] = "rxnbond"; + peratomflag[2] = 0; nvvec = 0; ncustomvars = 0; vvec = nullptr; @@ -204,7 +207,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : if (reset_mol_ids_flag) { delete reset_mol_ids; - reset_mol_ids = new ResetMolIDs(lmp); + reset_mol_ids = new ResetAtomsMol(lmp); reset_mol_ids->create_computes(id,group->names[igroup]); } @@ -224,8 +227,10 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : memory->create(nghostlyskips,nreacts,"bond/react:nghostlyskips"); memory->create(seed,nreacts,"bond/react:seed"); memory->create(limit_duration,nreacts,"bond/react:limit_duration"); + memory->create(rate_limit,3,nreacts,"bond/react:rate_limit"); memory->create(stabilize_steps_flag,nreacts,"bond/react:stabilize_steps_flag"); memory->create(custom_charges_fragid,nreacts,"bond/react:custom_charges_fragid"); + memory->create(rescale_charges_flag,nreacts,"bond/react:rescale_charges_flag"); memory->create(create_atoms_flag,nreacts,"bond/react:create_atoms_flag"); memory->create(modify_create_fragid,nreacts,"bond/react:modify_create_fragid"); memory->create(overlapsq,nreacts,"bond/react:overlapsq"); @@ -249,8 +254,11 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : fraction[i] = 1; seed[i] = 12345; max_rxn[i] = INT_MAX; + for (int j = 0; j < 3; j++) + rate_limit[j][i] = 0; stabilize_steps_flag[i] = 0; custom_charges_fragid[i] = -1; + rescale_charges_flag[i] = 0; create_atoms_flag[i] = 0; modify_create_fragid[i] = -1; overlapsq[i] = 0; @@ -286,58 +294,31 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : if (groupid == -1) error->all(FLERR,"Could not find fix group ID"); groupbits[rxn] = group->bitmask[groupid]; - if (strncmp(arg[iarg],"v_",2) == 0) { - char *str = utils::strdup(&arg[iarg][2]); - var_id[NEVERY][rxn] = input->variable->find(str); - if (var_id[NEVERY][rxn] < 0) - error->all(FLERR,"Fix bond/react: Variable name does not exist"); - if (!input->variable->equalstyle(var_id[NEVERY][rxn])) - error->all(FLERR,"Fix bond/react: Variable is not equal-style"); - var_flag[NEVERY][rxn] = 1; - delete [] str; - } else { + if (strncmp(arg[iarg],"v_",2) == 0) read_variable_keyword(&arg[iarg][2],NEVERY,rxn); + else { nevery[rxn] = utils::inumeric(FLERR,arg[iarg],false,lmp); if (nevery[rxn] <= 0) error->all(FLERR,"Illegal fix bond/react command: " "'Nevery' must be a positive integer"); } iarg++; + double cutoff; if (strncmp(arg[iarg],"v_",2) == 0) { - char *str = utils::strdup(&arg[iarg][2]); - var_id[RMIN][rxn] = input->variable->find(str); - if (var_id[RMIN][rxn] < 0) - error->all(FLERR,"Fix bond/react: Variable name does not exist"); - if (!input->variable->equalstyle(var_id[RMIN][rxn])) - error->all(FLERR,"Fix bond/react: Variable is not equal-style"); - double cutoff = input->variable->compute_equal(var_id[RMIN][rxn]); - cutsq[rxn][0] = cutoff*cutoff; - var_flag[RMIN][rxn] = 1; - delete [] str; - } else { - double cutoff = utils::numeric(FLERR,arg[iarg],false,lmp); + read_variable_keyword(&arg[iarg][2],RMIN,rxn); + cutoff = input->variable->compute_equal(var_id[RMIN][rxn]); + } else cutoff = utils::numeric(FLERR,arg[iarg],false,lmp); if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/react command: " "'Rmin' cannot be negative"); cutsq[rxn][0] = cutoff*cutoff; - } iarg++; if (strncmp(arg[iarg],"v_",2) == 0) { - char *str = utils::strdup(&arg[iarg][2]); - var_id[RMAX][rxn] = input->variable->find(str); - if (var_id[RMAX][rxn] < 0) - error->all(FLERR,"Fix bond/react: Variable name does not exist"); - if (!input->variable->equalstyle(var_id[RMAX][rxn])) - error->all(FLERR,"Fix bond/react: Variable is not equal-style"); - double cutoff = input->variable->compute_equal(var_id[RMAX][rxn]); - cutsq[rxn][1] = cutoff*cutoff; - var_flag[RMAX][rxn] = 1; - delete [] str; - } else { - double cutoff = utils::numeric(FLERR,arg[iarg],false,lmp); + read_variable_keyword(&arg[iarg][2],RMAX,rxn); + cutoff = input->variable->compute_equal(var_id[RMAX][rxn]); + } else cutoff = utils::numeric(FLERR,arg[iarg],false,lmp); if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/react command:" "'Rmax' cannot be negative"); cutsq[rxn][1] = cutoff*cutoff; - } iarg++; unreacted_mol[rxn] = atom->find_molecule(arg[iarg++]); @@ -347,7 +328,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : if (reacted_mol[rxn] == -1) error->all(FLERR,"Reacted molecule template ID for " "fix bond/react does not exist"); - //read superimpose file + //read map file files[rxn] = utils::strdup(arg[iarg]); iarg++; @@ -357,15 +338,8 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : "'prob' keyword has too few arguments"); // check if probability is a variable if (strncmp(arg[iarg+1],"v_",2) == 0) { - char *str = utils::strdup(&arg[iarg+1][2]); - var_id[PROB][rxn] = input->variable->find(str); - if (var_id[PROB][rxn] < 0) - error->all(FLERR,"Fix bond/react: Variable name does not exist"); - if (!input->variable->equalstyle(var_id[PROB][rxn])) - error->all(FLERR,"Fix bond/react: Variable is not equal-style"); + read_variable_keyword(&arg[iarg+1][2],PROB,rxn); fraction[rxn] = input->variable->compute_equal(var_id[PROB][rxn]); - var_flag[PROB][rxn] = 1; - delete [] str; } else { // otherwise probability should be a number fraction[rxn] = utils::numeric(FLERR,arg[iarg+1],false,lmp); @@ -384,6 +358,14 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : if (max_rxn[rxn] < 0) error->all(FLERR,"Illegal fix bond/react command: " "'max_rxn' cannot be negative"); iarg += 2; + } else if (strcmp(arg[iarg],"rate_limit") == 0) { + if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/react command: " + "'rate_limit' has too few arguments"); + rate_limit[0][rxn] = 1; // serves as flag for rate_limit keyword + if (strncmp(arg[iarg+1],"v_",2) == 0) read_variable_keyword(&arg[iarg+1][2],NRATE,rxn); + else rate_limit[1][rxn] = utils::numeric(FLERR,arg[iarg+1],false,lmp); + rate_limit[2][rxn] = utils::numeric(FLERR,arg[iarg+2],false,lmp); + iarg += 3; } else if (strcmp(arg[iarg],"stabilize_steps") == 0) { if (stabilization_flag == 0) error->all(FLERR,"Stabilize_steps keyword " "used without stabilization keyword"); @@ -402,6 +384,13 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : "'custom_charges' keyword does not exist"); } iarg += 2; + } else if (strcmp(arg[iarg],"rescale_charges") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: " + "'rescale_charges' has too few arguments"); + if (strcmp(arg[iarg+1],"no") == 0) rescale_charges_flag[rxn] = 0; //default + else if (strcmp(arg[iarg+1],"yes") == 0) rescale_charges_flag[rxn] = 1; + else error->one(FLERR,"Bond/react: Illegal option for 'rescale_charges' keyword"); + iarg += 2; } else if (strcmp(arg[iarg],"molecule") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: " "'molecule' has too few arguments"); @@ -437,21 +426,24 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : } max_natoms = 0; // the number of atoms in largest molecule template + max_rate_limit_steps = 0; for (int myrxn = 0; myrxn < nreacts; myrxn++) { twomol = atom->molecules[reacted_mol[myrxn]]; max_natoms = MAX(max_natoms,twomol->natoms); + max_rate_limit_steps = MAX(max_rate_limit_steps,rate_limit[2][myrxn]); } memory->create(equivalences,max_natoms,2,nreacts,"bond/react:equivalences"); memory->create(reverse_equiv,max_natoms,2,nreacts,"bond/react:reverse_equiv"); memory->create(edge,max_natoms,nreacts,"bond/react:edge"); memory->create(landlocked_atoms,max_natoms,nreacts,"bond/react:landlocked_atoms"); + memory->create(store_rxn_count,max_rate_limit_steps,nreacts,"bond/react:store_rxn_count"); memory->create(custom_charges,max_natoms,nreacts,"bond/react:custom_charges"); memory->create(delete_atoms,max_natoms,nreacts,"bond/react:delete_atoms"); memory->create(create_atoms,max_natoms,nreacts,"bond/react:create_atoms"); memory->create(chiral_atoms,max_natoms,6,nreacts,"bond/react:chiral_atoms"); - for (int j = 0; j < nreacts; j++) + for (int j = 0; j < nreacts; j++) { for (int i = 0; i < max_natoms; i++) { edge[i][j] = 0; custom_charges[i][j] = 1; // update all partial charges by default @@ -466,6 +458,10 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : equivalences[i][m][j] = i+1; } } + for (int i = 0; i < max_rate_limit_steps; i++) { + store_rxn_count[i][j] = -1; + } + } // read all map files afterward for (int i = 0; i < nreacts; i++) { @@ -475,7 +471,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : onemol->check_attributes(); twomol->check_attributes(); get_molxspecials(); - read(i); + read_map_file(i); fclose(fp); if (ncreate == 0 && onemol->natoms != twomol->natoms) error->all(FLERR,"Fix bond/react: Reaction templates must contain the same number of atoms"); @@ -497,7 +493,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : for (int i = 0; i < nreacts; i++) { for (int j = 0; j < nconstraints[i]; j++) { if (constraints[j][i].type == ARRHENIUS) { - rrhandom[tmp++] = new RanMars(lmp,(int) constraints[j][i].par[4] + me); + rrhandom[tmp++] = new RanMars(lmp,(int) constraints[j][i].par[4] + comm->me); } } } @@ -532,7 +528,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : random = new RanMars*[nreacts]; for (int i = 0; i < nreacts; i++) { - random[i] = new RanMars(lmp,seed[i] + me); + random[i] = new RanMars(lmp,seed[i] + comm->me); } // set comm sizes needed by this fix @@ -602,6 +598,7 @@ FixBondReact::~FixBondReact() memory->destroy(equivalences); memory->destroy(reverse_equiv); memory->destroy(landlocked_atoms); + memory->destroy(store_rxn_count); memory->destroy(custom_charges); memory->destroy(delete_atoms); memory->destroy(create_atoms); @@ -621,8 +618,10 @@ FixBondReact::~FixBondReact() memory->destroy(limit_duration); memory->destroy(var_flag); memory->destroy(var_id); + memory->destroy(rate_limit); memory->destroy(stabilize_steps_flag); memory->destroy(custom_charges_fragid); + memory->destroy(rescale_charges_flag); memory->destroy(molecule_keyword); memory->destroy(nconstraints); memory->destroy(constraintstr); @@ -662,27 +661,27 @@ FixBondReact::~FixBondReact() memory->destroy(global_mega_glove); if (stabilization_flag == 1) { - // check nfix in case all fixes have already been deleted - if (id_fix1 && modify->nfix) modify->delete_fix(id_fix1); - delete [] id_fix1; + // delete fixes if not already deleted + if (id_fix1 && modify->get_fix_by_id(id_fix1)) modify->delete_fix(id_fix1); + delete[] id_fix1; - if (id_fix3 && modify->nfix) modify->delete_fix(id_fix3); - delete [] id_fix3; + if (id_fix3 && modify->get_fix_by_id(id_fix3)) modify->delete_fix(id_fix3); + delete[] id_fix3; } - if (id_fix2 && modify->nfix) modify->delete_fix(id_fix2); - delete [] id_fix2; + if (id_fix2 && modify->get_fix_by_id(id_fix2)) modify->delete_fix(id_fix2); + delete[] id_fix2; - delete [] statted_id; - delete [] guess_branch; - delete [] pioneer_count; - delete [] set; + delete[] statted_id; + delete[] guess_branch; + delete[] pioneer_count; + delete[] set; if (group) { group->assign(std::string(master_group) + " delete"); if (stabilization_flag == 1) { group->assign(std::string(exclude_group) + " delete"); - delete [] exclude_group; + delete[] exclude_group; } } } @@ -708,8 +707,9 @@ void FixBondReact::post_constructor() { // let's add the limit_tags per-atom property fix id_fix2 = utils::strdup("bond_react_props_internal"); - if (modify->find_fix(id_fix2) < 0) - modify->add_fix(std::string(id_fix2)+" all property/atom i_limit_tags i_react_tags ghost yes"); + if (!modify->get_fix_by_id(id_fix2)) + fix2 = modify->add_fix(std::string(id_fix2) + + " all property/atom i_limit_tags i_react_tags ghost yes"); // create master_group if not already existing // NOTE: limit_tags and react_tags automaticaly intitialized to zero (unless read from restart) @@ -724,8 +724,9 @@ void FixBondReact::post_constructor() // create stabilization per-atom property id_fix3 = utils::strdup("bond_react_stabilization_internal"); - if (modify->find_fix(id_fix3) < 0) - fix3 = modify->add_fix(std::string(id_fix3) + " all property/atom i_statted_tags ghost yes"); + if (!modify->get_fix_by_id(id_fix3)) + fix3 = modify->add_fix(std::string(id_fix3) + + " all property/atom i_statted_tags ghost yes"); statted_id = utils::strdup("statted_tags"); @@ -733,7 +734,7 @@ void FixBondReact::post_constructor() // also, rename dynamic exclude_group by appending '_REACT' char *exclude_PARENT_group; exclude_PARENT_group = utils::strdup(exclude_group); - delete [] exclude_group; + delete[] exclude_group; exclude_group = utils::strdup(std::string(exclude_PARENT_group)+"_REACT"); group->find_or_create(exclude_group); @@ -742,7 +743,7 @@ void FixBondReact::post_constructor() else cmd = fmt::format("{} dynamic {} property statted_tags",exclude_group,exclude_PARENT_group); group->assign(cmd); - delete [] exclude_PARENT_group; + delete[] exclude_PARENT_group; // on to statted_tags (system-wide thermostat) // initialize per-atom statted_flags to 1 @@ -759,8 +760,7 @@ void FixBondReact::post_constructor() // sleeping code, for future capabilities custom_exclude_flag = 1; // first we have to find correct fix group reference - int ifix = modify->find_fix(std::string("GROUP_")+exclude_group); - Fix *fix = modify->fix[ifix]; + Fix *fix = modify->get_fix_by_id(std::string("GROUP_")+exclude_group); // this returns names of corresponding property int unused; @@ -779,10 +779,9 @@ void FixBondReact::post_constructor() // i_statted_tags[i] = 1; } - // let's create a new nve/limit fix to limit newly reacted atoms id_fix1 = utils::strdup("bond_react_MASTER_nve_limit"); - if (modify->find_fix(id_fix1) < 0) + if (!modify->get_fix_by_id(id_fix1)) fix1 = modify->add_fix(fmt::format("{} {} nve/limit {}", id_fix1,master_group,nve_limit_xmax)); } @@ -823,6 +822,16 @@ void FixBondReact::init_list(int /*id*/, NeighList *ptr) void FixBondReact::post_integrate() { + // update store_rxn_count on every step + for (int myrxn = 0; myrxn < nreacts; myrxn++) { + if (rate_limit[0][myrxn] == 1) { + for (int i = rate_limit[2][myrxn]-1; i > 0; i--) { + store_rxn_count[i][myrxn] = store_rxn_count[i-1][myrxn]; + } + store_rxn_count[0][myrxn] = reaction_count_total[myrxn]; + } + } + // check if any reactions could occur on this timestep int nevery_check = 1; for (int i = 0; i < nreacts; i++) { @@ -877,6 +886,8 @@ void FixBondReact::post_integrate() for (int i = 0; i < nreacts; i++) { nattempt[i] = 0; } + // reset per-bond compute map flag + atoms2bondflag = 0; int nlocal = atom->nlocal; int nall = atom->nlocal + atom->nghost; @@ -915,8 +926,22 @@ void FixBondReact::post_integrate() int j; for (rxnID = 0; rxnID < nreacts; rxnID++) { + int rate_limit_flag = 1; + if (rate_limit[0][rxnID] == 1) { + int myrxn_count = store_rxn_count[rate_limit[2][rxnID]-1][rxnID]; + if (myrxn_count == -1) rate_limit_flag = 0; + else { + int nrxns_delta = reaction_count_total[rxnID] - myrxn_count; + int my_nrate; + if (var_flag[NRATE][rxnID] == 1) { + my_nrate = input->variable->compute_equal(var_id[NRATE][rxnID]); + } else my_nrate = rate_limit[1][rxnID]; + if (nrxns_delta > my_nrate) rate_limit_flag = 0; + } + } if ((update->ntimestep % nevery[rxnID]) || - (max_rxn[rxnID] <= reaction_count_total[rxnID])) continue; + (max_rxn[rxnID] <= reaction_count_total[rxnID]) || + (rate_limit_flag == 0)) continue; for (int ii = 0; ii < nall; ii++) { partner[ii] = 0; finalpartner[ii] = 0; @@ -1225,6 +1250,7 @@ void FixBondReact::close_partner() void FixBondReact::superimpose_algorithm() { + const int nprocs = comm->nprocs; local_num_mega = 0; ghostly_num_mega = 0; @@ -1374,7 +1400,7 @@ void FixBondReact::superimpose_algorithm() MPI_Allreduce(&local_rxn_count[0],&reaction_count[0],nreacts,MPI_INT,MPI_SUM,world); int rxnflag = 0; - if (me == 0) + if (comm->me == 0) for (int i = 0; i < nreacts; i++) { reaction_count_total[i] += reaction_count[i] + ghostly_rxn_count[i]; rxnflag += reaction_count[i] + ghostly_rxn_count[i]; @@ -1389,18 +1415,37 @@ void FixBondReact::superimpose_algorithm() std::random_device rnd; std::minstd_rand park_rng(rnd()); - // check if we overstepped our reaction limit + // check if we overstepped our reaction limit, via either max_rxn or rate_limit for (int i = 0; i < nreacts; i++) { - if (reaction_count_total[i] > max_rxn[i]) { + int overstep = 0; + int max_rxn_overstep = reaction_count_total[i] - max_rxn[i]; + overstep = MAX(overstep,max_rxn_overstep); + if (rate_limit[0][i] == 1) { + int myrxn_count = store_rxn_count[rate_limit[2][i]-1][i]; + if (myrxn_count != -1) { + int nrxn_delta = reaction_count_total[i] - myrxn_count; + int my_nrate; + if (var_flag[NRATE][i] == 1) { + my_nrate = input->variable->compute_equal(var_id[NRATE][i]); + } else my_nrate = rate_limit[1][i]; + int rate_limit_overstep = nrxn_delta - my_nrate; + overstep = MAX(overstep,rate_limit_overstep); + } + } + + if (overstep > 0) { // let's randomly choose rxns to skip, unbiasedly from local and ghostly int *local_rxncounts; int *all_localskips; memory->create(local_rxncounts,nprocs,"bond/react:local_rxncounts"); memory->create(all_localskips,nprocs,"bond/react:all_localskips"); MPI_Gather(&local_rxn_count[i],1,MPI_INT,local_rxncounts,1,MPI_INT,0,world); - if (me == 0) { - int overstep = reaction_count_total[i] - max_rxn[i]; + if (comm->me == 0) { int delta_rxn = reaction_count[i] + ghostly_rxn_count[i]; + // when using variable input for rate_limit, rate_limit_overstep could be > delta_rxn (below) + // we need to limit overstep to the number of reactions on this timestep + // essentially skipping all reactions, would be more efficient to use a skip_all flag + if (overstep > delta_rxn) overstep = delta_rxn; int *rxn_by_proc; memory->create(rxn_by_proc,delta_rxn,"bond/react:rxn_by_proc"); for (int j = 0; j < delta_rxn; j++) @@ -1418,14 +1463,15 @@ void FixBondReact::superimpose_algorithm() else all_localskips[rxn_by_proc[j]]++; } memory->destroy(rxn_by_proc); + reaction_count_total[i] -= overstep; } - reaction_count_total[i] = max_rxn[i]; MPI_Scatter(&all_localskips[0],1,MPI_INT,&nlocalskips[i],1,MPI_INT,0,world); MPI_Bcast(&nghostlyskips[i],1,MPI_INT,0,world); memory->destroy(local_rxncounts); memory->destroy(all_localskips); } } + MPI_Bcast(&reaction_count_total[0], nreacts, MPI_INT, 0, world); // this updates topology next step next_reneighbor = update->ntimestep; @@ -1739,7 +1785,16 @@ void FixBondReact::inner_crosscheck_loop() // ...actually, avail_guesses should never be zero here anyway if (guess_branch[avail_guesses-1] == 0) guess_branch[avail_guesses-1] = num_choices; - std::sort(tag_choices, tag_choices + num_choices); + for (int i=1; i < num_choices; ++i) { + tagint hold = tag_choices[i]; + int j = i - 1; + while ((j >=0) && (tag_choices[j] > hold)) { + tag_choices[j+1] = tag_choices[j]; + --j; + } + tag_choices[j+1] = hold; + } + for (int i = guess_branch[avail_guesses-1]-1; i >= 0; i--) { int already_assigned = 0; for (int j = 0; j < onemol->natoms; j++) { @@ -2113,7 +2168,7 @@ double FixBondReact::get_temperature(tagint **myglove, int row_offset, int col) } /* ---------------------------------------------------------------------- -get per-atom variable names used by custom constraint +get per-atom variable names used by custom constraint ------------------------------------------------------------------------- */ void FixBondReact::customvarnames() @@ -2135,6 +2190,7 @@ void FixBondReact::customvarnames() // find next reaction special function occurrence pos1 = std::string::npos; for (int i = 0; i < nrxnfunction; i++) { + if (peratomflag[i] == 0) continue; pos = varstr.find(rxnfunclist[i],prev3+1); if (pos == std::string::npos) continue; if (pos < pos1) pos1 = pos; @@ -2216,7 +2272,6 @@ double FixBondReact::custom_constraint(const std::string& varstr) std::size_t pos,pos1,pos2,pos3; int irxnfunc; int prev3 = -1; - double val; std::string argstr,varid,fragid,evlcat; std::vector evlstr; @@ -2253,20 +2308,71 @@ double FixBondReact::custom_constraint(const std::string& varstr) evlstr.push_back(varstr.substr(prev3+1)); for (auto & evl : evlstr) evlcat += evl; - - char *cstr = utils::strdup(evlcat); - val = input->variable->compute_equal(cstr); - delete [] cstr; - return val; + return input->variable->compute_equal(evlcat); } /* ---------------------------------------------------------------------- -currently two 'rxn' functions: rxnsum and rxnave +currently three 'rxn' functions: rxnsum, rxnave, and rxnbond ------------------------------------------------------------------------- */ double FixBondReact::rxnfunction(const std::string& rxnfunc, const std::string& varid, const std::string& fragid) { + int ifrag = -1; + if (fragid != "all") { + ifrag = onemol->findfragment(fragid.c_str()); + if (ifrag < 0) error->one(FLERR,"Bond/react: Molecule fragment " + "in reaction special function does not exist"); + } + + // start with 'rxnbond' per-bond function + // for 'rxnbond', varid corresponds to 'compute bond/local' name, + // and fragid is a pre-reaction fragment containing the two atoms in the bond + if (rxnfunc == "rxnbond") { + int icompute,ibond,nsum; + double perbondval; + std::set aset; + std::string computeid = varid; + std::map,int>::iterator it; + + if (computeid.substr(0,2) != "c_") error->one(FLERR,"Bond/react: Reaction special function compute " + "name should begin with 'c_'"); + computeid = computeid.substr(2); + icompute = modify->find_compute(computeid); + if (icompute < 0) error->one(FLERR,"Bond/react: Reaction special function compute name does not exist"); + cperbond = modify->compute[icompute]; + std::string compute_style = cperbond->style; + if (compute_style != "bond/local") error->one(FLERR,"Bond/react: Compute used by reaction " + "special function 'rxnbond' must be of style 'bond/local'"); + if (cperbond->size_local_cols > 0) error->one(FLERR,"Bond/react: 'Compute bond/local' used by reaction " + "special function 'rxnbond' must compute one value"); + + if (atoms2bondflag == 0) { + atoms2bondflag = 1; + get_atoms2bond(cperbond->groupbit); + } + + nsum = 0; + for (int i = 0; i < onemol->natoms; i++) { + if (onemol->fragmentmask[ifrag][i]) { + aset.insert(glove[i][1]); + nsum++; + } + } + if (nsum != 2) error->one(FLERR,"Bond/react: Molecule fragment of reaction special function 'rxnbond' " + "must contain exactly two atoms"); + + if (cperbond->invoked_local != lmp->update->ntimestep) + cperbond->compute_local(); + + it = atoms2bond.find(aset); + if (it == atoms2bond.end()) error->one(FLERR,"Bond/react: Unable to locate bond referenced by " + "reaction special function 'rxnbond'"); + ibond = it->second; + perbondval = cperbond->vector_local[ibond]; + return perbondval; + } + int ivar = -1; for (int i = 0; i < ncustomvars; i++) { if (varid == customvarstrs[i]) { @@ -2280,13 +2386,6 @@ double FixBondReact::rxnfunction(const std::string& rxnfunc, const std::string& error->one(FLERR,"Fix bond/react: Reaction special function variable " "name does not exist"); - int ifrag = -1; - if (fragid != "all") { - ifrag = onemol->findfragment(fragid.c_str()); - if (ifrag < 0) error->one(FLERR,"Fix bond/react: Molecule fragment " - "in reaction special function does not exist"); - } - int iatom; int nsum = 0; double sumvvec = 0; @@ -2313,6 +2412,39 @@ double FixBondReact::rxnfunction(const std::string& rxnfunc, const std::string& return 0.0; } +/* ---------------------------------------------------------------------- +populate map to get bond index from atom IDs +------------------------------------------------------------------------- */ + +void FixBondReact::get_atoms2bond(int cgroupbit) +{ + int i,m,atom1,atom2,btype,nb; + std::set aset; + + int nlocal = atom->nlocal; + tagint *tag = atom->tag; + int *num_bond = atom->num_bond; + tagint **bond_atom = atom->bond_atom; + int **bond_type = atom->bond_type; + int *mask = atom->mask; + + m = 0; + atoms2bond.clear(); + for (atom1 = 0; atom1 < nlocal; atom1++) { + if (!(mask[atom1] & cgroupbit)) continue; + nb = num_bond[atom1]; + for (i = 0; i < nb; i++) { + btype = bond_type[atom1][i]; + atom2 = atom->map(bond_atom[atom1][i]); + if (atom2 < 0 || !(mask[atom2] & cgroupbit)) continue; + if (newton_bond == 0 && tag[atom1] > tag[atom2]) continue; + if (btype == 0) continue; + aset = {tag[atom1], tag[atom2]}; + atoms2bond.insert(std::make_pair(aset,m++)); + } + } +} + /* ---------------------------------------------------------------------- return handedness (1 or -1) of a chiral center, given ordered set of coordinates ------------------------------------------------------------------------- */ @@ -2483,7 +2615,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn) } // also, if atoms change number of bonds, but aren't landlocked, that could be bad - if (me == 0) + if (comm->me == 0) for (int i = 0; i < twomol->natoms; i++) { if ((create_atoms[i][myrxn] == 0) && (twomol_nxspecial[i][0] != onemol_nxspecial[equivalences[i][1][myrxn]-1][0]) && @@ -2774,7 +2906,7 @@ void FixBondReact::glove_ghostcheck() int ghostly = 0; #if !defined(MPI_STUBS) - if (comm->style == 0) { + if (comm->style == Comm::BRICK) { if (create_atoms_flag[rxnID] == 1) { ghostly = 1; } else { @@ -2815,6 +2947,7 @@ broadcast entries of mega_glove which contain nonlocal atoms for perusal by all void FixBondReact::ghost_glovecast() { #if !defined(MPI_STUBS) + const int nprocs = comm->nprocs; global_megasize = 0; @@ -2833,7 +2966,7 @@ void FixBondReact::ghost_glovecast() int *allstarts = new int[nprocs]; int start = 0; - for (int i = 0; i < me; i++) { + for (int i = 0; i < comm->me; i++) { start += allncols[i]; } MPI_Allgather(&start, 1, MPI_INT, allstarts, 1, MPI_INT, world); @@ -2861,7 +2994,7 @@ void FixBondReact::ghost_glovecast() } } // let's send to root, dedup, then broadcast - if (me == 0) { + if (comm->me == 0) { MPI_Gatherv(MPI_IN_PLACE, ghostly_num_mega, column, // Note: some values ignored for MPI_IN_PLACE &(global_mega_glove[0][0]), allncols, allstarts, column, 0, world); @@ -2871,7 +3004,7 @@ void FixBondReact::ghost_glovecast() column, 0, world); } - if (me == 0) dedup_mega_gloves(GLOBAL); // global_mega_glove mode + if (comm->me == 0) dedup_mega_gloves(GLOBAL); // global_mega_glove mode MPI_Bcast(&global_megasize,1,MPI_INT,0,world); MPI_Bcast(&(global_mega_glove[0][0]), global_megasize, column, 0, world); @@ -2985,6 +3118,8 @@ void FixBondReact::update_everything() } delete [] iskip; + if (update_num_mega == 0) continue; + // if inserted atoms and global map exists, reset map now instead // of waiting for comm since other pre-exchange fixes may use it // invoke map_init() b/c atom count has grown @@ -3012,6 +3147,33 @@ void FixBondReact::update_everything() } } + // get charge rescale delta + double charge_rescale_addend = 0; + if (rescale_charges_flag[rxnID] == 1) { + double sim_total_charge = 0; + double mol_total_charge = 0; + int n_custom_charge = 0; + for (int i = 0; i < update_num_mega; i++) { + rxnID = update_mega_glove[0][i]; + twomol = atom->molecules[reacted_mol[rxnID]]; + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (atom->map(update_mega_glove[jj+1][i]) >= 0 && + atom->map(update_mega_glove[jj+1][i]) < nlocal) { + if (landlocked_atoms[j][rxnID] == 1) + type[atom->map(update_mega_glove[jj+1][i])] = twomol->type[j]; + if (twomol->qflag && atom->q_flag && custom_charges[jj][rxnID] == 1) { + double *q = atom->q; + sim_total_charge += q[atom->map(update_mega_glove[jj+1][i])]; + mol_total_charge += twomol->q[j]; + n_custom_charge++; + } + } + } + } + charge_rescale_addend = (sim_total_charge-mol_total_charge)/n_custom_charge; + } + // update charges and types of landlocked atoms for (int i = 0; i < update_num_mega; i++) { rxnID = update_mega_glove[0][i]; @@ -3024,7 +3186,7 @@ void FixBondReact::update_everything() type[atom->map(update_mega_glove[jj+1][i])] = twomol->type[j]; if (twomol->qflag && atom->q_flag && custom_charges[jj][rxnID] == 1) { double *q = atom->q; - q[atom->map(update_mega_glove[jj+1][i])] = twomol->q[j]; + q[atom->map(update_mega_glove[jj+1][i])] = twomol->q[j]+charge_rescale_addend; } } } @@ -3584,7 +3746,7 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) Superpose3D superposer(n2superpose); int fitroot = 0; if (ifit >= 0 && ifit < atom->nlocal) { - fitroot = me; + fitroot = comm->me; // get 'temperatere' averaged over site, used for created atoms' vels t = get_temperature(my_mega_glove,1,iupdate); @@ -3602,7 +3764,8 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) int ipre = equivalences[j][1][rxnID]-1; // equiv pre-reaction template index if (!create_atoms[j][rxnID] && !delete_atoms[ipre][rxnID]) { if (atom->map(my_mega_glove[ipre+1][iupdate]) < 0) { - error->warning(FLERR," eligible atoms skipped for created-atoms fit on rank {}\n",me); + error->warning(FLERR," eligible atoms skipped for created-atoms fit on rank {}\n", + comm->me); continue; } iatom = atom->map(my_mega_glove[ipre+1][iupdate]); @@ -3630,7 +3793,7 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) if (create_atoms[m][rxnID] == 1) { // apply optimal rotation/translation for created atom coords // also map coords back into simulation box - if (fitroot == me) { + if (fitroot == comm->me) { MathExtra::matvec(rotmat,twomol->x[m],coords[m]); for (int i = 0; i < 3; i++) coords[m][i] += superposer.T[i]; imageflags[m] = atom->image[ifit]; @@ -3718,7 +3881,7 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) int root = 0; if (flag) { - root = me; + root = comm->me; atom->avec->create_atom(twomol->type[m],coords[m]); int n = atom->nlocal - 1; @@ -3795,10 +3958,24 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) } /* ---------------------------------------------------------------------- -read superimpose file +add equal-style variable to keyword argument list ------------------------------------------------------------------------- */ -void FixBondReact::read(int myrxn) +void FixBondReact::read_variable_keyword(const char *myarg, int keyword, int myrxn) +{ + var_id[keyword][myrxn] = input->variable->find(myarg); + if (var_id[keyword][myrxn] < 0) + error->all(FLERR,"Fix bond/react: Variable name {} does not exist",myarg); + if (!input->variable->equalstyle(var_id[keyword][myrxn])) + error->all(FLERR,"Fix bond/react: Variable {} is not equal-style",myarg); + var_flag[keyword][myrxn] = 1; +} + +/* ---------------------------------------------------------------------- +read map file +------------------------------------------------------------------------- */ + +void FixBondReact::read_map_file(int myrxn) { char line[MAXLINE],keyword[MAXLINE]; char *eof,*ptr; @@ -3850,7 +4027,7 @@ void FixBondReact::read(int myrxn) while (strlen(keyword)) { if (strcmp(keyword,"InitiatorIDs") == 0 || strcmp(keyword,"BondingIDs") == 0) { if (strcmp(keyword,"BondingIDs") == 0) - if (me == 0) error->warning(FLERR,"Fix bond/react: The BondingIDs section title has been deprecated. Please use InitiatorIDs instead."); + if (comm->me == 0) error->warning(FLERR,"Fix bond/react: The BondingIDs section title has been deprecated. Please use InitiatorIDs instead."); bondflag = 1; readline(line); sscanf(line,"%d",&ibonding[myrxn]); @@ -3937,6 +4114,8 @@ void FixBondReact::CreateAtoms(char *line, int myrxn) sscanf(line,"%d",&tmp); create_atoms[tmp-1][myrxn] = 1; } + if (twomol->xflag == 0) + error->one(FLERR,"Fix bond/react: 'Coords' section required in post-reaction template when creating new atoms"); } void FixBondReact::CustomCharges(int ifragment, int myrxn) @@ -4095,12 +4274,14 @@ void FixBondReact::readID(char *strarg, int iconstr, int myrxn, int i) if (isalpha(strarg[0])) { constraints[iconstr][myrxn].idtype[i] = FRAG; // fragment vs. atom ID flag int ifragment = onemol->findfragment(strarg); - if (ifragment < 0) error->one(FLERR,"Fix bond/react: Molecule fragment does not exist"); + if (ifragment < 0) + error->one(FLERR,"Fix bond/react: Molecule fragment {} does not exist", strarg); constraints[iconstr][myrxn].id[i] = ifragment; } else { constraints[iconstr][myrxn].idtype[i] = ATOM; // fragment vs. atom ID flag - int iatom = atoi(strarg); - if (iatom > onemol->natoms) error->one(FLERR,"Fix bond/react: Invalid template atom ID in map file"); + int iatom = utils::inumeric(FLERR, strarg, true, lmp); + if (iatom > onemol->natoms) + error->one(FLERR,"Fix bond/react: Invalid template atom ID {} in map file", strarg); constraints[iconstr][myrxn].id[i] = iatom; } } @@ -4108,13 +4289,13 @@ void FixBondReact::readID(char *strarg, int iconstr, int myrxn, int i) void FixBondReact::open(char *file) { fp = fopen(file,"r"); - if (fp == nullptr) error->one(FLERR, "Fix bond/react: Cannot open map file {}",file); + if (fp == nullptr) error->one(FLERR, "Fix bond/react: Cannot open map file {}", file); } void FixBondReact::readline(char *line) { int n; - if (me == 0) { + if (comm->me == 0) { if (fgets(line,MAXLINE,fp) == nullptr) n = 0; else n = strlen(line) + 1; } @@ -4131,7 +4312,7 @@ void FixBondReact::parse_keyword(int flag, char *line, char *keyword) // eof is set to 1 if any read hits end-of-file int eof = 0; - if (me == 0) { + if (comm->me == 0) { if (fgets(line,MAXLINE,fp) == nullptr) eof = 1; while (eof == 0 && strspn(line," \t\n\r") == strlen(line)) { if (fgets(line,MAXLINE,fp) == nullptr) eof = 1; @@ -4150,7 +4331,7 @@ void FixBondReact::parse_keyword(int flag, char *line, char *keyword) // bcast keyword line to all procs int n; - if (me == 0) n = strlen(line) + 1; + if (comm->me == 0) n = strlen(line) + 1; MPI_Bcast(&n,1,MPI_INT,0,world); MPI_Bcast(line,n,MPI_CHAR,0,world); } @@ -4297,34 +4478,71 @@ void FixBondReact::unpack_reverse_comm(int n, int *list, double *buf) void FixBondReact::write_restart(FILE *fp) { + int revision = 1; set[0].nreacts = nreacts; + set[0].max_rate_limit_steps = max_rate_limit_steps; + for (int i = 0; i < nreacts; i++) { set[i].reaction_count_total = reaction_count_total[i]; - strncpy(set[i].rxn_name,rxn_name[i],MAXLINE); + + strncpy(set[i].rxn_name,rxn_name[i],MAXLINE-1); set[i].rxn_name[MAXLINE-1] = '\0'; } - if (me == 0) { - int size = nreacts*sizeof(Set); - fwrite(&size,sizeof(int),1,fp); - fwrite(set,sizeof(Set),nreacts,fp); + int rbufcount = max_rate_limit_steps*nreacts; + int *rbuf; + if (rbufcount) { + memory->create(rbuf,rbufcount,"bond/react:rbuf"); + memcpy(rbuf,&store_rxn_count[0][0],sizeof(int)*rbufcount); } + + if (comm->me == 0) { + int size = nreacts*sizeof(Set)+(rbufcount+1)*sizeof(int); + fwrite(&size,sizeof(int),1,fp); + fwrite(&revision,sizeof(int),1,fp); + fwrite(set,sizeof(Set),nreacts,fp); + if (rbufcount) fwrite(rbuf,sizeof(int),rbufcount,fp); + } + if (rbufcount) memory->destroy(rbuf); } /* ---------------------------------------------------------------------- use selected state info from restart file to restart the Fix + bond/react restart revisions numbers added after LAMMPS version 3 Nov 2022 ------------------------------------------------------------------------- */ void FixBondReact::restart(char *buf) { - Set *set_restart = (Set *) buf; - for (int i = 0; i < set_restart[0].nreacts; i++) { + int n,revision,r_nreacts,r_max_rate_limit_steps,ibufcount,n2cpy; + int **ibuf; + + n = 0; + if (lmp->restart_ver > utils::date2num("3 Nov 2022")) revision = buf[n++]; + else revision = 0; + + Set *set_restart = (Set *) &buf[n*sizeof(int)]; + r_nreacts = set_restart[0].nreacts; + + if (revision > 0) { + r_max_rate_limit_steps = set_restart[0].max_rate_limit_steps; + ibufcount = r_max_rate_limit_steps*r_nreacts; + memory->create(ibuf,r_max_rate_limit_steps,r_nreacts,"bond/react:ibuf"); + memcpy(&ibuf[0][0],&buf[sizeof(int)+r_nreacts*sizeof(Set)],sizeof(int)*ibufcount); + n2cpy = r_max_rate_limit_steps; + } else n2cpy = 0; + + if (max_rate_limit_steps < n2cpy) n2cpy = max_rate_limit_steps; + for (int i = 0; i < r_nreacts; i++) { for (int j = 0; j < nreacts; j++) { if (strcmp(set_restart[i].rxn_name,rxn_name[j]) == 0) { reaction_count_total[j] = set_restart[i].reaction_count_total; + // read rate_limit restart information + for (int k = 0; k < n2cpy; k++) + store_rxn_count[k][j] = ibuf[k][i]; } } } + if (revision > 0) memory->destroy(ibuf); } /* ---------------------------------------------------------------------- diff --git a/src/REACTION/fix_bond_react.h b/src/REACTION/fix_bond_react.h index f38fa1f136..4751bc4eef 100644 --- a/src/REACTION/fix_bond_react.h +++ b/src/REACTION/fix_bond_react.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -26,6 +26,9 @@ FixStyle(bond/react,FixBondReact); #include "fix.h" +#include +#include + namespace LAMMPS_NS { class FixBondReact : public Fix { @@ -51,7 +54,6 @@ class FixBondReact : public Fix { double memory_usage() override; private: - int me, nprocs; int newton_bond; int nreacts; int *nevery; @@ -64,8 +66,11 @@ class FixBondReact : public Fix { int stabilization_flag; int reset_mol_ids_flag; int custom_exclude_flag; + int **rate_limit; + int **store_rxn_count; int *stabilize_steps_flag; int *custom_charges_fragid; + int *rescale_charges_flag; int *create_atoms_flag; int *modify_create_fragid; double *overlapsq; @@ -74,9 +79,11 @@ class FixBondReact : public Fix { int *nconstraints; char **constraintstr; int nrxnfunction; - std::vector rxnfunclist; + std::vector rxnfunclist; // lists current special rxn function + std::vector peratomflag; // 1 if special rxn function uses per-atom variable (vs. per-bond) + int atoms2bondflag; // 1 if atoms2bond map has been populated on this timestep int narrhenius; - int **var_flag, **var_id; // for keyword values with variable inputs + int **var_flag, **var_id; // for keyword values with variable inputs int status; int *groupbits; @@ -86,6 +93,7 @@ class FixBondReact : public Fix { int *reaction_count_total; int nmax; // max num local atoms int max_natoms; // max natoms in a molecule template + int max_rate_limit_steps; // max rate limit interval tagint *partner, *finalpartner; double **distsq; int *nattempt; @@ -102,7 +110,7 @@ class FixBondReact : public Fix { class RanMars **random; // random number for 'prob' keyword class RanMars **rrhandom; // random number for Arrhenius constraint class NeighList *list; - class ResetMolIDs *reset_mol_ids; // class for resetting mol IDs + class ResetAtomsMol *reset_mol_ids; // class for resetting mol IDs int *reacted_mol, *unreacted_mol; int *limit_duration; // indicates how long to relax @@ -160,7 +168,8 @@ class FixBondReact : public Fix { // but whose first neighbors haven't int glove_counter; // used to determine when to terminate Superimpose Algorithm - void read(int); + void read_variable_keyword(const char *, int, int); + void read_map_file(int); void EdgeIDs(char *, int); void Equivalences(char *, int); void DeleteAtoms(char *, int); @@ -184,6 +193,7 @@ class FixBondReact : public Fix { double custom_constraint(const std::string &); // evaulate expression for custom constraint double rxnfunction(const std::string &, const std::string &, const std::string &); // eval rxn_sum and rxn_ave + void get_atoms2bond(int); int get_chirality(double[12]); // get handedness given an ordered set of coordinates void open(char *); @@ -198,16 +208,18 @@ class FixBondReact : public Fix { void ghost_glovecast(); void update_everything(); int insert_atoms(tagint **, int); - void unlimit_bond(); + void unlimit_bond(); // removes atoms from stabilization, and other post-reaction every-step operations void limit_bond(int); void dedup_mega_gloves(int); //dedup global mega_glove void write_restart(FILE *) override; void restart(char *buf) override; + // store restart data struct Set { int nreacts; char rxn_name[MAXLINE]; int reaction_count_total; + int max_rate_limit_steps; }; Set *set; @@ -221,7 +233,9 @@ class FixBondReact : public Fix { int ncustomvars; std::vector customvarstrs; int nvvec; - double **vvec; // per-atom vector to store variable constraint atom-style variable values + double **vvec; // per-atom vector to store custom constraint atom-style variable values + class Compute *cperbond; // pointer to 'compute bond/local' used by custom constraint ('rxnbond' function) + std::map, int> atoms2bond; // maps atom pair to index of local bond array std::vector> constraints; // DEBUG diff --git a/src/REACTION/superpose3d.h b/src/REACTION/superpose3d.h index d3836691d1..32e48db9da 100644 --- a/src/REACTION/superpose3d.h +++ b/src/REACTION/superpose3d.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REAXFF/compute_spec_atom.cpp b/src/REAXFF/compute_spec_atom.cpp index 117ee0c862..a9cac4a753 100644 --- a/src/REAXFF/compute_spec_atom.cpp +++ b/src/REAXFF/compute_spec_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Labo0ratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REAXFF/compute_spec_atom.h b/src/REAXFF/compute_spec_atom.h index de3c0efb22..c2021d55a0 100644 --- a/src/REAXFF/compute_spec_atom.h +++ b/src/REAXFF/compute_spec_atom.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Labo0ratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REAXFF/fix_acks2_reaxff.cpp b/src/REAXFF/fix_acks2_reaxff.cpp index 9d1775c272..28733f0fe0 100644 --- a/src/REAXFF/fix_acks2_reaxff.cpp +++ b/src/REAXFF/fix_acks2_reaxff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REAXFF/fix_acks2_reaxff.h b/src/REAXFF/fix_acks2_reaxff.h index 27ba196bbd..cfb4c8680d 100644 --- a/src/REAXFF/fix_acks2_reaxff.h +++ b/src/REAXFF/fix_acks2_reaxff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REAXFF/fix_qeq_reaxff.cpp b/src/REAXFF/fix_qeq_reaxff.cpp index f0d58ae120..704b43e642 100644 --- a/src/REAXFF/fix_qeq_reaxff.cpp +++ b/src/REAXFF/fix_qeq_reaxff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REAXFF/fix_qeq_reaxff.h b/src/REAXFF/fix_qeq_reaxff.h index f0f46ed4ce..6d6f846793 100644 --- a/src/REAXFF/fix_qeq_reaxff.h +++ b/src/REAXFF/fix_qeq_reaxff.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REAXFF/fix_reaxff.cpp b/src/REAXFF/fix_reaxff.cpp index bd95dbcb38..06941cd8a0 100644 --- a/src/REAXFF/fix_reaxff.cpp +++ b/src/REAXFF/fix_reaxff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REAXFF/fix_reaxff.h b/src/REAXFF/fix_reaxff.h index 650b75c9d8..ebd352edba 100644 --- a/src/REAXFF/fix_reaxff.h +++ b/src/REAXFF/fix_reaxff.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REAXFF/fix_reaxff_bonds.cpp b/src/REAXFF/fix_reaxff_bonds.cpp index 3eba1e205d..393e22930f 100644 --- a/src/REAXFF/fix_reaxff_bonds.cpp +++ b/src/REAXFF/fix_reaxff_bonds.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REAXFF/fix_reaxff_bonds.h b/src/REAXFF/fix_reaxff_bonds.h index 7443db8658..659001263f 100644 --- a/src/REAXFF/fix_reaxff_bonds.h +++ b/src/REAXFF/fix_reaxff_bonds.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REAXFF/fix_reaxff_species.cpp b/src/REAXFF/fix_reaxff_species.cpp index 322ef8aadf..65a2e6d8ce 100644 --- a/src/REAXFF/fix_reaxff_species.cpp +++ b/src/REAXFF/fix_reaxff_species.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -132,13 +132,13 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) : setupflag = 0; // set default bond order cutoff - int n, i, j, itype, jtype; + int itype, jtype; double bo_cut; bg_cut = 0.30; - n = ntypes + 1; - memory->create(BOCut, n, n, "reaxff/species:BOCut"); - for (i = 1; i < n; i++) - for (j = 1; j < n; j++) BOCut[i][j] = bg_cut; + int np1 = ntypes + 1; + memory->create(BOCut, np1, np1, "reaxff/species:BOCut"); + for (int i = 1; i < np1; i++) + for (int j = 1; j < np1; j++) BOCut[i][j] = bg_cut; // optional args eletype = nullptr; @@ -213,7 +213,7 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) : if (comm->me == 0) { fprintf(fdel, "Timestep"); - for (i = 0; i < ndelspec; i++) fprintf(fdel, "\t%s", del_species[i].c_str()); + for (int i = 0; i < ndelspec; i++) fprintf(fdel, "\t%s", del_species[i].c_str()); fprintf(fdel, "\n"); fflush(fdel); } diff --git a/src/REAXFF/fix_reaxff_species.h b/src/REAXFF/fix_reaxff_species.h index 78eb39a0b6..65eeae4c60 100644 --- a/src/REAXFF/fix_reaxff_species.h +++ b/src/REAXFF/fix_reaxff_species.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REAXFF/pair_reaxff.cpp b/src/REAXFF/pair_reaxff.cpp index f3ab23bf06..ef859a0cda 100644 --- a/src/REAXFF/pair_reaxff.cpp +++ b/src/REAXFF/pair_reaxff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -587,8 +587,8 @@ void PairReaxFF::set_far_nbr(far_neighbor_data *fdest, int PairReaxFF::estimate_reax_lists() { int itr_i, itr_j, i, j; - int num_nbrs, num_marked; - int *ilist, *jlist, *numneigh, **firstneigh, *marked; + int num_nbrs; + int *ilist, *jlist, *numneigh, **firstneigh; double d_sqr; rvec dvec; double **x; @@ -602,15 +602,11 @@ int PairReaxFF::estimate_reax_lists() firstneigh = list->firstneigh; num_nbrs = 0; - num_marked = 0; - marked = (int*) calloc(api->system->N, sizeof(int)); int numall = list->inum + list->gnum; for (itr_i = 0; itr_i < numall; ++itr_i) { i = ilist[itr_i]; - marked[i] = 1; - ++num_marked; jlist = firstneigh[i]; for (itr_j = 0; itr_j < numneigh[i]; ++itr_j) { @@ -623,8 +619,6 @@ int PairReaxFF::estimate_reax_lists() } } - free(marked); - return static_cast (MAX(num_nbrs*safezone, mincap*REAX_MIN_NBRS)); } diff --git a/src/REAXFF/pair_reaxff.h b/src/REAXFF/pair_reaxff.h index 68d4588f6e..926e0060c9 100644 --- a/src/REAXFF/pair_reaxff.h +++ b/src/REAXFF/pair_reaxff.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REAXFF/reaxff_api.h b/src/REAXFF/reaxff_api.h index 52ee3df603..d6a0410622 100644 --- a/src/REAXFF/reaxff_api.h +++ b/src/REAXFF/reaxff_api.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REAXFF/reaxff_defs.h b/src/REAXFF/reaxff_defs.h index 0650c518fe..abde8e64db 100644 --- a/src/REAXFF/reaxff_defs.h +++ b/src/REAXFF/reaxff_defs.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REAXFF/reaxff_hydrogen_bonds.cpp b/src/REAXFF/reaxff_hydrogen_bonds.cpp index 5c7629ffb7..6f5c663da0 100644 --- a/src/REAXFF/reaxff_hydrogen_bonds.cpp +++ b/src/REAXFF/reaxff_hydrogen_bonds.cpp @@ -39,7 +39,6 @@ namespace ReaxFF { int start_j, end_j, hb_start_j, hb_end_j; int hblist[MAX_BONDS]; int itr, top; - int num_hb_intrs = 0; double r_jk, theta, cos_theta, sin_xhz4, cos_xhz1, sin_theta2; double e_hb, exp_hb2, exp_hb3, CEhb1, CEhb2, CEhb3; rvec dcos_theta_di, dcos_theta_dj, dcos_theta_dk; @@ -102,7 +101,6 @@ namespace ReaxFF { if (type_i < 0) continue; hbp = &(system->reax_param.hbp[type_i][type_j][type_k]); if (hbp->r0_hb <= 0.0) continue; - ++num_hb_intrs; Calculate_Theta(pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk, &theta, &cos_theta); diff --git a/src/REAXFF/reaxff_inline.h b/src/REAXFF/reaxff_inline.h index b07f02631d..b5b3091da6 100644 --- a/src/REAXFF/reaxff_inline.h +++ b/src/REAXFF/reaxff_inline.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REAXFF/reaxff_torsion_angles.cpp b/src/REAXFF/reaxff_torsion_angles.cpp index 2b94bf50ae..e9b6bc618d 100644 --- a/src/REAXFF/reaxff_torsion_angles.cpp +++ b/src/REAXFF/reaxff_torsion_angles.cpp @@ -119,7 +119,6 @@ namespace ReaxFF { int type_i, type_j, type_k, type_l; int start_j, end_j; int start_pj, end_pj, start_pk, end_pk; - int num_frb_intrs = 0; double Delta_j, Delta_k; double r_ij, r_jk, r_kl, r_li; @@ -242,7 +241,6 @@ namespace ReaxFF { if (i != l && fbh->cnt && bo_kl->BO > control->thb_cut/*0*/ && bo_ij->BO * bo_jk->BO * bo_kl->BO > control->thb_cut/*0*/) { - ++num_frb_intrs; r_kl = pbond_kl->d; BOA_kl = bo_kl->BO - control->thb_cut; diff --git a/src/REAXFF/reaxff_types.h b/src/REAXFF/reaxff_types.h index 7b090c79ce..abf2f68173 100644 --- a/src/REAXFF/reaxff_types.h +++ b/src/REAXFF/reaxff_types.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/compute_event_displace.cpp b/src/REPLICA/compute_event_displace.cpp index 7d08955803..20ec67500c 100644 --- a/src/REPLICA/compute_event_displace.cpp +++ b/src/REPLICA/compute_event_displace.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/compute_event_displace.h b/src/REPLICA/compute_event_displace.h index 990847194d..a8bb9f333a 100644 --- a/src/REPLICA/compute_event_displace.h +++ b/src/REPLICA/compute_event_displace.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/compute_pressure_grem.cpp b/src/REPLICA/compute_pressure_grem.cpp index 3657d6d028..50790ead2e 100644 --- a/src/REPLICA/compute_pressure_grem.cpp +++ b/src/REPLICA/compute_pressure_grem.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/compute_pressure_grem.h b/src/REPLICA/compute_pressure_grem.h index cf11ed2e17..dbcaf16731 100644 --- a/src/REPLICA/compute_pressure_grem.h +++ b/src/REPLICA/compute_pressure_grem.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/fix_event.cpp b/src/REPLICA/fix_event.cpp index 2f4f44d46f..a96f0e2b7c 100644 --- a/src/REPLICA/fix_event.cpp +++ b/src/REPLICA/fix_event.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/fix_event.h b/src/REPLICA/fix_event.h index 1eb2d75f84..45575d605f 100644 --- a/src/REPLICA/fix_event.h +++ b/src/REPLICA/fix_event.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/fix_event_hyper.cpp b/src/REPLICA/fix_event_hyper.cpp index 9cdb881d06..e388eb5e26 100644 --- a/src/REPLICA/fix_event_hyper.cpp +++ b/src/REPLICA/fix_event_hyper.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/fix_event_hyper.h b/src/REPLICA/fix_event_hyper.h index 8c65ef1c79..a8ca78e46d 100644 --- a/src/REPLICA/fix_event_hyper.h +++ b/src/REPLICA/fix_event_hyper.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/fix_event_prd.cpp b/src/REPLICA/fix_event_prd.cpp index 9e1aee90e6..783661dd68 100644 --- a/src/REPLICA/fix_event_prd.cpp +++ b/src/REPLICA/fix_event_prd.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/fix_event_prd.h b/src/REPLICA/fix_event_prd.h index 57ce9ede64..e3e98b4850 100644 --- a/src/REPLICA/fix_event_prd.h +++ b/src/REPLICA/fix_event_prd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/fix_event_tad.cpp b/src/REPLICA/fix_event_tad.cpp index 1ab34d3eed..6e02cebaa7 100644 --- a/src/REPLICA/fix_event_tad.cpp +++ b/src/REPLICA/fix_event_tad.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/fix_event_tad.h b/src/REPLICA/fix_event_tad.h index 5523df7107..ff5d4bb998 100644 --- a/src/REPLICA/fix_event_tad.h +++ b/src/REPLICA/fix_event_tad.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/fix_grem.cpp b/src/REPLICA/fix_grem.cpp index 8cc2ef27bc..4571afdcba 100644 --- a/src/REPLICA/fix_grem.cpp +++ b/src/REPLICA/fix_grem.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/fix_grem.h b/src/REPLICA/fix_grem.h index a1ffae353a..e33a2f247d 100644 --- a/src/REPLICA/fix_grem.h +++ b/src/REPLICA/fix_grem.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/fix_hyper.cpp b/src/REPLICA/fix_hyper.cpp index dc458dd3c6..f334f6a592 100644 --- a/src/REPLICA/fix_hyper.cpp +++ b/src/REPLICA/fix_hyper.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/fix_hyper.h b/src/REPLICA/fix_hyper.h index 9d646f9927..a5e9e2e093 100644 --- a/src/REPLICA/fix_hyper.h +++ b/src/REPLICA/fix_hyper.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/fix_hyper_global.cpp b/src/REPLICA/fix_hyper_global.cpp index 232a72a9ad..d262c49fda 100644 --- a/src/REPLICA/fix_hyper_global.cpp +++ b/src/REPLICA/fix_hyper_global.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/fix_hyper_global.h b/src/REPLICA/fix_hyper_global.h index 89e17b5ef0..123a879b83 100644 --- a/src/REPLICA/fix_hyper_global.h +++ b/src/REPLICA/fix_hyper_global.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/fix_hyper_local.cpp b/src/REPLICA/fix_hyper_local.cpp index 9364a2f753..0ed3c14451 100644 --- a/src/REPLICA/fix_hyper_local.cpp +++ b/src/REPLICA/fix_hyper_local.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/fix_hyper_local.h b/src/REPLICA/fix_hyper_local.h index ea7b3e3dfe..0ef54fbf1a 100644 --- a/src/REPLICA/fix_hyper_local.h +++ b/src/REPLICA/fix_hyper_local.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/fix_neb.cpp b/src/REPLICA/fix_neb.cpp index bb15e99fd2..3ebf64d609 100644 --- a/src/REPLICA/fix_neb.cpp +++ b/src/REPLICA/fix_neb.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/fix_neb.h b/src/REPLICA/fix_neb.h index 80ffc130d9..a5aa831163 100644 --- a/src/REPLICA/fix_neb.h +++ b/src/REPLICA/fix_neb.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/fix_pimd.cpp b/src/REPLICA/fix_pimd.cpp index 32c468765e..40e203d3c2 100644 --- a/src/REPLICA/fix_pimd.cpp +++ b/src/REPLICA/fix_pimd.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -102,6 +102,9 @@ FixPIMD::FixPIMD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) error->universe_all(FLERR, fmt::format("Unknown keyword {} for fix pimd", arg[i])); } + if (strcmp(update->unit_style, "lj") == 0) + error->all(FLERR, "Fix pimd does not support lj units"); + /* Initiation */ size_peratom_cols = 12 * nhc_nchain + 3; diff --git a/src/REPLICA/fix_pimd.h b/src/REPLICA/fix_pimd.h index ad3c7d31b0..384bc2ce25 100644 --- a/src/REPLICA/fix_pimd.h +++ b/src/REPLICA/fix_pimd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/hyper.cpp b/src/REPLICA/hyper.cpp index 7b402a1729..2c7d13766f 100644 --- a/src/REPLICA/hyper.cpp +++ b/src/REPLICA/hyper.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -22,7 +22,6 @@ #include "fix_event_hyper.h" #include "fix_hyper.h" #include "integrate.h" -#include "memory.h" #include "min.h" #include "modify.h" #include "neighbor.h" diff --git a/src/REPLICA/hyper.h b/src/REPLICA/hyper.h index 28229d819e..651c1ebdcb 100644 --- a/src/REPLICA/hyper.h +++ b/src/REPLICA/hyper.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp index e80668a687..9c5befaf36 100644 --- a/src/REPLICA/neb.cpp +++ b/src/REPLICA/neb.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -108,9 +108,9 @@ NEB::~NEB() void NEB::command(int narg, char **arg) { if (domain->box_exist == 0) - error->all(FLERR,"NEB command before simulation box is defined"); + error->universe_all(FLERR,"NEB command before simulation box is defined"); - if (narg < 6) error->universe_all(FLERR,"Illegal NEB command"); + if (narg < 6) error->universe_all(FLERR,"Illegal NEB command: missing argument(s)"); etol = utils::numeric(FLERR,arg[0],false,lmp); ftol = utils::numeric(FLERR,arg[1],false,lmp); @@ -120,11 +120,14 @@ void NEB::command(int narg, char **arg) // error checks - if (etol < 0.0) error->all(FLERR,"Illegal NEB command"); - if (ftol < 0.0) error->all(FLERR,"Illegal NEB command"); - if (nevery <= 0) error->universe_all(FLERR,"Illegal NEB command"); - if (n1steps % nevery || n2steps % nevery) - error->universe_all(FLERR,"Illegal NEB command"); + if (etol < 0.0) error->universe_all(FLERR, fmt::format("Illegal NEB energy tolerance: {}", etol)); + if (ftol < 0.0) error->universe_all(FLERR, fmt::format("Illegal NEB force tolerance: {}", ftol)); + if (nevery <= 0) + error->universe_all(FLERR,fmt::format("Illegal NEB command every parameter: {}", nevery)); + if (n1steps % nevery) + error->all(FLERR, fmt::format("NEB N1 value {} incompatible with every {}", n1steps, nevery)); + if (n2steps % nevery) + error->all(FLERR, fmt::format("NEB N2 value {} incompatible with every {}", n2steps, nevery)); // replica info @@ -136,26 +139,38 @@ void NEB::command(int narg, char **arg) // error checks - if (nreplica == 1) error->all(FLERR,"Cannot use NEB with a single replica"); + if (nreplica == 1) error->universe_all(FLERR,"Cannot use NEB with a single replica"); if (atom->map_style == Atom::MAP_NONE) - error->all(FLERR,"Cannot use NEB unless atom map exists"); + error->universe_all(FLERR,"Cannot use NEB without an atom map"); // process file-style setting to setup initial configs for all replicas - - if (strcmp(arg[5],"final") == 0) { - if (narg != 7 && narg !=8) error->universe_all(FLERR,"Illegal NEB command"); - inpfile = arg[6]; - readfile(inpfile,0); - } else if (strcmp(arg[5],"each") == 0) { - if (narg != 7 && narg !=8) error->universe_all(FLERR,"Illegal NEB command"); - inpfile = arg[6]; - readfile(inpfile,1); - } else if (strcmp(arg[5],"none") == 0) { - if (narg != 6 && narg !=7) error->universe_all(FLERR,"Illegal NEB command"); - } else error->universe_all(FLERR,"Illegal NEB command"); - + int iarg = 5; + int filecmd = 0; verbose=false; - if (strcmp(arg[narg-1],"verbose") == 0) verbose=true; + while (iarg < narg) { + if (strcmp(arg[iarg],"final") == 0) { + if (iarg + 2 > narg) error->universe_all(FLERR,"Illegal NEB command: missing arguments"); + inpfile = arg[iarg+1]; + readfile(inpfile,0); + filecmd = 1; + iarg += 2; + } else if (strcmp(arg[iarg],"each") == 0) { + if (iarg + 2 > narg) error->universe_all(FLERR,"Illegal NEB command: missing arguments"); + inpfile = arg[iarg+1]; + readfile(inpfile,1); + filecmd = 1; + iarg += 2; + } else if (strcmp(arg[iarg],"none") == 0) { + filecmd = 1; + ++iarg; + } else if (strcmp(arg[iarg],"verbose") == 0) { + verbose=true; + ++iarg; + } else error->universe_all(FLERR,fmt::format("Unknown NEB command keyword: {}", arg[iarg])); + } + + if (!filecmd) error->universe_all(FLERR, "NEB is missing 'final', 'each', or 'none' keyword"); + // run the NEB calculation run(); @@ -176,7 +191,7 @@ void NEB::run() auto fixes = modify->get_fix_by_style("^neb$"); if (fixes.size() != 1) - error->all(FLERR,"NEB requires use of exactly one fix neb instance"); + error->universe_all(FLERR,"NEB requires use of exactly one fix neb instance"); fneb = dynamic_cast(fixes[0]); if (verbose) numall =7; @@ -194,7 +209,7 @@ void NEB::run() lmp->init(); if (update->minimize->searchflag) - error->all(FLERR,"NEB requires damped dynamics minimizer"); + error->universe_all(FLERR,"NEB requires a damped dynamics minimizer"); // setup regular NEB minimization FILE *uscreen = universe->uscreen; @@ -207,38 +222,43 @@ void NEB::run() update->endstep = update->laststep = update->firststep + n1steps; update->nsteps = n1steps; update->max_eval = n1steps; - if (update->laststep < 0) - error->all(FLERR,"Too many timesteps for NEB"); + if (update->laststep < 0) error->universe_all(FLERR,"Too many timesteps for NEB"); update->minimize->setup(); if (me_universe == 0) { if (uscreen) { + fmt::print(uscreen," Step {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} ", + "MaxReplicaForce", "MaxAtomForce", "GradV0","GradV1","GradVc","EBF", "EBR", "RDT"); + for (int i = 1; i <= nreplica; ++i) + fmt::print(uscreen, "{:^14} {:^14} ", "RD"+std::to_string(i), "PE"+std::to_string(i)); + if (verbose) { - fprintf(uscreen,"Step MaxReplicaForce MaxAtomForce " - "GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... " - "RDN PEN pathangle1 angletangrad1 anglegrad1 gradV1 " - "ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 " - "... ReplicaForceN MaxAtomForceN\n"); - } else { - fprintf(uscreen,"Step MaxReplicaForce MaxAtomForce " - "GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... " - "RDN PEN\n"); + for (int i = 1; i <= nreplica; ++i) { + auto idx = std::to_string(i); + fmt::print(uscreen, "{:^12}{:^12}{:^12} {:^12} {:^12}{:^12} ", + "pathangle"+idx, "angletangrad"+idx, "anglegrad"+idx, "gradV"+idx, + "RepForce"+idx, "MaxAtomForce"+idx); + } } + fprintf(uscreen,"\n"); } if (ulogfile) { + fmt::print(ulogfile," Step {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} ", + "MaxReplicaForce", "MaxAtomForce", "GradV0","GradV1","GradVc","EBF", "EBR", "RDT"); + for (int i = 1; i <= nreplica; ++i) + fmt::print(ulogfile, "{:^14} {:^14} ", "RD"+std::to_string(i), "PE"+std::to_string(i)); + if (verbose) { - fprintf(ulogfile,"Step MaxReplicaForce MaxAtomForce " - "GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... " - "RDN PEN pathangle1 angletangrad1 anglegrad1 gradV1 " - "ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 " - "... ReplicaForceN MaxAtomForceN\n"); - } else { - fprintf(ulogfile,"Step MaxReplicaForce MaxAtomForce " - "GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... " - "RDN PEN\n"); + for (int i = 1; i <= nreplica; ++i) { + auto idx = std::to_string(i); + fmt::print(ulogfile, "{:^12}{:^12}{:^12} {:^12} {:^12}{:^12} ", + "pathangle"+idx, "angletangrad"+idx, "anglegrad"+idx, "gradV"+idx, + "RepForce"+idx, "MaxAtomForce"+idx); + } } + fprintf(ulogfile,"\n"); } } print_status(); @@ -292,8 +312,7 @@ void NEB::run() update->endstep = update->laststep = update->firststep + n2steps; update->nsteps = n2steps; update->max_eval = n2steps; - if (update->laststep < 0) - error->all(FLERR,"Too many timesteps"); + if (update->laststep < 0) error->universe_all(FLERR,"Too many timesteps"); update->minimize->init(); fneb->rclimber = top; @@ -301,34 +320,37 @@ void NEB::run() if (me_universe == 0) { if (uscreen) { + fmt::print(uscreen," Step {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} ", + "MaxReplicaForce", "MaxAtomForce", "GradV0","GradV1","GradVc","EBF", "EBR", "RDT"); + for (int i = 1; i <= nreplica; ++i) + fmt::print(uscreen, "{:^14} {:^14} ", "RD"+std::to_string(i), "PE"+std::to_string(i)); + if (verbose) { - fprintf(uscreen,"Step MaxReplicaForce MaxAtomForce " - "GradV0 GradV1 GradVc EBF EBR RDT " - "RD1 PE1 RD2 PE2 ... RDN PEN " - "pathangle1 angletangrad1 anglegrad1 gradV1 " - "ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 " - "... ReplicaForceN MaxAtomForceN\n"); - } else { - fprintf(uscreen,"Step MaxReplicaForce MaxAtomForce " - "GradV0 GradV1 GradVc " - "EBF EBR RDT " - "RD1 PE1 RD2 PE2 ... RDN PEN\n"); + for (int i = 1; i <= nreplica; ++i) { + auto idx = std::to_string(i); + fmt::print(uscreen, "{:^12}{:^12}{:^12} {:^12} {:^12}{:^12} ", + "pathangle"+idx, "angletangrad"+idx, "anglegrad"+idx, "gradV"+idx, + "RepForce"+idx, "MaxAtomForce"+idx); + } } + fprintf(uscreen,"\n"); } + if (ulogfile) { + fmt::print(ulogfile," Step {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} {:^14} ", + "MaxReplicaForce", "MaxAtomForce", "GradV0","GradV1","GradVc","EBF", "EBR", "RDT"); + for (int i = 1; i <= nreplica; ++i) + fmt::print(ulogfile, "{:^14} {:^14} ", "RD"+std::to_string(i), "PE"+std::to_string(i)); + if (verbose) { - fprintf(ulogfile,"Step MaxReplicaForce MaxAtomForce " - "GradV0 GradV1 GradVc EBF EBR RDT " - "RD1 PE1 RD2 PE2 ... RDN PEN " - "pathangle1 angletangrad1 anglegrad1 gradV1 " - "ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 " - "... ReplicaForceN MaxAtomForceN\n"); - } else { - fprintf(ulogfile,"Step MaxReplicaForce MaxAtomForce " - "GradV0 GradV1 GradVc " - "EBF EBR RDT " - "RD1 PE1 RD2 PE2 ... RDN PEN\n"); + for (int i = 1; i <= nreplica; ++i) { + auto idx = std::to_string(i); + fmt::print(ulogfile, "{:^12}{:^12}{:^12} {:^12} {:^12}{:^12} ", + "pathangle"+idx, "angletangrad"+idx, "anglegrad"+idx, "gradV"+idx, + "RepForce"+idx, "MaxAtomForce"+idx); + } } + fprintf(ulogfile,"\n"); } } print_status(); @@ -420,7 +442,7 @@ void NEB::readfile(char *file, int flag) } MPI_Bcast(&nlines,1,MPI_INT,0,world); if (nlines < 0) - error->all(FLERR,"Incorrectly formatted NEB file"); + error->universe_all(FLERR,"Incorrectly formatted NEB file"); } auto buffer = new char[CHUNK*MAXLINE]; @@ -542,11 +564,11 @@ void NEB::open(char *file) if (platform::has_compress_extension(file)) { compressed = 1; fp = platform::compressed_read(file); - if (!fp) error->one(FLERR,"Cannot open compressed file"); + if (!fp) error->one(FLERR,"Cannot open compressed file {}: {}", file, utils::getsyserror()); } else fp = fopen(file,"r"); if (fp == nullptr) - error->one(FLERR,"Cannot open file {}: {}",file,utils::getsyserror()); + error->one(FLERR,"Cannot open file {}: {}", file, utils::getsyserror()); } /* ---------------------------------------------------------------------- @@ -626,19 +648,19 @@ void NEB::print_status() if (me_universe == 0) { constexpr double todeg=180.0/MY_PI; - std::string mesg = fmt::format("{} {:12.8g} {:12.8g} ",update->ntimestep,fmaxreplica,fmaxatom); - mesg += fmt::format("{:12.8g} {:12.8g} {:12.8g} ",gradvnorm0,gradvnorm1,gradvnormc); - mesg += fmt::format("{:12.8g} {:12.8g} {:12.8g} ",ebf,ebr,endpt); - for (int i = 0; i < nreplica; i++) mesg += fmt::format("{:12.8g} {:12.8g} ",rdist[i],all[i][0]); + std::string mesg = fmt::format("{:10} {:<14.8g} {:<14.8g} ",update->ntimestep,fmaxreplica,fmaxatom); + mesg += fmt::format("{:<14.8g} {:<14.8g} {:<14.8g} ",gradvnorm0,gradvnorm1,gradvnormc); + mesg += fmt::format("{:<14.8g} {:<14.8g} {:<14.8g} ",ebf,ebr,endpt); + for (int i = 0; i < nreplica; i++) mesg += fmt::format("{:<14.8g} {:<14.8g} ",rdist[i],all[i][0]); if (verbose) { - mesg += fmt::format("{:12.5g} {:12.5g} {:12.5g} {:12.5g} {:12.5g} {:12.5g}", + mesg += fmt::format("{:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g}", NAN,180-acos(all[0][5])*todeg,180-acos(all[0][6])*todeg, all[0][3],freplica[0],fmaxatomInRepl[0]); for (int i = 1; i < nreplica-1; i++) - mesg += fmt::format("{:12.5g} {:12.5g} {:12.5g} {:12.5g} {:12.5g} {:12.5g}", + mesg += fmt::format("{:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g}", 180-acos(all[i][4])*todeg,180-acos(all[i][5])*todeg, 180-acos(all[i][6])*todeg,all[i][3],freplica[i],fmaxatomInRepl[i]); - mesg += fmt::format("{:12.5g} {:12.5g} {:12.5g} {:12.5g} {:12.5g} {:12.5g}", + mesg += fmt::format("{:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g} {:<12.5g}", NAN,180-acos(all[nreplica-1][5])*todeg,NAN,all[nreplica-1][3], freplica[nreplica-1],fmaxatomInRepl[nreplica-1]); } @@ -650,4 +672,8 @@ void NEB::print_status() fflush(universe->ulogfile); } } + if (verbose) { + delete[] freplica; + delete[] fmaxatomInRepl; + } } diff --git a/src/REPLICA/neb.h b/src/REPLICA/neb.h index 9bbd6966e6..cad0ac7122 100644 --- a/src/REPLICA/neb.h +++ b/src/REPLICA/neb.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp index e09807e565..f1af019fb2 100644 --- a/src/REPLICA/prd.cpp +++ b/src/REPLICA/prd.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/prd.h b/src/REPLICA/prd.h index 2284b93aaa..1509d87107 100644 --- a/src/REPLICA/prd.h +++ b/src/REPLICA/prd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/tad.cpp b/src/REPLICA/tad.cpp index ceda4fb592..da4a3b1355 100644 --- a/src/REPLICA/tad.cpp +++ b/src/REPLICA/tad.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/tad.h b/src/REPLICA/tad.h index 07c8764686..8f51ca8c91 100644 --- a/src/REPLICA/tad.h +++ b/src/REPLICA/tad.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp index 1bac1aea92..9e7e67d79d 100644 --- a/src/REPLICA/temper.cpp +++ b/src/REPLICA/temper.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/temper.h b/src/REPLICA/temper.h index 39e4661fcd..b557e8ddd8 100644 --- a/src/REPLICA/temper.h +++ b/src/REPLICA/temper.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/temper_grem.cpp b/src/REPLICA/temper_grem.cpp index 72dd331491..68fbb4eef6 100644 --- a/src/REPLICA/temper_grem.cpp +++ b/src/REPLICA/temper_grem.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/temper_grem.h b/src/REPLICA/temper_grem.h index f372a75feb..3c41f9b082 100644 --- a/src/REPLICA/temper_grem.h +++ b/src/REPLICA/temper_grem.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/temper_npt.cpp b/src/REPLICA/temper_npt.cpp index eaf429380f..6567cb83e1 100644 --- a/src/REPLICA/temper_npt.cpp +++ b/src/REPLICA/temper_npt.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/temper_npt.h b/src/REPLICA/temper_npt.h index b6e92f7d83..3a51fc74e4 100644 --- a/src/REPLICA/temper_npt.h +++ b/src/REPLICA/temper_npt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/REPLICA/verlet_split.cpp b/src/REPLICA/verlet_split.cpp index 661b86129c..dbb91a95be 100644 --- a/src/REPLICA/verlet_split.cpp +++ b/src/REPLICA/verlet_split.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -52,9 +52,8 @@ VerletSplit::VerletSplit(LAMMPS *lmp, int narg, char **arg) : if (universe->procs_per_world[0] % universe->procs_per_world[1]) error->universe_all(FLERR,"Verlet/split requires Rspace partition " "size be multiple of Kspace partition size"); - if (comm->style != 0) - error->universe_all(FLERR,"Verlet/split can only currently be used with " - "comm_style brick"); + if (comm->style != Comm::BRICK) + error->universe_all(FLERR,"Verlet/split can only currently be used with comm_style brick"); // master = 1 for Rspace procs, 0 for Kspace procs @@ -217,11 +216,10 @@ VerletSplit::~VerletSplit() void VerletSplit::init() { - if (comm->style != 0) - error->universe_all(FLERR,"Verlet/split can only currently be used with " - "comm_style brick"); + if (comm->style != Comm::BRICK) + error->universe_all(FLERR,"Verlet/split can only currently be used with comm_style brick"); if (!force->kspace && comm->me == 0) - error->warning(FLERR,"No Kspace calculation with verlet/split"); + error->warning(FLERR,"A KSpace style must be defined with verlet/split"); if (force->kspace_match("/tip4p",0)) tip4p_flag = 1; else tip4p_flag = 0; diff --git a/src/REPLICA/verlet_split.h b/src/REPLICA/verlet_split.h index 2ab679472b..6bffac1d38 100644 --- a/src/REPLICA/verlet_split.h +++ b/src/REPLICA/verlet_split.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/compute_erotate_rigid.cpp b/src/RIGID/compute_erotate_rigid.cpp index 0d0ad038b1..6c4f395c68 100644 --- a/src/RIGID/compute_erotate_rigid.cpp +++ b/src/RIGID/compute_erotate_rigid.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/compute_erotate_rigid.h b/src/RIGID/compute_erotate_rigid.h index ea160df17f..cab00da740 100644 --- a/src/RIGID/compute_erotate_rigid.h +++ b/src/RIGID/compute_erotate_rigid.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/compute_ke_rigid.cpp b/src/RIGID/compute_ke_rigid.cpp index b0342ec1f9..fa86b996b5 100644 --- a/src/RIGID/compute_ke_rigid.cpp +++ b/src/RIGID/compute_ke_rigid.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/compute_ke_rigid.h b/src/RIGID/compute_ke_rigid.h index 71fecb0d09..6b05d301a3 100644 --- a/src/RIGID/compute_ke_rigid.h +++ b/src/RIGID/compute_ke_rigid.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/compute_rigid_local.cpp b/src/RIGID/compute_rigid_local.cpp index 4254acc025..bd0db29d20 100644 --- a/src/RIGID/compute_rigid_local.cpp +++ b/src/RIGID/compute_rigid_local.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/compute_rigid_local.h b/src/RIGID/compute_rigid_local.h index 3314307f2c..b1e1ef0433 100644 --- a/src/RIGID/compute_rigid_local.h +++ b/src/RIGID/compute_rigid_local.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_ehex.cpp b/src/RIGID/fix_ehex.cpp index fd52de7d84..dc5f220a87 100644 --- a/src/RIGID/fix_ehex.cpp +++ b/src/RIGID/fix_ehex.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_ehex.h b/src/RIGID/fix_ehex.h index bbaddd5118..f24d1616f8 100644 --- a/src/RIGID/fix_ehex.h +++ b/src/RIGID/fix_ehex.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rattle.cpp b/src/RIGID/fix_rattle.cpp index 1d6336712b..0027b537ee 100644 --- a/src/RIGID/fix_rattle.cpp +++ b/src/RIGID/fix_rattle.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rattle.h b/src/RIGID/fix_rattle.h index 3e96e41efd..aad2f98b03 100644 --- a/src/RIGID/fix_rattle.h +++ b/src/RIGID/fix_rattle.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index f0bcf630b7..4ea43cf6c8 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rigid.h b/src/RIGID/fix_rigid.h index 027c3eb59c..1e94adec09 100644 --- a/src/RIGID/fix_rigid.h +++ b/src/RIGID/fix_rigid.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rigid_nh.cpp b/src/RIGID/fix_rigid_nh.cpp index 61491688e9..9c9d582d94 100644 --- a/src/RIGID/fix_rigid_nh.cpp +++ b/src/RIGID/fix_rigid_nh.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rigid_nh.h b/src/RIGID/fix_rigid_nh.h index ea628355dc..94600f97d1 100644 --- a/src/RIGID/fix_rigid_nh.h +++ b/src/RIGID/fix_rigid_nh.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp index ba4de80d15..f0bfa1f50a 100644 --- a/src/RIGID/fix_rigid_nh_small.cpp +++ b/src/RIGID/fix_rigid_nh_small.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rigid_nh_small.h b/src/RIGID/fix_rigid_nh_small.h index edc7f7694b..3d637b6aea 100644 --- a/src/RIGID/fix_rigid_nh_small.h +++ b/src/RIGID/fix_rigid_nh_small.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rigid_nph.cpp b/src/RIGID/fix_rigid_nph.cpp index 6fcdc66fec..08d1d81a26 100644 --- a/src/RIGID/fix_rigid_nph.cpp +++ b/src/RIGID/fix_rigid_nph.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rigid_nph.h b/src/RIGID/fix_rigid_nph.h index 0d0e22c2f6..fa8c53ea06 100644 --- a/src/RIGID/fix_rigid_nph.h +++ b/src/RIGID/fix_rigid_nph.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rigid_nph_small.cpp b/src/RIGID/fix_rigid_nph_small.cpp index 7f6f81d858..f44e894f43 100644 --- a/src/RIGID/fix_rigid_nph_small.cpp +++ b/src/RIGID/fix_rigid_nph_small.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rigid_nph_small.h b/src/RIGID/fix_rigid_nph_small.h index f6e99db2a7..ba354c95b3 100644 --- a/src/RIGID/fix_rigid_nph_small.h +++ b/src/RIGID/fix_rigid_nph_small.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rigid_npt.cpp b/src/RIGID/fix_rigid_npt.cpp index 342144f82f..4b568d63e1 100644 --- a/src/RIGID/fix_rigid_npt.cpp +++ b/src/RIGID/fix_rigid_npt.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rigid_npt.h b/src/RIGID/fix_rigid_npt.h index c079751012..cd0afec1dd 100644 --- a/src/RIGID/fix_rigid_npt.h +++ b/src/RIGID/fix_rigid_npt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rigid_npt_small.cpp b/src/RIGID/fix_rigid_npt_small.cpp index 701ed0c9f2..00643bcbd1 100644 --- a/src/RIGID/fix_rigid_npt_small.cpp +++ b/src/RIGID/fix_rigid_npt_small.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rigid_npt_small.h b/src/RIGID/fix_rigid_npt_small.h index 77a74f2265..6acd22025e 100644 --- a/src/RIGID/fix_rigid_npt_small.h +++ b/src/RIGID/fix_rigid_npt_small.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rigid_nve.cpp b/src/RIGID/fix_rigid_nve.cpp index 1d16eed335..9f7b841271 100644 --- a/src/RIGID/fix_rigid_nve.cpp +++ b/src/RIGID/fix_rigid_nve.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rigid_nve.h b/src/RIGID/fix_rigid_nve.h index b38203c114..4f3fe5ee04 100644 --- a/src/RIGID/fix_rigid_nve.h +++ b/src/RIGID/fix_rigid_nve.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rigid_nve_small.cpp b/src/RIGID/fix_rigid_nve_small.cpp index 67b4e5204e..483bf942fd 100644 --- a/src/RIGID/fix_rigid_nve_small.cpp +++ b/src/RIGID/fix_rigid_nve_small.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rigid_nve_small.h b/src/RIGID/fix_rigid_nve_small.h index 0255d1d750..97ae70cec5 100644 --- a/src/RIGID/fix_rigid_nve_small.h +++ b/src/RIGID/fix_rigid_nve_small.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rigid_nvt.cpp b/src/RIGID/fix_rigid_nvt.cpp index 6cc436734d..e7ee90e576 100644 --- a/src/RIGID/fix_rigid_nvt.cpp +++ b/src/RIGID/fix_rigid_nvt.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rigid_nvt.h b/src/RIGID/fix_rigid_nvt.h index be01a3c72b..73e266b2d6 100644 --- a/src/RIGID/fix_rigid_nvt.h +++ b/src/RIGID/fix_rigid_nvt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rigid_nvt_small.cpp b/src/RIGID/fix_rigid_nvt_small.cpp index c3a7aed35f..f568255a3f 100644 --- a/src/RIGID/fix_rigid_nvt_small.cpp +++ b/src/RIGID/fix_rigid_nvt_small.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rigid_nvt_small.h b/src/RIGID/fix_rigid_nvt_small.h index 89b71a1470..39e1a71e75 100644 --- a/src/RIGID/fix_rigid_nvt_small.h +++ b/src/RIGID/fix_rigid_nvt_small.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index d39102f5dc..f0449a00ba 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_rigid_small.h b/src/RIGID/fix_rigid_small.h index e669867e1b..b473026fdb 100644 --- a/src/RIGID/fix_rigid_small.h +++ b/src/RIGID/fix_rigid_small.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp index 82f35eab59..1678a36e02 100644 --- a/src/RIGID/fix_shake.cpp +++ b/src/RIGID/fix_shake.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -869,13 +869,11 @@ void FixShake::find_clusters() // else it's an error flag = 0; - int flag2 = 0; for (i = 0; i < nlocal; i++) for (j = 0; j < npartner[i]; j++) { if (partner_type[i][j] == 0) flag++; if (!(mask[i] & groupbit)) continue; if (!(partner_mask[i][j] & groupbit)) continue; - if (partner_bondtype[i][j] == 0) flag2++; } MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world); diff --git a/src/RIGID/fix_shake.h b/src/RIGID/fix_shake.h index 2cfedcbf29..3e9c213578 100644 --- a/src/RIGID/fix_shake.h +++ b/src/RIGID/fix_shake.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/RIGID/rigid_const.h b/src/RIGID/rigid_const.h index 16f20d567e..690848663c 100644 --- a/src/RIGID/rigid_const.h +++ b/src/RIGID/rigid_const.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SCAFACOS/scafacos.cpp b/src/SCAFACOS/scafacos.cpp index 5e4981663f..d8e5c92ad9 100644 --- a/src/SCAFACOS/scafacos.cpp +++ b/src/SCAFACOS/scafacos.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SCAFACOS/scafacos.h b/src/SCAFACOS/scafacos.h index 2d6cf0b1d4..82e506bedc 100644 --- a/src/SCAFACOS/scafacos.h +++ b/src/SCAFACOS/scafacos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SHOCK/fix_append_atoms.cpp b/src/SHOCK/fix_append_atoms.cpp index 63a3d8c839..9ab788b352 100644 --- a/src/SHOCK/fix_append_atoms.cpp +++ b/src/SHOCK/fix_append_atoms.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SHOCK/fix_append_atoms.h b/src/SHOCK/fix_append_atoms.h index d2118c1975..5fbe9e904b 100644 --- a/src/SHOCK/fix_append_atoms.h +++ b/src/SHOCK/fix_append_atoms.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SHOCK/fix_msst.cpp b/src/SHOCK/fix_msst.cpp index 3b682f7df5..a4c9db3fd7 100644 --- a/src/SHOCK/fix_msst.cpp +++ b/src/SHOCK/fix_msst.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SHOCK/fix_msst.h b/src/SHOCK/fix_msst.h index 96cf8e0e96..8cd3f79a89 100644 --- a/src/SHOCK/fix_msst.h +++ b/src/SHOCK/fix_msst.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SHOCK/fix_nphug.cpp b/src/SHOCK/fix_nphug.cpp index 46a3ccf0ef..0f9bb3ba93 100644 --- a/src/SHOCK/fix_nphug.cpp +++ b/src/SHOCK/fix_nphug.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SHOCK/fix_nphug.h b/src/SHOCK/fix_nphug.h index 80972b5aa2..039f59e19f 100644 --- a/src/SHOCK/fix_nphug.h +++ b/src/SHOCK/fix_nphug.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SHOCK/fix_wall_piston.cpp b/src/SHOCK/fix_wall_piston.cpp index d27a58e6d9..82cec907f4 100644 --- a/src/SHOCK/fix_wall_piston.cpp +++ b/src/SHOCK/fix_wall_piston.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SHOCK/fix_wall_piston.h b/src/SHOCK/fix_wall_piston.h index 3c6908840a..d2eaedae82 100644 --- a/src/SHOCK/fix_wall_piston.h +++ b/src/SHOCK/fix_wall_piston.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SMTBQ/pair_smatb.cpp b/src/SMTBQ/pair_smatb.cpp index 85ae93239a..85446b7a62 100644 --- a/src/SMTBQ/pair_smatb.cpp +++ b/src/SMTBQ/pair_smatb.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SMTBQ/pair_smatb.h b/src/SMTBQ/pair_smatb.h index 198ea10559..7d98d8afd9 100644 --- a/src/SMTBQ/pair_smatb.h +++ b/src/SMTBQ/pair_smatb.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SMTBQ/pair_smatb_single.cpp b/src/SMTBQ/pair_smatb_single.cpp index 426c0a2442..756941b2b7 100644 --- a/src/SMTBQ/pair_smatb_single.cpp +++ b/src/SMTBQ/pair_smatb_single.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SMTBQ/pair_smatb_single.h b/src/SMTBQ/pair_smatb_single.h index 619192b31f..d012cd9ef5 100644 --- a/src/SMTBQ/pair_smatb_single.h +++ b/src/SMTBQ/pair_smatb_single.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SMTBQ/pair_smtbq.cpp b/src/SMTBQ/pair_smtbq.cpp index 988958ca36..494e86a0ad 100644 --- a/src/SMTBQ/pair_smtbq.cpp +++ b/src/SMTBQ/pair_smtbq.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SMTBQ/pair_smtbq.h b/src/SMTBQ/pair_smtbq.h index 2809405697..62d2ea86e5 100644 --- a/src/SMTBQ/pair_smtbq.h +++ b/src/SMTBQ/pair_smtbq.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPH/atom_vec_sph.cpp b/src/SPH/atom_vec_sph.cpp index a26967a57b..8d92558655 100644 --- a/src/SPH/atom_vec_sph.cpp +++ b/src/SPH/atom_vec_sph.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -15,6 +15,8 @@ #include "atom.h" +#include + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/SPH/atom_vec_sph.h b/src/SPH/atom_vec_sph.h index 18d82d76de..e2b15709c5 100644 --- a/src/SPH/atom_vec_sph.h +++ b/src/SPH/atom_vec_sph.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,7 @@ AtomStyle(sph,AtomVecSPH); namespace LAMMPS_NS { -class AtomVecSPH : public AtomVec { +class AtomVecSPH : virtual public AtomVec { public: AtomVecSPH(class LAMMPS *); diff --git a/src/SPH/compute_sph_e_atom.cpp b/src/SPH/compute_sph_e_atom.cpp index 24f81c7997..05e752c49b 100644 --- a/src/SPH/compute_sph_e_atom.cpp +++ b/src/SPH/compute_sph_e_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPH/compute_sph_e_atom.h b/src/SPH/compute_sph_e_atom.h index 00ff5550d7..884678f366 100644 --- a/src/SPH/compute_sph_e_atom.h +++ b/src/SPH/compute_sph_e_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPH/compute_sph_rho_atom.cpp b/src/SPH/compute_sph_rho_atom.cpp index 08d47326e1..9c596bdfc3 100644 --- a/src/SPH/compute_sph_rho_atom.cpp +++ b/src/SPH/compute_sph_rho_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPH/compute_sph_rho_atom.h b/src/SPH/compute_sph_rho_atom.h index a3a366df07..3bd82a3f27 100644 --- a/src/SPH/compute_sph_rho_atom.h +++ b/src/SPH/compute_sph_rho_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPH/compute_sph_t_atom.cpp b/src/SPH/compute_sph_t_atom.cpp index 88e6e3443a..4a83013434 100644 --- a/src/SPH/compute_sph_t_atom.cpp +++ b/src/SPH/compute_sph_t_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPH/compute_sph_t_atom.h b/src/SPH/compute_sph_t_atom.h index 786fb8b063..499061db03 100644 --- a/src/SPH/compute_sph_t_atom.h +++ b/src/SPH/compute_sph_t_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPH/fix_sph.cpp b/src/SPH/fix_sph.cpp index 9711653951..0dafcee7c0 100644 --- a/src/SPH/fix_sph.cpp +++ b/src/SPH/fix_sph.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPH/fix_sph.h b/src/SPH/fix_sph.h index 0bb9f2f965..415e38bd21 100644 --- a/src/SPH/fix_sph.h +++ b/src/SPH/fix_sph.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPH/fix_sph_stationary.cpp b/src/SPH/fix_sph_stationary.cpp index bb3fc6547a..673a7d50bf 100644 --- a/src/SPH/fix_sph_stationary.cpp +++ b/src/SPH/fix_sph_stationary.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPH/fix_sph_stationary.h b/src/SPH/fix_sph_stationary.h index b558aba917..51e336a038 100644 --- a/src/SPH/fix_sph_stationary.h +++ b/src/SPH/fix_sph_stationary.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPH/pair_sph_heatconduction.cpp b/src/SPH/pair_sph_heatconduction.cpp index 7a7a5774bd..cb27982fa3 100644 --- a/src/SPH/pair_sph_heatconduction.cpp +++ b/src/SPH/pair_sph_heatconduction.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPH/pair_sph_heatconduction.h b/src/SPH/pair_sph_heatconduction.h index de35075680..16d1bada7c 100644 --- a/src/SPH/pair_sph_heatconduction.h +++ b/src/SPH/pair_sph_heatconduction.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPH/pair_sph_idealgas.cpp b/src/SPH/pair_sph_idealgas.cpp index 41e0f011b7..114d323bbd 100644 --- a/src/SPH/pair_sph_idealgas.cpp +++ b/src/SPH/pair_sph_idealgas.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPH/pair_sph_idealgas.h b/src/SPH/pair_sph_idealgas.h index a9c1e25b05..3d61d76616 100644 --- a/src/SPH/pair_sph_idealgas.h +++ b/src/SPH/pair_sph_idealgas.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPH/pair_sph_lj.cpp b/src/SPH/pair_sph_lj.cpp index 4ace66809d..d59a3ad992 100644 --- a/src/SPH/pair_sph_lj.cpp +++ b/src/SPH/pair_sph_lj.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPH/pair_sph_lj.h b/src/SPH/pair_sph_lj.h index 7fe51ed39f..47c34159e1 100644 --- a/src/SPH/pair_sph_lj.h +++ b/src/SPH/pair_sph_lj.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPH/pair_sph_rhosum.cpp b/src/SPH/pair_sph_rhosum.cpp index 30fac93036..34adf3ce87 100644 --- a/src/SPH/pair_sph_rhosum.cpp +++ b/src/SPH/pair_sph_rhosum.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPH/pair_sph_rhosum.h b/src/SPH/pair_sph_rhosum.h index f2021360ca..d1e1a95fce 100644 --- a/src/SPH/pair_sph_rhosum.h +++ b/src/SPH/pair_sph_rhosum.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPH/pair_sph_taitwater.cpp b/src/SPH/pair_sph_taitwater.cpp index eb05ab6f93..9a5991718d 100644 --- a/src/SPH/pair_sph_taitwater.cpp +++ b/src/SPH/pair_sph_taitwater.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPH/pair_sph_taitwater.h b/src/SPH/pair_sph_taitwater.h index 40cda898b7..c618469cbe 100644 --- a/src/SPH/pair_sph_taitwater.h +++ b/src/SPH/pair_sph_taitwater.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPH/pair_sph_taitwater_morris.cpp b/src/SPH/pair_sph_taitwater_morris.cpp index 0cbecc1dcb..50fcd270f6 100644 --- a/src/SPH/pair_sph_taitwater_morris.cpp +++ b/src/SPH/pair_sph_taitwater_morris.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPH/pair_sph_taitwater_morris.h b/src/SPH/pair_sph_taitwater_morris.h index 1bd0153b5f..92de298ed9 100644 --- a/src/SPH/pair_sph_taitwater_morris.h +++ b/src/SPH/pair_sph_taitwater_morris.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp index 209704fef8..9a7e4c6aac 100644 --- a/src/SPIN/atom_vec_spin.cpp +++ b/src/SPIN/atom_vec_spin.cpp @@ -2,7 +2,7 @@ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -28,6 +28,7 @@ #include "atom.h" #include +#include using namespace LAMMPS_NS; diff --git a/src/SPIN/atom_vec_spin.h b/src/SPIN/atom_vec_spin.h index c6ce33a10e..bf11d5856e 100644 --- a/src/SPIN/atom_vec_spin.h +++ b/src/SPIN/atom_vec_spin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,7 @@ AtomStyle(spin,AtomVecSpin); namespace LAMMPS_NS { -class AtomVecSpin : public AtomVec { +class AtomVecSpin : virtual public AtomVec { public: AtomVecSpin(class LAMMPS *); @@ -32,7 +32,7 @@ class AtomVecSpin : public AtomVec { void force_clear(int, size_t) override; void data_atom_post(int) override; - private: + protected: double **sp, **fm, **fm_long; }; diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp index b674598265..1c92d284f0 100644 --- a/src/SPIN/compute_spin.cpp +++ b/src/SPIN/compute_spin.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/compute_spin.h b/src/SPIN/compute_spin.h index 45aac3c89f..9c90b1951e 100644 --- a/src/SPIN/compute_spin.h +++ b/src/SPIN/compute_spin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp index 397c3c618f..6fa29f705d 100644 --- a/src/SPIN/fix_langevin_spin.cpp +++ b/src/SPIN/fix_langevin_spin.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/fix_langevin_spin.h b/src/SPIN/fix_langevin_spin.h index 478ad09c94..ddf2bc9790 100644 --- a/src/SPIN/fix_langevin_spin.h +++ b/src/SPIN/fix_langevin_spin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/fix_neb_spin.cpp b/src/SPIN/fix_neb_spin.cpp index 0a96227c46..ea8ce9c1fc 100644 --- a/src/SPIN/fix_neb_spin.cpp +++ b/src/SPIN/fix_neb_spin.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/fix_neb_spin.h b/src/SPIN/fix_neb_spin.h index 86e633b3b2..e621b7579d 100644 --- a/src/SPIN/fix_neb_spin.h +++ b/src/SPIN/fix_neb_spin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index 20240ab2ea..297e81b424 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/fix_nve_spin.h b/src/SPIN/fix_nve_spin.h index d1b03b2518..ab7a0b415b 100644 --- a/src/SPIN/fix_nve_spin.h +++ b/src/SPIN/fix_nve_spin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp index 8902857433..486ece82b2 100644 --- a/src/SPIN/fix_precession_spin.cpp +++ b/src/SPIN/fix_precession_spin.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/fix_precession_spin.h b/src/SPIN/fix_precession_spin.h index cd891f8670..b578079a7e 100644 --- a/src/SPIN/fix_precession_spin.h +++ b/src/SPIN/fix_precession_spin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/fix_setforce_spin.cpp b/src/SPIN/fix_setforce_spin.cpp index a88a84f0bb..156fe6afbe 100644 --- a/src/SPIN/fix_setforce_spin.cpp +++ b/src/SPIN/fix_setforce_spin.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,6 @@ #include "fix_setforce_spin.h" #include "atom.h" -#include "domain.h" #include "input.h" #include "memory.h" #include "modify.h" diff --git a/src/SPIN/fix_setforce_spin.h b/src/SPIN/fix_setforce_spin.h index b927d1bee3..c8855e14f7 100644 --- a/src/SPIN/fix_setforce_spin.h +++ b/src/SPIN/fix_setforce_spin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/min_spin.cpp b/src/SPIN/min_spin.cpp index 4f28db2296..a2202cba32 100644 --- a/src/SPIN/min_spin.cpp +++ b/src/SPIN/min_spin.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/min_spin.h b/src/SPIN/min_spin.h index 14117d9189..d9cb0be7d1 100644 --- a/src/SPIN/min_spin.h +++ b/src/SPIN/min_spin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/min_spin_cg.cpp b/src/SPIN/min_spin_cg.cpp index 84540a4a7f..06e829fc85 100644 --- a/src/SPIN/min_spin_cg.cpp +++ b/src/SPIN/min_spin_cg.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/min_spin_cg.h b/src/SPIN/min_spin_cg.h index 581a343233..7ea0fc1905 100644 --- a/src/SPIN/min_spin_cg.h +++ b/src/SPIN/min_spin_cg.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/min_spin_lbfgs.cpp b/src/SPIN/min_spin_lbfgs.cpp index 9972af0a7a..58bdf72899 100644 --- a/src/SPIN/min_spin_lbfgs.cpp +++ b/src/SPIN/min_spin_lbfgs.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/min_spin_lbfgs.h b/src/SPIN/min_spin_lbfgs.h index bc8ae42567..cd3a051208 100644 --- a/src/SPIN/min_spin_lbfgs.h +++ b/src/SPIN/min_spin_lbfgs.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/neb_spin.cpp b/src/SPIN/neb_spin.cpp index c67ba36d59..fa42fc7a57 100644 --- a/src/SPIN/neb_spin.cpp +++ b/src/SPIN/neb_spin.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/neb_spin.h b/src/SPIN/neb_spin.h index 544d2c7c63..3491dfb32b 100644 --- a/src/SPIN/neb_spin.h +++ b/src/SPIN/neb_spin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/pair_spin.cpp b/src/SPIN/pair_spin.cpp index 4ee6110659..909d9a977a 100644 --- a/src/SPIN/pair_spin.cpp +++ b/src/SPIN/pair_spin.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -32,7 +32,6 @@ #include "math_const.h" #include "memory.h" #include "modify.h" -#include "neigh_request.h" #include "neighbor.h" #include "pair.h" #include "update.h" diff --git a/src/SPIN/pair_spin.h b/src/SPIN/pair_spin.h index 03756236be..de2888f8e2 100644 --- a/src/SPIN/pair_spin.h +++ b/src/SPIN/pair_spin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/pair_spin_dipole_cut.cpp b/src/SPIN/pair_spin_dipole_cut.cpp index b4e1e17b88..8470bbcfcc 100644 --- a/src/SPIN/pair_spin_dipole_cut.cpp +++ b/src/SPIN/pair_spin_dipole_cut.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + LAMMPS development team: developers@lammps.org, Sandia National Laboratories Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/pair_spin_dipole_cut.h b/src/SPIN/pair_spin_dipole_cut.h index dd21d68374..891f40d522 100644 --- a/src/SPIN/pair_spin_dipole_cut.h +++ b/src/SPIN/pair_spin_dipole_cut.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - www.cs.sandia.gov/~sjplimp/lammps.html - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/pair_spin_dipole_long.cpp b/src/SPIN/pair_spin_dipole_long.cpp index e551f7c4fe..b125d2b49a 100644 --- a/src/SPIN/pair_spin_dipole_long.cpp +++ b/src/SPIN/pair_spin_dipole_long.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + LAMMPS development team: developers@lammps.org, Sandia National Laboratories Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/pair_spin_dipole_long.h b/src/SPIN/pair_spin_dipole_long.h index c3337327ff..6d2d9610f7 100644 --- a/src/SPIN/pair_spin_dipole_long.h +++ b/src/SPIN/pair_spin_dipole_long.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - www.cs.sandia.gov/~sjplimp/lammps.html - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp index 2b1fd39a05..6dec238163 100644 --- a/src/SPIN/pair_spin_dmi.cpp +++ b/src/SPIN/pair_spin_dmi.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/pair_spin_dmi.h b/src/SPIN/pair_spin_dmi.h index bddb1ea652..560b57ab72 100644 --- a/src/SPIN/pair_spin_dmi.h +++ b/src/SPIN/pair_spin_dmi.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp index 329ad5e100..b113b17d10 100644 --- a/src/SPIN/pair_spin_exchange.cpp +++ b/src/SPIN/pair_spin_exchange.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/pair_spin_exchange.h b/src/SPIN/pair_spin_exchange.h index 1631cdd7f9..568b07b755 100644 --- a/src/SPIN/pair_spin_exchange.h +++ b/src/SPIN/pair_spin_exchange.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/pair_spin_exchange_biquadratic.cpp b/src/SPIN/pair_spin_exchange_biquadratic.cpp index fb727e1939..51df3294d7 100644 --- a/src/SPIN/pair_spin_exchange_biquadratic.cpp +++ b/src/SPIN/pair_spin_exchange_biquadratic.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/pair_spin_exchange_biquadratic.h b/src/SPIN/pair_spin_exchange_biquadratic.h index b14cc4c11b..0030362991 100644 --- a/src/SPIN/pair_spin_exchange_biquadratic.h +++ b/src/SPIN/pair_spin_exchange_biquadratic.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/pair_spin_magelec.cpp b/src/SPIN/pair_spin_magelec.cpp index 5ea66e7d7d..3d22a652b3 100644 --- a/src/SPIN/pair_spin_magelec.cpp +++ b/src/SPIN/pair_spin_magelec.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/pair_spin_magelec.h b/src/SPIN/pair_spin_magelec.h index 0041e9e4a5..d1d920b8ae 100644 --- a/src/SPIN/pair_spin_magelec.h +++ b/src/SPIN/pair_spin_magelec.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/pair_spin_neel.cpp b/src/SPIN/pair_spin_neel.cpp index 78717777d4..a9ed7d6966 100644 --- a/src/SPIN/pair_spin_neel.cpp +++ b/src/SPIN/pair_spin_neel.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SPIN/pair_spin_neel.h b/src/SPIN/pair_spin_neel.h index 7be0f718a3..10a8e8b993 100644 --- a/src/SPIN/pair_spin_neel.h +++ b/src/SPIN/pair_spin_neel.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp index 544c92a702..0822b4a9f9 100644 --- a/src/SRD/fix_srd.cpp +++ b/src/SRD/fix_srd.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -355,7 +355,7 @@ void FixSRD::init() error->all(FLERR, "Fix srd no-slip requires atom attribute torque"); if (initflag && update->dt != dt_big) error->all(FLERR, "Cannot change timestep once fix srd is setup"); - if (comm->style != 0) + if (comm->style != Comm::BRICK) error->universe_all(FLERR, "Fix srd can only currently be used with comm_style brick"); // orthogonal vs triclinic simulation box diff --git a/src/SRD/fix_srd.h b/src/SRD/fix_srd.h index 9088999f3e..1a06b7cae4 100644 --- a/src/SRD/fix_srd.h +++ b/src/SRD/fix_srd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SRD/fix_wall_srd.cpp b/src/SRD/fix_wall_srd.cpp index d284aaa0ad..ccce252e5d 100644 --- a/src/SRD/fix_wall_srd.cpp +++ b/src/SRD/fix_wall_srd.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/SRD/fix_wall_srd.h b/src/SRD/fix_wall_srd.h index e93f6920a1..3a96a73be4 100644 --- a/src/SRD/fix_wall_srd.h +++ b/src/SRD/fix_wall_srd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/STUBS/mpi.cpp b/src/STUBS/mpi.cpp index e914063889..53b83236ba 100644 --- a/src/STUBS/mpi.cpp +++ b/src/STUBS/mpi.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -19,7 +19,6 @@ #include #include -#include #include #if defined(_WIN32) diff --git a/src/STUBS/mpi.h b/src/STUBS/mpi.h index 1d0ab8413d..71da393642 100644 --- a/src/STUBS/mpi.h +++ b/src/STUBS/mpi.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ----------------------------------------------------------- - LAMMPS 2003 (July 31) - Molecular Dynamics Simulator - Sandia National Laboratories, www.cs.sandia.gov/~sjplimp/lammps.html - Steve Plimpton, sjplimp@sandia.gov + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/TALLY/compute_force_tally.cpp b/src/TALLY/compute_force_tally.cpp index 052bb267fa..8346edf928 100644 --- a/src/TALLY/compute_force_tally.cpp +++ b/src/TALLY/compute_force_tally.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/TALLY/compute_force_tally.h b/src/TALLY/compute_force_tally.h index 9cddb6ed15..d639d691bc 100644 --- a/src/TALLY/compute_force_tally.h +++ b/src/TALLY/compute_force_tally.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/TALLY/compute_heat_flux_tally.cpp b/src/TALLY/compute_heat_flux_tally.cpp index 5a2211216e..2af809af22 100644 --- a/src/TALLY/compute_heat_flux_tally.cpp +++ b/src/TALLY/compute_heat_flux_tally.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/TALLY/compute_heat_flux_tally.h b/src/TALLY/compute_heat_flux_tally.h index d7296e36d7..5afc79f446 100644 --- a/src/TALLY/compute_heat_flux_tally.h +++ b/src/TALLY/compute_heat_flux_tally.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/TALLY/compute_heat_flux_virial_tally.cpp b/src/TALLY/compute_heat_flux_virial_tally.cpp index 1eac3ac307..29d409c660 100644 --- a/src/TALLY/compute_heat_flux_virial_tally.cpp +++ b/src/TALLY/compute_heat_flux_virial_tally.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/TALLY/compute_heat_flux_virial_tally.h b/src/TALLY/compute_heat_flux_virial_tally.h index d4e9064791..0386d73e5c 100644 --- a/src/TALLY/compute_heat_flux_virial_tally.h +++ b/src/TALLY/compute_heat_flux_virial_tally.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/TALLY/compute_pe_mol_tally.cpp b/src/TALLY/compute_pe_mol_tally.cpp index 7267272c99..b4f2ccd832 100644 --- a/src/TALLY/compute_pe_mol_tally.cpp +++ b/src/TALLY/compute_pe_mol_tally.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/TALLY/compute_pe_mol_tally.h b/src/TALLY/compute_pe_mol_tally.h index 73e188088e..9a83066cd6 100644 --- a/src/TALLY/compute_pe_mol_tally.h +++ b/src/TALLY/compute_pe_mol_tally.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/TALLY/compute_pe_tally.cpp b/src/TALLY/compute_pe_tally.cpp index bc31890dcc..d6af993afe 100644 --- a/src/TALLY/compute_pe_tally.cpp +++ b/src/TALLY/compute_pe_tally.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/TALLY/compute_pe_tally.h b/src/TALLY/compute_pe_tally.h index ad7658e0f2..db4287cc5e 100644 --- a/src/TALLY/compute_pe_tally.h +++ b/src/TALLY/compute_pe_tally.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/TALLY/compute_stress_tally.cpp b/src/TALLY/compute_stress_tally.cpp index ea9a02b6ee..f04640a2d2 100644 --- a/src/TALLY/compute_stress_tally.cpp +++ b/src/TALLY/compute_stress_tally.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/TALLY/compute_stress_tally.h b/src/TALLY/compute_stress_tally.h index 4bf29dfd42..c836aa132f 100644 --- a/src/TALLY/compute_stress_tally.h +++ b/src/TALLY/compute_stress_tally.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/UEF/compute_pressure_uef.cpp b/src/UEF/compute_pressure_uef.cpp index feb524904d..16fe6137bf 100644 --- a/src/UEF/compute_pressure_uef.cpp +++ b/src/UEF/compute_pressure_uef.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/UEF/compute_pressure_uef.h b/src/UEF/compute_pressure_uef.h index 391fd60f9b..588a39f759 100644 --- a/src/UEF/compute_pressure_uef.h +++ b/src/UEF/compute_pressure_uef.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/UEF/compute_temp_uef.cpp b/src/UEF/compute_temp_uef.cpp index 9b7e83f920..4ca84b2044 100644 --- a/src/UEF/compute_temp_uef.cpp +++ b/src/UEF/compute_temp_uef.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/UEF/compute_temp_uef.h b/src/UEF/compute_temp_uef.h index 3bee5e9f3c..f17d575ddd 100644 --- a/src/UEF/compute_temp_uef.h +++ b/src/UEF/compute_temp_uef.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/UEF/dump_cfg_uef.cpp b/src/UEF/dump_cfg_uef.cpp index f5803b499b..d72225b238 100644 --- a/src/UEF/dump_cfg_uef.cpp +++ b/src/UEF/dump_cfg_uef.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/UEF/dump_cfg_uef.h b/src/UEF/dump_cfg_uef.h index 20fbab5d7e..c1b3be9514 100644 --- a/src/UEF/dump_cfg_uef.h +++ b/src/UEF/dump_cfg_uef.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/UEF/fix_nh_uef.cpp b/src/UEF/fix_nh_uef.cpp index ac866e945e..b8b1fd07d6 100644 --- a/src/UEF/fix_nh_uef.cpp +++ b/src/UEF/fix_nh_uef.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + LAMMPS development team: developers@lammps.org, Sandia National Laboratories Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/UEF/fix_nh_uef.h b/src/UEF/fix_nh_uef.h index 02e9fd05e8..b7bce8f502 100644 --- a/src/UEF/fix_nh_uef.h +++ b/src/UEF/fix_nh_uef.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - www.cs.sandia.gov/~sjplimp/lammps.html - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/UEF/fix_npt_uef.cpp b/src/UEF/fix_npt_uef.cpp index cc7b14c015..54ea4ef98f 100644 --- a/src/UEF/fix_npt_uef.cpp +++ b/src/UEF/fix_npt_uef.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/UEF/fix_npt_uef.h b/src/UEF/fix_npt_uef.h index 665c96f06e..2008492685 100644 --- a/src/UEF/fix_npt_uef.h +++ b/src/UEF/fix_npt_uef.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/UEF/fix_nvt_uef.cpp b/src/UEF/fix_nvt_uef.cpp index fee8f711fa..b0cb92f838 100644 --- a/src/UEF/fix_nvt_uef.cpp +++ b/src/UEF/fix_nvt_uef.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/UEF/fix_nvt_uef.h b/src/UEF/fix_nvt_uef.h index 9dd26a8905..3f83cfd967 100644 --- a/src/UEF/fix_nvt_uef.h +++ b/src/UEF/fix_nvt_uef.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/UEF/uef_utils.cpp b/src/UEF/uef_utils.cpp index 68829c9e78..d8e65eab91 100644 --- a/src/UEF/uef_utils.cpp +++ b/src/UEF/uef_utils.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/UEF/uef_utils.h b/src/UEF/uef_utils.h index 073fbf6d0a..5f18431670 100644 --- a/src/UEF/uef_utils.h +++ b/src/UEF/uef_utils.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/VORONOI/Install.sh b/src/VORONOI/Install.sh index 6373506b19..c7f897e5e6 100755 --- a/src/VORONOI/Install.sh +++ b/src/VORONOI/Install.sh @@ -48,7 +48,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*voronoi.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*voronoi.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/voronoi\/Makefile.lammps @@ -63,7 +63,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*voronoi.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*voronoi.*$/d' ../Makefile.package.settings fi fi diff --git a/src/VORONOI/compute_voronoi_atom.cpp b/src/VORONOI/compute_voronoi_atom.cpp index c95d8da491..d2f60a8586 100644 --- a/src/VORONOI/compute_voronoi_atom.cpp +++ b/src/VORONOI/compute_voronoi_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/VORONOI/compute_voronoi_atom.h b/src/VORONOI/compute_voronoi_atom.h index 0a60b5b224..fbcf14c9bc 100644 --- a/src/VORONOI/compute_voronoi_atom.h +++ b/src/VORONOI/compute_voronoi_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/VTK/Install.sh b/src/VTK/Install.sh index 3749242fb2..fda4287d51 100755 --- a/src/VTK/Install.sh +++ b/src/VTK/Install.sh @@ -43,7 +43,7 @@ if (test $1 = 1) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*vtk.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*vtk.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/vtk\/Makefile.lammps @@ -58,7 +58,7 @@ elif (test $1 = 0) then fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*vtk.*$/d' ../Makefile.package.settings + sed -i -e '/^[ \t]*include.*vtk.*$/d' ../Makefile.package.settings fi fi diff --git a/src/VTK/dump_vtk.cpp b/src/VTK/dump_vtk.cpp index 61897735c7..4b26086c3b 100644 --- a/src/VTK/dump_vtk.cpp +++ b/src/VTK/dump_vtk.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/VTK/dump_vtk.h b/src/VTK/dump_vtk.h index 264becfff6..8db08ae82a 100644 --- a/src/VTK/dump_vtk.h +++ b/src/VTK/dump_vtk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/YAFF/angle_cross.cpp b/src/YAFF/angle_cross.cpp index 7ba687ca34..46833b7f74 100644 --- a/src/YAFF/angle_cross.cpp +++ b/src/YAFF/angle_cross.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/YAFF/angle_cross.h b/src/YAFF/angle_cross.h index b371e525a9..fea7c0fbc4 100644 --- a/src/YAFF/angle_cross.h +++ b/src/YAFF/angle_cross.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/YAFF/angle_mm3.cpp b/src/YAFF/angle_mm3.cpp index 9bfce2a841..c75a0d8308 100644 --- a/src/YAFF/angle_mm3.cpp +++ b/src/YAFF/angle_mm3.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/YAFF/angle_mm3.h b/src/YAFF/angle_mm3.h index ef9d88d4c9..95009a9cf6 100644 --- a/src/YAFF/angle_mm3.h +++ b/src/YAFF/angle_mm3.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/YAFF/bond_mm3.cpp b/src/YAFF/bond_mm3.cpp index 7d6cb7cfff..a5ef6fb8bc 100644 --- a/src/YAFF/bond_mm3.cpp +++ b/src/YAFF/bond_mm3.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/YAFF/bond_mm3.h b/src/YAFF/bond_mm3.h index 48ab6d28cc..302c4052d0 100644 --- a/src/YAFF/bond_mm3.h +++ b/src/YAFF/bond_mm3.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/YAFF/improper_distharm.cpp b/src/YAFF/improper_distharm.cpp index 3a176c1f23..3e67b6a436 100644 --- a/src/YAFF/improper_distharm.cpp +++ b/src/YAFF/improper_distharm.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/YAFF/improper_distharm.h b/src/YAFF/improper_distharm.h index ebc4c701d5..911bbadb0d 100644 --- a/src/YAFF/improper_distharm.h +++ b/src/YAFF/improper_distharm.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/YAFF/improper_sqdistharm.cpp b/src/YAFF/improper_sqdistharm.cpp index f542ec5f6c..1b366c058f 100644 --- a/src/YAFF/improper_sqdistharm.cpp +++ b/src/YAFF/improper_sqdistharm.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/YAFF/improper_sqdistharm.h b/src/YAFF/improper_sqdistharm.h index e7a1e62661..4cd89a294e 100644 --- a/src/YAFF/improper_sqdistharm.h +++ b/src/YAFF/improper_sqdistharm.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/YAFF/pair_lj_switch3_coulgauss_long.cpp index 5a3102a96f..0aed883dd6 100644 --- a/src/YAFF/pair_lj_switch3_coulgauss_long.cpp +++ b/src/YAFF/pair_lj_switch3_coulgauss_long.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/YAFF/pair_lj_switch3_coulgauss_long.h b/src/YAFF/pair_lj_switch3_coulgauss_long.h index cb831ed021..01e8cde6be 100644 --- a/src/YAFF/pair_lj_switch3_coulgauss_long.h +++ b/src/YAFF/pair_lj_switch3_coulgauss_long.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/YAFF/pair_mm3_switch3_coulgauss_long.cpp b/src/YAFF/pair_mm3_switch3_coulgauss_long.cpp index 85908d4d81..e68d53cb21 100644 --- a/src/YAFF/pair_mm3_switch3_coulgauss_long.cpp +++ b/src/YAFF/pair_mm3_switch3_coulgauss_long.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/YAFF/pair_mm3_switch3_coulgauss_long.h b/src/YAFF/pair_mm3_switch3_coulgauss_long.h index 3c6d1f019c..2b04728bdb 100644 --- a/src/YAFF/pair_mm3_switch3_coulgauss_long.h +++ b/src/YAFF/pair_mm3_switch3_coulgauss_long.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/accelerator_kokkos.h b/src/accelerator_kokkos.h index a6cfdd12df..c064d73728 100644 --- a/src/accelerator_kokkos.h +++ b/src/accelerator_kokkos.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/accelerator_omp.h b/src/accelerator_omp.h index 0a85816684..a0b294b57c 100644 --- a/src/accelerator_omp.h +++ b/src/accelerator_omp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/angle.cpp b/src/angle.cpp index 7044459f9f..93d217237e 100644 --- a/src/angle.cpp +++ b/src/angle.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/angle.h b/src/angle.h index 5abc31bc81..542bad4911 100644 --- a/src/angle.h +++ b/src/angle.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/angle_deprecated.cpp b/src/angle_deprecated.cpp index 60cdab3398..eaf50387c3 100644 --- a/src/angle_deprecated.cpp +++ b/src/angle_deprecated.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/angle_deprecated.h b/src/angle_deprecated.h index 51c5cdc0ab..01c9fc2c7e 100644 --- a/src/angle_deprecated.h +++ b/src/angle_deprecated.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/angle_hybrid.cpp b/src/angle_hybrid.cpp index b3ca095795..7419139942 100644 --- a/src/angle_hybrid.cpp +++ b/src/angle_hybrid.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -20,7 +20,6 @@ #include "memory.h" #include "neighbor.h" -#include #include using namespace LAMMPS_NS; @@ -306,6 +305,16 @@ void AngleHybrid::coeff(int narg, char **arg) void AngleHybrid::init_style() { + // error if sub-style is not used + + int used; + for (int istyle = 0; istyle < nstyles; ++istyle) { + used = 0; + for (int itype = 1; itype <= atom->nangletypes; ++itype) + if (map[itype] == istyle) used = 1; + if (used == 0) error->all(FLERR, "Angle hybrid sub-style {} is not used", keywords[istyle]); + } + for (int m = 0; m < nstyles; m++) if (styles[m]) styles[m]->init_style(); } diff --git a/src/angle_hybrid.h b/src/angle_hybrid.h index c66952208b..474ce89673 100644 --- a/src/angle_hybrid.h +++ b/src/angle_hybrid.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/angle_zero.cpp b/src/angle_zero.cpp index 53f5176d30..aad7f36d05 100644 --- a/src/angle_zero.cpp +++ b/src/angle_zero.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/angle_zero.h b/src/angle_zero.h index 2306fd4085..85638a6f9a 100644 --- a/src/angle_zero.h +++ b/src/angle_zero.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/arg_info.cpp b/src/arg_info.cpp index 86becc1da5..2a20bea945 100644 --- a/src/arg_info.cpp +++ b/src/arg_info.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/arg_info.h b/src/arg_info.h index e9d976db8d..5045c70fcf 100644 --- a/src/arg_info.h +++ b/src/arg_info.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/atom.cpp b/src/atom.cpp index 0fde1d3f8b..947023b496 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -680,7 +680,8 @@ void Atom::create_avec(const std::string &style, int narg, char **arg, int trysu if (sflag) { std::string estyle = style + "/"; if (sflag == 1) estyle += lmp->suffix; - else estyle += lmp->suffix2; + else if (sflag == 2) estyle += lmp->suffix2; + else if (sflag == 3) estyle += lmp->non_pair_suffix(); atom_style = utils::strdup(estyle); } else { atom_style = utils::strdup(style); @@ -704,9 +705,9 @@ void Atom::create_avec(const std::string &style, int narg, char **arg, int trysu AtomVec *Atom::new_avec(const std::string &style, int trysuffix, int &sflag) { if (trysuffix && lmp->suffix_enable) { - if (lmp->suffix) { - sflag = 1; - std::string estyle = style + "/" + lmp->suffix; + if (lmp->non_pair_suffix()) { + sflag = 1 + 2*lmp->pair_only_flag; + std::string estyle = style + "/" + lmp->non_pair_suffix(); if (avec_map->find(estyle) != avec_map->end()) { AtomVecCreator &avec_creator = (*avec_map)[estyle]; return avec_creator(lmp); @@ -2470,7 +2471,7 @@ void Atom::setup_sort_bins() /* ---------------------------------------------------------------------- register a callback to a fix so it can manage atom-based arrays happens when fix is created - flag = 0 for grow, 1 for restart, 2 for border comm + flag = Atom::GROW for grow, Atom::RESTART for restart, Atom::BORDER for border comm ------------------------------------------------------------------------- */ void Atom::add_callback(int flag) diff --git a/src/atom.h b/src/atom.h index 61ae0d047b..2e663c628a 100644 --- a/src/atom.h +++ b/src/atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -21,9 +21,10 @@ namespace LAMMPS_NS { -// forward declaration +// forward declarations class AtomVec; +class Molecule; class Atom : protected Pointers { public: @@ -252,7 +253,7 @@ class Atom : protected Pointers { // 1st molecule in template stores nset = # in set int nmolecule; - class Molecule **molecules; + Molecule **molecules; // type label maps @@ -354,7 +355,7 @@ class Atom : protected Pointers { void add_molecule(int, char **); int find_molecule(const char *); std::vector get_molecule_by_id(const std::string &); - void add_molecule_atom(class Molecule *, int, int, tagint); + void add_molecule_atom(Molecule *, int, int, tagint); void add_label_map(); diff --git a/src/atom_map.cpp b/src/atom_map.cpp index 2eb4a08ea6..0cfed5a595 100644 --- a/src/atom_map.cpp +++ b/src/atom_map.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/atom_map.h b/src/atom_map.h index 1a1bf3fe84..987e6f96c9 100644 --- a/src/atom_map.h +++ b/src/atom_map.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/atom_masks.h b/src/atom_masks.h index 00ad0e6e0f..f94ecd6cbd 100644 --- a/src/atom_masks.h +++ b/src/atom_masks.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index 586235d088..bfda951823 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -20,12 +20,8 @@ #include "fix.h" #include "force.h" #include "label_map.h" -#include "math_const.h" #include "memory.h" #include "modify.h" -#include "tokenizer.h" - -#include using namespace LAMMPS_NS; diff --git a/src/atom_vec.h b/src/atom_vec.h index 8101eadcc0..a4db054752 100644 --- a/src/atom_vec.h +++ b/src/atom_vec.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -157,21 +157,6 @@ class AtomVec : protected Pointers { virtual double memory_usage(); virtual double memory_usage_bonus() { return 0; } - // old hybrid functions, needed by Kokkos package - - virtual int pack_comm_hybrid(int, int *, double *) { return 0; } - virtual int unpack_comm_hybrid(int, int, double *) { return 0; } - virtual int pack_reverse_hybrid(int, int, double *) { return 0; } - virtual int unpack_reverse_hybrid(int, int *, double *) { return 0; } - virtual int pack_border_hybrid(int, int *, double *) { return 0; } - virtual int unpack_border_hybrid(int, int, double *) { return 0; } - virtual int data_atom_hybrid(int, const std::vector &, int) { return 0; } - virtual int data_vel_hybrid(int, const std::vector &, int) { return 0; } - virtual int pack_data_hybrid(int, double *) { return 0; } - virtual int write_data_hybrid(FILE *, double *) { return 0; } - virtual int pack_vel_hybrid(int, double *) { return 0; } - virtual int write_vel_hybrid(FILE *, double *) { return 0; } - protected: int nmax; // local copy of atom->nmax int deform_vremap; // local copy of domain properties diff --git a/src/atom_vec_atomic.cpp b/src/atom_vec_atomic.cpp index 44fb7d2fee..30c67a56f3 100644 --- a/src/atom_vec_atomic.cpp +++ b/src/atom_vec_atomic.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/atom_vec_atomic.h b/src/atom_vec_atomic.h index cba25e11ec..6fdd570c2e 100644 --- a/src/atom_vec_atomic.h +++ b/src/atom_vec_atomic.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,7 @@ AtomStyle(atomic,AtomVecAtomic); namespace LAMMPS_NS { -class AtomVecAtomic : public AtomVec { +class AtomVecAtomic : virtual public AtomVec { public: AtomVecAtomic(class LAMMPS *); }; diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index 0726468c4f..538e9783df 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -22,6 +22,8 @@ #include "modify.h" #include "my_pool_chunk.h" +#include + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/atom_vec_body.h b/src/atom_vec_body.h index f9a4df9a31..e02fd3bbb0 100644 --- a/src/atom_vec_body.h +++ b/src/atom_vec_body.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/atom_vec_charge.cpp b/src/atom_vec_charge.cpp index 73164b6273..e3a558cd12 100644 --- a/src/atom_vec_charge.cpp +++ b/src/atom_vec_charge.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/atom_vec_charge.h b/src/atom_vec_charge.h index 40bfb5622c..2953b7cfcb 100644 --- a/src/atom_vec_charge.h +++ b/src/atom_vec_charge.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,7 @@ AtomStyle(charge,AtomVecCharge); namespace LAMMPS_NS { -class AtomVecCharge : public AtomVec { +class AtomVecCharge : virtual public AtomVec { public: AtomVecCharge(class LAMMPS *); }; diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp index cae0d1bc11..59b8310d3f 100644 --- a/src/atom_vec_ellipsoid.cpp +++ b/src/atom_vec_ellipsoid.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -25,6 +25,8 @@ #include "memory.h" #include "modify.h" +#include + using namespace LAMMPS_NS; using MathConst::MY_PI; diff --git a/src/atom_vec_ellipsoid.h b/src/atom_vec_ellipsoid.h index 0fb3ac2f71..6e06d773fc 100644 --- a/src/atom_vec_ellipsoid.h +++ b/src/atom_vec_ellipsoid.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp index c4f6711db0..c81ea56202 100644 --- a/src/atom_vec_hybrid.cpp +++ b/src/atom_vec_hybrid.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -16,7 +16,6 @@ #include "atom.h" #include "comm.h" #include "error.h" -#include "tokenizer.h" #include #include diff --git a/src/atom_vec_hybrid.h b/src/atom_vec_hybrid.h index 913b3c8fea..afe44bae6e 100644 --- a/src/atom_vec_hybrid.h +++ b/src/atom_vec_hybrid.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,7 @@ AtomStyle(hybrid,AtomVecHybrid); namespace LAMMPS_NS { -class AtomVecHybrid : public AtomVec { +class AtomVecHybrid : virtual public AtomVec { public: int nstyles; class AtomVec **styles; diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp index 2f05684c69..ff09bed6d0 100644 --- a/src/atom_vec_line.cpp +++ b/src/atom_vec_line.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -22,6 +22,7 @@ #include "modify.h" #include +#include using namespace LAMMPS_NS; using MathConst::MY_PI; diff --git a/src/atom_vec_line.h b/src/atom_vec_line.h index 2d4969b1bf..740c541916 100644 --- a/src/atom_vec_line.h +++ b/src/atom_vec_line.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp index 2a3c58e77e..d2f9c51880 100644 --- a/src/atom_vec_sphere.cpp +++ b/src/atom_vec_sphere.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -20,6 +20,8 @@ #include "math_const.h" #include "modify.h" +#include + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/atom_vec_sphere.h b/src/atom_vec_sphere.h index 619c1f6851..88a879d611 100644 --- a/src/atom_vec_sphere.h +++ b/src/atom_vec_sphere.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,7 @@ AtomStyle(sphere,AtomVecSphere); namespace LAMMPS_NS { -class AtomVecSphere : public AtomVec { +class AtomVecSphere : virtual public AtomVec { public: AtomVecSphere(class LAMMPS *); void process_args(int, char **) override; @@ -36,7 +36,7 @@ class AtomVecSphere : public AtomVec { void pack_data_pre(int) override; void pack_data_post(int) override; - private: + protected: double *radius, *rmass; double **omega; diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp index 4dbd0dd677..a46609b02c 100644 --- a/src/atom_vec_tri.cpp +++ b/src/atom_vec_tri.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,6 +24,7 @@ #include "modify.h" #include +#include using namespace LAMMPS_NS; using MathConst::MY_PI; diff --git a/src/atom_vec_tri.h b/src/atom_vec_tri.h index d9e56f438f..424bd8ea0a 100644 --- a/src/atom_vec_tri.h +++ b/src/atom_vec_tri.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/balance.cpp b/src/balance.cpp index c67e561738..ac609cce5d 100644 --- a/src/balance.cpp +++ b/src/balance.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -27,6 +27,7 @@ #include "comm.h" #include "domain.h" #include "fix_store_peratom.h" +#include "force.h" #include "imbalance.h" #include "imbalance_group.h" #include "imbalance_neigh.h" @@ -36,6 +37,7 @@ #include "irregular.h" #include "memory.h" #include "modify.h" +#include "pair.h" #include "rcb.h" #include "error.h" @@ -245,7 +247,7 @@ void Balance::command(int narg, char **arg) } } - if (style == BISECTION && comm->style == 0) + if (style == BISECTION && comm->style == Comm::BRICK) error->all(FLERR,"Balance rcb cannot be used with comm_style brick"); // process remaining optional args @@ -366,6 +368,13 @@ void Balance::command(int narg, char **arg) if (outflag) dumpout(update->ntimestep); + // notify all classes that store distributed grids + // so they can adjust to new proc sub-domains + // no need to invoke kspace->reset_grid() b/c it does this in its init() + + modify->reset_grid(); + if (force->pair) force->pair->reset_grid(); + // check if any particles were lost bigint natoms; diff --git a/src/balance.h b/src/balance.h index 29870ea52a..a21f8992f2 100644 --- a/src/balance.h +++ b/src/balance.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/body.cpp b/src/body.cpp index f59acdfc66..8ef1da0111 100644 --- a/src/body.cpp +++ b/src/body.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/body.h b/src/body.h index 9911c425ff..3a9cb283c6 100644 --- a/src/body.h +++ b/src/body.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/bond.cpp b/src/bond.cpp index 1a184e1ed1..99e95124e3 100644 --- a/src/bond.cpp +++ b/src/bond.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -255,11 +255,10 @@ void Bond::ev_tally(int i, int j, int nlocal, int newton_bond, double ebond, dou for virial, have delx,dely,delz and fx,fy,fz ------------------------------------------------------------------------- */ -void Bond::ev_tally_xyz(int i, int j, int nlocal, int newton_bond, - double ebond, double fx, double fy, double fz, - double delx, double dely, double delz) +void Bond::ev_tally_xyz(int i, int j, int nlocal, int newton_bond, double ebond, double fx, + double fy, double fz, double delx, double dely, double delz) { - double ebondhalf,v[6]; + double ebondhalf, v[6]; if (eflag_either) { if (eflag_global) { diff --git a/src/bond.h b/src/bond.h index 3bae8f48b9..be6d737597 100644 --- a/src/bond.h +++ b/src/bond.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/bond_deprecated.cpp b/src/bond_deprecated.cpp index 6d4c17b5d0..adf645622c 100644 --- a/src/bond_deprecated.cpp +++ b/src/bond_deprecated.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/bond_deprecated.h b/src/bond_deprecated.h index 2d348b1190..c72acf2fcb 100644 --- a/src/bond_deprecated.h +++ b/src/bond_deprecated.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/bond_hybrid.cpp b/src/bond_hybrid.cpp index ec49871506..4e477ab3a6 100644 --- a/src/bond_hybrid.cpp +++ b/src/bond_hybrid.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -20,7 +20,6 @@ #include "memory.h" #include "neighbor.h" -#include #include using namespace LAMMPS_NS; @@ -257,10 +256,9 @@ void BondHybrid::flags() // set comm_forward, comm_reverse, comm_reverse_off to max of any sub-style for (m = 0; m < nstyles; m++) { - if (styles[m]) comm_forward = MAX(comm_forward,styles[m]->comm_forward); - if (styles[m]) comm_reverse = MAX(comm_reverse,styles[m]->comm_reverse); - if (styles[m]) comm_reverse_off = MAX(comm_reverse_off, - styles[m]->comm_reverse_off); + if (styles[m]) comm_forward = MAX(comm_forward, styles[m]->comm_forward); + if (styles[m]) comm_reverse = MAX(comm_reverse, styles[m]->comm_reverse); + if (styles[m]) comm_reverse_off = MAX(comm_reverse_off, styles[m]->comm_reverse_off); } init_svector(); @@ -276,8 +274,7 @@ void BondHybrid::init_svector() // allocate svector single_extra = 0; - for (int m = 0; m < nstyles; m++) - single_extra = MAX(single_extra,styles[m]->single_extra); + for (int m = 0; m < nstyles; m++) single_extra = MAX(single_extra, styles[m]->single_extra); if (single_extra) { delete[] svector; @@ -336,6 +333,16 @@ void BondHybrid::coeff(int narg, char **arg) void BondHybrid::init_style() { + // error if sub-style is not used + + int used; + for (int istyle = 0; istyle < nstyles; ++istyle) { + used = 0; + for (int itype = 1; itype <= atom->nbondtypes; ++itype) + if (map[itype] == istyle) used = 1; + if (used == 0) error->all(FLERR, "Bond hybrid sub-style {} is not used", keywords[istyle]); + } + for (int m = 0; m < nstyles; m++) if (styles[m]) styles[m]->init_style(); @@ -415,14 +422,12 @@ double BondHybrid::single(int type, double rsq, int i, int j, double &fforce) void BondHybrid::copy_svector(int type) { - memset(svector,0,single_extra*sizeof(double)); + memset(svector, 0, single_extra * sizeof(double)); // there is only one style in bond style hybrid for a bond type Bond *this_style = styles[map[type]]; - for (int l = 0; this_style->single_extra; ++l) { - svector[l] = this_style->svector[l]; - } + for (int l = 0; this_style->single_extra; ++l) { svector[l] = this_style->svector[l]; } } /* ---------------------------------------------------------------------- diff --git a/src/bond_hybrid.h b/src/bond_hybrid.h index ce689488b0..df1437c038 100644 --- a/src/bond_hybrid.h +++ b/src/bond_hybrid.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/bond_zero.cpp b/src/bond_zero.cpp index 3307831331..66cedd4a29 100644 --- a/src/bond_zero.cpp +++ b/src/bond_zero.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/bond_zero.h b/src/bond_zero.h index 67fc4b63cb..d1cb2c4125 100644 --- a/src/bond_zero.h +++ b/src/bond_zero.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/change_box.cpp b/src/change_box.cpp index b26d7803ed..1cef7c96a5 100644 --- a/src/change_box.cpp +++ b/src/change_box.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -281,9 +281,7 @@ void ChangeBox::command(int narg, char **arg) } else if (ops[m].style == BOUNDARY) { domain->set_boundary(3,&arg[ops[m].boundindex],1); if (domain->dimension == 2 && domain->zperiodic == 0) - error->all(FLERR, - "Cannot change box z boundary to " - "non-periodic for a 2d simulation"); + error->all(FLERR, "Cannot change box z boundary to non-periodic for a 2d simulation"); domain->set_initial_box(); domain->set_global_box(); domain->set_local_box(); diff --git a/src/change_box.h b/src/change_box.h index 85b4b302fa..7deb12c40f 100644 --- a/src/change_box.h +++ b/src/change_box.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/citeme.cpp b/src/citeme.cpp index e1032f7143..894fce84fd 100644 --- a/src/citeme.cpp +++ b/src/citeme.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/citeme.h b/src/citeme.h index 7a8b456eb8..f5b22d614f 100644 --- a/src/citeme.h +++ b/src/citeme.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/comm.cpp b/src/comm.cpp index 402cf8c7fb..3debdd36cb 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -796,103 +796,6 @@ int Comm::coord2proc(double *x, int &igx, int &igy, int &igz) return grid2proc[igx][igy][igz]; } -/* ---------------------------------------------------------------------- - partition a global regular grid into one brick-shaped sub-grid per proc - if grid point is inside my sub-domain I own it, - this includes sub-domain lo boundary but excludes hi boundary - nx,ny,nz = extent of global grid - indices into the global grid range from 0 to N-1 in each dim - zfactor = 0.0 if the grid exactly covers the simulation box - zfactor > 1.0 if the grid extends beyond the +z boundary by this factor - used by 2d slab-mode PPPM - this effectively maps proc sub-grids to a smaller subset of the grid - nxyz lo/hi = inclusive lo/hi bounds of global grid sub-brick I own - if proc owns no grid cells in a dim, then nlo > nhi - special case: 2 procs share boundary which a grid point is exactly on - 2 equality if tests insure a consistent decision as to which proc owns it -------------------------------------------------------------------------- */ - -void Comm::partition_grid(int nx, int ny, int nz, double zfactor, - int &nxlo, int &nxhi, int &nylo, int &nyhi, - int &nzlo, int &nzhi) -{ - double xfraclo,xfrachi,yfraclo,yfrachi,zfraclo,zfrachi; - - if (layout != LAYOUT_TILED) { - xfraclo = xsplit[myloc[0]]; - xfrachi = xsplit[myloc[0]+1]; - yfraclo = ysplit[myloc[1]]; - yfrachi = ysplit[myloc[1]+1]; - zfraclo = zsplit[myloc[2]]; - zfrachi = zsplit[myloc[2]+1]; - } else { - xfraclo = mysplit[0][0]; - xfrachi = mysplit[0][1]; - yfraclo = mysplit[1][0]; - yfrachi = mysplit[1][1]; - zfraclo = mysplit[2][0]; - zfrachi = mysplit[2][1]; - } - - nxlo = static_cast (xfraclo * nx); - if (1.0*nxlo != xfraclo*nx) nxlo++; - nxhi = static_cast (xfrachi * nx); - if (1.0*nxhi == xfrachi*nx) nxhi--; - - nylo = static_cast (yfraclo * ny); - if (1.0*nylo != yfraclo*ny) nylo++; - nyhi = static_cast (yfrachi * ny); - if (1.0*nyhi == yfrachi*ny) nyhi--; - - if (zfactor == 0.0) { - nzlo = static_cast (zfraclo * nz); - if (1.0*nzlo != zfraclo*nz) nzlo++; - nzhi = static_cast (zfrachi * nz); - if (1.0*nzhi == zfrachi*nz) nzhi--; - } else { - nzlo = static_cast (zfraclo * nz/zfactor); - if (1.0*nzlo != zfraclo*nz) nzlo++; - nzhi = static_cast (zfrachi * nz/zfactor); - if (1.0*nzhi == zfrachi*nz) nzhi--; - } - - // OLD code - // could sometimes map grid points slightly outside a proc to the proc - - /* - if (layout != LAYOUT_TILED) { - nxlo = static_cast (xsplit[myloc[0]] * nx); - nxhi = static_cast (xsplit[myloc[0]+1] * nx) - 1; - - nylo = static_cast (ysplit[myloc[1]] * ny); - nyhi = static_cast (ysplit[myloc[1]+1] * ny) - 1; - - if (zfactor == 0.0) { - nzlo = static_cast (zsplit[myloc[2]] * nz); - nzhi = static_cast (zsplit[myloc[2]+1] * nz) - 1; - } else { - nzlo = static_cast (zsplit[myloc[2]] * nz/zfactor); - nzhi = static_cast (zsplit[myloc[2]+1] * nz/zfactor) - 1; - } - - } else { - nxlo = static_cast (mysplit[0][0] * nx); - nxhi = static_cast (mysplit[0][1] * nx) - 1; - - nylo = static_cast (mysplit[1][0] * ny); - nyhi = static_cast (mysplit[1][1] * ny) - 1; - - if (zfactor == 0.0) { - nzlo = static_cast (mysplit[2][0] * nz); - nzhi = static_cast (mysplit[2][1] * nz) - 1; - } else { - nzlo = static_cast (mysplit[2][0] * nz/zfactor); - nzhi = static_cast (mysplit[2][1] * nz/zfactor) - 1; - } - } - */ -} - /* ---------------------------------------------------------------------- communicate inbuf around full ring of processors with messtag nbytes = size of inbuf = n datums * nper bytes diff --git a/src/comm.h b/src/comm.h index 43fabb1b67..7bbf4a55b5 100644 --- a/src/comm.h +++ b/src/comm.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -20,13 +20,18 @@ namespace LAMMPS_NS { class Comm : protected Pointers { public: - int style; // comm pattern: 0 = 6-way stencil, 1 = irregular tiling + enum { BRICK, TILED }; + int style; // BRICK = 6-way stencil communication + // TILED = irregular tiling communication + + enum { LAYOUT_UNIFORM, LAYOUT_NONUNIFORM, LAYOUT_TILED }; int layout; // LAYOUT_UNIFORM = equal-sized bricks // LAYOUT_NONUNIFORM = logical bricks, but diff sizes via LB // LAYOUT_TILED = general tiling, due to RCB LB - enum { LAYOUT_UNIFORM, LAYOUT_NONUNIFORM, LAYOUT_TILED }; - int mode; // 0 = single cutoff, 1 = multi-collection cutoff, 2 = multiold-type cutoff enum { SINGLE, MULTI, MULTIOLD }; + int mode; // SINGLE = single cutoff + // MULTI = multi-collection cutoff + // MULTIOLD = multiold-type cutoff int me, nprocs; // proc info int ghost_velocity; // 1 if ghost atoms have velocity, 0 if not @@ -46,11 +51,11 @@ class Comm : protected Pointers { // public settings specific to layout = UNIFORM, NONUNIFORM - int procgrid[3]; // procs assigned in each dim of 3d grid - int user_procgrid[3]; // user request for procs in each dim - int myloc[3]; // which proc I am in each dim + int procgrid[3]; // proc count assigned to each dim of 3d grid + int user_procgrid[3]; // user request for proc counts in each dim + int myloc[3]; // which proc I am in each dim, 0 to N-1 int procneigh[3][2]; // my 6 neighboring procs, 0/1 = left/right - double *xsplit, *ysplit, *zsplit; // fractional (0-1) sub-domain sizes + double *xsplit, *ysplit, *zsplit; // fractional (0-1) sub-domain sizes, includes 0/1 int ***grid2proc; // which proc owns i,j,k loc in 3d grid // public settings specific to layout = TILED @@ -106,10 +111,6 @@ class Comm : protected Pointers { virtual void coord2proc_setup() {} virtual int coord2proc(double *, int &, int &, int &); - // partition a global regular grid by proc sub-domains - - void partition_grid(int, int, int, double, int &, int &, int &, int &, int &, int &); - // memory usage virtual double memory_usage() = 0; diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index b4a0cddda8..5e4e83cda7 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -50,7 +50,7 @@ CommBrick::CommBrick(LAMMPS *lmp) : pbc_flag(nullptr), pbc(nullptr), firstrecv(nullptr), sendlist(nullptr), localsendlist(nullptr), maxsendlist(nullptr), buf_send(nullptr), buf_recv(nullptr) { - style = 0; + style = Comm::BRICK; layout = Comm::LAYOUT_UNIFORM; pbc_flag = nullptr; init_buffers(); @@ -92,7 +92,7 @@ CommBrick::CommBrick(LAMMPS * /*lmp*/, Comm *oldcomm) : Comm(*oldcomm) if (oldcomm->layout == Comm::LAYOUT_TILED) error->all(FLERR,"Cannot change to comm_style brick from tiled layout"); - style = 0; + style = Comm::BRICK; layout = oldcomm->layout; Comm::copy_arrays(oldcomm); init_buffers(); diff --git a/src/comm_brick.h b/src/comm_brick.h index cbd08126b4..38483af9de 100644 --- a/src/comm_brick.h +++ b/src/comm_brick.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 8088ada44b..517b48c9a1 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -47,7 +47,7 @@ using namespace LAMMPS_NS; CommTiled::CommTiled(LAMMPS *lmp) : Comm(lmp) { - style = 1; + style = Comm::TILED; layout = Comm::LAYOUT_UNIFORM; pbc_flag = nullptr; buf_send = nullptr; @@ -68,7 +68,7 @@ CommTiled::CommTiled(LAMMPS *lmp) : Comm(lmp) CommTiled::CommTiled(LAMMPS * /*lmp*/, Comm *oldcomm) : Comm(*oldcomm) { - style = 1; + style = Comm::TILED; layout = oldcomm->layout; Comm::copy_arrays(oldcomm); init_buffers(); diff --git a/src/comm_tiled.h b/src/comm_tiled.h index 0339991331..526c6166a8 100644 --- a/src/comm_tiled.h +++ b/src/comm_tiled.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/command.h b/src/command.h index fb0d9dc415..1b5cea5ccb 100644 --- a/src/command.h +++ b/src/command.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute.cpp b/src/compute.cpp index 7200f66dc8..d7e8e8d5a4 100644 --- a/src/compute.cpp +++ b/src/compute.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -62,7 +62,7 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) : // set child class defaults scalar_flag = vector_flag = array_flag = 0; - peratom_flag = local_flag = 0; + peratom_flag = local_flag = pergrid_flag = 0; size_vector_variable = size_array_rows_variable = 0; tempflag = pressflag = peflag = 0; diff --git a/src/compute.h b/src/compute.h index 90b88c7d1d..72b0075fd6 100644 --- a/src/compute.h +++ b/src/compute.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -30,6 +30,7 @@ class Compute : protected Pointers { INVOKED_ARRAY = 1<<2, INVOKED_PERATOM = 1<<3, INVOKED_LOCAL = 1<<4, + INVOKED_PERGRID = 1<<5, }; // clang-format on static int instance_total; // # of Compute classes ever instantiated @@ -61,6 +62,8 @@ class Compute : protected Pointers { int size_local_rows; // rows in local vector or array int size_local_cols; // 0 = vector, N = columns in local array + int pergrid_flag; // 0/1 if compute_pergrid() function exists + int extscalar; // 0/1 if global scalar is intensive/extensive int extvector; // 0/1/-1 if global vector is all int/ext/extlist int *extlist; // list of 0/1 int/ext for each vec component @@ -91,6 +94,7 @@ class Compute : protected Pointers { bigint invoked_array; // ditto for compute_array() bigint invoked_peratom; // ditto for compute_peratom() bigint invoked_local; // ditto for compute_local() + bigint invoked_pergrid; // ditto for compute_grid() double dof; // degrees-of-freedom for temperature @@ -118,6 +122,7 @@ class Compute : protected Pointers { virtual void compute_array() {} virtual void compute_peratom() {} virtual void compute_local() {} + virtual void compute_pergrid() {} virtual void set_arrays(int) {} virtual int pack_forward_comm(int, int *, double *, int, int *) { return 0; } @@ -125,6 +130,13 @@ class Compute : protected Pointers { virtual int pack_reverse_comm(int, int, double *) { return 0; } virtual void unpack_reverse_comm(int, int *, double *) {} + virtual void reset_grid(){}; + + virtual int get_grid_by_name(const std::string &, int &) { return -1; }; + virtual void *get_grid_by_index(int) { return nullptr; }; + virtual int get_griddata_by_name(int, const std::string &, int &) { return -1; }; + virtual void *get_griddata_by_index(int) { return nullptr; }; + virtual void dof_remove_pre() {} virtual int dof_remove(int) { return 0; } virtual void remove_bias(int, double *) {} diff --git a/src/compute_aggregate_atom.cpp b/src/compute_aggregate_atom.cpp index 6811ae2d87..9298a17530 100644 --- a/src/compute_aggregate_atom.cpp +++ b/src/compute_aggregate_atom.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_aggregate_atom.h b/src/compute_aggregate_atom.h index 253c1aa24b..7a0aab03b5 100644 --- a/src/compute_aggregate_atom.h +++ b/src/compute_aggregate_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_angle.cpp b/src/compute_angle.cpp index bf1241754d..71c13ebc7f 100644 --- a/src/compute_angle.cpp +++ b/src/compute_angle.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_angle.h b/src/compute_angle.h index fc5b8e21ce..aa4e41f4ba 100644 --- a/src/compute_angle.h +++ b/src/compute_angle.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_angle_local.cpp b/src/compute_angle_local.cpp index 2bceb91dd5..3600562664 100644 --- a/src/compute_angle_local.cpp +++ b/src/compute_angle_local.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_angle_local.h b/src/compute_angle_local.h index c9d71c3ce6..2f4a47c539 100644 --- a/src/compute_angle_local.h +++ b/src/compute_angle_local.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_angmom_chunk.cpp b/src/compute_angmom_chunk.cpp index 75e73d280d..12489920fc 100644 --- a/src/compute_angmom_chunk.cpp +++ b/src/compute_angmom_chunk.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_angmom_chunk.h b/src/compute_angmom_chunk.h index ca8867dd45..04023dbe44 100644 --- a/src/compute_angmom_chunk.h +++ b/src/compute_angmom_chunk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -23,6 +23,7 @@ ComputeStyle(angmom/chunk,ComputeAngmomChunk); #include "compute.h" namespace LAMMPS_NS { + class Fix; class ComputeAngmomChunk : public Compute { public: @@ -34,8 +35,8 @@ class ComputeAngmomChunk : public Compute { void lock_enable() override; void lock_disable() override; int lock_length() override; - void lock(class Fix *, bigint, bigint) override; - void unlock(class Fix *) override; + void lock(Fix *, bigint, bigint) override; + void unlock(Fix *) override; double memory_usage() override; diff --git a/src/compute_bond.cpp b/src/compute_bond.cpp index c0d65c55d5..8070c13231 100644 --- a/src/compute_bond.cpp +++ b/src/compute_bond.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_bond.h b/src/compute_bond.h index 51a6c1bc5f..039fd1c353 100644 --- a/src/compute_bond.h +++ b/src/compute_bond.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp index 19561cc6bf..f2603e8cdd 100644 --- a/src/compute_bond_local.cpp +++ b/src/compute_bond_local.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_bond_local.h b/src/compute_bond_local.h index 078c957dcd..1012e405cd 100644 --- a/src/compute_bond_local.h +++ b/src/compute_bond_local.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_centro_atom.cpp b/src/compute_centro_atom.cpp index b3cedae89e..e9edc97d71 100644 --- a/src/compute_centro_atom.cpp +++ b/src/compute_centro_atom.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_centro_atom.h b/src/compute_centro_atom.h index 30e28b376a..92335b5eb0 100644 --- a/src/compute_centro_atom.h +++ b/src/compute_centro_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_centroid_stress_atom.cpp b/src/compute_centroid_stress_atom.cpp index 911f6f58ac..8aa2e45807 100644 --- a/src/compute_centroid_stress_atom.cpp +++ b/src/compute_centroid_stress_atom.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_centroid_stress_atom.h b/src/compute_centroid_stress_atom.h index 16de7f3713..12128dc71e 100644 --- a/src/compute_centroid_stress_atom.h +++ b/src/compute_centroid_stress_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp index 013efb8c50..f9723497b1 100644 --- a/src/compute_chunk_atom.cpp +++ b/src/compute_chunk_atom.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -629,6 +629,7 @@ void ComputeChunkAtom::compute_peratom() to return the number of chunks, we first need to make certain that compute_peratom() has been called. ------------------------------------------------------------------------- */ + double ComputeChunkAtom::compute_scalar() { if (invoked_peratom != update->ntimestep) compute_peratom(); diff --git a/src/compute_chunk_atom.h b/src/compute_chunk_atom.h index 2c1f3ef000..6850003b3e 100644 --- a/src/compute_chunk_atom.h +++ b/src/compute_chunk_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_chunk_spread_atom.cpp b/src/compute_chunk_spread_atom.cpp index c34da3e2c0..933cf0af0c 100644 --- a/src/compute_chunk_spread_atom.cpp +++ b/src/compute_chunk_spread_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -63,8 +63,7 @@ ComputeChunkSpreadAtom(LAMMPS *lmp, int narg, char **arg) : val.id = argi.get_name(); val.val.c = nullptr; - if ((val.which == ArgInfo::UNKNOWN) || (val.which == ArgInfo::NONE) - || (argi.get_dim() > 1)) + if ((val.which == ArgInfo::UNKNOWN) || (val.which == ArgInfo::NONE) || (argi.get_dim() > 1)) error->all(FLERR,"Illegal compute chunk/spread/atom argument: {}", arg[iarg]); values.push_back(val); @@ -153,7 +152,7 @@ void ComputeChunkSpreadAtom::init() { init_chunk(); - // set indices of all computes,fixes,variables + // store references of all computes and fixes for (auto &val : values) { if (val.which == ArgInfo::COMPUTE) { diff --git a/src/compute_chunk_spread_atom.h b/src/compute_chunk_spread_atom.h index 870fa47c9c..4ea88e89ec 100644 --- a/src/compute_chunk_spread_atom.h +++ b/src/compute_chunk_spread_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_cluster_atom.cpp b/src/compute_cluster_atom.cpp index c2cb2816d3..0a0a36debd 100644 --- a/src/compute_cluster_atom.cpp +++ b/src/compute_cluster_atom.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -17,7 +17,6 @@ #include "comm.h" #include "error.h" #include "force.h" -#include "group.h" #include "memory.h" #include "modify.h" #include "neigh_list.h" diff --git a/src/compute_cluster_atom.h b/src/compute_cluster_atom.h index 9e6e757b01..6f45d558f4 100644 --- a/src/compute_cluster_atom.h +++ b/src/compute_cluster_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_cna_atom.cpp b/src/compute_cna_atom.cpp index 4b9c28362c..ccb4183707 100644 --- a/src/compute_cna_atom.cpp +++ b/src/compute_cna_atom.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_cna_atom.h b/src/compute_cna_atom.h index d9c1e50afa..095571ab89 100644 --- a/src/compute_cna_atom.h +++ b/src/compute_cna_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_com.cpp b/src/compute_com.cpp index 539fd5dcd9..88bb73912a 100644 --- a/src/compute_com.cpp +++ b/src/compute_com.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_com.h b/src/compute_com.h index 0966247f1e..c958d1fa68 100644 --- a/src/compute_com.h +++ b/src/compute_com.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_com_chunk.cpp b/src/compute_com_chunk.cpp index 7a1308366e..2a024fd214 100644 --- a/src/compute_com_chunk.cpp +++ b/src/compute_com_chunk.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_com_chunk.h b/src/compute_com_chunk.h index 8e870392db..c617e181fe 100644 --- a/src/compute_com_chunk.h +++ b/src/compute_com_chunk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -23,6 +23,7 @@ ComputeStyle(com/chunk,ComputeCOMChunk); #include "compute.h" namespace LAMMPS_NS { +class Fix; class ComputeCOMChunk : public Compute { public: @@ -38,8 +39,8 @@ class ComputeCOMChunk : public Compute { void lock_enable() override; void lock_disable() override; int lock_length() override; - void lock(class Fix *, bigint, bigint) override; - void unlock(class Fix *) override; + void lock(Fix *, bigint, bigint) override; + void unlock(Fix *) override; double memory_usage() override; diff --git a/src/compute_coord_atom.cpp b/src/compute_coord_atom.cpp index 7bf749b1be..0d56ea6573 100644 --- a/src/compute_coord_atom.cpp +++ b/src/compute_coord_atom.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_coord_atom.h b/src/compute_coord_atom.h index 63ffd56c82..6aed13dd59 100644 --- a/src/compute_coord_atom.h +++ b/src/compute_coord_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_deprecated.cpp b/src/compute_deprecated.cpp index fca119a456..8a32130b43 100644 --- a/src/compute_deprecated.cpp +++ b/src/compute_deprecated.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_deprecated.h b/src/compute_deprecated.h index 3267e78880..0e19cca3f0 100644 --- a/src/compute_deprecated.h +++ b/src/compute_deprecated.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_dihedral.cpp b/src/compute_dihedral.cpp index 2fda5b1f1c..39d5179d30 100644 --- a/src/compute_dihedral.cpp +++ b/src/compute_dihedral.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_dihedral.h b/src/compute_dihedral.h index 3120734c0f..376bce2a7e 100644 --- a/src/compute_dihedral.h +++ b/src/compute_dihedral.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_dihedral_local.cpp b/src/compute_dihedral_local.cpp index 062741bad1..a6bcbccf00 100644 --- a/src/compute_dihedral_local.cpp +++ b/src/compute_dihedral_local.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_dihedral_local.h b/src/compute_dihedral_local.h index 48b24b4465..a9eb6af9d7 100644 --- a/src/compute_dihedral_local.h +++ b/src/compute_dihedral_local.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_dipole.cpp b/src/compute_dipole.cpp index 7486baefd6..b8d03dfe75 100644 --- a/src/compute_dipole.cpp +++ b/src/compute_dipole.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_dipole.h b/src/compute_dipole.h index 61e07f2514..c6ab891d6f 100644 --- a/src/compute_dipole.h +++ b/src/compute_dipole.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_dipole_chunk.cpp b/src/compute_dipole_chunk.cpp index 3517fb1781..a7609842d1 100644 --- a/src/compute_dipole_chunk.cpp +++ b/src/compute_dipole_chunk.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_dipole_chunk.h b/src/compute_dipole_chunk.h index c0ae6409de..42198fe478 100644 --- a/src/compute_dipole_chunk.h +++ b/src/compute_dipole_chunk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -23,6 +23,7 @@ ComputeStyle(dipole/chunk,ComputeDipoleChunk); #include "compute.h" namespace LAMMPS_NS { +class Fix; class ComputeDipoleChunk : public Compute { public: @@ -34,8 +35,8 @@ class ComputeDipoleChunk : public Compute { void lock_enable() override; void lock_disable() override; int lock_length() override; - void lock(class Fix *, bigint, bigint) override; - void unlock(class Fix *) override; + void lock(Fix *, bigint, bigint) override; + void unlock(Fix *) override; double memory_usage() override; diff --git a/src/compute_displace_atom.cpp b/src/compute_displace_atom.cpp index 6322bc1c00..0b1ffff687 100644 --- a/src/compute_displace_atom.cpp +++ b/src/compute_displace_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_displace_atom.h b/src/compute_displace_atom.h index b0e6710d8d..dc1be7434f 100644 --- a/src/compute_displace_atom.h +++ b/src/compute_displace_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_erotate_sphere.cpp b/src/compute_erotate_sphere.cpp index 3e863eaf65..b020fc4e0e 100644 --- a/src/compute_erotate_sphere.cpp +++ b/src/compute_erotate_sphere.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_erotate_sphere.h b/src/compute_erotate_sphere.h index b27b726578..06262b89ef 100644 --- a/src/compute_erotate_sphere.h +++ b/src/compute_erotate_sphere.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_erotate_sphere_atom.cpp b/src/compute_erotate_sphere_atom.cpp index af4f902f83..fc9016c06a 100644 --- a/src/compute_erotate_sphere_atom.cpp +++ b/src/compute_erotate_sphere_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_erotate_sphere_atom.h b/src/compute_erotate_sphere_atom.h index eab3410bf2..e4e7f2c451 100644 --- a/src/compute_erotate_sphere_atom.h +++ b/src/compute_erotate_sphere_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_fragment_atom.cpp b/src/compute_fragment_atom.cpp index 8317d8251d..a1fd19d7af 100644 --- a/src/compute_fragment_atom.cpp +++ b/src/compute_fragment_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -148,11 +148,7 @@ void ComputeFragmentAtom::compute_peratom() commflag = 1; - int iteration = 0; - while (true) { - iteration++; - comm->forward_comm(this); done = 1; diff --git a/src/compute_fragment_atom.h b/src/compute_fragment_atom.h index 2e948a9371..2312fd8c69 100644 --- a/src/compute_fragment_atom.h +++ b/src/compute_fragment_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_global_atom.cpp b/src/compute_global_atom.cpp index b72f5a28f6..c2880763a3 100644 --- a/src/compute_global_atom.cpp +++ b/src/compute_global_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -26,19 +26,12 @@ using namespace LAMMPS_NS; -enum{VECTOR,ARRAY}; - - -#define BIG 1.0e20 - /* ---------------------------------------------------------------------- */ ComputeGlobalAtom::ComputeGlobalAtom(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg), - idref(nullptr), which(nullptr), argindex(nullptr), value2index(nullptr), ids(nullptr), - indices(nullptr), varatom(nullptr), vecglobal(nullptr) + Compute(lmp, narg, arg), indices(nullptr), varatom(nullptr), vecglobal(nullptr) { - if (narg < 5) error->all(FLERR,"Illegal compute global/atom command"); + if (narg < 5) utils::missing_cmd_args(FLERR,"compute global/atom", error); peratom_flag = 1; @@ -47,13 +40,13 @@ ComputeGlobalAtom::ComputeGlobalAtom(LAMMPS *lmp, int narg, char **arg) : int iarg = 3; ArgInfo argi(arg[iarg]); - whichref = argi.get_type(); - indexref = argi.get_index1(); - idref = argi.copy_name(); + reference.which = argi.get_type(); + reference.argindex = argi.get_index1(); + reference.id = argi.get_name(); - if ((whichref == ArgInfo::UNKNOWN) || (whichref == ArgInfo::NONE) + if ((reference.which == ArgInfo::UNKNOWN) || (reference.which == ArgInfo::NONE) || (argi.get_dim() > 1)) - error->all(FLERR,"Illegal compute global/atom command"); + error->all(FLERR,"Illegal compute global/atom index property: {}", arg[iarg]); iarg++; @@ -68,24 +61,22 @@ ComputeGlobalAtom::ComputeGlobalAtom(LAMMPS *lmp, int narg, char **arg) : // parse values until one isn't recognized - which = new int[nargnew]; - argindex = new int[nargnew]; - ids = new char*[nargnew]; - value2index = new int[nargnew]; - nvalues = 0; + values.clear(); for (iarg = 0; iarg < nargnew; iarg++) { ArgInfo argi2(arg[iarg]); - which[nvalues] = argi2.get_type(); - argindex[nvalues] = argi2.get_index1(); - ids[nvalues] = argi2.copy_name(); + value_t val; + val.which = argi2.get_type(); + val.argindex = argi2.get_index1(); + val.id = argi2.get_name(); + val.val.c = nullptr; - if ((which[nvalues] == ArgInfo::UNKNOWN) || (which[nvalues] == ArgInfo::NONE) + if ((val.which == ArgInfo::UNKNOWN) || (val.which == ArgInfo::NONE) || (argi2.get_dim() > 1)) - error->all(FLERR,"Illegal compute slice command"); + error->all(FLERR,"Illegal compute global/atom global property: {}", arg[iarg]); - nvalues++; + values.push_back(val); } // if wildcard expansion occurred, free earg memory from expand_args() @@ -95,94 +86,97 @@ ComputeGlobalAtom::ComputeGlobalAtom(LAMMPS *lmp, int narg, char **arg) : memory->sfree(earg); } - // setup and error check both index arg and values + // setup and error check for both, index arg and values - if (whichref == ArgInfo::COMPUTE) { - int icompute = modify->find_compute(idref); - if (icompute < 0) - error->all(FLERR,"Compute ID for compute global/atom does not exist"); + if (reference.which == ArgInfo::COMPUTE) { + reference.val.c = modify->get_compute_by_id(reference.id); + if (!reference.val.c) + error->all(FLERR,"Compute ID {} for compute global/atom index", reference.id); - if (!modify->compute[icompute]->peratom_flag) - error->all(FLERR,"Compute global/atom compute does not " - "calculate a per-atom vector or array"); - if (indexref == 0 && - modify->compute[icompute]->size_peratom_cols != 0) - error->all(FLERR,"Compute global/atom compute does not " - "calculate a per-atom vector"); - if (indexref && modify->compute[icompute]->size_peratom_cols == 0) - error->all(FLERR,"Compute global/atom compute does not " - "calculate a per-atom array"); - if (indexref && indexref > modify->compute[icompute]->size_peratom_cols) - error->all(FLERR, - "Compute global/atom compute array is accessed out-of-range"); + if (!reference.val.c->peratom_flag) + error->all(FLERR,"Compute global/atom compute {} does not calculate a per-atom " + "vector or array", reference.id); + if ((reference.argindex == 0) && (reference.val.c->size_peratom_cols != 0)) + error->all(FLERR,"Compute global/atom compute {} does not calculate a per-atom " + "vector", reference.id); + if (reference.argindex && (reference.val.c->size_peratom_cols == 0)) + error->all(FLERR,"Compute global/atom compute does not calculate a per-atom " + "array", reference.id); + if (reference.argindex && (reference.argindex > reference.val.c->size_peratom_cols)) + error->all(FLERR, "Compute global/atom compute array {} is accessed out-of-range", + reference.id); - } else if (whichref == ArgInfo::FIX) { - auto ifix = modify->get_fix_by_id(idref); - if (!ifix) - error->all(FLERR,"Fix ID {} for compute global/atom does not exist", idref); - if (!ifix->peratom_flag) - error->all(FLERR,"Compute global/atom fix {} does not calculate a per-atom vector or array", idref); - if (indexref == 0 && (ifix->size_peratom_cols != 0)) - error->all(FLERR,"Compute global/atom fix {} does not calculate a per-atom vector", idref); - if (indexref && (ifix->size_peratom_cols == 0)) - error->all(FLERR,"Compute global/atom fix {} does not calculate a per-atom array", idref); - if (indexref && indexref > ifix->size_peratom_cols) - error->all(FLERR, "Compute global/atom fix {} array is accessed out-of-range", idref); + } else if (reference.which == ArgInfo::FIX) { + reference.val.f =modify->get_fix_by_id(reference.id); + if (!reference.val.f) + error->all(FLERR,"Fix ID {} for compute global/atom does not exist", reference.id); + if (!reference.val.f->peratom_flag) + error->all(FLERR,"Compute global/atom fix {} does not calculate a per-atom vector " + "or array", reference.id); + if (reference.argindex == 0 && (reference.val.f->size_peratom_cols != 0)) + error->all(FLERR,"Compute global/atom fix {} does not calculate a per-atom vector", + reference.id); + if (reference.argindex && (reference.val.f->size_peratom_cols == 0)) + error->all(FLERR,"Compute global/atom fix {} does not calculate a per-atom array", + reference.id); + if (reference.argindex && (reference.argindex > reference.val.f->size_peratom_cols)) + error->all(FLERR, "Compute global/atom fix {} array is accessed out-of-range", reference.id); - } else if (whichref == ArgInfo::VARIABLE) { - int ivariable = input->variable->find(idref); - if (ivariable < 0) - error->all(FLERR,"Variable name for compute global/atom does not exist"); - if (input->variable->atomstyle(ivariable) == 0) - error->all(FLERR,"Compute global/atom variable is not " - "atom-style variable"); + } else if (reference.which == ArgInfo::VARIABLE) { + reference.val.v = input->variable->find(reference.id.c_str()); + if (reference.val.v < 0) + error->all(FLERR,"Variable name {} for compute global/atom index does not exist", + reference.id); + if (input->variable->atomstyle(reference.val.v) == 0) + error->all(FLERR,"Compute global/atom index variable {} is not atom-style variable", + reference.id); } - for (int i = 0; i < nvalues; i++) { - if (which[i] == ArgInfo::COMPUTE) { - int icompute = modify->find_compute(ids[i]); - if (icompute < 0) - error->all(FLERR,"Compute ID for compute global/atom does not exist"); - if (argindex[i] == 0) { - if (!modify->compute[icompute]->vector_flag) - error->all(FLERR,"Compute global/atom compute does not " - "calculate a global vector"); + for (auto &val : values) { + if (val.which == ArgInfo::COMPUTE) { + val.val.c = modify->get_compute_by_id(val.id); + if (!val.val.c) + error->all(FLERR,"Compute ID {} for compute global/atom does not exist", val.id); + if (val.argindex == 0) { + if (!val.val.c->vector_flag) + error->all(FLERR,"Compute ID {} for global/atom compute does not calculate " + "a global vector", val.id); } else { - if (!modify->compute[icompute]->array_flag) - error->all(FLERR,"Compute global/atom compute does not " - "calculate a global array"); - if (argindex[i] > modify->compute[icompute]->size_array_cols) - error->all(FLERR,"Compute global/atom compute array is " - "accessed out-of-range"); + if (!val.val.c->array_flag) + error->all(FLERR,"Compute ID {} for global/atom compute does not calculate " + "a global array", val.id); + if (val.argindex > val.val.c->size_array_cols) + error->all(FLERR,"Compute global/atom compute {} array is accessed out-of-range", val.id); } - } else if (which[i] == ArgInfo::FIX) { - auto ifix = modify->get_fix_by_id(ids[i]); - if (!ifix) - error->all(FLERR,"Fix ID for compute global/atom does not exist"); - if (argindex[i] == 0) { - if (!ifix->vector_flag) - error->all(FLERR,"Compute global/atom fix {} does not calculate a global vector", ids[i]); + } else if (val.which == ArgInfo::FIX) { + val.val.f = modify->get_fix_by_id(val.id); + if (!val.val.f) error->all(FLERR,"Fix ID {} for compute global/atom does not exist", val.id); + if (val.argindex == 0) { + if (!val.val.f->vector_flag) + error->all(FLERR,"Fix ID {} for compute global/atom compute does not calculate " + "a global vector", val.id); } else { - if (!ifix->array_flag) - error->all(FLERR,"Compute global/atom fix {} does not calculate a global array", ids[i]); - if (argindex[i] > ifix->size_array_cols) - error->all(FLERR,"Compute global/atom fix {} array is accessed out-of-range", ids[i]); + if (!val.val.f->array_flag) + error->all(FLERR,"Fix ID {} for compute global/atom compute does not calculate " + "a global array", val.id); + if (val.argindex > val.val.f->size_array_cols) + error->all(FLERR,"Compute global/atom fix {} array is accessed out-of-range", val.id); } - } else if (which[i] == ArgInfo::VARIABLE) { - int ivariable = input->variable->find(ids[i]); - if (ivariable < 0) - error->all(FLERR,"Variable name for compute global/atom does not exist"); - if (input->variable->vectorstyle(ivariable) == 0) - error->all(FLERR,"Compute global/atom variable is not vector-style variable"); + } else if (val.which == ArgInfo::VARIABLE) { + val.val.v = input->variable->find(val.id.c_str()); + if (val.val.v < 0) + error->all(FLERR,"Variable name {} for compute global/atom does not exist", val.id); + if (input->variable->vectorstyle(val.val.v) == 0) + error->all(FLERR,"Compute global/atom variable {} is not vector-style variable", val.id); } } // this compute produces either a peratom vector or array - if (nvalues == 1) size_peratom_cols = 0; - else size_peratom_cols = nvalues; + if (values.size() == 1) size_peratom_cols = 0; + else size_peratom_cols = values.size(); nmax = maxvector = 0; vector_atom = nullptr; @@ -193,14 +187,6 @@ ComputeGlobalAtom::ComputeGlobalAtom(LAMMPS *lmp, int narg, char **arg) : ComputeGlobalAtom::~ComputeGlobalAtom() { - delete [] idref; - - delete [] which; - delete [] argindex; - for (int m = 0; m < nvalues; m++) delete [] ids[m]; - delete [] ids; - delete [] value2index; - memory->destroy(indices); memory->destroy(varatom); memory->destroy(vecglobal); @@ -212,44 +198,38 @@ ComputeGlobalAtom::~ComputeGlobalAtom() void ComputeGlobalAtom::init() { - // set indices of all computes,fixes,variables + // store references of all computes, fixes, or variables - if (whichref == ArgInfo::COMPUTE) { - int icompute = modify->find_compute(idref); - if (icompute < 0) - error->all(FLERR,"Compute ID for compute global/atom does not exist"); - ref2index = icompute; - } else if (whichref == ArgInfo::FIX) { - int ifix = modify->find_fix(idref); - if (ifix < 0) - error->all(FLERR,"Fix ID for compute global/atom does not exist"); - ref2index = ifix; - } else if (whichref == ArgInfo::VARIABLE) { - int ivariable = input->variable->find(idref); - if (ivariable < 0) - error->all(FLERR,"Variable name for compute global/atom does not exist"); - ref2index = ivariable; + if (reference.which == ArgInfo::COMPUTE) { + reference.val.c = modify->get_compute_by_id(reference.id); + if (!reference.val.c) + error->all(FLERR,"Compute ID {} for compute global/atom index does not exist", reference.id); + } else if (reference.which == ArgInfo::FIX) { + reference.val.f = modify->get_fix_by_id(reference.id); + if (reference.val.f) + error->all(FLERR,"Fix ID {} for compute global/atom index does not exist", reference.id); + } else if (reference.which == ArgInfo::VARIABLE) { + reference.val.v = input->variable->find(reference.id.c_str()); + if (reference.val.v < 0) + error->all(FLERR,"Variable name {} for compute global/atom index does not exist", + reference.id); } - for (int m = 0; m < nvalues; m++) { - if (which[m] == ArgInfo::COMPUTE) { - int icompute = modify->find_compute(ids[m]); - if (icompute < 0) - error->all(FLERR,"Compute ID for compute global/atom does not exist"); - value2index[m] = icompute; + for (auto &val : values) { + if (val.which == ArgInfo::COMPUTE) { + val.val.c = modify->get_compute_by_id(val.id); + if (!val.val.c) + error->all(FLERR,"Compute ID {} for compute global/atom does not exist", val.id); - } else if (which[m] == ArgInfo::FIX) { - int ifix = modify->find_fix(ids[m]); - if (ifix < 0) - error->all(FLERR,"Fix ID for compute global/atom does not exist"); - value2index[m] = ifix; + } else if (val.which == ArgInfo::FIX) { + val.val.f = modify->get_fix_by_id(val.id); + if (!val.val.f) + error->all(FLERR,"Fix ID {} for compute global/atom does not exist", val.id); - } else if (which[m] == ArgInfo::VARIABLE) { - int ivariable = input->variable->find(ids[m]); - if (ivariable < 0) - error->all(FLERR,"Variable name for compute global/atom " - "does not exist"); - value2index[m] = ivariable; + } else if (val.which == ArgInfo::VARIABLE) { + val.val.v = input->variable->find(val.id.c_str()); + if (val.val.v < 0) + error->all(FLERR,"Variable name {} for compute global/atom does not exist", val.id); } } } @@ -258,8 +238,6 @@ void ComputeGlobalAtom::init() void ComputeGlobalAtom::compute_peratom() { - int i,j; - invoked_peratom = update->ntimestep; // grow indices and output vector or array if necessary @@ -268,16 +246,16 @@ void ComputeGlobalAtom::compute_peratom() nmax = atom->nmax; memory->destroy(indices); memory->create(indices,nmax,"global/atom:indices"); - if (whichref == ArgInfo::VARIABLE) { + if (reference.which == ArgInfo::VARIABLE) { memory->destroy(varatom); memory->create(varatom,nmax,"global/atom:varatom"); } - if (nvalues == 1) { + if (values.size() == 1) { memory->destroy(vector_atom); memory->create(vector_atom,nmax,"global/atom:vector_atom"); } else { memory->destroy(array_atom); - memory->create(array_atom,nmax,nvalues,"global/atom:array_atom"); + memory->create(array_atom,nmax,values.size(),"global/atom:array_atom"); } } @@ -286,81 +264,79 @@ void ComputeGlobalAtom::compute_peratom() // indices are decremented from 1 to N -> 0 to N-1 int *mask = atom->mask; - int nlocal = atom->nlocal; + const int nlocal = atom->nlocal; - if (whichref == ArgInfo::COMPUTE) { - Compute *compute = modify->compute[ref2index]; + if (reference.which == ArgInfo::COMPUTE) { - if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) { - compute->compute_peratom(); - compute->invoked_flag |= Compute::INVOKED_PERATOM; + if (!(reference.val.c->invoked_flag & Compute::INVOKED_PERATOM)) { + reference.val.c->compute_peratom(); + reference.val.c->invoked_flag |= Compute::INVOKED_PERATOM; } - if (indexref == 0) { - double *compute_vector = compute->vector_atom; - for (i = 0; i < nlocal; i++) + if (reference.argindex == 0) { + double *compute_vector = reference.val.c->vector_atom; + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) indices[i] = static_cast (compute_vector[i]) - 1; } else { - double **compute_array = compute->array_atom; - int im1 = indexref - 1; - for (i = 0; i < nlocal; i++) + double **compute_array = reference.val.c->array_atom; + int im1 = reference.argindex - 1; + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) indices[i] = static_cast (compute_array[i][im1]) - 1; } - } else if (whichref == ArgInfo::FIX) { - if (update->ntimestep % modify->fix[ref2index]->peratom_freq) - error->all(FLERR,"Fix used in compute global/atom not " - "computed at compatible time"); - Fix *fix = modify->fix[ref2index]; + } else if (reference.which == ArgInfo::FIX) { + if (update->ntimestep % reference.val.f->peratom_freq) + error->all(FLERR,"Fix {} used in compute global/atom not computed at compatible time", + reference.id); - if (indexref == 0) { - double *fix_vector = fix->vector_atom; - for (i = 0; i < nlocal; i++) + if (reference.argindex == 0) { + double *fix_vector = reference.val.f->vector_atom; + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) indices[i] = static_cast (fix_vector[i]) - 1; } else { - double **fix_array = fix->array_atom; - int im1 = indexref - 1; - for (i = 0; i < nlocal; i++) + double **fix_array = reference.val.f->array_atom; + int im1 = reference.argindex - 1; + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) indices[i] = static_cast (fix_array[i][im1]) - 1; } - } else if (whichref == ArgInfo::VARIABLE) { - input->variable->compute_atom(ref2index,igroup,varatom,1,0); - for (i = 0; i < nlocal; i++) + } else if (reference.which == ArgInfo::VARIABLE) { + input->variable->compute_atom(reference.val.v, igroup, varatom, 1, 0); + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) indices[i] = static_cast (varatom[i]) - 1; } // loop over values to fill output vector or array - for (int m = 0; m < nvalues; m++) { + int m = 0; + for (auto &val : values) { // output = vector - if (argindex[m] == 0) { + if (val.argindex == 0) { int vmax; double *source; - if (which[m] == ArgInfo::COMPUTE) { - Compute *compute = modify->compute[value2index[m]]; + if (val.which == ArgInfo::COMPUTE) { - if (!(compute->invoked_flag & Compute::INVOKED_VECTOR)) { - compute->compute_vector(); - compute->invoked_flag |= Compute::INVOKED_VECTOR; + if (!(val.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { + val.val.c->compute_vector(); + val.val.c->invoked_flag |= Compute::INVOKED_VECTOR; } - source = compute->vector; - vmax = compute->size_vector; + source = val.val.c->vector; + vmax = val.val.c->size_vector; - } else if (which[m] == ArgInfo::FIX) { - if (update->ntimestep % modify->fix[value2index[m]]->peratom_freq) - error->all(FLERR,"Fix used in compute global/atom not computed at compatible time"); - Fix *fix = modify->fix[value2index[m]]; - vmax = fix->size_vector; + } else if (val.which == ArgInfo::FIX) { + if (update->ntimestep % val.val.f->peratom_freq) + error->all(FLERR,"Fix {} used in compute global/atom not computed at compatible time", + val.id); + vmax = reference.val.f->size_vector; if (vmax > maxvector) { maxvector = vmax; @@ -368,28 +344,28 @@ void ComputeGlobalAtom::compute_peratom() memory->create(vecglobal,maxvector,"global/atom:vecglobal"); } - for (i = 0; i < vmax; i++) - vecglobal[i] = fix->compute_vector(i); + for (int i = 0; i < vmax; i++) + vecglobal[i] = val.val.f->compute_vector(i); source = vecglobal; - } else if (which[m] == ArgInfo::VARIABLE) { - vmax = input->variable->compute_vector(value2index[m],&source); + } else if (val.which == ArgInfo::VARIABLE) { + vmax = input->variable->compute_vector(val.val.v, &source); } - if (nvalues == 1) { - for (i = 0; i < nlocal; i++) { + if (values.size() == 1) { + for (int i = 0; i < nlocal; i++) { vector_atom[i] = 0.0; if (mask[i] & groupbit) { - j = indices[i]; + int j = indices[i]; if (j >= 0 && j < vmax) vector_atom[i] = source[j]; } } } else { - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { array_atom[i][m] = 0.0; if (mask[i] & groupbit) { - j = indices[i]; + int j = indices[i]; if (j >= 0 && j < vmax) array_atom[i][m] = source[j]; } } @@ -400,18 +376,17 @@ void ComputeGlobalAtom::compute_peratom() } else { int vmax; double *source; - int col = argindex[m] - 1; + int col = val.argindex - 1; - if (which[m] == ArgInfo::COMPUTE) { - Compute *compute = modify->compute[value2index[m]]; + if (val.which == ArgInfo::COMPUTE) { - if (!(compute->invoked_flag & Compute::INVOKED_ARRAY)) { - compute->compute_array(); - compute->invoked_flag |= Compute::INVOKED_ARRAY; + if (!(val.val.c->invoked_flag & Compute::INVOKED_ARRAY)) { + val.val.c->compute_array(); + val.val.c->invoked_flag |= Compute::INVOKED_ARRAY; } - double **compute_array = compute->array; - vmax = compute->size_array_rows; + double **compute_array = val.val.c->array; + vmax = val.val.c->size_array_rows; if (vmax > maxvector) { maxvector = vmax; @@ -419,17 +394,16 @@ void ComputeGlobalAtom::compute_peratom() memory->create(vecglobal,maxvector,"global/atom:vecglobal"); } - for (i = 0; i < vmax; i++) + for (int i = 0; i < vmax; i++) vecglobal[i] = compute_array[i][col]; source = vecglobal; - } else if (which[m] == ArgInfo::FIX) { - if (update->ntimestep % modify->fix[value2index[m]]->peratom_freq) - error->all(FLERR,"Fix used in compute global/atom not " - "computed at compatible time"); - Fix *fix = modify->fix[value2index[m]]; - vmax = fix->size_array_rows; + } else if (val.which == ArgInfo::FIX) { + if (update->ntimestep % val.val.f->peratom_freq) + error->all(FLERR,"Fix {} used in compute global/atom not computed at compatible time", + val.id); + vmax = val.val.f->size_array_rows; if (vmax > maxvector) { maxvector = vmax; @@ -437,34 +411,35 @@ void ComputeGlobalAtom::compute_peratom() memory->create(vecglobal,maxvector,"global/atom:vecglobal"); } - for (i = 0; i < vmax; i++) - vecglobal[i] = fix->compute_array(i,col); + for (int i = 0; i < vmax; i++) + vecglobal[i] = val.val.f->compute_array(i,col); source = vecglobal; - } else if (which[m] == ArgInfo::VARIABLE) { - vmax = input->variable->compute_vector(value2index[m],&source); + } else if (val.which == ArgInfo::VARIABLE) { + vmax = input->variable->compute_vector(val.val.v, &source); } - if (nvalues == 1) { - for (i = 0; i < nlocal; i++) { + if (values.size() == 1) { + for (int i = 0; i < nlocal; i++) { vector_atom[i] = 0.0; if (mask[i] & groupbit) { - j = indices[i]; + int j = indices[i]; if (j >= 0 && j < vmax) vector_atom[i] = source[j]; } } } else { - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { array_atom[i][m] = 0.0; if (mask[i] & groupbit) { - j = indices[i]; + int j = indices[i]; if (j >= 0 && j < vmax) array_atom[i][m] = source[j]; } } } } } + ++m; } /* ---------------------------------------------------------------------- @@ -473,7 +448,7 @@ void ComputeGlobalAtom::compute_peratom() double ComputeGlobalAtom::memory_usage() { - double bytes = (double)nmax*nvalues * sizeof(double); + double bytes = (double)nmax*values.size() * sizeof(double); bytes += (double)nmax * sizeof(int); // indices if (varatom) bytes += (double)nmax * sizeof(double); // varatom bytes += (double)maxvector * sizeof(double); // vecglobal diff --git a/src/compute_global_atom.h b/src/compute_global_atom.h index 67b499dc3c..3a4808bddd 100644 --- a/src/compute_global_atom.h +++ b/src/compute_global_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -33,12 +33,18 @@ class ComputeGlobalAtom : public Compute { double memory_usage() override; protected: - int whichref, indexref, ref2index; - char *idref; - - int nvalues; - int *which, *argindex, *value2index; - char **ids; + struct value_t { + int which; + int argindex; + std::string id; + union { + class Compute *c; + class Fix *f; + int v; + } val; + }; + std::vector values; + value_t reference; int nmax, maxvector; int *indices; diff --git a/src/compute_group_group.cpp b/src/compute_group_group.cpp index 2fcd3b9c22..31bbc81597 100644 --- a/src/compute_group_group.cpp +++ b/src/compute_group_group.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_group_group.h b/src/compute_group_group.h index b813ca1e2c..3e66484368 100644 --- a/src/compute_group_group.h +++ b/src/compute_group_group.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_gyration.cpp b/src/compute_gyration.cpp index 623f7b9c92..74220fb9f6 100644 --- a/src/compute_gyration.cpp +++ b/src/compute_gyration.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_gyration.h b/src/compute_gyration.h index 4d014eb31a..3c061f1b85 100644 --- a/src/compute_gyration.h +++ b/src/compute_gyration.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_gyration_chunk.cpp b/src/compute_gyration_chunk.cpp index 8dd28ca4e6..5432a15fa6 100644 --- a/src/compute_gyration_chunk.cpp +++ b/src/compute_gyration_chunk.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_gyration_chunk.h b/src/compute_gyration_chunk.h index 0a560a3e39..c455f5a100 100644 --- a/src/compute_gyration_chunk.h +++ b/src/compute_gyration_chunk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_heat_flux.cpp b/src/compute_heat_flux.cpp index d363d0ae5d..b1d26b6b95 100644 --- a/src/compute_heat_flux.cpp +++ b/src/compute_heat_flux.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_heat_flux.h b/src/compute_heat_flux.h index 83a2c800c3..4fbc8f0827 100644 --- a/src/compute_heat_flux.h +++ b/src/compute_heat_flux.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_improper.cpp b/src/compute_improper.cpp index d2b426c5b3..36a38a48f8 100644 --- a/src/compute_improper.cpp +++ b/src/compute_improper.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_improper.h b/src/compute_improper.h index 3deb23db77..6e4237720a 100644 --- a/src/compute_improper.h +++ b/src/compute_improper.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_improper_local.cpp b/src/compute_improper_local.cpp index 7a80ce982a..48070a4f7c 100644 --- a/src/compute_improper_local.cpp +++ b/src/compute_improper_local.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_improper_local.h b/src/compute_improper_local.h index 899aaf17f5..26b6072421 100644 --- a/src/compute_improper_local.h +++ b/src/compute_improper_local.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_inertia_chunk.cpp b/src/compute_inertia_chunk.cpp index 275ef66071..ee94231c5b 100644 --- a/src/compute_inertia_chunk.cpp +++ b/src/compute_inertia_chunk.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_inertia_chunk.h b/src/compute_inertia_chunk.h index 7ada8e634e..6ec318833a 100644 --- a/src/compute_inertia_chunk.h +++ b/src/compute_inertia_chunk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_ke.cpp b/src/compute_ke.cpp index c515522195..e6525d6b4e 100644 --- a/src/compute_ke.cpp +++ b/src/compute_ke.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_ke.h b/src/compute_ke.h index d428aa71da..7fa530b333 100644 --- a/src/compute_ke.h +++ b/src/compute_ke.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_ke_atom.cpp b/src/compute_ke_atom.cpp index 3f0a0f85ab..2db93f81fe 100644 --- a/src/compute_ke_atom.cpp +++ b/src/compute_ke_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_ke_atom.h b/src/compute_ke_atom.h index e967ef9bc3..1653a2e8c6 100644 --- a/src/compute_ke_atom.h +++ b/src/compute_ke_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_msd.cpp b/src/compute_msd.cpp index 90d8f47b7a..8b7043e20d 100644 --- a/src/compute_msd.cpp +++ b/src/compute_msd.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_msd.h b/src/compute_msd.h index 11ac804259..a273e9cf58 100644 --- a/src/compute_msd.h +++ b/src/compute_msd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_msd_chunk.cpp b/src/compute_msd_chunk.cpp index 14f8786db5..cc718d1b53 100644 --- a/src/compute_msd_chunk.cpp +++ b/src/compute_msd_chunk.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_msd_chunk.h b/src/compute_msd_chunk.h index 5e745bb39a..7357f440a1 100644 --- a/src/compute_msd_chunk.h +++ b/src/compute_msd_chunk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_omega_chunk.cpp b/src/compute_omega_chunk.cpp index 0378fa19ef..50c42b6501 100644 --- a/src/compute_omega_chunk.cpp +++ b/src/compute_omega_chunk.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_omega_chunk.h b/src/compute_omega_chunk.h index 0184637595..cbd158c525 100644 --- a/src/compute_omega_chunk.h +++ b/src/compute_omega_chunk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp index e224c0d509..7821d0683e 100644 --- a/src/compute_orientorder_atom.cpp +++ b/src/compute_orientorder_atom.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_orientorder_atom.h b/src/compute_orientorder_atom.h index adf27a2faa..5fd3e7e6dd 100644 --- a/src/compute_orientorder_atom.h +++ b/src/compute_orientorder_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_pair.cpp b/src/compute_pair.cpp index 7e1b6fc062..7088787e6d 100644 --- a/src/compute_pair.cpp +++ b/src/compute_pair.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_pair.h b/src/compute_pair.h index 2a2f42f299..3c146749af 100644 --- a/src/compute_pair.h +++ b/src/compute_pair.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_pair_local.cpp b/src/compute_pair_local.cpp index 3176bb667b..f106e6a879 100644 --- a/src/compute_pair_local.cpp +++ b/src/compute_pair_local.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_pair_local.h b/src/compute_pair_local.h index 84adfaaf50..ce1459b8eb 100644 --- a/src/compute_pair_local.h +++ b/src/compute_pair_local.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_pe.cpp b/src/compute_pe.cpp index 2385f1e94e..f4207408f9 100644 --- a/src/compute_pe.cpp +++ b/src/compute_pe.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_pe.h b/src/compute_pe.h index 0ad8097226..4df58c6475 100644 --- a/src/compute_pe.h +++ b/src/compute_pe.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_pe_atom.cpp b/src/compute_pe_atom.cpp index b1b62ec16d..2e1973ceca 100644 --- a/src/compute_pe_atom.cpp +++ b/src/compute_pe_atom.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_pe_atom.h b/src/compute_pe_atom.h index 03e04dfd1a..f1f3f9f2fa 100644 --- a/src/compute_pe_atom.h +++ b/src/compute_pe_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp index 53ac58e505..4c63505954 100644 --- a/src/compute_pressure.cpp +++ b/src/compute_pressure.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_pressure.h b/src/compute_pressure.h index 8338922471..88d50471fa 100644 --- a/src/compute_pressure.h +++ b/src/compute_pressure.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_property_atom.cpp b/src/compute_property_atom.cpp index f6ed867c63..fc7089fa01 100644 --- a/src/compute_property_atom.cpp +++ b/src/compute_property_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_property_atom.h b/src/compute_property_atom.h index 0e551e2818..034b2901c2 100644 --- a/src/compute_property_atom.h +++ b/src/compute_property_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_property_chunk.cpp b/src/compute_property_chunk.cpp index 46914ca358..909ffdbc9e 100644 --- a/src/compute_property_chunk.cpp +++ b/src/compute_property_chunk.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_property_chunk.h b/src/compute_property_chunk.h index 0d299a6026..7339d6479a 100644 --- a/src/compute_property_chunk.h +++ b/src/compute_property_chunk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_property_grid.cpp b/src/compute_property_grid.cpp new file mode 100644 index 0000000000..2b8df955ef --- /dev/null +++ b/src/compute_property_grid.cpp @@ -0,0 +1,559 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "compute_property_grid.h" + +#include "domain.h" +#include "error.h" +#include "grid2d.h" +#include "grid3d.h" +#include "memory.h" +#include "update.h" + +#include + +using namespace LAMMPS_NS; + +enum { LOW, CTR }; +enum { UNSCALED, SCALED }; + +#define DELTA 10000 + +/* ---------------------------------------------------------------------- */ + +ComputePropertyGrid::ComputePropertyGrid(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg), grid2d(nullptr), grid3d(nullptr), vec2d(nullptr), vec3d(nullptr), + array2d(nullptr), array3d(nullptr), pack_choice(nullptr) +{ + if (narg < 7) utils::missing_cmd_args(FLERR, "compute property/grid", error); + + pergrid_flag = 1; + + dimension = domain->dimension; + + nxgrid = utils::inumeric(FLERR, arg[3], false, lmp); + nygrid = utils::inumeric(FLERR, arg[4], false, lmp); + nzgrid = utils::inumeric(FLERR, arg[5], false, lmp); + + if (dimension == 2 && nzgrid != 1) + error->all(FLERR, "Compute property/grid for 2d requires nz = 1"); + + if (nxgrid <= 0 || nygrid <= 0 || nzgrid <= 0) + error->all(FLERR, "All compute property/grid grid counts must be > 0"); + + nvalues = narg - 6; + pack_choice = new FnPtrPack[nvalues]; + + for (int iarg = 6; iarg < narg; iarg++) { + int jarg = iarg - 6; + + if (strcmp(arg[iarg], "id") == 0) { + pack_choice[jarg] = &ComputePropertyGrid::pack_id; + + } else if (strcmp(arg[iarg], "ix") == 0) { + pack_choice[jarg] = &ComputePropertyGrid::pack_indices<0>; + } else if (strcmp(arg[iarg], "iy") == 0) { + pack_choice[jarg] = &ComputePropertyGrid::pack_indices<1>; + } else if (strcmp(arg[iarg], "iz") == 0) { + if (dimension == 2) error->all(FLERR, "Compute property/grid for 2d cannot use z coord"); + pack_choice[jarg] = &ComputePropertyGrid::pack_indices<2>; + + } else if (strcmp(arg[iarg], "x") == 0) { + pack_choice[jarg] = &ComputePropertyGrid::pack_coords; + } else if (strcmp(arg[iarg], "y") == 0) { + pack_choice[jarg] = &ComputePropertyGrid::pack_coords; + } else if (strcmp(arg[iarg], "z") == 0) { + if (dimension == 2) error->all(FLERR, "Compute property/grid for 2d cannot use z coord"); + pack_choice[jarg] = &ComputePropertyGrid::pack_coords; + + } else if (strcmp(arg[iarg], "xs") == 0) { + pack_choice[jarg] = &ComputePropertyGrid::pack_coords; + } else if (strcmp(arg[iarg], "ys") == 0) { + pack_choice[jarg] = &ComputePropertyGrid::pack_coords; + } else if (strcmp(arg[iarg], "zs") == 0) { + if (dimension == 2) error->all(FLERR, "Compute property/grid for 2d cannot use z coord"); + pack_choice[jarg] = &ComputePropertyGrid::pack_coords; + + } else if (strcmp(arg[iarg], "xc") == 0) { + pack_choice[jarg] = &ComputePropertyGrid::pack_coords; + } else if (strcmp(arg[iarg], "yc") == 0) { + pack_choice[jarg] = &ComputePropertyGrid::pack_coords; + } else if (strcmp(arg[iarg], "zc") == 0) { + if (dimension == 2) error->all(FLERR, "Compute property/grid for 2d cannot use z coord"); + pack_choice[jarg] = &ComputePropertyGrid::pack_coords; + + } else if (strcmp(arg[iarg], "xsc") == 0) { + pack_choice[jarg] = &ComputePropertyGrid::pack_coords; + } else if (strcmp(arg[iarg], "ysc") == 0) { + pack_choice[jarg] = &ComputePropertyGrid::pack_coords; + } else if (strcmp(arg[iarg], "zsc") == 0) { + if (dimension == 2) error->all(FLERR, "Compute property/grid for 2d cannot use z coord"); + pack_choice[jarg] = &ComputePropertyGrid::pack_coords; + + } else + error->all(FLERR, "Unknown compute property/grid keyword: {}", arg[iarg]); + } + + // initial setup of distributed grid + + allocate_grid(); +} + +/* ---------------------------------------------------------------------- */ + +ComputePropertyGrid::~ComputePropertyGrid() +{ + delete[] pack_choice; + + deallocate_grid(); +} + +/* ---------------------------------------------------------------------- */ + +void ComputePropertyGrid::init() +{ + triclinic = domain->triclinic; +} + +/* ---------------------------------------------------------------------- */ + +void ComputePropertyGrid::compute_pergrid() +{ + invoked_pergrid = update->ntimestep; + + // fill data vector or array with values for my grid pts + + if (nvalues == 1) { + (this->*pack_choice[0])(0); + } else { + for (int n = 0; n < nvalues; n++) (this->*pack_choice[n])(n); + } +} + +/* ---------------------------------------------------------------------- + subset of grid assigned to each proc may have changed + deallocate and reallocate Grid class and local data structs + called by load balancer when proc subdomains are adjusted +---------------------------------------------------------------------- */ + +void ComputePropertyGrid::reset_grid() +{ + deallocate_grid(); + allocate_grid(); +} + +/* ---------------------------------------------------------------------- + return index of grid associated with name + this class can store M named grids, indexed 0 to M-1 + also set dim for 2d vs 3d grid + return -1 if grid name not found +------------------------------------------------------------------------- */ + +int ComputePropertyGrid::get_grid_by_name(const std::string &name, int &dim) +{ + if (name == "grid") { + dim = dimension; + return 0; + } + + return -1; +} + +/* ---------------------------------------------------------------------- + return ptr to Grid data struct for grid with index + this class can store M named grids, indexed 0 to M-1 + return nullptr if index is invalid +------------------------------------------------------------------------- */ + +void *ComputePropertyGrid::get_grid_by_index(int index) +{ + if (index == 0) { + if (dimension == 2) + return grid2d; + else + return grid3d; + } + + return nullptr; +} + +/* ---------------------------------------------------------------------- + return index of data associated with name in grid with index igrid + this class can store M named grids, indexed 0 to M-1 + each grid can store G named data sets, indexed 0 to G-1 + a data set name can be associated with multiple grids + set ncol for data set, 0 = vector, 1-N for array with N columns + vector = single value per grid pt, array = N values per grid pt + return -1 if data name not found +------------------------------------------------------------------------- */ + +int ComputePropertyGrid::get_griddata_by_name(int igrid, const std::string &name, int &ncol) +{ + if ((igrid == 0) && (name == "data")) { + if (nvalues == 1) + ncol = 0; + else + ncol = nvalues; + return 0; + } + + return -1; +} + +/* ---------------------------------------------------------------------- + return ptr to multidim data array associated with index + this class can store G named data sets, indexed 0 to M-1 + return nullptr if index is invalid +------------------------------------------------------------------------- */ + +void *ComputePropertyGrid::get_griddata_by_index(int index) +{ + if (index == 0) { + if (dimension == 2) { + if (nvalues == 1) + return vec2d; + else + return array2d; + } else { + if (nvalues == 1) + return vec3d; + else + return array3d; + } + } + + return nullptr; +} + +/* ---------------------------------------------------------------------- + instantiate the Grid class and allocate local per-grid memory +---------------------------------------------------------------------- */ + +void ComputePropertyGrid::allocate_grid() +{ + if (dimension == 2) { + grid2d = new Grid2d(lmp, world, nxgrid, nygrid); + grid2d->setup_grid(nxlo_in, nxhi_in, nylo_in, nyhi_in, nxlo_out, nxhi_out, nylo_out, nyhi_out); + + if (nvalues == 1) + memory->create2d_offset(vec2d, nylo_out, nyhi_out, nxlo_out, nxhi_out, "property/grid:vec2d"); + else + memory->create3d_offset_last(array2d, nylo_out, nyhi_out, nxlo_out, nxhi_out, nvalues, + "property/grid:array2d"); + ngridout = (nxhi_out - nxlo_out + 1) * (nyhi_out - nylo_out + 1); + + } else { + grid3d = new Grid3d(lmp, world, nxgrid, nygrid, nzgrid); + grid3d->setup_grid(nxlo_in, nxhi_in, nylo_in, nyhi_in, nzlo_in, nzhi_in, + nxlo_out, nxhi_out, nylo_out, nyhi_out, nzlo_out, nzhi_out); + if (nvalues == 1) + memory->create3d_offset(vec3d, nzlo_out, nzhi_out, nylo_out, nyhi_out, nxlo_out, nxhi_out, + "property/grid:vec3d"); + else + memory->create4d_offset_last(array3d, nzlo_out, nzhi_out, nylo_out, nyhi_out, nxlo_out, + nxhi_out, nvalues, "property/grid:array3d"); + ngridout = (nxhi_out - nxlo_out + 1) * (nyhi_out - nylo_out + 1) * (nzhi_out - nzlo_out + 1); + } +} + +/* ---------------------------------------------------------------------- */ + +void ComputePropertyGrid::deallocate_grid() +{ + delete grid2d; + delete grid3d; + memory->destroy2d_offset(vec2d, nylo_out, nxlo_out); + memory->destroy3d_offset_last(array2d, nylo_out, nxlo_out); + memory->destroy3d_offset(vec3d, nzlo_out, nylo_out, nxlo_out); + memory->destroy4d_offset_last(array3d, nzlo_out, nylo_out, nxlo_out); +} + +/* ---------------------------------------------------------------------- + memory usage of grid data +------------------------------------------------------------------------- */ + +double ComputePropertyGrid::memory_usage() +{ + double bytes = (double) ngridout * nvalues * sizeof(double); + return bytes; +} + +// ---------------------------------------------------------------------- +// pack methods for all values +// ---------------------------------------------------------------------- + +/* ---------------------------------------------------------------------- + grid point IDs +------------------------------------------------------------------------- */ + +void ComputePropertyGrid::pack_id(int n) +{ + if (dimension == 2) { + if (nvalues == 1) { + for (int iy = nylo_in; iy <= nyhi_in; iy++) + for (int ix = nxlo_in; ix <= nxhi_in; ix++) vec2d[iy][ix] = iy * nxgrid + ix + 1; + } else { + for (int iy = nylo_in; iy <= nyhi_in; iy++) + for (int ix = nxlo_in; ix <= nxhi_in; ix++) array2d[iy][ix][n] = iy * nxgrid + ix + 1; + } + } else if (dimension == 3) { + if (nvalues == 1) { + for (int iz = nzlo_in; iz <= nzhi_in; iz++) + for (int iy = nylo_in; iy <= nyhi_in; iy++) + for (int ix = nxlo_in; ix <= nxhi_in; ix++) + vec3d[iz][iy][ix] = iz * nygrid * nxgrid + iy * nxgrid + ix + 1; + } else { + for (int iz = nzlo_in; iz <= nzhi_in; iz++) + for (int iy = nylo_in; iy <= nyhi_in; iy++) + for (int ix = nxlo_in; ix <= nxhi_in; ix++) + array3d[iz][iy][ix][n] = iz * nygrid * nxgrid + iy * nxgrid + ix + 1; + } + } +} + +/* ---------------------------------------------------------------------- + grid indices via templating +------------------------------------------------------------------------- */ + +template void ComputePropertyGrid::pack_indices(int n) +{ + if (dimension == 2) { + if (nvalues == 1) { + for (int iy = nylo_in; iy <= nyhi_in; iy++) + for (int ix = nxlo_in; ix <= nxhi_in; ix++) { + if (IDIM == 0) vec2d[iy][ix] = ix + 1; + if (IDIM == 1) vec2d[iy][ix] = iy + 1; + } + } else { + for (int iy = nylo_in; iy <= nyhi_in; iy++) + for (int ix = nxlo_in; ix <= nxhi_in; ix++) { + if (IDIM == 0) array2d[iy][ix][n] = ix + 1; + if (IDIM == 1) array2d[iy][ix][n] = iy + 1; + } + } + + } else if (dimension == 3) { + if (nvalues == 1) { + for (int iz = nzlo_in; iz <= nzhi_in; iz++) + for (int iy = nylo_in; iy <= nyhi_in; iy++) + for (int ix = nxlo_in; ix <= nxhi_in; ix++) { + if (IDIM == 0) vec3d[iz][iy][ix] = ix + 1; + if (IDIM == 1) vec3d[iz][iy][ix] = iy + 1; + if (IDIM == 2) vec3d[iz][iy][ix] = iz + 1; + } + } else { + for (int iz = nzlo_in; iz <= nzhi_in; iz++) + for (int iy = nylo_in; iy <= nyhi_in; iy++) + for (int ix = nxlo_in; ix <= nxhi_in; ix++) { + if (IDIM == 0) array3d[iz][iy][ix][n] = ix + 1; + if (IDIM == 1) array3d[iz][iy][ix][n] = iy + 1; + if (IDIM == 2) array3d[iz][iy][ix][n] = iz + 1; + } + } + } +} + +/* ---------------------------------------------------------------------- + grid point coords + LOW/CTR, SCALED/UNSCALED, DIM = 0/1 via templating + dimension and orthogonal/tricilic in code logic +------------------------------------------------------------------------- */ + +template void ComputePropertyGrid::pack_coords(int n) +{ + double boxlo, delta; + double lamda[3], xone[3]; + + // 2d grid + + if (dimension == 2) { + + // for coords which are orthogonal OR scaled + + if (!triclinic || MODE == SCALED) { + + if (MODE == UNSCALED) { + boxlo = domain->boxlo[IDIM]; + if (IDIM == 0) delta = domain->prd[IDIM] / nxgrid; + if (IDIM == 1) delta = domain->prd[IDIM] / nygrid; + } + if (MODE == SCALED) { + boxlo = 0.0; + if (IDIM == 0) delta = 1.0 / nxgrid; + if (IDIM == 1) delta = 1.0 / nygrid; + } + + if (nvalues == 1) { + for (int iy = nylo_in; iy <= nyhi_in; iy++) + for (int ix = nxlo_in; ix <= nxhi_in; ix++) { + if (POS == LOW) { + if (IDIM == 0) vec2d[iy][ix] = boxlo + ix * delta; + if (IDIM == 1) vec2d[iy][ix] = boxlo + iy * delta; + } + if (POS == CTR) { + if (IDIM == 0) vec2d[iy][ix] = boxlo + (ix + 0.5) * delta; + if (IDIM == 1) vec2d[iy][ix] = boxlo + (iy + 0.5) * delta; + } + } + + } else { + for (int iy = nylo_in; iy <= nyhi_in; iy++) + for (int ix = nxlo_in; ix <= nxhi_in; ix++) { + if (POS == LOW) { + if (IDIM == 0) array2d[iy][ix][n] = boxlo + ix * delta; + if (IDIM == 1) array2d[iy][ix][n] = boxlo + iy * delta; + } + if (POS == CTR) { + if (IDIM == 0) array2d[iy][ix][n] = boxlo + (ix + 0.5) * delta; + if (IDIM == 1) array2d[iy][ix][n] = boxlo + (iy + 0.5) * delta; + } + } + } + + // only for coords which are triclinic AND unscaled + + } else { + + double dx = 1.0 / nxgrid; + double dy = 1.0 / nygrid; + lamda[2] = 0.0; + + if (nvalues == 1) { + for (int iy = nylo_in; iy <= nyhi_in; iy++) { + if (POS == LOW) lamda[1] = iy * dy; + else lamda[1] = (iy + 0.5) * dy; + for (int ix = nxlo_in; ix <= nxhi_in; ix++) { + if (POS == LOW) lamda[0] = ix * dx; + else lamda[0] = (ix + 0.5) * dx; + domain->lamda2x(lamda, xone); + if (IDIM == 0) vec2d[iy][ix] = xone[0]; + if (IDIM == 1) vec2d[iy][ix] = xone[1]; + } + } + + } else { + for (int iy = nylo_in; iy <= nyhi_in; iy++) { + if (POS == LOW) lamda[1] = iy * dy; + else lamda[1] = (iy + 0.5) * dy; + for (int ix = nxlo_in; ix <= nxhi_in; ix++) { + if (POS == LOW) lamda[0] = ix * dx; + else lamda[0] = (ix + 0.5) * dx; + domain->lamda2x(lamda, xone); + if (IDIM == 0) array2d[iy][ix][n] = xone[0]; + if (IDIM == 1) array2d[iy][ix][n] = xone[1]; + } + } + } + } + + // 3d grid + + } else if (dimension == 3) { + + // for coords which are orthogonal OR scaled + + if (!triclinic || MODE == SCALED) { + + if (MODE == UNSCALED) { + boxlo = domain->boxlo[IDIM]; + if (IDIM == 0) delta = domain->prd[IDIM] / nxgrid; + if (IDIM == 1) delta = domain->prd[IDIM] / nygrid; + if (IDIM == 2) delta = domain->prd[IDIM] / nzgrid; + } + if (MODE == SCALED) { + boxlo = 0.0; + if (IDIM == 0) delta = 1.0 / nxgrid; + if (IDIM == 1) delta = 1.0 / nygrid; + if (IDIM == 2) delta = 1.0 / nzgrid; + } + + if (nvalues == 1) { + for (int iz = nzlo_in; iz <= nzhi_in; iz++) + for (int iy = nylo_in; iy <= nyhi_in; iy++) + for (int ix = nxlo_in; ix <= nxhi_in; ix++) { + if (POS == LOW) { + if (IDIM == 0) vec3d[iz][iy][ix] = boxlo + ix * delta; + if (IDIM == 1) vec3d[iz][iy][ix] = boxlo + iy * delta; + if (IDIM == 2) vec3d[iz][iy][ix] = boxlo + iz * delta; + } + if (POS == CTR) { + if (IDIM == 0) vec3d[iz][iy][ix] = boxlo + (ix + 0.5) * delta; + if (IDIM == 1) vec3d[iz][iy][ix] = boxlo + (iy + 0.5) * delta; + if (IDIM == 2) vec3d[iz][iy][ix] = boxlo + (iz + 0.5) * delta; + } + } + + } else { + for (int iz = nzlo_in; iz <= nzhi_in; iz++) + for (int iy = nylo_in; iy <= nyhi_in; iy++) + for (int ix = nxlo_in; ix <= nxhi_in; ix++) { + if (POS == LOW) { + if (IDIM == 0) array3d[iz][iy][ix][n] = boxlo + ix * delta; + if (IDIM == 1) array3d[iz][iy][ix][n] = boxlo + iy * delta; + if (IDIM == 2) array3d[iz][iy][ix][n] = boxlo + iz * delta; + } + if (POS == CTR) { + if (IDIM == 0) array3d[iz][iy][ix][n] = boxlo + (ix + 0.5) * delta; + if (IDIM == 1) array3d[iz][iy][ix][n] = boxlo + (iy + 0.5) * delta; + if (IDIM == 2) array3d[iz][iy][ix][n] = boxlo + (iz + 0.5) * delta; + } + } + } + + // only for coords which are triclinic AND unscaled + + } else { + + double dx = 1.0 / nxgrid; + double dy = 1.0 / nygrid; + double dz = 1.0 / nzgrid; + + if (nvalues == 1) { + for (int iz = nzlo_in; iz <= nzhi_in; iz++) { + if (POS == LOW) lamda[2] = iz * dz; + else lamda[2] = (iz + 0.5) * dz; + for (int iy = nylo_in; iy <= nyhi_in; iy++) { + if (POS == LOW) lamda[1] = iy * dy; + else lamda[1] = (iy + 0.5) * dy; + for (int ix = nxlo_in; ix <= nxhi_in; ix++) { + if (POS == LOW) lamda[0] = ix * dx; + else lamda[0] = (ix + 0.5) * dx; + domain->lamda2x(lamda, xone); + if (IDIM == 0) vec3d[iz][iy][ix] = xone[0]; + if (IDIM == 1) vec3d[iz][iy][ix] = xone[1]; + if (IDIM == 2) vec3d[iz][iy][ix] = xone[2]; + } + } + } + + } else { + for (int iz = nzlo_in; iz <= nzhi_in; iz++) { + if (POS == LOW) lamda[2] = iz * dz; + else lamda[2] = (iz + 0.5) * dz; + for (int iy = nylo_in; iy <= nyhi_in; iy++) { + if (POS == LOW) lamda[1] = iy * dy; + else lamda[1] = (iy + 0.5) * dy; + for (int ix = nxlo_in; ix <= nxhi_in; ix++) { + if (POS == LOW) lamda[0] = ix * dx; + else lamda[0] = (ix + 0.5) * dx; + domain->lamda2x(lamda, xone); + if (IDIM == 0) array3d[iz][iy][ix][n] = xone[0]; + if (IDIM == 1) array3d[iz][iy][ix][n] = xone[1]; + if (IDIM == 2) array3d[iz][iy][ix][n] = xone[2]; + } + } + } + } + } + } +} diff --git a/src/compute_property_grid.h b/src/compute_property_grid.h new file mode 100644 index 0000000000..8a0ef63090 --- /dev/null +++ b/src/compute_property_grid.h @@ -0,0 +1,75 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + 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 COMPUTE_CLASS +// clang-format off +ComputeStyle(property/grid,ComputePropertyGrid); +// clang-format on +#else + +#ifndef LMP_COMPUTE_PROPERTY_GRID_H +#define LMP_COMPUTE_PROPERTY_GRID_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputePropertyGrid : public Compute { + public: + ComputePropertyGrid(class LAMMPS *, int, char **); + ~ComputePropertyGrid() override; + void init() override; + void compute_pergrid() override; + + void reset_grid() override; + + int get_grid_by_name(const std::string &, int &) override; + void *get_grid_by_index(int) override; + int get_griddata_by_name(int, const std::string &, int &) override; + void *get_griddata_by_index(int) override; + + double memory_usage() override; + + private: + int nxgrid,nygrid,nzgrid; + int nvalues; + int dimension; + int triclinic; + + class Grid2d *grid2d; + class Grid3d *grid3d; + + int nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in; + int nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out; + int ngridout; + + double **vec2d,***vec3d; + double ***array2d,****array3d; + + // local methods + + void allocate_grid(); + void deallocate_grid(); + + typedef void (ComputePropertyGrid::*FnPtrPack)(int); + FnPtrPack *pack_choice; // ptrs to pack functions + + void pack_id(int); + template void pack_indices(int); + template void pack_coords(int); +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/compute_property_local.cpp b/src/compute_property_local.cpp index b00535d5ed..c4f0c547a3 100644 --- a/src/compute_property_local.cpp +++ b/src/compute_property_local.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_property_local.h b/src/compute_property_local.h index 4b669ca72d..b1a9902f58 100644 --- a/src/compute_property_local.h +++ b/src/compute_property_local.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp index a5068b5acd..17fe450fe5 100644 --- a/src/compute_rdf.cpp +++ b/src/compute_rdf.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_rdf.h b/src/compute_rdf.h index a8cdb6b89c..d2914ca6c6 100644 --- a/src/compute_rdf.h +++ b/src/compute_rdf.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp index c8426673ab..f2afeab3e6 100644 --- a/src/compute_reduce.cpp +++ b/src/compute_reduce.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -15,6 +15,7 @@ #include "arg_info.h" #include "atom.h" +#include "comm.h" #include "domain.h" #include "error.h" #include "fix.h" @@ -25,6 +26,7 @@ #include "update.h" #include "variable.h" +#include #include using namespace LAMMPS_NS; @@ -34,16 +36,15 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg), nvalues(0), which(nullptr), argindex(nullptr), flavor(nullptr), - value2index(nullptr), ids(nullptr), onevec(nullptr), replace(nullptr), indices(nullptr), + Compute(lmp, narg, arg), nvalues(0), onevec(nullptr), replace(nullptr), indices(nullptr), owner(nullptr), idregion(nullptr), region(nullptr), varatom(nullptr) { int iarg = 0; if (strcmp(style, "reduce") == 0) { - if (narg < 5) error->all(FLERR, "Illegal compute reduce command"); + if (narg < 5) utils::missing_cmd_args(FLERR, "compute reduce", error); iarg = 3; } else if (strcmp(style, "reduce/region") == 0) { - if (narg < 6) error->all(FLERR, "Illegal compute reduce/region command"); + if (narg < 6) utils::missing_cmd_args(FLERR, "compute reduce/region", error); if (!domain->get_region_by_id(arg[3])) error->all(FLERR, "Region {} for compute reduce/region does not exist", arg[3]); idregion = utils::strdup(arg[3]); @@ -67,11 +68,9 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) : else if (strcmp(arg[iarg], "aveabs") == 0) mode = AVEABS; else - error->all(FLERR, "Illegal compute {} operation {}", style, arg[iarg]); + error->all(FLERR, "Unknown compute {} mode: {}", style, arg[iarg]); iarg++; - MPI_Comm_rank(world, &me); - // expand args if any have wildcard character "*" int expand = 0; @@ -81,95 +80,92 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) : if (earg != &arg[iarg]) expand = 1; arg = earg; - // parse values until one isn't recognized + // parse values - which = new int[nargnew]; - argindex = new int[nargnew]; - flavor = new int[nargnew]; - ids = new char *[nargnew]; - value2index = new int[nargnew]; - for (int i = 0; i < nargnew; ++i) { - which[i] = argindex[i] = flavor[i] = value2index[i] = ArgInfo::UNKNOWN; - ids[i] = nullptr; - } + values.clear(); nvalues = 0; + for (int iarg = 0; iarg < nargnew; ++iarg) { + value_t val; - iarg = 0; - while (iarg < nargnew) { - ids[nvalues] = nullptr; + val.id = ""; + val.flavor = 0; + val.val.c = nullptr; if (strcmp(arg[iarg], "x") == 0) { - which[nvalues] = ArgInfo::X; - argindex[nvalues++] = 0; + val.which = ArgInfo::X; + val.argindex = 0; } else if (strcmp(arg[iarg], "y") == 0) { - which[nvalues] = ArgInfo::X; - argindex[nvalues++] = 1; + val.which = ArgInfo::X; + val.argindex = 1; } else if (strcmp(arg[iarg], "z") == 0) { - which[nvalues] = ArgInfo::X; - argindex[nvalues++] = 2; + val.which = ArgInfo::X; + val.argindex = 2; } else if (strcmp(arg[iarg], "vx") == 0) { - which[nvalues] = ArgInfo::V; - argindex[nvalues++] = 0; + val.which = ArgInfo::V; + val.argindex = 0; } else if (strcmp(arg[iarg], "vy") == 0) { - which[nvalues] = ArgInfo::V; - argindex[nvalues++] = 1; + val.which = ArgInfo::V; + val.argindex = 1; } else if (strcmp(arg[iarg], "vz") == 0) { - which[nvalues] = ArgInfo::V; - argindex[nvalues++] = 2; + val.which = ArgInfo::V; + val.argindex = 2; } else if (strcmp(arg[iarg], "fx") == 0) { - which[nvalues] = ArgInfo::F; - argindex[nvalues++] = 0; + val.which = ArgInfo::F; + val.argindex = 0; } else if (strcmp(arg[iarg], "fy") == 0) { - which[nvalues] = ArgInfo::F; - argindex[nvalues++] = 1; + val.which = ArgInfo::F; + val.argindex = 1; } else if (strcmp(arg[iarg], "fz") == 0) { - which[nvalues] = ArgInfo::F; - argindex[nvalues++] = 2; + val.which = ArgInfo::F; + val.argindex = 2; } else { ArgInfo argi(arg[iarg]); - which[nvalues] = argi.get_type(); - argindex[nvalues] = argi.get_index1(); - ids[nvalues] = argi.copy_name(); + val.which = argi.get_type(); + val.argindex = argi.get_index1(); + val.id = argi.get_name(); - if ((which[nvalues] == ArgInfo::UNKNOWN) || (argi.get_dim() > 1)) - error->all(FLERR, "Illegal compute reduce command"); + if ((val.which == ArgInfo::UNKNOWN) || (argi.get_dim() > 1)) + error->all(FLERR, "Illegal compute {} argument: {}", style, arg[iarg]); - if (which[nvalues] == ArgInfo::NONE) break; - nvalues++; + if (val.which == ArgInfo::NONE) break; } - - iarg++; + values.push_back(val); } // optional args + nvalues = values.size(); replace = new int[nvalues]; - for (int i = 0; i < nvalues; i++) replace[i] = -1; + for (int i = 0; i < nvalues; ++i) replace[i] = -1; + std::string mycmd = "compute "; + mycmd += style; - while (iarg < nargnew) { + for (int iarg = nvalues; iarg < nargnew; iarg++) { if (strcmp(arg[iarg], "replace") == 0) { - if (iarg + 3 > narg) error->all(FLERR, "Illegal compute reduce command"); + if (iarg + 3 > narg) utils::missing_cmd_args(FLERR, mycmd + " replace", error); if (mode != MINN && mode != MAXX) - error->all(FLERR, "Compute reduce replace requires min or max mode"); + error->all(FLERR, "Compute {} replace requires min or max mode", style); int col1 = utils::inumeric(FLERR, arg[iarg + 1], false, lmp) - 1; int col2 = utils::inumeric(FLERR, arg[iarg + 2], false, lmp) - 1; - if (col1 < 0 || col1 >= nvalues || col2 < 0 || col2 >= nvalues) - error->all(FLERR, "Illegal compute reduce command"); - if (col1 == col2) error->all(FLERR, "Illegal compute reduce command"); - if (replace[col1] >= 0 || replace[col2] >= 0) - error->all(FLERR, "Invalid replace values in compute reduce"); + if ((col1 < 0) || (col1 >= nvalues)) + error->all(FLERR, "Invalid compute {} replace first column index {}", style, col1); + if ((col2 < 0) || (col2 >= nvalues)) + error->all(FLERR, "Invalid compute {} replace second column index {}", style, col2); + if (col1 == col2) error->all(FLERR, "Compute {} replace columns must be different"); + if ((replace[col1] >= 0) || (replace[col2] >= 0)) + error->all(FLERR, "Compute {} replace column already used for another replacement"); replace[col1] = col2; - iarg += 3; + iarg += 2; } else - error->all(FLERR, "Illegal compute reduce command"); + error->all(FLERR, "Unknown compute {} keyword: {}", style, arg[iarg]); } - // delete replace if not set + // delete replace list if not set int flag = 0; for (int i = 0; i < nvalues; i++) @@ -188,68 +184,67 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) : // setup and error check - for (int i = 0; i < nvalues; i++) { - if (which[i] == ArgInfo::X || which[i] == ArgInfo::V || which[i] == ArgInfo::F) - flavor[i] = PERATOM; + for (auto &val : values) { + if (val.which == ArgInfo::X || val.which == ArgInfo::V || val.which == ArgInfo::F) + val.flavor = PERATOM; - else if (which[i] == ArgInfo::COMPUTE) { - int icompute = modify->find_compute(ids[i]); - if (icompute < 0) error->all(FLERR, "Compute ID for compute reduce does not exist"); - if (modify->compute[icompute]->peratom_flag) { - flavor[i] = PERATOM; - if (argindex[i] == 0 && modify->compute[icompute]->size_peratom_cols != 0) - error->all(FLERR, - "Compute reduce compute does not " - "calculate a per-atom vector"); - if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0) - error->all(FLERR, - "Compute reduce compute does not " - "calculate a per-atom array"); - if (argindex[i] && argindex[i] > modify->compute[icompute]->size_peratom_cols) - error->all(FLERR, "Compute reduce compute array is accessed out-of-range"); - } else if (modify->compute[icompute]->local_flag) { - flavor[i] = LOCAL; - if (argindex[i] == 0 && modify->compute[icompute]->size_local_cols != 0) - error->all(FLERR, - "Compute reduce compute does not " - "calculate a local vector"); - if (argindex[i] && modify->compute[icompute]->size_local_cols == 0) - error->all(FLERR, - "Compute reduce compute does not " - "calculate a local array"); - if (argindex[i] && argindex[i] > modify->compute[icompute]->size_local_cols) - error->all(FLERR, "Compute reduce compute array is accessed out-of-range"); + else if (val.which == ArgInfo::COMPUTE) { + val.val.c = modify->get_compute_by_id(val.id); + if (!val.val.c) + error->all(FLERR, "Compute ID {} for compute {} does not exist", val.id, style); + if (val.val.c->peratom_flag) { + val.flavor = PERATOM; + if (val.argindex == 0 && val.val.c->size_peratom_cols != 0) + error->all(FLERR, "Compute {} compute {} does not calculate a per-atom vector", style, + val.id); + if (val.argindex && val.val.c->size_peratom_cols == 0) + error->all(FLERR, "Compute {} compute {} does not calculate a per-atom array", style, + val.id); + if (val.argindex && val.argindex > val.val.c->size_peratom_cols) + error->all(FLERR, "Compute {} compute {} array is accessed out-of-range", style, val.id); + } else if (val.val.c->local_flag) { + val.flavor = LOCAL; + if (val.argindex == 0 && val.val.c->size_local_cols != 0) + error->all(FLERR, "Compute {} compute {} does not calculate a local vector", style, + val.id); + if (val.argindex && val.val.c->size_local_cols == 0) + error->all(FLERR, "Compute {} compute {} does not calculate a local array", style, + val.id); + if (val.argindex && val.argindex > val.val.c->size_local_cols) + error->all(FLERR, "Compute {} compute {} array is accessed out-of-range", style, val.id); } else - error->all(FLERR, "Compute reduce compute calculates global values"); + error->all(FLERR, "Compute {} compute {} calculates global values", style, val.id); - } else if (which[i] == ArgInfo::FIX) { - auto ifix = modify->get_fix_by_id(ids[i]); - if (!ifix) error->all(FLERR, "Fix ID {} for compute reduce does not exist", ids[i]); - if (ifix->peratom_flag) { - flavor[i] = PERATOM; - if (argindex[i] == 0 && (ifix->size_peratom_cols != 0)) - error->all(FLERR, "Compute reduce fix {} does not calculate a per-atom vector", ids[i]); - if (argindex[i] && (ifix->size_peratom_cols == 0)) - error->all(FLERR, "Compute reduce fix {} does not calculate a per-atom array", ids[i]); - if (argindex[i] && (argindex[i] > ifix->size_peratom_cols)) - error->all(FLERR, "Compute reduce fix {} array is accessed out-of-range", ids[i]); - } else if (ifix->local_flag) { - flavor[i] = LOCAL; - if (argindex[i] == 0 && (ifix->size_local_cols != 0)) - error->all(FLERR, "Compute reduce fix {} does not calculate a local vector", ids[i]); - if (argindex[i] && (ifix->size_local_cols == 0)) - error->all(FLERR, "Compute reduce fix {} does not calculate a local array", ids[i]); - if (argindex[i] && (argindex[i] > ifix->size_local_cols)) - error->all(FLERR, "Compute reduce fix {} array is accessed out-of-range", ids[i]); + } else if (val.which == ArgInfo::FIX) { + val.val.f = modify->get_fix_by_id(val.id); + if (!val.val.f) error->all(FLERR, "Fix ID {} for compute {} does not exist", val.id, style); + if (val.val.f->peratom_flag) { + val.flavor = PERATOM; + if (val.argindex == 0 && (val.val.f->size_peratom_cols != 0)) + error->all(FLERR, "Compute {} fix {} does not calculate a per-atom vector", style, + val.id); + if (val.argindex && (val.val.f->size_peratom_cols == 0)) + error->all(FLERR, "Compute {} fix {} does not calculate a per-atom array", style, val.id); + if (val.argindex && (val.argindex > val.val.f->size_peratom_cols)) + error->all(FLERR, "Compute {} fix {} array is accessed out-of-range", style, val.id); + } else if (val.val.f->local_flag) { + val.flavor = LOCAL; + if (val.argindex == 0 && (val.val.f->size_local_cols != 0)) + error->all(FLERR, "Compute {} fix {} does not calculate a local vector", style, val.id); + if (val.argindex && (val.val.f->size_local_cols == 0)) + error->all(FLERR, "Compute {} fix {} does not calculate a local array", style, val.id); + if (val.argindex && (val.argindex > val.val.f->size_local_cols)) + error->all(FLERR, "Compute {} fix {} array is accessed out-of-range", style, val.id); } else - error->all(FLERR, "Compute reduce fix {} calculates global values", ids[i]); + error->all(FLERR, "Compute {} fix {} calculates global values", style, val.id); - } else if (which[i] == ArgInfo::VARIABLE) { - int ivariable = input->variable->find(ids[i]); - if (ivariable < 0) error->all(FLERR, "Variable name for compute reduce does not exist"); - if (input->variable->atomstyle(ivariable) == 0) - error->all(FLERR, "Compute reduce variable is not atom-style variable"); - flavor[i] = PERATOM; + } else if (val.which == ArgInfo::VARIABLE) { + val.val.v = input->variable->find(val.id.c_str()); + if (val.val.v < 0) + error->all(FLERR, "Variable name {} for compute {} does not exist", val.id, style); + if (input->variable->atomstyle(val.val.v) == 0) + error->all(FLERR, "Compute {} variable {} is not atom-style variable", style, val.id); + val.flavor = PERATOM; } } @@ -284,12 +279,6 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) : ComputeReduce::~ComputeReduce() { - delete[] which; - delete[] argindex; - delete[] flavor; - for (int m = 0; m < nvalues; m++) delete[] ids[m]; - delete[] ids; - delete[] value2index; delete[] replace; delete[] idregion; @@ -307,24 +296,21 @@ void ComputeReduce::init() { // set indices of all computes,fixes,variables - for (int m = 0; m < nvalues; m++) { - if (which[m] == ArgInfo::COMPUTE) { - int icompute = modify->find_compute(ids[m]); - if (icompute < 0) error->all(FLERR, "Compute ID for compute reduce does not exist"); - value2index[m] = icompute; + for (auto &val : values) { + if (val.which == ArgInfo::COMPUTE) { + val.val.c = modify->get_compute_by_id(val.id); + if (!val.val.c) + error->all(FLERR, "Compute ID {} for compute {} does not exist", val.id, style); - } else if (which[m] == ArgInfo::FIX) { - int ifix = modify->find_fix(ids[m]); - if (ifix < 0) error->all(FLERR, "Fix ID for compute reduce does not exist"); - value2index[m] = ifix; + } else if (val.which == ArgInfo::FIX) { + val.val.f = modify->get_fix_by_id(val.id); + if (!val.val.f) error->all(FLERR, "Fix ID {} for compute {} does not exist", val.id, style); - } else if (which[m] == ArgInfo::VARIABLE) { - int ivariable = input->variable->find(ids[m]); - if (ivariable < 0) error->all(FLERR, "Variable name for compute reduce does not exist"); - value2index[m] = ivariable; - - } else - value2index[m] = ArgInfo::UNKNOWN; + } else if (val.which == ArgInfo::VARIABLE) { + val.val.v = input->variable->find(val.id.c_str()); + if (val.val.v < 0) + error->all(FLERR, "Variable name {} for compute {} does not exist", val.id, style); + } } // set index and check validity of region @@ -383,14 +369,14 @@ void ComputeReduce::compute_vector() for (int m = 0; m < nvalues; m++) if (replace[m] < 0) { pairme.value = onevec[m]; - pairme.proc = me; + pairme.proc = comm->me; MPI_Allreduce(&pairme, &pairall, 1, MPI_DOUBLE_INT, MPI_MINLOC, world); vector[m] = pairall.value; owner[m] = pairall.proc; } for (int m = 0; m < nvalues; m++) if (replace[m] >= 0) { - if (me == owner[replace[m]]) vector[m] = compute_one(m, indices[replace[m]]); + if (comm->me == owner[replace[m]]) vector[m] = compute_one(m, indices[replace[m]]); MPI_Bcast(&vector[m], 1, MPI_DOUBLE, owner[replace[m]], world); } } @@ -404,14 +390,14 @@ void ComputeReduce::compute_vector() for (int m = 0; m < nvalues; m++) if (replace[m] < 0) { pairme.value = onevec[m]; - pairme.proc = me; + pairme.proc = comm->me; MPI_Allreduce(&pairme, &pairall, 1, MPI_DOUBLE_INT, MPI_MAXLOC, world); vector[m] = pairall.value; owner[m] = pairall.proc; } for (int m = 0; m < nvalues; m++) if (replace[m] >= 0) { - if (me == owner[replace[m]]) vector[m] = compute_one(m, indices[replace[m]]); + if (comm->me == owner[replace[m]]) vector[m] = compute_one(m, indices[replace[m]]); MPI_Bcast(&vector[m], 1, MPI_DOUBLE, owner[replace[m]], world); } } @@ -436,24 +422,21 @@ void ComputeReduce::compute_vector() double ComputeReduce::compute_one(int m, int flag) { - int i; - // invoke the appropriate attribute,compute,fix,variable // for flag = -1, compute scalar quantity by scanning over atom properties // only include atoms in group for atom properties and per-atom quantities index = -1; - int vidx = value2index[m]; + auto &val = values[m]; // initialization in case it has not yet been run, e.g. when // the compute was invoked right after it has been created - if (vidx == ArgInfo::UNKNOWN) { - init(); - vidx = value2index[m]; + if ((val.which == ArgInfo::COMPUTE) || (val.which == ArgInfo::FIX)) { + if (val.val.c == nullptr) init(); } - int aidx = argindex[m]; + int aidx = val.argindex; int *mask = atom->mask; int nlocal = atom->nlocal; @@ -461,77 +444,76 @@ double ComputeReduce::compute_one(int m, int flag) if (mode == MINN) one = BIG; if (mode == MAXX) one = -BIG; - if (which[m] == ArgInfo::X) { + if (val.which == ArgInfo::X) { double **x = atom->x; if (flag < 0) { - for (i = 0; i < nlocal; i++) + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) combine(one, x[i][aidx], i); } else one = x[flag][aidx]; - } else if (which[m] == ArgInfo::V) { + } else if (val.which == ArgInfo::V) { double **v = atom->v; if (flag < 0) { - for (i = 0; i < nlocal; i++) + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) combine(one, v[i][aidx], i); } else one = v[flag][aidx]; - } else if (which[m] == ArgInfo::F) { + } else if (val.which == ArgInfo::F) { double **f = atom->f; if (flag < 0) { - for (i = 0; i < nlocal; i++) + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) combine(one, f[i][aidx], i); } else one = f[flag][aidx]; // invoke compute if not previously invoked - } else if (which[m] == ArgInfo::COMPUTE) { - Compute *compute = modify->compute[vidx]; + } else if (val.which == ArgInfo::COMPUTE) { - if (flavor[m] == PERATOM) { - if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) { - compute->compute_peratom(); - compute->invoked_flag |= Compute::INVOKED_PERATOM; + if (val.flavor == PERATOM) { + if (!(val.val.c->invoked_flag & Compute::INVOKED_PERATOM)) { + val.val.c->compute_peratom(); + val.val.c->invoked_flag |= Compute::INVOKED_PERATOM; } if (aidx == 0) { - double *comp_vec = compute->vector_atom; + double *comp_vec = val.val.c->vector_atom; int n = nlocal; if (flag < 0) { - for (i = 0; i < n; i++) + for (int i = 0; i < n; i++) if (mask[i] & groupbit) combine(one, comp_vec[i], i); } else one = comp_vec[flag]; } else { - double **carray_atom = compute->array_atom; + double **carray_atom = val.val.c->array_atom; int n = nlocal; int aidxm1 = aidx - 1; if (flag < 0) { - for (i = 0; i < n; i++) + for (int i = 0; i < n; i++) if (mask[i] & groupbit) combine(one, carray_atom[i][aidxm1], i); } else one = carray_atom[flag][aidxm1]; } - } else if (flavor[m] == LOCAL) { - if (!(compute->invoked_flag & Compute::INVOKED_LOCAL)) { - compute->compute_local(); - compute->invoked_flag |= Compute::INVOKED_LOCAL; + } else if (val.flavor == LOCAL) { + if (!(val.val.c->invoked_flag & Compute::INVOKED_LOCAL)) { + val.val.c->compute_local(); + val.val.c->invoked_flag |= Compute::INVOKED_LOCAL; } if (aidx == 0) { - double *comp_vec = compute->vector_local; - int n = compute->size_local_rows; + double *comp_vec = val.val.c->vector_local; + int n = val.val.c->size_local_rows; if (flag < 0) - for (i = 0; i < n; i++) combine(one, comp_vec[i], i); + for (int i = 0; i < n; i++) combine(one, comp_vec[i], i); else one = comp_vec[flag]; } else { - double **carray_local = compute->array_local; - int n = compute->size_local_rows; + double **carray_local = val.val.c->array_local; + int n = val.val.c->size_local_rows; int aidxm1 = aidx - 1; if (flag < 0) - for (i = 0; i < n; i++) combine(one, carray_local[i][aidxm1], i); + for (int i = 0; i < n; i++) combine(one, carray_local[i][aidxm1], i); else one = carray_local[flag][aidxm1]; } @@ -539,46 +521,42 @@ double ComputeReduce::compute_one(int m, int flag) // access fix fields, check if fix frequency is a match - } else if (which[m] == ArgInfo::FIX) { - if (update->ntimestep % modify->fix[vidx]->peratom_freq) - error->all(FLERR, - "Fix used in compute reduce not " - "computed at compatible time"); - Fix *fix = modify->fix[vidx]; + } else if (val.which == ArgInfo::FIX) { + if (update->ntimestep % val.val.f->peratom_freq) + error->all(FLERR, "Fix {} used in compute {} not computed at compatible time", val.id, style); - if (flavor[m] == PERATOM) { + if (val.flavor == PERATOM) { if (aidx == 0) { - double *fix_vector = fix->vector_atom; - int n = nlocal; + double *fix_vector = val.val.f->vector_atom; if (flag < 0) { - for (i = 0; i < n; i++) + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) combine(one, fix_vector[i], i); } else one = fix_vector[flag]; } else { - double **fix_array = fix->array_atom; + double **fix_array = val.val.f->array_atom; int aidxm1 = aidx - 1; if (flag < 0) { - for (i = 0; i < nlocal; i++) + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) combine(one, fix_array[i][aidxm1], i); } else one = fix_array[flag][aidxm1]; } - } else if (flavor[m] == LOCAL) { + } else if (val.flavor == LOCAL) { if (aidx == 0) { - double *fix_vector = fix->vector_local; - int n = fix->size_local_rows; + double *fix_vector = val.val.f->vector_local; + int n = val.val.f->size_local_rows; if (flag < 0) - for (i = 0; i < n; i++) combine(one, fix_vector[i], i); + for (int i = 0; i < n; i++) combine(one, fix_vector[i], i); else one = fix_vector[flag]; } else { - double **fix_array = fix->array_local; - int n = fix->size_local_rows; + double **fix_array = val.val.f->array_local; + int n = val.val.f->size_local_rows; int aidxm1 = aidx - 1; if (flag < 0) - for (i = 0; i < n; i++) combine(one, fix_array[i][aidxm1], i); + for (int i = 0; i < n; i++) combine(one, fix_array[i][aidxm1], i); else one = fix_array[flag][aidxm1]; } @@ -586,16 +564,16 @@ double ComputeReduce::compute_one(int m, int flag) // evaluate atom-style variable - } else if (which[m] == ArgInfo::VARIABLE) { + } else if (val.which == ArgInfo::VARIABLE) { if (atom->nmax > maxatom) { maxatom = atom->nmax; memory->destroy(varatom); memory->create(varatom, maxatom, "reduce:varatom"); } - input->variable->compute_atom(vidx, igroup, varatom, 1, 0); + input->variable->compute_atom(val.val.v, igroup, varatom, 1, 0); if (flag < 0) { - for (i = 0; i < nlocal; i++) + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) combine(one, varatom[i], i); } else one = varatom[flag]; @@ -608,31 +586,28 @@ double ComputeReduce::compute_one(int m, int flag) bigint ComputeReduce::count(int m) { - int vidx = value2index[m]; - - if (which[m] == ArgInfo::X || which[m] == ArgInfo::V || which[m] == ArgInfo::F) + auto &val = values[m]; + if ((val.which == ArgInfo::X) || (val.which == ArgInfo::V) || (val.which == ArgInfo::F)) return group->count(igroup); - else if (which[m] == ArgInfo::COMPUTE) { - Compute *compute = modify->compute[vidx]; - if (flavor[m] == PERATOM) { + else if (val.which == ArgInfo::COMPUTE) { + if (val.flavor == PERATOM) { return group->count(igroup); - } else if (flavor[m] == LOCAL) { - bigint ncount = compute->size_local_rows; + } else if (val.flavor == LOCAL) { + bigint ncount = val.val.c->size_local_rows; bigint ncountall; MPI_Allreduce(&ncount, &ncountall, 1, MPI_LMP_BIGINT, MPI_SUM, world); return ncountall; } - } else if (which[m] == ArgInfo::FIX) { - Fix *fix = modify->fix[vidx]; - if (flavor[m] == PERATOM) { + } else if (val.which == ArgInfo::FIX) { + if (val.flavor == PERATOM) { return group->count(igroup); - } else if (flavor[m] == LOCAL) { - bigint ncount = fix->size_local_rows; + } else if (val.flavor == LOCAL) { + bigint ncount = val.val.f->size_local_rows; bigint ncountall; MPI_Allreduce(&ncount, &ncountall, 1, MPI_LMP_BIGINT, MPI_SUM, world); return ncountall; } - } else if (which[m] == ArgInfo::VARIABLE) + } else if (val.which == ArgInfo::VARIABLE) return group->count(igroup); bigint dummy = 0; diff --git a/src/compute_reduce.h b/src/compute_reduce.h index dc4ee1ef2c..74313514f0 100644 --- a/src/compute_reduce.h +++ b/src/compute_reduce.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -37,30 +37,38 @@ class ComputeReduce : public Compute { double memory_usage() override; protected: - int me; int mode, nvalues; - int *which, *argindex, *flavor, *value2index; - char **ids; + struct value_t { + int which; + int argindex; + std::string id; + int flavor; + union { + class Compute *c; + class Fix *f; + int v; + } val; + }; + std::vector values; double *onevec; int *replace, *indices, *owner; + int index; char *idregion; class Region *region; int maxatom; double *varatom; - struct Pair { + struct valpair { double value; int proc; }; - Pair pairme, pairall; + valpair pairme, pairall; virtual double compute_one(int, int); virtual bigint count(int); void combine(double &, double, int); }; - } // namespace LAMMPS_NS - #endif #endif diff --git a/src/compute_reduce_chunk.cpp b/src/compute_reduce_chunk.cpp index 11604998c8..bafffed038 100644 --- a/src/compute_reduce_chunk.cpp +++ b/src/compute_reduce_chunk.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -30,19 +30,17 @@ using namespace LAMMPS_NS; -enum{SUM,MINN,MAXX}; - +enum{ SUM, MINN, MAXX }; #define BIG 1.0e20 /* ---------------------------------------------------------------------- */ ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg), - which(nullptr), argindex(nullptr), value2index(nullptr), idchunk(nullptr), ids(nullptr), - vlocal(nullptr), vglobal(nullptr), alocal(nullptr), aglobal(nullptr), varatom(nullptr) + Compute(lmp, narg, arg), idchunk(nullptr), vlocal(nullptr), vglobal(nullptr), + alocal(nullptr), aglobal(nullptr), varatom(nullptr), cchunk(nullptr), ichunk(nullptr) { - if (narg < 6) error->all(FLERR,"Illegal compute reduce/chunk command"); + if (narg < 6) utils::missing_cmd_args(FLERR,"compute reduce/chunk", error); // ID of compute chunk/atom @@ -54,7 +52,7 @@ ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) : if (strcmp(arg[4],"sum") == 0) mode = SUM; else if (strcmp(arg[4],"min") == 0) mode = MINN; else if (strcmp(arg[4],"max") == 0) mode = MAXX; - else error->all(FLERR,"Illegal compute reduce/chunk command"); + else error->all(FLERR,"Unknown compute reduce/chunk mode: {}", arg[4]); int iarg = 5; @@ -67,30 +65,22 @@ ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) : if (earg != &arg[iarg]) expand = 1; arg = earg; - // parse values until one isn't recognized - - which = new int[nargnew]; - argindex = new int[nargnew]; - ids = new char*[nargnew]; - value2index = new int[nargnew]; - for (int i=0; i < nargnew; ++i) { - which[i] = argindex[i] = value2index[i] = ArgInfo::UNKNOWN; - ids[i] = nullptr; - } - nvalues = 0; + // parse values + values.clear(); for (iarg = 0; iarg < nargnew; iarg++) { ArgInfo argi(arg[iarg]); - which[nvalues] = argi.get_type(); - argindex[nvalues] = argi.get_index1(); - ids[nvalues] = argi.copy_name(); + value_t val; + val.which = argi.get_type(); + val.argindex = argi.get_index1(); + val.id = argi.get_name(); + val.val.c = nullptr; - if ((which[nvalues] == ArgInfo::UNKNOWN) || (which[nvalues] == ArgInfo::NONE) - || (argi.get_dim() > 1)) - error->all(FLERR,"Illegal compute reduce/chunk command"); + if ((val.which == ArgInfo::UNKNOWN) || (val.which == ArgInfo::NONE) || (argi.get_dim() > 1)) + error->all(FLERR,"Illegal compute reduce/chunk argument: {}", arg[iarg]); - nvalues++; + values.push_back(val); } // if wildcard expansion occurred, free earg memory from expand_args() @@ -102,58 +92,55 @@ ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) : // error check - for (int i = 0; i < nvalues; i++) { - if (which[i] == ArgInfo::COMPUTE) { - int icompute = modify->find_compute(ids[i]); - if (icompute < 0) - error->all(FLERR,"Compute ID for compute reduce/chunk does not exist"); - if (!modify->compute[icompute]->peratom_flag) - error->all(FLERR,"Compute reduce/chunk compute does not " - "calculate per-atom values"); - if (argindex[i] == 0 && - modify->compute[icompute]->size_peratom_cols != 0) - error->all(FLERR,"Compute reduce/chunk compute does not " - "calculate a per-atom vector"); - if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0) - error->all(FLERR,"Compute reduce/chunk compute does not " - "calculate a per-atom array"); - if (argindex[i] && - argindex[i] > modify->compute[icompute]->size_peratom_cols) - error->all(FLERR, - "Compute reduce/chunk compute array is accessed out-of-range"); + for (auto &val : values) { + if (val.which == ArgInfo::COMPUTE) { + val.val.c = modify->get_compute_by_id(val.id); + if (!val.val.c) + error->all(FLERR,"Compute ID {} for compute reduce/chunk does not exist", val.id); + if (!val.val.c->peratom_flag) + error->all(FLERR,"Compute reduce/chunk compute {} does not calculate per-atom values", + val.id); + if ((val.argindex == 0) && (val.val.c->size_peratom_cols != 0)) + error->all(FLERR,"Compute reduce/chunk compute {} does not calculate a per-atom vector", + val.id); + if (val.argindex && (val.val.c->size_peratom_cols == 0)) + error->all(FLERR,"Compute reduce/chunk compute {} does not calculate a per-atom array", + val.id); + if (val.argindex && (val.argindex > val.val.c->size_peratom_cols)) + error->all(FLERR, "Compute reduce/chunk compute array {} is accessed out-of-range", val.id); - } else if (which[i] == ArgInfo::FIX) { - auto ifix = modify->get_fix_by_id(ids[i]); - if (!ifix) - error->all(FLERR,"Fix ID {} for compute reduce/chunk does not exist", ids[i]); - if (!ifix->peratom_flag) - error->all(FLERR,"Compute reduce/chunk fix {} does not calculate per-atom values", ids[i]); - if ((argindex[i] == 0) && (ifix->size_peratom_cols != 0)) - error->all(FLERR,"Compute reduce/chunk fix {} does not calculate a per-atom vector", ids[i]); - if (argindex[i] && (ifix->size_peratom_cols == 0)) - error->all(FLERR,"Compute reduce/chunk fix {} does not calculate a per-atom array", ids[i]); - if (argindex[i] && (argindex[i] > ifix->size_peratom_cols)) - error->all(FLERR,"Compute reduce/chunk fix {} array is accessed out-of-range", ids[i]); + } else if (val.which == ArgInfo::FIX) { + val.val.f = modify->get_fix_by_id(val.id); + if (!val.val.f) + error->all(FLERR,"Fix ID {} for compute reduce/chunk does not exist", val.id); + if (!val.val.f->peratom_flag) + error->all(FLERR,"Compute reduce/chunk fix {} does not calculate per-atom values", val.id); + if ((val.argindex == 0) && (val.val.f->size_peratom_cols != 0)) + error->all(FLERR,"Compute reduce/chunk fix {} does not calculate a per-atom vector", val.id); + if (val.argindex && (val.val.f->size_peratom_cols == 0)) + error->all(FLERR,"Compute reduce/chunk fix {} does not calculate a per-atom array", val.id); + if (val.argindex && (val.argindex > val.val.f->size_peratom_cols)) + error->all(FLERR,"Compute reduce/chunk fix {} array is accessed out-of-range", val.id); - } else if (which[i] == ArgInfo::VARIABLE) { - int ivariable = input->variable->find(ids[i]); - if (ivariable < 0) - error->all(FLERR,"Variable name for compute reduce/chunk does not exist"); - if (input->variable->atomstyle(ivariable) == 0) + } else if (val.which == ArgInfo::VARIABLE) { + val.val.v = input->variable->find(val.id.c_str()); + if (val.val.v < 0) + error->all(FLERR,"Variable name {} for compute reduce/chunk does not exist", val.id); + if (input->variable->atomstyle(val.val.v) == 0) error->all(FLERR,"Compute reduce/chunk variable is not atom-style variable"); } } // this compute produces either a vector or array - if (nvalues == 1) { + if (values.size() == 1) { vector_flag = 1; size_vector_variable = 1; extvector = 0; } else { array_flag = 1; size_array_rows_variable = 1; - size_array_cols = nvalues; + size_array_cols = values.size(); extarray = 0; } @@ -175,13 +162,7 @@ ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) : ComputeReduceChunk::~ComputeReduceChunk() { - delete [] idchunk; - - delete [] which; - delete [] argindex; - for (int m = 0; m < nvalues; m++) delete [] ids[m]; - delete [] ids; - delete [] value2index; + delete[] idchunk; memory->destroy(vlocal); memory->destroy(vglobal); @@ -199,24 +180,21 @@ void ComputeReduceChunk::init() // set indices of all computes,fixes,variables - for (int m = 0; m < nvalues; m++) { - if (which[m] == ArgInfo::COMPUTE) { - int icompute = modify->find_compute(ids[m]); - if (icompute < 0) - error->all(FLERR,"Compute ID for compute reduce/chunk does not exist"); - value2index[m] = icompute; + for (auto &val : values) { + if (val.which == ArgInfo::COMPUTE) { + val.val.c = modify->get_compute_by_id(val.id); + if (!val.val.c) + error->all(FLERR,"Compute ID {} for compute reduce/chunk does not exist", val.id); - } else if (which[m] == ArgInfo::FIX) { - int ifix = modify->find_fix(ids[m]); - if (ifix < 0) - error->all(FLERR,"Fix ID for compute reduce/chunk does not exist"); - value2index[m] = ifix; + } else if (val.which == ArgInfo::FIX) { + val.val.f = modify->get_fix_by_id(val.id); + if (!val.val.f) + error->all(FLERR,"Fix ID {} for compute reduce/chunk does not exist", val.id); - } else if (which[m] == ArgInfo::VARIABLE) { - int ivariable = input->variable->find(ids[m]); - if (ivariable < 0) - error->all(FLERR,"Variable name for compute reduce/chunk does not exist"); - value2index[m] = ivariable; + } else if (val.which == ArgInfo::VARIABLE) { + val.val.v = input->variable->find(val.id.c_str()); + if (val.val.v < 0) + error->all(FLERR,"Variable name {} for compute reduce/chunk does not exist", val.id); } } } @@ -225,13 +203,10 @@ void ComputeReduceChunk::init() void ComputeReduceChunk::init_chunk() { - int icompute = modify->find_compute(idchunk); - if (icompute < 0) - error->all(FLERR,"Chunk/atom compute does not exist for " - "compute reduce/chunk"); - cchunk = dynamic_cast(modify->compute[icompute]); - if (strcmp(cchunk->style,"chunk/atom") != 0) - error->all(FLERR,"Compute reduce/chunk does not use chunk/atom compute"); + cchunk = dynamic_cast(modify->get_compute_by_id(idchunk)); + if (!cchunk) + error->all(FLERR,"Compute chunk/atom {} does not exist or is incorrect style for " + "compute reduce/chunk", idchunk); } /* ---------------------------------------------------------------------- */ @@ -295,26 +270,23 @@ void ComputeReduceChunk::compute_array() memory->destroy(alocal); memory->destroy(aglobal); maxchunk = nchunk; - memory->create(alocal,maxchunk,nvalues,"reduce/chunk:alocal"); - memory->create(aglobal,maxchunk,nvalues,"reduce/chunk:aglobal"); + memory->create(alocal,maxchunk,values.size(),"reduce/chunk:alocal"); + memory->create(aglobal,maxchunk,values.size(),"reduce/chunk:aglobal"); array = aglobal; } // perform local reduction of all peratom values - for (int m = 0; m < nvalues; m++) compute_one(m,&alocal[0][m],nvalues); + for (std::size_t m = 0; m < values.size(); m++) compute_one(m,&alocal[0][m],values.size()); // reduce the per-chunk values across all procs if (mode == SUM) - MPI_Allreduce(&alocal[0][0],&aglobal[0][0],nchunk*nvalues, - MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(&alocal[0][0],&aglobal[0][0],nchunk*values.size(),MPI_DOUBLE,MPI_SUM,world); else if (mode == MINN) - MPI_Allreduce(&alocal[0][0],&aglobal[0][0],nchunk*nvalues, - MPI_DOUBLE,MPI_MIN,world); + MPI_Allreduce(&alocal[0][0],&aglobal[0][0],nchunk*values.size(),MPI_DOUBLE,MPI_MIN,world); else if (mode == MAXX) - MPI_Allreduce(&alocal[0][0],&aglobal[0][0],nchunk*nvalues, - MPI_DOUBLE,MPI_MAX,world); + MPI_Allreduce(&alocal[0][0],&aglobal[0][0],nchunk*values.size(),MPI_DOUBLE,MPI_MAX,world); } /* ---------------------------------------------------------------------- */ @@ -323,7 +295,7 @@ void ComputeReduceChunk::compute_one(int m, double *vchunk, int nstride) { // initialize per-chunk values in accumulation vector - for (int i = 0; i < nvalues*nchunk; i += nstride) vchunk[i] = initvalue; + for (std::size_t i = 0; i < values.size()*nchunk; i += nstride) vchunk[i] = initvalue; // loop over my atoms // use peratom input and chunk ID of each atom to update vector @@ -331,27 +303,22 @@ void ComputeReduceChunk::compute_one(int m, double *vchunk, int nstride) int *mask = atom->mask; int nlocal = atom->nlocal; + auto &val = values[m]; int index = -1; - int vidx = value2index[m]; // initialization in case it has not yet been run, e.g. when // the compute was invoked right after it has been created - if (vidx == ArgInfo::UNKNOWN) { - init(); - vidx = value2index[m]; - } + if (val.val.c == nullptr) init(); - if (which[m] == ArgInfo::COMPUTE) { - Compute *compute = modify->compute[vidx]; - - if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) { - compute->compute_peratom(); - compute->invoked_flag |= Compute::INVOKED_PERATOM; + if (val.which == ArgInfo::COMPUTE) { + if (!(val.val.c->invoked_flag & Compute::INVOKED_PERATOM)) { + val.val.c->compute_peratom(); + val.val.c->invoked_flag |= Compute::INVOKED_PERATOM; } - if (argindex[m] == 0) { - double *vcompute = compute->vector_atom; + if (val.argindex == 0) { + double *vcompute = val.val.c->vector_atom; for (int i = 0; i < nlocal; i++) { if (!(mask[i] & groupbit)) continue; index = ichunk[i]-1; @@ -359,8 +326,8 @@ void ComputeReduceChunk::compute_one(int m, double *vchunk, int nstride) combine(vchunk[index*nstride],vcompute[i]); } } else { - double **acompute = compute->array_atom; - int argindexm1 = argindex[m] - 1; + double **acompute = val.val.c->array_atom; + int argindexm1 = val.argindex - 1; for (int i = 0; i < nlocal; i++) { if (!(mask[i] & groupbit)) continue; index = ichunk[i]-1; @@ -371,13 +338,12 @@ void ComputeReduceChunk::compute_one(int m, double *vchunk, int nstride) // access fix fields, check if fix frequency is a match - } else if (which[m] == ArgInfo::FIX) { - Fix *fix = modify->fix[vidx]; - if (update->ntimestep % fix->peratom_freq) + } else if (val.which == ArgInfo::FIX) { + if (update->ntimestep % val.val.f->peratom_freq) error->all(FLERR,"Fix used in compute reduce/chunk not computed at compatible time"); - if (argindex[m] == 0) { - double *vfix = fix->vector_atom; + if (val.argindex == 0) { + double *vfix = val.val.f->vector_atom; for (int i = 0; i < nlocal; i++) { if (!(mask[i] & groupbit)) continue; index = ichunk[i]-1; @@ -385,8 +351,8 @@ void ComputeReduceChunk::compute_one(int m, double *vchunk, int nstride) combine(vchunk[index*nstride],vfix[i]); } } else { - double **afix = fix->array_atom; - int argindexm1 = argindex[m] - 1; + double **afix = val.val.f->array_atom; + int argindexm1 = val.argindex - 1; for (int i = 0; i < nlocal; i++) { if (!(mask[i] & groupbit)) continue; index = ichunk[i]-1; @@ -397,14 +363,14 @@ void ComputeReduceChunk::compute_one(int m, double *vchunk, int nstride) // evaluate atom-style variable - } else if (which[m] == ArgInfo::VARIABLE) { + } else if (val.which == ArgInfo::VARIABLE) { if (atom->nmax > maxatom) { memory->destroy(varatom); maxatom = atom->nmax; memory->create(varatom,maxatom,"reduce/chunk:varatom"); } - input->variable->compute_atom(vidx,igroup,varatom,1,0); + input->variable->compute_atom(val.val.v,igroup,varatom,1,0); for (int i = 0; i < nlocal; i++) { if (!(mask[i] & groupbit)) continue; index = ichunk[i]-1; @@ -449,11 +415,8 @@ void ComputeReduceChunk::lock_enable() void ComputeReduceChunk::lock_disable() { - int icompute = modify->find_compute(idchunk); - if (icompute >= 0) { - cchunk = dynamic_cast(modify->compute[icompute]); - cchunk->lockcount--; - } + cchunk = dynamic_cast(modify->get_compute_by_id(idchunk)); + if (cchunk) cchunk->lockcount--; } /* ---------------------------------------------------------------------- @@ -491,7 +454,7 @@ void ComputeReduceChunk::unlock(Fix *fixptr) double ComputeReduceChunk::memory_usage() { double bytes = (bigint) maxatom * sizeof(double); - if (nvalues == 1) bytes += (double) maxchunk * 2 * sizeof(double); - else bytes += (double) maxchunk * nvalues * 2 * sizeof(double); + if (values.size() == 1) bytes += (double) maxchunk * 2 * sizeof(double); + else bytes += (double) maxchunk * values.size() * 2 * sizeof(double); return bytes; } diff --git a/src/compute_reduce_chunk.h b/src/compute_reduce_chunk.h index 4c83093c6b..505e2b4a21 100644 --- a/src/compute_reduce_chunk.h +++ b/src/compute_reduce_chunk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -41,12 +41,21 @@ class ComputeReduceChunk : public Compute { double memory_usage() override; private: - int mode, nvalues; - int *which, *argindex, *value2index; - char *idchunk; - char **ids; + struct value_t { + int which; + int argindex; + std::string id; + union { + class Compute *c; + class Fix *f; + int v; + } val; + }; + std::vector values; - int nchunk; + char *idchunk; + + int mode, nchunk; int maxchunk, maxatom; double initvalue; double *vlocal, *vglobal; @@ -60,8 +69,6 @@ class ComputeReduceChunk : public Compute { void compute_one(int, double *, int); void combine(double &, double); }; - } // namespace LAMMPS_NS - #endif #endif diff --git a/src/compute_reduce_region.cpp b/src/compute_reduce_region.cpp index f8a92c7bf3..efce00ff66 100644 --- a/src/compute_reduce_region.cpp +++ b/src/compute_reduce_region.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -15,13 +15,11 @@ #include "arg_info.h" #include "atom.h" -#include "domain.h" #include "error.h" #include "fix.h" #include "group.h" #include "input.h" #include "memory.h" -#include "modify.h" #include "region.h" #include "update.h" #include "variable.h" @@ -55,62 +53,58 @@ double ComputeReduceRegion::compute_one(int m, int flag) // only include atoms in group index = -1; + auto &val = values[m]; + + // initialization in case it has not yet been run, e.g. when + // the compute was invoked right after it has been created + if ((val.which == ArgInfo::COMPUTE) || (val.which == ArgInfo::FIX)) { + if (val.val.c == nullptr) init(); + } + + int aidx = val.argindex; double **x = atom->x; int *mask = atom->mask; int nlocal = atom->nlocal; - int n = value2index[m]; - - // initialization in case it has not yet been run, - // e.g. when invoked - if (n == ArgInfo::UNKNOWN) { - init(); - n = value2index[m]; - } - - int j = argindex[m]; - double one = 0.0; if (mode == MINN) one = BIG; if (mode == MAXX) one = -BIG; - if (which[m] == ArgInfo::X) { + if (val.which == ArgInfo::X) { if (flag < 0) { for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2])) - combine(one, x[i][j], i); + combine(one, x[i][aidx], i); } else - one = x[flag][j]; - } else if (which[m] == ArgInfo::V) { + one = x[flag][aidx]; + } else if (val.which == ArgInfo::V) { double **v = atom->v; if (flag < 0) { for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2])) - combine(one, v[i][j], i); + combine(one, v[i][aidx], i); } else - one = v[flag][j]; - } else if (which[m] == ArgInfo::F) { + one = v[flag][aidx]; + } else if (val.which == ArgInfo::F) { double **f = atom->f; if (flag < 0) { for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2])) - combine(one, f[i][j], i); + combine(one, f[i][aidx], i); } else - one = f[flag][j]; + one = f[flag][aidx]; // invoke compute if not previously invoked - } else if (which[m] == ArgInfo::COMPUTE) { - Compute *compute = modify->compute[n]; - - if (flavor[m] == PERATOM) { - if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) { - compute->compute_peratom(); - compute->invoked_flag |= Compute::INVOKED_PERATOM; + } else if (val.which == ArgInfo::COMPUTE) { + if (val.flavor == PERATOM) { + if (!(val.val.c->invoked_flag & Compute::INVOKED_PERATOM)) { + val.val.c->compute_peratom(); + val.val.c->invoked_flag |= Compute::INVOKED_PERATOM; } - if (j == 0) { - double *compute_vector = compute->vector_atom; + if (aidx == 0) { + double *compute_vector = val.val.c->vector_atom; if (flag < 0) { for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2])) @@ -118,48 +112,48 @@ double ComputeReduceRegion::compute_one(int m, int flag) } else one = compute_vector[flag]; } else { - double **compute_array = compute->array_atom; - int jm1 = j - 1; + double **compute_array = val.val.c->array_atom; + int aidxm1 = aidx - 1; if (flag < 0) { for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2])) - combine(one, compute_array[i][jm1], i); + combine(one, compute_array[i][aidxm1], i); } else - one = compute_array[flag][jm1]; + one = compute_array[flag][aidxm1]; } - } else if (flavor[m] == LOCAL) { - if (!(compute->invoked_flag & Compute::INVOKED_LOCAL)) { - compute->compute_local(); - compute->invoked_flag |= Compute::INVOKED_LOCAL; + } else if (val.flavor == LOCAL) { + if (!(val.val.c->invoked_flag & Compute::INVOKED_LOCAL)) { + val.val.c->compute_local(); + val.val.c->invoked_flag |= Compute::INVOKED_LOCAL; } - if (j == 0) { - double *compute_vector = compute->vector_local; + if (aidx == 0) { + double *compute_vector = val.val.c->vector_local; if (flag < 0) - for (int i = 0; i < compute->size_local_rows; i++) combine(one, compute_vector[i], i); + for (int i = 0; i < val.val.c->size_local_rows; i++) combine(one, compute_vector[i], i); else one = compute_vector[flag]; } else { - double **compute_array = compute->array_local; - int jm1 = j - 1; + double **compute_array = val.val.c->array_local; + int aidxm1 = aidx - 1; if (flag < 0) - for (int i = 0; i < compute->size_local_rows; i++) combine(one, compute_array[i][jm1], i); + for (int i = 0; i < val.val.c->size_local_rows; i++) + combine(one, compute_array[i][aidxm1], i); else - one = compute_array[flag][jm1]; + one = compute_array[flag][aidxm1]; } } // check if fix frequency is a match - } else if (which[m] == ArgInfo::FIX) { - if (update->ntimestep % modify->fix[n]->peratom_freq) - error->all(FLERR, "Fix used in compute reduce not computed at compatible time"); - Fix *fix = modify->fix[n]; + } else if (val.which == ArgInfo::FIX) { + if (update->ntimestep % val.val.f->peratom_freq) + error->all(FLERR, "Fix {} used in compute {} not computed at compatible time", val.id, style); - if (flavor[m] == PERATOM) { - if (j == 0) { - double *fix_vector = fix->vector_atom; + if (val.flavor == PERATOM) { + if (aidx == 0) { + double *fix_vector = val.val.f->vector_atom; if (flag < 0) { for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2])) @@ -167,43 +161,44 @@ double ComputeReduceRegion::compute_one(int m, int flag) } else one = fix_vector[flag]; } else { - double **fix_array = fix->array_atom; - int jm1 = j - 1; + double **fix_array = val.val.f->array_atom; + int aidxm1 = aidx - 1; if (flag < 0) { for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2])) - combine(one, fix_array[i][jm1], i); + combine(one, fix_array[i][aidxm1], i); } else - one = fix_array[flag][jm1]; + one = fix_array[flag][aidxm1]; } - } else if (flavor[m] == LOCAL) { - if (j == 0) { - double *fix_vector = fix->vector_local; + } else if (val.flavor == LOCAL) { + if (aidx == 0) { + double *fix_vector = val.val.f->vector_local; if (flag < 0) - for (int i = 0; i < fix->size_local_rows; i++) combine(one, fix_vector[i], i); + for (int i = 0; i < val.val.f->size_local_rows; i++) combine(one, fix_vector[i], i); else one = fix_vector[flag]; } else { - double **fix_array = fix->array_local; - int jm1 = j - 1; + double **fix_array = val.val.f->array_local; + int aidxm1 = aidx - 1; if (flag < 0) - for (int i = 0; i < fix->size_local_rows; i++) combine(one, fix_array[i][jm1], i); + for (int i = 0; i < val.val.f->size_local_rows; i++) + combine(one, fix_array[i][aidxm1], i); else - one = fix_array[flag][jm1]; + one = fix_array[flag][aidxm1]; } } // evaluate atom-style variable - } else if (which[m] == ArgInfo::VARIABLE) { + } else if (val.which == ArgInfo::VARIABLE) { if (atom->nmax > maxatom) { maxatom = atom->nmax; memory->destroy(varatom); memory->create(varatom, maxatom, "reduce/region:varatom"); } - input->variable->compute_atom(n, igroup, varatom, 1, 0); + input->variable->compute_atom(val.val.v, igroup, varatom, 1, 0); if (flag < 0) { for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2])) @@ -219,31 +214,29 @@ double ComputeReduceRegion::compute_one(int m, int flag) bigint ComputeReduceRegion::count(int m) { - int n = value2index[m]; + auto &val = values[m]; - if (which[m] == ArgInfo::X || which[m] == ArgInfo::V || which[m] == ArgInfo::F) + if (val.which == ArgInfo::X || val.which == ArgInfo::V || val.which == ArgInfo::F) return group->count(igroup, region); - else if (which[m] == ArgInfo::COMPUTE) { - Compute *compute = modify->compute[n]; - if (flavor[m] == PERATOM) { + else if (val.which == ArgInfo::COMPUTE) { + if (val.flavor == PERATOM) { return group->count(igroup, region); - } else if (flavor[m] == LOCAL) { - bigint ncount = compute->size_local_rows; + } else if (val.flavor == LOCAL) { + bigint ncount = val.val.c->size_local_rows; bigint ncountall; MPI_Allreduce(&ncount, &ncountall, 1, MPI_DOUBLE, MPI_SUM, world); return ncountall; } - } else if (which[m] == ArgInfo::FIX) { - Fix *fix = modify->fix[n]; - if (flavor[m] == PERATOM) { + } else if (val.which == ArgInfo::FIX) { + if (val.flavor == PERATOM) { return group->count(igroup, region); - } else if (flavor[m] == LOCAL) { - bigint ncount = fix->size_local_rows; + } else if (val.flavor == LOCAL) { + bigint ncount = val.val.f->size_local_rows; bigint ncountall; MPI_Allreduce(&ncount, &ncountall, 1, MPI_DOUBLE, MPI_SUM, world); return ncountall; } - } else if (which[m] == ArgInfo::VARIABLE) + } else if (val.which == ArgInfo::VARIABLE) return group->count(igroup, region); bigint dummy = 0; diff --git a/src/compute_reduce_region.h b/src/compute_reduce_region.h index 05ebc693fe..92a0312ad1 100644 --- a/src/compute_reduce_region.h +++ b/src/compute_reduce_region.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_slice.cpp b/src/compute_slice.cpp index f37bff1e17..9851c430c4 100644 --- a/src/compute_slice.cpp +++ b/src/compute_slice.cpp @@ -1,8 +1,7 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -27,96 +26,84 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -ComputeSlice::ComputeSlice(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg), - nvalues(0), which(nullptr), argindex(nullptr), value2index(nullptr), ids(nullptr) +ComputeSlice::ComputeSlice(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg) { - if (narg < 7) error->all(FLERR,"Illegal compute slice command"); + if (narg < 7) utils::missing_cmd_args(FLERR, "compute slice", error); - MPI_Comm_rank(world,&me); + nstart = utils::inumeric(FLERR, arg[3], false, lmp); + nstop = utils::inumeric(FLERR, arg[4], false, lmp); + nskip = utils::inumeric(FLERR, arg[5], false, lmp); - nstart = utils::inumeric(FLERR,arg[3],false,lmp); - nstop = utils::inumeric(FLERR,arg[4],false,lmp); - nskip = utils::inumeric(FLERR,arg[5],false,lmp); + if (nstart < 1) error->all(FLERR, "Invalid compute slice nstart value {} < 1", nstart); + if (nstop < nstart) error->all(FLERR, "Invalid compute slice nstop value {} < {}", nstop, nstart); + if (nskip < 1) error->all(FLERR, "Invalid compute slice nskip value < 1: {}", nskip); - if (nstart < 1 || nstop < nstart || nskip < 1) - error->all(FLERR,"Illegal compute slice command"); - - // parse remaining values until one isn't recognized - - which = new int[narg-6]; - argindex = new int[narg-6]; - ids = new char*[narg-6]; - value2index = new int[narg-6]; - nvalues = 0; + // parse values + values.clear(); for (int iarg = 6; iarg < narg; iarg++) { ArgInfo argi(arg[iarg]); - which[nvalues] = argi.get_type(); - argindex[nvalues] = argi.get_index1(); - ids[nvalues] = argi.copy_name(); + value_t val; + val.which = argi.get_type(); + val.argindex = argi.get_index1(); + val.id = argi.get_name(); + val.val.c = nullptr; - if ((which[nvalues] == ArgInfo::UNKNOWN) || (which[nvalues] == ArgInfo::NONE) - || (argi.get_dim() > 1)) - error->all(FLERR,"Illegal compute slice command"); + if ((val.which == ArgInfo::UNKNOWN) || (val.which == ArgInfo::NONE) || (argi.get_dim() > 1)) + error->all(FLERR, "Illegal compute slice argument: {}", arg[iarg]); - nvalues++; + values.push_back(val); } // setup and error check - for (int i = 0; i < nvalues; i++) { - if (which[i] == ArgInfo::COMPUTE) { - int icompute = modify->find_compute(ids[i]); - if (icompute < 0) - error->all(FLERR,"Compute ID for compute slice does not exist"); - if (modify->compute[icompute]->vector_flag) { - if (argindex[i]) - error->all(FLERR,"Compute slice compute does not " - "calculate a global array"); - if (nstop > modify->compute[icompute]->size_vector) - error->all(FLERR,"Compute slice compute vector is " - "accessed out-of-range"); - } else if (modify->compute[icompute]->array_flag) { - if (argindex[i] == 0) - error->all(FLERR,"Compute slice compute does not " - "calculate a global vector"); - if (argindex[i] > modify->compute[icompute]->size_array_cols) - error->all(FLERR,"Compute slice compute array is " - "accessed out-of-range"); - if (nstop > modify->compute[icompute]->size_array_rows) - error->all(FLERR,"Compute slice compute array is " - "accessed out-of-range"); - } else error->all(FLERR,"Compute slice compute does not calculate " - "global vector or array"); - - } else if (which[i] == ArgInfo::FIX) { - auto ifix = modify->get_fix_by_id(ids[i]); - if (!ifix) - error->all(FLERR,"Fix ID {} for compute slice does not exist", ids[i]); - if (ifix->vector_flag) { - if (argindex[i]) - error->all(FLERR,"Compute slice fix {} does not calculate a global array", ids[i]); - if (nstop > ifix->size_vector) - error->all(FLERR,"Compute slice fix {} vector is accessed out-of-range", ids[i]); - } else if (ifix->array_flag) { - if (argindex[i] == 0) - error->all(FLERR,"Compute slice fix {} does not calculate a global vector", ids[i]); - if (argindex[i] > ifix->size_array_cols) - error->all(FLERR,"Compute slice fix {} array is accessed out-of-range", ids[i]); - if (nstop > ifix->size_array_rows) - error->all(FLERR,"Compute slice fix {} array is accessed out-of-range", ids[i]); - } else error->all(FLERR,"Compute slice fix {} does not calculate global vector or array", ids[i]); - - } else if (which[i] == ArgInfo::VARIABLE) { - int ivariable = input->variable->find(ids[i]); - if (ivariable < 0) - error->all(FLERR,"Variable name for compute slice does not exist"); - if (argindex[i] == 0 && input->variable->vectorstyle(ivariable) == 0) - error->all(FLERR,"Compute slice variable is not vector-style variable"); - if (argindex[i]) - error->all(FLERR,"Compute slice vector variable cannot be indexed"); + for (auto &val : values) { + if (val.which == ArgInfo::COMPUTE) { + val.val.c = modify->get_compute_by_id(val.id); + if (!val.val.c) error->all(FLERR, "Compute ID {} for compute slice does not exist", val.id); + if (val.val.c->vector_flag) { + if (val.argindex) + error->all(FLERR, "Compute slice compute {} does not calculate a global array", val.id); + if (nstop > val.val.c->size_vector) + error->all(FLERR, "Compute slice compute {} vector is accessed out-of-range", val.id); + } else if (val.val.c->array_flag) { + if (val.argindex == 0) + error->all(FLERR, "Compute slice compute {} does not calculate a global vector", val.id); + if (val.argindex > val.val.c->size_array_cols) + error->all(FLERR, "Compute slice compute {} array is accessed out-of-range", val.id); + if (nstop > val.val.c->size_array_rows) + error->all(FLERR, "Compute slice compute {} array is accessed out-of-range", val.id); + } else { + error->all(FLERR, "Compute slice compute {} does not calculate global vector or array", + val.id); + } + } else if (val.which == ArgInfo::FIX) { + val.val.f = modify->get_fix_by_id(val.id); + if (!val.val.f) error->all(FLERR, "Fix ID {} for compute slice does not exist", val.id); + if (val.val.f->vector_flag) { + if (val.argindex) + error->all(FLERR, "Compute slice fix {} does not calculate a global array", val.id); + if (nstop > val.val.f->size_vector) + error->all(FLERR, "Compute slice fix {} vector is accessed out-of-range", val.id); + } else if (val.val.f->array_flag) { + if (val.argindex == 0) + error->all(FLERR, "Compute slice fix {} does not calculate a global vector", val.id); + if (val.argindex > val.val.f->size_array_cols) + error->all(FLERR, "Compute slice fix {} array is accessed out-of-range", val.id); + if (nstop > val.val.f->size_array_rows) + error->all(FLERR, "Compute slice fix {} array is accessed out-of-range", val.id); + } else { + error->all(FLERR, "Compute slice fix {} does not calculate global vector or array", val.id); + } + } else if (val.which == ArgInfo::VARIABLE) { + val.val.v = input->variable->find(val.id.c_str()); + if (val.val.v < 0) + error->all(FLERR, "Variable name {} for compute slice does not exist", val.id); + if (val.argindex == 0 && input->variable->vectorstyle(val.val.v) == 0) + error->all(FLERR, "Compute slice variable {} is not vector-style variable", val.id); + if (val.argindex) + error->all(FLERR, "Compute slice vector variable {} cannot be indexed", val.id); } } @@ -124,68 +111,65 @@ ComputeSlice::ComputeSlice(LAMMPS *lmp, int narg, char **arg) : // for vector, set intensive/extensive to mirror input values // for array, set intensive if all input values are intensive, else extensive - if (nvalues == 1) { + if (values.size() == 1) { + auto &val = values[0]; vector_flag = 1; - size_vector = (nstop-nstart) / nskip; - memory->create(vector,size_vector,"slice:vector"); + size_vector = (nstop - nstart) / nskip; + memory->create(vector, size_vector, "slice:vector"); - if (which[0] == ArgInfo::COMPUTE) { - int icompute = modify->find_compute(ids[0]); - if (argindex[0] == 0) { - extvector = modify->compute[icompute]->extvector; - if (modify->compute[icompute]->extvector == -1) { + if (val.which == ArgInfo::COMPUTE) { + if (val.argindex == 0) { + extvector = val.val.c->extvector; + if (val.val.c->extvector == -1) { extlist = new int[size_vector]; int j = 0; - for (int i = nstart; i < nstop; i += nskip) - extlist[j++] = modify->compute[icompute]->extlist[i-1]; + for (int i = nstart; i < nstop; i += nskip) extlist[j++] = val.val.c->extlist[i - 1]; } - } else extvector = modify->compute[icompute]->extarray; - } else if (which[0] == ArgInfo::FIX) { - auto ifix = modify->get_fix_by_id(ids[0]); - if (argindex[0] == 0) { - extvector = ifix->extvector; - if (ifix->extvector == -1) { + } else + extvector = val.val.c->extarray; + } else if (val.which == ArgInfo::FIX) { + if (val.argindex == 0) { + extvector = val.val.f->extvector; + if (val.val.f->extvector == -1) { extlist = new int[size_vector]; int j = 0; - for (int i = nstart; i < nstop; i += nskip) - extlist[j++] = ifix->extlist[i-1]; + for (int i = nstart; i < nstop; i += nskip) extlist[j++] = val.val.f->extlist[i - 1]; } - } else extvector = ifix->extarray; - } else if (which[0] == ArgInfo::VARIABLE) { + } else + extvector = val.val.f->extarray; + } else if (val.which == ArgInfo::VARIABLE) { extvector = 0; } } else { array_flag = 1; - size_array_rows = (nstop-nstart) / nskip; - size_array_cols = nvalues; - memory->create(array,size_array_rows,size_array_cols,"slice:array"); + size_array_rows = (nstop - nstart) / nskip; + size_array_cols = values.size(); + memory->create(array, size_array_rows, size_array_cols, "slice:array"); extarray = 0; - for (int i = 0; i < nvalues; i++) { - if (which[i] == ArgInfo::COMPUTE) { - int icompute = modify->find_compute(ids[i]); - if (argindex[i] == 0) { - if (modify->compute[icompute]->extvector == 1) extarray = 1; - if (modify->compute[icompute]->extvector == -1) { - for (int j = 0; j < modify->compute[icompute]->size_vector; j++) - if (modify->compute[icompute]->extlist[j]) extarray = 1; + for (auto &val : values) { + if (val.which == ArgInfo::COMPUTE) { + if (val.argindex == 0) { + if (val.val.c->extvector == 1) extarray = 1; + if (val.val.c->extvector == -1) { + for (int j = 0; j < val.val.c->size_vector; j++) + if (val.val.c->extlist[j]) extarray = 1; } } else { - if (modify->compute[icompute]->extarray) extarray = 1; + if (val.val.c->extarray) extarray = 1; } - } else if (which[i] == ArgInfo::FIX) { - auto ifix = modify->get_fix_by_id(ids[i]); - if (argindex[i] == 0) { - if (ifix->extvector == 1) extarray = 1; - if (ifix->extvector == -1) { - for (int j = 0; j < ifix->size_vector; j++) - if (ifix->extlist[j]) extarray = 1; + } else if (val.which == ArgInfo::FIX) { + if (val.argindex == 0) { + if (val.val.f->extvector == 1) extarray = 1; + if (val.val.f->extvector == -1) { + for (int j = 0; j < val.val.f->size_vector; j++) + if (val.val.f->extlist[j]) extarray = 1; } } else { - if (ifix->extarray) extarray = 1; + if (val.val.f->extarray) extarray = 1; } - } else if (which[i] == ArgInfo::VARIABLE) { + } else if (val.which == ArgInfo::VARIABLE) { // variable is always intensive, does not change extarray } } @@ -196,12 +180,7 @@ ComputeSlice::ComputeSlice(LAMMPS *lmp, int narg, char **arg) : ComputeSlice::~ComputeSlice() { - delete [] which; - delete [] argindex; - for (int m = 0; m < nvalues; m++) delete [] ids[m]; - delete [] ids; - delete [] value2index; - delete [] extlist; + delete[] extlist; memory->destroy(vector); memory->destroy(array); @@ -213,22 +192,17 @@ void ComputeSlice::init() { // set indices and check validity of all computes,fixes - for (int m = 0; m < nvalues; m++) { - if (which[m] == ArgInfo::COMPUTE) { - int icompute = modify->find_compute(ids[m]); - if (icompute < 0) - error->all(FLERR,"Compute ID for compute slice does not exist"); - value2index[m] = icompute; - } else if (which[m] == ArgInfo::FIX) { - int ifix = modify->find_fix(ids[m]); - if (ifix < 0) - error->all(FLERR,"Fix ID for compute slice does not exist"); - value2index[m] = ifix; - } else if (which[m] == ArgInfo::VARIABLE) { - int ivariable = input->variable->find(ids[m]); - if (ivariable < 0) - error->all(FLERR,"Variable name for compute slice does not exist"); - value2index[m] = ivariable; + for (auto &val : values) { + if (val.which == ArgInfo::COMPUTE) { + val.val.c = modify->get_compute_by_id(val.id); + if (!val.val.c) error->all(FLERR, "Compute ID {} for compute slice does not exist", val.id); + } else if (val.which == ArgInfo::FIX) { + val.val.f = modify->get_fix_by_id(val.id); + if (!val.val.f) error->all(FLERR, "Fix ID {} for compute slice does not exist", val.id); + } else if (val.which == ArgInfo::VARIABLE) { + val.val.v = input->variable->find(val.id.c_str()); + if (val.val.v < 0) + error->all(FLERR, "Variable name {} for compute slice does not exist", val.id); } } } @@ -239,7 +213,7 @@ void ComputeSlice::compute_vector() { invoked_vector = update->ntimestep; - extract_one(0,vector,1); + extract_one(0, vector, 1); } /* ---------------------------------------------------------------------- */ @@ -248,8 +222,7 @@ void ComputeSlice::compute_array() { invoked_array = update->ntimestep; - for (int m = 0; m < nvalues; m++) - extract_one(0,&array[m][0],nvalues); + for (std::size_t m = 0; m < values.size(); m++) extract_one(0, &array[m][0], values.size()); } /* ---------------------------------------------------------------------- @@ -259,72 +232,67 @@ void ComputeSlice::compute_array() void ComputeSlice::extract_one(int m, double *vec, int stride) { - int i,j; + auto &val = values[m]; // invoke the appropriate compute if needed - if (which[m] == ArgInfo::COMPUTE) { - Compute *compute = modify->compute[value2index[m]]; - - if (argindex[m] == 0) { - if (!(compute->invoked_flag & Compute::INVOKED_VECTOR)) { - compute->compute_vector(); - compute->invoked_flag |= Compute::INVOKED_VECTOR; + if (val.which == ArgInfo::COMPUTE) { + if (val.argindex == 0) { + if (!(val.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { + val.val.c->compute_vector(); + val.val.c->invoked_flag |= Compute::INVOKED_VECTOR; } - double *cvector = compute->vector; - j = 0; - for (i = nstart; i < nstop; i += nskip) { - vec[j] = cvector[i-1]; + double *cvector = val.val.c->vector; + int j = 0; + for (int i = nstart; i < nstop; i += nskip) { + vec[j] = cvector[i - 1]; j += stride; } } else { - if (!(compute->invoked_flag & Compute::INVOKED_ARRAY)) { - compute->compute_array(); - compute->invoked_flag |= Compute::INVOKED_ARRAY; + if (!(val.val.c->invoked_flag & Compute::INVOKED_ARRAY)) { + val.val.c->compute_array(); + val.val.c->invoked_flag |= Compute::INVOKED_ARRAY; } - double **carray = compute->array; - int icol = argindex[m]-1; - j = 0; - for (i = nstart; i < nstop; i += nskip) { - vec[j] = carray[i-1][icol]; + double **carray = val.val.c->array; + int icol = val.argindex - 1; + int j = 0; + for (int i = nstart; i < nstop; i += nskip) { + vec[j] = carray[i - 1][icol]; j += stride; } } - // access fix fields, check if fix frequency is a match + // access fix fields, check if fix frequency is a match - } else if (which[m] == ArgInfo::FIX) { - if (update->ntimestep % modify->fix[value2index[m]]->global_freq) - error->all(FLERR,"Fix used in compute slice not " - "computed at compatible time"); - Fix *fix = modify->fix[value2index[m]]; + } else if (val.which == ArgInfo::FIX) { + if (update->ntimestep % val.val.f->global_freq) + error->all(FLERR, "Fix {} used in compute slice not computed at compatible time", val.id); - if (argindex[m] == 0) { - j = 0; - for (i = nstart; i < nstop; i += nskip) { - vec[j] = fix->compute_vector(i-1); + if (val.argindex == 0) { + int j = 0; + for (int i = nstart; i < nstop; i += nskip) { + vec[j] = val.val.f->compute_vector(i - 1); j += stride; } } else { - int icol = argindex[m]-1; - j = 0; - for (i = nstart; i < nstop; i += nskip) { - vec[j] = fix->compute_array(i-1,icol); + int icol = val.argindex - 1; + int j = 0; + for (int i = nstart; i < nstop; i += nskip) { + vec[j] = val.val.f->compute_array(i - 1, icol); j += stride; } } // invoke vector-style variable - } else if (which[m] == ArgInfo::VARIABLE) { + } else if (val.which == ArgInfo::VARIABLE) { double *varvec; - int nvec = input->variable->compute_vector(value2index[m],&varvec); - if (nvec < nstop) - error->all(FLERR,"Compute slice variable is not long enough"); - j = 0; - for (i = nstart; i < nstop; i += nskip) { - vec[j] = varvec[i-1]; + int nvec = input->variable->compute_vector(val.val.v, &varvec); + if (nvec < nstop) error->all(FLERR, "Compute slice variable {} is not long enough", val.id); + int j = 0; + for (int i = nstart; i < nstop; i += nskip) { + vec[j] = varvec[i - 1]; j += stride; } } diff --git a/src/compute_slice.h b/src/compute_slice.h index fd82df2d4e..c1575f4fc8 100644 --- a/src/compute_slice.h +++ b/src/compute_slice.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -33,10 +33,18 @@ class ComputeSlice : public Compute { void compute_array() override; private: - int me; - int nstart, nstop, nskip, nvalues; - int *which, *argindex, *value2index; - char **ids; + struct value_t { + int which; + int argindex; + std::string id; + union { + class Compute *c; + class Fix *f; + int v; + } val; + }; + std::vector values; + int nstart, nstop, nskip; void extract_one(int, double *, int); }; diff --git a/src/compute_stress_atom.cpp b/src/compute_stress_atom.cpp index f9c24847a1..1867e2c0aa 100644 --- a/src/compute_stress_atom.cpp +++ b/src/compute_stress_atom.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_stress_atom.h b/src/compute_stress_atom.h index a160785c3e..19f31c3016 100644 --- a/src/compute_stress_atom.h +++ b/src/compute_stress_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_temp.cpp b/src/compute_temp.cpp index b225cee2a1..2aa8782002 100644 --- a/src/compute_temp.cpp +++ b/src/compute_temp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_temp.h b/src/compute_temp.h index 98a5ee8325..367983cf58 100644 --- a/src/compute_temp.h +++ b/src/compute_temp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_temp_chunk.cpp b/src/compute_temp_chunk.cpp index c174c11ef9..54bf930f96 100644 --- a/src/compute_temp_chunk.cpp +++ b/src/compute_temp_chunk.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_temp_chunk.h b/src/compute_temp_chunk.h index 354966039a..fc9b6d78fd 100644 --- a/src/compute_temp_chunk.h +++ b/src/compute_temp_chunk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_temp_com.cpp b/src/compute_temp_com.cpp index 4ed4a669a5..a6d38a8167 100644 --- a/src/compute_temp_com.cpp +++ b/src/compute_temp_com.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_temp_com.h b/src/compute_temp_com.h index e02a1adce5..5ccefda99c 100644 --- a/src/compute_temp_com.h +++ b/src/compute_temp_com.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_temp_deform.cpp b/src/compute_temp_deform.cpp index a9617596dd..7c7404732d 100644 --- a/src/compute_temp_deform.cpp +++ b/src/compute_temp_deform.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_temp_deform.h b/src/compute_temp_deform.h index ec9b5a4a85..f024b0dbae 100644 --- a/src/compute_temp_deform.h +++ b/src/compute_temp_deform.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_temp_partial.cpp b/src/compute_temp_partial.cpp index 72297c8379..3773a39f40 100644 --- a/src/compute_temp_partial.cpp +++ b/src/compute_temp_partial.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_temp_partial.h b/src/compute_temp_partial.h index 7bd82b7027..191292f24e 100644 --- a/src/compute_temp_partial.h +++ b/src/compute_temp_partial.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_temp_profile.cpp b/src/compute_temp_profile.cpp index 4b8e77029b..f159f2f79a 100644 --- a/src/compute_temp_profile.cpp +++ b/src/compute_temp_profile.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_temp_profile.h b/src/compute_temp_profile.h index 13c7f030fd..1ce28ed290 100644 --- a/src/compute_temp_profile.h +++ b/src/compute_temp_profile.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_temp_ramp.cpp b/src/compute_temp_ramp.cpp index 9630b70cf9..5382c03389 100644 --- a/src/compute_temp_ramp.cpp +++ b/src/compute_temp_ramp.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_temp_ramp.h b/src/compute_temp_ramp.h index 8cc0e3fd44..b8e8d89463 100644 --- a/src/compute_temp_ramp.h +++ b/src/compute_temp_ramp.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_temp_region.cpp b/src/compute_temp_region.cpp index d65ac67147..47a060c088 100644 --- a/src/compute_temp_region.cpp +++ b/src/compute_temp_region.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_temp_region.h b/src/compute_temp_region.h index 784af5ddf2..be0642b6c6 100644 --- a/src/compute_temp_region.h +++ b/src/compute_temp_region.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_temp_sphere.cpp b/src/compute_temp_sphere.cpp index 7e5e97a42f..0cfc9a93ba 100644 --- a/src/compute_temp_sphere.cpp +++ b/src/compute_temp_sphere.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_temp_sphere.h b/src/compute_temp_sphere.h index 483a7e20f1..cfcb27e739 100644 --- a/src/compute_temp_sphere.h +++ b/src/compute_temp_sphere.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_torque_chunk.cpp b/src/compute_torque_chunk.cpp index 01e91e0797..febc286984 100644 --- a/src/compute_torque_chunk.cpp +++ b/src/compute_torque_chunk.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_torque_chunk.h b/src/compute_torque_chunk.h index a0b5f72db4..c810f7dc03 100644 --- a/src/compute_torque_chunk.h +++ b/src/compute_torque_chunk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_vacf.cpp b/src/compute_vacf.cpp index 07669ec84f..4e209f8612 100644 --- a/src/compute_vacf.cpp +++ b/src/compute_vacf.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government ret diff --git a/src/compute_vacf.h b/src/compute_vacf.h index b48bfcf475..42b3ed4adc 100644 --- a/src/compute_vacf.h +++ b/src/compute_vacf.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_vcm_chunk.cpp b/src/compute_vcm_chunk.cpp index 66e7dbeb48..a7678a5315 100644 --- a/src/compute_vcm_chunk.cpp +++ b/src/compute_vcm_chunk.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/compute_vcm_chunk.h b/src/compute_vcm_chunk.h index 02c280df04..418ae63c3a 100644 --- a/src/compute_vcm_chunk.h +++ b/src/compute_vcm_chunk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index 9fb3916965..f070d0a53f 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -38,7 +38,9 @@ #include "text_file_reader.h" #include "variable.h" +#include #include +#include using namespace LAMMPS_NS; using MathConst::MY_2PI; @@ -439,10 +441,12 @@ void CreateAtoms::command(int narg, char **arg) MPI_Barrier(world); double time1 = platform::walltime(); + // clear global->local map for owned and ghost atoms // clear ghost count and any ghost bonus data internal to AtomVec // same logic as beginning of Comm::exchange() // do it now b/c creating atoms will overwrite ghost atoms + if (atom->map_style != Atom::MAP_NONE) atom->map_clear(); atom->nghost = 0; atom->avec->clear_bonus(); diff --git a/src/create_atoms.h b/src/create_atoms.h index 826be1b8c4..ae6f1b9d33 100644 --- a/src/create_atoms.h +++ b/src/create_atoms.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp index 275463f4de..c6d3f1838e 100644 --- a/src/create_bonds.cpp +++ b/src/create_bonds.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -26,7 +26,6 @@ #include "force.h" #include "group.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "special.h" diff --git a/src/create_bonds.h b/src/create_bonds.h index 84a853cfde..03cbea5ccc 100644 --- a/src/create_bonds.h +++ b/src/create_bonds.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/create_box.cpp b/src/create_box.cpp index 679c1f31bd..fbf40c41ef 100644 --- a/src/create_box.cpp +++ b/src/create_box.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/create_box.h b/src/create_box.h index 3aaac1d004..66b613d7eb 100644 --- a/src/create_box.h +++ b/src/create_box.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp index f9a4197b71..e6b95f312e 100644 --- a/src/delete_atoms.cpp +++ b/src/delete_atoms.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/delete_atoms.h b/src/delete_atoms.h index 26754a5492..0aef095327 100644 --- a/src/delete_atoms.h +++ b/src/delete_atoms.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/delete_bonds.cpp b/src/delete_bonds.cpp index 2dcbd4af56..c4f55d47ef 100644 --- a/src/delete_bonds.cpp +++ b/src/delete_bonds.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/delete_bonds.h b/src/delete_bonds.h index 1b9c011e67..72d2d92722 100644 --- a/src/delete_bonds.h +++ b/src/delete_bonds.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/deprecated.cpp b/src/deprecated.cpp index 4e19f39894..c39cab1104 100644 --- a/src/deprecated.cpp +++ b/src/deprecated.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -32,16 +32,29 @@ void Deprecated::command(int narg, char **arg) if (cmd == "DEPRECATED") { if (lmp->comm->me == 0) utils::logmesg(lmp, "\nCommand 'DEPRECATED' is a dummy command\n\n"); return; - } else if (cmd == "reset_ids") { + } else if (cmd == "box") { if (lmp->comm->me == 0) - utils::logmesg(lmp, "\n'reset_ids' has been renamed to 'reset_atom_ids'\n\n"); + utils::logmesg(lmp, "\nThe 'box' command has been removed and will be ignored\n\n"); + return; } else if (utils::strmatch(cmd, "^kim_")) { - if (lmp->comm->me == 0) - utils::logmesg(lmp, - "\nWARNING: 'kim_' has been renamed to 'kim '. " - "Please update your input.\n\n"); std::string newcmd("kim"); newcmd += " " + cmd.substr(4); + if (lmp->comm->me == 0) + utils::logmesg(lmp, "\nWARNING: '{}' has been renamed to '{}'. Please update your input.\n\n", + cmd, newcmd); + for (int i = 0; i < narg; ++i) { + newcmd.append(1, ' '); + newcmd.append(arg[i]); + } + input->one(newcmd); + return; + } else if (utils::strmatch(cmd, "^reset_")) { + std::string newcmd("reset_atoms"); + if ((cmd == "reset_ids") || (cmd == "reset_atom_ids")) newcmd += " id"; + if (cmd == "reset_mol_ids") newcmd += " mol"; + if (lmp->comm->me == 0) + utils::logmesg(lmp, "\nWARNING: '{}' has been renamed to '{}'. Please update your input.\n\n", + cmd, newcmd); for (int i = 0; i < narg; ++i) { newcmd.append(1, ' '); newcmd.append(arg[i]); diff --git a/src/deprecated.h b/src/deprecated.h index 0e99512a9d..085bf5d47d 100644 --- a/src/deprecated.h +++ b/src/deprecated.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -14,12 +14,15 @@ #ifdef COMMAND_CLASS // clang-format off CommandStyle(DEPRECATED,Deprecated); -CommandStyle(reset_ids,Deprecated); +CommandStyle(box,Deprecated); CommandStyle(kim_init,Deprecated); CommandStyle(kim_interactions,Deprecated); CommandStyle(kim_param,Deprecated); CommandStyle(kim_property,Deprecated); CommandStyle(kim_query,Deprecated); +CommandStyle(reset_ids,Deprecated); +CommandStyle(reset_atom_ids,Deprecated); +CommandStyle(reset_mol_ids,Deprecated); CommandStyle(message,Deprecated); CommandStyle(server,Deprecated); // clang-format on diff --git a/src/dihedral.cpp b/src/dihedral.cpp index a59f83f37d..3e995fc405 100644 --- a/src/dihedral.cpp +++ b/src/dihedral.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/dihedral.h b/src/dihedral.h index 07e9fcba22..cf3d3f7d9a 100644 --- a/src/dihedral.h +++ b/src/dihedral.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/dihedral_deprecated.cpp b/src/dihedral_deprecated.cpp index 63afe28dff..4c10ca6dd1 100644 --- a/src/dihedral_deprecated.cpp +++ b/src/dihedral_deprecated.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/dihedral_deprecated.h b/src/dihedral_deprecated.h index 10af862990..41cf8f892c 100644 --- a/src/dihedral_deprecated.h +++ b/src/dihedral_deprecated.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/dihedral_hybrid.cpp b/src/dihedral_hybrid.cpp index 9925df6f81..d38ccf5d52 100644 --- a/src/dihedral_hybrid.cpp +++ b/src/dihedral_hybrid.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -20,7 +20,6 @@ #include "memory.h" #include "neighbor.h" -#include #include using namespace LAMMPS_NS; @@ -313,6 +312,16 @@ void DihedralHybrid::coeff(int narg, char **arg) void DihedralHybrid::init_style() { + // error if sub-style is not used + + int used; + for (int istyle = 0; istyle < nstyles; ++istyle) { + used = 0; + for (int itype = 1; itype <= atom->ndihedraltypes; ++itype) + if (map[itype] == istyle) used = 1; + if (used == 0) error->all(FLERR, "Dihedral hybrid sub-style {} is not used", keywords[istyle]); + } + for (int m = 0; m < nstyles; m++) if (styles[m]) styles[m]->init_style(); } diff --git a/src/dihedral_hybrid.h b/src/dihedral_hybrid.h index 5c3ed584bc..b7d4013afe 100644 --- a/src/dihedral_hybrid.h +++ b/src/dihedral_hybrid.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/dihedral_zero.cpp b/src/dihedral_zero.cpp index b995e2f935..d6d8349b0e 100644 --- a/src/dihedral_zero.cpp +++ b/src/dihedral_zero.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/dihedral_zero.h b/src/dihedral_zero.h index b338a92981..4a65e9567b 100644 --- a/src/dihedral_zero.h +++ b/src/dihedral_zero.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/displace_atoms.cpp b/src/displace_atoms.cpp index 5dc862a023..fa333f1bc2 100644 --- a/src/displace_atoms.cpp +++ b/src/displace_atoms.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/displace_atoms.h b/src/displace_atoms.h index 869f155190..38991f0ed5 100644 --- a/src/displace_atoms.h +++ b/src/displace_atoms.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/domain.cpp b/src/domain.cpp index 8df73852c2..97f626cbcd 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -82,7 +82,6 @@ Domain::Domain(LAMMPS *lmp) : Pointers(lmp) minzlo = minzhi = 0.0; triclinic = 0; - tiltsmall = 1; boxlo[0] = boxlo[1] = boxlo[2] = -0.5; boxhi[0] = boxhi[1] = boxhi[2] = 0.5; @@ -212,16 +211,13 @@ void Domain::set_initial_box(int expandflag) if (dimension == 2 && (xz != 0.0 || yz != 0.0)) error->all(FLERR,"Cannot skew triclinic box in z for 2d simulation"); - // error check or warning on triclinic tilt factors + // check on triclinic tilt factors if (triclinic) { - if ((fabs(xy/(boxhi[0]-boxlo[0])) > 0.5 && xperiodic) || - (fabs(xz/(boxhi[0]-boxlo[0])) > 0.5 && xperiodic) || - (fabs(yz/(boxhi[1]-boxlo[1])) > 0.5 && yperiodic)) { - if (tiltsmall) - error->all(FLERR,"Triclinic box skew is too large"); - else if (comm->me == 0) - error->warning(FLERR,"Triclinic box skew is large"); + if ((fabs(xy/(boxhi[1]-boxlo[1])) > 0.5 && yperiodic) || + ((fabs(xz)+fabs(yz))/(boxhi[2]-boxlo[2]) > 0.5 && zperiodic)) { + if (comm->me == 0) + error->warning(FLERR,"Triclinic box skew is large. LAMMPS will run inefficiently."); } } @@ -981,25 +977,33 @@ void Domain::subbox_too_small_check(double thresh) this should not be used if atom has moved infinitely far outside box b/c while could iterate forever e.g. fix shake prediction of new position with highly overlapped atoms - use minimum_image_once() instead + uses minimum_image_once() instead ------------------------------------------------------------------------- */ +static constexpr double MAXIMGCOUNT = 16; + void Domain::minimum_image(double &dx, double &dy, double &dz) { if (triclinic == 0) { if (xperiodic) { + if (fabs(dx) > (MAXIMGCOUNT * xprd)) + error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dx); while (fabs(dx) > xprd_half) { if (dx < 0.0) dx += xprd; else dx -= xprd; } } if (yperiodic) { + if (fabs(dy) > (MAXIMGCOUNT * yprd)) + error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dy); while (fabs(dy) > yprd_half) { if (dy < 0.0) dy += yprd; else dy -= yprd; } } if (zperiodic) { + if (fabs(dz) > (MAXIMGCOUNT * zprd)) + error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dz); while (fabs(dz) > zprd_half) { if (dz < 0.0) dz += zprd; else dz -= zprd; @@ -1008,6 +1012,8 @@ void Domain::minimum_image(double &dx, double &dy, double &dz) } else { if (zperiodic) { + if (fabs(dz) > (MAXIMGCOUNT * zprd)) + error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dz); while (fabs(dz) > zprd_half) { if (dz < 0.0) { dz += zprd; @@ -1021,6 +1027,8 @@ void Domain::minimum_image(double &dx, double &dy, double &dz) } } if (yperiodic) { + if (fabs(dy) > (MAXIMGCOUNT * yprd)) + error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dy); while (fabs(dy) > yprd_half) { if (dy < 0.0) { dy += yprd; @@ -1032,6 +1040,8 @@ void Domain::minimum_image(double &dx, double &dy, double &dz) } } if (xperiodic) { + if (fabs(dx) > (MAXIMGCOUNT * xprd)) + error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dx); while (fabs(dx) > xprd_half) { if (dx < 0.0) dx += xprd; else dx -= xprd; @@ -1040,75 +1050,6 @@ void Domain::minimum_image(double &dx, double &dy, double &dz) } } -/* ---------------------------------------------------------------------- - minimum image convention in periodic dimensions - use 1/2 of box size as test - for triclinic, also add/subtract tilt factors in other dims as needed - changed "if" to "while" to enable distance to - far-away ghost atom returned by atom->map() to be wrapped back into box - could be problem for looking up atom IDs when cutoff > boxsize - this should not be used if atom has moved infinitely far outside box - b/c while could iterate forever - e.g. fix shake prediction of new position with highly overlapped atoms - use minimum_image_once() instead -------------------------------------------------------------------------- */ - -void Domain::minimum_image(double *delta) -{ - if (triclinic == 0) { - if (xperiodic) { - while (fabs(delta[0]) > xprd_half) { - if (delta[0] < 0.0) delta[0] += xprd; - else delta[0] -= xprd; - } - } - if (yperiodic) { - while (fabs(delta[1]) > yprd_half) { - if (delta[1] < 0.0) delta[1] += yprd; - else delta[1] -= yprd; - } - } - if (zperiodic) { - while (fabs(delta[2]) > zprd_half) { - if (delta[2] < 0.0) delta[2] += zprd; - else delta[2] -= zprd; - } - } - - } else { - if (zperiodic) { - while (fabs(delta[2]) > zprd_half) { - if (delta[2] < 0.0) { - delta[2] += zprd; - delta[1] += yz; - delta[0] += xz; - } else { - delta[2] -= zprd; - delta[1] -= yz; - delta[0] -= xz; - } - } - } - if (yperiodic) { - while (fabs(delta[1]) > yprd_half) { - if (delta[1] < 0.0) { - delta[1] += yprd; - delta[0] += xy; - } else { - delta[1] -= yprd; - delta[0] -= xy; - } - } - } - if (xperiodic) { - while (fabs(delta[0]) > xprd_half) { - if (delta[0] < 0.0) delta[0] += xprd; - else delta[0] -= xprd; - } - } - } -} - /* ---------------------------------------------------------------------- minimum image convention in periodic dimensions use 1/2 of box size as test @@ -1760,8 +1701,8 @@ void Domain::add_region(int narg, char **arg) Region *newregion = nullptr; if (lmp->suffix_enable) { - if (lmp->suffix) { - std::string estyle = std::string(arg[1]) + "/" + lmp->suffix; + if (lmp->non_pair_suffix()) { + std::string estyle = std::string(arg[1]) + "/" + lmp->non_pair_suffix(); if (region_map->find(estyle) != region_map->end()) { RegionCreator ®ion_creator = (*region_map)[estyle]; newregion = region_creator(lmp, narg, arg); @@ -1929,26 +1870,6 @@ void Domain::set_boundary(int narg, char **arg, int flag) } } -/* ---------------------------------------------------------------------- - set domain attributes -------------------------------------------------------------------------- */ - -void Domain::set_box(int narg, char **arg) -{ - if (narg < 1) utils::missing_cmd_args(FLERR, "box", error); - - int iarg = 0; - while (iarg < narg) { - if (strcmp(arg[iarg],"tilt") == 0) { - if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "box tilt", error); - if (strcmp(arg[iarg+1],"small") == 0) tiltsmall = 1; - else if (strcmp(arg[iarg+1],"large") == 0) tiltsmall = 0; - else error->all(FLERR,"Unknown box tilt argument: {}", arg[iarg+1]); - iarg += 2; - } else error->all(FLERR,"Unknown box keyword: {}", arg[iarg]); - } -} - /* ---------------------------------------------------------------------- print box info, orthogonal or triclinic ------------------------------------------------------------------------- */ diff --git a/src/domain.h b/src/domain.h index 649849e961..1999baac2b 100644 --- a/src/domain.h +++ b/src/domain.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -19,7 +19,6 @@ #include #include #include -#include namespace LAMMPS_NS { class Region; @@ -41,7 +40,6 @@ class Domain : protected Pointers { // 3 = shrink-wrap non-per w/ min int triclinic; // 0 = orthog box, 1 = triclinic - int tiltsmall; // 1 if limit tilt, else 0 // orthogonal box @@ -120,7 +118,7 @@ class Domain : protected Pointers { void box_too_small_check(); void subbox_too_small_check(double); void minimum_image(double &, double &, double &); - void minimum_image(double *); + void minimum_image(double *delta) { minimum_image(delta[0], delta[1], delta[2]); } void minimum_image_once(double *); int closest_image(int, int); int closest_image(const double *const, int); @@ -141,7 +139,6 @@ class Domain : protected Pointers { const std::vector get_region_by_style(const std::string &) const; const std::vector get_region_list(); void set_boundary(int, char **, int); - void set_box(int, char **); void print_box(const std::string &); void boundary_string(char *); diff --git a/src/dump.cpp b/src/dump.cpp index 42d7186bcc..82a25c31f2 100644 --- a/src/dump.cpp +++ b/src/dump.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -29,6 +29,7 @@ #include "variable.h" #include +#include using namespace LAMMPS_NS; diff --git a/src/dump.h b/src/dump.h index ecff27f7dd..4f0019ca2c 100644 --- a/src/dump.h +++ b/src/dump.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -45,9 +45,15 @@ class Dump : protected Pointers { void init(); virtual void write(); - virtual int pack_forward_comm(int, int *, double *, int, int *) { return 0; } + virtual int pack_forward_comm(int, int *, double *, int, int *) + { + return 0; + } virtual void unpack_forward_comm(int, int, double *) {} - virtual int pack_reverse_comm(int, int, double *) { return 0; } + virtual int pack_reverse_comm(int, int, double *) + { + return 0; + } virtual void unpack_reverse_comm(int, int *, double *) {} void modify_params(int, char **); @@ -91,9 +97,9 @@ class Dump : protected Pointers { char *refresh; // compute ID to invoke refresh() on int irefresh; // index of compute - int skipflag; // 1 if skip condition defined - char *skipvar; // name of variable to check for skip condition - int skipindex; // index of skip variable + int skipflag; // 1 if skip condition defined + char *skipvar; // name of variable to check for skip condition + int skipindex; // index of skip variable char boundstr[9]; // encoding of boundary flags @@ -151,11 +157,17 @@ class Dump : protected Pointers { virtual void init_style() = 0; virtual void openfile(); - virtual int modify_param(int, char **) { return 0; } + virtual int modify_param(int, char **) + { + return 0; + } virtual void write_header(bigint) = 0; virtual int count(); virtual void pack(tagint *) = 0; - virtual int convert_string(int, double *) { return 0; } + virtual int convert_string(int, double *) + { + return 0; + } virtual void write_data(int, double *) = 0; virtual void write_footer() {} diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp index 8daf2d1d0a..1d3862ab26 100644 --- a/src/dump_atom.cpp +++ b/src/dump_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/dump_atom.h b/src/dump_atom.h index 335557ea95..e28b390520 100644 --- a/src/dump_atom.h +++ b/src/dump_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/dump_cfg.cpp b/src/dump_cfg.cpp index c5a122b2ef..a64507dc16 100644 --- a/src/dump_cfg.cpp +++ b/src/dump_cfg.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/dump_cfg.h b/src/dump_cfg.h index f2df772319..0298ccf798 100644 --- a/src/dump_cfg.h +++ b/src/dump_cfg.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index 2417a05c2c..d2b091eb6d 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -1150,6 +1150,7 @@ int DumpCustom::count() void DumpCustom::pack(tagint *ids) { for (int n = 0; n < size_one; n++) (this->*pack_choice[n])(n); + if (ids) { tagint *tag = atom->tag; for (int i = 0; i < nchoose; i++) diff --git a/src/dump_custom.h b/src/dump_custom.h index 92c50fc173..da49ffdc22 100644 --- a/src/dump_custom.h +++ b/src/dump_custom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/dump_deprecated.cpp b/src/dump_deprecated.cpp index 1c4fb59390..64d50fff6a 100644 --- a/src/dump_deprecated.cpp +++ b/src/dump_deprecated.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/dump_deprecated.h b/src/dump_deprecated.h index 85a4d17d7f..4a081e8854 100644 --- a/src/dump_deprecated.h +++ b/src/dump_deprecated.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/dump_grid.cpp b/src/dump_grid.cpp new file mode 100644 index 0000000000..996c7f1301 --- /dev/null +++ b/src/dump_grid.cpp @@ -0,0 +1,882 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "dump_grid.h" + +#include "arg_info.h" +#include "compute.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "grid2d.h" +#include "grid3d.h" +#include "memory.h" +#include "modify.h" +#include "region.h" +#include "update.h" + +#include + +using namespace LAMMPS_NS; + +// customize by adding keyword +// also customize compute_atom_property.cpp + +enum {COMPUTE,FIX}; + +#define ONEFIELD 32 +#define DELTA 1048576 + +/* ---------------------------------------------------------------------- */ + +DumpGrid::DumpGrid(LAMMPS *lmp, int narg, char **arg) : + Dump(lmp, narg, arg), idregion(nullptr), earg(nullptr), vtype(nullptr), + vformat(nullptr), columns(nullptr), columns_default(nullptr), + field2index(nullptr), field2grid(nullptr), field2data(nullptr), + argindex(nullptr), id_compute(nullptr), id_fix(nullptr), pack_choice(nullptr) +{ + if (narg == 5) error->all(FLERR,"No dump grid arguments specified"); + + clearstep = 1; + + nevery = utils::inumeric(FLERR,arg[3],false,lmp); + if (nevery <= 0) error->all(FLERR,"Illegal dump grid nevery value: {}", nevery); + + // expand args if any have wildcard character "*" + // ok to include trailing optional args, + // so long as they do not have "*" between square brackets + // nfield may be shrunk below if extra optional args exist + + expand = 0; + nfield = nargnew = utils::expand_args(FLERR,narg-5,&arg[5],1,earg,lmp); + if (earg != &arg[5]) expand = 1; + + // allocate field vectors + + pack_choice = new FnPtrPack[nfield]; + vtype = new int[nfield]; + field2source = new int[nfield]; + field2index = new int[nfield]; + field2grid = new int[nfield]; + field2data = new int[nfield]; + argindex = new int[nfield]; + + buffer_allow = 1; + buffer_flag = 1; + + dimension = domain->dimension; + + // for 2d, set nzgrid = 1 for dump grid and grid/vtk files + + if (dimension == 2) nzgrid = 1; + + // computes and fixes which the dump accesses + + ncompute = 0; + nfix = 0; + + // process attributes + // ioptional = start of additional optional args in expanded args + + ioptional = parse_fields(nfield,earg); + + if (ioptional < nfield && + strcmp(style,"image") != 0 && strcmp(style,"movie") != 0) + error->all(FLERR,"Invalid attribute {} in dump {} command", earg[ioptional],style); + + // noptional = # of optional args + // reset nfield to subtract off optional args + // reset ioptional to what it would be in original arg list + // only dump image and dump movie styles process optional args, + // they do not use expanded earg list + + int noptional = nfield - ioptional; + nfield -= noptional; + size_one = nfield; + ioptional = narg - noptional; + + // setup format strings + + vformat = new char*[nfield]; + std::string cols; + + cols.clear(); + for (int i = 0; i < nfield; i++) { + if (vtype[i] == Dump::INT) cols += "%d "; + else if (vtype[i] == Dump::DOUBLE) cols += "%g "; + else if (vtype[i] == Dump::STRING) cols += "%s "; + else if (vtype[i] == Dump::BIGINT) cols += BIGINT_FORMAT " "; + vformat[i] = nullptr; + } + cols.resize(cols.size()-1); + format_default = utils::strdup(cols); + + format_column_user = new char*[nfield]; + for (int i = 0; i < nfield; i++) format_column_user[i] = nullptr; + + // setup column string + + cols.clear(); + keyword_user.resize(nfield); + for (int iarg = 0; iarg < nfield; iarg++) { + key2col[earg[iarg]] = iarg; + keyword_user[iarg].clear(); + if (cols.size()) cols += " "; + cols += earg[iarg]; + } + columns_default = utils::strdup(cols); +} + +/* ---------------------------------------------------------------------- */ + +DumpGrid::~DumpGrid() +{ + // if wildcard expansion occurred, free earg memory from expand_args() + // could not do in constructor, b/c some derived classes process earg + + if (expand) { + for (int i = 0; i < nargnew; i++) delete[] earg[i]; + memory->sfree(earg); + } + + delete[] pack_choice; + delete[] vtype; + delete[] field2source; + delete[] field2index; + delete[] field2grid; + delete[] field2data; + delete[] argindex; + + delete[] idregion; + + for (int i = 0; i < ncompute; i++) delete[] id_compute[i]; + memory->sfree(id_compute); + + for (int i = 0; i < nfix; i++) delete[] id_fix[i]; + memory->sfree(id_fix); + + if (vformat) { + for (int i = 0; i < nfield; i++) delete[] vformat[i]; + delete[] vformat; + } + + if (format_column_user) { + for (int i = 0; i < nfield; i++) delete[] format_column_user[i]; + delete[] format_column_user; + } + + delete[] columns_default; + delete[] columns; +} + +/* ---------------------------------------------------------------------- */ + +void DumpGrid::init_style() +{ + // assemble ITEMS: column string from defaults and user values + + delete[] columns; + std::string combined; + int icol = 0; + for (const auto &item : utils::split_words(columns_default)) { + if (combined.size()) combined += " "; + if (keyword_user[icol].size()) combined += keyword_user[icol]; + else combined += item; + ++icol; + } + columns = utils::strdup(combined); + + // format = copy of default or user-specified line format + + delete[] format; + if (format_line_user) format = utils::strdup(format_line_user); + else format = utils::strdup(format_default); + + // tokenize the format string and add space at end of each format element + // if user-specified int/float format exists, use it instead + // if user-specified column format exists, use it instead + // lo priority = line, medium priority = int/float, hi priority = column + + auto words = utils::split_words(format); + if ((int) words.size() < nfield) + error->all(FLERR,"Dump_modify format line is too short"); + + int i=0; + for (const auto &word : words) { + delete[] vformat[i]; + + if (format_column_user[i]) + vformat[i] = utils::strdup(std::string(format_column_user[i]) + " "); + else if (vtype[i] == Dump::INT && format_int_user) + vformat[i] = utils::strdup(std::string(format_int_user) + " "); + else if (vtype[i] == Dump::DOUBLE && format_float_user) + vformat[i] = utils::strdup(std::string(format_float_user) + " "); + else if (vtype[i] == Dump::BIGINT && format_bigint_user) + vformat[i] = utils::strdup(std::string(format_bigint_user) + " "); + else vformat[i] = utils::strdup(word + " "); + + // remove trailing blank on last column's format + if (i == nfield-1) vformat[i][strlen(vformat[i])-1] = '\0'; + + ++i; + } + + // setup boundary string + + domain->boundary_string(boundstr); + + // setup function ptrs + + if (binary && domain->triclinic == 0) + header_choice = &DumpGrid::header_binary; + else if (binary && domain->triclinic == 1) + header_choice = &DumpGrid::header_binary_triclinic; + else if (!binary && domain->triclinic == 0) + header_choice = &DumpGrid::header_item; + else if (!binary && domain->triclinic == 1) + header_choice = &DumpGrid::header_item_triclinic; + + if (binary) write_choice = &DumpGrid::write_binary; + else if (buffer_flag == 1) write_choice = &DumpGrid::write_string; + else write_choice = &DumpGrid::write_lines; + + // find current ptr for each compute and fix + + for (i = 0; i < ncompute; i++) { + compute[i] = modify->get_compute_by_id(id_compute[i]); + if (!compute[i]) + error->all(FLERR,"Could not find dump grid compute ID {}",id_compute[i]); + } + + for (i = 0; i < nfix; i++) { + fix[i] = modify->get_fix_by_id(id_fix[i]); + if (!fix[i]) + error->all(FLERR,"Could not find dump grid fix ID {}", id_fix[i]); + } + + // check that grid sizes for all fields are the same + + Grid2d *grid2d = nullptr; + Grid3d *grid3d = nullptr; + int nxtmp,nytmp,nztmp; + for (int i = 0; i < nfield; i++) { + if (dimension == 2) { + if (field2source[i] == COMPUTE) + grid2d = (Grid2d *) compute[field2index[i]]->get_grid_by_index(field2grid[i]); + else + grid2d = (Grid2d *) fix[field2index[i]]->get_grid_by_index(field2grid[i]); + if (i == 0) grid2d->get_size(nxgrid,nygrid); + else { + grid2d->get_size(nxtmp,nytmp); + if ((nxtmp != nxgrid) || (nytmp != nygrid)) + error->all(FLERR,"Dump grid field grid sizes do not match"); + } + + } else { + if (field2source[i] == COMPUTE) + grid3d = (Grid3d *) compute[field2index[i]]->get_grid_by_index(field2grid[i]); + else + grid3d = (Grid3d *) fix[field2index[i]]->get_grid_by_index(field2grid[i]); + if (i == 0) grid3d->get_size(nxgrid,nygrid,nzgrid); + else { + grid3d->get_size(nxtmp,nytmp,nztmp); + if ((nxtmp != nxgrid) || (nytmp != nygrid) || (nztmp != nzgrid)) + error->all(FLERR,"Dump grid field grid sizes do not match"); + } + } + } + + // check validity of region + + if (idregion && !domain->get_region_by_id(idregion)) + error->all(FLERR,"Region {} for dump grid does not exist", idregion); + + // open single file, one time only + + if (multifile == 0) openfile(); +} + +/* ---------------------------------------------------------------------- */ + +void DumpGrid::write_header(bigint ndump) +{ + if (multiproc) (this->*header_choice)(ndump); + else if (me == 0) (this->*header_choice)(ndump); +} + +/* ---------------------------------------------------------------------- */ + +void DumpGrid::header_unit_style_binary() +{ + int len = 0; + if (unit_flag && !unit_count) { + ++unit_count; + len = strlen(update->unit_style); + fwrite(&len, sizeof(int), 1, fp); + fwrite(update->unit_style, sizeof(char), len, fp); + } else { + fwrite(&len, sizeof(int), 1, fp); + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpGrid::header_columns_binary() +{ + int len = strlen(columns); + fwrite(&len, sizeof(int), 1, fp); + fwrite(columns, sizeof(char), len, fp); +} + +/* ---------------------------------------------------------------------- */ + +void DumpGrid::header_time_binary() +{ + char flag = time_flag ? 1 : 0; + fwrite(&flag, sizeof(char), 1, fp); + + if (time_flag) { + double t = compute_time(); + fwrite(&t, sizeof(double), 1, fp); + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpGrid::header_format_binary() +{ + format_magic_string_binary(); + format_endian_binary(); + format_revision_binary(); +} + +/* ---------------------------------------------------------------------- */ + +void DumpGrid::header_binary(bigint ndump) +{ + header_format_binary(); + + fwrite(&update->ntimestep,sizeof(bigint),1,fp); + fwrite(&ndump,sizeof(bigint),1,fp); + fwrite(&domain->triclinic,sizeof(int),1,fp); + fwrite(&domain->boundary[0][0],6*sizeof(int),1,fp); + fwrite(&boxxlo,sizeof(double),1,fp); + fwrite(&boxxhi,sizeof(double),1,fp); + fwrite(&boxylo,sizeof(double),1,fp); + fwrite(&boxyhi,sizeof(double),1,fp); + fwrite(&boxzlo,sizeof(double),1,fp); + fwrite(&boxzhi,sizeof(double),1,fp); + fwrite(&nxgrid,sizeof(int),1,fp); + fwrite(&nygrid,sizeof(int),1,fp); + fwrite(&nzgrid,sizeof(int),1,fp); + fwrite(&nfield,sizeof(int),1,fp); + + header_unit_style_binary(); + header_time_binary(); + header_columns_binary(); + + if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp); + else fwrite(&nprocs,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- */ + +void DumpGrid::header_binary_triclinic(bigint ndump) +{ + header_format_binary(); + + fwrite(&update->ntimestep,sizeof(bigint),1,fp); + fwrite(&ndump,sizeof(bigint),1,fp); + fwrite(&domain->triclinic,sizeof(int),1,fp); + fwrite(&domain->boundary[0][0],6*sizeof(int),1,fp); + fwrite(&boxxlo,sizeof(double),1,fp); + fwrite(&boxxhi,sizeof(double),1,fp); + fwrite(&boxylo,sizeof(double),1,fp); + fwrite(&boxyhi,sizeof(double),1,fp); + fwrite(&boxzlo,sizeof(double),1,fp); + fwrite(&boxzhi,sizeof(double),1,fp); + fwrite(&boxxy,sizeof(double),1,fp); + fwrite(&boxxz,sizeof(double),1,fp); + fwrite(&boxyz,sizeof(double),1,fp); + fwrite(&nxgrid,sizeof(int),1,fp); + fwrite(&nygrid,sizeof(int),1,fp); + fwrite(&nzgrid,sizeof(int),1,fp); + fwrite(&nfield,sizeof(int),1,fp); + + header_unit_style_binary(); + header_time_binary(); + header_columns_binary(); + + if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp); + else fwrite(&nprocs,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- */ + +void DumpGrid::header_item(bigint /*ndump*/) +{ + if (unit_flag && !unit_count) { + ++unit_count; + fmt::print(fp,"ITEM: UNITS\n{}\n",update->unit_style); + } + if (time_flag) fmt::print(fp,"ITEM: TIME\n{:.16}\n",compute_time()); + + fmt::print(fp,"ITEM: TIMESTEP\n{}\n",update->ntimestep); + fmt::print(fp,"ITEM: BOX BOUNDS {}\n" + "{:>1.16e} {:>1.16e}\n" + "{:>1.16e} {:>1.16e}\n" + "{:>1.16e} {:>1.16e}\n", + boundstr,boxxlo,boxxhi,boxylo,boxyhi,boxzlo,boxzhi); + fmt::print(fp,"ITEM: GRID SIZE nx ny nz\n{} {} {}\n",nxgrid,nygrid,nzgrid); + fmt::print(fp,"ITEM: GRID CELLS {}\n",columns); +} + +/* ---------------------------------------------------------------------- */ + +void DumpGrid::header_item_triclinic(bigint /*ndump*/) +{ + if (unit_flag && !unit_count) { + ++unit_count; + fmt::print(fp,"ITEM: UNITS\n{}\n",update->unit_style); + } + if (time_flag) fmt::print(fp,"ITEM: TIME\n{:.16}\n",compute_time()); + + fmt::print(fp,"ITEM: TIMESTEP\n{}\n",update->ntimestep); + fmt::print(fp,"ITEM: BOX BOUNDS xy xz yz {}\n" + "{:>1.16e} {:>1.16e} {:>1.16e}\n" + "{:>1.16e} {:>1.16e} {:>1.16e}\n" + "{:>1.16e} {:>1.16e} {:>1.16e}\n", + boundstr,boxxlo,boxxhi,boxxy,boxylo,boxyhi,boxxz,boxzlo,boxzhi,boxyz); + fmt::print(fp,"ITEM: GRID SIZE nx ny nz\n{} {} {}\n",nxgrid,nygrid,nzgrid); + fmt::print(fp,"ITEM: GRID CELLS {}\n",columns); +} + +/* ---------------------------------------------------------------------- */ + +void DumpGrid::format_magic_string_binary() +{ + // use negative ntimestep as marker for new format + bigint fmtlen = strlen(MAGIC_STRING); + bigint marker = -fmtlen; + fwrite(&marker, sizeof(bigint), 1, fp); + fwrite(MAGIC_STRING, sizeof(char), fmtlen, fp); +} + +/* ---------------------------------------------------------------------- */ + +void DumpGrid::format_endian_binary() +{ + int endian = ENDIAN; + fwrite(&endian, sizeof(int), 1, fp); +} + +/* ---------------------------------------------------------------------- */ + +void DumpGrid::format_revision_binary() +{ + int revision = FORMAT_REVISION; + fwrite(&revision, sizeof(int), 1, fp); +} + +/* ---------------------------------------------------------------------- */ + +int DumpGrid::count() +{ + int i; + + // set current size for portion of grid on each proc + // may change between dump snapshots due to load balancing + + Grid2d *grid2d = nullptr; + Grid3d *grid3d = nullptr; + + if (dimension == 2) { + if (field2source[0] == COMPUTE) + grid2d = (Grid2d *) compute[field2index[0]]->get_grid_by_index(field2grid[0]); + else if (field2source[0] == FIX) + grid2d = (Grid2d *) fix[field2index[0]]->get_grid_by_index(field2grid[0]); + else error->all(FLERR, "Unsupported grid data source type {}", field2source[0]); + grid2d->get_bounds_owned(nxlo_in,nxhi_in,nylo_in,nyhi_in); + } else { + if (field2source[0] == COMPUTE) + grid3d = (Grid3d *) compute[field2index[0]]->get_grid_by_index(field2grid[0]); + else if (field2source[0] == FIX) + grid3d = (Grid3d *) fix[field2index[0]]->get_grid_by_index(field2grid[0]); + else error->all(FLERR, "Unsupported grid data source type {}", field2source[0]); + grid3d->get_bounds_owned(nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in); + } + + // invoke Computes for per-grid quantities + // only if within a run or minimize + // else require that computes are current + // this prevents a compute from being invoked by the WriteDump class + + if (ncompute) { + if (update->whichflag == 0) { + for (i = 0; i < ncompute; i++) + if (compute[i]->invoked_pergrid != update->ntimestep) + error->all(FLERR,"Compute {} used in dump between runs is not current", compute[i]->id); + } else { + for (i = 0; i < ncompute; i++) { + if (!(compute[i]->invoked_flag & Compute::INVOKED_PERGRID)) { + compute[i]->compute_pergrid(); + compute[i]->invoked_flag |= Compute::INVOKED_PERGRID; + } + } + } + } + + // return count of grid points I own + + int ngrid; + if (dimension == 2) + ngrid = (nxhi_in-nxlo_in+1) * (nyhi_in-nylo_in+1); + else + ngrid = (nxhi_in-nxlo_in+1) * (nyhi_in-nylo_in+1) * (nzhi_in-nzlo_in+1); + + return ngrid; +} + +/* ---------------------------------------------------------------------- */ + +void DumpGrid::pack(tagint *ids) +{ + for (int n = 0; n < size_one; n++) (this->*pack_choice[n])(n); + + // ids = list of my grid IDs + + if (ids) { + int m = 0; + if (dimension == 2) { + for (int iy = nylo_in; iy <= nyhi_in; iy++) + for (int ix = nxlo_in; ix <= nxhi_in; ix++) + ids[m++] = iy*nxgrid + ix + 1; + } else if (dimension == 3) { + for (int iz = nzlo_in; iz <= nzhi_in; iz++) + for (int iy = nylo_in; iy <= nyhi_in; iy++) + for (int ix = nxlo_in; ix <= nxhi_in; ix++) + ids[m++] = iz*nygrid*nxgrid + iy*nxgrid + ix + 1; + } + } +} + +/* ---------------------------------------------------------------------- + convert mybuf of doubles to one big formatted string in sbuf + return -1 if strlen exceeds an int, since used as arg in MPI calls in Dump +------------------------------------------------------------------------- */ + +int DumpGrid::convert_string(int n, double *mybuf) +{ + int i,j; + + int offset = 0; + int m = 0; + for (i = 0; i < n; i++) { + if (offset + nfield*ONEFIELD > maxsbuf) { + if ((bigint) maxsbuf + DELTA > MAXSMALLINT) return -1; + maxsbuf += DELTA; + memory->grow(sbuf,maxsbuf,"dump:sbuf"); + } + + for (j = 0; j < nfield; j++) { + if (vtype[j] == Dump::INT) + offset += sprintf(&sbuf[offset],vformat[j],static_cast (mybuf[m])); + else if (vtype[j] == Dump::DOUBLE) + offset += sprintf(&sbuf[offset],vformat[j],mybuf[m]); + else if (vtype[j] == Dump::BIGINT) + offset += sprintf(&sbuf[offset],vformat[j], static_cast (mybuf[m])); + m++; + } + offset += sprintf(&sbuf[offset],"\n"); + } + + return offset; +} + +/* ---------------------------------------------------------------------- */ + +void DumpGrid::write_data(int n, double *mybuf) +{ + (this->*write_choice)(n,mybuf); +} + +/* ---------------------------------------------------------------------- */ + +void DumpGrid::write_binary(int n, double *mybuf) +{ + n *= size_one; + fwrite(&n,sizeof(int),1,fp); + fwrite(mybuf,sizeof(double),n,fp); +} + +/* ---------------------------------------------------------------------- */ + +void DumpGrid::write_string(int n, double *mybuf) +{ + if (mybuf) + fwrite(mybuf,sizeof(char),n,fp); +} + +/* ---------------------------------------------------------------------- */ + +void DumpGrid::write_lines(int n, double *mybuf) +{ + int i,j; + + int m = 0; + for (i = 0; i < n; i++) { + for (j = 0; j < nfield; j++) { + if (vtype[j] == Dump::INT) fprintf(fp,vformat[j],static_cast (mybuf[m])); + else if (vtype[j] == Dump::DOUBLE) fprintf(fp,vformat[j],mybuf[m]); + else if (vtype[j] == Dump::BIGINT) fprintf(fp,vformat[j],static_cast (mybuf[m])); + m++; + } + fprintf(fp,"\n"); + } +} + +/* ---------------------------------------------------------------------- */ + +int DumpGrid::parse_fields(int narg, char **arg) +{ + // customize by adding to if statement + + for (int iarg = 0; iarg < narg; iarg++) { + + char *id; + int igrid,idata,index; + int iflag = + utils::check_grid_reference((char *) "Dump grid", + arg[iarg],nevery,id,igrid,idata,index,lmp); + + // arg is not a valid Grid reference + // assume it's an additional dump grid option and return + + if (iflag < 0) return iarg; + + // grid reference is to a compute or fix + + if (iflag == ArgInfo::COMPUTE) { + auto icompute = lmp->modify->get_compute_by_id(id); + field2index[iarg] = add_compute(id,icompute); + field2source[iarg] = COMPUTE; + } else if (iflag == ArgInfo::FIX) { + auto ifix = modify->get_fix_by_id(id); + field2index[iarg] = add_fix(id,ifix); + field2source[iarg] = FIX; + } + + delete [] id; + argindex[iarg] = index; + vtype[iarg] = Dump::DOUBLE; + field2grid[iarg] = igrid; + field2data[iarg] = idata; + + if (dimension == 2) pack_choice[iarg] = &DumpGrid::pack_grid2d; + else pack_choice[iarg] = &DumpGrid::pack_grid3d; + } + + return narg; +} + +/* ---------------------------------------------------------------------- + add Compute to list of Compute objects used by dump + return index of where this Compute is in list + if already in list, do not add, just return index, else add to list +------------------------------------------------------------------------- */ + +int DumpGrid::add_compute(const std::string &id, Compute *cptr) +{ + int icompute; + for (icompute = 0; icompute < ncompute; icompute++) + if (id == id_compute[icompute]) break; + if (icompute < ncompute) return icompute; + + id_compute = (char **) memory->srealloc(id_compute,(ncompute+1)*sizeof(char *),"dump:id_compute"); + id_compute[ncompute] = utils::strdup(id); + compute.push_back(cptr); + + ncompute++; + return ncompute-1; +} + +/* ---------------------------------------------------------------------- + add Fix to list of Fix objects used by dump + return index of where this Fix is in list + if already in list, do not add, just return index, else add to list +------------------------------------------------------------------------- */ + +int DumpGrid::add_fix(const std::string &id, Fix *fptr) +{ + int ifix; + for (ifix = 0; ifix < nfix; ifix++) + if (id == id_fix[ifix]) break; + if (ifix < nfix) return ifix; + + id_fix = (char **) memory->srealloc(id_fix,(nfix+1)*sizeof(char *),"dump:id_fix"); + id_fix[nfix] = utils::strdup(id); + fix.push_back(fptr); + + nfix++; + return nfix-1; +} + +/* ---------------------------------------------------------------------- */ + +int DumpGrid::modify_param(int narg, char **arg) +{ + if (strcmp(arg[0],"region") == 0) { + if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); + if (strcmp(arg[1],"none") == 0) { + delete[] idregion; + idregion = nullptr; + } else { + delete[] idregion; + if (!domain->get_region_by_id(arg[1])) + error->all(FLERR,"Dump_modify region {} does not exist", arg[1]); + idregion = utils::strdup(arg[1]); + } + return 2; + } + + if (strcmp(arg[0],"format") == 0) { + if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); + + if (strcmp(arg[1],"none") == 0) { + // just clear format_column_user allocated by this dump child class + for (int i = 0; i < nfield; i++) { + delete[] format_column_user[i]; + format_column_user[i] = nullptr; + } + return 2; + } + + if (narg < 3) error->all(FLERR,"Illegal dump_modify command"); + + if (strcmp(arg[1],"int") == 0) { + delete[] format_int_user; + format_int_user = utils::strdup(arg[2]); + delete[] format_bigint_user; + int n = strlen(format_int_user) + 8; + format_bigint_user = new char[n]; + // replace "d" in format_int_user with bigint format specifier + // use of &str[1] removes leading '%' from BIGINT_FORMAT string + char *ptr = strchr(format_int_user,'d'); + if (ptr == nullptr) + error->all(FLERR,"Dump_modify int format does not contain d character"); + char str[8]; + sprintf(str,"%s",BIGINT_FORMAT); + *ptr = '\0'; + sprintf(format_bigint_user,"%s%s%s",format_int_user,&str[1],ptr+1); + *ptr = 'd'; + + } else if (strcmp(arg[1],"float") == 0) { + delete[] format_float_user; + format_float_user = utils::strdup(arg[2]); + + } else { + int i = utils::inumeric(FLERR,arg[1],false,lmp) - 1; + if (i < 0 || i >= nfield) + error->all(FLERR,"Illegal dump_modify command"); + delete[] format_column_user[i]; + format_column_user[i] = utils::strdup(arg[2]); + } + return 3; + } + + return 0; +} + +/* ---------------------------------------------------------------------- + return # of bytes of allocated memory in buf, choose, variable arrays +------------------------------------------------------------------------- */ + +double DumpGrid::memory_usage() +{ + double bytes = Dump::memory_usage(); + return bytes; +} + +/* ---------------------------------------------------------------------- + extraction of 2d and 3d grid data + from either compute or fix +------------------------------------------------------------------------- */ + +void DumpGrid::pack_grid2d(int n) +{ + int index = argindex[n]; + + if (index == 0) { + double **vec2d; + if (field2source[n] == COMPUTE) + vec2d = (double **) compute[field2index[n]]->get_griddata_by_index(field2data[n]); + else if (field2source[n] == FIX) + vec2d = (double **) fix[field2index[n]]->get_griddata_by_index(field2data[n]); + else error->all(FLERR, "Unsupported grid data source type {}", field2source[n]); + for (int iy = nylo_in; iy <= nyhi_in; iy++) + for (int ix = nxlo_in; ix <= nxhi_in; ix++) { + buf[n] = vec2d[iy][ix]; + n += size_one; + } + } else { + double ***array2d; + if (field2source[n] == COMPUTE) + array2d = (double ***) compute[field2index[n]]->get_griddata_by_index(field2data[n]); + else if (field2source[n] == FIX) + array2d = (double ***) fix[field2index[n]]->get_griddata_by_index(field2data[n]); + else error->all(FLERR, "Unsupported grid data source type {}", field2source[n]); + index--; + for (int iy = nylo_in; iy <= nyhi_in; iy++) + for (int ix = nxlo_in; ix <= nxhi_in; ix++) { + buf[n] = array2d[iy][ix][index]; + n += size_one; + } + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpGrid::pack_grid3d(int n) +{ + int index = argindex[n]; + + if (index == 0) { + double ***vec3d; + if (field2source[n] == COMPUTE) + vec3d = (double ***) compute[field2index[n]]->get_griddata_by_index(field2data[n]); + else if (field2source[n] == FIX) + vec3d = (double ***) fix[field2index[n]]->get_griddata_by_index(field2data[n]); + else error->all(FLERR, "Unsupported grid data source type {}", field2source[n]); + for (int iz = nzlo_in; iz <= nzhi_in; iz++) + for (int iy = nylo_in; iy <= nyhi_in; iy++) + for (int ix = nxlo_in; ix <= nxhi_in; ix++) { + buf[n] = vec3d[iz][iy][ix]; + n += size_one; + } + } else { + double ****array3d; + if (field2source[n] == COMPUTE) + array3d = (double ****) compute[field2index[n]]->get_griddata_by_index(field2data[n]); + else if (field2source[n] == FIX) + array3d = (double ****) fix[field2index[n]]->get_griddata_by_index(field2data[n]); + else error->all(FLERR, "Unsupported grid data source type {}", field2source[n]); + index--; + for (int iz = nzlo_in; iz <= nzhi_in; iz++) + for (int iy = nylo_in; iy <= nyhi_in; iy++) + for (int ix = nxlo_in; ix <= nxhi_in; ix++) { + buf[n] = array3d[iz][iy][ix][index]; + n += size_one; + } + } +} diff --git a/src/dump_grid.h b/src/dump_grid.h new file mode 100644 index 0000000000..019553264c --- /dev/null +++ b/src/dump_grid.h @@ -0,0 +1,126 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + 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 DUMP_CLASS +// clang-format off +DumpStyle(grid,DumpGrid); +// clang-format on +#else + +#ifndef LMP_DUMP_GRID_H +#define LMP_DUMP_GRID_H + +#include "dump.h" + +namespace LAMMPS_NS { + +class DumpGrid : public Dump { + public: + DumpGrid(class LAMMPS *, int, char **); + ~DumpGrid() override; + + const char *MAGIC_STRING = "DUMPGRID"; + const int FORMAT_REVISION = 0x0002; + const int ENDIAN = 0x0001; + + protected: + int nevery; // dump frequency for output + char *idregion; // region ID, nullptr if no region + + int expand; // flag for whether field args were expanded + char **earg; // field names with wildcard expansion + int nargnew; // size of earg + // + int *vtype; // type of each vector (INT, DOUBLE) + char **vformat; // format string for each vector element + // + char *columns; // column labels + char *columns_default; + + int dimension; + + int nxgrid, nygrid, nzgrid; // global grid size + + int nfield; // # of keywords listed by user + int ioptional; // index of start of optional args + + // per field info + int *field2index; // which compute/fix + int *field2source; // COMPUTE or FIX + int *field2grid; // index of grid within compute/fix + int *field2data; // index of data within compute/fix + int *argindex; // index into compute,fix,custom per-atom data + // 0 for per-atom vector, 1-N for cols of per-atom array + + int ncompute; // # of Computes accessed by dump + char **id_compute; // their IDs + std::vector compute; // list of ptrs to the Computes + + int nfix; // # of Fixes used by dump + char **id_fix; // their IDs + std::vector fix; // list of ptrs to the Fixes + + int nxlo_in, nxhi_in; // bounds of this proc's portion of grids + int nylo_in, nyhi_in; + int nzlo_in, nzhi_in; + + // methods + + void init_style() override; + void write_header(bigint) override; + int count() override; + void pack(tagint *) override; + int convert_string(int, double *) override; + void write_data(int, double *) override; + double memory_usage() override; + + int parse_fields(int, char **); + int add_compute(const std::string &, class Compute *); + int add_fix(const std::string &, class Fix *); + int modify_param(int, char **) override; + + void header_format_binary(); + void header_unit_style_binary(); + void header_time_binary(); + void header_columns_binary(); + + typedef void (DumpGrid::*FnPtrHeader)(bigint); + FnPtrHeader header_choice; // ptr to write header functions + void header_binary(bigint); + void header_binary_triclinic(bigint); + void header_item(bigint); + void header_item_triclinic(bigint); + + void format_magic_string_binary(); + void format_endian_binary(); + void format_revision_binary(); + + typedef void (DumpGrid::*FnPtrWrite)(int, double *); + FnPtrWrite write_choice; // ptr to write data functions + void write_binary(int, double *); + void write_string(int, double *); + void write_lines(int, double *); + + // customize by adding a method prototype + + typedef void (DumpGrid::*FnPtrPack)(int); + FnPtrPack *pack_choice; // ptrs to pack functions + + void pack_grid2d(int); + void pack_grid3d(int); +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/dump_grid_vtk.cpp b/src/dump_grid_vtk.cpp new file mode 100644 index 0000000000..8c74024485 --- /dev/null +++ b/src/dump_grid_vtk.cpp @@ -0,0 +1,156 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "dump_grid_vtk.h" + +#include "domain.h" +#include "error.h" +#include "memory.h" + +using namespace LAMMPS_NS; + +enum { SCALAR, VECTOR }; + +/* ---------------------------------------------------------------------- */ + +DumpGridVTK::DumpGridVTK(LAMMPS *lmp, int narg, char **arg) : + DumpGrid(lmp, narg, arg), xcoord(nullptr), ycoord(nullptr), zcoord(nullptr) +{ + if (binary || multiproc) error->all(FLERR, "Invalid dump grid/vtk filename: {}", filename); + if (nfield != 1 && nfield != 3) error->all(FLERR, "Dump grid/vtk requires one or three fields\n"); + + buffer_allow = 0; + buffer_flag = 0; + sort_flag = 1; + sortcol = 0; + + mode = (nfield == 1) ? SCALAR : VECTOR; +} + +/* ---------------------------------------------------------------------- */ + +DumpGridVTK::~DumpGridVTK() +{ + memory->destroy(xcoord); + memory->destroy(ycoord); + memory->destroy(zcoord); +} + +/* ---------------------------------------------------------------------- */ + +void DumpGridVTK::init_style() +{ + DumpGrid::init_style(); + + if (multifile == 0) error->all(FLERR, "Dump grid/vtk requires one snapshot per file"); + if (sort_flag == 0 || sortcol > 0) error->all(FLERR, "Dump grid/vtk requires sorting on IDs"); + if (domain->triclinic) + error->all(FLERR, + "Dump grid/vtk does not support triclinic simulation boxes, use dump grid instead"); + if (binary) error->all(FLERR, "Dump grid/vtk cannot write binary files\n"); + + if (!xcoord) { + memory->create(xcoord, nxgrid + 1, "dumpgridVTK:xcoord"); + memory->create(ycoord, nygrid + 1, "dumpgridVTK:ycoord"); + memory->create(zcoord, nzgrid + 1, "dumpgridVTK:zcoord"); + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpGridVTK::write_header(bigint /*ndump*/) +{ + if (me) return; + + xyz_grid(); + + fprintf(fp, "\n"); + fprintf(fp, "\n"); + fprintf(fp, + "\n", + nxgrid, nygrid, nzgrid); + fprintf(fp, "\n", nxgrid, nygrid, nzgrid); + fprintf(fp, "\n"); + fprintf(fp, "\n"); + fprintf(fp, "\n"); + + // coords of center point of grid cells in each of xyz dimensions + + fprintf(fp, "\n"); + for (int i = 0; i <= nxgrid; i++) fprintf(fp, "%g ", xcoord[i]); + fprintf(fp, "\n\n"); + fprintf(fp, "\n"); + for (int i = 0; i <= nygrid; i++) fprintf(fp, "%g ", ycoord[i]); + fprintf(fp, "\n\n"); + fprintf(fp, "\n"); + for (int i = 0; i <= nzgrid; i++) fprintf(fp, "%g ", zcoord[i]); + fprintf(fp, "\n\n"); + + fprintf(fp, "\n"); + + fprintf(fp, "\n"); + if (mode == SCALAR) + fprintf(fp, "\n"); + else if (mode == VECTOR) + fprintf(fp, + "\n"); +} + +/* ---------------------------------------------------------------------- */ + +void DumpGridVTK::write_footer() +{ + if (me) return; + + fprintf(fp, "\n"); + fprintf(fp, "\n"); + fprintf(fp, "\n"); + fprintf(fp, "\n"); + fprintf(fp, "\n"); +} + +/* ---------------------------------------------------------------------- */ + +void DumpGridVTK::write_data(int n, double *mybuf) +{ + int m = 0; + for (int i = 0; i < n; i++) { + for (int j = 0; j < nfield; j++) { + if (vtype[j] == Dump::INT) + fprintf(fp, vformat[j], static_cast(mybuf[m])); + else if (vtype[j] == Dump::DOUBLE) + fprintf(fp, vformat[j], mybuf[m]); + else if (vtype[j] == Dump::BIGINT) + fprintf(fp, vformat[j], static_cast(mybuf[m])); + m++; + } + fprintf(fp, "\n"); + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpGridVTK::xyz_grid() +{ + double *boxlo = domain->boxlo; + + double dx = domain->prd[0] / nxgrid; + double dy = domain->prd[1] / nygrid; + double dz = domain->prd[2] / nzgrid; + + for (int ix = 0; ix <= nxgrid; ix++) xcoord[ix] = boxlo[0] + ix * dx; + for (int iy = 0; iy <= nygrid; iy++) ycoord[iy] = boxlo[1] + iy * dy; + for (int iz = 0; iz <= nzgrid; iz++) zcoord[iz] = boxlo[2] + iz * dz; +} diff --git a/src/dump_grid_vtk.h b/src/dump_grid_vtk.h new file mode 100644 index 0000000000..4f4da3fd4e --- /dev/null +++ b/src/dump_grid_vtk.h @@ -0,0 +1,49 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + 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 DUMP_CLASS +// clang-format off +DumpStyle(grid/vtk,DumpGridVTK); +// clang-format on +#else + +#ifndef LMP_DUMP_GRID_VTK_H +#define LMP_DUMP_GRID_VTK_H + +#include "dump_grid.h" + +namespace LAMMPS_NS { + +class DumpGridVTK : public DumpGrid { + public: + DumpGridVTK(class LAMMPS *, int, char **); + ~DumpGridVTK() override; + + protected: + int mode; + double *xcoord, *ycoord, *zcoord; + + // methods + + void init_style() override; + void write_header(bigint) override; + void write_data(int, double *) override; + void write_footer() override; + + void xyz_grid(); +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/dump_image.cpp b/src/dump_image.cpp index 3f4e5c7457..36cafc9b73 100644 --- a/src/dump_image.cpp +++ b/src/dump_image.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -14,6 +14,7 @@ #include "dump_image.h" +#include "arg_info.h" #include "atom.h" #include "atom_vec.h" #include "atom_vec_body.h" @@ -21,10 +22,13 @@ #include "atom_vec_tri.h" #include "body.h" #include "comm.h" +#include "compute.h" #include "domain.h" #include "error.h" #include "fix.h" #include "force.h" +#include "grid2d.h" +#include "grid3d.h" #include "image.h" #include "input.h" #include "math_const.h" @@ -33,6 +37,7 @@ #include "modify.h" #include "molecule.h" #include "tokenizer.h" +#include "update.h" #include "variable.h" #include @@ -104,10 +109,10 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) : if (strcmp(arg[6],"type") == 0) adiam = TYPE; else if (strcmp(arg[6],"element") == 0) adiam = ELEMENT; - // create Image class with single colormap for atoms + // create Image class with two colormaps for atoms and grid cells // change defaults for 2d - image = new Image(lmp,1); + image = new Image(lmp,2); if (domain->dimension == 2) { image->theta = 0.0; @@ -118,7 +123,10 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) : // set defaults for optional args atomflag = YES; + gridflag = NO; lineflag = triflag = bodyflag = fixflag = NO; + id_grid_compute = id_grid_fix = nullptr; + if (atom->nbondtypes == 0) bondflag = NO; else { bondflag = YES; @@ -175,6 +183,25 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) : else error->all(FLERR,"Illegal dump image command"); iarg += 3; + } else if (strcmp(arg[iarg],"grid") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal dump image command"); + gridflag = YES; + + char *id; + int igrid,idata,index; + int iflag = + utils::check_grid_reference((char *) "Dump image", + arg[iarg+1],nevery,id, + igrid,idata,index,lmp); + if (iflag < 0) error->all(FLERR,"Invalid grid reference in dump image command"); + + if (iflag == ArgInfo::COMPUTE) id_grid_compute = utils::strdup(id); + else if (iflag == ArgInfo::FIX) id_grid_fix = utils::strdup(id); + delete [] id; + grid_igrid = igrid; + grid_idata = idata; + grid_index = index; + iarg += 2; } else if (strcmp(arg[iarg],"line") == 0) { if (iarg+3 > narg) error->all(FLERR,"Illegal dump image command"); @@ -413,9 +440,15 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) : // local data + grid_compute = nullptr; + grid_fix = nullptr; + maxbufcopy = 0; chooseghost = nullptr; bufcopy = nullptr; + + maxgrid = 0; + gbuf = nullptr; } /* ---------------------------------------------------------------------- */ @@ -432,6 +465,10 @@ DumpImage::~DumpImage() delete [] bcolortype; memory->destroy(chooseghost); memory->destroy(bufcopy); + memory->destroy(gbuf); + + delete [] id_grid_compute; + delete [] id_grid_fix; } /* ---------------------------------------------------------------------- */ @@ -444,7 +481,23 @@ void DumpImage::init_style() DumpCustom::init_style(); - // check variables + // for grid output, find current ptr for compute or fix + // check that fix frequency is acceptable + + if (gridflag) { + if (id_grid_compute) { + grid_compute = modify->get_compute_by_id(id_grid_compute); + if (!grid_compute) + error->all(FLERR,"Could not find dump image grid compute ID {}",id_grid_compute); + } else if (id_grid_fix) { + grid_fix = modify->get_fix_by_id(id_grid_fix); + if (!grid_fix) error->all(FLERR,"Could not find dump image fix ID {}",id_grid_fix); + if (nevery % grid_fix->peratom_freq) + error->all(FLERR,"Dump image and grid fix not computed at compatible times"); + } + } + + // check image variables if (thetastr) { thetavar = input->variable->find(thetastr); @@ -553,7 +606,7 @@ void DumpImage::write() memory->create(buf,maxbuf*size_one,"dump:buf"); } - // pack buf with color & diameter + // pack atom buf with color & diameter pack(nullptr); @@ -573,7 +626,135 @@ void DumpImage::write() two[1] = hi; MPI_Allreduce(two,twoall,2,MPI_DOUBLE,MPI_MAX,world); int flag = image->map_minmax(0,-twoall[0],twoall[1]); - if (flag) error->all(FLERR,"Invalid color map min/max values"); + if (flag) error->all(FLERR,"Invalid atom color map min/max values"); + } + + // pack grid gbuf with grid cell values + // ngrid = # of grid cells this proc owns + + if (gridflag) { + if (domain->dimension == 2) { + if (grid_compute) + grid2d = (Grid2d *) grid_compute->get_grid_by_index(grid_igrid); + else if (grid_fix) + grid2d = (Grid2d *) grid_fix->get_grid_by_index(grid_igrid); + grid2d->get_size(nxgrid,nygrid); + grid2d->get_bounds_owned(nxlo_in,nxhi_in,nylo_in,nyhi_in); + ngrid = (nxhi_in-nxlo_in+1) * (nyhi_in-nylo_in+1); + } else { + if (grid_compute) + grid3d = (Grid3d *) grid_compute->get_grid_by_index(grid_igrid); + else if (grid_fix) + grid3d = (Grid3d *) grid_fix->get_grid_by_index(grid_igrid); + grid3d->get_size(nxgrid,nygrid,nzgrid); + grid3d->get_bounds_owned(nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in); + ngrid = (nxhi_in-nxlo_in+1) * (nyhi_in-nylo_in+1) * (nzhi_in-nzlo_in+1); + } + + // insure gbuf is large enough + + if (ngrid > maxgrid) { + memory->destroy(gbuf); + maxgrid = ngrid; + memory->create(gbuf,maxgrid,"dump/image:gbuf"); + } + + // invoke Compute for per-grid quantities + // only if within a run or minimize + // else require the compute is current + // this prevents the compute from being invoked by the WriteDump class + + if (grid_compute) { + if (update->whichflag == 0) { + if (grid_compute->invoked_pergrid != update->ntimestep) + error->all(FLERR,"Grid compute {} used in dump image between runs is not current", + grid_compute->id); + } else { + if (!(grid_compute->invoked_flag & Compute::INVOKED_PERGRID)) { + grid_compute->compute_pergrid(); + grid_compute->invoked_flag |= Compute::INVOKED_PERGRID; + } + } + } + + // access grid data and load gbuf + + if (domain->dimension == 2) { + if (grid_index == 0) { + double **vec2d; + if (grid_compute) + vec2d = (double **) + grid_compute->get_griddata_by_index(grid_idata); + else if (grid_fix) + vec2d = (double **) + grid_fix->get_griddata_by_index(grid_idata); + int n = 0; + for (int iy = nylo_in; iy <= nyhi_in; iy++) + for (int ix = nxlo_in; ix <= nxhi_in; ix++) + gbuf[n++] = vec2d[iy][ix]; + } else { + double ***array2d; + if (grid_compute) + array2d = (double ***) + grid_compute->get_griddata_by_index(grid_idata); + else if (grid_fix) + array2d = (double ***) + grid_fix->get_griddata_by_index(grid_idata); + int index = grid_index - 1; + int n = 0; + for (int iy = nylo_in; iy <= nyhi_in; iy++) + for (int ix = nxlo_in; ix <= nxhi_in; ix++) + gbuf[n++] = array2d[iy][ix][index]; + } + + } else if (domain->dimension == 3) { + if (grid_index == 0) { + double ***vec3d; + if (grid_compute) + vec3d = (double ***) + grid_compute->get_griddata_by_index(grid_idata); + else if (grid_fix) + vec3d = (double ***) + grid_fix->get_griddata_by_index(grid_idata); + int n = 0; + for (int iz = nzlo_in; iz <= nzhi_in; iz++) + for (int iy = nylo_in; iy <= nyhi_in; iy++) + for (int ix = nxlo_in; ix <= nxhi_in; ix++) + gbuf[n++] = vec3d[iz][iy][ix]; + + } + } else { + double ****array3d; + if (grid_compute) + array3d = (double ****) + grid_compute->get_griddata_by_index(grid_idata); + else if (grid_fix) + array3d = (double ****) + grid_fix->get_griddata_by_index(grid_idata); + int index = grid_index - 1; + int n = 0; + for (int iz = nzlo_in; iz <= nzhi_in; iz++) + for (int iy = nylo_in; iy <= nyhi_in; iy++) + for (int ix = nxlo_in; ix <= nxhi_in; ix++) + gbuf[n++] = array3d[iz][iy][ix][index]; + } + } + + // set minmax color range if using dynamic grid color map + + if (gridflag && image->map_dynamic(1)) { + double two[2],twoall[2]; + double lo = BIG; + double hi = -BIG; + for (int i = 0; i < ngrid; i++) { + lo = MIN(lo,gbuf[i]); + hi = MAX(hi,gbuf[i]); + } + two[0] = -lo; + two[1] = hi; + MPI_Allreduce(two,twoall,2,MPI_DOUBLE,MPI_MAX,world); + int flag = image->map_minmax(1,-twoall[0],twoall[1]); + if (flag) error->all(FLERR,"Invalid grid color map min/max values"); } // create image on each proc, then merge them @@ -674,8 +855,9 @@ void DumpImage::view_params() } /* ---------------------------------------------------------------------- - create image for atoms on this proc - every pixel has depth + create image for all data this proc owns + all procs draw simulation box edges if requested + every drawn pixel has depth so merge can decide which to keep ------------------------------------------------------------------------- */ void DumpImage::create_image() @@ -739,6 +921,64 @@ void DumpImage::create_image() } } + // render my grid cells + // 2 triangles for 2d rectangle, 12 triangles for 3d cube surface + // grid_cell_corners_2d/3d calculates orthogonal vs triclinic corner pts + // for 3d, outward normals on all 6 faces + + if (gridflag) { + + // reset lighting for flat surfaces to make them brighter + + image->ambientColor[0] = image->ambientColor[1] = image->ambientColor[2] = 0.9; + image->keyLightColor[0] = image->keyLightColor[1] = image->keyLightColor[2] = 0.3; + image->fillLightColor[0] = image->fillLightColor[1] = image->fillLightColor[2] = 0.3; + image->backLightColor[0] = image->backLightColor[1] = image->backLightColor[2] = 0.3; + + int n = 0; + if (domain->dimension == 2) { + for (int iy = nylo_in; iy <= nyhi_in; iy++) + for (int ix = nxlo_in; ix <= nxhi_in; ix++) { + grid_cell_corners_2d(ix,iy); + color = image->map_value2color(1,gbuf[n++]); + image->draw_triangle(gcorners[0],gcorners[1],gcorners[3],color); + image->draw_triangle(gcorners[0],gcorners[3],gcorners[2],color); + } + } else { + for (int iz = nzlo_in; iz <= nzhi_in; iz++) + for (int iy = nylo_in; iy <= nyhi_in; iy++) + for (int ix = nxlo_in; ix <= nxhi_in; ix++) { + grid_cell_corners_3d(ix,iy,iz); + color = image->map_value2color(1,gbuf[n++]); + // lower x face + image->draw_triangle(gcorners[0],gcorners[4],gcorners[6],color); + image->draw_triangle(gcorners[0],gcorners[6],gcorners[2],color); + // upper x face + image->draw_triangle(gcorners[1],gcorners[5],gcorners[7],color); + image->draw_triangle(gcorners[1],gcorners[7],gcorners[3],color); + // lower y face + image->draw_triangle(gcorners[0],gcorners[1],gcorners[5],color); + image->draw_triangle(gcorners[0],gcorners[5],gcorners[4],color); + // upper y face + image->draw_triangle(gcorners[2],gcorners[6],gcorners[7],color); + image->draw_triangle(gcorners[2],gcorners[7],gcorners[3],color); + // lower z face + image->draw_triangle(gcorners[0],gcorners[2],gcorners[3],color); + image->draw_triangle(gcorners[0],gcorners[3],gcorners[1],color); + // upper z face + image->draw_triangle(gcorners[4],gcorners[5],gcorners[7],color); + image->draw_triangle(gcorners[4],gcorners[7],gcorners[6],color); + } + } + + // restore lighting for curved objects + + image->ambientColor[0] = image->ambientColor[1] = image->ambientColor[2] = 0.0; + image->keyLightColor[0] = image->keyLightColor[1] = image->keyLightColor[2] = 0.9; + image->fillLightColor[0] = image->fillLightColor[1] = image->fillLightColor[2] = 0.45; + image->backLightColor[0] = image->backLightColor[1] = image->backLightColor[2] = 0.9; + } + // render atoms that are lines if (lineflag) { @@ -1135,6 +1375,86 @@ void DumpImage::create_image() /* ---------------------------------------------------------------------- */ +void DumpImage::grid_cell_corners_2d(int ix, int iy) +{ + double *boxlo = domain->boxlo; + double *prd = domain->prd; + + if (!domain->triclinic) { + double xdelta = prd[0] / nxgrid; + double ydelta = prd[1] / nygrid; + + int n = 0; + for (int y = 0; y < 2; y++) + for (int x = 0; x < 2; x++) { + gcorners[n][0] = boxlo[0] + (ix+x) * xdelta; + gcorners[n][1] = boxlo[1] + (iy+y) * ydelta; + gcorners[n][2] = 0.0; + n++; + } + + } else { + double lamda[3]; + lamda[2] = 0.0; + + double dx = 1.0 / nxgrid; + double dy = 1.0 / nygrid; + + int n = 0; + for (int y = 0; y < 2; y++) + for (int x = 0; x < 2; x++) { + lamda[0] = (ix+x) * dx; + lamda[1] = (iy+y) * dy; + domain->lamda2x(lamda,gcorners[n]); + n++; + } + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpImage::grid_cell_corners_3d(int ix, int iy, int iz) +{ + double *boxlo = domain->boxlo; + double *prd = domain->prd; + + if (!domain->triclinic) { + double xdelta = prd[0] / nxgrid; + double ydelta = prd[1] / nygrid; + double zdelta = prd[2] / nzgrid; + + int n = 0; + for (int z = 0; z < 2; z++) + for (int y = 0; y < 2; y++) + for (int x = 0; x < 2; x++) { + gcorners[n][0] = boxlo[0] + (ix+x) * xdelta; + gcorners[n][1] = boxlo[1] + (iy+y) * ydelta; + gcorners[n][2] = boxlo[2] + (iz+z) * zdelta; + n++; + } + + } else { + double lamda[3]; + + double dx = 1.0 / nxgrid; + double dy = 1.0 / nygrid; + double dz = 1.0 / nzgrid; + + int n = 0; + for (int z = 0; z < 2; z++) + for (int y = 0; y < 2; y++) + for (int x = 0; x < 2; x++) { + lamda[0] = (ix+x) * dx; + lamda[1] = (iy+y) * dy; + lamda[2] = (iz+z) * dz; + domain->lamda2x(lamda,gcorners[n]); + n++; + } + } +} + +/* ---------------------------------------------------------------------- */ + int DumpImage::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { @@ -1217,7 +1537,7 @@ int DumpImage::modify_param(int narg, char **arg) return 3; } - if (strcmp(arg[0],"amap") == 0) { + if ((strcmp(arg[0],"amap") == 0) || (strcmp(arg[0],"gmap") == 0)) { if (narg < 6) error->all(FLERR,"Illegal dump_modify command"); if (strlen(arg[3]) != 2) error->all(FLERR,"Illegal dump_modify command"); int factor = 0; @@ -1229,7 +1549,9 @@ int DumpImage::modify_param(int narg, char **arg) if (nentry < 1) error->all(FLERR,"Illegal dump_modify command"); n = 6 + factor*nentry; if (narg < n) error->all(FLERR,"Illegal dump_modify command"); - int flag = image->map_reset(0,n-1,&arg[1]); + int flag; + if (strcmp(arg[0],"amap") == 0) flag = image->map_reset(0,n-1,&arg[1]); + if (strcmp(arg[0],"gmap") == 0) flag = image->map_reset(1,n-1,&arg[1]); if (flag) error->all(FLERR,"Illegal dump_modify command"); return n; } diff --git a/src/dump_image.h b/src/dump_image.h index dc91d43aea..efac5e97d3 100644 --- a/src/dump_image.h +++ b/src/dump_image.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -79,16 +79,29 @@ class DumpImage : public DumpCustom { double *diamtype, *diamelement, *bdiamtype; // per-type diameters double **colortype, **colorelement, **bcolortype; // per-type colors + int gridflag; // 0/1 for draw grid cells + class Grid2d *grid2d; + class Grid3d *grid3d; + char *id_grid_compute,*id_grid_fix; + class Compute *grid_compute; + class Fix *grid_fix; + int grid_igrid,grid_idata,grid_index; + int nxgrid,nygrid,nzgrid; + int nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in; + double *gbuf; + int ngrid,maxgrid; + double gcorners[8][3]; + class AtomVecLine *avec_line; // ptrs to atom style (sub)classes class AtomVecTri *avec_tri; class AtomVecBody *avec_body; class Fix *fixptr; // ptr to Fix that provides image data - class Image *image; // class that renders each image + class Image *image; // class that renders each image - int *chooseghost; // extended choose array for comm - double **bufcopy; // buffer for communicating bond/atom info + int *chooseghost; // extended choose array for comm + double **bufcopy; // buffer for communicating bond/atom info int maxbufcopy; void init_style() override; @@ -100,6 +113,8 @@ class DumpImage : public DumpCustom { void box_bounds(); void create_image(); + void grid_cell_corners_2d(int, int); + void grid_cell_corners_3d(int, int, int); }; } // namespace LAMMPS_NS diff --git a/src/dump_local.cpp b/src/dump_local.cpp index b7a390a749..9c18b7f94f 100644 --- a/src/dump_local.cpp +++ b/src/dump_local.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/dump_local.h b/src/dump_local.h index da06092522..ca7f450148 100644 --- a/src/dump_local.h +++ b/src/dump_local.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/dump_movie.cpp b/src/dump_movie.cpp index 52c0522289..e442823113 100644 --- a/src/dump_movie.cpp +++ b/src/dump_movie.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/dump_movie.h b/src/dump_movie.h index cb0be72cdf..bebd53e18a 100644 --- a/src/dump_movie.h +++ b/src/dump_movie.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/dump_xyz.cpp b/src/dump_xyz.cpp index 12ab962a82..83c4d180d6 100644 --- a/src/dump_xyz.cpp +++ b/src/dump_xyz.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/dump_xyz.h b/src/dump_xyz.h index c85d13bb44..b5f8105114 100644 --- a/src/dump_xyz.h +++ b/src/dump_xyz.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/error.cpp b/src/error.cpp index 912093c865..c49bc6ce58 100644 --- a/src/error.cpp +++ b/src/error.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -122,7 +122,7 @@ void Error::universe_one(const std::string &file, int line, const std::string &s void Error::universe_warn(const std::string &file, int line, const std::string &str) { ++numwarn; - if ((numwarn > maxwarn) || (allwarn > maxwarn) || (maxwarn < 0)) return; + if ((maxwarn != 0) && ((numwarn > maxwarn) || (allwarn > maxwarn) || (maxwarn < 0))) return; if (universe->uscreen) fmt::print(universe->uscreen,"WARNING on proc {}: {} ({}:{})\n", universe->me,str,truncpath(file),line); @@ -254,7 +254,7 @@ void Error::_one(const std::string &file, int line, fmt::string_view format, void Error::warning(const std::string &file, int line, const std::string &str) { ++numwarn; - if ((numwarn > maxwarn) || (allwarn > maxwarn) || (maxwarn < 0)) return; + if ((maxwarn != 0) && ((numwarn > maxwarn) || (allwarn > maxwarn) || (maxwarn < 0))) return; std::string mesg = fmt::format("WARNING: {} ({}:{})\n", str,truncpath(file),line); if (screen) fputs(mesg.c_str(),screen); diff --git a/src/error.h b/src/error.h index 61d4e5a243..bb3d8705cb 100644 --- a/src/error.h +++ b/src/error.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/exceptions.h b/src/exceptions.h index f10f4ecf89..5c4aa99971 100644 --- a/src/exceptions.h +++ b/src/exceptions.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/file_writer.h b/src/file_writer.h index 3b34fb1f17..0d68603838 100644 --- a/src/file_writer.h +++ b/src/file_writer.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/finish.cpp b/src/finish.cpp index b35fed0dde..554f250fe1 100644 --- a/src/finish.cpp +++ b/src/finish.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,8 +24,6 @@ #include "memory.h" // IWYU pragma: keep #include "min.h" #include "molecule.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" // IWYU pragma: keep #include "output.h" #include "pair.h" @@ -141,21 +139,34 @@ void Finish::end(int flag) (strcmp(update->unit_style,"real") == 0))) { double one_fs = force->femtosecond; double t_step = ((double) time_loop) / ((double) update->nsteps); - double step_t = 1.0/t_step; + double step_t = 1.0 / t_step; + double atomstep_s = (double)atom->natoms * step_t; + std::string atomstep_u = "atom-step/s"; + if (atomstep_s > 1000000000.0) { + atomstep_u = "Gatom-step/s"; + atomstep_s /= 1000000000.0; + } else if (atomstep_s > 1000000.0) { + atomstep_u = "Matom-step/s"; + atomstep_s /= 1000000.0; + } else if (atomstep_s > 1000.0) { + atomstep_u = "katom-step/s"; + atomstep_s /= 1000.0; + } if (strcmp(update->unit_style,"lj") == 0) { double tau_day = 24.0*3600.0 / t_step * update->dt / one_fs; - utils::logmesg(lmp,"Performance: {:.3f} tau/day, {:.3f} timesteps/s\n",tau_day,step_t); + utils::logmesg(lmp, "Performance: {:.3f} tau/day, {:.3f} timesteps/s, {:.3f} {}\n", + tau_day, step_t, atomstep_s, atomstep_u); } else if (strcmp(update->unit_style,"electron") == 0) { double hrs_fs = t_step / update->dt * one_fs / 3600.0; double fs_day = 24.0*3600.0 / t_step * update->dt / one_fs; - utils::logmesg(lmp,"Performance: {:.3f} fs/day, {:.3f} hours/fs, " - "{:.3f} timesteps/s\n",fs_day,hrs_fs,step_t); + utils::logmesg(lmp,"Performance: {:.3f} fs/day, {:.3f} hours/fs, {:.3f} timesteps/s, " + "{:.3f} {}\n", fs_day, hrs_fs, step_t, atomstep_s, atomstep_u); } else { double hrs_ns = t_step / update->dt * 1000000.0 * one_fs / 3600.0; double ns_day = 24.0*3600.0 / t_step * update->dt / one_fs/1000000.0; - utils::logmesg(lmp,"Performance: {:.3f} ns/day, {:.3f} hours/ns, " - "{:.3f} timesteps/s\n",ns_day,hrs_ns,step_t); + utils::logmesg(lmp,"Performance: {:.3f} ns/day, {:.3f} hours/ns, {:.3f} timesteps/s, " + "{:.3f} {}\n", ns_day, hrs_ns, step_t, atomstep_s, atomstep_u); } } diff --git a/src/finish.h b/src/finish.h index 3e41287680..53d9c5b1b4 100644 --- a/src/finish.h +++ b/src/finish.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix.cpp b/src/fix.cpp index 83e0650483..9b50d872ea 100644 --- a/src/fix.cpp +++ b/src/fix.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -81,8 +81,8 @@ Fix::Fix(LAMMPS *lmp, int /*narg*/, char **arg) : stores_ids = 0; scalar_flag = vector_flag = array_flag = 0; - peratom_flag = local_flag = 0; - global_freq = local_freq = peratom_freq = -1; + peratom_flag = local_flag = pergrid_flag = 0; + global_freq = local_freq = peratom_freq = pergrid_freq = -1; size_vector_variable = size_array_rows_variable = 0; comm_forward = comm_reverse = comm_border = 0; diff --git a/src/fix.h b/src/fix.h index 41a30d2d60..ea82c1677b 100644 --- a/src/fix.h +++ b/src/fix.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -99,6 +99,9 @@ class Fix : protected Pointers { int size_local_cols; // 0 = vector, N = columns in local array int local_freq; // frequency local data is available at + int pergrid_flag; // 0/1 if per-grid data is stored + int pergrid_freq; // frequency per-grid data is available at + int extscalar; // 0/1 if global scalar is intensive/extensive int extvector; // 0/1/-1 if global vector is all int/ext/extlist int *extlist; // list of 0/1 int/ext for each vec component @@ -208,12 +211,22 @@ class Fix : protected Pointers { virtual int pack_reverse_comm(int, int, double *) { return 0; } virtual void unpack_reverse_comm(int, int *, double *) {} + virtual void reset_grid(){}; + virtual void pack_forward_grid(int, void *, int, int *){}; virtual void unpack_forward_grid(int, void *, int, int *){}; virtual void pack_reverse_grid(int, void *, int, int *){}; virtual void unpack_reverse_grid(int, void *, int, int *){}; - virtual void pack_gather_grid(int, void *){}; - virtual void unpack_gather_grid(int, void *, void *, int, int, int, int, int, int){}; + virtual void pack_remap_grid(int, void *, int, int *){}; + virtual void unpack_remap_grid(int, void *, int, int *){}; + virtual int unpack_read_grid(int, char *) {return 0;}; + virtual void pack_write_grid(int, void *){}; + virtual void unpack_write_grid(int, void *, int *){}; + + virtual int get_grid_by_name(const std::string &, int &) { return -1; }; + virtual void *get_grid_by_index(int) { return nullptr; }; + virtual int get_griddata_by_name(int, const std::string &, int &) { return -1; }; + virtual void *get_griddata_by_index(int) { return nullptr; }; virtual double compute_scalar() { return 0.0; } virtual double compute_vector(int) { return 0.0; } diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp index 75817ec083..f82e5a644a 100644 --- a/src/fix_adapt.cpp +++ b/src/fix_adapt.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_adapt.h b/src/fix_adapt.h index d4db692895..82dc739c67 100644 --- a/src/fix_adapt.h +++ b/src/fix_adapt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_addforce.cpp b/src/fix_addforce.cpp index b4d13ff5fa..5c60fbab2d 100644 --- a/src/fix_addforce.cpp +++ b/src/fix_addforce.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_addforce.h b/src/fix_addforce.h index 780d679686..2a876abb6a 100644 --- a/src/fix_addforce.h +++ b/src/fix_addforce.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_ave_atom.cpp b/src/fix_ave_atom.cpp index a5661b1f52..aec6867755 100644 --- a/src/fix_ave_atom.cpp +++ b/src/fix_ave_atom.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -31,149 +31,135 @@ using namespace FixConst; /* ---------------------------------------------------------------------- */ -FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg), - nvalues(0), which(nullptr), argindex(nullptr), value2index(nullptr), - ids(nullptr), array(nullptr) +FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), array(nullptr) { - if (narg < 7) error->all(FLERR,"Illegal fix ave/atom command"); + if (narg < 7) utils::missing_cmd_args(FLERR, "fix ave/atom", error); - nevery = utils::inumeric(FLERR,arg[3],false,lmp); - nrepeat = utils::inumeric(FLERR,arg[4],false,lmp); - peratom_freq = utils::inumeric(FLERR,arg[5],false,lmp); + nevery = utils::inumeric(FLERR, arg[3], false, lmp); + nrepeat = utils::inumeric(FLERR, arg[4], false, lmp); + peratom_freq = utils::inumeric(FLERR, arg[5], false, lmp); time_depend = 1; - nvalues = narg - 6; - // expand args if any have wildcard character "*" // this can reset nvalues int expand = 0; char **earg; - nvalues = utils::expand_args(FLERR,nvalues,&arg[6],1,earg,lmp); + int nvalues = utils::expand_args(FLERR, narg - 6, &arg[6], 1, earg, lmp); if (earg != &arg[6]) expand = 1; arg = earg; // parse values - which = new int[nvalues]; - argindex = new int[nvalues]; - ids = new char*[nvalues]; - value2index = new int[nvalues]; - + values.clear(); for (int i = 0; i < nvalues; i++) { - ids[i] = nullptr; - if (strcmp(arg[i],"x") == 0) { - which[i] = ArgInfo::X; - argindex[i] = 0; - } else if (strcmp(arg[i],"y") == 0) { - which[i] = ArgInfo::X; - argindex[i] = 1; - } else if (strcmp(arg[i],"z") == 0) { - which[i] = ArgInfo::X; - argindex[i] = 2; + value_t val; + val.id = ""; + val.val.c = nullptr; - } else if (strcmp(arg[i],"vx") == 0) { - which[i] = ArgInfo::V; - argindex[i] = 0; - } else if (strcmp(arg[i],"vy") == 0) { - which[i] = ArgInfo::V; - argindex[i] = 1; - } else if (strcmp(arg[i],"vz") == 0) { - which[i] = ArgInfo::V; - argindex[i] = 2; + if (strcmp(arg[i], "x") == 0) { + val.which = ArgInfo::X; + val.argindex = 0; + } else if (strcmp(arg[i], "y") == 0) { + val.which = ArgInfo::X; + val.argindex = 1; + } else if (strcmp(arg[i], "z") == 0) { + val.which = ArgInfo::X; + val.argindex = 2; - } else if (strcmp(arg[i],"fx") == 0) { - which[i] = ArgInfo::F; - argindex[i] = 0; - } else if (strcmp(arg[i],"fy") == 0) { - which[i] = ArgInfo::F; - argindex[i] = 1; - } else if (strcmp(arg[i],"fz") == 0) { - which[i] = ArgInfo::F; - argindex[i] = 2; + } else if (strcmp(arg[i], "vx") == 0) { + val.which = ArgInfo::V; + val.argindex = 0; + } else if (strcmp(arg[i], "vy") == 0) { + val.which = ArgInfo::V; + val.argindex = 1; + } else if (strcmp(arg[i], "vz") == 0) { + val.which = ArgInfo::V; + val.argindex = 2; + + } else if (strcmp(arg[i], "fx") == 0) { + val.which = ArgInfo::F; + val.argindex = 0; + } else if (strcmp(arg[i], "fy") == 0) { + val.which = ArgInfo::F; + val.argindex = 1; + } else if (strcmp(arg[i], "fz") == 0) { + val.which = ArgInfo::F; + val.argindex = 2; } else { ArgInfo argi(arg[i]); - which[i] = argi.get_type(); - argindex[i] = argi.get_index1(); - ids[i] = argi.copy_name(); + val.which = argi.get_type(); + val.argindex = argi.get_index1(); + val.id = argi.get_name(); - if ((which[i] == ArgInfo::UNKNOWN) || (which[i] == ArgInfo::NONE) - || (argi.get_dim() > 1)) - error->all(FLERR,"Illegal fix ave/atom command"); + if ((val.which == ArgInfo::UNKNOWN) || (val.which == ArgInfo::NONE) || (argi.get_dim() > 1)) + error->all(FLERR, "Invalid fix ave/atom argument: {}", arg[i]); } + values.push_back(val); } // if wildcard expansion occurred, free earg memory from exapnd_args() if (expand) { - for (int i = 0; i < nvalues; i++) delete [] earg[i]; + for (int i = 0; i < nvalues; i++) delete[] earg[i]; memory->sfree(earg); } // setup and error check // for fix inputs, check that fix frequency is acceptable - if (nevery <= 0 || nrepeat <= 0 || peratom_freq <= 0) - error->all(FLERR,"Illegal fix ave/atom command"); + if (nevery <= 0) error->all(FLERR,"Illegal fix ave/atom nevery value: {}", nevery); + if (nrepeat <= 0) error->all(FLERR,"Illegal fix ave/atom nrepeat value: {}", nrepeat); + if (peratom_freq <= 0) error->all(FLERR,"Illegal fix ave/atom nfreq value: {}", peratom_freq); if (peratom_freq % nevery || nrepeat*nevery > peratom_freq) - error->all(FLERR,"Illegal fix ave/atom command"); + error->all(FLERR,"Inconsistent fix ave/atom nevery/nrepeat/nfreq values"); - for (int i = 0; i < nvalues; i++) { - if (which[i] == ArgInfo::COMPUTE) { - int icompute = modify->find_compute(ids[i]); - if (icompute < 0) - error->all(FLERR,"Compute ID for fix ave/atom does not exist"); - if (modify->compute[icompute]->peratom_flag == 0) - error->all(FLERR, - "Fix ave/atom compute does not calculate per-atom values"); - if (argindex[i] == 0 && - modify->compute[icompute]->size_peratom_cols != 0) - error->all(FLERR,"Fix ave/atom compute does not " - "calculate a per-atom vector"); - if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0) - error->all(FLERR,"Fix ave/atom compute does not " - "calculate a per-atom array"); - if (argindex[i] && - argindex[i] > modify->compute[icompute]->size_peratom_cols) - error->all(FLERR,"Fix ave/atom compute array is accessed out-of-range"); + for (auto &val : values) { - } else if (which[i] == ArgInfo::FIX) { - int ifix = modify->find_fix(ids[i]); - if (ifix < 0) - error->all(FLERR,"Fix ID for fix ave/atom does not exist"); - if (modify->fix[ifix]->peratom_flag == 0) - error->all(FLERR,"Fix ave/atom fix does not calculate per-atom values"); - if (argindex[i] == 0 && modify->fix[ifix]->size_peratom_cols != 0) - error->all(FLERR, - "Fix ave/atom fix does not calculate a per-atom vector"); - if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0) - error->all(FLERR, - "Fix ave/atom fix does not calculate a per-atom array"); - if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols) - error->all(FLERR,"Fix ave/atom fix array is accessed out-of-range"); - if (nevery % modify->fix[ifix]->peratom_freq) - error->all(FLERR, - "Fix for fix ave/atom not computed at compatible time"); + if (val.which == ArgInfo::COMPUTE) { + val.val.c = modify->get_compute_by_id(val.id); + if (!val.val.c) error->all(FLERR,"Compute ID {} for fix ave/atom does not exist", val.id); + if (val.val.c->peratom_flag == 0) + error->all(FLERR, "Fix ave/atom compute {} does not calculate per-atom values", val.id); + if (val.argindex == 0 && val.val.c->size_peratom_cols != 0) + error->all(FLERR,"Fix ave/atom compute {} does not calculate a per-atom vector", val.id); + if (val.argindex && val.val.c->size_peratom_cols == 0) + error->all(FLERR,"Fix ave/atom compute {} does not calculate a per-atom array", val.id); + if (val.argindex && val.argindex > val.val.c->size_peratom_cols) + error->all(FLERR,"Fix ave/atom compute {} array is accessed out-of-range", val.id); - } else if (which[i] == ArgInfo::VARIABLE) { - int ivariable = input->variable->find(ids[i]); - if (ivariable < 0) - error->all(FLERR,"Variable name for fix ave/atom does not exist"); - if (input->variable->atomstyle(ivariable) == 0) - error->all(FLERR,"Fix ave/atom variable is not atom-style variable"); + } else if (val.which == ArgInfo::FIX) { + val.val.f = modify->get_fix_by_id(val.id); + if (!val.val.f) error->all(FLERR, "Fix ID {} for fix ave/atom does not exist", val.id); + if (val.val.f->peratom_flag == 0) + error->all(FLERR, "Fix ave/atom fix {} does not calculate per-atom values", val.id); + if (val.argindex == 0 && val.val.f->size_peratom_cols != 0) + error->all(FLERR, "Fix ave/atom fix {} does not calculate a per-atom vector", val.id); + if (val.argindex && val.val.f->size_peratom_cols == 0) + error->all(FLERR, "Fix ave/atom fix {} does not calculate a per-atom array", val.id); + if (val.argindex && val.argindex > val.val.f->size_peratom_cols) + error->all(FLERR,"Fix ave/atom fix {} array is accessed out-of-range", val.id); + if (nevery % val.val.f->peratom_freq) + error->all(FLERR, "Fix {} for fix ave/atom not computed at compatible time", val.id); + + } else if (val.which == ArgInfo::VARIABLE) { + val.val.v = input->variable->find(val.id.c_str()); + if (val.val.v < 0) + error->all(FLERR,"Variable name {} for fix ave/atom does not exist", val.id); + if (input->variable->atomstyle(val.val.v) == 0) + error->all(FLERR,"Fix ave/atom variable {} is not atom-style variable", val.id); } } // this fix produces either a per-atom vector or array peratom_flag = 1; - if (nvalues == 1) size_peratom_cols = 0; - else size_peratom_cols = nvalues; + if (values.size() == 1) size_peratom_cols = 0; + else size_peratom_cols = values.size(); // perform initial allocation of atom-based array // register with Atom class @@ -186,7 +172,7 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) : int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) - for (int m = 0; m < nvalues; m++) + for (std::size_t m = 0; m < values.size(); m++) array[i][m] = 0.0; // nvalid = next step on which end_of_step does something @@ -207,13 +193,6 @@ FixAveAtom::~FixAveAtom() // unregister callback to this fix from Atom class atom->delete_callback(id,Atom::GROW); - - delete [] which; - delete [] argindex; - for (int m = 0; m < nvalues; m++) delete [] ids[m]; - delete [] ids; - delete [] value2index; - memory->destroy(array); } @@ -232,26 +211,20 @@ void FixAveAtom::init() { // set indices and check validity of all computes,fixes,variables - for (int m = 0; m < nvalues; m++) { - if (which[m] == ArgInfo::COMPUTE) { - int icompute = modify->find_compute(ids[m]); - if (icompute < 0) - error->all(FLERR,"Compute ID for fix ave/atom does not exist"); - value2index[m] = icompute; + for (auto &val : values) { + if (val.which == ArgInfo::COMPUTE) { + val.val.c = modify->get_compute_by_id(val.id); + if (!val.val.c) error->all(FLERR, "Compute ID {} for fix ave/atom does not exist", val.id); - } else if (which[m] == ArgInfo::FIX) { - int ifix = modify->find_fix(ids[m]); - if (ifix < 0) - error->all(FLERR,"Fix ID for fix ave/atom does not exist"); - value2index[m] = ifix; + } else if (val.which == ArgInfo::FIX) { + val.val.f = modify->get_fix_by_id(val.id); + if (!val.val.f) error->all(FLERR, "Fix ID {} for fix ave/atom does not exist", val.id); - } else if (which[m] == ArgInfo::VARIABLE) { - int ivariable = input->variable->find(ids[m]); - if (ivariable < 0) - error->all(FLERR,"Variable name for fix ave/atom does not exist"); - value2index[m] = ivariable; - - } else value2index[m] = -1; + } else if (val.which == ArgInfo::VARIABLE) { + val.val.v = input->variable->find(val.id.c_str()); + if (val.val.v < 0) + error->all(FLERR,"Variable name {} for fix ave/atom does not exist", val.id); + } } // need to reset nvalid if nvalid < ntimestep b/c minimize was performed @@ -276,8 +249,6 @@ void FixAveAtom::setup(int /*vflag*/) void FixAveAtom::end_of_step() { - int i,j,m,n; - // skip if not step which requires doing something bigint ntimestep = update->ntimestep; @@ -289,8 +260,8 @@ void FixAveAtom::end_of_step() int nlocal = atom->nlocal; if (irepeat == 0) - for (i = 0; i < nlocal; i++) - for (m = 0; m < nvalues; m++) + for (int i = 0; i < nlocal; i++) + for (std::size_t m = 0; m < values.size(); m++) array[i][m] = 0.0; // accumulate results of attributes,computes,fixes,variables to local copy @@ -300,55 +271,54 @@ void FixAveAtom::end_of_step() int *mask = atom->mask; - for (m = 0; m < nvalues; m++) { - n = value2index[m]; - j = argindex[m]; + int i, j, m = 0; + for (auto &val : values) { + j = val.argindex; - if (which[m] == ArgInfo::X) { + if (val.which == ArgInfo::X) { double **x = atom->x; for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) array[i][m] += x[i][j]; - } else if (which[m] == ArgInfo::V) { + } else if (val.which == ArgInfo::V) { double **v = atom->v; for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) array[i][m] += v[i][j]; - } else if (which[m] == ArgInfo::F) { + } else if (val.which == ArgInfo::F) { double **f = atom->f; for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) array[i][m] += f[i][j]; // invoke compute if not previously invoked - } else if (which[m] == ArgInfo::COMPUTE) { - Compute *compute = modify->compute[n]; - if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) { - compute->compute_peratom(); - compute->invoked_flag |= Compute::INVOKED_PERATOM; + } else if (val.which == ArgInfo::COMPUTE) { + if (!(val.val.c->invoked_flag & Compute::INVOKED_PERATOM)) { + val.val.c->compute_peratom(); + val.val.c->invoked_flag |= Compute::INVOKED_PERATOM; } if (j == 0) { - double *compute_vector = compute->vector_atom; + double *compute_vector = val.val.c->vector_atom; for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) array[i][m] += compute_vector[i]; } else { int jm1 = j - 1; - double **compute_array = compute->array_atom; + double **compute_array = val.val.c->array_atom; for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) array[i][m] += compute_array[i][jm1]; } // access fix fields, guaranteed to be ready - } else if (which[m] == ArgInfo::FIX) { + } else if (val.which == ArgInfo::FIX) { if (j == 0) { - double *fix_vector = modify->fix[n]->vector_atom; + double *fix_vector = val.val.f->vector_atom; for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) array[i][m] += fix_vector[i]; } else { int jm1 = j - 1; - double **fix_array = modify->fix[n]->array_atom; + double **fix_array = val.val.f->array_atom; for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) array[i][m] += fix_array[i][jm1]; } @@ -356,10 +326,11 @@ void FixAveAtom::end_of_step() // evaluate atom-style variable // final argument = 1 sums result to array - } else if (which[m] == ArgInfo::VARIABLE) { - if (array) input->variable->compute_atom(n,igroup,&array[0][m],nvalues,1); - else input->variable->compute_atom(n,igroup,nullptr,nvalues,1); + } else if (val.which == ArgInfo::VARIABLE) { + if (array) input->variable->compute_atom(val.val.v,igroup,&array[0][m],values.size(),1); + else input->variable->compute_atom(val.val.v,igroup,nullptr,values.size(),1); } + ++m; } // done if irepeat < nrepeat @@ -382,7 +353,7 @@ void FixAveAtom::end_of_step() double repeat = nrepeat; for (i = 0; i < nlocal; i++) - for (m = 0; m < nvalues; m++) + for (m = 0; m < (int)values.size(); m++) array[i][m] /= repeat; } @@ -393,7 +364,7 @@ void FixAveAtom::end_of_step() double FixAveAtom::memory_usage() { double bytes; - bytes = (double)atom->nmax*nvalues * sizeof(double); + bytes = (double)atom->nmax*values.size() * sizeof(double); return bytes; } @@ -403,7 +374,7 @@ double FixAveAtom::memory_usage() void FixAveAtom::grow_arrays(int nmax) { - memory->grow(array,nmax,nvalues,"fix_ave/atom:array"); + memory->grow(array,nmax,values.size(),"fix_ave/atom:array"); array_atom = array; if (array) vector_atom = array[0]; else vector_atom = nullptr; @@ -415,7 +386,7 @@ void FixAveAtom::grow_arrays(int nmax) void FixAveAtom::copy_arrays(int i, int j, int /*delflag*/) { - for (int m = 0; m < nvalues; m++) + for (std::size_t m = 0; m < values.size(); m++) array[j][m] = array[i][m]; } @@ -425,8 +396,8 @@ void FixAveAtom::copy_arrays(int i, int j, int /*delflag*/) int FixAveAtom::pack_exchange(int i, double *buf) { - for (int m = 0; m < nvalues; m++) buf[m] = array[i][m]; - return nvalues; + for (std::size_t m = 0; m < values.size(); m++) buf[m] = array[i][m]; + return values.size(); } /* ---------------------------------------------------------------------- @@ -435,8 +406,8 @@ int FixAveAtom::pack_exchange(int i, double *buf) int FixAveAtom::unpack_exchange(int nlocal, double *buf) { - for (int m = 0; m < nvalues; m++) array[nlocal][m] = buf[m]; - return nvalues; + for (std::size_t m = 0; m < values.size(); m++) array[nlocal][m] = buf[m]; + return values.size(); } /* ---------------------------------------------------------------------- diff --git a/src/fix_ave_atom.h b/src/fix_ave_atom.h index f285004305..8edf632b00 100644 --- a/src/fix_ave_atom.h +++ b/src/fix_ave_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -40,11 +40,20 @@ class FixAveAtom : public Fix { int unpack_exchange(int, double *) override; private: - int nvalues; + struct value_t { + int which; // type of data: COMPUTE, FIX, VARIABLE + int argindex; // 1-based index if data is vector, else 0 + std::string id; // compute/fix/variable ID + union { + class Compute *c; + class Fix *f; + int v; + } val; + }; + std::vector values; + int nrepeat, irepeat; bigint nvalid, nvalid_last; - int *which, *argindex, *value2index; - char **ids; double **array; bigint nextvalid(); diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp index 688c4676e1..7c37bbaaff 100644 --- a/src/fix_ave_chunk.cpp +++ b/src/fix_ave_chunk.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -33,29 +33,24 @@ using namespace LAMMPS_NS; using namespace FixConst; -enum{SCALAR,VECTOR}; -enum{SAMPLE,ALL}; -enum{NOSCALE,ATOM}; -enum{ONE,RUNNING,WINDOW}; - +enum { SCALAR, VECTOR }; +enum { SAMPLE, ALL }; +enum { NOSCALE, ATOM }; +enum { ONE, RUNNING, WINDOW }; /* ---------------------------------------------------------------------- */ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg), - nvalues(0), nrepeat(0), - which(nullptr), argindex(nullptr), value2index(nullptr), ids(nullptr), - fp(nullptr), idchunk(nullptr), varatom(nullptr), - count_one(nullptr), count_many(nullptr), count_sum(nullptr), - values_one(nullptr), values_many(nullptr), values_sum(nullptr), - count_total(nullptr), count_list(nullptr), - values_total(nullptr), values_list(nullptr) + Fix(lmp, narg, arg), nvalues(0), nrepeat(0), fp(nullptr), idchunk(nullptr), varatom(nullptr), + count_one(nullptr), count_many(nullptr), count_sum(nullptr), values_one(nullptr), + values_many(nullptr), values_sum(nullptr), count_total(nullptr), count_list(nullptr), + values_total(nullptr), values_list(nullptr) { - if (narg < 7) error->all(FLERR,"Illegal fix ave/chunk command"); + if (narg < 7) utils::missing_cmd_args(FLERR, "fix ave/chunk", error); - nevery = utils::inumeric(FLERR,arg[3],false,lmp); - nrepeat = utils::inumeric(FLERR,arg[4],false,lmp); - nfreq = utils::inumeric(FLERR,arg[5],false,lmp); + nevery = utils::inumeric(FLERR, arg[3], false, lmp); + nrepeat = utils::inumeric(FLERR, arg[4], false, lmp); + nfreq = utils::inumeric(FLERR, arg[5], false, lmp); idchunk = utils::strdup(arg[6]); @@ -63,82 +58,81 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) : no_change_box = 1; time_depend = 1; - char * group = arg[1]; + char *group = arg[1]; // expand args if any have wildcard character "*" int expand = 0; char **earg; - int nargnew = utils::expand_args(FLERR,narg-7,&arg[7],1,earg,lmp); + int nargnew = utils::expand_args(FLERR, narg - 7, &arg[7], 1, earg, lmp); if (earg != &arg[7]) expand = 1; arg = earg; // parse values until one isn't recognized - which = new int[nargnew]; - argindex = new int[nargnew]; - ids = new char*[nargnew]; - value2index = new int[nargnew]; densityflag = 0; int iarg = 0; + values.clear(); while (iarg < nargnew) { - ids[nvalues] = nullptr; + value_t val; + val.id = ""; + val.val.c = nullptr; if (strcmp(arg[iarg],"vx") == 0) { - which[nvalues] = ArgInfo::V; - argindex[nvalues++] = 0; + val.which = ArgInfo::V; + val.argindex = 0; } else if (strcmp(arg[iarg],"vy") == 0) { - which[nvalues] = ArgInfo::V; - argindex[nvalues++] = 1; + val.which = ArgInfo::V; + val.argindex = 1; } else if (strcmp(arg[iarg],"vz") == 0) { - which[nvalues] = ArgInfo::V; - argindex[nvalues++] = 2; + val.which = ArgInfo::V; + val.argindex = 2; } else if (strcmp(arg[iarg],"fx") == 0) { - which[nvalues] = ArgInfo::F; - argindex[nvalues++] = 0; + val.which = ArgInfo::F; + val.argindex = 0; } else if (strcmp(arg[iarg],"fy") == 0) { - which[nvalues] = ArgInfo::F; - argindex[nvalues++] = 1; + val.which = ArgInfo::F; + val.argindex = 1; } else if (strcmp(arg[iarg],"fz") == 0) { - which[nvalues] = ArgInfo::F; - argindex[nvalues++] = 2; + val.which = ArgInfo::F; + val.argindex = 2; } else if (strcmp(arg[iarg],"mass") == 0) { - which[nvalues] = ArgInfo::MASS; - argindex[nvalues++] = 0; + val.which = ArgInfo::MASS; + val.argindex = 0; } else if (strcmp(arg[iarg],"density/number") == 0) { densityflag = 1; - which[nvalues] = ArgInfo::DENSITY_NUMBER; - argindex[nvalues++] = 0; + val.which = ArgInfo::DENSITY_NUMBER; + val.argindex = 0; } else if (strcmp(arg[iarg],"density/mass") == 0) { densityflag = 1; - which[nvalues] = ArgInfo::DENSITY_MASS; - argindex[nvalues++] = 0; + val.which = ArgInfo::DENSITY_MASS; + val.argindex = 0; } else if (strcmp(arg[iarg],"temp") == 0) { - which[nvalues] = ArgInfo::TEMPERATURE; - argindex[nvalues++] = 0; + val.which = ArgInfo::TEMPERATURE; + val.argindex = 0; } else { ArgInfo argi(arg[iarg]); if (argi.get_type() == ArgInfo::NONE) break; if ((argi.get_type() == ArgInfo::UNKNOWN) || (argi.get_dim() > 1)) - error->all(FLERR,"Invalid fix ave/chunk command"); + error->all(FLERR,"Unknown fix ave/chunk data value: {}", arg[iarg]); - which[nvalues] = argi.get_type(); - argindex[nvalues] = argi.get_index1(); - ids[nvalues] = argi.copy_name(); - - nvalues++; + val.which = argi.get_type(); + val.argindex = argi.get_index1(); + val.id = argi.get_name(); } + values.push_back(val); iarg++; } - if (nvalues == 0) error->all(FLERR,"No values in fix ave/chunk command"); + nvalues = values.size(); + if (nvalues == 0) error->all(FLERR, "No values in fix ave/chunk command"); // optional args @@ -159,7 +153,7 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) : while (iarg < nargnew) { if (strcmp(arg[iarg],"norm") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/chunk command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/chunk norm", error); if (strcmp(arg[iarg+1],"all") == 0) { normflag = ALL; scaleflag = ATOM; @@ -169,127 +163,124 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) : } else if (strcmp(arg[iarg+1],"none") == 0) { normflag = SAMPLE; scaleflag = NOSCALE; - } else error->all(FLERR,"Illegal fix ave/chunk command"); + } else error->all(FLERR,"Unknown fix ave/chunk norm mode: {}", arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"ave") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/chunk command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/chunk ave", error); if (strcmp(arg[iarg+1],"one") == 0) ave = ONE; else if (strcmp(arg[iarg+1],"running") == 0) ave = RUNNING; else if (strcmp(arg[iarg+1],"window") == 0) ave = WINDOW; - else error->all(FLERR,"Illegal fix ave/chunk command"); + else error->all(FLERR,"Unknown fix ave/chunk ave mode: {}", arg[iarg+1]); if (ave == WINDOW) { - if (iarg+3 > narg) error->all(FLERR,"Illegal fix ave/chunk command"); + if (iarg+3 > narg) utils::missing_cmd_args(FLERR, "fix ave/chunk ave window", error); nwindow = utils::inumeric(FLERR,arg[iarg+2],false,lmp); - if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/chunk command"); + if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/chunk number of windows: {}", nwindow); } iarg += 2; if (ave == WINDOW) iarg++; } else if (strcmp(arg[iarg],"bias") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal fix ave/chunk command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/chunk bias", error); biasflag = 1; id_bias = utils::strdup(arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"adof") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal fix ave/chunk command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/chunk adof", error); adof = utils::numeric(FLERR,arg[iarg+1],false,lmp); iarg += 2; } else if (strcmp(arg[iarg],"cdof") == 0) { - if (iarg+2 > narg) - error->all(FLERR,"Illegal fix ave/chunk command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/chunk cdof", error); cdof = utils::numeric(FLERR,arg[iarg+1],false,lmp); iarg += 2; } else if (strcmp(arg[iarg],"file") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/chunk command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/chunk file", error); if (comm->me == 0) { fp = fopen(arg[iarg+1],"w"); if (fp == nullptr) - error->one(FLERR,"Cannot open fix ave/chunk file {}: {}", - arg[iarg+1], utils::getsyserror()); + error->one(FLERR, "Cannot open fix ave/chunk file {}: {}", + arg[iarg+1], utils::getsyserror()); } iarg += 2; } else if (strcmp(arg[iarg],"overwrite") == 0) { overwrite = 1; iarg += 1; } else if (strcmp(arg[iarg],"format") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/chunk command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/chunk format", error); delete[] format_user; format_user = utils::strdup(arg[iarg+1]); format = format_user; iarg += 2; } else if (strcmp(arg[iarg],"title1") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/chunk command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/chunk title1", error); delete[] title1; title1 = utils::strdup(arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"title2") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/chunk command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/chunk title2", error); delete[] title2; title2 = utils::strdup(arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"title3") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/chunk command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/chunk title3", error); delete[] title3; title3 = utils::strdup(arg[iarg+1]); iarg += 2; - } else error->all(FLERR,"Illegal fix ave/chunk command"); + } else error->all(FLERR,"Unknown fix ave/chunk keyword: {}", arg[iarg]); } // setup and error check - if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0) - error->all(FLERR,"Illegal fix ave/chunk command"); + if (nevery <= 0) error->all(FLERR,"Illegal fix ave/chunk nevery value: {}", nevery); + if (nrepeat <= 0) error->all(FLERR,"Illegal fix ave/chunk nrepeat value: {}", nrepeat); + if (nfreq <= 0) error->all(FLERR,"Illegal fix ave/chunk nfreq value: {}", nfreq); if (nfreq % nevery || nrepeat*nevery > nfreq) - error->all(FLERR,"Illegal fix ave/chunk command"); + error->all(FLERR,"Inconsistent fix ave/chunk nevery/nrepeat/nfreq values"); if (ave != RUNNING && overwrite) - error->all(FLERR,"Illegal fix ave/chunk command"); + error->all(FLERR,"Fix ave/chunk overwrite keyword requires ave running setting"); if (biasflag) { - int i = modify->find_compute(id_bias); - if (i < 0) - error->all(FLERR,"Could not find compute ID for temperature bias"); - tbias = modify->compute[i]; + tbias = modify->get_compute_by_id(id_bias); + if (!tbias) error->all(FLERR,"Could not find compute ID {} for temperature bias", id_bias); if (tbias->tempflag == 0) - error->all(FLERR,"Bias compute does not calculate temperature"); + error->all(FLERR,"Bias compute {} does not calculate temperature", id_bias); if (tbias->tempbias == 0) - error->all(FLERR,"Bias compute does not calculate a velocity bias"); + error->all(FLERR,"Bias compute {} does not calculate a velocity bias", id_bias); } - for (int i = 0; i < nvalues; i++) { - if (which[i] == ArgInfo::COMPUTE) { - auto icompute = modify->get_compute_by_id(ids[i]); - if (!icompute) - error->all(FLERR,"Compute ID {} for fix ave/chunk does not exist",ids[i]); - if (icompute->peratom_flag == 0) - error->all(FLERR,"Fix ave/chunk compute {} does not calculate per-atom values",ids[i]); - if (argindex[i] == 0 && (icompute->size_peratom_cols != 0)) - error->all(FLERR,"Fix ave/chunk compute {} does not calculate a per-atom vector",ids[i]); - if (argindex[i] && (icompute->size_peratom_cols == 0)) - error->all(FLERR,"Fix ave/chunk compute {} does not calculate a per-atom array",ids[i]); - if (argindex[i] && (argindex[i] > icompute->size_peratom_cols)) - error->all(FLERR,"Fix ave/chunk compute {} vector is accessed out-of-range",ids[i]); + for (auto &val : values) { - } else if (which[i] == ArgInfo::FIX) { - auto ifix = modify->get_fix_by_id(ids[i]); - if (!ifix) - error->all(FLERR, "Fix ID {} for fix ave/chunk does not exist",ids[i]); - if (ifix->peratom_flag == 0) - error->all(FLERR, "Fix ave/chunk fix {} does not calculate per-atom values",ids[i]); - if (argindex[i] == 0 && (ifix->size_peratom_cols != 0)) - error->all(FLERR, "Fix ave/chunk fix {} does not calculate a per-atom vector",ids[i]); - if (argindex[i] && (ifix->size_peratom_cols == 0)) - error->all(FLERR, "Fix ave/chunk fix {} does not calculate a per-atom array",ids[i]); - if (argindex[i] && argindex[i] > ifix->size_peratom_cols) - error->all(FLERR,"Fix ave/chunk fix {} vector is accessed out-of-range",ids[i]); - } else if (which[i] == ArgInfo::VARIABLE) { - int ivariable = input->variable->find(ids[i]); - if (ivariable < 0) - error->all(FLERR,"Variable name {} for fix ave/chunk does not exist",ids[i]); - if (input->variable->atomstyle(ivariable) == 0) - error->all(FLERR,"Fix ave/chunk variable {} is not atom-style variable",ids[i]); + if (val.which == ArgInfo::COMPUTE) { + val.val.c = modify->get_compute_by_id(val.id); + if (!val.val.c) + error->all(FLERR,"Compute ID {} for fix ave/chunk does not exist",val.id); + if (val.val.c->peratom_flag == 0) + error->all(FLERR,"Fix ave/chunk compute {} does not calculate per-atom values",val.id); + if (val.argindex == 0 && (val.val.c->size_peratom_cols != 0)) + error->all(FLERR,"Fix ave/chunk compute {} does not calculate a per-atom vector",val.id); + if (val.argindex && (val.val.c->size_peratom_cols == 0)) + error->all(FLERR,"Fix ave/chunk compute {} does not calculate a per-atom array",val.id); + if (val.argindex && (val.argindex > val.val.c->size_peratom_cols)) + error->all(FLERR,"Fix ave/chunk compute {} vector is accessed out-of-range",val.id); + + } else if (val.which == ArgInfo::FIX) { + val.val.f = modify->get_fix_by_id(val.id); + if (!val.val.f) + error->all(FLERR, "Fix ID {} for fix ave/chunk does not exist",val.id); + if (val.val.f->peratom_flag == 0) + error->all(FLERR, "Fix ave/chunk fix {} does not calculate per-atom values",val.id); + if (val.argindex == 0 && (val.val.f->size_peratom_cols != 0)) + error->all(FLERR, "Fix ave/chunk fix {} does not calculate a per-atom vector",val.id); + if (val.argindex && (val.val.f->size_peratom_cols == 0)) + error->all(FLERR, "Fix ave/chunk fix {} does not calculate a per-atom array",val.id); + if (val.argindex && val.argindex > val.val.f->size_peratom_cols) + error->all(FLERR,"Fix ave/chunk fix {} vector is accessed out-of-range",val.id); + } else if (val.which == ArgInfo::VARIABLE) { + val.val.v = input->variable->find(val.id.c_str()); + if (val.val.v < 0) + error->all(FLERR,"Variable name {} for fix ave/chunk does not exist",val.id); + if (input->variable->atomstyle(val.val.v) == 0) + error->all(FLERR,"Fix ave/chunk variable {} is not atom-style variable",val.id); } } @@ -396,12 +387,6 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) : FixAveChunk::~FixAveChunk() { - delete[] which; - delete[] argindex; - for (int i = 0; i < nvalues; i++) delete[] ids[i]; - delete[] ids; - delete[] value2index; - if (fp && comm->me == 0) fclose(fp); memory->destroy(varatom); @@ -427,10 +412,6 @@ FixAveChunk::~FixAveChunk() } delete[] idchunk; - which = nullptr; - argindex = nullptr; - ids = nullptr; - value2index = nullptr; fp = nullptr; varatom = nullptr; count_one = nullptr; @@ -463,42 +444,34 @@ void FixAveChunk::init() // set indices and check validity of all computes,fixes,variables // check that fix frequency is acceptable - int icompute = modify->find_compute(idchunk); - if (icompute < 0) - error->all(FLERR,"Chunk/atom compute does not exist for fix ave/chunk"); - cchunk = dynamic_cast(modify->compute[icompute]); + cchunk = dynamic_cast(modify->get_compute_by_id(idchunk)); + if (!cchunk) + error->all(FLERR,"Chunk/atom compute {} does not exist or is " + "incorrect style for fix ave/chunk",idchunk); if (biasflag) { - int i = modify->find_compute(id_bias); - if (i < 0) - error->all(FLERR,"Could not find compute ID for temperature bias"); - tbias = modify->compute[i]; + tbias = modify->get_compute_by_id(id_bias); + if (!tbias) + error->all(FLERR,"Could not find compute ID {} for temperature bias", id_bias); } - for (int m = 0; m < nvalues; m++) { - if (which[m] == ArgInfo::COMPUTE) { - icompute = modify->find_compute(ids[m]); - if (icompute < 0) - error->all(FLERR,"Compute ID for fix ave/chunk does not exist"); - value2index[m] = icompute; + for (auto &val : values) { + if (val.which == ArgInfo::COMPUTE) { + val.val.c = modify->get_compute_by_id(val.id); + if (!val.val.c) error->all(FLERR,"Compute ID {} for fix ave/chunk does not exist", val.id); - } else if (which[m] == ArgInfo::FIX) { - int ifix = modify->find_fix(ids[m]); - if (ifix < 0) - error->all(FLERR,"Fix ID for fix ave/chunk does not exist"); - value2index[m] = ifix; + } else if (val.which == ArgInfo::FIX) { + val.val.f = modify->get_fix_by_id(val.id); + if (!val.val.f) error->all(FLERR,"Fix ID {} for fix ave/chunk does not exist", val.id); - if (nevery % modify->fix[ifix]->peratom_freq) - error->all(FLERR, - "Fix for fix ave/chunk not computed at compatible time"); + if (nevery % val.val.f->peratom_freq) + error->all(FLERR, "Fix {} for fix ave/chunk not computed at compatible time", val.id); - } else if (which[m] == ArgInfo::VARIABLE) { - int ivariable = input->variable->find(ids[m]); - if (ivariable < 0) - error->all(FLERR,"Variable name for fix ave/chunk does not exist"); - value2index[m] = ivariable; - - } else value2index[m] = -1; + } else if (val.which == ArgInfo::VARIABLE) { + val.val.v = input->variable->find(val.id.c_str()); + if (val.val.v < 0) + error->all(FLERR,"Variable name {} for fix ave/chunk does not exist", val.id); + } } // need to reset nvalid if nvalid < ntimestep b/c minimize was performed @@ -527,7 +500,7 @@ void FixAveChunk::setup(int /*vflag*/) void FixAveChunk::end_of_step() { - int i,j,m,n,index; + int i,j,m,index; // skip if not step which requires doing something @@ -609,15 +582,15 @@ void FixAveChunk::end_of_step() modify->clearstep_compute(); - for (m = 0; m < nvalues; m++) { - n = value2index[m]; - j = argindex[m]; + m = 0; + for (auto &val : values) { + j = val.argindex; // V,F adds velocities,forces to values - if (which[m] == ArgInfo::V || which[m] == ArgInfo::F) { + if (val.which == ArgInfo::V || val.which == ArgInfo::F) { double **attribute; - if (which[m] == ArgInfo::V) attribute = atom->v; + if (val.which == ArgInfo::V) attribute = atom->v; else attribute = atom->f; for (i = 0; i < nlocal; i++) @@ -628,7 +601,7 @@ void FixAveChunk::end_of_step() // DENSITY_NUMBER adds 1 to values - } else if (which[m] == ArgInfo::DENSITY_NUMBER) { + } else if (val.which == ArgInfo::DENSITY_NUMBER) { for (i = 0; i < nlocal; i++) if (mask[i] & groupbit && ichunk[i] > 0) { @@ -638,8 +611,7 @@ void FixAveChunk::end_of_step() // DENSITY_MASS or MASS adds mass to values - } else if ((which[m] == ArgInfo::DENSITY_MASS) - || (which[m] == ArgInfo::MASS)) { + } else if ((val.which == ArgInfo::DENSITY_MASS) || (val.which == ArgInfo::MASS)) { int *type = atom->type; double *mass = atom->mass; double *rmass = atom->rmass; @@ -661,7 +633,7 @@ void FixAveChunk::end_of_step() // TEMPERATURE adds KE to values // subtract and restore velocity bias if requested - } else if (which[m] == ArgInfo::TEMPERATURE) { + } else if (val.which == ArgInfo::TEMPERATURE) { if (biasflag) { if (tbias->invoked_scalar != ntimestep) tbias->compute_scalar(); @@ -695,14 +667,13 @@ void FixAveChunk::end_of_step() // COMPUTE adds its scalar or vector component to values // invoke compute if not previously invoked - } else if (which[m] == ArgInfo::COMPUTE) { - Compute *compute = modify->compute[n]; - if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) { - compute->compute_peratom(); - compute->invoked_flag |= Compute::INVOKED_PERATOM; + } else if (val.which == ArgInfo::COMPUTE) { + if (!(val.val.c->invoked_flag & Compute::INVOKED_PERATOM)) { + val.val.c->compute_peratom(); + val.val.c->invoked_flag |= Compute::INVOKED_PERATOM; } - double *vector = compute->vector_atom; - double **array = compute->array_atom; + double *vector = val.val.c->vector_atom; + double **array = val.val.c->array_atom; int jm1 = j - 1; for (i = 0; i < nlocal; i++) @@ -715,9 +686,9 @@ void FixAveChunk::end_of_step() // FIX adds its scalar or vector component to values // access fix fields, guaranteed to be ready - } else if (which[m] == ArgInfo::FIX) { - double *vector = modify->fix[n]->vector_atom; - double **array = modify->fix[n]->array_atom; + } else if (val.which == ArgInfo::FIX) { + double *vector = val.val.f->vector_atom; + double **array = val.val.f->array_atom; int jm1 = j - 1; for (i = 0; i < nlocal; i++) @@ -730,14 +701,14 @@ void FixAveChunk::end_of_step() // VARIABLE adds its per-atom quantities to values // evaluate atom-style variable - } else if (which[m] == ArgInfo::VARIABLE) { + } else if (val.which == ArgInfo::VARIABLE) { if (atom->nmax > maxvar) { maxvar = atom->nmax; memory->destroy(varatom); memory->create(varatom,maxvar,"ave/chunk:varatom"); } - input->variable->compute_atom(n,igroup,varatom,1,0); + input->variable->compute_atom(val.val.v,igroup,varatom,1,0); for (i = 0; i < nlocal; i++) if (mask[i] & groupbit && ichunk[i] > 0) { @@ -745,6 +716,7 @@ void FixAveChunk::end_of_step() values_one[index][m] += varatom[i]; } } + ++m; } // process the current sample @@ -784,14 +756,14 @@ void FixAveChunk::end_of_step() for (m = 0; m < nchunk; m++) { if (count_many[m] > 0.0) for (j = 0; j < nvalues; j++) { - if (which[j] == ArgInfo::TEMPERATURE) { + if (values[j].which == ArgInfo::TEMPERATURE) { values_many[m][j] += mvv2e*values_one[m][j] / ((cdof + adof*count_many[m]) * boltz); - } else if (which[j] == ArgInfo::DENSITY_NUMBER) { + } else if (values[j].which == ArgInfo::DENSITY_NUMBER) { if (volflag == SCALAR) values_one[m][j] /= chunk_volume_scalar; else values_one[m][j] /= chunk_volume_vec[m]; values_many[m][j] += values_one[m][j]; - } else if (which[j] == ArgInfo::DENSITY_MASS) { + } else if (values[j].which == ArgInfo::DENSITY_MASS) { if (volflag == SCALAR) values_one[m][j] /= chunk_volume_scalar; else values_one[m][j] /= chunk_volume_vec[m]; values_many[m][j] += mv2d*values_one[m][j]; @@ -854,13 +826,13 @@ void FixAveChunk::end_of_step() for (m = 0; m < nchunk; m++) { if (count_sum[m] > 0.0) for (j = 0; j < nvalues; j++) { - if (which[j] == ArgInfo::TEMPERATURE) { + if (values[j].which == ArgInfo::TEMPERATURE) { values_sum[m][j] *= mvv2e/((repeat*cdof + adof*count_sum[m])*boltz); - } else if (which[j] == ArgInfo::DENSITY_NUMBER) { + } else if (values[j].which == ArgInfo::DENSITY_NUMBER) { if (volflag == SCALAR) values_sum[m][j] /= chunk_volume_scalar; else values_sum[m][j] /= chunk_volume_vec[m]; values_sum[m][j] /= repeat; - } else if (which[j] == ArgInfo::DENSITY_MASS) { + } else if (values[j].which == ArgInfo::DENSITY_MASS) { if (volflag == SCALAR) values_sum[m][j] /= chunk_volume_scalar; else values_sum[m][j] /= chunk_volume_vec[m]; values_sum[m][j] *= mv2d/repeat; @@ -1045,8 +1017,7 @@ void FixAveChunk::allocate() if (ave == WINDOW) { memory->create(count_list,nwindow,nchunk,"ave/chunk:count_list"); - memory->create(values_list,nwindow,nchunk,nvalues, - "ave/chunk:values_list"); + memory->create(values_list,nwindow,nchunk,nvalues,"ave/chunk:values_list"); } // reinitialize regrown count/values total since they accumulate diff --git a/src/fix_ave_chunk.h b/src/fix_ave_chunk.h index 1183b089e8..0919a17acf 100644 --- a/src/fix_ave_chunk.h +++ b/src/fix_ave_chunk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -36,15 +36,24 @@ class FixAveChunk : public Fix { double memory_usage() override; private: - int nvalues; - int nrepeat, nfreq, irepeat; + struct value_t { + int which; // type of data: COMPUTE, FIX, VARIABLE + int argindex; // 1-based index if data is vector, else 0 + std::string id; // compute/fix/variable ID + union { + class Compute *c; + class Fix *f; + int v; + } val; + }; + std::vector values; + + int nvalues, nrepeat, nfreq, irepeat; int normflag, scaleflag, overwrite, biasflag, colextra; bigint nvalid, nvalid_last; double adof, cdof; char *format, *format_user; char *tstring, *sstring, *id_bias; - int *which, *argindex, *value2index; - char **ids; class Compute *tbias; // ptr to additional bias compute FILE *fp; diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp index 17182c8667..d506e17761 100644 --- a/src/fix_ave_correlate.cpp +++ b/src/fix_ave_correlate.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -21,6 +21,7 @@ #include "fix_ave_correlate.h" #include "arg_info.h" +#include "comm.h" #include "compute.h" #include "error.h" #include "input.h" @@ -34,23 +35,20 @@ using namespace LAMMPS_NS; using namespace FixConst; -enum{ONE,RUNNING}; -enum{AUTO,UPPER,LOWER,AUTOUPPER,AUTOLOWER,FULL}; +enum { ONE, RUNNING }; +enum { AUTO, UPPER, LOWER, AUTOUPPER, AUTOLOWER, FULL }; /* ---------------------------------------------------------------------- */ -FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg): - Fix (lmp, narg, arg), - nvalues(0), which(nullptr), argindex(nullptr), value2index(nullptr), ids(nullptr), fp(nullptr), - count(nullptr), values(nullptr), corr(nullptr), save_count(nullptr), save_corr(nullptr) +FixAveCorrelate::FixAveCorrelate(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg), fp(nullptr), count(nullptr), cvalues(nullptr), corr(nullptr), + save_count(nullptr), save_corr(nullptr) { - if (narg < 7) error->all(FLERR,"Illegal fix ave/correlate command"); + if (narg < 7) utils::missing_cmd_args(FLERR, "fix ave/correlate", error); - MPI_Comm_rank(world,&me); - - nevery = utils::inumeric(FLERR,arg[3],false,lmp); - nrepeat = utils::inumeric(FLERR,arg[4],false,lmp); - nfreq = utils::inumeric(FLERR,arg[5],false,lmp); + nevery = utils::inumeric(FLERR, arg[3], false, lmp); + nrepeat = utils::inumeric(FLERR, arg[4], false, lmp); + nfreq = utils::inumeric(FLERR, arg[5], false, lmp); time_depend = 1; global_freq = nfreq; @@ -59,34 +57,31 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg): int expand = 0; char **earg; - int nargnew = utils::expand_args(FLERR,narg-6,&arg[6],0,earg,lmp); + int nargnew = utils::expand_args(FLERR, narg - 6, &arg[6], 0, earg, lmp); if (earg != &arg[6]) expand = 1; arg = earg; - // parse values until one isn't recognized - - which = new int[nargnew]; - argindex = new int[nargnew]; - ids = new char*[nargnew]; - value2index = new int[nargnew]; - nvalues = 0; + // parse values int iarg = 0; while (iarg < nargnew) { ArgInfo argi(arg[iarg]); + value_t val; if (argi.get_type() == ArgInfo::NONE) break; if ((argi.get_type() == ArgInfo::UNKNOWN) || (argi.get_dim() > 1)) - error->all(FLERR,"Invalid fix ave/correlate command"); + error->all(FLERR, "Unknown fix ave/correlate data type: {}", arg[iarg]); - which[nvalues] = argi.get_type(); - argindex[nvalues] = argi.get_index1(); - ids[nvalues] = argi.copy_name(); + val.which = argi.get_type(); + val.argindex = argi.get_index1(); + val.id = argi.get_name(); + val.val.c = nullptr; - nvalues++; + values.push_back(val); iarg++; } + nvalues = values.size(); // optional args @@ -102,32 +97,32 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg): while (iarg < nargnew) { if (strcmp(arg[iarg],"type") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/correlate command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate type", error); if (strcmp(arg[iarg+1],"auto") == 0) type = AUTO; else if (strcmp(arg[iarg+1],"upper") == 0) type = UPPER; else if (strcmp(arg[iarg+1],"lower") == 0) type = LOWER; else if (strcmp(arg[iarg+1],"auto/upper") == 0) type = AUTOUPPER; else if (strcmp(arg[iarg+1],"auto/lower") == 0) type = AUTOLOWER; else if (strcmp(arg[iarg+1],"full") == 0) type = FULL; - else error->all(FLERR,"Illegal fix ave/correlate command"); + else error->all(FLERR,"Unknown fix ave/correlate type: {}"); iarg += 2; } else if (strcmp(arg[iarg],"ave") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/correlate command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate ave", error); if (strcmp(arg[iarg+1],"one") == 0) ave = ONE; else if (strcmp(arg[iarg+1],"running") == 0) ave = RUNNING; - else error->all(FLERR,"Illegal fix ave/correlate command"); + else error->all(FLERR,"Unknown fix ave/correlate ave mode: {}", arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"start") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/correlate command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate start", error); startstep = utils::inumeric(FLERR,arg[iarg+1],false,lmp); iarg += 2; } else if (strcmp(arg[iarg],"prefactor") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/correlate command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate prefactor", error); prefactor = utils::numeric(FLERR,arg[iarg+1],false,lmp); iarg += 2; } else if (strcmp(arg[iarg],"file") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/correlate command"); - if (me == 0) { + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate file", error); + if (comm->me == 0) { fp = fopen(arg[iarg+1],"w"); if (fp == nullptr) error->one(FLERR,"Cannot open fix ave/correlate file {}:"" {}", @@ -138,75 +133,67 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg): overwrite = 1; iarg += 1; } else if (strcmp(arg[iarg],"title1") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/correlate command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate title1", error); delete[] title1; title1 = utils::strdup(arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"title2") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/correlate command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate title2", error); delete[] title2; title2 = utils::strdup(arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"title3") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/correlate command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate title3", error); delete[] title3; title3 = utils::strdup(arg[iarg+1]); iarg += 2; - } else error->all(FLERR,"Illegal fix ave/correlate command"); + } else error->all(FLERR,"Unkown fix ave/correlate keyword: {}", arg[iarg]); } // setup and error check // for fix inputs, check that fix frequency is acceptable - if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0) - error->all(FLERR,"Illegal fix ave/correlate command"); - if (nfreq % nevery) - error->all(FLERR,"Illegal fix ave/correlate command"); - if (ave == ONE && nfreq < (nrepeat-1)*nevery) - error->all(FLERR,"Illegal fix ave/correlate command"); + if (nevery <= 0) error->all(FLERR,"Illegal fix ave/correlate nevery value: {}", nevery); + if (nrepeat <= 0) error->all(FLERR,"Illegal fix ave/correlate nrepeat value: {}", nrepeat); + if (nfreq <= 0) error->all(FLERR,"Illegal fix ave/correlate nfreq value: {}", nfreq); + if (nfreq % nevery || nrepeat*nevery > nfreq) + error->all(FLERR,"Inconsistent fix ave/correlate nevery/nrepeat/nfreq values"); if (ave != RUNNING && overwrite) - error->all(FLERR,"Illegal fix ave/correlate command"); + error->all(FLERR,"Fix ave/correlate overwrite keyword requires ave running setting"); - for (int i = 0; i < nvalues; i++) { - if (which[i] == ArgInfo::COMPUTE) { - int icompute = modify->find_compute(ids[i]); - if (icompute < 0) - error->all(FLERR,"Compute ID for fix ave/correlate does not exist"); - if (argindex[i] == 0 && modify->compute[icompute]->scalar_flag == 0) - error->all(FLERR, - "Fix ave/correlate compute does not calculate a scalar"); - if (argindex[i] && modify->compute[icompute]->vector_flag == 0) - error->all(FLERR, - "Fix ave/correlate compute does not calculate a vector"); - if (argindex[i] && argindex[i] > modify->compute[icompute]->size_vector) - error->all(FLERR,"Fix ave/correlate compute vector " - "is accessed out-of-range"); + for (auto &val : values) { - } else if (which[i] == ArgInfo::FIX) { - int ifix = modify->find_fix(ids[i]); - if (ifix < 0) - error->all(FLERR,"Fix ID for fix ave/correlate does not exist"); - if (argindex[i] == 0 && modify->fix[ifix]->scalar_flag == 0) - error->all(FLERR,"Fix ave/correlate fix does not calculate a scalar"); - if (argindex[i] && modify->fix[ifix]->vector_flag == 0) - error->all(FLERR,"Fix ave/correlate fix does not calculate a vector"); - if (argindex[i] && argindex[i] > modify->fix[ifix]->size_vector) - error->all(FLERR, - "Fix ave/correlate fix vector is accessed out-of-range"); - if (nevery % modify->fix[ifix]->global_freq) - error->all(FLERR,"Fix for fix ave/correlate " - "not computed at compatible time"); + if (val.which == ArgInfo::COMPUTE) { + val.val.c = modify->get_compute_by_id(val.id); + if (!val.val.c) + error->all(FLERR, "Compute ID {} for fix ave/correlate does not exist", val.id); + if (val.argindex == 0 && val.val.c->scalar_flag == 0) + error->all(FLERR, "Fix ave/correlate compute {} does not calculate a scalar", val.id); + if (val.argindex && val.val.c->vector_flag == 0) + error->all(FLERR, "Fix ave/correlate compute {} does not calculate a vector", val.id); + if (val.argindex && val.argindex > val.val.c->size_vector) + error->all(FLERR, "Fix ave/correlate compute {} vector is accessed out-of-range", val.id); - } else if (which[i] == ArgInfo::VARIABLE) { - int ivariable = input->variable->find(ids[i]); - if (ivariable < 0) - error->all(FLERR,"Variable name for fix ave/correlate does not exist"); - if (argindex[i] == 0 && input->variable->equalstyle(ivariable) == 0) - error->all(FLERR, - "Fix ave/correlate variable is not equal-style variable"); - if (argindex[i] && input->variable->vectorstyle(ivariable) == 0) - error->all(FLERR, - "Fix ave/correlate variable is not vector-style variable"); + } else if (val.which == ArgInfo::FIX) { + val.val.f = modify->get_fix_by_id(val.id); + if (!val.val.f) error->all(FLERR, "Fix ID {} for fix ave/correlate does not exist", val.id); + if (val.argindex == 0 && val.val.f->scalar_flag == 0) + error->all(FLERR, "Fix ave/correlate fix {} does not calculate a scalar", val.id); + if (val.argindex && val.val.f->vector_flag == 0) + error->all(FLERR, "Fix ave/correlate fix {} does not calculate a vector", val.id); + if (val.argindex && val.argindex > val.val.f->size_vector) + error->all(FLERR, "Fix ave/correlate fix {} vector is accessed out-of-range", val.id); + if (nevery % val.val.f->global_freq) + error->all(FLERR, "Fix {} for fix ave/correlate not computed at compatible time", val.id); + + } else if (val.which == ArgInfo::VARIABLE) { + val.val.v = input->variable->find(val.id.c_str()); + if (val.val.v < 0) + error->all(FLERR, "Variable name {} for fix ave/correlate does not exist", val.id); + if (val.argindex == 0 && input->variable->equalstyle(val.val.v) == 0) + error->all(FLERR, "Fix ave/correlate variable {} is not equal-style variable", val.id); + if (val.argindex && input->variable->vectorstyle(val.val.v) == 0) + error->all(FLERR, "Fix ave/correlate variable {} is not vector-style variable", val.id); } } @@ -219,7 +206,7 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg): // print file comment lines - if (fp && me == 0) { + if (fp && comm->me == 0) { clearerr(fp); if (title1) fprintf(fp,"%s\n",title1); else fprintf(fp,"# Time-correlated data for fix %s\n",id); @@ -254,7 +241,7 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg): fprintf(fp,"\n"); } if (ferror(fp)) - error->one(FLERR,"Error writing file header"); + error->one(FLERR,"Error writing ave/correlate header: {}", utils::getsyserror()); filepos = platform::ftell(fp); } @@ -275,7 +262,7 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg): // set count and corr to zero since they accumulate // also set save versions to zero in case accessed via compute_array() - memory->create(values,nrepeat,nvalues,"ave/correlate:values"); + memory->create(cvalues,nrepeat,nvalues,"ave/correlate:cvalues"); memory->create(count,nrepeat,"ave/correlate:count"); memory->create(save_count,nrepeat,"ave/correlate:save_count"); memory->create(corr,nrepeat,npair,"ave/correlate:corr"); @@ -312,19 +299,13 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg): FixAveCorrelate::~FixAveCorrelate() { - delete[] which; - delete[] argindex; - delete[] value2index; - for (int i = 0; i < nvalues; i++) delete[] ids[i]; - delete[] ids; - - memory->destroy(values); + memory->destroy(cvalues); memory->destroy(count); memory->destroy(save_count); memory->destroy(corr); memory->destroy(save_corr); - if (fp && me == 0) fclose(fp); + if (fp && comm->me == 0) fclose(fp); } /* ---------------------------------------------------------------------- */ @@ -342,24 +323,21 @@ void FixAveCorrelate::init() { // set current indices for all computes,fixes,variables - for (int i = 0; i < nvalues; i++) { - if (which[i] == ArgInfo::COMPUTE) { - int icompute = modify->find_compute(ids[i]); - if (icompute < 0) - error->all(FLERR,"Compute ID for fix ave/correlate does not exist"); - value2index[i] = icompute; + for (auto &val : values) { - } else if (which[i] == ArgInfo::FIX) { - int ifix = modify->find_fix(ids[i]); - if (ifix < 0) - error->all(FLERR,"Fix ID for fix ave/correlate does not exist"); - value2index[i] = ifix; + if (val.which == ArgInfo::COMPUTE) { + val.val.c = modify->get_compute_by_id(val.id); + if (!val.val.c) + error->all(FLERR, "Compute ID {} for fix ave/correlate does not exist", val.id); - } else if (which[i] == ArgInfo::VARIABLE) { - int ivariable = input->variable->find(ids[i]); - if (ivariable < 0) - error->all(FLERR,"Variable name for fix ave/correlate does not exist"); - value2index[i] = ivariable; + } else if (val.which == ArgInfo::FIX) { + val.val.f = modify->get_fix_by_id(val.id); + if (!val.val.f) error->all(FLERR,"Fix ID {} for fix ave/correlate does not exist", val.id); + + } else if (val.which == ArgInfo::VARIABLE) { + val.val.v = input->variable->find(val.id.c_str()); + if (val.val.v < 0) + error->all(FLERR,"Variable name {} for fix ave/correlate does not exist", val.id); } } @@ -387,8 +365,7 @@ void FixAveCorrelate::setup(int /*vflag*/) void FixAveCorrelate::end_of_step() { - int i,j,m; - double scalar; + int i,j; // skip if not step which requires doing something @@ -406,51 +383,51 @@ void FixAveCorrelate::end_of_step() lastindex++; if (lastindex == nrepeat) lastindex = 0; - for (i = 0; i < nvalues; i++) { - m = value2index[i]; + i = 0; + for (auto &val : values) { + double scalar = 0.0; // invoke compute if not previously invoked - if (which[i] == ArgInfo::COMPUTE) { - Compute *compute = modify->compute[m]; + if (val.which == ArgInfo::COMPUTE) { - if (argindex[i] == 0) { - if (!(compute->invoked_flag & Compute::INVOKED_SCALAR)) { - compute->compute_scalar(); - compute->invoked_flag |= Compute::INVOKED_SCALAR; + if (val.argindex == 0) { + if (!(val.val.c->invoked_flag & Compute::INVOKED_SCALAR)) { + val.val.c->compute_scalar(); + val.val.c->invoked_flag |= Compute::INVOKED_SCALAR; } - scalar = compute->scalar; + scalar = val.val.c->scalar; } else { - if (!(compute->invoked_flag & Compute::INVOKED_VECTOR)) { - compute->compute_vector(); - compute->invoked_flag |= Compute::INVOKED_VECTOR; + if (!(val.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { + val.val.c->compute_vector(); + val.val.c->invoked_flag |= Compute::INVOKED_VECTOR; } - scalar = compute->vector[argindex[i]-1]; + scalar = val.val.c->vector[val.argindex-1]; } // access fix fields, guaranteed to be ready - } else if (which[i] == ArgInfo::FIX) { - if (argindex[i] == 0) - scalar = modify->fix[m]->compute_scalar(); + } else if (val.which == ArgInfo::FIX) { + if (val.argindex == 0) + scalar = val.val.f->compute_scalar(); else - scalar = modify->fix[m]->compute_vector(argindex[i]-1); + scalar = val.val.f->compute_vector(val.argindex-1); // evaluate equal-style or vector-style variable - } else if (which[i] == ArgInfo::VARIABLE) { - if (argindex[i] == 0) - scalar = input->variable->compute_equal(m); + } else if (val.which == ArgInfo::VARIABLE) { + if (val.argindex == 0) + scalar = input->variable->compute_equal(val.val.v); else { double *varvec; - int nvec = input->variable->compute_vector(m,&varvec); - int index = argindex[i]; + int nvec = input->variable->compute_vector(val.val.v,&varvec); + int index = val.argindex; if (nvec < index) scalar = 0.0; else scalar = varvec[index-1]; } } - values[lastindex][i] = scalar; + cvalues[lastindex][i++] = scalar; } // fistindex = index in values ring of earliest time sample @@ -484,7 +461,7 @@ void FixAveCorrelate::end_of_step() // output result to file - if (fp && me == 0) { + if (fp && comm->me == 0) { clearerr(fp); if (overwrite) platform::fseek(fp,filepos); fmt::print(fp,"{} {}\n",ntimestep,nrepeat); @@ -499,7 +476,7 @@ void FixAveCorrelate::end_of_step() fprintf(fp,"\n"); } if (ferror(fp)) - error->one(FLERR,"Error writing out correlation data"); + error->one(FLERR,"Error writing out fix ave/correlate data: {}", utils::getsyserror()); fflush(fp); @@ -539,7 +516,7 @@ void FixAveCorrelate::accumulate() for (k = 0; k < nsample; k++) { ipair = 0; for (i = 0; i < nvalues; i++) { - corr[k][ipair++] += values[m][i]*values[n][i]; + corr[k][ipair++] += cvalues[m][i]*cvalues[n][i]; } m--; if (m < 0) m = nrepeat-1; @@ -550,7 +527,7 @@ void FixAveCorrelate::accumulate() ipair = 0; for (i = 0; i < nvalues; i++) for (j = i+1; j < nvalues; j++) - corr[k][ipair++] += values[m][i]*values[n][j]; + corr[k][ipair++] += cvalues[m][i]*cvalues[n][j]; m--; if (m < 0) m = nrepeat-1; } @@ -560,7 +537,7 @@ void FixAveCorrelate::accumulate() ipair = 0; for (i = 0; i < nvalues; i++) for (j = 0; j < i; j++) - corr[k][ipair++] += values[m][i]*values[n][j]; + corr[k][ipair++] += cvalues[m][i]*cvalues[n][j]; m--; if (m < 0) m = nrepeat-1; } @@ -570,7 +547,7 @@ void FixAveCorrelate::accumulate() ipair = 0; for (i = 0; i < nvalues; i++) for (j = i; j < nvalues; j++) - corr[k][ipair++] += values[m][i]*values[n][j]; + corr[k][ipair++] += cvalues[m][i]*cvalues[n][j]; m--; if (m < 0) m = nrepeat-1; } @@ -580,7 +557,7 @@ void FixAveCorrelate::accumulate() ipair = 0; for (i = 0; i < nvalues; i++) for (j = 0; j <= i; j++) - corr[k][ipair++] += values[m][i]*values[n][j]; + corr[k][ipair++] += cvalues[m][i]*cvalues[n][j]; m--; if (m < 0) m = nrepeat-1; } @@ -590,7 +567,7 @@ void FixAveCorrelate::accumulate() ipair = 0; for (i = 0; i < nvalues; i++) for (j = 0; j < nvalues; j++) - corr[k][ipair++] += values[m][i]*values[n][j]; + corr[k][ipair++] += cvalues[m][i]*cvalues[n][j]; m--; if (m < 0) m = nrepeat-1; } diff --git a/src/fix_ave_correlate.h b/src/fix_ave_correlate.h index 517740a121..8637988b8b 100644 --- a/src/fix_ave_correlate.h +++ b/src/fix_ave_correlate.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -35,11 +35,20 @@ class FixAveCorrelate : public Fix { double compute_array(int, int) override; private: - int me, nvalues; - int nrepeat, nfreq; + struct value_t { + int which; // type of data: COMPUTE, FIX, VARIABLE + int argindex; // 1-based index if data is vector, else 0 + std::string id; // compute/fix/variable ID + union { + class Compute *c; + class Fix *f; + int v; + } val; + }; + std::vector values; + + int nvalues, nrepeat, nfreq; bigint nvalid, nvalid_last; - int *which, *argindex, *value2index; - char **ids; FILE *fp; int type, ave, startstep, overwrite; @@ -52,7 +61,7 @@ class FixAveCorrelate : public Fix { int npair; // number of correlation pairs to calculate int *count; - double **values, **corr; + double **cvalues, **corr; int *save_count; // saved values at Nfreq for output via compute_array() double **save_corr; diff --git a/src/fix_ave_grid.cpp b/src/fix_ave_grid.cpp new file mode 100644 index 0000000000..524def73a4 --- /dev/null +++ b/src/fix_ave_grid.cpp @@ -0,0 +1,2233 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "fix_ave_grid.h" + +#include "arg_info.h" +#include "atom.h" +#include "compute.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "grid2d.h" +#include "grid3d.h" +#include "input.h" +#include "memory.h" +#include "modify.h" +#include "neighbor.h" +#include "update.h" +#include "variable.h" + +#include + +using namespace LAMMPS_NS; +using namespace FixConst; + +enum{ALL,SAMPLE,NONORM}; +enum{ONE,RUNNING,WINDOW}; +enum{DISCARD,KEEP}; + +// OFFSET avoids outside-of-box atoms being rounded to grid pts incorrectly + +static constexpr int OFFSET = 16384; + +/* ---------------------------------------------------------------------- */ + +FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg), id_bias(nullptr), which(nullptr), argindex(nullptr), ids(nullptr), + value2index(nullptr), value2grid(nullptr), value2data(nullptr), grid2d(nullptr), grid3d(nullptr), + grid_buf1(nullptr), grid_buf2(nullptr), grid_output(nullptr), grid_sample(nullptr), + grid_nfreq(nullptr), grid_running(nullptr), grid_window(nullptr), grid2d_previous(nullptr), + grid3d_previous(nullptr), grid_sample_previous(nullptr), grid_nfreq_previous(nullptr), + grid_running_previous(nullptr), grid_window_previous(nullptr), bin(nullptr), skip(nullptr), + vresult(nullptr) +{ + if (narg < 10) utils::missing_cmd_args(FLERR,"fix ave/grid", error); + + pergrid_flag = 1; + nevery = utils::inumeric(FLERR,arg[3],false,lmp); + nrepeat = utils::inumeric(FLERR,arg[4],false,lmp); + pergrid_freq = utils::inumeric(FLERR,arg[5],false,lmp); + time_depend = 1; + + if (nevery <= 0 || nrepeat <= 0 || pergrid_freq <= 0) + error->all(FLERR,"Illegal fix ave/grid command"); + if (pergrid_freq % nevery || nrepeat*nevery > pergrid_freq) + error->all(FLERR,"Illegal fix ave/grid command"); + + // NOTE: allow Dxyz as well at some point ? + + nxgrid = utils::inumeric(FLERR,arg[6],false,lmp); + nygrid = utils::inumeric(FLERR,arg[7],false,lmp); + nzgrid = utils::inumeric(FLERR,arg[8],false,lmp); + + // expand args if any have wildcard character "*" + // this can reset nvalues + + int expand = 0; + char **earg; + int nargnew = utils::expand_args(FLERR,narg-9,&arg[9],1,earg,lmp); + + if (earg != &arg[9]) expand = 1; + arg = earg; + + // parse values until one isn't recognized (optional keyword) + + which = new int[nargnew]; + argindex = new int[nargnew]; + ids = new char*[nargnew]; + value2index = new int[nargnew]; + value2grid = new int[nargnew]; + value2data = new int[nargnew]; + + modeatom = modegrid = 0; + nvalues = 0; + + int iarg = 0; + while (iarg < nargnew) { + ids[nvalues] = nullptr; + + if (strcmp(arg[iarg],"vx") == 0) { + which[nvalues] = ArgInfo::V; + argindex[nvalues] = 0; + modeatom = 1; + } else if (strcmp(arg[iarg],"vy") == 0) { + which[nvalues] = ArgInfo::V; + argindex[nvalues] = 1; + modeatom = 1; + } else if (strcmp(arg[iarg],"vz") == 0) { + which[nvalues] = ArgInfo::V; + argindex[nvalues] = 2; + modeatom = 1; + + } else if (strcmp(arg[iarg],"fx") == 0) { + which[nvalues] = ArgInfo::F; + argindex[nvalues] = 0; + modeatom = 1; + } else if (strcmp(arg[iarg],"fy") == 0) { + which[nvalues] = ArgInfo::F; + argindex[nvalues] = 1; + modeatom = 1; + } else if (strcmp(arg[iarg],"fz") == 0) { + which[nvalues] = ArgInfo::F; + argindex[nvalues] = 2; + modeatom = 1; + + } else if (strcmp(arg[iarg],"density/number") == 0) { + which[nvalues] = ArgInfo::DENSITY_NUMBER; + argindex[nvalues] = 0; + modeatom = 1; + } else if (strcmp(arg[iarg],"density/mass") == 0) { + which[nvalues] = ArgInfo::DENSITY_MASS; + argindex[nvalues] = 0; + modeatom = 1; + } else if (strcmp(arg[iarg],"mass") == 0) { + which[nvalues] = ArgInfo::MASS; + argindex[nvalues] = 0; + modeatom = 1; + } else if (strcmp(arg[iarg],"temp") == 0) { + which[nvalues] = ArgInfo::TEMPERATURE; + argindex[nvalues] = 0; + modeatom = 1; + + } else { + + // if arg is not a per-atom or per-grid value + // then it's an optional arg after the values + + ArgInfo argi(arg[iarg]); + if (argi.get_type() == ArgInfo::NONE || argi.get_type() == ArgInfo::UNKNOWN) break; + if (argi.get_dim() > 1) error->all(FLERR,"Invalid fix ave/grid command"); + + // atom value has no colon + + if (!strchr(arg[iarg],':')) { + modeatom = 1; + ids[nvalues] = argi.copy_name(); + which[nvalues] = argi.get_type(); + argindex[nvalues] = argi.get_index1(); + + // per-grid value has colons + + } else { + modegrid = 1; + + int igrid,idata,index; + int iflag = + utils::check_grid_reference((char *) "Fix ave/grid", + arg[iarg],nevery,ids[nvalues],igrid,idata,index,lmp); + if (iflag < 0) error->all(FLERR,"Invalid grid reference in fix ave/grid command"); + + which[nvalues] = iflag; + value2grid[nvalues] = igrid; + value2data[nvalues] = idata; + argindex[nvalues] = index; + } + } + + nvalues++; + iarg++; + } + + if (nvalues == 0) error->all(FLERR,"No values in fix ave/grid command"); + + if (modeatom && modegrid) + error->all(FLERR,"Fix ave/grid cannot operate on per-atom and " + "per-grid values"); + + // optional args + + discardflag = DISCARD; + normflag = ALL; + aveflag = ONE; + nwindow = 0; + biasflag = 0; + id_bias = nullptr; + adof = domain->dimension; + cdof = 0.0; + + while (iarg < nargnew) { + if (strcmp(arg[iarg],"discard") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/grid command"); + if (strcmp(arg[iarg+1],"yes") == 0) discardflag = DISCARD; + else if (strcmp(arg[iarg+1],"no") == 0) discardflag = KEEP; + else error->all(FLERR,"Illegal fix ave/grid command"); + iarg += 2; + + } else if (strcmp(arg[iarg],"norm") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/grid command"); + if (strcmp(arg[iarg+1],"all") == 0) normflag = ALL; + else if (strcmp(arg[iarg+1],"sample") == 0) normflag = SAMPLE; + else if (strcmp(arg[iarg+1],"none") == 0) normflag = NONORM; + else error->all(FLERR,"Illegal fix ave/grid command"); + iarg += 2; + + } else if (strcmp(arg[iarg],"ave") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/grid command"); + if (strcmp(arg[iarg+1],"one") == 0) aveflag = ONE; + else if (strcmp(arg[iarg+1],"running") == 0) aveflag = RUNNING; + else if (strcmp(arg[iarg+1],"window") == 0) aveflag = WINDOW; + else error->all(FLERR,"Illegal fix ave/grid command"); + if (aveflag == WINDOW) { + if (iarg+3 > narg) error->all(FLERR,"Illegal fix ave/grid command"); + nwindow = utils::inumeric(FLERR,arg[iarg+2],false,lmp); + if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/grid command"); + iarg++; + } + iarg += 2; + + } else if (strcmp(arg[iarg],"bias") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal fix ave/grid command"); + biasflag = 1; + id_bias = utils::strdup(arg[iarg+1]); + iarg += 2; + + } else if (strcmp(arg[iarg],"adof") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal fix ave/grid command"); + adof = utils::numeric(FLERR,arg[iarg+1],false,lmp); + iarg += 2; + } else if (strcmp(arg[iarg],"cdof") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal fix ave/grid command"); + cdof = utils::numeric(FLERR,arg[iarg+1],false,lmp); + iarg += 2; + + } else error->all(FLERR,"Illegal fix ave/grid command"); + } + + // if wildcard expansion occurred, free earg memory from exapnd_args() + + if (expand) { + for (int i = 0; i < nvalues; i++) delete[] earg[i]; + memory->sfree(earg); + } + + // more error checks + // for fix inputs, check that fix frequency is acceptable + + dimension = domain->dimension; + + if ((nxgrid < 1) || (nygrid < 1) || (nzgrid < 1)) + error->all(FLERR,"Invalid fix ave/grid grid size"); + if (dimension == 2 && nzgrid != 1) + error->all(FLERR,"Fix ave/grid grid Nz must be 1 for 2d simulation"); + + if (biasflag) { + tbias = modify->get_compute_by_id(id_bias); + if (!tbias) + error->all(FLERR,"Could not find compute ID for temperature bias"); + if (tbias->tempflag == 0) + error->all(FLERR,"Bias compute does not calculate temperature"); + if (tbias->tempbias == 0) + error->all(FLERR,"Bias compute does not calculate a velocity bias"); + } + + // error checks for ATOM mode + + if (modeatom) { + for (int i = 0; i < nvalues; i++) { + if (which[i] == ArgInfo::COMPUTE) { + int icompute = modify->find_compute(ids[i]); + if (icompute < 0) + error->all(FLERR,"Compute ID for fix ave/grid does not exist"); + if (modify->compute[icompute]->peratom_flag == 0) + error->all(FLERR, "Fix ave/atom compute does not calculate per-atom values"); + if (argindex[i] == 0 && + modify->compute[icompute]->size_peratom_cols != 0) + error->all(FLERR,"Fix ave/atom compute does not calculate a per-atom vector"); + if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0) + error->all(FLERR,"Fix ave/atom compute does not calculate a per-atom array"); + if (argindex[i] && argindex[i] > modify->compute[icompute]->size_peratom_cols) + error->all(FLERR,"Fix ave/atom compute array is accessed out-of-range"); + + } else if (which[i] == ArgInfo::FIX) { + int ifix = modify->find_fix(ids[i]); + if (ifix < 0) + error->all(FLERR,"Fix ID for fix ave/atom does not exist"); + if (modify->fix[ifix]->peratom_flag == 0) + error->all(FLERR,"Fix ave/atom fix does not calculate per-atom values"); + if (argindex[i] == 0 && modify->fix[ifix]->size_peratom_cols != 0) + error->all(FLERR, "Fix ave/atom fix does not calculate a per-atom vector"); + if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0) + error->all(FLERR, "Fix ave/atom fix does not calculate a per-atom array"); + if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols) + error->all(FLERR,"Fix ave/atom fix array is accessed out-of-range"); + if (nevery % modify->fix[ifix]->peratom_freq) + error->all(FLERR, "Fix for fix ave/atom not computed at compatible time"); + + } else if (which[i] == ArgInfo::VARIABLE) { + int ivariable = input->variable->find(ids[i]); + if (ivariable < 0) + error->all(FLERR,"Variable name for fix ave/atom does not exist"); + if (input->variable->atomstyle(ivariable) == 0) + error->all(FLERR,"Fix ave/atom variable is not atom-style variable"); + } + } + } + + // instantiate Grid class and buffers + // allocate/zero per-grid data + + allocate_grid(); + + grid_sample = allocate_one_grid(); + grid_nfreq = allocate_one_grid(); + if (aveflag == RUNNING || aveflag == WINDOW) grid_running = allocate_one_grid(); + if (aveflag == WINDOW) { + grid_window = new GridData*[nwindow]; + for (int i = 0; i < nwindow; i++) + grid_window[i] = allocate_one_grid(); + } + + // output may occur via dump on timestep 0 + + grid_output = new GridData(); + output_grid(grid_nfreq); + + // initialize running and window values + + running_count = 0; + window_count = 0; + window_oldest = -1; + window_newest = 0; + + // bin indices and skip flags for ATOM mode + // vresult for per-atom variable evaluation + + maxatom = 0; + bin = nullptr; + skip = nullptr; + + maxvar = 0; + vresult = nullptr; + + // nvalid = next step on which end_of_step does something + // add nvalid to all computes that store invocation times + // since don't know a priori which are invoked by this fix + // once in end_of_step() can set timestep for ones actually invoked + + irepeat = 0; + nvalid_last = -1; + nvalid = nextvalid(); + modify->addstep_compute_all(nvalid); +} + +/* ---------------------------------------------------------------------- */ + +FixAveGrid::~FixAveGrid() +{ + delete[] which; + delete[] argindex; + for (int m = 0; m < nvalues; m++) delete[] ids[m]; + delete[] ids; + delete[] value2index; + delete[] value2grid; + delete[] value2data; + + // deallocate Grid class and buffers + + if (dimension == 2) delete grid2d; + else delete grid3d; + + memory->destroy(grid_buf1); + memory->destroy(grid_buf2); + + // deallocate per-grid data + + deallocate_one_grid(grid_sample,nxlo_out,nylo_out,nzlo_out); + deallocate_one_grid(grid_nfreq,nxlo_out,nylo_out,nzlo_out); + if (aveflag == RUNNING || aveflag == WINDOW) + deallocate_one_grid(grid_running,nxlo_out,nylo_out,nzlo_out); + if (aveflag == WINDOW) { + for (int i = 0; i < nwindow; i++) + deallocate_one_grid(grid_window[i],nxlo_out,nylo_out,nzlo_out); + delete [] grid_window; + } + + delete grid_output; + + if (modeatom) { + memory->destroy(bin); + memory->destroy(skip); + memory->destroy(vresult); + } +} + +/* ---------------------------------------------------------------------- */ + +int FixAveGrid::setmask() +{ + int mask = 0; + mask |= END_OF_STEP; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixAveGrid::init() +{ + if (biasflag) { + tbias = modify->get_compute_by_id(id_bias); + if (!tbias) + error->all(FLERR,"Could not find compute ID for temperature bias"); + } + + // set indices and check validity of all computes,fixes,variables + + for (int m = 0; m < nvalues; m++) { + if (which[m] == ArgInfo::COMPUTE) { + int icompute = modify->find_compute(ids[m]); + if (icompute < 0) + error->all(FLERR,"Compute ID for fix ave/grid does not exist"); + value2index[m] = icompute; + + } else if (which[m] == ArgInfo::FIX) { + int ifix = modify->find_fix(ids[m]); + if (ifix < 0) + error->all(FLERR,"Fix ID for fix ave/grid does not exist"); + value2index[m] = ifix; + + } else if (which[m] == ArgInfo::VARIABLE) { + int ivariable = input->variable->find(ids[m]); + if (ivariable < 0) + error->all(FLERR,"Variable name for fix ave/grid does not exist"); + value2index[m] = ivariable; + + } else value2index[m] = -1; + } + + // check that grid sizes for all fields match grid size for this fix + + if (modegrid) { + Compute *compute; + Fix *fix; + Grid2d *grid2d; + Grid3d *grid3d; + + int nxtmp,nytmp,nztmp; + + for (int m = 0; m < nvalues; m++) { + if (dimension == 2) { + if (which[m] == ArgInfo::COMPUTE) { + compute = modify->compute[value2index[m]]; + grid2d = (Grid2d *) compute->get_grid_by_index(value2grid[m]); + } else { + fix = modify->fix[value2index[m]]; + grid2d = (Grid2d *) fix->get_grid_by_index(value2grid[m]); + } + grid2d->get_size(nxtmp,nytmp); + if (nxtmp != nxgrid || nytmp != nygrid) + error->all(FLERR,"Fix ave/grid value grid sizes do not match"); + + } else { + if (which[m] == ArgInfo::COMPUTE) { + compute = modify->compute[value2index[m]]; + grid3d = (Grid3d *) compute->get_grid_by_index(value2grid[m]); + } else { + fix = modify->fix[value2index[m]]; + grid3d = (Grid3d *) fix->get_grid_by_index(value2grid[m]); + } + grid3d->get_size(nxtmp,nytmp,nztmp); + if (nxtmp != nxgrid || nytmp != nygrid || nztmp != nzgrid) + error->all(FLERR,"Fix ave/grid value grid sizes do not match"); + } + } + } + + // set triclinic flag + + triclinic = domain->triclinic; + + // need to reset nvalid if nvalid < ntimestep b/c minimize was performed + + if (nvalid < update->ntimestep) { + irepeat = 0; + nvalid = nextvalid(); + modify->addstep_compute_all(nvalid); + } +} + +/* ---------------------------------------------------------------------- + only does something if nvalid = current timestep +------------------------------------------------------------------------- */ + +void FixAveGrid::setup(int /*vflag*/) +{ + end_of_step(); +} + +/* ---------------------------------------------------------------------- */ + +void FixAveGrid::end_of_step() +{ + // skip if not step which requires doing something + + bigint ntimestep = update->ntimestep; + if (ntimestep != nvalid) return; + nvalid_last = nvalid; + + // if first sample in nfreq, zero owned and ghost grid points + + if (irepeat == 0) { + zero_grid(grid_sample); + if (normflag == SAMPLE) zero_grid(grid_nfreq); + } + + // accumulate per-grid values for one sample for either ATOM or GRID mode + // per-atom compute/fix/variable may invoke computes so wrap with clear/add + + if (modeatom) { + modify->clearstep_compute(); + atom2grid(); + } else { + grid2grid(); + } + + // return if irepeat < nrepeat + // unless ATOM mode and norm = SAMPLE + + irepeat++; + if (irepeat < nrepeat && (modegrid || normflag != SAMPLE)) { + nvalid += nevery; + if (modeatom) modify->addstep_compute(nvalid); + return; + } + + // for ATOM mode, perform ghost to owned grid communication + // done once per Nfreq for norm = ONE + // done every sample for norm = SAMPLE + // nvalues+1 includes atom count + + if (modeatom) { + if (dimension == 2) + grid2d->reverse_comm(Grid2d::FIX,this,0,nvalues+1,sizeof(double), + grid_buf1,grid_buf2,MPI_DOUBLE); + else + grid3d->reverse_comm(Grid3d::FIX,this,0,nvalues+1,sizeof(double), + grid_buf1,grid_buf2,MPI_DOUBLE); + } + + // if ATOM mode and norm = SAMPLE: + // normalize the single sample + // sum sample grid to Nfreq grid + // return if irepeat < nrepeat + + if (modeatom && normflag == SAMPLE) { + normalize_atom(1,grid_sample); + add_grid(grid_sample,grid_nfreq); + zero_grid(grid_sample); + + if (irepeat < nrepeat) { + nvalid += nevery; + modify->addstep_compute(nvalid); + return; + } + } + + // this is an Nfreq timestep + // reset irepeat and nvalid + + irepeat = 0; + nvalid = ntimestep+pergrid_freq - ((bigint) nrepeat-1)*nevery; + if (modeatom) modify->addstep_compute(nvalid); + + // just return if this proc owns no grid points + + if (ngridout == 0) return; + + // average final results over the entire Nfreq of samples + // store final result in Nfreq grid + // for ATOM mode: + // for norm = ALL, normalize sample grid by counts over all samples + // for norm = SAMPLE, normalize Nfreq grid by Nrepeat + // for norm = NONORM, normalize sample grid by Nrepeat, not by counts + // this check is made inside normalize_atom() + // for GRID mode: + // normalize sample grid by Nrepeat + + if (modeatom) { + if (normflag == ALL) { + normalize_atom(nrepeat,grid_sample); + normalize_count(nrepeat,grid_sample); + copy_grid(grid_sample,grid_nfreq); + + } else if (normflag == SAMPLE) { + normalize_grid(nrepeat,grid_nfreq); + normalize_count(nrepeat,grid_nfreq); + + } else if (normflag == NONORM) { + normalize_atom(nrepeat,grid_sample); + normalize_count(nrepeat,grid_sample); + copy_grid(grid_sample,grid_nfreq); + } + } + + if (modegrid) { + normalize_grid(nrepeat,grid_sample); + copy_grid(grid_sample,grid_nfreq); + } + + // create Nfreq output + // for aveflag == RUNNING + // running_count = # of Nfreq entries in grid_running + // for aveflag == WINDOW + // window_count = # of Nfreq entries in grid_window + + if (aveflag == ONE) { + output_grid(grid_nfreq); + + } else if (aveflag == RUNNING) { + running_count++; + add_grid(grid_nfreq,grid_running); + copy_grid(grid_running,grid_nfreq); + normalize_grid(running_count,grid_nfreq); + if (modeatom) normalize_count(running_count,grid_nfreq); + output_grid(grid_nfreq); + + } else if (aveflag == WINDOW) { + + // update grid_running to be sum over grid_window entries + // add grid_nfreq to grid_running + // if window is full, subtract oldest window entry from grid_running + // copy grid_nfreq into window + + add_grid(grid_nfreq,grid_running); + if (window_count == nwindow) + subtract_grid(grid_window[window_oldest],grid_running); + copy_grid(grid_nfreq,grid_window[window_newest]); + + // update status of window + // window_count = # of entries in window + // window_oldest = index of oldest entry in grid_window + // window_newest = index in window where next grid_nfreq will be copied + + if (window_count < nwindow) window_count++; + if (window_count == nwindow) window_oldest++; + if (window_oldest == nwindow) window_oldest = 0; + window_newest++; + if (window_newest == nwindow) window_newest = 0; + + // copy grid running to grid_nfreq and perform normalization + + copy_grid(grid_running,grid_nfreq); + normalize_grid(window_count,grid_nfreq); + output_grid(grid_nfreq); + } +} + +/* ---------------------------------------------------------------------- + sum per-atom contributions to owned+ghost grid cells + sets one of vec2d,array2d,vec3d,array3d sample + also set count2d or count3d for atom count per bin +------------------------------------------------------------------------- */ + +void FixAveGrid::atom2grid() +{ + int i,j,m,n,ix,iy,iz; + + double **count2d = grid_sample->count2d; + double **vec2d = grid_sample->vec2d; + double ***array2d = grid_sample->array2d; + double ***count3d = grid_sample->count3d; + double ***vec3d = grid_sample->vec3d; + double ****array3d = grid_sample->array3d; + + // bin[i][dim] = indices of bin each atom is in + // skip atom if group mask does not match + // check if any atom is out of bounds for my local grid + // for nonperiodic dim, remap atom to first/last bin if out of bounds + // count atoms contributing to each bin + + double *boxlo,*prd; + int *periodicity = domain->periodicity; + + if (triclinic) { + boxlo = domain->boxlo_lamda; + prd = domain->prd_lamda; + } else { + boxlo = domain->boxlo; + prd = domain->prd; + } + + double dxinv = nxgrid/prd[0]; + double dyinv = nygrid/prd[1]; + double dzinv = nzgrid/prd[2]; + + double **x = atom->x; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + if (nlocal > maxatom) { + memory->destroy(bin); + memory->destroy(skip); + maxatom = atom->nmax; + memory->create(bin,maxatom,dimension,"ave/grid:bin"); + memory->create(skip,maxatom,"ave/grid:skip"); + } + + if (triclinic) domain->x2lamda(nlocal); + + int flag = 0; + + if (dimension == 2) { + for (i = 0; i < nlocal; i++) { + if (!(mask[i] & groupbit)) { + skip[i] = 1; + continue; + } + + ix = static_cast ((x[i][0]-boxlo[0])*dxinv + OFFSET) - OFFSET; + iy = static_cast ((x[i][1]-boxlo[1])*dyinv + OFFSET) - OFFSET; + + if (ix < nxlo_out || ix > nxhi_out) { + if (periodicity[0]) flag = 1; + else if (discardflag == KEEP) { + if (ix < nxlo_out && nxlo_out == 0) ix = 0; + else if (ix > nxhi_out && nxhi_out == nxgrid-1) ix = nxgrid-1; + else flag = 1; + } else skip[i] = 1; + continue; + } + if (iy < nylo_out || iy > nyhi_out) { + if (periodicity[1]) flag = 1; + else if (discardflag == KEEP) { + if (iy < nylo_out && nylo_out == 0) iy = 0; + else if (iy > nyhi_out && nyhi_out == nygrid-1) iy = nygrid-1; + else flag = 1; + } else skip[i] = 1; + continue; + } + + skip[i] = 0; + count2d[iy][ix] += 1.0; + bin[i][0] = iy; + bin[i][1] = ix; + } + + } else { + for (i = 0; i < nlocal; i++) { + if (!(mask[i] & groupbit)) { + skip[i] = 1; + continue; + } + + ix = static_cast ((x[i][0]-boxlo[0])*dxinv + OFFSET) - OFFSET; + iy = static_cast ((x[i][1]-boxlo[1])*dyinv + OFFSET) - OFFSET; + iz = static_cast ((x[i][2]-boxlo[2])*dzinv + OFFSET) - OFFSET; + + if (ix < nxlo_out || ix > nxhi_out) { + if (periodicity[0]) flag = 1; + else if (discardflag == KEEP) { + if (ix < nxlo_out && nxlo_out == 0) ix = 0; + else if (ix > nxhi_out && nxhi_out == nxgrid-1) ix = nxgrid-1; + else flag = 1; + } else skip[i] = 1; + } + + if (iy < nylo_out || iy > nyhi_out) { + if (periodicity[1]) flag = 1; + else if (discardflag == KEEP) { + if (iy < nylo_out && nylo_out == 0) iy = 0; + else if (iy > nyhi_out && nyhi_out == nygrid-1) iy = nygrid-1; + else flag = 1; + } else skip[i] = 1; + continue; + } + + if (iz < nzlo_out || iz > nzhi_out) { + if (periodicity[2]) flag = 1; + else if (discardflag == KEEP) { + if (iz < nzlo_out && nzlo_out == 0) iz = 0; + else if (iz > nzhi_out && nzhi_out == nzgrid-1) iz = nzgrid-1; + else flag = 1; + } else skip[i] = 1; + continue; + } + + skip[i] = 0; + count3d[iz][iy][ix] += 1.0; + bin[i][0] = iz; + bin[i][1] = iy; + bin[i][2] = ix; + } + } + + if (flag) error->one(FLERR,"Out of range fix ave/grid atoms"); + + if (triclinic) domain->lamda2x(nlocal); + + // loop over user-specified values + + for (m = 0; m < nvalues; m++) { + n = value2index[m]; + j = argindex[m]; + + // V,F adds velocity,force to value + + if (which[m] == ArgInfo::V || which[m] == ArgInfo::F) { + + double **attribute; + if (which[m] == ArgInfo::V) attribute = atom->v; + else if (which[m] == ArgInfo::F) attribute = atom->f; + + if (dimension == 2) { + if (nvalues == 1) { + for (i = 0; i < nlocal; i++) { + if (!skip[i]) + vec2d[bin[i][0]][bin[i][1]] += attribute[i][j]; + } + } else + for (i = 0; i < nlocal; i++) { + if (!skip[i]) + array2d[bin[i][0]][bin[i][1]][m] += attribute[i][j]; + } + } else { + if (nvalues == 1) { + for (i = 0; i < nlocal; i++) { + if (!skip[i]) + vec3d[bin[i][0]][bin[i][1]][bin[i][2]] += attribute[i][j]; + } + } else + for (i = 0; i < nlocal; i++) { + if (!skip[i]) + array3d[bin[i][0]][bin[i][1]][bin[i][2]][m] += attribute[i][j]; + } + } + + // DENSITY_NUMBER adds 1 to value + // DENSITY_MASS or MASS adds mass to value + + } else if ((which[m] == ArgInfo::DENSITY_NUMBER) || + (which[m] == ArgInfo::DENSITY_MASS) || + (which[m] == ArgInfo::MASS)) { + + int *type = atom->type; + double *mass = atom->mass; + double *rmass = atom->rmass; + double one; + + if (dimension == 2) { + if (nvalues == 1) { + for (i = 0; i < nlocal; i++) { + if (!skip[i]) { + if (which[m] == ArgInfo::DENSITY_NUMBER) one = 1.0; + else if (rmass) one = rmass[i]; + else one = mass[type[i]]; + vec2d[bin[i][0]][bin[i][1]] += one; + } + } + } else + for (i = 0; i < nlocal; i++) { + if (!skip[i]) { + if (which[m] == ArgInfo::DENSITY_NUMBER) one = 1.0; + else if (rmass) one = rmass[i]; + else one = mass[type[i]]; + array2d[bin[i][0]][bin[i][1]][m] += one; + } + } + } else { + if (nvalues == 1) { + for (i = 0; i < nlocal; i++) { + if (!skip[i]) { + if (which[m] == ArgInfo::DENSITY_NUMBER) one = 1.0; + else if (rmass) one = rmass[i]; + else one = mass[type[i]]; + vec3d[bin[i][0]][bin[i][1]][bin[i][2]] += one; + } + } + } else + for (i = 0; i < nlocal; i++) { + if (!skip[i]) { + if (which[m] == ArgInfo::DENSITY_NUMBER) one = 1.0; + else if (rmass) one = rmass[i]; + else one = mass[type[i]]; + array3d[bin[i][0]][bin[i][1]][bin[i][2]][m] += one; + } + } + } + + // TEMPERATURE adds KE to values + // subtract and restore velocity bias if requested + + } else if (which[m] == ArgInfo::TEMPERATURE) { + + if (biasflag) { + if (tbias->invoked_scalar != update->ntimestep) tbias->compute_scalar(); + tbias->remove_bias_all(); + } + + double **v = atom->v; + int *type = atom->type; + double *mass = atom->mass; + double *rmass = atom->rmass; + double vsq,one; + + if (dimension == 2) { + if (nvalues == 1) { + for (i = 0; i < nlocal; i++) { + if (!skip[i]) { + vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]; + if (rmass) one = rmass[i]; + else one = mass[type[i]]; + vec2d[bin[i][0]][bin[i][1]] += one*vsq; + } + } + } else + for (i = 0; i < nlocal; i++) { + if (!skip[i]) { + vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]; + if (rmass) one = rmass[i]; + else one = mass[type[i]]; + array2d[bin[i][0]][bin[i][1]][m] += one*vsq;; + } + } + } else { + if (nvalues == 1) { + for (i = 0; i < nlocal; i++) { + if (!skip[i]) { + vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]; + if (rmass) one = rmass[i]; + else one = mass[type[i]]; + vec3d[bin[i][0]][bin[i][1]][bin[i][2]] += one*vsq; + } + } + } else + for (i = 0; i < nlocal; i++) { + if (!skip[i]) { + vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]; + if (rmass) one = rmass[i]; + else one = mass[type[i]]; + array3d[bin[i][0]][bin[i][1]][bin[i][2]][m] += one*vsq; + } + } + } + + if (biasflag) tbias->restore_bias_all(); + + // per-atom compute or fix or variable + // invoke compute if not previously invoked + // evaluate atom-style variable + + } else if (which[m] == ArgInfo::COMPUTE || which[m] == ArgInfo::FIX || + which[m] == ArgInfo::VARIABLE) { + double *ovector,**oarray; + + if (which[m] == ArgInfo::COMPUTE) { + Compute *compute = modify->compute[n]; + if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) { + compute->compute_peratom(); + compute->invoked_flag |= Compute::INVOKED_PERATOM; + } + if (j == 0) ovector = compute->vector_atom; + else oarray = compute->array_atom; + + } else if (which[m] == ArgInfo::FIX) { + Fix *fix = modify->fix[n]; + if (j == 0) ovector = fix->vector_atom; + else oarray = fix->array_atom; + } else if (which[m] == ArgInfo::VARIABLE) { + if (nlocal > maxvar) { + memory->destroy(vresult); + maxvar = atom->nmax; + memory->create(vresult,maxvar,"ave/grid:vresult"); + } + input->variable->compute_atom(n,igroup,vresult,1,0); + ovector = vresult; + } + + if (dimension == 2) { + if (nvalues == 1) { + if (j == 0) { + for (i = 0; i < nlocal; i++) { + if (!skip[i]) + vec2d[bin[i][0]][bin[i][1]] += ovector[i]; + } + } else { + int jm1 = j = 1; + for (i = 0; i < nlocal; i++) { + if (!skip[i]) + vec2d[bin[i][0]][bin[i][1]] += oarray[i][jm1]; + } + } + } else { + if (j == 0) { + for (i = 0; i < nlocal; i++) { + if (!skip[i]) + array2d[bin[i][0]][bin[i][1]][m] += ovector[i]; + } + } else { + int jm1 = j - 1; + for (i = 0; i < nlocal; i++) { + if (!skip[i]) + array2d[bin[i][0]][bin[i][1]][m] += oarray[i][jm1]; + } + } + } + + } else { + if (nvalues == 1) { + if (j == 0) { + for (i = 0; i < nlocal; i++) { + if (!skip[i]) + vec3d[bin[i][0]][bin[i][1]][bin[i][2]] += ovector[i]; + } + } else { + int jm1 = j - 1; + for (i = 0; i < nlocal; i++) { + if (!skip[i]) + vec3d[bin[i][0]][bin[i][1]][bin[i][2]] += oarray[i][jm1]; + } + } + } else { + if (j == 0) { + for (i = 0; i < nlocal; i++) { + if (!skip[i]) + array3d[bin[i][0]][bin[i][1]][bin[i][2]][m] += ovector[i]; + } + } else { + int jm1 = j - 1; + for (i = 0; i < nlocal; i++) { + if (!skip[i]) + array3d[bin[i][0]][bin[i][1]][bin[i][2]][m] += oarray[i][jm1]; + } + } + } + } + } + } +} + +/* ---------------------------------------------------------------------- + copy per-grid values from other computes/fixes to owned grid cells + sets one of vec2d,array2d,vec3d,array3d +------------------------------------------------------------------------- */ + +void FixAveGrid::grid2grid() +{ + int j,m,n,ix,iy,iz; + + double **vec2d = grid_sample->vec2d; + double ***array2d = grid_sample->array2d; + double ***vec3d = grid_sample->vec3d; + double ****array3d = grid_sample->array3d; + + // loop over user-specified values + + for (m = 0; m < nvalues; m++) { + n = value2index[m]; + j = argindex[m]; + int idata = value2data[m]; + + Compute *compute; + Fix *fix; + + if (which[m] == ArgInfo::COMPUTE) { + compute = modify->compute[n]; + if (!(compute->invoked_flag & Compute::INVOKED_PERGRID)) { + compute->compute_pergrid(); + compute->invoked_flag |= Compute::INVOKED_PERGRID; + } + } else if (which[m] == ArgInfo::FIX) fix = modify->fix[n]; + + if (dimension == 2) { + double **ovec2d,***oarray2d; + if (which[m] == ArgInfo::COMPUTE) { + if (j == 0) + ovec2d = (double **) compute->get_griddata_by_index(idata); + else + oarray2d = (double ***) compute->get_griddata_by_index(idata); + } else { + if (j == 0) + ovec2d = (double **) fix->get_griddata_by_index(idata); + else + oarray2d = (double ***) fix->get_griddata_by_index(idata); + } + + if (nvalues == 1) { + if (j == 0) { + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + vec2d[iy][ix] += ovec2d[iy][ix]; + } else { + int jm1 = j - 1; + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + vec2d[iy][ix] += oarray2d[iy][ix][jm1]; + } + } else { + if (j == 0) { + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + array2d[iy][ix][m] += ovec2d[iy][ix]; + } else { + int jm1 = j - 1; + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + array2d[iy][ix][m] += oarray2d[iy][ix][jm1]; + } + } + + } else { + double ***ovec3d,****oarray3d; + if (which[m] == ArgInfo::COMPUTE) { + if (j == 0) + ovec3d = (double ***) compute->get_griddata_by_index(idata); + else + oarray3d = (double ****) compute->get_griddata_by_index(idata); + } else { + if (j == 0) { + ovec3d = (double ***) fix->get_griddata_by_index(idata); + } else + oarray3d = (double ****) fix->get_griddata_by_index(idata); + } + + if (nvalues == 1) { + if (j == 0) { + for (iz = nzlo_in; iz <= nzhi_in; iz++) + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + vec3d[iz][iy][ix] += ovec3d[iz][iy][ix]; + } else { + int jm1 = j - 1; + for (iz = nzlo_in; iz <= nzhi_in; iz++) + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + vec3d[iz][iy][ix] += oarray3d[iz][iy][ix][jm1]; + } + } else { + if (j == 0) { + for (iz = nzlo_in; iz <= nzhi_in; iz++) + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + array3d[iz][iy][ix][m] += ovec3d[iz][iy][ix]; + } else { + int jm1 = j - 1; + for (iz = nzlo_in; iz <= nzhi_in; iz++) + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + array3d[iz][iy][ix][m] += oarray3d[iz][iy][ix][jm1]; + } + } + } + } +} + +/* ---------------------------------------------------------------------- + normalize grid values for ATOM mode for owned cells + grid values are summed over numsamples (can be 1 or Nrepeat) + result = sample_value / count + exception is DENSITY_NUMBER: + result = value / (current binvol * Nrepeat) + exception is DENSITY_MASS: + result = (value * mv2d) / (current binvol * Nrepeat) + exception is TEMPERATURE: + result = (value * mvv2e) / (Nrepeat*cdof + adof*count) * boltz) + exception normalization is same for norm = ALL, SAMPLE, NONORM + so NONORM if test is after exception if tests +------------------------------------------------------------------------- */ + +void FixAveGrid::normalize_atom(int numsamples, GridData *grid) +{ + int ix,iy,iz,m; + double count,norm; + + double mvv2e = force->mvv2e; + double mv2d = force->mv2d; + double boltz = force->boltz; + + double *prd = domain->prd; + double dx = prd[0]/nxgrid; + double dy = prd[1]/nygrid; + double dz = prd[2]/nzgrid; + + double repeat = numsamples; + double invrepeat = 1.0/repeat; + + double binvol; + if (dimension == 2) binvol = dx*dy; + else binvol = dx*dy*dz; + + double density_number_norm = 1.0 / (binvol * repeat); + double density_mass_norm = mv2d / (binvol * repeat); + + if (dimension == 2) { + double **count2d = grid->count2d; + + if (nvalues == 1) { + double **vec2d = grid->vec2d; + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) { + count = count2d[iy][ix]; + if (count) { + if (which[0] == ArgInfo::DENSITY_NUMBER) + norm = density_number_norm; + else if (which[0] == ArgInfo::DENSITY_MASS) + norm = density_mass_norm; + else if (which[0] == ArgInfo::TEMPERATURE) + norm = mvv2e / ((repeat*cdof + adof*count) * boltz); + else if (normflag == NONORM) + norm = invrepeat; + else + norm = 1.0/count; + vec2d[iy][ix] *= norm; + } + } + + } else { + double ***array2d = grid->array2d; + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) { + count = count2d[iy][ix]; + if (count) { + for (m = 0; m < nvalues; m++) { + if (which[m] == ArgInfo::DENSITY_NUMBER) + norm = density_number_norm; + else if (which[m] == ArgInfo::DENSITY_MASS) + norm = density_mass_norm; + else if (which[m] == ArgInfo::TEMPERATURE) + norm = mvv2e / ((repeat*cdof + adof*count) * boltz); + else if (normflag == NONORM) + norm = invrepeat; + else + norm = 1.0/count; + array2d[iy][ix][m] *= norm; + } + } + } + } + + } else if (dimension == 3) { + double ***count3d = grid->count3d; + + if (nvalues == 1) { + double ***vec3d = grid->vec3d; + for (iz = nzlo_in; iz <= nzhi_in; iz++) + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) { + count = count3d[iz][iy][ix]; + if (count) { + if (which[0] == ArgInfo::DENSITY_NUMBER) + norm = density_number_norm; + else if (which[0] == ArgInfo::DENSITY_MASS) + norm = density_mass_norm; + else if (which[0] == ArgInfo::TEMPERATURE) + norm = mvv2e / ((repeat*cdof + adof*count) * boltz); + else if (normflag == NONORM) + norm = invrepeat; + else + norm = 1.0/count; + vec3d[iz][iy][ix] *= norm; + } + } + + } else { + double ****array3d = grid->array3d; + for (iz = nzlo_in; iz <= nzhi_in; iz++) + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) { + count = count3d[iz][iy][ix]; + if (count) { + for (m = 0; m < nvalues; m++) { + if (which[m] == ArgInfo::DENSITY_NUMBER) + norm = density_number_norm; + else if (which[m] == ArgInfo::DENSITY_MASS) + norm = density_mass_norm; + else if (which[m] == ArgInfo::TEMPERATURE) + norm = mvv2e / ((repeat*cdof + adof*count) * boltz); + else if (normflag == NONORM) + norm = invrepeat; + else + norm = 1.0/count; + array3d[iz][iy][ix][m] *= norm; + } + } + } + } + } +} + +/* ---------------------------------------------------------------------- + normalize grid values by numsamples + used for ATOM MODE when norm = SAMPLE + used for GRID mode +------------------------------------------------------------------------- */ + +void FixAveGrid::normalize_grid(int numsamples, GridData *grid) +{ + int ix,iy,iz,m; + + double invrepeat = 1.0/numsamples; + + if (dimension == 2) { + if (nvalues == 1) { + double **vec2d = grid->vec2d; + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + vec2d[iy][ix] *= invrepeat; + } else { + double ***array2d = grid->array2d; + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + for (m = 0; m < nvalues; m++) + array2d[iy][ix][m] *= invrepeat; + } + + } else if (dimension == 3) { + if (nvalues == 1) { + double ***vec3d = grid->vec3d; + for (iz = nzlo_in; iz <= nzhi_in; iz++) + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + vec3d[iz][iy][ix] *= invrepeat; + } else { + double ****array3d = grid->array3d; + for (iz = nzlo_in; iz <= nzhi_in; iz++) + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + for (m = 0; m < nvalues; m++) + array3d[iz][iy][ix][m] *= invrepeat; + } + } +} + +/* ---------------------------------------------------------------------- + normalize grid counts by numsamples + used for ATOM mode +------------------------------------------------------------------------- */ + +void FixAveGrid::normalize_count(int numsamples, GridData *grid) +{ + int ix,iy,iz; + + double invrepeat = 1.0/numsamples; + + if (dimension == 2) { + double **count2d = grid->count2d; + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + count2d[iy][ix] *= invrepeat; + + } else if (dimension == 3) { + double ***count3d = grid->count3d; + for (iz = nzlo_in; iz <= nzhi_in; iz++) + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + count3d[iz][iy][ix] *= invrepeat; + } +} + +/* ---------------------------------------------------------------------- + allocate instance of Grid2d or Grid3d +------------------------------------------------------------------------- */ + +void FixAveGrid::allocate_grid() +{ + if (modeatom) maxdist = 0.5 * neighbor->skin; + else if (modegrid) maxdist = 0.0; + + if (dimension == 2) { + grid2d = new Grid2d(lmp, world, nxgrid, nygrid); + grid2d->set_distance(maxdist); + grid2d->setup_grid(nxlo_in, nxhi_in, nylo_in, nyhi_in, + nxlo_out, nxhi_out, nylo_out, nyhi_out); + + // ngrid_buf12 converted to nvalues + count + + grid2d->setup_comm(ngrid_buf1, ngrid_buf2); + ngrid_buf1 *= nvalues + 1; + ngrid_buf2 *= nvalues + 1; + + grid_buf1 = grid_buf2 = nullptr; + if (ngrid_buf1) memory->create(grid_buf1, ngrid_buf1, "ave/grid:grid_buf1"); + if (ngrid_buf2) memory->create(grid_buf2, ngrid_buf2, "ave/grid:grid_buf2"); + + ngridout = (nxhi_out - nxlo_out + 1) * (nyhi_out - nylo_out + 1); + + } else { + grid3d = new Grid3d(lmp, world, nxgrid, nygrid, nzgrid); + grid3d->set_distance(maxdist); + grid3d->setup_grid(nxlo_in, nxhi_in, nylo_in, nyhi_in, nzlo_in, nzhi_in, + nxlo_out, nxhi_out, nylo_out, nyhi_out, nzlo_out, nzhi_out); + + // ngrid_buf12 converted to nvalues + count + + grid3d->setup_comm(ngrid_buf1, ngrid_buf2); + ngrid_buf1 *= nvalues + 1; + ngrid_buf2 *= nvalues + 1; + + grid_buf1 = grid_buf2 = nullptr; + if (ngrid_buf1) memory->create(grid_buf1, ngrid_buf1, "ave/grid:grid_buf1"); + if (ngrid_buf2) memory->create(grid_buf2, ngrid_buf2, "ave/grid:grid_buf2"); + + ngridout = (nxhi_out - nxlo_out + 1) * (nyhi_out - nylo_out + 1) * + (nzhi_out - nzlo_out + 1); + } +} + +/* ---------------------------------------------------------------------- + allocate a data grid and zero its values + if ATOM mode, also allocate per-grid count +------------------------------------------------------------------------- */ + +FixAveGrid::GridData *FixAveGrid::allocate_one_grid() +{ + GridData *grid = new GridData(); + + grid->vec2d = nullptr; + grid->array2d = nullptr; + grid->count2d = nullptr; + grid->vec3d = nullptr; + grid->array3d = nullptr; + grid->count3d = nullptr; + + if (dimension == 2) { + if (nvalues == 1) + memory->create2d_offset(grid->vec2d, nylo_out, nyhi_out, + nxlo_out, nxhi_out, "ave/grid:vec2d"); + else + memory->create3d_offset_last(grid->array2d, nylo_out, nyhi_out, + nxlo_out, nxhi_out, + nvalues, "ave/grid:array3d"); + if (modeatom) + memory->create2d_offset(grid->count2d, nylo_out, nyhi_out, + nxlo_out, nxhi_out, "ave/grid:count2d"); + + } else if (dimension == 3) { + if (nvalues == 1) + memory->create3d_offset(grid->vec3d, nzlo_out, nzhi_out, nylo_out, + nyhi_out, nxlo_out, nxhi_out, "ave/grid:vec3d"); + else + memory->create4d_offset_last(grid->array3d, nzlo_out, nzhi_out, nylo_out, + nyhi_out, nxlo_out, nxhi_out, nvalues, + "ave/grid:array3d"); + if (modeatom) + memory->create3d_offset(grid->count3d, nzlo_out, nzhi_out, nylo_out, + nyhi_out, nxlo_out, nxhi_out, "ave/grid:count3d"); + } + + zero_grid(grid); + + return grid; +} + + +/* ---------------------------------------------------------------------- + create clone of a data grid + allocate a new grid and copy only the pointers from the source grid + used by reset_grid() to keep old data values until remap is complete +------------------------------------------------------------------------- */ + +FixAveGrid::GridData *FixAveGrid::clone_one_grid(GridData *src) +{ + GridData *grid = new GridData(); + + grid->vec2d = src->vec2d; + grid->array2d = src->array2d; + grid->count2d = src->count2d; + grid->vec3d = src->vec3d; + grid->array3d = src->array3d; + grid->count3d = src->count3d; + + return grid; +} + +/* ---------------------------------------------------------------------- + deallocate a data grid and all its memory + if ATOM mode, also deallocate per-grid count +------------------------------------------------------------------------- */ + +void FixAveGrid::deallocate_one_grid(GridData *grid, + int xoffset, int yoffset, int zoffset) +{ + if (dimension == 2) { + if (nvalues == 1) + memory->destroy2d_offset(grid->vec2d,yoffset,xoffset); + else + memory->destroy3d_offset_last(grid->array2d,yoffset,xoffset); + if (modeatom) + memory->destroy2d_offset(grid->count2d,yoffset,xoffset); + + } else if (dimension == 3) { + if (nvalues == 1) + memory->destroy3d_offset(grid->vec3d,zoffset,yoffset,xoffset); + else + memory->destroy4d_offset_last(grid->array3d,zoffset,yoffset,xoffset); + if (modeatom) + memory->destroy3d_offset(grid->count3d,zoffset,yoffset,xoffset); + } + + delete grid; +} + +/* ---------------------------------------------------------------------- + size of a data grid + if ATOM mode, also include per-grid count +------------------------------------------------------------------------- */ + +double FixAveGrid::size_grid(GridData * /*grid*/) +{ + int nper = nvalues; + if (modeatom) nper++; + + double bytes; + if (dimension == 2) + bytes = sizeof(double) * nper * (nxhi_out - nxlo_out + 1) * (nyhi_out - nylo_out + 1); + else + bytes = sizeof(double) * nper * (nxhi_out - nxlo_out + 1) * (nyhi_out - nylo_out + 1) * + (nzhi_out - nzlo_out + 1); + + return bytes; +} + +/* ---------------------------------------------------------------------- + zero values for a data grid including ghost cells + for ATOM mode, also zero per-grid count +------------------------------------------------------------------------- */ + +void FixAveGrid::zero_grid(GridData *grid) +{ + if (!ngridout) return; + + if (dimension == 2) { + if (nvalues == 1) + memset(&grid->vec2d[nylo_out][nxlo_out], 0, sizeof(double) * ngridout); + else + memset(&grid->array2d[nylo_out][nxlo_out][0], 0, sizeof(double) * ngridout * nvalues); + if (modeatom) memset(&grid->count2d[nylo_out][nxlo_out], 0, sizeof(double) * ngridout); + + } else { + if (nvalues == 1) + memset(&grid->vec3d[nzlo_out][nylo_out][nxlo_out], 0, sizeof(double) * ngridout); + else + memset(&grid->array3d[nzlo_out][nylo_out][nxlo_out][0], 0, sizeof(double)* ngridout * nvalues); + if (modeatom) + memset(&grid->count3d[nzlo_out][nylo_out][nxlo_out], 0, sizeof(double) * ngridout); + } +} + +/* ---------------------------------------------------------------------- + copy src grid values to result grid, just for owned grid cells + for ATOM mode, also copy per-grid count +------------------------------------------------------------------------- */ + +void FixAveGrid::copy_grid(GridData *src, GridData *result) +{ + int ix,iy,iz,m; + + if (!ngridout) return; + + if (dimension == 2) { + if (nvalues == 1) { + double **vsrc = src->vec2d; + double **vresult = result->vec2d; + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + vresult[iy][ix] = vsrc[iy][ix]; + } else { + double ***asrc = src->array2d; + double ***aresult = result->array2d; + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + for (m = 0; m < nvalues; m++) + aresult[iy][ix][m] = asrc[iy][ix][m]; + } + if (modeatom) { + double **csrc = src->count2d; + double **cresult = result->count2d; + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + cresult[iy][ix] = csrc[iy][ix]; + } + + } else if (dimension == 3) { + if (nvalues == 1) { + double ***vsrc = src->vec3d; + double ***vresult = result->vec3d; + for (iz = nzlo_in; iz <= nzhi_in; iz++) + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + vresult[iz][iy][ix] = vsrc[iz][iy][ix]; + } else { + double ****asrc = src->array3d; + double ****aresult = result->array3d; + for (iz = nzlo_in; iz <= nzhi_in; iz++) + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + for (m = 0; m < nvalues; m++) + aresult[iz][iy][ix][m] = asrc[iz][iy][ix][m]; + } + if (modeatom) { + double ***csrc = src->count3d; + double ***cresult = result->count3d; + for (iz = nzlo_in; iz <= nzhi_in; iz++) + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + cresult[iz][iy][ix] = csrc[iz][iy][ix]; + } + } +} + +/* ---------------------------------------------------------------------- + add values in src grid to result grid, just for owned grid cells + for ATOM mode, also sum per-grid count +------------------------------------------------------------------------- */ + +void FixAveGrid::add_grid(GridData *src, GridData *result) +{ + int ix,iy,iz,m; + + if (!ngridout) return; + + if (dimension == 2) { + if (nvalues == 1) { + double **vsrc = src->vec2d; + double **vresult = result->vec2d; + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + vresult[iy][ix] += vsrc[iy][ix]; + } else { + double ***asrc = src->array2d; + double ***aresult = result->array2d; + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + for (m = 0; m < nvalues; m++) + aresult[iy][ix][m] += asrc[iy][ix][m]; + } + if (modeatom) { + double **csrc = src->count2d; + double **cresult = result->count2d; + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + cresult[iy][ix] += csrc[iy][ix]; + } + + } else if (dimension == 3) { + if (nvalues == 1) { + double ***vsrc = src->vec3d; + double ***vresult = result->vec3d; + for (iz = nzlo_in; iz <= nzhi_in; iz++) + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + vresult[iz][iy][ix] += vsrc[iz][iy][ix]; + } else { + double ****asrc = src->array3d; + double ****aresult = result->array3d; + for (iz = nzlo_in; iz <= nzhi_in; iz++) + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + for (m = 0; m < nvalues; m++) + aresult[iz][iy][ix][m] += asrc[iz][iy][ix][m]; + } + if (modeatom) { + double ***csrc = src->count3d; + double ***cresult = result->count3d; + for (iz = nzlo_in; iz <= nzhi_in; iz++) + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + cresult[iz][iy][ix] += csrc[iz][iy][ix]; + } + } +} + +/* ---------------------------------------------------------------------- + subtact values in src grid from result grid, just for owned grid cells + for ATOM mode, also sum per-grid count +------------------------------------------------------------------------- */ + +void FixAveGrid::subtract_grid(GridData *src, GridData *result) +{ + int ix,iy,iz,m; + + if (!ngridout) return; + + if (dimension == 2) { + if (nvalues == 1) { + double **vsrc = src->vec2d; + double **vresult = result->vec2d; + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + vresult[iy][ix] -= vsrc[iy][ix]; + } else { + double ***asrc = src->array2d; + double ***aresult = result->array2d; + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + for (m = 0; m < nvalues; m++) + aresult[iy][ix][m] -= asrc[iy][ix][m]; + } + if (modeatom) { + double **csrc = src->count2d; + double **cresult = result->count2d; + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + cresult[iy][ix] -= csrc[iy][ix]; + } + + } else if (dimension == 3) { + if (nvalues == 1) { + double ***vsrc = src->vec3d; + double ***vresult = result->vec3d; + for (iz = nzlo_in; iz <= nzhi_in; iz++) + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + vresult[iz][iy][ix] -= vsrc[iz][iy][ix]; + } else { + double ****asrc = src->array3d; + double ****aresult = result->array3d; + for (iz = nzlo_in; iz <= nzhi_in; iz++) + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + for (m = 0; m < nvalues; m++) + aresult[iz][iy][ix][m] -= asrc[iz][iy][ix][m]; + } + if (modeatom) { + double ***csrc = src->count3d; + double ***cresult = result->count3d; + for (iz = nzlo_in; iz <= nzhi_in; iz++) + for (iy = nylo_in; iy <= nyhi_in; iy++) + for (ix = nxlo_in; ix <= nxhi_in; ix++) + cresult[iz][iy][ix] -= csrc[iz][iy][ix]; + } + } +} + +/* ---------------------------------------------------------------------- + set output grid pointers to src grid data + for ATOM mode, also set pointers to per-grid count +------------------------------------------------------------------------- */ + +void FixAveGrid::output_grid(GridData *src) +{ + if (dimension == 2) { + if (nvalues == 1) + grid_output->vec2d = src->vec2d; + else + grid_output->array2d = src->array2d; + if (modeatom) + grid_output->count2d = src->count2d; + + } else if (dimension == 3) { + if (nvalues == 1) + grid_output->vec3d = src->vec3d; + else + grid_output->array3d = src->array3d; + if (modeatom) + grid_output->count3d = src->count3d; + } +} + +/* ---------------------------------------------------------------------- + pack ghost values into buf to send to another proc + nvalues per grid point + count- + only invoked for ATOM mode +------------------------------------------------------------------------ */ + +void FixAveGrid::pack_reverse_grid(int /*which*/, void *vbuf, int nlist, int *list) +{ + int i,j,m; + + auto buf = (double *) vbuf; + double *count,*data,*values; + m = 0; + + if (dimension == 2) { + count = &grid_sample->count2d[nylo_out][nxlo_out]; + if (nvalues == 1) data = &grid_sample->vec2d[nylo_out][nxlo_out]; + else data = &grid_sample->array2d[nylo_out][nxlo_out][0]; + } else { + count = &grid_sample->count3d[nzlo_out][nylo_out][nxlo_out]; + if (nvalues == 1) data = &grid_sample->vec3d[nzlo_out][nylo_out][nxlo_out]; + else data = &grid_sample->array3d[nzlo_out][nylo_out][nxlo_out][0]; + } + + if (nvalues == 1) { + for (i = 0; i < nlist; i++) { + buf[m++] = count[list[i]]; + buf[m++] = data[list[i]]; + } + } else { + for (i = 0; i < nlist; i++) { + buf[m++] = count[list[i]]; + values = &data[nvalues*list[i]]; + for (j = 0; j < nvalues; j++) + buf[m++] = values[j]; + } + } +} + +/* ---------------------------------------------------------------------- + unpack another proc's ghost values from buf and add to own values + nvalues per grid point + count + only invoked for ATOM mode +------------------------------------------------------------------------- */ + +void FixAveGrid::unpack_reverse_grid(int /*which*/, void *vbuf, int nlist, int *list) +{ + int i,j,m; + + auto buf = (double *) vbuf; + double *count,*data,*values; + + if (dimension == 2) { + count = &grid_sample->count2d[nylo_out][nxlo_out]; + if (nvalues == 1) data = &grid_sample->vec2d[nylo_out][nxlo_out]; + else data = &grid_sample->array2d[nylo_out][nxlo_out][0]; + } else { + count = &grid_sample->count3d[nzlo_out][nylo_out][nxlo_out]; + if (nvalues == 1) data = &grid_sample->vec3d[nzlo_out][nylo_out][nxlo_out]; + else data = &grid_sample->array3d[nzlo_out][nylo_out][nxlo_out][0]; + } + + m = 0; + if (nvalues == 1) { + for (i = 0; i < nlist; i++) { + count[list[i]] += buf[m++]; + data[list[i]] += buf[m++]; + } + } else { + for (i = 0; i < nlist; i++) { + count[list[i]] += buf[m++]; + values = &data[nvalues*list[i]]; + for (j = 0; j < nvalues; j++) + values[j] += buf[m++]; + } + } +} + +/* ---------------------------------------------------------------------- + pack old grid values to buf to send to another proc + invoked for both GRID and ATOM mode +------------------------------------------------------------------------- */ + +void FixAveGrid::pack_remap_grid(int /*which*/, void *vbuf, int nlist, int *list) +{ + auto buf = (double *) vbuf; + + int running_flag = 0; + if (aveflag == RUNNING || aveflag == WINDOW) running_flag = 1; + int window_flag = 0; + if (aveflag == WINDOW) window_flag = 1; + + int m = 0; + for (int i = 0; i < nlist; i++) { + m += pack_one_grid(grid_sample_previous,list[i],&buf[m]); + m += pack_one_grid(grid_nfreq_previous,list[i],&buf[m]); + if (running_flag) m += pack_one_grid(grid_running_previous,list[i],&buf[m]); + if (window_flag) + for (int iwindow = 0; iwindow < nwindow; iwindow++) + m += pack_one_grid(grid_window_previous[iwindow],list[i],&buf[m]); + } +} + +/* ---------------------------------------------------------------------- + unpack received owned values from buf into new grid + invoked for both GRID and ATOM mode +------------------------------------------------------------------------- */ + +void FixAveGrid::unpack_remap_grid(int /*which*/, void *vbuf, int nlist, int *list) +{ + auto buf = (double *) vbuf; + + int running_flag = 0; + if (aveflag == RUNNING || aveflag == WINDOW) running_flag = 1; + int window_flag = 0; + if (aveflag == WINDOW) window_flag = 1; + + int m = 0; + for (int i = 0; i < nlist; i++) { + m += unpack_one_grid(&buf[m],grid_sample,list[i]); + m += unpack_one_grid(&buf[m],grid_nfreq,list[i]); + if (running_flag) m += unpack_one_grid(&buf[m],grid_running,list[i]); + if (window_flag) + for (int iwindow = 0; iwindow < nwindow; iwindow++) + m += unpack_one_grid(&buf[m],grid_window[iwindow],list[i]); + } +} + +/* ---------------------------------------------------------------------- + pack values for a single grid cell to buf + return number of values packed +------------------------------------------------------------------------- */ + +int FixAveGrid::pack_one_grid(GridData *grid, int index, double *buf) +{ + double *count,*data,*values; + + if (dimension == 2) { + count = &grid->count2d[nylo_out_previous][nxlo_out_previous]; + if (nvalues == 1) data = &grid->vec2d[nylo_out_previous][nxlo_out_previous]; + else data = &grid->array2d[nylo_out_previous][nxlo_out_previous][0]; + } else { + count = &grid->count3d[nzlo_out_previous][nylo_out_previous][nxlo_out_previous]; + if (nvalues == 1) data = &grid->vec3d[nzlo_out_previous][nylo_out_previous][nxlo_out_previous]; + else data = &grid->array3d[nzlo_out_previous][nylo_out_previous][nxlo_out_previous][0]; + } + + int m = 0; + if (modeatom) buf[m++] = count[index]; + if (nvalues == 1) buf[m++] = data[index]; + else { + values = &data[nvalues*index]; + for (int j = 0; j < nvalues; j++) + buf[m++] = values[j]; + } + + return m; +} + +/* ---------------------------------------------------------------------- + unpack values for a single grid cell from buf + return number of values unpacked +------------------------------------------------------------------------- */ + +int FixAveGrid::unpack_one_grid(double *buf, GridData *grid, int index) +{ + double *count,*data,*values; + + if (dimension == 2) { + count = &grid->count2d[nylo_out][nxlo_out]; + if (nvalues == 1) data = &grid->vec2d[nylo_out][nxlo_out]; + else data = &grid->array2d[nylo_out][nxlo_out][0]; + } else { + count = &grid->count3d[nzlo_out][nylo_out][nxlo_out]; + if (nvalues == 1) data = &grid->vec3d[nzlo_out][nylo_out][nxlo_out]; + else data = &grid->array3d[nzlo_out][nylo_out][nxlo_out][0]; + } + + int m = 0; + if (modeatom) count[index] = buf[m++]; + if (nvalues == 1) data[index] = buf[m++]; + else { + values = &data[nvalues*index]; + for (int j = 0; j < nvalues; j++) + values[j] = buf[m++]; + } + + return m; +} + +/* ---------------------------------------------------------------------- + subset of grid assigned to each proc may have changed + called by load balancer when proc subdomains are adjusted + persist per-grid data by performing a grid remap +------------------------------------------------------------------------- */ + +void FixAveGrid::reset_grid() +{ + // check if new grid partitioning is different on any proc + // if not, just return + + if (dimension == 2) { + int tmp[8]; + Grid2d *gridnew = new Grid2d(lmp, world, nxgrid, nygrid); + gridnew->set_distance(maxdist); + gridnew->setup_grid(tmp[0], tmp[1], tmp[2], tmp[3], + tmp[4], tmp[5], tmp[6], tmp[7]); + + if (grid2d->identical(gridnew)) { + delete gridnew; + return; + } else delete gridnew; + + } else { + + int tmp[12]; + Grid3d *gridnew = new Grid3d(lmp, world, nxgrid, nygrid, nzgrid); + gridnew->set_distance(maxdist); + gridnew->setup_grid(tmp[0], tmp[1], tmp[2], tmp[3], tmp[4], tmp[5], + tmp[6], tmp[7], tmp[8], tmp[9], tmp[10], tmp[11]); + + if (grid3d->identical(gridnew)) { + delete gridnew; + return; + } else delete gridnew; + } + + // for ATOM mode, perform ghost to owned grid comm for grid_sample + // necessary b/c remap will only communicate owned grid cell data + // so can't lose ghost data not yet summed to owned cells + // nvalues+1 includes atom count + + if (modeatom) { + if (dimension == 2) + grid2d->reverse_comm(Grid2d::FIX,this,0,nvalues+1,sizeof(double), + grid_buf1,grid_buf2,MPI_DOUBLE); + else + grid3d->reverse_comm(Grid3d::FIX,this,0,nvalues+1,sizeof(double), + grid_buf1,grid_buf2,MPI_DOUBLE); + } + + // deallocate local comm buffers b/c new ones will be allocated + + memory->destroy(grid_buf1); + memory->destroy(grid_buf2); + + // make copy of ptrs to grid data which needs to persist + + if (dimension == 2) grid2d_previous = grid2d; + else grid3d_previous = grid3d; + + nxlo_out_previous = nxlo_out; + nylo_out_previous = nylo_out; + nzlo_out_previous = nzlo_out; + + grid_sample_previous = clone_one_grid(grid_sample); + grid_nfreq_previous = clone_one_grid(grid_nfreq); + if (aveflag == RUNNING || aveflag == WINDOW) + grid_running_previous = clone_one_grid(grid_running); + if (aveflag == WINDOW) { + grid_window_previous = new GridData*[nwindow]; + for (int i = 0; i < nwindow; i++) + grid_window_previous[i] = clone_one_grid(grid_window[i]); + } + + delete grid_sample; + delete grid_nfreq; + if (aveflag == RUNNING || aveflag == WINDOW) delete grid_running; + if (aveflag == WINDOW) { + for (int i = 0; i < nwindow; i++) + delete grid_window[i]; + delete [] grid_window; + } + + // allocate grid instance and grid data for new decomposition + + allocate_grid(); + + grid_sample = allocate_one_grid(); + grid_nfreq = allocate_one_grid(); + if (aveflag == RUNNING || aveflag == WINDOW) grid_running = allocate_one_grid(); + if (aveflag == WINDOW) { + grid_window = new GridData*[nwindow]; + for (int i = 0; i < nwindow; i++) + grid_window[i] = allocate_one_grid(); + } + + // perform remap from previous decomp to new decomp + // nper = # of remapped values per grid cell + // depends on atom vs grid mode, and running/window options + + int nremap_buf1,nremap_buf2; + if (dimension == 2) + grid2d->setup_remap(grid2d_previous,nremap_buf1,nremap_buf2); + else + grid3d->setup_remap(grid3d_previous,nremap_buf1,nremap_buf2); + + int n = 2; // grid_sample & grid_nfreq + if (aveflag == RUNNING || aveflag == WINDOW) n++; // grid_running + if (aveflag == WINDOW) n += nwindow; // grid_window + int nper = n*nvalues; + if (modeatom) nper += n; + + double *remap_buf1 = nullptr; + double *remap_buf2 = nullptr; + if (nremap_buf1) memory->create(remap_buf1, nper*nremap_buf1, "ave/grid:remap_buf1"); + if (nremap_buf2) memory->create(remap_buf2, nper*nremap_buf2, "ave/grid:remap_buf2"); + + if (dimension == 2) + grid2d->remap(Grid2d::FIX,this,0,nper,sizeof(double),remap_buf1,remap_buf2,MPI_DOUBLE); + else + grid3d->remap(Grid3d::FIX,this,0,nper,sizeof(double),remap_buf1,remap_buf2,MPI_DOUBLE); + + memory->destroy(remap_buf1); + memory->destroy(remap_buf2); + + // delete grid instance and grid data for previous decomposition + + if (dimension == 2) delete grid2d_previous; + else delete grid3d_previous; + + deallocate_one_grid(grid_sample_previous,nxlo_out_previous,nylo_out_previous,nzlo_out_previous); + deallocate_one_grid(grid_nfreq_previous,nxlo_out_previous,nylo_out_previous,nzlo_out_previous); + if (aveflag == RUNNING || aveflag == WINDOW) + deallocate_one_grid(grid_running_previous,nxlo_out_previous,nylo_out_previous,nzlo_out_previous); + if (aveflag == WINDOW) { + for (int i = 0; i < nwindow; i++) + deallocate_one_grid(grid_window_previous[i],nxlo_out_previous,nylo_out_previous,nzlo_out_previous); + delete [] grid_window_previous; + } + + // set output data in case load balance fix comes after fix ave/grid + + output_grid(grid_nfreq); +} + +/* ---------------------------------------------------------------------- + return index of grid associated with name + this class can store M named grids, indexed 0 to M-1 + also set dim for 2d vs 3d grid + return -1 if grid name not found +------------------------------------------------------------------------- */ + +int FixAveGrid::get_grid_by_name(const std::string &name, int &dim) +{ + if (name == "grid") { + dim = dimension; + return 0; + } + + return -1; +} + +/* ---------------------------------------------------------------------- + return ptr to Grid data struct for grid with index + this class can store M named grids, indexed 0 to M-1 + return nullptr if index is invalid +------------------------------------------------------------------------- */ + +void *FixAveGrid::get_grid_by_index(int index) +{ + if (index == 0) { + if (dimension == 2) return grid2d; + else return grid3d; + } + + return nullptr; +} + +/* ---------------------------------------------------------------------- + return index of data associated with name in grid with index igrid + this class can store M named grids, indexed 0 to M-1 + each grid can store G named data sets, indexed 0 to G-1 + a data set name can be associated with multiple grids + set ncol for data set, 0 = vector, 1-N for array with N columns + vector = single value per grid pt, array = N values per grid pt + return -1 if data name not found +------------------------------------------------------------------------- */ + +int FixAveGrid::get_griddata_by_name(int igrid, const std::string &name, int &ncol) +{ + if ((igrid == 0) && (name == "data")) { + if (nvalues == 1) ncol = 0; + else ncol = nvalues; + return 0; + } + + // count is only produced for ATOM mode + + if (modeatom && (igrid == 0) && (name == "count")) { + ncol = 0; + return 1; + } + + return -1; +} + +/* ---------------------------------------------------------------------- + return ptr to multidim data array associated with index + this class can store G named data sets, indexed 0 to M-1 + return nullptr if index is invalid +------------------------------------------------------------------------- */ + +void *FixAveGrid::get_griddata_by_index(int index) +{ + if (index == 0) { + if (dimension == 2) { + if (nvalues == 1) return grid_output->vec2d; + else return grid_output->array2d; + } else { + if (nvalues == 1) return grid_output->vec3d; + else return grid_output->array3d; + } + } + if (index == 1) { + if (dimension == 2) return grid_output->count2d; + else return grid_output->count3d; + } + + return nullptr; +} + +/* ---------------------------------------------------------------------- + memory usage of local per-grid data +------------------------------------------------------------------------- */ + +double FixAveGrid::memory_usage() +{ + double bytes = 0.0; + + bytes += size_grid(grid_sample); + bytes += size_grid(grid_nfreq); + if (aveflag == RUNNING || aveflag == WINDOW) + bytes += size_grid(grid_running); + if (aveflag == WINDOW) + bytes += nwindow * size_grid(grid_window[0]); + + if (modeatom) { + bytes += sizeof(int) * maxatom * dimension; // bin array + bytes += sizeof(int) * maxatom; // skip vector + bytes += sizeof(double) * maxvar; // vresult for per-atom variable + } + + return bytes; +} + +/* ---------------------------------------------------------------------- + calculate nvalid = next step on which end_of_step does something + can be this timestep if multiple of nfreq and nrepeat = 1 + else backup from next multiple of nfreq +------------------------------------------------------------------------- */ + +bigint FixAveGrid::nextvalid() +{ + bigint nvalid = (update->ntimestep/pergrid_freq)*pergrid_freq + pergrid_freq; + if (nvalid-pergrid_freq == update->ntimestep && nrepeat == 1) + nvalid = update->ntimestep; + else + nvalid -= ((bigint)nrepeat-1)*nevery; + if (nvalid < update->ntimestep) nvalid += pergrid_freq; + return nvalid; +} diff --git a/src/fix_ave_grid.h b/src/fix_ave_grid.h new file mode 100644 index 0000000000..326adb9f0b --- /dev/null +++ b/src/fix_ave_grid.h @@ -0,0 +1,135 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS +// clang-format off +FixStyle(ave/grid,FixAveGrid); +// clang-format on +#else + +#ifndef LMP_FIX_AVE_GRID_H +#define LMP_FIX_AVE_GRID_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixAveGrid : public Fix { + public: + FixAveGrid(class LAMMPS *, int, char **); + ~FixAveGrid() override; + int setmask() override; + void init() override; + void setup(int) override; + void end_of_step() override; + + void pack_reverse_grid(int, void *, int, int *) override; + void unpack_reverse_grid(int, void *, int, int *) override; + void pack_remap_grid(int, void *, int, int *) override; + void unpack_remap_grid(int, void *, int, int *) override; + + void reset_grid() override; + + int get_grid_by_name(const std::string &, int &) override; + void *get_grid_by_index(int) override; + int get_griddata_by_name(int, const std::string &, int &) override; + void *get_griddata_by_index(int) override; + + double memory_usage() override; + + private: + int nxgrid,nygrid,nzgrid; + int nvalues; + int nrepeat, irepeat; + bigint nvalid, nvalid_last; + int modeatom, modegrid; + int discardflag, normflag, aveflag, nwindow; + + double maxdist; + int running_count; + int window_count,window_oldest,window_newest; + + int biasflag; + char *id_bias; + class Compute *tbias; // ptr to additional bias compute + double adof,cdof; + + int dimension,triclinic; + + int *which, *argindex; + char **ids; + int *value2index, *value2grid, *value2data; + + class Grid2d *grid2d; + class Grid3d *grid3d; + int ngrid_buf1, ngrid_buf2; + double *grid_buf1, *grid_buf2; + + int nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in; + int nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out; + int ngridout; + + struct GridData { + double **vec2d,***vec3d; + double ***array2d,****array3d; + double **count2d,***count3d; + }; + + GridData *grid_output; + GridData *grid_sample,*grid_nfreq,*grid_running; + GridData **grid_window; + + // old grid data for remap operation + + class Grid2d *grid2d_previous; + class Grid3d *grid3d_previous; + int nxlo_out_previous,nylo_out_previous,nzlo_out_previous; + GridData *grid_sample_previous,*grid_nfreq_previous,*grid_running_previous; + GridData **grid_window_previous; + + int **bin; + int *skip; + int maxatom; + + double *vresult; + int maxvar; + + void atom2grid(); + void grid2grid(); + + void normalize_atom(int, GridData *); + void normalize_grid(int, GridData *); + void normalize_count(int, GridData *); + + void allocate_grid(); + GridData *allocate_one_grid(); + GridData *clone_one_grid(GridData *); + void deallocate_one_grid(GridData *, int, int, int); + + int pack_one_grid(GridData *, int, double *); + int unpack_one_grid(double *, GridData *, int); + + double size_grid(GridData *); + void zero_grid(GridData *); + void copy_grid(GridData *, GridData *); + void add_grid(GridData *, GridData *); + void subtract_grid(GridData *, GridData *); + void output_grid(GridData *); + + bigint nextvalid(); +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp index c2acd652ad..157e43610a 100644 --- a/src/fix_ave_histo.cpp +++ b/src/fix_ave_histo.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -16,6 +16,7 @@ #include "arg_info.h" #include "atom.h" +#include "comm.h" #include "compute.h" #include "error.h" #include "input.h" @@ -29,29 +30,24 @@ using namespace LAMMPS_NS; using namespace FixConst; -enum{ONE,RUNNING}; -enum{SCALAR,VECTOR,WINDOW}; -enum{DEFAULT,GLOBAL,PERATOM,LOCAL}; -enum{IGNORE,END,EXTRA}; - +enum { ONE, RUNNING }; +enum { SCALAR, VECTOR, WINDOW }; +enum { DEFAULT, GLOBAL, PERATOM, LOCAL }; +enum { IGNORE, END, EXTRA }; #define BIG 1.0e20 /* ---------------------------------------------------------------------- */ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg), - nvalues(0), which(nullptr), argindex(nullptr), value2index(nullptr), - ids(nullptr), fp(nullptr), stats_list(nullptr), - bin(nullptr), bin_total(nullptr), bin_all(nullptr), bin_list(nullptr), - coord(nullptr), vector(nullptr) + Fix(lmp, narg, arg), nvalues(0), fp(nullptr), stats_list(nullptr), bin(nullptr), + bin_total(nullptr), bin_all(nullptr), bin_list(nullptr), coord(nullptr), vector(nullptr) { - if (narg < 10) error->all(FLERR,"Illegal fix ave/histo command"); + auto mycmd = fmt::format("fix {}", style); + if (narg < 10) utils::missing_cmd_args(FLERR, mycmd, error); - MPI_Comm_rank(world,&me); - - nevery = utils::inumeric(FLERR,arg[3],false,lmp); - nrepeat = utils::inumeric(FLERR,arg[4],false,lmp); - nfreq = utils::inumeric(FLERR,arg[5],false,lmp); + nevery = utils::inumeric(FLERR, arg[3], false, lmp); + nrepeat = utils::inumeric(FLERR, arg[4], false, lmp); + nfreq = utils::inumeric(FLERR, arg[5], false, lmp); global_freq = nfreq; vector_flag = 1; @@ -63,9 +59,9 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) : dynamic_group_allow = 1; time_depend = 1; - lo = utils::numeric(FLERR,arg[6],false,lmp); - hi = utils::numeric(FLERR,arg[7],false,lmp); - nbins = utils::inumeric(FLERR,arg[8],false,lmp); + lo = utils::numeric(FLERR, arg[6], false, lmp); + hi = utils::numeric(FLERR, arg[7], false, lmp); + nbins = utils::inumeric(FLERR, arg[8], false, lmp); // scan values to count them // then read options so know mode = SCALAR/VECTOR before re-reading values @@ -91,7 +87,7 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) : } else break; } - if (nvalues == 0) error->all(FLERR,"No values in fix ave/histo command"); + if (nvalues == 0) error->all(FLERR,"No values in {} command", mycmd); options(iarg,narg,arg); @@ -100,70 +96,65 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) : int expand = 0; char **earg; - nvalues = utils::expand_args(FLERR,nvalues,&arg[9],mode,earg,lmp); + nvalues = utils::expand_args(FLERR, nvalues, &arg[9], mode, earg, lmp); if (earg != &arg[9]) expand = 1; arg = earg; // parse values - which = new int[nvalues]; - argindex = new int[nvalues]; - value2index = new int[nvalues]; - ids = new char*[nvalues]; + values.clear(); for (int i = 0; i < nvalues; i++) { + value_t val; + val.id = ""; + val.val.c = nullptr; + if (strcmp(arg[i],"x") == 0) { - which[i] = ArgInfo::X; - argindex[i] = 0; - ids[i] = nullptr; + val.which = ArgInfo::X; + val.argindex = 0; } else if (strcmp(arg[i],"y") == 0) { - which[i] = ArgInfo::X; - argindex[i] = 1; - ids[i] = nullptr; + val.which = ArgInfo::X; + val.argindex = 1; } else if (strcmp(arg[i],"z") == 0) { - which[i] = ArgInfo::X; - argindex[i] = 2; - ids[i] = nullptr; + val.which = ArgInfo::X; + val.argindex = 2; } else if (strcmp(arg[i],"vx") == 0) { - which[i] = ArgInfo::V; - argindex[i] = 0; - ids[i] = nullptr; + val.which = ArgInfo::V; + val.argindex = 0; } else if (strcmp(arg[i],"vy") == 0) { - which[i] = ArgInfo::V; - argindex[i] = 1; - ids[i] = nullptr; + val.which = ArgInfo::V; + val.argindex = 1; } else if (strcmp(arg[i],"vz") == 0) { - which[i] = ArgInfo::V; - argindex[i] = 2; - ids[i] = nullptr; + val.which = ArgInfo::V; + val.argindex = 2; } else if (strcmp(arg[i],"fx") == 0) { - which[i] = ArgInfo::F; - argindex[i] = 0; - ids[i] = nullptr; + val.which = ArgInfo::F; + val.argindex = 0; } else if (strcmp(arg[i],"fy") == 0) { - which[i] = ArgInfo::F; - argindex[i] = 1; - ids[i] = nullptr; + val.which = ArgInfo::F; + val.argindex = 1; } else if (strcmp(arg[i],"fz") == 0) { - which[i] = ArgInfo::F; - argindex[i] = 2; - ids[i] = nullptr; + val.which = ArgInfo::F; + val.argindex = 2; } else { ArgInfo argi(arg[i]); if (argi.get_type() == ArgInfo::NONE) break; if ((argi.get_type() == ArgInfo::UNKNOWN) || (argi.get_dim() > 1)) - error->all(FLERR,"Invalid fix ave/histo command"); + error->all(FLERR,"Invalid {} argument: {}", mycmd, arg[i]); - which[i] = argi.get_type(); - argindex[i] = argi.get_index1(); - ids[i] = argi.copy_name(); + val.which = argi.get_type(); + val.argindex = argi.get_index1(); + val.id = argi.get_name(); } + values.push_back(val); } + if (nvalues != (int)values.size()) + error->all(FLERR, "Could not parse value data consistently for {}", mycmd); // if wildcard expansion occurred, free earg memory from expand_args() @@ -175,69 +166,67 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) : // check input args for kind consistency // all inputs must all be global, per-atom, or local - if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0) - error->all(FLERR,"Illegal fix ave/histo command"); + if (nevery <= 0) + error->all(FLERR,"Illegal {} nevery value: {}", mycmd, nevery); + if (nrepeat <= 0) + error->all(FLERR,"Illegal {} nrepeat value: {}", mycmd, nrepeat); + if (nfreq <= 0) + error->all(FLERR,"Illegal {} nfreq value: {}", mycmd, nfreq); if (nfreq % nevery || nrepeat*nevery > nfreq) - error->all(FLERR,"Illegal fix ave/histo command"); - if (lo >= hi) error->all(FLERR,"Illegal fix ave/histo command"); - if (nbins <= 0) error->all(FLERR,"Illegal fix ave/histo command"); + error->all(FLERR,"Inconsistent {} nevery/nrepeat/nfreq values", mycmd); if (ave != RUNNING && overwrite) - error->all(FLERR,"Illegal fix ave/histo command"); + error->all(FLERR,"{} overwrite keyword requires ave running setting", mycmd); int kindglobal,kindperatom,kindlocal; - - for (int i = 0; i < nvalues; i++) { + for (auto &val : values) { kindglobal = kindperatom = kindlocal = 0; - if ((which[i] == ArgInfo::X) || (which[i] == ArgInfo::V) - || (which[i] == ArgInfo::F)) { + if ((val.which == ArgInfo::X) || (val.which == ArgInfo::V) || (val.which == ArgInfo::F)) { kindperatom = 1; - } else if (which[i] == ArgInfo::COMPUTE) { - int c_id = modify->find_compute(ids[i]); - if (c_id < 0) error->all(FLERR,"Fix ave/histo input is invalid compute"); - Compute *compute = modify->compute[c_id]; + } else if (val.which == ArgInfo::COMPUTE) { + val.val.c = modify->get_compute_by_id(val.id); + if (!val.val.c) error->all(FLERR,"Compute ID {} for {} does not exist", val.id, mycmd); // computes can produce multiple kinds of output - if (compute->scalar_flag || compute->vector_flag || compute->array_flag) + if (val.val.c->scalar_flag || val.val.c->vector_flag || val.val.c->array_flag) kindglobal = 1; - if (compute->peratom_flag) kindperatom = 1; - if (compute->local_flag) kindlocal = 1; + if (val.val.c->peratom_flag) kindperatom = 1; + if (val.val.c->local_flag) kindlocal = 1; - } else if (which[i] == ArgInfo::FIX) { - int f_id = modify->find_fix(ids[i]); - if (f_id < 0) error->all(FLERR,"Fix ave/histo input is invalid fix"); - Fix *fix = modify->fix[f_id]; + } else if (val.which == ArgInfo::FIX) { + val.val.f = modify->get_fix_by_id(val.id); + if (!val.val.f) error->all(FLERR,"Fix ID {} for {} does not exist", val.id, mycmd); // fixes can produce multiple kinds of output - if (fix->scalar_flag || fix->vector_flag || fix->array_flag) + if (val.val.f->scalar_flag || val.val.f->vector_flag || val.val.f->array_flag) kindglobal = 1; - if (fix->peratom_flag) kindperatom = 1; - if (fix->local_flag) kindlocal = 1; + if (val.val.f->peratom_flag) kindperatom = 1; + if (val.val.f->local_flag) kindlocal = 1; - } else if (which[i] == ArgInfo::VARIABLE) { - int ivariable = input->variable->find(ids[i]); - if (ivariable < 0) - error->all(FLERR,"Fix ave/histo input is invalid variable"); + } else if (val.which == ArgInfo::VARIABLE) { + val.val.v = input->variable->find(val.id.c_str()); + if (val.val.v < 0) + error->all(FLERR,"Variable name {} for {} does not exist", val.id, mycmd); // variables only produce one kind of output - if (input->variable->equalstyle(ivariable)) kindglobal = 1; - else if (input->variable->atomstyle(ivariable)) kindperatom = 1; - else error->all(FLERR,"Fix ave/histo input is invalid kind of variable"); + if (input->variable->equalstyle(val.val.v)) kindglobal = 1; + else if (input->variable->atomstyle(val.val.v)) kindperatom = 1; + else error->all(FLERR,"{} variable {} is incompatible style", mycmd, val.id); } if (kind == DEFAULT) { if (kindglobal + kindperatom + kindlocal > 1) - error->all(FLERR,"Fix ave/histo input kind is ambiguous"); + error->all(FLERR,"{} input kind is ambiguous", mycmd); if (kindglobal) kind = GLOBAL; if (kindperatom) kind = PERATOM; if (kindlocal) kind = LOCAL; } else if (kind == GLOBAL) { if (!kindglobal) - error->all(FLERR,"Fix ave/histo input kind is invalid"); + error->all(FLERR,"{} input kind is not global", mycmd); } else if (kind == PERATOM) { if (!kindperatom) - error->all(FLERR,"Fix ave/histo input kind is invalid"); + error->all(FLERR,"{} input kind is not peratom", mycmd); } else if (kind == LOCAL) { if (!kindlocal) - error->all(FLERR,"Fix ave/histo input kind is invalid"); + error->all(FLERR,"{} input kind is not local", mycmd); } } @@ -245,183 +234,112 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) : // for fix inputs, check that fix frequency is acceptable if (kind == PERATOM && mode == SCALAR) - error->all(FLERR, - "Fix ave/histo cannot input per-atom values in scalar mode"); + error->all(FLERR, "{} cannot process per-atom values in scalar mode", mycmd); if (kind == LOCAL && mode == SCALAR) - error->all(FLERR,"Fix ave/histo cannot input local values in scalar mode"); + error->all(FLERR,"{} cannot process local values in scalar mode", mycmd); - for (int i = 0; i < nvalues; i++) { - if (which[i] == ArgInfo::COMPUTE && kind == GLOBAL && mode == SCALAR) { - int icompute = modify->find_compute(ids[i]); - if (icompute < 0) - error->all(FLERR,"Compute ID for fix ave/histo does not exist"); - if (argindex[i] == 0 && modify->compute[icompute]->scalar_flag == 0) - error->all(FLERR, - "Fix ave/histo compute does not calculate a global scalar"); - if (argindex[i] && modify->compute[icompute]->vector_flag == 0) - error->all(FLERR, - "Fix ave/histo compute does not calculate a global vector"); - if (argindex[i] && argindex[i] > modify->compute[icompute]->size_vector) - error->all(FLERR, - "Fix ave/histo compute vector is accessed out-of-range"); + for (auto &val : values) { + if (val.which == ArgInfo::COMPUTE && kind == GLOBAL && mode == SCALAR) { + if (val.argindex == 0 && val.val.c->scalar_flag == 0) + error->all(FLERR, "{} compute {} does not calculate a global scalar", mycmd, val.id); + if (val.argindex && val.val.c->vector_flag == 0) + error->all(FLERR, "{} compute {} does not calculate a global vector", mycmd, val.id); + if (val.argindex && val.argindex > val.val.c->size_vector) + error->all(FLERR, "{} compute {} vector is accessed out-of-range", mycmd, val.id); - } else if (which[i] == ArgInfo::COMPUTE && kind == GLOBAL && mode == VECTOR) { - int icompute = modify->find_compute(ids[i]); - if (icompute < 0) - error->all(FLERR,"Compute ID for fix ave/histo does not exist"); - if (argindex[i] == 0 && modify->compute[icompute]->vector_flag == 0) - error->all(FLERR, - "Fix ave/histo compute does not calculate a global vector"); - if (argindex[i] && modify->compute[icompute]->array_flag == 0) - error->all(FLERR, - "Fix ave/histo compute does not calculate a global array"); - if (argindex[i] && - argindex[i] > modify->compute[icompute]->size_array_cols) - error->all(FLERR, - "Fix ave/histo compute array is accessed out-of-range"); + } else if (val.which == ArgInfo::COMPUTE && kind == GLOBAL && mode == VECTOR) { + if (val.argindex == 0 && val.val.c->vector_flag == 0) + error->all(FLERR, "{} compute {} does not calculate a global vector", mycmd, val.id); + if (val.argindex && val.val.c->array_flag == 0) + error->all(FLERR, "{} compute {} does not calculate a global array", mycmd, val.id); + if (val.argindex && val.argindex > val.val.c->size_array_cols) + error->all(FLERR, "{} compute {} array is accessed out-of-range", mycmd, val.id); - } else if (which[i] == ArgInfo::COMPUTE && kind == PERATOM) { - int icompute = modify->find_compute(ids[i]); - if (icompute < 0) - error->all(FLERR,"Compute ID for fix ave/histo does not exist"); - if (modify->compute[icompute]->peratom_flag == 0) - error->all(FLERR, - "Fix ave/histo compute does not calculate per-atom values"); - if (argindex[i] == 0 && - modify->compute[icompute]->size_peratom_cols != 0) - error->all(FLERR,"Fix ave/histo compute does not " - "calculate a per-atom vector"); - if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0) - error->all(FLERR,"Fix ave/histo compute does not " - "calculate a per-atom array"); - if (argindex[i] && - argindex[i] > modify->compute[icompute]->size_peratom_cols) - error->all(FLERR, - "Fix ave/histo compute array is accessed out-of-range"); + } else if (val.which == ArgInfo::COMPUTE && kind == PERATOM) { + if (val.val.c->peratom_flag == 0) + error->all(FLERR, "{} compute {} does not calculate per-atom values", mycmd, val.id); + if (val.argindex == 0 && val.val.c->size_peratom_cols != 0) + error->all(FLERR, "{} compute {} does not calculate a per-atom vector", mycmd, val.id); + if (val.argindex && val.val.c->size_peratom_cols == 0) + error->all(FLERR, "{} compute {} does not calculate a per-atom array", mycmd, val.id); + if (val.argindex && val.argindex > val.val.c->size_peratom_cols) + error->all(FLERR, "{} compute {} array is accessed out-of-range", mycmd, val.id); - } else if (which[i] == ArgInfo::COMPUTE && kind == LOCAL) { - int icompute = modify->find_compute(ids[i]); - if (icompute < 0) - error->all(FLERR,"Compute ID for fix ave/histo does not exist"); - if (modify->compute[icompute]->local_flag == 0) - error->all(FLERR, - "Fix ave/histo compute does not calculate local values"); - if (argindex[i] == 0 && - modify->compute[icompute]->size_local_cols != 0) - error->all(FLERR,"Fix ave/histo compute does not " - "calculate a local vector"); - if (argindex[i] && modify->compute[icompute]->size_local_cols == 0) - error->all(FLERR,"Fix ave/histo compute does not " - "calculate a local array"); - if (argindex[i] && - argindex[i] > modify->compute[icompute]->size_local_cols) - error->all(FLERR, - "Fix ave/histo compute array is accessed out-of-range"); + } else if (val.which == ArgInfo::COMPUTE && kind == LOCAL) { + if (val.val.c->local_flag == 0) + error->all(FLERR, "{} compute {} does not calculate local values", mycmd, val.id); + if (val.argindex == 0 && val.val.c->size_local_cols != 0) + error->all(FLERR, "{} compute {} does not calculate a local vector", mycmd, val.id); + if (val.argindex && val.val.c->size_local_cols == 0) + error->all(FLERR, "{} compute {} does not calculate a local array", mycmd, val.id); + if (val.argindex && val.argindex > val.val.c->size_local_cols) + error->all(FLERR, "{} compute {} array is accessed out-of-range", mycmd, val.id); - } else if (which[i] == ArgInfo::FIX && kind == GLOBAL && mode == SCALAR) { - int ifix = modify->find_fix(ids[i]); - if (ifix < 0) - error->all(FLERR,"Fix ID for fix ave/histo does not exist"); - if (argindex[i] == 0 && modify->fix[ifix]->scalar_flag == 0) - error->all(FLERR, - "Fix ave/histo fix does not calculate a global scalar"); - if (argindex[i] && modify->fix[ifix]->vector_flag == 0) - error->all(FLERR, - "Fix ave/histo fix does not calculate a global vector"); - if (argindex[i] && argindex[i] > modify->fix[ifix]->size_vector) - error->all(FLERR,"Fix ave/histo fix vector is accessed out-of-range"); - if (nevery % modify->fix[ifix]->global_freq) - error->all(FLERR, - "Fix for fix ave/histo not computed at compatible time"); + } else if (val.which == ArgInfo::FIX && kind == GLOBAL && mode == SCALAR) { + if (val.argindex == 0 && val.val.f->scalar_flag == 0) + error->all(FLERR, "{} fix {} does not calculate a global scalar", mycmd, val.id); + if (val.argindex && val.val.f->vector_flag == 0) + error->all(FLERR, "{} fix {} does not calculate a global vector", mycmd, val.id); + if (val.argindex && val.argindex > val.val.f->size_vector) + error->all(FLERR, "{} fix {} vector is accessed out-of-range", mycmd, val.id); + if (nevery % val.val.f->global_freq) + error->all(FLERR, "Fix {} for {} not computed at compatible time", val.id, mycmd); - } else if (which[i] == ArgInfo::FIX && kind == GLOBAL && mode == VECTOR) { - int ifix = modify->find_fix(ids[i]); - if (ifix < 0) - error->all(FLERR,"Fix ID for fix ave/histo does not exist"); - if (argindex[i] == 0 && modify->fix[ifix]->vector_flag == 0) - error->all(FLERR, - "Fix ave/histo fix does not calculate a global vector"); - if (argindex[i] && modify->fix[ifix]->array_flag == 0) - error->all(FLERR,"Fix ave/histo fix does not calculate a global array"); - if (argindex[i] && argindex[i] > modify->fix[ifix]->size_array_cols) - error->all(FLERR,"Fix ave/histo fix array is accessed out-of-range"); - if (nevery % modify->fix[ifix]->global_freq) - error->all(FLERR, - "Fix for fix ave/histo not computed at compatible time"); + } else if (val.which == ArgInfo::FIX && kind == GLOBAL && mode == VECTOR) { + if (val.argindex == 0 && val.val.f->vector_flag == 0) + error->all(FLERR, "{} fix {} does not calculate a global vector", mycmd, val.id); + if (val.argindex && val.val.f->array_flag == 0) + error->all(FLERR, "{} fix {} does not calculate a global array", mycmd, val.id); + if (val.argindex && val.argindex > val.val.f->size_array_cols) + error->all(FLERR, "{} fix {} array is accessed out-of-range", mycmd, val.id); + if (nevery % val.val.f->global_freq) + error->all(FLERR, "Fix {} for {} not computed at compatible time", val.id, mycmd); - } else if (which[i] == ArgInfo::FIX && kind == PERATOM) { - int ifix = modify->find_fix(ids[i]); - if (ifix < 0) - error->all(FLERR,"Fix ID for fix ave/histo does not exist"); - if (modify->fix[ifix]->peratom_flag == 0) - error->all(FLERR, - "Fix ave/histo fix does not calculate per-atom values"); - if (argindex[i] == 0 && - modify->fix[ifix]->size_peratom_cols != 0) - error->all(FLERR,"Fix ave/histo fix does not " - "calculate a per-atom vector"); - if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0) - error->all(FLERR,"Fix ave/histo fix does not " - "calculate a per-atom array"); - if (argindex[i] && - argindex[i] > modify->fix[ifix]->size_peratom_cols) - error->all(FLERR,"Fix ave/histo fix array is accessed out-of-range"); - if (nevery % modify->fix[ifix]->global_freq) - error->all(FLERR, - "Fix for fix ave/histo not computed at compatible time"); + } else if (val.which == ArgInfo::FIX && kind == PERATOM) { + if (val.val.f->peratom_flag == 0) + error->all(FLERR, "{} fix {} does not calculate per-atom values", mycmd, val.id); + if (val.argindex == 0 && val.val.f->size_peratom_cols != 0) + error->all(FLERR," {} fix {} does not calculate a per-atom vector", mycmd, val.id); + if (val.argindex && val.val.f->size_peratom_cols == 0) + error->all(FLERR, "{} fix {} does not ""calculate a per-atom array", mycmd, val.id); + if (val.argindex && val.argindex > val.val.f->size_peratom_cols) + error->all(FLERR, "{} fix {} array is accessed out-of-range", mycmd, val.id); + if (nevery % val.val.f->global_freq) + error->all(FLERR, "Fix {} for {} not computed at compatible time", val.id, mycmd); - } else if (which[i] == ArgInfo::FIX && kind == LOCAL) { - int ifix = modify->find_fix(ids[i]); - if (ifix < 0) - error->all(FLERR,"Fix ID for fix ave/histo does not exist"); - if (modify->fix[ifix]->local_flag == 0) - error->all(FLERR,"Fix ave/histo fix does not calculate local values"); - if (argindex[i] == 0 && - modify->fix[ifix]->size_local_cols != 0) - error->all(FLERR,"Fix ave/histo fix does not " - "calculate a local vector"); - if (argindex[i] && modify->fix[ifix]->size_local_cols == 0) - error->all(FLERR,"Fix ave/histo fix does not " - "calculate a local array"); - if (argindex[i] && - argindex[i] > modify->fix[ifix]->size_local_cols) - error->all(FLERR,"Fix ave/histo fix array is accessed out-of-range"); - if (nevery % modify->fix[ifix]->global_freq) - error->all(FLERR, - "Fix for fix ave/histo not computed at compatible time"); + } else if (val.which == ArgInfo::FIX && kind == LOCAL) { + if (val.val.f->local_flag == 0) + error->all(FLERR, "{} fix {} does not calculate local values", mycmd, val.id); + if (val.argindex == 0 && val.val.f->size_local_cols != 0) + error->all(FLERR, "{} fix {} does not calculate a local vector", mycmd, val.id); + if (val.argindex && val.val.f->size_local_cols == 0) + error->all(FLERR, "{} fix does not calculate a local array", mycmd, val.id); + if (val.argindex && val.argindex > val.val.f->size_local_cols) + error->all(FLERR, "{} fix {} array is accessed out-of-range", mycmd, val.id); + if (nevery % val.val.f->global_freq) + error->all(FLERR, "Fix {} for {} not computed at compatible time", val.id, mycmd); - } else if (which[i] == ArgInfo::VARIABLE && kind == GLOBAL && mode == SCALAR) { - int ivariable = input->variable->find(ids[i]); - if (ivariable < 0) - error->all(FLERR,"Variable name for fix ave/histo does not exist"); - if (argindex[i] == 0 && input->variable->equalstyle(ivariable) == 0) - error->all(FLERR,"Fix ave/histo variable is not equal-style variable"); - if (argindex[i] && input->variable->vectorstyle(ivariable) == 0) - error->all(FLERR,"Fix ave/histo variable is not vector-style variable"); + } else if (val.which == ArgInfo::VARIABLE && kind == GLOBAL && mode == SCALAR) { + if (val.argindex == 0 && input->variable->equalstyle(val.val.v) == 0) + error->all(FLERR,"{} variable {} is not equal-style variable", mycmd, val.id); + if (val.argindex && input->variable->vectorstyle(val.val.v) == 0) + error->all(FLERR,"{} variable {} is not vector-style variable" , mycmd, val.id); - } else if (which[i] == ArgInfo::VARIABLE && kind == GLOBAL && mode == VECTOR) { - int ivariable = input->variable->find(ids[i]); - if (ivariable < 0) - error->all(FLERR,"Variable name for fix ave/histo does not exist"); - if (argindex[i] == 0 && input->variable->vectorstyle(ivariable) == 0) - error->all(FLERR,"Fix ave/histo variable is not vector-style variable"); - if (argindex[i]) - error->all(FLERR,"Fix ave/histo variable cannot be indexed"); + } else if (val.which == ArgInfo::VARIABLE && kind == GLOBAL && mode == VECTOR) { + if (val.argindex == 0 && input->variable->vectorstyle(val.val.v) == 0) + error->all(FLERR,"{} variable {} is not vector-style variable", mycmd, val.id); + if (val.argindex) error->all(FLERR,"{} variable {} cannot be indexed", mycmd, val.id); - } else if (which[i] == ArgInfo::VARIABLE && kind == PERATOM) { - int ivariable = input->variable->find(ids[i]); - if (ivariable < 0) - error->all(FLERR,"Variable name for fix ave/histo does not exist"); - if (argindex[i] == 0 && input->variable->atomstyle(ivariable) == 0) - error->all(FLERR,"Fix ave/histo variable is not atom-style variable"); - if (argindex[i]) - error->all(FLERR,"Fix ave/histo variable cannot be indexed"); + } else if (val.which == ArgInfo::VARIABLE && kind == PERATOM) { + if (val.argindex == 0 && input->variable->atomstyle(val.val.v) == 0) + error->all(FLERR,"{} variable {} is not atom-style variable", mycmd, val.id); + if (val.argindex) error->all(FLERR,"{} variable {} cannot be indexed", mycmd, val.id); } } // print file comment lines - if (fp && me == 0) { + if (fp && comm->me == 0) { clearerr(fp); if (title1) fprintf(fp,"%s\n",title1); else fprintf(fp,"# Histogrammed data for fix %s\n",id); @@ -431,9 +349,7 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) : if (title3) fprintf(fp,"%s\n",title3); else fprintf(fp,"# Bin Coord Count Count/Total\n"); - if (ferror(fp)) - error->one(FLERR,"Error writing file header"); - + if (ferror(fp)) error->one(FLERR,"Error writing file header: {}", utils::getsyserror()); filepos = platform::ftell(fp); } @@ -502,13 +418,7 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) : FixAveHisto::~FixAveHisto() { - delete[] which; - delete[] argindex; - delete[] value2index; - for (int i = 0; i < nvalues; i++) delete[] ids[i]; - delete[] ids; - - if (fp && me == 0) fclose(fp); + if (fp && comm->me == 0) fclose(fp); delete[] bin; delete[] bin_total; @@ -532,26 +442,20 @@ int FixAveHisto::setmask() void FixAveHisto::init() { - // set current indices for all computes,fixes,variables + auto mycmd = fmt::format("fix {}", style); - for (int i = 0; i < nvalues; i++) { - if (which[i] == ArgInfo::COMPUTE) { - int icompute = modify->find_compute(ids[i]); - if (icompute < 0) - error->all(FLERR,"Compute ID for fix ave/histo does not exist"); - value2index[i] = icompute; + // update indices/pointers for all computes,fixes,variables - } else if (which[i] == ArgInfo::FIX) { - int ifix = modify->find_fix(ids[i]); - if (ifix < 0) - error->all(FLERR,"Fix ID for fix ave/histo does not exist"); - value2index[i] = ifix; - - } else if (which[i] == ArgInfo::VARIABLE) { - int ivariable = input->variable->find(ids[i]); - if (ivariable < 0) - error->all(FLERR,"Variable name for fix ave/histo does not exist"); - value2index[i] = ivariable; + for (auto &val : values) { + if (val.which == ArgInfo::COMPUTE) { + val.val.c = modify->get_compute_by_id(val.id); + if (!val.val.c) error->all(FLERR,"Compute ID {} for {} does not exist", val.id, mycmd); + } else if (val.which == ArgInfo::FIX) { + val.val.f = modify->get_fix_by_id(val.id); + if (!val.val.f) error->all(FLERR,"Fix ID {} for {} does not exist", val.id, mycmd); + } else if (val.which == ArgInfo::VARIABLE) { + val.val.v = input->variable->find(val.id.c_str()); + if (val.val.v < 0) error->all(FLERR,"Variable name {} for {} does not exist", val.id, mycmd); } } @@ -577,8 +481,6 @@ void FixAveHisto::setup(int /*vflag*/) void FixAveHisto::end_of_step() { - int i,j,m; - // skip if not step which requires doing something bigint ntimestep = update->ntimestep; @@ -591,7 +493,7 @@ void FixAveHisto::end_of_step() stats[0] = stats[1] = 0.0; stats[2] = BIG; stats[3] = -BIG; - for (i = 0; i < nbins; i++) bin[i] = 0.0; + for (int i = 0; i < nbins; i++) bin[i] = 0.0; } // accumulate results of computes,fixes,variables to local copy @@ -599,132 +501,128 @@ void FixAveHisto::end_of_step() modify->clearstep_compute(); - for (i = 0; i < nvalues; i++) { - m = value2index[i]; - j = argindex[i]; + for (auto &val : values) { + int j = val.argindex; // atom attributes - if (which[i] == ArgInfo::X) + if (val.which == ArgInfo::X) bin_atoms(&atom->x[0][j],3); - else if (which[i] == ArgInfo::V) + else if (val.which == ArgInfo::V) bin_atoms(&atom->v[0][j],3); - else if (which[i] == ArgInfo::F) + else if (val.which == ArgInfo::F) bin_atoms(&atom->f[0][j],3); // invoke compute if not previously invoked - if (which[i] == ArgInfo::COMPUTE) { - Compute *compute = modify->compute[m]; + if (val.which == ArgInfo::COMPUTE) { if (kind == GLOBAL && mode == SCALAR) { if (j == 0) { - if (!(compute->invoked_flag & Compute::INVOKED_SCALAR)) { - compute->compute_scalar(); - compute->invoked_flag |= Compute::INVOKED_SCALAR; + if (!(val.val.c->invoked_flag & Compute::INVOKED_SCALAR)) { + val.val.c->compute_scalar(); + val.val.c->invoked_flag |= Compute::INVOKED_SCALAR; } - bin_one(compute->scalar); + bin_one(val.val.c->scalar); } else { - if (!(compute->invoked_flag & Compute::INVOKED_VECTOR)) { - compute->compute_vector(); - compute->invoked_flag |= Compute::INVOKED_VECTOR; + if (!(val.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { + val.val.c->compute_vector(); + val.val.c->invoked_flag |= Compute::INVOKED_VECTOR; } - bin_one(compute->vector[j-1]); + bin_one(val.val.c->vector[j-1]); } } else if (kind == GLOBAL && mode == VECTOR) { if (j == 0) { - if (!(compute->invoked_flag & Compute::INVOKED_VECTOR)) { - compute->compute_vector(); - compute->invoked_flag |= Compute::INVOKED_VECTOR; + if (!(val.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { + val.val.c->compute_vector(); + val.val.c->invoked_flag |= Compute::INVOKED_VECTOR; } - bin_vector(compute->size_vector,compute->vector,1); + bin_vector(val.val.c->size_vector,val.val.c->vector,1); } else { - if (!(compute->invoked_flag & Compute::INVOKED_ARRAY)) { - compute->compute_array(); - compute->invoked_flag |= Compute::INVOKED_ARRAY; + if (!(val.val.c->invoked_flag & Compute::INVOKED_ARRAY)) { + val.val.c->compute_array(); + val.val.c->invoked_flag |= Compute::INVOKED_ARRAY; } - if (compute->array) - bin_vector(compute->size_array_rows,&compute->array[0][j-1], - compute->size_array_cols); + if (val.val.c->array) + bin_vector(val.val.c->size_array_rows,&val.val.c->array[0][j-1], + val.val.c->size_array_cols); } } else if (kind == PERATOM) { - if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) { - compute->compute_peratom(); - compute->invoked_flag |= Compute::INVOKED_PERATOM; + if (!(val.val.c->invoked_flag & Compute::INVOKED_PERATOM)) { + val.val.c->compute_peratom(); + val.val.c->invoked_flag |= Compute::INVOKED_PERATOM; } if (j == 0) - bin_atoms(compute->vector_atom,1); - else if (compute->array_atom) - bin_atoms(&compute->array_atom[0][j-1],compute->size_peratom_cols); + bin_atoms(val.val.c->vector_atom,1); + else if (val.val.c->array_atom) + bin_atoms(&val.val.c->array_atom[0][j-1],val.val.c->size_peratom_cols); } else if (kind == LOCAL) { - if (!(compute->invoked_flag & Compute::INVOKED_LOCAL)) { - compute->compute_local(); - compute->invoked_flag |= Compute::INVOKED_LOCAL; + if (!(val.val.c->invoked_flag & Compute::INVOKED_LOCAL)) { + val.val.c->compute_local(); + val.val.c->invoked_flag |= Compute::INVOKED_LOCAL; } if (j == 0) - bin_vector(compute->size_local_rows,compute->vector_local,1); - else if (compute->array_local) - bin_vector(compute->size_local_rows,&compute->array_local[0][j-1], - compute->size_local_cols); + bin_vector(val.val.c->size_local_rows,val.val.c->vector_local,1); + else if (val.val.c->array_local) + bin_vector(val.val.c->size_local_rows,&val.val.c->array_local[0][j-1], + val.val.c->size_local_cols); } // access fix fields, guaranteed to be ready - } else if (which[i] == ArgInfo::FIX) { - - Fix *fix = modify->fix[m]; + } else if (val.which == ArgInfo::FIX) { if (kind == GLOBAL && mode == SCALAR) { - if (j == 0) bin_one(fix->compute_scalar()); - else bin_one(fix->compute_vector(j-1)); + if (j == 0) bin_one(val.val.f->compute_scalar()); + else bin_one(val.val.f->compute_vector(j-1)); } else if (kind == GLOBAL && mode == VECTOR) { if (j == 0) { - int n = fix->size_vector; - for (i = 0; i < n; i++) bin_one(fix->compute_vector(i)); + int n = val.val.f->size_vector; + for (int i = 0; i < n; i++) bin_one(val.val.f->compute_vector(i)); } else { - int n = fix->size_vector; - for (i = 0; i < n; i++) bin_one(fix->compute_array(i,j-1)); + int n = val.val.f->size_vector; + for (int i = 0; i < n; i++) bin_one(val.val.f->compute_array(i,j-1)); } } else if (kind == PERATOM) { - if (j == 0) bin_atoms(fix->vector_atom,1); - else if (fix->array_atom) - bin_atoms(fix->array_atom[j-1],fix->size_peratom_cols); + if (j == 0) bin_atoms(val.val.f->vector_atom,1); + else if (val.val.f->array_atom) + bin_atoms(val.val.f->array_atom[j-1],val.val.f->size_peratom_cols); } else if (kind == LOCAL) { - if (j == 0) bin_vector(fix->size_local_rows,fix->vector_local,1); - else if (fix->array_local) - bin_vector(fix->size_local_rows,&fix->array_local[0][j-1], - fix->size_local_cols); + if (j == 0) bin_vector(val.val.f->size_local_rows,val.val.f->vector_local,1); + else if (val.val.f->array_local) + bin_vector(val.val.f->size_local_rows,&val.val.f->array_local[0][j-1], + val.val.f->size_local_cols); } // evaluate equal-style or vector-style or atom-style variable - } else if (which[i] == ArgInfo::VARIABLE) { + } else if (val.which == ArgInfo::VARIABLE) { if (kind == GLOBAL && mode == SCALAR) { - if (j == 0) bin_one(input->variable->compute_equal(m)); + if (j == 0) bin_one(input->variable->compute_equal(val.val.v)); else { double *varvec; - int nvec = input->variable->compute_vector(m,&varvec); + int nvec = input->variable->compute_vector(val.val.v,&varvec); if (nvec < j) bin_one(0.0); else bin_one(varvec[j-1]); } } else if (kind == GLOBAL && mode == VECTOR) { double *varvec; - int nvec = input->variable->compute_vector(m,&varvec); + int nvec = input->variable->compute_vector(val.val.v,&varvec); bin_vector(nvec,varvec,1); - } else if (which[i] == ArgInfo::VARIABLE && kind == PERATOM) { + } else if (val.which == ArgInfo::VARIABLE && kind == PERATOM) { if (atom->nmax > maxatom) { memory->destroy(vector); maxatom = atom->nmax; memory->create(vector,maxatom,"ave/histo:vector"); } - input->variable->compute_atom(m,igroup,vector,1,0); + input->variable->compute_atom(val.val.v,igroup,vector,1,0); bin_atoms(vector,1); } } @@ -756,7 +654,7 @@ void FixAveHisto::end_of_step() stats[1] = stats_all[1]; stats[2] = stats_all[2]; stats[3] = stats_all[3]; - for (i = 0; i < nbins; i++) bin[i] = bin_all[i]; + for (int i = 0; i < nbins; i++) bin[i] = bin_all[i]; } // if ave = ONE, only single Nfreq timestep value is needed @@ -768,16 +666,17 @@ void FixAveHisto::end_of_step() stats_total[1] = stats[1]; stats_total[2] = stats[2]; stats_total[3] = stats[3]; - for (i = 0; i < nbins; i++) bin_total[i] = bin[i]; + for (int i = 0; i < nbins; i++) bin_total[i] = bin[i]; } else if (ave == RUNNING) { stats_total[0] += stats[0]; stats_total[1] += stats[1]; stats_total[2] = MIN(stats_total[2],stats[2]); stats_total[3] = MAX(stats_total[3],stats[3]); - for (i = 0; i < nbins; i++) bin_total[i] += bin[i]; + for (int i = 0; i < nbins; i++) bin_total[i] += bin[i]; } else if (ave == WINDOW) { + int m; stats_total[0] += stats[0]; if (window_limit) stats_total[0] -= stats_list[iwindow][0]; stats_list[iwindow][0] = stats[0]; @@ -790,14 +689,14 @@ void FixAveHisto::end_of_step() stats_list[iwindow][2] = stats[2]; stats_total[2] = stats_list[0][2]; - for (i = 1; i < m; i++) + for (int i = 1; i < m; i++) stats_total[2] = MIN(stats_total[2],stats_list[i][2]); stats_list[iwindow][3] = stats[3]; stats_total[3] = stats_list[0][3]; - for (i = 1; i < m; i++) + for (int i = 1; i < m; i++) stats_total[3] = MAX(stats_total[3],stats_list[i][3]); - for (i = 0; i < nbins; i++) { + for (int i = 0; i < nbins; i++) { bin_total[i] += bin[i]; if (window_limit) bin_total[i] -= bin_list[iwindow][i]; bin_list[iwindow][i] = bin[i]; @@ -812,17 +711,17 @@ void FixAveHisto::end_of_step() // output result to file - if (fp && me == 0) { + if (fp && comm->me == 0) { clearerr(fp); if (overwrite) platform::fseek(fp,filepos); fmt::print(fp,"{} {} {} {} {} {}\n",ntimestep,nbins, stats_total[0],stats_total[1],stats_total[2],stats_total[3]); if (stats_total[0] != 0.0) - for (i = 0; i < nbins; i++) + for (int i = 0; i < nbins; i++) fprintf(fp,"%d %g %g %g\n", i+1,coord[i],bin_total[i],bin_total[i]/stats_total[0]); else - for (i = 0; i < nbins; i++) + for (int i = 0; i < nbins; i++) fprintf(fp,"%d %g %g %g\n",i+1,coord[i],0.0,0.0); if (ferror(fp)) @@ -937,73 +836,74 @@ void FixAveHisto::options(int iarg, int narg, char **arg) title3 = nullptr; // optional args + auto mycmd = fmt::format("fix {}", style); while (iarg < narg) { if (strcmp(arg[iarg],"file") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/histo command"); - if (me == 0) { + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, mycmd + " file", error); + if (comm->me == 0) { fp = fopen(arg[iarg+1],"w"); if (fp == nullptr) - error->one(FLERR,"Cannot open fix ave/histo file {}: {}", - arg[iarg+1], utils::getsyserror()); + error->one(FLERR, "Cannot open fix ave/histo file {}: {}", + arg[iarg+1], utils::getsyserror()); } iarg += 2; } else if (strcmp(arg[iarg],"kind") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/histo command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, mycmd + " kind", error); if (strcmp(arg[iarg+1],"global") == 0) kind = GLOBAL; else if (strcmp(arg[iarg+1],"peratom") == 0) kind = PERATOM; else if (strcmp(arg[iarg+1],"local") == 0) kind = LOCAL; - else error->all(FLERR,"Illegal fix ave/histo command"); + else error->all(FLERR,"Unknown fix ave/histo kind option: {}", arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"ave") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/histo command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, mycmd + " ave", error); if (strcmp(arg[iarg+1],"one") == 0) ave = ONE; else if (strcmp(arg[iarg+1],"running") == 0) ave = RUNNING; else if (strcmp(arg[iarg+1],"window") == 0) ave = WINDOW; - else error->all(FLERR,"Illegal fix ave/histo command"); + else error->all(FLERR,"Unknown fix ave/histo ave option: {}", arg[iarg+1]); if (ave == WINDOW) { - if (iarg+3 > narg) error->all(FLERR,"Illegal fix ave/histo command"); + if (iarg+3 > narg) utils::missing_cmd_args(FLERR, mycmd + " ave window", error); nwindow = utils::inumeric(FLERR,arg[iarg+2],false,lmp); - if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/histo command"); + if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/histo ave window size: {}", nwindow); } iarg += 2; if (ave == WINDOW) iarg++; } else if (strcmp(arg[iarg],"start") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/histo command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, mycmd + " start", error); startstep = utils::inumeric(FLERR,arg[iarg+1],false,lmp); iarg += 2; } else if (strcmp(arg[iarg],"mode") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/histo command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, mycmd + " mode", error); if (strcmp(arg[iarg+1],"scalar") == 0) mode = SCALAR; else if (strcmp(arg[iarg+1],"vector") == 0) mode = VECTOR; - else error->all(FLERR,"Illegal fix ave/histo command"); + else error->all(FLERR,"Unknown fix ave/histo mode option: {}", arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"beyond") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/histo command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, mycmd + " beyond", error); if (strcmp(arg[iarg+1],"ignore") == 0) beyond = IGNORE; else if (strcmp(arg[iarg+1],"end") == 0) beyond = END; else if (strcmp(arg[iarg+1],"extra") == 0) beyond = EXTRA; - else error->all(FLERR,"Illegal fix ave/histo command"); + else error->all(FLERR,"Unknown fix ave/histo beyond option: {}", arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"overwrite") == 0) { overwrite = 1; iarg += 1; } else if (strcmp(arg[iarg],"title1") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/histo command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, mycmd + " title1", error); delete[] title1; title1 = utils::strdup(arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"title2") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/histo command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, mycmd + " title2", error); delete[] title2; title2 = utils::strdup(arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"title3") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/histo command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, mycmd + " title3", error); delete[] title3; title3 = utils::strdup(arg[iarg+1]); iarg += 2; - } else error->all(FLERR,"Illegal fix ave/histo command"); + } else error->all(FLERR,"Unknown {} option: {}", mycmd, arg[iarg]); } } diff --git a/src/fix_ave_histo.h b/src/fix_ave_histo.h index ed64c8562d..d112223dce 100644 --- a/src/fix_ave_histo.h +++ b/src/fix_ave_histo.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -36,11 +36,21 @@ class FixAveHisto : public Fix { double compute_array(int, int) override; protected: - int me, nvalues; - int nrepeat, nfreq, irepeat; + struct value_t { + int which; // type of data: COMPUTE, FIX, VARIABLE + int argindex; // 1-based index if data is vector, else 0 + std::string id; // compute/fix/variable ID + union { + class Compute *c; + class Fix *f; + int v; + } val; + }; + std::vector values; + + int nvalues, nrepeat, nfreq, irepeat; bigint nvalid, nvalid_last; - int *which, *argindex, *value2index; - char **ids; + FILE *fp; double lo, hi, binsize, bininv; int kind, beyond, overwrite; diff --git a/src/fix_ave_histo_weight.cpp b/src/fix_ave_histo_weight.cpp index f90551b52f..17dd00440e 100644 --- a/src/fix_ave_histo_weight.cpp +++ b/src/fix_ave_histo_weight.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -19,6 +19,7 @@ #include "arg_info.h" #include "atom.h" +#include "comm.h" #include "compute.h" #include "error.h" #include "fix.h" @@ -31,68 +32,61 @@ using namespace LAMMPS_NS; using namespace FixConst; -enum{ONE,RUNNING}; -enum{SCALAR,VECTOR,WINDOW}; -enum{DEFAULT,GLOBAL,PERATOM,LOCAL}; -enum{IGNORE,END,EXTRA}; -enum{SINGLE,VALUE}; +enum { ONE, RUNNING }; +enum { SCALAR, VECTOR, WINDOW }; +enum { DEFAULT, GLOBAL, PERATOM, LOCAL }; +enum { IGNORE, END, EXTRA }; +enum { SINGLE, VALUE }; #define BIG 1.0e20 /* ---------------------------------------------------------------------- */ FixAveHistoWeight::FixAveHistoWeight(LAMMPS *lmp, int narg, char **arg) : - FixAveHisto(lmp, narg, arg) + FixAveHisto(lmp, narg, arg) { // nvalues = 2 required for histo/weight - if (nvalues != 2) error->all(FLERR,"Illegal fix ave/histo/weight command"); + if (nvalues != 2) + error->all(FLERR, "Illegal fix ave/histo/weight command: must have two data arguments"); // check that length of 2 values is the same - int size[2] = {0,0}; + int size[2] = {0, 0}; for (int i = 0; i < nvalues; i++) { - if (which[i] == ArgInfo::X || which[i] == ArgInfo::V || which[i] == ArgInfo::F) { + auto &val = values[i]; + if (val.which == ArgInfo::X || val.which == ArgInfo::V || val.which == ArgInfo::F) { size[i] = atom->nlocal; - } else if (which[i] == ArgInfo::COMPUTE && kind == GLOBAL && mode == SCALAR) { - int icompute = modify->find_compute(ids[i]); - size[i] = modify->compute[icompute]->size_vector; - } else if (which[i] == ArgInfo::COMPUTE && kind == GLOBAL && mode == VECTOR) { - int icompute = modify->find_compute(ids[i]); - size[i] = modify->compute[icompute]->size_array_rows; - } else if (which[i] == ArgInfo::COMPUTE && kind == PERATOM) { + } else if (val.which == ArgInfo::COMPUTE && kind == GLOBAL && mode == SCALAR) { + size[i] = val.val.c->size_vector; + } else if (val.which == ArgInfo::COMPUTE && kind == GLOBAL && mode == VECTOR) { + size[i] = val.val.c->size_array_rows; + } else if (val.which == ArgInfo::COMPUTE && kind == PERATOM) { size[i] = atom->nlocal; - } else if (which[i] == ArgInfo::COMPUTE && kind == LOCAL) { - int icompute = modify->find_compute(ids[i]); - size[i] = modify->compute[icompute]->size_local_rows; - } else if (which[i] == ArgInfo::FIX && kind == GLOBAL && mode == SCALAR) { - int ifix = modify->find_fix(ids[i]); - size[i] = modify->fix[ifix]->size_vector; - } else if (which[i] == ArgInfo::FIX && kind == GLOBAL && mode == VECTOR) { - int ifix = modify->find_fix(ids[i]); - size[i]= modify->fix[ifix]->size_array_rows; - } else if (which[i] == ArgInfo::FIX && kind == PERATOM) { + } else if (val.which == ArgInfo::COMPUTE && kind == LOCAL) { + size[i] = val.val.c->size_local_rows; + } else if (val.which == ArgInfo::FIX && kind == GLOBAL && mode == SCALAR) { + size[i] = val.val.f->size_vector; + } else if (val.which == ArgInfo::FIX && kind == GLOBAL && mode == VECTOR) { + size[i]= val.val.f->size_array_rows; + } else if (val.which == ArgInfo::FIX && kind == PERATOM) { size[i] = atom->nlocal; - } else if (which[i] == ArgInfo::FIX && kind == LOCAL) { - int ifix = modify->find_fix(ids[i]); - size[i] = modify->fix[ifix]->size_local_rows; - } else if (which[i] == ArgInfo::VARIABLE && kind == PERATOM) { + } else if (val.which == ArgInfo::FIX && kind == LOCAL) { + size[i] = val.val.f->size_local_rows; + } else if (val.which == ArgInfo::VARIABLE && kind == PERATOM) { size[i] = atom->nlocal; } } if (size[0] != size[1]) - error->all(FLERR,"Fix ave/histo/weight value and weight vector " - "lengths do not match"); + error->all(FLERR,"Fix ave/histo/weight value and weight vector lengths do not match"); } /* ---------------------------------------------------------------------- */ void FixAveHistoWeight::end_of_step() { - int i,j,m; - // skip if not step which requires doing something bigint ntimestep = update->ntimestep; @@ -105,7 +99,7 @@ void FixAveHistoWeight::end_of_step() stats[0] = stats[1] = 0.0; stats[2] = BIG; stats[3] = -BIG; - for (i = 0; i < nbins; i++) bin[i] = 0.0; + for (int i = 0; i < nbins; i++) bin[i] = 0.0; } // first calculate weight factors, then bin single value @@ -119,265 +113,256 @@ void FixAveHistoWeight::end_of_step() double weight = 0.0; double *weights = nullptr; int stride = 0; - i = 1; - - m = value2index[i]; - j = argindex[i]; + auto &val = values[1]; + int j = val.argindex; // atom attributes - if (which[i] == ArgInfo::X) { + if (val.which == ArgInfo::X) { weights = &atom->x[0][j]; stride = 3; - } else if (which[i] == ArgInfo::V) { + } else if (val.which == ArgInfo::V) { weights = &atom->v[0][j]; stride = 3; bin_atoms(&atom->v[0][j],3); - } else if (which[i] == ArgInfo::F) { + } else if (val.which == ArgInfo::F) { weights = &atom->f[0][j]; stride = 3; } // invoke compute if not previously invoked - if (which[i] == ArgInfo::COMPUTE) { - - Compute *compute = modify->compute[m]; + if (val.which == ArgInfo::COMPUTE) { if (kind == GLOBAL && mode == SCALAR) { if (j == 0) { - if (!(compute->invoked_flag & Compute::INVOKED_SCALAR)) { - compute->compute_scalar(); - compute->invoked_flag |= Compute::INVOKED_SCALAR; + if (!(val.val.c->invoked_flag & Compute::INVOKED_SCALAR)) { + val.val.c->compute_scalar(); + val.val.c->invoked_flag |= Compute::INVOKED_SCALAR; } - weight = compute->scalar; + weight = val.val.c->scalar; } else { - if (!(compute->invoked_flag & Compute::INVOKED_VECTOR)) { - compute->compute_vector(); - compute->invoked_flag |= Compute::INVOKED_VECTOR; + if (!(val.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { + val.val.c->compute_vector(); + val.val.c->invoked_flag |= Compute::INVOKED_VECTOR; } - weight = compute->vector[j-1]; + weight = val.val.c->vector[j-1]; } } else if (kind == GLOBAL && mode == VECTOR) { if (j == 0) { - if (!(compute->invoked_flag & Compute::INVOKED_VECTOR)) { - compute->compute_vector(); - compute->invoked_flag |= Compute::INVOKED_VECTOR; + if (!(val.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { + val.val.c->compute_vector(); + val.val.c->invoked_flag |= Compute::INVOKED_VECTOR; } - weights = compute->vector; + weights = val.val.c->vector; stride = 1; } else { - if (!(compute->invoked_flag & Compute::INVOKED_ARRAY)) { - compute->compute_array(); - compute->invoked_flag |= Compute::INVOKED_ARRAY; + if (!(val.val.c->invoked_flag & Compute::INVOKED_ARRAY)) { + val.val.c->compute_array(); + val.val.c->invoked_flag |= Compute::INVOKED_ARRAY; } - if (compute->array) weights = &compute->array[0][j-1]; - stride = compute->size_array_cols; + if (val.val.c->array) weights = &val.val.c->array[0][j-1]; + stride = val.val.c->size_array_cols; } } else if (kind == PERATOM) { - if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) { - compute->compute_peratom(); - compute->invoked_flag |= Compute::INVOKED_PERATOM; + if (!(val.val.c->invoked_flag & Compute::INVOKED_PERATOM)) { + val.val.c->compute_peratom(); + val.val.c->invoked_flag |= Compute::INVOKED_PERATOM; } if (j == 0) { - weights = compute->vector_atom; + weights = val.val.c->vector_atom; stride = 1; - } else if (compute->array_atom) { - weights = &compute->array_atom[0][j-1]; - stride = compute->size_peratom_cols; + } else if (val.val.c->array_atom) { + weights = &val.val.c->array_atom[0][j-1]; + stride = val.val.c->size_peratom_cols; } } else if (kind == LOCAL) { - if (!(compute->invoked_flag & Compute::INVOKED_LOCAL)) { - compute->compute_local(); - compute->invoked_flag |= Compute::INVOKED_LOCAL; + if (!(val.val.c->invoked_flag & Compute::INVOKED_LOCAL)) { + val.val.c->compute_local(); + val.val.c->invoked_flag |= Compute::INVOKED_LOCAL; } if (j == 0) { - weights = compute->vector_local; + weights = val.val.c->vector_local; stride = 1; - } else if (compute->array_local) { - weights = &compute->array_local[0][j-1]; - stride = compute->size_local_cols; + } else if (val.val.c->array_local) { + weights = &val.val.c->array_local[0][j-1]; + stride = val.val.c->size_local_cols; } } // access fix fields, guaranteed to be ready - } else if (which[i] == ArgInfo::FIX) { - - Fix *fix = modify->fix[m]; + } else if (val.which == ArgInfo::FIX) { if (kind == GLOBAL && mode == SCALAR) { - if (j == 0) weight = fix->compute_scalar(); - else weight = fix->compute_vector(j-1); + if (j == 0) weight = val.val.f->compute_scalar(); + else weight = val.val.f->compute_vector(j-1); } else if (kind == GLOBAL && mode == VECTOR) { error->all(FLERR,"Fix ave/histo/weight option not yet supported"); // NOTE: need to allocate local storage if (j == 0) { - int n = fix->size_vector; - for (i = 0; i < n; i++) weights[n] = fix->compute_vector(i); + int n = val.val.f->size_vector; + for (int i = 0; i < n; i++) weights[n] = val.val.f->compute_vector(i); } else { - int n = fix->size_vector; - for (i = 0; i < n; i++) weights[n] = fix->compute_array(i,j-1); + int n = val.val.f->size_vector; + for (int i = 0; i < n; i++) weights[n] = val.val.f->compute_array(i,j-1); } } else if (kind == PERATOM) { if (j == 0) { - weights = fix->vector_atom; + weights = val.val.f->vector_atom; stride = 1; - } else if (fix->array_atom) { - weights = fix->array_atom[j-1]; - stride = fix->size_peratom_cols; + } else if (val.val.f->array_atom) { + weights = val.val.f->array_atom[j-1]; + stride = val.val.f->size_peratom_cols; } } else if (kind == LOCAL) { if (j == 0) { - weights = fix->vector_local; + weights = val.val.f->vector_local; stride = 1; - } else if (fix->array_local) { - weights = &fix->array_local[0][j-1]; - stride = fix->size_local_cols; + } else if (val.val.f->array_local) { + weights = &val.val.f->array_local[0][j-1]; + stride = val.val.f->size_local_cols; } } // evaluate equal-style variable - } else if (which[i] == ArgInfo::VARIABLE && kind == GLOBAL) { - weight = input->variable->compute_equal(m); + } else if (val.which == ArgInfo::VARIABLE && kind == GLOBAL) { + weight = input->variable->compute_equal(val.val.v); - } else if (which[i] == ArgInfo::VARIABLE && kind == PERATOM) { + } else if (val.which == ArgInfo::VARIABLE && kind == PERATOM) { if (atom->nmax > maxatom) { memory->destroy(vector); maxatom = atom->nmax; memory->create(vector,maxatom,"ave/histo/weight:vector"); } - input->variable->compute_atom(m,igroup,vector,1,0); + input->variable->compute_atom(val.val.v,igroup,vector,1,0); weights = vector; stride = 1; } // bin values using weights, values are 1st value (i = 0) - i = 0; - m = value2index[i]; - j = argindex[i]; + val = values[0]; + j = val.argindex; // atom attributes - if (which[i] == ArgInfo::X && weights != nullptr) + if (val.which == ArgInfo::X && weights != nullptr) bin_atoms_weights(&atom->x[0][j],3,weights,stride); - else if (which[i] == ArgInfo::V && weights != nullptr) + else if (val.which == ArgInfo::V && weights != nullptr) bin_atoms_weights(&atom->v[0][j],3,weights,stride); - else if (which[i] == ArgInfo::F && weights != nullptr) + else if (val.which == ArgInfo::F && weights != nullptr) bin_atoms_weights(&atom->f[0][j],3,weights,stride); // invoke compute if not previously invoked - if (which[i] == ArgInfo::COMPUTE) { - Compute *compute = modify->compute[m]; + if (val.which == ArgInfo::COMPUTE) { + if (kind == GLOBAL && mode == SCALAR) { if (j == 0) { - if (!(compute->invoked_flag & Compute::INVOKED_SCALAR)) { - compute->compute_scalar(); - compute->invoked_flag |= Compute::INVOKED_SCALAR; + if (!(val.val.c->invoked_flag & Compute::INVOKED_SCALAR)) { + val.val.c->compute_scalar(); + val.val.c->invoked_flag |= Compute::INVOKED_SCALAR; } - bin_one_weights(compute->scalar,weight); + bin_one_weights(val.val.c->scalar,weight); } else { - if (!(compute->invoked_flag & Compute::INVOKED_VECTOR)) { - compute->compute_vector(); - compute->invoked_flag |= Compute::INVOKED_VECTOR; + if (!(val.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { + val.val.c->compute_vector(); + val.val.c->invoked_flag |= Compute::INVOKED_VECTOR; } - bin_one_weights(compute->vector[j-1],weight); + bin_one_weights(val.val.c->vector[j-1],weight); } } else if (kind == GLOBAL && mode == VECTOR) { if (j == 0) { - if (!(compute->invoked_flag & Compute::INVOKED_VECTOR)) { - compute->compute_vector(); - compute->invoked_flag |= Compute::INVOKED_VECTOR; + if (!(val.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { + val.val.c->compute_vector(); + val.val.c->invoked_flag |= Compute::INVOKED_VECTOR; } - bin_vector_weights(compute->size_vector,compute->vector,1, + bin_vector_weights(val.val.c->size_vector,val.val.c->vector,1, weights,stride); } else { - if (!(compute->invoked_flag & Compute::INVOKED_ARRAY)) { - compute->compute_array(); - compute->invoked_flag |= Compute::INVOKED_ARRAY; + if (!(val.val.c->invoked_flag & Compute::INVOKED_ARRAY)) { + val.val.c->compute_array(); + val.val.c->invoked_flag |= Compute::INVOKED_ARRAY; } - if (compute->array) - bin_vector_weights(compute->size_array_rows,&compute->array[0][j-1], - compute->size_array_cols,weights,stride); + if (val.val.c->array) + bin_vector_weights(val.val.c->size_array_rows,&val.val.c->array[0][j-1], + val.val.c->size_array_cols,weights,stride); } } else if (kind == PERATOM) { - if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) { - compute->compute_peratom(); - compute->invoked_flag |= Compute::INVOKED_PERATOM; + if (!(val.val.c->invoked_flag & Compute::INVOKED_PERATOM)) { + val.val.c->compute_peratom(); + val.val.c->invoked_flag |= Compute::INVOKED_PERATOM; } if (j == 0) - bin_atoms_weights(compute->vector_atom,1,weights, stride); - else if (compute->array_atom) - bin_atoms_weights(&compute->array_atom[0][j-1], - compute->size_peratom_cols,weights,stride); + bin_atoms_weights(val.val.c->vector_atom,1,weights, stride); + else if (val.val.c->array_atom) + bin_atoms_weights(&val.val.c->array_atom[0][j-1], + val.val.c->size_peratom_cols,weights,stride); } else if (kind == LOCAL) { - if (!(compute->invoked_flag & Compute::INVOKED_LOCAL)) { - compute->compute_local(); - compute->invoked_flag |= Compute::INVOKED_LOCAL; + if (!(val.val.c->invoked_flag & Compute::INVOKED_LOCAL)) { + val.val.c->compute_local(); + val.val.c->invoked_flag |= Compute::INVOKED_LOCAL; } if (j == 0) - bin_vector_weights(compute->size_local_rows, - compute->vector_local,1,weights,stride); - else if (compute->array_local) - bin_vector_weights(compute->size_local_rows, - &compute->array_local[0][j-1], - compute->size_local_cols,weights,stride); + bin_vector_weights(val.val.c->size_local_rows, + val.val.c->vector_local,1,weights,stride); + else if (val.val.c->array_local) + bin_vector_weights(val.val.c->size_local_rows, + &val.val.c->array_local[0][j-1], + val.val.c->size_local_cols,weights,stride); } // access fix fields, guaranteed to be ready - } else if (which[i] == ArgInfo::FIX) { - - Fix *fix = modify->fix[m]; + } else if (val.which == ArgInfo::FIX) { if (kind == GLOBAL && mode == SCALAR) { - if (j == 0) bin_one_weights(fix->compute_scalar(),weight); - else bin_one_weights(fix->compute_vector(j-1),weight); + if (j == 0) bin_one_weights(val.val.f->compute_scalar(),weight); + else bin_one_weights(val.val.f->compute_vector(j-1),weight); } else if (kind == GLOBAL && mode == VECTOR) { if (j == 0) { - int n = fix->size_vector; - for (i = 0; i < n; i++) - bin_one_weights(fix->compute_vector(i),weights[i*stride]); + int n = val.val.f->size_vector; + for (int i = 0; i < n; i++) + bin_one_weights(val.val.f->compute_vector(i),weights[i*stride]); } else { - int n = fix->size_vector; - for (i = 0; i < n; i++) - bin_one_weights(fix->compute_array(i,j-1),weights[i*stride]); + int n = val.val.f->size_vector; + for (int i = 0; i < n; i++) + bin_one_weights(val.val.f->compute_array(i,j-1),weights[i*stride]); } } else if (kind == PERATOM) { if (j == 0) - bin_atoms_weights(fix->vector_atom,1,weights,stride); - else if (fix->array_atom) - bin_atoms_weights(fix->array_atom[j-1],fix->size_peratom_cols, + bin_atoms_weights(val.val.f->vector_atom,1,weights,stride); + else if (val.val.f->array_atom) + bin_atoms_weights(val.val.f->array_atom[j-1],val.val.f->size_peratom_cols, weights,stride); } else if (kind == LOCAL) { - if (j == 0) bin_vector_weights(fix->size_local_rows,fix->vector_local,1, + if (j == 0) bin_vector_weights(val.val.f->size_local_rows,val.val.f->vector_local,1, weights,stride); - else if (fix->array_local) - bin_vector_weights(fix->size_local_rows,&fix->array_local[0][j-1], - fix->size_local_cols,weights,stride); + else if (val.val.f->array_local) + bin_vector_weights(val.val.f->size_local_rows,&val.val.f->array_local[0][j-1], + val.val.f->size_local_cols,weights,stride); } // evaluate equal-style variable - } else if (which[i] == ArgInfo::VARIABLE && kind == GLOBAL) { - bin_one_weights(input->variable->compute_equal(m),weight); + } else if (val.which == ArgInfo::VARIABLE && kind == GLOBAL) { + bin_one_weights(input->variable->compute_equal(val.val.v),weight); - } else if (which[i] == ArgInfo::VARIABLE && kind == PERATOM) { + } else if (val.which == ArgInfo::VARIABLE && kind == PERATOM) { if (atom->nmax > maxatom) { memory->destroy(vector); maxatom = atom->nmax; memory->create(vector,maxatom,"ave/histo/weight:vector"); } - input->variable->compute_atom(m,igroup,vector,1,0); + input->variable->compute_atom(val.val.v,igroup,vector,1,0); bin_atoms_weights(vector,1,weights,stride); } @@ -409,7 +394,7 @@ void FixAveHistoWeight::end_of_step() stats[1] = stats_all[1]; stats[2] = stats_all[2]; stats[3] = stats_all[3]; - for (i = 0; i < nbins; i++) bin[i] = bin_all[i]; + for (int i = 0; i < nbins; i++) bin[i] = bin_all[i]; } // if ave = ONE, only single Nfreq timestep value is needed @@ -421,14 +406,14 @@ void FixAveHistoWeight::end_of_step() stats_total[1] = stats[1]; stats_total[2] = stats[2]; stats_total[3] = stats[3]; - for (i = 0; i < nbins; i++) bin_total[i] = bin[i]; + for (int i = 0; i < nbins; i++) bin_total[i] = bin[i]; } else if (ave == RUNNING) { stats_total[0] += stats[0]; stats_total[1] += stats[1]; stats_total[2] = MIN(stats_total[2],stats[2]); stats_total[3] = MAX(stats_total[3],stats[3]); - for (i = 0; i < nbins; i++) bin_total[i] += bin[i]; + for (int i = 0; i < nbins; i++) bin_total[i] += bin[i]; } else if (ave == WINDOW) { stats_total[0] += stats[0]; @@ -438,19 +423,20 @@ void FixAveHistoWeight::end_of_step() if (window_limit) stats_total[1] -= stats_list[iwindow][1]; stats_list[iwindow][1] = stats[1]; + int m; if (window_limit) m = nwindow; else m = iwindow+1; stats_list[iwindow][2] = stats[2]; stats_total[2] = stats_list[0][2]; - for (i = 1; i < m; i++) + for (int i = 1; i < m; i++) stats_total[2] = MIN(stats_total[2],stats_list[i][2]); stats_list[iwindow][3] = stats[3]; stats_total[3] = stats_list[0][3]; - for (i = 1; i < m; i++) + for (int i = 1; i < m; i++) stats_total[3] = MAX(stats_total[3],stats_list[i][3]); - for (i = 0; i < nbins; i++) { + for (int i = 0; i < nbins; i++) { bin_total[i] += bin[i]; if (window_limit) bin_total[i] -= bin_list[iwindow][i]; bin_list[iwindow][i] = bin[i]; @@ -465,17 +451,17 @@ void FixAveHistoWeight::end_of_step() // output result to file - if (fp && me == 0) { + if (fp && comm->me == 0) { clearerr(fp); if (overwrite) platform::fseek(fp,filepos); fmt::print(fp,"{} {} {} {} {} {}\n",ntimestep,nbins, stats_total[0],stats_total[1],stats_total[2],stats_total[3]); if (stats_total[0] != 0.0) - for (i = 0; i < nbins; i++) + for (int i = 0; i < nbins; i++) fprintf(fp,"%d %g %g %g\n", i+1,coord[i],bin_total[i],bin_total[i]/stats_total[0]); else - for (i = 0; i < nbins; i++) + for (int i = 0; i < nbins; i++) fprintf(fp,"%d %g %g %g\n",i+1,coord[i],0.0,0.0); if (ferror(fp)) diff --git a/src/fix_ave_histo_weight.h b/src/fix_ave_histo_weight.h index ea2f42e041..087c7c2dc5 100644 --- a/src/fix_ave_histo_weight.h +++ b/src/fix_ave_histo_weight.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp index bd8ed1468d..6c0397c74b 100644 --- a/src/fix_ave_time.cpp +++ b/src/fix_ave_time.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -29,6 +29,7 @@ #include "variable.h" #include +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -92,14 +93,12 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) : value_t val; val.keyword = arg[i]; + val.which = argi.get_type(); key2col[arg[i]] = i; - if ((argi.get_type() == ArgInfo::NONE) - || (argi.get_type() == ArgInfo::UNKNOWN) - || (argi.get_dim() > 1)) + if ((val.which == ArgInfo::NONE) || (val.which == ArgInfo::UNKNOWN) || (argi.get_dim() > 1)) error->all(FLERR,"Invalid fix ave/time argument: {}", arg[i]); - val.which = argi.get_type(); val.argindex = argi.get_index1(); val.varlen = 0; val.offcol = 0; @@ -123,12 +122,9 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) : // for fix inputs, check that fix frequency is acceptable // set variable_length if any compute is variable length - if (nevery <= 0) - error->all(FLERR,"Illegal fix ave/time nevery value: {}", nevery); - if (nrepeat <= 0) - error->all(FLERR,"Illegal fix ave/time nrepeat value: {}", nrepeat); - if (nfreq <= 0) - error->all(FLERR,"Illegal fix ave/time nfreq value: {}", nfreq); + if (nevery <= 0) error->all(FLERR,"Illegal fix ave/time nevery value: {}", nevery); + if (nrepeat <= 0) error->all(FLERR,"Illegal fix ave/time nrepeat value: {}", nrepeat); + if (nfreq <= 0) error->all(FLERR,"Illegal fix ave/time nfreq value: {}", nfreq); if (nfreq % nevery || nrepeat*nevery > nfreq) error->all(FLERR,"Inconsistent fix ave/time nevery/nrepeat/nfreq values"); if (ave != RUNNING && overwrite) diff --git a/src/fix_ave_time.h b/src/fix_ave_time.h index 9bc46a0b4f..5b25a68ab5 100644 --- a/src/fix_ave_time.h +++ b/src/fix_ave_time.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_aveforce.cpp b/src/fix_aveforce.cpp index e2369697ca..bc5a6ea344 100644 --- a/src/fix_aveforce.cpp +++ b/src/fix_aveforce.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_aveforce.h b/src/fix_aveforce.h index a28566709b..23e008bf8e 100644 --- a/src/fix_aveforce.h +++ b/src/fix_aveforce.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_balance.cpp b/src/fix_balance.cpp index 1ce3c212d4..692ba45e42 100644 --- a/src/fix_balance.cpp +++ b/src/fix_balance.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -25,6 +25,7 @@ #include "kspace.h" #include "modify.h" #include "neighbor.h" +#include "pair.h" #include "rcb.h" #include "update.h" @@ -94,7 +95,7 @@ FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) : } } - if (lbstyle == BISECTION && comm->style == 0) + if (lbstyle == BISECTION && comm->style == Comm::BRICK) error->all(FLERR,"Fix balance rcb cannot be used with comm_style brick"); // create instance of Balance class @@ -155,9 +156,6 @@ void FixBalance::post_constructor() void FixBalance::init() { - if (force->kspace) kspace_flag = 1; - else kspace_flag = 0; - balance->init_imbalance(1); } @@ -278,11 +276,13 @@ void FixBalance::rebalance() } // reset proc sub-domains - // check and warn if any proc's subbox is smaller than neigh skin - // since may lead to lost atoms in comm->exchange() if (domain->triclinic) domain->set_lamda_box(); domain->set_local_box(); + + // check and warn if any proc's subbox is smaller than neigh skin + // since may lead to lost atoms in comm->exchange() + domain->subbox_too_small_check(neighbor->skin); // output of new decomposition @@ -303,9 +303,12 @@ void FixBalance::rebalance() else if (irregular->migrate_check()) irregular->migrate_atoms(); if (domain->triclinic) domain->lamda2x(atom->nlocal); - // invoke KSpace setup_grid() to adjust to new proc sub-domains + // notify all classes that store distributed grids + // so they can adjust to new proc sub-domains - if (kspace_flag) force->kspace->setup_grid(); + modify->reset_grid(); + if (force->pair) force->pair->reset_grid(); + if (force->kspace) force->kspace->reset_grid(); // pending triggers pre_neighbor() to compute final imbalance factor // can only be done after atoms migrate in comm->exchange() diff --git a/src/fix_balance.h b/src/fix_balance.h index 0a67825daa..f1a8db57ae 100644 --- a/src/fix_balance.h +++ b/src/fix_balance.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -43,16 +43,15 @@ class FixBalance : public Fix { int nevery, lbstyle, nitermax; double thresh, stopthresh; char bstr[4]; - int wtflag; // 1 for weighted balancing + int wtflag; // 1 for weighted balancing double imbnow; // current imbalance factor double imbprev; // imbalance factor before last rebalancing double imbfinal; // imbalance factor after last rebalancing double maxloadperproc; // max load on any processor int itercount; // iteration count of last call to Balance - int kspace_flag; // 1 if KSpace solver defined int pending; - bigint lastbalance; // last timestep balancing was attempted + bigint lastbalance; // last timestep balancing was attempted class Balance *balance; class Irregular *irregular; diff --git a/src/fix_bond_history.cpp b/src/fix_bond_history.cpp index b5b51a963c..cae9dc744d 100644 --- a/src/fix_bond_history.cpp +++ b/src/fix_bond_history.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -87,8 +87,8 @@ void FixBondHistory::post_constructor() id_fix = utils::strdup(id + std::string("_FIX_PROP_ATOM")); id_array = utils::strdup(std::string("d2_") + id); - modify->add_fix(fmt::format("{} {} property/atom {} {} writedata no", id_fix, group->names[igroup], id_array, - nbond * ndata)); + modify->add_fix(fmt::format("{} {} property/atom {} {} writedata no", id_fix, + group->names[igroup], id_array, nbond * ndata)); int tmp1, tmp2; index = atom->find_custom(&id_array[3], tmp1, tmp2); } @@ -264,6 +264,9 @@ void FixBondHistory::write_restart(FILE *fp) double list[1]; list[n++] = stored_flag; + // Update stored values if needed + pre_exchange(); + if (comm->me == 0) { int size = n * sizeof(double); fwrite(&size, sizeof(int), 1, fp); diff --git a/src/fix_bond_history.h b/src/fix_bond_history.h index 8237f01aea..fafcf52bd9 100644 --- a/src/fix_bond_history.h +++ b/src/fix_bond_history.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -24,7 +24,6 @@ FixStyle(BOND_HISTORY,FixBondHistory); #include #include -#include namespace LAMMPS_NS { diff --git a/src/fix_box_relax.cpp b/src/fix_box_relax.cpp index 756a62bb51..fba050e89c 100644 --- a/src/fix_box_relax.cpp +++ b/src/fix_box_relax.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_box_relax.h b/src/fix_box_relax.h index 922d3a3190..bedf7faef3 100644 --- a/src/fix_box_relax.h +++ b/src/fix_box_relax.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp index bc6e61a69e..1243fef79a 100644 --- a/src/fix_deform.cpp +++ b/src/fix_deform.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_deform.h b/src/fix_deform.h index 76f5fc9d4a..20f6ac5901 100644 --- a/src/fix_deform.h +++ b/src/fix_deform.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_deposit.cpp b/src/fix_deposit.cpp index be30fbc97b..35bc48fe89 100644 --- a/src/fix_deposit.cpp +++ b/src/fix_deposit.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_deposit.h b/src/fix_deposit.h index a9d3d01b34..ba5078dbbe 100644 --- a/src/fix_deposit.h +++ b/src/fix_deposit.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_deprecated.cpp b/src/fix_deprecated.cpp index 23e219c7c1..fc80dba99e 100644 --- a/src/fix_deprecated.cpp +++ b/src/fix_deprecated.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_deprecated.h b/src/fix_deprecated.h index e7ee0ba43c..9e9d369d28 100644 --- a/src/fix_deprecated.h +++ b/src/fix_deprecated.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_dt_reset.cpp b/src/fix_dt_reset.cpp index 2c73cc07ce..b56ae4f846 100644 --- a/src/fix_dt_reset.cpp +++ b/src/fix_dt_reset.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_dt_reset.h b/src/fix_dt_reset.h index d500f97035..00070dac4b 100644 --- a/src/fix_dt_reset.h +++ b/src/fix_dt_reset.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -34,7 +34,7 @@ class FixDtReset : public Fix { void end_of_step() override; double compute_scalar() override; - private: + protected: bigint laststep; int minbound, maxbound; double tmin, tmax, xmax, emax; diff --git a/src/fix_dummy.cpp b/src/fix_dummy.cpp index eb8c08f43e..90110245f8 100644 --- a/src/fix_dummy.cpp +++ b/src/fix_dummy.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_dummy.h b/src/fix_dummy.h index a7012138be..b04f878c04 100644 --- a/src/fix_dummy.h +++ b/src/fix_dummy.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_efield.cpp b/src/fix_efield.cpp index 3a2d8cfb5c..e1d70e832f 100644 --- a/src/fix_efield.cpp +++ b/src/fix_efield.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_efield.h b/src/fix_efield.h index fc92766b80..2ebdcbfaed 100644 --- a/src/fix_efield.h +++ b/src/fix_efield.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_enforce2d.cpp b/src/fix_enforce2d.cpp index fc8240ae44..c6816c2355 100644 --- a/src/fix_enforce2d.cpp +++ b/src/fix_enforce2d.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_enforce2d.h b/src/fix_enforce2d.h index ac0b11f611..4572785158 100644 --- a/src/fix_enforce2d.h +++ b/src/fix_enforce2d.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_evaporate.cpp b/src/fix_evaporate.cpp index ec3a85b259..5311461467 100644 --- a/src/fix_evaporate.cpp +++ b/src/fix_evaporate.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_evaporate.h b/src/fix_evaporate.h index 776097d3a4..25aa76e615 100644 --- a/src/fix_evaporate.h +++ b/src/fix_evaporate.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_external.cpp b/src/fix_external.cpp index ecc1aaa670..c9d019d963 100644 --- a/src/fix_external.cpp +++ b/src/fix_external.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_external.h b/src/fix_external.h index 4ee42da2c7..c06d0753f6 100644 --- a/src/fix_external.h +++ b/src/fix_external.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp index 7d8b5aa906..3f3f63363f 100644 --- a/src/fix_gravity.cpp +++ b/src/fix_gravity.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_gravity.h b/src/fix_gravity.h index ef92baa377..cf984c76c0 100644 --- a/src/fix_gravity.h +++ b/src/fix_gravity.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_group.cpp b/src/fix_group.cpp index 00deab3ef8..5d86de3e88 100644 --- a/src/fix_group.cpp +++ b/src/fix_group.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_group.h b/src/fix_group.h index f343be2344..7cab08683c 100644 --- a/src/fix_group.h +++ b/src/fix_group.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_halt.cpp b/src/fix_halt.cpp index 08713cf6ad..fcfefe102d 100644 --- a/src/fix_halt.cpp +++ b/src/fix_halt.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_halt.h b/src/fix_halt.h index 648c3b745b..d6c46778e4 100644 --- a/src/fix_halt.h +++ b/src/fix_halt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_heat.cpp b/src/fix_heat.cpp index db77dd7bdc..f63d689f3c 100644 --- a/src/fix_heat.cpp +++ b/src/fix_heat.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_heat.h b/src/fix_heat.h index cc901545ed..d525ec8047 100644 --- a/src/fix_heat.h +++ b/src/fix_heat.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_indent.cpp b/src/fix_indent.cpp index ab9ef08e30..9adb337dd6 100644 --- a/src/fix_indent.cpp +++ b/src/fix_indent.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_indent.h b/src/fix_indent.h index d06132b80b..527e9ec277 100644 --- a/src/fix_indent.h +++ b/src/fix_indent.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp index 84a628eefe..adfa651147 100644 --- a/src/fix_langevin.cpp +++ b/src/fix_langevin.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_langevin.h b/src/fix_langevin.h index 9eba98135d..477081450e 100644 --- a/src/fix_langevin.h +++ b/src/fix_langevin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_lineforce.cpp b/src/fix_lineforce.cpp index fa284d3ed2..c0a6fb5a42 100644 --- a/src/fix_lineforce.cpp +++ b/src/fix_lineforce.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_lineforce.h b/src/fix_lineforce.h index ae0ae3b6a4..4dece5dec1 100644 --- a/src/fix_lineforce.h +++ b/src/fix_lineforce.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_minimize.cpp b/src/fix_minimize.cpp index 43f0943b14..e011c79d9d 100644 --- a/src/fix_minimize.cpp +++ b/src/fix_minimize.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_minimize.h b/src/fix_minimize.h index 4cafc0e0d6..7bc1ccd46b 100644 --- a/src/fix_minimize.h +++ b/src/fix_minimize.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_momentum.cpp b/src/fix_momentum.cpp index 19a9bd0acd..284d77e2a8 100644 --- a/src/fix_momentum.cpp +++ b/src/fix_momentum.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_momentum.h b/src/fix_momentum.h index dcf9b3dbbb..bc0b251e94 100644 --- a/src/fix_momentum.h +++ b/src/fix_momentum.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_move.cpp b/src/fix_move.cpp index 37e8647671..36bba410fc 100644 --- a/src/fix_move.cpp +++ b/src/fix_move.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_move.h b/src/fix_move.h index e6b253a2a2..e3c018f54d 100644 --- a/src/fix_move.h +++ b/src/fix_move.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_neigh_history.cpp b/src/fix_neigh_history.cpp index 7413b590a7..6b103f9f80 100644 --- a/src/fix_neigh_history.cpp +++ b/src/fix_neigh_history.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_neigh_history.h b/src/fix_neigh_history.h index 0cfa6c399c..bd029ef529 100644 --- a/src/fix_neigh_history.h +++ b/src/fix_neigh_history.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index a1b46c51fb..d0356f10f3 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_nh.h b/src/fix_nh.h index 422eb9d317..3e406929b2 100644 --- a/src/fix_nh.h +++ b/src/fix_nh.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_nh_sphere.cpp b/src/fix_nh_sphere.cpp index 3aa22ffe3e..f39de6c656 100644 --- a/src/fix_nh_sphere.cpp +++ b/src/fix_nh_sphere.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_nh_sphere.h b/src/fix_nh_sphere.h index a63e2e1e11..e1ebbd8711 100644 --- a/src/fix_nh_sphere.h +++ b/src/fix_nh_sphere.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_nph.cpp b/src/fix_nph.cpp index 0a8f67e4b0..91ffabeb17 100644 --- a/src/fix_nph.cpp +++ b/src/fix_nph.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_nph.h b/src/fix_nph.h index 93d94da161..7d7f837ca1 100644 --- a/src/fix_nph.h +++ b/src/fix_nph.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_nph_sphere.cpp b/src/fix_nph_sphere.cpp index 75aab70f06..84b5e7c156 100644 --- a/src/fix_nph_sphere.cpp +++ b/src/fix_nph_sphere.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_nph_sphere.h b/src/fix_nph_sphere.h index 34eb62387f..a68387fbce 100644 --- a/src/fix_nph_sphere.h +++ b/src/fix_nph_sphere.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_npt.cpp b/src/fix_npt.cpp index ff94ae678d..b2b02cb5bc 100644 --- a/src/fix_npt.cpp +++ b/src/fix_npt.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_npt.h b/src/fix_npt.h index b234a8afd1..c0e61e07fa 100644 --- a/src/fix_npt.h +++ b/src/fix_npt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_npt_sphere.cpp b/src/fix_npt_sphere.cpp index 64279b1099..1fa7ca44d7 100644 --- a/src/fix_npt_sphere.cpp +++ b/src/fix_npt_sphere.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_npt_sphere.h b/src/fix_npt_sphere.h index 087c47ccb1..9beaba96a6 100644 --- a/src/fix_npt_sphere.h +++ b/src/fix_npt_sphere.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_nve.cpp b/src/fix_nve.cpp index fd8c4a4099..30c1f24867 100644 --- a/src/fix_nve.cpp +++ b/src/fix_nve.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -15,7 +15,6 @@ #include "fix_nve.h" #include "atom.h" -#include "error.h" #include "force.h" #include "respa.h" #include "update.h" diff --git a/src/fix_nve.h b/src/fix_nve.h index 461455f76c..b54e225c88 100644 --- a/src/fix_nve.h +++ b/src/fix_nve.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_nve_limit.cpp b/src/fix_nve_limit.cpp index 0ce217168e..331d50631b 100644 --- a/src/fix_nve_limit.cpp +++ b/src/fix_nve_limit.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_nve_limit.h b/src/fix_nve_limit.h index 93e2d615eb..2a32aee975 100644 --- a/src/fix_nve_limit.h +++ b/src/fix_nve_limit.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_nve_noforce.cpp b/src/fix_nve_noforce.cpp index 9124dfac3e..27fcc49f13 100644 --- a/src/fix_nve_noforce.cpp +++ b/src/fix_nve_noforce.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -14,7 +14,6 @@ #include "fix_nve_noforce.h" #include "atom.h" -#include "error.h" #include "respa.h" #include "update.h" diff --git a/src/fix_nve_noforce.h b/src/fix_nve_noforce.h index 0c96dc3503..a5d554a1da 100644 --- a/src/fix_nve_noforce.h +++ b/src/fix_nve_noforce.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_nve_sphere.cpp b/src/fix_nve_sphere.cpp index 8ece78d011..ea57028af4 100644 --- a/src/fix_nve_sphere.cpp +++ b/src/fix_nve_sphere.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_nve_sphere.h b/src/fix_nve_sphere.h index 388443e338..d12d9846db 100644 --- a/src/fix_nve_sphere.h +++ b/src/fix_nve_sphere.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_nvt.cpp b/src/fix_nvt.cpp index 11404bf90d..bb3754f9cf 100644 --- a/src/fix_nvt.cpp +++ b/src/fix_nvt.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_nvt.h b/src/fix_nvt.h index e5f7051015..30c41f8b12 100644 --- a/src/fix_nvt.h +++ b/src/fix_nvt.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_nvt_sllod.cpp b/src/fix_nvt_sllod.cpp index 610d310e3f..bb4b6c4273 100644 --- a/src/fix_nvt_sllod.cpp +++ b/src/fix_nvt_sllod.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + LAMMPS development team: developers@lammps.org, Sandia National Laboratories Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_nvt_sllod.h b/src/fix_nvt_sllod.h index 13d002af82..e13eb11311 100644 --- a/src/fix_nvt_sllod.h +++ b/src/fix_nvt_sllod.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - www.cs.sandia.gov/~sjplimp/lammps.html - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_nvt_sphere.cpp b/src/fix_nvt_sphere.cpp index 349da470c7..5818d369dc 100644 --- a/src/fix_nvt_sphere.cpp +++ b/src/fix_nvt_sphere.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_nvt_sphere.h b/src/fix_nvt_sphere.h index f8deede163..98aa55d244 100644 --- a/src/fix_nvt_sphere.h +++ b/src/fix_nvt_sphere.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_pair.cpp b/src/fix_pair.cpp index b71e65b4b7..5e5ccbf810 100644 --- a/src/fix_pair.cpp +++ b/src/fix_pair.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -15,19 +15,12 @@ #include "fix_pair.h" #include "atom.h" -#include "dump.h" #include "error.h" #include "force.h" #include "fix.h" -#include "input.h" #include "memory.h" #include "pair.h" -#include "output.h" -#include "variable.h" #include "update.h" -#include "variable.h" - -#include using namespace LAMMPS_NS; using namespace FixConst; @@ -240,15 +233,19 @@ void FixPair::post_force(int /*vflag*/) // extract pair style fields one by one // store their values in this fix - int nlocal = atom->nlocal; + const int nlocal = atom->nlocal; int icol = 0; int columns; for (int ifield = 0; ifield < nfield; ifield++) { void *pvoid = pstyle->extract_peratom(fieldname[ifield],columns); - if (pvoid == nullptr) - error->all(FLERR,"Fix pair pair style cannot extract {}",fieldname[ifield]); + + // Pair::extract_peratom() may return a null pointer if there are no atoms the sub-domain + // so returning null is only an error if there are local atoms. + + if ((pvoid == nullptr) && (nlocal > 0)) + error->one(FLERR, "Fix pair cannot extract property {} from pair style", fieldname[ifield]); if (columns == 0) { double *pvector = (double *) pvoid; diff --git a/src/fix_pair.h b/src/fix_pair.h index c3d8454185..765b261ee5 100644 --- a/src/fix_pair.h +++ b/src/fix_pair.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -46,10 +46,10 @@ class FixPair : public Fix { double memory_usage() override; private: - int nevery,nfield,ncols; + int nevery, nfield, ncols; bigint lasttime; char *pairname; - char **fieldname,**triggername; + char **fieldname, **triggername; int *trigger; int **triggerptr; diff --git a/src/fix_planeforce.cpp b/src/fix_planeforce.cpp index c58b87630a..6cf5b61368 100644 --- a/src/fix_planeforce.cpp +++ b/src/fix_planeforce.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_planeforce.h b/src/fix_planeforce.h index 3709c25a4c..806200d414 100644 --- a/src/fix_planeforce.h +++ b/src/fix_planeforce.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_press_berendsen.cpp b/src/fix_press_berendsen.cpp index 67802654ba..b2b9797451 100644 --- a/src/fix_press_berendsen.cpp +++ b/src/fix_press_berendsen.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_press_berendsen.h b/src/fix_press_berendsen.h index 87364ac601..85a4895901 100644 --- a/src/fix_press_berendsen.h +++ b/src/fix_press_berendsen.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_print.cpp b/src/fix_print.cpp index 47810c7e48..023b9355cd 100644 --- a/src/fix_print.cpp +++ b/src/fix_print.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_print.h b/src/fix_print.h index c73cd7d28b..48eda897b5 100644 --- a/src/fix_print.h +++ b/src/fix_print.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp index 38dd00c364..95e25c59b2 100644 --- a/src/fix_property_atom.cpp +++ b/src/fix_property_atom.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -154,8 +154,8 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) : border = utils::logical(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "writedata") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix property/atom command"); - wd_section = utils::logical(FLERR,arg[iarg+1],false,lmp); + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix property/atom command"); + wd_section = utils::logical(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else error->all(FLERR, "Illegal fix property/atom command"); @@ -275,6 +275,7 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf, tagint for (int i = 0; i < n; i++) { next = strchr(buf, '\n'); + if (!next) error->all(FLERR, "Unexpected end of file while reading data section"); *next = '\0'; try { @@ -324,12 +325,12 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf, tagint } /* ---------------------------------------------------------------------- - return # of lines in section of data file labeled by keyword + return # of lines in section of data file labeled by keyword. -1 signals use # of added atoms ------------------------------------------------------------------------- */ bigint FixPropertyAtom::read_data_skip_lines(char * /*keyword*/) { - return atom->natoms; + return -1; } /* ---------------------------------------------------------------------- diff --git a/src/fix_property_atom.h b/src/fix_property_atom.h index 760daa4b34..18a4b61529 100644 --- a/src/fix_property_atom.h +++ b/src/fix_property_atom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_read_restart.cpp b/src/fix_read_restart.cpp index 20daa94f84..6d03394a08 100644 --- a/src/fix_read_restart.cpp +++ b/src/fix_read_restart.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_read_restart.h b/src/fix_read_restart.h index 0eb740f4d6..918d9e5cb5 100644 --- a/src/fix_read_restart.h +++ b/src/fix_read_restart.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_recenter.cpp b/src/fix_recenter.cpp index b5a1d39d1a..bee7f55823 100644 --- a/src/fix_recenter.cpp +++ b/src/fix_recenter.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_recenter.h b/src/fix_recenter.h index 6a4a7f0a2c..a45f0201bf 100644 --- a/src/fix_recenter.h +++ b/src/fix_recenter.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_respa.cpp b/src/fix_respa.cpp index dba09b3c78..100acafd94 100644 --- a/src/fix_respa.cpp +++ b/src/fix_respa.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_respa.h b/src/fix_respa.h index e5756e6be7..8fd230e61c 100644 --- a/src/fix_respa.h +++ b/src/fix_respa.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_restrain.cpp b/src/fix_restrain.cpp index 0dde6a7f39..f252134aa9 100644 --- a/src/fix_restrain.cpp +++ b/src/fix_restrain.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_restrain.h b/src/fix_restrain.h index 35bb9abc5c..fe34514d7d 100644 --- a/src/fix_restrain.h +++ b/src/fix_restrain.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_setforce.cpp b/src/fix_setforce.cpp index 8bd5477f76..2078bcb5e1 100644 --- a/src/fix_setforce.cpp +++ b/src/fix_setforce.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_setforce.h b/src/fix_setforce.h index 5dc29509af..adde21ba1d 100644 --- a/src/fix_setforce.h +++ b/src/fix_setforce.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp index ccc2b288a9..3a14ec8de1 100644 --- a/src/fix_spring.cpp +++ b/src/fix_spring.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_spring.h b/src/fix_spring.h index 07f9e010f2..a086a04dc1 100644 --- a/src/fix_spring.h +++ b/src/fix_spring.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_spring_chunk.cpp b/src/fix_spring_chunk.cpp index c727b14bad..3deedcffac 100644 --- a/src/fix_spring_chunk.cpp +++ b/src/fix_spring_chunk.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_spring_chunk.h b/src/fix_spring_chunk.h index a025a85c28..ebde4d806b 100644 --- a/src/fix_spring_chunk.h +++ b/src/fix_spring_chunk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_spring_self.cpp b/src/fix_spring_self.cpp index 2c62bdc3c0..550b3afc4d 100644 --- a/src/fix_spring_self.cpp +++ b/src/fix_spring_self.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_spring_self.h b/src/fix_spring_self.h index 20d97d80bf..59dba78e43 100644 --- a/src/fix_spring_self.h +++ b/src/fix_spring_self.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_store_force.cpp b/src/fix_store_force.cpp index d63d5e67ea..09406bb4f1 100644 --- a/src/fix_store_force.cpp +++ b/src/fix_store_force.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_store_force.h b/src/fix_store_force.h index 4b5aefcbda..927ad76f38 100644 --- a/src/fix_store_force.h +++ b/src/fix_store_force.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_store_global.cpp b/src/fix_store_global.cpp index 4926ce2c5a..cebf4f7690 100644 --- a/src/fix_store_global.cpp +++ b/src/fix_store_global.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -13,7 +13,6 @@ #include "fix_store_global.h" -#include "atom.h" #include "comm.h" #include "error.h" #include "memory.h" diff --git a/src/fix_store_global.h b/src/fix_store_global.h index 0da1a869b3..bad314fbc8 100644 --- a/src/fix_store_global.h +++ b/src/fix_store_global.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_store_local.cpp b/src/fix_store_local.cpp index a3a6906325..d32f0e8178 100644 --- a/src/fix_store_local.cpp +++ b/src/fix_store_local.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -14,7 +14,6 @@ #include "fix_store_local.h" #include "atom.h" -#include "comm.h" #include "error.h" #include "memory.h" #include "update.h" diff --git a/src/fix_store_local.h b/src/fix_store_local.h index 33b4b5a802..2e841e63fd 100644 --- a/src/fix_store_local.h +++ b/src/fix_store_local.h @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_store_peratom.cpp b/src/fix_store_peratom.cpp index 2af87d8b4c..6f5637e3f6 100644 --- a/src/fix_store_peratom.cpp +++ b/src/fix_store_peratom.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -14,7 +14,6 @@ #include "fix_store_peratom.h" #include "atom.h" -#include "comm.h" #include "error.h" #include "memory.h" diff --git a/src/fix_store_peratom.h b/src/fix_store_peratom.h index fcabae75b7..d3efe4142b 100644 --- a/src/fix_store_peratom.h +++ b/src/fix_store_peratom.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_store_state.cpp b/src/fix_store_state.cpp index cd29e785ec..92aee9c1c9 100644 --- a/src/fix_store_state.cpp +++ b/src/fix_store_state.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -35,175 +35,188 @@ using namespace FixConst; /* ---------------------------------------------------------------------- */ FixStoreState::FixStoreState(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg), - nvalues(0), which(nullptr), argindex(nullptr), value2index(nullptr), - ids(nullptr), values(nullptr), - vbuf(nullptr), pack_choice(nullptr) + Fix(lmp, narg, arg), avalues(nullptr), vbuf(nullptr) { - if (narg < 5) error->all(FLERR,"Illegal fix store/state command"); + if (narg < 5) utils::missing_cmd_args(FLERR,"fix store/state", error); restart_peratom = 1; peratom_freq = 1; nevery = utils::inumeric(FLERR,arg[3],false,lmp); - if (nevery < 0) error->all(FLERR,"Illegal fix store/state command"); + if (nevery < 0) error->all(FLERR,"Invalid fix store/state never value {}", nevery); - // parse values until one isn't recognized + // parse values // customize a new keyword by adding to if statement - pack_choice = new FnPtrPack[narg-4]; - which = new int[narg-4]; - argindex = new int[narg-4]; - ids = new char*[narg-4]; - value2index = new int[narg-4]; - nvalues = 0; + values.clear(); cfv_any = 0; int iarg = 4; while (iarg < narg) { - which[nvalues] = ArgInfo::KEYWORD; - ids[nvalues] = nullptr; + + value_t val; + val.which = ArgInfo::KEYWORD; + val.argindex = -1; + val.id = ""; + val.val.c = nullptr; + val.pack_choice = nullptr; if (strcmp(arg[iarg],"id") == 0) { - pack_choice[nvalues++] = &FixStoreState::pack_id; + val.pack_choice = &FixStoreState::pack_id; } else if (strcmp(arg[iarg],"mol") == 0) { if (!atom->molecule_flag) - error->all(FLERR, - "Fix store/state for atom property that isn't allocated"); - pack_choice[nvalues++] = &FixStoreState::pack_molecule; + error->all(FLERR, "Cannot use fix store/state {} for atom style {}", + arg[iarg], atom->get_style()); + val.pack_choice = &FixStoreState::pack_molecule; } else if (strcmp(arg[iarg],"type") == 0) { - pack_choice[nvalues++] = &FixStoreState::pack_type; + val.pack_choice = &FixStoreState::pack_type; } else if (strcmp(arg[iarg],"mass") == 0) { - pack_choice[nvalues++] = &FixStoreState::pack_mass; + val.pack_choice = &FixStoreState::pack_mass; } else if (strcmp(arg[iarg],"x") == 0) { - pack_choice[nvalues++] = &FixStoreState::pack_x; + val.pack_choice = &FixStoreState::pack_x; } else if (strcmp(arg[iarg],"y") == 0) { - pack_choice[nvalues++] = &FixStoreState::pack_y; + val.pack_choice = &FixStoreState::pack_y; } else if (strcmp(arg[iarg],"z") == 0) { - pack_choice[nvalues++] = &FixStoreState::pack_z; + val.pack_choice = &FixStoreState::pack_z; } else if (strcmp(arg[iarg],"xs") == 0) { if (domain->triclinic) - pack_choice[nvalues++] = &FixStoreState::pack_xs_triclinic; - else pack_choice[nvalues++] = &FixStoreState::pack_xs; + val.pack_choice = &FixStoreState::pack_xs_triclinic; + else val.pack_choice = &FixStoreState::pack_xs; } else if (strcmp(arg[iarg],"ys") == 0) { if (domain->triclinic) - pack_choice[nvalues++] = &FixStoreState::pack_ys_triclinic; - else pack_choice[nvalues++] = &FixStoreState::pack_ys; + val.pack_choice = &FixStoreState::pack_ys_triclinic; + else val.pack_choice = &FixStoreState::pack_ys; } else if (strcmp(arg[iarg],"zs") == 0) { if (domain->triclinic) - pack_choice[nvalues++] = &FixStoreState::pack_zs_triclinic; - else pack_choice[nvalues++] = &FixStoreState::pack_zs; + val.pack_choice = &FixStoreState::pack_zs_triclinic; + else val.pack_choice = &FixStoreState::pack_zs; } else if (strcmp(arg[iarg],"xu") == 0) { if (domain->triclinic) - pack_choice[nvalues++] = &FixStoreState::pack_xu_triclinic; - else pack_choice[nvalues++] = &FixStoreState::pack_xu; + val.pack_choice = &FixStoreState::pack_xu_triclinic; + else val.pack_choice = &FixStoreState::pack_xu; } else if (strcmp(arg[iarg],"yu") == 0) { if (domain->triclinic) - pack_choice[nvalues++] = &FixStoreState::pack_yu_triclinic; - else pack_choice[nvalues++] = &FixStoreState::pack_yu; + val.pack_choice = &FixStoreState::pack_yu_triclinic; + else val.pack_choice = &FixStoreState::pack_yu; } else if (strcmp(arg[iarg],"zu") == 0) { if (domain->triclinic) - pack_choice[nvalues++] = &FixStoreState::pack_zu_triclinic; - else pack_choice[nvalues++] = &FixStoreState::pack_zu; + val.pack_choice = &FixStoreState::pack_zu_triclinic; + else val.pack_choice = &FixStoreState::pack_zu; } else if (strcmp(arg[iarg],"xsu") == 0) { if (domain->triclinic) - pack_choice[nvalues++] = &FixStoreState::pack_xsu_triclinic; - else pack_choice[nvalues++] = &FixStoreState::pack_xsu; + val.pack_choice = &FixStoreState::pack_xsu_triclinic; + else val.pack_choice = &FixStoreState::pack_xsu; } else if (strcmp(arg[iarg],"ysu") == 0) { if (domain->triclinic) - pack_choice[nvalues++] = &FixStoreState::pack_ysu_triclinic; - else pack_choice[nvalues++] = &FixStoreState::pack_ysu; + val.pack_choice = &FixStoreState::pack_ysu_triclinic; + else val.pack_choice = &FixStoreState::pack_ysu; } else if (strcmp(arg[iarg],"zsu") == 0) { if (domain->triclinic) - pack_choice[nvalues++] = &FixStoreState::pack_zsu_triclinic; - else pack_choice[nvalues++] = &FixStoreState::pack_zsu; + val.pack_choice = &FixStoreState::pack_zsu_triclinic; + else val.pack_choice = &FixStoreState::pack_zsu; } else if (strcmp(arg[iarg],"ix") == 0) { - pack_choice[nvalues++] = &FixStoreState::pack_ix; + val.pack_choice = &FixStoreState::pack_ix; } else if (strcmp(arg[iarg],"iy") == 0) { - pack_choice[nvalues++] = &FixStoreState::pack_iy; + val.pack_choice = &FixStoreState::pack_iy; } else if (strcmp(arg[iarg],"iz") == 0) { - pack_choice[nvalues++] = &FixStoreState::pack_iz; + val.pack_choice = &FixStoreState::pack_iz; } else if (strcmp(arg[iarg],"vx") == 0) { - pack_choice[nvalues++] = &FixStoreState::pack_vx; + val.pack_choice = &FixStoreState::pack_vx; } else if (strcmp(arg[iarg],"vy") == 0) { - pack_choice[nvalues++] = &FixStoreState::pack_vy; + val.pack_choice = &FixStoreState::pack_vy; } else if (strcmp(arg[iarg],"vz") == 0) { - pack_choice[nvalues++] = &FixStoreState::pack_vz; + val.pack_choice = &FixStoreState::pack_vz; } else if (strcmp(arg[iarg],"fx") == 0) { - pack_choice[nvalues++] = &FixStoreState::pack_fx; + val.pack_choice = &FixStoreState::pack_fx; } else if (strcmp(arg[iarg],"fy") == 0) { - pack_choice[nvalues++] = &FixStoreState::pack_fy; + val.pack_choice = &FixStoreState::pack_fy; } else if (strcmp(arg[iarg],"fz") == 0) { - pack_choice[nvalues++] = &FixStoreState::pack_fz; + val.pack_choice = &FixStoreState::pack_fz; } else if (strcmp(arg[iarg],"q") == 0) { if (!atom->q_flag) - error->all(FLERR,"Fix store/state for atom property that isn't allocated"); - pack_choice[nvalues++] = &FixStoreState::pack_q; + error->all(FLERR, "Cannot use fix store/state {} for atom style {}", + arg[iarg], atom->get_style()); + val.pack_choice = &FixStoreState::pack_q; } else if (strcmp(arg[iarg],"mux") == 0) { if (!atom->mu_flag) - error->all(FLERR,"Fix store/state for atom property that isn't allocated"); - pack_choice[nvalues++] = &FixStoreState::pack_mux; + error->all(FLERR, "Cannot use fix store/state {} for atom style {}", + arg[iarg], atom->get_style()); + val.pack_choice = &FixStoreState::pack_mux; } else if (strcmp(arg[iarg],"muy") == 0) { if (!atom->mu_flag) - error->all(FLERR,"Fix store/state for atom property that isn't allocated"); - pack_choice[nvalues++] = &FixStoreState::pack_muy; + error->all(FLERR, "Cannot use fix store/state {} for atom style {}", + arg[iarg], atom->get_style()); + val.pack_choice = &FixStoreState::pack_muy; } else if (strcmp(arg[iarg],"muz") == 0) { if (!atom->mu_flag) - error->all(FLERR,"Fix store/state for atom property that isn't allocated"); - pack_choice[nvalues++] = &FixStoreState::pack_muz; + error->all(FLERR, "Cannot use fix store/state {} for atom style {}", + arg[iarg], atom->get_style()); + val.pack_choice = &FixStoreState::pack_muz; } else if (strcmp(arg[iarg],"mu") == 0) { if (!atom->mu_flag) - error->all(FLERR,"Fix store/state for atom property that isn't allocated"); - pack_choice[nvalues++] = &FixStoreState::pack_mu; + error->all(FLERR, "Cannot use fix store/state {} for atom style {}", + arg[iarg], atom->get_style()); + val.pack_choice = &FixStoreState::pack_mu; } else if (strcmp(arg[iarg],"radius") == 0) { if (!atom->radius_flag) - error->all(FLERR,"Fix store/state for atom property that isn't allocated"); - pack_choice[nvalues++] = &FixStoreState::pack_radius; + error->all(FLERR, "Cannot use fix store/state {} for atom style {}", + arg[iarg], atom->get_style()); + val.pack_choice = &FixStoreState::pack_radius; } else if (strcmp(arg[iarg],"diameter") == 0) { if (!atom->radius_flag) - error->all(FLERR,"Fix store/state for atom property that isn't allocated"); - pack_choice[nvalues++] = &FixStoreState::pack_diameter; + error->all(FLERR, "Cannot use fix store/state {} for atom style {}", + arg[iarg], atom->get_style()); + val.pack_choice = &FixStoreState::pack_diameter; } else if (strcmp(arg[iarg],"omegax") == 0) { if (!atom->omega_flag) - error->all(FLERR,"Fix store/state for atom property that isn't allocated"); - pack_choice[nvalues++] = &FixStoreState::pack_omegax; + error->all(FLERR, "Cannot use fix store/state {} for atom style {}", + arg[iarg], atom->get_style()); + val.pack_choice = &FixStoreState::pack_omegax; } else if (strcmp(arg[iarg],"omegay") == 0) { if (!atom->omega_flag) - error->all(FLERR,"Fix store/state for atom property that isn't allocated"); - pack_choice[nvalues++] = &FixStoreState::pack_omegay; + error->all(FLERR, "Cannot use fix store/state {} for atom style {}", + arg[iarg], atom->get_style()); + val.pack_choice = &FixStoreState::pack_omegay; } else if (strcmp(arg[iarg],"omegaz") == 0) { if (!atom->omega_flag) - error->all(FLERR,"Fix store/state for atom property that isn't allocated"); - pack_choice[nvalues++] = &FixStoreState::pack_omegaz; + error->all(FLERR, "Cannot use fix store/state {} for atom style {}", + arg[iarg], atom->get_style()); + val.pack_choice = &FixStoreState::pack_omegaz; } else if (strcmp(arg[iarg],"angmomx") == 0) { if (!atom->angmom_flag) - error->all(FLERR,"Fix store/state for atom property that isn't allocated"); - pack_choice[nvalues++] = &FixStoreState::pack_angmomx; + error->all(FLERR, "Cannot use fix store/state {} for atom style {}", + arg[iarg], atom->get_style()); + val.pack_choice = &FixStoreState::pack_angmomx; } else if (strcmp(arg[iarg],"angmomy") == 0) { if (!atom->angmom_flag) - error->all(FLERR,"Fix store/state for atom property that isn't allocated"); - pack_choice[nvalues++] = &FixStoreState::pack_angmomy; + error->all(FLERR, "Cannot use fix store/state {} for atom style {}", + arg[iarg], atom->get_style()); + val.pack_choice = &FixStoreState::pack_angmomy; } else if (strcmp(arg[iarg],"angmomz") == 0) { if (!atom->angmom_flag) - error->all(FLERR,"Fix store/state for atom property that isn't allocated"); - pack_choice[nvalues++] = &FixStoreState::pack_angmomz; + error->all(FLERR, "Cannot use fix store/state {} for atom style {}", + arg[iarg], atom->get_style()); + val.pack_choice = &FixStoreState::pack_angmomz; } else if (strcmp(arg[iarg],"tqx") == 0) { if (!atom->torque_flag) - error->all(FLERR,"Fix store/state for atom property that isn't allocated"); - pack_choice[nvalues++] = &FixStoreState::pack_tqx; + error->all(FLERR, "Cannot use fix store/state {} for atom style {}", + arg[iarg], atom->get_style()); + val.pack_choice = &FixStoreState::pack_tqx; } else if (strcmp(arg[iarg],"tqy") == 0) { if (!atom->torque_flag) - error->all(FLERR,"Fix store/state for atom property that isn't allocated"); - pack_choice[nvalues++] = &FixStoreState::pack_tqy; + error->all(FLERR, "Cannot use fix store/state {} for atom style {}", + arg[iarg], atom->get_style()); + val.pack_choice = &FixStoreState::pack_tqy; } else if (strcmp(arg[iarg],"tqz") == 0) { if (!atom->torque_flag) - error->all(FLERR,"Fix store/state for atom property that isn't allocated"); - pack_choice[nvalues++] = &FixStoreState::pack_tqz; + error->all(FLERR, "Cannot use fix store/state {} for atom style {}", + arg[iarg], atom->get_style()); + val.pack_choice = &FixStoreState::pack_tqz; // compute or fix or variable or custom per-atom vector or array @@ -211,16 +224,15 @@ FixStoreState::FixStoreState(LAMMPS *lmp, int narg, char **arg) : ArgInfo argi(arg[iarg],ArgInfo::COMPUTE|ArgInfo::FIX|ArgInfo::VARIABLE |ArgInfo::DNAME|ArgInfo::INAME); - if (argi.get_type() == ArgInfo::NONE) break; - if ((argi.get_type() == ArgInfo::UNKNOWN) || (argi.get_dim() > 1)) - error->all(FLERR,"Illegal fix store/state command"); + val.which = argi.get_type(); + val.argindex = argi.get_index1(); + val.id = argi.get_name(); - which[nvalues] = argi.get_type(); - argindex[nvalues] = argi.get_index1(); - ids[nvalues] = argi.copy_name(); - nvalues++; + if (val.which == ArgInfo::NONE) break; + if ((val.which == ArgInfo::UNKNOWN) || (argi.get_dim() > 1)) + error->all(FLERR,"Illegal fix store/state argument: {}", arg[iarg]); } - + values.push_back(val); iarg++; } @@ -230,94 +242,79 @@ FixStoreState::FixStoreState(LAMMPS *lmp, int narg, char **arg) : while (iarg < narg) { if (strcmp(arg[iarg],"com") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix store/state command"); + if (iarg+2 > narg) utils::missing_cmd_args(FLERR,"fix store/state com", error); comflag = utils::logical(FLERR,arg[iarg+1],false,lmp); iarg += 2; - } else error->all(FLERR,"Illegal fix store/state command"); + } else error->all(FLERR,"Unknown fix store/state keyword: {}", arg[iarg]); } // error check - for (int i = 0; i < nvalues; i++) { - if (which[i] == ArgInfo::COMPUTE) { - int icompute = modify->find_compute(ids[i]); - if (icompute < 0) - error->all(FLERR,"Compute ID for fix store/state does not exist"); - if (modify->compute[icompute]->peratom_flag == 0) - error->all(FLERR,"Fix store/state compute does not calculate per-atom values"); - if (argindex[i] == 0 && - modify->compute[icompute]->size_peratom_cols != 0) - error->all(FLERR,"Fix store/state compute does not calculate a per-atom vector"); - if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0) - error->all(FLERR, - "Fix store/state compute does not calculate a per-atom array"); - if (argindex[i] && - argindex[i] > modify->compute[icompute]->size_peratom_cols) - error->all(FLERR, - "Fix store/state compute array is accessed out-of-range"); + for (auto &val : values) { + if (val.which == ArgInfo::COMPUTE) { + val.val.c = modify->get_compute_by_id(val.id); + if (!val.val.c) + error->all(FLERR,"Compute ID {} for fix store/state does not exist", val.id); + if (val.val.c->peratom_flag == 0) + error->all(FLERR,"Fix store/state compute {} does not calculate per-atom values", val.id); + if (val.argindex == 0 && + val.val.c->size_peratom_cols != 0) + error->all(FLERR,"Fix store/state compute {} does not calculate per-atom vector", val.id); + if (val.argindex && val.val.c->size_peratom_cols == 0) + error->all(FLERR, "Fix store/state compute {} does not calculate per-atom array", val.id); + if (val.argindex && (val.argindex > val.val.c->size_peratom_cols)) + error->all(FLERR, "Fix store/state compute array {} is accessed out-of-range", val.id); - } else if (which[i] == ArgInfo::FIX) { - int ifix = modify->find_fix(ids[i]); - if (ifix < 0) - error->all(FLERR, - "Fix ID for fix store/state does not exist"); - if (modify->fix[ifix]->peratom_flag == 0) - error->all(FLERR, - "Fix store/state fix does not calculate per-atom values"); - if (argindex[i] == 0 && modify->fix[ifix]->size_peratom_cols != 0) - error->all(FLERR, - "Fix store/state fix does not calculate a per-atom vector"); - if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0) - error->all(FLERR, - "Fix store/state fix does not calculate a per-atom array"); - if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols) - error->all(FLERR, - "Fix store/state fix array is accessed out-of-range"); - if (nevery % modify->fix[ifix]->peratom_freq) - error->all(FLERR, - "Fix for fix store/state not computed at compatible time"); + } else if (val.which == ArgInfo::FIX) { + val.val.f = modify->get_fix_by_id(val.id); + if (!val.val.f) + error->all(FLERR, "Fix ID {} for fix store/state does not exist", val.id); + if (val.val.f->peratom_flag == 0) + error->all(FLERR, "Fix store/state fix {} does not calculate per-atom values", val.id); + if (val.argindex == 0 && val.val.f->size_peratom_cols != 0) + error->all(FLERR, "Fix store/state fix {} does not calculate per-atom vector", val.id); + if (val.argindex && val.val.f->size_peratom_cols == 0) + error->all(FLERR, "Fix store/state fix {} does not calculate per-atom array", val.id); + if (val.argindex && (val.argindex > val.val.f->size_peratom_cols)) + error->all(FLERR, "Fix store/state fix {} array is accessed out-of-range", val.id); + if (nevery % val.val.f->peratom_freq) + error->all(FLERR, "Fix {} for fix store/state not computed at compatible time", val.id); - } else if (which[i] == ArgInfo::VARIABLE) { - int ivariable = input->variable->find(ids[i]); - if (ivariable < 0) - error->all(FLERR,"Variable name for fix store/state does not exist"); - if (input->variable->atomstyle(ivariable) == 0) - error->all(FLERR,"Fix store/state variable is not atom-style variable"); + } else if (val.which == ArgInfo::VARIABLE) { + val.val.v = input->variable->find(val.id.c_str()); + if (val.val.v < 0) + error->all(FLERR, "Variable name {} for fix store/state does not exist", val.id); + if (input->variable->atomstyle(val.val.v) == 0) + error->all(FLERR,"Fix store/state variable {} is not atom-style variable", val.id); - } else if (which[i] == ArgInfo::DNAME) { - int icustom,iflag,icol; - icustom = atom->find_custom(ids[i],iflag,icol); - if (icustom < 0) - error->all(FLERR,"Custom vector/array for fix store/state does not exist"); - if (argindex[i] == 0) { + } else if (val.which == ArgInfo::DNAME) { + int iflag,icol; + val.val.d = atom->find_custom(val.id.c_str(),iflag,icol); + if (val.val.d < 0) + error->all(FLERR,"Custom vector/array {} for fix store/state does not exist", val.id); + if (val.argindex == 0) { if (!iflag || icol) - error->all(FLERR, - "Custom double vector for fix store/state does not exist"); + error->all(FLERR, "Custom property {} for fix store/state is not double vector", val.id); } else { if (!iflag || !icol) - error->all(FLERR, - "Custom double array for fix store/state does not exist"); - if (argindex[i] > atom->dcols[icustom]) - error->all(FLERR, - "Fix store/state custom array is accessed out-of-range"); + error->all(FLERR, "Custom property {} for fix store/state is not double array", val.id); + if (val.argindex > atom->dcols[val.val.d]) + error->all(FLERR, "Fix store/state custom array {} is accessed out-of-range", val.id); } - } else if (which[i] == ArgInfo::INAME) { - int icustom,iflag,icol; - icustom = atom->find_custom(ids[i],iflag,icol); - if (icustom < 0) - error->all(FLERR,"Custom vector/array for fix store/state does not exist"); - if (argindex[i] == 0) { + } else if (val.which == ArgInfo::INAME) { + int iflag,icol; + val.val.i = atom->find_custom(val.id.c_str(),iflag,icol); + if (val.val.i < 0) + error->all(FLERR, "Custom vector/array {} for fix store/state does not exist", val.id); + if (val.argindex == 0) { if (iflag || icol) - error->all(FLERR, - "Custom integer vector for fix store/state does not exist"); + error->all(FLERR, "Custom property {} for fix store/state is not integer vector", val.id); } else { if (iflag || !icol) - error->all(FLERR, - "Custom integer array for fix store/state does not exist"); - if (argindex[i] > atom->icols[icustom]) - error->all(FLERR, - "Fix store/state custom array is accessed out-of-range"); + error->all(FLERR, "Custom property {} for fix store/state is not integer array", val.id); + if (val.argindex > atom->icols[val.val.i]) + error->all(FLERR, "Fix store/state custom array {} is accessed out-of-range", val.id); } } } @@ -325,13 +322,13 @@ FixStoreState::FixStoreState(LAMMPS *lmp, int narg, char **arg) : // this fix produces either a per-atom vector or array peratom_flag = 1; - if (nvalues == 1) size_peratom_cols = 0; - else size_peratom_cols = nvalues; + if (values.size() == 1) size_peratom_cols = 0; + else size_peratom_cols = values.size(); // perform initial allocation of atom-based array // register with Atom class - values = nullptr; + avalues = nullptr; FixStoreState::grow_arrays(atom->nmax); atom->add_callback(Atom::GROW); atom->add_callback(Atom::RESTART); @@ -341,8 +338,8 @@ FixStoreState::FixStoreState(LAMMPS *lmp, int narg, char **arg) : int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) - for (int m = 0; m < nvalues; m++) - values[i][m] = 0.0; + for (std::size_t m = 0; m < values.size(); m++) + avalues[i][m] = 0.0; // store current values for keywords but not for compute, fix, variable @@ -361,14 +358,7 @@ FixStoreState::~FixStoreState() atom->delete_callback(id,Atom::GROW); atom->delete_callback(id,Atom::RESTART); - delete [] which; - delete [] argindex; - for (int m = 0; m < nvalues; m++) delete [] ids[m]; - delete [] ids; - delete [] value2index; - delete [] pack_choice; - - memory->destroy(values); + memory->destroy(avalues); } /* ---------------------------------------------------------------------- */ @@ -389,31 +379,33 @@ void FixStoreState::init() if (!firstflag && nevery == 0) return; - for (int m = 0; m < nvalues; m++) { - if (which[m] == ArgInfo::COMPUTE) { - int icompute = modify->find_compute(ids[m]); - if (icompute < 0) - error->all(FLERR,"Compute ID for fix store/state does not exist"); - value2index[m] = icompute; + for (auto &val : values) { + if (val.which == ArgInfo::COMPUTE) { + val.val.c = modify->get_compute_by_id(val.id); + if (!val.val.c) + error->all(FLERR,"Compute ID {} for fix store/state does not exist", val.id); - } else if (which[m] == ArgInfo::FIX) { - int ifix = modify->find_fix(ids[m]); - if (ifix < 0) - error->all(FLERR,"Fix ID for fix store/state does not exist"); - value2index[m] = ifix; + } else if (val.which == ArgInfo::FIX) { + val.val.f = modify->get_fix_by_id(val.id); + if (!val.val.f) + error->all(FLERR,"Fix ID {} for fix store/state does not exist", val.id); - } else if (which[m] == ArgInfo::VARIABLE) { - int ivariable = input->variable->find(ids[m]); - if (ivariable < 0) - error->all(FLERR,"Variable name for fix store/state does not exist"); - value2index[m] = ivariable; + } else if (val.which == ArgInfo::VARIABLE) { + val.val.v = input->variable->find(val.id.c_str()); + if (val.val.v < 0) + error->all(FLERR,"Variable name {} for fix store/state does not exist", val.id); - } else if (which[m] == ArgInfo::INAME || which[m] == ArgInfo::DNAME) { - int icustom,iflag,cols; - icustom = atom->find_custom(ids[m],iflag,cols); - if (icustom < 0) - error->all(FLERR,"Custom vector/array for fix store/state does not exist"); - value2index[m] = icustom; + } else if (val.which == ArgInfo::DNAME) { + int iflag,cols; + val.val.d = atom->find_custom(val.id.c_str(), iflag, cols); + if (val.val.d < 0) + error->all(FLERR,"Custom vector/array {} for fix store/state does not exist", val.id); + + } else if (val.which == ArgInfo::INAME) { + int iflag,cols; + val.val.i = atom->find_custom(val.id.c_str(), iflag, cols); + if (val.val.i < 0) + error->all(FLERR,"Custom vector/array {} for fix store/state does not exist", val.id); } } } @@ -437,8 +429,6 @@ void FixStoreState::setup(int /*vflag*/) void FixStoreState::end_of_step() { - int i,j,n; - // compute com if comflag set if (comflag) { @@ -452,86 +442,85 @@ void FixStoreState::end_of_step() // fill vector or array with per-atom values - if (values) vbuf = &values[0][0]; + if (avalues) vbuf = &avalues[0][0]; else vbuf = nullptr; - for (int m = 0; m < nvalues; m++) { - if (which[m] == ArgInfo::KEYWORD && kflag) (this->*pack_choice[m])(m); + int m = 0; + for (auto &val : values) { + if (val.which == ArgInfo::KEYWORD && kflag) + (this->*val.pack_choice)(m); else if (cfv_flag) { - n = value2index[m]; - j = argindex[m]; int *mask = atom->mask; int nlocal = atom->nlocal; - // invoke compute if not previously invoked + // invoke compute if not previously invoked, then access fields - if (which[m] == ArgInfo::COMPUTE) { - Compute *compute = modify->compute[n]; - if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) { - compute->compute_peratom(); - compute->invoked_flag |= Compute::INVOKED_PERATOM; + if (val.which == ArgInfo::COMPUTE) { + if (!(val.val.c->invoked_flag & Compute::INVOKED_PERATOM)) { + val.val.c->compute_peratom(); + val.val.c->invoked_flag |= Compute::INVOKED_PERATOM; } - if (j == 0) { - double *compute_vector = compute->vector_atom; - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit) values[i][m] = compute_vector[i]; + if (val.argindex == 0) { + double *compute_vector = val.val.c->vector_atom; + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) avalues[i][m] = compute_vector[i]; } else { - int jm1 = j - 1; - double **compute_array = compute->array_atom; - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit) values[i][m] = compute_array[i][jm1]; + int jm1 = val.argindex - 1; + double **compute_array = val.val.c->array_atom; + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) avalues[i][m] = compute_array[i][jm1]; } // access fix fields, guaranteed to be ready - } else if (which[m] == ArgInfo::FIX) { - if (j == 0) { - double *fix_vector = modify->fix[n]->vector_atom; - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit) values[i][m] = fix_vector[i]; + } else if (val.which == ArgInfo::FIX) { + if (val.argindex == 0) { + double *fix_vector = val.val.f->vector_atom; + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) avalues[i][m] = fix_vector[i]; } else { - int jm1 = j - 1; - double **fix_array = modify->fix[n]->array_atom; - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit) values[i][m] = fix_array[i][jm1]; + int jm1 = val.argindex - 1; + double **fix_array = val.val.f->array_atom; + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) avalues[i][m] = fix_array[i][jm1]; } // evaluate atom-style variable - } else if (which[m] == ArgInfo::VARIABLE) { - input->variable->compute_atom(n,igroup,&values[0][m],nvalues,0); - + } else if (val.which == ArgInfo::VARIABLE) { + input->variable->compute_atom(val.val.v, igroup, &avalues[0][m], values.size(),0); // access custom atom vector/array fields - } else if (which[m] == ArgInfo::DNAME) { - if (j == 0) { - double *dvector = atom->dvector[n]; - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit) values[i][m] = dvector[i]; + } else if (val.which == ArgInfo::DNAME) { + if (val.argindex == 0) { + double *dvector = atom->dvector[val.val.d]; + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) avalues[i][m] = dvector[i]; } else { - double **darray = atom->darray[n]; - int jm1 = j - 1; - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit) values[i][m] = darray[i][jm1]; + double **darray = atom->darray[val.val.d]; + int jm1 = val.argindex - 1; + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) avalues[i][m] = darray[i][jm1]; } - } else if (which[m] == ArgInfo::INAME) { - if (j == 0) { - int *ivector = atom->ivector[n]; - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit) values[i][m] = ivector[i]; + } else if (val.which == ArgInfo::INAME) { + if (val.argindex == 0) { + int *ivector = atom->ivector[val.val.i]; + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) avalues[i][m] = ivector[i]; } else { - int **iarray = atom->iarray[n]; - int jm1 = j - 1; - for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit) values[i][m] = iarray[i][jm1]; + int **iarray = atom->iarray[val.val.i]; + int jm1 = val.argindex - 1; + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) avalues[i][m] = iarray[i][jm1]; } } } + ++m; } // if any compute/fix/variable and nevery, wrap with clear/add @@ -548,7 +537,7 @@ void FixStoreState::end_of_step() double FixStoreState::memory_usage() { - double bytes = (double)atom->nmax*nvalues * sizeof(double); + double bytes = (double)atom->nmax*values.size() * sizeof(double); return bytes; } @@ -558,11 +547,11 @@ double FixStoreState::memory_usage() void FixStoreState::grow_arrays(int nmax) { - memory->grow(values,nmax,nvalues,"store/state:values"); - if (nvalues == 1) { - if (nmax) vector_atom = &values[0][0]; + memory->grow(avalues,nmax,values.size(),"store/state:avalues"); + if (values.size() == 1) { + if (nmax) vector_atom = &avalues[0][0]; else vector_atom = nullptr; - } else array_atom = values; + } else array_atom = avalues; } /* ---------------------------------------------------------------------- @@ -571,7 +560,7 @@ void FixStoreState::grow_arrays(int nmax) void FixStoreState::copy_arrays(int i, int j, int /*delflag*/) { - for (int m = 0; m < nvalues; m++) values[j][m] = values[i][m]; + for (std::size_t m = 0; m < values.size(); m++) avalues[j][m] = avalues[i][m]; } /* ---------------------------------------------------------------------- @@ -580,8 +569,8 @@ void FixStoreState::copy_arrays(int i, int j, int /*delflag*/) int FixStoreState::pack_exchange(int i, double *buf) { - for (int m = 0; m < nvalues; m++) buf[m] = values[i][m]; - return nvalues; + for (std::size_t m = 0; m < values.size(); m++) buf[m] = avalues[i][m]; + return values.size(); } /* ---------------------------------------------------------------------- @@ -590,8 +579,8 @@ int FixStoreState::pack_exchange(int i, double *buf) int FixStoreState::unpack_exchange(int nlocal, double *buf) { - for (int m = 0; m < nvalues; m++) values[nlocal][m] = buf[m]; - return nvalues; + for (std::size_t m = 0; m < values.size(); m++) avalues[nlocal][m] = buf[m]; + return values.size(); } /* ---------------------------------------------------------------------- @@ -601,9 +590,9 @@ int FixStoreState::unpack_exchange(int nlocal, double *buf) int FixStoreState::pack_restart(int i, double *buf) { // pack buf[0] this way because other fixes unpack it - buf[0] = nvalues+1; - for (int m = 0; m < nvalues; m++) buf[m+1] = values[i][m]; - return nvalues+1; + buf[0] = values.size()+1; + for (std::size_t m = 0; m < values.size(); m++) buf[m+1] = avalues[i][m]; + return values.size()+1; } /* ---------------------------------------------------------------------- @@ -618,10 +607,10 @@ void FixStoreState::unpack_restart(int nlocal, int nth) // unpack the Nth first values this way because other fixes pack them int m = 0; - for (int i = 0; i < nth; i++) m += static_cast (extra[nlocal][m]); + for (int i = 0; i < nth; i++) m += static_cast(extra[nlocal][m]); m++; - for (int i = 0; i < nvalues; i++) values[nlocal][i] = extra[nlocal][m++]; + for (std::size_t i = 0; i < values.size(); i++) avalues[nlocal][i] = extra[nlocal][m++]; } /* ---------------------------------------------------------------------- @@ -630,7 +619,7 @@ void FixStoreState::unpack_restart(int nlocal, int nth) int FixStoreState::maxsize_restart() { - return nvalues+1; + return values.size()+1; } /* ---------------------------------------------------------------------- @@ -639,12 +628,12 @@ int FixStoreState::maxsize_restart() int FixStoreState::size_restart(int /*nlocal*/) { - return nvalues+1; + return values.size()+1; } /* ---------------------------------------------------------------------- one method for every keyword fix store/state can archive - the atom property is packed into buf starting at n with stride nvalues + the atom property is packed into buf starting at n with stride values.size() customize a new keyword by adding a method ------------------------------------------------------------------------- */ @@ -659,7 +648,7 @@ void FixStoreState::pack_id(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = tag[i]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -674,7 +663,7 @@ void FixStoreState::pack_molecule(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = molecule[i]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -689,7 +678,7 @@ void FixStoreState::pack_type(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = type[i]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -707,13 +696,13 @@ void FixStoreState::pack_mass(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = rmass[i]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } else { for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = mass[type[i]]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } } @@ -729,7 +718,7 @@ void FixStoreState::pack_x(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = x[i][0]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -744,7 +733,7 @@ void FixStoreState::pack_y(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = x[i][1]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -759,7 +748,7 @@ void FixStoreState::pack_z(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = x[i][2]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -777,7 +766,7 @@ void FixStoreState::pack_xs(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = (x[i][0] - boxxlo) * invxprd; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -795,7 +784,7 @@ void FixStoreState::pack_ys(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = (x[i][1] - boxylo) * invyprd; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -813,7 +802,7 @@ void FixStoreState::pack_zs(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = (x[i][2] - boxzlo) * invzprd; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -833,7 +822,7 @@ void FixStoreState::pack_xs_triclinic(int n) vbuf[n] = h_inv[0]*(x[i][0]-boxlo[0]) + h_inv[5]*(x[i][1]-boxlo[1]) + h_inv[4]*(x[i][2]-boxlo[2]); else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -852,7 +841,7 @@ void FixStoreState::pack_ys_triclinic(int n) if (mask[i] & groupbit) vbuf[n] = h_inv[1]*(x[i][1]-boxlo[1]) + h_inv[3]*(x[i][2]-boxlo[2]); else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -871,7 +860,7 @@ void FixStoreState::pack_zs_triclinic(int n) if (mask[i] & groupbit) vbuf[n] = h_inv[2]*(x[i][2]-boxlo[2]); else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -891,7 +880,7 @@ void FixStoreState::pack_xu(int n) vbuf[n] = x[i][0] + ((image[i] & IMGMASK) - IMGMAX) * xprd; if (comflag) vbuf[n] -= cm[0]; } else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -911,7 +900,7 @@ void FixStoreState::pack_yu(int n) vbuf[n] = x[i][1] + ((image[i] >> IMGBITS & IMGMASK) - IMGMAX) * yprd; if (comflag) vbuf[n] -= cm[1]; } else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -931,7 +920,7 @@ void FixStoreState::pack_zu(int n) vbuf[n] = x[i][2] + ((image[i] >> IMG2BITS) - IMGMAX) * zprd; if (comflag) vbuf[n] -= cm[2]; } else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -955,7 +944,7 @@ void FixStoreState::pack_xu_triclinic(int n) vbuf[n] = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox; if (comflag) vbuf[n] -= cm[0]; } else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -978,7 +967,7 @@ void FixStoreState::pack_yu_triclinic(int n) vbuf[n] = x[i][1] + h[1]*ybox + h[3]*zbox; if (comflag) vbuf[n] -= cm[1]; } else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1000,7 +989,7 @@ void FixStoreState::pack_zu_triclinic(int n) vbuf[n] = x[i][2] + h[2]*zbox; if (comflag) vbuf[n] -= cm[2]; } else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1020,7 +1009,7 @@ void FixStoreState::pack_xsu(int n) if (mask[i] & groupbit) vbuf[n] = (x[i][0]-boxxlo)*invxprd + ((image[i] & IMGMASK) - IMGMAX); else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1041,7 +1030,7 @@ void FixStoreState::pack_ysu(int n) vbuf[n] = (x[i][1]-boxylo)*invyprd + (image[i] >> IMGBITS & IMGMASK) - IMGMAX; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1061,7 +1050,7 @@ void FixStoreState::pack_zsu(int n) if (mask[i] & groupbit) vbuf[n] = (x[i][2]-boxzlo)*invzprd + (image[i] >> IMG2BITS) - IMGMAX; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1082,7 +1071,7 @@ void FixStoreState::pack_xsu_triclinic(int n) vbuf[n] = h_inv[0]*(x[i][0]-boxlo[0]) + h_inv[5]*(x[i][1]-boxlo[1]) + h_inv[4]*(x[i][2]-boxlo[2]) + (image[i] & IMGMASK) - IMGMAX; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1103,7 +1092,7 @@ void FixStoreState::pack_ysu_triclinic(int n) vbuf[n] = h_inv[1]*(x[i][1]-boxlo[1]) + h_inv[3]*(x[i][2]-boxlo[2]) + (image[i] >> IMGBITS & IMGMASK) - IMGMAX; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1123,7 +1112,7 @@ void FixStoreState::pack_zsu_triclinic(int n) if (mask[i] & groupbit) vbuf[n] = h_inv[2]*(x[i][2]-boxlo[2]) + (image[i] >> IMG2BITS) - IMGMAX; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1138,7 +1127,7 @@ void FixStoreState::pack_ix(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = (image[i] & IMGMASK) - IMGMAX; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1154,7 +1143,7 @@ void FixStoreState::pack_iy(int n) if (mask[i] & groupbit) vbuf[n] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1169,7 +1158,7 @@ void FixStoreState::pack_iz(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = (image[i] >> IMG2BITS) - IMGMAX; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1184,7 +1173,7 @@ void FixStoreState::pack_vx(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = v[i][0]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1199,7 +1188,7 @@ void FixStoreState::pack_vy(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = v[i][1]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1214,7 +1203,7 @@ void FixStoreState::pack_vz(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = v[i][2]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1229,7 +1218,7 @@ void FixStoreState::pack_fx(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = f[i][0]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1244,7 +1233,7 @@ void FixStoreState::pack_fy(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = f[i][1]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1259,7 +1248,7 @@ void FixStoreState::pack_fz(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = f[i][2]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1274,7 +1263,7 @@ void FixStoreState::pack_q(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = q[i]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1289,7 +1278,7 @@ void FixStoreState::pack_mux(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = mu[i][0]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1304,7 +1293,7 @@ void FixStoreState::pack_muy(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = mu[i][1]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1319,7 +1308,7 @@ void FixStoreState::pack_muz(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = mu[i][2]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1334,7 +1323,7 @@ void FixStoreState::pack_mu(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = mu[i][3]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1349,7 +1338,7 @@ void FixStoreState::pack_radius(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = radius[i]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1364,7 +1353,7 @@ void FixStoreState::pack_diameter(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = 2.0*radius[i]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1379,7 +1368,7 @@ void FixStoreState::pack_omegax(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = omega[i][0]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1394,7 +1383,7 @@ void FixStoreState::pack_omegay(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = omega[i][1]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1409,7 +1398,7 @@ void FixStoreState::pack_omegaz(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = omega[i][2]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1424,7 +1413,7 @@ void FixStoreState::pack_angmomx(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = angmom[i][0]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1439,7 +1428,7 @@ void FixStoreState::pack_angmomy(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = angmom[i][1]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1454,7 +1443,7 @@ void FixStoreState::pack_angmomz(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = angmom[i][2]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1469,7 +1458,7 @@ void FixStoreState::pack_tqx(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = torque[i][0]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1484,7 +1473,7 @@ void FixStoreState::pack_tqy(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = torque[i][1]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } @@ -1499,6 +1488,6 @@ void FixStoreState::pack_tqz(int n) for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) vbuf[n] = torque[i][2]; else vbuf[n] = 0.0; - n += nvalues; + n += values.size(); } } diff --git a/src/fix_store_state.h b/src/fix_store_state.h index 245d54c8e5..8bb23ecc95 100644 --- a/src/fix_store_state.h +++ b/src/fix_store_state.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -44,10 +44,22 @@ class FixStoreState : public Fix { int maxsize_restart() override; private: - int nvalues; - int *which, *argindex, *value2index; - char **ids; - double **values; // archived atom properties + struct value_t { + int which; + int argindex; + std::string id; + union { + class Compute *c; + class Fix *f; + int v; + int d; + int i; + } val; + void (FixStoreState::* pack_choice)(int); // ptr to pack function + }; + std::vector values; + + double **avalues; // archived atom properties double *vbuf; // 1d ptr to values int comflag; @@ -56,9 +68,6 @@ class FixStoreState : public Fix { int kflag, cfv_flag, firstflag; int cfv_any; // 1 if any compute/fix/variable specified - typedef void (FixStoreState::*FnPtrPack)(int); - FnPtrPack *pack_choice; // ptrs to pack functions - void pack_id(int); void pack_molecule(int); void pack_type(int); @@ -113,8 +122,6 @@ class FixStoreState : public Fix { void pack_tqy(int); void pack_tqz(int); }; - } // namespace LAMMPS_NS - #endif #endif diff --git a/src/fix_temp_berendsen.cpp b/src/fix_temp_berendsen.cpp index 07ad556943..ea2ffeb2c0 100644 --- a/src/fix_temp_berendsen.cpp +++ b/src/fix_temp_berendsen.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_temp_berendsen.h b/src/fix_temp_berendsen.h index a2fe84ad26..78ece2af22 100644 --- a/src/fix_temp_berendsen.h +++ b/src/fix_temp_berendsen.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_temp_rescale.cpp b/src/fix_temp_rescale.cpp index e248dfe92c..1a8993675a 100644 --- a/src/fix_temp_rescale.cpp +++ b/src/fix_temp_rescale.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_temp_rescale.h b/src/fix_temp_rescale.h index b1ca81e724..a448c55605 100644 --- a/src/fix_temp_rescale.h +++ b/src/fix_temp_rescale.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_thermal_conductivity.cpp b/src/fix_thermal_conductivity.cpp index bdd516ae80..5fcb59d276 100644 --- a/src/fix_thermal_conductivity.cpp +++ b/src/fix_thermal_conductivity.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_thermal_conductivity.h b/src/fix_thermal_conductivity.h index 6d7cfc39ad..536de1e56b 100644 --- a/src/fix_thermal_conductivity.h +++ b/src/fix_thermal_conductivity.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_update_special_bonds.cpp b/src/fix_update_special_bonds.cpp index 78c520344c..1c2f91f06b 100644 --- a/src/fix_update_special_bonds.cpp +++ b/src/fix_update_special_bonds.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -15,11 +15,11 @@ #include "atom.h" #include "atom_vec.h" +#include "comm.h" #include "error.h" #include "force.h" #include "modify.h" #include "neigh_list.h" -#include "neighbor.h" #include "pair.h" #include @@ -35,6 +35,8 @@ FixUpdateSpecialBonds::FixUpdateSpecialBonds(LAMMPS *lmp, int narg, char **arg) Fix(lmp, narg, arg) { if (narg != 3) error->all(FLERR, "Illegal fix update/special/bonds command"); + + restart_global = 1; } /* ---------------------------------------------------------------------- */ @@ -54,7 +56,7 @@ void FixUpdateSpecialBonds::setup(int /*vflag*/) // error if more than one fix update/special/bonds if (modify->get_fix_by_style("UPDATE_SPECIAL_BONDS").size() > 1) - error->all(FLERR,"More than one fix update/special/bonds"); + error->all(FLERR, "More than one fix update/special/bonds"); // Require atoms know about all of their bonds and if they break if (force->newton_bond) error->all(FLERR, "Fix update/special/bonds requires Newton bond off"); @@ -70,12 +72,6 @@ void FixUpdateSpecialBonds::setup(int /*vflag*/) force->special_coul[3] != 1.0) error->all(FLERR, "Fix update/special/bonds requires special Coulomb weights = 1,1,1"); // Implies neighbor->special_flag = [X, 2, 1, 1] - - new_broken_pairs.clear(); - broken_pairs.clear(); - - new_created_pairs.clear(); - created_pairs.clear(); } /* ---------------------------------------------------------------------- @@ -131,14 +127,14 @@ void FixUpdateSpecialBonds::pre_exchange() // ignore n2, n3 since 1-3, 1-4 special factors required to be 1.0 n1 = nspecial[i][0]; if (n1 >= atom->maxspecial) - error->one(FLERR,"Special list size exceeded in fix update/special/bond"); + error->one(FLERR, "Special list size exceeded in fix update/special/bond"); special[i][n1] = tagj; nspecial[i][0] += 1; nspecial[i][1] = nspecial[i][2] = nspecial[i][0]; n1 = nspecial[j][0]; if (n1 >= atom->maxspecial) - error->one(FLERR,"Special list size exceeded in fix update/special/bond"); + error->one(FLERR, "Special list size exceeded in fix update/special/bond"); special[j][n1] = tagi; nspecial[j][0] += 1; nspecial[j][1] = nspecial[j][2] = nspecial[j][0]; @@ -210,8 +206,8 @@ void FixUpdateSpecialBonds::pre_force(int /*vflag*/) jnum = numneigh[i1]; for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; - if (((j >> SBBITS) & 3) != 0) continue; // Skip bonded pairs - if (tag[j] == tag2) jlist[jj] = j ^ (1 << SBBITS); // Add 1-2 special bond bits + if (((j >> SBBITS) & 3) != 0) continue; // Skip bonded pairs + if (tag[j] == tag2) jlist[jj] = j ^ (1 << SBBITS); // Add 1-2 special bond bits } } @@ -220,8 +216,8 @@ void FixUpdateSpecialBonds::pre_force(int /*vflag*/) jnum = numneigh[i2]; for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; - if (((j >> SBBITS) & 3) != 0) continue; // Skip bonded pairs - if (tag[j] == tag1) jlist[jj] = j ^ (1 << SBBITS); // Add 1-2 special bond bits + if (((j >> SBBITS) & 3) != 0) continue; // Skip bonded pairs + if (tag[j] == tag1) jlist[jj] = j ^ (1 << SBBITS); // Add 1-2 special bond bits } } } @@ -247,3 +243,18 @@ void FixUpdateSpecialBonds::add_created_bond(int i, int j) new_created_pairs.push_back(tag_pair); created_pairs.push_back(tag_pair); } + +/* ---------------------------------------------------------------------- + Use write_restart to invoke pre_exchange +------------------------------------------------------------------------- */ + +void FixUpdateSpecialBonds::write_restart(FILE *fp) +{ + // Call pre-exchange to process any broken/created bonds + + pre_exchange(); + if (comm->me == 0) { + int size = 0; + fwrite(&size,sizeof(int),1,fp); + } +} diff --git a/src/fix_update_special_bonds.h b/src/fix_update_special_bonds.h index 825977d37f..30d0faeb4b 100644 --- a/src/fix_update_special_bonds.h +++ b/src/fix_update_special_bonds.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -23,7 +23,6 @@ FixStyle(UPDATE_SPECIAL_BONDS,FixUpdateSpecialBonds); #include "fix.h" #include -#include namespace LAMMPS_NS { @@ -36,6 +35,7 @@ class FixUpdateSpecialBonds : public Fix { void pre_force(int) override; void add_broken_bond(int, int); void add_created_bond(int, int); + void write_restart(FILE *) override; protected: // Create two arrays to store bonds broken this timestep (new) diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp index f1da015382..6d561a58df 100644 --- a/src/fix_vector.cpp +++ b/src/fix_vector.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -47,8 +47,7 @@ FixVector::FixVector(LAMMPS *lmp, int narg, char **arg) : val.id = argi.get_name(); val.val.c = nullptr; - if ((val.which == ArgInfo::UNKNOWN) || (val.which == ArgInfo::NONE) || - (argi.get_dim() > 1)) + if ((val.which == ArgInfo::UNKNOWN) || (val.which == ArgInfo::NONE) || (argi.get_dim() > 1)) error->all(FLERR, "Invalid fix vector argument: {}", arg[iarg]); values.push_back(val); diff --git a/src/fix_vector.h b/src/fix_vector.h index 3c2f69b21b..5d29492aa8 100644 --- a/src/fix_vector.h +++ b/src/fix_vector.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_viscous.cpp b/src/fix_viscous.cpp index 65515f2802..fb0b38f264 100644 --- a/src/fix_viscous.cpp +++ b/src/fix_viscous.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -61,6 +61,8 @@ FixViscous::FixViscous(LAMMPS *lmp, int narg, char **arg) : FixViscous::~FixViscous() { + if (copymode) return; + delete [] gamma; } diff --git a/src/fix_viscous.h b/src/fix_viscous.h index 7d7608621c..4c04d979cb 100644 --- a/src/fix_viscous.h +++ b/src/fix_viscous.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp index 0eee94b1f7..d624ee9ff7 100644 --- a/src/fix_wall.cpp +++ b/src/fix_wall.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_wall.h b/src/fix_wall.h index 2aeaf040e7..32fccea2b3 100644 --- a/src/fix_wall.h +++ b/src/fix_wall.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_wall_harmonic.cpp b/src/fix_wall_harmonic.cpp index 4b55dde8aa..a8e4127523 100644 --- a/src/fix_wall_harmonic.cpp +++ b/src/fix_wall_harmonic.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_wall_harmonic.h b/src/fix_wall_harmonic.h index 37038fa9ef..34e9a9a2df 100644 --- a/src/fix_wall_harmonic.h +++ b/src/fix_wall_harmonic.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_wall_lj1043.cpp b/src/fix_wall_lj1043.cpp index 592636b937..dd6b5122f0 100644 --- a/src/fix_wall_lj1043.cpp +++ b/src/fix_wall_lj1043.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_wall_lj1043.h b/src/fix_wall_lj1043.h index 9e09a4b6b9..a0dc983114 100644 --- a/src/fix_wall_lj1043.h +++ b/src/fix_wall_lj1043.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_wall_lj126.cpp b/src/fix_wall_lj126.cpp index 068663bd85..78d9656e7f 100644 --- a/src/fix_wall_lj126.cpp +++ b/src/fix_wall_lj126.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_wall_lj126.h b/src/fix_wall_lj126.h index 93a529e358..01999a5f82 100644 --- a/src/fix_wall_lj126.h +++ b/src/fix_wall_lj126.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_wall_lj93.cpp b/src/fix_wall_lj93.cpp index 5a93732461..1e02b61fe1 100644 --- a/src/fix_wall_lj93.cpp +++ b/src/fix_wall_lj93.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_wall_lj93.h b/src/fix_wall_lj93.h index 8dae6ade30..147795368f 100644 --- a/src/fix_wall_lj93.h +++ b/src/fix_wall_lj93.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_wall_morse.cpp b/src/fix_wall_morse.cpp index 942e8e0e04..a1427b380f 100644 --- a/src/fix_wall_morse.cpp +++ b/src/fix_wall_morse.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_wall_morse.h b/src/fix_wall_morse.h index 518ece2302..b80bff0742 100644 --- a/src/fix_wall_morse.h +++ b/src/fix_wall_morse.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_wall_reflect.cpp b/src/fix_wall_reflect.cpp index 27f3b41f8b..60a055fbd6 100644 --- a/src/fix_wall_reflect.cpp +++ b/src/fix_wall_reflect.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_wall_reflect.h b/src/fix_wall_reflect.h index 6021bfa10d..05acfe94cf 100644 --- a/src/fix_wall_reflect.h +++ b/src/fix_wall_reflect.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_wall_region.cpp b/src/fix_wall_region.cpp index 41a96fe374..ad94c3985f 100644 --- a/src/fix_wall_region.cpp +++ b/src/fix_wall_region.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fix_wall_region.h b/src/fix_wall_region.h index 43671c83b1..77b82d012c 100644 --- a/src/fix_wall_region.h +++ b/src/fix_wall_region.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/fmt/core.h b/src/fmt/core.h index 39000078c0..0634f94412 100644 --- a/src/fmt/core.h +++ b/src/fmt/core.h @@ -291,8 +291,9 @@ #endif // Enable minimal optimizations for more compact code in debug mode. +// LAMMPS customization: exclude __NVCC__ in addition to __NVCOMPILER for nvcc from CUDA toolkit FMT_GCC_PRAGMA("GCC push_options") -#if !defined(__OPTIMIZE__) && !defined(__NVCOMPILER) +#if !defined(__OPTIMIZE__) && !defined(__NVCOMPILER) && !defined(__NVCC__) FMT_GCC_PRAGMA("GCC optimize(\"Og\")") #endif diff --git a/src/force.cpp b/src/force.cpp index 3c5e6fe7c8..347b3087cf 100644 --- a/src/force.cpp +++ b/src/force.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -237,22 +237,13 @@ void Force::create_pair(const std::string &style, int trysuffix) /* ---------------------------------------------------------------------- generate a pair class if trysuffix = 1, try first with suffix1/2 appended - return sflag = 0 for no suffix added, 1 or 2 or 3 for suffix1/2/p added - special case: if suffixp exists only try suffixp, not suffix + return sflag = 0 for no suffix added, 1 or 2 for suffix1/2 added ------------------------------------------------------------------------- */ Pair *Force::new_pair(const std::string &style, int trysuffix, int &sflag) { if (trysuffix && lmp->suffix_enable) { - if (lmp->suffixp) { - sflag = 3; - std::string estyle = style + "/" + lmp->suffixp; - if (pair_map->find(estyle) != pair_map->end()) { - PairCreator &pair_creator = (*pair_map)[estyle]; - return pair_creator(lmp); - } - } - if (lmp->suffix && !lmp->suffixp) { + if (lmp->suffix) { sflag = 1; std::string estyle = style + "/" + lmp->suffix; if (pair_map->find(estyle) != pair_map->end()) { @@ -354,9 +345,9 @@ void Force::create_bond(const std::string &style, int trysuffix) Bond *Force::new_bond(const std::string &style, int trysuffix, int &sflag) { if (trysuffix && lmp->suffix_enable) { - if (lmp->suffix) { - sflag = 1; - std::string estyle = style + "/" + lmp->suffix; + if (lmp->non_pair_suffix()) { + sflag = 1 + 2*lmp->pair_only_flag; + std::string estyle = style + "/" + lmp->non_pair_suffix(); if (bond_map->find(estyle) != bond_map->end()) { BondCreator &bond_creator = (*bond_map)[estyle]; return bond_creator(lmp); @@ -422,9 +413,9 @@ void Force::create_angle(const std::string &style, int trysuffix) Angle *Force::new_angle(const std::string &style, int trysuffix, int &sflag) { if (trysuffix && lmp->suffix_enable) { - if (lmp->suffix) { - sflag = 1; - std::string estyle = style + "/" + lmp->suffix; + if (lmp->non_pair_suffix()) { + sflag = 1 + 2*lmp->pair_only_flag; + std::string estyle = style + "/" + lmp->non_pair_suffix(); if (angle_map->find(estyle) != angle_map->end()) { AngleCreator &angle_creator = (*angle_map)[estyle]; return angle_creator(lmp); @@ -490,9 +481,9 @@ void Force::create_dihedral(const std::string &style, int trysuffix) Dihedral *Force::new_dihedral(const std::string &style, int trysuffix, int &sflag) { if (trysuffix && lmp->suffix_enable) { - if (lmp->suffix) { - sflag = 1; - std::string estyle = style + "/" + lmp->suffix; + if (lmp->non_pair_suffix()) { + sflag = 1 + 2*lmp->pair_only_flag; + std::string estyle = style + "/" + lmp->non_pair_suffix(); if (dihedral_map->find(estyle) != dihedral_map->end()) { DihedralCreator &dihedral_creator = (*dihedral_map)[estyle]; return dihedral_creator(lmp); @@ -558,9 +549,9 @@ void Force::create_improper(const std::string &style, int trysuffix) Improper *Force::new_improper(const std::string &style, int trysuffix, int &sflag) { if (trysuffix && lmp->suffix_enable) { - if (lmp->suffix) { - sflag = 1; - std::string estyle = style + "/" + lmp->suffix; + if (lmp->non_pair_suffix()) { + sflag = 1 + 2*lmp->pair_only_flag; + std::string estyle = style + "/" + lmp->non_pair_suffix(); if (improper_map->find(estyle) != improper_map->end()) { ImproperCreator &improper_creator = (*improper_map)[estyle]; return improper_creator(lmp); @@ -626,9 +617,9 @@ void Force::create_kspace(const std::string &style, int trysuffix) KSpace *Force::new_kspace(const std::string &style, int trysuffix, int &sflag) { if (trysuffix && lmp->suffix_enable) { - if (lmp->suffix) { - sflag = 1; - std::string estyle = style + "/" + lmp->suffix; + if (lmp->non_pair_suffix()) { + sflag = 1 + 2*lmp->pair_only_flag; + std::string estyle = style + "/" + lmp->non_pair_suffix(); if (kspace_map->find(estyle) != kspace_map->end()) { KSpaceCreator &kspace_creator = (*kspace_map)[estyle]; return kspace_creator(lmp); @@ -676,7 +667,7 @@ KSpace *Force::kspace_match(const std::string &word, int exact) /* ---------------------------------------------------------------------- store style name in str allocated here if sflag = 0, no suffix - if sflag = 1/2/3, append suffix or suffix2 or suffixp to style + if sflag = 1/2, append suffix or suffix2 to style ------------------------------------------------------------------------- */ char *Force::store_style(const std::string &style, int sflag) @@ -687,8 +678,8 @@ char *Force::store_style(const std::string &style, int sflag) estyle += std::string("/") + lmp->suffix; else if (sflag == 2) estyle += std::string("/") + lmp->suffix2; - else if (sflag == 3) - estyle += std::string("/") + lmp->suffixp; + else if ((sflag == 3) && lmp->non_pair_suffix()) + estyle += std::string("/") + lmp->non_pair_suffix(); return utils::strdup(estyle); } diff --git a/src/force.h b/src/force.h index 23eeb7e167..a076519e44 100644 --- a/src/force.h +++ b/src/force.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/grid2d.cpp b/src/grid2d.cpp new file mode 100644 index 0000000000..7858ed3a3a --- /dev/null +++ b/src/grid2d.cpp @@ -0,0 +1,1961 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "grid2d.h" + +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "irregular.h" +#include "kspace.h" +#include "math_extra.h" +#include "memory.h" +#include "pair.h" + +using namespace LAMMPS_NS; + +#define DELTA 16 + +static constexpr int OFFSET = 16384; + +/* ---------------------------------------------------------------------- + NOTES: + if o indices for ghosts are < 0 or hi indices are >= N, + then grid is treated as periodic in that dimension, + comm is done across the periodic boundaries + tiled implementations only work for RCB, not general tilings + b/c RCB tree is used to find neighboring tiles +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + constructor to create a 2d distributed grid + Grid3d assigns owned/ghost cells to each proc via setup_grid() + it MUST be called after constructor + gcomm = caller's communicator + gnx,gny,gnz = global grid size +------------------------------------------------------------------------- */ + +Grid2d::Grid2d(LAMMPS *lmp, MPI_Comm gcomm, int gnx, int gny) : + Pointers(lmp), swap(nullptr), requests(nullptr), srequest(nullptr), rrequest(nullptr), + sresponse(nullptr), rresponse(nullptr), send(nullptr), recv(nullptr), copy(nullptr), + send_remap(nullptr), recv_remap(nullptr), overlap_procs(nullptr), xsplit(nullptr), + ysplit(nullptr), zsplit(nullptr), grid2proc(nullptr), rcbinfo(nullptr), overlap_list(nullptr) +{ + gridcomm = gcomm; + MPI_Comm_rank(gridcomm, &me); + MPI_Comm_size(gridcomm, &nprocs); + + nx = gnx; + ny = gny; + + // default settings, can be overridden by set() methods + // these affect assignment of owned and ghost cells + + maxdist = 0.0; + stencil_grid_lo = stencil_grid_hi = 0; + stencil_atom_lo = stencil_atom_hi = 0; + shift_grid = 0.5; + shift_atom_lo = shift_atom_hi = 0.0; + yextra = 0; + yfactor = 1.0; +} + +/* ---------------------------------------------------------------------- + alternate constructor to create a 2d distributed grid + caller assigns owned/ghost cells to each proc + setup_grid() must NOT be called + gcomm = caller's communicator + gnx,gny = global grid size + i xy lo/hi = extent of owned grid cells on this proc + o xy lo/hi = extent of owned+ghost grid cells on this proc + owned and ghost indices are inclusive + owned indices range from 0 to N-1 + ghost indices can extend < 0 or >= N +------------------------------------------------------------------------- */ + +Grid2d::Grid2d(LAMMPS *lmp, MPI_Comm gcomm, int gnx, int gny, int ixlo, int ixhi, int iylo, + int iyhi, int oxlo, int oxhi, int oylo, int oyhi) : + Pointers(lmp), + swap(nullptr), requests(nullptr), srequest(nullptr), rrequest(nullptr), sresponse(nullptr), + rresponse(nullptr), send(nullptr), recv(nullptr), copy(nullptr), send_remap(nullptr), + recv_remap(nullptr), overlap_procs(nullptr), xsplit(nullptr), ysplit(nullptr), zsplit(nullptr), + grid2proc(nullptr), rcbinfo(nullptr), overlap_list(nullptr) +{ + gridcomm = gcomm; + MPI_Comm_rank(gridcomm, &me); + MPI_Comm_size(gridcomm, &nprocs); + + nx = gnx; + ny = gny; + + // store owned/ghost indices provided by caller + + inxlo = ixlo; + inxhi = ixhi; + inylo = iylo; + inyhi = iyhi; + + outxlo = oxlo; + outxhi = oxhi; + outylo = oylo; + outyhi = oyhi; + + // additional intialization + // other constructor invokes this from setup_grid() + + initialize(); +} + +/* ---------------------------------------------------------------------- */ + +Grid2d::~Grid2d() +{ + // brick comm data structs + + for (int i = 0; i < nswap; i++) { + memory->destroy(swap[i].packlist); + memory->destroy(swap[i].unpacklist); + } + memory->sfree(swap); + + delete[] xsplit; + delete[] ysplit; + memory->destroy(grid2proc); + + // tiled comm data structs + + for (int i = 0; i < nsend; i++) memory->destroy(send[i].packlist); + memory->sfree(send); + + for (int i = 0; i < nrecv; i++) memory->destroy(recv[i].unpacklist); + memory->sfree(recv); + + for (int i = 0; i < ncopy; i++) { + memory->destroy(copy[i].packlist); + memory->destroy(copy[i].unpacklist); + } + memory->sfree(copy); + + delete[] requests; + delete[] requests_remap; + + memory->sfree(rcbinfo); + + // remap data structs + + deallocate_remap(); +} + +// ---------------------------------------------------------------------- +// set Grid parameters +// ---------------------------------------------------------------------- + +/* ---------------------------------------------------------------------- + maxdist = max distance outside proc subdomain a particle can be + used to determine extent of ghost cells +------------------------------------------------------------------------- */ + +void Grid2d::set_distance(double distance) +{ + maxdist = distance; +} + +/* ---------------------------------------------------------------------- + # of grid cells beyond an owned grid cell that caller accesses + can be different in lo vs hi direction +------------------------------------------------------------------------- */ + +void Grid2d::set_stencil_grid(int lo, int hi) +{ + stencil_grid_lo = lo; + stencil_grid_hi = hi; +} + +/* ---------------------------------------------------------------------- + # of grid cells beyond a particle's grid cell that caller accesses + can be different in lo vs hi direction +------------------------------------------------------------------------- */ + +void Grid2d::set_stencil_atom(int lo, int hi) +{ + stencil_atom_lo = lo; + stencil_atom_hi = hi; +} + +/* ---------------------------------------------------------------------- + shift_grid = offset within grid cell of position of grid point + 0.5 = cell center (default), 0.0 = lower-left corner of cell + used to decide which proc owns a grid cell (grid pt within subdomain) +------------------------------------------------------------------------- */ + +void Grid2d::set_shift_grid(double shift) +{ + shift_grid = shift; +} + +/* ---------------------------------------------------------------------- + shift_atom = offset added to atoms when caller maps them to grid cells + 0.5 = half a grid cell, 0.0 = no offset + used to compute maximum possible ghost extents + use of lo/hi allows max ghost extent on each side to be different +------------------------------------------------------------------------- */ + +void Grid2d::set_shift_atom(double shift_lo, double shift_hi) +{ + shift_atom_lo = shift_lo; + shift_atom_hi = shift_hi; +} + +/* ---------------------------------------------------------------------- + enable extra grid cells in Y + factor = muliplication factor on box size Y and thus grid size + factor > 1.0 when grid extends beyond Y box size (3.0 = tripled in size) + only enable yextra if factor > 1.0 + default zextra = 0, factor = 1.0 (no extra grid cells in Y) +------------------------------------------------------------------------- */ + +void Grid2d::set_yfactor(double factor) +{ + if (factor == 1.0) + yextra = 0; + else + yextra = 1; + yfactor = factor; +} + +/* ---------------------------------------------------------------------- + set IDs of proc neighbors used in uniform local owned/ghost comm + must be called BEFORE setup_comm() to override + the processor neighbors stored by extract_comm_info() +------------------------------------------------------------------------- */ + +void Grid2d::set_proc_neighs(int pxlo, int pxhi, int pylo, int pyhi) +{ + procxlo = pxlo; + procxhi = pxhi; + procylo = pylo; + procyhi = pyhi; +} + +/* ---------------------------------------------------------------------- + set allocation dimensions of caller grid used by indices() to setup pack/unpack + must be called BEFORE setup_comm() to override + the caller grid size used in indices() +------------------------------------------------------------------------- */ + +void Grid2d::set_caller_grid(int fxlo, int fxhi, int fylo, int fyhi) +{ + fullxlo = fxlo; + fullxhi = fxhi; + fullylo = fylo; + fullyhi = fyhi; +} + +// ---------------------------------------------------------------------- +// retrieve Grid parameters +// ---------------------------------------------------------------------- + +int Grid2d::identical(Grid2d *grid2) +{ + int inxlo2, inxhi2, inylo2, inyhi2; + int outxlo2, outxhi2, outylo2, outyhi2; + + grid2->get_bounds_owned(inxlo2, inxhi2, inylo2, inyhi2); + grid2->get_bounds_ghost(outxlo2, outxhi2, outylo2, outyhi2); + + int flag = 0; + if ((inxlo != inxlo2) || (inxhi != inxhi2) || (inylo != inylo2) || (inyhi != inyhi2)) flag = 1; + if ((outxlo != outxlo2) || (outxhi != outxhi2) || (outylo != outylo2) || (outyhi != outyhi2)) + flag = 1; + + int flagall; + MPI_Allreduce(&flag, &flagall, 1, MPI_INT, MPI_SUM, gridcomm); + + if (flagall) return 0; + return 1; +} + +/* ---------------------------------------------------------------------- */ + +void Grid2d::get_size(int &nxgrid, int &nygrid) +{ + nxgrid = nx; + nygrid = ny; +} + +/* ---------------------------------------------------------------------- */ + +void Grid2d::get_bounds_owned(int &xlo, int &xhi, int &ylo, int &yhi) +{ + xlo = inxlo; + xhi = inxhi; + ylo = inylo; + yhi = inyhi; +} + +/* ---------------------------------------------------------------------- */ + +void Grid2d::get_bounds_ghost(int &xlo, int &xhi, int &ylo, int &yhi) +{ + xlo = outxlo; + xhi = outxhi; + ylo = outylo; + yhi = outyhi; +} + +// ---------------------------------------------------------------------- +// define owned and ghost grid cells +// also store comm and grid partitioning info +// ---------------------------------------------------------------------- + +/* ---------------------------------------------------------------------- + setup grid partition for each proc = owned + ghost cells + return: + i xy lohi = portion of global grid this proc owns, 0 <= index < N + o xy lohi = owned + ghost grid cells in all directions + for periodic dims, o indices can be < 0 or >= N + for non-periodic dims, o indices will be >= 0 and < N + since no grid comm is done across non-periodic boundaries +------------------------------------------------------------------------- */ + +void Grid2d::setup_grid(int &ixlo, int &ixhi, int &iylo, int &iyhi, int &oxlo, int &oxhi, int &oylo, + int &oyhi) +{ + // owned grid cells = those whose grid point is within proc subdomain + // shift_grid = 0.5 for grid point at cell center, 0.0 for lower-left corner + + double fraclo, frachi; + + if (comm->layout != Comm::LAYOUT_TILED) { + fraclo = comm->xsplit[comm->myloc[0]]; + frachi = comm->xsplit[comm->myloc[0] + 1]; + partition_grid(nx, fraclo, frachi, shift_grid, 0, inxlo, inxhi); + fraclo = comm->ysplit[comm->myloc[1]]; + frachi = comm->ysplit[comm->myloc[1] + 1]; + partition_grid(ny, fraclo, frachi, shift_grid, yextra, inylo, inyhi); + } else { + fraclo = comm->mysplit[0][0]; + frachi = comm->mysplit[0][1]; + partition_grid(nx, fraclo, frachi, shift_grid, 0, inxlo, inxhi); + fraclo = comm->mysplit[1][0]; + frachi = comm->mysplit[1][1]; + partition_grid(ny, fraclo, frachi, shift_grid, yextra, inylo, inyhi); + } + + // extend owned grid bounds with ghost grid cells in each direction + + ghost_grid(); + + // additional intialization + // other constructor invokes this directly + + initialize(); + + // return values + + ixlo = inxlo; + ixhi = inxhi; + iylo = inylo; + iyhi = inyhi; + + oxlo = outxlo; + oxhi = outxhi; + oylo = outylo; + oyhi = outyhi; +} + +/* ---------------------------------------------------------------------- + additional one-time setup common to both constructors + ---------------------------------------------------------------------- */ + +void Grid2d::initialize() +{ + // error check on size of grid stored by this proc + + bigint total = (bigint) (outxhi - outxlo + 1) * (outyhi - outylo + 1); + if (total > MAXSMALLINT) error->one(FLERR, "Too many owned+ghost grid2d points"); + + // default = caller grid is allocated to ghost grid + // used when computing pack/unpack lists in indices() + // these values can be overridden using set_caller_grid() + + fullxlo = outxlo; + fullxhi = outxhi; + fullylo = outylo; + fullyhi = outyhi; + + // initialize data structs + + nswap = maxswap = 0; + swap = nullptr; + + nsend = nrecv = ncopy = 0; + send = nullptr; + recv = nullptr; + copy = nullptr; + requests = nullptr; + requests_remap = nullptr; + + xsplit = ysplit = zsplit = nullptr; + grid2proc = nullptr; + rcbinfo = nullptr; + + nsend_remap = nrecv_remap = self_remap = 0; + send_remap = nullptr; + recv_remap = nullptr; + + // store info about Comm decomposition needed for remap operation + // two Grid instances will exist for duration of remap + // each must know Comm decomp at time Grid instance was created + + extract_comm_info(); +} + +/* ---------------------------------------------------------------------- + partition a global regular grid into one brick-shaped sub-grid per proc + if grid point is inside my sub-domain I own it, + this includes sub-domain lo boundary but excludes hi boundary + ngrid = extent of global grid in a dimension + indices into the global grid range from 0 to Ngrid-1 in that dim + shift determines position of grid pt within grid cell + shift = 0.5 for cell center, 0.0 for lower-left corner + extra = 0 if grid exactly covers the simulation box + extra = 1 if grid extends beyond the +y boundary by yfactor + effectively maps proc partitions to the box-size subset of the grid + lo/hi = inclusive lo/hi bounds for brick of global grid cells I own + lo grid index = first grid pt >= fraclo*bound + hi grid index = last grid pt < frachi*bound + if proc owns no grid cells in a dim, then inlo > inhi + special case: 2 procs share boundary which a grid point is exactly on + 2 if test equalties insure a consistent decision as to which proc owns it +------------------------------------------------------------------------- */ + +void Grid2d::partition_grid(int ngrid, double fraclo, double frachi, double shift, int extra, + int &lo, int &hi) +{ + if (extra == 0) { + lo = static_cast(fraclo * ngrid); + while (lo + shift < fraclo * ngrid) lo++; + hi = static_cast(frachi * ngrid); + while (hi + shift >= frachi * ngrid) hi--; + } else { + lo = static_cast(fraclo * ngrid / yfactor); + while (lo + shift < fraclo * ngrid / yfactor) lo++; + hi = static_cast(frachi * ngrid / yfactor); + while (hi + shift >= frachi * ngrid / yfactor) hi--; + } +} + +// clang-format off +/* ---------------------------------------------------------------------- + extend ghost grid cells in each direction beyond owned grid + indices into the global grid range from 0 to N-1 in each dim + ghost cell indices for periodic systems can be < 0 or >= N +------------------------------------------------------------------------- */ + +void Grid2d::ghost_grid() +{ + double *prd,*boxlo,*sublo,*subhi; + int triclinic = domain->triclinic; + + if (triclinic == 0) { + prd = domain->prd; + boxlo = domain->boxlo; + sublo = domain->sublo; + subhi = domain->subhi; + } else { + prd = domain->prd_lamda; + boxlo = domain->boxlo_lamda; + sublo = domain->sublo_lamda; + subhi = domain->subhi_lamda; + } + + // for triclinic, maxdist = different value in each orthogonal direction + + double dist[3] = {0.0,0.0,0.0}; + if (triclinic == 0) dist[0] = dist[1] = dist[2] = maxdist; + else MathExtra::tribbox(domain->h,maxdist,&dist[0]); + + // lo/hi = min/max index of global grid cells my owned atoms can be mapped to + // includes effects of maxdist and shift_atom settings + // lo/hi can be further extended by stencil_atom and stencil_grid settings + // all those settings are set by caller + // ghost cell layers needed in each dim/dir = max of two extension effects + // OFFSET allows generation of negative indices with static_cast + // out xyz lo/hi = index range of owned + ghost cells + // if yextra, ny and effective prd[1] are both larger, so dyinv is the same + + double dxinv = nx / prd[0]; + double dyinv = ny / prd[1]; + if (yextra) dyinv = ny / (prd[1] * yfactor); + + int lo, hi; + + lo = static_cast((sublo[0]-dist[0]-boxlo[0]) * dxinv + shift_atom_lo + OFFSET) - OFFSET; + hi = static_cast((subhi[0]+dist[0]-boxlo[0]) * dxinv + shift_atom_hi + OFFSET) - OFFSET; + outxlo = MIN(lo - stencil_atom_lo, inxlo - stencil_grid_lo); + outxhi = MAX(hi + stencil_atom_hi, inxhi + stencil_grid_hi); + + lo = static_cast((sublo[1]-dist[1]-boxlo[1]) * dyinv + shift_atom_lo + OFFSET) - OFFSET; + hi = static_cast((subhi[1]+dist[1]-boxlo[1]) * dyinv + shift_atom_hi + OFFSET) - OFFSET; + outylo = MIN(lo - stencil_atom_lo, inylo - stencil_grid_lo); + outyhi = MAX(hi + stencil_atom_hi, inyhi + stencil_grid_hi); + + // if yextra = 1: + // adjust grid boundaries for processors at +y end, + // to include added empty grid cells between periodically repeating slabs + // in this case: + // want grid data forward communicated from +y proc to -y proc, but not vice versa + // want grid data reverse communicated from -y proc to +y proc, but not vice versa + // this is accomplished by inyhi = outyhi on +y end (no ghost cells) + // also insure no other procs use ghost cells beyond +y limit + + if (yextra) { + if (layout != Comm::LAYOUT_TILED) { + if (comm->myloc[1] == comm->procgrid[1]-1) inyhi = outyhi = ny - 1; + } else { + if (comm->mysplit[1][1] == 1.0) inyhi = outyhi = ny - 1; + } + outyhi = MIN(outyhi,ny-1); + } + + // limit out xyz lo/hi indices to global grid for non-periodic dims + // if yextra = 1, treat y-dimension as if periodic + + int *periodicity = domain->periodicity; + + if (!periodicity[0]) { + outxlo = MAX(0,outxlo); + outxhi = MIN(nx-1,outxhi); + } + + if (!periodicity[1] && !yextra) { + outylo = MAX(0,outylo); + outyhi = MIN(ny-1,outyhi); + } +} + +/* ---------------------------------------------------------------------- + store copy of info from Comm class about processor partitioning + used when a remap is performed between two Grid instances, old and new +------------------------------------------------------------------------- */ + +void Grid2d::extract_comm_info() +{ + layout = comm->layout; + + // for non TILED layout: + // proc xyz lohi = my 4 neighbor procs in this MPI_Comm + // these proc IDs can be overridden by caller using set_proc_neighs() + // xyz split = copy of 1d vectors in Comm + // grid2proc = copy of 3d array in Comm + + if (layout != Comm::LAYOUT_TILED) { + procxlo = comm->procneigh[0][0]; + procxhi = comm->procneigh[0][1]; + procylo = comm->procneigh[1][0]; + procyhi = comm->procneigh[1][1]; + + xsplit = new double[comm->procgrid[0]+1]; + ysplit = new double[comm->procgrid[1]+1]; + memcpy(xsplit, comm->xsplit, sizeof(double) * (comm->procgrid[0]+1)); + memcpy(ysplit, comm->ysplit, sizeof(double) * (comm->procgrid[1]+1)); + + memory->create(grid2proc,comm->procgrid[0],comm->procgrid[1],comm->procgrid[2], + "grid3d:grid2proc"); + memcpy(&grid2proc[0][0][0],&comm->grid2proc[0][0][0], + sizeof(int) * comm->procgrid[0] * comm->procgrid[1] * comm->procgrid[2]); + } + + // for TILED layout: + // create RCB tree of grid partitioning info for grid decomp + // Comm provides dim info for this proc, stored as RCBinfo.dim + // dim is -1 for proc 0, but never accessed + // RCBinfo.cut = this proc's inlo in that dim + // Allgather creates the tree of dims and cuts + + if (layout == Comm::LAYOUT_TILED) { + rcbinfo = (RCBinfo *) + memory->smalloc(nprocs*sizeof(RCBinfo),"grid3d:rcbinfo"); + RCBinfo rcbone; + rcbone.dim = comm->rcbcutdim; + if (rcbone.dim <= 0) rcbone.cut = inxlo; + else if (rcbone.dim == 1) rcbone.cut = inylo; + MPI_Allgather(&rcbone,sizeof(RCBinfo),MPI_CHAR, + rcbinfo,sizeof(RCBinfo),MPI_CHAR,gridcomm); + } +} + +// ---------------------------------------------------------------------- +// setup of local owned/ghost grid comm +// ---------------------------------------------------------------------- + +/* ---------------------------------------------------------------------- + setup communication of owned/ghost grid cells + either for brick decomp or tiled decomp + return sizes of two buffers needed for communication + nbuf1 = largest pack or unpack in any Send or Recv or Copy + nbuf2 = larget of sum of all packs or unpacks in Send or Recv + for brick comm, nbuf1 = nbuf2 + for tiling comm, nbuf2 >= nbuf2 + nbuf1,nbuf2 are counts of grid cells + caller converts them to message sizes for grid data it stores +------------------------------------------------------------------------- */ + +void Grid2d::setup_comm(int &nbuf1, int &nbuf2) +{ + if (layout != Comm::LAYOUT_TILED) setup_comm_brick(nbuf1,nbuf2); + else setup_comm_tiled(nbuf1,nbuf2); +} + +/* ---------------------------------------------------------------------- + setup owned/ghost comm for brick comm + each proc has 4 neighbors + comm pattern = series of swaps with one of those 4 procs + can be multiple swaps with same proc if ghost extent is large + swap may not be symmetric if both procs do not need same layers of ghosts + all procs perform same # of swaps in a direction, even if some don't need it +------------------------------------------------------------------------- */ + +void Grid2d::setup_comm_brick(int &nbuf1, int &nbuf2) +{ + int nsent,sendfirst,sendlast,recvfirst,recvlast; + int sendplanes,recvplanes; + int notdoneme,notdone; + + // notify 4 neighbor procs how many ghost grid planes I need from them + // ghost xy lo = # of my lower grid planes that proc xy lo needs as its ghosts + // ghost xy hi = # of my upper grid planes that proc xy hi needs as its ghosts + // if this proc is its own neighbor across periodic bounary, value is from self + + int nplanes = inxlo - outxlo; + if (procxlo != me) + MPI_Sendrecv(&nplanes,1,MPI_INT,procxlo,0, + &ghostxhi,1,MPI_INT,procxhi,0,gridcomm,MPI_STATUS_IGNORE); + else ghostxhi = nplanes; + + nplanes = outxhi - inxhi; + if (procxhi != me) + MPI_Sendrecv(&nplanes,1,MPI_INT,procxhi,0, + &ghostxlo,1,MPI_INT,procxlo,0,gridcomm,MPI_STATUS_IGNORE); + else ghostxlo = nplanes; + + nplanes = inylo - outylo; + if (procylo != me) + MPI_Sendrecv(&nplanes,1,MPI_INT,procylo,0, + &ghostyhi,1,MPI_INT,procyhi,0,gridcomm,MPI_STATUS_IGNORE); + else ghostyhi = nplanes; + + nplanes = outyhi - inyhi; + if (procyhi != me) + MPI_Sendrecv(&nplanes,1,MPI_INT,procyhi,0, + &ghostylo,1,MPI_INT,procylo,0,gridcomm,MPI_STATUS_IGNORE); + else ghostylo = nplanes; + + // setup swaps = exchange of grid data with one of 6 neighobr procs + // can be more than one in a direction if ghost region extends beyond neigh proc + // all procs have same swap count, but swapsize npack/nunpack can be empty + + nswap = 0; + + // send own grid pts to -x processor, recv ghost grid pts from +x processor + + nsent = 0; + sendfirst = inxlo; + sendlast = inxhi; + recvfirst = inxhi+1; + notdone = 1; + + while (notdone) { + if (nswap == maxswap) grow_swap(); + + swap[nswap].sendproc = procxlo; + swap[nswap].recvproc = procxhi; + sendplanes = MIN(sendlast-sendfirst+1,ghostxlo-nsent); + swap[nswap].npack = + indices(swap[nswap].packlist, + sendfirst,sendfirst+sendplanes-1,inylo,inyhi); + + if (procxlo != me) + MPI_Sendrecv(&sendplanes,1,MPI_INT,procxlo,0, + &recvplanes,1,MPI_INT,procxhi,0,gridcomm,MPI_STATUS_IGNORE); + else recvplanes = sendplanes; + + swap[nswap].nunpack = + indices(swap[nswap].unpacklist, + recvfirst,recvfirst+recvplanes-1,inylo,inyhi); + + nsent += sendplanes; + sendfirst += sendplanes; + sendlast += recvplanes; + recvfirst += recvplanes; + nswap++; + + if (nsent < ghostxlo) notdoneme = 1; + else notdoneme = 0; + MPI_Allreduce(¬doneme,¬done,1,MPI_INT,MPI_SUM,gridcomm); + } + + // send own grid pts to +x processor, recv ghost grid pts from -x processor + + nsent = 0; + sendfirst = inxlo; + sendlast = inxhi; + recvlast = inxlo-1; + notdone = 1; + + while (notdone) { + if (nswap == maxswap) grow_swap(); + + swap[nswap].sendproc = procxhi; + swap[nswap].recvproc = procxlo; + sendplanes = MIN(sendlast-sendfirst+1,ghostxhi-nsent); + swap[nswap].npack = + indices(swap[nswap].packlist, + sendlast-sendplanes+1,sendlast,inylo,inyhi); + + if (procxhi != me) + MPI_Sendrecv(&sendplanes,1,MPI_INT,procxhi,0, + &recvplanes,1,MPI_INT,procxlo,0,gridcomm,MPI_STATUS_IGNORE); + else recvplanes = sendplanes; + + swap[nswap].nunpack = + indices(swap[nswap].unpacklist, + recvlast-recvplanes+1,recvlast,inylo,inyhi); + + nsent += sendplanes; + sendfirst -= recvplanes; + sendlast -= sendplanes; + recvlast -= recvplanes; + nswap++; + + if (nsent < ghostxhi) notdoneme = 1; + else notdoneme = 0; + MPI_Allreduce(¬doneme,¬done,1,MPI_INT,MPI_SUM,gridcomm); + } + + // send own grid pts to -y processor, recv ghost grid pts from +y processor + + nsent = 0; + sendfirst = inylo; + sendlast = inyhi; + recvfirst = inyhi+1; + notdone = 1; + + while (notdone) { + if (nswap == maxswap) grow_swap(); + + swap[nswap].sendproc = procylo; + swap[nswap].recvproc = procyhi; + sendplanes = MIN(sendlast-sendfirst+1,ghostylo-nsent); + swap[nswap].npack = + indices(swap[nswap].packlist, + outxlo,outxhi,sendfirst,sendfirst+sendplanes-1); + + if (procylo != me) + MPI_Sendrecv(&sendplanes,1,MPI_INT,procylo,0, + &recvplanes,1,MPI_INT,procyhi,0,gridcomm,MPI_STATUS_IGNORE); + else recvplanes = sendplanes; + + swap[nswap].nunpack = + indices(swap[nswap].unpacklist, + outxlo,outxhi,recvfirst,recvfirst+recvplanes-1); + + nsent += sendplanes; + sendfirst += sendplanes; + sendlast += recvplanes; + recvfirst += recvplanes; + nswap++; + + if (nsent < ghostylo) notdoneme = 1; + else notdoneme = 0; + MPI_Allreduce(¬doneme,¬done,1,MPI_INT,MPI_SUM,gridcomm); + } + + // send own grid pts to +y processor, recv ghost grid pts from -y processor + + nsent = 0; + sendfirst = inylo; + sendlast = inyhi; + recvlast = inylo-1; + notdone = 1; + + while (notdone) { + if (nswap == maxswap) grow_swap(); + + swap[nswap].sendproc = procyhi; + swap[nswap].recvproc = procylo; + sendplanes = MIN(sendlast-sendfirst+1,ghostyhi-nsent); + swap[nswap].npack = + indices(swap[nswap].packlist, + outxlo,outxhi,sendlast-sendplanes+1,sendlast); + + if (procyhi != me) + MPI_Sendrecv(&sendplanes,1,MPI_INT,procyhi,0, + &recvplanes,1,MPI_INT,procylo,0,gridcomm,MPI_STATUS_IGNORE); + else recvplanes = sendplanes; + + swap[nswap].nunpack = + indices(swap[nswap].unpacklist, + outxlo,outxhi,recvlast-recvplanes+1,recvlast); + + nsent += sendplanes; + sendfirst -= recvplanes; + sendlast -= sendplanes; + recvlast -= recvplanes; + nswap++; + + if (nsent < ghostyhi) notdoneme = 1; + else notdoneme = 0; + MPI_Allreduce(¬doneme,¬done,1,MPI_INT,MPI_SUM,gridcomm); + } + + // ngrid = max of any forward/reverse pack/unpack grid points + + int ngrid = 0; + for (int i = 0; i < nswap; i++) { + ngrid = MAX(ngrid,swap[i].npack); + ngrid = MAX(ngrid,swap[i].nunpack); + } + + nbuf1 = nbuf2 = ngrid; +} + +/* ---------------------------------------------------------------------- + setup owned/ghost comm for tiled comm + each proc has arbitrary # of neighbors that overlap its ghost extent + identify which procs will send me ghost cells, and vice versa + may not be symmetric if both procs do not need same layers of ghosts + comm pattern = post recvs for all my ghosts, send my owned, wait on recvs + no exchanges by dimension, unlike CommTiled forward/reverse comm of particles +------------------------------------------------------------------------- */ + +void Grid2d::setup_comm_tiled(int &nbuf1, int &nbuf2) +{ + int i,m; + double xlo,xhi,ylo,yhi; + int ghostbox[4],pbc[2]; + + // find overlaps of my extended ghost box with all owned boxes + // accounts for ghost box overlapping periodic boundaries + // noverlap = # of overlaps, including self + // overlap = vector of overlap info using Overlap data struct + + ghostbox[0] = outxlo; + ghostbox[1] = outxhi; + ghostbox[2] = outylo; + ghostbox[3] = outyhi; + + pbc[0] = pbc[1] = 0; + + Overlap *overlap; + int noverlap = compute_overlap(1,ghostbox,pbc,overlap); + + // send each proc an overlap message + // content: me, index of my overlap, box that overlaps with its owned cells + // ncopy = # of overlaps with myself, across a periodic boundary + // skip copy to self when non-PBC + + int *proclist; + memory->create(proclist,noverlap,"grid2d:proclist"); + srequest = (Request *) + memory->smalloc(noverlap*sizeof(Request),"grid2d:srequest"); + + int nsend_request = 0; + ncopy = 0; + + for (m = 0; m < noverlap; m++) { + if (overlap[m].proc == me) { + if (overlap[m].pbc[0] == 0 && overlap[m].pbc[1] == 0) continue; + ncopy++; + } else { + proclist[nsend_request] = overlap[m].proc; + srequest[nsend_request].sender = me; + srequest[nsend_request].index = m; + for (i = 0; i < 4; i++) + srequest[nsend_request].box[i] = overlap[m].box[i]; + nsend_request++; + } + } + + auto irregular = new Irregular(lmp); + int nrecv_request = irregular->create_data(nsend_request,proclist,1); + auto rrequest = (Request *) memory->smalloc(nrecv_request*sizeof(Request),"grid2d:rrequest"); + irregular->exchange_data((char *) srequest,sizeof(Request),(char *) rrequest); + irregular->destroy_data(); + + // compute overlaps between received ghost boxes and my owned box + // overlap box used to setup my Send data struct and respond to requests + + send = (Send *) memory->smalloc(nrecv_request*sizeof(Send),"grid2d:send"); + sresponse = (Response *) memory->smalloc(nrecv_request*sizeof(Response),"grid2d:sresponse"); + memory->destroy(proclist); + memory->create(proclist,nrecv_request,"grid2d:proclist"); + + for (m = 0; m < nrecv_request; m++) { + send[m].proc = rrequest[m].sender; + xlo = MAX(rrequest[m].box[0],inxlo); + xhi = MIN(rrequest[m].box[1],inxhi); + ylo = MAX(rrequest[m].box[2],inylo); + yhi = MIN(rrequest[m].box[3],inyhi); + send[m].npack = indices(send[m].packlist,xlo,xhi,ylo,yhi); + + proclist[m] = rrequest[m].sender; + sresponse[m].index = rrequest[m].index; + sresponse[m].box[0] = xlo; + sresponse[m].box[1] = xhi; + sresponse[m].box[2] = ylo; + sresponse[m].box[3] = yhi; + } + + nsend = nrecv_request; + + // reply to each Request message with a Response message + // content: index for the overlap on requestor, overlap box on my owned grid + + int nsend_response = nrecv_request; + int nrecv_response = irregular->create_data(nsend_response,proclist,1); + auto rresponse = (Response *) memory->smalloc(nrecv_response*sizeof(Response),"grid2d:rresponse"); + irregular->exchange_data((char *) sresponse,sizeof(Response),(char *) rresponse); + irregular->destroy_data(); + delete irregular; + + // process received responses + // box used to setup my Recv data struct after unwrapping via PBC + // adjacent = 0 if any box of ghost cells does not adjoin my owned cells + + recv = (Recv *) memory->smalloc(nrecv_response*sizeof(Recv),"grid2d:recv"); + adjacent = 1; + + for (i = 0; i < nrecv_response; i++) { + m = rresponse[i].index; + recv[i].proc = overlap[m].proc; + xlo = rresponse[i].box[0] + overlap[m].pbc[0] * nx; + xhi = rresponse[i].box[1] + overlap[m].pbc[0] * nx; + ylo = rresponse[i].box[2] + overlap[m].pbc[1] * ny; + yhi = rresponse[i].box[3] + overlap[m].pbc[1] * ny; + recv[i].nunpack = indices(recv[i].unpacklist,xlo,xhi,ylo,yhi); + + if (xlo != inxhi+1 && xhi != inxlo-1 && + ylo != inyhi+1 && yhi != inylo-1) adjacent = 0; + } + + nrecv = nrecv_response; + + // create Copy data struct from overlaps with self + // skip copy to self when non-PBC + + copy = (Copy *) memory->smalloc(ncopy*sizeof(Copy),"grid2d:copy"); + + ncopy = 0; + for (m = 0; m < noverlap; m++) { + if (overlap[m].proc != me) continue; + if (overlap[m].pbc[0] == 0 && overlap[m].pbc[1] == 0) continue; + xlo = overlap[m].box[0]; + xhi = overlap[m].box[1]; + ylo = overlap[m].box[2]; + yhi = overlap[m].box[3]; + copy[ncopy].npack = indices(copy[ncopy].packlist,xlo,xhi,ylo,yhi); + xlo = overlap[m].box[0] + overlap[m].pbc[0] * nx; + xhi = overlap[m].box[1] + overlap[m].pbc[0] * nx; + ylo = overlap[m].box[2] + overlap[m].pbc[1] * ny; + yhi = overlap[m].box[3] + overlap[m].pbc[1] * ny; + copy[ncopy].nunpack = indices(copy[ncopy].unpacklist,xlo,xhi,ylo,yhi); + ncopy++; + } + + // set offsets for received data + + int offset = 0; + for (m = 0; m < nsend; m++) { + send[m].offset = offset; + offset += send[m].npack; + } + + offset = 0; + for (m = 0; m < nrecv; m++) { + recv[m].offset = offset; + offset += recv[m].nunpack; + } + + // length of MPI requests vector is max of nsend, nrecv + + int nrequest = MAX(nsend,nrecv); + requests = new MPI_Request[nrequest]; + + // clean-up + + clean_overlap(); + memory->destroy(proclist); + memory->sfree(srequest); + memory->sfree(rrequest); + memory->sfree(sresponse); + memory->sfree(rresponse); + + // nbuf1 = largest pack or unpack in any Send or Recv or Copy + // nbuf2 = larget of sum of all packs or unpacks in Send or Recv + + nbuf1 = 0; + + for (m = 0; m < ncopy; m++) { + nbuf1 = MAX(nbuf1,copy[m].npack); + nbuf1 = MAX(nbuf1,copy[m].nunpack); + } + + int nbufs = 0; + for (m = 0; m < nsend; m++) { + nbuf1 = MAX(nbuf1,send[m].npack); + nbufs += send[m].npack; + } + + int nbufr = 0; + for (m = 0; m < nrecv; m++) { + nbuf1 = MAX(nbuf1,recv[m].nunpack); + nbufr += recv[m].nunpack; + } + + nbuf2 = MAX(nbufs,nbufr); +} + +// ---------------------------------------------------------------------- +// query locality of forwrd/reverse grid comm +// ---------------------------------------------------------------------- + +/* ---------------------------------------------------------------------- + check if all procs only need ghost info from adjacent procs + return 1 if yes, 0 if no +------------------------------------------------------------------------- */ + +int Grid2d::ghost_adjacent() +{ + if (layout != Comm::LAYOUT_TILED) return ghost_adjacent_brick(); + return ghost_adjacent_tiled(); +} + +/* ---------------------------------------------------------------------- + adjacent = 0 if a proc's ghost xy lohi values exceed its subdomain size + return 0 if adjacent=0 for any proc, else 1 +------------------------------------------------------------------------- */ + +int Grid2d::ghost_adjacent_brick() +{ + adjacent = 1; + if (ghostxlo > inxhi-inxlo+1) adjacent = 0; + if (ghostxhi > inxhi-inxlo+1) adjacent = 0; + if (ghostylo > inyhi-inylo+1) adjacent = 0; + if (ghostyhi > inyhi-inylo+1) adjacent = 0; + + int adjacent_all; + MPI_Allreduce(&adjacent,&adjacent_all,1,MPI_INT,MPI_MIN,gridcomm); + return adjacent_all; +} + +/* ---------------------------------------------------------------------- + adjacent = 0 if a proc's received ghosts were flagged + as non-adjacent in setup_tiled() + return 0 if adjacent=0 for any proc, else 1 +------------------------------------------------------------------------- */ + +int Grid2d::ghost_adjacent_tiled() +{ + int adjacent_all; + MPI_Allreduce(&adjacent,&adjacent_all,1,MPI_INT,MPI_MIN,gridcomm); + return adjacent_all; +} + +// ---------------------------------------------------------------------- +// forward/reverse comm of owned/ghost grid data via callbacks +// ---------------------------------------------------------------------- + +/* ---------------------------------------------------------------------- + forward comm of my owned cells to other's ghost cells +------------------------------------------------------------------------- */ + +void Grid2d::forward_comm(int caller, void *ptr, int which, int nper, int nbyte, + void *buf1, void *buf2, MPI_Datatype datatype) +{ + if (layout != Comm::LAYOUT_TILED) { + if (caller == KSPACE) + forward_comm_brick((KSpace *) ptr,which,nper,nbyte, + buf1,buf2,datatype); + else if (caller == PAIR) + forward_comm_brick((Pair *) ptr,which,nper,nbyte, + buf1,buf2,datatype); + else if (caller == FIX) + forward_comm_brick((Fix *) ptr,which,nper,nbyte, + buf1,buf2,datatype); + } else { + if (caller == KSPACE) + forward_comm_tiled((KSpace *) ptr,which,nper,nbyte, + buf1,buf2,datatype); + else if (caller == PAIR) + forward_comm_tiled((Pair *) ptr,which,nper,nbyte, + buf1,buf2,datatype); + else if (caller == FIX) + forward_comm_tiled((Fix *) ptr,which,nper,nbyte, + buf1,buf2,datatype); + } +} + +/* ---------------------------------------------------------------------- + forward comm for brick decomp via list of swaps with 6 neighbor procs +------------------------------------------------------------------------- */ + +template < class T > +void Grid2d:: +forward_comm_brick(T *ptr, int which, int nper, int /*nbyte*/, + void *buf1, void *buf2, MPI_Datatype datatype) +{ + int m; + MPI_Request request; + + for (m = 0; m < nswap; m++) { + if (swap[m].sendproc == me) + ptr->pack_forward_grid(which,buf2,swap[m].npack,swap[m].packlist); + else + ptr->pack_forward_grid(which,buf1,swap[m].npack,swap[m].packlist); + + if (swap[m].sendproc != me) { + if (swap[m].nunpack) MPI_Irecv(buf2,nper*swap[m].nunpack,datatype, + swap[m].recvproc,0,gridcomm,&request); + if (swap[m].npack) MPI_Send(buf1,nper*swap[m].npack,datatype, + swap[m].sendproc,0,gridcomm); + if (swap[m].nunpack) MPI_Wait(&request,MPI_STATUS_IGNORE); + } + + ptr->unpack_forward_grid(which,buf2,swap[m].nunpack,swap[m].unpacklist); + } +} + +/* ---------------------------------------------------------------------- + forward comm for tiled decomp via Send/Recv lists of each neighbor proc +------------------------------------------------------------------------- */ + +template < class T > +void Grid2d:: +forward_comm_tiled(T *ptr, int which, int nper, int nbyte, + void *buf1, void *vbuf2, MPI_Datatype datatype) +{ + int i,m,offset; + + auto buf2 = (char *) vbuf2; + + // post all receives + + for (m = 0; m < nrecv; m++) { + offset = nper * recv[m].offset * nbyte; + MPI_Irecv((void *) &buf2[offset],nper*recv[m].nunpack,datatype, + recv[m].proc,0,gridcomm,&requests[m]); + } + + // perform all sends to other procs + + for (m = 0; m < nsend; m++) { + ptr->pack_forward_grid(which,buf1,send[m].npack,send[m].packlist); + MPI_Send(buf1,nper*send[m].npack,datatype,send[m].proc,0,gridcomm); + } + + // perform all copies to self + + for (m = 0; m < ncopy; m++) { + ptr->pack_forward_grid(which,buf1,copy[m].npack,copy[m].packlist); + ptr->unpack_forward_grid(which,buf1,copy[m].nunpack,copy[m].unpacklist); + } + + // unpack all received data + + for (i = 0; i < nrecv; i++) { + MPI_Waitany(nrecv,requests,&m,MPI_STATUS_IGNORE); + offset = nper * recv[m].offset * nbyte; + ptr->unpack_forward_grid(which,(void *) &buf2[offset], + recv[m].nunpack,recv[m].unpacklist); + } +} + +/* ---------------------------------------------------------------------- + reverse comm of my ghost cells to sum to owner cells +------------------------------------------------------------------------- */ + +void Grid2d::reverse_comm(int caller, void *ptr, int which, int nper, int nbyte, + void *buf1, void *buf2, MPI_Datatype datatype) +{ + if (layout != Comm::LAYOUT_TILED) { + if (caller == KSPACE) + reverse_comm_brick((KSpace *) ptr,which,nper,nbyte, + buf1,buf2,datatype); + else if (caller == PAIR) + reverse_comm_brick((Pair *) ptr,which,nper,nbyte, + buf1,buf2,datatype); + else if (caller == FIX) + reverse_comm_brick((Fix *) ptr,which,nper,nbyte, + buf1,buf2,datatype); + } else { + if (caller == KSPACE) + reverse_comm_tiled((KSpace *) ptr,which,nper,nbyte, + buf1,buf2,datatype); + else if (caller == PAIR) + reverse_comm_tiled((Pair *) ptr,which,nper,nbyte, + buf1,buf2,datatype); + else if (caller == FIX) + reverse_comm_tiled((Fix *) ptr,which,nper,nbyte, + buf1,buf2,datatype); + } +} + +/* ---------------------------------------------------------------------- + reverse comm for brick decomp via list of swaps with 6 neighbor procs +------------------------------------------------------------------------- */ + +template < class T > +void Grid2d:: +reverse_comm_brick(T *ptr, int which, int nper, int /*nbyte*/, + void *buf1, void *buf2, MPI_Datatype datatype) +{ + int m; + MPI_Request request; + + for (m = nswap-1; m >= 0; m--) { + if (swap[m].recvproc == me) + ptr->pack_reverse_grid(which,buf2,swap[m].nunpack,swap[m].unpacklist); + else + ptr->pack_reverse_grid(which,buf1,swap[m].nunpack,swap[m].unpacklist); + + if (swap[m].recvproc != me) { + if (swap[m].npack) MPI_Irecv(buf2,nper*swap[m].npack,datatype, + swap[m].sendproc,0,gridcomm,&request); + if (swap[m].nunpack) MPI_Send(buf1,nper*swap[m].nunpack,datatype, + swap[m].recvproc,0,gridcomm); + if (swap[m].npack) MPI_Wait(&request,MPI_STATUS_IGNORE); + } + + ptr->unpack_reverse_grid(which,buf2,swap[m].npack,swap[m].packlist); + } +} + +/* ---------------------------------------------------------------------- + reverse comm for tiled decomp via Send/Recv lists of each neighbor proc +------------------------------------------------------------------------- */ + +template < class T > +void Grid2d:: +reverse_comm_tiled(T *ptr, int which, int nper, int nbyte, + void *buf1, void *vbuf2, MPI_Datatype datatype) +{ + int i,m,offset; + + auto buf2 = (char *) vbuf2; + + // post all receives + + for (m = 0; m < nsend; m++) { + offset = nper * send[m].offset * nbyte; + MPI_Irecv((void *) &buf2[offset],nper*send[m].npack,datatype, + send[m].proc,0,gridcomm,&requests[m]); + } + + // perform all sends to other procs + + for (m = 0; m < nrecv; m++) { + ptr->pack_reverse_grid(which,buf1,recv[m].nunpack,recv[m].unpacklist); + MPI_Send(buf1,nper*recv[m].nunpack,datatype,recv[m].proc,0,gridcomm); + } + + // perform all copies to self + + for (m = 0; m < ncopy; m++) { + ptr->pack_reverse_grid(which,buf1,copy[m].nunpack,copy[m].unpacklist); + ptr->unpack_reverse_grid(which,buf1,copy[m].npack,copy[m].packlist); + } + + // unpack all received data + + for (i = 0; i < nsend; i++) { + MPI_Waitany(nsend,requests,&m,MPI_STATUS_IGNORE); + offset = nper * send[m].offset * nbyte; + ptr->unpack_reverse_grid(which,(void *) &buf2[offset], + send[m].npack,send[m].packlist); + } +} + +// ---------------------------------------------------------------------- +// remap comm between 2 old/new grid decomposition of owned grid data +// ---------------------------------------------------------------------- + +/* ---------------------------------------------------------------------- + setup remap from old grid decomposition to this grid decomposition + return sizes of two buffers needed for communication + either for brick decomp or tiling decomp + nbuf1 = largest pack or unpack in any Send or Recv or Copy + nbuf2 = larget of sum of all packs or unpacks in Send or Recv + for brick comm, nbuf1 = nbuf2 + for tiled comm, nbuf2 >= nbuf2 + nbuf1,nbuf2 are just count of grid points + caller converts them to message size for grid data it stores +------------------------------------------------------------------------- */ + +void Grid2d::setup_remap(Grid2d *old, int &nremap_buf1, int &nremap_buf2) +{ + int m; + int pbc[2]; + int *box; + + // deallocated existing remap data structs + + deallocate_remap(); + + // set layout to current Comm layout + + layout = comm->layout; + + // overlaps of my old decomp owned box with all owned boxes in new decomp + // noverlap_old = # of overlaps, including self + // overlap_old = vector of overlap info in Overlap data struct + + int oldbox[4]; + old->get_bounds_owned(oldbox[0],oldbox[1],oldbox[2],oldbox[3]); + pbc[0] = pbc[1] = 0; + + Overlap *overlap_old; + int noverlap_old = compute_overlap(0,oldbox,pbc,overlap_old); + + // use overlap_old to construct send and copy lists + // skip overlaps that contain no grid cells + + self_remap = 0; + + nsend_remap = 0; + for (m = 0; m < noverlap_old; m++) { + box = overlap_old[m].box; + if (box[0] > box[1] || box[2] > box[3]) continue; + if (overlap_old[m].proc == me) self_remap =1; + else nsend_remap++; + } + + send_remap = new Send[nsend_remap]; + + nsend_remap = 0; + for (m = 0; m < noverlap_old; m++) { + box = overlap_old[m].box; + if (box[0] > box[1] || box[2] > box[3]) continue; + if (overlap_old[m].proc == me) { + copy_remap.npack = + old->indices(copy_remap.packlist,box[0],box[1],box[2],box[3]); + } else { + send_remap[nsend_remap].proc = overlap_old[m].proc; + send_remap[nsend_remap].npack = + old->indices(send_remap[nsend_remap].packlist, + box[0],box[1],box[2],box[3]); + nsend_remap++; + } + } + + // overlaps of my new decomp owned box with all owned boxes in old decomp + // noverlap_new = # of overlaps, including self + // overlap_new = vector of overlap info in Overlap data struct + + int newbox[4]; + get_bounds_owned(newbox[0],newbox[1],newbox[2],newbox[3]); + pbc[0] = pbc[1] = 0; + + Overlap *overlap_new; + int noverlap_new = old->compute_overlap(0,newbox,pbc,overlap_new); + + // use overlap_new to construct recv and copy lists + // skip overlaps that contain no grid cells + // set offsets for Recv data + + nrecv_remap = 0; + for (m = 0; m < noverlap_new; m++) { + box = overlap_new[m].box; + if (box[0] > box[1] || box[2] > box[3]) continue; + if (overlap_new[m].proc != me) nrecv_remap++; + } + + recv_remap = new Recv[nrecv_remap]; + + nrecv_remap = 0; + for (m = 0; m < noverlap_new; m++) { + box = overlap_new[m].box; + if (box[0] > box[1] || box[2] > box[3]) continue; + if (overlap_new[m].proc == me) { + copy_remap.nunpack = + indices(copy_remap.unpacklist,box[0],box[1],box[2],box[3]); + } else { + recv_remap[nrecv_remap].proc = overlap_new[m].proc; + recv_remap[nrecv_remap].nunpack = + indices(recv_remap[nrecv_remap].unpacklist, + box[0],box[1],box[2],box[3]); + nrecv_remap++; + } + } + + // set offsets for received data + + int offset = 0; + for (m = 0; m < nrecv_remap; m++) { + recv_remap[m].offset = offset; + offset += recv_remap[m].nunpack; + } + + // length of MPI requests vector = nrecv_remap + + delete [] requests_remap; + requests_remap = new MPI_Request[nrecv_remap]; + + // clean-up + + clean_overlap(); + old->clean_overlap(); + + // nremap_buf1 = largest pack or unpack in any Send or Recv or Copy + // nremap_buf2 = sum of all unpacks in Recv + + nremap_buf1 = 0; + + if (self_remap) { + nremap_buf1 = MAX(nremap_buf1,copy_remap.npack); + nremap_buf1 = MAX(nremap_buf1,copy_remap.nunpack); + } + + for (m = 0; m < nsend_remap; m++) + nremap_buf1 = MAX(nremap_buf1,send_remap[m].npack); + + nremap_buf2 = 0; + for (m = 0; m < nrecv_remap; m++) { + nremap_buf1 = MAX(nremap_buf1,recv_remap[m].nunpack); + nremap_buf2 += recv_remap[m].nunpack; + } +} + +/* ---------------------------------------------------------------------- + perform remap from old grid decomposition to this grid decomposition + pack/unpack operations are performed by caller via callbacks +------------------------------------------------------------------------- */ + +void Grid2d::remap(int caller, void *ptr, int which, int nper, int nbyte, + void *buf1, void *buf2, MPI_Datatype datatype) +{ + if (caller == FIX) remap_style((Fix *) ptr,which,nper,nbyte,buf1,buf2,datatype); +} + +/* ------------------------------------------------------------------------- */ + +template < class T > +void Grid2d::remap_style(T *ptr, int which, int nper, int nbyte, + void *buf1, void *vbuf2, MPI_Datatype datatype) +{ + int i,m,offset; + + auto buf2 = (char *) vbuf2; + + // post all receives + + for (m = 0; m < nrecv_remap; m++) { + offset = nper * recv_remap[m].offset * nbyte; + MPI_Irecv((void *) &buf2[offset],nper*recv_remap[m].nunpack,datatype, + recv_remap[m].proc,0,gridcomm,&requests_remap[m]); + } + + // perform all sends to other procs + + for (m = 0; m < nsend_remap; m++) { + ptr->pack_remap_grid(which,buf1,send_remap[m].npack,send_remap[m].packlist); + MPI_Send(buf1,nper*send_remap[m].npack,datatype,send_remap[m].proc,0,gridcomm); + } + + // perform remap to self if defined + + if (self_remap) { + ptr->pack_remap_grid(which,buf1,copy_remap.npack,copy_remap.packlist); + ptr->unpack_remap_grid(which,buf1,copy_remap.nunpack,copy_remap.unpacklist); + } + + // unpack all received data + + for (i = 0; i < nrecv_remap; i++) { + MPI_Waitany(nrecv_remap,requests_remap,&m,MPI_STATUS_IGNORE); + offset = nper * recv_remap[m].offset * nbyte; + ptr->unpack_remap_grid(which,(void *) &buf2[offset], + recv_remap[m].nunpack,recv_remap[m].unpacklist); + } +} + +// ---------------------------------------------------------------------- +// grid I/O methods +// ---------------------------------------------------------------------- + +/* ---------------------------------------------------------------------- + read grid values from a file +------------------------------------------------------------------------- */ + +void Grid2d::read_file(int caller, void *ptr, FILE *fp, int nchunk, int maxline) +{ + if (caller == FIX) + read_file_style((Fix *) ptr,fp,nchunk,maxline); +} + +/* ---------------------------------------------------------------------- + proc 0 reads one chunk of lines at a time from file + broadcast chunk buffer to other procs + call back to caller so it can process the chunk of lines + caller returns count of grid-value lines in chunk +------------------------------------------------------------------------- */ + +template < class T > +void Grid2d::read_file_style(T *ptr, FILE *fp, int nchunk, int maxline) +{ + auto buffer = new char[nchunk * maxline]; + bigint ntotal = (bigint) nx * ny; + bigint nread = 0; + + while (nread < ntotal) { + int mychunk = MIN(ntotal - nread, nchunk); + int eof = utils::read_lines_from_file(fp, mychunk, maxline, buffer, me, world); + if (eof) error->all(FLERR, "Unexpected end of grid data file"); + + nread += ptr->unpack_read_grid(nchunk,buffer); + } + + delete [] buffer; +} + +/* ---------------------------------------------------------------------- + write grid values to a file +------------------------------------------------------------------------- */ + +void Grid2d::write_file(int caller, void *ptr, int which, + int nper, int nbyte, MPI_Datatype datatype) +{ + if (caller == FIX) + write_file_style((Fix *) ptr, which, nper, nbyte, datatype); +} + +/* ---------------------------------------------------------------------- + proc 0 reads one chunk of lines at a time from file + broadcast chunk buffer to other procs + call back to caller so it can process the chunk of lines + caller returns count of grid-value lines in chunk +------------------------------------------------------------------------- */ + +template < class T > +void Grid2d::write_file_style(T *ptr, int which, + int nper, int nbyte, MPI_Datatype datatype) +{ + // maxsize = max size of grid data owned by any proc + + int mysize = (inxhi-inxlo+1) * (inyhi-inylo+1); + mysize *= nper; + int maxsize; + MPI_Allreduce(&mysize,&maxsize,1,MPI_INT,MPI_MAX,world); + + // pack my grid data via callback to caller + + char *onebuf; + if (me == 0) memory->create(onebuf,maxsize*nbyte,"grid3d:onebuf"); + else memory->create(onebuf,mysize*nbyte,"grid3d:onebuf"); + ptr->pack_write_grid(which,onebuf); + + // ping each proc for its grid data + // call back to caller with each proc's grid data + + int tmp; + int bounds[4]; + + if (me == 0) { + MPI_Status status; + MPI_Request request; + + for (int iproc = 0; iproc < nprocs; iproc++) { + if (iproc) { + MPI_Irecv(onebuf,maxsize,datatype,iproc,0,world,&request); + MPI_Send(&tmp,0,MPI_INT,iproc,0,world); + MPI_Wait(&request,&status); + MPI_Recv(bounds,4,MPI_INT,iproc,0,world,&status); + } else { + bounds[0] = inxlo; + bounds[1] = inxhi; + bounds[2] = inylo; + bounds[3] = inyhi; + } + + ptr->unpack_write_grid(which,onebuf,bounds); + } + + } else { + MPI_Recv(&tmp,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE); + MPI_Rsend(onebuf,mysize,datatype,0,0,world); + bounds[0] = inxlo; + bounds[1] = inxhi; + bounds[2] = inylo; + bounds[3] = inyhi; + MPI_Send(bounds,4,MPI_INT,0,0,world); + } + + // clean up + + memory->destroy(onebuf); +} + +// ---------------------------------------------------------------------- +// overlap methods for brick and tiled RCB decompositions +// overlap = overlap of owned or owned+ghost box with all boxes of a decomposition +// for owned/ghost grid comm, called only by tiled decomposition +// brick decomp uses one or more comm passes with neigh procs +// like forward/reverse comm for atoms +// for remap, called by both brick and tiled decompositions +// ---------------------------------------------------------------------- + +/* ---------------------------------------------------------------------- + compute list of overlaps between box and the owned grid boxes of all procs + ghostflag = 1 if box includes ghost grid pts, called by setup_tiled() + ghostflag = 0 if box has no ghost grid pts, called by setup_remap() + layout != LAYOUT_TILED is only invoked by setup_remap() + for brick decomp of Grid, done using xyz split + grid2proc copied from Comm + for tiled decomp of Grid, done via recursive box drop on RCB tree + box = 4 integers = (xlo,xhi,ylo,yhi) + box can be owned cells or owned + ghost cells + pbc = flags for grid periodicity in each dim + if box includes ghost cells, it can overlap PBCs (only for setup_tiled) + each lo/hi value may extend beyond 0 to N-1 into another periodic image + return # of overlaps including with self, caller handles self overlaps as needed + return list of overlaps + for setup_tiled() this is what box_drop() computes + entire box for each overlap + caller will determine extent of overlap using PBC info + for setup_remap(), return extent of overlap (no PBC info involved) + use proc_box_uniform() or tiled() and MAX/MIN to determine this +------------------------------------------------------------------------- */ + +int Grid2d::compute_overlap(int ghostflag, int *box, int *pbc, Overlap *&overlap) +{ + int obox[4]; + + memory->create(overlap_procs,nprocs,"grid2d:overlap_procs"); + noverlap_list = maxoverlap_list = 0; + overlap_list = nullptr; + + // skip overlap check if box contains no grid cells + + if (box[0] > box[1] || box[2] > box[3]) { + overlap = overlap_list; + return noverlap_list; + } + + // test obox against appropriate layout + + if (layout != Comm::LAYOUT_TILED) { + + // find comm->procgrid indices in each dim for box bounds + + int iproclo = proc_index_uniform(box[0],nx,shift_grid,0,xsplit); + int iprochi = proc_index_uniform(box[1],nx,shift_grid,0,xsplit); + int jproclo = proc_index_uniform(box[2],ny,shift_grid,1,ysplit); + int jprochi = proc_index_uniform(box[3],ny,shift_grid,1,ysplit); + + // compute extent of overlap of box with with each proc's obox + + for (int j = jproclo; j <= jprochi; j++) + for (int i = iproclo; i <= iprochi; i++) { + partition_grid(nx,xsplit[i],xsplit[i+1],shift_grid,0,obox[0],obox[1]); + partition_grid(ny,ysplit[j],ysplit[j+1],shift_grid,yextra,obox[2],obox[3]); + + if (noverlap_list == maxoverlap_list) grow_overlap(); + overlap_list[noverlap_list].proc = grid2proc[i][j][0]; + overlap_list[noverlap_list].box[0] = MAX(box[0],obox[0]); + overlap_list[noverlap_list].box[1] = MIN(box[1],obox[1]); + overlap_list[noverlap_list].box[2] = MAX(box[2],obox[2]); + overlap_list[noverlap_list].box[3] = MIN(box[3],obox[3]); + noverlap_list++; + } + + } else { + box_drop(box,pbc); + + // compute extent of overlap of box with with each proc's obox + + if (ghostflag == 0) { + for (int m = 0; m < noverlap_list; m++) { + obox[0] = 0; + obox[1] = nx-1; + obox[2] = 0; + obox[3] = ny-1; + + partition_tiled(overlap_list[m].proc,0,nprocs-1,obox); + + overlap_list[m].box[0] = MAX(box[0],obox[0]); + overlap_list[m].box[1] = MIN(box[1],obox[1]); + overlap_list[m].box[2] = MAX(box[2],obox[2]); + overlap_list[m].box[3] = MIN(box[3],obox[3]); + } + } + } + + overlap = overlap_list; + return noverlap_list; +} + +/* ---------------------------------------------------------------------- + deallocate data created by recursive overlap computation +------------------------------------------------------------------------- */ + +void Grid2d::clean_overlap() +{ + memory->destroy(overlap_procs); + memory->sfree(overlap_list); +} + +/* ---------------------------------------------------------------------- + recursively split a box until it doesn't overlap any periodic boundaries + box = 4 integers = (xlo,xhi,ylo,yhi) + each lo/hi value may extend beyonw 0 to N-1 into another periodic image + pbc = flags in each dim of which periodic image the caller box was in + when a box straddles a periodic bounadry, split it in two + when a box does not straddle, drop it down RCB tree + add all the procs it overlaps with to Overlap list +------------------------------------------------------------------------- */ + +void Grid2d::box_drop(int *box, int *pbc) +{ + int i,m; + + // newbox12 and newpbc are initially copies of caller box and pbc + + int newbox1[4],newbox2[4],newpbc[2]; + + for (i = 0; i < 4; i++) newbox1[i] = newbox2[i] = box[i]; + for (i = 0; i < 2; i++) newpbc[i] = pbc[i]; + + // 4 if tests to see if box needs to be split across a periodic boundary + // newbox1 and 2 = new split boxes, newpbc increments current pbc + // final else is no split + + int splitflag = 1; + + if (box[0] < 0) { + newbox1[0] = 0; + newbox2[0] = box[0] + nx; + newbox2[1] = nx - 1; + newpbc[0]--; + } else if (box[1] >= nx) { + newbox1[1] = nx - 1; + newbox2[0] = 0; + newbox2[1] = box[1] - nx; + newpbc[0]++; + } else if (box[2] < 0) { + newbox1[2] = 0; + newbox2[2] = box[2] + ny; + newbox2[3] = ny - 1; + newpbc[1]--; + } else if (box[3] >= ny) { + newbox1[3] = ny - 1; + newbox2[2] = 0; + newbox2[3] = box[3] - ny; + newpbc[1]++; + + // box is not split, drop on RCB tree + // returns np = # of procs it overlaps, including self + // returns proc_overlap = list of proc IDs it overlaps + // add each overlap to overlap list + + } else { + splitflag = 0; + int np = 0; + box_drop_grid(box,0,nprocs-1,np,overlap_procs); + for (m = 0; m < np; m++) { + if (noverlap_list == maxoverlap_list) grow_overlap(); + overlap_list[noverlap_list].proc = overlap_procs[m]; + for (i = 0; i < 4; i++) overlap_list[noverlap_list].box[i] = box[i]; + for (i = 0; i < 2; i++) overlap_list[noverlap_list].pbc[i] = pbc[i]; + noverlap_list++; + } + } + + // recurse with 2 split boxes + + if (splitflag) { + box_drop(newbox1,pbc); + box_drop(newbox2,newpbc); + } +} + +/* ---------------------------------------------------------------------- + recursively drop a box down the RCB tree to find all procs it overlaps with + box = 4 integers = (xlo,xhi,ylo,yhi) + each lo/hi value ranges from 0 to N-1 in a dim, N = grid size in that dim + box is guaranteed to be wholly within the global domain + return Np = # of procs, plist = proc IDs +------------------------------------------------------------------------- */ + +void Grid2d::box_drop_grid(int *box, int proclower, int procupper, + int &np, int *plist) +{ + // end recursion when partition is a single proc + // add proclower to plist + + if (proclower == procupper) { + plist[np++] = proclower; + return; + } + + // drop box on each side of cut it extends beyond + // use < and >= criteria so does not include a box it only touches + // procmid = 1st processor in upper half of partition + // = location in tree that stores this cut + // cut = index of first grid cell in upper partition + // dim = 0,1,2 dimension of cut + + int procmid = proclower + (procupper - proclower) / 2 + 1; + int dim = rcbinfo[procmid].dim; + int cut = rcbinfo[procmid].cut; + + if (box[2*dim] < cut) box_drop_grid(box,proclower,procmid-1,np,plist); + if (box[2*dim+1] >= cut) box_drop_grid(box,procmid,procupper,np,plist); +} + +// ---------------------------------------------------------------------- +// miscellaneous methods +// ---------------------------------------------------------------------- + +/* ---------------------------------------------------------------------- + grow list of swaps by DELTA +------------------------------------------------------------------------- */ + +void Grid2d::grow_swap() +{ + maxswap += DELTA; + swap = (Swap *) memory->srealloc(swap,maxswap*sizeof(Swap),"grid2d:swap"); +} + +/* ---------------------------------------------------------------------- + grow list of overlaps by DELTA +------------------------------------------------------------------------- */ + +void Grid2d::grow_overlap() +{ + maxoverlap_list += DELTA; + overlap_list = (Overlap *) + memory->srealloc(overlap_list,maxoverlap_list*sizeof(Overlap),"grid2d:overlap"); +} + +/* ---------------------------------------------------------------------- + deallocate remap data structs +------------------------------------------------------------------------- */ + +void Grid2d::deallocate_remap() +{ + for (int i = 0; i < nsend_remap; i++) + memory->destroy(send_remap[i].packlist); + delete [] send_remap; + + for (int i = 0; i < nrecv_remap; i++) + memory->destroy(recv_remap[i].unpacklist); + delete [] recv_remap; + + if (self_remap) { + memory->destroy(copy_remap.packlist); + memory->destroy(copy_remap.unpacklist); + } +} + +/* ---------------------------------------------------------------------- + create 1d list of offsets into 2d array section (xlo:xhi,ylo:yhi) + assume caller's 2d array is allocated as + (fullxlo:fullxhi,fullylo:fullyhi) +------------------------------------------------------------------------- */ + +int Grid2d::indices(int *&list, int xlo, int xhi, int ylo, int yhi) +{ + int nmax = (xhi-xlo+1) * (yhi-ylo+1); + memory->create(list,nmax,"grid2d:indices"); + if (nmax == 0) return 0; + + int nx = (fullxhi-fullxlo+1); + + int n = 0; + int ix,iy; + for (iy = ylo; iy <= yhi; iy++) + for (ix = xlo; ix <= xhi; ix++) + list[n++] = (iy-fullylo)*nx + (ix-fullxlo); + + return nmax; +} + +/* ---------------------------------------------------------------------- + find the comm->procgrid index = which proc owns the igrid index + igrid = grid index (0 to N-1) in dim + n = # of grid points in dim + shift determines position of grid pt within grid cell + shift = 0.5 for cell center, 0.0 for lower-left corner + dim = which dimension (0,1) + split = comm->x/y/z split for fractional bounds of each proc domain +------------------------------------------------------------------------- */ + +int Grid2d::proc_index_uniform(int igrid, int n, double shift, int dim, double *split) +{ + int lo,hi; + double fraclo,frachi; + + // loop over # of procs in this dime + // compute the grid bounds for that proc + // if igrid falls within those bounds, return m = proc index + // same logic as in partition_grid() + + int m; + for (m = 0; m < comm->procgrid[dim]; m++) { + fraclo = split[m]; + frachi = split[m+1]; + + lo = static_cast (fraclo * n); + while (lo+shift < fraclo*n) lo++; + hi = static_cast (frachi * n); + if (hi+shift >= frachi*n) hi--; + + if (igrid >= lo && igrid <= hi) break; + } + + return m; +} + +/* ---------------------------------------------------------------------- + compute the grid box owned by proc within tiled decomposition + performed recursively until proclower = procupper = proc + return box = lo/hi bounds of proc's box in 2 dims +------------------------------------------------------------------------- */ + +void Grid2d::partition_tiled(int proc, int proclower, int procupper, int *box) +{ + // end recursion when partition is a single proc + + if (proclower == procupper) return; + + // split processor partition + // procmid = 1st processor in upper half of partition + // = location in tree that stores this cut + // cut = index of first grid cell in upper partition + // dim = 0,1 dimension of cut + + int procmid = proclower + (procupper - proclower) / 2 + 1; + int dim = rcbinfo[procmid].dim; + int cut = rcbinfo[procmid].cut; + + // adjust box to reflect which half of partition the proc is in + + if (proc < procmid) { + box[2*dim+1] = cut-1; + partition_tiled(proc,proclower,procmid-1,box); + } else { + box[2*dim] = cut; + partition_tiled(proc,procmid,procupper,box); + } +} diff --git a/src/grid2d.h b/src/grid2d.h new file mode 100644 index 0000000000..bb1bfb25e1 --- /dev/null +++ b/src/grid2d.h @@ -0,0 +1,266 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_GRID2D_H +#define LMP_GRID2D_H + +#include "pointers.h" + +namespace LAMMPS_NS { + +class Grid2d : protected Pointers { + public: + enum { KSPACE = 0, PAIR = 1, FIX = 2 }; // calling classes + + Grid2d(class LAMMPS *, MPI_Comm, int, int); + Grid2d(class LAMMPS *, MPI_Comm, int, int, int, int, int, int, int, int, int, int); + ~Grid2d() override; + + void set_distance(double); + void set_stencil_grid(int, int); + void set_stencil_atom(int, int); + void set_shift_grid(double); + void set_shift_atom(double, double); + void set_yfactor(double); + void set_caller_grid(int, int, int, int); + void set_proc_neighs(int, int, int, int); + + int identical(Grid2d *); + void get_size(int &, int &); + void get_bounds_owned(int &, int &, int &, int &); + void get_bounds_ghost(int &, int &, int &, int &); + + void setup_grid(int &, int &, int &, int &, int &, int &, int &, int &); + + void setup_comm(int &, int &); + int ghost_adjacent(); + void forward_comm(int, void *, int, int, int, void *, void *, MPI_Datatype); + void reverse_comm(int, void *, int, int, int, void *, void *, MPI_Datatype); + + void setup_remap(Grid2d *, int &, int &); + void remap(int, void *, int, int, int, void *, void *, MPI_Datatype); + + void read_file(int, void *, FILE *, int, int); + void write_file(int, void *, int, int, int, MPI_Datatype); + +protected: + int me, nprocs; + int layout; // not TILED or TILED, same as Comm class + MPI_Comm gridcomm; // communicator for this class + // usually world, but MSM calls with subset + + // inputs from caller via constructor + + int nx, ny; // size of global grid in both dims + double maxdist; // distance owned atoms can move outside subdomain + int stencil_atom_lo,stencil_atom_hi; // grid cells accessed beyond atom's cell + int stencil_grid_lo,stencil_grid_hi; // grid cells accessed beyond owned cell + double shift_grid; // location of grid point within grid cell + // only affects which proc owns grid cell + double shift_atom_lo,shift_atom_hi;; // max shift applied to atoms + // when mapped to grid cell by caller + // can be different in lo/hi directions + // only affects extent of ghost cells + int yextra; // 1 if extra grid cells in Y, 0 if not + double yfactor; // multiplier on extent of grid in Y direction + + // extent of my owned and ghost cells + + int inxlo, inxhi; // inclusive extent of my grid chunk, 0 <= in <= N-1 + int inylo, inyhi; + int outxlo, outxhi; // inclusive extent of my grid chunk plus + int outylo, outyhi; // ghost cells in all 4 directions + // lo indices can be < 0, hi indices can be >= N + int fullxlo, fullxhi; // extent of grid chunk that caller stores + int fullylo, fullyhi; // can be same as out indices or larger + + // ------------------------------------------- + // internal variables for BRICK layout + // ------------------------------------------- + + int procxlo, procxhi; // 4 neighbor procs that adjoin me + int procylo, procyhi; // not used for comm_style = tiled + + int ghostxlo, ghostxhi; // # of my owned grid planes needed + int ghostylo, ghostyhi; // by neighobr procs in each dir as their ghost planes + + // swap = exchange of owned and ghost grid cells between 2 procs, including self + + struct Swap { + int sendproc; // proc to send to for forward comm + int recvproc; // proc to recv from for forward comm + int npack; // # of datums to pack + int nunpack; // # of datums to unpack + int *packlist; // 3d array offsets to pack + int *unpacklist; // 3d array offsets to unpack + }; + + int nswap, maxswap; + Swap *swap; + + // ------------------------------------------- + // internal variables for TILED layout + // ------------------------------------------- + + MPI_Request *requests; // length of max messages this proc receives + + // request = sent to each proc whose owned cells overlap my ghost cells + + struct Request { + int sender; // sending proc + int index; // index of overlap on sender + int box[4]; // box that overlaps receiver's owned cells + // wholly contained within global grid + }; + + Request *srequest, *rrequest; + + // response = reply from each proc whose owned cells overlap my ghost cells + + struct Response { + int index; // index of my overlap for the initial request + int box[4]; // box that overlaps responder's owned cells + // wholly contained within global grid + // has to unwrapped by PBC to map to my ghost cells + }; + + Response *sresponse, *rresponse; + + // send = proc to send a subset of my owned cells to, for forward comm + // for reverse comm, proc I receive ghost overlaps with my owned cells from + // offset used in reverse comm to recv a message in middle of a large buffer + + struct Send { + int proc; + int npack; + int *packlist; + int offset; + }; + + // recv = proc to recv a subset of my ghost cells from, for forward comm + // for reverse comm, proc I send a subset of my ghost cells to + // offset used in forward comm to recv a message in middle of a large buffer + + struct Recv { + int proc; + int nunpack; + int *unpacklist; + int offset; + }; + + int adjacent; // 0 on a proc who receives ghosts from a non-neighbor proc + + // copy = subset of my owned cells to copy into subset of my ghost cells + // that describes forward comm, for reverse comm it is the opposite + + struct Copy { + int npack; + int nunpack; + int *packlist; + int *unpacklist; + }; + + int nsend, nrecv, ncopy; + Send *send; + Recv *recv; + Copy *copy; + + // ------------------------------------------- + // internal variables for REMAP operation + // ------------------------------------------- + + MPI_Request *requests_remap; // length of max messages this proc receives + + int nsend_remap, nrecv_remap, self_remap; + Send *send_remap; + Recv *recv_remap; + Copy copy_remap; + + // ------------------------------------------- + // internal variables for OVERLAP operation + // ------------------------------------------- + + int *overlap_procs; // length of Nprocs in communicator + + // BRICK decomposition + + double *xsplit,*ysplit,*zsplit; + int ***grid2proc; + + // TILED decomposition + + // RCB tree of cut info + // each proc contributes one value, except proc 0 + + struct RCBinfo { + int dim; // 0,1 = which dim the cut is in + int cut; // grid index of lowest cell in upper half of cut + }; + + RCBinfo *rcbinfo; + + // overlap = a proc whose owned cells overlap with my owned or ghost box + // includes overlaps across periodic boundaries, can also be self + + struct Overlap { + int proc; // proc whose cells overlap my cells + int box[4]; // box of my cells which overlap proc's cells + // this box is wholly contained within global grid + int pbc[2]; // PBC offsets to convert my box to a portion of my ghost box + // my ghost box may extend beyond global grid + }; + + int noverlap_list, maxoverlap_list; + Overlap *overlap_list; + + // ------------------------------------------- + // internal methods + // ------------------------------------------- + + void initialize(); + void partition_grid(int, double, double, double, int, int &, int &); + void ghost_grid(); + void extract_comm_info(); + + void setup_comm_brick(int &, int &); + void setup_comm_tiled(int &, int &); + int ghost_adjacent_brick(); + int ghost_adjacent_tiled(); + + template void forward_comm_brick(T *, int, int, int, void *, void *, MPI_Datatype); + template void forward_comm_tiled(T *, int, int, int, void *, void *, MPI_Datatype); + template void reverse_comm_brick(T *, int, int, int, void *, void *, MPI_Datatype); + template void reverse_comm_tiled(T *, int, int, int, void *, void *, MPI_Datatype); + + template void remap_style(T *, int, int, int, void *, void *, MPI_Datatype); + + template void read_file_style(T *, FILE *, int, int); + template void write_file_style(T *, int, int, int, MPI_Datatype); + + int compute_overlap(int, int *, int *, Overlap *&); + void clean_overlap(); + void box_drop(int *, int *); + void box_drop_grid(int *, int, int, int &, int *); + + void grow_swap(); + void grow_overlap(); + void deallocate_remap(); + + int indices(int *&, int, int, int, int); + int proc_index_uniform(int, int, double, int, double *); + void partition_tiled(int, int, int, int *); +}; + +} // namespace LAMMPS_NS + +#endif diff --git a/src/grid3d.cpp b/src/grid3d.cpp new file mode 100644 index 0000000000..3654830549 --- /dev/null +++ b/src/grid3d.cpp @@ -0,0 +1,2159 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS Development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "grid3d.h" + +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "irregular.h" +#include "pair.h" +#include "kspace.h" +#include "fix.h" +#include "math_extra.h" +#include "memory.h" + +using namespace LAMMPS_NS; + +#define DELTA 16 + +static constexpr int OFFSET = 16384; + +/* ---------------------------------------------------------------------- + NOTES: + if o indices for ghosts are < 0 or hi indices are >= N, + then grid is treated as periodic in that dimension, + comm is done across the periodic boundaries + tiled implementations only work for RCB, not general tilings + b/c RCB tree is used to find neighboring tiles +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + constructor to create a 3d distributed grid + Grid3d assigns owned/ghost cells to each proc via setup_grid() + it MUST be called after constructor + gcomm = caller's communicator + gnx,gny,gnz = global grid size +------------------------------------------------------------------------- */ + +Grid3d::Grid3d(LAMMPS *lmp, MPI_Comm gcomm, int gnx, int gny, int gnz) : + Pointers(lmp), swap(nullptr), requests(nullptr), srequest(nullptr), rrequest(nullptr), + sresponse(nullptr), rresponse(nullptr), send(nullptr), recv(nullptr), copy(nullptr), + send_remap(nullptr), recv_remap(nullptr), overlap_procs(nullptr), xsplit(nullptr), + ysplit(nullptr), zsplit(nullptr), grid2proc(nullptr), rcbinfo(nullptr), overlap_list(nullptr) + +{ + gridcomm = gcomm; + MPI_Comm_rank(gridcomm,&me); + MPI_Comm_size(gridcomm,&nprocs); + + nx = gnx; + ny = gny; + nz = gnz; + + // default settings, can be overridden by set() methods + // these affect assignment of owned and ghost cells + + maxdist = 0.0; + stencil_grid_lo = stencil_grid_hi = 0; + stencil_atom_lo = stencil_atom_hi = 0; + shift_grid = 0.5; + shift_atom_lo = shift_atom_hi = 0.0; + zextra = 0; + zfactor = 1.0; +} + +/* ---------------------------------------------------------------------- + alternate constructor to create a 3d distributed grid + caller assigns owned/ghost cells to each proc + setup_grid() must NOT be called + used by MSM and PPPM/Electrode b/c their definition of ghost cells is complex + gcomm = caller's communicator + gnx,gny,gnz = global grid size + i xyz lo/hi = extent of owned grid cells on this proc + o xyz lo/hi = extent of owned+ghost grid cells on this proc + owned and ghost indices are inclusive + owned indices range from 0 to N-1 + ghost indices can extend < 0 or >= N +------------------------------------------------------------------------- */ + +Grid3d::Grid3d(LAMMPS *lmp, MPI_Comm gcomm, int gnx, int gny, int gnz, + int ixlo, int ixhi, int iylo, int iyhi, int izlo, int izhi, + int oxlo, int oxhi, int oylo, int oyhi, int ozlo, int ozhi) : + Pointers(lmp), swap(nullptr), requests(nullptr), srequest(nullptr), rrequest(nullptr), + sresponse(nullptr), rresponse(nullptr), send(nullptr), recv(nullptr), copy(nullptr), + send_remap(nullptr), recv_remap(nullptr), overlap_procs(nullptr), xsplit(nullptr), + ysplit(nullptr), zsplit(nullptr), grid2proc(nullptr), rcbinfo(nullptr), overlap_list(nullptr) +{ + gridcomm = gcomm; + MPI_Comm_rank(gridcomm,&me); + MPI_Comm_size(gridcomm,&nprocs); + + nx = gnx; + ny = gny; + nz = gnz; + + // store owned/ghost indices provided by caller + + inxlo = ixlo; + inxhi = ixhi; + inylo = iylo; + inyhi = iyhi; + inzlo = izlo; + inzhi = izhi; + + outxlo = oxlo; + outxhi = oxhi; + outylo = oylo; + outyhi = oyhi; + outzlo = ozlo; + outzhi = ozhi; + + // additional intialization + // other constructor invokes this from setup_grid() + + initialize(); +} + +/* ---------------------------------------------------------------------- */ + +Grid3d::~Grid3d() +{ + // brick comm data structs + + for (int i = 0; i < nswap; i++) { + memory->destroy(swap[i].packlist); + memory->destroy(swap[i].unpacklist); + } + memory->sfree(swap); + + delete [] xsplit; + delete [] ysplit; + delete [] zsplit; + memory->destroy(grid2proc); + + // tiled comm data structs + + for (int i = 0; i < nsend; i++) + memory->destroy(send[i].packlist); + memory->sfree(send); + + for (int i = 0; i < nrecv; i++) + memory->destroy(recv[i].unpacklist); + memory->sfree(recv); + + for (int i = 0; i < ncopy; i++) { + memory->destroy(copy[i].packlist); + memory->destroy(copy[i].unpacklist); + } + memory->sfree(copy); + + delete [] requests; + delete [] requests_remap; + + memory->sfree(rcbinfo); + + // remap data structs + + deallocate_remap(); +} + +// ---------------------------------------------------------------------- +// set Grid parameters +// ---------------------------------------------------------------------- + +/* ---------------------------------------------------------------------- + maxdist = max distance outside proc subdomain a particle can be + used to determine extent of ghost cells +------------------------------------------------------------------------- */ + +void Grid3d::set_distance(double distance) +{ + maxdist = distance; +} + +/* ---------------------------------------------------------------------- + # of grid cells beyond an owned grid cell that caller accesses + used by FixTTMGrid for a finite different stencil + can be different in lo vs hi direction +------------------------------------------------------------------------- */ + +void Grid3d::set_stencil_grid(int lo, int hi) +{ + stencil_grid_lo = lo; + stencil_grid_hi = hi; +} + +/* ---------------------------------------------------------------------- + # of grid cells beyond a particle's grid cell that caller accesses + used by PPPM for smearing a point charge to the grid + can be different in lo vs hi direction +------------------------------------------------------------------------- */ + +void Grid3d::set_stencil_atom(int lo, int hi) +{ + stencil_atom_lo = lo; + stencil_atom_hi = hi; +} + +/* ---------------------------------------------------------------------- + shift_grid = offset within grid cell of position of grid point + 0.5 = cell center (default), 0.0 = lower-left corner of cell + used to decide which proc owns a grid cell (grid pt within subdomain) +------------------------------------------------------------------------- */ + +void Grid3d::set_shift_grid(double shift) +{ + shift_grid = shift; +} + +/* ---------------------------------------------------------------------- + shift_atom = offset added to atoms when caller maps them to grid cells + 0.5 = half a grid cell, 0.0 = no offset + used to compute maximum possible ghost extents + use of lo/hi allows max ghost extent on each side to be different + PPPM uses 0.5 when stencil order is odd, 0.0 when order is even + PPPM/stagger applies different shift values for 2 stagger iterations +------------------------------------------------------------------------- */ + +void Grid3d::set_shift_atom(double shift_lo, double shift_hi) +{ + shift_atom_lo = shift_lo; + shift_atom_hi = shift_hi; +} + +/* ---------------------------------------------------------------------- + enable extra grid cells in Z + factor = muliplication factor on box size Z and thus grid size + factor > 1.0 when grid extends beyond Z box size (3.0 = tripled in size) + used by PPPM for 2d periodic slab geometries + only enable zextra if factor > 1.0 + default zextra = 0, factor = 1.0 (no extra grid cells in Z) +------------------------------------------------------------------------- */ + +void Grid3d::set_zfactor(double factor) +{ + if (factor == 1.0) zextra = 0; + else zextra = 1; + zfactor = factor; +} + +/* ---------------------------------------------------------------------- + set IDs of proc neighbors used in uniform local owned/ghost comm + must be called BEFORE setup_comm() to override + the processor neighbors stored by extract_comm_info() + used by MSM to exclude non-participating procs for coarse grid comm +------------------------------------------------------------------------- */ + +void Grid3d::set_proc_neighs(int pxlo, int pxhi, int pylo, int pyhi, + int pzlo, int pzhi) +{ + procxlo = pxlo; + procxhi = pxhi; + procylo = pylo; + procyhi = pyhi; + proczlo = pzlo; + proczhi = pzhi; +} + +/* ---------------------------------------------------------------------- + set allocation dimensions of caller grid used by indices() to setup pack/unpack + must be called BEFORE setup_comm() to override + the caller grid size used in indices() + used by MSM to allow a larger level 0 grid to be allocated + with more ghost cells for other operations +------------------------------------------------------------------------- */ + +void Grid3d::set_caller_grid(int fxlo, int fxhi, int fylo, int fyhi, + int fzlo, int fzhi) +{ + fullxlo = fxlo; + fullxhi = fxhi; + fullylo = fylo; + fullyhi = fyhi; + fullzlo = fzlo; + fullzhi = fzhi; +} + +// ---------------------------------------------------------------------- +// retrieve Grid parameters +// ---------------------------------------------------------------------- + +int Grid3d::identical(Grid3d *grid2) +{ + int inxlo2,inxhi2,inylo2,inyhi2,inzlo2,inzhi2; + int outxlo2,outxhi2,outylo2,outyhi2,outzlo2,outzhi2; + + grid2->get_bounds_owned(inxlo2,inxhi2,inylo2,inyhi2,inzlo2,inzhi2); + grid2->get_bounds_ghost(outxlo2,outxhi2,outylo2,outyhi2,outzlo2,outzhi2); + + int flag = 0; + if (inxlo != inxlo2 || inxhi != inxhi2 || + inylo != inylo2 || inyhi != inyhi2 || + inzlo != inzlo2 || inzhi != inzhi2) flag = 1; + if (outxlo != outxlo2 || outxhi != outxhi2 || + outylo != outylo2 || outyhi != outyhi2 || + outzlo != outzlo2 || outzhi != outzhi2) flag = 1; + + int flagall; + MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,gridcomm); + + if (flagall) return 0; + return 1; +} + +/* ---------------------------------------------------------------------- */ + +void Grid3d::get_size(int &nxgrid, int &nygrid, int &nzgrid) +{ + nxgrid = nx; + nygrid = ny; + nzgrid = nz; +} + +/* ---------------------------------------------------------------------- */ + +void Grid3d::get_bounds_owned(int &xlo, int &xhi, int &ylo, int &yhi, + int &zlo, int &zhi) +{ + xlo = inxlo; + xhi = inxhi; + ylo = inylo; + yhi = inyhi; + zlo = inzlo; + zhi = inzhi; +} + +/* ---------------------------------------------------------------------- */ + +void Grid3d::get_bounds_ghost(int &xlo, int &xhi, int &ylo, int &yhi, + int &zlo, int &zhi) +{ + xlo = outxlo; + xhi = outxhi; + ylo = outylo; + yhi = outyhi; + zlo = outzlo; + zhi = outzhi; +} + +// ---------------------------------------------------------------------- +// define owned and ghost grid cells +// also store comm and grid partitioning info +// ---------------------------------------------------------------------- + +/* ---------------------------------------------------------------------- + setup grid partition for each proc = owned + ghost cells + return: + i xyz lohi = portion of global grid this proc owns, 0 <= index < N + o xyz lohi = owned + ghost grid cells in all directions + for periodic dims, o indices can be < 0 or >= N + for non-periodic dims, o indices will be >= 0 and < N + since no grid comm is done across non-periodic boundaries +------------------------------------------------------------------------- */ + +void Grid3d::setup_grid(int &ixlo, int &ixhi, int &iylo, int &iyhi, + int &izlo, int &izhi, + int &oxlo, int &oxhi, int &oylo, int &oyhi, + int &ozlo, int &ozhi) +{ + // owned grid cells = those whose grid point is within proc subdomain + // shift_grid = 0.5 for grid point at cell center, 0.0 for lower-left corner + + double fraclo,frachi; + + if (comm->layout != Comm::LAYOUT_TILED) { + fraclo = comm->xsplit[comm->myloc[0]]; + frachi = comm->xsplit[comm->myloc[0]+1]; + partition_grid(nx,fraclo,frachi,shift_grid,0,inxlo,inxhi); + fraclo = comm->ysplit[comm->myloc[1]]; + frachi = comm->ysplit[comm->myloc[1]+1]; + partition_grid(ny,fraclo,frachi,shift_grid,0,inylo,inyhi); + fraclo = comm->zsplit[comm->myloc[2]]; + frachi = comm->zsplit[comm->myloc[2]+1]; + partition_grid(nz,fraclo,frachi,shift_grid,zextra,inzlo,inzhi); + } else { + fraclo = comm->mysplit[0][0]; + frachi = comm->mysplit[0][1]; + partition_grid(nx,fraclo,frachi,shift_grid,0,inxlo,inxhi); + fraclo = comm->mysplit[1][0]; + frachi = comm->mysplit[1][1]; + partition_grid(ny,fraclo,frachi,shift_grid,0,inylo,inyhi); + fraclo = comm->mysplit[2][0]; + frachi = comm->mysplit[2][1]; + partition_grid(nz,fraclo,frachi,shift_grid,zextra,inzlo,inzhi); + } + + // extend owned grid bounds with ghost grid cells in each direction + + ghost_grid(); + + // additional intialization + // other constructor invokes this directly + + initialize(); + + // return values + + ixlo = inxlo; + ixhi = inxhi; + iylo = inylo; + iyhi = inyhi; + izlo = inzlo; + izhi = inzhi; + + oxlo = outxlo; + oxhi = outxhi; + oylo = outylo; + oyhi = outyhi; + ozlo = outzlo; + ozhi = outzhi; +} + +/* ---------------------------------------------------------------------- + additional one-time setup common to both constructors + ---------------------------------------------------------------------- */ + +void Grid3d::initialize() +{ + // error check on size of grid stored by this proc + + bigint total = (bigint) + (outxhi - outxlo + 1) * (outyhi - outylo + 1) * (outzhi - outzlo + 1); + if (total > MAXSMALLINT) + error->one(FLERR, "Too many owned+ghost grid3d points"); + + // default = caller grid is allocated to ghost grid + // used when computing pack/unpack lists in indices() + // these values can be overridden using set_caller_grid() + + fullxlo = outxlo; + fullxhi = outxhi; + fullylo = outylo; + fullyhi = outyhi; + fullzlo = outzlo; + fullzhi = outzhi; + + // initialize data structs + + nswap = maxswap = 0; + swap = nullptr; + + nsend = nrecv = ncopy = 0; + send = nullptr; + recv = nullptr; + copy = nullptr; + requests = nullptr; + requests_remap = nullptr; + + xsplit = ysplit = zsplit = nullptr; + grid2proc = nullptr; + rcbinfo = nullptr; + + nsend_remap = nrecv_remap = self_remap = 0; + send_remap = nullptr; + recv_remap = nullptr; + + // store info about Comm decomposition needed for remap operation + // two Grid instances will exist for duration of remap + // each must know Comm decomp at time Grid instance was created + + extract_comm_info(); +} + +/* ---------------------------------------------------------------------- + partition a global regular grid into one brick-shaped sub-grid per proc + if grid point is inside my sub-domain I own it, + this includes sub-domain lo boundary but excludes hi boundary + ngrid = extent of global grid in a dimension + indices into the global grid range from 0 to Ngrid-1 in that dim + shift determines position of grid pt within grid cell + shift = 0.5 for cell center, 0.0 for lower-left corner + extra = 0 if grid exactly covers the simulation box + extra = 1 if grid extends beyond the +z boundary by zfactor (PPPM slab) + effectively maps proc partitions to the box-size subset of the grid + lo/hi = inclusive lo/hi bounds for brick of global grid cells I own + lo grid index = first grid pt >= fraclo*bound + hi grid index = last grid pt < frachi*bound + if proc owns no grid cells in a dim, then inlo > inhi + special case: 2 procs share boundary which a grid point is exactly on + 2 if test equalties insure a consistent decision as to which proc owns it +------------------------------------------------------------------------- */ + +void Grid3d::partition_grid(int ngrid, double fraclo, double frachi, + double shift, int extra, int &lo, int &hi) +{ + if (extra == 0) { + lo = static_cast (fraclo * ngrid); + while (lo+shift < fraclo*ngrid) lo++; + hi = static_cast (frachi * ngrid); + while (hi+shift >= frachi*ngrid) hi--; + } else { + lo = static_cast (fraclo * ngrid/zfactor); + while (lo+shift < fraclo*ngrid/zfactor) lo++; + hi = static_cast (frachi * ngrid/zfactor); + while (hi+shift >= frachi*ngrid/zfactor) hi--; + } +} + +/* ---------------------------------------------------------------------- + extend ghost grid cells in each direction beyond owned grid + indices into the global grid range from 0 to N-1 in each dim + ghost cell indices for periodic systems can be < 0 or >= N +------------------------------------------------------------------------- */ + +void Grid3d::ghost_grid() +{ + double *prd,*boxlo,*sublo,*subhi; + int triclinic = domain->triclinic; + + if (triclinic == 0) { + prd = domain->prd; + boxlo = domain->boxlo; + sublo = domain->sublo; + subhi = domain->subhi; + } else { + prd = domain->prd_lamda; + boxlo = domain->boxlo_lamda; + sublo = domain->sublo_lamda; + subhi = domain->subhi_lamda; + } + + // for triclinic, maxdist = different value in each orthogonal direction + + double dist[3] = {0.0,0.0,0.0}; + if (triclinic == 0) dist[0] = dist[1] = dist[2] = maxdist; + else MathExtra::tribbox(domain->h,maxdist,&dist[0]); + + // lo/hi = min/max index of global grid cells my owned atoms can be mapped to + // includes effects of maxdist and shift_atom settings + // lo/hi can be further extended by stencil_atom and stencil_grid settings + // all those settings are set by caller + // ghost cell layers needed in each dim/dir = max of two extension effects + // OFFSET allows generation of negative indices with static_cast + // out xyz lo/hi = index range of owned + ghost cells + // if zextra, nz and effective prd[2] are both larger, so dzinv is the same + + double dxinv = nx / prd[0]; + double dyinv = ny / prd[1]; + double dzinv = nz / prd[2]; + if (zextra) dzinv = nz / (prd[2] * zfactor); + + int lo, hi; + + lo = static_cast((sublo[0]-dist[0]-boxlo[0]) * dxinv + shift_atom_lo + OFFSET) - OFFSET; + hi = static_cast((subhi[0]+dist[0]-boxlo[0]) * dxinv + shift_atom_hi + OFFSET) - OFFSET; + outxlo = MIN(lo - stencil_atom_lo, inxlo - stencil_grid_lo); + outxhi = MAX(hi + stencil_atom_hi, inxhi + stencil_grid_hi); + + lo = static_cast((sublo[1]-dist[1]-boxlo[1]) * dyinv + shift_atom_lo + OFFSET) - OFFSET; + hi = static_cast((subhi[1]+dist[1]-boxlo[1]) * dyinv + shift_atom_hi + OFFSET) - OFFSET; + outylo = MIN(lo - stencil_atom_lo, inylo - stencil_grid_lo); + outyhi = MAX(hi + stencil_atom_hi, inyhi + stencil_grid_hi); + + lo = static_cast((sublo[2]-dist[2]-boxlo[2]) * dzinv + shift_atom_lo + OFFSET) - OFFSET; + hi = static_cast((subhi[2]+dist[2]-boxlo[2]) * dzinv + shift_atom_hi + OFFSET) - OFFSET; + outzlo = MIN(lo - stencil_atom_lo, inzlo - stencil_grid_lo); + outzhi = MAX(hi + stencil_atom_hi, inzhi + stencil_grid_hi); + + // if zextra = 1: + // adjust grid boundaries for processors at +z end, + // to include added empty grid cells between periodically repeating slabs + // in this case: + // want grid data forward communicated from +z proc to -z proc, but not vice versa + // want grid data reverse communicated from -z proc to +z proc, but not vice versa + // this is accomplished by inzhi = outzhi on +z end (no ghost cells) + // also insure no other procs use ghost cells beyond +z limit + + if (zextra) { + if (layout != Comm::LAYOUT_TILED) { + if (comm->myloc[2] == comm->procgrid[2]-1) inzhi = outzhi = nz - 1; + } else { + if (comm->mysplit[2][1] == 1.0) inzhi = outzhi = nz - 1; + } + outzhi = MIN(outzhi,nz-1); + } + + // limit out xyz lo/hi indices to global grid for non-periodic dims + // if zextra = 1 (e.g. PPPM), treat z-dimension as if periodic + + int *periodicity = domain->periodicity; + + if (!periodicity[0]) { + outxlo = MAX(0,outxlo); + outxhi = MIN(nx-1,outxhi); + } + + if (!periodicity[1]) { + outylo = MAX(0,outylo); + outyhi = MIN(ny-1,outyhi); + } + + if (!periodicity[2] && !zextra) { + outzlo = MAX(0,outzlo); + outzhi = MIN(nz-1,outzhi); + } +} + +/* ---------------------------------------------------------------------- + store copy of info from Comm class about processor partitioning + used when a remap is performed between two Grid instances, old and new +------------------------------------------------------------------------- */ + +void Grid3d::extract_comm_info() +{ + layout = comm->layout; + + // for non TILED layout: + // proc xyz lohi = my 6 neighbor procs in this MPI_Comm + // these proc IDs can be overridden by caller using set_proc_neighs() + // xyz split = copy of 1d vectors in Comm + // grid2proc = copy of 3d array in Comm + + if (layout != Comm::LAYOUT_TILED) { + procxlo = comm->procneigh[0][0]; + procxhi = comm->procneigh[0][1]; + procylo = comm->procneigh[1][0]; + procyhi = comm->procneigh[1][1]; + proczlo = comm->procneigh[2][0]; + proczhi = comm->procneigh[2][1]; + + xsplit = new double[comm->procgrid[0]+1]; + ysplit = new double[comm->procgrid[1]+1]; + zsplit = new double[comm->procgrid[2]+1]; + memcpy(xsplit, comm->xsplit, sizeof(double) * (comm->procgrid[0]+1)); + memcpy(ysplit, comm->ysplit, sizeof(double) * (comm->procgrid[1]+1)); + memcpy(zsplit, comm->zsplit, sizeof(double) * (comm->procgrid[2]+1)); + + memory->create(grid2proc,comm->procgrid[0],comm->procgrid[1],comm->procgrid[2], + "grid3d:grid2proc"); + memcpy(&grid2proc[0][0][0],&comm->grid2proc[0][0][0], + sizeof(int) * comm->procgrid[0] * comm->procgrid[1] * comm->procgrid[2]); + } + + // for TILED layout: + // create RCB tree of grid partitioning info for grid decomp + // Comm provides dim info for this proc, stored as RCBinfo.dim + // dim is -1 for proc 0, but never accessed + // RCBinfo.cut = this proc's inlo in that dim + // Allgather creates the tree of dims and cuts + + if (layout == Comm::LAYOUT_TILED) { + rcbinfo = (RCBinfo *) + memory->smalloc(nprocs*sizeof(RCBinfo),"grid3d:rcbinfo"); + RCBinfo rcbone; + rcbone.dim = comm->rcbcutdim; + if (rcbone.dim <= 0) rcbone.cut = inxlo; + else if (rcbone.dim == 1) rcbone.cut = inylo; + else if (rcbone.dim == 2) rcbone.cut = inzlo; + MPI_Allgather(&rcbone,sizeof(RCBinfo),MPI_CHAR, + rcbinfo,sizeof(RCBinfo),MPI_CHAR,gridcomm); + } +} + +// ---------------------------------------------------------------------- +// setup of local owned/ghost grid comm +// ---------------------------------------------------------------------- + +/* ---------------------------------------------------------------------- + setup commmunication of owned/ghost grid cells + either for brick decomp or tiled decomp + return sizes of two buffers needed for communication + nbuf1 = largest pack or unpack in any Send or Recv or Copy + nbuf2 = larget of sum of all packs or unpacks in Send or Recv + for brick comm, nbuf1 = nbuf2 + for tiling comm, nbuf2 >= nbuf2 + nbuf1,nbuf2 are counts of grid cells + caller converts them to message sizes for grid data it stores +------------------------------------------------------------------------- */ + +void Grid3d::setup_comm(int &nbuf1, int &nbuf2) +{ + if (layout != Comm::LAYOUT_TILED) setup_comm_brick(nbuf1,nbuf2); + else setup_comm_tiled(nbuf1,nbuf2); +} + +/* ---------------------------------------------------------------------- + setup owned/ghost comm for brick comm + each proc has 6 neighbors + comm pattern = series of swaps with one of those 6 procs + can be multiple swaps with same proc if ghost extent is large + swap may not be symmetric if both procs do not need same layers of ghosts + all procs perform same # of swaps in a direction, even if some don't need it +------------------------------------------------------------------------- */ + +void Grid3d::setup_comm_brick(int &nbuf1, int &nbuf2) +{ + int nsent,sendfirst,sendlast,recvfirst,recvlast; + int sendplanes,recvplanes; + int notdoneme,notdone; + + // notify 6 neighbor procs how many ghost grid planes I need from them + // ghost xyz lo = # of my lower grid planes that proc xyz lo needs as its ghosts + // ghost xyz hi = # of my upper grid planes that proc xyz hi needs as its ghosts + // if this proc is its own neighbor across periodic bounary, value is from self + + int nplanes = inxlo - outxlo; + if (procxlo != me) + MPI_Sendrecv(&nplanes,1,MPI_INT,procxlo,0, + &ghostxhi,1,MPI_INT,procxhi,0,gridcomm,MPI_STATUS_IGNORE); + else ghostxhi = nplanes; + + nplanes = outxhi - inxhi; + if (procxhi != me) + MPI_Sendrecv(&nplanes,1,MPI_INT,procxhi,0, + &ghostxlo,1,MPI_INT,procxlo,0,gridcomm,MPI_STATUS_IGNORE); + else ghostxlo = nplanes; + + nplanes = inylo - outylo; + if (procylo != me) + MPI_Sendrecv(&nplanes,1,MPI_INT,procylo,0, + &ghostyhi,1,MPI_INT,procyhi,0,gridcomm,MPI_STATUS_IGNORE); + else ghostyhi = nplanes; + + nplanes = outyhi - inyhi; + if (procyhi != me) + MPI_Sendrecv(&nplanes,1,MPI_INT,procyhi,0, + &ghostylo,1,MPI_INT,procylo,0,gridcomm,MPI_STATUS_IGNORE); + else ghostylo = nplanes; + + nplanes = inzlo - outzlo; + if (proczlo != me) + MPI_Sendrecv(&nplanes,1,MPI_INT,proczlo,0, + &ghostzhi,1,MPI_INT,proczhi,0,gridcomm,MPI_STATUS_IGNORE); + else ghostzhi = nplanes; + + nplanes = outzhi - inzhi; + if (proczhi != me) + MPI_Sendrecv(&nplanes,1,MPI_INT,proczhi,0, + &ghostzlo,1,MPI_INT,proczlo,0,gridcomm,MPI_STATUS_IGNORE); + else ghostzlo = nplanes; + + // setup swaps = exchange of grid data with one of 6 neighobr procs + // can be more than one in a direction if ghost region extends beyond neigh proc + // all procs have same swap count, but swapsize npack/nunpack can be empty + + nswap = 0; + + // send own grid pts to -x processor, recv ghost grid pts from +x processor + + nsent = 0; + sendfirst = inxlo; + sendlast = inxhi; + recvfirst = inxhi+1; + notdone = 1; + + while (notdone) { + if (nswap == maxswap) grow_swap(); + + swap[nswap].sendproc = procxlo; + swap[nswap].recvproc = procxhi; + sendplanes = MIN(sendlast-sendfirst+1,ghostxlo-nsent); + swap[nswap].npack = + indices(swap[nswap].packlist, + sendfirst,sendfirst+sendplanes-1,inylo,inyhi,inzlo,inzhi); + + if (procxlo != me) + MPI_Sendrecv(&sendplanes,1,MPI_INT,procxlo,0, + &recvplanes,1,MPI_INT,procxhi,0,gridcomm,MPI_STATUS_IGNORE); + else recvplanes = sendplanes; + + swap[nswap].nunpack = + indices(swap[nswap].unpacklist, + recvfirst,recvfirst+recvplanes-1,inylo,inyhi,inzlo,inzhi); + + nsent += sendplanes; + sendfirst += sendplanes; + sendlast += recvplanes; + recvfirst += recvplanes; + nswap++; + + if (nsent < ghostxlo) notdoneme = 1; + else notdoneme = 0; + MPI_Allreduce(¬doneme,¬done,1,MPI_INT,MPI_SUM,gridcomm); + } + + // send own grid pts to +x processor, recv ghost grid pts from -x processor + + nsent = 0; + sendfirst = inxlo; + sendlast = inxhi; + recvlast = inxlo-1; + notdone = 1; + + while (notdone) { + if (nswap == maxswap) grow_swap(); + + swap[nswap].sendproc = procxhi; + swap[nswap].recvproc = procxlo; + sendplanes = MIN(sendlast-sendfirst+1,ghostxhi-nsent); + swap[nswap].npack = + indices(swap[nswap].packlist, + sendlast-sendplanes+1,sendlast,inylo,inyhi,inzlo,inzhi); + + if (procxhi != me) + MPI_Sendrecv(&sendplanes,1,MPI_INT,procxhi,0, + &recvplanes,1,MPI_INT,procxlo,0,gridcomm,MPI_STATUS_IGNORE); + else recvplanes = sendplanes; + + swap[nswap].nunpack = + indices(swap[nswap].unpacklist, + recvlast-recvplanes+1,recvlast,inylo,inyhi,inzlo,inzhi); + + nsent += sendplanes; + sendfirst -= recvplanes; + sendlast -= sendplanes; + recvlast -= recvplanes; + nswap++; + + if (nsent < ghostxhi) notdoneme = 1; + else notdoneme = 0; + MPI_Allreduce(¬doneme,¬done,1,MPI_INT,MPI_SUM,gridcomm); + } + + // send own grid pts to -y processor, recv ghost grid pts from +y processor + + nsent = 0; + sendfirst = inylo; + sendlast = inyhi; + recvfirst = inyhi+1; + notdone = 1; + + while (notdone) { + if (nswap == maxswap) grow_swap(); + + swap[nswap].sendproc = procylo; + swap[nswap].recvproc = procyhi; + sendplanes = MIN(sendlast-sendfirst+1,ghostylo-nsent); + swap[nswap].npack = + indices(swap[nswap].packlist, + outxlo,outxhi,sendfirst,sendfirst+sendplanes-1,inzlo,inzhi); + + if (procylo != me) + MPI_Sendrecv(&sendplanes,1,MPI_INT,procylo,0, + &recvplanes,1,MPI_INT,procyhi,0,gridcomm,MPI_STATUS_IGNORE); + else recvplanes = sendplanes; + + swap[nswap].nunpack = + indices(swap[nswap].unpacklist, + outxlo,outxhi,recvfirst,recvfirst+recvplanes-1,inzlo,inzhi); + + nsent += sendplanes; + sendfirst += sendplanes; + sendlast += recvplanes; + recvfirst += recvplanes; + nswap++; + + if (nsent < ghostylo) notdoneme = 1; + else notdoneme = 0; + MPI_Allreduce(¬doneme,¬done,1,MPI_INT,MPI_SUM,gridcomm); + } + + // send own grid pts to +y processor, recv ghost grid pts from -y processor + + nsent = 0; + sendfirst = inylo; + sendlast = inyhi; + recvlast = inylo-1; + notdone = 1; + + while (notdone) { + if (nswap == maxswap) grow_swap(); + + swap[nswap].sendproc = procyhi; + swap[nswap].recvproc = procylo; + sendplanes = MIN(sendlast-sendfirst+1,ghostyhi-nsent); + swap[nswap].npack = + indices(swap[nswap].packlist, + outxlo,outxhi,sendlast-sendplanes+1,sendlast,inzlo,inzhi); + + if (procyhi != me) + MPI_Sendrecv(&sendplanes,1,MPI_INT,procyhi,0, + &recvplanes,1,MPI_INT,procylo,0,gridcomm,MPI_STATUS_IGNORE); + else recvplanes = sendplanes; + + swap[nswap].nunpack = + indices(swap[nswap].unpacklist, + outxlo,outxhi,recvlast-recvplanes+1,recvlast,inzlo,inzhi); + + nsent += sendplanes; + sendfirst -= recvplanes; + sendlast -= sendplanes; + recvlast -= recvplanes; + nswap++; + + if (nsent < ghostyhi) notdoneme = 1; + else notdoneme = 0; + MPI_Allreduce(¬doneme,¬done,1,MPI_INT,MPI_SUM,gridcomm); + } + + // send own grid pts to -z processor, recv ghost grid pts from +z processor + + nsent = 0; + sendfirst = inzlo; + sendlast = inzhi; + recvfirst = inzhi+1; + notdone = 1; + + while (notdone) { + if (nswap == maxswap) grow_swap(); + + swap[nswap].sendproc = proczlo; + swap[nswap].recvproc = proczhi; + sendplanes = MIN(sendlast-sendfirst+1,ghostzlo-nsent); + swap[nswap].npack = + indices(swap[nswap].packlist, + outxlo,outxhi,outylo,outyhi,sendfirst,sendfirst+sendplanes-1); + + if (proczlo != me) + MPI_Sendrecv(&sendplanes,1,MPI_INT,proczlo,0, + &recvplanes,1,MPI_INT,proczhi,0,gridcomm,MPI_STATUS_IGNORE); + else recvplanes = sendplanes; + + swap[nswap].nunpack = + indices(swap[nswap].unpacklist, + outxlo,outxhi,outylo,outyhi,recvfirst,recvfirst+recvplanes-1); + + nsent += sendplanes; + sendfirst += sendplanes; + sendlast += recvplanes; + recvfirst += recvplanes; + nswap++; + + if (nsent < ghostzlo) notdoneme = 1; + else notdoneme = 0; + MPI_Allreduce(¬doneme,¬done,1,MPI_INT,MPI_SUM,gridcomm); + } + + // send own grid pts to +z processor, recv ghost grid pts from -z processor + + nsent = 0; + sendfirst = inzlo; + sendlast = inzhi; + recvlast = inzlo-1; + notdone = 1; + + while (notdone) { + if (nswap == maxswap) grow_swap(); + + swap[nswap].sendproc = proczhi; + swap[nswap].recvproc = proczlo; + sendplanes = MIN(sendlast-sendfirst+1,ghostzhi-nsent); + swap[nswap].npack = + indices(swap[nswap].packlist, + outxlo,outxhi,outylo,outyhi,sendlast-sendplanes+1,sendlast); + + if (proczhi != me) + MPI_Sendrecv(&sendplanes,1,MPI_INT,proczhi,0, + &recvplanes,1,MPI_INT,proczlo,0,gridcomm,MPI_STATUS_IGNORE); + else recvplanes = sendplanes; + + swap[nswap].nunpack = + indices(swap[nswap].unpacklist, + outxlo,outxhi,outylo,outyhi,recvlast-recvplanes+1,recvlast); + + nsent += sendplanes; + sendfirst -= recvplanes; + sendlast -= sendplanes; + recvlast -= recvplanes; + nswap++; + + if (nsent < ghostzhi) notdoneme = 1; + else notdoneme = 0; + MPI_Allreduce(¬doneme,¬done,1,MPI_INT,MPI_SUM,gridcomm); + } + + // ngrid = max of any forward/reverse pack/unpack grid points + + int ngrid = 0; + for (int i = 0; i < nswap; i++) { + ngrid = MAX(ngrid,swap[i].npack); + ngrid = MAX(ngrid,swap[i].nunpack); + } + + nbuf1 = nbuf2 = ngrid; +} + +/* ---------------------------------------------------------------------- + setup owned/ghost comm for tiled comm + each proc has arbitrary # of neighbors that overlap its ghost extent + identify which procs will send me ghost cells, and vice versa + may not be symmetric if both procs do not need same layers of ghosts + comm pattern = post recvs for all my ghosts, send my owned, wait on recvs + no exchanges by dimension, unlike CommTiled forward/reverse comm of particles +------------------------------------------------------------------------- */ + +void Grid3d::setup_comm_tiled(int &nbuf1, int &nbuf2) +{ + int i,m; + double xlo,xhi,ylo,yhi,zlo,zhi; + int ghostbox[6],pbc[3]; + + // find overlaps of my extended ghost box with all owned boxes + // accounts for ghost box overlapping periodic boundaries + // noverlap = # of overlaps, including self + // overlap = vector of overlap info using Overlap data struct + + ghostbox[0] = outxlo; + ghostbox[1] = outxhi; + ghostbox[2] = outylo; + ghostbox[3] = outyhi; + ghostbox[4] = outzlo; + ghostbox[5] = outzhi; + + pbc[0] = pbc[1] = pbc[2] = 0; + + Overlap *overlap; + int noverlap = compute_overlap(1,ghostbox,pbc,overlap); + + // send each proc an overlap message + // content: me, index of my overlap, box that overlaps with its owned cells + // ncopy = # of overlaps with myself across a periodic boundary + // skip copy to self when non-PBC + + int *proclist; + memory->create(proclist,noverlap,"grid3d:proclist"); + srequest = (Request *) + memory->smalloc(noverlap*sizeof(Request),"grid3d:srequest"); + + int nsend_request = 0; + ncopy = 0; + + for (m = 0; m < noverlap; m++) { + if (overlap[m].proc == me) { + if (overlap[m].pbc[0] == 0 && overlap[m].pbc[1] == 0 && + overlap[m].pbc[2] == 0) continue; + ncopy++; + } else { + proclist[nsend_request] = overlap[m].proc; + srequest[nsend_request].sender = me; + srequest[nsend_request].index = m; + for (i = 0; i < 6; i++) + srequest[nsend_request].box[i] = overlap[m].box[i]; + nsend_request++; + } + } + + auto irregular = new Irregular(lmp); + int nrecv_request = irregular->create_data(nsend_request,proclist,1); + auto rrequest = (Request *) memory->smalloc(nrecv_request*sizeof(Request),"grid3d:rrequest"); + irregular->exchange_data((char *) srequest,sizeof(Request),(char *) rrequest); + irregular->destroy_data(); + + // compute overlaps between received ghost boxes and my owned box + // overlap box used to setup my Send data struct and respond to requests + + send = (Send *) memory->smalloc(nrecv_request*sizeof(Send),"grid3d:send"); + sresponse = (Response *) memory->smalloc(nrecv_request*sizeof(Response),"grid3d:sresponse"); + memory->destroy(proclist); + memory->create(proclist,nrecv_request,"grid3d:proclist"); + + for (m = 0; m < nrecv_request; m++) { + send[m].proc = rrequest[m].sender; + xlo = MAX(rrequest[m].box[0],inxlo); + xhi = MIN(rrequest[m].box[1],inxhi); + ylo = MAX(rrequest[m].box[2],inylo); + yhi = MIN(rrequest[m].box[3],inyhi); + zlo = MAX(rrequest[m].box[4],inzlo); + zhi = MIN(rrequest[m].box[5],inzhi); + send[m].npack = indices(send[m].packlist,xlo,xhi,ylo,yhi,zlo,zhi); + + proclist[m] = rrequest[m].sender; + sresponse[m].index = rrequest[m].index; + sresponse[m].box[0] = xlo; + sresponse[m].box[1] = xhi; + sresponse[m].box[2] = ylo; + sresponse[m].box[3] = yhi; + sresponse[m].box[4] = zlo; + sresponse[m].box[5] = zhi; + } + + nsend = nrecv_request; + + // reply to each Request message with a Response message + // content: index for the overlap on requestor, overlap box on my owned grid + + int nsend_response = nrecv_request; + int nrecv_response = irregular->create_data(nsend_response,proclist,1); + auto rresponse = (Response *) memory->smalloc(nrecv_response*sizeof(Response),"grid3d:rresponse"); + irregular->exchange_data((char *) sresponse,sizeof(Response),(char *) rresponse); + irregular->destroy_data(); + delete irregular; + + // process received responses + // box used to setup my Recv data struct after unwrapping via PBC + // adjacent = 0 if any box of ghost cells does not adjoin my owned cells + + recv = (Recv *) memory->smalloc(nrecv_response*sizeof(Recv),"grid3d:recv"); + adjacent = 1; + + for (i = 0; i < nrecv_response; i++) { + m = rresponse[i].index; + recv[i].proc = overlap[m].proc; + xlo = rresponse[i].box[0] + overlap[m].pbc[0] * nx; + xhi = rresponse[i].box[1] + overlap[m].pbc[0] * nx; + ylo = rresponse[i].box[2] + overlap[m].pbc[1] * ny; + yhi = rresponse[i].box[3] + overlap[m].pbc[1] * ny; + zlo = rresponse[i].box[4] + overlap[m].pbc[2] * nz; + zhi = rresponse[i].box[5] + overlap[m].pbc[2] * nz; + recv[i].nunpack = indices(recv[i].unpacklist,xlo,xhi,ylo,yhi,zlo,zhi); + + if (xlo != inxhi+1 && xhi != inxlo-1 && + ylo != inyhi+1 && yhi != inylo-1 && + zlo != inzhi+1 && zhi != inzlo-1) adjacent = 0; + } + + nrecv = nrecv_response; + + // create Copy data struct from overlaps with self + // skip copy to self when non-PBC + + copy = (Copy *) memory->smalloc(ncopy*sizeof(Copy),"grid3d:copy"); + + ncopy = 0; + for (m = 0; m < noverlap; m++) { + if (overlap[m].proc != me) continue; + if (overlap[m].pbc[0] == 0 && overlap[m].pbc[1] == 0 && + overlap[m].pbc[2] == 0) continue; + xlo = overlap[m].box[0]; + xhi = overlap[m].box[1]; + ylo = overlap[m].box[2]; + yhi = overlap[m].box[3]; + zlo = overlap[m].box[4]; + zhi = overlap[m].box[5]; + copy[ncopy].npack = indices(copy[ncopy].packlist,xlo,xhi,ylo,yhi,zlo,zhi); + xlo = overlap[m].box[0] + overlap[m].pbc[0] * nx; + xhi = overlap[m].box[1] + overlap[m].pbc[0] * nx; + ylo = overlap[m].box[2] + overlap[m].pbc[1] * ny; + yhi = overlap[m].box[3] + overlap[m].pbc[1] * ny; + zlo = overlap[m].box[4] + overlap[m].pbc[2] * nz; + zhi = overlap[m].box[5] + overlap[m].pbc[2] * nz; + copy[ncopy].nunpack = indices(copy[ncopy].unpacklist,xlo,xhi,ylo,yhi,zlo,zhi); + ncopy++; + } + + // set offsets for received data + + int offset = 0; + for (m = 0; m < nsend; m++) { + send[m].offset = offset; + offset += send[m].npack; + } + + offset = 0; + for (m = 0; m < nrecv; m++) { + recv[m].offset = offset; + offset += recv[m].nunpack; + } + + // length of MPI requests vector is max of nsend, nrecv + + int nrequest = MAX(nsend,nrecv); + requests = new MPI_Request[nrequest]; + + // clean-up + + clean_overlap(); + memory->destroy(proclist); + memory->sfree(srequest); + memory->sfree(rrequest); + memory->sfree(sresponse); + memory->sfree(rresponse); + + // nbuf1 = largest pack or unpack in any Send or Recv or Copy + // nbuf2 = larget of sum of all packs or unpacks in Send or Recv + + nbuf1 = 0; + + for (m = 0; m < ncopy; m++) { + nbuf1 = MAX(nbuf1,copy[m].npack); + nbuf1 = MAX(nbuf1,copy[m].nunpack); + } + + int nbufs = 0; + for (m = 0; m < nsend; m++) { + nbuf1 = MAX(nbuf1,send[m].npack); + nbufs += send[m].npack; + } + + int nbufr = 0; + for (m = 0; m < nrecv; m++) { + nbuf1 = MAX(nbuf1,recv[m].nunpack); + nbufr += recv[m].nunpack; + } + + nbuf2 = MAX(nbufs,nbufr); +} + +// ---------------------------------------------------------------------- +// query locality of forward/reverse grid comm +// ---------------------------------------------------------------------- + +/* ---------------------------------------------------------------------- + check if all procs only need ghost info from adjacent procs + return 1 if yes, 0 if no +------------------------------------------------------------------------- */ + +int Grid3d::ghost_adjacent() +{ + if (layout != Comm::LAYOUT_TILED) return ghost_adjacent_brick(); + return ghost_adjacent_tiled(); +} + +/* ---------------------------------------------------------------------- + adjacent = 0 if a proc's ghost xyz lohi values exceed its subdomain size + return 0 if adjacent=0 for any proc, else 1 +------------------------------------------------------------------------- */ + +int Grid3d::ghost_adjacent_brick() +{ + adjacent = 1; + if (ghostxlo > inxhi-inxlo+1) adjacent = 0; + if (ghostxhi > inxhi-inxlo+1) adjacent = 0; + if (ghostylo > inyhi-inylo+1) adjacent = 0; + if (ghostyhi > inyhi-inylo+1) adjacent = 0; + if (ghostzlo > inzhi-inzlo+1) adjacent = 0; + if (ghostzhi > inzhi-inzlo+1) adjacent = 0; + + int adjacent_all; + MPI_Allreduce(&adjacent,&adjacent_all,1,MPI_INT,MPI_MIN,gridcomm); + return adjacent_all; +} + +/* ---------------------------------------------------------------------- + adjacent = 0 if a proc's received ghosts were flagged + as non-adjacent in setup_tiled() + return 0 if adjacent=0 for any proc, else 1 +------------------------------------------------------------------------- */ + +int Grid3d::ghost_adjacent_tiled() +{ + int adjacent_all; + MPI_Allreduce(&adjacent,&adjacent_all,1,MPI_INT,MPI_MIN,gridcomm); + return adjacent_all; +} + +// ---------------------------------------------------------------------- +// forward/reverse comm of owned/ghost grid data via callbacks +// ---------------------------------------------------------------------- + +/* ---------------------------------------------------------------------- + forward comm of my owned cells to other's ghost cells +------------------------------------------------------------------------- */ + +void Grid3d::forward_comm(int caller, void *ptr, int which, int nper, int nbyte, + void *buf1, void *buf2, MPI_Datatype datatype) +{ + if (layout != Comm::LAYOUT_TILED) { + if (caller == KSPACE) + forward_comm_brick((KSpace *) ptr,which,nper,nbyte, + buf1,buf2,datatype); + else if (caller == PAIR) + forward_comm_brick((Pair *) ptr,which,nper,nbyte, + buf1,buf2,datatype); + else if (caller == FIX) + forward_comm_brick((Fix *) ptr,which,nper,nbyte, + buf1,buf2,datatype); + } else { + if (caller == KSPACE) + forward_comm_tiled((KSpace *) ptr,which,nper,nbyte, + buf1,buf2,datatype); + else if (caller == PAIR) + forward_comm_tiled((Pair *) ptr,which,nper,nbyte, + buf1,buf2,datatype); + else if (caller == FIX) + forward_comm_tiled((Fix *) ptr,which,nper,nbyte, + buf1,buf2,datatype); + } +} + +/* ---------------------------------------------------------------------- + forward comm for brick decomp via list of swaps with 6 neighbor procs +------------------------------------------------------------------------- */ + +template < class T > +void Grid3d:: +forward_comm_brick(T *ptr, int which, int nper, int /*nbyte*/, + void *buf1, void *buf2, MPI_Datatype datatype) +{ + int m; + MPI_Request request; + + for (m = 0; m < nswap; m++) { + if (swap[m].sendproc == me) + ptr->pack_forward_grid(which,buf2,swap[m].npack,swap[m].packlist); + else + ptr->pack_forward_grid(which,buf1,swap[m].npack,swap[m].packlist); + + if (swap[m].sendproc != me) { + if (swap[m].nunpack) MPI_Irecv(buf2,nper*swap[m].nunpack,datatype, + swap[m].recvproc,0,gridcomm,&request); + if (swap[m].npack) MPI_Send(buf1,nper*swap[m].npack,datatype, + swap[m].sendproc,0,gridcomm); + if (swap[m].nunpack) MPI_Wait(&request,MPI_STATUS_IGNORE); + } + + ptr->unpack_forward_grid(which,buf2,swap[m].nunpack,swap[m].unpacklist); + } +} + +/* ---------------------------------------------------------------------- + forward comm for tiled decomp via Send/Recv lists of each neighbor proc +------------------------------------------------------------------------- */ + +template < class T > +void Grid3d:: +forward_comm_tiled(T *ptr, int which, int nper, int nbyte, + void *buf1, void *vbuf2, MPI_Datatype datatype) +{ + int i,m,offset; + + auto buf2 = (char *) vbuf2; + + // post all receives + + for (m = 0; m < nrecv; m++) { + offset = nper * recv[m].offset * nbyte; + MPI_Irecv((void *) &buf2[offset],nper*recv[m].nunpack,datatype, + recv[m].proc,0,gridcomm,&requests[m]); + } + + // perform all sends to other procs + + for (m = 0; m < nsend; m++) { + ptr->pack_forward_grid(which,buf1,send[m].npack,send[m].packlist); + MPI_Send(buf1,nper*send[m].npack,datatype,send[m].proc,0,gridcomm); + } + + // perform all copies to self + + for (m = 0; m < ncopy; m++) { + ptr->pack_forward_grid(which,buf1,copy[m].npack,copy[m].packlist); + ptr->unpack_forward_grid(which,buf1,copy[m].nunpack,copy[m].unpacklist); + } + + // unpack all received data + + for (i = 0; i < nrecv; i++) { + MPI_Waitany(nrecv,requests,&m,MPI_STATUS_IGNORE); + offset = nper * recv[m].offset * nbyte; + ptr->unpack_forward_grid(which,(void *) &buf2[offset], + recv[m].nunpack,recv[m].unpacklist); + } +} + +/* ---------------------------------------------------------------------- + reverse comm of my ghost cells to sum to owner cells +------------------------------------------------------------------------- */ + +void Grid3d::reverse_comm(int caller, void *ptr, int which, int nper, int nbyte, + void *buf1, void *buf2, MPI_Datatype datatype) +{ + if (layout != Comm::LAYOUT_TILED) { + if (caller == KSPACE) + reverse_comm_brick((KSpace *) ptr,which,nper,nbyte, + buf1,buf2,datatype); + else if (caller == PAIR) + reverse_comm_brick((Pair *) ptr,which,nper,nbyte, + buf1,buf2,datatype); + else if (caller == FIX) + reverse_comm_brick((Fix *) ptr,which,nper,nbyte, + buf1,buf2,datatype); + } else { + if (caller == KSPACE) + reverse_comm_tiled((KSpace *) ptr,which,nper,nbyte, + buf1,buf2,datatype); + else if (caller == PAIR) + reverse_comm_tiled((Pair *) ptr,which,nper,nbyte, + buf1,buf2,datatype); + else if (caller == FIX) + reverse_comm_tiled((Fix *) ptr,which,nper,nbyte, + buf1,buf2,datatype); + } +} + +/* ---------------------------------------------------------------------- + reverse comm for brick decomp via list of swaps with 6 neighbor procs +------------------------------------------------------------------------- */ + +template < class T > +void Grid3d:: +reverse_comm_brick(T *ptr, int which, int nper, int /*nbyte*/, + void *buf1, void *buf2, MPI_Datatype datatype) +{ + int m; + MPI_Request request; + + for (m = nswap-1; m >= 0; m--) { + if (swap[m].recvproc == me) + ptr->pack_reverse_grid(which,buf2,swap[m].nunpack,swap[m].unpacklist); + else + ptr->pack_reverse_grid(which,buf1,swap[m].nunpack,swap[m].unpacklist); + + if (swap[m].recvproc != me) { + if (swap[m].npack) MPI_Irecv(buf2,nper*swap[m].npack,datatype, + swap[m].sendproc,0,gridcomm,&request); + if (swap[m].nunpack) MPI_Send(buf1,nper*swap[m].nunpack,datatype, + swap[m].recvproc,0,gridcomm); + if (swap[m].npack) MPI_Wait(&request,MPI_STATUS_IGNORE); + } + + ptr->unpack_reverse_grid(which,buf2,swap[m].npack,swap[m].packlist); + } +} + +/* ---------------------------------------------------------------------- + reverse comm for tiled decomp via Send/Recv lists of each neighbor proc +------------------------------------------------------------------------- */ + +template < class T > +void Grid3d:: +reverse_comm_tiled(T *ptr, int which, int nper, int nbyte, + void *buf1, void *vbuf2, MPI_Datatype datatype) +{ + int i,m,offset; + + auto buf2 = (char *) vbuf2; + + // post all receives + + for (m = 0; m < nsend; m++) { + offset = nper * send[m].offset * nbyte; + MPI_Irecv((void *) &buf2[offset],nper*send[m].npack,datatype, + send[m].proc,0,gridcomm,&requests[m]); + } + + // perform all sends to other procs + + for (m = 0; m < nrecv; m++) { + ptr->pack_reverse_grid(which,buf1,recv[m].nunpack,recv[m].unpacklist); + MPI_Send(buf1,nper*recv[m].nunpack,datatype,recv[m].proc,0,gridcomm); + } + + // perform all copies to self + + for (m = 0; m < ncopy; m++) { + ptr->pack_reverse_grid(which,buf1,copy[m].nunpack,copy[m].unpacklist); + ptr->unpack_reverse_grid(which,buf1,copy[m].npack,copy[m].packlist); + } + + // unpack all received data + + for (i = 0; i < nsend; i++) { + MPI_Waitany(nsend,requests,&m,MPI_STATUS_IGNORE); + offset = nper * send[m].offset * nbyte; + ptr->unpack_reverse_grid(which,(void *) &buf2[offset], + send[m].npack,send[m].packlist); + } +} + +// ---------------------------------------------------------------------- +// remap comm between 2 old/new grid decomposition of owned grid data +// ---------------------------------------------------------------------- + +/* ---------------------------------------------------------------------- + setup remap from old grid decomposition to this grid decomposition + return sizes of two buffers needed for communication + either for brick decomp or tiling decomp + nbuf1 = largest pack or unpack in any Send or Recv or Copy + nbuf2 = larget of sum of all packs or unpacks in Send or Recv + for brick comm, nbuf1 = nbuf2 + for tiled comm, nbuf2 >= nbuf2 + nbuf1,nbuf2 are just count of grid points + caller converts them to message size for grid data it stores +------------------------------------------------------------------------- */ + +void Grid3d::setup_remap(Grid3d *old, int &nremap_buf1, int &nremap_buf2) +{ + int m; + int pbc[3]; + int *box; + + // deallocated existing remap data structs + + deallocate_remap(); + + // set layout to current Comm layout + + layout = comm->layout; + + // overlaps of my old decomp owned box with all owned boxes in new decomp + // noverlap_old = # of overlaps, including self + // overlap_old = vector of overlap info in Overlap data struct + + int oldbox[6]; + old->get_bounds_owned(oldbox[0],oldbox[1],oldbox[2],oldbox[3], + oldbox[4],oldbox[5]); + pbc[0] = pbc[1] = pbc[2] = 0; + + Overlap *overlap_old; + int noverlap_old = compute_overlap(0,oldbox,pbc,overlap_old); + + // use overlap_old to construct send and copy lists + // skip overlaps that contain no grid cells + + self_remap = 0; + + nsend_remap = 0; + for (m = 0; m < noverlap_old; m++) { + box = overlap_old[m].box; + if (box[0] > box[1] || box[2] > box[3] || box[4] > box[5]) continue; + if (overlap_old[m].proc == me) self_remap = 1; + else nsend_remap++; + } + + send_remap = new Send[nsend_remap]; + + nsend_remap = 0; + for (m = 0; m < noverlap_old; m++) { + box = overlap_old[m].box; + if (box[0] > box[1] || box[2] > box[3] || box[4] > box[5]) continue; + if (overlap_old[m].proc == me) { + copy_remap.npack = + old->indices(copy_remap.packlist, + box[0],box[1],box[2],box[3],box[4],box[5]); + } else { + send_remap[nsend_remap].proc = overlap_old[m].proc; + send_remap[nsend_remap].npack = + old->indices(send_remap[nsend_remap].packlist, + box[0],box[1],box[2],box[3],box[4],box[5]); + nsend_remap++; + } + } + + // overlaps of my new decomp owned box with all owned boxes in old decomp + // noverlap_new = # of overlaps, including self + // overlap_new = vector of overlap info in Overlap data struct + + int newbox[6]; + get_bounds_owned(newbox[0],newbox[1],newbox[2],newbox[3],newbox[4],newbox[5]); + pbc[0] = pbc[1] = pbc[2] = 0; + + Overlap *overlap_new; + int noverlap_new = old->compute_overlap(0,newbox,pbc,overlap_new); + + // use overlap_new to construct recv and copy lists + // skip overlaps that contain no grid cells + // set offsets for Recv data + + nrecv_remap = 0; + for (m = 0; m < noverlap_new; m++) { + box = overlap_new[m].box; + if (box[0] > box[1] || box[2] > box[3] || box[4] > box[5]) continue; + if (overlap_new[m].proc != me) nrecv_remap++; + } + + recv_remap = new Recv[nrecv_remap]; + + nrecv_remap = 0; + for (m = 0; m < noverlap_new; m++) { + box = overlap_new[m].box; + if (box[0] > box[1] || box[2] > box[3] || box[4] > box[5]) continue; + if (overlap_new[m].proc == me) { + copy_remap.nunpack = + indices(copy_remap.unpacklist, + box[0],box[1],box[2],box[3],box[4],box[5]); + } else { + recv_remap[nrecv_remap].proc = overlap_new[m].proc; + recv_remap[nrecv_remap].nunpack = + indices(recv_remap[nrecv_remap].unpacklist, + box[0],box[1],box[2],box[3],box[4],box[5]); + nrecv_remap++; + } + } + + // set offsets for received data + + int offset = 0; + for (m = 0; m < nrecv_remap; m++) { + recv_remap[m].offset = offset; + offset += recv_remap[m].nunpack; + } + + // length of MPI requests vector = nrecv_remap + + delete [] requests_remap; + requests_remap = new MPI_Request[nrecv_remap]; + + // clean-up + + clean_overlap(); + old->clean_overlap(); + + // nremap_buf1 = largest pack or unpack in any Send or Recv or Copy + // nremap_buf2 = sum of all unpacks in Recv + + nremap_buf1 = 0; + + if (self_remap) { + nremap_buf1 = MAX(nremap_buf1,copy_remap.npack); + nremap_buf1 = MAX(nremap_buf1,copy_remap.nunpack); + } + + for (m = 0; m < nsend_remap; m++) + nremap_buf1 = MAX(nremap_buf1,send_remap[m].npack); + + nremap_buf2 = 0; + for (m = 0; m < nrecv_remap; m++) { + nremap_buf1 = MAX(nremap_buf1,recv_remap[m].nunpack); + nremap_buf2 += recv_remap[m].nunpack; + } +} + +/* ---------------------------------------------------------------------- + perform remap from old grid decomposition to this grid decomposition + pack/unpack operations are performed by caller via callbacks +------------------------------------------------------------------------- */ + +void Grid3d::remap(int caller, void *ptr, int which, int nper, int nbyte, + void *buf1, void *buf2, MPI_Datatype datatype) +{ + if (caller == FIX) remap_style((Fix *) ptr,which,nper,nbyte,buf1,buf2,datatype); +} + +/* ------------------------------------------------------------------------- */ + +template < class T > +void Grid3d::remap_style(T *ptr, int which, int nper, int nbyte, + void *buf1, void *vbuf2, MPI_Datatype datatype) +{ + int i,m,offset; + + auto buf2 = (char *) vbuf2; + + // post all receives + + for (m = 0; m < nrecv_remap; m++) { + offset = nper * recv_remap[m].offset * nbyte; + MPI_Irecv((void *) &buf2[offset],nper*recv_remap[m].nunpack,datatype, + recv_remap[m].proc,0,gridcomm,&requests_remap[m]); + } + + // perform all sends to other procs + + for (m = 0; m < nsend_remap; m++) { + ptr->pack_remap_grid(which,buf1,send_remap[m].npack,send_remap[m].packlist); + MPI_Send(buf1,nper*send_remap[m].npack,datatype,send_remap[m].proc,0,gridcomm); + } + + // perform remap to self if defined + + if (self_remap) { + ptr->pack_remap_grid(which,buf1,copy_remap.npack,copy_remap.packlist); + ptr->unpack_remap_grid(which,buf1,copy_remap.nunpack,copy_remap.unpacklist); + } + + // unpack all received data + + for (i = 0; i < nrecv_remap; i++) { + MPI_Waitany(nrecv_remap,requests_remap,&m,MPI_STATUS_IGNORE); + offset = nper * recv_remap[m].offset * nbyte; + ptr->unpack_remap_grid(which,(void *) &buf2[offset], + recv_remap[m].nunpack,recv_remap[m].unpacklist); + } +} + +// ---------------------------------------------------------------------- +// grid I/O methods +// ---------------------------------------------------------------------- + +/* ---------------------------------------------------------------------- + read grid values from a file +------------------------------------------------------------------------- */ + +void Grid3d::read_file(int caller, void *ptr, FILE *fp, int nchunk, int maxline) +{ + if (caller == FIX) + read_file_style((Fix *) ptr,fp,nchunk,maxline); +} + +/* ---------------------------------------------------------------------- + proc 0 reads one chunk of lines at a time from file + broadcast chunk buffer to other procs + call back to caller so it can process the chunk of lines + caller returns count of grid-value lines in chunk +------------------------------------------------------------------------- */ + +template < class T > +void Grid3d::read_file_style(T *ptr, FILE *fp, int nchunk, int maxline) +{ + auto buffer = new char[nchunk * maxline]; + bigint ntotal = (bigint) nx * ny * nz; + bigint nread = 0; + + while (nread < ntotal) { + int mychunk = MIN(ntotal - nread, nchunk); + int eof = utils::read_lines_from_file(fp, mychunk, maxline, buffer, me, world); + if (eof) error->all(FLERR, "Unexpected end of grid data file"); + + nread += ptr->unpack_read_grid(nchunk,buffer); + } + + delete [] buffer; +} + +/* ---------------------------------------------------------------------- + write grid values to a file +------------------------------------------------------------------------- */ + +void Grid3d::write_file(int caller, void *ptr, int which, + int nper, int nbyte, MPI_Datatype datatype) +{ + if (caller == FIX) + write_file_style((Fix *) ptr, which, nper, nbyte, datatype); +} + +/* ---------------------------------------------------------------------- + proc 0 reads one chunk of lines at a time from file + broadcast chunk buffer to other procs + call back to caller so it can process the chunk of lines + caller returns count of grid-value lines in chunk +------------------------------------------------------------------------- */ + +template < class T > +void Grid3d::write_file_style(T *ptr, int which, + int nper, int nbyte, MPI_Datatype datatype) +{ + // maxsize = max size of grid data owned by any proc + + int mysize = (inxhi-inxlo+1) * (inyhi-inylo+1) * (inzhi-inzlo+1); + mysize *= nper; + int maxsize; + MPI_Allreduce(&mysize,&maxsize,1,MPI_INT,MPI_MAX,world); + + // pack my grid data via callback to caller + + char *onebuf; + if (me == 0) memory->create(onebuf,maxsize*nbyte,"grid3d:onebuf"); + else memory->create(onebuf,mysize*nbyte,"grid3d:nebuf"); + ptr->pack_write_grid(which,onebuf); + + // ping each proc for its grid data + // call back to caller with each proc's grid data + + int tmp; + int bounds[6]; + + if (me == 0) { + MPI_Status status; + MPI_Request request; + + for (int iproc = 0; iproc < nprocs; iproc++) { + if (iproc) { + MPI_Irecv(onebuf,maxsize,datatype,iproc,0,world,&request); + MPI_Send(&tmp,0,MPI_INT,iproc,0,world); + MPI_Wait(&request,&status); + MPI_Recv(bounds,6,MPI_INT,iproc,0,world,&status); + } else { + bounds[0] = inxlo; + bounds[1] = inxhi; + bounds[2] = inylo; + bounds[3] = inyhi; + bounds[4] = inzlo; + bounds[5] = inzhi; + } + + ptr->unpack_write_grid(which,onebuf,bounds); + } + + } else { + MPI_Recv(&tmp,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE); + MPI_Rsend(onebuf,mysize,datatype,0,0,world); + bounds[0] = inxlo; + bounds[1] = inxhi; + bounds[2] = inylo; + bounds[3] = inyhi; + bounds[4] = inzlo; + bounds[5] = inzhi; + MPI_Send(bounds,6,MPI_INT,0,0,world); + } + + // clean up + + memory->destroy(onebuf); +} + +// ---------------------------------------------------------------------- +// overlap methods for brick and tiled RCB decompositions +// overlap = overlap of owned or owned+ghost box with all boxes of a decomposition +// for owned/ghost grid comm, called only by tiled decomposition +// brick decomp uses one or more comm passes with neigh procs +// like forward/reverse comm for atoms +// for remap, called by both brick and tiled decompositions +// ---------------------------------------------------------------------- + +/* ---------------------------------------------------------------------- + compute list of overlaps between box and the owned grid boxes of all procs + ghostflag = 1 if box includes ghost grid pts, called by setup_tiled() + ghostflag = 0 if box has no ghost grid pts, called by setup_remap() + layout != LAYOUT_TILED is only invoked by setup_remap() + for brick decomp of Grid, done using xyz split + grid2proc copied from Comm + for tiled decomp of Grid, done via recursive box drop on RCB tree + box = 6 integers = (xlo,xhi,ylo,yhi,zlo,zhi) + box can be owned cells or owned + ghost cells + pbc = flags for grid periodicity in each dim + if box includes ghost cells, it can overlap PBCs (only for setup_tiled) + each lo/hi value may extend beyond 0 to N-1 into another periodic image + return # of overlaps including with self, caller handles self overlaps as needed + return list of overlaps + for setup_tiled() this is what box_drop() computes + entire box for each overlap + caller will determine extent of overlap using PBC info + for setup_remap(), return extent of overlap (no PBC info involved) + use proc_box_uniform() or tiled() and MAX/MIN to determine this +------------------------------------------------------------------------- */ + +int Grid3d::compute_overlap(int ghostflag, int *box, int *pbc, Overlap *&overlap) +{ + int obox[6]; + + memory->create(overlap_procs,nprocs,"grid3d:overlap_procs"); + noverlap_list = maxoverlap_list = 0; + overlap_list = nullptr; + + // skip overlap check if box contains no grid cells + + if (box[0] > box[1] || box[2] > box[3] || box[4] > box[5]) { + overlap = overlap_list; + return noverlap_list; + } + + if (layout != Comm::LAYOUT_TILED) { + + // find comm->procgrid indices in each dim for box bounds + + int iproclo = proc_index_uniform(box[0],nx,shift_grid,0,xsplit); + int iprochi = proc_index_uniform(box[1],nx,shift_grid,0,xsplit); + int jproclo = proc_index_uniform(box[2],ny,shift_grid,1,ysplit); + int jprochi = proc_index_uniform(box[3],ny,shift_grid,1,ysplit); + int kproclo = proc_index_uniform(box[4],nz,shift_grid,2,zsplit); + int kprochi = proc_index_uniform(box[5],nz,shift_grid,2,zsplit); + + // compute extent of overlap of box with with each proc's obox + + for (int k = kproclo; k <= kprochi; k++) + for (int j = jproclo; j <= jprochi; j++) + for (int i = iproclo; i <= iprochi; i++) { + partition_grid(nx,xsplit[i],xsplit[i+1],shift_grid,0,obox[0],obox[1]); + partition_grid(ny,ysplit[j],ysplit[j+1],shift_grid,0,obox[2],obox[3]); + partition_grid(nz,zsplit[k],zsplit[k+1],shift_grid,zextra,obox[4],obox[5]); + + if (noverlap_list == maxoverlap_list) grow_overlap(); + overlap_list[noverlap_list].proc = grid2proc[i][j][k]; + overlap_list[noverlap_list].box[0] = MAX(box[0],obox[0]); + overlap_list[noverlap_list].box[1] = MIN(box[1],obox[1]); + overlap_list[noverlap_list].box[2] = MAX(box[2],obox[2]); + overlap_list[noverlap_list].box[3] = MIN(box[3],obox[3]); + overlap_list[noverlap_list].box[4] = MAX(box[4],obox[4]); + overlap_list[noverlap_list].box[5] = MIN(box[5],obox[5]); + noverlap_list++; + } + + } else { + box_drop(box,pbc); + + // compute extent of overlap of box with with each proc's obox + + if (ghostflag == 0) { + for (int m = 0; m < noverlap_list; m++) { + obox[0] = 0; + obox[1] = nx-1; + obox[2] = 0; + obox[3] = ny-1; + obox[4] = 0; + obox[5] = nz-1; + + partition_tiled(overlap_list[m].proc,0,nprocs-1,obox); + + overlap_list[m].box[0] = MAX(box[0],obox[0]); + overlap_list[m].box[1] = MIN(box[1],obox[1]); + overlap_list[m].box[2] = MAX(box[2],obox[2]); + overlap_list[m].box[3] = MIN(box[3],obox[3]); + overlap_list[m].box[4] = MAX(box[4],obox[4]); + overlap_list[m].box[5] = MIN(box[5],obox[5]); + } + } + } + + overlap = overlap_list; + return noverlap_list; +} + +/* ---------------------------------------------------------------------- + deallocate data created by recursive overlap computation +------------------------------------------------------------------------- */ + +void Grid3d::clean_overlap() +{ + memory->destroy(overlap_procs); + memory->sfree(overlap_list); +} + +/* ---------------------------------------------------------------------- + recursively split a box until it doesn't overlap any periodic boundaries + box = 6 integers = (xlo,xhi,ylo,yhi,zlo,zhi) + each lo/hi value may extend beyonw 0 to N-1 into another periodic image + pbc = flags in each dim of which periodic image the caller box was in + when a box straddles a periodic bounadry, split it in two + when a box does not straddle, drop it down RCB tree + add all the procs it overlaps with to Overlap list +------------------------------------------------------------------------- */ + +void Grid3d::box_drop(int *box, int *pbc) +{ + int i,m; + + // newbox12 and newpbc are initially copies of caller box and pbc + + int newbox1[6],newbox2[6],newpbc[3]; + + for (i = 0; i < 6; i++) newbox1[i] = newbox2[i] = box[i]; + for (i = 0; i < 3; i++) newpbc[i] = pbc[i]; + + // 6 if tests to see if box needs to be split across a periodic boundary + // newbox1 and 2 = new split boxes, newpbc increments current pbc + // final else is no split + + int splitflag = 1; + + if (box[0] < 0) { + newbox1[0] = 0; + newbox2[0] = box[0] + nx; + newbox2[1] = nx - 1; + newpbc[0]--; + } else if (box[1] >= nx) { + newbox1[1] = nx - 1; + newbox2[0] = 0; + newbox2[1] = box[1] - nx; + newpbc[0]++; + } else if (box[2] < 0) { + newbox1[2] = 0; + newbox2[2] = box[2] + ny; + newbox2[3] = ny - 1; + newpbc[1]--; + } else if (box[3] >= ny) { + newbox1[3] = ny - 1; + newbox2[2] = 0; + newbox2[3] = box[3] - ny; + newpbc[1]++; + } else if (box[4] < 0) { + newbox1[4] = 0; + newbox2[4] = box[4] + nz; + newbox2[5] = nz - 1; + newpbc[2]--; + } else if (box[5] >= nz) { + newbox1[5] = nz - 1; + newbox2[4] = 0; + newbox2[5] = box[5] - nz; + newpbc[2]++; + + // box is not split, drop on RCB tree + // returns np = # of procs it overlaps, including self + // returns proc_overlap = list of proc IDs it overlaps + // add each overlap to overlap list + + } else { + splitflag = 0; + int np = 0; + box_drop_grid(box,0,nprocs-1,np,overlap_procs); + for (m = 0; m < np; m++) { + if (noverlap_list == maxoverlap_list) grow_overlap(); + overlap_list[noverlap_list].proc = overlap_procs[m]; + for (i = 0; i < 6; i++) overlap_list[noverlap_list].box[i] = box[i]; + for (i = 0; i < 3; i++) overlap_list[noverlap_list].pbc[i] = pbc[i]; + noverlap_list++; + } + } + + // recurse with 2 split boxes + + if (splitflag) { + box_drop(newbox1,pbc); + box_drop(newbox2,newpbc); + } +} + +/* ---------------------------------------------------------------------- + recursively drop a box down the RCB tree to find all procs it overlaps with + box = 6 integers = (xlo,xhi,ylo,yhi,zlo,zhi) + each lo/hi value ranges from 0 to N-1 in a dim, N = grid size in that dim + box is guaranteed to be wholly within the global domain + return Np = # of procs, plist = proc IDs +------------------------------------------------------------------------- */ + +void Grid3d::box_drop_grid(int *box, int proclower, int procupper, + int &np, int *plist) +{ + // end recursion when partition is a single proc + // add proclower to plist + + if (proclower == procupper) { + plist[np++] = proclower; + return; + } + + // drop box on each side of cut it extends beyond + // use < and >= criteria so does not include a box it only touches + // procmid = 1st processor in upper half of partition + // = location in tree that stores this cut + // cut = index of first grid cell in upper partition + // dim = 0,1,2 dimension of cut + + int procmid = proclower + (procupper - proclower) / 2 + 1; + int dim = rcbinfo[procmid].dim; + int cut = rcbinfo[procmid].cut; + + if (box[2*dim] < cut) box_drop_grid(box,proclower,procmid-1,np,plist); + if (box[2*dim+1] >= cut) box_drop_grid(box,procmid,procupper,np,plist); +} + +// ---------------------------------------------------------------------- +// miscellaneous methods +// ---------------------------------------------------------------------- + +/* ---------------------------------------------------------------------- + grow list of swaps by DELTA +------------------------------------------------------------------------- */ + +void Grid3d::grow_swap() +{ + maxswap += DELTA; + swap = (Swap *) memory->srealloc(swap,maxswap*sizeof(Swap),"grid3d:swap"); +} + +/* ---------------------------------------------------------------------- + grow list of overlaps by DELTA +------------------------------------------------------------------------- */ + +void Grid3d::grow_overlap() +{ + maxoverlap_list += DELTA; + overlap_list = (Overlap *) + memory->srealloc(overlap_list,maxoverlap_list*sizeof(Overlap),"grid3d:overlap_list"); +} + +/* ---------------------------------------------------------------------- + deallocate remap data structs +------------------------------------------------------------------------- */ + +void Grid3d::deallocate_remap() +{ + for (int i = 0; i < nsend_remap; i++) + memory->destroy(send_remap[i].packlist); + delete [] send_remap; + + for (int i = 0; i < nrecv_remap; i++) + memory->destroy(recv_remap[i].unpacklist); + delete [] recv_remap; + + if (self_remap) { + memory->destroy(copy_remap.packlist); + memory->destroy(copy_remap.unpacklist); + } +} + +/* ---------------------------------------------------------------------- + create 1d list of offsets into 3d array section (xlo:xhi,ylo:yhi,zlo:zhi) + assume caller's 3d array is allocated as + (fullxlo:fullxhi,fullylo:fullyhi,fullzlo:fullzhi) +------------------------------------------------------------------------- */ + +int Grid3d::indices(int *&list, + int xlo, int xhi, int ylo, int yhi, int zlo, int zhi) +{ + int nmax = (xhi-xlo+1) * (yhi-ylo+1) * (zhi-zlo+1); + memory->create(list,nmax,"grid3d:indices"); + if (nmax == 0) return 0; + + int nx = (fullxhi-fullxlo+1); + int ny = (fullyhi-fullylo+1); + + int n = 0; + int ix,iy,iz; + for (iz = zlo; iz <= zhi; iz++) + for (iy = ylo; iy <= yhi; iy++) + for (ix = xlo; ix <= xhi; ix++) + list[n++] = (iz-fullzlo)*ny*nx + (iy-fullylo)*nx + (ix-fullxlo); + + return nmax; +} + +/* ---------------------------------------------------------------------- + find the comm->procgrid index = which proc owns the igrid index + igrid = grid index (0 to N-1) in dim + n = # of grid points in dim + shift determines position of grid pt within grid cell + shift = 0.5 for cell center, 0.0 for lower-left corner + dim = which dimension (0,1,2) + split = comm->x/y/z split for fractional bounds of each proc domain +------------------------------------------------------------------------- */ + +int Grid3d::proc_index_uniform(int igrid, int n, double shift, int dim, double *split) +{ + int lo,hi; + double fraclo,frachi; + + // loop over # of procs in this dime + // compute the grid bounds for that proc + // if igrid falls within those bounds, return m = proc index + // same logic as in partition_grid() + + int m; + for (m = 0; m < comm->procgrid[dim]; m++) { + fraclo = split[m]; + frachi = split[m+1]; + + lo = static_cast (fraclo * n); + while (lo+shift < fraclo*n) lo++; + hi = static_cast (frachi * n); + if (hi+shift >= frachi*n) hi--; + + if (igrid >= lo && igrid <= hi) break; + } + + return m; +} + +/* ---------------------------------------------------------------------- + compute the grid box owned by proc within tiled decomposition + performed recursively until proclower = procupper = proc + return box = lo/hi bounds of proc's box in 3 dims +------------------------------------------------------------------------- */ + +void Grid3d::partition_tiled(int proc, int proclower, int procupper, int *box) +{ + // end recursion when partition is a single proc + + if (proclower == procupper) return; + + // split processor partition + // procmid = 1st processor in upper half of partition + // = location in tree that stores this cut + // cut = index of first grid cell in upper partition + // dim = 0,1,2 dimension of cut + + int procmid = proclower + (procupper - proclower) / 2 + 1; + int dim = rcbinfo[procmid].dim; + int cut = rcbinfo[procmid].cut; + + // adjust box to reflect which half of partition the proc is in + + if (proc < procmid) { + box[2*dim+1] = cut-1; + partition_tiled(proc,proclower,procmid-1,box); + } else { + box[2*dim] = cut; + partition_tiled(proc,procmid,procupper,box); + } +} diff --git a/src/gridcomm.h b/src/grid3d.h similarity index 57% rename from src/gridcomm.h rename to src/grid3d.h index 011faad9fb..97fcf5992a 100644 --- a/src/gridcomm.h +++ b/src/grid3d.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -11,39 +11,75 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#ifndef LMP_GRIDCOMM_H -#define LMP_GRIDCOMM_H +#ifndef LMP_GRID3D_H +#define LMP_GRID3D_H #include "pointers.h" namespace LAMMPS_NS { -class GridComm : protected Pointers { +class Grid3d : protected Pointers { public: enum { KSPACE = 0, PAIR = 1, FIX = 2 }; // calling classes - GridComm(class LAMMPS *, MPI_Comm, int, int, int, int, int, int, int, int, int, int, int, int, - int, int, int); - GridComm(class LAMMPS *, MPI_Comm, int, int, int, int, int, int, int, int, int, int, int, int, - int, int, int, int, int, int, int, int, int, int); - ~GridComm() override; - void setup(int &, int &); + Grid3d(class LAMMPS *, MPI_Comm, int, int, int); + Grid3d(class LAMMPS *, MPI_Comm, int, int, int, + int, int, int, int, int, int, int, int, int, int, int, int); + ~Grid3d(); + + void set_distance(double); + void set_stencil_grid(int, int); + void set_stencil_atom(int, int); + void set_shift_grid(double); + void set_shift_atom(double, double); + void set_zfactor(double); + void set_caller_grid(int, int, int, int, int, int); + void set_proc_neighs(int, int, int, int, int, int); + + int identical(Grid3d *); + void get_size(int &, int &, int &); + void get_bounds_owned(int &, int &, int &, int &, int &, int &); + void get_bounds_ghost(int &, int &, int &, int &, int &, int &); + + void setup_grid(int &, int &, int &, int &, int &, int &, + int &, int &, int &, int &, int &, int &); + + void setup_comm(int &, int &); int ghost_adjacent(); void forward_comm(int, void *, int, int, int, void *, void *, MPI_Datatype); void reverse_comm(int, void *, int, int, int, void *, void *, MPI_Datatype); - void gather(int, void *, int, int, int, void *, MPI_Datatype); + + void setup_remap(Grid3d *, int &, int &); + void remap(int, void *, int, int, int, void *, void *, MPI_Datatype); + + void read_file(int, void *, FILE *, int, int); + void write_file(int, void *, int, int, int, MPI_Datatype); protected: int me, nprocs; - int layout; // REGULAR or TILED + int layout; // not TILED or TILED, same as Comm class MPI_Comm gridcomm; // communicator for this class // usually world, but MSM calls with subset - // inputs from caller via constructor + // input from caller int nx, ny, nz; // size of global grid in all 3 dims - int inxlo, inxhi; // inclusive extent of my grid chunk - int inylo, inyhi; // 0 <= in <= N-1 + double maxdist; // distance owned atoms can move outside subdomain + int stencil_atom_lo,stencil_atom_hi; // grid cells accessed beyond atom's cell + int stencil_grid_lo,stencil_grid_hi; // grid cells accessed beyond owned cell + double shift_grid; // location of grid point within grid cell + // only affects which proc owns grid cell + double shift_atom_lo,shift_atom_hi;; // max shift applied to atoms + // when mapped to grid cell by caller + // can be different in lo/hi directions + // only affects extent of ghost cells + int zextra; // 1 if extra grid cells in Z, 0 if not + double zfactor; // multiplier on extent of grid in Z direction + + // extent of my owned and ghost cells + + int inxlo, inxhi; // inclusive extent of my grid chunk, 0 <= in <= N-1 + int inylo, inyhi; int inzlo, inzhi; int outxlo, outxhi; // inclusive extent of my grid chunk plus int outylo, outyhi; // ghost cells in all 6 directions @@ -53,7 +89,7 @@ class GridComm : protected Pointers { int fullzlo, fullzhi; // ------------------------------------------- - // internal variables for REGULAR layout + // internal variables for BRICK layout // ------------------------------------------- int procxlo, procxhi; // 6 neighbor procs that adjoin me @@ -82,33 +118,8 @@ class GridComm : protected Pointers { // internal variables for TILED layout // ------------------------------------------- - int *overlap_procs; // length of Nprocs in communicator MPI_Request *requests; // length of max messages this proc receives - // RCB tree of cut info - // each proc contributes one value, except proc 0 - - struct RCBinfo { - int dim; // 0,1,2 = which dim the cut is in - int cut; // grid index of lowest cell in upper half of cut - }; - - RCBinfo *rcbinfo; - - // overlap = a proc whose owned cells overlap with my extended ghost box - // includes overlaps across periodic boundaries, can also be self - - struct Overlap { - int proc; // proc whose owned cells overlap my ghost cells - int box[6]; // box that overlaps otherproc's owned cells - // this box is wholly contained within global grid - int pbc[3]; // PBC offsets to convert box to a portion of my ghost box - // my ghost box may extend beyond global grid - }; - - int noverlap, maxoverlap; - Overlap *overlap; - // request = sent to each proc whose owned cells overlap my ghost cells struct Request { @@ -170,29 +181,89 @@ class GridComm : protected Pointers { Recv *recv; Copy *copy; + // ------------------------------------------- + // internal variables for REMAP operation + // ------------------------------------------- + + MPI_Request *requests_remap; // length of max messages this proc receives + + int nsend_remap, nrecv_remap, self_remap; + Send *send_remap; + Recv *recv_remap; + Copy copy_remap; + + // ------------------------------------------- + // internal variables for OVERLAP operation + // ------------------------------------------- + + int *overlap_procs; // length of Nprocs in communicator + + // BRICK decomposition + + double *xsplit,*ysplit,*zsplit; + int ***grid2proc; + + // TILED decomposition + // RCB tree of cut info + // each proc contributes one value, except proc 0 + + struct RCBinfo { + int dim; // 0,1,2 = which dim the cut is in + int cut; // grid index of lowest cell in upper half of cut + }; + + RCBinfo *rcbinfo; + + // overlap = a proc whose owned cells overlap with my owned or ghost box + // includes overlaps across periodic boundaries, can also be self + + struct Overlap { + int proc; // proc whose cells overlap my cells + int box[6]; // box of my cells which overlap proc's cells + // this box is wholly contained within global grid + int pbc[3]; // PBC offsets to convert my box to a portion of my ghost box + // my ghost box may extend beyond global grid + }; + + int noverlap_list, maxoverlap_list; + Overlap *overlap_list; + // ------------------------------------------- // internal methods // ------------------------------------------- - void initialize(MPI_Comm, int, int, int, int, int, int, int, int, int, int, int, int, int, int, - int, int, int, int, int, int, int, int, int, int, int, int, int); - virtual void setup_regular(int &, int &); - virtual void setup_tiled(int &, int &); - void ghost_box_drop(int *, int *); - void box_drop_grid(int *, int, int, int &, int *); + void initialize(); + void partition_grid(int, double, double, double, int, int &, int &); + void ghost_grid(); + void extract_comm_info(); - int ghost_adjacent_regular(); + virtual void setup_comm_brick(int &, int &); + virtual void setup_comm_tiled(int &, int &); + int ghost_adjacent_brick(); int ghost_adjacent_tiled(); - template void forward_comm_regular(T *, int, int, int, void *, void *, MPI_Datatype); + template void forward_comm_brick(T *, int, int, int, void *, void *, MPI_Datatype); template void forward_comm_tiled(T *, int, int, int, void *, void *, MPI_Datatype); - template void reverse_comm_regular(T *, int, int, int, void *, void *, MPI_Datatype); + template void reverse_comm_brick(T *, int, int, int, void *, void *, MPI_Datatype); template void reverse_comm_tiled(T *, int, int, int, void *, void *, MPI_Datatype); + template void remap_style(T *, int, int, int, void *, void *, MPI_Datatype); + + template void read_file_style(T *, FILE *, int, int); + template void write_file_style(T *, int, int, int, MPI_Datatype); + + int compute_overlap(int, int *, int *, Overlap *&); + void clean_overlap(); + void box_drop(int *, int *); + void box_drop_grid(int *, int, int, int &, int *); + virtual void grow_swap(); void grow_overlap(); + void deallocate_remap(); int indices(int *&, int, int, int, int, int, int); + int proc_index_uniform(int, int, double, int, double *); + void partition_tiled(int, int, int, int *); }; } // namespace LAMMPS_NS diff --git a/src/gridcomm.cpp b/src/gridcomm.cpp deleted file mode 100644 index fc53026cc8..0000000000 --- a/src/gridcomm.cpp +++ /dev/null @@ -1,1267 +0,0 @@ -// 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. -------------------------------------------------------------------------- */ - -#include "gridcomm.h" - -#include "comm.h" -#include "error.h" -#include "irregular.h" -#include "pair.h" -#include "kspace.h" -#include "fix.h" -#include "memory.h" - -using namespace LAMMPS_NS; - -enum{REGULAR,TILED}; - -#define DELTA 16 - -/* ---------------------------------------------------------------------- - NOTES - tiled implementation only currently works for RCB, not general tiled - b/c RCB tree is used to find neighboring tiles - if o indices for ghosts are < 0 or hi indices are >= N, - then grid is treated as periodic in that dimension, - communication is done across the periodic boundaries -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - constructor called by all classes except MSM - gcomm = world communicator - gn xyz = size of global grid - i xyz lohi = portion of global grid this proc owns, 0 <= index < N - o xyz lohi = owned grid portion + ghost grid cells needed in all directions - if o indices are < 0 or hi indices are >= N, - then grid is treated as periodic in that dimension, - communication is done across the periodic boundaries -------------------------------------------------------------------------- */ - -GridComm::GridComm(LAMMPS *lmp, MPI_Comm gcomm, - int gnx, int gny, int gnz, - int ixlo, int ixhi, int iylo, int iyhi, int izlo, int izhi, - int oxlo, int oxhi, int oylo, int oyhi, int ozlo, int ozhi) - : Pointers(lmp) -{ - if (comm->layout == Comm::LAYOUT_TILED) layout = TILED; - else layout = REGULAR; - - if (layout == REGULAR) { - int (*procneigh)[2] = comm->procneigh; - initialize(gcomm,gnx,gny,gnz, - ixlo,ixhi,iylo,iyhi,izlo,izhi, - oxlo,oxhi,oylo,oyhi,ozlo,ozhi, - oxlo,oxhi,oylo,oyhi,ozlo,ozhi, - procneigh[0][0],procneigh[0][1], - procneigh[1][0],procneigh[1][1], - procneigh[2][0],procneigh[2][1]); - } else { - initialize(gcomm,gnx,gny,gnz, - ixlo,ixhi,iylo,iyhi,izlo,izhi, - oxlo,oxhi,oylo,oyhi,ozlo,ozhi, - oxlo,oxhi,oylo,oyhi,ozlo,ozhi, - 0,0,0,0,0,0); - } -} - -/* ---------------------------------------------------------------------- - constructor called by MSM - gcomm = world communicator or sub-communicator for a hierarchical grid - flag = 1 if e xyz lohi values = larger grid stored by caller in gcomm = world - flag = 2 if e xyz lohi values = 6 neighbor procs in gcomm - gn xyz = size of global grid - i xyz lohi = portion of global grid this proc owns, 0 <= index < N - o xyz lohi = owned grid portion + ghost grid cells needed in all directions - e xyz lohi for flag = 1: extent of larger grid stored by caller - e xyz lohi for flag = 2: 6 neighbor procs -------------------------------------------------------------------------- */ - -GridComm::GridComm(LAMMPS *lmp, MPI_Comm gcomm, int flag, - int gnx, int gny, int gnz, - int ixlo, int ixhi, int iylo, int iyhi, int izlo, int izhi, - int oxlo, int oxhi, int oylo, int oyhi, int ozlo, int ozhi, - int exlo, int exhi, int eylo, int eyhi, int ezlo, int ezhi) - : Pointers(lmp) -{ - if (comm->layout == Comm::LAYOUT_TILED) layout = TILED; - else layout = REGULAR; - - if (flag == 1) { - if (layout == REGULAR) { - // this assumes gcomm = world - int (*procneigh)[2] = comm->procneigh; - initialize(gcomm,gnx,gny,gnz, - ixlo,ixhi,iylo,iyhi,izlo,izhi, - oxlo,oxhi,oylo,oyhi,ozlo,ozhi, - exlo,exhi,eylo,eyhi,ezlo,ezhi, - procneigh[0][0],procneigh[0][1], - procneigh[1][0],procneigh[1][1], - procneigh[2][0],procneigh[2][1]); - } else { - initialize(gcomm,gnx,gny,gnz, - ixlo,ixhi,iylo,iyhi,izlo,izhi, - oxlo,oxhi,oylo,oyhi,ozlo,ozhi, - exlo,exhi,eylo,eyhi,ezlo,ezhi, - 0,0,0,0,0,0); - } - - } else if (flag == 2) { - if (layout == REGULAR) { - initialize(gcomm,gnx,gny,gnz, - ixlo,ixhi,iylo,iyhi,izlo,izhi, - oxlo,oxhi,oylo,oyhi,ozlo,ozhi, - oxlo,oxhi,oylo,oyhi,ozlo,ozhi, - exlo,exhi,eylo,eyhi,ezlo,ezhi); - } else { - error->all(FLERR,"GridComm does not support tiled layout with neighbor procs"); - } - } -} - -/* ---------------------------------------------------------------------- */ - -GridComm::~GridComm() -{ - // regular comm data struct - - for (int i = 0; i < nswap; i++) { - memory->destroy(swap[i].packlist); - memory->destroy(swap[i].unpacklist); - } - memory->sfree(swap); - - // tiled comm data structs - - for (int i = 0; i < nsend; i++) - memory->destroy(send[i].packlist); - memory->sfree(send); - - for (int i = 0; i < nrecv; i++) - memory->destroy(recv[i].unpacklist); - memory->sfree(recv); - - for (int i = 0; i < ncopy; i++) { - memory->destroy(copy[i].packlist); - memory->destroy(copy[i].unpacklist); - } - memory->sfree(copy); - - delete [] requests; -} - -/* ---------------------------------------------------------------------- - store constructor args in local variables -------------------------------------------------------------------------- */ - -void GridComm::initialize(MPI_Comm gcomm, - int gnx, int gny, int gnz, - int ixlo, int ixhi, int iylo, int iyhi, - int izlo, int izhi, - int oxlo, int oxhi, int oylo, int oyhi, - int ozlo, int ozhi, - int fxlo, int fxhi, int fylo, int fyhi, - int fzlo, int fzhi, - int pxlo, int pxhi, int pylo, int pyhi, - int pzlo, int pzhi) -{ - gridcomm = gcomm; - MPI_Comm_rank(gridcomm,&me); - MPI_Comm_size(gridcomm,&nprocs); - - nx = gnx; - ny = gny; - nz = gnz; - - inxlo = ixlo; - inxhi = ixhi; - inylo = iylo; - inyhi = iyhi; - inzlo = izlo; - inzhi = izhi; - - outxlo = oxlo; - outxhi = oxhi; - outylo = oylo; - outyhi = oyhi; - outzlo = ozlo; - outzhi = ozhi; - - fullxlo = fxlo; - fullxhi = fxhi; - fullylo = fylo; - fullyhi = fyhi; - fullzlo = fzlo; - fullzhi = fzhi; - - // for REGULAR layout, proc xyz lohi = my 6 neighbor procs in this MPI_Comm - - if (layout == REGULAR) { - procxlo = pxlo; - procxhi = pxhi; - procylo = pylo; - procyhi = pyhi; - proczlo = pzlo; - proczhi = pzhi; - } - - // internal data initializations - - nswap = maxswap = 0; - swap = nullptr; - - nsend = nrecv = ncopy = 0; - send = nullptr; - recv = nullptr; - copy = nullptr; - requests = nullptr; -} - -/* ---------------------------------------------------------------------- */ - -void GridComm::setup(int &nbuf1, int &nbuf2) -{ - if (layout == REGULAR) setup_regular(nbuf1,nbuf2); - else setup_tiled(nbuf1,nbuf2); -} - -/* ---------------------------------------------------------------------- - setup comm for a regular grid of procs - each proc has 6 neighbors - comm pattern = series of swaps with one of those 6 procs - can be multiple swaps with same proc if ghost extent is large - swap may not be symmetric if both procs do not need same layers of ghosts - all procs perform same # of swaps in a direction, even if some don't need it -------------------------------------------------------------------------- */ - -void GridComm::setup_regular(int &nbuf1, int &nbuf2) -{ - int nsent,sendfirst,sendlast,recvfirst,recvlast; - int sendplanes,recvplanes; - int notdoneme,notdone; - - // notify 6 neighbor procs how many ghost grid planes I need from them - // ghost xyz lo = # of my lower grid planes that proc xyz lo needs as its ghosts - // ghost xyz hi = # of my upper grid planes that proc xyz hi needs as its ghosts - // if this proc is its own neighbor across periodic bounary, value is from self - - int nplanes = inxlo - outxlo; - if (procxlo != me) - MPI_Sendrecv(&nplanes,1,MPI_INT,procxlo,0, - &ghostxhi,1,MPI_INT,procxhi,0,gridcomm,MPI_STATUS_IGNORE); - else ghostxhi = nplanes; - - nplanes = outxhi - inxhi; - if (procxhi != me) - MPI_Sendrecv(&nplanes,1,MPI_INT,procxhi,0, - &ghostxlo,1,MPI_INT,procxlo,0,gridcomm,MPI_STATUS_IGNORE); - else ghostxlo = nplanes; - - nplanes = inylo - outylo; - if (procylo != me) - MPI_Sendrecv(&nplanes,1,MPI_INT,procylo,0, - &ghostyhi,1,MPI_INT,procyhi,0,gridcomm,MPI_STATUS_IGNORE); - else ghostyhi = nplanes; - - nplanes = outyhi - inyhi; - if (procyhi != me) - MPI_Sendrecv(&nplanes,1,MPI_INT,procyhi,0, - &ghostylo,1,MPI_INT,procylo,0,gridcomm,MPI_STATUS_IGNORE); - else ghostylo = nplanes; - - nplanes = inzlo - outzlo; - if (proczlo != me) - MPI_Sendrecv(&nplanes,1,MPI_INT,proczlo,0, - &ghostzhi,1,MPI_INT,proczhi,0,gridcomm,MPI_STATUS_IGNORE); - else ghostzhi = nplanes; - - nplanes = outzhi - inzhi; - if (proczhi != me) - MPI_Sendrecv(&nplanes,1,MPI_INT,proczhi,0, - &ghostzlo,1,MPI_INT,proczlo,0,gridcomm,MPI_STATUS_IGNORE); - else ghostzlo = nplanes; - - // setup swaps = exchange of grid data with one of 6 neighobr procs - // can be more than one in a direction if ghost region extends beyond neigh proc - // all procs have same swap count, but swapsize npack/nunpack can be empty - - nswap = 0; - - // send own grid pts to -x processor, recv ghost grid pts from +x processor - - nsent = 0; - sendfirst = inxlo; - sendlast = inxhi; - recvfirst = inxhi+1; - notdone = 1; - - while (notdone) { - if (nswap == maxswap) grow_swap(); - - swap[nswap].sendproc = procxlo; - swap[nswap].recvproc = procxhi; - sendplanes = MIN(sendlast-sendfirst+1,ghostxlo-nsent); - swap[nswap].npack = - indices(swap[nswap].packlist, - sendfirst,sendfirst+sendplanes-1,inylo,inyhi,inzlo,inzhi); - - if (procxlo != me) - MPI_Sendrecv(&sendplanes,1,MPI_INT,procxlo,0, - &recvplanes,1,MPI_INT,procxhi,0,gridcomm,MPI_STATUS_IGNORE); - else recvplanes = sendplanes; - - swap[nswap].nunpack = - indices(swap[nswap].unpacklist, - recvfirst,recvfirst+recvplanes-1,inylo,inyhi,inzlo,inzhi); - - nsent += sendplanes; - sendfirst += sendplanes; - sendlast += recvplanes; - recvfirst += recvplanes; - nswap++; - - if (nsent < ghostxlo) notdoneme = 1; - else notdoneme = 0; - MPI_Allreduce(¬doneme,¬done,1,MPI_INT,MPI_SUM,gridcomm); - } - - // send own grid pts to +x processor, recv ghost grid pts from -x processor - - nsent = 0; - sendfirst = inxlo; - sendlast = inxhi; - recvlast = inxlo-1; - notdone = 1; - - while (notdone) { - if (nswap == maxswap) grow_swap(); - - swap[nswap].sendproc = procxhi; - swap[nswap].recvproc = procxlo; - sendplanes = MIN(sendlast-sendfirst+1,ghostxhi-nsent); - swap[nswap].npack = - indices(swap[nswap].packlist, - sendlast-sendplanes+1,sendlast,inylo,inyhi,inzlo,inzhi); - - if (procxhi != me) - MPI_Sendrecv(&sendplanes,1,MPI_INT,procxhi,0, - &recvplanes,1,MPI_INT,procxlo,0,gridcomm,MPI_STATUS_IGNORE); - else recvplanes = sendplanes; - - swap[nswap].nunpack = - indices(swap[nswap].unpacklist, - recvlast-recvplanes+1,recvlast,inylo,inyhi,inzlo,inzhi); - - nsent += sendplanes; - sendfirst -= recvplanes; - sendlast -= sendplanes; - recvlast -= recvplanes; - nswap++; - - if (nsent < ghostxhi) notdoneme = 1; - else notdoneme = 0; - MPI_Allreduce(¬doneme,¬done,1,MPI_INT,MPI_SUM,gridcomm); - } - - // send own grid pts to -y processor, recv ghost grid pts from +y processor - - nsent = 0; - sendfirst = inylo; - sendlast = inyhi; - recvfirst = inyhi+1; - notdone = 1; - - while (notdone) { - if (nswap == maxswap) grow_swap(); - - swap[nswap].sendproc = procylo; - swap[nswap].recvproc = procyhi; - sendplanes = MIN(sendlast-sendfirst+1,ghostylo-nsent); - swap[nswap].npack = - indices(swap[nswap].packlist, - outxlo,outxhi,sendfirst,sendfirst+sendplanes-1,inzlo,inzhi); - - if (procylo != me) - MPI_Sendrecv(&sendplanes,1,MPI_INT,procylo,0, - &recvplanes,1,MPI_INT,procyhi,0,gridcomm,MPI_STATUS_IGNORE); - else recvplanes = sendplanes; - - swap[nswap].nunpack = - indices(swap[nswap].unpacklist, - outxlo,outxhi,recvfirst,recvfirst+recvplanes-1,inzlo,inzhi); - - nsent += sendplanes; - sendfirst += sendplanes; - sendlast += recvplanes; - recvfirst += recvplanes; - nswap++; - - if (nsent < ghostylo) notdoneme = 1; - else notdoneme = 0; - MPI_Allreduce(¬doneme,¬done,1,MPI_INT,MPI_SUM,gridcomm); - } - - // send own grid pts to +y processor, recv ghost grid pts from -y processor - - nsent = 0; - sendfirst = inylo; - sendlast = inyhi; - recvlast = inylo-1; - notdone = 1; - - while (notdone) { - if (nswap == maxswap) grow_swap(); - - swap[nswap].sendproc = procyhi; - swap[nswap].recvproc = procylo; - sendplanes = MIN(sendlast-sendfirst+1,ghostyhi-nsent); - swap[nswap].npack = - indices(swap[nswap].packlist, - outxlo,outxhi,sendlast-sendplanes+1,sendlast,inzlo,inzhi); - - if (procyhi != me) - MPI_Sendrecv(&sendplanes,1,MPI_INT,procyhi,0, - &recvplanes,1,MPI_INT,procylo,0,gridcomm,MPI_STATUS_IGNORE); - else recvplanes = sendplanes; - - swap[nswap].nunpack = - indices(swap[nswap].unpacklist, - outxlo,outxhi,recvlast-recvplanes+1,recvlast,inzlo,inzhi); - - nsent += sendplanes; - sendfirst -= recvplanes; - sendlast -= sendplanes; - recvlast -= recvplanes; - nswap++; - - if (nsent < ghostyhi) notdoneme = 1; - else notdoneme = 0; - MPI_Allreduce(¬doneme,¬done,1,MPI_INT,MPI_SUM,gridcomm); - } - - // send own grid pts to -z processor, recv ghost grid pts from +z processor - - nsent = 0; - sendfirst = inzlo; - sendlast = inzhi; - recvfirst = inzhi+1; - notdone = 1; - - while (notdone) { - if (nswap == maxswap) grow_swap(); - - swap[nswap].sendproc = proczlo; - swap[nswap].recvproc = proczhi; - sendplanes = MIN(sendlast-sendfirst+1,ghostzlo-nsent); - swap[nswap].npack = - indices(swap[nswap].packlist, - outxlo,outxhi,outylo,outyhi,sendfirst,sendfirst+sendplanes-1); - - if (proczlo != me) - MPI_Sendrecv(&sendplanes,1,MPI_INT,proczlo,0, - &recvplanes,1,MPI_INT,proczhi,0,gridcomm,MPI_STATUS_IGNORE); - else recvplanes = sendplanes; - - swap[nswap].nunpack = - indices(swap[nswap].unpacklist, - outxlo,outxhi,outylo,outyhi,recvfirst,recvfirst+recvplanes-1); - - nsent += sendplanes; - sendfirst += sendplanes; - sendlast += recvplanes; - recvfirst += recvplanes; - nswap++; - - if (nsent < ghostzlo) notdoneme = 1; - else notdoneme = 0; - MPI_Allreduce(¬doneme,¬done,1,MPI_INT,MPI_SUM,gridcomm); - } - - // send own grid pts to +z processor, recv ghost grid pts from -z processor - - nsent = 0; - sendfirst = inzlo; - sendlast = inzhi; - recvlast = inzlo-1; - notdone = 1; - - while (notdone) { - if (nswap == maxswap) grow_swap(); - - swap[nswap].sendproc = proczhi; - swap[nswap].recvproc = proczlo; - sendplanes = MIN(sendlast-sendfirst+1,ghostzhi-nsent); - swap[nswap].npack = - indices(swap[nswap].packlist, - outxlo,outxhi,outylo,outyhi,sendlast-sendplanes+1,sendlast); - - if (proczhi != me) - MPI_Sendrecv(&sendplanes,1,MPI_INT,proczhi,0, - &recvplanes,1,MPI_INT,proczlo,0,gridcomm,MPI_STATUS_IGNORE); - else recvplanes = sendplanes; - - swap[nswap].nunpack = - indices(swap[nswap].unpacklist, - outxlo,outxhi,outylo,outyhi,recvlast-recvplanes+1,recvlast); - - nsent += sendplanes; - sendfirst -= recvplanes; - sendlast -= sendplanes; - recvlast -= recvplanes; - nswap++; - - if (nsent < ghostzhi) notdoneme = 1; - else notdoneme = 0; - MPI_Allreduce(¬doneme,¬done,1,MPI_INT,MPI_SUM,gridcomm); - } - - // ngrid = max of any forward/reverse pack/unpack grid points - - int ngrid = 0; - for (int i = 0; i < nswap; i++) { - ngrid = MAX(ngrid,swap[i].npack); - ngrid = MAX(ngrid,swap[i].nunpack); - } - - nbuf1 = nbuf2 = ngrid; -} - -/* ---------------------------------------------------------------------- - setup comm for RCB tiled proc domains - each proc has arbitrary # of neighbors that overlap its ghost extent - identify which procs will send me ghost cells, and vice versa - may not be symmetric if both procs do not need same layers of ghosts - comm pattern = post recvs for all my ghosts, send my owned, wait on recvs - no exchanges by dimension, unlike CommTiled forward/reverse comm of particles -------------------------------------------------------------------------- */ - -void GridComm::setup_tiled(int &nbuf1, int &nbuf2) -{ - int i,m; - double xlo,xhi,ylo,yhi,zlo,zhi; - int ghostbox[6],pbc[3]; - - // setup RCB tree of cut info for grid - // access CommTiled to get cut dimension - // cut = this proc's inlo in that dim - // dim is -1 for proc 0, but never accessed - - rcbinfo = (RCBinfo *) - memory->smalloc(nprocs*sizeof(RCBinfo),"GridComm:rcbinfo"); - RCBinfo rcbone; - rcbone.dim = comm->rcbcutdim; - if (rcbone.dim <= 0) rcbone.cut = inxlo; - else if (rcbone.dim == 1) rcbone.cut = inylo; - else if (rcbone.dim == 2) rcbone.cut = inzlo; - MPI_Allgather(&rcbone,sizeof(RCBinfo),MPI_CHAR, - rcbinfo,sizeof(RCBinfo),MPI_CHAR,gridcomm); - - // find overlaps of my extended ghost box with all other procs - // accounts for crossings of periodic boundaries - // noverlap = # of overlaps, including self - // overlap = vector of overlap info using Overlap data struct - - ghostbox[0] = outxlo; - ghostbox[1] = outxhi; - ghostbox[2] = outylo; - ghostbox[3] = outyhi; - ghostbox[4] = outzlo; - ghostbox[5] = outzhi; - - pbc[0] = pbc[1] = pbc[2] = 0; - - memory->create(overlap_procs,nprocs,"GridComm:overlap_procs"); - noverlap = maxoverlap = 0; - overlap = nullptr; - - ghost_box_drop(ghostbox,pbc); - - // send each proc an overlap message - // content: me, index of my overlap, box that overlaps with its owned cells - // ncopy = # of overlaps with myself, across a periodic boundary - - int *proclist; - memory->create(proclist,noverlap,"GridComm:proclist"); - srequest = (Request *) - memory->smalloc(noverlap*sizeof(Request),"GridComm:srequest"); - - int nsend_request = 0; - ncopy = 0; - - for (m = 0; m < noverlap; m++) { - if (overlap[m].proc == me) ncopy++; - else { - proclist[nsend_request] = overlap[m].proc; - srequest[nsend_request].sender = me; - srequest[nsend_request].index = m; - for (i = 0; i < 6; i++) - srequest[nsend_request].box[i] = overlap[m].box[i]; - nsend_request++; - } - } - - auto irregular = new Irregular(lmp); - int nrecv_request = irregular->create_data(nsend_request,proclist,1); - auto rrequest = (Request *) memory->smalloc(nrecv_request*sizeof(Request),"GridComm:rrequest"); - irregular->exchange_data((char *) srequest,sizeof(Request),(char *) rrequest); - irregular->destroy_data(); - - // compute overlaps between received ghost boxes and my owned box - // overlap box used to setup my Send data struct and respond to requests - - send = (Send *) memory->smalloc(nrecv_request*sizeof(Send),"GridComm:send"); - sresponse = (Response *) memory->smalloc(nrecv_request*sizeof(Response),"GridComm:sresponse"); - memory->destroy(proclist); - memory->create(proclist,nrecv_request,"GridComm:proclist"); - - for (m = 0; m < nrecv_request; m++) { - send[m].proc = rrequest[m].sender; - xlo = MAX(rrequest[m].box[0],inxlo); - xhi = MIN(rrequest[m].box[1],inxhi); - ylo = MAX(rrequest[m].box[2],inylo); - yhi = MIN(rrequest[m].box[3],inyhi); - zlo = MAX(rrequest[m].box[4],inzlo); - zhi = MIN(rrequest[m].box[5],inzhi); - send[m].npack = indices(send[m].packlist,xlo,xhi,ylo,yhi,zlo,zhi); - - proclist[m] = rrequest[m].sender; - sresponse[m].index = rrequest[m].index; - sresponse[m].box[0] = xlo; - sresponse[m].box[1] = xhi; - sresponse[m].box[2] = ylo; - sresponse[m].box[3] = yhi; - sresponse[m].box[4] = zlo; - sresponse[m].box[5] = zhi; - } - - nsend = nrecv_request; - - // reply to each Request message with a Response message - // content: index for the overlap on requestor, overlap box on my owned grid - - int nsend_response = nrecv_request; - int nrecv_response = irregular->create_data(nsend_response,proclist,1); - auto rresponse = (Response *) memory->smalloc(nrecv_response*sizeof(Response),"GridComm:rresponse"); - irregular->exchange_data((char *) sresponse,sizeof(Response),(char *) rresponse); - irregular->destroy_data(); - delete irregular; - - // process received responses - // box used to setup my Recv data struct after unwrapping via PBC - // adjacent = 0 if any box of ghost cells does not adjoin my owned cells - - recv = (Recv *) memory->smalloc(nrecv_response*sizeof(Recv),"GridComm:recv"); - adjacent = 1; - - for (i = 0; i < nrecv_response; i++) { - m = rresponse[i].index; - recv[i].proc = overlap[m].proc; - xlo = rresponse[i].box[0] + overlap[m].pbc[0] * nx; - xhi = rresponse[i].box[1] + overlap[m].pbc[0] * nx; - ylo = rresponse[i].box[2] + overlap[m].pbc[1] * ny; - yhi = rresponse[i].box[3] + overlap[m].pbc[1] * ny; - zlo = rresponse[i].box[4] + overlap[m].pbc[2] * nz; - zhi = rresponse[i].box[5] + overlap[m].pbc[2] * nz; - recv[i].nunpack = indices(recv[i].unpacklist,xlo,xhi,ylo,yhi,zlo,zhi); - - if (xlo != inxhi+1 && xhi != inxlo-1 && - ylo != inyhi+1 && yhi != inylo-1 && - zlo != inzhi+1 && zhi != inzlo-1) adjacent = 0; - } - - nrecv = nrecv_response; - - // create Copy data struct from overlaps with self - - copy = (Copy *) memory->smalloc(ncopy*sizeof(Copy),"GridComm:copy"); - - ncopy = 0; - for (m = 0; m < noverlap; m++) { - if (overlap[m].proc != me) continue; - xlo = overlap[m].box[0]; - xhi = overlap[m].box[1]; - ylo = overlap[m].box[2]; - yhi = overlap[m].box[3]; - zlo = overlap[m].box[4]; - zhi = overlap[m].box[5]; - copy[ncopy].npack = indices(copy[ncopy].packlist,xlo,xhi,ylo,yhi,zlo,zhi); - xlo = overlap[m].box[0] + overlap[m].pbc[0] * nx; - xhi = overlap[m].box[1] + overlap[m].pbc[0] * nx; - ylo = overlap[m].box[2] + overlap[m].pbc[1] * ny; - yhi = overlap[m].box[3] + overlap[m].pbc[1] * ny; - zlo = overlap[m].box[4] + overlap[m].pbc[2] * nz; - zhi = overlap[m].box[5] + overlap[m].pbc[2] * nz; - copy[ncopy].nunpack = indices(copy[ncopy].unpacklist,xlo,xhi,ylo,yhi,zlo,zhi); - ncopy++; - } - - // set offsets for received data - - int offset = 0; - for (m = 0; m < nsend; m++) { - send[m].offset = offset; - offset += send[m].npack; - } - - offset = 0; - for (m = 0; m < nrecv; m++) { - recv[m].offset = offset; - offset += recv[m].nunpack; - } - - // length of MPI requests vector is max of nsend, nrecv - - int nrequest = MAX(nsend,nrecv); - requests = new MPI_Request[nrequest]; - - // clean-up - - memory->sfree(rcbinfo); - memory->destroy(proclist); - memory->destroy(overlap_procs); - memory->sfree(overlap); - memory->sfree(srequest); - memory->sfree(rrequest); - memory->sfree(sresponse); - memory->sfree(rresponse); - - // nbuf1 = largest pack or unpack in any Send or Recv or Copy - // nbuf2 = larget of sum of all packs or unpacks in Send or Recv - - nbuf1 = 0; - - for (m = 0; m < ncopy; m++) { - nbuf1 = MAX(nbuf1,copy[m].npack); - nbuf1 = MAX(nbuf1,copy[m].nunpack); - } - - int nbufs = 0; - for (m = 0; m < nsend; m++) { - nbuf1 = MAX(nbuf1,send[m].npack); - nbufs += send[m].npack; - } - - int nbufr = 0; - for (m = 0; m < nrecv; m++) { - nbuf1 = MAX(nbuf1,recv[m].nunpack); - nbufr += recv[m].nunpack; - } - - nbuf2 = MAX(nbufs,nbufr); -} - -/* ---------------------------------------------------------------------- - recursively split a box until it doesn't overlap any periodic boundaries - box = 6 integers = (xlo,xhi,ylo,yhi,zlo,zhi) - each lo/hi value may extend beyonw 0 to N-1 into another periodic image - pbc = flags in each dim of which periodic image the caller box was in - when a box straddles a periodic bounadry, split it in two - when a box does not straddle, drop it down RCB tree - add all the procs it overlaps with to Overlap list -------------------------------------------------------------------------- */ - -void GridComm::ghost_box_drop(int *box, int *pbc) -{ - int i,m; - - // newbox12 and newpbc are initially copies of caller box and pbc - - int newbox1[6],newbox2[6],newpbc[3]; - - for (i = 0; i < 6; i++) newbox1[i] = newbox2[i] = box[i]; - for (i = 0; i < 3; i++) newpbc[i] = pbc[i]; - - // 6 if tests to see if box needs to be split across a periodic boundary - // newbox1 and 2 = new split boxes, newpbc increments current pbc - // final else is no split - - int splitflag = 1; - - if (box[0] < 0) { - newbox1[0] = 0; - newbox2[0] = box[0] + nx; - newbox2[1] = nx - 1; - newpbc[0]--; - } else if (box[1] >= nx) { - newbox1[1] = nx - 1; - newbox2[0] = 0; - newbox2[1] = box[1] - nx; - newpbc[0]++; - } else if (box[2] < 0) { - newbox1[2] = 0; - newbox2[2] = box[2] + ny; - newbox2[3] = ny - 1; - newpbc[1]--; - } else if (box[3] >= ny) { - newbox1[3] = ny - 1; - newbox2[2] = 0; - newbox2[3] = box[3] - ny; - newpbc[1]++; - } else if (box[4] < 0) { - newbox1[4] = 0; - newbox2[4] = box[4] + nz; - newbox2[5] = nz - 1; - newpbc[2]--; - } else if (box[5] >= nz) { - newbox1[5] = nz - 1; - newbox2[4] = 0; - newbox2[5] = box[5] - nz; - newpbc[2]++; - - // box is not split, drop on RCB tree - // returns nprocs = # of procs it overlaps, including self - // returns proc_overlap = list of proc IDs it overlaps - // skip self overlap if no crossing of periodic boundaries - // do not skip self if overlap is in another periodic image - - } else { - splitflag = 0; - int np = 0; - box_drop_grid(box,0,nprocs-1,np,overlap_procs); - for (m = 0; m < np; m++) { - if (noverlap == maxoverlap) grow_overlap(); - if (overlap_procs[m] == me && - pbc[0] == 0 && pbc[1] == 0 && pbc[2] == 0) continue; - overlap[noverlap].proc = overlap_procs[m]; - for (i = 0; i < 6; i++) overlap[noverlap].box[i] = box[i]; - for (i = 0; i < 3; i++) overlap[noverlap].pbc[i] = pbc[i]; - noverlap++; - } - } - - // recurse with 2 split boxes - - if (splitflag) { - ghost_box_drop(newbox1,pbc); - ghost_box_drop(newbox2,newpbc); - } -} - -/* ---------------------------------------------------------------------- - recursively drop a box down the RCB tree to find all procs it overlaps with - box = 6 integers = (xlo,xhi,ylo,yhi,zlo,zhi) - each lo/hi value ranges from 0 to N-1 in a dim, N = grid size in that dim - box is guaranteed to be wholly within the global domain - return Np = # of procs, plist = proc IDs -------------------------------------------------------------------------- */ - -void GridComm::box_drop_grid(int *box, int proclower, int procupper, - int &np, int *plist) -{ - // end recursion when partition is a single proc - // add proclower to plist - - if (proclower == procupper) { - plist[np++] = proclower; - return; - } - - // drop box on each side of cut it extends beyond - // use < and >= criteria so does not include a box it only touches - // procmid = 1st processor in upper half of partition - // = location in tree that stores this cut - // cut = index of first grid cell in upper partition - // dim = 0,1,2 dimension of cut - - int procmid = proclower + (procupper - proclower) / 2 + 1; - int dim = rcbinfo[procmid].dim; - int cut = rcbinfo[procmid].cut; - - if (box[2*dim] < cut) box_drop_grid(box,proclower,procmid-1,np,plist); - if (box[2*dim+1] >= cut) box_drop_grid(box,procmid,procupper,np,plist); -} - -/* ---------------------------------------------------------------------- - check if all procs only need ghost info from adjacent procs - return 1 if yes, 0 if no -------------------------------------------------------------------------- */ - -int GridComm::ghost_adjacent() -{ - if (layout == REGULAR) return ghost_adjacent_regular(); - return ghost_adjacent_tiled(); -} - -/* ---------------------------------------------------------------------- - adjacent = 0 if a proc's ghost xyz lohi values exceed its subdomain size - return 0 if adjacent=0 for any proc, else 1 -------------------------------------------------------------------------- */ - -int GridComm::ghost_adjacent_regular() -{ - adjacent = 1; - if (ghostxlo > inxhi-inxlo+1) adjacent = 0; - if (ghostxhi > inxhi-inxlo+1) adjacent = 0; - if (ghostylo > inyhi-inylo+1) adjacent = 0; - if (ghostyhi > inyhi-inylo+1) adjacent = 0; - if (ghostzlo > inzhi-inzlo+1) adjacent = 0; - if (ghostzhi > inzhi-inzlo+1) adjacent = 0; - - int adjacent_all; - MPI_Allreduce(&adjacent,&adjacent_all,1,MPI_INT,MPI_MIN,gridcomm); - return adjacent_all; -} - -/* ---------------------------------------------------------------------- - adjacent = 0 if a proc's received ghosts were flagged - as non-adjacent in setup_tiled() - return 0 if adjacent=0 for any proc, else 1 -------------------------------------------------------------------------- */ - -int GridComm::ghost_adjacent_tiled() -{ - int adjacent_all; - MPI_Allreduce(&adjacent,&adjacent_all,1,MPI_INT,MPI_MIN,gridcomm); - return adjacent_all; -} - -/* ---------------------------------------------------------------------- - forward comm of my owned cells to other's ghost cells -------------------------------------------------------------------------- */ - -void GridComm::forward_comm(int caller, void *ptr, int nper, int nbyte, int which, - void *buf1, void *buf2, MPI_Datatype datatype) -{ - if (layout == REGULAR) { - if (caller == KSPACE) - forward_comm_regular((KSpace *) ptr,nper,nbyte,which, - buf1,buf2,datatype); - else if (caller == PAIR) - forward_comm_regular((Pair *) ptr,nper,nbyte,which, - buf1,buf2,datatype); - else if (caller == FIX) - forward_comm_regular((Fix *) ptr,nper,nbyte,which, - buf1,buf2,datatype); - } else { - if (caller == KSPACE) - forward_comm_tiled((KSpace *) ptr,nper,nbyte,which, - buf1,buf2,datatype); - else if (caller == PAIR) - forward_comm_tiled((Pair *) ptr,nper,nbyte,which, - buf1,buf2,datatype); - else if (caller == FIX) - forward_comm_tiled((Fix *) ptr,nper,nbyte, - which,buf1,buf2,datatype); - } -} - -/* ---------------------------------------------------------------------- - forward comm on regular grid of procs via list of swaps with 6 neighbor procs -------------------------------------------------------------------------- */ - -template < class T > -void GridComm:: -forward_comm_regular(T *ptr, int nper, int /*nbyte*/, int which, - void *buf1, void *buf2, MPI_Datatype datatype) -{ - int m; - MPI_Request request; - - for (m = 0; m < nswap; m++) { - if (swap[m].sendproc == me) - ptr->pack_forward_grid(which,buf2,swap[m].npack,swap[m].packlist); - else - ptr->pack_forward_grid(which,buf1,swap[m].npack,swap[m].packlist); - - if (swap[m].sendproc != me) { - if (swap[m].nunpack) MPI_Irecv(buf2,nper*swap[m].nunpack,datatype, - swap[m].recvproc,0,gridcomm,&request); - if (swap[m].npack) MPI_Send(buf1,nper*swap[m].npack,datatype, - swap[m].sendproc,0,gridcomm); - if (swap[m].nunpack) MPI_Wait(&request,MPI_STATUS_IGNORE); - } - - ptr->unpack_forward_grid(which,buf2,swap[m].nunpack,swap[m].unpacklist); - } -} - -/* ---------------------------------------------------------------------- - forward comm on tiled grid decomp via Send/Recv lists of each neighbor proc -------------------------------------------------------------------------- */ - -template < class T > -void GridComm:: -forward_comm_tiled(T *ptr, int nper, int nbyte, int which, - void *buf1, void *vbuf2, MPI_Datatype datatype) -{ - int i,m,offset; - - auto buf2 = (char *) vbuf2; - - // post all receives - - for (m = 0; m < nrecv; m++) { - offset = nper * recv[m].offset * nbyte; - MPI_Irecv((void *) &buf2[offset],nper*recv[m].nunpack,datatype, - recv[m].proc,0,gridcomm,&requests[m]); - } - - // perform all sends to other procs - - for (m = 0; m < nsend; m++) { - ptr->pack_forward_grid(which,buf1,send[m].npack,send[m].packlist); - MPI_Send(buf1,nper*send[m].npack,datatype,send[m].proc,0,gridcomm); - } - - // perform all copies to self - - for (m = 0; m < ncopy; m++) { - ptr->pack_forward_grid(which,buf1,copy[m].npack,copy[m].packlist); - ptr->unpack_forward_grid(which,buf1,copy[m].nunpack,copy[m].unpacklist); - } - - // unpack all received data - - for (i = 0; i < nrecv; i++) { - MPI_Waitany(nrecv,requests,&m,MPI_STATUS_IGNORE); - offset = nper * recv[m].offset * nbyte; - ptr->unpack_forward_grid(which,(void *) &buf2[offset], - recv[m].nunpack,recv[m].unpacklist); - } -} - -/* ---------------------------------------------------------------------- - reverse comm of my ghost cells to sum to owner cells -------------------------------------------------------------------------- */ - -void GridComm::reverse_comm(int caller, void *ptr, int nper, int nbyte, int which, - void *buf1, void *buf2, MPI_Datatype datatype) -{ - if (layout == REGULAR) { - if (caller == KSPACE) - reverse_comm_regular((KSpace *) ptr,nper,nbyte,which, - buf1,buf2,datatype); - else if (caller == PAIR) - reverse_comm_regular((Pair *) ptr,nper,nbyte,which, - buf1,buf2,datatype); - else if (caller == FIX) - reverse_comm_regular((Fix *) ptr,nper,nbyte,which, - buf1,buf2,datatype); - } else { - if (caller == KSPACE) - reverse_comm_tiled((KSpace *) ptr,nper,nbyte,which, - buf1,buf2,datatype); - else if (caller == PAIR) - reverse_comm_tiled((Pair *) ptr,nper,nbyte,which, - buf1,buf2,datatype); - else if (caller == FIX) - reverse_comm_tiled((Fix *) ptr,nper,nbyte,which, - buf1,buf2,datatype); - } -} - -/* ---------------------------------------------------------------------- - reverse comm on regular grid of procs via list of swaps with 6 neighbor procs -------------------------------------------------------------------------- */ - -template < class T > -void GridComm:: -reverse_comm_regular(T *ptr, int nper, int /*nbyte*/, int which, - void *buf1, void *buf2, MPI_Datatype datatype) -{ - int m; - MPI_Request request; - - for (m = nswap-1; m >= 0; m--) { - if (swap[m].recvproc == me) - ptr->pack_reverse_grid(which,buf2,swap[m].nunpack,swap[m].unpacklist); - else - ptr->pack_reverse_grid(which,buf1,swap[m].nunpack,swap[m].unpacklist); - - if (swap[m].recvproc != me) { - if (swap[m].npack) MPI_Irecv(buf2,nper*swap[m].npack,datatype, - swap[m].sendproc,0,gridcomm,&request); - if (swap[m].nunpack) MPI_Send(buf1,nper*swap[m].nunpack,datatype, - swap[m].recvproc,0,gridcomm); - if (swap[m].npack) MPI_Wait(&request,MPI_STATUS_IGNORE); - } - - ptr->unpack_reverse_grid(which,buf2,swap[m].npack,swap[m].packlist); - } -} - -/* ---------------------------------------------------------------------- - reverse comm on tiled grid decomp via Send/Recv lists of each neighbor proc -------------------------------------------------------------------------- */ - -template < class T > -void GridComm:: -reverse_comm_tiled(T *ptr, int nper, int nbyte, int which, - void *buf1, void *vbuf2, MPI_Datatype datatype) -{ - int i,m,offset; - - auto buf2 = (char *) vbuf2; - - // post all receives - - for (m = 0; m < nsend; m++) { - offset = nper * send[m].offset * nbyte; - MPI_Irecv((void *) &buf2[offset],nper*send[m].npack,datatype, - send[m].proc,0,gridcomm,&requests[m]); - } - - // perform all sends to other procs - - for (m = 0; m < nrecv; m++) { - ptr->pack_reverse_grid(which,buf1,recv[m].nunpack,recv[m].unpacklist); - MPI_Send(buf1,nper*recv[m].nunpack,datatype,recv[m].proc,0,gridcomm); - } - - // perform all copies to self - - for (m = 0; m < ncopy; m++) { - ptr->pack_reverse_grid(which,buf1,copy[m].nunpack,copy[m].unpacklist); - ptr->unpack_reverse_grid(which,buf1,copy[m].npack,copy[m].packlist); - } - - // unpack all received data - - for (i = 0; i < nsend; i++) { - MPI_Waitany(nsend,requests,&m,MPI_STATUS_IGNORE); - offset = nper * send[m].offset * nbyte; - ptr->unpack_reverse_grid(which,(void *) &buf2[offset], - send[m].npack,send[m].packlist); - } -} - -/* ---------------------------------------------------------------------- - gather global grid values to proc 0, one grid chunk at a time - proc 0 pings each proc for its grid chunk - pack/unpack operations are performed by caller via callbacks - caller can decide whether to store chunks, output them, etc -------------------------------------------------------------------------- */ - -void GridComm::gather(int /*caller*/, void *ptr, int nper, int nbyte, - int which, void *buf, MPI_Datatype datatype) -{ - int me = comm->me; - Fix *fptr = (Fix *) ptr; - - // maxsize = max grid data owned by any proc - - int mysize = (inxhi-inxlo+1) * (inyhi-inylo+1) * (inzhi-inzlo+1); - mysize *= nper; - int maxsize; - MPI_Allreduce(&mysize,&maxsize,1,MPI_INT,MPI_MAX,world); - - // pack my data via callback to caller - - char *mybuf; - if (me == 0) memory->create(mybuf,maxsize*nbyte,"GridComm:mybuf"); - else memory->create(mybuf,mysize*nbyte,"GridComm:mybuf"); - fptr->pack_gather_grid(which,mybuf); - - // ping each proc for its data - // unpack into full buffer via callback to caller - - int xlo,xhi,ylo,yhi,zlo,zhi,tmp; - int bounds[6]; - - if (me == 0) { - MPI_Status status; - MPI_Request request; - - for (int iproc = 0; iproc < nprocs; iproc++) { - if (iproc) { - MPI_Irecv(mybuf,maxsize,datatype,iproc,0,world,&request); - MPI_Send(&tmp,0,MPI_INT,iproc,0,world); - MPI_Wait(&request,&status); - MPI_Recv(bounds,6,MPI_INT,iproc,0,world,&status); - xlo = bounds[0]; - xhi = bounds[1]; - ylo = bounds[2]; - yhi = bounds[3]; - zlo = bounds[4]; - zhi = bounds[5]; - } else { - xlo = inxlo; - xhi = inxhi; - ylo = inylo; - yhi = inyhi; - zlo = inzlo; - zhi = inzhi; - } - - fptr->unpack_gather_grid(which,mybuf,buf,xlo,xhi,ylo,yhi,zlo,zhi); - } - - } else { - MPI_Recv(&tmp,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE); - MPI_Rsend(mybuf,mysize,datatype,0,0,world); - bounds[0] = inxlo; - bounds[1] = inxhi; - bounds[2] = inylo; - bounds[3] = inyhi; - bounds[4] = inzlo; - bounds[5] = inzhi; - MPI_Send(bounds,6,MPI_INT,0,0,world); - } - - memory->destroy(mybuf); -} - -/* ---------------------------------------------------------------------- - create swap stencil for grid own/ghost communication - swaps covers all 3 dimensions and both directions - swaps cover multiple iterations in a direction if need grid pts - from further away than nearest-neighbor proc - same swap list used by forward and reverse communication -------------------------------------------------------------------------- */ - -void GridComm::grow_swap() -{ - maxswap += DELTA; - swap = (Swap *) memory->srealloc(swap,maxswap*sizeof(Swap),"GridComm:swap"); -} - -/* ---------------------------------------------------------------------- - create swap stencil for grid own/ghost communication - swaps covers all 3 dimensions and both directions - swaps cover multiple iterations in a direction if need grid pts - from further away than nearest-neighbor proc - same swap list used by forward and reverse communication -------------------------------------------------------------------------- */ - -void GridComm::grow_overlap() -{ - maxoverlap += DELTA; - overlap = (Overlap *) - memory->srealloc(overlap,maxoverlap*sizeof(Overlap),"GridComm:overlap"); -} - -/* ---------------------------------------------------------------------- - create 1d list of offsets into 3d array section (xlo:xhi,ylo:yhi,zlo:zhi) - assume 3d array is allocated as - (fullxlo:fullxhi,fullylo:fullyhi,fullzlo:fullzhi) -------------------------------------------------------------------------- */ - -int GridComm::indices(int *&list, - int xlo, int xhi, int ylo, int yhi, int zlo, int zhi) -{ - int nmax = (xhi-xlo+1) * (yhi-ylo+1) * (zhi-zlo+1); - memory->create(list,nmax,"GridComm:indices"); - if (nmax == 0) return 0; - - int nx = (fullxhi-fullxlo+1); - int ny = (fullyhi-fullylo+1); - - int n = 0; - int ix,iy,iz; - for (iz = zlo; iz <= zhi; iz++) - for (iy = ylo; iy <= yhi; iy++) - for (ix = xlo; ix <= xhi; ix++) - list[n++] = (iz-fullzlo)*ny*nx + (iy-fullylo)*nx + (ix-fullxlo); - - return nmax; -} diff --git a/src/group.cpp b/src/group.cpp index 4179797d35..55ac809d5b 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/group.h b/src/group.h index ac6a0736ac..0820c7d4b2 100644 --- a/src/group.h +++ b/src/group.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/image.cpp b/src/image.cpp index b542290e0d..1c23939781 100644 --- a/src/image.cpp +++ b/src/image.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -815,26 +815,34 @@ void Image::draw_triangle(double *x, double *y, double *z, double *surfaceColor) double s1[3], s2[3], s3[3]; double c1[3], c2[3]; + // for grid cell viz: + // using <= if test can leave single-pixel gaps between 2 tris + // using < if test fixes it + // suggested by Nathan Fabian, Nov 2022 + MathExtra::sub3 (zlocal, xlocal, s1); MathExtra::sub3 (ylocal, xlocal, s2); MathExtra::sub3 (p, xlocal, s3); MathExtra::cross3 (s1, s2, c1); MathExtra::cross3 (s1, s3, c2); - if (MathExtra::dot3 (c1, c2) <= 0) continue; + if (MathExtra::dot3 (c1, c2) < 0) continue; + //if (MathExtra::dot3 (c1, c2) <= 0) continue; MathExtra::sub3 (xlocal, ylocal, s1); MathExtra::sub3 (zlocal, ylocal, s2); MathExtra::sub3 (p, ylocal, s3); MathExtra::cross3 (s1, s2, c1); MathExtra::cross3 (s1, s3, c2); - if (MathExtra::dot3 (c1, c2) <= 0) continue; + if (MathExtra::dot3 (c1, c2) < 0) continue; + //if (MathExtra::dot3 (c1, c2) <= 0) continue; MathExtra::sub3 (ylocal, zlocal, s1); MathExtra::sub3 (xlocal, zlocal, s2); MathExtra::sub3 (p, zlocal, s3); MathExtra::cross3 (s1, s2, c1); MathExtra::cross3 (s1, s3, c2); - if (MathExtra::dot3 (c1, c2) <= 0) continue; + if (MathExtra::dot3 (c1, c2) < 0) continue; + //if (MathExtra::dot3 (c1, c2) <= 0) continue; double cNormal[3]; cNormal[0] = MathExtra::dot3(camRight, normal); @@ -981,7 +989,6 @@ void Image::compute_SSAO() double minPeak = -1; double peakLen = 0.0; - int stepsTaken = 1; while ((small > 0 && ind <= end) || (small < 0 && ind >= end)) { if (ind < 0 || ind >= (width*height)) { break; @@ -1001,7 +1008,6 @@ void Image::compute_SSAO() ind += large; err -= 1.0; } - stepsTaken ++; } if (peakLen > 0) { diff --git a/src/image.h b/src/image.h index 1d2ad272ae..51a0acc61c 100644 --- a/src/image.h +++ b/src/image.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -34,6 +34,11 @@ class Image : protected Pointers { double *boxcolor; // color to draw box outline with int background[3]; // RGB values of background + double ambientColor[3]; // light color settings (adjustable by caller) + double keyLightColor[3]; + double fillLightColor[3]; + double backLightColor[3]; + Image(class LAMMPS *, int); ~Image() override; void buffers(); @@ -80,19 +85,19 @@ class Image : protected Pointers { // constant view params double FOV; - double ambientColor[3]; + //double ambientColor[3]; double keyLightTheta; double keyLightPhi; - double keyLightColor[3]; + //double keyLightColor[3]; double fillLightTheta; double fillLightPhi; - double fillLightColor[3]; + //double fillLightColor[3]; double backLightTheta; double backLightPhi; - double backLightColor[3]; + //double backLightColor[3]; double specularHardness; double specularIntensity; diff --git a/src/imbalance.cpp b/src/imbalance.cpp index e6ecacbfa0..a741c104a1 100644 --- a/src/imbalance.cpp +++ b/src/imbalance.cpp @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/imbalance.h b/src/imbalance.h index 72037d110c..5ef19a5cfd 100644 --- a/src/imbalance.h +++ b/src/imbalance.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/imbalance_group.cpp b/src/imbalance_group.cpp index d69bc34ea7..85b465be51 100644 --- a/src/imbalance_group.cpp +++ b/src/imbalance_group.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/imbalance_group.h b/src/imbalance_group.h index d6e80cda7e..6a2e059fd7 100644 --- a/src/imbalance_group.h +++ b/src/imbalance_group.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/imbalance_neigh.cpp b/src/imbalance_neigh.cpp index 8b5dace4d2..40b7f6b249 100644 --- a/src/imbalance_neigh.cpp +++ b/src/imbalance_neigh.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -17,8 +17,6 @@ #include "atom.h" #include "comm.h" #include "error.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/imbalance_neigh.h b/src/imbalance_neigh.h index 629e0f39f9..bd289794a4 100644 --- a/src/imbalance_neigh.h +++ b/src/imbalance_neigh.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/imbalance_store.cpp b/src/imbalance_store.cpp index 598fb88bee..7b97ab3d73 100644 --- a/src/imbalance_store.cpp +++ b/src/imbalance_store.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/imbalance_store.h b/src/imbalance_store.h index 6575cf7162..1cbc1bb050 100644 --- a/src/imbalance_store.h +++ b/src/imbalance_store.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/imbalance_time.cpp b/src/imbalance_time.cpp index 8f27938a68..4e16ae3e1f 100644 --- a/src/imbalance_time.cpp +++ b/src/imbalance_time.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/imbalance_time.h b/src/imbalance_time.h index 67213ffedd..edd5fd1230 100644 --- a/src/imbalance_time.h +++ b/src/imbalance_time.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/imbalance_var.cpp b/src/imbalance_var.cpp index 4b1099c767..8e3f29780a 100644 --- a/src/imbalance_var.cpp +++ b/src/imbalance_var.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/imbalance_var.h b/src/imbalance_var.h index 6f158a80e3..c35cd9d97a 100644 --- a/src/imbalance_var.h +++ b/src/imbalance_var.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/improper.cpp b/src/improper.cpp index 68b83a69c3..b135dfbac8 100644 --- a/src/improper.cpp +++ b/src/improper.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/improper.h b/src/improper.h index 2013c7e548..59302485e2 100644 --- a/src/improper.h +++ b/src/improper.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/improper_deprecated.cpp b/src/improper_deprecated.cpp index 5012d1d2a3..84334b03da 100644 --- a/src/improper_deprecated.cpp +++ b/src/improper_deprecated.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/improper_deprecated.h b/src/improper_deprecated.h index 214d2ff67c..02252a74b3 100644 --- a/src/improper_deprecated.h +++ b/src/improper_deprecated.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/improper_hybrid.cpp b/src/improper_hybrid.cpp index 9b97c82957..9aa20d236e 100644 --- a/src/improper_hybrid.cpp +++ b/src/improper_hybrid.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -20,7 +20,6 @@ #include "memory.h" #include "neighbor.h" -#include #include using namespace LAMMPS_NS; @@ -305,6 +304,16 @@ void ImproperHybrid::coeff(int narg, char **arg) void ImproperHybrid::init_style() { + // error if sub-style is not used + + int used; + for (int istyle = 0; istyle < nstyles; ++istyle) { + used = 0; + for (int itype = 1; itype <= atom->nimpropertypes; ++itype) + if (map[itype] == istyle) used = 1; + if (used == 0) error->all(FLERR, "Improper hybrid sub-style {} is not used", keywords[istyle]); + } + for (int m = 0; m < nstyles; m++) if (styles[m]) styles[m]->init_style(); } diff --git a/src/improper_hybrid.h b/src/improper_hybrid.h index 4317b5e76c..e7cb8383d4 100644 --- a/src/improper_hybrid.h +++ b/src/improper_hybrid.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/improper_zero.cpp b/src/improper_zero.cpp index a29396d18d..3a80cbeb72 100644 --- a/src/improper_zero.cpp +++ b/src/improper_zero.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/improper_zero.h b/src/improper_zero.h index 16b6f6f316..74e55f082a 100644 --- a/src/improper_zero.h +++ b/src/improper_zero.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/info.cpp b/src/info.cpp index a93c57780e..cd1b2eddf6 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -63,7 +63,9 @@ #endif #if defined(__linux__) +#include #include +#include #endif namespace LAMMPS_NS { @@ -1185,11 +1187,10 @@ bool Info::has_accelerator_feature(const std::string &package, } if (category == "api") { #if defined(_OPENMP) - if (setting == "openmp") return true; + return setting == "openmp"; #else - if (setting == "serial") return true; + return setting == "serial"; #endif - return false; } } #endif @@ -1198,7 +1199,7 @@ bool Info::has_accelerator_feature(const std::string &package, if (category == "precision") { if (setting == "double") return true; else if (setting == "mixed") return true; - else if (setting == "single")return true; + else if (setting == "single") return true; else return false; } if (category == "api") { diff --git a/src/info.h b/src/info.h index ffe1907fae..40ec2cf23c 100644 --- a/src/info.h +++ b/src/info.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/input.cpp b/src/input.cpp index 4c88579dfc..e653704ae3 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -749,77 +749,77 @@ int Input::execute_command() { int flag = 1; - if (!strcmp(command,"clear")) clear(); - else if (!strcmp(command,"echo")) echo(); - else if (!strcmp(command,"if")) ifthenelse(); - else if (!strcmp(command,"include")) include(); - else if (!strcmp(command,"jump")) jump(); - else if (!strcmp(command,"label")) label(); - else if (!strcmp(command,"log")) log(); - else if (!strcmp(command,"next")) next_command(); - else if (!strcmp(command,"partition")) partition(); - else if (!strcmp(command,"print")) print(); - else if (!strcmp(command,"python")) python(); - else if (!strcmp(command,"quit")) quit(); - else if (!strcmp(command,"shell")) shell(); - else if (!strcmp(command,"variable")) variable_command(); + std::string mycmd = command; + if (mycmd == "clear") clear(); + else if (mycmd == "echo") echo(); + else if (mycmd == "if") ifthenelse(); + else if (mycmd == "include") include(); + else if (mycmd == "jump") jump(); + else if (mycmd == "label") label(); + else if (mycmd == "log") log(); + else if (mycmd == "next") next_command(); + else if (mycmd == "partition") partition(); + else if (mycmd == "print") print(); + else if (mycmd == "python") python(); + else if (mycmd == "quit") quit(); + else if (mycmd == "shell") shell(); + else if (mycmd == "variable") variable_command(); - else if (!strcmp(command,"angle_coeff")) angle_coeff(); - else if (!strcmp(command,"angle_style")) angle_style(); - else if (!strcmp(command,"atom_modify")) atom_modify(); - else if (!strcmp(command,"atom_style")) atom_style(); - else if (!strcmp(command,"bond_coeff")) bond_coeff(); - else if (!strcmp(command,"bond_style")) bond_style(); - else if (!strcmp(command,"bond_write")) bond_write(); - else if (!strcmp(command,"boundary")) boundary(); - else if (!strcmp(command,"box")) box(); - else if (!strcmp(command,"comm_modify")) comm_modify(); - else if (!strcmp(command,"comm_style")) comm_style(); - else if (!strcmp(command,"compute")) compute(); - else if (!strcmp(command,"compute_modify")) compute_modify(); - else if (!strcmp(command,"dielectric")) dielectric(); - else if (!strcmp(command,"dihedral_coeff")) dihedral_coeff(); - else if (!strcmp(command,"dihedral_style")) dihedral_style(); - else if (!strcmp(command,"dimension")) dimension(); - else if (!strcmp(command,"dump")) dump(); - else if (!strcmp(command,"dump_modify")) dump_modify(); - else if (!strcmp(command,"fix")) fix(); - else if (!strcmp(command,"fix_modify")) fix_modify(); - else if (!strcmp(command,"group")) group_command(); - else if (!strcmp(command,"improper_coeff")) improper_coeff(); - else if (!strcmp(command,"improper_style")) improper_style(); - else if (!strcmp(command,"kspace_modify")) kspace_modify(); - else if (!strcmp(command,"kspace_style")) kspace_style(); - else if (!strcmp(command,"labelmap")) labelmap(); - else if (!strcmp(command,"lattice")) lattice(); - else if (!strcmp(command,"mass")) mass(); - else if (!strcmp(command,"min_modify")) min_modify(); - else if (!strcmp(command,"min_style")) min_style(); - else if (!strcmp(command,"molecule")) molecule(); - else if (!strcmp(command,"neigh_modify")) neigh_modify(); - else if (!strcmp(command,"neighbor")) neighbor_command(); - else if (!strcmp(command,"newton")) newton(); - else if (!strcmp(command,"package")) package(); - else if (!strcmp(command,"pair_coeff")) pair_coeff(); - else if (!strcmp(command,"pair_modify")) pair_modify(); - else if (!strcmp(command,"pair_style")) pair_style(); - else if (!strcmp(command,"pair_write")) pair_write(); - else if (!strcmp(command,"processors")) processors(); - else if (!strcmp(command,"region")) region(); - else if (!strcmp(command,"reset_timestep")) reset_timestep(); - else if (!strcmp(command,"restart")) restart(); - else if (!strcmp(command,"run_style")) run_style(); - else if (!strcmp(command,"special_bonds")) special_bonds(); - else if (!strcmp(command,"suffix")) suffix(); - else if (!strcmp(command,"thermo")) thermo(); - else if (!strcmp(command,"thermo_modify")) thermo_modify(); - else if (!strcmp(command,"thermo_style")) thermo_style(); - else if (!strcmp(command,"timestep")) timestep(); - else if (!strcmp(command,"timer")) timer_command(); - else if (!strcmp(command,"uncompute")) uncompute(); - else if (!strcmp(command,"undump")) undump(); - else if (!strcmp(command,"unfix")) unfix(); - else if (!strcmp(command,"units")) units(); + else if (mycmd == "angle_coeff") angle_coeff(); + else if (mycmd == "angle_style") angle_style(); + else if (mycmd == "atom_modify") atom_modify(); + else if (mycmd == "atom_style") atom_style(); + else if (mycmd == "bond_coeff") bond_coeff(); + else if (mycmd == "bond_style") bond_style(); + else if (mycmd == "bond_write") bond_write(); + else if (mycmd == "boundary") boundary(); + else if (mycmd == "comm_modify") comm_modify(); + else if (mycmd == "comm_style") comm_style(); + else if (mycmd == "compute") compute(); + else if (mycmd == "compute_modify") compute_modify(); + else if (mycmd == "dielectric") dielectric(); + else if (mycmd == "dihedral_coeff") dihedral_coeff(); + else if (mycmd == "dihedral_style") dihedral_style(); + else if (mycmd == "dimension") dimension(); + else if (mycmd == "dump") dump(); + else if (mycmd == "dump_modify") dump_modify(); + else if (mycmd == "fix") fix(); + else if (mycmd == "fix_modify") fix_modify(); + else if (mycmd == "group") group_command(); + else if (mycmd == "improper_coeff") improper_coeff(); + else if (mycmd == "improper_style") improper_style(); + else if (mycmd == "kspace_modify") kspace_modify(); + else if (mycmd == "kspace_style") kspace_style(); + else if (mycmd == "labelmap") labelmap(); + else if (mycmd == "lattice") lattice(); + else if (mycmd == "mass") mass(); + else if (mycmd == "min_modify") min_modify(); + else if (mycmd == "min_style") min_style(); + else if (mycmd == "molecule") molecule(); + else if (mycmd == "neigh_modify") neigh_modify(); + else if (mycmd == "neighbor") neighbor_command(); + else if (mycmd == "newton") newton(); + else if (mycmd == "package") package(); + else if (mycmd == "pair_coeff") pair_coeff(); + else if (mycmd == "pair_modify") pair_modify(); + else if (mycmd == "pair_style") pair_style(); + else if (mycmd == "pair_write") pair_write(); + else if (mycmd == "processors") processors(); + else if (mycmd == "region") region(); + else if (mycmd == "reset_timestep") reset_timestep(); + else if (mycmd == "restart") restart(); + else if (mycmd == "run_style") run_style(); + else if (mycmd == "special_bonds") special_bonds(); + else if (mycmd == "suffix") suffix(); + else if (mycmd == "thermo") thermo(); + else if (mycmd == "thermo_modify") thermo_modify(); + else if (mycmd == "thermo_style") thermo_style(); + else if (mycmd == "timestep") timestep(); + else if (mycmd == "timer") timer_command(); + else if (mycmd == "uncompute") uncompute(); + else if (mycmd == "undump") undump(); + else if (mycmd == "unfix") unfix(); + else if (mycmd == "units") units(); else flag = 0; @@ -827,12 +827,17 @@ int Input::execute_command() if (flag) return 0; + // process "meta-commands", i.e. commands that may have sub-commands + // they return 1 if there was a match and 0 if not + + if (mycmd == "reset_atoms") flag = meta(mycmd); + if (flag) return 0; + // invoke commands added via style_command.h // try suffixed version first - std::string mycmd = command; - if (lmp->suffix_enable && lmp->suffix) { - mycmd = command + std::string("/") + lmp->suffix; + if (lmp->suffix_enable && lmp->non_pair_suffix()) { + mycmd = command + std::string("/") + lmp->non_pair_suffix(); if (command_map->find(mycmd) == command_map->end()) { if (lmp->suffix2) { mycmd = command + std::string("/") + lmp->suffix2; @@ -1411,15 +1416,6 @@ void Input::boundary() /* ---------------------------------------------------------------------- */ -void Input::box() -{ - if (domain->box_exist) - error->all(FLERR,"Box command after simulation box is defined"); - domain->set_box(narg,arg); -} - -/* ---------------------------------------------------------------------- */ - void Input::comm_modify() { comm->modify_params(narg,arg); @@ -1429,21 +1425,19 @@ void Input::comm_modify() void Input::comm_style() { - if (narg < 1) error->all(FLERR,"Illegal comm_style command"); + if (narg < 1) utils::missing_cmd_args(FLERR, "comm_style", error); if (strcmp(arg[0],"brick") == 0) { - if (comm->style == 0) return; + if (comm->style == Comm::BRICK) return; Comm *oldcomm = comm; comm = new CommBrick(lmp,oldcomm); delete oldcomm; } else if (strcmp(arg[0],"tiled") == 0) { - if (comm->style == 1) return; + if (comm->style == Comm::TILED) return; Comm *oldcomm = comm; - if (lmp->kokkos) comm = new CommTiledKokkos(lmp,oldcomm); else comm = new CommTiled(lmp,oldcomm); - delete oldcomm; - } else error->all(FLERR,"Illegal comm_style command"); + } else error->all(FLERR,"Unknown comm_style argument: {}", arg[0]); } /* ---------------------------------------------------------------------- */ @@ -1499,7 +1493,7 @@ void Input::dihedral_style() void Input::dimension() { - if (narg != 1) error->all(FLERR,"Illegal dimension command: expected 1 argument but found {}", narg); + if (narg != 1) error->all(FLERR, "Dimension command expects exactly 1 argument"); if (domain->box_exist) error->all(FLERR,"Dimension command after simulation box is defined"); domain->dimension = utils::inumeric(FLERR,arg[0],false,lmp); @@ -1509,8 +1503,7 @@ void Input::dimension() // must reset default extra_dof of all computes // since some were created before dimension command is encountered - for (int i = 0; i < modify->ncompute; i++) - modify->compute[i]->reset_extra_dof(); + for (auto &c : modify->get_compute_list()) c->reset_extra_dof(); } /* ---------------------------------------------------------------------- */ @@ -1729,7 +1722,7 @@ void Input::pair_coeff() if (force->pair == nullptr) error->all(FLERR,"Pair_coeff command without a pair style"); if (narg < 2) utils::missing_cmd_args(FLERR,"pair_coeff", error); if (force->pair->one_coeff && ((strcmp(arg[0],"*") != 0) || (strcmp(arg[1],"*") != 0))) - error->all(FLERR,"Pair_coeff must start with * * for this pair style"); + error->all(FLERR,"Pair_coeff must start with * * for pair style {}", force->pair_style); char *newarg0 = utils::expand_type(FLERR, arg[0], Atom::ATOM, lmp); if (newarg0) arg[0] = newarg0; @@ -1776,10 +1769,7 @@ void Input::pair_style() int match = 0; if (style == force->pair_style) match = 1; if (!match && lmp->suffix_enable) { - if (lmp->suffixp) - if (style + "/" + lmp->suffixp == force->pair_style) match = 1; - - if (lmp->suffix && !lmp->suffixp) + if (lmp->suffix) if (style + "/" + lmp->suffix == force->pair_style) match = 1; if (lmp->suffix2) @@ -1992,3 +1982,21 @@ void Input::units() error->all(FLERR,"Units command after simulation box is defined"); update->set_units(arg[0]); } + +/* ---------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + function for meta commands +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- */ + +int Input::meta(const std::string &prefix) +{ + auto mycmd = fmt::format("{}_{}", utils::uppercase(prefix), utils::uppercase(arg[0])); + if (command_map->find(mycmd) != command_map->end()) { + CommandCreator &command_creator = (*command_map)[mycmd]; + Command *cmd = command_creator(lmp); + cmd->command(narg-1,arg+1); + delete cmd; + return 1; + } else return 0; +} diff --git a/src/input.h b/src/input.h index 5bd531ca0a..5a29484cbc 100644 --- a/src/input.h +++ b/src/input.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -70,6 +70,8 @@ class Input : protected Pointers { void reallocate(char *&, int &, int); // reallocate a char string int execute_command(); // execute a single command + int meta(const std::string &); // process meta-commands + void clear(); // input script commands void echo(); void ifthenelse(); @@ -94,7 +96,6 @@ class Input : protected Pointers { void bond_style(); void bond_write(); void boundary(); - void box(); void comm_modify(); void comm_style(); void compute(); @@ -143,7 +144,5 @@ class Input : protected Pointers { void unfix(); void units(); }; - } // namespace LAMMPS_NS - #endif diff --git a/src/integrate.cpp b/src/integrate.cpp index 256291ed3b..98ea7a09f9 100644 --- a/src/integrate.cpp +++ b/src/integrate.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/integrate.h b/src/integrate.h index 6905b6ddcc..85d4bec65b 100644 --- a/src/integrate.h +++ b/src/integrate.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/irregular.cpp b/src/irregular.cpp index 3d4719aa02..8a18098c14 100644 --- a/src/irregular.cpp +++ b/src/irregular.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/irregular.h b/src/irregular.h index c88471017f..2e6186d0a9 100644 --- a/src/irregular.h +++ b/src/irregular.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/kspace.cpp b/src/kspace.cpp index 99eb4c1ac9..583df478e7 100644 --- a/src/kspace.cpp +++ b/src/kspace.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -429,31 +429,6 @@ void KSpace::lamda2xvector(double *lamda, double *v) v[2] = h[2]*lamda[2]; } -/* ---------------------------------------------------------------------- - convert a sphere in box coords to an ellipsoid in lamda (0-1) - coords and return the tight (axis-aligned) bounding box, does not - preserve vector magnitude see: - http://www.loria.fr/~shornus/ellipsoid-bbox.html (no longer online) and - https://yiningkarlli.blogspot.com/2013/02/bounding-boxes-for-ellipsoidsfigure.html -------------------------------------------------------------------------- */ - -void KSpace::kspacebbox(double r, double *b) -{ - double *h = domain->h; - double lx,ly,lz,xy,xz,yz; - lx = h[0]; - ly = h[1]; - lz = h[2]; - yz = h[3]; - xz = h[4]; - xy = h[5]; - - b[0] = r*sqrt(ly*ly*lz*lz + ly*ly*xz*xz - 2.0*ly*xy*xz*yz + lz*lz*xy*xy + - xy*xy*yz*yz)/(lx*ly*lz); - b[1] = r*sqrt(lz*lz + yz*yz)/(ly*lz); - b[2] = r/lz; -} - /* ---------------------------------------------------------------------- modify parameters of the KSpace style ------------------------------------------------------------------------- */ diff --git a/src/kspace.h b/src/kspace.h index bc85436eb9..61ab15c1d9 100644 --- a/src/kspace.h +++ b/src/kspace.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -113,7 +113,6 @@ class KSpace : protected Pointers { void x2lamdaT(double *, double *); void lamda2xT(double *, double *); void lamda2xvector(double *, double *); - void kspacebbox(double, double *); // public so can be called by commands that change charge @@ -124,7 +123,7 @@ class KSpace : protected Pointers { virtual void settings(int, char **){}; virtual void init() = 0; virtual void setup() = 0; - virtual void setup_grid(){}; + virtual void reset_grid(){}; virtual void compute(int, int) = 0; virtual void compute_group_group(int, int, int){}; diff --git a/src/kspace_deprecated.cpp b/src/kspace_deprecated.cpp index 62605542d8..5db642e945 100644 --- a/src/kspace_deprecated.cpp +++ b/src/kspace_deprecated.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/kspace_deprecated.h b/src/kspace_deprecated.h index 9c140af808..0165dc6da8 100644 --- a/src/kspace_deprecated.h +++ b/src/kspace_deprecated.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/label_map.cpp b/src/label_map.cpp index 392a9b7ddd..67b1ae480d 100644 --- a/src/label_map.cpp +++ b/src/label_map.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -17,7 +17,6 @@ #include "comm.h" #include "error.h" #include "force.h" -#include "memory.h" #include diff --git a/src/label_map.h b/src/label_map.h index 9354306c56..a96fcc255c 100644 --- a/src/label_map.h +++ b/src/label_map.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/lammps.cpp b/src/lammps.cpp index 83f00ecefd..cc32578f22 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -50,6 +50,7 @@ #include "timer.h" #include "universe.h" #include "update.h" +#include "variable.h" #include "version.h" #if defined(LMP_PLUGIN) @@ -129,6 +130,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) : version = (const char *) LAMMPS_VERSION; num_ver = utils::date2num(version); + restart_ver = -1; external_comm = 0; mdicomm = nullptr; @@ -199,8 +201,9 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) : int helpflag = 0; int nonbufflag = 0; - suffix = suffix2 = suffixp = nullptr; + suffix = suffix2 = nullptr; suffix_enable = 0; + pair_only_flag = 0; if (arg) exename = arg[0]; else exename = nullptr; packargs = nullptr; @@ -416,8 +419,8 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) : strcmp(arg[iarg],"-sf") == 0) { if (iarg+2 > narg) error->universe_all(FLERR,"Invalid command-line argument"); - delete [] suffix; - delete [] suffix2; + delete[] suffix; + delete[] suffix2; suffix = suffix2 = nullptr; suffix_enable = 1; // hybrid option to set fall-back for suffix2 @@ -520,10 +523,11 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) : error->one(FLERR,"Cannot open input script {}: {}", arg[inflag], utils::getsyserror()); if (!helpflag) utils::logmesg(this,fmt::format("LAMMPS ({}{})\n",version,UPDATE_STRING)); - // warn against using I/O redirection in parallel runs + + // warn against using I/O redirection in parallel runs if ((inflag == 0) && (universe->nprocs > 1)) error->warning(FLERR, "Using I/O redirection is unreliable with parallel runs. " - "Better use -in switch to read input file."); + "Better to use the -in switch to read input files."); utils::flush_buffers(this); } @@ -773,9 +777,8 @@ LAMMPS::~LAMMPS() delete python; delete kokkos; - delete [] suffix; - delete [] suffix2; - delete [] suffixp; + delete[] suffix; + delete[] suffix2; // free the MPI comm created by -mpicolor cmdline arg processed in constructor // it was passed to universe as if original universe world @@ -886,30 +889,27 @@ void LAMMPS::post_create() } } - // either suffix or suffixp will be set if suffix_enable = 1 // check that KOKKOS package classes were instantiated // check that GPU, INTEL, OPENMP fixes were compiled with LAMMPS // do not re-issue package command if already issued if (suffix_enable) { - const char *mysuffix = suffix; - if (suffixp) mysuffix = suffixp; - if (strcmp(mysuffix,"gpu") == 0 && !modify->check_package("GPU")) + if (strcmp(suffix,"gpu") == 0 && !modify->check_package("GPU")) error->all(FLERR,"Using suffix gpu without GPU package installed"); - if (strcmp(mysuffix,"intel") == 0 && !modify->check_package("INTEL")) + if (strcmp(suffix,"intel") == 0 && !modify->check_package("INTEL")) error->all(FLERR,"Using suffix intel without INTEL package installed"); - if (strcmp(mysuffix,"kk") == 0 && + if (strcmp(suffix,"kk") == 0 && (kokkos == nullptr || kokkos->kokkos_exists == 0)) error->all(FLERR,"Using suffix kk without KOKKOS package enabled"); - if (strcmp(mysuffix,"omp") == 0 && !modify->check_package("OMP")) + if (strcmp(suffix,"omp") == 0 && !modify->check_package("OMP")) error->all(FLERR,"Using suffix omp without OPENMP package installed"); - if (strcmp(mysuffix,"gpu") == 0 && !(package_issued & Suffix::GPU)) + if (strcmp(suffix,"gpu") == 0 && !(package_issued & Suffix::GPU)) input->one("package gpu 0"); - if (strcmp(mysuffix,"intel") == 0 && !(package_issued & Suffix::INTEL)) + if (strcmp(suffix,"intel") == 0 && !(package_issued & Suffix::INTEL)) input->one("package intel 1"); - if (strcmp(mysuffix,"omp") == 0 && !(package_issued & Suffix::OMP)) + if (strcmp(suffix,"omp") == 0 && !(package_issued & Suffix::OMP)) input->one("package omp 0"); if (suffix2) { @@ -970,6 +970,9 @@ void LAMMPS::destroy() delete output; output = nullptr; + // undefine atomfile variables because they use a fix for backing storage + input->variable->purge_atomfile(); + delete modify; // modify must come after output, force, update // since they delete fixes modify = nullptr; @@ -991,6 +994,8 @@ void LAMMPS::destroy() delete python; python = nullptr; + + restart_ver = -1; // reset last restart version id } /* ---------------------------------------------------------------------- @@ -1151,6 +1156,26 @@ const char *LAMMPS::match_style(const char *style, const char *name) return nullptr; } +/** \brief Return suffix for non-pair styles depending on pair_only_flag + * + * \return suffix or null pointer + */ +const char *LAMMPS::non_pair_suffix() const +{ + const char *mysuffix; + if (pair_only_flag) { +#ifdef LMP_KOKKOS_GPU + if (utils::strmatch(suffix,"^kk")) mysuffix = "kk/host"; + else mysuffix = nullptr; +#else + mysuffix = nullptr; +#endif + } else { + mysuffix = suffix; + } + return mysuffix; +} + /* ---------------------------------------------------------------------- help message for command line options and styles present in executable ------------------------------------------------------------------------- */ @@ -1206,6 +1231,7 @@ void _noopt LAMMPS::help() "-mpicolor color : which exe in a multi-exe mpirun cmd (-m)\n" "-cite : select citation reminder style (-c)\n" "-nocite : disable citation reminder (-nc)\n" + "-nonbuf : disable screen/logfile buffering (-nb)\n" "-package style ... : invoke package command (-pk)\n" "-partition size1 size2 ... : assign partition sizes (-p)\n" "-plog basename : basename for partition logs (-pl)\n" diff --git a/src/lammps.h b/src/lammps.h index 811d313d91..03b019ed43 100644 --- a/src/lammps.h +++ b/src/lammps.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -49,6 +49,8 @@ class LAMMPS { // that is constructed so that will be greater // for newer versions in numeric or string // value comparisons + int restart_ver; // -1 or numeric version id of LAMMPS version in restart + // file, in case LAMMPS was initialized from a restart // MPI_Comm world; // MPI communicator FILE *infile; // infile @@ -58,9 +60,11 @@ class LAMMPS { double initclock; // wall clock at instantiation int skiprunflag; // 1 inserts timer command to skip run and minimize loops - char *suffix, *suffix2, *suffixp; // suffixes to add to input script style names - int suffix_enable; // 1 if suffixes are enabled, 0 if disabled - char *exename; // pointer to argv[0] + char *suffix, *suffix2; // suffixes to add to input script style names + int suffix_enable; // 1 if suffixes are enabled, 0 if disabled + int pair_only_flag; // 1 if only force field pair styles are accelerated, 0 if all + const char *non_pair_suffix() const; + char *exename; // pointer to argv[0] char ***packargs; // arguments for cmdline package commands int num_package; // number of cmdline package commands diff --git a/src/lammpsplugin.h b/src/lammpsplugin.h index 5df0172763..2c1dedf3fb 100644 --- a/src/lammpsplugin.h +++ b/src/lammpsplugin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/lattice.cpp b/src/lattice.cpp index 65864f66d8..edb482cfac 100644 --- a/src/lattice.cpp +++ b/src/lattice.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -53,14 +53,7 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) if (style == NONE) { if (narg != 2) error->all(FLERR,"Illegal lattice command: expected 2 arguments but found {}", narg); - // Domain creates a default lattice of style "none" - // before Force class is instantiated, just use atof() in that case - - if (force) - xlattice = ylattice = zlattice = utils::numeric(FLERR,arg[1],false,lmp); - else - xlattice = ylattice = zlattice = atof(arg[1]); - + xlattice = ylattice = zlattice = utils::numeric(FLERR,arg[1],false,lmp); if (xlattice <= 0.0) error->all(FLERR, "Invalid lattice none argument: {}", arg[1]); return; } diff --git a/src/lattice.h b/src/lattice.h index 67b9ce61ea..5b98f580b7 100644 --- a/src/lattice.h +++ b/src/lattice.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/library.cpp b/src/library.cpp index 03f6c0e211..2c16cc6615 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -435,7 +435,7 @@ of constants from :cpp:enum:`_LMP_ERROR_CONST`. If the value does not match any valid combination of constants a warning is printed and the function returns. -.. versionadded:: TBD +.. versionadded:: 3Nov2022 \endverbatim * @@ -685,7 +685,7 @@ void lammps_commands_string(void *handle, const char *str) \verbatim embed:rst This number may be very large when running large simulations across -multiple processors. Depending on compile time choices, LAMMPS may be +multiple processes. Depending on compile time choices, LAMMPS may be using either 32-bit or a 64-bit integer to store this number. For portability this function returns thus a double precision floating point number, which can represent up to a 53-bit signed @@ -953,6 +953,7 @@ not recognized, the function returns -1. The integer sizes functions may be called without a valid LAMMPS object handle (it is ignored). * :ref:`Integer sizes ` +* :ref:`Image masks ` * :ref:`System status ` * :ref:`System sizes ` * :ref:`Atom style flags ` @@ -977,6 +978,28 @@ be called without a valid LAMMPS object handle (it is ignored). - size of the ``imageint`` integer type, 4 or 8 bytes. Set at :ref:`compile time `. +.. _extract_image_masks: + +**Image masks** + +These settings are related to how LAMMPS stores and interprets periodic images. The values are used +internally by the :doc:`Fortran interface ` and are not likely to be useful to users. + +.. list-table:: + :header-rows: 1 + :widths: auto + + * - Keyword + - Description / Return value + * - IMGMASK + - Bit-mask used to convert image flags to a single integer + * - IMGMAX + - Maximum allowed image number for a particular atom + * - IMGBITS + - Bits used in image counts + * - IMG2BITS + - Second bitmask used in image counts + .. _extract_system_status: **System status** @@ -992,8 +1015,17 @@ be called without a valid LAMMPS object handle (it is ignored). * - box_exist - 1 if the simulation box is defined, 0 if not. See :doc:`create_box`. + * - kokkos_active + - 1 if the KOKKOS package is compiled in **and** activated, 0 if not. + See :doc:`Speed_kokkos`. + * - kokkos_nthreads + - Number of Kokkos threads per MPI process, 0 if Kokkos is not active. + See :doc:`Speed_kokkos`. + * - kokkos_ngpus + - Number of Kokkos gpus per physical node, 0 if Kokkos is not active or no GPU support. + See :doc:`Speed_kokkos`. * - nthreads - - Number of requested OpenMP threads for LAMMPS' execution + - Number of requested OpenMP threads per MPI process for LAMMPS' execution * - newton_bond - 1 if Newton's 3rd law is applied to bonded interactions, 0 if not. * - newton_pair @@ -1096,8 +1128,16 @@ int lammps_extract_setting(void *handle, const char *keyword) if (strcmp(keyword,"tagint") == 0) return sizeof(tagint); if (strcmp(keyword,"imageint") == 0) return sizeof(imageint); + if (strcmp(keyword,"IMGMASK") == 0) return IMGMASK; + if (strcmp(keyword,"IMGBITS") == 0) return IMGBITS; + if (strcmp(keyword,"IMG2BITS") == 0) return IMG2BITS; + if (strcmp(keyword,"IMGMAX") == 0) return IMGMAX; + if (strcmp(keyword,"dimension") == 0) return lmp->domain->dimension; if (strcmp(keyword,"box_exist") == 0) return lmp->domain->box_exist; + if (strcmp(keyword,"kokkos_active") == 0) return (lmp->kokkos) ? 1 : 0; + if (strcmp(keyword,"kokkos_nthreads") == 0) return (lmp->kokkos) ? lmp->kokkos->nthreads : 0; + if (strcmp(keyword,"kokkos_ngpus") == 0) return (lmp->kokkos) ? lmp->kokkos->ngpus : 0; if (strcmp(keyword,"newton_bond") == 0) return lmp->force->newton_bond; if (strcmp(keyword,"newton_pair") == 0) return lmp->force->newton_pair; if (strcmp(keyword,"triclinic") == 0) return lmp->domain->triclinic; @@ -2160,7 +2200,7 @@ with the specified name. See :cpp:enum:`_LMP_VAR_CONST` for valid values. Callers of :cpp:func:`lammps_extract_variable` can use this information to decide how to cast the ``void *`` pointer and access the data. -.. versionadded:: TBD +.. versionadded:: 3Nov2022 \endverbatim * @@ -2223,7 +2263,7 @@ int lammps_set_variable(void *handle, char *name, char *str) // Library functions for scatter/gather operations of data // ---------------------------------------------------------------------- -/** Gather the named atom-based entity for all atoms across all processors, +/** Gather the named atom-based entity for all atoms across all processes, * in order. * \verbatim embed:rst @@ -2242,6 +2282,8 @@ x[0][2], x[1][0], x[1][1], x[1][2], x[2][0], :math:`\dots`); *natoms*), as queried by :cpp:func:`lammps_get_natoms`, :cpp:func:`lammps_extract_global`, or :cpp:func:`lammps_extract_setting`. +This function is not compatible with ``-DLAMMPS_BIGBIG``. + \endverbatim * * \param handle pointer to a previously created LAMMPS instance @@ -2261,7 +2303,8 @@ x[0][2], x[1][0], x[1][1], x[1][2], x[2][0], :math:`\dots`); Allreduce to sum vector into data across all procs ------------------------------------------------------------------------- */ -void lammps_gather_atoms(void *handle, char *name, int type, int count, void *data) +void lammps_gather_atoms(void *handle, const char *name, int type, int count, + void *data) { auto lmp = (LAMMPS *) handle; @@ -2375,7 +2418,7 @@ void lammps_gather_atoms(void *handle, char *name, int type, int count, void *da END_CAPTURE } -/** Gather the named atom-based entity for all atoms across all processors, +/** Gather the named atom-based entity for all atoms across all processes, * unordered. * \verbatim embed:rst @@ -2392,12 +2435,14 @@ of atoms, use :cpp:func:`lammps_gather_atoms_subset`. The *data* array will be in groups of *count* values, with *natoms* groups total, but not in order by atom ID (e.g., if *name* is *x* and *count* -is 3, then *data* might be something like = x[10][0], x[10][1], x[10][2], +is 3, then *data* might be something like x[10][0], x[10][1], x[10][2], x[2][0], x[2][1], x[2][2], x[4][0], :math:`\dots`); *data* must be pre-allocated by the caller to length (*count* :math:`\times` *natoms*), as queried by :cpp:func:`lammps_get_natoms`, :cpp:func:`lammps_extract_global`, or :cpp:func:`lammps_extract_setting`. +This function is not compatible with ``-DLAMMPS_BIGBIG``. + \endverbatim * * \param handle: pointer to a previously created LAMMPS instance @@ -2416,7 +2461,8 @@ queried by :cpp:func:`lammps_get_natoms`, Allgather Nlocal atoms from each proc into data ------------------------------------------------------------------------- */ -void lammps_gather_atoms_concat(void *handle, char *name, int type, int count, void *data) +void lammps_gather_atoms_concat(void *handle, const char *name, int type, + int count, void *data) { auto lmp = (LAMMPS *) handle; @@ -2559,6 +2605,8 @@ x[100][2], x[57][0], x[57][1], x[57][2], x[210][0], :math:`\dots`); *data* must be pre-allocated by the caller to length (*count* :math:`\times` *ndata*). +This function is not compatible with ``-DLAMMPS_BIGBIG``. + \endverbatim * * \param handle: pointer to a previously created LAMMPS instance @@ -2581,8 +2629,8 @@ x[100][2], x[57][0], x[57][1], x[57][2], x[210][0], :math:`\dots`); Allreduce to sum vector into data across all procs ------------------------------------------------------------------------- */ -void lammps_gather_atoms_subset(void *handle, char *name, int type, int count, - int ndata, int *ids, void *data) +void lammps_gather_atoms_subset(void *handle, const char *name, int type, + int count, int ndata, int *ids, void *data) { auto lmp = (LAMMPS *) handle; @@ -2705,20 +2753,22 @@ void lammps_gather_atoms_subset(void *handle, char *name, int type, int count, END_CAPTURE } -/** Scatter the named atom-based entities in *data* to all processors. +/** Scatter the named atom-based entities in *data* to all processes. * \verbatim embed:rst This subroutine takes data stored in a one-dimensional array supplied by the -user and scatters them to all atoms on all processors. The data must be +user and scatters them to all atoms on all processes. The data must be ordered by atom ID, with the requirement that the IDs be consecutive. Use :cpp:func:`lammps_scatter_atoms_subset` to scatter data for some (or all) atoms, unordered. The *data* array needs to be ordered in groups of *count* values, sorted by atom ID (e.g., if *name* is *x* and *count* = 3, then -*data* = x[0][0], x[0][1], x[0][2], x[1][0], x[1][1], x[1][2], x[2][0], -:math:`\dots`); *data* must be of length (*count* :math:`\times` *natoms*). +*data* = {x[0][0], x[0][1], x[0][2], x[1][0], x[1][1], x[1][2], x[2][0], +:math:`\dots`}); *data* must be of length (*count* :math:`\times` *natoms*). + +This function is not compatible with ``-DLAMMPS_BIGBIG``. \endverbatim * @@ -2728,7 +2778,7 @@ atom ID (e.g., if *name* is *x* and *count* = 3, then * \param count number of per-atom values (e.g., 1 for *type* or *charge*, * 3 for *x* or *f*); use *count* = 3 with *image* if you have * a single image flag packed into (*x*,*y*,*z*) components. - * \param data per-atom values packed in a 1-dimensional array of length + * \param data per-atom values packed in a one-dimensional array of length * *natoms* \* *count*. * */ @@ -2738,7 +2788,8 @@ atom ID (e.g., if *name* is *x* and *count* = 3, then loop over Natoms, if I own atom ID, set its values from data ------------------------------------------------------------------------- */ -void lammps_scatter_atoms(void *handle, char *name, int type, int count, void *data) +void lammps_scatter_atoms(void *handle, const char *name, int type, int count, + void *data) { auto lmp = (LAMMPS *) handle; @@ -2839,12 +2890,12 @@ void lammps_scatter_atoms(void *handle, char *name, int type, int count, void *d } /** Scatter the named atom-based entities in *data* from a subset of atoms - * to all processors. + * to all processes. * \verbatim embed:rst This subroutine takes data stored in a one-dimensional array supplied by the -user and scatters them to a subset of atoms on all processors. The array +user and scatters them to a subset of atoms on all processes. The array *data* contains data associated with atom IDs, but there is no requirement that the IDs be consecutive, as they are provided in a separate array. Use :cpp:func:`lammps_scatter_atoms` to scatter data for all atoms, in order. @@ -2855,6 +2906,8 @@ to be the array {x[1][0], x[1][1], x[1][2], x[100][0], x[100][1], x[100][2], x[57][0], x[57][1], x[57][2]}, then *count* = 3, *ndata* = 3, and *ids* would be {1, 100, 57}. +This function is not compatible with ``-DLAMMPS_BIGBIG``. + \endverbatim * * \param handle: pointer to a previously created LAMMPS instance @@ -2888,8 +2941,8 @@ be {1, 100, 57}. loop over Ndata, if I own atom ID, set its values from data ------------------------------------------------------------------------- */ -void lammps_scatter_atoms_subset(void *handle, char *name, int type, int count, - int ndata, int *ids, void *data) +void lammps_scatter_atoms_subset(void *handle, const char *name, int type, + int count, int ndata, int *ids, void *data) { auto lmp = (LAMMPS *) handle; @@ -3020,10 +3073,11 @@ Below is a brief C code demonstrating accessing this collected bond information. .. code-block:: c + #include "library.h" + + #include #include #include - #include - #include "library.h" int main(int argc, char **argv) { @@ -3105,6 +3159,43 @@ void lammps_gather_bonds(void *handle, void *data) END_CAPTURE } +/** Gather the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entities + * from all processes, in order by atom ID. + * +\verbatim embed:rst + +This subroutine gathers data from all processes and stores them in a one-dimensional array +allocated by the user. The array *data* will be ordered by atom ID, which requires consecutive IDs +(1 to *natoms*\ ). If you need a similar array but for non-consecutive atom IDs, see +:cpp:func:`lammps_gather_concat`; for a similar array but for a subset of atoms, see +:cpp:func:`lammps_gather_subset`. + +The *data* array will be ordered in groups of *count* values, sorted by atom ID (e.g., if *name* is +*x*, then *data* is {x[0][0], x[0][1], x[0][2], x[1][0], x[1][1], x[1][2], x[2][0], +:math:`\dots`}); *data* must be pre-allocated by the caller to the correct length +(*count*\ :math:`{}\times{}`\ *natoms*), as queried by :cpp:func:`lammps_get_natoms`, +:cpp:func:`lammps_extract_global`, or :cpp:func:`lammps_extract_setting`. + +This function will return an error if fix or compute data are requested and the fix or compute ID +given does not have per-atom data. + +This function is not compatible with ``-DLAMMPS_BIGBIG``. + +\endverbatim + * + * \param handle pointer to a previously created LAMMPS instance + * \param name desired quantity (e.g., "x" or "f" for atom properties, "f_id" for per-atom fix + * data, "c_id" for per-atom compute data, "d_name" or "i_name" for fix + * property/atom vectors with *count* = 1, "d2_name" or "i2_name" for fix + * property/atom vectors with *count* > 1) + * \param type 0 for ``int`` values, 1 for ``double`` values + * \param count number of per-atom values (e.g., 1 for *type* or *charge*, 3 for *x* or *f*); + * use *count* = 3 with *image* if you want the image flags unpacked into + * (*x*,*y*,*z*) components. + * \param data per-atom values packed into a one-dimensional array of length + * *natoms* \* *count*. + * + */ /* ---------------------------------------------------------------------- Contributing author: Thomas Swinburne (CNRS & CINaM, Marseille, France) gather the named atom-based entity for all atoms @@ -3131,7 +3222,7 @@ void lammps_gather_bonds(void *handle, void *data) Allreduce to sum vector into data across all procs ------------------------------------------------------------------------- */ -void lammps_gather(void *handle, char *name, int type, int count, void *data) +void lammps_gather(void *handle, const char *name, int type, int count, void *data) { auto lmp = (LAMMPS *) handle; @@ -3340,6 +3431,44 @@ void lammps_gather(void *handle, char *name, int type, int count, void *data) END_CAPTURE } +/** Gather the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entities + * from all processes, unordered. + * +\verbatim embed:rst + +This subroutine gathers data for all atoms and stores them in a one-dimensional array allocated by +the user. The data will be a concatenation of chunks from each processor's owned atoms, in +whatever order the atoms are in on each processor. This process has no requirement that the atom +IDs be consecutive. If you need the ID of each atom, you can do another call to either +:cpp:func:`lammps_gather_atoms_concat` or :cpp:func:`lammps_gather_concat` with *name* set to +``id``. If you have consecutive IDs and want the data to be in order, use +:cpp:func:`lammps_gather`; for a similar array but for a subset of atoms, use +:cpp:func:`lammps_gather_subset`. + +The *data* array will be in groups of *count* values, with *natoms* groups total, but not in order +by atom ID (e.g., if *name* is *x* and *count* is 3, then *data* might be something like +{x[10][0], x[10][1], x[10][2], x[2][0], x[2][1], x[2][2], x[4][0], :math:`\dots`}); *data* must be +pre-allocated by the caller to length (*count* :math:`\times` *natoms*), as queried by +:cpp:func:`lammps_get_natoms`, :cpp:func:`lammps_extract_global`, or +:cpp:func:`lammps_extract_setting`. + +This function is not compatible with ``-DLAMMPS_BIGBIG``. + +\endverbatim + * + * \param handle: pointer to a previously created LAMMPS instance + * \param name: desired quantity (e.g., "x" or "f" for atom properties, "f_id" for per-atom fix + * data, "c_id" for per-atom compute data, "d_name" or "i_name" for fix + * property/atom vectors with count = 1, "d2_name" or "i2_name" for fix + * property/atom vectors with count > 1) + * \param type: 0 for ``int`` values, 1 for ``double`` values + * \param count: number of per-atom values (e.g., 1 for *type* or *charge*, 3 for *x* or *f*); + * use *count* = 3 with *image* if you want the image flags unpacked into + * (*x*,*y*,*z*) components. + * \param data: per-atom values packed into a one-dimensional array of length + * *natoms* \* *count*. + * + */ /* ---------------------------------------------------------------------- Contributing author: Thomas Swinburne (CNRS & CINaM, Marseille, France) gather the named atom-based entity for all atoms @@ -3366,7 +3495,8 @@ void lammps_gather(void *handle, char *name, int type, int count, void *data) Allreduce to sum vector into data across all procs ------------------------------------------------------------------------- */ -void lammps_gather_concat(void *handle, char *name, int type, int count, void *data) +void lammps_gather_concat(void *handle, const char *name, int type, int count, + void *data) { auto lmp = (LAMMPS *) handle; @@ -3592,6 +3722,41 @@ void lammps_gather_concat(void *handle, char *name, int type, int count, void *d END_CAPTURE } +/** Gather the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entities + * from all processes for a subset of atoms. + * +\verbatim embed:rst + +This subroutine gathers data for the requested atom IDs and stores them in a one-dimensional array +allocated by the user. The data will be ordered by atom ID, but there is no requirement that the +IDs be consecutive. If you wish to return a similar array for *all* the atoms, use +:cpp:func:`lammps_gather` or :cpp:func:`lammps_gather_concat`. + +The *data* array will be in groups of *count* values, sorted by atom ID in the same order as the +array *ids* (e.g., if *name* is *x*, *count* = 3, and *ids* is {100, 57, 210}, then *data* might +look like {x[100][0], x[100][1], x[100][2], x[57][0], x[57][1], x[57][2], x[210][0], +:math:`\dots`}); *ids* must be provided by the user with length *ndata*, and *data* must be +pre-allocated by the caller to length (*count*\ :math:`{}\times{}`\ *ndata*). + +This function is not compatible with ``-DLAMMPS_BIGBIG``. + +\endverbatim + * + * \param handle: pointer to a previously created LAMMPS instance + * \param name desired quantity (e.g., "x" or "f" for atom properties, "f_id" for per-atom fix + * data, "c_id" for per-atom compute data, "d_name" or "i_name" for fix + * property/atom vectors with *count* = 1, "d2_name" or "i2_name" for fix + * property/atom vectors with *count* > 1) + * \param type 0 for ``int`` values, 1 for ``double`` values + * \param count number of per-atom values (e.g., 1 for *type* or *charge*, 3 for *x* or *f*); + * use *count* = 3 with *image* if you want the image flags unpacked into + * (*x*,*y*,*z*) components. + * \param ndata: number of atoms for which to return data (can be all of them) + * \param ids: list of *ndata* atom IDs for which to return data + * \param data per-atom values packed into a one-dimensional array of length + * *ndata* \* *count*. + * + */ /* ---------------------------------------------------------------------- Contributing author: Thomas Swinburne (CNRS & CINaM, Marseille, France) gather the named atom-based entity for all atoms @@ -3618,9 +3783,8 @@ void lammps_gather_concat(void *handle, char *name, int type, int count, void *d Allreduce to sum vector into data across all procs ------------------------------------------------------------------------- */ -void lammps_gather_subset(void *handle, char *name, - int type, int count, - int ndata, int *ids, void *data) +void lammps_gather_subset(void *handle, const char *name, int type, int count, + int ndata, int *ids, void *data) { auto lmp = (LAMMPS *) handle; @@ -3843,6 +4007,37 @@ void lammps_gather_subset(void *handle, char *name, END_CAPTURE } +/** Scatter the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based + * entity in *data* to all processes. + * +\verbatim embed:rst + +This subroutine takes data stored in a one-dimensional array supplied by the user and scatters +them to all atoms on all processes. The data must be ordered by atom ID, with the requirement that +the IDs be consecutive. Use :cpp:func:`lammps_scatter_subset` to scatter data for some (or all) +atoms, unordered. + +The *data* array needs to be ordered in groups of *count* values, sorted by atom ID (e.g., if +*name* is *x* and *count* = 3, then *data* = {x[0][0], x[0][1], x[0][2], x[1][0], x[1][1], +x[1][2], x[2][0], :math:`\dots`}); *data* must be of length (*count* :math:`\times` *natoms*). + +This function is not compatible with ``-DLAMMPS_BIGBIG``. + +\endverbatim + * + * \param handle pointer to a previously created LAMMPS instance + * \param name desired quantity (e.g., "x" or "f" for atom properties, "f_id" for per-atom fix + * data, "c_id" for per-atom compute data, "d_name" or "i_name" for fix + * property/atom vectors with *count* = 1, "d2_name" or "i2_name" for fix + * property/atom vectors with *count* > 1) + * \param type 0 for ``int`` values, 1 for ``double`` values + * \param count number of per-atom values (e.g., 1 for *type* or *charge*, + * 3 for *x* or *f*); use *count* = 3 with *image* if you have + * a single image flag packed into (*x*,*y*,*z*) components. + * \param data per-atom values packed in a one-dimensional array of length + * *natoms* \* *count*. + * + */ /* ---------------------------------------------------------------------- Contributing author: Thomas Swinburne (CNRS & CINaM, Marseille, France) scatter the named atom-based entity in data to all atoms @@ -3867,7 +4062,8 @@ void lammps_gather_subset(void *handle, char *name, Allreduce to sum vector into data across all procs ------------------------------------------------------------------------- */ -void lammps_scatter(void *handle, char *name, int type, int count, void *data) +void lammps_scatter(void *handle, const char *name, int type, int count, + void *data) { auto lmp = (LAMMPS *) handle; @@ -4062,6 +4258,42 @@ void lammps_scatter(void *handle, char *name, int type, int count, void *data) END_CAPTURE } +/** Scatter the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based + * entities in *data* from a subset of atoms to all processes. + * +\verbatim embed:rst + +This subroutine takes data stored in a one-dimensional array supplied by the +user and scatters them to a subset of atoms on all processes. The array +*data* contains data associated with atom IDs, but there is no requirement that +the IDs be consecutive, as they are provided in a separate array. +Use :cpp:func:`lammps_scatter` to scatter data for all atoms, in order. + +The *data* array needs to be organized in groups of *count* values, with the +groups in the same order as the array *ids*. For example, if you want *data* +to be the array {x[1][0], x[1][1], x[1][2], x[100][0], x[100][1], x[100][2], +x[57][0], x[57][1], x[57][2]}, then *count* = 3, *ndata* = 3, and *ids* would +be {1, 100, 57}. + +This function is not compatible with ``-DLAMMPS_BIGBIG``. + +\endverbatim + * + * \param handle: pointer to a previously created LAMMPS instance + * \param name desired quantity (e.g., "x" or "f" for atom properties, "f_id" for per-atom fix + * data, "c_id" for per-atom compute data, "d_name" or "i_name" for fix + * property/atom vectors with *count* = 1, "d2_name" or "i2_name" for fix + * property/atom vectors with *count* > 1) + * \param type: 0 for ``int`` values, 1 for ``double`` values + * \param count: number of per-atom values (e.g., 1 for *type* or *charge*, + * 3 for *x* or *f*); use *count* = 3 with "image" if you want + * single image flags unpacked into (*x*,*y*,*z*) + * \param ndata: number of atoms listed in *ids* and *data* arrays + * \param ids: list of *ndata* atom IDs to scatter data to + * \param data per-atom values packed in a 1-dimensional array of length + * *ndata* \* *count*. + * + */ /* ---------------------------------------------------------------------- Contributing author: Thomas Swinburne (CNRS & CINaM, Marseille, France) scatter the named atom-based entity in data to a subset of atoms @@ -4084,7 +4316,7 @@ void lammps_scatter(void *handle, char *name, int type, int count, void *data) loop over Ndata, if I own atom ID, set its values from data ------------------------------------------------------------------------- */ -void lammps_scatter_subset(void *handle, char *name,int type, int count, +void lammps_scatter_subset(void *handle, const char *name,int type, int count, int ndata, int *ids, void *data) { auto lmp = (LAMMPS *) handle; @@ -5836,7 +6068,7 @@ This function is used by the ML-IAP python code (mliappy) to verify the API version of the embedded python interpreter of the PYTHON package. It returns -1 if the PYTHON package is not enabled. -.. versionadded:: TBD +.. versionadded:: 3Nov2022 \endverbatim * diff --git a/src/library.h b/src/library.h index 814c24210d..9cd2f34d73 100644 --- a/src/library.h +++ b/src/library.h @@ -1,7 +1,7 @@ /* -*- c -*- ------------------------------------------------------------ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -40,8 +40,9 @@ /** Data type constants for extracting data from atoms, computes and fixes * - * Must be kept in sync with the equivalent constants in python/lammps/constants.py, - * fortran/lammps.f90, and tools/swig/lammps.i */ + * Must be kept in sync with the equivalent constants in ``python/lammps/constants.py``, + * ``fortran/lammps.f90``, ``tools/swig/lammps.i``, and + *``examples/COUPLE/plugin/liblammpsplugin.h`` */ enum _LMP_DATATYPE_CONST { LAMMPS_INT = 0, /*!< 32-bit integer (array) */ @@ -55,8 +56,9 @@ enum _LMP_DATATYPE_CONST { /** Style constants for extracting data from computes and fixes. * - * Must be kept in sync with the equivalent constants in python/lammps/constants.py, - * fortran/lammps.f90, and tools/swig/lammps.i */ + * Must be kept in sync with the equivalent constants in ``python/lammps/constants.py``, + * ``fortran/lammps.f90``, ``tools/swig/lammps.i``, and + * ``examples/COUPLE/plugin/liblammpsplugin.h`` */ enum _LMP_STYLE_CONST { LMP_STYLE_GLOBAL = 0, /*!< return global data */ @@ -66,8 +68,9 @@ enum _LMP_STYLE_CONST { /** Type and size constants for extracting data from computes and fixes. * - * Must be kept in sync with the equivalent constants in python/lammps/constants.py, - * fortran/lammps.f90, and tools/swig/lammps.i */ + * Must be kept in sync with the equivalent constants in ``python/lammps/constants.py``, + * ``fortran/lammps.f90``, ``tools/swig/lammps.i``, and + * ``examples/COUPLE/plugin/liblammpsplugin.h`` */ enum _LMP_TYPE_CONST { LMP_TYPE_SCALAR = 0, /*!< return scalar */ @@ -80,8 +83,9 @@ enum _LMP_TYPE_CONST { /** Error codes to select the suitable function in the Error class * - * Must be kept in sync with the equivalent constants in python/lammps/constants.py, - * fortran/lammps.f90, and tools/swig/lammps.i */ + * Must be kept in sync with the equivalent constants in ``python/lammps/constants.py``, + * ``fortran/lammps.f90``, ``tools/swig/lammps.i``, and + * ``examples/COUPLE/plugin/liblammpsplugin.h`` */ enum _LMP_ERROR_CONST { LMP_ERROR_WARNING = 0, /*!< call Error::warning() */ @@ -93,8 +97,9 @@ enum _LMP_ERROR_CONST { /** Variable style constants for extracting data from variables. * - * Must be kept in sync with the equivalent constants in python/lammps/constants.py, - * fortran/lammps.f90, and tools/swig/lammps.i */ + * Must be kept in sync with the equivalent constants in ``python/lammps/constants.py``, + * ``fortran/lammps.f90``, ``tools/swig/lammps.i``, and + * ``examples/COUPLE/plugin/liblammpsplugin.h`` */ enum _LMP_VAR_CONST { LMP_VAR_EQUAL = 0, /*!< compatible with equal-style variables */ @@ -176,23 +181,23 @@ int lammps_set_variable(void *, char *, char *); * Library functions for scatter/gather operations of data * ---------------------------------------------------------------------- */ -void lammps_gather_atoms(void *handle, char *name, int type, int count, void *data); -void lammps_gather_atoms_concat(void *handle, char *name, int type, int count, void *data); -void lammps_gather_atoms_subset(void *handle, char *name, int type, int count, int ndata, int *ids, - void *data); -void lammps_scatter_atoms(void *handle, char *name, int type, int count, void *data); -void lammps_scatter_atoms_subset(void *handle, char *name, int type, int count, int ndata, int *ids, - void *data); +void lammps_gather_atoms(void *handle, const char *name, int type, int count, void *data); +void lammps_gather_atoms_concat(void *handle, const char *name, int type, int count, void *data); +void lammps_gather_atoms_subset(void *handle, const char *name, int type, int count, int ndata, + int *ids, void *data); +void lammps_scatter_atoms(void *handle, const char *name, int type, int count, void *data); +void lammps_scatter_atoms_subset(void *handle, const char *name, int type, int count, int ndata, + int *ids, void *data); void lammps_gather_bonds(void *handle, void *data); -void lammps_gather(void *handle, char *name, int type, int count, void *data); -void lammps_gather_concat(void *handle, char *name, int type, int count, void *data); -void lammps_gather_subset(void *handle, char *name, int type, int count, int ndata, int *ids, - void *data); -void lammps_scatter(void *handle, char *name, int type, int count, void *data); -void lammps_scatter_subset(void *handle, char *name, int type, int count, int ndata, int *ids, - void *data); +void lammps_gather(void *handle, const char *name, int type, int count, void *data); +void lammps_gather_concat(void *handle, const char *name, int type, int count, void *data); +void lammps_gather_subset(void *handle, const char *name, int type, int count, int ndata, + int *ids, void *data); +void lammps_scatter(void *handle, const char *name, int type, int count, void *data); +void lammps_scatter_subset(void *handle, const char *name, int type, int count, int ndata, + int *ids, void *data); #if !defined(LAMMPS_BIGBIG) int lammps_create_atoms(void *handle, int n, const int *id, const int *type, const double *x, @@ -260,15 +265,14 @@ void lammps_decode_image_flags(int64_t image, int *flags); #if defined(LAMMPS_BIGBIG) typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **); -void lammps_set_fix_external_callback(void *handle, const char *id, FixExternalFnPtr funcptr, - void *ptr); #elif defined(LAMMPS_SMALLBIG) typedef void (*FixExternalFnPtr)(void *, int64_t, int, int *, double **, double **); -void lammps_set_fix_external_callback(void *, const char *, FixExternalFnPtr, void *); #else typedef void (*FixExternalFnPtr)(void *, int, int, int *, double **, double **); -void lammps_set_fix_external_callback(void *, const char *, FixExternalFnPtr, void *); #endif + +void lammps_set_fix_external_callback(void *handle, const char *id, FixExternalFnPtr funcptr, + void *ptr); double **lammps_fix_external_get_force(void *handle, const char *id); void lammps_fix_external_set_energy_global(void *handle, const char *id, double eng); void lammps_fix_external_set_energy_peratom(void *handle, const char *id, double *eng); diff --git a/src/lmpfftsettings.h b/src/lmpfftsettings.h index 7c33d2b26c..7fad0de8c7 100644 --- a/src/lmpfftsettings.h +++ b/src/lmpfftsettings.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/lmppython.cpp b/src/lmppython.cpp index daebf23c23..b3c52111fe 100644 --- a/src/lmppython.cpp +++ b/src/lmppython.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/lmppython.h b/src/lmppython.h index 145c06a6af..8eb490f9dc 100644 --- a/src/lmppython.h +++ b/src/lmppython.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/lmprestart.h b/src/lmprestart.h index 61c96acd75..e5e1da7edf 100644 --- a/src/lmprestart.h +++ b/src/lmprestart.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/lmptype.h b/src/lmptype.h index 2781de28a9..bf56d07d77 100644 --- a/src/lmptype.h +++ b/src/lmptype.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/lmpwindows.h b/src/lmpwindows.h index 9568866eda..34e90a140f 100644 --- a/src/lmpwindows.h +++ b/src/lmpwindows.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/main.cpp b/src/main.cpp index 19ccbb465a..e263938e57 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/math_const.h b/src/math_const.h index 1a6b5c3b47..2c5c65f98f 100644 --- a/src/math_const.h +++ b/src/math_const.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -30,7 +30,8 @@ namespace MathConst { static constexpr double MY_ISPI4 = 1.12837916709551257389; // 1/sqrt(pi/4) static constexpr double MY_SQRT2 = 1.41421356237309504880; // sqrt(2) static constexpr double MY_ISQRT2 = 0.707106781186547524401; // 1/sqrt(2) - static constexpr double MY_CUBEROOT2 = 1.25992104989487316476; // 2*(1/3) + static constexpr double MY_CUBEROOT2 = 1.25992104989487316476; // 2^(1/3) + static constexpr double MY_TWOBYSIXTH = 1.12246204830937298142; // 2^(1/6) // static constexpr double DEG2RAD = MY_PI / 180.0; // degree to radians static constexpr double RAD2DEG = 180.0 / MY_PI; // radians to degree } // namespace MathConst diff --git a/src/math_eigen.cpp b/src/math_eigen.cpp index f8fed1853b..967739ded9 100644 --- a/src/math_eigen.cpp +++ b/src/math_eigen.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/math_eigen.h b/src/math_eigen.h index 756ec78f5c..9f2431e14a 100644 --- a/src/math_eigen.h +++ b/src/math_eigen.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/math_eigen_impl.h b/src/math_eigen_impl.h index a3dbf3d323..57fb5f860c 100644 --- a/src/math_eigen_impl.h +++ b/src/math_eigen_impl.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/math_extra.cpp b/src/math_extra.cpp index 15d6e472c9..83e548f79f 100644 --- a/src/math_extra.cpp +++ b/src/math_extra.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -577,8 +577,8 @@ void inertia_triangle(double *idiag, double *quat, double /*mass*/, } /* ---------------------------------------------------------------------- - Build rotation matrix for a small angle rotation around the X axis - ------------------------------------------------------------------------- */ + build rotation matrix for a small angle rotation around the X axis +------------------------------------------------------------------------- */ void BuildRxMatrix(double R[3][3], const double angle) { @@ -592,8 +592,8 @@ void BuildRxMatrix(double R[3][3], const double angle) } /* ---------------------------------------------------------------------- - Build rotation matrix for a small angle rotation around the Y axis - ------------------------------------------------------------------------- */ + build rotation matrix for a small angle rotation around the Y axis +------------------------------------------------------------------------- */ void BuildRyMatrix(double R[3][3], const double angle) { @@ -607,8 +607,8 @@ void BuildRyMatrix(double R[3][3], const double angle) } /* ---------------------------------------------------------------------- - Build rotation matrix for a small angle rotation around the Z axis - ------------------------------------------------------------------------- */ + build rotation matrix for a small angle rotation around the Z axis +------------------------------------------------------------------------- */ void BuildRzMatrix(double R[3][3], const double angle) { @@ -621,6 +621,31 @@ void BuildRzMatrix(double R[3][3], const double angle) R[2][0] = 0.0; R[2][1] = 0.0; R[2][2] = 1.0; } +/* ---------------------------------------------------------------------- + convert a sphere in box coords to an ellipsoid in triclinic lamda (0-1) coords + h[6] = domain->h for size and shape of triclinic box + radius = radius of sphere in box coords + return dist[3] = tight (axis-aligned) bounding box in triclinic lamda coords + see: http://www.loria.fr/~shornus/ellipsoid-bbox.html (no longer online) + https://yiningkarlli.blogspot.com/2013/02/bounding-boxes-for-ellipsoidsfigure.html +------------------------------------------------------------------------- */ + +void tribbox(double *h, double radius, double *dist) +{ + double lx = h[0]; + double ly = h[1]; + double lz = h[2]; + double yz = h[3]; + double xz = h[4]; + double xy = h[5]; + + dist[0] = radius * sqrt(ly*ly*lz*lz + ly*ly*xz*xz - 2.0*ly*xy*xz*yz + + lz*lz*xy*xy + xy*xy*yz*yz) / (lx*ly*lz); + dist[1] = radius * sqrt(lz*lz + yz*yz) / (ly*lz); + dist[2] = radius / lz; +} + /* ---------------------------------------------------------------------- */ + } diff --git a/src/math_extra.h b/src/math_extra.h index cbf9f78e53..1efacea463 100644 --- a/src/math_extra.h +++ b/src/math_extra.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -119,6 +119,11 @@ void inertia_ellipsoid(double *shape, double *quat, double mass, double *inertia void inertia_line(double length, double theta, double mass, double *inertia); void inertia_triangle(double *v0, double *v1, double *v2, double mass, double *inertia); void inertia_triangle(double *idiag, double *quat, double mass, double *inertia); + +// triclinic bounding box of a spher + +void tribbox(double *, double, double *); + } // namespace MathExtra /* ---------------------------------------------------------------------- diff --git a/src/math_special.h b/src/math_special.h index 6931a8e19e..b190a4b622 100644 --- a/src/math_special.h +++ b/src/math_special.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/memory.cpp b/src/memory.cpp index 2a053e3dbd..c2d8163ece 100644 --- a/src/memory.cpp +++ b/src/memory.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/memory.h b/src/memory.h index 5493b5fa57..7d6217b04a 100644 --- a/src/memory.h +++ b/src/memory.h @@ -1,7 +1,8 @@ +// clang-format off /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -36,6 +37,10 @@ class Memory : protected Pointers { for these other cases, use smalloc/srealloc/sfree directly ------------------------------------------------------------------------- */ +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- + /* ---------------------------------------------------------------------- create a 1d array ------------------------------------------------------------------------- */ @@ -91,6 +96,10 @@ class Memory : protected Pointers { array = nullptr; } +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- + /* ---------------------------------------------------------------------- create a 1d array with index from nlo to nhi inclusive cannot grow it @@ -124,6 +133,10 @@ class Memory : protected Pointers { array = nullptr; } +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- + /* ---------------------------------------------------------------------- create a 2d array ------------------------------------------------------------------------- */ @@ -200,6 +213,10 @@ class Memory : protected Pointers { array = nullptr; } +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- + /* ---------------------------------------------------------------------- create a 2d array with a ragged 2nd dimension ------------------------------------------------------------------------- */ @@ -259,6 +276,10 @@ class Memory : protected Pointers { return array; } +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- + /* ---------------------------------------------------------------------- create a 2d array with 2nd index from n2lo to n2hi inclusive cannot grow it @@ -296,6 +317,57 @@ class Memory : protected Pointers { array = nullptr; } +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- + +/* ---------------------------------------------------------------------- + create a 2d array with both indices offset + 1st index from n1lo to n1hi inclusive + 2nd index from n2lo to n2hi inclusive + cannot grow it +------------------------------------------------------------------------- */ + + template + TYPE **create2d_offset(TYPE **&array, int n1lo, int n1hi, int n2lo, int n2hi, + const char *name) + { + if (n1lo > n1hi || n2lo > n2hi) return nullptr; + + int n1 = n1hi - n1lo + 1; + int n2 = n2hi - n2lo + 1; + create(array, n1, n2, name); + + for (int i = 0; i < n1; i++) array[i] -= n2lo; + array -= n1lo; + return array; + } + + template + TYPE ***create2d_offset(TYPE ***& /*array*/, int /*n1lo*/, int /*n1hi*/, int /*n2lo*/, + int /*n2hi*/, const char *name) + { + fail(name); + return nullptr; + } + + /* ---------------------------------------------------------------------- + free a 2d array with both indices offset +------------------------------------------------------------------------- */ + + template + void destroy2d_offset(TYPE **&array, int n1_offset, int n2_offset) + { + if (array == nullptr) return; + sfree(&array[n1_offset][n2_offset]); + sfree(&array[n1_offset]); + array = nullptr; + } + +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- + /* ---------------------------------------------------------------------- create a 3d array ------------------------------------------------------------------------- */ @@ -389,6 +461,10 @@ class Memory : protected Pointers { array = nullptr; } +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- + /* ---------------------------------------------------------------------- create a 3d array with 1st index from n1lo to n1hi inclusive cannot grow it @@ -426,6 +502,10 @@ class Memory : protected Pointers { array = nullptr; } +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- + /* ---------------------------------------------------------------------- create a 3d array with all 3 indices offset 1st index from n1lo to n1hi inclusive @@ -474,6 +554,57 @@ class Memory : protected Pointers { array = nullptr; } +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- + +/* ---------------------------------------------------------------------- + create a 3d array with indices 1,2 offset, but not last + 1st index from n1lo to n1hi inclusive + 2nd index from n2lo to n2hi inclusive + cannot grow it +------------------------------------------------------------------------- */ + + template + TYPE ***create3d_offset_last(TYPE ***&array, int n1lo, int n1hi, + int n2lo, int n2hi, int n3, + const char *name) + { + if (n1lo > n1hi || n2lo > n2hi || n3 < 0) return nullptr; + + int n1 = n1hi - n1lo + 1; + int n2 = n2hi - n2lo + 1; + create(array,n1,n2,n3,name); + + for (int i = 0; i < n1; i++) array[i] -= n2lo; + array -= n1lo; + return array; + } + + template + TYPE ***create3d_offset_last(TYPE ****& /*array*/, int /*n1lo*/, int /*n1hi*/, + int /*n2lo*/, int /*n2hi*/, int /*n3*/, + const char *name) + {fail(name); return nullptr;} + +/* ---------------------------------------------------------------------- + free a 3d array with indices 1,2 offset, but not last +------------------------------------------------------------------------- */ + + template + void destroy3d_offset_last(TYPE ***&array, int n1_offset, int n2_offset) + { + if (array == nullptr) return; + sfree(&array[n1_offset][n2_offset][0]); + sfree(&array[n1_offset][n2_offset]); + sfree(&array[n1_offset]); + array = nullptr; + } + +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- + /* ---------------------------------------------------------------------- create a 4d array ------------------------------------------------------------------------- */ @@ -588,8 +719,12 @@ class Memory : protected Pointers { array = nullptr; } +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- + /* ---------------------------------------------------------------------- - create a 4d array with indices 2,3,4 offset + create a 4d array with indices 2,3,4 offset, but not first 2nd index from n2lo to n2hi inclusive 3rd index from n3lo to n3hi inclusive 4th index from n4lo to n4hi inclusive @@ -624,7 +759,7 @@ class Memory : protected Pointers { } /* ---------------------------------------------------------------------- - free a 4d array with indices 2,3,4 offset + free a 4d array with indices 2,3,4 offset, but not first ------------------------------------------------------------------------- */ template @@ -638,25 +773,28 @@ class Memory : protected Pointers { array = nullptr; } +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- + /* ---------------------------------------------------------------------- - create a 4d array with indices 1,2,3 offset - 1st index from n1lo to n2hi inclusive - 2nd index from n3lo to n3hi inclusive - 3rd index from n4lo to n4hi inclusive + create a 4d array with indices 1,2,3 offset, but not last + 1st index from n1lo to n1hi inclusive + 2nd index from n2lo to n2hi inclusive + 3rd index from n3lo to n3hi inclusive cannot grow it ------------------------------------------------------------------------- */ template - TYPE ****create4d_offset_last(TYPE ****&array, int n1lo, int n1hi, - int n2lo, int n2hi, int n3lo, int n3hi, int n4, - const char *name) + TYPE ****create4d_offset_last(TYPE ****&array, int n1lo, int n1hi, int n2lo, int n2hi, int n3lo, + int n3hi, int n4, const char *name) { if (n1lo > n1hi || n2lo > n2hi || n3lo > n3hi || n4 <= 0) return nullptr; int n1 = n1hi - n1lo + 1; int n2 = n2hi - n2lo + 1; int n3 = n3hi - n3lo + 1; - create(array,n1,n2,n3,n4,name); + create(array, n1, n2, n3, n4, name); bigint m = ((bigint) n1) * n2; for (bigint i = 0; i < m; i++) array[0][i] -= n3lo; @@ -666,19 +804,20 @@ class Memory : protected Pointers { } template - TYPE ****create4d_offset_last(TYPE *****& /*array*/, int /*n1lo*/, int /*n1hi*/, - int /*n2lo*/, int /*n2hi*/, - int /*n3lo*/, int /*n3hi*/, int /*n4*/, + TYPE ****create4d_offset_last(TYPE *****& /*array*/, int /*n1lo*/, int /*n1hi*/, int /*n2lo*/, + int /*n2hi*/, int /*n3lo*/, int /*n3hi*/, int /*n4*/, const char *name) - {fail(name); return nullptr;} + { + fail(name); + return nullptr; + } /* ---------------------------------------------------------------------- - free a 4d array with indices 1,2,3 offset + free a 4d array with indices 1,2,3 offset, but not last ------------------------------------------------------------------------- */ template - void destroy4d_offset_last(TYPE ****&array, - int n1_offset, int n2_offset, int n3_offset) + void destroy4d_offset_last(TYPE ****&array, int n1_offset, int n2_offset, int n3_offset) { if (array == nullptr) return; sfree(&array[n1_offset][n2_offset][n3_offset][0]); @@ -688,6 +827,10 @@ class Memory : protected Pointers { array = nullptr; } +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- + /* ---------------------------------------------------------------------- create a 5d array ------------------------------------------------------------------------- */ @@ -757,6 +900,10 @@ class Memory : protected Pointers { array = nullptr; } +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- +// ------------------------------------------------------------------------- + /* ---------------------------------------------------------------------- memory usage of arrays, including pointers ------------------------------------------------------------------------- */ diff --git a/src/min.cpp b/src/min.cpp index 62333b215c..0813c2184a 100644 --- a/src/min.cpp +++ b/src/min.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/min.h b/src/min.h index 169e7fb7e8..a9ddc03950 100644 --- a/src/min.h +++ b/src/min.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/min_cg.cpp b/src/min_cg.cpp index 1c7ab8b8d5..782ab04c44 100644 --- a/src/min_cg.cpp +++ b/src/min_cg.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/min_cg.h b/src/min_cg.h index f203c0fbd6..9e543daddb 100644 --- a/src/min_cg.h +++ b/src/min_cg.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/min_fire.cpp b/src/min_fire.cpp index 8999d2a4a6..c7b8503800 100644 --- a/src/min_fire.cpp +++ b/src/min_fire.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/min_fire.h b/src/min_fire.h index c415ec8fb9..39f9636a2b 100644 --- a/src/min_fire.h +++ b/src/min_fire.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/min_fire_old.cpp b/src/min_fire_old.cpp index 40fc11de66..daa269d8b8 100644 --- a/src/min_fire_old.cpp +++ b/src/min_fire_old.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/min_fire_old.h b/src/min_fire_old.h index 0d9d7ee2ec..f5eba75003 100644 --- a/src/min_fire_old.h +++ b/src/min_fire_old.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/min_hftn.cpp b/src/min_hftn.cpp index d49821bedd..19adb345c0 100644 --- a/src/min_hftn.cpp +++ b/src/min_hftn.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/min_hftn.h b/src/min_hftn.h index 360f52a03d..f7bf087cd7 100644 --- a/src/min_hftn.h +++ b/src/min_hftn.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/min_linesearch.cpp b/src/min_linesearch.cpp index 2e7066daed..8ce927bea3 100644 --- a/src/min_linesearch.cpp +++ b/src/min_linesearch.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/min_linesearch.h b/src/min_linesearch.h index ff8a24fab0..c9c0b1c158 100644 --- a/src/min_linesearch.h +++ b/src/min_linesearch.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/min_quickmin.cpp b/src/min_quickmin.cpp index 3191cb1429..99d95be57d 100644 --- a/src/min_quickmin.cpp +++ b/src/min_quickmin.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/min_quickmin.h b/src/min_quickmin.h index d1b415313b..417fb6f9d2 100644 --- a/src/min_quickmin.h +++ b/src/min_quickmin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/min_sd.cpp b/src/min_sd.cpp index eed6793b63..f8e9c44794 100644 --- a/src/min_sd.cpp +++ b/src/min_sd.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/min_sd.h b/src/min_sd.h index 39d2c5f529..973efa36bd 100644 --- a/src/min_sd.h +++ b/src/min_sd.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/minimize.cpp b/src/minimize.cpp index 7412347c34..d13429804c 100644 --- a/src/minimize.cpp +++ b/src/minimize.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/minimize.h b/src/minimize.h index 5fbcb8d61e..8cfb3f66b6 100644 --- a/src/minimize.h +++ b/src/minimize.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/modify.cpp b/src/modify.cpp index aa978641a1..bd62b03597 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -791,6 +791,19 @@ int Modify::min_reset_ref() return itmpall; } +/* ---------------------------------------------------------------------- + reset grids for any Fix or Compute that uses distributed grids + called by load balancer when proc sub-domains change +------------------------------------------------------------------------- */ + +void Modify::reset_grid() +{ + for (int i = 0; i < nfix; i++) + if (fix[i]->pergrid_flag) fix[i]->reset_grid(); + for (int i = 0; i < ncompute; i++) + if (compute[i]->pergrid_flag) compute[i]->reset_grid(); +} + /* ---------------------------------------------------------------------- add a new fix or replace one with same ID ------------------------------------------------------------------------- */ @@ -806,10 +819,12 @@ Fix *Modify::add_fix(int narg, char **arg, int trysuffix) // since some fixes access domain settings in their constructor // nullptr must be last entry in this list + // clang-format off const char *exceptions[] = {"GPU", "OMP", "INTEL", "property/atom", "cmap", "cmap3", "rx", "deprecated", "STORE/KIM", "amoeba/pitorsion", "amoeba/bitorsion", nullptr}; + // clang-format on if (domain->box_exist == 0) { int m; @@ -846,8 +861,8 @@ Fix *Modify::add_fix(int narg, char **arg, int trysuffix) int match = 0; if (strcmp(arg[2], fix[ifix]->style) == 0) match = 1; if (!match && trysuffix && lmp->suffix_enable) { - if (lmp->suffix) { - std::string estyle = arg[2] + std::string("/") + lmp->suffix; + if (lmp->non_pair_suffix()) { + std::string estyle = arg[2] + std::string("/") + lmp->non_pair_suffix(); if (estyle == fix[ifix]->style) match = 1; } if (lmp->suffix2) { @@ -877,8 +892,8 @@ Fix *Modify::add_fix(int narg, char **arg, int trysuffix) fix[ifix] = nullptr; if (trysuffix && lmp->suffix_enable) { - if (lmp->suffix) { - std::string estyle = arg[2] + std::string("/") + lmp->suffix; + if (lmp->non_pair_suffix()) { + std::string estyle = arg[2] + std::string("/") + lmp->non_pair_suffix(); if (fix_map->find(estyle) != fix_map->end()) { FixCreator &fix_creator = (*fix_map)[estyle]; fix[ifix] = fix_creator(lmp, narg, arg); @@ -923,8 +938,8 @@ Fix *Modify::add_fix(int narg, char **arg, int trysuffix) // if yes, pass state info to the Fix so it can reset itself for (int i = 0; i < nfix_restart_global; i++) - if (strcmp(id_restart_global[i], fix[ifix]->id) == 0 && - strcmp(style_restart_global[i], fix[ifix]->style) == 0) { + if ((strcmp(id_restart_global[i], fix[ifix]->id) == 0) && + (utils::strip_style_suffix(fix[ifix]->style, lmp) == style_restart_global[i])) { fix[ifix]->restart(state_restart_global[i]); used_restart_global[i] = 1; fix[ifix]->restart_reset = 1; @@ -1241,8 +1256,8 @@ Compute *Modify::add_compute(int narg, char **arg, int trysuffix) compute[ncompute] = nullptr; if (trysuffix && lmp->suffix_enable) { - if (lmp->suffix) { - std::string estyle = arg[2] + std::string("/") + lmp->suffix; + if (lmp->non_pair_suffix()) { + std::string estyle = arg[2] + std::string("/") + lmp->non_pair_suffix(); if (compute_map->find(estyle) != compute_map->end()) { ComputeCreator &compute_creator = (*compute_map)[estyle]; compute[ncompute] = compute_creator(lmp, narg, arg); @@ -1446,9 +1461,10 @@ void Modify::write_restart(FILE *fp) n = strlen(fix[i]->id) + 1; fwrite(&n, sizeof(int), 1, fp); fwrite(fix[i]->id, sizeof(char), n, fp); - n = strlen(fix[i]->style) + 1; + auto fix_style = utils::strip_style_suffix(fix[i]->style, lmp); + n = fix_style.size() + 1; fwrite(&n, sizeof(int), 1, fp); - fwrite(fix[i]->style, sizeof(char), n, fp); + fwrite(fix_style.c_str(), sizeof(char), n, fp); } fix[i]->write_restart(fp); } diff --git a/src/modify.h b/src/modify.h index 820b957033..7a3f54c277 100644 --- a/src/modify.h +++ b/src/modify.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -17,7 +17,6 @@ #include "pointers.h" #include -#include namespace LAMMPS_NS { @@ -101,6 +100,8 @@ class Modify : protected Pointers { virtual int min_dof(); virtual int min_reset_ref(); + void reset_grid(); + Fix *add_fix(int, char **, int trysuffix = 1); Fix *add_fix(const std::string &, int trysuffix = 1); Fix *replace_fix(const char *, int, char **, int trysuffix = 1); diff --git a/src/molecule.cpp b/src/molecule.cpp index df7d8ac415..6e2d3891d3 100644 --- a/src/molecule.cpp +++ b/src/molecule.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/molecule.h b/src/molecule.h index b4a8e642cc..06a1211ea3 100644 --- a/src/molecule.h +++ b/src/molecule.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/mpiio.h b/src/mpiio.h index db5fa0847f..923aff0bbe 100644 --- a/src/mpiio.h +++ b/src/mpiio.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/my_page.cpp b/src/my_page.cpp index b407e279a9..94412aee0b 100644 --- a/src/my_page.cpp +++ b/src/my_page.cpp @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/my_page.h b/src/my_page.h index fcb7b63cff..6c06abd71e 100644 --- a/src/my_page.h +++ b/src/my_page.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/my_pool_chunk.cpp b/src/my_pool_chunk.cpp index 74d2d037e0..4ec8ea60bb 100644 --- a/src/my_pool_chunk.cpp +++ b/src/my_pool_chunk.cpp @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/my_pool_chunk.h b/src/my_pool_chunk.h index ba71d6ac55..fa0a4e2506 100644 --- a/src/my_pool_chunk.h +++ b/src/my_pool_chunk.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nbin.cpp b/src/nbin.cpp index 89c0cfc851..6a0c98e603 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nbin.h b/src/nbin.h index 73100d2c34..72e9b6fadb 100644 --- a/src/nbin.h +++ b/src/nbin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nbin_multi.cpp b/src/nbin_multi.cpp index f5e79bcda6..24edfcb03b 100644 --- a/src/nbin_multi.cpp +++ b/src/nbin_multi.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nbin_multi.h b/src/nbin_multi.h index 057acc72eb..087dc980a5 100644 --- a/src/nbin_multi.h +++ b/src/nbin_multi.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nbin_standard.cpp b/src/nbin_standard.cpp index aa2a9f6686..eec17ae29a 100644 --- a/src/nbin_standard.cpp +++ b/src/nbin_standard.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nbin_standard.h b/src/nbin_standard.h index cb5e19517b..9e9e7f7df4 100644 --- a/src/nbin_standard.h +++ b/src/nbin_standard.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/neigh_list.cpp b/src/neigh_list.cpp index d8fe7a8c27..2d91eebdef 100644 --- a/src/neigh_list.cpp +++ b/src/neigh_list.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/neigh_list.h b/src/neigh_list.h index 9b1bc238e6..01e9a1c6a7 100644 --- a/src/neigh_list.h +++ b/src/neigh_list.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/neigh_request.cpp b/src/neigh_request.cpp index dc38205d55..280b5c54ae 100644 --- a/src/neigh_request.cpp +++ b/src/neigh_request.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/neigh_request.h b/src/neigh_request.h index 9f2d56add8..a3114dff82 100644 --- a/src/neigh_request.h +++ b/src/neigh_request.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 6af4094a21..19a09aacde 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -119,7 +119,7 @@ pairclass(nullptr), pairnames(nullptr), pairmasks(nullptr) style = Neighbor::BIN; every = 1; - delay = 10; + delay = 0; dist_check = 1; pgsize = 100000; oneatom = 2000; diff --git a/src/neighbor.h b/src/neighbor.h index 1fa8a28d53..241f44be06 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair.cpp b/src/npair.cpp index 24dde8c741..c1615411c0 100644 --- a/src/npair.cpp +++ b/src/npair.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair.h b/src/npair.h index 9e7384ade3..3eeb1d48f4 100644 --- a/src/npair.h +++ b/src/npair.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_copy.cpp b/src/npair_copy.cpp index 38a36d0ba5..84eb2c13aa 100644 --- a/src/npair_copy.cpp +++ b/src/npair_copy.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_copy.h b/src/npair_copy.h index d696206186..7371494616 100644 --- a/src/npair_copy.h +++ b/src/npair_copy.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_full_bin.cpp b/src/npair_full_bin.cpp index 64404ccf8d..152033cdc1 100644 --- a/src/npair_full_bin.cpp +++ b/src/npair_full_bin.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_full_bin.h b/src/npair_full_bin.h index 465bb82786..7ee37c8ec5 100644 --- a/src/npair_full_bin.h +++ b/src/npair_full_bin.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_full_bin_atomonly.cpp b/src/npair_full_bin_atomonly.cpp index aa7a91dbbe..825b25fe56 100644 --- a/src/npair_full_bin_atomonly.cpp +++ b/src/npair_full_bin_atomonly.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_full_bin_atomonly.h b/src/npair_full_bin_atomonly.h index ffb979743d..b30d0433e0 100644 --- a/src/npair_full_bin_atomonly.h +++ b/src/npair_full_bin_atomonly.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_full_bin_ghost.cpp b/src/npair_full_bin_ghost.cpp index e051a1d75a..fc2f325c48 100644 --- a/src/npair_full_bin_ghost.cpp +++ b/src/npair_full_bin_ghost.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_full_bin_ghost.h b/src/npair_full_bin_ghost.h index 9c2e3d2155..7fedb1e0c5 100644 --- a/src/npair_full_bin_ghost.h +++ b/src/npair_full_bin_ghost.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_full_multi.cpp b/src/npair_full_multi.cpp index 34b7a7bfa8..5df1c5b200 100644 --- a/src/npair_full_multi.cpp +++ b/src/npair_full_multi.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_full_multi.h b/src/npair_full_multi.h index 942f9e47c9..c3c707a91d 100644 --- a/src/npair_full_multi.h +++ b/src/npair_full_multi.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_full_multi_old.cpp b/src/npair_full_multi_old.cpp index 7b89f35268..2d529627f2 100644 --- a/src/npair_full_multi_old.cpp +++ b/src/npair_full_multi_old.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_full_multi_old.h b/src/npair_full_multi_old.h index 6697f3163b..cb78cf3d76 100644 --- a/src/npair_full_multi_old.h +++ b/src/npair_full_multi_old.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_full_nsq.cpp b/src/npair_full_nsq.cpp index c6427366f4..6743961d38 100644 --- a/src/npair_full_nsq.cpp +++ b/src/npair_full_nsq.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_full_nsq.h b/src/npair_full_nsq.h index 78cef5fac3..0f6665826d 100644 --- a/src/npair_full_nsq.h +++ b/src/npair_full_nsq.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_full_nsq_ghost.cpp b/src/npair_full_nsq_ghost.cpp index 9550ae54f3..1ea118bc85 100644 --- a/src/npair_full_nsq_ghost.cpp +++ b/src/npair_full_nsq_ghost.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_full_nsq_ghost.h b/src/npair_full_nsq_ghost.h index 9b97579e74..0e26d8c5df 100644 --- a/src/npair_full_nsq_ghost.h +++ b/src/npair_full_nsq_ghost.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_bin_atomonly_newton.cpp b/src/npair_half_bin_atomonly_newton.cpp index db84d38f6e..d69dba4643 100644 --- a/src/npair_half_bin_atomonly_newton.cpp +++ b/src/npair_half_bin_atomonly_newton.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_bin_atomonly_newton.h b/src/npair_half_bin_atomonly_newton.h index 2033710601..b17f7608fc 100644 --- a/src/npair_half_bin_atomonly_newton.h +++ b/src/npair_half_bin_atomonly_newton.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_bin_newtoff.cpp b/src/npair_half_bin_newtoff.cpp index 00318b2aa7..240d6e4909 100644 --- a/src/npair_half_bin_newtoff.cpp +++ b/src/npair_half_bin_newtoff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_bin_newtoff.h b/src/npair_half_bin_newtoff.h index e4d56b79b1..ce551b1b95 100644 --- a/src/npair_half_bin_newtoff.h +++ b/src/npair_half_bin_newtoff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_bin_newtoff_ghost.cpp b/src/npair_half_bin_newtoff_ghost.cpp index b85e3328e1..6672e8fd5b 100644 --- a/src/npair_half_bin_newtoff_ghost.cpp +++ b/src/npair_half_bin_newtoff_ghost.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_bin_newtoff_ghost.h b/src/npair_half_bin_newtoff_ghost.h index e6ae0b216c..c581ba86fe 100644 --- a/src/npair_half_bin_newtoff_ghost.h +++ b/src/npair_half_bin_newtoff_ghost.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_bin_newton.cpp b/src/npair_half_bin_newton.cpp index d07ebf01f9..201b1d2e27 100644 --- a/src/npair_half_bin_newton.cpp +++ b/src/npair_half_bin_newton.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_bin_newton.h b/src/npair_half_bin_newton.h index faf8c90af6..bbb4f825a0 100644 --- a/src/npair_half_bin_newton.h +++ b/src/npair_half_bin_newton.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_bin_newton_tri.cpp b/src/npair_half_bin_newton_tri.cpp index ef2e48a417..88ef993a41 100644 --- a/src/npair_half_bin_newton_tri.cpp +++ b/src/npair_half_bin_newton_tri.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_bin_newton_tri.h b/src/npair_half_bin_newton_tri.h index 2e733b6ad1..fbc3703f64 100644 --- a/src/npair_half_bin_newton_tri.h +++ b/src/npair_half_bin_newton_tri.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_multi_newtoff.cpp b/src/npair_half_multi_newtoff.cpp index cef28f4cb4..5cacd8015d 100644 --- a/src/npair_half_multi_newtoff.cpp +++ b/src/npair_half_multi_newtoff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_multi_newtoff.h b/src/npair_half_multi_newtoff.h index ccb8763eac..cfb3ba9e60 100644 --- a/src/npair_half_multi_newtoff.h +++ b/src/npair_half_multi_newtoff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_multi_newton.cpp b/src/npair_half_multi_newton.cpp index 3ee4ce5fde..dad42ffb7f 100644 --- a/src/npair_half_multi_newton.cpp +++ b/src/npair_half_multi_newton.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_multi_newton.h b/src/npair_half_multi_newton.h index 315ddde617..98552db81a 100644 --- a/src/npair_half_multi_newton.h +++ b/src/npair_half_multi_newton.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_multi_newton_tri.cpp b/src/npair_half_multi_newton_tri.cpp index 4a8bb8e19f..9bebfe71e2 100644 --- a/src/npair_half_multi_newton_tri.cpp +++ b/src/npair_half_multi_newton_tri.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_multi_newton_tri.h b/src/npair_half_multi_newton_tri.h index b16a2a66b6..a26087465f 100644 --- a/src/npair_half_multi_newton_tri.h +++ b/src/npair_half_multi_newton_tri.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_multi_old_newtoff.cpp b/src/npair_half_multi_old_newtoff.cpp index eb6c7d9069..69c9543838 100644 --- a/src/npair_half_multi_old_newtoff.cpp +++ b/src/npair_half_multi_old_newtoff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_multi_old_newtoff.h b/src/npair_half_multi_old_newtoff.h index fc6f50557b..d81d2d685a 100644 --- a/src/npair_half_multi_old_newtoff.h +++ b/src/npair_half_multi_old_newtoff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_multi_old_newton.cpp b/src/npair_half_multi_old_newton.cpp index 9708b3e879..e9556d50ff 100644 --- a/src/npair_half_multi_old_newton.cpp +++ b/src/npair_half_multi_old_newton.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_multi_old_newton.h b/src/npair_half_multi_old_newton.h index e8ca998c25..1b8bff5080 100644 --- a/src/npair_half_multi_old_newton.h +++ b/src/npair_half_multi_old_newton.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_multi_old_newton_tri.cpp b/src/npair_half_multi_old_newton_tri.cpp index 683cc5f53c..fbb9a8e504 100644 --- a/src/npair_half_multi_old_newton_tri.cpp +++ b/src/npair_half_multi_old_newton_tri.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_multi_old_newton_tri.h b/src/npair_half_multi_old_newton_tri.h index b6d884a708..bb15724074 100644 --- a/src/npair_half_multi_old_newton_tri.h +++ b/src/npair_half_multi_old_newton_tri.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_nsq_newtoff.cpp b/src/npair_half_nsq_newtoff.cpp index affcdcf39f..c08147cc06 100644 --- a/src/npair_half_nsq_newtoff.cpp +++ b/src/npair_half_nsq_newtoff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_nsq_newtoff.h b/src/npair_half_nsq_newtoff.h index 348b4fd4fc..157d9c3835 100644 --- a/src/npair_half_nsq_newtoff.h +++ b/src/npair_half_nsq_newtoff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_nsq_newtoff_ghost.cpp b/src/npair_half_nsq_newtoff_ghost.cpp index eebee1208b..cef9d5203c 100644 --- a/src/npair_half_nsq_newtoff_ghost.cpp +++ b/src/npair_half_nsq_newtoff_ghost.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_nsq_newtoff_ghost.h b/src/npair_half_nsq_newtoff_ghost.h index db2045f512..86f3f9e36f 100644 --- a/src/npair_half_nsq_newtoff_ghost.h +++ b/src/npair_half_nsq_newtoff_ghost.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_nsq_newton.cpp b/src/npair_half_nsq_newton.cpp index 5263903657..e5f3138f0a 100644 --- a/src/npair_half_nsq_newton.cpp +++ b/src/npair_half_nsq_newton.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_nsq_newton.h b/src/npair_half_nsq_newton.h index befa527ada..8f6952ff01 100644 --- a/src/npair_half_nsq_newton.h +++ b/src/npair_half_nsq_newton.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_respa_bin_newtoff.cpp b/src/npair_half_respa_bin_newtoff.cpp index b0fb7cb097..11d9e916e7 100644 --- a/src/npair_half_respa_bin_newtoff.cpp +++ b/src/npair_half_respa_bin_newtoff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_respa_bin_newtoff.h b/src/npair_half_respa_bin_newtoff.h index c0ca235deb..a6d8b10de0 100644 --- a/src/npair_half_respa_bin_newtoff.h +++ b/src/npair_half_respa_bin_newtoff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_respa_bin_newton.cpp b/src/npair_half_respa_bin_newton.cpp index 0bb6756497..6f829660bd 100644 --- a/src/npair_half_respa_bin_newton.cpp +++ b/src/npair_half_respa_bin_newton.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_respa_bin_newton.h b/src/npair_half_respa_bin_newton.h index fd25f1c537..2cd68446a8 100644 --- a/src/npair_half_respa_bin_newton.h +++ b/src/npair_half_respa_bin_newton.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_respa_bin_newton_tri.cpp b/src/npair_half_respa_bin_newton_tri.cpp index c6c569d794..b2749bd7a7 100644 --- a/src/npair_half_respa_bin_newton_tri.cpp +++ b/src/npair_half_respa_bin_newton_tri.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_respa_bin_newton_tri.h b/src/npair_half_respa_bin_newton_tri.h index f0af474444..68289c2d37 100644 --- a/src/npair_half_respa_bin_newton_tri.h +++ b/src/npair_half_respa_bin_newton_tri.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_respa_nsq_newtoff.cpp b/src/npair_half_respa_nsq_newtoff.cpp index ff512be7d9..7bbd9dbece 100644 --- a/src/npair_half_respa_nsq_newtoff.cpp +++ b/src/npair_half_respa_nsq_newtoff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_respa_nsq_newtoff.h b/src/npair_half_respa_nsq_newtoff.h index e1ab752d35..e0f3ae8380 100644 --- a/src/npair_half_respa_nsq_newtoff.h +++ b/src/npair_half_respa_nsq_newtoff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_respa_nsq_newton.cpp b/src/npair_half_respa_nsq_newton.cpp index 941ce41159..77d6af141f 100644 --- a/src/npair_half_respa_nsq_newton.cpp +++ b/src/npair_half_respa_nsq_newton.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_respa_nsq_newton.h b/src/npair_half_respa_nsq_newton.h index 7b13e5356e..e5233f5e9d 100644 --- a/src/npair_half_respa_nsq_newton.h +++ b/src/npair_half_respa_nsq_newton.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_size_bin_newtoff.cpp b/src/npair_half_size_bin_newtoff.cpp index de063c1eb9..b4842337ca 100644 --- a/src/npair_half_size_bin_newtoff.cpp +++ b/src/npair_half_size_bin_newtoff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_size_bin_newtoff.h b/src/npair_half_size_bin_newtoff.h index 6dd8914ed7..ac68f699ca 100644 --- a/src/npair_half_size_bin_newtoff.h +++ b/src/npair_half_size_bin_newtoff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_size_bin_newton.cpp b/src/npair_half_size_bin_newton.cpp index fbf5ce14d4..11ac30ed30 100644 --- a/src/npair_half_size_bin_newton.cpp +++ b/src/npair_half_size_bin_newton.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_size_bin_newton.h b/src/npair_half_size_bin_newton.h index 65bbf1b5bf..de11284a8a 100644 --- a/src/npair_half_size_bin_newton.h +++ b/src/npair_half_size_bin_newton.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_size_bin_newton_tri.cpp b/src/npair_half_size_bin_newton_tri.cpp index 15728a596a..47bb9d01e1 100644 --- a/src/npair_half_size_bin_newton_tri.cpp +++ b/src/npair_half_size_bin_newton_tri.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_size_bin_newton_tri.h b/src/npair_half_size_bin_newton_tri.h index 86e100406a..ad35b7ac36 100644 --- a/src/npair_half_size_bin_newton_tri.h +++ b/src/npair_half_size_bin_newton_tri.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_size_multi_newtoff.cpp b/src/npair_half_size_multi_newtoff.cpp index ecb70cd6c4..0c22a49ed0 100644 --- a/src/npair_half_size_multi_newtoff.cpp +++ b/src/npair_half_size_multi_newtoff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_size_multi_newtoff.h b/src/npair_half_size_multi_newtoff.h index 06347bf462..89ca0eae4e 100644 --- a/src/npair_half_size_multi_newtoff.h +++ b/src/npair_half_size_multi_newtoff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_size_multi_newton.cpp b/src/npair_half_size_multi_newton.cpp index ee100596bc..ff9df7e2cf 100644 --- a/src/npair_half_size_multi_newton.cpp +++ b/src/npair_half_size_multi_newton.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_size_multi_newton.h b/src/npair_half_size_multi_newton.h index dc9f3ebdbf..2f892e37ee 100644 --- a/src/npair_half_size_multi_newton.h +++ b/src/npair_half_size_multi_newton.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_size_multi_newton_tri.cpp b/src/npair_half_size_multi_newton_tri.cpp index 9a170948b9..5d8a0f05ef 100644 --- a/src/npair_half_size_multi_newton_tri.cpp +++ b/src/npair_half_size_multi_newton_tri.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_size_multi_newton_tri.h b/src/npair_half_size_multi_newton_tri.h index 7d9c24d604..70563147dc 100644 --- a/src/npair_half_size_multi_newton_tri.h +++ b/src/npair_half_size_multi_newton_tri.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_size_multi_old_newtoff.cpp b/src/npair_half_size_multi_old_newtoff.cpp index 4f8e4a8078..158ddc0f10 100644 --- a/src/npair_half_size_multi_old_newtoff.cpp +++ b/src/npair_half_size_multi_old_newtoff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_size_multi_old_newtoff.h b/src/npair_half_size_multi_old_newtoff.h index eaaa3f6cba..051d5d47de 100644 --- a/src/npair_half_size_multi_old_newtoff.h +++ b/src/npair_half_size_multi_old_newtoff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_size_multi_old_newton.cpp b/src/npair_half_size_multi_old_newton.cpp index 753c8c7d44..cbb75f568d 100644 --- a/src/npair_half_size_multi_old_newton.cpp +++ b/src/npair_half_size_multi_old_newton.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_size_multi_old_newton.h b/src/npair_half_size_multi_old_newton.h index 408b4bdb69..082e752e80 100644 --- a/src/npair_half_size_multi_old_newton.h +++ b/src/npair_half_size_multi_old_newton.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_size_multi_old_newton_tri.cpp b/src/npair_half_size_multi_old_newton_tri.cpp index ee7a11a36e..ea3f271956 100644 --- a/src/npair_half_size_multi_old_newton_tri.cpp +++ b/src/npair_half_size_multi_old_newton_tri.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_size_multi_old_newton_tri.h b/src/npair_half_size_multi_old_newton_tri.h index 828c2ab7f1..354832e07d 100644 --- a/src/npair_half_size_multi_old_newton_tri.h +++ b/src/npair_half_size_multi_old_newton_tri.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_size_nsq_newtoff.cpp b/src/npair_half_size_nsq_newtoff.cpp index 9ace347901..f34c9e6323 100644 --- a/src/npair_half_size_nsq_newtoff.cpp +++ b/src/npair_half_size_nsq_newtoff.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_size_nsq_newtoff.h b/src/npair_half_size_nsq_newtoff.h index d0777b16c9..d84d7d62dd 100644 --- a/src/npair_half_size_nsq_newtoff.h +++ b/src/npair_half_size_nsq_newtoff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_size_nsq_newton.cpp b/src/npair_half_size_nsq_newton.cpp index 05409a0bab..8b596e6968 100644 --- a/src/npair_half_size_nsq_newton.cpp +++ b/src/npair_half_size_nsq_newton.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_half_size_nsq_newton.h b/src/npair_half_size_nsq_newton.h index 0f058cecb5..d55785bd72 100644 --- a/src/npair_half_size_nsq_newton.h +++ b/src/npair_half_size_nsq_newton.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_halffull_newtoff.cpp b/src/npair_halffull_newtoff.cpp index 57c121b933..a5f0e1624a 100644 --- a/src/npair_halffull_newtoff.cpp +++ b/src/npair_halffull_newtoff.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_halffull_newtoff.h b/src/npair_halffull_newtoff.h index 3254006e2f..d2b42f2370 100644 --- a/src/npair_halffull_newtoff.h +++ b/src/npair_halffull_newtoff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_halffull_newtoff_trim.cpp b/src/npair_halffull_newtoff_trim.cpp index af1f1d7304..8ed392da2f 100644 --- a/src/npair_halffull_newtoff_trim.cpp +++ b/src/npair_halffull_newtoff_trim.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_halffull_newtoff_trim.h b/src/npair_halffull_newtoff_trim.h index a5e39e4800..0fe730f9c1 100644 --- a/src/npair_halffull_newtoff_trim.h +++ b/src/npair_halffull_newtoff_trim.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_halffull_newton.cpp b/src/npair_halffull_newton.cpp index d9ba02d5b0..3232b79db1 100644 --- a/src/npair_halffull_newton.cpp +++ b/src/npair_halffull_newton.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_halffull_newton.h b/src/npair_halffull_newton.h index 736985466a..3a9462f8b4 100644 --- a/src/npair_halffull_newton.h +++ b/src/npair_halffull_newton.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_halffull_newton_trim.cpp b/src/npair_halffull_newton_trim.cpp index 26e46a0525..d52806bdfa 100644 --- a/src/npair_halffull_newton_trim.cpp +++ b/src/npair_halffull_newton_trim.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_halffull_newton_trim.h b/src/npair_halffull_newton_trim.h index 344ed618a8..aad3edcbfb 100644 --- a/src/npair_halffull_newton_trim.h +++ b/src/npair_halffull_newton_trim.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_skip.cpp b/src/npair_skip.cpp index 4ef0573dbb..b901611518 100644 --- a/src/npair_skip.cpp +++ b/src/npair_skip.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_skip.h b/src/npair_skip.h index 03e912fcc4..4e85174730 100644 --- a/src/npair_skip.h +++ b/src/npair_skip.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_skip_respa.cpp b/src/npair_skip_respa.cpp index 373fe3f8db..022c0d5f60 100644 --- a/src/npair_skip_respa.cpp +++ b/src/npair_skip_respa.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_skip_respa.h b/src/npair_skip_respa.h index 4d03f33462..822fcc290b 100644 --- a/src/npair_skip_respa.h +++ b/src/npair_skip_respa.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_skip_size.cpp b/src/npair_skip_size.cpp index b0134fd82c..22883b4e60 100644 --- a/src/npair_skip_size.cpp +++ b/src/npair_skip_size.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_skip_size.h b/src/npair_skip_size.h index 8cc993e2f3..9c2f23447b 100644 --- a/src/npair_skip_size.h +++ b/src/npair_skip_size.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_skip_size_off2on.cpp b/src/npair_skip_size_off2on.cpp index e48ca345ff..00538b68c1 100644 --- a/src/npair_skip_size_off2on.cpp +++ b/src/npair_skip_size_off2on.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_skip_size_off2on.h b/src/npair_skip_size_off2on.h index ee491700c2..faed76f6c3 100644 --- a/src/npair_skip_size_off2on.h +++ b/src/npair_skip_size_off2on.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_skip_size_off2on_oneside.cpp b/src/npair_skip_size_off2on_oneside.cpp index 1e4b4ac78d..eecf293755 100644 --- a/src/npair_skip_size_off2on_oneside.cpp +++ b/src/npair_skip_size_off2on_oneside.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_skip_size_off2on_oneside.h b/src/npair_skip_size_off2on_oneside.h index 7e73b06892..48eccf7faf 100644 --- a/src/npair_skip_size_off2on_oneside.h +++ b/src/npair_skip_size_off2on_oneside.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_trim.cpp b/src/npair_trim.cpp index 82078ff1be..14974d72ab 100644 --- a/src/npair_trim.cpp +++ b/src/npair_trim.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Trimright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/npair_trim.h b/src/npair_trim.h index d8510051c8..2a7c9285e0 100644 --- a/src/npair_trim.h +++ b/src/npair_trim.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Trimright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 944c94f983..e89f014f29 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil.h b/src/nstencil.h index ac48eb6316..6ae7f05dfb 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_full_bin_2d.cpp b/src/nstencil_full_bin_2d.cpp index 5c79f3ae8a..cbcdc6e797 100644 --- a/src/nstencil_full_bin_2d.cpp +++ b/src/nstencil_full_bin_2d.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_full_bin_2d.h b/src/nstencil_full_bin_2d.h index d30dfac59f..c3cdbb3b9b 100644 --- a/src/nstencil_full_bin_2d.h +++ b/src/nstencil_full_bin_2d.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_full_bin_3d.cpp b/src/nstencil_full_bin_3d.cpp index 837bf109f2..e305abc764 100644 --- a/src/nstencil_full_bin_3d.cpp +++ b/src/nstencil_full_bin_3d.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_full_bin_3d.h b/src/nstencil_full_bin_3d.h index 1939bef184..73da08b840 100644 --- a/src/nstencil_full_bin_3d.h +++ b/src/nstencil_full_bin_3d.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_full_ghost_bin_2d.cpp b/src/nstencil_full_ghost_bin_2d.cpp index 32c4440647..0429624cb1 100644 --- a/src/nstencil_full_ghost_bin_2d.cpp +++ b/src/nstencil_full_ghost_bin_2d.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_full_ghost_bin_2d.h b/src/nstencil_full_ghost_bin_2d.h index 558d4af0ef..2907880c92 100644 --- a/src/nstencil_full_ghost_bin_2d.h +++ b/src/nstencil_full_ghost_bin_2d.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_full_ghost_bin_3d.cpp b/src/nstencil_full_ghost_bin_3d.cpp index 3d43e35e04..866f391b90 100644 --- a/src/nstencil_full_ghost_bin_3d.cpp +++ b/src/nstencil_full_ghost_bin_3d.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_full_ghost_bin_3d.h b/src/nstencil_full_ghost_bin_3d.h index 7a3479747b..5fea44f48e 100644 --- a/src/nstencil_full_ghost_bin_3d.h +++ b/src/nstencil_full_ghost_bin_3d.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_full_multi_2d.cpp b/src/nstencil_full_multi_2d.cpp index d6e5fd2a9d..b49e245d25 100644 --- a/src/nstencil_full_multi_2d.cpp +++ b/src/nstencil_full_multi_2d.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_full_multi_2d.h b/src/nstencil_full_multi_2d.h index 0ba95c9b02..6b9c98bd89 100644 --- a/src/nstencil_full_multi_2d.h +++ b/src/nstencil_full_multi_2d.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_full_multi_3d.cpp b/src/nstencil_full_multi_3d.cpp index d48cf0c8d7..107e3e6d13 100644 --- a/src/nstencil_full_multi_3d.cpp +++ b/src/nstencil_full_multi_3d.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_full_multi_3d.h b/src/nstencil_full_multi_3d.h index 4517ed72cb..e4d4691139 100644 --- a/src/nstencil_full_multi_3d.h +++ b/src/nstencil_full_multi_3d.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_full_multi_old_2d.cpp b/src/nstencil_full_multi_old_2d.cpp index 3747e99699..80d7275279 100644 --- a/src/nstencil_full_multi_old_2d.cpp +++ b/src/nstencil_full_multi_old_2d.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_full_multi_old_2d.h b/src/nstencil_full_multi_old_2d.h index ae5967fb9f..713a88d549 100644 --- a/src/nstencil_full_multi_old_2d.h +++ b/src/nstencil_full_multi_old_2d.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_full_multi_old_3d.cpp b/src/nstencil_full_multi_old_3d.cpp index 04f10c5362..c733bc8e88 100644 --- a/src/nstencil_full_multi_old_3d.cpp +++ b/src/nstencil_full_multi_old_3d.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_full_multi_old_3d.h b/src/nstencil_full_multi_old_3d.h index 2dcdcdf9f5..9ebaed6154 100644 --- a/src/nstencil_full_multi_old_3d.h +++ b/src/nstencil_full_multi_old_3d.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_half_bin_2d.cpp b/src/nstencil_half_bin_2d.cpp index b1ad0237a7..c65095a3b0 100644 --- a/src/nstencil_half_bin_2d.cpp +++ b/src/nstencil_half_bin_2d.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_half_bin_2d.h b/src/nstencil_half_bin_2d.h index 4ad4d356a2..506136b41d 100644 --- a/src/nstencil_half_bin_2d.h +++ b/src/nstencil_half_bin_2d.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_half_bin_2d_tri.cpp b/src/nstencil_half_bin_2d_tri.cpp index 7b7ce962a2..06831730fd 100644 --- a/src/nstencil_half_bin_2d_tri.cpp +++ b/src/nstencil_half_bin_2d_tri.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_half_bin_2d_tri.h b/src/nstencil_half_bin_2d_tri.h index 844f8100a9..2873b7d92f 100644 --- a/src/nstencil_half_bin_2d_tri.h +++ b/src/nstencil_half_bin_2d_tri.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_half_bin_3d.cpp b/src/nstencil_half_bin_3d.cpp index 736bf151ee..90d8e45053 100644 --- a/src/nstencil_half_bin_3d.cpp +++ b/src/nstencil_half_bin_3d.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_half_bin_3d.h b/src/nstencil_half_bin_3d.h index 0347e203b6..2b612a4a0a 100644 --- a/src/nstencil_half_bin_3d.h +++ b/src/nstencil_half_bin_3d.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_half_bin_3d_tri.cpp b/src/nstencil_half_bin_3d_tri.cpp index a5376d0208..d066a24ee6 100644 --- a/src/nstencil_half_bin_3d_tri.cpp +++ b/src/nstencil_half_bin_3d_tri.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_half_bin_3d_tri.h b/src/nstencil_half_bin_3d_tri.h index 2b0e3c9e10..ad24ab0a06 100644 --- a/src/nstencil_half_bin_3d_tri.h +++ b/src/nstencil_half_bin_3d_tri.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_half_multi_2d.cpp b/src/nstencil_half_multi_2d.cpp index 81713e183d..e8e452d8fc 100644 --- a/src/nstencil_half_multi_2d.cpp +++ b/src/nstencil_half_multi_2d.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_half_multi_2d.h b/src/nstencil_half_multi_2d.h index 11447c8952..a87f517b5b 100644 --- a/src/nstencil_half_multi_2d.h +++ b/src/nstencil_half_multi_2d.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_half_multi_2d_tri.cpp b/src/nstencil_half_multi_2d_tri.cpp index d53c503fad..9a63331f18 100644 --- a/src/nstencil_half_multi_2d_tri.cpp +++ b/src/nstencil_half_multi_2d_tri.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_half_multi_2d_tri.h b/src/nstencil_half_multi_2d_tri.h index 4e93e940a0..6067afbb50 100644 --- a/src/nstencil_half_multi_2d_tri.h +++ b/src/nstencil_half_multi_2d_tri.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_half_multi_3d.cpp b/src/nstencil_half_multi_3d.cpp index ca4b4c4111..446f740617 100644 --- a/src/nstencil_half_multi_3d.cpp +++ b/src/nstencil_half_multi_3d.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_half_multi_3d.h b/src/nstencil_half_multi_3d.h index 30c197e9e4..c9281cab19 100644 --- a/src/nstencil_half_multi_3d.h +++ b/src/nstencil_half_multi_3d.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_half_multi_3d_tri.cpp b/src/nstencil_half_multi_3d_tri.cpp index 60df9199a2..4298353a86 100644 --- a/src/nstencil_half_multi_3d_tri.cpp +++ b/src/nstencil_half_multi_3d_tri.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_half_multi_3d_tri.h b/src/nstencil_half_multi_3d_tri.h index 914be51825..9a55c10f1d 100644 --- a/src/nstencil_half_multi_3d_tri.h +++ b/src/nstencil_half_multi_3d_tri.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_half_multi_old_2d.cpp b/src/nstencil_half_multi_old_2d.cpp index b4869b37f4..6bf9e5c5b1 100644 --- a/src/nstencil_half_multi_old_2d.cpp +++ b/src/nstencil_half_multi_old_2d.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_half_multi_old_2d.h b/src/nstencil_half_multi_old_2d.h index 13f5579a7d..a3825bcb71 100644 --- a/src/nstencil_half_multi_old_2d.h +++ b/src/nstencil_half_multi_old_2d.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_half_multi_old_2d_tri.cpp b/src/nstencil_half_multi_old_2d_tri.cpp index e6cf2d311e..1438aef843 100644 --- a/src/nstencil_half_multi_old_2d_tri.cpp +++ b/src/nstencil_half_multi_old_2d_tri.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_half_multi_old_2d_tri.h b/src/nstencil_half_multi_old_2d_tri.h index 9701cbf449..a65eb21ff7 100644 --- a/src/nstencil_half_multi_old_2d_tri.h +++ b/src/nstencil_half_multi_old_2d_tri.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_half_multi_old_3d.cpp b/src/nstencil_half_multi_old_3d.cpp index ada8c66610..99e72610f0 100644 --- a/src/nstencil_half_multi_old_3d.cpp +++ b/src/nstencil_half_multi_old_3d.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_half_multi_old_3d.h b/src/nstencil_half_multi_old_3d.h index e47239ec4a..3b93d3cd6c 100644 --- a/src/nstencil_half_multi_old_3d.h +++ b/src/nstencil_half_multi_old_3d.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_half_multi_old_3d_tri.cpp b/src/nstencil_half_multi_old_3d_tri.cpp index c58fe509ef..836eee6039 100644 --- a/src/nstencil_half_multi_old_3d_tri.cpp +++ b/src/nstencil_half_multi_old_3d_tri.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/nstencil_half_multi_old_3d_tri.h b/src/nstencil_half_multi_old_3d_tri.h index 53889e1392..89fc167959 100644 --- a/src/nstencil_half_multi_old_3d_tri.h +++ b/src/nstencil_half_multi_old_3d_tri.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo.cpp b/src/ntopo.cpp index f1cd547e44..6f96587f08 100644 --- a/src/ntopo.cpp +++ b/src/ntopo.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo.h b/src/ntopo.h index e03cf809a9..cf81738251 100644 --- a/src/ntopo.h +++ b/src/ntopo.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo_angle_all.cpp b/src/ntopo_angle_all.cpp index 915cbb5cb3..a4b7ffd973 100644 --- a/src/ntopo_angle_all.cpp +++ b/src/ntopo_angle_all.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo_angle_all.h b/src/ntopo_angle_all.h index 3c81d6907a..28c2a74cd6 100644 --- a/src/ntopo_angle_all.h +++ b/src/ntopo_angle_all.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo_angle_partial.cpp b/src/ntopo_angle_partial.cpp index 5a09d15909..4b59dce86f 100644 --- a/src/ntopo_angle_partial.cpp +++ b/src/ntopo_angle_partial.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo_angle_partial.h b/src/ntopo_angle_partial.h index 94d5ac09b1..8153fafa81 100644 --- a/src/ntopo_angle_partial.h +++ b/src/ntopo_angle_partial.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo_angle_template.cpp b/src/ntopo_angle_template.cpp index ff0b499c9e..4ef188a2fc 100644 --- a/src/ntopo_angle_template.cpp +++ b/src/ntopo_angle_template.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo_angle_template.h b/src/ntopo_angle_template.h index 60bb6d3109..777a2cfd9e 100644 --- a/src/ntopo_angle_template.h +++ b/src/ntopo_angle_template.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo_bond_all.cpp b/src/ntopo_bond_all.cpp index b3cd3011a5..c52309f8cf 100644 --- a/src/ntopo_bond_all.cpp +++ b/src/ntopo_bond_all.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo_bond_all.h b/src/ntopo_bond_all.h index 52a64da8b3..d8937bce01 100644 --- a/src/ntopo_bond_all.h +++ b/src/ntopo_bond_all.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo_bond_partial.cpp b/src/ntopo_bond_partial.cpp index de6d0bf151..e020137f90 100644 --- a/src/ntopo_bond_partial.cpp +++ b/src/ntopo_bond_partial.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo_bond_partial.h b/src/ntopo_bond_partial.h index f035143a2a..efe7009481 100644 --- a/src/ntopo_bond_partial.h +++ b/src/ntopo_bond_partial.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo_bond_template.cpp b/src/ntopo_bond_template.cpp index e2cb4d87c5..263feb2a1d 100644 --- a/src/ntopo_bond_template.cpp +++ b/src/ntopo_bond_template.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo_bond_template.h b/src/ntopo_bond_template.h index 6be277cbbc..3c3832818a 100644 --- a/src/ntopo_bond_template.h +++ b/src/ntopo_bond_template.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo_dihedral_all.cpp b/src/ntopo_dihedral_all.cpp index e378e82d45..a281ac97df 100644 --- a/src/ntopo_dihedral_all.cpp +++ b/src/ntopo_dihedral_all.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo_dihedral_all.h b/src/ntopo_dihedral_all.h index 420c3962b4..2416a0d638 100644 --- a/src/ntopo_dihedral_all.h +++ b/src/ntopo_dihedral_all.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo_dihedral_partial.cpp b/src/ntopo_dihedral_partial.cpp index c8c94b45e5..04280c412e 100644 --- a/src/ntopo_dihedral_partial.cpp +++ b/src/ntopo_dihedral_partial.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo_dihedral_partial.h b/src/ntopo_dihedral_partial.h index b0b540a86e..768d279dd7 100644 --- a/src/ntopo_dihedral_partial.h +++ b/src/ntopo_dihedral_partial.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo_dihedral_template.cpp b/src/ntopo_dihedral_template.cpp index f7f7d7594a..5c92ae6bed 100644 --- a/src/ntopo_dihedral_template.cpp +++ b/src/ntopo_dihedral_template.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo_dihedral_template.h b/src/ntopo_dihedral_template.h index 484635e6b7..003efebaad 100644 --- a/src/ntopo_dihedral_template.h +++ b/src/ntopo_dihedral_template.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo_improper_all.cpp b/src/ntopo_improper_all.cpp index ec9aab9827..13229bd179 100644 --- a/src/ntopo_improper_all.cpp +++ b/src/ntopo_improper_all.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo_improper_all.h b/src/ntopo_improper_all.h index dd4ba81587..5d4d1d3aa5 100644 --- a/src/ntopo_improper_all.h +++ b/src/ntopo_improper_all.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo_improper_partial.cpp b/src/ntopo_improper_partial.cpp index be7f2531da..17dc507ccc 100644 --- a/src/ntopo_improper_partial.cpp +++ b/src/ntopo_improper_partial.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo_improper_partial.h b/src/ntopo_improper_partial.h index e4e181d09f..fcf87643d7 100644 --- a/src/ntopo_improper_partial.h +++ b/src/ntopo_improper_partial.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo_improper_template.cpp b/src/ntopo_improper_template.cpp index c714d6fef8..9be6cd1813 100644 --- a/src/ntopo_improper_template.cpp +++ b/src/ntopo_improper_template.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/ntopo_improper_template.h b/src/ntopo_improper_template.h index 1bdc0fe572..fe5bfeb512 100644 --- a/src/ntopo_improper_template.h +++ b/src/ntopo_improper_template.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/omp_compat.h b/src/omp_compat.h index f7c33cedb6..1d35ee34e5 100644 --- a/src/omp_compat.h +++ b/src/omp_compat.h @@ -2,7 +2,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2020) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/output.cpp b/src/output.cpp index 9442311724..1036ff26e5 100644 --- a/src/output.cpp +++ b/src/output.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/output.h b/src/output.h index adbfd1b165..32f3a0a48a 100644 --- a/src/output.h +++ b/src/output.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pack.h b/src/pack.h index a3a4ddd90a..58284f83fa 100644 --- a/src/pack.h +++ b/src/pack.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair.cpp b/src/pair.cpp index c5aed7ee65..fc7232d615 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -821,7 +821,7 @@ void Pair::map_element2type(int narg, char **arg, bool update_setflag) // elements = list of element names if (narg != ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Number of element to type mappings does not match number of atom types"); if (elements) { for (i = 0; i < nelements; i++) delete[] elements[i]; diff --git a/src/pair.h b/src/pair.h index 4f4d66ed97..73fa7e4d29 100644 --- a/src/pair.h +++ b/src/pair.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -203,6 +203,8 @@ class Pair : protected Pointers { virtual int pack_reverse_comm(int, int, double *) { return 0; } virtual void unpack_reverse_comm(int, int *, double *) {} + virtual void reset_grid() {} + virtual void pack_forward_grid(int, void *, int, int *) {} virtual void unpack_forward_grid(int, void *, int, int *) {} virtual void pack_reverse_grid(int, void *, int, int *) {} diff --git a/src/pair_born.cpp b/src/pair_born.cpp index dd2292a4e7..7a76e5f547 100644 --- a/src/pair_born.cpp +++ b/src/pair_born.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_born.h b/src/pair_born.h index 0c6bbb88d4..acfa3ccfc9 100644 --- a/src/pair_born.h +++ b/src/pair_born.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_buck.cpp b/src/pair_buck.cpp index 8c6a4afd19..dcd4e5f079 100644 --- a/src/pair_buck.cpp +++ b/src/pair_buck.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_buck.h b/src/pair_buck.h index 1df96e09e2..1fdaf1a0e5 100644 --- a/src/pair_buck.h +++ b/src/pair_buck.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_buck_coul_cut.cpp b/src/pair_buck_coul_cut.cpp index 7926b01c91..4f85ccd430 100644 --- a/src/pair_buck_coul_cut.cpp +++ b/src/pair_buck_coul_cut.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_buck_coul_cut.h b/src/pair_buck_coul_cut.h index 9460e89df7..b5f19def38 100644 --- a/src/pair_buck_coul_cut.h +++ b/src/pair_buck_coul_cut.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp index daca6374c5..9246e535fe 100644 --- a/src/pair_coul_cut.cpp +++ b/src/pair_coul_cut.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_coul_cut.h b/src/pair_coul_cut.h index 2eb08e73b2..dc3a3df64f 100644 --- a/src/pair_coul_cut.h +++ b/src/pair_coul_cut.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_coul_debye.cpp b/src/pair_coul_debye.cpp index 4320233569..0f375f6e00 100644 --- a/src/pair_coul_debye.cpp +++ b/src/pair_coul_debye.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_coul_debye.h b/src/pair_coul_debye.h index f045849503..0f28efb46a 100644 --- a/src/pair_coul_debye.h +++ b/src/pair_coul_debye.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_coul_dsf.cpp b/src/pair_coul_dsf.cpp index 9617cc1331..8e42cdadee 100644 --- a/src/pair_coul_dsf.cpp +++ b/src/pair_coul_dsf.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_coul_dsf.h b/src/pair_coul_dsf.h index 8b562ecf02..7a1cfa10a1 100644 --- a/src/pair_coul_dsf.h +++ b/src/pair_coul_dsf.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_coul_wolf.cpp b/src/pair_coul_wolf.cpp index 3d8ade8110..2bd3094a7c 100644 --- a/src/pair_coul_wolf.cpp +++ b/src/pair_coul_wolf.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_coul_wolf.h b/src/pair_coul_wolf.h index 97fe0be429..afe3c0e1ef 100644 --- a/src/pair_coul_wolf.h +++ b/src/pair_coul_wolf.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_deprecated.cpp b/src/pair_deprecated.cpp index cafb0ce7c0..eeb36d2171 100644 --- a/src/pair_deprecated.cpp +++ b/src/pair_deprecated.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_deprecated.h b/src/pair_deprecated.h index 2af100ee74..3f6e72ab0f 100644 --- a/src/pair_deprecated.h +++ b/src/pair_deprecated.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index a4a7528d14..0c1bf1b6d5 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -3,7 +3,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -271,10 +271,9 @@ void PairHybrid::allocate() void PairHybrid::settings(int narg, char **arg) { - if (narg < 1) error->all(FLERR,"Illegal pair_style command"); + if (narg < 1) utils::missing_cmd_args(FLERR, "pair_style hybrid", error); if (lmp->kokkos && !utils::strmatch(force->pair_style,"^hybrid.*/kk$")) - error->all(FLERR,"Must use pair_style {}/kk with Kokkos", - force->pair_style); + error->all(FLERR,"Must use pair_style {}/kk with Kokkos", force->pair_style); // delete old lists, since cannot just change settings @@ -326,9 +325,9 @@ void PairHybrid::settings(int narg, char **arg) nstyles = 0; while (iarg < narg) { if (utils::strmatch(arg[iarg],"^hybrid")) - error->all(FLERR,"Pair style hybrid cannot have hybrid as an argument"); + error->all(FLERR,"Pair style hybrid cannot have hybrid as a sub-style"); if (strcmp(arg[iarg],"none") == 0) - error->all(FLERR,"Pair style hybrid cannot have none as an argument"); + error->all(FLERR,"Pair style hybrid cannot have none as a sub-style"); styles[nstyles] = force->new_pair(arg[iarg],1,dummy); keywords[nstyles] = force->store_style(arg[iarg],0); @@ -478,7 +477,7 @@ void PairHybrid::init_svector() void PairHybrid::coeff(int narg, char **arg) { - if (narg < 3) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 3) utils::missing_cmd_args(FLERR,"pair_coeff", error); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -497,7 +496,7 @@ void PairHybrid::coeff(int narg, char **arg) if (strcmp(arg[2],keywords[m]) == 0) { if (multiple[m]) { multflag = 1; - if (narg < 4) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 4) utils::missing_cmd_args(FLERR, "pair_coeff", error); if (multiple[m] == utils::inumeric(FLERR,arg[3],false,lmp)) break; else continue; } else break; @@ -507,7 +506,7 @@ void PairHybrid::coeff(int narg, char **arg) int none = 0; if (m == nstyles) { if (strcmp(arg[2],"none") == 0) none = 1; - else error->all(FLERR,"Pair coeff for hybrid has invalid style: {}",arg[2]); + else error->all(FLERR,"Pair coeff for hybrid has invalid style: {}", arg[2]); } // move 1st/2nd args to 2nd/3rd args @@ -527,7 +526,7 @@ void PairHybrid::coeff(int narg, char **arg) if (!none && styles[m]->one_coeff) { if ((strcmp(arg[0],"*") != 0) || (strcmp(arg[1],"*") != 0)) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR,"Pair_coeff must start with * * for sub-style {}", keywords[m]); for (int i = 1; i <= atom->ntypes; i++) for (int j = i; j <= atom->ntypes; j++) if (nmap[i][j] && map[i][j][0] == m) { @@ -578,7 +577,7 @@ void PairHybrid::init_style() for (jtype = itype; jtype <= ntypes; jtype++) for (m = 0; m < nmap[itype][jtype]; m++) if (map[itype][jtype][m] == istyle) used = 1; - if (used == 0) error->all(FLERR,"Pair hybrid sub-style is not used"); + if (used == 0) error->all(FLERR,"Pair hybrid sub-style {} is not used", keywords[istyle]); } // The GPU library uses global data for each pair style, so the diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h index 37b79e5917..d3a7693f9b 100644 --- a/src/pair_hybrid.h +++ b/src/pair_hybrid.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_hybrid_overlay.cpp b/src/pair_hybrid_overlay.cpp index e93473e3c9..12c84c3a71 100644 --- a/src/pair_hybrid_overlay.cpp +++ b/src/pair_hybrid_overlay.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_hybrid_overlay.h b/src/pair_hybrid_overlay.h index 8debcb2056..ea0babbde5 100644 --- a/src/pair_hybrid_overlay.h +++ b/src/pair_hybrid_overlay.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_hybrid_scaled.cpp b/src/pair_hybrid_scaled.cpp index 5c20bff5e2..7cfc4a4c48 100644 --- a/src/pair_hybrid_scaled.cpp +++ b/src/pair_hybrid_scaled.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_hybrid_scaled.h b/src/pair_hybrid_scaled.h index 14d8ede71f..64fd938822 100644 --- a/src/pair_hybrid_scaled.h +++ b/src/pair_hybrid_scaled.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp index 73d46b26ce..fae308c57f 100644 --- a/src/pair_lj_cut.cpp +++ b/src/pair_lj_cut.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_lj_cut.h b/src/pair_lj_cut.h index 3ab865650f..94480d9a4b 100644 --- a/src/pair_lj_cut.h +++ b/src/pair_lj_cut.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_lj_cut_coul_cut.cpp b/src/pair_lj_cut_coul_cut.cpp index 264a31b2c6..bc5f5ed93e 100644 --- a/src/pair_lj_cut_coul_cut.cpp +++ b/src/pair_lj_cut_coul_cut.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_lj_cut_coul_cut.h b/src/pair_lj_cut_coul_cut.h index 7ad725845a..b4e1bfb5c9 100644 --- a/src/pair_lj_cut_coul_cut.h +++ b/src/pair_lj_cut_coul_cut.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_lj_expand.cpp b/src/pair_lj_expand.cpp index 9276e0804e..ea2801abb3 100644 --- a/src/pair_lj_expand.cpp +++ b/src/pair_lj_expand.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_lj_expand.h b/src/pair_lj_expand.h index 84c1aafdd2..8a8ed1838b 100644 --- a/src/pair_lj_expand.h +++ b/src/pair_lj_expand.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp index 64c5339950..2332d7fa6c 100644 --- a/src/pair_morse.cpp +++ b/src/pair_morse.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_morse.h b/src/pair_morse.h index 9a818c7d4e..43fece47bb 100644 --- a/src/pair_morse.h +++ b/src/pair_morse.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_soft.cpp b/src/pair_soft.cpp index 5802cfaf19..66c4c1f9cd 100644 --- a/src/pair_soft.cpp +++ b/src/pair_soft.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_soft.h b/src/pair_soft.h index 08ace01cbc..8fd1654609 100644 --- a/src/pair_soft.h +++ b/src/pair_soft.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_table.cpp b/src/pair_table.cpp index 11bd986822..3e293cb414 100644 --- a/src/pair_table.cpp +++ b/src/pair_table.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -398,6 +398,9 @@ void PairTable::read_table(Table *tb, char *file, char *keyword) reader.skip_line(); for (int i = 0; i < tb->ninput; i++) { line = reader.next_line(); + if (!line) + error->one(FLERR, "Data missing when parsing pair table '{}' line {} of {}.", keyword, i + 1, + tb->ninput); try { ValueTokenizer values(line); values.next_int(); diff --git a/src/pair_table.h b/src/pair_table.h index 529a4a93e2..36c8d04b1f 100644 --- a/src/pair_table.h +++ b/src/pair_table.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp index e1190b614f..55a686e5f0 100644 --- a/src/pair_yukawa.cpp +++ b/src/pair_yukawa.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_yukawa.h b/src/pair_yukawa.h index 64c7166331..5a2e282ef1 100644 --- a/src/pair_yukawa.h +++ b/src/pair_yukawa.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_zbl.cpp b/src/pair_zbl.cpp index 292b3e8ad0..bbbeea18d7 100644 --- a/src/pair_zbl.cpp +++ b/src/pair_zbl.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_zbl.h b/src/pair_zbl.h index f51e6ba93b..e0409c687b 100644 --- a/src/pair_zbl.h +++ b/src/pair_zbl.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_zbl_const.h b/src/pair_zbl_const.h index 325c30034f..61f05174be 100644 --- a/src/pair_zbl_const.h +++ b/src/pair_zbl_const.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pair_zero.cpp b/src/pair_zero.cpp index b554f78b7f..c62479d1c4 100644 --- a/src/pair_zero.cpp +++ b/src/pair_zero.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -21,7 +21,6 @@ #include "comm.h" #include "error.h" #include "memory.h" -#include "neigh_list.h" #include "neighbor.h" #include diff --git a/src/pair_zero.h b/src/pair_zero.h index 06d7b2ab72..e70ece0190 100644 --- a/src/pair_zero.h +++ b/src/pair_zero.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/platform.cpp b/src/platform.cpp index 667481b94d..861e3d7722 100644 --- a/src/platform.cpp +++ b/src/platform.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -16,6 +16,8 @@ * the "utils" namespace with convenience and utility functions. */ #include "platform.h" + +#include "fmt/format.h" #include "text_file_reader.h" #include "utils.h" @@ -229,6 +231,8 @@ std::string platform::os_info() buf = "Windows 10 21H1"; } else if (build == "19044") { buf = "Windows 10 21H2"; + } else if (build == "19045") { + buf = "Windows 10 22H2"; } else if (build == "20348") { buf = "Windows Server 2022"; } else if (build == "22000") { diff --git a/src/platform.h b/src/platform.h index 82835fb4dc..7a8dcea24e 100644 --- a/src/platform.h +++ b/src/platform.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/pointers.h b/src/pointers.h index 5f82872514..09efa49cbc 100644 --- a/src/pointers.h +++ b/src/pointers.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -28,6 +28,7 @@ #include // IWYU pragme: export #include // IWYU pragma: export #include // IWYU pragma: export +#include // IWYU pragma: export #include "fmt/format.h" // IWYU pragma: export #include "lammps.h" // IWYU pragma: export diff --git a/src/potential_file_reader.cpp b/src/potential_file_reader.cpp index 8d190efdef..2c0b9a6a55 100644 --- a/src/potential_file_reader.cpp +++ b/src/potential_file_reader.cpp @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/potential_file_reader.h b/src/potential_file_reader.h index 466419b676..c07b4b83f6 100644 --- a/src/potential_file_reader.h +++ b/src/potential_file_reader.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/procmap.cpp b/src/procmap.cpp index 801a18c7a5..6fcea50315 100644 --- a/src/procmap.cpp +++ b/src/procmap.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/procmap.h b/src/procmap.h index df8b9431d3..06867837c6 100644 --- a/src/procmap.h +++ b/src/procmap.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/random_mars.cpp b/src/random_mars.cpp index a0eb24eed3..8f1105e0d9 100644 --- a/src/random_mars.cpp +++ b/src/random_mars.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -187,7 +187,7 @@ double RanMars::besselexp(double theta, double alpha, double cp) void RanMars::select_subset(bigint ntarget, int nmine, int *mark, int *next) { - int mode,index,oldindex,newvalue,nflip,which,niter; + int mode,index,oldindex,newvalue,nflip,which; int active[2],first[2]; int newactive[2],newfirst[2],newlast[2]; bigint nmark,nflipall; @@ -209,8 +209,6 @@ void RanMars::select_subset(bigint ntarget, int nmine, int *mark, int *next) if (nmine > 0) next[nmine-1] = -1; nmark = 0; - niter = 0; - while (nmark != ntarget) { // choose to ADD or SUBTRACT from current nmark @@ -285,13 +283,6 @@ void RanMars::select_subset(bigint ntarget, int nmine, int *mark, int *next) if (mode == ADD) nmark += nflipall; else if (mode == SUBTRACT) nmark -= nflipall; - - niter++; - - // DEBUG output of stats - - //if (comm->me == 0) printf("%d %ld %ld %g %ld\n", - // niter,nmark,nactiveall,thresh,nflipall); } } diff --git a/src/random_mars.h b/src/random_mars.h index 91fad5a2f3..0b89c18c72 100644 --- a/src/random_mars.h +++ b/src/random_mars.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/random_park.cpp b/src/random_park.cpp index 34f8396e44..f11515ff8c 100644 --- a/src/random_park.cpp +++ b/src/random_park.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/random_park.h b/src/random_park.h index 0abe2e4fd3..fa703e035e 100644 --- a/src/random_park.h +++ b/src/random_park.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/rcb.cpp b/src/rcb.cpp index ef326793cc..85a7c72f74 100644 --- a/src/rcb.cpp +++ b/src/rcb.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/rcb.h b/src/rcb.h index e6f187799a..34a33f6b52 100644 --- a/src/rcb.h +++ b/src/rcb.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/read_data.cpp b/src/read_data.cpp index 63d291a5dc..85f5accc4b 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -41,6 +41,7 @@ #include #include +#include #include using namespace LAMMPS_NS; @@ -374,6 +375,16 @@ void ReadData::command(int narg, char **arg) if (addflag == NONE) { domain->box_exist = 1; update->ntimestep = 0; + } else { + + // clear global->local map for owned and ghost atoms + // clear ghost count and any ghost bonus data internal to AtomVec + // same logic as beginning of Comm::exchange() + // do it now b/c adding atoms will overwrite ghost atoms + + if (atom->map_style != Atom::MAP_NONE) atom->map_clear(); + atom->nghost = 0; + atom->avec->clear_bonus(); } // compute atomID and optionally moleculeID offset for addflag = APPEND @@ -550,6 +561,8 @@ void ReadData::command(int narg, char **arg) // only done if firstpass and not first data file if (firstpass && addflag != NONE) { + double oldboxlo[3] = { domain->boxlo[0], domain->boxlo[1] , domain->boxlo[2]}; + double oldboxhi[3] = { domain->boxhi[0], domain->boxhi[1] , domain->boxhi[2]}; domain->boxlo[0] = MIN(domain->boxlo[0], boxlo[0] + shift[0]); domain->boxhi[0] = MAX(domain->boxhi[0], boxhi[0] + shift[0]); domain->boxlo[1] = MIN(domain->boxlo[1], boxlo[1] + shift[1]); @@ -557,6 +570,25 @@ void ReadData::command(int narg, char **arg) domain->boxlo[2] = MIN(domain->boxlo[2], boxlo[2] + shift[2]); domain->boxhi[2] = MAX(domain->boxhi[2], boxhi[2] + shift[2]); + // check of box has changed. If yes, warn about non-zero image flags + if ((oldboxlo[0] != domain->boxlo[0]) || (oldboxlo[1] != domain->boxlo[1]) || + (oldboxlo[2] != domain->boxlo[2]) || (oldboxhi[0] != domain->boxhi[0]) || + (oldboxhi[1] != domain->boxhi[1]) || (oldboxhi[2] != domain->boxhi[2])) { + int iflag = 1; + for (int i=0; i < atom->nlocal; ++i) { + int xbox = (atom->image[i] & IMGMASK) - IMGMAX; + int ybox = (atom->image[i] >> IMGBITS & IMGMASK) - IMGMAX; + int zbox = (atom->image[i] >> IMG2BITS) - IMGMAX; + if (xbox != 0) iflag = 1; + if (ybox != 0) iflag = 1; + if (zbox != 0) iflag = 1; + } + int flag_all; + MPI_Allreduce(&iflag,&flag_all, 1, MPI_INT, MPI_SUM, world); + if ((flag_all > 0) && (comm->me == 0)) + error->warning(FLERR,"Non-zero image flags with growing box leads to bad coordinates"); + } + // NOTE: not sure what to do about tilt value in subsequent data files //if (triclinic) { // domain->xy = xy; domain->xz = xz; domain->yz = yz; @@ -875,10 +907,13 @@ void ReadData::command(int narg, char **arg) int i; for (i = 0; i < nfix; i++) if (strcmp(keyword, fix_section[i]) == 0) { - if (firstpass) + if (firstpass) { fix(fix_index[i], keyword); - else - skip_lines(fix_index[i]->read_data_skip_lines(keyword)); + } else { + auto nskip = fix_index[i]->read_data_skip_lines(keyword); + if (nskip < 0) nskip = natoms; + skip_lines(nskip); + } break; } if (i == nfix) @@ -2225,6 +2260,7 @@ void ReadData::fix(Fix *ifix, char *keyword) int nchunk, eof; bigint nline = ifix->read_data_skip_lines(keyword); + if (nline < 0) nline = natoms; bigint nread = 0; while (nread < nline) { diff --git a/src/read_data.h b/src/read_data.h index aef35f99a1..c630c027bc 100644 --- a/src/read_data.h +++ b/src/read_data.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/read_dump.cpp b/src/read_dump.cpp index aa9ec0bbf0..71ea0288e5 100644 --- a/src/read_dump.cpp +++ b/src/read_dump.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/read_dump.h b/src/read_dump.h index 506cd197c1..f9a9f0ba57 100644 --- a/src/read_dump.h +++ b/src/read_dump.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 98f594ac5c..aa9f5fe8ee 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -599,6 +599,8 @@ void ReadRestart::header() if (flag == VERSION) { char *version = read_string(); + lmp->restart_ver = utils::date2num(version); + if (me == 0) utils::logmesg(lmp," restart file = {}, LAMMPS = {}\n", version, lmp->version); delete[] version; @@ -767,7 +769,7 @@ void ReadRestart::header() argcopy[i] = read_string(); atom->create_avec(style,nargcopy,argcopy,1); if (comm->me ==0) - utils::logmesg(lmp," restoring atom style {} from restart\n",style); + utils::logmesg(lmp," restoring atom style {} from restart\n",atom->atom_style); for (int i = 0; i < nargcopy; i++) delete[] argcopy[i]; delete[] argcopy; delete[] style; diff --git a/src/read_restart.h b/src/read_restart.h index 65459fc0cb..573f49016a 100644 --- a/src/read_restart.h +++ b/src/read_restart.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/reader.cpp b/src/reader.cpp index 025445ca24..3caafc62f4 100644 --- a/src/reader.cpp +++ b/src/reader.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/reader.h b/src/reader.h index 753b6956f7..e8483b76cd 100644 --- a/src/reader.h +++ b/src/reader.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/reader_native.cpp b/src/reader_native.cpp index 911de417eb..3e7d01550d 100644 --- a/src/reader_native.cpp +++ b/src/reader_native.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -19,6 +19,7 @@ #include "tokenizer.h" #include +#include #include using namespace LAMMPS_NS; diff --git a/src/reader_native.h b/src/reader_native.h index df8eede311..55a434ed14 100644 --- a/src/reader_native.h +++ b/src/reader_native.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/reader_xyz.cpp b/src/reader_xyz.cpp index 7add54fdb9..c11ec3a1a9 100644 --- a/src/reader_xyz.cpp +++ b/src/reader_xyz.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/reader_xyz.h b/src/reader_xyz.h index 5f943413b8..372c41baad 100644 --- a/src/reader_xyz.h +++ b/src/reader_xyz.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/region.cpp b/src/region.cpp index 1f328df155..abddfa4b83 100644 --- a/src/region.cpp +++ b/src/region.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/region.h b/src/region.h index b74d839049..f273485dce 100644 --- a/src/region.h +++ b/src/region.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/region_block.cpp b/src/region_block.cpp index 76c27fbd55..42c1269f9b 100644 --- a/src/region_block.cpp +++ b/src/region_block.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/region_block.h b/src/region_block.h index c342bebc3d..a1078176e1 100644 --- a/src/region_block.h +++ b/src/region_block.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/region_cone.cpp b/src/region_cone.cpp index 84da1bae56..e71a6a72a3 100644 --- a/src/region_cone.cpp +++ b/src/region_cone.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/region_cone.h b/src/region_cone.h index 7b1a1f7078..25fdcc9713 100644 --- a/src/region_cone.h +++ b/src/region_cone.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/region_cylinder.cpp b/src/region_cylinder.cpp index 0f7df1e3af..259b855a66 100644 --- a/src/region_cylinder.cpp +++ b/src/region_cylinder.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/region_cylinder.h b/src/region_cylinder.h index f9f1e3d4a5..816cbda3de 100644 --- a/src/region_cylinder.h +++ b/src/region_cylinder.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/region_deprecated.cpp b/src/region_deprecated.cpp index bc59d77259..00142b13ed 100644 --- a/src/region_deprecated.cpp +++ b/src/region_deprecated.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/region_deprecated.h b/src/region_deprecated.h index d2ef9cd1b7..218de907ea 100644 --- a/src/region_deprecated.h +++ b/src/region_deprecated.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/region_ellipsoid.cpp b/src/region_ellipsoid.cpp index ee622aad85..7ad3860f32 100644 --- a/src/region_ellipsoid.cpp +++ b/src/region_ellipsoid.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -16,7 +16,6 @@ #include "domain.h" #include "error.h" #include "input.h" -#include "update.h" #include "variable.h" #include @@ -198,39 +197,29 @@ int RegEllipsoid::surface_interior(double *x, double cutoff) if (r_r > rc_r) { // sort the values - int sorting[3] = {0, 1, 2}; - double axes[3] = {c, b, a}; - double coords[3] = {fabs(x[2] - zc), fabs(x[1] - yc), fabs(x[0] - xc)}; + double axes[3] = {a, b, c}; + double coords[3] = {fabs(x[0] - xc), fabs(x[1] - yc), fabs(x[2] - zc)}; - if (axes[1] < axes[0]) { - sorting[0] = 1; - sorting[1] = 0; - axes[0] = b; - axes[1] = c; - } - - if (axes[2] < axes[1]) { - int ti = sorting[2]; - sorting[2] = sorting[1]; - sorting[1] = ti; - double td = axes[2]; - axes[2] = axes[1]; - axes[1] = td; - if (axes[1] < axes[0]) ti = sorting[1]; - sorting[1] = sorting[0]; - sorting[0] = ti; - td = axes[1]; - axes[1] = axes[0]; - axes[0] = td; + int min, max; + if (axes[0] < axes[1]) { + min = 0; + max = 1; + } else { + min = 1; + max = 0; } + if (axes[min] > axes[2]) { min = 2; } + if (axes[max] < axes[2]) { max = 2; } + int mid = 3 - min - max; + int sorting[3] = {min, mid, max}; double x0[3]; - contact[0].r = - DistancePointEllipsoid(axes[2], axes[1], axes[0], coords[sorting[2]], coords[sorting[1]], - coords[sorting[0]], x0[2], x0[1], x0[0]); - contact[0].delx = copysign(x0[sorting[2]], x[0] - xc) + xc; - contact[0].dely = copysign(x0[sorting[1]], x[1] - yc) + yc; - contact[0].delz = copysign(x0[sorting[0]], x[2] - zc) + zc; + contact[0].r = DistancePointEllipsoid( + axes[sorting[2]], axes[sorting[1]], axes[sorting[0]], coords[sorting[2]], + coords[sorting[1]], coords[sorting[0]], x0[sorting[2]], x0[sorting[1]], x0[sorting[0]]); + contact[0].delx = x[0] - (copysign(x0[sorting[2]], x[0] - xc) + xc); + contact[0].dely = x[1] - (copysign(x0[sorting[1]], x[1] - yc) + yc); + contact[0].delz = x[2] - (copysign(x0[sorting[0]], x[2] - zc) + zc); // contact[0].radius = -radius; contact[0].iwall = 0; contact[0].varflag = 1; @@ -255,12 +244,12 @@ int RegEllipsoid::surface_interior(double *x, double cutoff) double x0, x1; if (a >= b) { contact[0].r = DistancePointEllipse(a, b, fabs(x[0] - xc), fabs(x[1] - yc), x0, x1); - contact[0].delx = copysign(x0, x[0] - xc) + xc; - contact[0].dely = copysign(x1, x[1] - yc) + yc; + contact[0].delx = x[0] - (copysign(x0, x[0] - xc) + xc); + contact[0].dely = x[1] - (copysign(x1, x[1] - yc) + yc); } else { contact[0].r = DistancePointEllipse(b, a, fabs(x[1] - yc), fabs(x[0] - xc), x0, x1); - contact[0].delx = copysign(x1, x[0] - xc) + xc; - contact[0].dely = copysign(x0, x[1] - yc) + yc; + contact[0].delx = x[0] - (copysign(x1, x[0] - xc) + xc); + contact[0].dely = x[1] - (copysign(x0, x[1] - yc) + yc); } contact[0].delz = 0; // contact[0].radius = -radius; @@ -299,39 +288,29 @@ int RegEllipsoid::surface_exterior(double *x, double cutoff) if (r_r < rc_r) { // sort the values - int sorting[3] = {0, 1, 2}; - double axes[3] = {c, b, a}; - double coords[3] = {fabs(x[2] - zc), fabs(x[1] - yc), fabs(x[0] - xc)}; + double axes[3] = {a, b, c}; + double coords[3] = {fabs(x[0] - xc), fabs(x[1] - yc), fabs(x[2] - zc)}; - if (axes[1] < axes[0]) { - sorting[0] = 1; - sorting[1] = 0; - axes[0] = b; - axes[1] = c; - } - - if (axes[2] < axes[1]) { - int ti = sorting[2]; - sorting[2] = sorting[1]; - sorting[1] = ti; - double td = axes[2]; - axes[2] = axes[1]; - axes[1] = td; - if (axes[1] < axes[0]) ti = sorting[1]; - sorting[1] = sorting[0]; - sorting[0] = ti; - td = axes[1]; - axes[1] = axes[0]; - axes[0] = td; + int min, max; + if (axes[0] < axes[1]) { + min = 0; + max = 1; + } else { + min = 1; + max = 0; } + if (axes[min] > axes[2]) { min = 2; } + if (axes[max] < axes[2]) { max = 2; } + int mid = 3 - min - max; + int sorting[3] = {min, mid, max}; double x0[3]; - contact[0].r = - DistancePointEllipsoid(axes[2], axes[1], axes[0], coords[sorting[2]], coords[sorting[1]], - coords[sorting[0]], x0[2], x0[1], x0[0]); - contact[0].delx = copysign(x0[sorting[2]], x[0] - xc) + xc; - contact[0].dely = copysign(x0[sorting[1]], x[1] - yc) + yc; - contact[0].delz = copysign(x0[sorting[0]], x[2] - zc) + zc; + contact[0].r = DistancePointEllipsoid( + axes[sorting[2]], axes[sorting[1]], axes[sorting[0]], coords[sorting[2]], + coords[sorting[1]], coords[sorting[0]], x0[sorting[2]], x0[sorting[1]], x0[sorting[0]]); + contact[0].delx = x[0] - (copysign(x0[sorting[2]], x[0] - xc) + xc); + contact[0].dely = x[1] - (copysign(x0[sorting[1]], x[1] - yc) + yc); + contact[0].delz = x[2] - (copysign(x0[sorting[0]], x[2] - zc) + zc); // contact[0].radius = radius; contact[0].iwall = 0; contact[0].varflag = 1; @@ -356,12 +335,12 @@ int RegEllipsoid::surface_exterior(double *x, double cutoff) double x0, x1; if (a >= b) { contact[0].r = DistancePointEllipse(a, b, fabs(x[0] - xc), fabs(x[1] - yc), x0, x1); - contact[0].delx = copysign(x0, x[0] - xc) + xc; - contact[0].dely = copysign(x1, x[1] - yc) + yc; + contact[0].delx = x[0] - (copysign(x0, x[0] - xc) + xc); + contact[0].dely = x[1] - (copysign(x1, x[1] - yc) + yc); } else { contact[0].r = DistancePointEllipse(b, a, fabs(x[1] - yc), fabs(x[0] - xc), x0, x1); - contact[0].delx = copysign(x1, x[0] - xc) + xc; - contact[0].dely = copysign(x0, x[1] - yc) + yc; + contact[0].delx = x[0] - (copysign(x1, x[0] - xc) + xc); + contact[0].dely = x[1] - (copysign(x0, x[1] - yc) + yc); } contact[0].delz = 0; // contact[0].radius = radius; @@ -405,44 +384,44 @@ void RegEllipsoid::variable_check() { if (xstyle == VARIABLE) { xvar = input->variable->find(xstr); - if (xvar < 0) error->all(FLERR, "Variable name for region ellipsoid does not exist"); + if (xvar < 0) error->all(FLERR, "Variable name {} for region ellipsoid does not exist", xstr); if (!input->variable->equalstyle(xvar)) - error->all(FLERR, "Variable for region ellipsoid is invalid style"); + error->all(FLERR, "Variable {} for region ellipsoid is invalid style", xstr); } if (ystyle == VARIABLE) { yvar = input->variable->find(ystr); - if (yvar < 0) error->all(FLERR, "Variable name for region ellipsoid does not exist"); + if (yvar < 0) error->all(FLERR, "Variable name {} for region ellipsoid does not exist", ystr); if (!input->variable->equalstyle(yvar)) - error->all(FLERR, "Variable for region ellipsoid is invalid style"); + error->all(FLERR, "Variable {} for region ellipsoid is invalid style", ystr); } if (zstyle == VARIABLE) { zvar = input->variable->find(zstr); - if (zvar < 0) error->all(FLERR, "Variable name for region ellipsoid does not exist"); + if (zvar < 0) error->all(FLERR, "Variable name {} for region ellipsoid does not exist", zstr); if (!input->variable->equalstyle(zvar)) - error->all(FLERR, "Variable for region ellipsoid is invalid style"); + error->all(FLERR, "Variable {} for region ellipsoid is invalid style", zstr); } if (astyle == VARIABLE) { avar = input->variable->find(astr); - if (avar < 0) error->all(FLERR, "Variable name for region ellipsoid does not exist"); + if (avar < 0) error->all(FLERR, "Variable name {} for region ellipsoid does not exist", astr); if (!input->variable->equalstyle(avar)) - error->all(FLERR, "Variable for region ellipsoid is invalid style"); + error->all(FLERR, "Variable {} for region ellipsoid is invalid style", astr); } if (bstyle == VARIABLE) { bvar = input->variable->find(bstr); - if (bvar < 0) error->all(FLERR, "Variable name for region ellipsoid does not exist"); + if (bvar < 0) error->all(FLERR, "Variable name {} for region ellipsoid does not exist", bstr); if (!input->variable->equalstyle(bvar)) - error->all(FLERR, "Variable for region ellipsoid is invalid style"); + error->all(FLERR, "Variable {} for region ellipsoid is invalid style", cstr); } if (cstyle == VARIABLE) { cvar = input->variable->find(cstr); - if (cvar < 0) error->all(FLERR, "Variable name for region ellipsoid does not exist"); + if (cvar < 0) error->all(FLERR, "Variable name {} for region ellipsoid does not exist", cstr); if (!input->variable->equalstyle(cvar)) - error->all(FLERR, "Variable for region ellipsoid is invalid style"); + error->all(FLERR, "Variable {} for region ellipsoid is invalid style", cstr); } } diff --git a/src/region_ellipsoid.h b/src/region_ellipsoid.h index 0b63e66133..033d30234f 100644 --- a/src/region_ellipsoid.h +++ b/src/region_ellipsoid.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/region_intersect.cpp b/src/region_intersect.cpp index 50c5f9fc68..b41f2a2ead 100644 --- a/src/region_intersect.cpp +++ b/src/region_intersect.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/region_intersect.h b/src/region_intersect.h index b4084db633..57582ceabc 100644 --- a/src/region_intersect.h +++ b/src/region_intersect.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/region_plane.cpp b/src/region_plane.cpp index a5163796d0..06e7c467d7 100644 --- a/src/region_plane.cpp +++ b/src/region_plane.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/region_plane.h b/src/region_plane.h index a1f19d151d..2025586a7c 100644 --- a/src/region_plane.h +++ b/src/region_plane.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/region_prism.cpp b/src/region_prism.cpp index f83da54e34..7c06c0aa7d 100644 --- a/src/region_prism.cpp +++ b/src/region_prism.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/region_prism.h b/src/region_prism.h index 8b92425c86..fd1e8b17b0 100644 --- a/src/region_prism.h +++ b/src/region_prism.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/region_sphere.cpp b/src/region_sphere.cpp index bbe8400f90..03eb762266 100644 --- a/src/region_sphere.cpp +++ b/src/region_sphere.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/region_sphere.h b/src/region_sphere.h index 09f5df386b..f0e0bd195c 100644 --- a/src/region_sphere.h +++ b/src/region_sphere.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/region_union.cpp b/src/region_union.cpp index c14a9ef714..9d79b139f5 100644 --- a/src/region_union.cpp +++ b/src/region_union.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/region_union.h b/src/region_union.h index 641eac09d4..970ba45132 100644 --- a/src/region_union.h +++ b/src/region_union.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/replicate.cpp b/src/replicate.cpp index 80edd7bcbc..eb7047e777 100644 --- a/src/replicate.cpp +++ b/src/replicate.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -47,8 +47,6 @@ void Replicate::command(int narg, char **arg) int me = comm->me; int nprocs = comm->nprocs; - if (me == 0) utils::logmesg(lmp,"Replicating atoms ...\n"); - // nrep = total # of replications int nx = utils::inumeric(FLERR,arg[0],false,lmp); @@ -56,6 +54,10 @@ void Replicate::command(int narg, char **arg) int nz = utils::inumeric(FLERR,arg[2],false,lmp); int nrep = nx*ny*nz; + if (me == 0) + utils::logmesg(lmp, "Replication is creating a {}x{}x{} = {} times larger system...\n", + nx, ny, nz, nrep); + int bbox_flag = 0; if (narg == 4) if (strcmp(arg[3],"bbox") == 0) bbox_flag = 1; diff --git a/src/replicate.h b/src/replicate.h index d120b18b98..8d71ba6584 100644 --- a/src/replicate.h +++ b/src/replicate.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/rerun.cpp b/src/rerun.cpp index f0048a3ce2..50088a9c2c 100644 --- a/src/rerun.cpp +++ b/src/rerun.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/rerun.h b/src/rerun.h index d6707078e8..d5f34a3daf 100644 --- a/src/rerun.h +++ b/src/rerun.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/reset_atom_ids.cpp b/src/reset_atoms_id.cpp similarity index 65% rename from src/reset_atom_ids.cpp rename to src/reset_atoms_id.cpp index 5a6e5170bd..c0fce95326 100644 --- a/src/reset_atom_ids.cpp +++ b/src/reset_atoms_id.cpp @@ -1,8 +1,7 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -12,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "reset_atom_ids.h" +#include "reset_atoms_id.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +31,7 @@ using namespace LAMMPS_NS; #if defined(LMP_QSORT) // allocate space for static class variable // prototype for non-class function -ResetIDs::AtomRvous *ResetIDs::sortrvous; +ResetAtomsID::AtomRvous *ResetAtomsID::sortrvous; static int compare_coords(const void *, const void *); #else // prototype for non-class function @@ -44,22 +43,23 @@ static int compare_coords(const int, const int, void *); /* ---------------------------------------------------------------------- */ -ResetIDs::ResetIDs(LAMMPS *lmp) : Command(lmp) {} +ResetAtomsID::ResetAtomsID(LAMMPS *lmp) : Command(lmp) { + binlo = binhi = -1; +} /* ---------------------------------------------------------------------- */ -void ResetIDs::command(int narg, char **arg) +void ResetAtomsID::command(int narg, char **arg) { if (domain->box_exist == 0) - error->all(FLERR,"Reset_ids command before simulation box is defined"); - if (atom->tag_enable == 0) - error->all(FLERR,"Cannot use reset_atom_ids unless atoms have IDs"); + error->all(FLERR, "Reset_atoms id command before simulation box is defined"); + if (atom->tag_enable == 0) error->all(FLERR, "Cannot use reset_atoms id unless atoms have IDs"); for (int i = 0; i < modify->nfix; i++) if (modify->fix[i]->stores_ids) - error->all(FLERR,"Cannot use reset_atom_ids when a fix exists that stores atom IDs"); + error->all(FLERR, "Cannot use reset_atoms id when a fix exists that stores atom IDs"); - if (comm->me == 0) utils::logmesg(lmp,"Resetting atom IDs ...\n"); + if (comm->me == 0) utils::logmesg(lmp, "Resetting atom IDs ...\n"); // process args @@ -67,11 +67,12 @@ void ResetIDs::command(int narg, char **arg) int iarg = 0; while (iarg < narg) { - if (strcmp(arg[iarg],"sort") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal reset_atom_ids command"); - sortflag = utils::logical(FLERR,arg[iarg+1],false,lmp); + if (strcmp(arg[iarg], "sort") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "reset_atoms id", error); + sortflag = utils::logical(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else error->all(FLERR,"Illegal reset_atom_ids command"); + } else + error->all(FLERR, "Unknown reset_atoms id keyword: {}", arg[iarg]); } // create an atom map if one doesn't exist already @@ -99,7 +100,7 @@ void ResetIDs::command(int narg, char **arg) comm->setup(); comm->exchange(); comm->borders(); - if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost); + if (domain->triclinic) domain->lamda2x(atom->nlocal + atom->nghost); // oldIDs = copy of current owned IDs @@ -108,7 +109,7 @@ void ResetIDs::command(int narg, char **arg) int nall = nlocal + atom->nghost; tagint *oldIDs; - memory->create(oldIDs,nlocal,"reset_atom_ids:oldIDs"); + memory->create(oldIDs, nlocal, "reset_atom_ids:oldIDs"); for (int i = 0; i < nlocal; i++) { oldIDs[i] = tag[i]; @@ -119,22 +120,24 @@ void ResetIDs::command(int narg, char **arg) // if sortflag = no: use fast tag_extend() // if sortflag = yes: use slower full spatial sort plus rendezvous comm - if (sortflag == 0) atom->tag_extend(); - else sort(); + if (sortflag == 0) + atom->tag_extend(); + else + sort(); // newIDs = copy of new IDs // restore old IDs, consistent with existing atom map // forward_comm_array acquires new IDs for ghost atoms double **newIDs; - memory->create(newIDs,nall,1,"reset_atom_ids:newIDs"); + memory->create(newIDs, nall, 1, "reset_atom_ids:newIDs"); for (int i = 0; i < nlocal; i++) { newIDs[i][0] = ubuf(tag[i]).d; tag[i] = oldIDs[i]; } - comm->forward_comm_array(1,newIDs); + comm->forward_comm_array(1, newIDs); // loop over bonds, angles, etc and reset IDs in stored topology arrays // only necessary for molecular = Atom::MOLECULAR, not molecular = Atom::TEMPLATE @@ -143,7 +146,7 @@ void ResetIDs::command(int narg, char **arg) int badcount = 0; if (atom->molecular == Atom::MOLECULAR) { - int j,m; + int j, m; tagint oldID; if (atom->avec->bonds_allow) { @@ -153,8 +156,10 @@ void ResetIDs::command(int narg, char **arg) for (j = 0; j < num_bond[i]; j++) { oldID = bond_atom[i][j]; m = atom->map(oldID); - if (m >= 0) bond_atom[i][j] = (tagint) ubuf(newIDs[m][0]).i; - else badcount++; + if (m >= 0) + bond_atom[i][j] = (tagint) ubuf(newIDs[m][0]).i; + else + badcount++; } } } @@ -168,18 +173,24 @@ void ResetIDs::command(int narg, char **arg) for (j = 0; j < num_angle[i]; j++) { oldID = angle_atom1[i][j]; m = atom->map(oldID); - if (m >= 0) angle_atom1[i][j] = (tagint) ubuf(newIDs[m][0]).i; - else badcount++; + if (m >= 0) + angle_atom1[i][j] = (tagint) ubuf(newIDs[m][0]).i; + else + badcount++; oldID = angle_atom2[i][j]; m = atom->map(oldID); - if (m >= 0) angle_atom2[i][j] = (tagint) ubuf(newIDs[m][0]).i; - else badcount++; + if (m >= 0) + angle_atom2[i][j] = (tagint) ubuf(newIDs[m][0]).i; + else + badcount++; oldID = angle_atom3[i][j]; m = atom->map(oldID); - if (m >= 0) angle_atom3[i][j] = (tagint) ubuf(newIDs[m][0]).i; - else badcount++; + if (m >= 0) + angle_atom3[i][j] = (tagint) ubuf(newIDs[m][0]).i; + else + badcount++; } } } @@ -194,23 +205,31 @@ void ResetIDs::command(int narg, char **arg) for (j = 0; j < num_dihedral[i]; j++) { oldID = dihedral_atom1[i][j]; m = atom->map(oldID); - if (m >= 0) dihedral_atom1[i][j] = (tagint) ubuf(newIDs[m][0]).i; - else badcount++; + if (m >= 0) + dihedral_atom1[i][j] = (tagint) ubuf(newIDs[m][0]).i; + else + badcount++; oldID = dihedral_atom2[i][j]; m = atom->map(oldID); - if (m >= 0) dihedral_atom2[i][j] = (tagint) ubuf(newIDs[m][0]).i; - else badcount++; + if (m >= 0) + dihedral_atom2[i][j] = (tagint) ubuf(newIDs[m][0]).i; + else + badcount++; oldID = dihedral_atom3[i][j]; m = atom->map(oldID); - if (m >= 0) dihedral_atom3[i][j] = (tagint) ubuf(newIDs[m][0]).i; - else badcount++; + if (m >= 0) + dihedral_atom3[i][j] = (tagint) ubuf(newIDs[m][0]).i; + else + badcount++; oldID = dihedral_atom4[i][j]; m = atom->map(oldID); - if (m >= 0) dihedral_atom4[i][j] = (tagint) ubuf(newIDs[m][0]).i; - else badcount++; + if (m >= 0) + dihedral_atom4[i][j] = (tagint) ubuf(newIDs[m][0]).i; + else + badcount++; } } } @@ -225,23 +244,31 @@ void ResetIDs::command(int narg, char **arg) for (j = 0; j < num_improper[i]; j++) { oldID = improper_atom1[i][j]; m = atom->map(oldID); - if (m >= 0) improper_atom1[i][j] = (tagint) ubuf(newIDs[m][0]).i; - else badcount++; + if (m >= 0) + improper_atom1[i][j] = (tagint) ubuf(newIDs[m][0]).i; + else + badcount++; oldID = improper_atom2[i][j]; m = atom->map(oldID); - if (m >= 0) improper_atom2[i][j] = (tagint) ubuf(newIDs[m][0]).i; - else badcount++; + if (m >= 0) + improper_atom2[i][j] = (tagint) ubuf(newIDs[m][0]).i; + else + badcount++; oldID = improper_atom3[i][j]; m = atom->map(oldID); - if (m >= 0) improper_atom3[i][j] = (tagint) ubuf(newIDs[m][0]).i; - else badcount++; + if (m >= 0) + improper_atom3[i][j] = (tagint) ubuf(newIDs[m][0]).i; + else + badcount++; oldID = improper_atom4[i][j]; m = atom->map(oldID); - if (m >= 0) improper_atom4[i][j] = (tagint) ubuf(newIDs[m][0]).i; - else badcount++; + if (m >= 0) + improper_atom4[i][j] = (tagint) ubuf(newIDs[m][0]).i; + else + badcount++; } } } @@ -250,10 +277,10 @@ void ResetIDs::command(int narg, char **arg) // error check int all; - MPI_Allreduce(&badcount,&all,1,MPI_INT,MPI_SUM,world); + MPI_Allreduce(&badcount, &all, 1, MPI_INT, MPI_SUM, world); if (all) - error->all(FLERR,"Reset_ids missing {} bond topology atom IDs - " - "use comm_modify cutoff",all); + error->all(FLERR, + "reset_atoms id is missing {} bond topology atom IDs - use comm_modify cutoff", all); // reset IDs and atom map for owned atoms @@ -287,9 +314,9 @@ void ResetIDs::command(int narg, char **arg) spatial sort of atoms followed by rendezvous comm to reset atom IDs ------------------------------------------------------------------------- */ -void ResetIDs::sort() +void ResetAtomsID::sort() { - double mylo[3],myhi[3],bboxlo[3],bboxhi[3]; + double mylo[3], myhi[3], bboxlo[3], bboxhi[3]; int me = comm->me; int nprocs = comm->nprocs; @@ -306,12 +333,12 @@ void ResetIDs::sort() myhi[0] = myhi[1] = myhi[2] = -BIG; for (int i = 0; i < nlocal; i++) { - mylo[0] = MIN(mylo[0],x[i][0]); - mylo[1] = MIN(mylo[1],x[i][1]); - mylo[2] = MIN(mylo[2],x[i][2]); - myhi[0] = MAX(myhi[0],x[i][0]); - myhi[1] = MAX(myhi[1],x[i][1]); - myhi[2] = MAX(myhi[2],x[i][2]); + mylo[0] = MIN(mylo[0], x[i][0]); + mylo[1] = MIN(mylo[1], x[i][1]); + mylo[2] = MIN(mylo[2], x[i][2]); + myhi[0] = MAX(myhi[0], x[i][0]); + myhi[1] = MAX(myhi[1], x[i][1]); + myhi[2] = MAX(myhi[2], x[i][2]); } if (dim == 2) mylo[2] = myhi[2] = 0.0; @@ -325,15 +352,15 @@ void ResetIDs::sort() } } - MPI_Allreduce(mylo,bboxlo,3,MPI_DOUBLE,MPI_MIN,world); - MPI_Allreduce(myhi,bboxhi,3,MPI_DOUBLE,MPI_MAX,world); + MPI_Allreduce(mylo, bboxlo, 3, MPI_DOUBLE, MPI_MIN, world); + MPI_Allreduce(myhi, bboxhi, 3, MPI_DOUBLE, MPI_MAX, world); - bboxlo[0] -= 0.0001 * (bboxhi[0]-bboxlo[0]); - bboxlo[1] -= 0.0001 * (bboxhi[1]-bboxlo[1]); - bboxlo[2] -= 0.0001 * (bboxhi[2]-bboxlo[2]); - bboxhi[0] += 0.0001 * (bboxhi[0]-bboxlo[0]); - bboxhi[1] += 0.0001 * (bboxhi[1]-bboxlo[1]); - bboxhi[2] += 0.0001 * (bboxhi[2]-bboxlo[2]); + bboxlo[0] -= 0.0001 * (bboxhi[0] - bboxlo[0]); + bboxlo[1] -= 0.0001 * (bboxhi[1] - bboxlo[1]); + bboxlo[2] -= 0.0001 * (bboxhi[2] - bboxlo[2]); + bboxhi[0] += 0.0001 * (bboxhi[0] - bboxlo[0]); + bboxhi[1] += 0.0001 * (bboxhi[1] - bboxlo[1]); + bboxhi[2] += 0.0001 * (bboxhi[2] - bboxlo[2]); // nbin_estimate = estimate of total number of bins, each with PERBIN atoms // binsize = edge length of a cubic bin @@ -342,19 +369,23 @@ void ResetIDs::sort() bigint nbin_estimate = atom->natoms / PERBIN + 1; double vol; - if (dim == 2) vol = (bboxhi[0]-bboxlo[0]) * (bboxhi[1]-bboxlo[1]); - else vol = (bboxhi[0]-bboxlo[0]) * (bboxhi[1]-bboxlo[1]) * (bboxhi[2]-bboxlo[2]); - double binsize = pow(vol/nbin_estimate,1.0/dim); + if (dim == 2) + vol = (bboxhi[0] - bboxlo[0]) * (bboxhi[1] - bboxlo[1]); + else + vol = (bboxhi[0] - bboxlo[0]) * (bboxhi[1] - bboxlo[1]) * (bboxhi[2] - bboxlo[2]); + double binsize = pow(vol / nbin_estimate, 1.0 / dim); - int nbinx = static_cast ((bboxhi[0]-bboxlo[0]) / binsize) + 1; - int nbiny = static_cast ((bboxhi[1]-bboxlo[1]) / binsize) + 1; - int nbinz = static_cast ((bboxhi[2]-bboxlo[2]) / binsize) + 1; + int nbinx = static_cast((bboxhi[0] - bboxlo[0]) / binsize) + 1; + int nbiny = static_cast((bboxhi[1] - bboxlo[1]) / binsize) + 1; + int nbinz = static_cast((bboxhi[2] - bboxlo[2]) / binsize) + 1; - double invx = 1.0 / (bboxhi[0]-bboxlo[0]); - double invy = 1.0 / (bboxhi[1]-bboxlo[1]); + double invx = 1.0 / (bboxhi[0] - bboxlo[0]); + double invy = 1.0 / (bboxhi[1] - bboxlo[1]); double invz; - if (dim == 2) invz = 0.0; - else invz = 1.0 / (bboxhi[2]-bboxlo[2]); + if (dim == 2) + invz = 0.0; + else + invz = 1.0 / (bboxhi[2] - bboxlo[2]); // nbins = actual total number of bins // bins are split evenly across procs @@ -366,18 +397,18 @@ void ResetIDs::sort() // binlo to binhi-1 = bin indices this proc will own in Rvous decomp // bins are numbered from 0 to Nbins-1 - bigint nbins = (bigint) nbinx*nbiny*nbinz; + bigint nbins = (bigint) nbinx * nbiny * nbinz; bigint nlo = nbins / nprocs; bigint nhi = nlo + 1; bigint nplo = nprocs - (nbins % nprocs); - bigint nbinlo = nplo*nlo; + bigint nbinlo = nplo * nlo; if (me < nplo) { binlo = me * nlo; - binhi = (me+1) * nlo; + binhi = (me + 1) * nlo; } else { - binlo = nbinlo + (me-nplo) * nhi; - binhi = nbinlo + (me+1-nplo) * nhi; + binlo = nbinlo + (me - nplo) * nhi; + binhi = nbinlo + (me + 1 - nplo) * nhi; } // fill atombuf with info on my atoms @@ -385,20 +416,23 @@ void ResetIDs::sort() // proclist = proc that owns ibin int *proclist; - memory->create(proclist,nlocal,"special:proclist"); - auto atombuf = (AtomRvous *) memory->smalloc((bigint) nlocal*sizeof(AtomRvous),"resetIDs:idbuf"); + memory->create(proclist, nlocal, "special:proclist"); + auto atombuf = + (AtomRvous *) memory->smalloc((bigint) nlocal * sizeof(AtomRvous), "resetIDs:idbuf"); - int ibinx,ibiny,ibinz,iproc; + int ibinx, ibiny, ibinz, iproc; bigint ibin; for (int i = 0; i < nlocal; i++) { - ibinx = static_cast ((x[i][0]-bboxlo[0])*invx * nbinx); - ibiny = static_cast ((x[i][1]-bboxlo[1])*invy * nbiny); - ibinz = static_cast ((x[i][2]-bboxlo[2])*invz * nbinz); - ibin = (bigint) ibinz*nbiny*nbinx + (bigint) ibiny*nbinx + ibinx; + ibinx = static_cast((x[i][0] - bboxlo[0]) * invx * nbinx); + ibiny = static_cast((x[i][1] - bboxlo[1]) * invy * nbiny); + ibinz = static_cast((x[i][2] - bboxlo[2]) * invz * nbinz); + ibin = (bigint) ibinz * nbiny * nbinx + (bigint) ibiny * nbinx + ibinx; - if (ibin < nbinlo) iproc = ibin / nlo; - else iproc = nplo + (ibin-nbinlo) / nhi; + if (ibin < nbinlo) + iproc = ibin / nlo; + else + iproc = nplo + (ibin - nbinlo) / nhi; proclist[i] = iproc; atombuf[i].ibin = ibin; @@ -412,8 +446,8 @@ void ResetIDs::sort() // perform rendezvous operation, send atombuf to other procs char *buf; - int nreturn = comm->rendezvous(1,nlocal,(char *) atombuf,sizeof(AtomRvous),0,proclist, - sort_bins,0,buf,sizeof(IDRvous),(void *) this); + int nreturn = comm->rendezvous(1, nlocal, (char *) atombuf, sizeof(AtomRvous), 0, proclist, + sort_bins, 0, buf, sizeof(IDRvous), (void *) this); auto outbuf = (IDRvous *) buf; memory->destroy(proclist); @@ -437,27 +471,30 @@ void ResetIDs::sort() outbuf = list of N IDRvous datums, sent back to sending proc ------------------------------------------------------------------------- */ -int ResetIDs::sort_bins(int n, char *inbuf, int &flag, int *&proclist, char *&outbuf, void *ptr) +int ResetAtomsID::sort_bins(int n, char *inbuf, int &flag, int *&proclist, char *&outbuf, void *ptr) { - int i,ibin,index; + int i, ibin, index; - auto rptr = (ResetIDs *) ptr; + auto rptr = (ResetAtomsID *) ptr; Memory *memory = rptr->memory; Error *error = rptr->error; MPI_Comm world = rptr->world; bigint binlo = rptr->binlo; bigint binhi = rptr->binhi; + if ((binlo < 0) || (binhi < 0)) + error->one(FLERR, "Called sort_bins without previous setup of bins"); + // nbins = my subset of bins from binlo to binhi-1 // initialize linked lists of my Rvous atoms in each bin - int *next,*head,*last,*count; + int *next, *head, *last, *count; int nbins = binhi - binlo; - memory->create(next,n,"resetIDs:next"); - memory->create(head,nbins,"resetIDs:head"); - memory->create(last,nbins,"resetIDs:last"); - memory->create(count,nbins,"resetIDs:count"); + memory->create(next, n, "resetIDs:next"); + memory->create(head, nbins, "resetIDs:head"); + memory->create(last, nbins, "resetIDs:last"); + memory->create(count, nbins, "resetIDs:count"); for (i = 0; i < n; i++) next[i] = -1; @@ -472,7 +509,7 @@ int ResetIDs::sort_bins(int n, char *inbuf, int &flag, int *&proclist, char *&ou if (in[i].ibin < binlo || in[i].ibin >= binhi) { //printf("BAD me %d i %d %d ibin %d binlohi %d %d\n", // rptr->comm->me,i,n,in[i].ibin,binlo,binhi); - error->one(FLERR,"Bad spatial bin assignment in reset_atom_ids sort"); + error->one(FLERR, "Bad spatial bin assignment in reset_atoms id sort"); } ibin = in[i].ibin - binlo; if (head[ibin] < 0) head[ibin] = i; @@ -482,11 +519,10 @@ int ResetIDs::sort_bins(int n, char *inbuf, int &flag, int *&proclist, char *&ou } int maxcount = 0; - for (ibin = 0; ibin < nbins; ibin++) - maxcount = MAX(maxcount,count[ibin]); + for (ibin = 0; ibin < nbins; ibin++) maxcount = MAX(maxcount, count[ibin]); int *order; - memory->create(order,maxcount,"resetIDs:order"); + memory->create(order, maxcount, "resetIDs:order"); // sort atoms in each bin by their spatial position // recreate linked list for each bin based on sorted order @@ -498,12 +534,11 @@ int ResetIDs::sort_bins(int n, char *inbuf, int &flag, int *&proclist, char *&ou index = next[index]; } - #if defined(LMP_QSORT) sortrvous = in; - qsort(order,count[ibin],sizeof(int),compare_coords); + qsort(order, count[ibin], sizeof(int), compare_coords); #else - utils::merge_sort(order,count[ibin],(void *) in,compare_coords); + utils::merge_sort(order, count[ibin], (void *) in, compare_coords); #endif head[ibin] = last[ibin] = -1; @@ -518,15 +553,15 @@ int ResetIDs::sort_bins(int n, char *inbuf, int &flag, int *&proclist, char *&ou tagint ntag = n; tagint nprev; - MPI_Scan(&ntag,&nprev,1,MPI_LMP_TAGINT,MPI_SUM,world); + MPI_Scan(&ntag, &nprev, 1, MPI_LMP_TAGINT, MPI_SUM, world); nprev -= n; // loop over bins and sorted atoms in each bin, reset ids to be consecutive // pass outbuf of IDRvous datums back to comm->rendezvous int nout = n; - memory->create(proclist,nout,"resetIDs:proclist"); - auto out = (IDRvous *) memory->smalloc(nout*sizeof(IDRvous),"resetIDs:out"); + memory->create(proclist, nout, "resetIDs:proclist"); + auto out = (IDRvous *) memory->smalloc(nout * sizeof(IDRvous), "resetIDs:out"); tagint one = nprev + 1; for (ibin = 0; ibin < nbins; ibin++) { @@ -567,7 +602,7 @@ int compare_coords(const void *iptr, const void *jptr) { int i = *((int *) iptr); int j = *((int *) jptr); - ResetIDs::AtomRvous *rvous = ResetIDs::sortrvous; + ResetAtomsID::AtomRvous *rvous = ResetAtomsID::sortrvous; double *xi = rvous[i].x; double *xj = rvous[j].x; if (xi[0] < xj[0]) return -1; @@ -588,7 +623,7 @@ int compare_coords(const void *iptr, const void *jptr) int compare_coords(const int i, const int j, void *ptr) { - auto rvous = (ResetIDs::AtomRvous *) ptr; + auto rvous = (ResetAtomsID::AtomRvous *) ptr; double *xi = rvous[i].x; double *xj = rvous[j].x; if (xi[0] < xj[0]) return -1; diff --git a/src/reset_atom_ids.h b/src/reset_atoms_id.h similarity index 84% rename from src/reset_atom_ids.h rename to src/reset_atoms_id.h index 6ba833e7a6..9d80505586 100644 --- a/src/reset_atom_ids.h +++ b/src/reset_atoms_id.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -13,18 +13,18 @@ #ifdef COMMAND_CLASS // clang-format off -CommandStyle(reset_atom_ids,ResetIDs); +CommandStyle(RESET_ATOMS_ID,ResetAtomsID); // clang-format on #else -#ifndef LMP_RESET_IDS_H -#define LMP_RESET_IDS_H +#ifndef LMP_RESET_ATOMS_ID_H +#define LMP_RESET_ATOMS_ID_H #include "command.h" namespace LAMMPS_NS { -class ResetIDs : public Command { +class ResetAtomsID : public Command { public: struct AtomRvous { bigint ibin; @@ -42,7 +42,7 @@ class ResetIDs : public Command { static AtomRvous *sortrvous; #endif - ResetIDs(class LAMMPS *); + ResetAtomsID(class LAMMPS *); void command(int, char **) override; private: @@ -54,8 +54,6 @@ class ResetIDs : public Command { void sort(); }; - } // namespace LAMMPS_NS - #endif #endif diff --git a/src/reset_atoms_image.cpp b/src/reset_atoms_image.cpp new file mode 100644 index 0000000000..56a1bf9f99 --- /dev/null +++ b/src/reset_atoms_image.cpp @@ -0,0 +1,140 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "reset_atoms_image.h" + +#include "atom.h" +#include "atom_vec.h" +#include "comm.h" +#include "compute.h" +#include "domain.h" +#include "error.h" +#include "group.h" +#include "input.h" +#include "modify.h" +#include "variable.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ResetAtomsImage::ResetAtomsImage(LAMMPS *lmp) : Command(lmp) {} + +/* ---------------------------------------------------------------------- + called as reset_atoms image command in input script +------------------------------------------------------------------------- */ + +void ResetAtomsImage::command(int narg, char **arg) +{ + if (domain->box_exist == 0) + error->all(FLERR, "Reset_atoms image command before simulation box is defined"); + if (atom->tag_enable == 0) + error->all(FLERR, "Cannot use reset_atoms image unless atoms have IDs"); + if (atom->avec->bonds_allow == 0) + error->all(FLERR, "Cannot use reset_atoms image used when bonds are not allowed"); + + // process args + + if (narg < 1) utils::missing_cmd_args(FLERR, "reset_atoms image", error); + if (narg > 1) error->all(FLERR, "Unknown reset_atoms image keyword: {}", arg[1]); + int igroup = group->find(arg[0]); + if (igroup < 0) error->all(FLERR, "Could not find reset_atoms image group {}", arg[0]); + int groupbit = group->bitmask[igroup]; + + if (comm->me == 0) utils::logmesg(lmp, "Resetting image flags ...\n"); + + // record wall time for resetting molecule IDs + + MPI_Barrier(world); + double time1 = platform::walltime(); + + // initialize system since comm->borders() will be invoked + + lmp->init(); + + // setup domain, communication + // exchange will clear map, borders will reset + // this is the map needed to lookup current global IDs for bond topology + + if (domain->triclinic) domain->x2lamda(atom->nlocal); + domain->pbc(); + domain->reset_box(); + comm->setup(); + comm->exchange(); + comm->borders(); + if (domain->triclinic) domain->lamda2x(atom->nlocal + atom->nghost); + + // create computes and variables + + auto frags = modify->add_compute("frags_r_i_f all fragment/atom single yes"); + auto chunk = modify->add_compute("chunk_r_i_f all chunk/atom c_frags_r_i_f compress yes"); + auto flags = modify->add_compute("flags_r_i_f all property/atom ix iy iz"); + input->variable->set("ix_r_i_f atom c_flags_r_i_f[1]"); + input->variable->set("iy_r_i_f atom c_flags_r_i_f[2]"); + input->variable->set("iz_r_i_f atom c_flags_r_i_f[3]"); + auto ifmin = modify->add_compute("ifmin_r_i_f all reduce/chunk chunk_r_i_f min " + "v_ix_r_i_f v_iy_r_i_f v_iz_r_i_f"); + auto ifmax = modify->add_compute("ifmax_r_i_f all reduce/chunk chunk_r_i_f max " + "v_ix_r_i_f v_iy_r_i_f v_iz_r_i_f"); + auto cdist = modify->add_compute("cdist_r_i_f all chunk/spread/atom chunk_r_i_f " + "c_ifmax_r_i_f[*] c_ifmin_r_i_f[*]"); + + // trigger computes + + frags->compute_peratom(); + chunk->compute_peratom(); + flags->compute_peratom(); + ifmin->compute_array(); + ifmax->compute_array(); + cdist->compute_peratom(); + + // reset image flags for atoms in group + + const int *const mask = atom->mask; + const int nlocal = atom->nlocal; + imageint *image = atom->image; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + int ix = (image[i] & IMGMASK) - IMGMAX; + int iy = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; + int iz = (image[i] >> IMG2BITS) - IMGMAX; + ix -= (int) floor(0.5 * (cdist->array_atom[i][0] + cdist->array_atom[i][3])); + iy -= (int) floor(0.5 * (cdist->array_atom[i][1] + cdist->array_atom[i][4])); + iz -= (int) floor(0.5 * (cdist->array_atom[i][2] + cdist->array_atom[i][5])); + image[i] = ((imageint) (ix + IMGMAX) & IMGMASK) | + (((imageint) (iy + IMGMAX) & IMGMASK) << IMGBITS) | + (((imageint) (iz + IMGMAX) & IMGMASK) << IMG2BITS); + } + } + + // cleanup + + modify->delete_compute("cdist_r_i_f"); + modify->delete_compute("ifmax_r_i_f"); + modify->delete_compute("ifmin_r_i_f"); + modify->delete_compute("flags_r_i_f"); + modify->delete_compute("chunk_r_i_f"); + modify->delete_compute("frags_r_i_f"); + input->variable->set("ix_r_i_f delete"); + input->variable->set("iy_r_i_f delete"); + input->variable->set("iz_r_i_f delete"); + + // total time + + MPI_Barrier(world); + if (comm->me == 0) + utils::logmesg(lmp, " reset_atoms image CPU = {:.3f} seconds\n", platform::walltime() - time1); +} diff --git a/src/reset_atoms_image.h b/src/reset_atoms_image.h new file mode 100644 index 0000000000..314f2dd086 --- /dev/null +++ b/src/reset_atoms_image.h @@ -0,0 +1,34 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + 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 COMMAND_CLASS +// clang-format off +CommandStyle(RESET_ATOMS_IMAGE,ResetAtomsImage); +// clang-format on +#else + +#ifndef LMP_RESET_ATOMS_IMAGE_H +#define LMP_RESET_ATOMS_IMAGE_H + +#include "command.h" + +namespace LAMMPS_NS { + +class ResetAtomsImage : public Command { + public: + ResetAtomsImage(class LAMMPS *); + void command(int, char **) override; +}; +} // namespace LAMMPS_NS +#endif +#endif diff --git a/src/reset_mol_ids.cpp b/src/reset_atoms_mol.cpp similarity index 61% rename from src/reset_mol_ids.cpp rename to src/reset_atoms_mol.cpp index 30a817433e..66dd886059 100644 --- a/src/reset_mol_ids.cpp +++ b/src/reset_atoms_mol.cpp @@ -1,8 +1,7 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -16,7 +15,7 @@ Contributing author: Jacob Gissinger (jacob.gissinger@colorado.edu) ------------------------------------------------------------------------- */ -#include "reset_mol_ids.h" +#include "reset_atoms_mol.h" #include "atom.h" #include "comm.h" @@ -33,65 +32,65 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -ResetMolIDs::ResetMolIDs(LAMMPS *lmp) : Command(lmp) { - cfa = nullptr; - cca = nullptr; - +ResetAtomsMol::ResetAtomsMol(LAMMPS *lmp) : Command(lmp), cfa(nullptr), cca(nullptr) +{ // default settings compressflag = 1; singleflag = 0; offset = -1; + groupbit = group->bitmask[0]; idfrag.clear(); idchunk.clear(); + nchunk = 0; } /* ---------------------------------------------------------------------- */ -ResetMolIDs::~ResetMolIDs() +ResetAtomsMol::~ResetAtomsMol() { if (!idfrag.empty()) modify->delete_compute(idfrag); if (compressflag && !idchunk.empty()) modify->delete_compute(idchunk); } /* ---------------------------------------------------------------------- - called as reset_mol_ids command in input script + called as reset_atoms mol command in input script ------------------------------------------------------------------------- */ -void ResetMolIDs::command(int narg, char **arg) +void ResetAtomsMol::command(int narg, char **arg) { if (domain->box_exist == 0) - error->all(FLERR,"Reset_mol_ids command before simulation box is defined"); - if (atom->tag_enable == 0) - error->all(FLERR,"Cannot use reset_mol_ids unless atoms have IDs"); + error->all(FLERR, "Reset_atoms mol command before simulation box is defined"); + if (atom->tag_enable == 0) error->all(FLERR, "Cannot use reset_atoms mol unless atoms have IDs"); if (atom->molecular != Atom::MOLECULAR) - error->all(FLERR,"Can only use reset_mol_ids on molecular systems"); + error->all(FLERR, "Can only use reset_atoms mol on molecular systems"); // process args - if (narg < 1) error->all(FLERR,"Illegal reset_mol_ids command"); + if (narg < 1) utils::missing_cmd_args(FLERR, "reset_atoms mol", error); char *groupid = arg[0]; int iarg = 1; while (iarg < narg) { - if (strcmp(arg[iarg],"compress") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal reset_mol_ids command"); - compressflag = utils::logical(FLERR,arg[iarg+1],false,lmp); + if (strcmp(arg[iarg], "compress") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "reset_atoms mol compress", error); + compressflag = utils::logical(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"single") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal reset_mol_ids command"); - singleflag = utils::logical(FLERR,arg[iarg+1],false,lmp); + } else if (strcmp(arg[iarg], "single") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "reset_atoms mol single", error); + singleflag = utils::logical(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"offset") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal reset_mol_ids command"); - offset = utils::tnumeric(FLERR,arg[iarg+1],true,lmp); - if (offset < -1) error->all(FLERR,"Illegal reset_mol_ids command"); + } else if (strcmp(arg[iarg], "offset") == 0) { + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "reset_atoms mol offset", error); + offset = utils::tnumeric(FLERR, arg[iarg + 1], true, lmp); + if (offset < -1) error->all(FLERR, "Illegal reset_atoms mol offset: {}", offset); iarg += 2; - } else error->all(FLERR,"Illegal reset_mol_ids command"); + } else + error->all(FLERR, "Unknown reset_atoms mol keyword: {}", arg[iarg]); } - if (comm->me == 0) utils::logmesg(lmp,"Resetting molecule IDs ...\n"); + if (comm->me == 0) utils::logmesg(lmp, "Resetting molecule IDs ...\n"); // record wall time for resetting molecule IDs @@ -112,11 +111,11 @@ void ResetMolIDs::command(int narg, char **arg) comm->setup(); comm->exchange(); comm->borders(); - if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost); + if (domain->triclinic) domain->lamda2x(atom->nlocal + atom->nghost); // create computes - create_computes((char *) "COMMAND",groupid); + create_computes((char *) "COMMAND", groupid); // reset molecule IDs @@ -128,44 +127,43 @@ void ResetMolIDs::command(int narg, char **arg) if (comm->me == 0) { if (nchunk < 0) - utils::logmesg(lmp," number of new molecule IDs = unknown\n"); + utils::logmesg(lmp, " number of new molecule IDs = unknown\n"); else - utils::logmesg(lmp," number of new molecule IDs = {}\n",nchunk); - utils::logmesg(lmp," reset_mol_ids CPU = {:.3f} seconds\n", - platform::walltime()-time1); + utils::logmesg(lmp, " number of new molecule IDs = {}\n", nchunk); + utils::logmesg(lmp, " reset_atoms mol CPU = {:.3f} seconds\n", platform::walltime() - time1); } } /* ---------------------------------------------------------------------- - create computes used by reset_mol_ids + create computes used by reset_atoms_mol ------------------------------------------------------------------------- */ -void ResetMolIDs::create_computes(char *fixid, char *groupid) +void ResetAtomsMol::create_computes(char *fixid, char *groupid) { int igroup = group->find(groupid); - if (igroup == -1) error->all(FLERR,"Could not find reset_mol_ids group ID"); + if (igroup < 0) error->all(FLERR, "Could not find reset_atoms mol group {}", groupid); groupbit = group->bitmask[igroup]; // create instances of compute fragment/atom, compute reduce (if needed), // and compute chunk/atom. all use the group-ID for this command. // 'fixid' allows for creating independent instances of the computes - idfrag = fmt::format("{}_reset_mol_ids_FRAGMENT_ATOM",fixid); + idfrag = fmt::format("{}_reset_atoms_mol_FRAGMENT_ATOM", fixid); auto use_single = singleflag ? "yes" : "no"; - cfa = dynamic_cast( - modify->add_compute(fmt::format("{} {} fragment/atom single {}",idfrag,groupid,use_single))); + cfa = dynamic_cast(modify->add_compute( + fmt::format("{} {} fragment/atom single {}", idfrag, groupid, use_single))); - idchunk = fmt::format("{}_reset_mol_ids_CHUNK_ATOM",fixid); + idchunk = fmt::format("{}_reset_atoms_mol_CHUNK_ATOM", fixid); if (compressflag) - cca = dynamic_cast( - modify->add_compute(fmt::format("{} {} chunk/atom molecule compress yes",idchunk,groupid))); + cca = dynamic_cast(modify->add_compute( + fmt::format("{} {} chunk/atom molecule compress yes", idchunk, groupid))); } /* ---------------------------------------------------------------------- called from command() and directly from fixes that update molecules ------------------------------------------------------------------------- */ -void ResetMolIDs::reset() +void ResetAtomsMol::reset() { // invoke peratom method of compute fragment/atom // walks bond connectivity and assigns each atom a fragment ID @@ -181,8 +179,7 @@ void ResetMolIDs::reset() int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit) - molecule[i] = static_cast (fragIDs[i]); + if (mask[i] & groupbit) molecule[i] = static_cast(fragIDs[i]); // if compressflag = 0, done // set nchunk = -1 since cannot easily determine # of new molecule IDs @@ -208,7 +205,7 @@ void ResetMolIDs::reset() for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) if (fragIDs[i] == 0.0) mysingle = 1; - MPI_Allreduce(&mysingle,&singleexist,1,MPI_INT,MPI_MAX,world); + MPI_Allreduce(&mysingle, &singleexist, 1, MPI_INT, MPI_MAX, world); if (singleexist) nchunk--; } @@ -220,10 +217,10 @@ void ResetMolIDs::reset() if (groupbit != 1) { tagint mymol = 0; for (int i = 0; i < nlocal; i++) - if (!(mask[i] & groupbit)) - mymol = MAX(mymol,molecule[i]); - MPI_Allreduce(&mymol,&offset,1,MPI_LMP_TAGINT,MPI_MAX,world); - } else offset = 0; + if (!(mask[i] & groupbit)) mymol = MAX(mymol, molecule[i]); + MPI_Allreduce(&mymol, &offset, 1, MPI_LMP_TAGINT, MPI_MAX, world); + } else + offset = 0; } // reset molecule ID for all atoms in group @@ -231,11 +228,14 @@ void ResetMolIDs::reset() for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { - auto newid = static_cast(chunkIDs[i]); + auto newid = static_cast(chunkIDs[i]); if (singleexist) { - if (newid == 1) newid = 0; - else newid += offset - 1; - } else newid += offset; + if (newid == 1) + newid = 0; + else + newid += offset - 1; + } else + newid += offset; molecule[i] = newid; } } diff --git a/src/reset_mol_ids.h b/src/reset_atoms_mol.h similarity index 82% rename from src/reset_mol_ids.h rename to src/reset_atoms_mol.h index fb0d507931..3fad2560df 100644 --- a/src/reset_mol_ids.h +++ b/src/reset_atoms_mol.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -13,21 +13,21 @@ #ifdef COMMAND_CLASS // clang-format off -CommandStyle(reset_mol_ids,ResetMolIDs); +CommandStyle(RESET_ATOMS_MOL,ResetAtomsMol); // clang-format on #else -#ifndef LMP_RESET_MOL_IDS_H -#define LMP_RESET_MOL_IDS_H +#ifndef LMP_RESET_ATOMS_MOL_H +#define LMP_RESET_ATOMS_MOL_H #include "command.h" namespace LAMMPS_NS { -class ResetMolIDs : public Command { +class ResetAtomsMol : public Command { public: - ResetMolIDs(class LAMMPS *); - ~ResetMolIDs() override; + ResetAtomsMol(class LAMMPS *); + ~ResetAtomsMol() override; void command(int, char **) override; void create_computes(char *, char *); void reset(); @@ -43,7 +43,6 @@ class ResetMolIDs : public Command { class ComputeFragmentAtom *cfa; class ComputeChunkAtom *cca; }; - } // namespace LAMMPS_NS #endif diff --git a/src/respa.cpp b/src/respa.cpp index 650b04e6d6..71878a5af3 100644 --- a/src/respa.cpp +++ b/src/respa.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -372,7 +372,7 @@ void Respa::setup(int flag) mesg += fmt::format(" {}:{}", ilevel + 1, step[ilevel]); mesg += "\n r-RESPA fixes :"; - for (int l = 0; l < modify->n_post_force_respa_any; ++l) { + for (int l = 0; l < modify->n_post_force_respa; ++l) { Fix *f = modify->get_fix_by_index(modify->list_post_force_respa[l]); if (f->respa_level >= 0) mesg += fmt::format(" {}:{}[{}]", MIN(f->respa_level + 1, nlevels), f->style, f->id); diff --git a/src/respa.h b/src/respa.h index 68df9c179b..a0d16c451a 100644 --- a/src/respa.h +++ b/src/respa.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/run.cpp b/src/run.cpp index 3a9a4dc32e..516bce5d0b 100644 --- a/src/run.cpp +++ b/src/run.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/run.h b/src/run.h index 48b99b226f..a4be485395 100644 --- a/src/run.h +++ b/src/run.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/set.cpp b/src/set.cpp index b45b6e5798..65c215badf 100644 --- a/src/set.cpp +++ b/src/set.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/set.h b/src/set.h index fee69a3c86..b00dfb9854 100644 --- a/src/set.h +++ b/src/set.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/special.cpp b/src/special.cpp index 76091d10af..a210b6a82a 100644 --- a/src/special.cpp +++ b/src/special.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/special.h b/src/special.h index 49be187ec4..8b813f2a02 100644 --- a/src/special.h +++ b/src/special.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/suffix.h b/src/suffix.h index eaed5ffd4d..8df694157f 100644 --- a/src/suffix.h +++ b/src/suffix.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/table_file_reader.cpp b/src/table_file_reader.cpp index c3ff91d6a8..ab36036d6c 100644 --- a/src/table_file_reader.cpp +++ b/src/table_file_reader.cpp @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/table_file_reader.h b/src/table_file_reader.h index 51e10189ee..6ebb70dc19 100644 --- a/src/table_file_reader.h +++ b/src/table_file_reader.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/tabular_function.cpp b/src/tabular_function.cpp index 07df49729a..69265a61fd 100644 --- a/src/tabular_function.cpp +++ b/src/tabular_function.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/tabular_function.h b/src/tabular_function.h index 734424a8e6..05f75a31e4 100644 --- a/src/tabular_function.h +++ b/src/tabular_function.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/text_file_reader.cpp b/src/text_file_reader.cpp index 26124fb924..46a5fd33a9 100644 --- a/src/text_file_reader.cpp +++ b/src/text_file_reader.cpp @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/text_file_reader.h b/src/text_file_reader.h index e96387d423..cc62471f66 100644 --- a/src/text_file_reader.h +++ b/src/text_file_reader.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -21,6 +21,8 @@ #include "tokenizer.h" // IWYU pragma: export #include +#include +#include namespace LAMMPS_NS { class TextFileReader { diff --git a/src/thermo.cpp b/src/thermo.cpp index 518deab618..122463a25f 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -47,6 +47,7 @@ #include #include +#include using namespace LAMMPS_NS; using namespace MathConst; @@ -678,6 +679,19 @@ void Thermo::modify_params(int narg, char **arg) format_int_user.replace(found, 1, std::string(BIGINT_FORMAT).substr(1)); } else if (strcmp(arg[iarg + 1], "float") == 0) { format_float_user = arg[iarg + 2]; + } else if (utils::strmatch(arg[iarg + 1], "^\\d*\\*\\d*$")) { + // handles cases such as 2*6; currently doesn't allow negatives + int nlo, nhi; + utils::bounds(FLERR, arg[iarg + 1], 1, nfield_initial, nlo, nhi, error); + int icol = -1; + for (int i = nlo - 1; i < nhi; i++) { + if (i < 0) icol = nfield_initial + i + 1; // doesn't happen currently + else icol = i; + if (icol < 0 || (icol >= nfield_initial)) + error->all(FLERR, "Invalid thermo_modify format argument: {}", + arg[iarg + 1]); + format_column_user[icol] = arg[iarg + 2]; + } } else { int icol = -1; if (utils::is_integer(arg[iarg + 1])) { @@ -691,7 +705,7 @@ void Thermo::modify_params(int narg, char **arg) icol = -1; } } - if (icol < 0 || icol >= nfield_initial + 1) + if ((icol < 0) || (icol >= nfield_initial)) error->all(FLERR, "Invalid thermo_modify format argument: {}", arg[iarg + 1]); format_column_user[icol] = arg[iarg + 2]; } diff --git a/src/thermo.h b/src/thermo.h index 903a103c52..eaec3eb9f8 100644 --- a/src/thermo.h +++ b/src/thermo.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/timer.cpp b/src/timer.cpp index 785d345512..5bc397714a 100644 --- a/src/timer.cpp +++ b/src/timer.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -18,6 +18,7 @@ #include "fmt/chrono.h" #include +#include using namespace LAMMPS_NS; diff --git a/src/timer.h b/src/timer.h index a4b48716d5..5c100db1c0 100644 --- a/src/timer.h +++ b/src/timer.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/tokenizer.cpp b/src/tokenizer.cpp index 89c5b99dfb..00f0b0b761 100644 --- a/src/tokenizer.cpp +++ b/src/tokenizer.cpp @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/tokenizer.h b/src/tokenizer.h index b267e89b23..b5d9abf1f7 100644 --- a/src/tokenizer.h +++ b/src/tokenizer.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/universe.cpp b/src/universe.cpp index bd06300d12..e743816d92 100644 --- a/src/universe.cpp +++ b/src/universe.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/universe.h b/src/universe.h index faca04b398..8fd289ef65 100644 --- a/src/universe.h +++ b/src/universe.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/update.cpp b/src/update.cpp index 8b8dd3d49b..a7c06a1429 100644 --- a/src/update.cpp +++ b/src/update.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -346,8 +346,10 @@ void Update::create_integrate(int narg, char **arg, int trysuffix) estyle += "/"; if (sflag == 1) estyle += lmp->suffix; - else + else if (sflag == 2) estyle += lmp->suffix2; + else if ((sflag == 3) && lmp->non_pair_suffix()) + estyle += lmp->non_pair_suffix(); } integrate_style = utils::strdup(estyle); } @@ -359,9 +361,9 @@ void Update::create_integrate(int narg, char **arg, int trysuffix) void Update::new_integrate(char *style, int narg, char **arg, int trysuffix, int &sflag) { if (trysuffix && lmp->suffix_enable) { - if (lmp->suffix) { - sflag = 1; - std::string estyle = style + std::string("/") + lmp->suffix; + if (lmp->non_pair_suffix()) { + sflag = 1 + 2*lmp->pair_only_flag; + std::string estyle = style + std::string("/") + lmp->non_pair_suffix(); if (integrate_map->find(estyle) != integrate_map->end()) { IntegrateCreator &integrate_creator = (*integrate_map)[estyle]; integrate = integrate_creator(lmp, narg, arg); @@ -407,8 +409,10 @@ void Update::create_minimize(int narg, char **arg, int trysuffix) estyle += "/"; if (sflag == 1) estyle += lmp->suffix; - else + else if (sflag == 2) estyle += lmp->suffix2; + else if ((sflag == 3) && lmp->non_pair_suffix()) + estyle += lmp->non_pair_suffix(); } minimize_style = utils::strdup(estyle); } @@ -420,9 +424,9 @@ void Update::create_minimize(int narg, char **arg, int trysuffix) void Update::new_minimize(char *style, int /* narg */, char ** /* arg */, int trysuffix, int &sflag) { if (trysuffix && lmp->suffix_enable) { - if (lmp->suffix) { - sflag = 1; - std::string estyle = style + std::string("/") + lmp->suffix; + if (lmp->non_pair_suffix()) { + sflag = 1 + 2*lmp->pair_only_flag; + std::string estyle = style + std::string("/") + lmp->non_pair_suffix(); if (minimize_map->find(estyle) != minimize_map->end()) { MinimizeCreator &minimize_creator = (*minimize_map)[estyle]; minimize = minimize_creator(lmp); diff --git a/src/update.h b/src/update.h index b88e70134c..7ed61ba296 100644 --- a/src/update.h +++ b/src/update.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/utils.cpp b/src/utils.cpp index e293b6c67b..11a1abffb8 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -13,6 +13,7 @@ #include "utils.h" +#include "arg_info.h" #include "atom.h" #include "comm.h" #include "compute.h" @@ -381,7 +382,7 @@ double utils::numeric(const char *file, int line, const std::string &str, bool d std::string buf(str); if (has_utf8(buf)) buf = utf8_subst(buf); - if (buf.find_first_not_of("0123456789-+.eE") != std::string::npos) { + if (!is_double(buf)) { std::string msg("Expected floating point parameter instead of '"); msg += buf + "' in input script or data file"; if (do_abort) @@ -425,7 +426,7 @@ int utils::inumeric(const char *file, int line, const std::string &str, bool do_ std::string buf(str); if (has_utf8(buf)) buf = utf8_subst(buf); - if (buf.find_first_not_of("0123456789-+") != std::string::npos) { + if (!is_integer(buf)) { std::string msg("Expected integer parameter instead of '"); msg += buf + "' in input script or data file"; if (do_abort) @@ -470,7 +471,7 @@ bigint utils::bnumeric(const char *file, int line, const std::string &str, bool std::string buf(str); if (has_utf8(buf)) buf = utf8_subst(buf); - if (buf.find_first_not_of("0123456789-+") != std::string::npos) { + if (!is_integer(buf)) { std::string msg("Expected integer parameter instead of '"); msg += buf + "' in input script or data file"; if (do_abort) @@ -515,7 +516,7 @@ tagint utils::tnumeric(const char *file, int line, const std::string &str, bool std::string buf(str); if (has_utf8(buf)) buf = utf8_subst(buf); - if (buf.find_first_not_of("0123456789-+") != std::string::npos) { + if (!is_integer(buf)) { std::string msg("Expected integer parameter instead of '"); msg += buf + "' in input script or data file"; if (do_abort) @@ -629,11 +630,79 @@ int utils::expand_args(const char *file, int line, int narg, char **arg, int mod std::string word(arg[iarg]); expandflag = 0; - // match compute, fix, or custom property array reference with a '*' wildcard - // number range in the first pair of square brackets + // match grids - if (strmatch(word, "^[cfv]_\\w+\\[\\d*\\*\\d*\\]") || - strmatch(word, "^[id]2_\\w+\\[\\d*\\*\\d*\\]")) { + if (strmatch(word, "^[cf]_\\w+:\\w+:\\w+\\[\\d*\\*\\d*\\]")) { + auto gridid = utils::parse_grid_id(FLERR, word, lmp->error); + + size_t first = gridid[2].find('['); + size_t second = gridid[2].find(']', first + 1); + id = gridid[2].substr(0, first); + wc = gridid[2].substr(first + 1, second - first - 1); + tail = gridid[2].substr(second + 1); + + // grids from compute + + if (gridid[0][0] == 'c') { + + auto compute = lmp->modify->get_compute_by_id(gridid[0].substr(2)); + if (compute && compute->pergrid_flag) { + + int dim = 0; + int igrid = compute->get_grid_by_name(gridid[1], dim); + + if (igrid >= 0) { + + int ncol = 0; + compute->get_griddata_by_name(igrid, id, ncol); + nmax = ncol; + + expandflag = 1; + } + } + // grids from fix + + } else if (gridid[0][0] == 'f') { + + auto fix = lmp->modify->get_fix_by_id(gridid[0].substr(2)); + if (fix && fix->pergrid_flag) { + + int dim = 0; + int igrid = fix->get_grid_by_name(gridid[1], dim); + + if (igrid >= 0) { + + int ncol = 0; + fix->get_griddata_by_name(igrid, id, ncol); + nmax = ncol; + + expandflag = 1; + } + } + } + + // expand wild card string to nlo/nhi numbers + + if (expandflag) { + utils::bounds(file, line, wc, 1, nmax, nlo, nhi, lmp->error); + + if (newarg + nhi - nlo + 1 > maxarg) { + maxarg += nhi - nlo + 1; + earg = (char **) lmp->memory->srealloc(earg, maxarg * sizeof(char *), "input:earg"); + } + + for (int index = nlo; index <= nhi; index++) { + earg[newarg] = + utils::strdup(fmt::format("{}:{}:{}[{}]{}", gridid[0], gridid[1], id, index, tail)); + newarg++; + } + } + + // match compute, fix, or custom property array reference with a '*' wildcard + // number range in the first pair of square brackets + + } else if (strmatch(word, "^[cfv]_\\w+\\[\\d*\\*\\d*\\]") || + strmatch(word, "^[id]2_\\w+\\[\\d*\\*\\d*\\]")) { // split off the compute/fix/property ID, the wildcard and trailing text @@ -727,30 +796,33 @@ int utils::expand_args(const char *file, int line, int narg, char **arg, int mod } } } + + // expansion will take place + + if (expandflag) { + + // expand wild card string to nlo/nhi numbers + + utils::bounds(file, line, wc, 1, nmax, nlo, nhi, lmp->error); + + if (newarg + nhi - nlo + 1 > maxarg) { + maxarg += nhi - nlo + 1; + earg = (char **) lmp->memory->srealloc(earg, maxarg * sizeof(char *), "input:earg"); + } + + for (int index = nlo; index <= nhi; index++) { + if (word[1] == '2') + earg[newarg] = utils::strdup(fmt::format("{}2_{}[{}]{}", word[0], id, index, tail)); + else + earg[newarg] = utils::strdup(fmt::format("{}_{}[{}]{}", word[0], id, index, tail)); + newarg++; + } + } } - // expansion will take place + // no expansion: duplicate original string - if (expandflag) { - - // expand wild card string to nlo/nhi numbers - - utils::bounds(file, line, wc, 1, nmax, nlo, nhi, lmp->error); - - if (newarg + nhi - nlo + 1 > maxarg) { - maxarg += nhi - nlo + 1; - earg = (char **) lmp->memory->srealloc(earg, maxarg * sizeof(char *), "input:earg"); - } - - for (int index = nlo; index <= nhi; index++) { - if (word[1] == '2') - earg[newarg] = utils::strdup(fmt::format("{}2_{}[{}]{}", word[0], id, index, tail)); - else - earg[newarg] = utils::strdup(fmt::format("{}_{}[{}]{}", word[0], id, index, tail)); - newarg++; - } - } else { - // no expansion: duplicate original string + if (!expandflag) { if (newarg == maxarg) { maxarg++; earg = (char **) lmp->memory->srealloc(earg, maxarg * sizeof(char *), "input:earg"); @@ -760,10 +832,7 @@ int utils::expand_args(const char *file, int line, int narg, char **arg, int mod } } - //printf("NEWARG %d\n",newarg); - //for (int i = 0; i < newarg; i++) - // printf(" arg %d: %s\n",i,earg[i]); - + // printf("NEWARG %d\n",newarg); for (int i = 0; i < newarg; i++) printf(" arg %d: %s\n",i,earg[i]); return newarg; } @@ -795,6 +864,133 @@ char *utils::expand_type(const char *file, int line, const std::string &str, int return nullptr; } +/* ---------------------------------------------------------------------- + Check grid reference for valid Compute or Fix which produces per-grid data + errstr = name of calling command used if error is generated + ref = grid reference as it appears in an input script + e.g. c_myCompute:grid:data[2], ditto for a fix + nevery = frequency at which caller will access fix, not used if a compute + return arguments: + id = ID of compute or fix + igrid = index of which grid in compute/fix (0 to N-1) + idata = index of which data field in igrid (0 to N-1) + index = index into data field (0 for vector, 1-N for column of array) + method return = ArgInfo::COMPUTE or ArgInfo::FIX or -1 for neither + caller decides what to do if arg is not a COMPUTE or FIX reference +------------------------------------------------------------------------- */ + +int utils::check_grid_reference(char *errstr, char *ref, int nevery, + char *&id, int &igrid, int &idata, int &index, LAMMPS *lmp) +{ + ArgInfo argi(ref, ArgInfo::COMPUTE | ArgInfo::FIX); + index = argi.get_index1(); + auto name = argi.get_name(); + + switch (argi.get_type()) { + + case ArgInfo::UNKNOWN: { + lmp->error->all(FLERR,"%s grid reference %s is invalid",errstr,ref); + } break; + + // compute value = c_ID + + case ArgInfo::COMPUTE: { + + // split name = idcompute:gname:dname into 3 strings + + auto words = parse_grid_id(FLERR,name,lmp->error); + const auto &idcompute = words[0]; + const auto &gname = words[1]; + const auto &dname = words[2]; + + auto icompute = lmp->modify->get_compute_by_id(idcompute); + if (!icompute) lmp->error->all(FLERR,"{} compute ID {} not found",errstr,idcompute); + if (icompute->pergrid_flag == 0) + lmp->error->all(FLERR,"{} compute {} does not compute per-grid info",errstr,idcompute); + + int dim; + igrid = icompute->get_grid_by_name(gname,dim); + if (igrid < 0) + lmp->error->all(FLERR,"{} compute {} does not recognize grid name {}",errstr,idcompute,gname); + + int ncol; + idata = icompute->get_griddata_by_name(igrid,dname,ncol); + if (idata < 0) + lmp->error->all(FLERR,"{} compute {} does not recognize data name {}",errstr,idcompute,dname); + + if (argi.get_dim() == 0 && ncol) + lmp->error->all(FLERR,"{} compute {} data {} is not per-grid vector",errstr,idcompute,dname); + if (argi.get_dim() && ncol == 0) + lmp->error->all(FLERR,"{} compute {} data {} is not per-grid array",errstr,idcompute,dname); + if (argi.get_dim() && argi.get_index1() > ncol) + lmp->error->all(FLERR,"{} compute {} array {} is accessed out-of-range",errstr,idcompute,dname); + + id = utils::strdup(idcompute); + return ArgInfo::COMPUTE; + } break; + + // fix value = f_ID + + case ArgInfo::FIX: { + + // split name = idfix:gname:dname into 3 strings + + auto words = parse_grid_id(FLERR,name,lmp->error); + const auto &idfix = words[0]; + const auto &gname = words[1]; + const auto &dname = words[2]; + + auto ifix = lmp->modify->get_fix_by_id(idfix); + if (!ifix) lmp->error->all(FLERR,"{} fix ID {} not found",errstr,idfix); + if (ifix->pergrid_flag == 0) + lmp->error->all(FLERR,"{} fix {} does not compute per-grid info",errstr,idfix); + if (nevery % ifix->pergrid_freq) + lmp->error->all(FLERR,"{} fix {} not computed at compatible time",errstr,idfix); + + int dim; + igrid = ifix->get_grid_by_name(gname,dim); + if (igrid < 0) + lmp->error->all(FLERR,"{} fix {} does not recognize grid name {}",errstr,idfix,gname); + + int ncol; + idata = ifix->get_griddata_by_name(igrid,dname,ncol); + if (idata < 0) + lmp->error->all(FLERR,"{} fix {} does not recognize data name {}",errstr,idfix,dname); + + if (argi.get_dim() == 0 && ncol) + lmp->error->all(FLERR,"{} fix {} data {} is not per-grid vector",errstr,idfix,dname); + if (argi.get_dim() > 0 && ncol == 0) + lmp->error->all(FLERR,"{} fix {} data {} is not per-grid array",errstr,idfix,dname); + if (argi.get_dim() > 0 && argi.get_index1() > ncol) + lmp->error->all(FLERR,"{} fix {} array {} is accessed out-of-range",errstr,idfix,dname); + + id = utils::strdup(idfix); + return ArgInfo::FIX; + } break; + } + + return -1; +} + +/* ---------------------------------------------------------------------- + Parse grid reference into id:gridname:dataname + return vector of 3 substrings +------------------------------------------------------------------------- */ + +std::vector utils::parse_grid_id(const char *file, int line, const std::string &name, + Error *error) +{ + auto words = Tokenizer(name, ":").as_vector(); + if (words.size() != 3) { + if (error) + error->all(file, line, "Grid ID {} must be 3 strings separated by 2 ':'characters", name); + else + return {"", "", ""}; + } + + return words; +} + /* ---------------------------------------------------------------------- Make copy of string in new storage. Works like the (non-portable) C-style strdup() but also accepts a C++ string as argument. @@ -866,6 +1062,29 @@ std::string utils::star_subst(const std::string &name, bigint step, int pad) return fmt::format("{}{:0{}}{}", name.substr(0, star), step, pad, name.substr(star + 1)); } +/* ---------------------------------------------------------------------- + Remove accelerator style suffix from string +------------------------------------------------------------------------- */ +std::string utils::strip_style_suffix(const std::string &style, LAMMPS *lmp) +{ + std::string newstyle = style; + if (lmp->suffix_enable) { + if (lmp->suffix) { + if (utils::strmatch(style, fmt::format("/{}$", lmp->suffix))) { + newstyle.resize(style.size() - strlen(lmp->suffix) - 1); + return newstyle; + } + } + if (lmp->suffix2) { + if (utils::strmatch(style, fmt::format("/{}$", lmp->suffix2))) { + newstyle.resize(style.size() - strlen(lmp->suffix2) - 1); + return newstyle; + } + } + } + return newstyle; +} + /* ---------------------------------------------------------------------- Replace UTF-8 encoded chars with known ASCII equivalents ------------------------------------------------------------------------- */ @@ -1116,6 +1335,7 @@ std::vector utils::split_words(const std::string &text) /* ---------------------------------------------------------------------- Convert multi-line string into lines ------------------------------------------------------------------------- */ + std::vector utils::split_lines(const std::string &text) { return Tokenizer(text, "\r\n").as_vector(); @@ -1129,11 +1349,7 @@ bool utils::is_integer(const std::string &str) { if (str.empty()) return false; - for (const auto &c : str) { - if (isdigit(c) || c == '-' || c == '+') continue; - return false; - } - return true; + return strmatch(str, "^[+-]?\\d+$"); } /* ---------------------------------------------------------------------- @@ -1144,13 +1360,11 @@ bool utils::is_double(const std::string &str) { if (str.empty()) return false; - for (const auto &c : str) { - if (isdigit(c)) continue; - if (c == '-' || c == '+' || c == '.') continue; - if (c == 'e' || c == 'E') continue; + if (strmatch(str, "^[+-]?\\d+\\.?\\d*$") || strmatch(str, "^[+-]?\\d+\\.?\\d*[eE][+-]?\\d+$") || + strmatch(str, "^[+-]?\\d*\\.?\\d+$") || strmatch(str, "^[+-]?\\d*\\.?\\d+[eE][+-]?\\d+$")) + return true; + else return false; - } - return true; } /* ---------------------------------------------------------------------- @@ -1263,6 +1477,7 @@ std::string utils::get_potential_units(const std::string &path, const std::strin /* ---------------------------------------------------------------------- return bitmask of supported conversions for a given property ------------------------------------------------------------------------- */ + int utils::get_supported_conversions(const int property) { if (property == ENERGY) diff --git a/src/utils.h b/src/utils.h index 28f48d1ab2..335016831d 100644 --- a/src/utils.h +++ b/src/utils.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -334,13 +334,15 @@ namespace utils { /*! Expand list of arguments when containing fix/compute wildcards * * This function searches the list of arguments in *arg* for strings - * of the kind c_ID[*] or f_ID[*] referring to computes or fixes. + * of the kind c_ID[*], f_ID[*], v_ID[*], i2_ID[*], d2_ID[*], or + * c_ID:gname:dname[*] referring to computes, fixes, vector style + * variables, custom per-atom arrays, or grids, respectively. * Any such strings are replaced by one or more strings with the * '*' character replaced by the corresponding possible numbers as - * determined from the fix or compute instance. Other strings are - * just copied. If the *mode* parameter is set to 0, expand global - * vectors, but not global arrays; if it is set to 1, expand global - * arrays (by column) but not global vectors. + * determined from the fix, compute, variable, property, or grid instance. + * Unrecognized strings are just copied. If the *mode* parameter + * is set to 0, expand global vectors, but not global arrays; if it is + * set to 1, expand global arrays (by column) but not global vectors. * * If any expansion happens, the earg list and all its * strings are new allocations and must be freed explicitly by the @@ -377,6 +379,40 @@ namespace utils { char *expand_type(const char *file, int line, const std::string &str, int mode, LAMMPS *lmp); + /*! Check grid reference for valid Compute or Fix which produces per-grid data + * + * This function checks if a command argument in the input script + * is a valid reference to per-grid data produced by a Compute or Fix. + * If it is, the ID of the compute/fix is returned which the caller must + * free with delete []. It also returns igrid/idata/index integers + * which allow the caller to access the per-grid data. + * A flag is also returned to indicate compute vs fix vs error. + * + * \param errstr name of calling command, e.g. "Fix ave/grid" + * \param ref per-grid reference from input script, e.g. "c_10:grid:data[2]" + * \param nevery frequency at which caller will access fix for per-grid info, + * ignored when reference is to a compute + * \param lmp pointer to top-level LAMMPS class instance + * \return id ID of Compute or Fix + * \return igrid which grid is referenced (0 to N-1) + * \return idata which data on grid is referenced (0 to N-1) + * \return index which column of data is referenced (0 for vec, 1-N for array) + * \return ArgINFO::COMPUTE or FIX or UNKNOWN or NONE */ + + int check_grid_reference(char *errstr, char *ref, int nevery, + char *&id, int &igrid, int &idata, int &index, LAMMPS *lmp); + + /*! Parse grid reference into 3 sub-strings + * + * Format of grid ID reference = id:gname:dname + * Return vector with the 3 sub-strings + * + * \param name = complete grid ID + * \return std::vector containing the 3 sub-strings */ + + std::vector parse_grid_id(const char *file, int line, const std::string &name, + Error *error); + /*! Make C-style copy of string in new storage * * This allocates a storage buffer and copies the C-style or @@ -430,7 +466,23 @@ namespace utils { std::string star_subst(const std::string &name, bigint step, int pad); - /*! Check if a string will likely have UTF-8 encoded characters + /*! Remove style suffix from string if suffix flag is active + * + * +\verbatim embed:rst + +This will try to undo the effect from using the :doc:`suffix command ` +or the *-suffix/-sf* command line flag and return correspondingly modified string. + +\endverbatim + * + * \param style string of style name + * \param lmp pointer to the LAMMPS class (has suffix_flag and suffix strings) + * \return processed string */ + + std::string strip_style_suffix(const std::string &style, LAMMPS *lmp); + +/*! Check if a string will likely have UTF-8 encoded characters * * UTF-8 uses the 7-bit standard ASCII table for the first 127 characters and * all other characters are encoded as multiple bytes. For the multi-byte diff --git a/src/variable.cpp b/src/variable.cpp index e38dd4cd29..c07e62648b 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -832,6 +832,18 @@ void Variable::set_arrays(int /*i*/) reader[i]->fixstore->vstore[i] = 0.0; } +/* ---------------------------------------------------------------------- + delete all atomfile style variables. + must scan list in reverse since remove() will compact list. + called from LAMMPS::destroy() +------------------------------------------------------------------------- */ + +void Variable::purge_atomfile() +{ + for (int i = nvar-1; i >= 0; --i) + if (style[i] == ATOMFILE) remove(i); +} + /* ---------------------------------------------------------------------- called by python command in input script simply pass input script line args to Python class @@ -973,8 +985,21 @@ char *Variable::retrieve(const char *name) str = data[ivar][1] = utils::strdup(result); } else if (style[ivar] == PYTHON) { int ifunc = python->variable_match(data[ivar][0],name,0); - if (ifunc < 0) - error->all(FLERR,"Python variable {} does not match Python function {}", name, data[ivar][0]); + if (ifunc < 0) { + if (ifunc == -1) { + error->all(FLERR, "Could not find Python function {} linked to variable {}", + data[ivar][0], name); + } else if (ifunc == -2) { + error->all(FLERR, "Python function {} for variable {} does not have a return value", + data[ivar][0], name); + } else if (ifunc == -3) { + error->all(FLERR,"Python variable {} does not match variable name registered with " + "Python function {}", name, data[ivar][0]); + } else { + error->all(FLERR, "Unknown error verifying function {} linked to python style variable {}", + data[ivar][0],name); + } + } python->invoke_function(ifunc,data[ivar][1]); str = data[ivar][1]; // if Python func returns a string longer than VALUELENGTH @@ -4504,7 +4529,7 @@ void Variable::peratom2global(int flag, char *word, double *vector, int nstride, error->one(FLERR,"Variable uses atom property that isn't allocated"); mine = atom->q[index]; } - else error->one(FLERR,"Invalid atom vector in variable formula"); + else error->one(FLERR,"Invalid atom vector {} in variable formula", word); } else mine = vector[index*nstride]; diff --git a/src/variable.h b/src/variable.h index 1e05fd3904..6326c5cc78 100644 --- a/src/variable.h +++ b/src/variable.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -34,6 +34,7 @@ class Variable : protected Pointers { int find(const char *); void set_arrays(int); void python_command(int, char **); + void purge_atomfile(); int equalstyle(int); int atomstyle(int); diff --git a/src/velocity.cpp b/src/velocity.cpp index e11317dd09..421c494553 100644 --- a/src/velocity.cpp +++ b/src/velocity.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/velocity.h b/src/velocity.h index 669a0f947f..a2d42aef50 100644 --- a/src/velocity.h +++ b/src/velocity.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/verlet.cpp b/src/verlet.cpp index 15e1ab0800..0222a0d2a0 100644 --- a/src/verlet.cpp +++ b/src/verlet.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/verlet.h b/src/verlet.h index 98770f33f1..88bfd2fd58 100644 --- a/src/verlet.h +++ b/src/verlet.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/version.h b/src/version.h index 8f9e5a3941..d05bfe6f29 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "15 Sep 2022" +#define LAMMPS_VERSION "22 Dec 2022" diff --git a/src/write_coeff.cpp b/src/write_coeff.cpp index 9dfdeb5141..11987d4b37 100644 --- a/src/write_coeff.cpp +++ b/src/write_coeff.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/write_coeff.h b/src/write_coeff.h index 55c88c8149..5c1414c8ed 100644 --- a/src/write_coeff.h +++ b/src/write_coeff.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/write_data.cpp b/src/write_data.cpp index 2bc3a21627..8410fa7e81 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/write_data.h b/src/write_data.h index 74466dae05..f0df9b0c5f 100644 --- a/src/write_data.h +++ b/src/write_data.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/write_dump.cpp b/src/write_dump.cpp index a7f143aa43..89dd48e0ba 100644 --- a/src/write_dump.cpp +++ b/src/write_dump.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/write_dump.h b/src/write_dump.h index f8bbfefd13..a52da0d6ec 100644 --- a/src/write_dump.h +++ b/src/write_dump.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/src/write_restart.cpp b/src/write_restart.cpp index 2fe2f8d373..62cbe0078c 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -2,7 +2,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -399,7 +399,7 @@ void WriteRestart::write(const std::string &file) } } - // Check for I/O error status + // check for I/O error status int io_all = 0; MPI_Allreduce(&io_error,&io_all,1,MPI_INT,MPI_MAX,world); @@ -449,7 +449,7 @@ void WriteRestart::header() // write atom_style and its args - write_string(ATOM_STYLE,atom->atom_style); + write_string(ATOM_STYLE,utils::strip_style_suffix(atom->atom_style,lmp)); fwrite(&atom->avec->nargcopy,sizeof(int),1,fp); for (int i = 0; i < atom->avec->nargcopy; i++) { int n = strlen(atom->avec->argcopy[i]) + 1; @@ -542,26 +542,26 @@ void WriteRestart::force_fields() { if (force->pair) { if (force->pair->restartinfo) { - write_string(PAIR,force->pair_style); + write_string(PAIR,utils::strip_style_suffix(force->pair_style,lmp)); force->pair->write_restart(fp); } else { - write_string(NO_PAIR,force->pair_style); + write_string(NO_PAIR,utils::strip_style_suffix(force->pair_style,lmp)); } } if (atom->avec->bonds_allow && force->bond) { - write_string(BOND,force->bond_style); + write_string(BOND,utils::strip_style_suffix(force->bond_style,lmp)); force->bond->write_restart(fp); } if (atom->avec->angles_allow && force->angle) { - write_string(ANGLE,force->angle_style); + write_string(ANGLE,utils::strip_style_suffix(force->angle_style,lmp)); force->angle->write_restart(fp); } if (atom->avec->dihedrals_allow && force->dihedral) { - write_string(DIHEDRAL,force->dihedral_style); + write_string(DIHEDRAL,utils::strip_style_suffix(force->dihedral_style,lmp)); force->dihedral->write_restart(fp); } if (atom->avec->impropers_allow && force->improper) { - write_string(IMPROPER,force->improper_style); + write_string(IMPROPER,utils::strip_style_suffix(force->improper_style,lmp)); force->improper->write_restart(fp); } @@ -672,12 +672,12 @@ void WriteRestart::write_double(int flag, double value) byte) into the restart file ------------------------------------------------------------------------- */ -void WriteRestart::write_string(int flag, const char *value) +void WriteRestart::write_string(int flag, const std::string &value) { - int n = strlen(value) + 1; + int n = value.size() + 1; fwrite(&flag,sizeof(int),1,fp); fwrite(&n,sizeof(int),1,fp); - fwrite(value,sizeof(char),n,fp); + fwrite(value.c_str(),sizeof(char),n,fp); } /* ---------------------------------------------------------------------- diff --git a/src/write_restart.h b/src/write_restart.h index e1146653a5..390e143ed5 100644 --- a/src/write_restart.h +++ b/src/write_restart.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -62,7 +62,7 @@ class WriteRestart : public Command { void write_int(int, int); void write_bigint(int, bigint); void write_double(int, double); - void write_string(int, const char *); + void write_string(int, const std::string &); void write_int_vec(int, int, int *); void write_double_vec(int, int, double *); }; diff --git a/tools/README b/tools/README index 22d9c8ea18..82af6f3f66 100644 --- a/tools/README +++ b/tools/README @@ -48,6 +48,7 @@ smd convert Smooth Mach Dynamics triangles to VTK spin perform a cubic polynomial interpolation of a GNEB MEP stl_bin2txt convert binary STL files to ASCII swig Interface file and demo scripts for SWIG wrappers for the LAMMPS C library interface +tabulate Python scripts to generate tabulated potential files for LAMMPS tinker2lmp.py convert Tinker input files to LAMMPS input files valgrind suppression files for use with valgrind's memcheck tool vim add-ons to VIM editor for editing LAMMPS input scripts diff --git a/tools/binary2txt.cpp b/tools/binary2txt.cpp index b675fb5b5d..b77614a8fc 100644 --- a/tools/binary2txt.cpp +++ b/tools/binary2txt.cpp @@ -1,7 +1,7 @@ /* ----------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + LAMMPS development team: developers@lammps.org, Sandia National Laboratories Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/tools/coding_standard/homepage.py b/tools/coding_standard/homepage.py index 8d3f158a24..8cfc5192b9 100644 --- a/tools/coding_standard/homepage.py +++ b/tools/coding_standard/homepage.py @@ -24,9 +24,15 @@ include: - cmake/** - doc - doc/src/** - - python + - fortran + - lib/** + - python/** - src/** - - tools/coding_standard + - tools/** + - unittest/** + - examples/COUPLE/** + - examples/plugins/** + - examples/PACKAGES/** patterns: - "*.c" - "*.cmake" @@ -36,13 +42,26 @@ patterns: - "*.py" - "*.rst" - "*.sh" + - "*.f90" - ".gitignore" - "README" - "requirements.txt" """ def check_homepage(f): - pattern = re.compile(r'.*lammps.sandia.gov.*') # lgtm [py/incomplete-hostname-regexp] + pattern = re.compile(r'.*(lammps.sandia.gov|www.cs.sandia.gov).*') # lgtm [py/incomplete-hostname-regexp] + lineno = 1 + errors = set() + + for line in f: + if pattern.match(line): + errors.add(lineno) + lineno += 1 + + return errors + +def check_email(f): + pattern = re.compile(r'.*sjplimp@sandia.gov.*') # lgtm [py/incomplete-hostname-regexp] lineno = 1 errors = set() @@ -54,9 +73,10 @@ def check_homepage(f): return errors def check_file(path): - if path.find('homepage.py') >= 0: return { 'homepage_errors' : '' } + if path.find('homepage.py') >= 0: return { 'homepage_errors' : '', 'email_errors' : '' } encoding = 'UTF-8' homepage_errors = set() + email_errors = set() try: with open(path, 'r') as f: homepage_errors = check_homepage(f) @@ -67,9 +87,20 @@ def check_file(path): homepage_errors = check_homepage(f) except Exception: encoding = 'unknown' + try: + with open(path, 'r') as f: + email_errors = check_email(f) + except UnicodeDecodeError: + encoding = 'ISO-8859-1' + try: + with open(path, 'r', encoding=encoding) as f: + email_errors = check_email(f) + except Exception: + encoding = 'unknown' return { 'homepage_errors': homepage_errors, + 'email_errors': email_errors, 'encoding': encoding } @@ -84,6 +115,9 @@ def fix_file(path, check_result): newline = newline.replace("http://lammps.sandia.gov,","https://www.lammps.org/") newline = newline.replace("lammps.sandia.gov","www.lammps.org") newline = newline.replace("http://www.lammps.org","https://www.lammps.org") + newline = newline.replace("www.cs.sandia.gov/~sjplimp/lammps.html","https://www.lammps.org") + newline = newline.replace("Steve Plimpton, sjplimp@sandia.gov","LAMMPS Development team: developers@lammps.org") + newline = newline.replace("Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories","LAMMPS Development team: developers@lammps.org") print(newline, end='', file=out) shutil.copymode(path, newfile) shutil.move(newfile, path) @@ -104,13 +138,16 @@ def check_folder(directory, config, fix=False, verbose=False): print("Checking file:", path) result = check_file(path) - has_resolvable_errors = False for lineno in result['homepage_errors']: print("[Error] Incorrect LAMMPS homepage @ {}:{}".format(path, lineno)) has_resolvable_errors = True + for lineno in result['email_errors']: + print("[Error] Incorrect Developer email @ {}:{}".format(path, lineno)) + has_resolvable_errors = True + if has_resolvable_errors: if fix: print("Applying automatic fixes to file:", path) diff --git a/tools/coding_standard/versiontags.py b/tools/coding_standard/versiontags.py index 75a37dfbcc..0b4597046f 100644 --- a/tools/coding_standard/versiontags.py +++ b/tools/coding_standard/versiontags.py @@ -36,7 +36,7 @@ patterns: """ def check_pending_tag(f): - pattern = re.compile(r'^ *\.\. +version(changed|added):: +TBD') + pattern = re.compile(r'^ *\.\. +(version(changed|added)|deprecated):: +TBD') last_line = "\n" lineno = 1 errors = set() diff --git a/tools/eff/restart2data-pEFF.cpp b/tools/eff/restart2data-pEFF.cpp index db827b52a6..cdab025a59 100644 --- a/tools/eff/restart2data-pEFF.cpp +++ b/tools/eff/restart2data-pEFF.cpp @@ -1,7 +1,7 @@ /* ----------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + LAMMPS development team: developers@lammps.org, Sandia National Laboratories Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/tools/mesont/dump2vtk.cpp b/tools/mesont/dump2vtk.cpp index e2b16178b8..7b9984015d 100644 --- a/tools/mesont/dump2vtk.cpp +++ b/tools/mesont/dump2vtk.cpp @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/tools/python/README b/tools/python/README index 433b86b315..6840d5bae6 100644 --- a/tools/python/README +++ b/tools/python/README @@ -3,8 +3,7 @@ post-processing tasks. If you have suggestions or contributions for additional scripts or functionality that could be added, built on the Pizza.py modules (as -explained below), send email to Steve Plimpton (sjplimp at -sandia.gov). +explained below), send email to Steve Plimpton (sjplimp at gmail.com) log2txt.py convert thermo info in a LAMMPS log file to columns of numbers logplot.py plot 2 columns of thermo info from a LAMMPS log file diff --git a/tools/python/dump2cfg.py b/tools/python/dump2cfg.py index 8966f6a046..7d7ea5bab0 100755 --- a/tools/python/dump2cfg.py +++ b/tools/python/dump2cfg.py @@ -7,7 +7,7 @@ # Nid,Ntype,Nx,Ny,Nz = columns #s for ID,type,x,y,z # (usually 1,2,3,4,5) # cfgfile = new CFG file -# Author: Steve Plimpton (Sandia), sjplimp at sandia.gov +# Author: Steve Plimpton (Sandia), sjplimp at gmail.com import sys,os path = os.environ["LAMMPS_PYTHON_TOOLS"] diff --git a/tools/python/dump2pdb.py b/tools/python/dump2pdb.py index ff228ae93b..f9f606477d 100755 --- a/tools/python/dump2pdb.py +++ b/tools/python/dump2pdb.py @@ -9,7 +9,7 @@ # pdbfile = new PDB file # template = PDB file to use as template for creating new PDB file # this arg is optional, if not used a generic PDB file is created -# Author: Steve Plimpton (Sandia), sjplimp at sandia.gov +# Author: Steve Plimpton (Sandia), sjplimp at gmail.com import sys,os path = os.environ["LAMMPS_PYTHON_TOOLS"] diff --git a/tools/python/dump2xyz.py b/tools/python/dump2xyz.py index bf9f1a617f..aa6ab9e9f9 100755 --- a/tools/python/dump2xyz.py +++ b/tools/python/dump2xyz.py @@ -7,7 +7,7 @@ # Nid,Ntype,Nx,Ny,Nz = columns #s for ID,type,x,y,z # (usually 1,2,3,4,5) # xyzfile = new XYZ file -# Author: Steve Plimpton (Sandia), sjplimp at sandia.gov +# Author: Steve Plimpton (Sandia), sjplimp at gmail.com import sys,os path = os.environ["LAMMPS_PYTHON_TOOLS"] diff --git a/tools/python/dumpsort.py b/tools/python/dumpsort.py index 205d4de13a..040cdbd4a7 100755 --- a/tools/python/dumpsort.py +++ b/tools/python/dumpsort.py @@ -6,7 +6,7 @@ # oldfile = old LAMMPS dump file in native LAMMPS format # N = column # for atom ID (usually 1) # newfile = new sorted LAMMPS dump file -# Author: Steve Plimpton (Sandia), sjplimp at sandia.gov +# Author: Steve Plimpton (Sandia), sjplimp at gmail.com import sys,os path = os.environ["LAMMPS_PYTHON_TOOLS"] diff --git a/tools/python/log2txt.py b/tools/python/log2txt.py index acc9d61b73..5f4aa3908a 100755 --- a/tools/python/log2txt.py +++ b/tools/python/log2txt.py @@ -8,7 +8,7 @@ # data.txt = text file to create # X Y ... = columns to include (optional), X,Y are thermo keywords # if no columns listed, all columns are included -# Author: Steve Plimpton (Sandia), sjplimp at sandia.gov +# Author: Steve Plimpton (Sandia), sjplimp at gmail.com from __future__ import print_function diff --git a/tools/python/logplot.py b/tools/python/logplot.py index 858304f289..546bed51fe 100755 --- a/tools/python/logplot.py +++ b/tools/python/logplot.py @@ -6,7 +6,7 @@ # log.lammps = LAMMPS log file # X,Y = plot Y versus X where X,Y are thermo keywords # once plot appears, you are in Python interpreter, type C-D to exit -# Author: Steve Plimpton (Sandia), sjplimp at sandia.gov +# Author: Steve Plimpton (Sandia), sjplimp at gmail.com import sys,os,code path = os.environ["LAMMPS_PYTHON_TOOLS"] diff --git a/tools/python/neb_combine.py b/tools/python/neb_combine.py index 92a8b3f6f7..6b0d098e57 100755 --- a/tools/python/neb_combine.py +++ b/tools/python/neb_combine.py @@ -8,6 +8,7 @@ # can be in any order # -b dumpfile = background atoms (optional) # first snapshot in this file used as static non-NEB atoms +# Author: Steve Plimpton (Sandia), sjplimp at gmail.com import sys,os path = os.environ["LAMMPS_PYTHON_TOOLS"] diff --git a/tools/python/neb_final.py b/tools/python/neb_final.py index 6ba462df44..7b0cf3bdbb 100755 --- a/tools/python/neb_final.py +++ b/tools/python/neb_final.py @@ -8,6 +8,7 @@ # must be in correct sequence # -b dumpfile = background atoms (optional) # last snapshot in this file used as static non-NEB atoms +# Author: Steve Plimpton (Sandia), sjplimp at gmail.com import sys,os path = os.environ["LAMMPS_PYTHON_TOOLS"] diff --git a/tools/python/pizza/cfg.py b/tools/python/pizza/cfg.py index dc64ef50ff..ce1ce4f535 100644 --- a/tools/python/pizza/cfg.py +++ b/tools/python/pizza/cfg.py @@ -1,5 +1,5 @@ # Pizza.py toolkit, https://lammps.github.io/pizza -# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# LAMMPS development team: developers@lammps.org # # Copyright (2005) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/tools/python/pizza/dump.py b/tools/python/pizza/dump.py index 92df8fde6e..3dabc9b1b4 100644 --- a/tools/python/pizza/dump.py +++ b/tools/python/pizza/dump.py @@ -1,5 +1,5 @@ # Pizza.py toolkit, https://lammps.github.io/pizza -# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# LAMMPS development team: developers@lammps.org # # Copyright (2005) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/tools/python/pizza/gnu.py b/tools/python/pizza/gnu.py index 004c837f63..0609d1712d 100644 --- a/tools/python/pizza/gnu.py +++ b/tools/python/pizza/gnu.py @@ -1,5 +1,5 @@ # Pizza.py toolkit, https://lammps.github.io/pizza -# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# LAMMPS development team: developers@lammps.org # # Copyright (2005) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/tools/python/pizza/log.py b/tools/python/pizza/log.py index 874b70cca1..d136047091 100644 --- a/tools/python/pizza/log.py +++ b/tools/python/pizza/log.py @@ -1,5 +1,5 @@ # Pizza.py toolkit, https://lammps.github.io/pizza -# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# LAMMPS development team: developers@lammps.org # # Copyright (2005) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/tools/python/pizza/pdbfile.py b/tools/python/pizza/pdbfile.py index 893d7d8e58..a090bf6899 100644 --- a/tools/python/pizza/pdbfile.py +++ b/tools/python/pizza/pdbfile.py @@ -1,5 +1,5 @@ # Pizza.py toolkit, https://lammps.github.io/pizza -# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# LAMMPS development team: developers@lammps.org # # Copyright (2005) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/tools/python/pizza/xyz.py b/tools/python/pizza/xyz.py index 0d96e15096..a6029e9f1b 100644 --- a/tools/python/pizza/xyz.py +++ b/tools/python/pizza/xyz.py @@ -1,5 +1,5 @@ # Pizza.py toolkit, https://lammps.github.io/pizza -# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# LAMMPS development team: developers@lammps.org # # Copyright (2005) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/tools/singularity/almalinux9.def b/tools/singularity/almalinux9.def index 3078779957..e16ebbbdb5 100644 --- a/tools/singularity/almalinux9.def +++ b/tools/singularity/almalinux9.def @@ -44,7 +44,7 @@ From: library/almalinux:9 # manually install Plumed mkdir plumed cd plumed - version=2.8.0 + version=2.8.1 curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz tar -xzf plumed.tar.gz cd plumed-${version} diff --git a/tools/singularity/centos7.def b/tools/singularity/centos7.def index 9e2619e46d..c0fe278e94 100644 --- a/tools/singularity/centos7.def +++ b/tools/singularity/centos7.def @@ -1,5 +1,5 @@ -BootStrap: library -From: centos:7 +BootStrap: docker +From: library/centos:7 %post yum -y install epel-release @@ -37,7 +37,7 @@ From: centos:7 # manually install Plumed mkdir plumed cd plumed - version=2.8.0 + version=2.8.1 curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz tar -xzf plumed.tar.gz cd plumed-${version} diff --git a/tools/singularity/centos8.def b/tools/singularity/centos8.def index 081bee238c..7cb0c51a9e 100644 --- a/tools/singularity/centos8.def +++ b/tools/singularity/centos8.def @@ -42,7 +42,7 @@ From: centos:8 # manually install Plumed mkdir plumed cd plumed - version=2.8.0 + version=2.8.1 curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz tar -xzf plumed.tar.gz cd plumed-${version} diff --git a/tools/singularity/fedora35_mingw.def b/tools/singularity/fedora35_mingw.def index fd026c78d7..2661c77db4 100644 --- a/tools/singularity/fedora35_mingw.def +++ b/tools/singularity/fedora35_mingw.def @@ -49,7 +49,7 @@ From: fedora:35 # manually install Plumed mkdir plumed cd plumed - version=2.8.0 + version=2.8.1 curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz tar -xzf plumed.tar.gz cd plumed-${version} diff --git a/tools/singularity/fedora36_mingw.def b/tools/singularity/fedora36_mingw.def index 18acf35d4d..873b646e84 100644 --- a/tools/singularity/fedora36_mingw.def +++ b/tools/singularity/fedora36_mingw.def @@ -49,7 +49,7 @@ From: fedora:36 # manually install Plumed mkdir plumed cd plumed - version=2.8.0 + version=2.8.1 curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz tar -xzf plumed.tar.gz cd plumed-${version} diff --git a/tools/singularity/rocky8.def b/tools/singularity/rocky8.def index 8e74a28ddc..0882bfd72b 100644 --- a/tools/singularity/rocky8.def +++ b/tools/singularity/rocky8.def @@ -43,7 +43,7 @@ From: rockylinux/rockylinux:8 # manually install Plumed mkdir plumed cd plumed - version=2.8.0 + version=2.8.1 curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz tar -xzf plumed.tar.gz cd plumed-${version} diff --git a/tools/singularity/ubuntu18.04.def b/tools/singularity/ubuntu18.04.def index 81fd1159dc..02351d9ecb 100644 --- a/tools/singularity/ubuntu18.04.def +++ b/tools/singularity/ubuntu18.04.def @@ -5,7 +5,7 @@ From: ubuntu:18.04 export DEBIAN_FRONTEND=noninteractive apt-get update apt-get install --no-install-recommends -y software-properties-common - add-apt-repository ppa:openkim/latest + add-apt-repository ppa:openkim/latest -y apt-get update apt-get upgrade --no-install-recommends -y apt-get install --no-install-recommends -y \ @@ -107,7 +107,7 @@ From: ubuntu:18.04 # Plumed ########################################################################### - export PLUMED_PKG_VERSION=2.8.0 + export PLUMED_PKG_VERSION=2.8.1 mkdir plumed cd plumed diff --git a/tools/singularity/ubuntu18.04_amd_rocm.def b/tools/singularity/ubuntu18.04_amd_rocm.def index 88bed62aae..38eaa6e322 100644 --- a/tools/singularity/ubuntu18.04_amd_rocm.def +++ b/tools/singularity/ubuntu18.04_amd_rocm.def @@ -45,7 +45,7 @@ From: ubuntu:18.04 ########################################################################### # Common Software ########################################################################### - add-apt-repository ppa:openkim/latest + add-apt-repository ppa:openkim/latest -y apt-get update apt-get install --no-install-recommends -y \ bc \ @@ -136,7 +136,7 @@ From: ubuntu:18.04 # Plumed ########################################################################### - export PLUMED_PKG_VERSION=2.8.0 + export PLUMED_PKG_VERSION=2.8.1 mkdir plumed cd plumed diff --git a/tools/singularity/ubuntu18.04_gpu.def b/tools/singularity/ubuntu18.04_gpu.def index f189768be7..cab62c623f 100644 --- a/tools/singularity/ubuntu18.04_gpu.def +++ b/tools/singularity/ubuntu18.04_gpu.def @@ -48,7 +48,7 @@ From: ubuntu:18.04 ########################################################################### # Common Software ########################################################################### - add-apt-repository ppa:openkim/latest + add-apt-repository ppa:openkim/latest -y apt-get update apt-get install --no-install-recommends -y \ bc \ @@ -174,7 +174,7 @@ From: ubuntu:18.04 # Plumed ########################################################################### - export PLUMED_PKG_VERSION=2.8.0 + export PLUMED_PKG_VERSION=2.8.1 mkdir plumed cd plumed diff --git a/tools/singularity/ubuntu18.04_intel_opencl.def b/tools/singularity/ubuntu18.04_intel_opencl.def index 2b75cf09e1..2d562771bb 100644 --- a/tools/singularity/ubuntu18.04_intel_opencl.def +++ b/tools/singularity/ubuntu18.04_intel_opencl.def @@ -5,7 +5,7 @@ From: ubuntu:18.04 export DEBIAN_FRONTEND=noninteractive apt-get update apt-get install --no-install-recommends -y software-properties-common - add-apt-repository ppa:openkim/latest + add-apt-repository ppa:openkim/latest -y apt-get update apt-get upgrade --no-install-recommends -y apt-get install --no-install-recommends -y \ @@ -108,7 +108,7 @@ From: ubuntu:18.04 # Plumed ########################################################################### - export PLUMED_PKG_VERSION=2.8.0 + export PLUMED_PKG_VERSION=2.8.1 mkdir plumed cd plumed diff --git a/tools/singularity/ubuntu18.04_nvidia.def b/tools/singularity/ubuntu18.04_nvidia.def index bb2535a9c2..2a3a34b1b2 100644 --- a/tools/singularity/ubuntu18.04_nvidia.def +++ b/tools/singularity/ubuntu18.04_nvidia.def @@ -5,7 +5,7 @@ From: nvidia/cuda:11.6.2-devel-ubuntu18.04 export DEBIAN_FRONTEND=noninteractive apt-get update apt-get install --no-install-recommends -y software-properties-common - add-apt-repository ppa:openkim/latest + add-apt-repository ppa:openkim/latest -y apt-get update apt-get upgrade --no-install-recommends -y apt-get install --no-install-recommends -y \ @@ -107,7 +107,7 @@ From: nvidia/cuda:11.6.2-devel-ubuntu18.04 # Plumed ########################################################################### - export PLUMED_PKG_VERSION=2.8.0 + export PLUMED_PKG_VERSION=2.8.1 mkdir plumed cd plumed diff --git a/tools/singularity/ubuntu20.04.def b/tools/singularity/ubuntu20.04.def index 1d1d695b6b..2a2a1dd660 100644 --- a/tools/singularity/ubuntu20.04.def +++ b/tools/singularity/ubuntu20.04.def @@ -5,7 +5,7 @@ From: ubuntu:20.04 export DEBIAN_FRONTEND=noninteractive apt-get update apt-get install --no-install-recommends -y software-properties-common - add-apt-repository ppa:openkim/latest + add-apt-repository ppa:openkim/latest -y apt-get update apt-get upgrade --no-install-recommends -y apt-get install --no-install-recommends -y \ @@ -13,6 +13,7 @@ From: ubuntu:20.04 build-essential \ ccache \ clang \ + clang-format \ cmake \ cmake-curses-gui \ curl \ @@ -102,7 +103,7 @@ From: ubuntu:20.04 # Plumed ########################################################################### - export PLUMED_PKG_VERSION=2.8.0 + export PLUMED_PKG_VERSION=2.8.1 mkdir plumed cd plumed diff --git a/tools/singularity/ubuntu20.04_amd_rocm.def b/tools/singularity/ubuntu20.04_amd_rocm.def index f53e899d41..f947de9ee9 100644 --- a/tools/singularity/ubuntu20.04_amd_rocm.def +++ b/tools/singularity/ubuntu20.04_amd_rocm.def @@ -36,7 +36,7 @@ From: ubuntu:20.04 ########################################################################### # Common Software ########################################################################### - add-apt-repository ppa:openkim/latest + add-apt-repository ppa:openkim/latest -y apt-get update apt-get install --no-install-recommends -y \ bc \ @@ -123,7 +123,7 @@ From: ubuntu:20.04 # Plumed ########################################################################### - export PLUMED_PKG_VERSION=2.8.0 + export PLUMED_PKG_VERSION=2.8.1 mkdir plumed cd plumed diff --git a/tools/singularity/ubuntu20.04_gpu.def b/tools/singularity/ubuntu20.04_gpu.def index 5932bb03b5..f84c1f8926 100644 --- a/tools/singularity/ubuntu20.04_gpu.def +++ b/tools/singularity/ubuntu20.04_gpu.def @@ -39,7 +39,7 @@ From: ubuntu:20.04 # Common Software ########################################################################### apt-get install --no-install-recommends -y software-properties-common - add-apt-repository ppa:openkim/latest + add-apt-repository ppa:openkim/latest -y apt-get update apt-get install --no-install-recommends -y \ bc \ @@ -161,7 +161,7 @@ From: ubuntu:20.04 # Plumed ########################################################################### - export PLUMED_PKG_VERSION=2.8.0 + export PLUMED_PKG_VERSION=2.8.1 mkdir plumed cd plumed diff --git a/tools/singularity/ubuntu20.04_intel_opencl.def b/tools/singularity/ubuntu20.04_intel_opencl.def index 9049e87ebc..cc547fef29 100644 --- a/tools/singularity/ubuntu20.04_intel_opencl.def +++ b/tools/singularity/ubuntu20.04_intel_opencl.def @@ -5,7 +5,7 @@ From: ubuntu:20.04 export DEBIAN_FRONTEND=noninteractive apt-get update apt-get install --no-install-recommends -y software-properties-common - add-apt-repository ppa:openkim/latest + add-apt-repository ppa:openkim/latest -y apt-get update apt-get upgrade --no-install-recommends -y apt-get install --no-install-recommends -y \ @@ -101,7 +101,7 @@ From: ubuntu:20.04 # Plumed ########################################################################### - export PLUMED_PKG_VERSION=2.8.0 + export PLUMED_PKG_VERSION=2.8.1 mkdir plumed cd plumed diff --git a/tools/singularity/ubuntu20.04_nvidia.def b/tools/singularity/ubuntu20.04_nvidia.def index 9fb2de768b..8ec334ad8b 100644 --- a/tools/singularity/ubuntu20.04_nvidia.def +++ b/tools/singularity/ubuntu20.04_nvidia.def @@ -5,7 +5,7 @@ From: nvidia/cuda:11.6.2-devel-ubuntu20.04 export DEBIAN_FRONTEND=noninteractive apt-get update apt-get install --no-install-recommends -y software-properties-common - add-apt-repository ppa:openkim/latest + add-apt-repository ppa:openkim/latest -y apt-get update apt-get upgrade --no-install-recommends -y apt-get install --no-install-recommends -y \ @@ -103,7 +103,7 @@ From: nvidia/cuda:11.6.2-devel-ubuntu20.04 # Plumed ########################################################################### - export PLUMED_PKG_VERSION=2.8.0 + export PLUMED_PKG_VERSION=2.8.1 mkdir plumed cd plumed diff --git a/tools/singularity/ubuntu20.04_oneapi.def b/tools/singularity/ubuntu20.04_oneapi.def index 1f6d34f7d9..25c913f392 100644 --- a/tools/singularity/ubuntu20.04_oneapi.def +++ b/tools/singularity/ubuntu20.04_oneapi.def @@ -5,7 +5,7 @@ From: ubuntu:20.04 export DEBIAN_FRONTEND=noninteractive apt-get update apt-get install --no-install-recommends -y software-properties-common - add-apt-repository ppa:openkim/latest + add-apt-repository ppa:openkim/latest -y apt-get update apt-get upgrade --no-install-recommends -y apt-get install --no-install-recommends -y \ @@ -140,7 +140,7 @@ From: ubuntu:20.04 # Plumed ########################################################################### - export PLUMED_PKG_VERSION=2.8.0 + export PLUMED_PKG_VERSION=2.8.1 mkdir plumed cd plumed diff --git a/tools/singularity/ubuntu22.04.def b/tools/singularity/ubuntu22.04.def index f20b93c187..8a4f262f75 100644 --- a/tools/singularity/ubuntu22.04.def +++ b/tools/singularity/ubuntu22.04.def @@ -5,7 +5,7 @@ From: ubuntu:22.04 export DEBIAN_FRONTEND=noninteractive apt-get update apt-get install --no-install-recommends -y software-properties-common gpg gpg-agent - add-apt-repository ppa:openkim/latest + add-apt-repository ppa:openkim/latest -y apt-get update apt-get upgrade --no-install-recommends -y apt-get install --no-install-recommends -y \ @@ -13,6 +13,7 @@ From: ubuntu:22.04 build-essential \ ccache \ clang \ + clang-format \ cmake \ cmake-curses-gui \ curl \ @@ -102,7 +103,7 @@ From: ubuntu:22.04 # Plumed ########################################################################### - export PLUMED_PKG_VERSION=2.8.0 + export PLUMED_PKG_VERSION=2.8.1 mkdir plumed cd plumed diff --git a/tools/stl_bin2txt.cpp b/tools/stl_bin2txt.cpp index 976c3ad089..e614cde242 100644 --- a/tools/stl_bin2txt.cpp +++ b/tools/stl_bin2txt.cpp @@ -1,7 +1,7 @@ /* ----------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://www.lammps.org/ - Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/tools/swig/lammps.i b/tools/swig/lammps.i index 3c5f43ac2d..d085eb9283 100644 --- a/tools/swig/lammps.i +++ b/tools/swig/lammps.i @@ -24,8 +24,9 @@ /** Data type constants for extracting data from atoms, computes and fixes * - * Must be kept in sync with the equivalent constants in src/library.h, - * python/lammps/constants.py, and fortran/lammps.f90 */ + * Must be kept in sync with the equivalent constants in ``src/library.h``, + * ``python/lammps/constants.py``, ``examples/COUPLE/plugin/liblammpsplugin.h``, + * and ``fortran/lammps.f90`` */ enum _LMP_DATATYPE_CONST { LAMMPS_INT = 0, /*!< 32-bit integer (array) */ @@ -39,8 +40,9 @@ enum _LMP_DATATYPE_CONST { /** Style constants for extracting data from computes and fixes. * - * Must be kept in sync with the equivalent constants in src/library.h, - * python/lammps/constants.py, and fortran/lammps.f90 */ + * Must be kept in sync with the equivalent constants in ``src/library.h``, + * ``python/lammps/constants.py``, ``examples/COUPLE/plugin/liblammpsplugin.h``, + * and ``fortran/lammps.f90`` */ enum _LMP_STYLE_CONST { LMP_STYLE_GLOBAL = 0, /*!< return global data */ @@ -50,8 +52,9 @@ enum _LMP_STYLE_CONST { /** Type and size constants for extracting data from computes and fixes. * - * Must be kept in sync with the equivalent constants in src/library.h, - * python/lammps/constants.py, and fortran/lammps.f90 */ + * Must be kept in sync with the equivalent constants in ``src/library.h``, + * ``python/lammps/constants.py``, ``examples/COUPLE/plugin/liblammpsplugin.h``, + * and ``fortran/lammps.f90`` */ enum _LMP_TYPE_CONST { LMP_TYPE_SCALAR = 0, /*!< return scalar */ @@ -64,8 +67,9 @@ enum _LMP_TYPE_CONST { /** Error codes to select the suitable function in the Error class * - * Must be kept in sync with the equivalent constants in src/library.h, - * python/lammps/constants.py, and fortran/lammps.f90 */ + * Must be kept in sync with the equivalent constants in ``src/library.h``, + * ``python/lammps/constants.py``, ``examples/COUPLE/plugin/liblammpsplugin.h``, + * and ``fortran/lammps.f90`` */ enum _LMP_ERROR_CONST { LMP_ERROR_WARNING = 0, /*!< call Error::warning() */ @@ -77,8 +81,9 @@ enum _LMP_ERROR_CONST { /** Variable style constants for extracting data from variables. * - * Must be kept in sync with the equivalent constants in src/library.h, - * python/lammps/constants.py, and fortran/lammps.f90 */ + * Must be kept in sync with the equivalent constants in ``src/library.h``, + * ``python/lammps/constants.py``, ``examples/COUPLE/plugin/liblammpsplugin.h``, + * and ``fortran/lammps.f90`` */ enum _LMP_VAR_CONST { LMP_VAR_EQUAL = 0, /*!< compatible with equal-style variables */ diff --git a/tools/tabulate/README.md b/tools/tabulate/README.md new file mode 100644 index 0000000000..fb23e260a1 --- /dev/null +++ b/tools/tabulate/README.md @@ -0,0 +1,40 @@ +# Python scripts to generate tabulated potential files for LAMMPS + +This directory contains a Python module 'tabulate' that can be used to +generate tabulated potential files for pair style table, bond style +table, and angle style table + +To create tables, you need to define your energy and - optionally - +force functions and then an instance of either the PairTabulate(), +BondTabulate(), AngleTabulate(), or DihedralTabulate() class from the +tabulate module and call its run() method to generate the table. Most +of the settings (number of points, minimum, maximum etc.) are provided +as command line flags. The run() method may be called multiple times to +generate multiple tables, for instance after changing parameters of the +energy/force functions. If the force function is not provided, the +force will be determined through numerical differentiation. + +Please see the individual tabulation scripts in this folder for examples: + +| ------------------------------|-------------------------------------------------------------------------------| +| File | Description | +| ------------------------------|-------------------------------------------------------------------------------| +| pair_lj_tabulate.py | creates two Lennard-Jones pair potential tables with different parameters | +| bond_morse_tabulate.py | creates a table for a Morse bond potential table | +| angle_harmonic_tabulate.py | creates a table for a harmonic angle potential table | +| dihedral_harmonic_tabulate.py | creates a table for a harmonic dihedral potential table | +| pair_hybrid_tabulate.py | creates a Morse/Lennard-Jones hybrid potential table with smooth switching | +| pair_zbladd_tabulate.py | creates a table for hybrid/overlay to use ZBL repulsion with an EAM potential | +| ------------------------------|-------------------------------------------------------------------------------| + +Common command line flags: + +``` +options: + -h, --help show this help message and exit + --num-points NUM, -n NUM Number of tabulated points (default: 1000) + --filename FILENAME, -f FILENAME Name of output file (default: -) + --diff-num, -d Differentiate energy function numerically + --inner XMIN, -i XMIN Inner cutoff of table (required for pair) + --outer XMAX, -o XMAX Outer cutoff of table (required) +``` diff --git a/tools/tabulate/angle_harmonic_tabulate.py b/tools/tabulate/angle_harmonic_tabulate.py new file mode 100755 index 0000000000..f867acc391 --- /dev/null +++ b/tools/tabulate/angle_harmonic_tabulate.py @@ -0,0 +1,21 @@ +#!/usr/bin/env python + +from tabulate import AngleTabulate + +################################################################################ +import math + +def harmonic_energy(theta): + k = 100.0 + thetazero = 120.0 + # the force constant in LAMMPS is in energy per radians^2 so convert from degrees to radians + deg2rad = math.pi / 180.0 + t = (theta - thetazero) * deg2rad + f = k * t * t + return f + +################################################################################ + +if __name__ == "__main__": + atable = AngleTabulate(harmonic_energy, units='real') + atable.run('HARM') diff --git a/tools/tabulate/bond_morse_tabulate.py b/tools/tabulate/bond_morse_tabulate.py new file mode 100755 index 0000000000..14b6a2adf5 --- /dev/null +++ b/tools/tabulate/bond_morse_tabulate.py @@ -0,0 +1,28 @@ +#!/usr/bin/env python + +from tabulate import BondTabulate + +################################################################################ +import math + +def morse_energy(r): + depth = 1.0 + width = 2.0 + rzero = 1.2 + ralpha = math.exp(-width*(r-rzero)) + f = depth * (-1.0 + (1.0 - ralpha) * (1.0 - ralpha)) + return f + +def morse_force(r): + depth = 1.0 + width = 2.0 + rzero = 1.2 + ralpha = math.exp(-width*(r-rzero)) + f = -2.0 * depth * width * (1.0 -ralpha) * ralpha + return f + +################################################################################ + +if __name__ == "__main__": + btable = BondTabulate(morse_energy, morse_force, units='lj') + btable.run('MORSE') diff --git a/tools/tabulate/dihedral_harmonic_tabulate.py b/tools/tabulate/dihedral_harmonic_tabulate.py new file mode 100755 index 0000000000..29fc59dad2 --- /dev/null +++ b/tools/tabulate/dihedral_harmonic_tabulate.py @@ -0,0 +1,19 @@ +#!/usr/bin/env python + +from tabulate import DihedralTabulate + +################################################################################ +import math + +def harmonic_energy(theta): + k = 100.0 + # the force constant in LAMMPS is in energy per radians^2 so convert from degrees to radians + deg2rad = math.pi / 180.0 + f = k * (1 - math.cos(2.0 * deg2rad * theta)) + return f + +################################################################################ + +if __name__ == "__main__": + dtable = DihedralTabulate(harmonic_energy, units='metal') + dtable.run('HARM') diff --git a/tools/tabulate/pair_hybrid_tabulate.py b/tools/tabulate/pair_hybrid_tabulate.py new file mode 100755 index 0000000000..98e2814233 --- /dev/null +++ b/tools/tabulate/pair_hybrid_tabulate.py @@ -0,0 +1,31 @@ +#!/usr/bin/env python + +from tabulate import PairTabulate + +################################################################################ +import math + +# hybrid potential using Morse for repulsive and LJ for attractive. +# using tanh() as smooth switching function between the two. + +def hybrid_energy(r): + depth = 1.0 + width = 5.0 + epsilon = 1.0 + sigma = 1.0 + rzero = 1.2 + + f1 = 4.0*epsilon*(math.pow(sigma/r,12.0) - math.pow(sigma/r,6.0)) + + ralpha = math.exp(-width*(r-rzero)) + f2 = depth * (-1.0 + (1.0 - ralpha) * (1.0 - ralpha)) + + switch = 0.5*math.tanh(10.0*(r - rzero)) + 0.5 + f = switch*f1 + (1.0 - switch)*f2 + return f + +################################################################################ + +if __name__ == "__main__": + ptable = PairTabulate(hybrid_energy, units='lj', comment='Morse repulsion + LJ attraction') + ptable.run('MORSE_LJ') diff --git a/tools/tabulate/pair_lj_tabulate.py b/tools/tabulate/pair_lj_tabulate.py new file mode 100755 index 0000000000..713b10a761 --- /dev/null +++ b/tools/tabulate/pair_lj_tabulate.py @@ -0,0 +1,26 @@ +#!/usr/bin/env python + +from tabulate import PairTabulate + +################################################################################ +import math +epsilon = 1.0 +sigma = 1.0 + +def lj_energy(r): + f = 4.0*epsilon*(math.pow(sigma/r,12.0) - math.pow(sigma/r,6.0)) + return f + +def lj_force(r): + epsilon = 1.0 + sigma = 1.0 + f = -4.0*epsilon*(-12.0*math.pow(sigma/r,12.0)/r + 6.0*math.pow(sigma/r,6.0)/r) + return f +################################################################################ + +if __name__ == "__main__": + ptable = PairTabulate(lj_energy, lj_force) + ptable.run('LJ_11') + epsilon = 1.0 + sigma = 1.5 + ptable.run('LJ_12') diff --git a/tools/tabulate/pair_zbladd_tabulate.py b/tools/tabulate/pair_zbladd_tabulate.py new file mode 100755 index 0000000000..2791b1858f --- /dev/null +++ b/tools/tabulate/pair_zbladd_tabulate.py @@ -0,0 +1,59 @@ +#!/usr/bin/env python + +from tabulate import PairTabulate + +################################################################################ +import math + +# this table contains a correction to be added to the Al_zhou.eam.alloy potential via hybrid/overlay +# the purpose is to smoothly replace the original pairwise repulsion with the ZBL potential. +# the combined potential switches from ZBL to EAM w/o embedding and then subtracts the full EAM term. +# this way the table can be added to the eam/alloy pair style via hybrid/overlay +# due to using a Fermi-like switching function (tanh()) there are no discontinuities in energy or force + +def eam_2body(r): + biga = 0.251519 # metal units + bigb = 0.313394 # metal units + rzero = 2.886166 + alpha = 6.942419 + beta = 3.702623 + lamda = 0.790264 + kappa = 0.395132 + return (biga * math.exp(-alpha * (r/rzero - 1.0))) / (1.0 + math.pow(r/rzero - kappa, 20)) \ + - (bigb * math.exp(-beta * (r/rzero - 1.0))) / (1.0 + math.pow(r/rzero - lamda, 20)) + +def zbl_energy(r): + qqr2e = 14.399645 # for metal units + pzbl = 0.23 + a0 = 0.46850 + c1 = 0.02817 + c2 = 0.28022 + c3 = 0.50986 + c4 = 0.18175 + d1 = 0.20162 + d2 = 0.40290 + d3 = 0.94229 + d4 = 3.19980 + + zi = 13.0 # aluminium + zj = 13.0 # aluminium + + prefactor = zi * zj * qqr2e / r + rbya = r * (math.pow(zi, pzbl) + math.pow(zj, pzbl)) / a0 + f = prefactor * (c4*math.exp(-d4*rbya) + c3*math.exp(-d3*rbya) \ + + c2*math.exp(-d2*rbya) + c1*math.exp(-d1*rbya)) + return f + +def combined(r): + rmid = 2.886166 + switch_on = 0.5*(math.tanh(math.exp(1.0)*(r - rmid))+1.0) + return (1.0-switch_on)*zbl_energy(r) + (switch_on-1.0)*eam_2body(r) + +################################################################################ + +if __name__ == "__main__": + ptable = PairTabulate(combined, units='metal', \ + comment='Correct Al_zhou EAM with ZBL using hybrid/overlay') + ptable.run('AL_EAM_ZBL_CORR') + +# NOTE use/create table with an outer cutoff of 10.1025 to match the EAM potential cutoff. diff --git a/tools/tabulate/tabulate.py b/tools/tabulate/tabulate.py new file mode 100755 index 0000000000..3bba7c2ecf --- /dev/null +++ b/tools/tabulate/tabulate.py @@ -0,0 +1,284 @@ +#!/usr/bin/env python +# ---------------------------------------------------------------------- +# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator +# https://www.lammps.org/ Sandia National Laboratories +# LAMMPS Development team: developers@lammps.org +# +# 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. +# ------------------------------------------------------------------------- +""" +Python classes and support functions to generate tabulated potential files for LAMMPS. +""" + +# for python2/3 compatibility +from __future__ import print_function + +import sys +import argparse +from os import path +from datetime import datetime + +######################################################################## + +def numdiff(x, func): + """ Get the value of the first derivative of a function 'func(x)' at 'x' + from numerical differentiation.""" + + # optimal delta x value for 2-point numerical differentiation of two floating point numbers + epsilon = 6.05504e-6 + fval1 = func(x - epsilon) + fval2 = func(x + epsilon) + return 0.5 * (fval2-fval1) / epsilon + +######################################################################## + +def mktable(tstyle, label, num, xmin, xmax, efunc, diff=False, ffunc=None): + """ Do the tabulation of the provided energy function. Compute force from + numerical differentiation if no force function is provided. Also detect + minimum for use to determine potential shifting in bonded potentials.""" + + # must use numerical differentiation if no force function provided + if not ffunc: + diff = True + + print("# Creating %s table %s with %d points from %g to %g" % (tstyle, label, num, xmin, xmax)) + + table = [] + delx = (xmax - xmin) / (float(num) - 1.0) + emin = 999999999.0 + xzero = 0.0 + + for i in range(0,num): + x = xmin + i*delx + energy = efunc(x) + if energy < emin: + emin = energy + xzero = x + if diff: + force = -numdiff(x, efunc) + else: + force = ffunc(x) + table.append([i+1, x, energy, force]) + + return table, xzero + + +######################################################################## +# base class with shared functionality +class Tabulate(object): + """Base tabulation class. Contains all shared functionality: common argument parsing, + output file handling, table writing""" + + def __init__(self, style, efunc, ffunc=None, units=None, comment=None): + self.fp = sys.stdout + self.tstyle = style + self.energyfunc = efunc + self.forcefunc = ffunc + self.units = units + self.comment = comment + self.eshift = 0.0 + self.args = None + self.diff = True + + self.parser = argparse.ArgumentParser(description='Tool to generate tabulated ' + + self.tstyle + ' potential files for LAMMPS') + self.parser.add_argument('--num-points', '-n', dest='num', default=1000, type=int, + help="Number of tabulated points") + self.parser.add_argument('--filename', '-f', dest='filename', default='-', + help="Name of output file") + self.parser.add_argument('--diff-num', '-d', dest='diff',default=False, + action='store_true', + help="Differentiate energy function numerically") + self.parser.add_argument('--inner', '-i', dest='xmin', required=True, type=float, + help="Inner cutoff of table") + self.parser.add_argument('--outer', '-o', dest='xmax', required=True, type=float, + help="Outer cutoff of table") + + def openfile(self, label): + """Open table file, if needed and print label for new table entry""" + if self.args and self.args.filename != '-': + try: + if path.isfile(self.args.filename): + self.fp = open(self.args.filename, 'a') + print("# Appending table to file " + self.args.filename) + else: + self.fp = open(self.args.filename, 'w') + print("# Writing table to new file " + self.args.filename) + self.fp.write('# DATE: ' + datetime.now().date().isoformat()) + if self.units: + self.fp.write(' UNITS: ' + str(self.units)) + if self.comment: + self.fp.write(' COMMENT: ' + str(self.comment) + '\n') + except IOError: + sys.exit("Cannot open file %s for writing table data" % self.args.filename) + self.fp.write('\n' + label + '\n') + + def writetable(self, table, offset): + """ Formatted output tabulated data with 4 columns""" + for i,r,energy,force in table: + self.fp.write("%8d %- 22.15g %- 22.15g %- 22.15g\n" % (i, r, energy - offset, force)) + + def helpexit(self, text): + """ Convenience function to exit program with error and help message""" + sys.exit('\n' + text + '\n\n' + self.parser.format_help()) + +################################################################################ +# create tabulation for pair styles +class PairTabulate(Tabulate): + def __init__(self, efunc, ffunc=None, units=None, comment=None): + super(PairTabulate, self).__init__('pair', efunc, ffunc, units, comment) + self.parser.add_argument('--eshift', '-e', dest='eshift', default=False, + action='store_true', + help="Shift potential energy to be zero at outer cutoff") + try: + self.args = self.parser.parse_args() + except argparse.ArgumentError: + sys.exit() + + def run(self, label): + # sanity checks + if self.args.num < 2: + self.helpexit('Expect 2 or more points in table for tabulation') + if self.args.xmin <= 0.0: + self.helpexit('Inner tabulation cutoff must be > 0 for pair style table') + if self.args.xmax <= self.args.xmin: + self.helpexit('Outer cutoff must be larger than inner cutoff') + + self.diff = self.args.diff + if not self.forcefunc: + self.diff = True + offset = 0.0 + if self.args.eshift: + offset=self.energyfunc(self.args.xmax) + + table, dummy = mktable(self.tstyle, label, self.args.num, self.args.xmin, self.args.xmax, + self.energyfunc, self.args.diff, self.forcefunc) + + # open table file + self.openfile(label) + + # write pair style specific header + if self.forcefunc: + diffmin = -numdiff(self.args.xmin, self.forcefunc) + diffmax = -numdiff(self.args.xmax, self.forcefunc) + self.fp.write("N %d R %g %g FPRIME %- 22.15g %- 22.15g\n\n" + % (self.args.num, self.args.xmin, self.args.xmax, diffmin, diffmax)) + else: + self.fp.write("N %d R %g %g\n\n" % (self.args.num, self.args.xmin, self.args.xmax)) + + self.writetable(table, offset) + if self.args.filename != '-': + self.fp.close() + + +################################################################################ +# shared functionality to create tabulation for bond or angle styles +class BondAngleTabulate(Tabulate): + def __init__(self, style, efunc, ffunc=None, units=None, comment=None): + super(BondAngleTabulate, self).__init__(style, efunc, ffunc, units, comment) + self.parser.add_argument('--eshift', '-e', dest='eshift', default=False, + action='store_true', + help="Shift potential energy to be zero at minimum") + idx = [a.dest for a in self.parser._actions].index('xmin') + self.parser._actions[idx].required=False + self.parser._actions[idx].default=0.0 + if style == 'angle': + idx = [a.dest for a in self.parser._actions].index('xmax') + self.parser._actions[idx].required=False + self.parser._actions[idx].default=180.0 + try: + self.args = self.parser.parse_args() + except argparse.ArgumentError: + sys.exit() + + def run(self, label): + # sanity checks + if self.args.num < 2: + self.helpexit('Expect 2 or more points in table for tabulation') + if self.args.xmin < 0.0: + self.helpexit('Inner cutoff must not be negative') + if self.tstyle == 'angle' and self.args.xmax > 180.0: + self.helpexit('Outer cutoff must not be larger than 180.0 degrees') + + self.diff = self.args.diff + if not self.forcefunc: + self.diff = True + + table, xzero = mktable(self.tstyle, label, self.args.num, self.args.xmin, self.args.xmax, + self.energyfunc, self.args.diff, self.forcefunc) + print("# Minimum energy of tabulated potential is at %g" % xzero) + offset = 0.0 + if self.args.eshift: + offset=self.energyfunc(xzero) + + self.openfile(label) + + if self.forcefunc: + diffmin = -numdiff(self.args.xmin, self.forcefunc) + diffmax = -numdiff(self.args.xmax, self.forcefunc) + self.fp.write("N %d FP %- 22.15g %- 22.15g EQ %g\n\n" % + (self.args.num, diffmin, diffmax, xzero)) + else: + self.fp.write("N %d EQ %g\n\n" % (self.args.num, xzero)) + + self.writetable(table, offset) + if self.args.filename != '-': + self.fp.close() + +################################################################################ +class BondTabulate(BondAngleTabulate): + def __init__(self, efunc, ffunc=None, units=None, comment=None): + super(BondTabulate, self).__init__('bond', efunc, ffunc, units, comment) + +################################################################################ +class AngleTabulate(BondAngleTabulate): + def __init__(self, efunc, ffunc=None, units=None, comment=None): + super(AngleTabulate, self).__init__('angle', efunc, ffunc, units, comment) + +################################################################################ +# create tabulation for dihdedral +class DihedralTabulate(Tabulate): + def __init__(self, efunc, ffunc=None, units=None, comment=None): + super(DihedralTabulate, self).__init__('dihedral', efunc, ffunc, units, comment) + idx = [a.dest for a in self.parser._actions].index('xmin') + self.parser._actions[idx].required=False + self.parser._actions[idx].default=-180.0 + idx = [a.dest for a in self.parser._actions].index('xmax') + self.parser._actions[idx].required=False + self.parser._actions[idx].default=179.999999 + try: + self.args = self.parser.parse_args() + except argparse.ArgumentError: + sys.exit() + + def run(self, label): + # sanity checks + if self.args.num < 2: + self.helpexit('Expect 2 or more points in table for tabulation') + if self.args.xmin < -180 or self.args.xmin > 0.0: + self.helpexit('Inner cutoff must be within -180.0 and 0.0 degrees') + if self.args.xmax < 0.0 or self.args.xmin > 360.0: + self.helpexit('Outer cutoff must be within 0.0 and 360.0 degrees') + if (self.args.xmax - self.args.xmin) >= 360.0: + self.helpexit('Inner and outer cutoff range must be less than 360.0 degrees') + + self.diff = self.args.diff + if not self.forcefunc: + self.diff = True + + table, dummy = mktable(self.tstyle, label, self.args.num, self.args.xmin, self.args.xmax, + self.energyfunc, self.args.diff, self.forcefunc) + self.openfile(label) + self.fp.write("N %d DEGREES \n\n" % (self.args.num)) + self.writetable(table, 0.0) + if self.args.filename != '-': + self.fp.close() + +################################################################################ +if __name__ == "__main__": + sys.exit("The tabulate module is not meant to be executed directly") diff --git a/tools/tinker/data.py b/tools/tinker/data.py index 5d6951422f..cae94980eb 100644 --- a/tools/tinker/data.py +++ b/tools/tinker/data.py @@ -1,5 +1,5 @@ # Pizza.py toolkit, https://lammps.github.io/pizza -# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +# LAMMPS development team: developers@lammps.org, Sandia National Laboratories # # Copyright (2005) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/tools/valgrind/OpenMP.supp b/tools/valgrind/OpenMP.supp index 0227818262..703c71bf74 100644 --- a/tools/valgrind/OpenMP.supp +++ b/tools/valgrind/OpenMP.supp @@ -134,6 +134,16 @@ fun:GOMP_parallel obj:* } +{ + OpenMP_init_clang1 + Memcheck:Leak + match-leak-kinds: possible + fun:malloc + ... + fun:omp_set_num_threads + ... + obj:* +} { OpenMP_open_part1 Memcheck:Leak diff --git a/unittest/CMakeLists.txt b/unittest/CMakeLists.txt index 28b3e1c1cd..9819a53e10 100644 --- a/unittest/CMakeLists.txt +++ b/unittest/CMakeLists.txt @@ -4,6 +4,12 @@ # Created by Axel Kohlmeyer and Richard Berger ######################################## # download and build googletest framework + +# cannot compile googletest anymore with the default GCC on RHEL 7.x +if((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 6.0)) + message(FATAL_ERROR "Need GNU C++ compiler version 6.x or later for unit testing") +endif() + message(STATUS "Downloading and building googletest framework") set(GTEST_URL "https://github.com/google/googletest/archive/release-1.12.1.tar.gz" CACHE STRING "URL of googletest source") set(GTEST_MD5 "e82199374acdfda3f425331028eb4e2a" CACHE STRING "MD5 sum for googletest source") diff --git a/unittest/c-library/CMakeLists.txt b/unittest/c-library/CMakeLists.txt index e9409be0cc..966fac177f 100644 --- a/unittest/c-library/CMakeLists.txt +++ b/unittest/c-library/CMakeLists.txt @@ -71,3 +71,23 @@ add_executable(test_library_mpi test_library_mpi.cpp) target_link_libraries(test_library_mpi PRIVATE lammps GTest::GMock) target_compile_definitions(test_library_mpi PRIVATE ${TEST_CONFIG_DEFS}) add_mpi_test(NAME LibraryMPI NUM_PROCS 4 COMMAND $) + +# simple run tests for coupling to the LAMMPS library +if(BUILD_MPI) + if(BUILD_SHARED_LIBS) + add_subdirectory(${LAMMPS_DIR}/examples/COUPLE/plugin ${CMAKE_BINARY_DIR}/build-couple) + add_test(NAME RunCoupleSimplePlugin + COMMAND $ 1 ${LAMMPS_DIR}/examples/COUPLE/plugin/in.lj $) + set_tests_properties(RunCoupleSimplePlugin PROPERTIES + ENVIRONMENT "TSAN_OPTIONS=ignore_noninstrumented_modules=1;HWLOC_HIDE_ERRORS=2" + PASS_REGULAR_EXPRESSION "LAMMPS \\([0-9]+ [A-Za-z]+ 2[0-9][0-9][0-9]( - Update [0-9]+)?\\)") + endif() + add_subdirectory(${LAMMPS_DIR}/examples/COUPLE/simple ${CMAKE_BINARY_DIR}/build-simple) + add_test(NAME RunCoupleSimpleC + COMMAND $ 1 ${LAMMPS_DIR}/examples/COUPLE/simple/in.lj) + add_test(NAME RunCoupleSimpleCC + COMMAND $ 1 ${LAMMPS_DIR}/examples/COUPLE/simple/in.lj) + set_tests_properties(RunCoupleSimpleC RunCoupleSimpleCC PROPERTIES + ENVIRONMENT "TSAN_OPTIONS=ignore_noninstrumented_modules=1;HWLOC_HIDE_ERRORS=2" + PASS_REGULAR_EXPRESSION "LAMMPS \\([0-9]+ [A-Za-z]+ 2[0-9][0-9][0-9]( - Update [0-9]+)?\\)") +endif() diff --git a/unittest/c-library/test_library_properties.cpp b/unittest/c-library/test_library_properties.cpp index bbb363dfab..bb0f6e2894 100644 --- a/unittest/c-library/test_library_properties.cpp +++ b/unittest/c-library/test_library_properties.cpp @@ -209,6 +209,10 @@ TEST_F(LibraryProperties, setting) lammps_command(lmp, "dimension 3"); if (!verbose) ::testing::internal::GetCapturedStdout(); + EXPECT_EQ(lammps_extract_setting(lmp, "kokkos_active"), 0); + EXPECT_EQ(lammps_extract_setting(lmp, "kokkos_nthreads"), 0); + EXPECT_EQ(lammps_extract_setting(lmp, "kokkos_ngpus"), 0); + EXPECT_EQ(lammps_extract_setting(lmp, "world_size"), 1); EXPECT_EQ(lammps_extract_setting(lmp, "world_rank"), 0); EXPECT_EQ(lammps_extract_setting(lmp, "universe_size"), 1); @@ -545,3 +549,27 @@ TEST_F(AtomProperties, position) EXPECT_DOUBLE_EQ(x[1][1], 0.1); EXPECT_DOUBLE_EQ(x[1][2], 0.1); } + +TEST(SystemSettings, kokkos) +{ + if (!lammps_config_has_package("KOKKOS")) GTEST_SKIP(); + if (!lammps_config_accelerator("KOKKOS", "api", "openmp")) GTEST_SKIP(); + + // clang-format off + const char *args[] = {"SystemSettings", "-log", "none", "-echo", "screen", "-nocite", + "-k", "on", "t", "4", "-sf", "kk"}; + // clang-format on + char **argv = (char **)args; + int argc = sizeof(args) / sizeof(char *); + + ::testing::internal::CaptureStdout(); + void *lmp = lammps_open_no_mpi(argc, argv, nullptr); + std::string output = ::testing::internal::GetCapturedStdout(); + if (verbose) std::cout << output; + EXPECT_THAT(output, StartsWith("LAMMPS (")); + + EXPECT_EQ(lammps_extract_setting(lmp, "kokkos_active"), 1); + EXPECT_EQ(lammps_extract_setting(lmp, "kokkos_nthreads"), 4); + EXPECT_EQ(lammps_extract_setting(lmp, "kokkos_ngpus"), 0); + lammps_close(lmp); +} diff --git a/unittest/c-library/test_main.cpp b/unittest/c-library/test_main.cpp index 7e262cfe10..ef1f921680 100644 --- a/unittest/c-library/test_main.cpp +++ b/unittest/c-library/test_main.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/c-library/test_main.h b/unittest/c-library/test_main.h index 9a719e4b88..2cb72e1aff 100644 --- a/unittest/c-library/test_main.h +++ b/unittest/c-library/test_main.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/commands/CMakeLists.txt b/unittest/commands/CMakeLists.txt index c9a7c7df59..aa1bd22fa4 100644 --- a/unittest/commands/CMakeLists.txt +++ b/unittest/commands/CMakeLists.txt @@ -53,10 +53,10 @@ endif() target_link_libraries(test_kim_commands PRIVATE lammps GTest::GMock) add_test(NAME KimCommands COMMAND test_kim_commands) -add_executable(test_reset_ids test_reset_ids.cpp) -target_compile_definitions(test_reset_ids PRIVATE -DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR}) -target_link_libraries(test_reset_ids PRIVATE lammps GTest::GMock) -add_test(NAME ResetIDs COMMAND test_reset_ids) +add_executable(test_reset_atoms test_reset_atoms.cpp) +target_compile_definitions(test_reset_atoms PRIVATE -DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR}) +target_link_libraries(test_reset_atoms PRIVATE lammps GTest::GMock) +add_test(NAME ResetAtoms COMMAND test_reset_atoms) if(PKG_MOLECULE) add_executable(test_compute_global test_compute_global.cpp) diff --git a/unittest/commands/test_compute_chunk.cpp b/unittest/commands/test_compute_chunk.cpp index 5792ee725d..0a48087e81 100644 --- a/unittest/commands/test_compute_chunk.cpp +++ b/unittest/commands/test_compute_chunk.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -246,8 +246,8 @@ TEST_F(ComputeChunkTest, ChunkComputes) command("compute trq all torque/chunk mols"); command("compute vcm all vcm/chunk mols"); command("fix hist1 all ave/time 1 1 1 c_ang[*] c_com[*] c_dip[*] c_gyr c_mom[*] c_omg[*] " - "c_trq[*] c_vcm[*] mode vector file all_chunk.dat format %15.8f"); - command("fix hist2 all ave/time 1 1 1 c_tmp mode vector file vec_chunk.dat format %15.8f"); + "c_trq[*] c_vcm[*] mode vector"); + command("fix hist2 all ave/time 1 1 1 c_tmp mode vector"); command("run 0 post no"); END_HIDE_OUTPUT(); auto cang = get_array("ang"); @@ -314,6 +314,64 @@ TEST_F(ComputeChunkTest, ChunkComputes) EXPECT_NEAR(ctmp[4], -0.06062938, EPSILON); EXPECT_NEAR(ctmp[5], -0.09219489, EPSILON); } + +TEST_F(ComputeChunkTest, ChunkSpreadGlobal) +{ + if (lammps_get_natoms(lmp) == 0.0) GTEST_SKIP(); + + BEGIN_HIDE_OUTPUT(); + command("pair_style lj/cut/coul/cut 10.0"); + command("pair_coeff * * 0.01 3.0"); + command("bond_style harmonic"); + command("bond_coeff * 100.0 1.5"); + command("compute gyr all gyration/chunk mols"); + command("compute spr all chunk/spread/atom mols c_gyr"); + command("compute glb all global/atom c_mols c_gyr"); + command("variable odd atom ((id+1)%2)+1"); + command("compute odd all global/atom v_odd c_gyr"); + command("fix ave all ave/atom 1 1 1 c_spr c_glb c_odd"); + command("run 0 post no"); + END_HIDE_OUTPUT(); + + const int natoms = lammps_get_natoms(lmp); + + auto cgyr = get_vector("gyr"); + auto cspr = get_peratom("spr"); + auto cglb = get_peratom("glb"); + auto codd = get_peratom("odd"); + auto ctag = get_peratom("tags"); + + for (int i = 0; i < natoms; ++i) { + EXPECT_EQ(cspr[i], cgyr[chunkmol[(int)ctag[i]] - 1]); + EXPECT_EQ(cglb[i], cgyr[chunkmol[(int)ctag[i]] - 1]); + EXPECT_EQ(codd[i], cgyr[(((int)ctag[i] + 1) % 2)]); + } +} + +TEST_F(ComputeChunkTest, ChunkReduce) +{ + if (lammps_get_natoms(lmp) == 0.0) GTEST_SKIP(); + + BEGIN_HIDE_OUTPUT(); + command("pair_style lj/cut/coul/cut 10.0"); + command("pair_coeff * * 0.01 3.0"); + command("bond_style harmonic"); + command("bond_coeff * 100.0 1.5"); + command("compute prp all property/chunk mols count"); + command("variable one atom 1"); + command("compute red all reduce/chunk mols sum v_one"); + command("fix ave all ave/time 1 1 1 c_prp c_red mode vector"); + command("run 0 post no"); + END_HIDE_OUTPUT(); + + const int nchunks = get_scalar("mols"); + + auto cprp = get_vector("prp"); + auto cred = get_vector("red"); + + for (int i = 0; i < nchunks; ++i) + EXPECT_EQ(cprp[i], cred[i]); +} } // namespace LAMMPS_NS int main(int argc, char **argv) diff --git a/unittest/commands/test_compute_global.cpp b/unittest/commands/test_compute_global.cpp index 95164d4a09..d7573d8d16 100644 --- a/unittest/commands/test_compute_global.cpp +++ b/unittest/commands/test_compute_global.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -100,24 +100,24 @@ TEST_F(ComputeGlobalTest, Energy) EXPECT_DOUBLE_EQ(get_scalar("pe1"), 24155.155261642241); EXPECT_DOUBLE_EQ(get_scalar("pe2"), 361.37528652881286); EXPECT_DOUBLE_EQ(get_scalar("pe3"), 0.0); - EXPECT_NEAR(get_scalar("pr1"), 1956948.4735454607, 0.0000000005); - EXPECT_NEAR(get_scalar("pr2"), 1956916.7725807722, 0.0000000005); + EXPECT_NEAR(get_scalar("pr1"), 1956948.4735454607, 0.000000005); + EXPECT_NEAR(get_scalar("pr2"), 1956916.7725807722, 0.000000005); EXPECT_DOUBLE_EQ(get_scalar("pr3"), 0.0); auto pr1 = get_vector("pr1"); auto pr2 = get_vector("pr2"); auto pr3 = get_vector("pr3"); - EXPECT_NEAR(pr1[0], 2150600.9207200543, 0.0000000005); - EXPECT_NEAR(pr1[1], 1466949.7512112649, 0.0000000005); - EXPECT_NEAR(pr1[2], 2253294.7487050635, 0.0000000005); - EXPECT_NEAR(pr1[3], 856643.16926486336, 0.0000000005); - EXPECT_NEAR(pr1[4], 692710.86929464422, 0.0000000005); - EXPECT_NEAR(pr1[5], -44403.909298603547, 0.0000000005); - EXPECT_NEAR(pr2[0], 2150575.6989334146, 0.0000000005); - EXPECT_NEAR(pr2[1], 1466911.3911461537, 0.0000000005); - EXPECT_NEAR(pr2[2], 2253263.2276627473, 0.0000000005); - EXPECT_NEAR(pr2[3], 856632.34707690508, 0.0000000005); - EXPECT_NEAR(pr2[4], 692712.89222328411, 0.0000000005); - EXPECT_NEAR(pr2[5], -44399.277068014424, 0.0000000005); + EXPECT_NEAR(pr1[0], 2150600.9207200543, 0.000000005); + EXPECT_NEAR(pr1[1], 1466949.7512112649, 0.000000005); + EXPECT_NEAR(pr1[2], 2253294.7487050635, 0.000000005); + EXPECT_NEAR(pr1[3], 856643.16926486336, 0.000000005); + EXPECT_NEAR(pr1[4], 692710.86929464422, 0.000000005); + EXPECT_NEAR(pr1[5], -44403.909298603547, 0.000000005); + EXPECT_NEAR(pr2[0], 2150575.6989334146, 0.000000005); + EXPECT_NEAR(pr2[1], 1466911.3911461537, 0.000000005); + EXPECT_NEAR(pr2[2], 2253263.2276627473, 0.000000005); + EXPECT_NEAR(pr2[3], 856632.34707690508, 0.000000005); + EXPECT_NEAR(pr2[4], 692712.89222328411, 0.000000005); + EXPECT_NEAR(pr2[5], -44399.277068014424, 0.000000005); EXPECT_DOUBLE_EQ(pr3[0], 0.0); EXPECT_DOUBLE_EQ(pr3[1], 0.0); EXPECT_DOUBLE_EQ(pr3[2], 0.0); @@ -126,12 +126,12 @@ TEST_F(ComputeGlobalTest, Energy) EXPECT_DOUBLE_EQ(pr3[5], 0.0); if (has_tally) { - EXPECT_DOUBLE_EQ(get_scalar("pe4"), 15425.840923850392); + EXPECT_NEAR(get_scalar("pe4"), 15425.840923850392, 0.000000005); auto pe5 = get_vector("pe5"); - EXPECT_DOUBLE_EQ(pe5[0], 23803.966677151559); - EXPECT_DOUBLE_EQ(pe5[1], -94.210004432380643); - EXPECT_DOUBLE_EQ(pe5[2], 115.58040355478101); - EXPECT_DOUBLE_EQ(pe5[3], -31.557101160514257); + EXPECT_NEAR(pe5[0], 23803.966677151559, 0.000000005); + EXPECT_NEAR(pe5[1], -94.210004432380643, 0.000000005); + EXPECT_NEAR(pe5[2], 115.58040355478101, 0.000000005); + EXPECT_NEAR(pe5[3], -31.557101160514257, 0.000000005); } TEST_FAILURE(".*ERROR: Compute pressure must use group all.*", @@ -184,36 +184,36 @@ TEST_F(ComputeGlobalTest, Geometry) auto rg1 = get_vector("rg1"); auto rg2 = get_vector("rg2"); - EXPECT_DOUBLE_EQ(com1[0], 1.4300952724948282); - EXPECT_DOUBLE_EQ(com1[1], -0.29759806705328351); - EXPECT_DOUBLE_EQ(com1[2], -0.7245120195899285); - EXPECT_DOUBLE_EQ(com2[0], 1.7850913321989679); - EXPECT_DOUBLE_EQ(com2[1], -0.45168408952146238); - EXPECT_DOUBLE_EQ(com2[2], -0.60215022088294912); + EXPECT_NEAR(com1[0], 1.4300952724948282, 0.0000000005); + EXPECT_NEAR(com1[1], -0.29759806705328351, 0.0000000005); + EXPECT_NEAR(com1[2], -0.7245120195899285, 0.0000000005); + EXPECT_NEAR(com2[0], 1.7850913321989679, 0.0000000005); + EXPECT_NEAR(com2[1], -0.45168408952146238, 0.0000000005); + EXPECT_NEAR(com2[2], -0.60215022088294912, 0.0000000005); - EXPECT_DOUBLE_EQ(get_scalar("mu1"), 1.8335537504770163); - EXPECT_DOUBLE_EQ(get_scalar("mu2"), 1.7849382239204072); - EXPECT_DOUBLE_EQ(mu1[0], 0.41613191281297729); - EXPECT_DOUBLE_EQ(mu1[1], 1.0056523085627747); - EXPECT_DOUBLE_EQ(mu1[2], -1.4756073398127658); - EXPECT_DOUBLE_EQ(mu2[0], -0.029474795088977768); - EXPECT_DOUBLE_EQ(mu2[1], 1.153516133030746); - EXPECT_DOUBLE_EQ(mu2[2], -1.3618135814069394); + EXPECT_NEAR(get_scalar("mu1"), 1.8335537504770163, 0.0000000005); + EXPECT_NEAR(get_scalar("mu2"), 1.7849382239204072, 0.0000000005); + EXPECT_NEAR(mu1[0], 0.41613191281297729, 0.0000000005); + EXPECT_NEAR(mu1[1], 1.0056523085627747, 0.0000000005); + EXPECT_NEAR(mu1[2], -1.4756073398127658, 0.0000000005); + EXPECT_NEAR(mu2[0], -0.029474795088977768, 0.0000000005); + EXPECT_NEAR(mu2[1], 1.153516133030746, 0.0000000005); + EXPECT_NEAR(mu2[2], -1.3618135814069394, 0.0000000005); - EXPECT_DOUBLE_EQ(get_scalar("rg1"), 3.8495643473797196); - EXPECT_DOUBLE_EQ(get_scalar("rg2"), 5.4558163385611342); - EXPECT_DOUBLE_EQ(rg1[0], 3.6747807397432752); - EXPECT_DOUBLE_EQ(rg1[1], 6.5440303159316278); - EXPECT_DOUBLE_EQ(rg1[2], 4.6003346089421457); - EXPECT_DOUBLE_EQ(rg1[3], -0.4639249501367636); - EXPECT_DOUBLE_EQ(rg1[4], -1.8859032304357459); - EXPECT_DOUBLE_EQ(rg1[5], 0.2339161878440186); - EXPECT_DOUBLE_EQ(rg2[0], 6.2582260148310143); - EXPECT_DOUBLE_EQ(rg2[1], 13.353763805454184); - EXPECT_DOUBLE_EQ(rg2[2], 10.153942099825425); - EXPECT_DOUBLE_EQ(rg2[3], 1.2965604701522486); - EXPECT_DOUBLE_EQ(rg2[4], -5.0315240817290841); - EXPECT_DOUBLE_EQ(rg2[5], 1.1103378503822141); + EXPECT_NEAR(get_scalar("rg1"), 3.8495643473797196, 0.0000000005); + EXPECT_NEAR(get_scalar("rg2"), 5.4558163385611342, 0.0000000005); + EXPECT_NEAR(rg1[0], 3.6747807397432752, 0.0000000005); + EXPECT_NEAR(rg1[1], 6.5440303159316278, 0.0000000005); + EXPECT_NEAR(rg1[2], 4.6003346089421457, 0.0000000005); + EXPECT_NEAR(rg1[3], -0.4639249501367636, 0.0000000005); + EXPECT_NEAR(rg1[4], -1.8859032304357459, 0.0000000005); + EXPECT_NEAR(rg1[5], 0.2339161878440186, 0.0000000005); + EXPECT_NEAR(rg2[0], 6.2582260148310143, 0.0000000005); + EXPECT_NEAR(rg2[1], 13.353763805454184, 0.0000000005); + EXPECT_NEAR(rg2[2], 10.153942099825425, 0.0000000005); + EXPECT_NEAR(rg2[3], 1.2965604701522486, 0.0000000005); + EXPECT_NEAR(rg2[4], -5.0315240817290841, 0.0000000005); + EXPECT_NEAR(rg2[5], 1.1103378503822141, 0.0000000005); if (has_extra) { auto mom1 = get_vector("mom1"); auto mom2 = get_vector("mom2"); diff --git a/unittest/commands/test_delete_atoms.cpp b/unittest/commands/test_delete_atoms.cpp index 2a7cab4718..e348000969 100644 --- a/unittest/commands/test_delete_atoms.cpp +++ b/unittest/commands/test_delete_atoms.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/commands/test_groups.cpp b/unittest/commands/test_groups.cpp index 8247675b82..7751352a61 100644 --- a/unittest/commands/test_groups.cpp +++ b/unittest/commands/test_groups.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/commands/test_kim_commands.cpp b/unittest/commands/test_kim_commands.cpp index 1bb070ad6c..988b0db69a 100644 --- a/unittest/commands/test_kim_commands.cpp +++ b/unittest/commands/test_kim_commands.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -307,17 +307,17 @@ TEST_F(KimCommandsTest, kim_param) ASSERT_THAT(variable->retrieve("shift"), StrEq("2")); - TEST_FAILURE(".*ERROR: Illegal variable name in 'kim param get'.*", + TEST_FAILURE(".*ERROR: Illegal variable name 'list' in 'kim param get'.*", command("kim param get cutoffs 1:3 list");); - TEST_FAILURE(".*ERROR: Illegal variable name in 'kim param get'.*", + TEST_FAILURE(".*ERROR: Illegal variable name 'list' in 'kim param get'.*", command("kim param get cutoffs 1:3 cutoffs_1 cutoffs_2 list");); - TEST_FAILURE(".*ERROR: Illegal variable name in 'kim param get'.*", + TEST_FAILURE(".*ERROR: Illegal variable name 'split' in 'kim param get'.*", command("kim param get cutoffs 1:3 split");); - TEST_FAILURE(".*ERROR: Illegal variable name in 'kim param get'.*", + TEST_FAILURE(".*ERROR: Illegal variable name 'split' in 'kim param get'.*", command("kim param get cutoffs 1:3 cutoffs_1 cutoffs_2 split");); - TEST_FAILURE(".*ERROR: Illegal variable name in 'kim param get'.*", + TEST_FAILURE(".*ERROR: Illegal variable name 'explicit' in 'kim param get'.*", command("kim param get cutoffs 1:3 explicit");); - TEST_FAILURE(".*ERROR: Illegal variable name in 'kim param get'.*", + TEST_FAILURE(".*ERROR: Illegal variable name 'explicit' in 'kim param get'.*", command("kim param get cutoffs 1:3 cutoffs_1 cutoffs_2 explicit");); TEST_FAILURE(".*ERROR: Wrong number of arguments in 'kim param get' " "command.\nThe LAMMPS '3' variable names or 'cutoffs " diff --git a/unittest/commands/test_labelmap.cpp b/unittest/commands/test_labelmap.cpp index 8688575767..f25351e1d9 100644 --- a/unittest/commands/test_labelmap.cpp +++ b/unittest/commands/test_labelmap.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/commands/test_lattice_region.cpp b/unittest/commands/test_lattice_region.cpp index 257fe6a596..8dd15396b2 100644 --- a/unittest/commands/test_lattice_region.cpp +++ b/unittest/commands/test_lattice_region.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/commands/test_regions.cpp b/unittest/commands/test_regions.cpp index a39212efa8..8d5134535a 100644 --- a/unittest/commands/test_regions.cpp +++ b/unittest/commands/test_regions.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/commands/test_reset_ids.cpp b/unittest/commands/test_reset_atoms.cpp similarity index 68% rename from unittest/commands/test_reset_ids.cpp rename to unittest/commands/test_reset_atoms.cpp index cd311616aa..a0afe36324 100644 --- a/unittest/commands/test_reset_ids.cpp +++ b/unittest/commands/test_reset_atoms.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -17,6 +17,7 @@ #include "info.h" #include "input.h" #include "lammps.h" +#include "library.h" #include "output.h" #include "update.h" #include "utils.h" @@ -36,11 +37,11 @@ namespace LAMMPS_NS { #define STRINGIFY(val) XSTR(val) #define XSTR(val) #val -class ResetIDsTest : public LAMMPSTest { +class ResetAtomsIDTest : public LAMMPSTest { protected: void SetUp() override { - testbinary = "ResetIDsTest"; + testbinary = "ResetAtomsIDTest"; LAMMPSTest::SetUp(); if (info->has_style("atom", "full")) { BEGIN_HIDE_OUTPUT(); @@ -51,7 +52,7 @@ protected: } }; -TEST_F(ResetIDsTest, MolIDAll) +TEST_F(ResetAtomsIDTest, MolIDAll) { if (lmp->atom->natoms == 0) GTEST_SKIP(); @@ -89,7 +90,7 @@ TEST_F(ResetIDsTest, MolIDAll) // the original data file has two different molecule IDs // for two residues of the same molecule/fragment. BEGIN_HIDE_OUTPUT(); - command("reset_mol_ids all"); + command("reset_atoms mol all"); END_HIDE_OUTPUT(); ASSERT_EQ(molid[GETIDX(1)], 1); @@ -123,7 +124,7 @@ TEST_F(ResetIDsTest, MolIDAll) ASSERT_EQ(molid[GETIDX(29)], 5); } -TEST_F(ResetIDsTest, DeletePlusAtomID) +TEST_F(ResetAtomsIDTest, DeletePlusAtomID) { if (lmp->atom->natoms == 0) GTEST_SKIP(); @@ -134,7 +135,7 @@ TEST_F(ResetIDsTest, DeletePlusAtomID) command("group allwater molecule 3:6"); command("group twowater molecule 4:6:2"); command("delete_atoms group twowater compress no bond yes"); - command("reset_mol_ids all"); + command("reset_atoms mol all"); END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->natoms, 23); ASSERT_EQ(lmp->atom->map_tag_max, 26); @@ -193,7 +194,7 @@ TEST_F(ResetIDsTest, DeletePlusAtomID) ASSERT_GE(GETIDX(26), 0); BEGIN_HIDE_OUTPUT(); - command("reset_atom_ids"); + command("reset_atoms id"); END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->map_tag_max, 23); @@ -201,7 +202,7 @@ TEST_F(ResetIDsTest, DeletePlusAtomID) ASSERT_GE(GETIDX(i), 0); } -TEST_F(ResetIDsTest, PartialOffset) +TEST_F(ResetAtomsIDTest, PartialOffset) { if (lmp->atom->natoms == 0) GTEST_SKIP(); @@ -211,7 +212,7 @@ TEST_F(ResetIDsTest, PartialOffset) BEGIN_HIDE_OUTPUT(); command("group allwater molecule 3:6"); command("group nowater subtract all allwater"); - command("reset_mol_ids allwater offset 4"); + command("reset_atoms mol allwater offset 4"); END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->natoms, 29); ASSERT_EQ(lmp->atom->map_tag_max, 29); @@ -247,7 +248,7 @@ TEST_F(ResetIDsTest, PartialOffset) ASSERT_EQ(molid[GETIDX(29)], 8); BEGIN_HIDE_OUTPUT(); - command("reset_mol_ids nowater offset 0"); + command("reset_atoms mol nowater offset 0"); END_HIDE_OUTPUT(); ASSERT_EQ(molid[GETIDX(1)], 1); @@ -281,7 +282,7 @@ TEST_F(ResetIDsTest, PartialOffset) ASSERT_EQ(molid[GETIDX(29)], 8); } -TEST_F(ResetIDsTest, DeleteAdd) +TEST_F(ResetAtomsIDTest, DeleteAdd) { if (lmp->atom->natoms == 0) GTEST_SKIP(); @@ -293,7 +294,7 @@ TEST_F(ResetIDsTest, DeleteAdd) command("group twowater molecule 4:6:2"); command("group nowater subtract all allwater"); command("delete_atoms group twowater compress no bond yes mol yes"); - command("reset_mol_ids allwater"); + command("reset_atoms mol allwater"); END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->natoms, 23); ASSERT_EQ(lmp->atom->map_tag_max, 26); @@ -352,7 +353,7 @@ TEST_F(ResetIDsTest, DeleteAdd) ASSERT_GE(GETIDX(26), 0); BEGIN_HIDE_OUTPUT(); - command("reset_atom_ids sort yes"); + command("reset_atoms id sort yes"); END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->map_tag_max, 23); @@ -360,7 +361,7 @@ TEST_F(ResetIDsTest, DeleteAdd) ASSERT_GE(GETIDX(i), 0); BEGIN_HIDE_OUTPUT(); - command("reset_mol_ids nowater offset 1"); + command("reset_atoms mol nowater offset 1"); END_HIDE_OUTPUT(); ASSERT_EQ(molid[GETIDX(1)], 2); @@ -392,7 +393,7 @@ TEST_F(ResetIDsTest, DeleteAdd) command("create_atoms 2 single 1.0 0.0 0.0"); command("create_atoms 3 single 2.0 0.0 0.0"); command("create_atoms 4 single 3.0 0.0 0.0"); - command("reset_mol_ids all single yes"); + command("reset_atoms mol all single yes"); END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->natoms, 27); ASSERT_EQ(lmp->atom->map_tag_max, 27); @@ -406,7 +407,7 @@ TEST_F(ResetIDsTest, DeleteAdd) ASSERT_EQ(molid[GETIDX(27)], 7); BEGIN_HIDE_OUTPUT(); - command("reset_mol_ids all single no"); + command("reset_atoms mol all single no"); END_HIDE_OUTPUT(); ASSERT_EQ(molid[GETIDX(21)], 3); @@ -418,7 +419,7 @@ TEST_F(ResetIDsTest, DeleteAdd) ASSERT_EQ(molid[GETIDX(27)], 0); BEGIN_HIDE_OUTPUT(); - command("reset_mol_ids all compress no single yes"); + command("reset_atoms mol all compress no single yes"); END_HIDE_OUTPUT(); ASSERT_EQ(molid[GETIDX(21)], 21); @@ -430,7 +431,7 @@ TEST_F(ResetIDsTest, DeleteAdd) ASSERT_EQ(molid[GETIDX(27)], 27); } -TEST_F(ResetIDsTest, TopologyData) +TEST_F(ResetAtomsIDTest, TopologyData) { if (lmp->atom->natoms == 0) GTEST_SKIP(); @@ -525,7 +526,7 @@ TEST_F(ResetIDsTest, TopologyData) ASSERT_EQ(angle_atom3[GETIDX(24)][0], 26); BEGIN_HIDE_OUTPUT(); - command("reset_atom_ids sort yes"); + command("reset_atoms id sort yes"); END_HIDE_OUTPUT(); num_bond = lmp->atom->num_bond; @@ -618,63 +619,186 @@ TEST_F(ResetIDsTest, TopologyData) ASSERT_EQ(angle_atom3[GETIDX(22)][0], 23); } -TEST_F(ResetIDsTest, DeathTests) +TEST_F(ResetAtomsIDTest, DeathTests) { if (lmp->atom->natoms == 0) GTEST_SKIP(); - TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", command("reset_mol_ids");); - TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", - command("reset_mol_ids all offset 1 1");); - TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", - command("reset_mol_ids all offset -2");); - TEST_FAILURE(".*ERROR on proc 0: Expected integer.*", command("reset_mol_ids all offset xxx");); + TEST_FAILURE(".*ERROR: Illegal reset_atoms mol command.*", command("reset_atoms mol");); + TEST_FAILURE(".*ERROR: Unknown reset_atoms mol keyword: 1.*", + command("reset_atoms mol all offset 1 1");); + TEST_FAILURE(".*ERROR: Illegal reset_atoms mol offset: -2.*", + command("reset_atoms mol all offset -2");); TEST_FAILURE(".*ERROR on proc 0: Expected integer.*", - command("reset_mol_ids all compress yes single no offset xxx");); - TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", command("reset_mol_ids all offset");); - TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", - command("reset_mol_ids all compress");); + command("reset_atoms mol all offset xxx");); + TEST_FAILURE(".*ERROR on proc 0: Expected integer.*", + command("reset_atoms mol all compress yes single no offset xxx");); + TEST_FAILURE(".*ERROR: Illegal reset_atoms mol offset command: missing argument.*", + command("reset_atoms mol all offset");); + TEST_FAILURE(".*ERROR: Illegal reset_atoms mol compress command: missing argument.*", + command("reset_atoms mol all compress");); TEST_FAILURE(".*ERROR: Expected boolean parameter instead of 'xxx'.*", - command("reset_mol_ids all compress xxx");); - TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", command("reset_mol_ids all single");); + command("reset_atoms mol all compress xxx");); + TEST_FAILURE(".*ERROR: Illegal reset_atoms mol single command: missing argument.*", + command("reset_atoms mol all single");); TEST_FAILURE(".*ERROR: Expected boolean parameter instead of 'xxx'.*", - command("reset_mol_ids all single xxx");); + command("reset_atoms mol all single xxx");); + + TEST_FAILURE(".*ERROR: Illegal reset_atoms image command: missing argument.*", + command("reset_atoms image");); + TEST_FAILURE(".*ERROR: Unknown reset_atoms image keyword: xxx.*", + command("reset_atoms image all xxx");); + TEST_FAILURE(".*ERROR: Could not find reset_atoms image group xxx.*", + command("reset_atoms image xxx");); } -class ResetMolIDsTest : public LAMMPSTest { +class ResetAtomsMolTest : public LAMMPSTest { protected: void SetUp() override { - testbinary = "ResetIDsTest"; + testbinary = "ResetAtomsMolTest"; LAMMPSTest::SetUp(); } }; -TEST_F(ResetMolIDsTest, FailBeforeBox) +TEST_F(ResetAtomsMolTest, FailBeforeBox) { - TEST_FAILURE(".*ERROR: Reset_mol_ids command before simulation box is.*", - command("reset_mol_ids all");); + TEST_FAILURE(".*ERROR: Reset_atoms id command before simulation box is.*", + command("reset_atoms id");); + TEST_FAILURE(".*ERROR: Reset_atoms mol command before simulation box is.*", + command("reset_atoms mol all");); + TEST_FAILURE(".*ERROR: Reset_atoms image command before simulation box is.*", + command("reset_atoms image all");); } -TEST_F(ResetMolIDsTest, FailMissingId) +TEST_F(ResetAtomsMolTest, FailMissingId) { BEGIN_HIDE_OUTPUT(); command("atom_modify id no"); command("region box block 0 1 0 1 0 1"); command("create_box 1 box"); END_HIDE_OUTPUT(); - TEST_FAILURE(".*ERROR: Cannot use reset_mol_ids unless.*", command("reset_mol_ids all");); + TEST_FAILURE(".*ERROR: Cannot use reset_atoms mol unless.*", command("reset_atoms mol all");); + TEST_FAILURE(".*ERROR: Cannot use reset_atoms image unless.*", + command("reset_atoms image all");); } -TEST_F(ResetMolIDsTest, FailOnlyMolecular) +TEST_F(ResetAtomsMolTest, FailOnlyMolecular) { BEGIN_HIDE_OUTPUT(); command("clear"); command("region box block 0 1 0 1 0 1"); command("create_box 1 box"); END_HIDE_OUTPUT(); - TEST_FAILURE(".*ERROR: Can only use reset_mol_ids.*", command("reset_mol_ids all");); + TEST_FAILURE(".*ERROR: Can only use reset_atoms mol.*", command("reset_atoms mol all");); } + +class ResetAtomsImageTest : public LAMMPSTest { +protected: + void SetUp() override + { + testbinary = "ResetAtomsImageTest"; + LAMMPSTest::SetUp(); + if (info->has_style("atom", "full")) { + BEGIN_HIDE_OUTPUT(); + command("variable input_dir index \"" STRINGIFY(TEST_INPUT_FOLDER) "\""); + command("include \"${input_dir}/in.fourmol\""); + command("create_atoms 1 single 1.0 1.0 1.0"); + command("create_atoms 1 single 2.0 1.0 1.0"); + command("create_atoms 1 single 1.0 2.0 1.0"); + command("set atom 1*7 image 1 1 -1"); + command("set atom 8*9 image 2 -1 0"); + command("set atom 8*9 image 2 -1 0"); + command("set atom 10 image 2 0 0"); + command("set atom 11*12 image 2 0 -1"); + command("set atom 13*15 image 1 0 0"); + command("set atom 16*17 image 0 1 1"); + command("set atom 18*19 image 0 1 0"); + command("set atom 20 image 0 2 0"); + command("set atom 21*23 image 20 -1 0"); + command("set atom 27*28 image 1 0 0"); + command("set atom 29 image 1 2 0"); + command("set atom 31 image -2 0 1"); + command("set atom 32 image 0 20 0"); + END_HIDE_OUTPUT(); + } + } +}; + +TEST_F(ResetAtomsImageTest, ResetAtomsImage) +{ + if (lmp->atom->natoms == 0) GTEST_SKIP(); + EXPECT_EQ(lmp->atom->image[GETIDX(1)], lammps_encode_image_flags(1, 1, -1)); + EXPECT_EQ(lmp->atom->image[GETIDX(2)], lammps_encode_image_flags(1, 1, -1)); + EXPECT_EQ(lmp->atom->image[GETIDX(3)], lammps_encode_image_flags(1, 1, -1)); + EXPECT_EQ(lmp->atom->image[GETIDX(4)], lammps_encode_image_flags(1, 1, -1)); + EXPECT_EQ(lmp->atom->image[GETIDX(5)], lammps_encode_image_flags(1, 1, -1)); + EXPECT_EQ(lmp->atom->image[GETIDX(6)], lammps_encode_image_flags(1, 1, -1)); + EXPECT_EQ(lmp->atom->image[GETIDX(7)], lammps_encode_image_flags(1, 1, -1)); + EXPECT_EQ(lmp->atom->image[GETIDX(8)], lammps_encode_image_flags(2, -1, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(9)], lammps_encode_image_flags(2, -1, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(10)], lammps_encode_image_flags(2, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(11)], lammps_encode_image_flags(2, 0, -1)); + EXPECT_EQ(lmp->atom->image[GETIDX(12)], lammps_encode_image_flags(2, 0, -1)); + EXPECT_EQ(lmp->atom->image[GETIDX(13)], lammps_encode_image_flags(1, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(14)], lammps_encode_image_flags(1, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(15)], lammps_encode_image_flags(1, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(16)], lammps_encode_image_flags(0, 1, 1)); + EXPECT_EQ(lmp->atom->image[GETIDX(17)], lammps_encode_image_flags(0, 1, 1)); + EXPECT_EQ(lmp->atom->image[GETIDX(18)], lammps_encode_image_flags(0, 1, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(19)], lammps_encode_image_flags(0, 1, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(20)], lammps_encode_image_flags(0, 2, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(21)], lammps_encode_image_flags(20, -1, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(22)], lammps_encode_image_flags(20, -1, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(23)], lammps_encode_image_flags(20, -1, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(24)], lammps_encode_image_flags(0, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(25)], lammps_encode_image_flags(0, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(26)], lammps_encode_image_flags(0, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(27)], lammps_encode_image_flags(1, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(28)], lammps_encode_image_flags(1, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(29)], lammps_encode_image_flags(1, 2, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(30)], lammps_encode_image_flags(0, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(31)], lammps_encode_image_flags(-2, 0, 1)); + EXPECT_EQ(lmp->atom->image[GETIDX(32)], lammps_encode_image_flags(0, 20, 0)); + BEGIN_HIDE_OUTPUT(); + command("group subset id 5:32"); + command("reset_atoms image subset"); + END_HIDE_OUTPUT(); + EXPECT_EQ(lmp->atom->image[GETIDX(1)], lammps_encode_image_flags(1, 1, -1)); + EXPECT_EQ(lmp->atom->image[GETIDX(2)], lammps_encode_image_flags(1, 1, -1)); + EXPECT_EQ(lmp->atom->image[GETIDX(3)], lammps_encode_image_flags(1, 1, -1)); + EXPECT_EQ(lmp->atom->image[GETIDX(4)], lammps_encode_image_flags(1, 1, -1)); + EXPECT_EQ(lmp->atom->image[GETIDX(5)], lammps_encode_image_flags(0, 1, -1)); + EXPECT_EQ(lmp->atom->image[GETIDX(6)], lammps_encode_image_flags(0, 1, -1)); + EXPECT_EQ(lmp->atom->image[GETIDX(7)], lammps_encode_image_flags(0, 1, -1)); + EXPECT_EQ(lmp->atom->image[GETIDX(8)], lammps_encode_image_flags(1, -1, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(9)], lammps_encode_image_flags(1, -1, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(10)], lammps_encode_image_flags(1, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(11)], lammps_encode_image_flags(1, 0, -1)); + EXPECT_EQ(lmp->atom->image[GETIDX(12)], lammps_encode_image_flags(1, 0, -1)); + EXPECT_EQ(lmp->atom->image[GETIDX(13)], lammps_encode_image_flags(0, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(14)], lammps_encode_image_flags(0, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(15)], lammps_encode_image_flags(0, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(16)], lammps_encode_image_flags(-1, 1, 1)); + EXPECT_EQ(lmp->atom->image[GETIDX(17)], lammps_encode_image_flags(-1, 1, 1)); + EXPECT_EQ(lmp->atom->image[GETIDX(18)], lammps_encode_image_flags(0, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(19)], lammps_encode_image_flags(0, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(20)], lammps_encode_image_flags(0, 1, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(21)], lammps_encode_image_flags(0, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(22)], lammps_encode_image_flags(0, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(23)], lammps_encode_image_flags(0, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(24)], lammps_encode_image_flags(0, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(25)], lammps_encode_image_flags(0, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(26)], lammps_encode_image_flags(0, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(27)], lammps_encode_image_flags(0, -1, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(28)], lammps_encode_image_flags(0, -1, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(29)], lammps_encode_image_flags(0, 1, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(30)], lammps_encode_image_flags(0, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(30)], lammps_encode_image_flags(0, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(31)], lammps_encode_image_flags(0, 0, 0)); + EXPECT_EQ(lmp->atom->image[GETIDX(32)], lammps_encode_image_flags(0, 0, 0)); +} + } // namespace LAMMPS_NS int main(int argc, char **argv) diff --git a/unittest/commands/test_set_property.cpp b/unittest/commands/test_set_property.cpp index 092a0172fc..dbe9f619b5 100644 --- a/unittest/commands/test_set_property.cpp +++ b/unittest/commands/test_set_property.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -107,6 +107,7 @@ TEST_F(SetTest, NoBoxNoAtoms) TEST_F(SetTest, StylesTypes) { + if (!Info::has_package("MOLECULE")) GTEST_SKIP(); atomic_system("molecular"); ASSERT_EQ(atom->natoms, 8); diff --git a/unittest/commands/test_simple_commands.cpp b/unittest/commands/test_simple_commands.cpp index 54ffbb6950..db6ee3c1e7 100644 --- a/unittest/commands/test_simple_commands.cpp +++ b/unittest/commands/test_simple_commands.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -20,6 +20,7 @@ #include "input.h" #include "output.h" #include "update.h" +#include "utils.h" #include "variable.h" #include "../testing/core.h" @@ -265,14 +266,22 @@ TEST_F(SimpleCommandsTest, Suffix) BEGIN_HIDE_OUTPUT(); command("suffix one"); + command("suffix yes"); END_HIDE_OUTPUT(); ASSERT_THAT(lmp->suffix, StrEq("one")); + ASSERT_EQ(lmp->suffix_enable, 1); + ASSERT_THAT(utils::strip_style_suffix("one/four", lmp), StrEq("one/four")); + ASSERT_THAT(utils::strip_style_suffix("four/one", lmp), StrEq("four")); BEGIN_HIDE_OUTPUT(); command("suffix hybrid two three"); END_HIDE_OUTPUT(); ASSERT_THAT(lmp->suffix, StrEq("two")); ASSERT_THAT(lmp->suffix2, StrEq("three")); + ASSERT_THAT(utils::strip_style_suffix("one/four", lmp), StrEq("one/four")); + ASSERT_THAT(utils::strip_style_suffix("one/two", lmp), StrEq("one")); + ASSERT_THAT(utils::strip_style_suffix("one/three", lmp), StrEq("one")); + ASSERT_THAT(utils::strip_style_suffix("four/one", lmp), StrEq("four/one")); BEGIN_HIDE_OUTPUT(); command("suffix four"); @@ -284,11 +293,13 @@ TEST_F(SimpleCommandsTest, Suffix) command("suffix off"); END_HIDE_OUTPUT(); ASSERT_EQ(lmp->suffix_enable, 0); + ASSERT_THAT(utils::strip_style_suffix("one/four", lmp), StrEq("one/four")); BEGIN_HIDE_OUTPUT(); command("suffix yes"); END_HIDE_OUTPUT(); ASSERT_EQ(lmp->suffix_enable, 1); + ASSERT_THAT(utils::strip_style_suffix("one/four", lmp), StrEq("one")); BEGIN_HIDE_OUTPUT(); command("suffix no"); diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp index c2a5acd1b8..8debb95b6a 100644 --- a/unittest/commands/test_variables.cpp +++ b/unittest/commands/test_variables.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/force-styles/CMakeLists.txt b/unittest/force-styles/CMakeLists.txt index 878492d6c7..b5bd92f2c7 100644 --- a/unittest/force-styles/CMakeLists.txt +++ b/unittest/force-styles/CMakeLists.txt @@ -49,7 +49,7 @@ else() target_compile_definitions(style_tests PRIVATE TEST_INPUT_FOLDER=${TEST_INPUT_FOLDER} YAML_DECLARE_STATIC) endif() target_include_directories(style_tests PRIVATE ${LAMMPS_SOURCE_DIR}) -target_link_libraries(style_tests PUBLIC gmock Yaml::Yaml lammps) +target_link_libraries(style_tests PUBLIC GTest::GMock Yaml::Yaml lammps) # propagate sanitizer options to test tools if(ENABLE_SANITIZER AND (NOT (ENABLE_SANITIZER STREQUAL "none"))) @@ -62,7 +62,7 @@ endif() # unit test for error stats class add_executable(test_error_stats test_error_stats.cpp) target_include_directories(test_error_stats PRIVATE ${CMAKE_CURRENT_SOURCE_DIR} ${LAMMPS_SOURCE_DIR}) -target_link_libraries(test_error_stats PRIVATE gtest_main) +target_link_libraries(test_error_stats PRIVATE GTest::GMockMain) add_test(NAME ErrorStats COMMAND test_error_stats) # pair style tester diff --git a/unittest/force-styles/error_stats.cpp b/unittest/force-styles/error_stats.cpp index af8eba5a66..df728e824f 100644 --- a/unittest/force-styles/error_stats.cpp +++ b/unittest/force-styles/error_stats.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/force-styles/error_stats.h b/unittest/force-styles/error_stats.h index 14038e23f6..987a0585ae 100644 --- a/unittest/force-styles/error_stats.h +++ b/unittest/force-styles/error_stats.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/force-styles/test_angle_style.cpp b/unittest/force-styles/test_angle_style.cpp index 1a97368e0a..36e281e100 100644 --- a/unittest/force-styles/test_angle_style.cpp +++ b/unittest/force-styles/test_angle_style.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/force-styles/test_bond_style.cpp b/unittest/force-styles/test_bond_style.cpp index 09ea62a909..d056fdc876 100644 --- a/unittest/force-styles/test_bond_style.cpp +++ b/unittest/force-styles/test_bond_style.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/force-styles/test_config.h b/unittest/force-styles/test_config.h index 18b4b4f0b2..b284052d6d 100644 --- a/unittest/force-styles/test_config.h +++ b/unittest/force-styles/test_config.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/force-styles/test_config_reader.cpp b/unittest/force-styles/test_config_reader.cpp index d920128862..3f99f251a5 100644 --- a/unittest/force-styles/test_config_reader.cpp +++ b/unittest/force-styles/test_config_reader.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/force-styles/test_config_reader.h b/unittest/force-styles/test_config_reader.h index 23da817622..1af7589add 100644 --- a/unittest/force-styles/test_config_reader.h +++ b/unittest/force-styles/test_config_reader.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/force-styles/test_dihedral_style.cpp b/unittest/force-styles/test_dihedral_style.cpp index 74438da356..2039155644 100644 --- a/unittest/force-styles/test_dihedral_style.cpp +++ b/unittest/force-styles/test_dihedral_style.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/force-styles/test_fix_timestep.cpp b/unittest/force-styles/test_fix_timestep.cpp index 981bc46eef..d2e35b463f 100644 --- a/unittest/force-styles/test_fix_timestep.cpp +++ b/unittest/force-styles/test_fix_timestep.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/force-styles/test_improper_style.cpp b/unittest/force-styles/test_improper_style.cpp index 740b75552b..259bd9008d 100644 --- a/unittest/force-styles/test_improper_style.cpp +++ b/unittest/force-styles/test_improper_style.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/force-styles/test_main.cpp b/unittest/force-styles/test_main.cpp index df6c79d4ef..80f1ca4e30 100644 --- a/unittest/force-styles/test_main.cpp +++ b/unittest/force-styles/test_main.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/force-styles/test_main.h b/unittest/force-styles/test_main.h index ff373e5174..36bcd7bdff 100644 --- a/unittest/force-styles/test_main.h +++ b/unittest/force-styles/test_main.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/force-styles/test_mliappy_unified.cpp b/unittest/force-styles/test_mliappy_unified.cpp index 1eb800a954..a8309feb21 100644 --- a/unittest/force-styles/test_mliappy_unified.cpp +++ b/unittest/force-styles/test_mliappy_unified.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/force-styles/test_pair_list.cpp b/unittest/force-styles/test_pair_list.cpp index 9e249613f3..ce0d9b4c08 100644 --- a/unittest/force-styles/test_pair_list.cpp +++ b/unittest/force-styles/test_pair_list.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/force-styles/test_pair_style.cpp b/unittest/force-styles/test_pair_style.cpp index 6f1061a5eb..385525c90b 100644 --- a/unittest/force-styles/test_pair_style.cpp +++ b/unittest/force-styles/test_pair_style.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -379,8 +379,9 @@ TEST(PairStyle, plain) EXPECT_FP_LE_WITH_EPS(pair->eng_vdwl, test_config.run_vdwl, epsilon); EXPECT_FP_LE_WITH_EPS(pair->eng_coul, test_config.run_coul, epsilon); // skip comparing per-atom energy with total energy for "kim" and "in.conp" - if (std::string("kim") != lmp->force->pair_style && - std::string("in.conp") != test_config.input_file) + if ((std::string("kim") != lmp->force->pair_style) && + (std::string("pod") != lmp->force->pair_style) && + (std::string("in.conp") != test_config.input_file)) EXPECT_FP_LE_WITH_EPS((pair->eng_vdwl + pair->eng_coul), energy, epsilon); if (print_stats) std::cerr << "run_energy stats, newton on: " << stats << std::endl; diff --git a/unittest/force-styles/tests/atomic-pair-meam_sc.yaml b/unittest/force-styles/tests/atomic-pair-meam_sc.yaml index 01e03e1715..bcd697c589 100644 --- a/unittest/force-styles/tests/atomic-pair-meam_sc.yaml +++ b/unittest/force-styles/tests/atomic-pair-meam_sc.yaml @@ -2,7 +2,7 @@ lammps_version: 3 Aug 2022 tags: slow date_generated: Thu Aug 18 22:46:30 2022 -epsilon: 7.5e-12 +epsilon: 1.0e-11 skip_tests: prerequisites: ! | pair meam diff --git a/unittest/force-styles/tests/atomic-pair-meam_sw_spline.yaml b/unittest/force-styles/tests/atomic-pair-meam_sw_spline.yaml index 0cc9619847..2ca499b4ce 100644 --- a/unittest/force-styles/tests/atomic-pair-meam_sw_spline.yaml +++ b/unittest/force-styles/tests/atomic-pair-meam_sw_spline.yaml @@ -1,7 +1,7 @@ --- -lammps_version: 17 Feb 2022 +lammps_version: 3 Nov 2022 tags: slow, unstable -date_generated: Fri Mar 18 22:17:38 2022 +date_generated: Sat Dec 17 23:00:39 2022 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -26,142 +26,142 @@ pair_coeff: ! | * * Si.b.meam.sw.spline Si extract: ! "" natoms: 64 -init_vdwl: -110.4685773088353 +init_vdwl: -110.45990817806636 init_coul: 0 init_stress: ! |2- - 2.0342092779841650e+02 2.9353890615210491e+02 1.9138584169384231e+02 -1.3797329301045073e+02 6.0306018863011829e+01 1.2377595362950453e+02 + 2.0350171190213450e+02 2.9342452017616694e+02 1.9128146785117693e+02 -1.3797012820305963e+02 6.0431847076778510e+01 1.2362227514422503e+02 init_forces: ! |2 - 1 -1.3233766738474692e+01 -1.2736008818268305e+01 -8.4807945144710555e+00 - 2 4.9498134298370466e-01 -4.8711972803905459e+00 1.9841873228328510e+00 - 3 -2.2604016428394664e+00 -2.3773175770601909e+00 -4.7907075017529648e+00 - 4 1.3198738000680255e+01 -1.3577671743256937e+01 1.6136271940741899e+01 - 5 1.3902528433647081e+01 1.1756623545348988e+01 1.8280754013108911e+01 - 6 6.8901540190015753e+00 5.2819576857359163e-01 -7.8675982110956089e-01 - 7 4.3967551798115430e+01 -4.9117468284031069e+01 -4.6363366102651781e+01 - 8 -3.1836191663317337e-01 3.0883879768115423e+00 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2.85 extract: ! 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"" +input_file: in.manybody +pair_style: pod +pair_coeff: ! | + * * Ta_param.pod Ta_coeff.pod Ta Ta Ta Ta Ta Ta Ta Ta +extract: ! 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7.3627368355304368e+00 + 36 9.8461575627457365e-01 -5.1895947221609999e+00 -1.7416681629788844e+00 + 37 -4.3479597602556987e+00 5.9771199348457786e+00 -6.4035952128921325e+00 + 38 5.4022686330729042e-01 -1.9715997267295688e+00 -8.5655067815022723e-01 + 39 3.9223699424296088e+00 -4.0527508147694391e+00 -9.4209981476048874e+00 + 40 1.1452927978439993e+01 -4.8883937399550499e+00 -3.5415966186040104e+00 + 41 9.6744931407782142e-01 -2.1966543538862224e-01 -2.7321296820305050e+00 + 42 -8.2423780480934816e+00 -5.1198905741883944e+00 -3.2132369293703431e+00 + 43 1.3449232112837139e-01 -1.4266031489439955e+01 9.0529636113665890e-01 + 44 9.2864716878942914e+00 -1.0653224674860530e+01 6.0756644746289155e+00 + 45 -7.3279419010510516e-01 6.2791577709783972e+00 -8.9108524114379080e+00 + 46 -1.9039679778788625e+00 -4.0528901631980760e+00 1.1630733460046352e+01 + 47 6.3763337760997540e+00 5.1233125844104510e+00 2.8138206914970656e+00 + 48 2.3380859800951628e+00 2.2326450966381390e+00 1.5287384487626418e-01 + 49 -2.8014223230382376e+00 -1.2044581352367127e+01 -8.0347575819620474e+00 + 50 2.1422145518477187e+00 7.2424826745901107e+00 -3.0637741546937911e+00 + 51 -4.1001979259164552e+00 8.5374368127020315e+00 8.7144930213835430e+00 + 52 1.1806523391252540e+01 -1.2284601329073553e+01 1.3944720496276224e+01 + 53 5.1475653317387939e+00 8.0227245379881804e+00 3.2309313222296896e+00 + 54 5.7087433874913218e+00 -5.6601583438330563e+00 -4.8237069484155661e+00 + 55 7.3380406496835295e+00 -8.4939091917007623e+00 -8.9244600192476753e+00 + 56 -1.2296439276523572e+00 2.7286867585656513e+00 -5.9003523038759793e+00 + 57 6.7476852384192298e-01 -3.7254641308262482e+00 2.8703807089098310e-02 + 58 7.1320373971199791e+00 -4.6322478918816286e+00 3.6412286305653043e+00 + 59 7.1937029046281671e+00 4.5742558433451368e+00 -3.7956679883677404e+00 + 60 -2.8288653495291820e+00 -1.3157182815231137e+01 -8.0095169657552905e+00 + 61 -9.9276745329887783e-01 3.0408835454693719e+00 7.7871977254688995e-01 + 62 -7.4381007616019534e+00 6.1448378054475778e+00 -4.6683183548425067e+00 + 63 5.5682593755810563e+00 -7.3119820285913608e+00 -2.0100166481798887e-01 + 64 6.5075012240147911e+00 6.2545959336473818e+00 1.4555696233577285e+01 +... diff --git a/unittest/force-styles/tests/mol-pair-coul_slater_long.yaml b/unittest/force-styles/tests/mol-pair-coul_slater_long.yaml index 52efdaa52d..ba11503a2c 100644 --- a/unittest/force-styles/tests/mol-pair-coul_slater_long.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_slater_long.yaml @@ -6,6 +6,7 @@ skip_tests: prerequisites: ! | atom full pair coul/slater/long + kspace ewald pre_commands: ! "" post_commands: ! | pair_modify mix arithmetic diff --git a/unittest/force-styles/tests/mol-pair-dpd_ext.yaml b/unittest/force-styles/tests/mol-pair-dpd_ext.yaml new file mode 100644 index 0000000000..8f07c88667 --- /dev/null +++ b/unittest/force-styles/tests/mol-pair-dpd_ext.yaml @@ -0,0 +1,94 @@ +--- +lammps_version: 3 Nov 2022 +date_generated: Sat Dec 17 15:41:37 2022 +epsilon: 5e-14 +skip_tests: gpu intel kokkos_omp single +prerequisites: ! | + atom full + pair dpd/ext +pre_commands: ! | + variable newton_pair delete + variable newton_pair index on + comm_modify vel yes +post_commands: ! "" +input_file: in.fourmol +pair_style: dpd/ext 100.0 8.0 55667788 +pair_coeff: ! | + * * 0.1 4.5 4.5 0.5 0.5 + 1 1 0.2 3.5 3.5 0.5 0.5 + 2 2 0.3 4.0 4.0 0.5 0.5 + 2 4 0.2 4.0 4.0 0.5 0.5 + 3 3 0.5 4.4 4.0 0.6 0.4 + 4 4 0.2 5.0 5.3 0.4 0.6 + 5 5 0.1 4.0 4.0 0.5 0.5 +extract: ! "" +natoms: 29 +init_vdwl: 33.88964374360757 +init_coul: 0 +init_stress: ! |2- + 3.8251398030273030e+01 1.0255447218676466e+02 9.1141445555187879e+00 -1.0350255887988475e+02 -7.0174884275309623e+01 4.5716673898956422e+01 +init_forces: ! |2 + 1 5.1498572672938039e+00 2.5703472206602790e+01 1.7551260448073723e+01 + 2 7.3736403442948868e+00 3.7099949433111239e+00 -3.3844562611278484e-01 + 3 -1.0939704157336930e+01 -3.6274831005384645e-02 -8.1581799650508113e+00 + 4 1.0546798203927455e+01 1.7539003794751913e+01 2.9994492538169113e+00 + 5 -1.0410959684004842e+01 -8.1769741369940423e+00 -5.2428230419297304e+00 + 6 9.9608775044461293e+00 -4.9278512001913999e+00 1.3146883289483814e+01 + 7 -6.4030495171728710e+00 -2.5387964373797569e+00 2.0140429133325867e+01 + 8 -4.5778825942774084e+00 -1.5770987190728489e+01 3.5045923269715251e+00 + 9 5.9908999094768181e+00 9.7332307249612149e-01 1.0060357557727691e+01 + 10 2.7253377841634489e+01 6.4127767911930995e+00 -1.0469797066097630e+01 + 11 1.3749322228418571e+01 1.5400413006506499e+01 7.1607935798767386e+00 + 12 -6.3010751860576750e+00 -3.4431826732902140e+00 -3.0942782086470420e+00 + 13 1.2526043516169834e+00 -9.6413955527851645e+00 1.5016970884444614e+01 + 14 1.1042419213961729e+01 -5.8227276839142634e+00 6.4364981814483899e+00 + 15 -2.3331556176574647e+01 3.5884413683136658e+00 -2.2544724990921903e+01 + 16 3.9618823632071987e+00 -3.2474498067579329e+00 -4.3843237827057759e+00 + 17 -3.0200667842357154e-01 -6.3764313595509456e+00 -7.0583460110929517e+00 + 18 1.1841351438192627e-01 1.9750953739057945e+01 -6.3192848067375609e+00 + 19 -5.6904071384394239e+00 -6.2917569004872265e+00 -1.1963208647112367e+01 + 20 -1.3902583843563816e+01 3.7924595629285376e+00 -2.9993634867248482e+00 + 21 1.1848803003107719e+01 3.8650194494042944e+00 -2.3931072468635392e+01 + 22 -6.8146144816873973e+00 -1.3419042942351584e+01 1.2608309005638453e+01 + 23 -3.0518458239020978e+00 7.1721772279611506e-01 3.9148450134713979e+00 + 24 9.4548676747643761e+00 -1.3834207645939959e+01 8.9087479013148609e+00 + 25 -7.7451277963340663e+00 -4.1099570091167834e+00 -1.8454479707717809e+01 + 26 -3.4603945899098898e+00 6.5339997484084289e-01 5.3617857889691987e+00 + 27 -6.0343949080994636e-02 6.6937405037029514e+00 4.7039728955452000e+00 + 28 -1.0240459623627199e+01 -1.0977733595975294e+00 -5.2443794968109296e+00 + 29 -4.4717521801392479e+00 -1.0065407405815222e+01 -1.3121879538108483e+00 +run_vdwl: 33.88366119853999 +run_coul: 0 +run_stress: ! |2- + 7.2919626053823890e+01 -2.7828917811551634e+01 1.7105017219881199e+02 3.0943069573372640e+01 -7.1432642261763988e+01 -1.2423392355535769e+02 +run_forces: ! |2 + 1 -1.4131674111536896e+01 -4.5307079930500205e+00 8.8553170111222954e+00 + 2 9.7772519012144627e+00 -7.6753209435892327e+00 2.2165445353219000e+00 + 3 3.7354251012742399e+00 4.0730926756541947e+00 -3.4731926524620276e+00 + 4 7.2336492368034024e+00 -1.6827826351167969e+00 2.4945502098538519e-01 + 5 -4.3208562921092657e+00 -5.5451228090627991e-01 1.7538935171390541e+01 + 6 -8.3623630071114459e+00 1.7132133728504200e+00 -1.4483310247648838e+01 + 7 1.3918955131102539e+01 2.0323073565411327e+01 -4.6282942080091303e+00 + 8 -1.0941054848703045e+01 1.2916076627428636e+01 2.5488491345468905e+01 + 9 1.0995769286479902e+01 -2.4561111179657743e+01 -3.6357241561659825e+00 + 10 6.5122254777210760e+00 -1.2205976065057740e+01 1.1048755663112694e+01 + 11 -9.6577339174027999e-01 -9.4121594793376318e+00 1.6872461982647906e+00 + 12 -1.2853351435795478e+01 -1.1661998374857859e+01 -9.6884410568153889e+00 + 13 -5.2341025813260380e+00 1.1186034190928794e+01 -7.3388432189309469e+00 + 14 1.8453686911180207e+00 3.6876241694906810e+01 -2.8491295602169469e+01 + 15 -5.9000405433533087e+00 1.8431521708956367e+01 -5.0964756582037101e+00 + 16 -1.9197033780653729e+01 2.0406043852115205e+00 2.7992914925840413e+00 + 17 -1.5914439243318078e+01 -1.2435145215277640e+01 2.0341321938884189e+01 + 18 1.4803582904257356e+01 -2.9511497655979561e+01 1.0215040560028893e+01 + 19 -1.0050999695673788e+01 6.1119983636964630e+00 -1.8429833349500644e+01 + 20 1.6443044975845829e+01 5.6146973572456416e+00 -9.2115937932282925e+00 + 21 1.2855031803629835e+01 -9.7066942571904633e+00 -3.9784057469393721e+00 + 22 5.5797621796998231e-01 1.4133831403887775e+01 5.3841248185420332e+00 + 23 1.3941797775857969e+01 -2.3195798716544669e+00 6.5317589855023881e+00 + 24 1.5442539735846905e-01 -1.4026916313486044e+01 6.4523748450131935e+00 + 25 1.5139211468268925e+00 8.9557892936032921e+00 -4.5731126870932428e+00 + 26 -2.9127736379450397e-01 -3.1195378063665529e+00 -4.9279042022816117e+00 + 27 1.1993002939972692e+00 -6.1439848849293170e+00 7.8038589020770974e+00 + 28 -2.0803097319420392e+00 -4.2219766348896366e+00 3.5494508593346126e+00 + 29 -5.2444493143993327e+00 1.1393726951565744e+01 -1.2205540768184314e+01 +... diff --git a/unittest/force-styles/tests/mol-pair-dpd_ext_tstat.yaml b/unittest/force-styles/tests/mol-pair-dpd_ext_tstat.yaml new file mode 100644 index 0000000000..2fcc640df5 --- /dev/null +++ b/unittest/force-styles/tests/mol-pair-dpd_ext_tstat.yaml @@ -0,0 +1,94 @@ +--- +lammps_version: 3 Nov 2022 +date_generated: Sat Dec 17 15:38:51 2022 +epsilon: 5e-14 +skip_tests: gpu intel kokkos_omp single +prerequisites: ! | + atom full + pair dpd/ext/tstat +pre_commands: ! | + variable newton_pair delete + variable newton_pair index on + comm_modify vel yes +post_commands: ! "" +input_file: in.fourmol +pair_style: dpd/ext/tstat 100.0 100.0 8.0 55667788 +pair_coeff: ! | + * * 4.5 4.5 0.5 0.5 + 1 1 3.5 3.5 0.5 0.5 + 2 2 4.0 4.0 0.5 0.5 + 2 4 4.0 4.0 0.5 0.5 + 3 3 4.4 4.0 0.6 0.4 + 4 4 5.0 5.3 0.4 0.6 + 5 5 4.0 4.0 0.5 0.5 +extract: ! "" +natoms: 29 +init_vdwl: 0 +init_coul: 0 +init_stress: ! |2- + 1.4574717693624876e+01 7.1252528106646366e+01 -1.6499215979159636e+01 -9.8805551174702813e+01 -6.2984101792184553e+01 4.6320747972221476e+01 +init_forces: ! |2 + 1 5.5624629707449236e+00 2.5267482418430543e+01 1.7455837636840936e+01 + 2 7.9890787589586321e+00 2.7334159704033394e+00 -4.4912609353132571e-01 + 3 -1.0425196835647425e+01 -2.6562178960112570e-01 -8.1895349238880719e+00 + 4 1.1707962985567560e+01 1.7218327488030280e+01 3.1325087294733294e+00 + 5 -9.3643110515778645e+00 -8.4559142280632553e+00 -5.6302526571777651e+00 + 6 1.0350319600938580e+01 -4.9631857700500754e+00 1.3208365081950475e+01 + 7 -5.6912844039900792e+00 -2.4251805995355227e+00 2.0613962020942797e+01 + 8 -4.5743413938317756e+00 -1.5518230536801214e+01 3.4794587310078304e+00 + 9 5.9805709630208952e+00 1.3393459078961725e+00 9.3707724473467930e+00 + 10 2.7103956409229447e+01 6.6911270479325857e+00 -1.0493307270086415e+01 + 11 1.3722558978526875e+01 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-1.4080250767719038e+01 8.5162255140264609e+00 + 25 -7.8427474971079656e+00 -4.7754637246776079e+00 -1.9403747740982496e+01 + 26 -3.7391228412677413e+00 1.9606663508176359e-01 4.7881550102383477e+00 + 27 1.0563289436921391e-01 6.9013112204358711e+00 4.5648539408008304e+00 + 28 -9.8360983166008218e+00 -7.1739355098872948e-01 -5.4182461340713486e+00 + 29 -4.1099028712689627e+00 -9.5274215037112846e+00 -1.7962811812418344e+00 +run_vdwl: 0 +run_coul: 0 +run_stress: ! |2- + 4.9266460967642843e+01 -5.9111413750583637e+01 1.4545481800287564e+02 3.5635963940478575e+01 -6.4251320017736717e+01 -1.2363508335441071e+02 +run_forces: ! |2 + 1 -1.3719442909413937e+01 -4.9666156334765059e+00 8.7599181534335386e+00 + 2 1.0391174870901938e+01 -8.6507911270806890e+00 2.1056097628746766e+00 + 3 4.2495251233698275e+00 3.8437663925916445e+00 -3.5045009657490156e+00 + 4 8.3932351062524155e+00 -2.0030337673750402e+00 3.8272790802088474e-01 + 5 -3.2757253735836840e+00 -8.3325031298511232e-01 1.7152252455143778e+01 + 6 -7.9733082813698939e+00 1.6777392958375097e+00 -1.4421849525714798e+01 + 7 1.4630307032129375e+01 2.0436521539550192e+01 -4.1549025034832399e+00 + 8 -1.0937454887747506e+01 1.3168617760103691e+01 2.5463421161558834e+01 + 9 1.0985589841094063e+01 -2.4195564454330718e+01 -4.3241673350660701e+00 + 10 6.3630015399831850e+00 -1.1927897676460454e+01 1.1025310238302538e+01 + 11 -9.9220745946968036e-01 -8.5794641759877450e+00 1.8650992727478291e+00 + 12 -1.3263925601780343e+01 -1.1515905270341566e+01 -9.6187877981563581e+00 + 13 -6.1625444464780745e+00 1.1413958091348704e+01 -7.3441718444905773e+00 + 14 1.3001579943448509e+00 3.7185212706389123e+01 -2.7912385686771604e+01 + 15 -6.8717194465009470e+00 1.8419025200600061e+01 -5.0795914343055593e+00 + 16 -1.9442609578275103e+01 2.4147187716181118e+00 2.5786155289050487e+00 + 17 -1.6260303719465991e+01 -1.1801162696943075e+01 1.9673377485657529e+01 + 18 1.4566204321128769e+01 -3.0235234907022587e+01 1.0905297377717281e+01 + 19 -1.0074685751023591e+01 5.3873018678994198e+00 -1.7378513715604424e+01 + 20 1.6064584839990744e+01 4.8406903684848972e+00 -8.5147142504480531e+00 + 21 1.2639813979842121e+01 -9.4362927696862950e+00 -3.7870406042380140e+00 + 22 3.1017290337441961e-01 1.4664671892692001e+01 5.8641592626050061e+00 + 23 1.3393222536146498e+01 -1.9013710469117922e+00 6.8765390626419194e+00 + 24 3.4310818063008952e-02 -1.4273017541160232e+01 6.0598981914849865e+00 + 25 1.4161064695435657e+00 8.2913896919499308e+00 -5.5215547745837821e+00 + 26 -5.6962178521803175e-01 -3.5765106637569533e+00 -5.5013272233283974e+00 + 27 1.3653624914977991e+00 -5.9363949579710917e+00 7.6647361174567505e+00 + 28 -1.6762592783918939e+00 -3.8420052862466951e+00 3.3757261594299082e+00 + 29 -4.8829613489439101e+00 1.1930898708671284e+01 -1.2689180476040610e+01 +... diff --git a/unittest/force-styles/tests/mol-pair-nm_cut_coul_cut.yaml b/unittest/force-styles/tests/mol-pair-nm_cut_coul_cut.yaml index e10d630408..dc09f6242b 100644 --- a/unittest/force-styles/tests/mol-pair-nm_cut_coul_cut.yaml +++ b/unittest/force-styles/tests/mol-pair-nm_cut_coul_cut.yaml @@ -1,7 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:17:35 2022 -epsilon: 5e-13 +lammps_version: 3 Nov 2022 +date_generated: Wed Nov 23 12:21:08 2022 +epsilon: 2e-12 skip_tests: prerequisites: ! | atom full @@ -33,72 +33,72 @@ extract: ! | nn 2 mm 2 natoms: 29 -init_vdwl: 184.28678589160327 -init_coul: -135.3222017722983 +init_vdwl: 184.287044185624 +init_coul: -137.87932620011787 init_stress: ! |2- - 5.1099535412443879e+02 4.9267015856417487e+02 1.0972826650625757e+03 -1.9179119371088936e+02 -3.5985836516943652e+00 1.6890666491875683e+02 + 5.0652399415102809e+02 4.9736621002026737e+02 1.0945023745733126e+03 -1.9301832865224381e+02 1.8762224642096914e-01 1.7162238049862481e+02 init_forces: ! |2 - 1 -3.3237622364758597e+00 6.7713954997753760e+01 8.3067188829067177e+01 - 2 3.9621008700560012e+01 3.0171229889604540e+01 -4.8145332639882334e+01 - 3 -3.5364644744971940e+01 -9.6539501255026011e+01 -3.5029548782863188e+01 - 4 -5.3015461109817663e-01 1.6289587757514515e-01 -7.2423374326431356e-01 - 5 -5.9482314827521177e-01 3.6012564229132904e-01 7.9763541784878933e-01 - 6 -2.0517469128198312e+02 2.3641073678086124e+02 2.8403110395134235e+02 - 7 1.4287738299209584e+01 -8.3042673557006708e+01 -4.2404138177988466e+02 - 8 3.4432579872496632e+01 -2.3062478463316680e+01 1.0196257581358861e+02 - 9 2.1504316475975024e+01 1.5520947058320779e+01 8.8721284584619994e+01 - 10 1.3156277736186865e+02 -1.5256269193303697e+02 -4.7528776206099316e+01 - 11 -1.1549608580120421e+00 7.0751627315313514e-01 -1.2306532477500820e+00 - 12 8.2305373454600836e+00 2.8332067643232048e+00 -1.6285990412442382e+00 - 13 2.2152653863898988e-01 -2.5442239617884921e-01 -1.7821156240885982e-02 - 14 -1.4864243248803288e+00 4.9691633196181018e-01 -6.5591950906426355e-01 - 15 1.9536455977505707e-01 4.6553673584615141e-01 -7.3823010387388632e-01 - 16 1.1408068052592634e+02 -8.3363365075734180e+01 -2.9358101411834207e+02 - 17 -1.1530269288646562e+02 8.4705249217102178e+01 2.9252691476710731e+02 - 18 1.2607896146319246e+00 6.6515350853351460e+00 -9.8941034529134715e+00 - 19 1.6182226631729169e+00 -1.6594283813607693e+00 5.6553541079235838e+00 - 20 -3.4521573063242741e+00 -3.1789176785999720e+00 4.2591620921699045e+00 - 21 -1.5230523428245663e+01 -1.8827777303529409e+01 4.5543598985413915e+01 - 22 -2.5331360436022880e+01 -5.4301878248720961e+00 -3.5349975516643234e+01 - 23 4.0112972843495513e+01 2.2949867135700025e+01 -9.6970781334064569e+00 + 1 -3.5396501309981954e+00 6.6944364611585584e+01 8.3059219120660856e+01 + 2 3.9621008700560019e+01 3.0171229889604543e+01 -4.8145332639882334e+01 + 3 -3.5309288471259912e+01 -9.6592073986045776e+01 -3.5059191984527324e+01 + 4 -5.3015461109817674e-01 1.6289587757514493e-01 -7.2423374326431356e-01 + 5 -5.9482314827521177e-01 3.6012564229132926e-01 7.9763541784878955e-01 + 6 -2.0517469128198312e+02 2.3641073678086121e+02 2.8403110395134229e+02 + 7 1.4287738299209584e+01 -8.3042673557006694e+01 -4.2404138177988466e+02 + 8 3.4432579872496632e+01 -2.3062478463316697e+01 1.0196257581358860e+02 + 9 2.1504316475975028e+01 1.5520947058320786e+01 8.8721284584619994e+01 + 10 1.3157989652366749e+02 -1.5248002606214345e+02 -4.7534699865938585e+01 + 11 -1.1549608580120423e+00 7.0751627315313514e-01 -1.2306532477500822e+00 + 12 7.2669942071383717e+00 2.0827730884953919e+00 -9.0483043978096866e-01 + 13 2.2152653863898994e-01 -2.5442239617884937e-01 -1.7821156240885788e-02 + 14 -1.4864243248803288e+00 4.9691633196180973e-01 -6.5591950906426388e-01 + 15 1.9536455977505737e-01 4.6553673584615107e-01 -7.3823010387388610e-01 + 16 1.1427944925864990e+02 -8.2676440560459525e+01 -2.9356712075009648e+02 + 17 -1.1530269288646562e+02 8.4705249217102164e+01 2.9252691476710731e+02 + 18 1.2607896146319251e+00 6.6515350853351460e+00 -9.8941034529134697e+00 + 19 1.6182226631729160e+00 -1.6594283813607693e+00 5.6553541079235821e+00 + 20 -3.4521573063242741e+00 -3.1789176785999724e+00 4.2591620921699054e+00 + 21 -1.5285879701957692e+01 -1.8775204572509647e+01 4.5573242187078066e+01 + 22 -2.5331360436022880e+01 -5.4301878248720943e+00 -3.5349975516643234e+01 + 23 4.0112972843495520e+01 2.2949867135700025e+01 -9.6970781334064569e+00 24 6.6473466694181287e+00 -4.2720688813774373e+01 2.5475101119120744e+01 25 -3.3278855135511762e+01 2.8247579501663811e+00 -2.7042493390233950e+01 26 2.5709355480930235e+01 3.9014887914531776e+01 2.6900053403817590e+00 - 27 1.0035511306793698e+01 -4.5249946085110551e+01 1.8136503701331897e+01 - 28 -3.9953070294941519e+01 1.3962092508592026e+01 -2.6231057257176037e+01 - 29 3.0657392434855581e+01 3.0940622604427993e+01 8.6697893689665211e+00 -run_vdwl: 182.40565476045293 -run_coul: -135.3428229317011 + 27 1.0999054445115412e+01 -4.4499512409282737e+01 1.7412735099868630e+01 + 28 -3.9953070294941519e+01 1.3962092508592027e+01 -2.6231057257176040e+01 + 29 3.0657392434855577e+01 3.0940622604427993e+01 8.6697893689665193e+00 +run_vdwl: 182.40627457531505 +run_coul: -137.89878255208336 run_stress: ! |2- - 5.0949331883645084e+02 4.9079274612266465e+02 1.0779924919705209e+03 -1.8978874005409725e+02 -2.3414288930535676e+00 1.6680086396779814e+02 + 5.0502284487804911e+02 4.9549254038893065e+02 1.0752131218453601e+03 -1.9101402318764428e+02 1.4448370451390913e+00 1.6951693900962570e+02 run_forces: ! |2 - 1 -3.0222512967714557e+00 6.7548505252631742e+01 8.2368596588550062e+01 - 2 3.9249247328631569e+01 2.9923489231546629e+01 -4.7570871930892892e+01 - 3 -3.5327226055520775e+01 -9.6102750283993871e+01 -3.4890589040756382e+01 - 4 -5.2696455605069259e-01 1.6213860296922811e-01 -7.2430457126338410e-01 - 5 -5.9400169113171586e-01 3.6136912208033589e-01 7.9530286564994024e-01 - 6 -2.0274433560773628e+02 2.3284786713406370e+02 2.7401951211582013e+02 - 7 1.4053553144930220e+01 -8.1102084254822103e+01 -4.1219124551744085e+02 - 8 3.2718675446198795e+01 -2.1551046804011083e+01 1.0097962112112319e+02 - 9 2.1323856224128093e+01 1.5222193966786529e+01 8.7834851199368813e+01 - 10 1.3130268818222987e+02 -1.5219622702094762e+02 -4.7515342312770102e+01 - 11 -1.1541261444752642e+00 7.1381752451384339e-01 -1.2230561924848902e+00 - 12 8.2264000446385346e+00 2.8299212831552727e+00 -1.6299507774035358e+00 - 13 2.1792987819368359e-01 -2.5267817510362128e-01 -1.9040070778804069e-02 - 14 -1.4863827602148627e+00 4.9691341825375590e-01 -6.4929126993868946e-01 - 15 1.9516446161304488e-01 4.6409461483290748e-01 -7.4066880359248788e-01 - 16 1.1245063534493042e+02 -8.2380964098503739e+01 -2.8939941367324343e+02 - 17 -1.1367888495468203e+02 8.3736413965239862e+01 2.8833591319216583e+02 - 18 1.2131213413750925e+00 6.6087858905244472e+00 -9.8443684782076062e+00 - 19 1.6546892701962139e+00 -1.6335518483372100e+00 5.6675264381026587e+00 - 20 -3.4406155231052553e+00 -3.1608955862760086e+00 4.2021081664244280e+00 - 21 -1.5380842837515630e+01 -1.8832663749099712e+01 4.5639191584555739e+01 - 22 -2.5437261250740086e+01 -5.4851555768258553e+00 -3.5409747254511750e+01 - 23 4.0368809860056317e+01 2.3008461599616822e+01 -9.7324663526701478e+00 - 24 7.1229399666679027e+00 -4.3444645139181588e+01 2.6085435505612736e+01 - 25 -3.4137823679541398e+01 2.8946896673905611e+00 -2.7774080649897098e+01 - 26 2.6093689208699011e+01 3.9671650206452789e+01 2.8124886686652082e+00 - 27 1.0189565500107717e+01 -4.5358416256293751e+01 1.8141445825723800e+01 - 28 -4.0123206182868742e+01 1.4015089779144132e+01 -2.6301107890805710e+01 - 29 3.0672957337757669e+01 3.0995677534193614e+01 8.7335515148952023e+00 + 1 -3.2370828229989943e+00 6.6780774771428867e+01 8.2360566992843957e+01 + 2 3.9248669659652556e+01 2.9923101710814461e+01 -4.7570156486162247e+01 + 3 -3.5272405495891725e+01 -9.6156898011190052e+01 -3.4920858821878639e+01 + 4 -5.2696307806019427e-01 1.6213782144861011e-01 -7.2430297098202856e-01 + 5 -5.9400132072875222e-01 3.6136881819958322e-01 7.9530174833943768e-01 + 6 -2.0274433109253258e+02 2.3284785750828254e+02 2.7401951291433039e+02 + 7 1.4053553193905296e+01 -8.1102076691627317e+01 -4.1219125509985423e+02 + 8 3.2718449282709940e+01 -2.1550864085726676e+01 1.0097970359571399e+02 + 9 2.1323849598698548e+01 1.5222193680732165e+01 8.7834847272654116e+01 + 10 1.3131984144877813e+02 -1.5211385896116542e+02 -4.7521267129265915e+01 + 11 -1.1541259655305498e+00 7.1381836660091746e-01 -1.2230539280652590e+00 + 12 7.2630852175005964e+00 2.0798061880380749e+00 -9.0633631991268937e-01 + 13 2.1792142656044974e-01 -2.5267485273151963e-01 -1.9040900180560982e-02 + 14 -1.4863809886398240e+00 4.9691277039032383e-01 -6.4928587974626595e-01 + 15 1.9516412586808574e-01 4.6408847437290568e-01 -7.4067142611860370e-01 + 16 1.1264998906650452e+02 -8.1693726909197835e+01 -2.8938652282069330e+02 + 17 -1.1367940494205878e+02 8.3736184613376594e+01 2.8833692617302631e+02 + 18 1.2131256191519586e+00 6.6087841118467869e+00 -9.8443636765781175e+00 + 19 1.6546867296048959e+00 -1.6335521580158148e+00 5.6675246971307507e+00 + 20 -3.4406162815803181e+00 -3.1608941993411719e+00 4.2021061175034422e+00 + 21 -1.5436168448451303e+01 -1.8780058922578032e+01 4.5668818732530838e+01 + 22 -2.5437256643599888e+01 -5.4851610900512116e+00 -3.5409746057405300e+01 + 23 4.0368779518163102e+01 2.3008433743607917e+01 -9.7324579117657564e+00 + 24 7.1229403171558960e+00 -4.3444642379685369e+01 2.6085431366299698e+01 + 25 -3.4137823381351410e+01 2.8946870622451546e+00 -2.7774076485443004e+01 + 26 2.6093689507109417e+01 3.9671649820489279e+01 2.8124906008412616e+00 + 27 1.1152133422843132e+01 -4.4609063038241878e+01 1.7417265391517304e+01 + 28 -4.0123145645809892e+01 1.4014953690801475e+01 -2.6300937504650808e+01 + 29 3.0673827973027787e+01 3.0996718146876649e+01 8.7338378159710270e+00 ... diff --git a/unittest/force-styles/tests/mol-pair-nm_cut_coul_long.yaml b/unittest/force-styles/tests/mol-pair-nm_cut_coul_long.yaml index b3c77b862c..8bc69e85f4 100644 --- a/unittest/force-styles/tests/mol-pair-nm_cut_coul_long.yaml +++ b/unittest/force-styles/tests/mol-pair-nm_cut_coul_long.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:17:35 2022 +lammps_version: 3 Nov 2022 +date_generated: Wed Nov 23 12:21:08 2022 epsilon: 7.5e-13 skip_tests: prerequisites: ! | @@ -39,72 +39,72 @@ extract: ! | mm 2 cut_coul 0 natoms: 29 -init_vdwl: 184.28678589160327 +init_vdwl: 184.287044185624 init_coul: 225.82181512692495 init_stress: ! |2- - 5.1535561642229106e+02 5.0058662653359033e+02 1.1159625282020661e+03 -1.8397466102442883e+02 -2.0220636765660638e+00 1.7544854550792292e+02 + 5.1535625659153879e+02 5.0058721227699067e+02 1.1159628277106565e+03 -1.8397448571567824e+02 -2.0224936628921029e+00 1.7544839728662993e+02 init_forces: ! |2 - 1 -3.0654526282473653e+00 6.6615864099533127e+01 8.2943973715838268e+01 - 2 3.9068866013811309e+01 2.9455617832505151e+01 -4.7591021495719247e+01 - 3 -3.5280048507313708e+01 -9.6589706921967377e+01 -3.5074530442718626e+01 - 4 -6.6290078829733745e-01 1.7069498108397532e-01 -6.5698974844320646e-01 - 5 -7.3666031116459629e-01 3.1866503947918778e-01 8.0597153193899140e-01 - 6 -2.0569141405030027e+02 2.3627567491105717e+02 2.8443813098936624e+02 - 7 1.4533357696957466e+01 -8.2901362570668283e+01 -4.2411675286042595e+02 - 8 3.4572734326141102e+01 -2.2709011166557751e+01 1.0190201388959704e+02 - 9 2.1302134918689685e+01 1.5382116555420744e+01 8.8486496066808485e+01 - 10 1.3163065394972341e+02 -1.5255187760681488e+02 -4.7566872183542166e+01 - 11 -1.0673114564038046e+00 6.0655281622864732e-01 -1.2545988594461333e+00 - 12 7.7809585200300058e+00 3.1160398793201316e+00 -1.4701791888504216e+00 - 13 5.3014557250212346e-01 -2.5075115207640880e-01 -1.8692015200156273e-01 - 14 -1.3123789187002088e+00 4.0626415990577358e-01 -7.3662740015731798e-01 - 15 3.2883564820812672e-01 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1.0861910045154971e+01 -4.6328889070692995e+01 1.8883074794015705e+01 + 28 -4.0470174882584466e+01 1.5020795051869364e+01 -2.6766823901697389e+01 + 29 2.9999319404392619e+01 3.1302945187447808e+01 7.8628922608669081e+00 +run_vdwl: 182.4028175410934 +run_coul: 225.8052312234039 run_stress: ! |2- - 5.1384631551491782e+02 4.9870417055031982e+02 1.0966342093912015e+03 -1.8197324336578851e+02 -7.7105078556388151e-01 1.7333789878387816e+02 + 5.1384695555524797e+02 4.9870475622702440e+02 1.0966345088415544e+03 -1.8197306815785140e+02 -7.7148065920433828e-01 1.7333775064278868e+02 run_forces: ! |2 - 1 -2.7683190788522740e+00 6.6449095933852917e+01 8.2247798763054263e+01 - 2 3.8702194737017720e+01 2.9212212087553127e+01 -4.7019606503568262e+01 - 3 -3.5243454712977965e+01 -9.6154953753202179e+01 -3.4936504547233788e+01 - 4 -6.5977694961123645e-01 1.7011044348999105e-01 -6.5636000725760957e-01 - 5 -7.3566520752177100e-01 3.2004552783623724e-01 8.0428279587216267e-01 - 6 -2.0326269571945986e+02 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a/unittest/force-styles/tests/mol-pair-nm_cut_coul_table.yaml b/unittest/force-styles/tests/mol-pair-nm_cut_coul_table.yaml index f53a664d2a..c6c13ec92a 100644 --- a/unittest/force-styles/tests/mol-pair-nm_cut_coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-nm_cut_coul_table.yaml @@ -1,6 +1,6 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:17:35 2022 +lammps_version: 3 Nov 2022 +date_generated: Wed Nov 23 12:21:08 2022 epsilon: 5e-12 skip_tests: gpu prerequisites: ! | @@ -39,72 +39,72 @@ extract: ! | mm 2 cut_coul 0 natoms: 29 -init_vdwl: 184.28678589160327 -init_coul: 225.82185134782813 +init_vdwl: 184.287044185624 +init_coul: 225.8218513478281 init_stress: ! |2- - 5.1535563668501300e+02 5.0058663228965906e+02 1.1159625416266908e+03 -1.8397465772983549e+02 -2.0220541814186075e+00 1.7544854959858193e+02 + 5.1535627685426095e+02 5.0058721803305957e+02 1.1159628411352805e+03 -1.8397448242108504e+02 -2.0224841677449517e+00 1.7544840137728934e+02 init_forces: 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a/unittest/force-styles/yaml_reader.h b/unittest/force-styles/yaml_reader.h index c31ee4ee9d..97d83fc1c4 100644 --- a/unittest/force-styles/yaml_reader.h +++ b/unittest/force-styles/yaml_reader.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/force-styles/yaml_writer.cpp b/unittest/force-styles/yaml_writer.cpp index b1165ff821..d2ac74f00d 100644 --- a/unittest/force-styles/yaml_writer.cpp +++ b/unittest/force-styles/yaml_writer.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/force-styles/yaml_writer.h b/unittest/force-styles/yaml_writer.h index ca95a578c1..be4861fcc0 100644 --- a/unittest/force-styles/yaml_writer.h +++ b/unittest/force-styles/yaml_writer.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/formats/compressed_dump_test.h b/unittest/formats/compressed_dump_test.h index b209097264..3c4376a5b8 100644 --- a/unittest/formats/compressed_dump_test.h +++ b/unittest/formats/compressed_dump_test.h @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/formats/compressed_dump_test_main.cpp b/unittest/formats/compressed_dump_test_main.cpp index 5f775a8843..53e3f7ff65 100644 --- a/unittest/formats/compressed_dump_test_main.cpp +++ b/unittest/formats/compressed_dump_test_main.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/formats/test_atom_styles.cpp b/unittest/formats/test_atom_styles.cpp index 4b726bb030..6d1c0f479e 100644 --- a/unittest/formats/test_atom_styles.cpp +++ b/unittest/formats/test_atom_styles.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -560,7 +560,6 @@ TEST_F(AtomStyleTest, atomic) auto x = lmp->atom->x; auto v = lmp->atom->v; - auto tag = lmp->atom->tag; EXPECT_NEAR(x[GETIDX(1)][0], -2.0, EPSILON); EXPECT_NEAR(x[GETIDX(1)][1], 2.0, EPSILON); EXPECT_NEAR(x[GETIDX(1)][2], 0.1, EPSILON); @@ -648,7 +647,6 @@ TEST_F(AtomStyleTest, atomic) END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->map_tag_max, 16); x = lmp->atom->x; - tag = lmp->atom->tag; EXPECT_NEAR(x[GETIDX(1)][0], -2.0, EPSILON); EXPECT_NEAR(x[GETIDX(1)][1], 2.0, EPSILON); EXPECT_NEAR(x[GETIDX(1)][2], 0.1, EPSILON); @@ -1149,7 +1147,7 @@ TEST_F(AtomStyleTest, ellipsoid) auto type = lmp->atom->type; auto ellipsoid = lmp->atom->ellipsoid; auto rmass = lmp->atom->rmass; - auto avec = (AtomVecEllipsoid *)lmp->atom->avec; + auto avec = dynamic_cast(lmp->atom->avec); auto bonus = avec->bonus; EXPECT_NEAR(x[GETIDX(1)][0], -2.0, EPSILON); EXPECT_NEAR(x[GETIDX(1)][1], 2.0, EPSILON); @@ -1260,7 +1258,7 @@ TEST_F(AtomStyleTest, ellipsoid) type = lmp->atom->type; ellipsoid = lmp->atom->ellipsoid; rmass = lmp->atom->rmass; - avec = (AtomVecEllipsoid *)lmp->atom->avec; + avec = dynamic_cast(lmp->atom->avec); bonus = avec->bonus; ASSERT_EQ(type[GETIDX(1)], 1); ASSERT_EQ(type[GETIDX(3)], 2); @@ -1325,7 +1323,7 @@ TEST_F(AtomStyleTest, ellipsoid) ellipsoid = lmp->atom->ellipsoid; rmass = lmp->atom->rmass; - avec = (AtomVecEllipsoid *)lmp->atom->avec; + avec = dynamic_cast(lmp->atom->avec); bonus = avec->bonus; ASSERT_EQ(type[GETIDX(1)], 1); ASSERT_EQ(type[GETIDX(2)], 3); @@ -1478,7 +1476,7 @@ TEST_F(AtomStyleTest, line) auto type = lmp->atom->type; auto line = lmp->atom->line; auto rmass = lmp->atom->rmass; - auto avec = (AtomVecLine *)lmp->atom->avec; + auto avec = dynamic_cast(lmp->atom->avec); auto bonus = avec->bonus; EXPECT_NEAR(x[GETIDX(1)][0], -2.0, EPSILON); EXPECT_NEAR(x[GETIDX(1)][1], 2.0, EPSILON); @@ -1571,7 +1569,7 @@ TEST_F(AtomStyleTest, line) type = lmp->atom->type; line = lmp->atom->line; rmass = lmp->atom->rmass; - avec = (AtomVecLine *)lmp->atom->avec; + avec = dynamic_cast(lmp->atom->avec); bonus = avec->bonus; ASSERT_EQ(type[GETIDX(1)], 1); ASSERT_EQ(type[GETIDX(3)], 2); @@ -1616,7 +1614,7 @@ TEST_F(AtomStyleTest, line) line = lmp->atom->line; rmass = lmp->atom->rmass; - avec = (AtomVecLine *)lmp->atom->avec; + avec = dynamic_cast(lmp->atom->avec); bonus = avec->bonus; ASSERT_EQ(type[GETIDX(1)], 1); ASSERT_EQ(type[GETIDX(2)], 3); @@ -1762,7 +1760,7 @@ TEST_F(AtomStyleTest, tri) auto tri = lmp->atom->tri; auto rmass = lmp->atom->rmass; auto radius = lmp->atom->radius; - auto avec = (AtomVecTri *)lmp->atom->avec; + auto avec = dynamic_cast(lmp->atom->avec); auto bonus = avec->bonus; EXPECT_NEAR(x[GETIDX(1)][0], -2.0, EPSILON); EXPECT_NEAR(x[GETIDX(1)][1], 2.0, EPSILON); @@ -1916,7 +1914,7 @@ TEST_F(AtomStyleTest, tri) tri = lmp->atom->tri; rmass = lmp->atom->rmass; radius = lmp->atom->radius; - avec = (AtomVecTri *)lmp->atom->avec; + avec = dynamic_cast(lmp->atom->avec); bonus = avec->bonus; ASSERT_EQ(type[GETIDX(1)], 1); ASSERT_EQ(type[GETIDX(3)], 2); @@ -2025,7 +2023,7 @@ TEST_F(AtomStyleTest, tri) tri = lmp->atom->tri; rmass = lmp->atom->rmass; - avec = (AtomVecTri *)lmp->atom->avec; + avec = dynamic_cast(lmp->atom->avec); bonus = avec->bonus; ASSERT_EQ(type[GETIDX(1)], 1); ASSERT_EQ(type[GETIDX(2)], 3); @@ -2083,7 +2081,7 @@ TEST_F(AtomStyleTest, body_nparticle) ASSERT_ATOM_STATE_EQ(lmp->atom, expected); - auto avec = (AtomVecBody *)lmp->atom->avec; + auto avec = dynamic_cast(lmp->atom->avec); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_NE(avec->bptr, nullptr); ASSERT_THAT(std::string(avec->bptr->style), Eq("nparticle")); @@ -2346,7 +2344,7 @@ TEST_F(AtomStyleTest, body_nparticle) rmass = lmp->atom->rmass; radius = lmp->atom->radius; angmom = lmp->atom->angmom; - avec = (AtomVecBody *)lmp->atom->avec; + avec = dynamic_cast(lmp->atom->avec); bonus = avec->bonus; EXPECT_NEAR(x[GETIDX(1)][0], -2.0, EPSILON); EXPECT_NEAR(x[GETIDX(1)][1], 2.0, EPSILON); @@ -2486,7 +2484,7 @@ TEST_F(AtomStyleTest, body_nparticle) command("replicate 1 1 2"); END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("body")); - avec = (AtomVecBody *)lmp->atom->avec; + avec = dynamic_cast(lmp->atom->avec); ASSERT_THAT(std::string(avec->bptr->style), Eq("nparticle")); ASSERT_NE(lmp->atom->avec, nullptr); ASSERT_EQ(lmp->atom->natoms, 8); @@ -2601,7 +2599,7 @@ TEST_F(AtomStyleTest, body_nparticle) body = lmp->atom->body; rmass = lmp->atom->rmass; radius = lmp->atom->radius; - avec = (AtomVecBody *)lmp->atom->avec; + avec = dynamic_cast(lmp->atom->avec); bonus = avec->bonus; ASSERT_EQ(type[GETIDX(1)], 1); ASSERT_EQ(type[GETIDX(2)], 3); @@ -3050,7 +3048,7 @@ TEST_F(AtomStyleTest, template_charge) ASSERT_ATOM_STATE_EQ(lmp->atom, expected); - auto hybrid = (AtomVecHybrid *)lmp->atom->avec; + auto hybrid = dynamic_cast(lmp->atom->avec); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("hybrid")); ASSERT_EQ(hybrid->nstyles, 2); ASSERT_THAT(std::string(hybrid->keywords[0]), Eq("template")); @@ -3081,7 +3079,7 @@ TEST_F(AtomStyleTest, template_charge) command("pair_coeff * *"); END_HIDE_OUTPUT(); ASSERT_NE(lmp->atom->avec, nullptr); - hybrid = (AtomVecHybrid *)lmp->atom->avec; + hybrid = dynamic_cast(lmp->atom->avec); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("hybrid")); ASSERT_EQ(hybrid->nstyles, 2); ASSERT_THAT(std::string(hybrid->keywords[0]), Eq("template")); @@ -4191,7 +4189,7 @@ TEST_F(AtomStyleTest, full_ellipsoid) ASSERT_ATOM_STATE_EQ(lmp->atom, expected); - auto hybrid = (AtomVecHybrid *)lmp->atom->avec; + auto hybrid = dynamic_cast(lmp->atom->avec); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("hybrid")); ASSERT_EQ(hybrid->nstyles, 2); ASSERT_THAT(std::string(hybrid->keywords[0]), Eq("full")); @@ -4278,7 +4276,7 @@ TEST_F(AtomStyleTest, full_ellipsoid) END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("hybrid")); ASSERT_NE(lmp->atom->avec, nullptr); - hybrid = (AtomVecHybrid *)lmp->atom->avec; + hybrid = dynamic_cast(lmp->atom->avec); ASSERT_EQ(hybrid->nstyles, 2); ASSERT_THAT(std::string(hybrid->keywords[0]), Eq("full")); ASSERT_THAT(std::string(hybrid->keywords[1]), Eq("ellipsoid")); @@ -4308,7 +4306,7 @@ TEST_F(AtomStyleTest, full_ellipsoid) auto ellipsoid = lmp->atom->ellipsoid; auto rmass = lmp->atom->rmass; - auto avec = (AtomVecEllipsoid *)hybrid->styles[1]; + auto avec = dynamic_cast(hybrid->styles[1]); auto bonus = avec->bonus; EXPECT_NEAR(x[GETIDX(1)][0], -2.0, EPSILON); EXPECT_NEAR(x[GETIDX(1)][1], 2.0, EPSILON); @@ -4410,7 +4408,7 @@ TEST_F(AtomStyleTest, full_ellipsoid) command("replicate 1 1 2 bbox"); END_HIDE_OUTPUT(); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("hybrid")); - hybrid = (AtomVecHybrid *)lmp->atom->avec; + hybrid = dynamic_cast(lmp->atom->avec); ASSERT_EQ(hybrid->nstyles, 2); ASSERT_THAT(std::string(hybrid->keywords[0]), Eq("full")); ASSERT_THAT(std::string(hybrid->keywords[1]), Eq("ellipsoid")); @@ -4431,7 +4429,7 @@ TEST_F(AtomStyleTest, full_ellipsoid) type = lmp->atom->type; ellipsoid = lmp->atom->ellipsoid; rmass = lmp->atom->rmass; - avec = (AtomVecEllipsoid *)hybrid->styles[1]; + avec = dynamic_cast(hybrid->styles[1]); bonus = avec->bonus; ASSERT_EQ(type[GETIDX(1)], 1); ASSERT_EQ(type[GETIDX(3)], 2); @@ -4496,8 +4494,8 @@ TEST_F(AtomStyleTest, full_ellipsoid) ellipsoid = lmp->atom->ellipsoid; rmass = lmp->atom->rmass; - hybrid = (AtomVecHybrid *)lmp->atom->avec; - avec = (AtomVecEllipsoid *)hybrid->styles[1]; + hybrid = dynamic_cast(lmp->atom->avec); + avec = dynamic_cast(hybrid->styles[1]); bonus = avec->bonus; ASSERT_EQ(type[GETIDX(1)], 1); ASSERT_EQ(type[GETIDX(2)], 3); @@ -4841,7 +4839,7 @@ TEST_F(AtomStyleTest, oxdna) ASSERT_ATOM_STATE_EQ(lmp->atom, expected); - auto hybrid = (AtomVecHybrid *)lmp->atom->avec; + auto hybrid = dynamic_cast(lmp->atom->avec); ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("hybrid")); ASSERT_EQ(hybrid->nstyles, 3); ASSERT_THAT(std::string(hybrid->keywords[0]), Eq("bond")); @@ -5016,7 +5014,7 @@ TEST_F(AtomStyleTest, oxdna) ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("hybrid")); ASSERT_NE(lmp->atom->avec, nullptr); - hybrid = (AtomVecHybrid *)lmp->atom->avec; + hybrid = dynamic_cast(lmp->atom->avec); ASSERT_EQ(hybrid->nstyles, 3); ASSERT_THAT(std::string(hybrid->keywords[0]), Eq("bond")); @@ -5060,7 +5058,7 @@ TEST_F(AtomStyleTest, oxdna) auto ellipsoid = lmp->atom->ellipsoid; auto rmass = lmp->atom->rmass; - auto avec = (AtomVecEllipsoid *)hybrid->styles[1]; + auto avec = dynamic_cast(hybrid->styles[1]); auto bonus = avec->bonus; EXPECT_NEAR(x[GETIDX(1)][0], -0.33741452300167507, EPSILON); diff --git a/unittest/formats/test_dump_atom.cpp b/unittest/formats/test_dump_atom.cpp index 683578d04f..a62bf12c80 100644 --- a/unittest/formats/test_dump_atom.cpp +++ b/unittest/formats/test_dump_atom.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -726,7 +726,7 @@ TEST_F(DumpAtomTest, frequency) values = extract_items(dump_file, "TIMESTEP"); expected = {"0", "5", "10", "15", "20", "25", "30", "10", "20"}; ASSERT_EQ(values.size(), expected.size()); - for (int i = 0; i < expected.size(); ++i) + for (std::size_t i = 0; i < expected.size(); ++i) ASSERT_THAT(values[i], Eq(expected[i])); BEGIN_HIDE_OUTPUT(); @@ -739,7 +739,7 @@ TEST_F(DumpAtomTest, frequency) values = extract_items(dump_file, "TIMESTEP"); expected = {"10", "20", "30"}; ASSERT_EQ(values.size(), expected.size()); - for (int i = 0; i < expected.size(); ++i) + for (std::size_t i = 0; i < expected.size(); ++i) ASSERT_THAT(values[i], Eq(expected[i])); BEGIN_HIDE_OUTPUT(); @@ -753,7 +753,7 @@ TEST_F(DumpAtomTest, frequency) values = extract_items(dump_file, "TIMESTEP"); expected = {"0", "10", "15", "20", "30"}; ASSERT_EQ(values.size(), expected.size()); - for (int i = 0; i < expected.size(); ++i) + for (std::size_t i = 0; i < expected.size(); ++i) ASSERT_THAT(values[i], Eq(expected[i])); delete_file(dump_file); @@ -777,7 +777,7 @@ TEST_F(DumpAtomTest, delay) values = extract_items(dump_file, "TIMESTEP"); expected = {"20", "30", "40", "50"}; ASSERT_EQ(values.size(), expected.size()); - for (int i = 0; i < expected.size(); ++i) + for (std::size_t i = 0; i < expected.size(); ++i) ASSERT_THAT(values[i], Eq(expected[i])); delete_file(dump_file); @@ -808,25 +808,25 @@ TEST_F(DumpAtomTest, colname) values = extract_items(dump_file, "ATOMS id type xs ys zs"); expected = {"1 1 0 0 0", "1 1 0 0 0"}; ASSERT_EQ(values.size(), expected.size()); - for (int i = 0; i < expected.size(); ++i) + for (std::size_t i = 0; i < expected.size(); ++i) ASSERT_THAT(values[i], Eq(expected[i])); values = extract_items(dump_file, "ATOMS AtomID type x-scaled ys z-scaled"); expected = {"1 1 0 0 0"}; ASSERT_EQ(values.size(), expected.size()); - for (int i = 0; i < expected.size(); ++i) + for (std::size_t i = 0; i < expected.size(); ++i) ASSERT_THAT(values[i], Eq(expected[i])); values = extract_items(dump_file, "ATOMS id type x y z ix iy iz"); expected = {"1 1 0 0 0 0 0 0", "1 1 0 0 0 0 0 0"}; ASSERT_EQ(values.size(), expected.size()); - for (int i = 0; i < expected.size(); ++i) + for (std::size_t i = 0; i < expected.size(); ++i) ASSERT_THAT(values[i], Eq(expected[i])); values = extract_items(dump_file, "ATOMS AtomID type X y Z img_x iy iz"); expected = {"1 1 0 0 0 0 0 0"}; ASSERT_EQ(values.size(), expected.size()); - for (int i = 0; i < expected.size(); ++i) + for (std::size_t i = 0; i < expected.size(); ++i) ASSERT_THAT(values[i], Eq(expected[i])); delete_file(dump_file); @@ -848,13 +848,13 @@ TEST_F(DumpAtomTest, units_time) values = extract_items(dump_file, "TIME"); expected = {"0", "0.05", "0.1", "0.15", "0.25", "0.35", "0.45"}; ASSERT_EQ(values.size(), expected.size()); - for (int i = 0; i < expected.size(); ++i) + for (std::size_t i = 0; i < expected.size(); ++i) ASSERT_THAT(values[i], Eq(expected[i])); values = extract_items(dump_file, "UNITS"); expected = {"lj"}; ASSERT_EQ(values.size(), expected.size()); - for (int i = 0; i < expected.size(); ++i) + for (std::size_t i = 0; i < expected.size(); ++i) ASSERT_THAT(values[i], Eq(expected[i])); delete_file(dump_file); @@ -877,7 +877,7 @@ TEST_F(DumpAtomTest, every) values = extract_items(dump_file, "TIMESTEP"); expected = {"0", "10", "20", "25", "30", "35", "40", "50", "60"}; ASSERT_EQ(values.size(), expected.size()); - for (int i = 0; i < expected.size(); ++i) + for (std::size_t i = 0; i < expected.size(); ++i) ASSERT_THAT(values[i], Eq(expected[i])); delete_file(dump_file); @@ -897,7 +897,7 @@ TEST_F(DumpAtomTest, every) values = extract_items(dump_file, "TIMESTEP"); expected = {"1", "4", "25", "60", "70", "100"}; ASSERT_EQ(values.size(), expected.size()); - for (int i = 0; i < expected.size(); ++i) + for (std::size_t i = 0; i < expected.size(); ++i) ASSERT_THAT(values[i], Eq(expected[i])); delete_file(dump_file); @@ -919,7 +919,7 @@ TEST_F(DumpAtomTest, every_time) values = extract_items(dump_file, "TIMESTEP"); expected = {"0", "20", "40", "50", "60"}; ASSERT_EQ(values.size(), expected.size()); - for (int i = 0; i < expected.size(); ++i) + for (std::size_t i = 0; i < expected.size(); ++i) ASSERT_THAT(values[i], Eq(expected[i])); delete_file(dump_file); @@ -940,7 +940,7 @@ TEST_F(DumpAtomTest, header) values = extract_items(dump_file, "TIMESTEP"); expected = {"10", "20", "30", "40"}; ASSERT_EQ(values.size(), expected.size()); - for (int i = 0; i < expected.size(); ++i) + for (std::size_t i = 0; i < expected.size(); ++i) ASSERT_THAT(values[i], Eq(expected[i])); BEGIN_HIDE_OUTPUT(); diff --git a/unittest/formats/test_dump_atom_compressed.cpp b/unittest/formats/test_dump_atom_compressed.cpp index 419ad0eb81..ea240ef4e4 100644 --- a/unittest/formats/test_dump_atom_compressed.cpp +++ b/unittest/formats/test_dump_atom_compressed.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/formats/test_dump_cfg.cpp b/unittest/formats/test_dump_cfg.cpp index 2a295163ab..fe08485ac4 100644 --- a/unittest/formats/test_dump_cfg.cpp +++ b/unittest/formats/test_dump_cfg.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/formats/test_dump_cfg_compressed.cpp b/unittest/formats/test_dump_cfg_compressed.cpp index 29afec06ce..158e8926bf 100644 --- a/unittest/formats/test_dump_cfg_compressed.cpp +++ b/unittest/formats/test_dump_cfg_compressed.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/formats/test_dump_custom.cpp b/unittest/formats/test_dump_custom.cpp index 3649dcfb02..08d5d65695 100644 --- a/unittest/formats/test_dump_custom.cpp +++ b/unittest/formats/test_dump_custom.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/formats/test_dump_custom_compressed.cpp b/unittest/formats/test_dump_custom_compressed.cpp index fec751b358..91d72e4483 100644 --- a/unittest/formats/test_dump_custom_compressed.cpp +++ b/unittest/formats/test_dump_custom_compressed.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/formats/test_dump_local.cpp b/unittest/formats/test_dump_local.cpp index 5685504cab..d138ee3ac3 100644 --- a/unittest/formats/test_dump_local.cpp +++ b/unittest/formats/test_dump_local.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/formats/test_dump_local_compressed.cpp b/unittest/formats/test_dump_local_compressed.cpp index b1161927c6..8523e99a30 100644 --- a/unittest/formats/test_dump_local_compressed.cpp +++ b/unittest/formats/test_dump_local_compressed.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/formats/test_dump_netcdf.cpp b/unittest/formats/test_dump_netcdf.cpp index bf14f8aa54..879d332250 100644 --- a/unittest/formats/test_dump_netcdf.cpp +++ b/unittest/formats/test_dump_netcdf.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/formats/test_dump_xyz_compressed.cpp b/unittest/formats/test_dump_xyz_compressed.cpp index 7c5b816639..ec47f0e180 100644 --- a/unittest/formats/test_dump_xyz_compressed.cpp +++ b/unittest/formats/test_dump_xyz_compressed.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/formats/test_eim_potential_file_reader.cpp b/unittest/formats/test_eim_potential_file_reader.cpp index 532df11c3f..9cc67b4e6d 100644 --- a/unittest/formats/test_eim_potential_file_reader.cpp +++ b/unittest/formats/test_eim_potential_file_reader.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/formats/test_file_operations.cpp b/unittest/formats/test_file_operations.cpp index ef954b51f3..d48dee34b2 100644 --- a/unittest/formats/test_file_operations.cpp +++ b/unittest/formats/test_file_operations.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -303,6 +303,7 @@ TEST_F(FileOperationsTest, error_all_one) TEST_F(FileOperationsTest, write_restart) { + ASSERT_EQ(lmp->restart_ver, -1); BEGIN_HIDE_OUTPUT(); command("echo none"); END_HIDE_OUTPUT(); @@ -356,6 +357,7 @@ TEST_F(FileOperationsTest, write_restart) BEGIN_HIDE_OUTPUT(); command("clear"); END_HIDE_OUTPUT(); + ASSERT_EQ(lmp->restart_ver, -1); ASSERT_EQ(lmp->atom->natoms, 0); ASSERT_EQ(lmp->update->ntimestep, 0); ASSERT_EQ(lmp->domain->triclinic, 0); @@ -369,18 +371,21 @@ TEST_F(FileOperationsTest, write_restart) command("change_box all triclinic"); command("write_restart triclinic.restart"); END_HIDE_OUTPUT(); + ASSERT_EQ(lmp->restart_ver, lmp->num_ver); ASSERT_EQ(lmp->atom->natoms, 1); ASSERT_EQ(lmp->update->ntimestep, 333); ASSERT_EQ(lmp->domain->triclinic, 1); BEGIN_HIDE_OUTPUT(); command("clear"); END_HIDE_OUTPUT(); + ASSERT_EQ(lmp->restart_ver, -1); ASSERT_EQ(lmp->atom->natoms, 0); ASSERT_EQ(lmp->update->ntimestep, 0); ASSERT_EQ(lmp->domain->triclinic, 0); BEGIN_HIDE_OUTPUT(); command("read_restart triclinic.restart"); END_HIDE_OUTPUT(); + ASSERT_EQ(lmp->restart_ver, lmp->num_ver); ASSERT_EQ(lmp->atom->natoms, 1); ASSERT_EQ(lmp->update->ntimestep, 333); ASSERT_EQ(lmp->domain->triclinic, 1); @@ -464,6 +469,8 @@ TEST_F(FileOperationsTest, write_data) TEST_FAILURE(".*ERROR: Cannot open file noexist.data: No such file or directory.*", command("read_data noexist.data");); + TEST_FAILURE(".*ERROR: Unknown read_data keyword xxx.*", + command("read_data noexist.data xxx");); BEGIN_HIDE_OUTPUT(); command("pair_style zero 1.0"); @@ -496,6 +503,116 @@ TEST_F(FileOperationsTest, write_data) delete_file("triclinic.data"); } +#define GETIDX(i) lmp->atom->map(i) +TEST_F(FileOperationsTest, read_data_fix) +{ + ASSERT_EQ(lmp->restart_ver, -1); + BEGIN_HIDE_OUTPUT(); + command("echo none"); + command("atom_modify map array"); + command("fix MoleculeIDs all property/atom mol"); + command("region box block -2 2 -2 2 -2 2"); + command("create_box 1 box"); + command("create_atoms 1 single 1.0 0.0 0.0"); + command("create_atoms 1 single 0.0 1.0 0.0"); + command("create_atoms 1 single 1.0 0.0 1.0"); + command("create_atoms 1 single 0.0 1.0 1.0"); + command("mass 1 1.0"); + command("set atom 1*2 mol 1"); + command("set atom 3*4 mol 2"); + command("write_data test_mol_id.data"); + lmp->atom->molecule[0] = 5; + lmp->atom->molecule[1] = 6; + lmp->atom->molecule[2] = 5; + lmp->atom->molecule[3] = 6; + lmp->atom->tag[0] = 9; + lmp->atom->tag[1] = 6; + lmp->atom->tag[2] = 7; + lmp->atom->tag[3] = 8; + lmp->atom->map_init(1); + lmp->atom->map_set(); + command("write_data test_mol_id_merge.data"); + command("clear"); + END_HIDE_OUTPUT(); + TEST_FAILURE(".*ERROR: Cannot use read_data add before simulation box is defined.*", + command("read_data test_mol_id.data add append");); + + BEGIN_HIDE_OUTPUT(); + command("atom_modify map array"); + command("fix MoleculeIDs all property/atom mol"); + command("read_data test_mol_id.data fix MoleculeIDs NULL Molecules"); + command("read_data test_mol_id_merge.data add merge fix MoleculeIDs NULL Molecules"); + END_HIDE_OUTPUT(); + + EXPECT_EQ(lmp->atom->natoms, 8); + EXPECT_EQ(lmp->atom->molecule[GETIDX(1)], 1); + EXPECT_EQ(lmp->atom->molecule[GETIDX(2)], 1); + EXPECT_EQ(lmp->atom->molecule[GETIDX(3)], 2); + EXPECT_EQ(lmp->atom->molecule[GETIDX(4)], 2); + EXPECT_EQ(lmp->atom->molecule[GETIDX(6)], 6); + EXPECT_EQ(lmp->atom->molecule[GETIDX(7)], 5); + EXPECT_EQ(lmp->atom->molecule[GETIDX(8)], 6); + EXPECT_EQ(lmp->atom->molecule[GETIDX(9)], 5); + EXPECT_EQ(lmp->atom->tag[GETIDX(1)], 1); + EXPECT_EQ(lmp->atom->tag[GETIDX(2)], 2); + EXPECT_EQ(lmp->atom->tag[GETIDX(3)], 3); + EXPECT_EQ(lmp->atom->tag[GETIDX(4)], 4); + EXPECT_EQ(lmp->atom->tag[GETIDX(6)], 6); + EXPECT_EQ(lmp->atom->tag[GETIDX(7)], 7); + EXPECT_EQ(lmp->atom->tag[GETIDX(8)], 8); + EXPECT_EQ(lmp->atom->tag[GETIDX(9)], 9); + + BEGIN_HIDE_OUTPUT(); + command("clear"); + command("atom_modify map array"); + command("fix MoleculeIDs all property/atom mol"); + command("read_data test_mol_id.data fix MoleculeIDs NULL Molecules"); + command("read_data test_mol_id.data add append fix MoleculeIDs NULL Molecules"); + END_HIDE_OUTPUT(); + EXPECT_EQ(lmp->atom->natoms, 8); + EXPECT_EQ(lmp->atom->molecule[GETIDX(1)], 1); + EXPECT_EQ(lmp->atom->molecule[GETIDX(2)], 1); + EXPECT_EQ(lmp->atom->molecule[GETIDX(3)], 2); + EXPECT_EQ(lmp->atom->molecule[GETIDX(4)], 2); + EXPECT_EQ(lmp->atom->molecule[GETIDX(5)], 1); + EXPECT_EQ(lmp->atom->molecule[GETIDX(6)], 1); + EXPECT_EQ(lmp->atom->molecule[GETIDX(7)], 2); + EXPECT_EQ(lmp->atom->molecule[GETIDX(8)], 2); + EXPECT_EQ(lmp->atom->tag[GETIDX(1)], 1); + EXPECT_EQ(lmp->atom->tag[GETIDX(2)], 2); + EXPECT_EQ(lmp->atom->tag[GETIDX(3)], 3); + EXPECT_EQ(lmp->atom->tag[GETIDX(4)], 4); + EXPECT_EQ(lmp->atom->tag[GETIDX(5)], 5); + EXPECT_EQ(lmp->atom->tag[GETIDX(6)], 6); + EXPECT_EQ(lmp->atom->tag[GETIDX(7)], 7); + EXPECT_EQ(lmp->atom->tag[GETIDX(8)], 8); + + BEGIN_HIDE_OUTPUT(); + command("clear"); + command("atom_modify map array"); + command("fix MoleculeIDs all property/atom mol"); + command("read_data test_mol_id.data fix MoleculeIDs NULL Molecules"); + command("read_data test_mol_id.data add 6 4 fix MoleculeIDs NULL Molecules"); + END_HIDE_OUTPUT(); + EXPECT_EQ(lmp->atom->natoms, 8); + EXPECT_EQ(lmp->atom->molecule[GETIDX(1)], 1); + EXPECT_EQ(lmp->atom->molecule[GETIDX(2)], 1); + EXPECT_EQ(lmp->atom->molecule[GETIDX(3)], 2); + EXPECT_EQ(lmp->atom->molecule[GETIDX(4)], 2); + EXPECT_EQ(lmp->atom->molecule[GETIDX(7)], 1); + EXPECT_EQ(lmp->atom->molecule[GETIDX(8)], 1); + EXPECT_EQ(lmp->atom->molecule[GETIDX(9)], 2); + EXPECT_EQ(lmp->atom->molecule[GETIDX(10)], 2); + EXPECT_EQ(lmp->atom->tag[GETIDX(1)], 1); + EXPECT_EQ(lmp->atom->tag[GETIDX(2)], 2); + EXPECT_EQ(lmp->atom->tag[GETIDX(3)], 3); + EXPECT_EQ(lmp->atom->tag[GETIDX(4)], 4); + EXPECT_EQ(lmp->atom->tag[GETIDX(7)], 7); + EXPECT_EQ(lmp->atom->tag[GETIDX(8)], 8); + EXPECT_EQ(lmp->atom->tag[GETIDX(9)], 9); + EXPECT_EQ(lmp->atom->tag[GETIDX(10)], 10); +} + int main(int argc, char **argv) { MPI_Init(&argc, &argv); diff --git a/unittest/formats/test_image_flags.cpp b/unittest/formats/test_image_flags.cpp index 2486d49031..c915a27c3e 100644 --- a/unittest/formats/test_image_flags.cpp +++ b/unittest/formats/test_image_flags.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/formats/test_input_convert.cpp b/unittest/formats/test_input_convert.cpp index 5930824735..858275a76f 100644 --- a/unittest/formats/test_input_convert.cpp +++ b/unittest/formats/test_input_convert.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/formats/test_molecule_file.cpp b/unittest/formats/test_molecule_file.cpp index 1b67d1eec2..6940908109 100644 --- a/unittest/formats/test_molecule_file.cpp +++ b/unittest/formats/test_molecule_file.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/formats/test_pair_unit_convert.cpp b/unittest/formats/test_pair_unit_convert.cpp index e989f5c7f6..c4900076dc 100644 --- a/unittest/formats/test_pair_unit_convert.cpp +++ b/unittest/formats/test_pair_unit_convert.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/formats/test_potential_file_reader.cpp b/unittest/formats/test_potential_file_reader.cpp index 9e07bbc951..b19c4166a1 100644 --- a/unittest/formats/test_potential_file_reader.cpp +++ b/unittest/formats/test_potential_file_reader.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/formats/test_text_file_reader.cpp b/unittest/formats/test_text_file_reader.cpp index ba1218b069..3146740b3a 100644 --- a/unittest/formats/test_text_file_reader.cpp +++ b/unittest/formats/test_text_file_reader.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/fortran/CMakeLists.txt b/unittest/fortran/CMakeLists.txt index 70ab462053..cec38ae55c 100644 --- a/unittest/fortran/CMakeLists.txt +++ b/unittest/fortran/CMakeLists.txt @@ -14,70 +14,85 @@ if(CMAKE_Fortran_COMPILER) message(STATUS "Skipping Tests for the LAMMPS Fortran Module: cannot identify Fortran compiler") return() endif() - get_filename_component(LAMMPS_FORTRAN_MODULE ${LAMMPS_SOURCE_DIR}/../fortran/lammps.f90 ABSOLUTE) - if(BUILD_MPI) - find_package(MPI REQUIRED) - if((NOT MPI_Fortran_FOUND) OR (NOT MPI_Fortran_HAVE_F77_HEADER)) - message(STATUS "Skipping Tests for the LAMMPS Fortran Module: no MPI support for Fortran") - return() - endif() - else() - add_library(fmpi_stubs STATIC mpi_stubs.f90) - get_filename_component(_tmp_fc ${CMAKE_Fortran_COMPILER} NAME) - if (_tmp_fc STREQUAL "flang") - target_link_libraries(fmpi_stubs PUBLIC gfortran) - endif() - add_library(MPI::MPI_Fortran ALIAS fmpi_stubs) + # GNU Fortran 4.8.x on RHEL/CentOS 7.x is not sufficient to compile the Fortran module. Work around flang being detected as GNU + get_filename_component(_tmp_fc ${CMAKE_Fortran_COMPILER} NAME) + if((CMAKE_Fortran_COMPILER_ID STREQUAL "GNU") AND (CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 6.0) AND NOT (_tmp_fc STREQUAL "flang")) + message(FATAL_ERROR "Need GNU Fortran compiler version 6.x or later for unit testing") endif() + get_filename_component(LAMMPS_FORTRAN_MODULE ${LAMMPS_SOURCE_DIR}/../fortran/lammps.f90 ABSOLUTE) + add_library(flammps STATIC ${LAMMPS_FORTRAN_MODULE} keepstuff.f90) + get_filename_component(_tmp_fc ${CMAKE_Fortran_COMPILER} NAME) + if (_tmp_fc STREQUAL "flang") + target_link_libraries(flammps PUBLIC gfortran) + endif() add_executable(test_fortran_create wrap_create.cpp test_fortran_create.f90) - target_link_libraries(test_fortran_create PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTestMain) + target_link_libraries(test_fortran_create PRIVATE flammps lammps GTest::GTestMain) target_include_directories(test_fortran_create PRIVATE "${LAMMPS_SOURCE_DIR}/../fortran") add_test(NAME FortranOpen COMMAND test_fortran_create) add_executable(test_fortran_commands wrap_commands.cpp test_fortran_commands.f90) - target_link_libraries(test_fortran_commands PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTestMain) + target_link_libraries(test_fortran_commands PRIVATE flammps lammps GTest::GTestMain) add_test(NAME FortranCommands COMMAND test_fortran_commands) add_executable(test_fortran_get_thermo wrap_get_thermo.cpp test_fortran_get_thermo.f90) - target_link_libraries(test_fortran_get_thermo PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTestMain) + target_link_libraries(test_fortran_get_thermo PRIVATE flammps lammps GTest::GTestMain) add_test(NAME FortranGetThermo COMMAND test_fortran_get_thermo) add_executable(test_fortran_box wrap_box.cpp test_fortran_box.f90) - target_link_libraries(test_fortran_box PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTestMain) + target_link_libraries(test_fortran_box PRIVATE flammps lammps GTest::GTestMain) add_test(NAME FortranBox COMMAND test_fortran_box) add_executable(test_fortran_properties wrap_properties.cpp test_fortran_properties.f90 test_fortran_commands.f90) - target_link_libraries(test_fortran_properties PRIVATE flammps lammps MPI::MPI_Fortran GTest::GMockMain) + target_link_libraries(test_fortran_properties PRIVATE flammps lammps GTest::GMockMain) add_test(NAME FortranProperties COMMAND test_fortran_properties) add_executable(test_fortran_extract_global wrap_extract_global.cpp test_fortran_extract_global.f90) - target_link_libraries(test_fortran_extract_global PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTestMain) + target_link_libraries(test_fortran_extract_global PRIVATE flammps lammps GTest::GTestMain) add_test(NAME FortranExtractGlobal COMMAND test_fortran_extract_global) add_executable(test_fortran_extract_atom wrap_extract_atom.cpp test_fortran_extract_atom.f90) - target_link_libraries(test_fortran_extract_atom PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTestMain) + target_link_libraries(test_fortran_extract_atom PRIVATE flammps lammps GTest::GTestMain) add_test(NAME FortranExtractAtom COMMAND test_fortran_extract_atom) add_executable(test_fortran_extract_compute wrap_extract_compute.cpp test_fortran_extract_compute.f90) - target_link_libraries(test_fortran_extract_compute PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTestMain) + target_link_libraries(test_fortran_extract_compute PRIVATE flammps lammps GTest::GTestMain) add_test(NAME FortranExtractCompute COMMAND test_fortran_extract_compute) add_executable(test_fortran_extract_fix wrap_extract_fix.cpp test_fortran_extract_fix.f90) - target_link_libraries(test_fortran_extract_fix PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTestMain) + target_link_libraries(test_fortran_extract_fix PRIVATE flammps lammps GTest::GTestMain) add_test(NAME FortranExtractFix COMMAND test_fortran_extract_fix) add_executable(test_fortran_extract_variable wrap_extract_variable.cpp test_fortran_extract_variable.f90) target_compile_definitions(test_fortran_extract_variable PRIVATE -DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR}) - target_link_libraries(test_fortran_extract_variable PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTestMain) + target_link_libraries(test_fortran_extract_variable PRIVATE flammps lammps GTest::GTestMain) add_test(NAME FortranExtractVariable COMMAND test_fortran_extract_variable) add_executable(test_fortran_gather_scatter wrap_gather_scatter.cpp test_fortran_gather_scatter.f90) - target_link_libraries(test_fortran_gather_scatter PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTestMain) + target_link_libraries(test_fortran_gather_scatter PRIVATE flammps lammps GTest::GTestMain) add_test(NAME FortranGatherScatter COMMAND test_fortran_gather_scatter) + add_executable(test_fortran_create_atoms wrap_create_atoms.cpp test_fortran_create_atoms.f90) + target_link_libraries(test_fortran_create_atoms PRIVATE flammps lammps GTest::GTestMain) + add_test(NAME FortranCreateAtoms COMMAND test_fortran_create_atoms) + + add_executable(test_fortran_configuration wrap_configuration.cpp test_fortran_configuration.f90 test_fortran_commands.f90) + target_link_libraries(test_fortran_configuration PRIVATE flammps lammps GTest::GMockMain) + add_test(NAME FortranConfiguration COMMAND test_fortran_configuration) + + add_executable(test_fortran_neighlist wrap_neighlist.cpp test_fortran_neighlist.f90) + target_link_libraries(test_fortran_neighlist PRIVATE flammps lammps GTest::GMockMain) + add_test(NAME FortranNeighlist COMMAND test_fortran_neighlist) + + # gfortran from GCC 9 on ubuntu has an ICE compiling this test. + if ((CMAKE_Fortran_COMPILER_ID STREQUAL "GNU") AND (CMAKE_Fortran_COMPILER_VERSION VERSION_GREATER 9.9)) + add_executable(test_fortran_fixexternal wrap_fixexternal.cpp test_fortran_fixexternal.f90) + target_link_libraries(test_fortran_fixexternal PRIVATE flammps lammps GTest::GMockMain) + add_test(NAME FortranFixExternal COMMAND test_fortran_fixexternal) + endif() + else() message(STATUS "Skipping Tests for the LAMMPS Fortran Module: no Fortran compiler") endif() diff --git a/unittest/fortran/keepstuff.f90 b/unittest/fortran/keepstuff.f90 index 6838d78955..63184e1006 100644 --- a/unittest/fortran/keepstuff.f90 +++ b/unittest/fortran/keepstuff.f90 @@ -1,8 +1,8 @@ MODULE keepstuff - USE liblammps + USE LIBLAMMPS IMPLICIT NONE - TYPE(LAMMPS) :: lmp - INTEGER :: mycomm + TYPE(LAMMPS), SAVE :: lmp + INTEGER, SAVE :: mycomm CHARACTER(LEN=40), DIMENSION(3), PARAMETER :: demo_input = & [ CHARACTER(LEN=40) :: & 'region box block 0 $x 0 2 0 2', & @@ -24,5 +24,43 @@ MODULE keepstuff 'pair_style lj/cut 2.5', & 'pair_coeff 1 1 1.0 1.0', & 'mass 1 2.0' ] + + INTERFACE + FUNCTION c_strlen(str) BIND(C,name='strlen') + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr, c_size_t + IMPLICIT NONE + TYPE(c_ptr), INTENT(IN), VALUE :: str + INTEGER(c_size_t) :: c_strlen + END FUNCTION c_strlen + END INTERFACE + +CONTAINS + + FUNCTION f2c_string(f_string) RESULT(ptr) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_char, c_ptr, c_size_t, & + c_null_char, C_F_POINTER + CHARACTER(LEN=*), INTENT(IN) :: f_string + CHARACTER(LEN=1, KIND=c_char), POINTER :: c_string(:) + TYPE(c_ptr) :: ptr + INTEGER(c_size_t) :: i, n + + INTERFACE + FUNCTION lammps_malloc(size) BIND(C, name='malloc') + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr, c_size_t + IMPLICIT NONE + INTEGER(c_size_t), VALUE :: size + TYPE(c_ptr) :: lammps_malloc + END FUNCTION lammps_malloc + END INTERFACE + + n = LEN_TRIM(f_string) + ptr = lammps_malloc(n+1) + CALL C_F_POINTER(ptr, c_string, [1]) + DO i=1, n + c_string(i) = f_string(i:i) + END DO + c_string(n+1) = c_null_char + END FUNCTION f2c_string + END MODULE keepstuff diff --git a/unittest/fortran/mpi_stubs.f90 b/unittest/fortran/mpi_stubs.f90 deleted file mode 100644 index 8601f436d2..0000000000 --- a/unittest/fortran/mpi_stubs.f90 +++ /dev/null @@ -1,20 +0,0 @@ -MODULE MPI - IMPLICIT NONE - PRIVATE - - INTEGER, PARAMETER :: MPI_COMM_WORLD=0 - INTEGER, PARAMETER :: MPI_SUCCESS=0 - - PUBLIC :: MPI_COMM_WORLD, MPI_SUCCESS, & - mpi_comm_split - -CONTAINS - - SUBROUTINE mpi_comm_split(comm,color,key,newcomm,ierr) - INTEGER, INTENT(in) :: comm,color,key - INTEGER, INTENT(out) :: newcomm,ierr - - newcomm = comm + 1 - ierr = 0 - END SUBROUTINE mpi_comm_split -END MODULE MPI diff --git a/unittest/fortran/test_fortran_configuration.f90 b/unittest/fortran/test_fortran_configuration.f90 new file mode 100644 index 0000000000..a3ccb876ec --- /dev/null +++ b/unittest/fortran/test_fortran_configuration.f90 @@ -0,0 +1,470 @@ +FUNCTION f_lammps_version() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int) :: f_lammps_version + + f_lammps_version = lmp%version() +END FUNCTION f_lammps_version + +FUNCTION f_lammps_os_info(ptr) BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr, c_char, c_int, c_size_t, & + C_F_POINTER + USE LIBLAMMPS + USE keepstuff, ONLY : lmp, c_strlen + IMPLICIT NONE + TYPE(c_ptr), INTENT(IN), VALUE :: ptr + INTEGER(c_int) :: f_lammps_os_info + CHARACTER(LEN=:), ALLOCATABLE :: string, os_info + CHARACTER(LEN=1, KIND=c_char), POINTER :: C_string(:) + INTEGER(c_size_t) :: length, i + + length = c_strlen(ptr) + CALL C_F_POINTER(ptr, C_string, [length]) + ALLOCATE(CHARACTER(LEN=length) :: string) + DO i = 1, length + string(i:i) = C_string(i) + END DO + + ALLOCATE(CHARACTER(LEN=1000) :: os_info) + CALL lmp%get_os_info(os_info) + os_info = TRIM(os_info) + + IF (os_info(1:length) == string) THEN + f_lammps_os_info = 1_c_int + ELSE + f_lammps_os_info = 0_c_int + END IF +END FUNCTION f_lammps_os_info + +FUNCTION f_lammps_mpi_support() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int) :: f_lammps_mpi_support + + IF (lmp%config_has_mpi_support()) THEN + f_lammps_mpi_support = 1_c_int + ELSE + f_lammps_mpi_support = 0_c_int + END IF +END FUNCTION f_lammps_mpi_support + +FUNCTION f_lammps_gzip_support() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int) :: f_lammps_gzip_support + + IF (lmp%config_has_gzip_support()) THEN + f_lammps_gzip_support = 1_c_int + ELSE + f_lammps_gzip_support = 0_c_int + END IF +END FUNCTION f_lammps_gzip_support + +FUNCTION f_lammps_png_support() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int) :: f_lammps_png_support + + IF (lmp%config_has_png_support()) THEN + f_lammps_png_support = 1_c_int + ELSE + f_lammps_png_support = 0_c_int + END IF +END FUNCTION f_lammps_png_support + +FUNCTION f_lammps_jpeg_support() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int) :: f_lammps_jpeg_support + + IF (lmp%config_has_jpeg_support()) THEN + f_lammps_jpeg_support = 1_c_int + ELSE + f_lammps_jpeg_support = 0_c_int + END IF +END FUNCTION f_lammps_jpeg_support + +FUNCTION f_lammps_ffmpeg_support() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int) :: f_lammps_ffmpeg_support + + IF (lmp%config_has_ffmpeg_support()) THEN + f_lammps_ffmpeg_support = 1_c_int + ELSE + f_lammps_ffmpeg_support = 0_c_int + END IF +END FUNCTION f_lammps_ffmpeg_support + +FUNCTION f_lammps_has_exceptions() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int) :: f_lammps_has_exceptions + + IF (lmp%config_has_exceptions()) THEN + f_lammps_has_exceptions = 1_c_int + ELSE + f_lammps_has_exceptions = 0_c_int + END IF +END FUNCTION f_lammps_has_exceptions + +FUNCTION f_lammps_has_package(Cname) BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_size_t, c_ptr, c_char, & + C_F_POINTER + USE LIBLAMMPS + USE keepstuff, ONLY : lmp, c_strlen + IMPLICIT NONE + TYPE(c_ptr), VALUE :: Cname + INTEGER(c_int) :: f_lammps_has_package + CHARACTER(LEN=1,KIND=c_char), DIMENSION(:), POINTER :: Fname + CHARACTER(LEN=:), ALLOCATABLE :: name + INTEGER(c_size_t) :: length, i + + length = c_strlen(Cname) + CALL C_F_POINTER(Cname, Fname, [length]) + ALLOCATE(CHARACTER(LEN=length) :: name) + DO i = 1, length + name(i:i) = Fname(i) + END DO + IF (lmp%config_has_package(name)) THEN + f_lammps_has_package = 1_c_int + ELSE + f_lammps_has_package = 0_c_int + END IF +END FUNCTION f_lammps_has_package + +FUNCTION f_lammps_package_count() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int) :: f_lammps_package_count + + f_lammps_package_count = lmp%config_package_count() +END FUNCTION f_lammps_package_count + +FUNCTION f_lammps_package_name(idx) BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr, c_null_ptr, c_int + USE keepstuff, ONLY : lmp, f2c_string + IMPLICIT NONE + INTEGER(c_int), VALUE :: idx + TYPE(c_ptr) :: f_lammps_package_name + CHARACTER(LEN=80) :: buffer + + CALL lmp%config_package_name(idx, buffer) + IF (LEN_TRIM(buffer) > 0) THEN + f_lammps_package_name = f2c_string(buffer) + ELSE + f_lammps_package_name = c_null_ptr + END IF +END FUNCTION f_lammps_package_name + +FUNCTION f_lammps_installed_packages(idx) BIND(C) RESULT(package) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_ptr, c_null_ptr + USE keepstuff, ONLY : lmp, f2c_string + IMPLICIT NONE + INTEGER(c_int), INTENT(IN), VALUE :: idx + TYPE(c_ptr) :: package + CHARACTER(LEN=:), DIMENSION(:), ALLOCATABLE :: all_packages + + CALL lmp%installed_packages(all_packages) + + IF (idx > SIZE(all_packages) .OR. idx <= 0) THEN + package = c_null_ptr + ELSE + package = f2c_string(all_packages(idx)) + END IF +END FUNCTION f_lammps_installed_packages + +FUNCTION f_lammps_config_accelerator(package, category, setting) BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_ptr, c_size_t, c_char, & + C_F_POINTER + USE keepstuff, ONLY : lmp, c_strlen + USE LIBLAMMPS + IMPLICIT NONE + TYPE(c_ptr), VALUE :: package, category, setting + INTEGER(c_int) :: f_lammps_config_accelerator + INTEGER(c_size_t) :: len_package, len_category, len_setting, i + CHARACTER(LEN=1,KIND=c_char), POINTER :: Cpackage(:),Ccategory(:),Csetting(:) + CHARACTER(LEN=:), ALLOCATABLE :: Fpackage, Fcategory, Fsetting + LOGICAL :: configured + + len_package = c_strlen(package) + len_category = c_strlen(category) + len_setting = c_strlen(setting) + ALLOCATE(CHARACTER(LEN=len_package) :: Fpackage) + ALLOCATE(CHARACTER(LEN=len_category) :: Fcategory) + ALLOCATE(CHARACTER(LEN=len_setting) :: Fsetting) + CALL C_F_POINTER(package, Cpackage, [len_package]) + CALL C_F_POINTER(category, Ccategory, [len_category]) + CALL C_F_POINTER(setting, Csetting, [len_setting]) + DO i = 1, len_package + Fpackage(i:i) = Cpackage(i) + END DO + DO i = 1, len_category + Fcategory(i:i) = Ccategory(i) + END DO + DO i = 1, len_setting + Fsetting(i:i) = Csetting(i) + END DO + + configured = lmp%config_accelerator(Fpackage, Fcategory, Fsetting) + + IF (configured) THEN + f_lammps_config_accelerator = 1_c_int + ELSE + f_lammps_config_accelerator = 0_c_int + END IF + +END FUNCTION f_lammps_config_accelerator + +FUNCTION f_lammps_has_gpu() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int) :: f_lammps_has_gpu + + IF (lmp%has_gpu_device()) THEN + f_lammps_has_gpu = 1_c_int + ELSE + f_lammps_has_gpu = 0_c_int + END IF +END FUNCTION f_lammps_has_gpu + +FUNCTION f_lammps_get_gpu_info(buf_size) RESULT(info) BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_size_t, c_ptr + USE keepstuff, ONLY : lmp, f2c_string + IMPLICIT NONE + INTEGER(c_size_t), VALUE :: buf_size + TYPE(c_ptr) :: info + CHARACTER(LEN=buf_size) :: string + + CALL lmp%get_gpu_device_info(string) + info = f2c_string(string) +END FUNCTION f_lammps_get_gpu_info + +FUNCTION f_lammps_has_style(Ccategory, Cname) BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_size_t, c_ptr, c_char, c_int, & + C_F_POINTER + USE keepstuff, ONLY : lmp, c_strlen + IMPLICIT NONE + TYPE(c_ptr), INTENT(IN), VALUE :: Ccategory, Cname + INTEGER(c_int) :: f_lammps_has_style + CHARACTER(LEN=1,KIND=c_char), DIMENSION(:), POINTER :: Fcategory, Fname + INTEGER(c_size_t) :: category_len, name_len, i + CHARACTER(LEN=:), ALLOCATABLE :: category, name + + category_len = c_strlen(Ccategory) + name_len = c_strlen(Cname) + CALL C_F_POINTER(Ccategory, Fcategory, [category_len]) + CALL C_F_POINTER(Cname, Fname, [name_len]) + ALLOCATE(CHARACTER(LEN=category_len) :: category) + ALLOCATE(CHARACTER(LEN=name_len) :: name) + DO i = 1, category_len + category(i:i) = Fcategory(i) + END DO + DO i = 1, name_len + name(i:i) = Fname(i) + END DO + IF (lmp%has_style(category, name)) THEN + f_lammps_has_style = 1_c_int + ELSE + f_lammps_has_style = 0_c_int + END IF +END FUNCTION f_lammps_has_style + +FUNCTION f_lammps_style_count(ptr) BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr, c_int, c_char, c_size_t, & + C_F_POINTER + USE LIBLAMMPS + USE keepstuff, ONLY : lmp, c_strlen + IMPLICIT NONE + TYPE(c_ptr), VALUE :: ptr + INTEGER(c_int) :: f_lammps_style_count + CHARACTER(LEN=1, KIND=c_char), DIMENSION(:), POINTER :: C_category + INTEGER(c_size_t) :: length, i + CHARACTER(LEN=:), ALLOCATABLE :: category + + length = c_strlen(ptr) + CALL C_F_POINTER(ptr, C_category, [length]) + ALLOCATE(CHARACTER(LEN=length) :: category) + DO i = 1, length + category(i:i) = C_category(i) + END DO + f_lammps_style_count = lmp%style_count(category) +END FUNCTION f_lammps_style_count + +FUNCTION f_lammps_style_name(category_ptr, idx) BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr, c_int, c_char, c_size_t, & + C_F_POINTER + USE LIBLAMMPS + USE keepstuff, ONLY : lmp, c_strlen, f2c_string + IMPLICIT NONE + TYPE(c_ptr), INTENT(IN), VALUE :: category_ptr + INTEGER(c_int), INTENT(IN), VALUE :: idx + TYPE(c_ptr) :: f_lammps_style_name + CHARACTER(LEN=1, KIND=c_char), DIMENSION(:), POINTER :: C_category + INTEGER(c_size_t) :: length, i + CHARACTER(LEN=:), ALLOCATABLE :: category + CHARACTER(LEN=100) :: buffer + + length = c_strlen(category_ptr) + CALL C_F_POINTER(category_ptr, C_category, [length]) + ALLOCATE(CHARACTER(LEN=length) :: category) + DO i = 1, length + category(i:i) = C_category(i) + END DO + CALL lmp%style_name(category, idx, buffer) + f_lammps_style_name = f2c_string(buffer) +END FUNCTION f_lammps_style_name + +SUBROUTINE f_setup_has_id() BIND(C) + USE keepstuff, ONLY : lmp + IMPLICIT NONE + CHARACTER(LEN=100), DIMENSION(14), PARAMETER :: setup_commands = & + [CHARACTER(LEN=100) :: 'units lj', & + 'region simbox block 0 2 0 3 0 4 units box', & + 'create_box 1 simbox', & + 'create_atoms 1 single 0.01 0.01 0.01 units box', & + 'create_atoms 1 single 1.0 1.0 1.0 units box', & + 'pair_style lj/cut 2.5', & + 'pair_coeff * * 1.0 1.0', & + 'mass * 1.0', & + 'compute COM all com', & + 'dump 1 all atom 1000 dump.tmp', & + 'fix 1 all nve', & + 'group one id 1', & + 'variable pi equal acos(-1)', & + 'run 0' & + ] + + CALL lmp%commands_list(setup_commands) +END SUBROUTINE + +FUNCTION f_lammps_has_id(Ccategory, Cname) BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr, c_int, c_size_t, c_char, & + C_F_POINTER + USE keepstuff, ONLY : lmp, c_strlen + IMPLICIT NONE + TYPE(c_ptr), VALUE :: Ccategory, Cname + INTEGER(c_int) :: f_lammps_has_id + INTEGER(c_size_t) :: len_cat, len_name, i + CHARACTER(LEN=:), ALLOCATABLE :: category, name + CHARACTER(LEN=1, KIND=c_char), DIMENSION(:), POINTER :: Fcategory, Fname + LOGICAL :: has_id + + len_cat = c_strlen(Ccategory) + len_name = c_strlen(Cname) + CALL C_F_POINTER(Ccategory, Fcategory, [len_cat]) + CALL C_F_POINTER(Cname, Fname, [len_name]) + ALLOCATE(CHARACTER(LEN=len_cat) :: category) + ALLOCATE(CHARACTER(LEN=len_name) :: name) + DO i = 1, len_cat + category(i:i) = Fcategory(i) + END DO + DO i = 1, len_name + name(i:i) = Fname(i) + END DO + has_id = lmp%has_id(category, name) + IF (has_id) THEN + f_lammps_has_id = 1_c_int + ELSE + f_lammps_has_id = 0_c_int + END IF +END FUNCTION f_lammps_has_id + +FUNCTION f_lammps_id_count(Ccategory) BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr, c_int, c_size_t, c_char, & + C_F_POINTER + USE keepstuff, ONLY : lmp, c_strlen + IMPLICIT NONE + TYPE(c_ptr), VALUE :: Ccategory + INTEGER(c_int) :: f_lammps_id_count + INTEGER(c_size_t) :: len_cat, i + CHARACTER(LEN=:), ALLOCATABLE :: category + CHARACTER(LEN=1, KIND=c_char), DIMENSION(:), POINTER :: Fcategory + + len_cat = c_strlen(Ccategory) + CALL C_F_POINTER(Ccategory, Fcategory, [len_cat]) + ALLOCATE(CHARACTER(LEN=len_cat) :: category) + DO i = 1, len_cat + category(i:i) = Fcategory(i) + END DO + f_lammps_id_count = lmp%id_count(category) +END FUNCTION f_lammps_id_count + +FUNCTION f_lammps_id_name(Ccategory, idx) BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr, c_int, c_size_t, c_char, & + C_F_POINTER + USE keepstuff, ONLY : lmp, c_strlen, f2c_string + IMPLICIT NONE + TYPE(c_ptr), VALUE :: Ccategory + INTEGER(c_int), VALUE :: idx + TYPE(c_ptr) :: f_lammps_id_name + INTEGER(c_size_t) :: len_cat, i + CHARACTER(LEN=:), ALLOCATABLE :: category + CHARACTER(LEN=1, KIND=c_char), DIMENSION(:), POINTER :: Fcategory + CHARACTER(LEN=100) :: buffer + + len_cat = c_strlen(Ccategory) + CALL C_F_POINTER(Ccategory, Fcategory, [len_cat]) + ALLOCATE(CHARACTER(LEN=len_cat) :: category) + DO i = 1, len_cat + category(i:i) = Fcategory(i) + END DO + CALL lmp%id_name(category, idx, buffer) + f_lammps_id_name = f2c_string(buffer) +END FUNCTION f_lammps_id_name + +FUNCTION f_lammps_plugin_count() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int + USE keepstuff, ONLY : lmp + INTEGER(c_int) :: f_lammps_plugin_count + + f_lammps_plugin_count = lmp%plugin_count(); +END FUNCTION f_lammps_plugin_count + +FUNCTION f_lammps_plugin_name(idx, Cstyle, Cname) BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr, c_int, c_size_t, c_char, & + C_F_POINTER + USE keepstuff, ONLY : lmp, c_strlen, f2c_string + IMPLICIT NONE + INTEGER(c_int), INTENT(IN), VALUE :: idx + TYPE(c_ptr), INTENT(IN), VALUE :: Cstyle, Cname + CHARACTER(LEN=1, KIND=c_char), DIMENSION(:), POINTER :: Fstyle, Fname + INTEGER(c_int) :: f_lammps_plugin_name + CHARACTER(LEN=100) :: style, name + INTEGER(c_size_t) :: len_style, len_name, i + LOGICAL :: all_are_identical + + CALL lmp%plugin_name(idx, style, name) + len_style = c_strlen(Cstyle) + len_name = c_strlen(Cname) + CALL C_F_POINTER(Cstyle, Fstyle, [len_style]) + CALL C_F_POINTER(Cname, Fname, [len_name]) + all_are_identical = .TRUE. + DO i = 1, len_style + all_are_identical = all_are_identical .AND. (style(i:i) == Fstyle(i)) + END DO + DO i = 1, len_name + all_are_identical = all_are_identical .AND. (name(i:i) == Fname(i)) + END DO + IF (all_are_identical) THEN + f_lammps_plugin_name = 1_c_int + ELSE + f_lammps_plugin_name = 0_c_int + END IF +END FUNCTION f_lammps_plugin_name diff --git a/unittest/fortran/test_fortran_create.f90 b/unittest/fortran/test_fortran_create.f90 index 4ea2a33cfe..fed67064f0 100644 --- a/unittest/fortran/test_fortran_create.f90 +++ b/unittest/fortran/test_fortran_create.f90 @@ -1,3 +1,20 @@ +MODULE MYMPI + USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_int + + IMPLICIT NONE + PRIVATE + PUBLIC :: lmp_comm_split + + INTERFACE + FUNCTION lmp_comm_split(color, key) BIND(C,name='create_mpi_comm_split') + IMPORT :: c_int + IMPLICIT NONE + INTEGER(c_int), VALUE, INTENT(IN) :: color, key + INTEGER(c_int) :: lmp_comm_split + END FUNCTION lmp_comm_split + END INTERFACE +END MODULE MYMPI + FUNCTION f_lammps_no_mpi_no_args() BIND(C, name="f_lammps_no_mpi_no_args") USE ISO_C_BINDING, ONLY: c_ptr USE liblammps @@ -25,35 +42,35 @@ END FUNCTION f_lammps_no_mpi_with_args FUNCTION f_lammps_open_no_args() BIND(C, name="f_lammps_open_no_args") USE ISO_C_BINDING, ONLY: c_ptr - USE MPI, ONLY: MPI_COMM_WORLD, mpi_comm_split + USE MYMPI, ONLY: lmp_comm_split USE liblammps USE keepstuff, ONLY: lmp,mycomm IMPLICIT NONE TYPE(c_ptr) :: f_lammps_open_no_args - INTEGER :: color, key, ierr + INTEGER :: color, key color = 1 key = 1 - CALL mpi_comm_split(MPI_COMM_WORLD, color, key, mycomm, ierr) + mycomm = lmp_comm_split(color, key) lmp = lammps(comm=mycomm) f_lammps_open_no_args = lmp%handle END FUNCTION f_lammps_open_no_args FUNCTION f_lammps_open_with_args() BIND(C, name="f_lammps_open_with_args") USE ISO_C_BINDING, ONLY: c_ptr - USE MPI, ONLY: MPI_COMM_WORLD, mpi_comm_split + USE MYMPI, ONLY: lmp_comm_split USE liblammps USE keepstuff, ONLY: lmp,mycomm IMPLICIT NONE TYPE(c_ptr) :: f_lammps_open_with_args - INTEGER :: color, key, ierr + INTEGER :: color, key CHARACTER(len=12), DIMENSION(4), PARAMETER :: args = & [ CHARACTER(len=12) :: 'liblammps', '-log', 'none', '-nocite' ] color = 2 key = 1 - CALL mpi_comm_split(MPI_COMM_WORLD, color, key, mycomm, ierr) + mycomm = lmp_comm_split(color, key) lmp = lammps(args,mycomm) f_lammps_open_with_args = lmp%handle END FUNCTION f_lammps_open_with_args diff --git a/unittest/fortran/test_fortran_create_atoms.f90 b/unittest/fortran/test_fortran_create_atoms.f90 new file mode 100644 index 0000000000..0a81bb39d7 --- /dev/null +++ b/unittest/fortran/test_fortran_create_atoms.f90 @@ -0,0 +1,157 @@ +FUNCTION f_lammps_with_args() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_ptr + USE LIBLAMMPS + USE keepstuff, ONLY: lmp + IMPLICIT NONE + TYPE(c_ptr) :: f_lammps_with_args + CHARACTER(len=12), DIMENSION(12), PARAMETER :: args = & + [ CHARACTER(len=12) :: 'liblammps', '-log', 'none', & + '-echo','screen','-nocite','-var','zpos','1.5','-var','x','2'] + + lmp = lammps(args) + f_lammps_with_args = lmp%handle +END FUNCTION f_lammps_with_args + +SUBROUTINE f_lammps_close() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_null_ptr + USE liblammps + USE keepstuff, ONLY: lmp + IMPLICIT NONE + + CALL lmp%close() + lmp%handle = c_null_ptr +END SUBROUTINE f_lammps_close + +SUBROUTINE f_lammps_setup_create_atoms() BIND(C) + USE LIBLAMMPS + USE keepstuff, ONLY : lmp, big_input, cont_input, more_input + IMPLICIT NONE + + !CALL lmp%command('atom_modify map array') + CALL lmp%commands_list(big_input) + CALL lmp%commands_list(cont_input) + CALL lmp%commands_list(more_input) +END SUBROUTINE f_lammps_setup_create_atoms + +SUBROUTINE f_lammps_create_three_atoms() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_double, c_int, c_int64_t + USE keepstuff, ONLY : lmp + USE LIBLAMMPS + IMPLICIT NONE + INTEGER(c_int), DIMENSION(3) :: new_ids, new_images, new_types + INTEGER(c_int64_t), DIMENSION(3) :: new_big_ids, new_big_images + REAL(c_double), DIMENSION(9) :: new_x, new_v + LOGICAL :: wrap + INTEGER(c_int) :: tagint_size + + new_ids = [4, 6, 5] + new_big_ids = [4, 6, 5] + tagint_size = lmp%extract_setting('tagint') + IF ( tagint_size == 4_c_int ) THEN + new_images(1) = lmp%encode_image_flags(1, -1, 3) + new_images(2) = lmp%encode_image_flags(-2, 0, 0) + new_images(3) = lmp%encode_image_flags(-2, -2, 1) + ELSE + new_big_images(1) = lmp%encode_image_flags(1, -1, 3) + new_big_images(2) = lmp%encode_image_flags(-2, 0, 0) + new_big_images(3) = lmp%encode_image_flags(-2, -2, 1) + END IF + new_types = [1, 1, 1] + new_x = [ 1.0_c_double, 1.8_c_double, 2.718281828_c_double, & + 0.6_c_double, 0.8_c_double, 2.2_c_double, & + 1.8_c_double, 0.1_c_double, 1.8_c_double ] + new_v = [ 0.0_c_double, 1.0_c_double, -1.0_c_double, & + 0.1_c_double, 0.2_c_double, -0.2_c_double, & + 1.0_c_double, -1.0_c_double, 3.0_c_double ] + wrap = .FALSE. + IF ( tagint_size == 4_c_int ) THEN + CALL lmp%create_atoms(new_ids, new_types, new_x, new_v, new_images, wrap) + ELSE + CALL lmp%create_atoms(new_big_ids, new_types, new_x, new_v, & + new_big_images, wrap) + END IF +END SUBROUTINE f_lammps_create_three_atoms + +SUBROUTINE f_lammps_create_two_more() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_double, c_int + USE keepstuff, ONLY : lmp + USE LIBLAMMPS + IMPLICIT NONE + INTEGER(c_int), DIMENSION(2) :: new_types + REAL(c_double), DIMENSION(6) :: new_x + + new_types = [1_c_int, 1_c_int] + new_x = [0.1_c_double, 1.9_c_double, 3.8_c_double, & + 1.2_c_double, 2.1_c_double, 1.25_c_double] + CALL lmp%create_atoms(type=new_types, x=new_x) +END SUBROUTINE f_lammps_create_two_more + +SUBROUTINE f_lammps_create_two_more_small() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_double, c_int + USE keepstuff, ONLY : lmp + USE LIBLAMMPS + IMPLICIT NONE + INTEGER(c_int), DIMENSION(2) :: new_types + REAL(c_double), DIMENSION(6) :: new_x + INTEGER(c_int), DIMENSION(2) :: new_id, new_image + + new_types = [1_c_int, 1_c_int] + new_x = [0.1_c_double, 1.9_c_double, 3.8_c_double, & + 1.2_c_double, 2.1_c_double, 1.25_c_double] + new_id = [8_c_int, 7_c_int] + new_image(1) = lmp%encode_image_flags(1,0,0) + new_image(2) = lmp%encode_image_flags(-1,0,0) + CALL lmp%create_atoms(id=new_id, image=new_image, type=new_types, x=new_x) +END SUBROUTINE f_lammps_create_two_more_small + +SUBROUTINE f_lammps_create_two_more_big() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_double, c_int, c_int64_t + USE keepstuff, ONLY : lmp + USE LIBLAMMPS + IMPLICIT NONE + INTEGER(c_int), DIMENSION(2) :: new_types + REAL(c_double), DIMENSION(6) :: new_x + INTEGER(c_int64_t), DIMENSION(2) :: new_id, new_image + + new_types = [1_c_int, 1_c_int] + new_x = [0.1_c_double, 1.9_c_double, 3.8_c_double, & + 1.2_c_double, 2.1_c_double, 1.25_c_double] + new_id = [8_c_int64_t, 7_c_int64_t] + new_image(1) = lmp%encode_image_flags(1,0,0) + new_image(2) = lmp%encode_image_flags(-1,0,0) + CALL lmp%create_atoms(id=new_id, image=new_image, type=new_types, x=new_x) +END SUBROUTINE f_lammps_create_two_more_big + +SUBROUTINE f_lammps_create_two_more_small2() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_double, c_int + USE keepstuff, ONLY : lmp + USE LIBLAMMPS + IMPLICIT NONE + INTEGER(c_int), DIMENSION(2) :: new_types + REAL(c_double), DIMENSION(6) :: new_x + INTEGER(c_int), DIMENSION(2) :: new_id + + new_types = [1_c_int, 1_c_int] + new_x = [0.1_c_double, 1.9_c_double, 3.8_c_double, & + 1.2_c_double, 2.1_c_double, 1.25_c_double] + new_id = [8_c_int, 7_c_int] + CALL lmp%create_atoms(id=new_id, type=new_types, x=new_x) +END SUBROUTINE f_lammps_create_two_more_small2 + +SUBROUTINE f_lammps_create_two_more_big2() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_double, c_int, c_int64_t + USE keepstuff, ONLY : lmp + USE LIBLAMMPS + IMPLICIT NONE + INTEGER(c_int), DIMENSION(2) :: new_types + REAL(c_double), DIMENSION(6) :: new_x + INTEGER(c_int64_t), DIMENSION(2) :: new_id + + new_types = [1_c_int, 1_c_int] + new_x = [0.1_c_double, 1.9_c_double, 3.8_c_double, & + 1.2_c_double, 2.1_c_double, 1.25_c_double] + new_id = [8_c_int64_t, 7_c_int64_t] + CALL lmp%create_atoms(id=new_id, type=new_types, x=new_x) +END SUBROUTINE f_lammps_create_two_more_big2 + +! vim: ts=2 sts=2 sw=2 et diff --git a/unittest/fortran/test_fortran_extract_variable.f90 b/unittest/fortran/test_fortran_extract_variable.f90 index c10e3eaa04..b4b5ab8727 100644 --- a/unittest/fortran/test_fortran_extract_variable.f90 +++ b/unittest/fortran/test_fortran_extract_variable.f90 @@ -10,13 +10,6 @@ MODULE keepvar TYPE(c_ptr) :: c_path_join END FUNCTION c_path_join - FUNCTION c_strlen(str) BIND(C,name='strlen') - IMPORT :: c_ptr, c_size_t - IMPLICIT NONE - TYPE(c_ptr), INTENT(IN), VALUE :: str - INTEGER(c_size_t) :: c_strlen - END FUNCTION c_strlen - SUBROUTINE c_free(ptr) BIND(C,name='free') IMPORT :: c_ptr TYPE(c_ptr), VALUE :: ptr @@ -27,7 +20,7 @@ CONTAINS FUNCTION absolute_path(filename) USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr, c_size_t, c_char, C_F_POINTER - USE keepstuff, ONLY : lmp + USE keepstuff, ONLY : lmp, f2c_string, c_strlen CHARACTER(LEN=:), ALLOCATABLE :: absolute_path CHARACTER(LEN=*), INTENT(IN) :: filename CHARACTER(LEN=256) :: test_input_directory @@ -50,38 +43,12 @@ CONTAINS CALL c_free(c_absolute_path) END FUNCTION absolute_path - FUNCTION f2c_string(f_string) RESULT(ptr) - USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_char, c_ptr, c_size_t, & - c_null_char, C_F_POINTER - CHARACTER(LEN=*), INTENT(IN) :: f_string - CHARACTER(LEN=1, KIND=c_char), POINTER :: c_string(:) - TYPE(c_ptr) :: ptr - INTEGER(c_size_t) :: i, n - - INTERFACE - FUNCTION lammps_malloc(size) BIND(C, name='malloc') - IMPORT :: c_ptr, c_size_t - IMPLICIT NONE - INTEGER(c_size_t), VALUE :: size - TYPE(c_ptr) :: lammps_malloc - END FUNCTION lammps_malloc - END INTERFACE - - n = LEN_TRIM(f_string) - ptr = lammps_malloc(n+1) - CALL C_F_POINTER(ptr, c_string, [1]) - DO i=1, n - c_string(i) = f_string(i:i) - END DO - c_string(n+1) = c_null_char - END FUNCTION f2c_string - END MODULE keepvar FUNCTION f_lammps_with_C_args(argc, argv) BIND(C) USE ISO_C_BINDING, ONLY: c_ptr, c_char, c_int, c_size_t, C_F_POINTER USE liblammps - USE keepstuff, ONLY: lmp + USE keepstuff, ONLY: lmp, c_strlen IMPLICIT NONE INTEGER(c_int), INTENT(IN), VALUE :: argc TYPE(c_ptr), VALUE :: argv @@ -92,15 +59,6 @@ FUNCTION f_lammps_with_C_args(argc, argv) BIND(C) CHARACTER(LEN=1,KIND=c_char), DIMENSION(:), POINTER :: Cstr INTEGER(c_size_t):: i, length, j - INTERFACE - FUNCTION c_strlen(str) BIND(C,name='strlen') - IMPORT :: c_ptr, c_size_t - IMPLICIT NONE - TYPE(c_ptr), INTENT(IN), VALUE :: str - INTEGER(c_size_t) :: c_strlen - END FUNCTION c_strlen - END INTERFACE - CALL C_F_POINTER(argv, Fargv, [argc]) DO i = 1, argc args(i) = '' @@ -219,8 +177,7 @@ END FUNCTION f_lammps_extract_variable_loop FUNCTION f_lammps_extract_variable_loop_pad() BIND(C) USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr USE LIBLAMMPS - USE keepstuff, ONLY : lmp - USE keepvar, ONLY : f2c_string + USE keepstuff, ONLY : lmp, f2c_string IMPLICIT NONE TYPE(c_ptr) :: f_lammps_extract_variable_loop_pad CHARACTER(LEN=20) :: loop @@ -232,8 +189,7 @@ END FUNCTION f_lammps_extract_variable_loop_pad FUNCTION f_lammps_extract_variable_world() BIND(C) USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr USE LIBLAMMPS - USE keepstuff, ONLY : lmp - USE keepvar, ONLY : f2c_string + USE keepstuff, ONLY : lmp, f2c_string IMPLICIT NONE TYPE(c_ptr) :: f_lammps_extract_variable_world CHARACTER(LEN=20) :: world @@ -245,8 +201,7 @@ END FUNCTION f_lammps_extract_variable_world FUNCTION f_lammps_extract_variable_universe() BIND(C) USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr USE LIBLAMMPS - USE keepstuff, ONLY : lmp - USE keepvar, ONLY : f2c_string + USE keepstuff, ONLY : lmp, f2c_string IMPLICIT NONE TYPE(c_ptr) :: f_lammps_extract_variable_universe CHARACTER(LEN=20) :: universe @@ -270,8 +225,7 @@ END FUNCTION f_lammps_extract_variable_uloop FUNCTION f_lammps_extract_variable_string() BIND(C) USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr USE LIBLAMMPS - USE keepstuff, ONLY : lmp - USE keepvar, ONLY : f2c_string + USE keepstuff, ONLY : lmp, f2c_string IMPLICIT NONE TYPE(c_ptr) :: f_lammps_extract_variable_string CHARACTER(LEN=256) :: string @@ -283,8 +237,7 @@ END FUNCTION f_lammps_extract_variable_string FUNCTION f_lammps_extract_variable_format() BIND(C) USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr USE LIBLAMMPS - USE keepstuff, ONLY : lmp - USE keepvar, ONLY : f2c_string + USE keepstuff, ONLY : lmp, f2c_string IMPLICIT NONE TYPE(c_ptr) :: f_lammps_extract_variable_format CHARACTER(LEN=20) :: form @@ -296,8 +249,7 @@ END FUNCTION f_lammps_extract_variable_format FUNCTION f_lammps_extract_variable_format_pad() BIND(C) USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr USE LIBLAMMPS - USE keepstuff, ONLY : lmp - USE keepvar, ONLY : f2c_string + USE keepstuff, ONLY : lmp, f2c_string IMPLICIT NONE TYPE(c_ptr) :: f_lammps_extract_variable_format_pad CHARACTER(LEN=20) :: form @@ -309,8 +261,7 @@ END FUNCTION f_lammps_extract_variable_format_pad FUNCTION f_lammps_extract_variable_getenv() BIND(C) USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr USE LIBLAMMPS - USE keepstuff, ONLY : lmp - USE keepvar, ONLY : f2c_string + USE keepstuff, ONLY : lmp, f2c_string IMPLICIT NONE TYPE(c_ptr) :: f_lammps_extract_variable_getenv CHARACTER(LEN=40) :: string @@ -322,8 +273,7 @@ END FUNCTION f_lammps_extract_variable_getenv FUNCTION f_lammps_extract_variable_file() BIND(C) USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_ptr USE LIBLAMMPS - USE keepstuff, ONLY : lmp - USE keepvar, ONLY : f2c_string + USE keepstuff, ONLY : lmp, f2c_string IMPLICIT NONE TYPE(c_ptr) :: f_lammps_extract_variable_file CHARACTER(LEN=40) :: string @@ -414,8 +364,7 @@ END FUNCTION f_lammps_extract_variable_vector SUBROUTINE f_lammps_set_variable_string() BIND(C) USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int USE LIBLAMMPS - USE keepstuff, ONLY : lmp - USE keepvar, ONLY : f2c_string + USE keepstuff, ONLY : lmp, f2c_string IMPLICIT NONE CHARACTER(LEN=40) :: string diff --git a/unittest/fortran/test_fortran_fixexternal.f90 b/unittest/fortran/test_fortran_fixexternal.f90 new file mode 100644 index 0000000000..d46e1ec673 --- /dev/null +++ b/unittest/fortran/test_fortran_fixexternal.f90 @@ -0,0 +1,424 @@ +MODULE ext_stuff + USE, INTRINSIC :: ISO_Fortran_ENV, ONLY : error_unit + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int, c_int64_t, c_loc + USE LIBLAMMPS + IMPLICIT NONE + + INTEGER, PARAMETER :: vec_length = 8 + REAL(c_double), SAVE :: direction = 1.0_c_double + REAL(c_double), DIMENSION(:,:), POINTER, SAVE :: f3 => NULL(), f4 => NULL() + +CONTAINS + + SUBROUTINE f_lammps_reverse_direction() BIND(C) + direction = -direction + END SUBROUTINE f_lammps_reverse_direction + + SUBROUTINE f_callback_ss(instance, timestep, id, x, f) + CLASS(*), INTENT(INOUT) :: instance + INTEGER(c_int) :: timestep + INTEGER(c_int), DIMENSION(:), INTENT(IN) :: id + REAL(c_double), DIMENSION(:,:), INTENT(IN) :: x + REAL(c_double), DIMENSION(:,:), INTENT(OUT) :: f + REAL(c_double), DIMENSION(SIZE(id)) :: e + REAL(c_double), DIMENSION(6,SIZE(id)) :: v + + WHERE (id == 1) + f(1,:) = 1.0_c_double + f(2,:) = -1.0_c_double + f(3,:) = 1.25_c_double + e = 1.0_c_double + v(1,:) = 1.0_c_double + v(2,:) = 2.0_c_double + v(3,:) = -1.0_c_double + v(4,:) = -2.0_c_double + v(5,:) = 3.0_c_double + v(6,:) = -3.0_c_double + ELSEWHERE + f(1,:) = -1.0_c_double + f(2,:) = +1.0_c_double + f(3,:) = -1.25_c_double + e = 10.0_c_double + v(1,:) = 10.0_c_double + v(2,:) = 20.0_c_double + v(3,:) = -10.0_c_double + v(4,:) = -20.0_c_double + v(5,:) = 30.0_c_double + v(6,:) = -30.0_c_double + END WHERE + SELECT TYPE (instance) + CLASS IS (lammps) + CALL instance%fix_external_set_energy_peratom('ext1', e) + CALL instance%fix_external_set_virial_peratom('ext1', v) + CLASS DEFAULT + WRITE(error_unit,*) 'UMM...this should never happen.' + STOP 1 + END SELECT + END SUBROUTINE f_callback_ss + + SUBROUTINE f_callback_sb(instance, timestep, id, x, f) + CLASS(*), INTENT(INOUT) :: instance + INTEGER(c_int64_t) :: timestep + INTEGER(c_int), DIMENSION(:), INTENT(IN) :: id + REAL(c_double), DIMENSION(:,:), INTENT(IN) :: x + REAL(c_double), DIMENSION(:,:), INTENT(OUT) :: f + REAL(c_double), DIMENSION(SIZE(id)) :: e + REAL(c_double), DIMENSION(6,SIZE(id)) :: v + + WHERE (id == 1_c_int) + f(1,:) = 1.0_c_double + f(2,:) = -1.0_c_double + f(3,:) = 1.25_c_double + e = 1.0_c_double + v(1,:) = 1.0_c_double + v(2,:) = 2.0_c_double + v(3,:) = -1.0_c_double + v(4,:) = -2.0_c_double + v(5,:) = 3.0_c_double + v(6,:) = -3.0_c_double + ELSEWHERE + f(1,:) = -1.0_c_double + f(2,:) = +1.0_c_double + f(3,:) = -1.25_c_double + e = 10.0_c_double + v(1,:) = 10.0_c_double + v(2,:) = 20.0_c_double + v(3,:) = -10.0_c_double + v(4,:) = -20.0_c_double + v(5,:) = 30.0_c_double + v(6,:) = -30.0_c_double + END WHERE + SELECT TYPE (instance) + CLASS IS (lammps) + CALL instance%fix_external_set_energy_peratom('ext1', e) + CALL instance%fix_external_set_virial_peratom('ext1', v) + CLASS DEFAULT + WRITE(error_unit,*) 'UMM...this should never happen.' + STOP 1 + END SELECT + END SUBROUTINE f_callback_sb + + SUBROUTINE f_callback_bb(instance, timestep, id, x, f) + CLASS(*), INTENT(INOUT) :: instance + INTEGER(c_int64_t) :: timestep + INTEGER(c_int64_t), DIMENSION(:), INTENT(IN) :: id + REAL(c_double), DIMENSION(:,:), INTENT(IN) :: x + REAL(c_double), DIMENSION(:,:), INTENT(OUT) :: f + REAL(c_double), DIMENSION(SIZE(id)) :: e + REAL(c_double), DIMENSION(6,SIZE(id)) :: v + + WHERE (id == 1_c_int64_t) + f(1,:) = 1.0_c_double + f(2,:) = -1.0_c_double + f(3,:) = 1.25_c_double + e = 1.0_c_double + v(1,:) = 1.0_c_double + v(2,:) = 2.0_c_double + v(3,:) = -1.0_c_double + v(4,:) = -2.0_c_double + v(5,:) = 3.0_c_double + v(6,:) = -3.0_c_double + ELSEWHERE + f(1,:) = -1.0_c_double + f(2,:) = +1.0_c_double + f(3,:) = -1.25_c_double + e = 10.0_c_double + v(1,:) = 10.0_c_double + v(2,:) = 20.0_c_double + v(3,:) = -10.0_c_double + v(4,:) = -20.0_c_double + v(5,:) = 30.0_c_double + v(6,:) = -30.0_c_double + END WHERE + SELECT TYPE (instance) + CLASS IS (lammps) + CALL instance%fix_external_set_energy_peratom('ext1', e) + CALL instance%fix_external_set_virial_peratom('ext1', v) + CLASS DEFAULT + WRITE(error_unit,*) 'UMM...this should never happen.' + STOP 1 + END SELECT + END SUBROUTINE f_callback_bb + + SUBROUTINE f_callback2_ss(entity, timestep, id, x, f) + CLASS(*), INTENT(INOUT), target :: entity + INTEGER(c_int) :: timestep + INTEGER(c_int), DIMENSION(:), INTENT(IN) :: id + REAL(c_double), DIMENSION(:,:), INTENT(IN) :: x + REAL(c_double), DIMENSION(:,:), INTENT(OUT) :: f + + SELECT TYPE (entity) + TYPE IS (REAL(c_double)) + WHERE (id == 1_c_int) + f(1,:) = SIGN(1.0_c_double, entity) * 2.0_c_double + f(2,:) = SIGN(1.0_c_double, entity) * (-2.0_c_double) + f(3,:) = SIGN(1.0_c_double, entity) * 2.5_c_double + ELSEWHERE + f(1,:) = SIGN(1.0_c_double, entity) * (-2.0_c_double) + f(2,:) = SIGN(1.0_c_double, entity) * 2.0_c_double + f(3,:) = SIGN(1.0_c_double, entity) * (-2.5_c_double) + END WHERE + CLASS DEFAULT + WRITE(error_unit,'(A)') 'ERROR: Failed to resolve "entity" in& + & f_callback2_ss' + STOP 1 + END SELECT + END SUBROUTINE f_callback2_ss + + SUBROUTINE f_callback2_sb(entity, timestep, id, x, f) + CLASS(*), INTENT(INOUT), target :: entity + INTEGER(c_int64_t) :: timestep + INTEGER(c_int), DIMENSION(:), INTENT(IN) :: id + REAL(c_double), DIMENSION(:,:), INTENT(IN) :: x + REAL(c_double), DIMENSION(:,:), INTENT(OUT) :: f + + SELECT TYPE (entity) + TYPE IS (REAL(c_double)) + WHERE (id == 1_c_int) + f(1,:) = SIGN(1.0_c_double, entity) * 2.0_c_double + f(2,:) = SIGN(1.0_c_double, entity) * (-2.0_c_double) + f(3,:) = SIGN(1.0_c_double, entity) * 2.5_c_double + ELSEWHERE + f(1,:) = SIGN(1.0_c_double, entity) * (-2.0_c_double) + f(2,:) = SIGN(1.0_c_double, entity) * 2.0_c_double + f(3,:) = SIGN(1.0_c_double, entity) * (-2.5_c_double) + END WHERE + CLASS DEFAULT + WRITE(error_unit,'(A)') 'ERROR: Failed to resolve "entity" in& + & f_callback2_sb' + STOP 1 + END SELECT + END SUBROUTINE f_callback2_sb + + SUBROUTINE f_callback2_bb(entity, timestep, id, x, f) + CLASS(*), INTENT(INOUT), target :: entity + INTEGER(c_int64_t) :: timestep + INTEGER(c_int64_t), DIMENSION(:), INTENT(IN) :: id + REAL(c_double), DIMENSION(:,:), INTENT(IN) :: x + REAL(c_double), DIMENSION(:,:), INTENT(OUT) :: f + + SELECT TYPE (entity) + TYPE IS (REAL(c_double)) + WHERE (id == 1_c_int64_t) + f(1,:) = SIGN(1.0_c_double, entity) * 2.0_c_double + f(2,:) = SIGN(1.0_c_double, entity) * (-2.0_c_double) + f(3,:) = SIGN(1.0_c_double, entity) * 2.5_c_double + ELSEWHERE + f(1,:) = SIGN(1.0_c_double, entity) * (-2.0_c_double) + f(2,:) = SIGN(1.0_c_double, entity) * 2.0_c_double + f(3,:) = SIGN(1.0_c_double, entity) * (-2.5_c_double) + END WHERE + CLASS DEFAULT + WRITE(error_unit,'(A)') 'ERROR: Failed to resolve "entity" in& + & f_callback2_sb' + STOP 1 + END SELECT + END SUBROUTINE f_callback2_bb +END MODULE ext_stuff + +FUNCTION f_lammps_with_args() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_ptr + USE liblammps + USE keepstuff, ONLY: lmp + IMPLICIT NONE + TYPE(c_ptr) :: f_lammps_with_args + + CHARACTER(len=12), DIMENSION(12), PARAMETER :: args = & + [ CHARACTER(len=12) :: 'liblammps', '-log', 'none', & + '-echo','screen','-nocite','-var','zpos','1.5','-var','x','2'] + + lmp = lammps(args) + f_lammps_with_args = lmp%handle +END FUNCTION f_lammps_with_args + +SUBROUTINE f_lammps_close() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_null_ptr + USE liblammps + USE keepstuff, ONLY: lmp + IMPLICIT NONE + + CALL lmp%close() + lmp%handle = c_null_ptr +END SUBROUTINE f_lammps_close + +SUBROUTINE f_lammps_setup_fix_external_callback() BIND(C) + USE LIBLAMMPS + USE keepstuff, ONLY : lmp, demo_input, cont_input, pair_input + USE ext_stuff, ONLY : vec_length + IMPLICIT NONE + + CALL lmp%commands_list(demo_input) + CALL lmp%commands_list(cont_input) + CALL lmp%commands_list(pair_input) + CALL lmp%command('neigh_modify exclude group all all') + CALL lmp%command('fix ext1 all external pf/callback 1 1') + CALL lmp%command('fix ext2 all external pf/callback 1 1') + CALL lmp%fix_external_set_vector_length('ext2', vec_length) +END SUBROUTINE f_lammps_setup_fix_external_callback + +SUBROUTINE f_lammps_setup_fix_external_array() BIND(C) + USE LIBLAMMPS + USE keepstuff, ONLY : lmp, demo_input, cont_input, pair_input + USE ext_stuff, ONLY : f3, f4 + IMPLICIT NONE + + CALL lmp%commands_list(demo_input) + CALL lmp%commands_list(cont_input) + CALL lmp%commands_list(pair_input) + CALL lmp%command('neigh_modify exclude group all all') + CALL lmp%command('fix ext3 all external pf/array 1') + CALL lmp%command('fix ext4 all external pf/array 1') + CALL lmp%command('thermo_style custom step pxx pe etotal') + CALL lmp%command('thermo_modify norm no') + CALL lmp%command('thermo 100') + f3 = lmp%fix_external_get_force('ext3') + f4 = lmp%fix_external_get_force('ext4') +END SUBROUTINE f_lammps_setup_fix_external_array + +SUBROUTINE f_lammps_set_fix_external_callbacks() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + USE ext_stuff + IMPLICIT NONE + INTEGER :: size_bigint, size_tagint, nlocal + + nlocal = lmp%extract_setting('nlocal') + + size_bigint = lmp%extract_setting('bigint') + size_tagint = lmp%extract_setting('tagint') + IF (size_bigint == 4_c_int .AND. size_tagint == 4_c_int) THEN + CALL lmp%set_fix_external_callback('ext1', f_callback_ss, lmp) + CALL lmp%set_fix_external_callback('ext2', f_callback2_ss, direction) + ELSE IF (size_bigint == 8_c_int .AND. size_tagint == 8_c_int) THEN + CALL lmp%set_fix_external_callback('ext1', f_callback_bb, lmp) + CALL lmp%set_fix_external_callback('ext2', f_callback2_bb, direction) + ELSE + CALL lmp%set_fix_external_callback('ext1', f_callback_sb, lmp) + CALL lmp%set_fix_external_callback('ext2', f_callback2_sb, direction) + END IF +END SUBROUTINE f_lammps_set_fix_external_callbacks + +SUBROUTINE f_lammps_get_force (i, ptr) BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double, c_ptr, C_F_POINTER + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int), INTENT(IN), VALUE :: i + TYPE(c_ptr), INTENT(IN), VALUE :: ptr + REAL(c_double), DIMENSION(:,:), POINTER :: force => NULL() + REAL(c_double), DIMENSION(:), POINTER :: f => NULL() + + CALL C_F_POINTER(ptr, f, [3]) + force = lmp%extract_atom('f') + f = force(:,i) +END SUBROUTINE f_lammps_get_force + +SUBROUTINE f_lammps_find_forces() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int, c_int64_t + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + USE ext_stuff, ONLY : f3, f4 + IMPLICIT NONE + INTEGER(c_int) :: size_tagint + INTEGER(c_int), DIMENSION(:), POINTER :: id + INTEGER(c_int64_t), DIMENSION(:), POINTER :: tag + + f3(:,:) = 0.0_c_double + f4(:,:) = 0.0_c_double + size_tagint = lmp%extract_setting('tagint') + IF (size_tagint == 4_c_int) THEN + id = lmp%extract_atom('id') + WHERE (id == 1_c_int) + f3(1,:) = 4.0_c_double + f3(2,:) = -4.0_c_double + f3(3,:) = 6.0_c_double + f4(1,:) = 10.0_c_double + f4(2,:) = -10.0_c_double + f4(3,:) = 12.0_c_double + ELSEWHERE + f3(1,:) = 5.0_c_double + f3(2,:) = -5.0_c_double + f3(3,:) = 7.0_c_double + f4(1,:) = 11.0_c_double + f4(2,:) = -11.0_c_double + f4(3,:) = 13.0_c_double + END WHERE + ELSE + tag = lmp%extract_atom('id') + WHERE (tag == 1_c_int64_t) + f3(1,:) = 4.0_c_double + f3(2,:) = -4.0_c_double + f3(3,:) = 6.0_c_double + f4(1,:) = 10.0_c_double + f4(2,:) = -10.0_c_double + f4(3,:) = 12.0_c_double + ELSEWHERE + f3(1,:) = 5.0_c_double + f3(2,:) = -5.0_c_double + f3(3,:) = 7.0_c_double + f4(1,:) = 11.0_c_double + f4(2,:) = -11.0_c_double + f4(3,:) = 13.0_c_double + END WHERE + END IF +END SUBROUTINE f_lammps_find_forces + +SUBROUTINE f_lammps_add_energy() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + + CALL lmp%fix_external_set_energy_global('ext3', -20.2_c_double); +END SUBROUTINE f_lammps_add_energy + +SUBROUTINE f_lammps_set_virial() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + + CALL lmp%fix_external_set_virial_global('ext4', [1.0_c_double, & + 2.0_c_double, 2.5_c_double, -1.0_c_double, -2.25_c_double, -3.02_c_double]) +END SUBROUTINE f_lammps_set_virial + +FUNCTION f_lammps_find_peratom_energy(i) RESULT(energy) BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int), INTENT(IN), VALUE :: i + REAL(c_double) :: energy + REAL(c_double), DIMENSION(:), POINTER :: e + + e = lmp%extract_compute('peratom', lmp%style%atom, lmp%type%vector) + energy = e(i) +END FUNCTION f_lammps_Find_peratom_energy + +SUBROUTINE f_lammps_find_peratom_virial(v, i) BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + REAL(c_double), DIMENSION(6) :: v + INTEGER(c_int), INTENT(IN), VALUE :: i + REAL(c_double), DIMENSION(:,:), POINTER :: virial + + virial = lmp%extract_compute('vperatom', lmp%style%atom, lmp%type%array) + v = virial(:,i) +END SUBROUTINE f_lammps_find_peratom_virial + +SUBROUTINE f_lammps_fixexternal_set_vector() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + USE ext_stuff, ONLY : vec_length + IMPLICIT NONE + REAL(c_double), DIMENSION(vec_length) :: v + INTEGER :: i + DO i = 1, vec_length + v(i) = REAL(i, c_double) + CALL lmp%fix_external_set_vector('ext2', i, v(i)) + END DO +END SUBROUTINE f_lammps_fixexternal_set_vector diff --git a/unittest/fortran/test_fortran_gather_scatter.f90 b/unittest/fortran/test_fortran_gather_scatter.f90 index ec1880c908..ab345127e5 100644 --- a/unittest/fortran/test_fortran_gather_scatter.f90 +++ b/unittest/fortran/test_fortran_gather_scatter.f90 @@ -24,13 +24,17 @@ END SUBROUTINE f_lammps_close SUBROUTINE f_lammps_setup_gather_scatter() BIND(C) USE LIBLAMMPS - USE keepstuff, ONLY : lmp, big_input, cont_input, more_input + USE keepstuff, ONLY : lmp, big_input, cont_input, more_input, pair_input IMPLICIT NONE CALL lmp%command('atom_modify map array') CALL lmp%commands_list(big_input) CALL lmp%commands_list(cont_input) CALL lmp%commands_list(more_input) + CALL lmp%commands_list(pair_input) + CALL lmp%command('mass 1 1.0') + CALL lmp%command("compute pe all pe/atom") + CALL lmp%command("fix dummy all ave/atom 1 1 1 c_pe") END SUBROUTINE f_lammps_setup_gather_scatter FUNCTION f_lammps_gather_atoms_mask(i) BIND(C) @@ -71,13 +75,13 @@ FUNCTION f_lammps_gather_atoms_concat_mask(i) BIND(C) CALL lmp%gather_atoms_concat('mask', 1_c_int, mask) CALL lmp%gather_atoms_concat('id', 1_c_int, tag) + f_lammps_gather_atoms_concat_mask = -1 DO j = 1, SIZE(tag) IF (tag(j) == i) THEN f_lammps_gather_atoms_concat_mask = mask(j) - RETURN + EXIT END IF END DO - f_lammps_gather_atoms_concat_mask = -1 END FUNCTION f_lammps_gather_atoms_concat_mask FUNCTION f_lammps_gather_atoms_concat_position(xyz, id) BIND(C) @@ -93,6 +97,7 @@ FUNCTION f_lammps_gather_atoms_concat_position(xyz, id) BIND(C) CALL lmp%gather_atoms_concat('x', 3_c_int, positions) CALL lmp%gather_atoms_concat('id', 1_c_int, tag) + f_lammps_gather_atoms_concat_position = -1.0_c_double DO j = 1, SIZE(tag) IF (tag(j) == id) THEN f_lammps_gather_atoms_concat_position = positions((j-1)*3 + xyz) @@ -109,16 +114,16 @@ FUNCTION f_lammps_gather_atoms_subset_mask(i) BIND(C) INTEGER(c_int) :: f_lammps_gather_atoms_subset_mask INTEGER(c_int), DIMENSION(:), ALLOCATABLE :: mask INTEGER :: j - INTEGER(c_int), DIMENSION(*), PARAMETER :: tag = [3,2] + INTEGER(c_int), DIMENSION(2), PARAMETER :: tag = [3,2] CALL lmp%gather_atoms_subset('mask', 1_c_int, tag, mask) + f_lammps_gather_atoms_subset_mask = -1 DO j = 1, SIZE(tag) IF (tag(j) == i) THEN f_lammps_gather_atoms_subset_mask = mask(j) - RETURN + EXIT END IF END DO - f_lammps_gather_atoms_subset_mask = -1 END FUNCTION f_lammps_gather_atoms_subset_mask FUNCTION f_lammps_gather_atoms_subset_position(xyz,id) BIND(C) @@ -129,17 +134,17 @@ FUNCTION f_lammps_gather_atoms_subset_position(xyz,id) BIND(C) INTEGER(c_int), INTENT(IN), VALUE :: id, xyz REAL(c_double) :: f_lammps_gather_atoms_subset_position REAL(c_double), DIMENSION(:), ALLOCATABLE :: positions - INTEGER(c_int), DIMENSION(*), PARAMETER :: tag = [3,2] + INTEGER(c_int), DIMENSION(2), PARAMETER :: tag = [3,2] INTEGER :: j CALL lmp%gather_atoms_subset('x', 3_c_int, tag, positions) + f_lammps_gather_atoms_subset_position = -1.0_c_double DO j = 1, SIZE(tag) IF (tag(j) == id) THEN f_lammps_gather_atoms_subset_position = positions((j-1)*3 + xyz) - RETURN + EXIT END IF END DO - f_lammps_gather_atoms_subset_position = -1.0D0 END FUNCTION f_lammps_gather_atoms_subset_position SUBROUTINE f_lammps_scatter_atoms_masks() BIND(C) @@ -188,7 +193,7 @@ SUBROUTINE f_lammps_scatter_atoms_subset_mask() BIND(C) USE keepstuff, ONLY : lmp IMPLICIT NONE INTEGER(c_int), DIMENSION(:), ALLOCATABLE :: all_masks - INTEGER(c_int), DIMENSION(*), PARAMETER :: tags = [3,1] + INTEGER(c_int), DIMENSION(2), PARAMETER :: tags = [3,1] INTEGER(c_int), DIMENSION(2) :: masks CALL lmp%gather_atoms('mask', 1_c_int, all_masks) @@ -199,3 +204,152 @@ SUBROUTINE f_lammps_scatter_atoms_subset_mask() BIND(C) CALL lmp%scatter_atoms_subset('mask', tags, masks) ! push the swap to LAMMPS END SUBROUTINE f_lammps_scatter_atoms_subset_mask + +SUBROUTINE f_lammps_setup_gather_bonds() BIND(C) + USE LIBLAMMPS + USE keepstuff, ONLY : lmp, cont_input, more_input, pair_input + IMPLICIT NONE + + INTERFACE + SUBROUTINE f_lammps_setup_gather_scatter() BIND(C) + END SUBROUTINE f_lammps_setup_gather_scatter + END INTERFACE + + CALL lmp%command('atom_modify map array') + CALL lmp%command('atom_style full') + CALL lmp%command('region simbox block 0 4 0 5 0 4') + CALL lmp%command('create_box 1 simbox bond/types 1 extra/bond/per/atom 2') + CALL lmp%command('create_atoms 1 single 1.0 1.0 ${zpos}') + CALL lmp%commands_list(cont_input) + CALL lmp%commands_list(more_input) + CALL lmp%commands_list(pair_input) + CALL lmp%command('bond_style zero') + CALL lmp%command('bond_coeff *') + CALL lmp%command('create_bonds many all all 1 0.0 1.5') + CALL lmp%command('run 0') +END SUBROUTINE f_lammps_setup_gather_bonds + +FUNCTION f_lammps_test_gather_bonds_small() BIND(C) RESULT(success) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_int64_t + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int) :: success + INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET :: bonds + INTEGER(c_int), DIMENSION(:,:), POINTER :: bonds_array + + CALL lmp%gather_bonds(bonds) + bonds_array(1:3,1:SIZE(bonds)/3) => bonds + IF ( ALL(bonds_array(:,1) == [INTEGER(c_int) :: 1,1,3]) & + .AND. ALL(bonds_array(:,2) == [INTEGER(c_int) :: 1,2,3])) THEN + success = 1_c_int + ELSE + success = 0_c_int + END IF +END FUNCTION f_lammps_test_gather_bonds_small + +FUNCTION f_lammps_test_gather_bonds_big() BIND(C) RESULT(success) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_int64_t + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int) :: success + INTEGER(c_int64_t), DIMENSION(:), ALLOCATABLE, TARGET :: bonds + INTEGER(c_int64_t), DIMENSION(:,:), POINTER :: bonds_array + + CALL lmp%gather_bonds(bonds) + bonds_array(1:3,1:SIZE(bonds)/3) => bonds + IF ( ALL(bonds_array(:,1) == [INTEGER(c_int64_t) :: 1,1,3]) & + .AND. ALL(bonds_array(:,2) == [INTEGER(c_int64_t) :: 1,2,3])) THEN + success = 1_c_int + ELSE + success = 0_c_int + END IF +END FUNCTION f_lammps_test_gather_bonds_big + +FUNCTION f_lammps_gather_pe_atom(i) BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int), INTENT(IN), VALUE :: i + REAL(c_double) :: f_lammps_gather_pe_atom + REAL(c_double), DIMENSION(:), ALLOCATABLE :: pe_atom + + CALL lmp%gather('c_pe', 1_c_int, pe_atom) + f_lammps_gather_pe_atom = pe_atom(i) +END FUNCTION f_lammps_gather_pe_atom + +FUNCTION f_lammps_gather_pe_atom_concat(i) BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int), INTENT(IN), VALUE :: i + REAL(c_double) :: f_lammps_gather_pe_atom_concat + REAL(c_double), DIMENSION(:), ALLOCATABLE :: pe_atom + INTEGER(c_int), DIMENSION(:), ALLOCATABLE :: tag + INTEGER :: j + + CALL lmp%gather_concat('id', 1_c_int, tag) + CALL lmp%gather_concat('c_pe', 1_c_int, pe_atom) + DO j = 1, SIZE(tag) + IF (tag(j) == i) THEN + f_lammps_gather_pe_atom_concat = pe_atom(j) + EXIT + END IF + END DO + f_lammps_gather_pe_atom_concat = pe_atom(i) +END FUNCTION f_lammps_gather_pe_atom_concat + +SUBROUTINE f_lammps_gather_pe_atom_subset(ids, pe) BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int), INTENT(IN) :: ids(2) + REAL(c_double), INTENT(OUT) :: pe(2) + REAL(c_double), DIMENSION(:), ALLOCATABLE :: pe_atom + INTEGER(c_int) :: natoms + + natoms = NINT(lmp%get_natoms(), c_int) + CALL lmp%gather_subset('c_pe', 1, ids, pe_atom) + pe(1:2) = pe_atom(1:2) +END SUBROUTINE f_lammps_gather_pe_atom_subset + +SUBROUTINE f_lammps_scatter_compute() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + REAL(c_double), DIMENSION(:), ALLOCATABLE :: pe_atom + REAL(c_double) :: swap + + CALL lmp%gather('c_pe', 1_c_int, pe_atom) + + ! swap the computed energy of atoms 1 and 3 + swap = pe_atom(1) + pe_atom(1) = pe_atom(3) + pe_atom(3) = swap + + CALL lmp%scatter('c_pe', pe_atom) ! push the swap back to LAMMPS +END SUBROUTINE f_lammps_scatter_compute + +SUBROUTINE f_lammps_scatter_subset_compute() BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int), PARAMETER :: ids(2) = [3,1] + REAL(c_double), DIMENSION(:), ALLOCATABLE :: pe_atom + REAL(c_double) :: swap + + CALL lmp%gather_subset('c_pe', 1_c_int, ids, pe_atom) + + ! swap the computed energy of atoms 1 and 3 + swap = pe_atom(1) + pe_atom(1) = pe_atom(2) + pe_atom(2) = swap + + CALL lmp%scatter_subset('c_pe', ids, pe_atom) ! push the swap back to LAMMPS +END SUBROUTINE f_lammps_scatter_subset_compute diff --git a/unittest/fortran/test_fortran_neighlist.f90 b/unittest/fortran/test_fortran_neighlist.f90 new file mode 100644 index 0000000000..efab39607e --- /dev/null +++ b/unittest/fortran/test_fortran_neighlist.f90 @@ -0,0 +1,86 @@ +FUNCTION f_lammps_with_args() BIND(C, name="f_lammps_with_args") + USE ISO_C_BINDING, ONLY: c_ptr + USE liblammps + USE keepstuff, ONLY: lmp + IMPLICIT NONE + TYPE(c_ptr) :: f_lammps_with_args + CHARACTER(len=12), DIMENSION(12), PARAMETER :: args = & + [ CHARACTER(len=12) :: 'liblammps', '-log', 'none', & + '-echo','screen','-nocite','-var','zpos','1.5','-var','x','2'] + + lmp = lammps(args) + f_lammps_with_args = lmp%handle +END FUNCTION f_lammps_with_args + +SUBROUTINE f_lammps_close() BIND(C, name="f_lammps_close") + USE ISO_C_BINDING, ONLY: c_null_ptr + USE liblammps + USE keepstuff, ONLY: lmp + IMPLICIT NONE + + CALL lmp%close() + lmp%handle = c_null_ptr +END SUBROUTINE f_lammps_close + +SUBROUTINE f_lammps_setup_neigh_tests() BIND(C) + USE LIBLAMMPS + USE keepstuff, ONLY : lmp, big_input, cont_input, pair_input + IMPLICIT NONE + + CALL lmp%command('atom_modify map array') + CALL lmp%commands_list(big_input) + CALL lmp%commands_list(cont_input) + CALL lmp%commands_list(pair_input) + CALL lmp%command('compute c all rdf 100') + ! We create one of the fixes that requests a neighbor list, none of which + ! is part of LAMMPS without additional packages; as such, we only do this + ! if REPLICA is included + IF (lmp%config_has_package('REPLICA')) THEN + CALL lmp%command('fix f all hyper/global 1.0 0.3 0.8 300.0') + CALL lmp%command('compute event all event/displace 1.0') + CALL lmp%command('hyper 0 100 f event') ! using "run 0" here segfaults (?) + ELSE + CALL lmp%command('run 0 post no') ! otherwise neighlists won't be requested + END IF +END SUBROUTINE f_lammps_setup_neigh_tests + +FUNCTION f_lammps_pair_neighlist_test() BIND(C) RESULT(nlist_id) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int) :: nlist_id + + nlist_id = lmp%find_pair_neighlist('lj/cut',.TRUE., 0, 0) +END FUNCTION f_lammps_pair_neighlist_test + +FUNCTION f_lammps_fix_neighlist_test() BIND(C) RESULT(nlist_id) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int) :: nlist_id + + nlist_id = lmp%find_fix_neighlist('f',0) +END FUNCTION f_lammps_fix_neighlist_test + +FUNCTION f_lammps_compute_neighlist_test() BIND(C) RESULT(nlist_id) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int) :: nlist_id + + nlist_id = lmp%find_compute_neighlist('c',0) +END FUNCTION f_lammps_compute_neighlist_test + +FUNCTION f_lammps_neighlist_num_elements(id) BIND(C) RESULT(nelements) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int + USE LIBLAMMPS + USE keepstuff, ONLY : lmp + IMPLICIT NONE + INTEGER(c_int), INTENT(IN), VALUE :: id + INTEGER(c_int) :: nelements + + nelements = lmp%neighlist_num_elements(id) +END FUNCTION f_lammps_neighlist_num_elements diff --git a/unittest/fortran/test_fortran_properties.f90 b/unittest/fortran/test_fortran_properties.f90 index 39606937a4..4f22321076 100644 --- a/unittest/fortran/test_fortran_properties.f90 +++ b/unittest/fortran/test_fortran_properties.f90 @@ -1,13 +1,3 @@ -FUNCTION f_lammps_version() BIND(C) - USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int - USE liblammps - USE keepstuff, ONLY : lmp - IMPLICIT NONE - INTEGER(c_int) :: f_lammps_version - - f_lammps_version = lmp%version() -END FUNCTION f_lammps_version - SUBROUTINE f_lammps_memory_usage(meminfo) BIND(C) USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double USE liblammps @@ -29,7 +19,7 @@ FUNCTION f_lammps_get_mpi_comm() BIND(C) END FUNCTION f_lammps_get_mpi_comm FUNCTION f_lammps_extract_setting(Cstr) BIND(C) - USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_char + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_char, c_null_char USE keepstuff, ONLY : lmp USE LIBLAMMPS IMPLICIT NONE @@ -39,7 +29,7 @@ FUNCTION f_lammps_extract_setting(Cstr) BIND(C) CHARACTER(LEN=:), ALLOCATABLE :: Fstr i = 1 - DO WHILE (Cstr(i) /= ACHAR(0)) + DO WHILE (Cstr(i) /= c_null_char) i = i + 1 END DO strlen = i @@ -66,7 +56,8 @@ FUNCTION f_lammps_has_error() BIND(C) END FUNCTION f_lammps_has_error FUNCTION f_lammps_get_last_error_message(errmesg, errlen) BIND(C) - USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_char, c_ptr, C_F_POINTER + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_char, c_ptr, C_F_POINTER, & + c_null_char USE keepstuff, ONLY : lmp USE LIBLAMMPS IMPLICIT NONE @@ -81,9 +72,55 @@ FUNCTION f_lammps_get_last_error_message(errmesg, errlen) BIND(C) CALL lmp%get_last_error_message(buffer, status) f_lammps_get_last_error_message = status ! and copy to C style string + errmesg(1:errlen) = c_null_char DO i=1, errlen errmesg(i) = buffer(i:i) - IF (buffer(i:i) == ACHAR(0)) EXIT + IF (buffer(i:i) == c_null_char) EXIT END DO + errmesg(errlen) = c_null_char DEALLOCATE(buffer) END FUNCTION f_lammps_get_last_error_message + +FUNCTION f_lammps_get_image_flags_int(ix, iy, iz) BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int + USE keepstuff, ONLY : lmp + USE LIBLAMMPS + IMPLICIT NONE + INTEGER(c_int), INTENT(IN), VALUE :: ix, iy, iz + INTEGER(c_int) :: f_lammps_get_image_flags_int + + f_lammps_get_image_flags_int = lmp%encode_image_flags(ix, iy, iz) +END FUNCTION f_lammps_get_image_flags_int + +FUNCTION f_lammps_get_image_flags_bigint(ix, iy, iz) BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_int64_t + USE keepstuff, ONLY : lmp + USE LIBLAMMPS + IMPLICIT NONE + INTEGER(c_int), INTENT(IN), VALUE :: ix, iy, iz + INTEGER(c_int64_t) :: f_lammps_get_image_flags_bigint + + f_lammps_get_image_flags_bigint = lmp%encode_image_flags(ix, iy, iz) +END FUNCTION f_lammps_get_image_flags_bigint + +SUBROUTINE f_lammps_decode_image_flags(image, flag) BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int + USE keepstuff, ONLY : lmp + USE LIBLAMMPS + IMPLICIT NONE + INTEGER(c_int), INTENT(IN), VALUE :: image + INTEGER(c_int), INTENT(OUT) :: flag(3) + + CALL lmp%decode_image_flags(image, flag) +END SUBROUTINE f_lammps_decode_image_flags + +SUBROUTINE f_lammps_decode_image_flags_bigbig(image, flag) BIND(C) + USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_int64_t + USE keepstuff, ONLY : lmp + USE LIBLAMMPS + IMPLICIT NONE + INTEGER(c_int64_t), INTENT(IN), VALUE :: image + INTEGER(c_int), INTENT(OUT) :: flag(3) + + CALL lmp%decode_image_flags(image, flag) +END SUBROUTINE f_lammps_decode_image_flags_bigbig diff --git a/unittest/fortran/wrap_configuration.cpp b/unittest/fortran/wrap_configuration.cpp new file mode 100644 index 0000000000..e542caf600 --- /dev/null +++ b/unittest/fortran/wrap_configuration.cpp @@ -0,0 +1,375 @@ +// unit tests for getting LAMMPS configuration through the Fortran wrapper + +#include "lammps.h" +#include "library.h" +#include "info.h" + +#ifdef LMP_PLUGIN +#include "plugin.h" +#endif + +#include + +#include "gmock/gmock.h" +#include "gtest/gtest.h" + +extern "C" { +void *f_lammps_with_args(); +void f_lammps_close(); +int f_lammps_version(); +int f_lammps_os_info(const char*); +int f_lammps_mpi_support(); +int f_lammps_gzip_support(); +int f_lammps_png_support(); +int f_lammps_jpeg_support(); +int f_lammps_ffmpeg_support(); +int f_lammps_has_exceptions(); +int f_lammps_has_package(const char*); +int f_lammps_package_count(); +char* f_lammps_package_name(int); +char* f_lammps_installed_packages(int); +int f_lammps_config_accelerator(const char*, const char*, const char*); +int f_lammps_has_gpu(); +char* f_lammps_get_gpu_info(size_t); +int f_lammps_has_style(const char*, const char*); +int f_lammps_style_count(const char*); +char* f_lammps_style_name(const char*, int); +void f_setup_has_id(); +int f_lammps_has_id(const char*, const char*); +int f_lammps_id_count(const char*); +char* f_lammps_id_name(const char*, int); +int f_lammps_plugin_count(); +int f_lammps_plugin_name(); +} +namespace LAMMPS_NS { + +using ::testing::ContainsRegex; + +class LAMMPS_configuration : public ::testing::Test { +protected: + LAMMPS *lmp; + std::vector style_category = {"atom","integrate","minimize", + "pair","bond","angle","dihedral","improper","kspace","fix","compute", + "region","dump","command"}; + + void SetUp() override + { + ::testing::internal::CaptureStdout(); + lmp = (LAMMPS *)f_lammps_with_args(); + + std::string output = ::testing::internal::GetCapturedStdout(); + EXPECT_STREQ(output.substr(0, 8).c_str(), "LAMMPS ("); + } + + void TearDown() override + { + ::testing::internal::CaptureStdout(); + f_lammps_close(); + std::string output = ::testing::internal::GetCapturedStdout(); + EXPECT_STREQ(output.substr(0, 16).c_str(), "Total wall time:"); + lmp = nullptr; + } +}; + +TEST_F(LAMMPS_configuration, version) +{ + EXPECT_LT(20200917, f_lammps_version()); + EXPECT_EQ(lmp->num_ver, f_lammps_version()); +}; + +TEST_F(LAMMPS_configuration, os_info) +{ + std::string str = platform::os_info(); + EXPECT_EQ(f_lammps_os_info(str.c_str()), 1); +}; + +TEST_F(LAMMPS_configuration, MPI_support) +{ +#ifdef MPI_STUBS + EXPECT_EQ(f_lammps_mpi_support(), 0); +#else + EXPECT_EQ(f_lammps_mpi_support(), 1); +#endif +}; + +TEST_F(LAMMPS_configuration, gzip_support) +{ + EXPECT_EQ(f_lammps_gzip_support(), Info::has_gzip_support()); +} + +TEST_F(LAMMPS_configuration, png_support) +{ + EXPECT_EQ(f_lammps_png_support(), Info::has_png_support()); +} + +TEST_F(LAMMPS_configuration, jpeg_support) +{ + EXPECT_EQ(f_lammps_jpeg_support(), Info::has_jpeg_support()); +} + +TEST_F(LAMMPS_configuration, ffmpeg_support) +{ + EXPECT_EQ(f_lammps_ffmpeg_support(), Info::has_ffmpeg_support()); +} + +TEST_F(LAMMPS_configuration, has_exceptions) +{ + EXPECT_EQ(f_lammps_has_exceptions(), Info::has_exceptions()); +} + +TEST_F(LAMMPS_configuration, has_package) +{ + std::vector pkg_name = {"ADIOS","ASPHERE","ATC","AWPMD","BOCS","BODY","BPM", + "BROWNIAN","CG-DNA","CLASS2","COLLOID","COLVARS","COMPRESS","CORESHELL","DEPEND", + "DIELECTRIC","DIFFRACTION","DIPOLE","DPD-BASIC","DPD-MESO","DPD-REACT","DPD-SMOOTH","DRUDE", + "EFF","ELECTRODE","EXTRA-COMPUTE","EXTRA-DUMP","EXTRA-FIX","EXTRA-MOLECULE","EXTRA-PAIR", + "FEP","GPU","GRANULAR","H5MD","INTEL","INTEL/TEST","INTERLAYER","KIM","KOKKOS","KSPACE", + "LATBOLTZ","LATTE","MACHDYN","MAKE","MAKE/MACHINES","MAKE/MINE","MAKE/OPTIONS","MANIFOLD", + "MANYBODY","MC","MDI","MEAM","MESONT","MGPT","MISC","ML-HDNNP","ML-IAP","ML-PACE","ML-QUIP", + "ML-RANN","ML-SNAP","MOFFF","MOLECULE","MOLFILE","MPIIO","MSCG","NETCDF","OPENMP","OPT", + "ORIENT","PERI","PHONON","PLUGIN","PLUMED","POEMS","PTM","PYTHON","QEQ","QMMM","QTB", + "REACTION","REAXFF","REPLICA","RIGID","SCAFACOS","SHOCK","SMTBQ","SPH","SPIN","SRD","STUBS", + "TALLY","UEF","VORONOI","VTK","YAFF","CG-SPICA","AMOEBA"}; + + for (std::size_t i = 0; i < pkg_name.size(); i++) + EXPECT_EQ(f_lammps_has_package(pkg_name[i].c_str()), + Info::has_package(pkg_name[i])); +} + +TEST_F(LAMMPS_configuration, package_count) +{ + int package_count = 0; + while (LAMMPS::installed_packages[package_count] != nullptr) + package_count++; + EXPECT_EQ(f_lammps_package_count(), package_count); +}; + +TEST_F(LAMMPS_configuration, package_name) +{ + int i = 0; + while (LAMMPS::installed_packages[i] != nullptr) + { + char* name = f_lammps_package_name(i+1); // 1 in Fortran is 0 in C + if (name) + EXPECT_STREQ(LAMMPS::installed_packages[i], name); + else + EXPECT_STREQ(LAMMPS::installed_packages[i], "NOT FOUND"); + std::free(name); + i++; + } +}; +TEST_F(LAMMPS_configuration, installed_packages) +{ + const char *package_name; + int npackages = lammps_config_package_count(); + char *pkg; + for (int i=0; i < npackages; i++) { + package_name = LAMMPS::installed_packages[i]; + pkg = f_lammps_installed_packages(i+1); + EXPECT_STREQ(package_name, pkg); + if (pkg) std::free(pkg); + } +}; + +TEST_F(LAMMPS_configuration, config_accelerator) +{ + const int npackage = 4; + const int ncategory = 2; + const int nsetting_api = 7; + const int nsetting_precision = 3; + const std::string package[] = {"GPU","KOKKOS","INTEL","OPENMP"}; + const std::string category[] = {"api","precision"}; + const std::string setting_api[] = {"cuda","hip","phi","pthreads","opencl", + "openmp","serial"}; + const std::string setting_precision[] = {"double","mixed","single"}; + + for (int p=0; p < npackage; p++) + { + for (int c=0; c < ncategory; c++) + { + if (category[c] == "api") + { + for (int s=0; s < nsetting_api; s++) + EXPECT_EQ(f_lammps_config_accelerator(package[p].c_str(), category[c].c_str(), + setting_api[s].c_str()), + Info::has_accelerator_feature(package[p], category[c], setting_api[s])); + } + else if (category[c] == "precision") + { + for (int s=0; s < nsetting_precision; s++) + EXPECT_EQ(f_lammps_config_accelerator(package[p].c_str(), category[c].c_str(), + setting_precision[s].c_str()), + Info::has_accelerator_feature(package[p],category[c],setting_precision[s])); + } + } + } +}; + +TEST_F(LAMMPS_configuration, has_gpu) +{ + EXPECT_EQ(Info::has_gpu_device(), f_lammps_has_gpu()); +}; + +TEST_F(LAMMPS_configuration, get_gpu_info) +{ + if (!Info::has_gpu_device()) GTEST_SKIP(); + size_t n; + std::string cpp_info = Info::get_gpu_device_info(); + n = cpp_info.size(); + char* f_string; + f_string = f_lammps_get_gpu_info(n); + EXPECT_STREQ(utils::trim(f_string).c_str(), utils::trim(cpp_info).c_str()); + std::free(f_string); + + if (n > 80) + { + f_string = f_lammps_get_gpu_info(80); + cpp_info.resize(80); + EXPECT_STREQ(utils::trim(f_string).c_str(), utils::trim(cpp_info).c_str()); + std::free(f_string); + } +}; + +TEST_F(LAMMPS_configuration, has_style) +{ + Info info(lmp); + for (std::size_t c = 0; c < style_category.size(); c++) + { + std::vector name = + info.get_available_styles(style_category[c]); + for (std::size_t s = 0; s < name.size(); s++) + { + EXPECT_EQ(f_lammps_has_style(style_category[c].c_str(), + name[s].c_str()), info.has_style(style_category[c], name[s])); + } + } + EXPECT_EQ(f_lammps_has_style("atom","none"), 0); +}; + +TEST_F(LAMMPS_configuration, style_count) +{ + Info info(lmp); + for (std::size_t i = 0; i < style_category.size(); i++) + EXPECT_EQ(f_lammps_style_count(style_category[i].c_str()), + info.get_available_styles(style_category[i].c_str()).size()); +}; + +TEST_F(LAMMPS_configuration, style_name) +{ + char *buffer; + Info info(lmp); + for (std::size_t c = 0; c < style_category.size(); c++) { + int nnames = f_lammps_style_count(style_category[c].c_str()); + auto styles = info.get_available_styles(style_category[c]); + for (int i = 0; i < nnames; i++) { + buffer = f_lammps_style_name(style_category[c].c_str(), i + 1); + EXPECT_STREQ(buffer, styles[i].c_str()); + std::free(buffer); + } + } + +}; + +TEST_F(LAMMPS_configuration, has_id) +{ + f_setup_has_id(); + EXPECT_EQ(f_lammps_has_id("compute","com"), 0); + EXPECT_EQ(f_lammps_has_id("compute","COM"), 1); + EXPECT_EQ(f_lammps_has_id("dump","atom"), 0); + EXPECT_EQ(f_lammps_has_id("dump","1"), 1); + EXPECT_EQ(f_lammps_has_id("fix","nve"), 0); + EXPECT_EQ(f_lammps_has_id("fix","1"), 1); + EXPECT_EQ(f_lammps_has_id("group","one"), 1); + EXPECT_EQ(f_lammps_has_id("group","all"), 1); + // Skip this one (we're testing thoroughly enough; molecules require files) + //EXPECT_EQ(f_lammps_has_id("molecule") + EXPECT_EQ(f_lammps_has_id("region","simbox"), 1); + EXPECT_EQ(f_lammps_has_id("region","box"), 0); + EXPECT_EQ(f_lammps_has_id("variable","pi"), 1); + EXPECT_EQ(f_lammps_has_id("variable","PI"), 0); +}; + +TEST_F(LAMMPS_configuration, id_count) +{ + f_setup_has_id(); + // computes: thermo_temp, thermo_press, thermo_pe, COM + EXPECT_EQ(f_lammps_id_count("compute"), 4); + EXPECT_EQ(f_lammps_id_count("dump"), 1); // only the one we defined + EXPECT_EQ(f_lammps_id_count("fix"), 1); // only the one we defined + EXPECT_EQ(f_lammps_id_count("group"), 2); // "one" and "all" + EXPECT_EQ(f_lammps_id_count("molecule"), 0); + EXPECT_EQ(f_lammps_id_count("region"), 1); // onle the one we created + EXPECT_EQ(f_lammps_id_count("variable"), 3); // "zpos", "x", and "pi" +}; + +TEST_F(LAMMPS_configuration, id_name) +{ + f_setup_has_id(); + char *name; + int nnames = f_lammps_id_count("compute"); + EXPECT_EQ(nnames, 4); + + name = f_lammps_id_name("compute",1); + EXPECT_STREQ(name, "thermo_temp"); + std::free(name); + + name = f_lammps_id_name("compute",2); + EXPECT_STREQ(name, "thermo_press"); + std::free(name); + + name = f_lammps_id_name("compute",3); + EXPECT_STREQ(name, "thermo_pe"); + std::free(name); + + name = f_lammps_id_name("compute",4); + EXPECT_STREQ(name, "COM"); + std::free(name); + + name = f_lammps_id_name("dump",1); + EXPECT_STREQ(name, "1"); + std::free(name); + + name = f_lammps_id_name("fix",1); + EXPECT_STREQ(name, "1"); + std::free(name); + + name = f_lammps_id_name("group",1); + EXPECT_STREQ(name, "all"); + std::free(name); + + name = f_lammps_id_name("group",2); + EXPECT_STREQ(name, "one"); + std::free(name); + + name = f_lammps_id_name("region",1); + EXPECT_STREQ(name, "simbox"); + std::free(name); + + name = f_lammps_id_name("variable",1); + EXPECT_STREQ(name, "zpos"); + std::free(name); + + name = f_lammps_id_name("variable",2); + EXPECT_STREQ(name, "x"); + std::free(name); + + name = f_lammps_id_name("variable",3); + EXPECT_STREQ(name, "pi"); + std::free(name); + +}; + +TEST_F(LAMMPS_configuration, plugins) +{ +#ifndef LMP_PLUGIN + GTEST_SKIP(); +#else + int nplugins = f_lammps_plugin_count(); + for (int n = 0; n < nplugins; n++) { + lammpsplugin_t *plugin = plugin_get_info(n); + EXPECT_EQ(f_lammps_plugin_name(n+1, plugin->style, plugin->name), 1); + } +#endif +}; + +} // namespace LAMMPS_NS diff --git a/unittest/fortran/wrap_create.cpp b/unittest/fortran/wrap_create.cpp index 04a62e4040..789e9fca6a 100644 --- a/unittest/fortran/wrap_create.cpp +++ b/unittest/fortran/wrap_create.cpp @@ -17,6 +17,14 @@ void f_lammps_close(); int f_lammps_get_comm(); } +// C wrapper to split MPI communicator w/o requiring a Fortran MPI lib +extern "C" int create_mpi_comm_split(int color, int key) +{ + MPI_Comm c_newcomm = MPI_COMM_NULL; + MPI_Comm_split(MPI_COMM_WORLD, color, key, &c_newcomm); + return MPI_Comm_c2f(c_newcomm); +} + TEST(open_no_mpi, no_args) { ::testing::internal::CaptureStdout(); diff --git a/unittest/fortran/wrap_create_atoms.cpp b/unittest/fortran/wrap_create_atoms.cpp new file mode 100644 index 0000000000..3addbcf070 --- /dev/null +++ b/unittest/fortran/wrap_create_atoms.cpp @@ -0,0 +1,219 @@ +// unit tests for creating atoms in a LAMMPS instance through the Fortran wrapper + +#include "lammps.h" +#include "library.h" +#include "atom.h" +#include +#include +#include +#include + +#include "gtest/gtest.h" + +// prototypes for Fortran reverse wrapper functions +extern "C" { +void *f_lammps_with_args(); +void f_lammps_close(); +void f_lammps_setup_create_atoms(); +void f_lammps_create_three_atoms(); +void f_lammps_create_two_more(); +void f_lammps_create_two_more_small(); +void f_lammps_create_two_more_big(); +void f_lammps_create_two_more_small2(); +void f_lammps_create_two_more_big2(); +} + +class LAMMPS_create_atoms : public ::testing::Test { +protected: + LAMMPS_NS::LAMMPS *lmp; + LAMMPS_create_atoms() = default; + ~LAMMPS_create_atoms() override = default; + + void SetUp() override + { + ::testing::internal::CaptureStdout(); + lmp = (LAMMPS_NS::LAMMPS *)f_lammps_with_args(); + std::string output = ::testing::internal::GetCapturedStdout(); + EXPECT_STREQ(output.substr(0, 8).c_str(), "LAMMPS ("); + } + void TearDown() override + { + ::testing::internal::CaptureStdout(); + f_lammps_close(); + std::string output = ::testing::internal::GetCapturedStdout(); + EXPECT_STREQ(output.substr(0, 16).c_str(), "Total wall time:"); + lmp = nullptr; + } +}; + +TEST_F(LAMMPS_create_atoms, create_three) +{ + f_lammps_setup_create_atoms(); +#ifdef LAMMPS_BIGBIG + int64_t *tag, *image; +#else + int *tag, *image; +#endif + double **x, **v; + EXPECT_EQ(lmp->atom->nlocal, 3); + tag = lmp->atom->tag; + image = lmp->atom->image; + x = lmp->atom->x; + v = lmp->atom->v; + f_lammps_create_three_atoms(); + EXPECT_EQ(lmp->atom->nlocal, 6); + for (int i = 0; i < lmp->atom->nlocal; i++) { + if (tag[i] == 4) { + EXPECT_EQ(image[i],lammps_encode_image_flags(1,-1,3)); + EXPECT_DOUBLE_EQ(x[i][0],1.0); + EXPECT_DOUBLE_EQ(x[i][1],1.8); + EXPECT_DOUBLE_EQ(x[i][2],2.718281828); + EXPECT_DOUBLE_EQ(v[i][0],0.0); + EXPECT_DOUBLE_EQ(v[i][1],1.0); + EXPECT_DOUBLE_EQ(v[i][2],-1.0); + } + if (tag[i] == 5) { + EXPECT_EQ(image[i],lammps_encode_image_flags(-2,-2,1)); + EXPECT_DOUBLE_EQ(x[i][0],1.8); + EXPECT_DOUBLE_EQ(x[i][1],0.1); + EXPECT_DOUBLE_EQ(x[i][2],1.8); + EXPECT_DOUBLE_EQ(v[i][0],1.0); + EXPECT_DOUBLE_EQ(v[i][1],-1.0); + EXPECT_DOUBLE_EQ(v[i][2],3.0); + } + if (tag[i] == 6) { + EXPECT_EQ(image[i],lammps_encode_image_flags(-2,0,0)); + EXPECT_DOUBLE_EQ(x[i][0],0.6); + EXPECT_DOUBLE_EQ(x[i][1],0.8); + EXPECT_DOUBLE_EQ(x[i][2],2.2); + EXPECT_DOUBLE_EQ(v[i][0],0.1); + EXPECT_DOUBLE_EQ(v[i][1],0.2); + EXPECT_DOUBLE_EQ(v[i][2],-0.2); + } + } +}; + +TEST_F(LAMMPS_create_atoms, create_two_more) +{ + f_lammps_setup_create_atoms(); +#ifdef LAMMPS_BIGBIG + int64_t *tag, *image; +#else + int *tag, *image; +#endif + double **x, **v; + f_lammps_create_three_atoms(); + EXPECT_EQ(lmp->atom->nlocal, 6); + f_lammps_create_two_more(); + EXPECT_EQ(lmp->atom->nlocal, 8); + tag = lmp->atom->tag; + image = lmp->atom->image; + x = lmp->atom->x; + v = lmp->atom->v; + for (int i = 0; i < lmp->atom->nlocal; i++) { + if (tag[i] == 7) { + EXPECT_EQ(image[i],lammps_encode_image_flags(0,0,0)); + EXPECT_DOUBLE_EQ(x[i][0],0.1); + EXPECT_DOUBLE_EQ(x[i][1],1.9); + EXPECT_DOUBLE_EQ(x[i][2],3.8); + EXPECT_DOUBLE_EQ(v[i][0],0.0); + EXPECT_DOUBLE_EQ(v[i][1],0.0); + EXPECT_DOUBLE_EQ(v[i][2],0.0); + } + if (tag[i] == 8) { + EXPECT_EQ(image[i],lammps_encode_image_flags(0,0,0)); + EXPECT_DOUBLE_EQ(x[i][0],1.2); + EXPECT_DOUBLE_EQ(x[i][1],2.1); + EXPECT_DOUBLE_EQ(x[i][2],1.25); + EXPECT_DOUBLE_EQ(v[i][0],0.0); + EXPECT_DOUBLE_EQ(v[i][1],0.0); + EXPECT_DOUBLE_EQ(v[i][2],0.0); + } + } +}; + +TEST_F(LAMMPS_create_atoms, create_two_more_bigsmall) +{ + f_lammps_setup_create_atoms(); +#ifdef LAMMPS_BIGBIG + int64_t *tag, *image; +#else + int *tag, *image; +#endif + double **x, **v; + f_lammps_create_three_atoms(); + EXPECT_EQ(lmp->atom->nlocal, 6); +#ifdef LAMMPS_BIGBIG + f_lammps_create_two_more_big(); +#else + f_lammps_create_two_more_small(); +#endif + EXPECT_EQ(lmp->atom->nlocal, 8); + tag = lmp->atom->tag; + image = lmp->atom->image; + x = lmp->atom->x; + v = lmp->atom->v; + for (int i = 0; i < lmp->atom->nlocal; i++) { + if (tag[i] == 7) { + EXPECT_EQ(image[i],lammps_encode_image_flags(-1,0,0)); + EXPECT_DOUBLE_EQ(x[i][0],1.2); + EXPECT_DOUBLE_EQ(x[i][1],2.1); + EXPECT_DOUBLE_EQ(x[i][2],1.25); + EXPECT_DOUBLE_EQ(v[i][0],0.0); + EXPECT_DOUBLE_EQ(v[i][1],0.0); + EXPECT_DOUBLE_EQ(v[i][2],0.0); + } + if (tag[i] == 8) { + EXPECT_EQ(image[i],lammps_encode_image_flags(1,0,0)); + EXPECT_DOUBLE_EQ(x[i][0],0.1); + EXPECT_DOUBLE_EQ(x[i][1],1.9); + EXPECT_DOUBLE_EQ(x[i][2],3.8); + EXPECT_DOUBLE_EQ(v[i][0],0.0); + EXPECT_DOUBLE_EQ(v[i][1],0.0); + EXPECT_DOUBLE_EQ(v[i][2],0.0); + } + } +}; + +TEST_F(LAMMPS_create_atoms, create_two_more_bigsmall2) +{ + f_lammps_setup_create_atoms(); +#ifdef LAMMPS_BIGBIG + int64_t *tag, *image; +#else + int *tag, *image; +#endif + double **x, **v; + f_lammps_create_three_atoms(); + EXPECT_EQ(lmp->atom->nlocal, 6); +#ifdef LAMMPS_BIGBIG + f_lammps_create_two_more_big2(); +#else + f_lammps_create_two_more_small2(); +#endif + EXPECT_EQ(lmp->atom->nlocal, 8); + tag = lmp->atom->tag; + image = lmp->atom->image; + x = lmp->atom->x; + v = lmp->atom->v; + for (int i = 0; i < lmp->atom->nlocal; i++) { + if (tag[i] == 7) { + EXPECT_EQ(image[i],lammps_encode_image_flags(0,0,0)); + EXPECT_DOUBLE_EQ(x[i][0],1.2); + EXPECT_DOUBLE_EQ(x[i][1],2.1); + EXPECT_DOUBLE_EQ(x[i][2],1.25); + EXPECT_DOUBLE_EQ(v[i][0],0.0); + EXPECT_DOUBLE_EQ(v[i][1],0.0); + EXPECT_DOUBLE_EQ(v[i][2],0.0); + } + if (tag[i] == 8) { + EXPECT_EQ(image[i],lammps_encode_image_flags(0,0,0)); + EXPECT_DOUBLE_EQ(x[i][0],0.1); + EXPECT_DOUBLE_EQ(x[i][1],1.9); + EXPECT_DOUBLE_EQ(x[i][2],3.8); + EXPECT_DOUBLE_EQ(v[i][0],0.0); + EXPECT_DOUBLE_EQ(v[i][1],0.0); + EXPECT_DOUBLE_EQ(v[i][2],0.0); + } + } +}; diff --git a/unittest/fortran/wrap_fixexternal.cpp b/unittest/fortran/wrap_fixexternal.cpp new file mode 100644 index 0000000000..694aceb009 --- /dev/null +++ b/unittest/fortran/wrap_fixexternal.cpp @@ -0,0 +1,194 @@ + +// unit tests for gathering and scattering data from a LAMMPS instance through +// the Fortran wrapper + +#include "lammps.h" +#include "library.h" +#include +#include +#include +#include + +#include "gtest/gtest.h" + +// prototypes for Fortran reverse wrapper functions +extern "C" { +void *f_lammps_with_args(); +void f_lammps_close(); +void f_lammps_setup_fix_external_callback(); +void f_lammps_setup_fix_external_array(); +void f_lammps_set_fix_external_callbacks(); +void f_lammps_get_force(int, double*); +void f_lammps_reverse_direction(); +void f_lammps_find_forces(); +void f_lammps_add_energy(); +void f_lammps_set_virial(); +double f_lammps_find_peratom_energy(int); +void f_lammps_find_peratom_virial(double[6], int); +void f_lammps_fixexternal_set_vector(); +} + +using namespace LAMMPS_NS; + +class LAMMPS_fixexternal : public ::testing::Test { +protected: + LAMMPS_NS::LAMMPS *lmp; + LAMMPS_fixexternal() = default; + ~LAMMPS_fixexternal() override = default; + + void SetUp() override + { + ::testing::internal::CaptureStdout(); + lmp = (LAMMPS_NS::LAMMPS *)f_lammps_with_args(); + std::string output = ::testing::internal::GetCapturedStdout(); + EXPECT_STREQ(output.substr(0, 8).c_str(), "LAMMPS ("); + } + void TearDown() override + { + ::testing::internal::CaptureStdout(); + f_lammps_close(); + std::string output = ::testing::internal::GetCapturedStdout(); + EXPECT_STREQ(output.substr(0, 16).c_str(), "Total wall time:"); + lmp = nullptr; + } +}; + +TEST_F(LAMMPS_fixexternal, callback) +{ + f_lammps_setup_fix_external_callback(); + f_lammps_set_fix_external_callbacks(); + lammps_command(lmp, "run 0"); + double f[3]; + f_lammps_get_force(1,f); + EXPECT_DOUBLE_EQ(f[0], 3.0); + EXPECT_DOUBLE_EQ(f[1], -3.0); + EXPECT_DOUBLE_EQ(f[2], 3.75); + f_lammps_get_force(2,f); + EXPECT_DOUBLE_EQ(f[0], -3.0); + EXPECT_DOUBLE_EQ(f[1], 3.0); + EXPECT_DOUBLE_EQ(f[2], -3.75); + + f_lammps_reverse_direction(); + f_lammps_set_fix_external_callbacks(); + lammps_command(lmp, "run 0"); + f_lammps_get_force(1,f); + EXPECT_DOUBLE_EQ(f[0], -1.0); + EXPECT_DOUBLE_EQ(f[1], 1.0); + EXPECT_DOUBLE_EQ(f[2], -1.25); + f_lammps_get_force(2,f); + EXPECT_DOUBLE_EQ(f[0], 1.0); + EXPECT_DOUBLE_EQ(f[1], -1.0); + EXPECT_DOUBLE_EQ(f[2], 1.25); +}; + +TEST_F(LAMMPS_fixexternal, array) +{ + f_lammps_setup_fix_external_array(); + double **f; + f = (double**) lammps_extract_atom(lmp, "f"); + f_lammps_find_forces(); + lammps_command(lmp, "run 0"); + EXPECT_DOUBLE_EQ(f[0][0], 14.0); + EXPECT_DOUBLE_EQ(f[0][1], -14.0); + EXPECT_DOUBLE_EQ(f[0][2], 18.0); + EXPECT_DOUBLE_EQ(f[1][0], 16.0); + EXPECT_DOUBLE_EQ(f[1][1], -16.0); + EXPECT_DOUBLE_EQ(f[1][2], 20.0); +}; + +TEST_F(LAMMPS_fixexternal, energy_global) +{ + f_lammps_setup_fix_external_array(); + double energy; + f_lammps_add_energy(); + lammps_command(lmp, "run 0"); + energy = lammps_get_thermo(lmp, "etotal"); + EXPECT_DOUBLE_EQ(energy, -20.2); +}; + +TEST_F(LAMMPS_fixexternal, virial_global) +{ + f_lammps_setup_fix_external_array(); + double virial[6], volume; + f_lammps_set_virial(); + lammps_command(lmp, "run 0"); + volume = lammps_get_thermo(lmp, "vol"); + virial[0] = lammps_get_thermo(lmp, "pxx"); + virial[1] = lammps_get_thermo(lmp, "pyy"); + virial[2] = lammps_get_thermo(lmp, "pzz"); + virial[3] = lammps_get_thermo(lmp, "pxy"); + virial[4] = lammps_get_thermo(lmp, "pxz"); + virial[5] = lammps_get_thermo(lmp, "pyz"); + EXPECT_DOUBLE_EQ(virial[0], 1.0/volume); + EXPECT_DOUBLE_EQ(virial[1], 2.0/volume); + EXPECT_DOUBLE_EQ(virial[2], 2.5/volume); + EXPECT_DOUBLE_EQ(virial[3], -1.0/volume); + EXPECT_DOUBLE_EQ(virial[4], -2.25/volume); + EXPECT_DOUBLE_EQ(virial[5], -3.02/volume); +}; + +TEST_F(LAMMPS_fixexternal, energy_peratom) +{ + f_lammps_setup_fix_external_callback(); + f_lammps_set_fix_external_callbacks(); + lammps_command(lmp, "compute peratom all pe/atom"); + double energy; + lammps_command(lmp, "run 0"); + int nlocal = lammps_extract_setting(lmp, "nlocal"); + for (int i = 1; i <= nlocal; i++) + { + energy = f_lammps_find_peratom_energy(i); + if (i == 1) + EXPECT_DOUBLE_EQ(energy, 1.0); + else + EXPECT_DOUBLE_EQ(energy, 10.0); + } +}; + +TEST_F(LAMMPS_fixexternal, virial_peratom) +{ + f_lammps_setup_fix_external_callback(); + f_lammps_set_fix_external_callbacks(); + lammps_command(lmp, "compute vperatom all stress/atom NULL"); + double virial[6]; + lammps_command(lmp, "run 0"); + int nlocal = lammps_extract_setting(lmp, "nlocal"); + for (int i = 1; i <= nlocal; i++) + { + f_lammps_find_peratom_virial(virial, i); + if (i == 1) + { + EXPECT_DOUBLE_EQ(virial[0], -1.0); + EXPECT_DOUBLE_EQ(virial[1], -2.0); + EXPECT_DOUBLE_EQ(virial[2], 1.0); + EXPECT_DOUBLE_EQ(virial[3], 2.0); + EXPECT_DOUBLE_EQ(virial[4], -3.0); + EXPECT_DOUBLE_EQ(virial[5], 3.0); + } + else + { + EXPECT_DOUBLE_EQ(virial[0], -10.0); + EXPECT_DOUBLE_EQ(virial[1], -20.0); + EXPECT_DOUBLE_EQ(virial[2], 10.0); + EXPECT_DOUBLE_EQ(virial[3], 20.0); + EXPECT_DOUBLE_EQ(virial[4], -30.0); + EXPECT_DOUBLE_EQ(virial[5], 30.0); + } + } +}; + +TEST_F(LAMMPS_fixexternal, vector) +{ + f_lammps_setup_fix_external_callback(); + f_lammps_set_fix_external_callbacks(); + f_lammps_fixexternal_set_vector(); + lammps_command(lmp, "run 0"); + double *v; + for (int i = 0; i < 8; i++) + { + v = (double*) lammps_extract_fix(lmp, "ext2", LMP_STYLE_GLOBAL, + LMP_TYPE_VECTOR, i, 1); + EXPECT_DOUBLE_EQ(i+1, *v); + std::free(v); + } +}; diff --git a/unittest/fortran/wrap_gather_scatter.cpp b/unittest/fortran/wrap_gather_scatter.cpp index 3b70c4393e..5eecf763a6 100644 --- a/unittest/fortran/wrap_gather_scatter.cpp +++ b/unittest/fortran/wrap_gather_scatter.cpp @@ -3,6 +3,7 @@ #include "lammps.h" #include "library.h" +#include "atom.h" #include #include #include @@ -23,8 +24,18 @@ int f_lammps_gather_atoms_subset_mask(int); double f_lammps_gather_atoms_subset_position(int, int); void f_lammps_scatter_atoms_masks(); void f_lammps_scatter_atoms_positions(); +void f_lammps_setup_gather_bonds(); +int f_lammps_test_gather_bonds_small(); +int f_lammps_test_gather_bonds_big(); +double f_lammps_gather_pe_atom(int); +double f_lammps_gather_pe_atom_concat(int); +void f_lammps_gather_pe_atom_subset(int*, double*); +void f_lammps_scatter_compute(); +void f_lammps_scatter_subset_compute(); } +using namespace LAMMPS_NS; + class LAMMPS_gather_scatter : public ::testing::Test { protected: LAMMPS_NS::LAMMPS *lmp; @@ -200,3 +211,124 @@ TEST_F(LAMMPS_gather_scatter, scatter_atoms_subset_mask) EXPECT_EQ(f_lammps_gather_atoms_mask(1), 9); EXPECT_EQ(f_lammps_gather_atoms_mask(3), 3); }; + +TEST_F(LAMMPS_gather_scatter, gather_bonds) +{ + if (!lammps_has_style(lmp, "atom", "full")) GTEST_SKIP(); + f_lammps_setup_gather_bonds(); +#ifdef LAMMPS_BIGBIG + EXPECT_EQ(f_lammps_test_gather_bonds_big(), 1); +#else + EXPECT_EQ(f_lammps_test_gather_bonds_small(), 1); +#endif +}; + +TEST_F(LAMMPS_gather_scatter, gather_compute) +{ +#ifdef LAMMPS_BIGBIG + GTEST_SKIP(); +#else + f_lammps_setup_gather_scatter(); + lammps_command(lmp, "run 0"); + int natoms = lmp->atom->natoms; + int *tag = lmp->atom->tag; + double *pe = (double*) lammps_extract_compute(lmp, "pe", LMP_STYLE_ATOM, + LMP_TYPE_VECTOR); + for (int i = 0; i < natoms; i++) + EXPECT_DOUBLE_EQ(f_lammps_gather_pe_atom(tag[i]), pe[i]); +#endif +}; + +TEST_F(LAMMPS_gather_scatter, gather_compute_concat) +{ +#ifdef LAMMPS_BIGBIG + GTEST_SKIP(); +#else + f_lammps_setup_gather_scatter(); + lammps_command(lmp, "run 0"); + int natoms = lmp->atom->natoms; + int *tag = lmp->atom->tag; + double *pe = (double*) lammps_extract_compute(lmp, "pe", LMP_STYLE_ATOM, + LMP_TYPE_VECTOR); + for (int i = 0; i < natoms; i++) + EXPECT_DOUBLE_EQ(f_lammps_gather_pe_atom(tag[i]), pe[i]); +#endif +}; + +TEST_F(LAMMPS_gather_scatter, gather_compute_subset) +{ +#ifdef LAMMPS_BIGBIG + GTEST_SKIP(); +#else + f_lammps_setup_gather_scatter(); + lammps_command(lmp, "run 0"); + int ids[2] = {3, 1}; + int *tag = lmp->atom->tag; + double pe[2] = {0.0, 0.0}; + int nlocal = lammps_extract_setting(lmp, "nlocal"); + double *pa_pe = (double*) lammps_extract_compute(lmp, "pe", LMP_STYLE_ATOM, + LMP_TYPE_VECTOR); + + for (int i = 0; i < nlocal; i++) { + if(tag[i] == ids[0]) pe[0] = pa_pe[i]; + if(tag[i] == ids[1]) pe[1] = pa_pe[i]; + } + + double ftn_pe[2]; + f_lammps_gather_pe_atom_subset(ids, ftn_pe); + EXPECT_DOUBLE_EQ(ftn_pe[0], pe[0]); + EXPECT_DOUBLE_EQ(ftn_pe[1], pe[1]); +#endif +}; + +TEST_F(LAMMPS_gather_scatter, scatter_compute) +{ +#ifdef LAMMPS_BIGBIG + GTEST_SKIP(); +#else + f_lammps_setup_gather_scatter(); + int natoms = lmp->atom->natoms; + double *pe = new double[natoms]; + lammps_command(lmp, "run 0"); + lammps_gather(lmp, "c_pe", 1, 1, pe); + double *old_pe = new double[natoms]; + for (int i = 0; i < natoms; i++) + old_pe[i] = pe[i]; + EXPECT_DOUBLE_EQ(pe[0], old_pe[0]); + EXPECT_DOUBLE_EQ(pe[1], old_pe[1]); + EXPECT_DOUBLE_EQ(pe[2], old_pe[2]); + f_lammps_scatter_compute(); + lammps_gather(lmp, "c_pe", 1, 1, pe); + EXPECT_DOUBLE_EQ(pe[0], old_pe[2]); + EXPECT_DOUBLE_EQ(pe[1], old_pe[1]); + EXPECT_DOUBLE_EQ(pe[2], old_pe[0]); + delete[] old_pe; + delete[] pe; +#endif +}; + +TEST_F(LAMMPS_gather_scatter, scatter_subset_compute) +{ +#ifdef LAMMPS_BIGBIG + GTEST_SKIP(); +#else + f_lammps_setup_gather_scatter(); + int natoms = lmp->atom->natoms; + double *pe = new double[natoms]; + lammps_command(lmp, "run 0"); + lammps_gather(lmp, "c_pe", 1, 1, pe); + double *old_pe = new double[natoms]; + for (int i = 0; i < natoms; i++) + old_pe[i] = pe[i]; + EXPECT_DOUBLE_EQ(pe[0], old_pe[0]); + EXPECT_DOUBLE_EQ(pe[1], old_pe[1]); + EXPECT_DOUBLE_EQ(pe[2], old_pe[2]); + f_lammps_scatter_subset_compute(); + lammps_gather(lmp, "c_pe", 1, 1, pe); + EXPECT_DOUBLE_EQ(pe[0], old_pe[2]); + EXPECT_DOUBLE_EQ(pe[1], old_pe[1]); + EXPECT_DOUBLE_EQ(pe[2], old_pe[0]); + delete[] old_pe; + delete[] pe; +#endif +}; diff --git a/unittest/fortran/wrap_neighlist.cpp b/unittest/fortran/wrap_neighlist.cpp new file mode 100644 index 0000000000..ce09dcccb6 --- /dev/null +++ b/unittest/fortran/wrap_neighlist.cpp @@ -0,0 +1,123 @@ +// unit tests for accessing neighbor lists in a LAMMPS instance through the Fortran wrapper + +#include "lammps.h" +#include "library.h" +#include "force.h" +#include "modify.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "info.h" +//#include +//#include +#include +#include + +#include "gtest/gtest.h" + +// prototypes for Fortran reverse wrapper functions +extern "C" { +void *f_lammps_with_args(); +void f_lammps_close(); +void f_lammps_setup_neigh_tests(); +int f_lammps_pair_neighlist_test(); +int f_lammps_fix_neighlist_test(); +int f_lammps_compute_neighlist_test(); +int f_lammps_neighlist_num_elements(int); +} + +namespace LAMMPS_NS { + +class LAMMPS_neighbors : public ::testing::Test { +protected: + LAMMPS_NS::LAMMPS *lmp; + LAMMPS_neighbors() = default; + ~LAMMPS_neighbors() override = default; + + void SetUp() override { + ::testing::internal::CaptureStdout(); + lmp = (LAMMPS_NS::LAMMPS *)f_lammps_with_args(); + std::string output = ::testing::internal::GetCapturedStdout(); + EXPECT_STREQ(output.substr(0, 8).c_str(), "LAMMPS ("); + } + void TearDown() override { + ::testing::internal::CaptureStdout(); + f_lammps_close(); + std::string output = ::testing::internal::GetCapturedStdout(); + EXPECT_STREQ(output.substr(0, 16).c_str(), "Total wall time:"); + lmp = nullptr; + } +}; + +TEST_F(LAMMPS_neighbors, pair) +{ + f_lammps_setup_neigh_tests(); + int pair_neighlist = f_lammps_pair_neighlist_test(); + Pair *pair = lmp->force->pair_match("lj/cut",1,0); + int index = -2; + if (pair != nullptr) { + for (int i = 0; i < lmp->neighbor->nlist; i++) { + NeighList *list = lmp->neighbor->lists[i]; + if ((list->requestor_type == NeighList::PAIR) + and (pair == list->requestor) + and (list->id == 0)) { + index = i; + break; + } + } + } + EXPECT_EQ(index, pair_neighlist); +}; + +TEST_F(LAMMPS_neighbors, fix) +{ + if (not Info::has_package("REPLICA")) GTEST_SKIP(); + f_lammps_setup_neigh_tests(); + auto fix = lmp->modify->get_fix_by_id("f"); + EXPECT_NE(fix, nullptr); + int ilist = -2; + for (int i = 0; i < lmp->neighbor->nlist; i++) { + NeighList *list = lmp->neighbor->lists[i]; + if ( (list->requestor_type == NeighList::FIX) + and (fix == list->requestor) and (list->id == 0) ) { + ilist = i; + break; + } + } + EXPECT_EQ(ilist, f_lammps_fix_neighlist_test()); +}; + +TEST_F(LAMMPS_neighbors, compute) +{ + f_lammps_setup_neigh_tests(); + auto compute = lmp->modify->get_compute_by_id("c"); + EXPECT_NE(compute,nullptr); + int ilist = -2; + for (int i=0; i < lmp->neighbor->nlist; i++) { + NeighList *list = lmp->neighbor->lists[i]; + if ( (list->requestor_type == NeighList::COMPUTE) + and (compute == list->requestor) and (list->id == 0) ) { + ilist = i; + break; + } + } + EXPECT_EQ(ilist, f_lammps_compute_neighlist_test()); +}; + +TEST_F(LAMMPS_neighbors, numelements) +{ + f_lammps_setup_neigh_tests(); + int num_neigh = 0; + int pair_id = f_lammps_pair_neighlist_test(); + num_neigh = f_lammps_neighlist_num_elements(pair_id); + EXPECT_EQ(num_neigh, lammps_neighlist_num_elements(lmp, pair_id)); + if (Info::has_package("REPLICA")) { + int fix_id = f_lammps_fix_neighlist_test(); + num_neigh = f_lammps_neighlist_num_elements(fix_id); + EXPECT_EQ(num_neigh, lammps_neighlist_num_elements(lmp, fix_id)); + } + int compute_id = f_lammps_compute_neighlist_test(); + num_neigh = f_lammps_neighlist_num_elements(compute_id); + EXPECT_EQ(num_neigh, lammps_neighlist_num_elements(lmp, compute_id)); +}; + +} // LAMMPS_NS diff --git a/unittest/fortran/wrap_properties.cpp b/unittest/fortran/wrap_properties.cpp index 5268548d48..50704d326a 100644 --- a/unittest/fortran/wrap_properties.cpp +++ b/unittest/fortran/wrap_properties.cpp @@ -2,7 +2,9 @@ #include "lammps.h" #include "library.h" +#include "info.h" +#include #include #include "gmock/gmock.h" @@ -12,12 +14,15 @@ extern "C" { void *f_lammps_with_args(); void f_lammps_close(); -int f_lammps_version(); void f_lammps_memory_usage(double *); int f_lammps_get_mpi_comm(); int f_lammps_extract_setting(const char *); int f_lammps_has_error(); int f_lammps_get_last_error_message(char *, int); +int f_lammps_get_image_flags_int(int, int, int); +int64_t f_lammps_get_image_flags_bigint(int, int, int); +void f_lammps_decode_image_flags(int, int*); +void f_lammps_decode_image_flags_bigbig(int64_t, int*); } namespace LAMMPS_NS { @@ -47,11 +52,6 @@ protected: } }; -TEST_F(LAMMPS_properties, version) -{ - EXPECT_LT(20200917, f_lammps_version()); -}; - TEST_F(LAMMPS_properties, memory_usage) { // copied from c-library, with a two-character modification @@ -85,9 +85,17 @@ TEST_F(LAMMPS_properties, extract_setting) #if defined(LAMMPS_BIGBIG) EXPECT_EQ(f_lammps_extract_setting("tagint"), 8); EXPECT_EQ(f_lammps_extract_setting("imageint"), 8); + EXPECT_EQ(f_lammps_extract_setting("IMGMASK"), 2097151); + EXPECT_EQ(f_lammps_extract_setting("IMGMAX"), 1048576); + EXPECT_EQ(f_lammps_extract_setting("IMGBITS"), 21); + EXPECT_EQ(f_lammps_extract_setting("IMG2BITS"), 42); #else EXPECT_EQ(f_lammps_extract_setting("tagint"), 4); EXPECT_EQ(f_lammps_extract_setting("imageint"), 4); + EXPECT_EQ(f_lammps_extract_setting("IMGMASK"), 1023); + EXPECT_EQ(f_lammps_extract_setting("IMGMAX"), 512); + EXPECT_EQ(f_lammps_extract_setting("IMGBITS"), 10); + EXPECT_EQ(f_lammps_extract_setting("IMG2BITS"), 20); #endif EXPECT_EQ(f_lammps_extract_setting("box_exist"), 0); @@ -141,4 +149,39 @@ TEST_F(LAMMPS_properties, has_error) EXPECT_EQ(err, 0); EXPECT_THAT(errmsg, ContainsRegex(" ")); }; + +TEST_F(LAMMPS_properties, get_image_flags) +{ +#ifdef LAMMPS_BIGBIG + int64_t image = f_lammps_get_image_flags_bigint(0,0,0); + int64_t Cimage = lammps_encode_image_flags(0,0,0); + EXPECT_EQ(image, Cimage); + image = f_lammps_get_image_flags_bigint(1,-1,1); + Cimage = lammps_encode_image_flags(1,-1,1); + EXPECT_EQ(image, Cimage); +#else + int image = f_lammps_get_image_flags_int(0,0,0); + int Cimage = lammps_encode_image_flags(0,0,0); + EXPECT_EQ(image, Cimage); + image = f_lammps_get_image_flags_int(1,-1,1); + Cimage = lammps_encode_image_flags(1,-1,1); + EXPECT_EQ(image, Cimage); +#endif +} + +TEST_F(LAMMPS_properties, decode_image_flags) +{ + int flag[3]; +#ifdef LAMMPS_BIGBIG + int64_t image = f_lammps_get_image_flags_bigint(1,3,-2); + f_lammps_decode_image_flags_bigbig(image, flag); +#else + int image = f_lammps_get_image_flags_int(1,3,-2); + f_lammps_decode_image_flags(image, flag); +#endif + EXPECT_EQ(flag[0], 1); + EXPECT_EQ(flag[1], 3); + EXPECT_EQ(flag[2], -2); +}; + } // namespace LAMMPS_NS diff --git a/unittest/python/python-capabilities.py b/unittest/python/python-capabilities.py index 3ac66ebdc6..be38a9f090 100644 --- a/unittest/python/python-capabilities.py +++ b/unittest/python/python-capabilities.py @@ -60,6 +60,13 @@ class PythonCapabilities(unittest.TestCase): for pkg in selected_packages: self.assertIn(pkg, installed_packages) + def test_has_package(self): + selected_packages = [key[4:] for key in self.cmake_cache.keys() if not key.startswith('PKG_CONFIG') and key.startswith('PKG_') and self.cmake_cache[key]] + self.assertFalse(self.lmp.has_package('XXXXXX')) + + for pkg in selected_packages: + self.assertTrue(self.lmp.has_package(pkg)) + def test_has_style(self): self.assertTrue(self.lmp.has_style('pair', 'lj/cut')) self.assertFalse(self.lmp.has_style('pair', 'lennard_jones')) diff --git a/unittest/python/python-pizza.py b/unittest/python/python-pizza.py index fd28ff9129..939c22a267 100644 --- a/unittest/python/python-pizza.py +++ b/unittest/python/python-pizza.py @@ -11,12 +11,21 @@ sys.path.insert(1,PIZZA_DIR) # dump class uses NumPy, so only load and test dump if NumPy is available has_numpy = False +has_molecule = False +machine = None +if 'LAMMPS_MACHINE_NAME' in os.environ: + machine=os.environ['LAMMPS_MACHINE_NAME'] +tmplmp = lammps(name=machine, cmdargs=['-nocite', '-log', 'none', '-echo', 'screen']) +has_molecule = tmplmp.has_package('MOLECULE') +tmplmp.close() + try: import numpy has_numpy = True import dump except: pass +do_dump_test = has_numpy and has_molecule import log @@ -116,11 +125,12 @@ class PythonDump(unittest.TestCase): if 'LAMMPS_MACHINE_NAME' in os.environ: machine=os.environ['LAMMPS_MACHINE_NAME'] self.lmp = lammps(name=machine, cmdargs=['-nocite', '-log', 'none', '-echo', 'screen']) + self.do_dump_test = self.lmp.has_package('MOLECULE') and has_numpy def tearDown(self): del self.lmp - @unittest.skipIf(not has_numpy,"Missing the NumPy python module") + @unittest.skipIf(not do_dump_test,"Missing the NumPy python module or MOLECULE package") def testDumpCustom(self): dumpfile = os.path.join(os.path.abspath('.'), 'dump.custom') self.lmp.command('shell cd ' + os.environ['TEST_INPUT_DIR']) diff --git a/unittest/python/test_python_package.cpp b/unittest/python/test_python_package.cpp index 377c3a7549..f998ebbcd8 100644 --- a/unittest/python/test_python_package.cpp +++ b/unittest/python/test_python_package.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -276,7 +276,7 @@ TEST_F(PythonPackageTest, RunSource) { // execute python script from file auto output = CAPTURE_OUTPUT([&] { - command("python xyz source ${input_dir}/run.py"); + command("python source ${input_dir}/run.py"); }); ASSERT_THAT(output, HasSubstr(LOREM_IPSUM)); @@ -286,7 +286,7 @@ TEST_F(PythonPackageTest, RunSourceInline) { // execute inline python script auto output = CAPTURE_OUTPUT([&] { - command("python xyz source \"\"\"\n" + command("python source here \"\"\"\n" "from __future__ import print_function\n" "print(2+2)\n" "\"\"\""); diff --git a/unittest/testing/core.h b/unittest/testing/core.h index 5b2aba6fd3..b64affc0c7 100644 --- a/unittest/testing/core.h +++ b/unittest/testing/core.h @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/testing/mpitesting.h b/unittest/testing/mpitesting.h index a69337e1c0..72f1dd9fa5 100644 --- a/unittest/testing/mpitesting.h +++ b/unittest/testing/mpitesting.h @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/testing/systems/melt.h b/unittest/testing/systems/melt.h index b61fec9927..dfebdb8c8f 100644 --- a/unittest/testing/systems/melt.h +++ b/unittest/testing/systems/melt.h @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/testing/test_mpi_main.h b/unittest/testing/test_mpi_main.h index ad78e3ace0..da30710b95 100644 --- a/unittest/testing/test_mpi_main.h +++ b/unittest/testing/test_mpi_main.h @@ -1,7 +1,7 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/testing/utils.h b/unittest/testing/utils.h index 46dc9b5694..a28348fce7 100644 --- a/unittest/testing/utils.h +++ b/unittest/testing/utils.h @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/utils/test_argutils.cpp b/unittest/utils/test_argutils.cpp index c5ef19bc10..2d7d83ef9d 100644 --- a/unittest/utils/test_argutils.cpp +++ b/unittest/utils/test_argutils.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/utils/test_fmtlib.cpp b/unittest/utils/test_fmtlib.cpp index fb4e58e6da..67cfad2f0b 100644 --- a/unittest/utils/test_fmtlib.cpp +++ b/unittest/utils/test_fmtlib.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/utils/test_mempool.cpp b/unittest/utils/test_mempool.cpp index 5c545023b0..9194ce3cd7 100644 --- a/unittest/utils/test_mempool.cpp +++ b/unittest/utils/test_mempool.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/utils/test_tokenizer.cpp b/unittest/utils/test_tokenizer.cpp index e895d96576..49cc771a25 100644 --- a/unittest/utils/test_tokenizer.cpp +++ b/unittest/utils/test_tokenizer.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains diff --git a/unittest/utils/test_utils.cpp b/unittest/utils/test_utils.cpp index 2881ad10de..58940f6600 100644 --- a/unittest/utils/test_utils.cpp +++ b/unittest/utils/test_utils.cpp @@ -1,7 +1,7 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov + LAMMPS Development team: developers@lammps.org Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains @@ -300,6 +300,26 @@ TEST(Utils, valid_double9) ASSERT_TRUE(utils::is_double("+.0")); } +TEST(Utils, valid_double10) +{ + ASSERT_TRUE(utils::is_double("-0.15")); +} + +TEST(Utils, valid_double11) +{ + ASSERT_TRUE(utils::is_double("-27.5")); +} + +TEST(Utils, valid_double12) +{ + ASSERT_TRUE(utils::is_double("+0.15")); +} + +TEST(Utils, valid_double13) +{ + ASSERT_TRUE(utils::is_double("+27.5")); +} + TEST(Utils, empty_not_an_integer) { ASSERT_FALSE(utils::is_integer("")); @@ -315,6 +335,66 @@ TEST(Utils, text_not_an_integer) ASSERT_FALSE(utils::is_integer("one")); } +TEST(Utils, minus_not_an_integer1) +{ + ASSERT_FALSE(utils::is_integer("1-")); +} + +TEST(Utils, plus_not_an_integer1) +{ + ASSERT_FALSE(utils::is_integer("1+")); +} + +TEST(Utils, minus_not_an_integer2) +{ + ASSERT_FALSE(utils::is_integer("--1")); +} + +TEST(Utils, plus_not_an_integer2) +{ + ASSERT_FALSE(utils::is_integer("++1")); +} + +TEST(Utils, plusminus_not_an_integer1) +{ + ASSERT_FALSE(utils::is_integer("-+1")); +} + +TEST(Utils, plusminus_not_an_integer2) +{ + ASSERT_FALSE(utils::is_integer("+-1")); +} + +TEST(Utils, minus_not_a_double1) +{ + ASSERT_FALSE(utils::is_double("1-")); +} + +TEST(Utils, plus_not_a_double1) +{ + ASSERT_FALSE(utils::is_double("1+")); +} + +TEST(Utils, minus_not_a_double2) +{ + ASSERT_FALSE(utils::is_double("--1")); +} + +TEST(Utils, plus_not_a_double2) +{ + ASSERT_FALSE(utils::is_double("++1")); +} + +TEST(Utils, plusminus_not_a_double1) +{ + ASSERT_FALSE(utils::is_double("+-1")); +} + +TEST(Utils, plusminus_not_a_double2) +{ + ASSERT_FALSE(utils::is_double("-+1")); +} + TEST(Utils, text_not_a_double) { ASSERT_FALSE(utils::is_double("half")); @@ -365,6 +445,11 @@ TEST(Utils, signed_double_and_exponential) ASSERT_TRUE(utils::is_double("-10E-22")); } +TEST(Utils, signed_double_and_broken_exponential) +{ + ASSERT_FALSE(utils::is_double("-10e10-2")); +} + TEST(Utils, is_double_with_d_exponential) { ASSERT_FALSE(utils::is_double("10d22")); @@ -631,6 +716,18 @@ TEST(Utils, strmatch_whitespace_nonwhitespace) ASSERT_TRUE(utils::strmatch(" 5.0 angles\n", "^\\s*\\S+\\s+\\S+\\s")); } +TEST(Utils, strmatch_range) +{ + ASSERT_TRUE(utils::strmatch("*11", "^\\d*\\*\\d*$")); + ASSERT_TRUE(utils::strmatch("2*11", "^\\d*\\*\\d*$")); + ASSERT_TRUE(utils::strmatch("5*", "^\\d*\\*\\d*$")); + ASSERT_TRUE(utils::strmatch("*", "^\\d*\\*\\d*$")); + ASSERT_FALSE(utils::strmatch("x5*", "^\\d*\\*\\d*$")); + ASSERT_FALSE(utils::strmatch("x*", "^\\d*\\*\\d*$")); + ASSERT_FALSE(utils::strmatch("*a", "^\\d*\\*\\d*$")); + ASSERT_FALSE(utils::strmatch("1*2d", "^\\d*\\*\\d*$")); +} + TEST(Utils, strfind_beg) { ASSERT_THAT(utils::strfind("rigid/small/omp", "^rigid"), StrEq("rigid")); @@ -832,6 +929,44 @@ TEST(Utils, boundsbig_case3) ASSERT_EQ(nhi, -1); } +TEST(Utils, parse_grid_id) +{ + auto words = utils::parse_grid_id(FLERR, "c_1:full:density", nullptr); + ASSERT_THAT(words[0], StrEq("c_1")); + ASSERT_THAT(words[1], StrEq("full")); + ASSERT_THAT(words[2], StrEq("density")); + + words = utils::parse_grid_id(FLERR, "c_1:full:density[1]", nullptr); + ASSERT_THAT(words[0], StrEq("c_1")); + ASSERT_THAT(words[1], StrEq("full")); + ASSERT_THAT(words[2], StrEq("density[1]")); + + words = utils::parse_grid_id(FLERR, "c_1:full:density[*]", nullptr); + ASSERT_THAT(words[0], StrEq("c_1")); + ASSERT_THAT(words[1], StrEq("full")); + ASSERT_THAT(words[2], StrEq("density[*]")); + + words = utils::parse_grid_id(FLERR, "c_1_full_density", nullptr); + ASSERT_THAT(words[0], StrEq("")); + ASSERT_THAT(words[1], StrEq("")); + ASSERT_THAT(words[0], StrEq("")); + + words = utils::parse_grid_id(FLERR, "c_1:full:", nullptr); + ASSERT_THAT(words[0], StrEq("")); + ASSERT_THAT(words[1], StrEq("")); + ASSERT_THAT(words[0], StrEq("")); + + words = utils::parse_grid_id(FLERR, ":full:density", nullptr); + ASSERT_THAT(words[0], StrEq("")); + ASSERT_THAT(words[1], StrEq("")); + ASSERT_THAT(words[0], StrEq("")); + + words = utils::parse_grid_id(FLERR, "c_1:full", nullptr); + ASSERT_THAT(words[0], StrEq("")); + ASSERT_THAT(words[1], StrEq("")); + ASSERT_THAT(words[0], StrEq("")); +} + TEST(Utils, errorurl) { auto errmesg = utils::errorurl(10); diff --git a/unittest/utils/testshared.c b/unittest/utils/testshared.c index 12922dea91..e778e671df 100644 --- a/unittest/utils/testshared.c +++ b/unittest/utils/testshared.c @@ -15,6 +15,3 @@ double some_double_function(double arg1, int arg2) sum += arg1; return sum; } - - -