mirror of https://github.com/phonopy/phonopy.git
Use nanobind for C binding
This commit is contained in:
Atsushi Togo
parent
a0873ec6cd
commit
2731d8c3f4
141
CMakeLists.txt
141
CMakeLists.txt
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@ -1,73 +1,128 @@
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cmake_minimum_required(VERSION 3.0)
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cmake_policy(SET CMP0007 NEW)
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cmake_minimum_required(VERSION 3.20)
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project(phonopy C)
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if(NOT SKBUILD_PROJECT_NAME)
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set(SKBUILD_PROJECT_NAME phonopy)
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endif()
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if(PHONOPY_LIBS)
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project(phonopy LANGUAGES C)
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set(CMAKE_MACOSX_RPATH 1)
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set(CMAKE_C_FLAGS_RELEASE "-Wall -O2")
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set(CMAKE_C_FLAGS_DEBUG "-g -DTHMWARNING")
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if(NOT CMAKE_BUILD_TYPE)
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set(CMAKE_BUILD_TYPE Release)
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endif(NOT CMAKE_BUILD_TYPE)
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message(STATUS "Build type: ${CMAKE_BUILD_TYPE}")
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message(STATUS "CMAKE_SYSTEM_PREFIX_PATH: ${CMAKE_SYSTEM_PREFIX_PATH}")
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include(GNUInstallDirs)
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# set(CMAKE_POSITION_INDEPENDENT_CODE ON)
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# Version numbers
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file(READ ${PROJECT_SOURCE_DIR}/phonopy/version.py version_file)
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string(REGEX MATCH "__version__.*([0-9]+)[.]([0-9]+)[.]([0-9]+)" phono3py_version ${version_file})
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string(REGEX MATCH "__version__.*([0-9]+)[.]([0-9]+)[.]([0-9]+)"
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phono3py_version ${version_file})
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set(phonopy_major_version ${CMAKE_MATCH_1})
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set(phonopy_minor_version ${CMAKE_MATCH_2})
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set(phonopy_micro_version ${CMAKE_MATCH_3})
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set(serial "${phonopy_major_version}.${phonopy_minor_version}.${phonopy_micro_version}")
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set(serial
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"${phonopy_major_version}.${phonopy_minor_version}.${phonopy_micro_version}"
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)
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set(soserial "1")
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else()
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project(${SKBUILD_PROJECT_NAME})
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set(DEV_MODULE Development.Module)
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find_package(
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Python 3.8
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REQUIRED COMPONENTS Interpreter ${DEV_MODULE}
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OPTIONAL_COMPONENTS Development.SABIModule
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)
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endif()
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cmake_policy(SET CMP0007 NEW)
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if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
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set(CMAKE_BUILD_TYPE
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Release
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CACHE STRING "Choose the type of build." FORCE)
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set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release"
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"MinSizeRel" "RelWithDebInfo")
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endif()
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message(STATUS "Build type: ${CMAKE_BUILD_TYPE}")
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message(STATUS "CMAKE_SYSTEM_PREFIX_PATH: ${CMAKE_SYSTEM_PREFIX_PATH}")
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find_package(OpenMP)
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if(OpenMP_FOUND)
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message(STATUS "OpenMP libs: ${OpenMP_C_LIBRARIES}")
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message(STATUS "OpenMP flags: ${OpenMP_C_FLAGS}")
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endif()
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if (PHONOPY)
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set(SOURCES_PHONOPY
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${PROJECT_SOURCE_DIR}/c/phonopy.c
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${PROJECT_SOURCE_DIR}/c/dynmat.c
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${PROJECT_SOURCE_DIR}/c/derivative_dynmat.c
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${PROJECT_SOURCE_DIR}/c/rgrid.c
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${PROJECT_SOURCE_DIR}/c/phonopy.c ${PROJECT_SOURCE_DIR}/c/dynmat.c
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${PROJECT_SOURCE_DIR}/c/derivative_dynmat.c ${PROJECT_SOURCE_DIR}/c/rgrid.c
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${PROJECT_SOURCE_DIR}/c/tetrahedron_method.c)
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if (BUILD_SHARED_LIBRARIES)
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if(BUILD_SHARED_LIBS)
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# Shared library
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add_library(phpy SHARED ${SOURCES_PHONOPY})
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add_library(phonopy_libs SHARED ${SOURCES_PHONOPY})
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if(OpenMP_FOUND)
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target_link_libraries(phpy m ${OpenMP_C_LIBRARIES})
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target_compile_options(phpy PRIVATE ${OpenMP_C_FLAGS})
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target_link_libraries(
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phonopy_libs
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PRIVATE m
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PRIVATE OpenMP::OpenMP_C)
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else()
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target_link_libraries(phpy m)
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endif()
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target_include_directories(phpy PRIVATE ${MY_INCLUDES})
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target_compile_definitions(phpy PRIVATE THM_EPSILON=1e-10)
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set_property(TARGET phpy PROPERTY VERSION ${serial})
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set_property(TARGET phpy PROPERTY SOVERSION ${soserial})
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install(TARGETS phpy LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
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target_link_libraries(phonopy_libs PRIVATE m)
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endif()
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target_compile_definitions(phonopy_libs PRIVATE THM_EPSILON=1e-10)
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else()
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# Static link library
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add_library(phpy_static STATIC ${SOURCES_PHONOPY})
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if (OpenMP_FOUND)
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target_link_libraries(phpy_static m ${OpenMP_C_LIBRARIES})
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target_compile_options(phpy_static PRIVATE ${OpenMP_C_FLAGS})
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else()
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target_link_libraries(phpy_static m)
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endif()
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target_include_directories(phpy_static PRIVATE ${MY_INCLUDES})
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target_compile_definitions(phpy_static PRIVATE THM_EPSILON=1e-10)
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set_property(TARGET phpy_static PROPERTY VERSION ${serial})
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set_property(TARGET phpy_static PROPERTY SOVERSION ${soserial})
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set_property(TARGET phpy_static PROPERTY OUTPUT_NAME phpy)
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install(TARGETS phpy_static ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
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add_library(phonopy_libs STATIC ${SOURCES_PHONOPY})
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# Header file
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install(FILES ${PROJECT_SOURCE_DIR}/c/phonopy.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
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if(OpenMP_FOUND)
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target_link_libraries(
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phonopy_libs
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PRIVATE m
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PRIVATE OpenMP::OpenMP_C)
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else()
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target_link_libraries(phonopy_libs PRIVATE m)
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endif()
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target_compile_definitions(phonopy_libs PRIVATE THM_EPSILON=1e-10)
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endif()
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if(PHONOPY_LIBS)
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install(FILES ${PROJECT_SOURCE_DIR}/c/phonopy.h
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DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
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if(BUILD_SHARED_LIBS)
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install(TARGETS phonopy_libs LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
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set_property(TARGET phonopy_libs PROPERTY VERSION ${serial})
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set_property(TARGET phonopy_libs PROPERTY SOVERSION ${soserial})
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else()
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install(TARGETS phonopy_libs ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
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set_property(TARGET phonopy_libs PROPERTY VERSION ${serial})
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set_property(TARGET phonopy_libs PROPERTY SOVERSION ${soserial})
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set_property(TARGET phonopy_libs PROPERTY OUTPUT_NAME phonopy_libs)
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endif()
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else()
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set_target_properties(phonopy_libs PROPERTIES POSITION_INDEPENDENT_CODE ON)
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execute_process(
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COMMAND "${Python_EXECUTABLE}" -m nanobind --cmake_dir
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OUTPUT_STRIP_TRAILING_WHITESPACE
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OUTPUT_VARIABLE NB_DIR)
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list(APPEND CMAKE_PREFIX_PATH "${NB_DIR}")
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find_package(nanobind CONFIG REQUIRED)
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nanobind_add_module(
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_phonopy
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STABLE_ABI
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${PROJECT_SOURCE_DIR}/c/phonopy.h
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${PROJECT_SOURCE_DIR}/c/_phonopy.cpp
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)
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if(OpenMP_FOUND)
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target_link_libraries(_phonopy PRIVATE phonopy_libs PRIVATE OpenMP::OpenMP_C)
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else()
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target_link_libraries(_phonopy PRIVATE phonopy_libs)
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endif()
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target_compile_definitions(_phonopy PRIVATE THM_EPSILON=1e-10)
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install(TARGETS _phonopy LIBRARY DESTINATION ${SKBUILD_PROJECT_NAME})
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endif()
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@ -0,0 +1,681 @@
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#include <nanobind/nanobind.h>
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#include <nanobind/ndarray.h>
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#include "phonopy.h"
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namespace nb = nanobind;
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void py_transform_dynmat_to_fc(nb::ndarray<> py_force_constants,
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nb::ndarray<> py_dynamical_matrices,
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nb::ndarray<> py_commensurate_points,
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nb::ndarray<> py_svecs, nb::ndarray<> py_multi,
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nb::ndarray<> py_masses,
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nb::ndarray<> py_s2pp_map,
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nb::ndarray<> py_fc_index_map, long use_openmp) {
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double *fc;
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double(*dm)[2];
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double(*comm_points)[3];
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double(*svecs)[3];
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double *masses;
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long(*multi)[2];
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long *s2pp_map;
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long *fc_index_map;
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long num_patom;
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long num_satom;
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fc = (double *)py_force_constants.data();
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dm = (double(*)[2])py_dynamical_matrices.data();
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comm_points = (double(*)[3])py_commensurate_points.data();
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svecs = (double(*)[3])py_svecs.data();
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masses = (double *)py_masses.data();
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multi = (long(*)[2])py_multi.data();
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s2pp_map = (long *)py_s2pp_map.data();
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fc_index_map = (long *)py_fc_index_map.data();
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num_patom = py_multi.shape(1);
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num_satom = py_multi.shape(0);
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phpy_transform_dynmat_to_fc(fc, dm, comm_points, svecs, multi, masses,
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s2pp_map, fc_index_map, num_patom, num_satom,
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use_openmp);
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};
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void py_perm_trans_symmetrize_fc(nb::ndarray<> py_force_constants, long level) {
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double *fc;
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int n_satom;
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fc = (double *)py_force_constants.data();
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n_satom = py_force_constants.shape(0);
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phpy_perm_trans_symmetrize_fc(fc, n_satom, level);
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}
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void py_perm_trans_symmetrize_compact_fc(nb::ndarray<> py_force_constants,
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nb::ndarray<> py_permutations,
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nb::ndarray<> py_s2pp_map,
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nb::ndarray<> py_p2s_map,
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nb::ndarray<> py_nsym_list,
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long level) {
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double *fc;
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int *perms;
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int *s2pp;
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int *p2s;
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int *nsym_list;
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int n_patom, n_satom;
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fc = (double *)py_force_constants.data();
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perms = (int *)py_permutations.data();
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s2pp = (int *)py_s2pp_map.data();
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p2s = (int *)py_p2s_map.data();
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nsym_list = (int *)py_nsym_list.data();
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n_patom = py_force_constants.shape(0);
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n_satom = py_force_constants.shape(1);
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phpy_perm_trans_symmetrize_compact_fc(fc, p2s, s2pp, nsym_list, perms,
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n_satom, n_patom, level);
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}
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void py_transpose_compact_fc(nb::ndarray<> py_force_constants,
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nb::ndarray<> py_permutations,
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nb::ndarray<> py_s2pp_map,
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nb::ndarray<> py_p2s_map,
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nb::ndarray<> py_nsym_list) {
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double *fc;
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int *s2pp;
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int *p2s;
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int *nsym_list;
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int *perms;
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int n_patom, n_satom;
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fc = (double *)py_force_constants.data();
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perms = (int *)py_permutations.data();
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s2pp = (int *)py_s2pp_map.data();
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p2s = (int *)py_p2s_map.data();
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nsym_list = (int *)py_nsym_list.data();
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n_patom = py_force_constants.shape(0);
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n_satom = py_force_constants.shape(1);
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phpy_set_index_permutation_symmetry_compact_fc(fc, p2s, s2pp, nsym_list,
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perms, n_satom, n_patom, 1);
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}
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void py_get_dynamical_matrices_with_dd_openmp_over_qpoints(
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nb::ndarray<> py_dynamical_matrix, nb::ndarray<> py_qpoints,
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nb::ndarray<> py_force_constants, nb::ndarray<> py_svecs,
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nb::ndarray<> py_multi, nb::ndarray<> py_positions, nb::ndarray<> py_masses,
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nb::ndarray<> py_s2p_map, nb::ndarray<> py_p2s_map,
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nb::ndarray<> py_q_direction, nb::ndarray<> py_born,
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nb::ndarray<> py_dielectric, nb::ndarray<> py_reciprocal_lattice,
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double nac_factor, nb::ndarray<> py_dd_q0, nb::ndarray<> py_G_list,
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double lambda, long use_Wang_NAC) {
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double(*dm)[2];
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double *fc;
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double *q_direction;
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double(*qpoints)[3];
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double(*svecs)[3];
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long(*multi)[2];
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double(*positions)[3];
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double *masses;
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double(*born)[3][3];
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double(*dielectric)[3];
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double(*reciprocal_lattice)[3];
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double(*dd_q0)[2];
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double(*G_list)[3];
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long *s2p_map;
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long *p2s_map;
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long num_patom;
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long num_satom;
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long n_qpoints;
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long n_Gpoints;
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dm = (double(*)[2])py_dynamical_matrix.data();
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qpoints = (double(*)[3])py_qpoints.data();
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n_qpoints = py_qpoints.shape(0);
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fc = (double *)py_force_constants.data();
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svecs = (double(*)[3])py_svecs.data();
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multi = (long(*)[2])py_multi.data();
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masses = (double *)py_masses.data();
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s2p_map = (long *)py_s2p_map.data();
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p2s_map = (long *)py_p2s_map.data();
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q_direction = (double *)py_q_direction.data();
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born = (double(*)[3][3])py_born.data();
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dielectric = (double(*)[3])py_dielectric.data();
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reciprocal_lattice = (double(*)[3])py_reciprocal_lattice.data();
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if (use_Wang_NAC) {
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positions = NULL;
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dd_q0 = NULL;
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G_list = NULL;
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n_Gpoints = 0;
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} else {
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positions = (double(*)[3])py_positions.data();
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dd_q0 = (double(*)[2])py_dd_q0.data();
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G_list = (double(*)[3])py_G_list.data();
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n_Gpoints = py_G_list.shape(0);
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}
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num_patom = py_p2s_map.shape(0);
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num_satom = py_s2p_map.shape(0);
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phpy_dynamical_matrices_with_dd_openmp_over_qpoints(
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dm, qpoints, n_qpoints, fc, svecs, multi, positions, num_patom,
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num_satom, masses, p2s_map, s2p_map, born, dielectric,
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reciprocal_lattice, q_direction, nac_factor, dd_q0, G_list, n_Gpoints,
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lambda, use_Wang_NAC);
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}
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void py_get_dynamical_matrix(nb::ndarray<> py_dynamical_matrix,
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nb::ndarray<> py_force_constants,
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nb::ndarray<> py_q, nb::ndarray<> py_svecs,
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nb::ndarray<> py_multi, nb::ndarray<> py_masses,
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nb::ndarray<> py_s2p_map, nb::ndarray<> py_p2s_map,
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long use_openmp) {
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double(*dm)[2];
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double *fc;
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double *q;
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double(*svecs)[3];
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double *m;
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long(*multi)[2];
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long *s2p_map;
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long *p2s_map;
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long num_patom;
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long num_satom;
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dm = (double(*)[2])py_dynamical_matrix.data();
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fc = (double *)py_force_constants.data();
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q = (double *)py_q.data();
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svecs = (double(*)[3])py_svecs.data();
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m = (double *)py_masses.data();
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multi = (long(*)[2])py_multi.data();
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s2p_map = (long *)py_s2p_map.data();
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p2s_map = (long *)py_p2s_map.data();
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num_patom = py_p2s_map.shape(0);
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num_satom = py_s2p_map.shape(0);
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if (py_q.ndim() == 1) {
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phpy_get_dynamical_matrix_at_q(dm, num_patom, num_satom, fc, q, svecs,
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multi, m, s2p_map, p2s_map, NULL,
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use_openmp);
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} else {
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phpy_get_dynamical_matrices_openmp_over_qpoints(
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dm, num_patom, num_satom, fc, (double(*)[3])q, py_q.shape(0), svecs,
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multi, m, s2p_map, p2s_map, NULL);
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}
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}
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void py_get_nac_dynamical_matrix(
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nb::ndarray<> py_dynamical_matrix, nb::ndarray<> py_force_constants,
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nb::ndarray<> py_q, nb::ndarray<> py_svecs, nb::ndarray<> py_multi,
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nb::ndarray<> py_masses, nb::ndarray<> py_s2p_map, nb::ndarray<> py_p2s_map,
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nb::ndarray<> py_q_cart, nb::ndarray<> py_born, double factor,
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long use_openmp) {
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double(*dm)[2];
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double *fc;
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double *q_cart;
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double *q;
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double(*svecs)[3];
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double *m;
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double(*born)[3][3];
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long(*multi)[2];
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long *s2p_map;
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long *p2s_map;
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long num_patom;
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long num_satom;
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long n;
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double(*charge_sum)[3][3];
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|
||||
dm = (double(*)[2])py_dynamical_matrix.data();
|
||||
fc = (double *)py_force_constants.data();
|
||||
q_cart = (double *)py_q_cart.data();
|
||||
q = (double *)py_q.data();
|
||||
svecs = (double(*)[3])py_svecs.data();
|
||||
m = (double *)py_masses.data();
|
||||
born = (double(*)[3][3])py_born.data();
|
||||
multi = (long(*)[2])py_multi.data();
|
||||
s2p_map = (long *)py_s2p_map.data();
|
||||
p2s_map = (long *)py_p2s_map.data();
|
||||
num_patom = py_p2s_map.shape(0);
|
||||
num_satom = py_s2p_map.shape(0);
|
||||
|
||||
charge_sum =
|
||||
(double(*)[3][3])malloc(sizeof(double[3][3]) * num_patom * num_patom);
|
||||
n = num_satom / num_patom;
|
||||
|
||||
phpy_get_charge_sum(charge_sum, num_patom, factor / n, q_cart, born);
|
||||
|
||||
if (py_q.ndim() == 1) {
|
||||
phpy_get_dynamical_matrix_at_q(dm, num_patom, num_satom, fc, q, svecs,
|
||||
multi, m, s2p_map, p2s_map, charge_sum,
|
||||
use_openmp);
|
||||
} else {
|
||||
phpy_get_dynamical_matrices_openmp_over_qpoints(
|
||||
dm, num_patom, num_satom, fc, (double(*)[3])q, py_q.shape(0), svecs,
|
||||
multi, m, s2p_map, p2s_map, charge_sum);
|
||||
}
|
||||
|
||||
free(charge_sum);
|
||||
charge_sum = NULL;
|
||||
}
|
||||
|
||||
void py_get_recip_dipole_dipole(
|
||||
nb::ndarray<> py_dd, nb::ndarray<> py_dd_q0, nb::ndarray<> py_G_list,
|
||||
nb::ndarray<> py_q_cart, nb::ndarray<> py_q_direction,
|
||||
nb::ndarray<> py_born, nb::ndarray<> py_dielectric,
|
||||
nb::ndarray<> py_positions, long is_q_zero, double factor, double lambda,
|
||||
double tolerance, long use_openmp) {
|
||||
double(*dd)[2];
|
||||
double(*dd_q0)[2];
|
||||
double(*G_list)[3];
|
||||
double *q_vector;
|
||||
double *q_direction;
|
||||
double(*born)[3][3];
|
||||
double(*dielectric)[3];
|
||||
double(*pos)[3];
|
||||
|
||||
long num_patom, num_G;
|
||||
|
||||
dd = (double(*)[2])py_dd.data();
|
||||
dd_q0 = (double(*)[2])py_dd_q0.data();
|
||||
G_list = (double(*)[3])py_G_list.data();
|
||||
if (is_q_zero) {
|
||||
q_direction = NULL;
|
||||
} else {
|
||||
q_direction = (double *)py_q_direction.data();
|
||||
}
|
||||
q_vector = (double *)py_q_cart.data();
|
||||
born = (double(*)[3][3])py_born.data();
|
||||
dielectric = (double(*)[3])py_dielectric.data();
|
||||
pos = (double(*)[3])py_positions.data();
|
||||
num_G = py_G_list.shape(0);
|
||||
num_patom = py_positions.shape(0);
|
||||
|
||||
phpy_get_recip_dipole_dipole(dd, /* [natom, 3, natom, 3, (real, imag)] */
|
||||
dd_q0, /* [natom, 3, 3, (real, imag)] */
|
||||
G_list, /* [num_kvec, 3] */
|
||||
num_G, num_patom, q_vector, q_direction, born,
|
||||
dielectric, pos, /* [natom, 3] */
|
||||
factor, /* 4pi/V*unit-conv */
|
||||
lambda, /* 4 * Lambda^2 */
|
||||
tolerance, use_openmp);
|
||||
}
|
||||
|
||||
void py_get_recip_dipole_dipole_q0(nb::ndarray<> py_dd_q0,
|
||||
nb::ndarray<> py_G_list,
|
||||
nb::ndarray<> py_born,
|
||||
nb::ndarray<> py_dielectric,
|
||||
nb::ndarray<> py_positions, double lambda,
|
||||
double tolerance, long use_openmp) {
|
||||
double(*dd_q0)[2];
|
||||
double(*G_list)[3];
|
||||
double(*born)[3][3];
|
||||
double(*dielectric)[3];
|
||||
double(*pos)[3];
|
||||
|
||||
long num_patom, num_G;
|
||||
|
||||
dd_q0 = (double(*)[2])py_dd_q0.data();
|
||||
G_list = (double(*)[3])py_G_list.data();
|
||||
born = (double(*)[3][3])py_born.data();
|
||||
dielectric = (double(*)[3])py_dielectric.data();
|
||||
pos = (double(*)[3])py_positions.data();
|
||||
num_G = py_G_list.shape(0);
|
||||
num_patom = py_positions.shape(0);
|
||||
|
||||
phpy_get_recip_dipole_dipole_q0(dd_q0, /* [natom, 3, 3, (real, imag)] */
|
||||
G_list, /* [num_kvec, 3] */
|
||||
num_G, num_patom, born, dielectric,
|
||||
pos, /* [natom, 3] */
|
||||
lambda, /* 4 * Lambda^2 */
|
||||
tolerance, use_openmp);
|
||||
}
|
||||
|
||||
void py_get_derivative_dynmat(
|
||||
nb::ndarray<> py_derivative_dynmat, nb::ndarray<> py_force_constants,
|
||||
nb::ndarray<> py_q_vector, nb::ndarray<> py_lattice, nb::ndarray<> py_svecs,
|
||||
nb::ndarray<> py_multi, nb::ndarray<> py_masses, nb::ndarray<> py_s2p_map,
|
||||
nb::ndarray<> py_p2s_map, double nac_factor, nb::ndarray<> py_born,
|
||||
nb::ndarray<> py_dielectric, nb::ndarray<> py_q_direction, long is_nac,
|
||||
long is_q_zero, long use_openmp) {
|
||||
double(*ddm)[2];
|
||||
double *fc;
|
||||
double *q_vector;
|
||||
double *lat;
|
||||
double(*svecs)[3];
|
||||
double *masses;
|
||||
long(*multi)[2];
|
||||
long *s2p_map;
|
||||
long *p2s_map;
|
||||
long num_patom;
|
||||
long num_satom;
|
||||
|
||||
double *born;
|
||||
double *epsilon;
|
||||
double *q_dir;
|
||||
|
||||
ddm = (double(*)[2])py_derivative_dynmat.data();
|
||||
fc = (double *)py_force_constants.data();
|
||||
q_vector = (double *)py_q_vector.data();
|
||||
lat = (double *)py_lattice.data();
|
||||
svecs = (double(*)[3])py_svecs.data();
|
||||
masses = (double *)py_masses.data();
|
||||
multi = (long(*)[2])py_multi.data();
|
||||
s2p_map = (long *)py_s2p_map.data();
|
||||
p2s_map = (long *)py_p2s_map.data();
|
||||
num_patom = py_p2s_map.shape(0);
|
||||
num_satom = py_s2p_map.shape(0);
|
||||
|
||||
epsilon = (double *)py_dielectric.data();
|
||||
born = (double *)py_born.data();
|
||||
if (is_q_zero) {
|
||||
q_dir = NULL;
|
||||
} else {
|
||||
q_dir = (double *)py_q_direction.data();
|
||||
}
|
||||
|
||||
phpy_get_derivative_dynmat_at_q(
|
||||
ddm, num_patom, num_satom, fc, q_vector, lat, svecs, multi, masses,
|
||||
s2p_map, p2s_map, nac_factor, born, epsilon, q_dir, is_nac, use_openmp);
|
||||
}
|
||||
|
||||
void py_get_thermal_properties(nb::ndarray<> py_thermal_props,
|
||||
nb::ndarray<> py_temperatures,
|
||||
nb::ndarray<> py_frequencies,
|
||||
nb::ndarray<> py_weights,
|
||||
double cutoff_frequency) {
|
||||
double *temperatures;
|
||||
double *freqs;
|
||||
double *thermal_props;
|
||||
long *weights;
|
||||
long num_qpoints;
|
||||
long num_bands;
|
||||
long num_temp;
|
||||
|
||||
thermal_props = (double *)py_thermal_props.data();
|
||||
temperatures = (double *)py_temperatures.data();
|
||||
num_temp = (long)py_temperatures.shape(0);
|
||||
freqs = (double *)py_frequencies.data();
|
||||
num_qpoints = (long)py_frequencies.shape(0);
|
||||
weights = (long *)py_weights.data();
|
||||
num_bands = (long)py_frequencies.shape(1);
|
||||
|
||||
phpy_get_thermal_properties(thermal_props, temperatures, freqs, weights,
|
||||
num_temp, num_qpoints, num_bands,
|
||||
cutoff_frequency);
|
||||
}
|
||||
|
||||
void py_distribute_fc2(nb::ndarray<> py_force_constants,
|
||||
nb::ndarray<> py_atom_list,
|
||||
nb::ndarray<> py_fc_indices_of_atom_list,
|
||||
nb::ndarray<> py_rotations_cart,
|
||||
nb::ndarray<> py_permutations,
|
||||
nb::ndarray<> py_map_atoms, nb::ndarray<> py_map_syms) {
|
||||
double(*r_carts)[3][3];
|
||||
double(*fc2)[3][3];
|
||||
int *permutations;
|
||||
int *map_atoms;
|
||||
int *map_syms;
|
||||
int *atom_list;
|
||||
int *fc_indices_of_atom_list;
|
||||
long num_pos, num_rot, len_atom_list;
|
||||
|
||||
fc2 = (double(*)[3][3])py_force_constants.data();
|
||||
atom_list = (int *)py_atom_list.data();
|
||||
len_atom_list = py_atom_list.shape(0);
|
||||
fc_indices_of_atom_list = (int *)py_fc_indices_of_atom_list.data();
|
||||
permutations = (int *)py_permutations.data();
|
||||
map_atoms = (int *)py_map_atoms.data();
|
||||
map_syms = (int *)py_map_syms.data();
|
||||
r_carts = (double(*)[3][3])py_rotations_cart.data();
|
||||
num_rot = py_permutations.shape(0);
|
||||
num_pos = py_permutations.shape(1);
|
||||
|
||||
phpy_distribute_fc2(fc2, atom_list, len_atom_list, fc_indices_of_atom_list,
|
||||
r_carts, permutations, map_atoms, map_syms, num_rot,
|
||||
num_pos);
|
||||
}
|
||||
|
||||
bool py_compute_permutation(nb::ndarray<> permutation, nb::ndarray<> lattice,
|
||||
nb::ndarray<> positions,
|
||||
nb::ndarray<> permuted_positions, double symprec) {
|
||||
int *rot_atoms;
|
||||
double(*lat)[3];
|
||||
double(*pos)[3];
|
||||
double(*rot_pos)[3];
|
||||
int num_pos;
|
||||
|
||||
int is_found;
|
||||
|
||||
rot_atoms = (int *)permutation.data();
|
||||
lat = (double(*)[3])lattice.data();
|
||||
pos = (double(*)[3])positions.data();
|
||||
rot_pos = (double(*)[3])permuted_positions.data();
|
||||
num_pos = positions.shape(0);
|
||||
|
||||
is_found = phpy_compute_permutation(rot_atoms, lat, pos, rot_pos, num_pos,
|
||||
symprec);
|
||||
|
||||
if (is_found) {
|
||||
return true;
|
||||
} else {
|
||||
return false;
|
||||
}
|
||||
}
|
||||
|
||||
void py_gsv_set_smallest_vectors_sparse(
|
||||
nb::ndarray<> py_smallest_vectors, nb::ndarray<> py_multiplicity,
|
||||
nb::ndarray<> py_pos_to, nb::ndarray<> py_pos_from,
|
||||
nb::ndarray<> py_lattice_points, nb::ndarray<> py_reduced_basis,
|
||||
nb::ndarray<> py_trans_mat, double symprec) {
|
||||
double(*smallest_vectors)[27][3];
|
||||
int *multiplicity;
|
||||
double(*pos_to)[3];
|
||||
double(*pos_from)[3];
|
||||
int(*lattice_points)[3];
|
||||
double(*reduced_basis)[3];
|
||||
int(*trans_mat)[3];
|
||||
int num_pos_to, num_pos_from, num_lattice_points;
|
||||
|
||||
smallest_vectors = (double(*)[27][3])py_smallest_vectors.data();
|
||||
multiplicity = (int *)py_multiplicity.data();
|
||||
pos_to = (double(*)[3])py_pos_to.data();
|
||||
pos_from = (double(*)[3])py_pos_from.data();
|
||||
num_pos_to = py_pos_to.shape(0);
|
||||
num_pos_from = py_pos_from.shape(0);
|
||||
lattice_points = (int(*)[3])py_lattice_points.data();
|
||||
num_lattice_points = py_lattice_points.shape(0);
|
||||
reduced_basis = (double(*)[3])py_reduced_basis.data();
|
||||
trans_mat = (int(*)[3])py_trans_mat.data();
|
||||
|
||||
phpy_set_smallest_vectors_sparse(smallest_vectors, multiplicity, pos_to,
|
||||
num_pos_to, pos_from, num_pos_from,
|
||||
lattice_points, num_lattice_points,
|
||||
reduced_basis, trans_mat, symprec);
|
||||
}
|
||||
|
||||
void py_gsv_set_smallest_vectors_dense(
|
||||
nb::ndarray<> py_smallest_vectors, nb::ndarray<> py_multiplicity,
|
||||
nb::ndarray<> py_pos_to, nb::ndarray<> py_pos_from,
|
||||
nb::ndarray<> py_lattice_points, nb::ndarray<> py_reduced_basis,
|
||||
nb::ndarray<> py_trans_mat, long initialize, double symprec) {
|
||||
double(*smallest_vectors)[3];
|
||||
long(*multiplicity)[2];
|
||||
double(*pos_to)[3];
|
||||
double(*pos_from)[3];
|
||||
long(*lattice_points)[3];
|
||||
double(*reduced_basis)[3];
|
||||
long(*trans_mat)[3];
|
||||
long num_pos_to, num_pos_from, num_lattice_points;
|
||||
|
||||
smallest_vectors = (double(*)[3])py_smallest_vectors.data();
|
||||
multiplicity = (long(*)[2])py_multiplicity.data();
|
||||
pos_to = (double(*)[3])py_pos_to.data();
|
||||
pos_from = (double(*)[3])py_pos_from.data();
|
||||
num_pos_to = py_pos_to.shape(0);
|
||||
num_pos_from = py_pos_from.shape(0);
|
||||
lattice_points = (long(*)[3])py_lattice_points.data();
|
||||
num_lattice_points = py_lattice_points.shape(0);
|
||||
reduced_basis = (double(*)[3])py_reduced_basis.data();
|
||||
trans_mat = (long(*)[3])py_trans_mat.data();
|
||||
|
||||
phpy_set_smallest_vectors_dense(
|
||||
smallest_vectors, multiplicity, pos_to, num_pos_to, pos_from,
|
||||
num_pos_from, lattice_points, num_lattice_points, reduced_basis,
|
||||
trans_mat, initialize, symprec);
|
||||
}
|
||||
|
||||
void py_thm_relative_grid_address(nb::ndarray<> py_relative_grid_address,
|
||||
nb::ndarray<> py_reciprocal_lattice_py) {
|
||||
long(*relative_grid_address)[4][3];
|
||||
double(*reciprocal_lattice)[3];
|
||||
|
||||
relative_grid_address = (long(*)[4][3])py_relative_grid_address.data();
|
||||
reciprocal_lattice = (double(*)[3])py_reciprocal_lattice_py.data();
|
||||
|
||||
phpy_get_relative_grid_address(relative_grid_address, reciprocal_lattice);
|
||||
}
|
||||
|
||||
void py_thm_all_relative_grid_address(nb::ndarray<> py_relative_grid_address) {
|
||||
long(*relative_grid_address)[24][4][3];
|
||||
|
||||
relative_grid_address = (long(*)[24][4][3])py_relative_grid_address.data();
|
||||
|
||||
phpy_get_all_relative_grid_address(relative_grid_address);
|
||||
}
|
||||
|
||||
double py_thm_integration_weight(double omega,
|
||||
nb::ndarray<> py_tetrahedra_omegas,
|
||||
const char *function) {
|
||||
double(*tetrahedra_omegas)[4];
|
||||
double iw;
|
||||
|
||||
tetrahedra_omegas = (double(*)[4])py_tetrahedra_omegas.data();
|
||||
|
||||
iw = phpy_get_integration_weight(omega, tetrahedra_omegas, function[0]);
|
||||
|
||||
return iw;
|
||||
}
|
||||
|
||||
void py_thm_integration_weight_at_omegas(nb::ndarray<> py_integration_weights,
|
||||
nb::ndarray<> py_omegas,
|
||||
nb::ndarray<> py_tetrahedra_omegas,
|
||||
const char *function) {
|
||||
double *omegas;
|
||||
double *iw;
|
||||
long num_omegas;
|
||||
double(*tetrahedra_omegas)[4];
|
||||
|
||||
long i;
|
||||
|
||||
omegas = (double *)py_omegas.data();
|
||||
iw = (double *)py_integration_weights.data();
|
||||
num_omegas = (long)py_omegas.shape(0);
|
||||
tetrahedra_omegas = (double(*)[4])py_tetrahedra_omegas.data();
|
||||
|
||||
#ifdef _OPENMP
|
||||
#pragma omp parallel for
|
||||
#endif
|
||||
for (i = 0; i < num_omegas; i++) {
|
||||
iw[i] = phpy_get_integration_weight(omegas[i], tetrahedra_omegas,
|
||||
function[0]);
|
||||
}
|
||||
}
|
||||
|
||||
void py_get_tetrahedra_frequenies(nb::ndarray<> py_freq_tetras,
|
||||
nb::ndarray<> py_grid_points,
|
||||
nb::ndarray<> py_mesh,
|
||||
nb::ndarray<> py_grid_address,
|
||||
nb::ndarray<> py_gp_ir_index,
|
||||
nb::ndarray<> py_relative_grid_address,
|
||||
nb::ndarray<> py_frequencies) {
|
||||
double *freq_tetras;
|
||||
long *grid_points;
|
||||
long *mesh;
|
||||
long(*grid_address)[3];
|
||||
long *gp_ir_index;
|
||||
long(*relative_grid_address)[3];
|
||||
double *frequencies;
|
||||
|
||||
long num_gp_in, num_band;
|
||||
|
||||
freq_tetras = (double *)py_freq_tetras.data();
|
||||
grid_points = (long *)py_grid_points.data();
|
||||
num_gp_in = py_grid_points.shape(0);
|
||||
mesh = (long *)py_mesh.data();
|
||||
grid_address = (long(*)[3])py_grid_address.data();
|
||||
gp_ir_index = (long *)py_gp_ir_index.data();
|
||||
relative_grid_address = (long(*)[3])py_relative_grid_address.data();
|
||||
frequencies = (double *)py_frequencies.data();
|
||||
num_band = py_frequencies.shape(1);
|
||||
|
||||
phpy_get_tetrahedra_frequenies(freq_tetras, mesh, grid_points, grid_address,
|
||||
relative_grid_address, gp_ir_index,
|
||||
frequencies, num_band, num_gp_in);
|
||||
}
|
||||
|
||||
void py_tetrahedron_method_dos(nb::ndarray<> py_dos, nb::ndarray<> py_mesh,
|
||||
nb::ndarray<> py_freq_points,
|
||||
nb::ndarray<> py_frequencies,
|
||||
nb::ndarray<> py_coef,
|
||||
nb::ndarray<> py_grid_address,
|
||||
nb::ndarray<> py_grid_mapping_table,
|
||||
nb::ndarray<> py_relative_grid_address) {
|
||||
double *dos;
|
||||
long *mesh;
|
||||
double *freq_points;
|
||||
double *frequencies;
|
||||
double *coef;
|
||||
long(*grid_address)[3];
|
||||
long num_gp, num_ir_gp, num_band, num_freq_points, num_coef;
|
||||
long *grid_mapping_table;
|
||||
long(*relative_grid_address)[4][3];
|
||||
|
||||
/* dos[num_ir_gp][num_band][num_freq_points][num_coef] */
|
||||
dos = (double *)py_dos.data();
|
||||
mesh = (long *)py_mesh.data();
|
||||
freq_points = (double *)py_freq_points.data();
|
||||
num_freq_points = (long)py_freq_points.shape(0);
|
||||
frequencies = (double *)py_frequencies.data();
|
||||
num_ir_gp = (long)py_frequencies.shape(0);
|
||||
num_band = (long)py_frequencies.shape(1);
|
||||
coef = (double *)py_coef.data();
|
||||
num_coef = (long)py_coef.shape(1);
|
||||
grid_address = (long(*)[3])py_grid_address.data();
|
||||
num_gp = (long)py_grid_address.shape(0);
|
||||
grid_mapping_table = (long *)py_grid_mapping_table.data();
|
||||
relative_grid_address = (long(*)[4][3])py_relative_grid_address.data();
|
||||
|
||||
phpy_tetrahedron_method_dos(dos, mesh, grid_address, relative_grid_address,
|
||||
grid_mapping_table, freq_points, frequencies,
|
||||
coef, num_freq_points, num_ir_gp, num_band,
|
||||
num_coef, num_gp);
|
||||
}
|
||||
|
||||
NB_MODULE(_phonopy, m) {
|
||||
m.def("transform_dynmat_to_fc", &py_transform_dynmat_to_fc);
|
||||
m.def("perm_trans_symmetrize_fc", &py_perm_trans_symmetrize_fc);
|
||||
m.def("perm_trans_symmetrize_compact_fc",
|
||||
&py_perm_trans_symmetrize_compact_fc);
|
||||
m.def("transpose_compact_fc", &py_transpose_compact_fc);
|
||||
m.def("dynamical_matrices_with_dd_openmp_over_qpoints",
|
||||
&py_get_dynamical_matrices_with_dd_openmp_over_qpoints);
|
||||
m.def("dynamical_matrix", &py_get_dynamical_matrix);
|
||||
m.def("nac_dynamical_matrix", &py_get_nac_dynamical_matrix);
|
||||
m.def("recip_dipole_dipole", &py_get_recip_dipole_dipole);
|
||||
m.def("recip_dipole_dipole_q0", &py_get_recip_dipole_dipole_q0);
|
||||
m.def("derivative_dynmat", &py_get_derivative_dynmat);
|
||||
m.def("thermal_properties", &py_get_thermal_properties);
|
||||
m.def("distribute_fc2", &py_distribute_fc2);
|
||||
m.def("compute_permutation", &py_compute_permutation);
|
||||
m.def("gsv_set_smallest_vectors_sparse",
|
||||
&py_gsv_set_smallest_vectors_sparse);
|
||||
m.def("gsv_set_smallest_vectors_dense", &py_gsv_set_smallest_vectors_dense);
|
||||
m.def("tetrahedra_relative_grid_address", &py_thm_relative_grid_address);
|
||||
m.def("all_tetrahedra_relative_grid_address",
|
||||
&py_thm_all_relative_grid_address);
|
||||
m.def("tetrahedra_integration_weight", &py_thm_integration_weight);
|
||||
m.def("tetrahedra_integration_weight_at_omegas",
|
||||
&py_thm_integration_weight_at_omegas);
|
||||
m.def("tetrahedra_frequencies", &py_get_tetrahedra_frequenies);
|
||||
m.def("tetrahedron_method_dos", &py_tetrahedron_method_dos);
|
||||
m.def("use_openmp", &phpy_use_openmp);
|
||||
m.def("get_max_threads", &phpy_get_max_threads);
|
||||
}
|
||||
|
|
@ -45,7 +45,7 @@ static void get_derivative_dynmat_at_q(
|
|||
const double *q, const double *lattice, /* column vector */
|
||||
const double (*svecs)[3], const long (*multi)[2], const double *mass,
|
||||
const long *s2p_map, const long *p2s_map, const double nac_factor,
|
||||
const double *born, const double *dielectric, const double *q_direction);
|
||||
const double *born, const double *dielectric);
|
||||
static void get_derivative_nac(double *ddnac, double *dnac,
|
||||
const long num_patom, const double *lattice,
|
||||
const double *mass, const double *q,
|
||||
|
|
@ -66,27 +66,11 @@ void ddm_get_derivative_dynmat_at_q(
|
|||
const double (*svecs)[3], const long (*multi)[2], const double *mass,
|
||||
const long *s2p_map, const long *p2s_map, const double nac_factor,
|
||||
const double *born, const double *dielectric, const double *q_direction,
|
||||
const long use_openmp) {
|
||||
long i, j, k, ij, adrs, adrsT, is_nac;
|
||||
const long is_nac, const long use_openmp) {
|
||||
long i, j, k, ij, adrs, adrsT;
|
||||
double factor;
|
||||
double *ddnac, *dnac;
|
||||
|
||||
if (born) {
|
||||
is_nac = 1;
|
||||
if (q_direction) {
|
||||
if (fabs(q_direction[0]) < 1e-5 && fabs(q_direction[1]) < 1e-5 &&
|
||||
fabs(q_direction[2]) < 1e-5) {
|
||||
is_nac = 0;
|
||||
}
|
||||
} else {
|
||||
if (fabs(q[0]) < 1e-5 && fabs(q[1]) < 1e-5 && fabs(q[2]) < 1e-5) {
|
||||
is_nac = 0;
|
||||
}
|
||||
}
|
||||
} else {
|
||||
is_nac = 0;
|
||||
}
|
||||
|
||||
if (is_nac) {
|
||||
ddnac = (double *)malloc(sizeof(double) * num_patom * num_patom * 27);
|
||||
dnac = (double *)malloc(sizeof(double) * num_patom * num_patom * 9);
|
||||
|
|
@ -102,10 +86,10 @@ void ddm_get_derivative_dynmat_at_q(
|
|||
for (ij = 0; ij < num_patom * num_patom; ij++) {
|
||||
i = ij / num_patom;
|
||||
j = ij % num_patom;
|
||||
get_derivative_dynmat_at_q(
|
||||
derivative_dynmat, i, j, ddnac, dnac, is_nac, num_patom,
|
||||
num_satom, fc, q, lattice, svecs, multi, mass, s2p_map, p2s_map,
|
||||
nac_factor, born, dielectric, q_direction);
|
||||
get_derivative_dynmat_at_q(derivative_dynmat, i, j, ddnac, dnac,
|
||||
is_nac, num_patom, num_satom, fc, q,
|
||||
lattice, svecs, multi, mass, s2p_map,
|
||||
p2s_map, nac_factor, born, dielectric);
|
||||
}
|
||||
} else {
|
||||
for (i = 0; i < num_patom; i++) {
|
||||
|
|
@ -113,7 +97,7 @@ void ddm_get_derivative_dynmat_at_q(
|
|||
get_derivative_dynmat_at_q(
|
||||
derivative_dynmat, i, j, ddnac, dnac, is_nac, num_patom,
|
||||
num_satom, fc, q, lattice, svecs, multi, mass, s2p_map,
|
||||
p2s_map, nac_factor, born, dielectric, q_direction);
|
||||
p2s_map, nac_factor, born, dielectric);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -149,7 +133,7 @@ void get_derivative_dynmat_at_q(
|
|||
const double *q, const double *lattice, /* column vector */
|
||||
const double (*svecs)[3], const long (*multi)[2], const double *mass,
|
||||
const long *s2p_map, const long *p2s_map, const double nac_factor,
|
||||
const double *born, const double *dielectric, const double *q_direction) {
|
||||
const double *born, const double *dielectric) {
|
||||
long k, l, m, n, adrs, m_pair, i_pair, svecs_adrs;
|
||||
double coef[3], real_coef[3], imag_coef[3];
|
||||
double c, s, phase, mass_sqrt, fc_elem, real_phase, imag_phase;
|
||||
|
|
|
|||
|
|
@ -42,6 +42,6 @@ void ddm_get_derivative_dynmat_at_q(
|
|||
const double (*svecs)[3], const long (*multi)[2], const double *mass,
|
||||
const long *s2p_map, const long *p2s_map, const double nac_factor,
|
||||
const double *born, const double *dielectric, const double *q_direction,
|
||||
const long use_openmp);
|
||||
const long is_nac, const long use_openmp);
|
||||
|
||||
#endif
|
||||
|
|
|
|||
|
|
@ -161,11 +161,11 @@ void phpy_get_derivative_dynmat_at_q(
|
|||
const double (*svecs)[3], const long (*multi)[2], const double *mass,
|
||||
const long *s2p_map, const long *p2s_map, const double nac_factor,
|
||||
const double *born, const double *dielectric, const double *q_direction,
|
||||
const long use_openmp) {
|
||||
const long is_nac, const long use_openmp) {
|
||||
ddm_get_derivative_dynmat_at_q(derivative_dynmat, num_patom, num_satom, fc,
|
||||
q, lattice, svecs, multi, mass, s2p_map,
|
||||
p2s_map, nac_factor, born, dielectric,
|
||||
q_direction, use_openmp);
|
||||
q_direction, is_nac, use_openmp);
|
||||
}
|
||||
|
||||
void phpy_get_relative_grid_address(long relative_grid_address[24][4][3],
|
||||
|
|
|
|||
11
c/phonopy.h
11
c/phonopy.h
|
|
@ -37,6 +37,10 @@
|
|||
#ifndef __phonopy_H__
|
||||
#define __phonopy_H__
|
||||
|
||||
#ifdef __cplusplus
|
||||
extern "C" {
|
||||
#endif
|
||||
|
||||
void phpy_transform_dynmat_to_fc(double *fc, const double (*dm)[2],
|
||||
const double (*comm_points)[3],
|
||||
const double (*svecs)[3],
|
||||
|
|
@ -94,7 +98,7 @@ void phpy_get_derivative_dynmat_at_q(
|
|||
const double (*svecs)[3], const long (*multi)[2], const double *mass,
|
||||
const long *s2p_map, const long *p2s_map, const double nac_factor,
|
||||
const double *born, const double *dielectric, const double *q_direction,
|
||||
const long use_openmp);
|
||||
const long is_nac, const long use_openmp);
|
||||
void phpy_get_neighboring_grid_points(
|
||||
size_t neighboring_grid_points[], const size_t grid_point,
|
||||
const int relative_grid_address[][3], const int num_relative_grid_address,
|
||||
|
|
@ -162,4 +166,9 @@ void phpy_set_index_permutation_symmetry_compact_fc(
|
|||
const int is_transpose);
|
||||
long phpy_use_openmp(void);
|
||||
long phpy_get_max_threads(void);
|
||||
|
||||
#ifdef __cplusplus
|
||||
}
|
||||
#endif
|
||||
|
||||
#endif
|
||||
|
|
|
|||
|
|
@ -141,18 +141,23 @@ class DerivativeOfDynamicalMatrix:
|
|||
dtype=("c%d" % (np.dtype("double").itemsize * 2)),
|
||||
)
|
||||
if isinstance(self._dynmat, DynamicalMatrixNAC):
|
||||
is_nac = True
|
||||
born = self._dynmat.born
|
||||
dielectric = self._dynmat.dielectric_constant
|
||||
nac_factor = self._dynmat.nac_factor
|
||||
if q_direction is None:
|
||||
q_dir = None
|
||||
q_dir = np.zerod(3)
|
||||
is_q_zero = True
|
||||
else:
|
||||
q_dir = np.array(q_direction, dtype="double", order="C")
|
||||
is_q_zero = False
|
||||
else:
|
||||
born = None
|
||||
dielectric = None
|
||||
nac_factor = 0
|
||||
q_dir = None
|
||||
born = np.zeros(0) # dummy value
|
||||
dielectric = np.zeros(0) # dummy value
|
||||
nac_factor = 0 # dummy value
|
||||
q_dir = np.zerod(3) # dummy value
|
||||
is_nac = False
|
||||
is_q_zero = True
|
||||
|
||||
if fc.shape[0] == fc.shape[1]: # full fc
|
||||
phonoc.derivative_dynmat(
|
||||
|
|
@ -169,6 +174,8 @@ class DerivativeOfDynamicalMatrix:
|
|||
born,
|
||||
dielectric,
|
||||
q_dir,
|
||||
is_nac * 1,
|
||||
is_q_zero * 1,
|
||||
self._dynmat.use_openmp * 1,
|
||||
)
|
||||
else:
|
||||
|
|
@ -186,6 +193,8 @@ class DerivativeOfDynamicalMatrix:
|
|||
born,
|
||||
dielectric,
|
||||
q_dir,
|
||||
is_nac * 1,
|
||||
is_q_zero * 1,
|
||||
self._dynmat.use_openmp * 1,
|
||||
)
|
||||
|
||||
|
|
|
|||
|
|
@ -802,7 +802,9 @@ class DynamicalMatrixGL(DynamicalMatrixNAC):
|
|||
|
||||
return C_dd
|
||||
|
||||
def _get_c_recip_dipole_dipole(self, q_cart, q_dir_cart):
|
||||
def _get_c_recip_dipole_dipole(
|
||||
self, q_cart: np.ndarray, q_dir_cart: Optional[np.ndarray]
|
||||
) -> np.ndarray:
|
||||
"""Reciprocal part of Eq.(71) on the right hand side.
|
||||
|
||||
This is subtracted from supercell force constants to create
|
||||
|
|
@ -828,15 +830,23 @@ class DynamicalMatrixGL(DynamicalMatrixNAC):
|
|||
else:
|
||||
dd_q0 = self._dd_q0
|
||||
|
||||
if q_dir_cart is None:
|
||||
is_q_zero = True
|
||||
_q_dir_cart = np.zeros(3, dtype="double")
|
||||
else:
|
||||
is_q_zero = False
|
||||
_q_dir_cart = q_dir_cart
|
||||
|
||||
phonoc.recip_dipole_dipole(
|
||||
dd.view(dtype="double"),
|
||||
dd_q0.view(dtype="double"),
|
||||
self._G_list,
|
||||
q_cart,
|
||||
q_dir_cart,
|
||||
_q_dir_cart,
|
||||
self._born,
|
||||
self._dielectric,
|
||||
np.array(pos, dtype="double", order="C"),
|
||||
is_q_zero * 1,
|
||||
self._unit_conversion * 4.0 * np.pi / volume,
|
||||
self._Lambda,
|
||||
self.Q_DIRECTION_TOLERANCE,
|
||||
|
|
@ -1224,10 +1234,9 @@ def run_dynamical_matrix_solver_c(
|
|||
) = gonze_nac_dataset # Convergence parameter
|
||||
fc = gonze_fc
|
||||
else:
|
||||
positions = None
|
||||
dd_q0 = None
|
||||
G_list = None
|
||||
Lambda = 0
|
||||
dd_q0 = np.zeros(2) # dummy value
|
||||
G_list = np.zeros(3) # dummy value
|
||||
Lambda = 0 # dummy value
|
||||
fc = dm.force_constants
|
||||
if isinstance(dm, DynamicalMatrixWang):
|
||||
use_Wang_NAC = True
|
||||
|
|
|
|||
|
|
@ -293,7 +293,7 @@ def distribute_force_constants(
|
|||
atom_list_done,
|
||||
lattice, # column vectors
|
||||
rotations, # scaled (fractional)
|
||||
permutations,
|
||||
permutations: np.ndarray,
|
||||
atom_list=None,
|
||||
fc_indices_of_atom_list=None,
|
||||
):
|
||||
|
|
@ -322,6 +322,16 @@ def distribute_force_constants(
|
|||
_fc_indices_of_atom_list = np.arange(len(targets), dtype="intc")
|
||||
else:
|
||||
_fc_indices_of_atom_list = np.array(fc_indices_of_atom_list, dtype="intc")
|
||||
|
||||
if map_atoms.ndim != 1 or map_atoms.shape[0] != permutations.shape[1]:
|
||||
raise ValueError("wrong shape for map_atoms")
|
||||
|
||||
if map_syms.ndim != 1 or map_syms.shape[0] != permutations.shape[1]:
|
||||
raise ValueError("wrong shape for map_syms")
|
||||
|
||||
if rots_cartesian.shape[0] != permutations.shape[0]:
|
||||
raise ValueError("permutations and rotations are different length")
|
||||
|
||||
import phonopy._phonopy as phonoc
|
||||
|
||||
phonoc.distribute_fc2(
|
||||
|
|
|
|||
|
|
@ -36,7 +36,9 @@
|
|||
|
||||
from phonopy.cui.phonopy_script import main
|
||||
|
||||
if __name__ == "__main__":
|
||||
|
||||
def run():
|
||||
"""Run phonopy script."""
|
||||
argparse_control = {
|
||||
"fc_symmetry": False,
|
||||
"is_nac": False,
|
||||
|
|
@ -36,7 +36,9 @@
|
|||
|
||||
from phonopy.cui.phonopy_script import main
|
||||
|
||||
if __name__ == "__main__":
|
||||
|
||||
def run():
|
||||
"""Run phonopy-load script."""
|
||||
argparse_control = {
|
||||
"fc_symmetry": True,
|
||||
"is_nac": True,
|
||||
|
|
@ -38,14 +38,6 @@ import warnings
|
|||
|
||||
import numpy as np
|
||||
|
||||
try:
|
||||
import phonopy._phonopy as phonoc
|
||||
except ImportError:
|
||||
import sys
|
||||
|
||||
print("Phonopy C-extension has to be built properly.")
|
||||
sys.exit(1)
|
||||
|
||||
|
||||
def get_tetrahedra_relative_grid_address(microzone_lattice, lang="C"):
|
||||
"""Return relative (differences of) grid addresses from the central.
|
||||
|
|
@ -57,6 +49,14 @@ def get_tetrahedra_relative_grid_address(microzone_lattice, lang="C"):
|
|||
microzone_lattice = np.linalg.inv(cell.get_cell()) / mesh
|
||||
|
||||
"""
|
||||
try:
|
||||
import phonopy._phonopy as phonoc
|
||||
except ImportError:
|
||||
import sys
|
||||
|
||||
print("Phonopy C-extension has to be built properly.")
|
||||
sys.exit(1)
|
||||
|
||||
relative_grid_address = np.zeros((24, 4, 3), dtype="int_", order="C")
|
||||
if lang == "C":
|
||||
phonoc.tetrahedra_relative_grid_address(
|
||||
|
|
@ -76,6 +76,14 @@ def get_all_tetrahedra_relative_grid_address(lang="C"):
|
|||
This exists only for the test.
|
||||
|
||||
"""
|
||||
try:
|
||||
import phonopy._phonopy as phonoc
|
||||
except ImportError:
|
||||
import sys
|
||||
|
||||
print("Phonopy C-extension has to be built properly.")
|
||||
sys.exit(1)
|
||||
|
||||
relative_grid_address = np.zeros((4, 24, 4, 3), dtype="int_", order="C")
|
||||
if lang == "C":
|
||||
phonoc.all_tetrahedra_relative_grid_address(relative_grid_address)
|
||||
|
|
@ -103,6 +111,14 @@ def get_tetrahedra_integration_weight(omegas, tetrahedra_omegas, function="I"):
|
|||
'J' is for intetration and 'I' is for its derivative.
|
||||
|
||||
"""
|
||||
try:
|
||||
import phonopy._phonopy as phonoc
|
||||
except ImportError:
|
||||
import sys
|
||||
|
||||
print("Phonopy C-extension has to be built properly.")
|
||||
sys.exit(1)
|
||||
|
||||
if isinstance(omegas, float):
|
||||
return phonoc.tetrahedra_integration_weight(
|
||||
omegas, np.array(tetrahedra_omegas, dtype="double", order="C"), function
|
||||
|
|
|
|||
|
|
@ -1,5 +1,53 @@
|
|||
[build-system]
|
||||
requires = ["setuptools", "wheel", "numpy"]
|
||||
requires = ["scikit-build-core", "nanobind", "numpy"]
|
||||
build-backend = "scikit_build_core.build"
|
||||
|
||||
[project]
|
||||
|
||||
name = "phonopy"
|
||||
dynamic = ["version"]
|
||||
readme = { file = "README.md", content-type = "text/markdown" }
|
||||
description = "This is the phonopy module."
|
||||
authors = [{ name = "Atsushi Togo", email = "atztogo@gmail.com" }]
|
||||
requires-python = ">=3.8"
|
||||
dependencies = [
|
||||
"numpy>=1.17.0",
|
||||
"PyYAML>=5.3",
|
||||
"matplotlib>=2.2.2",
|
||||
"h5py>=3.0",
|
||||
"spglib>=2.3",
|
||||
]
|
||||
license = { file = "LICENSE" }
|
||||
|
||||
[project.optional-dependencies]
|
||||
cp2k = ["cp2k-input-tools"]
|
||||
plot = ["seekpath"]
|
||||
|
||||
[project.scripts]
|
||||
phonopy = "phonopy.scripts.phonopy:run"
|
||||
phonopy-load = "phonopy.scripts.phonopy_load:run"
|
||||
# phonopy-qha = "phonopy.scripts.phonopy-qha"
|
||||
# phonopy-bandplot = "phonopy.scripts.phonopy-bandplot"
|
||||
# phonopy-vasp-born = "phonopy.scripts.phonopy-vasp-born"
|
||||
# phonopy-vasp-efe = "phonopy.scripts.phonopy-vasp-efe"
|
||||
# phonopy-crystal-born = "phonopy.scripts.phonopy-crystal-born"
|
||||
# phonopy-calc-convert = "phonopy.scripts.phonopy-calc-convert"
|
||||
# phonopy-propplot = "phonopy.scripts.phonopy-propplot"
|
||||
# phonopy-tdplot = "phonopy.scripts.phonopy-tdplot"
|
||||
# phonopy-gruneisen = "phonopy.scripts.phonopy-gruneisen"
|
||||
# phonopy-gruneisenplot = "phonopy.scripts.phonopy-gruneisenplot"
|
||||
# phonopy-pdosplot = "phonopy.scripts.phonopy-pdosplot"
|
||||
|
||||
[tool.sciki-build]
|
||||
cmake.verbose = true
|
||||
logging.level = "INFO"
|
||||
|
||||
[tool.scikit-build]
|
||||
metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"
|
||||
sdist.include = ["phonopy/_version.py"]
|
||||
|
||||
[tool.setuptools_scm]
|
||||
write_to = "phonopy/_version.py"
|
||||
|
||||
[tool.ruff]
|
||||
line-length = 88
|
||||
|
|
@ -10,10 +58,7 @@ lint.select = [
|
|||
"E", # pycodestyle-errors
|
||||
"D", # pydocstyle
|
||||
]
|
||||
lint.extend-ignore = [
|
||||
"D417",
|
||||
"D100",
|
||||
]
|
||||
lint.extend-ignore = ["D417", "D100"]
|
||||
exclude = [
|
||||
"test/phonon/test_irreps.py",
|
||||
"test/qha/test_electron.py",
|
||||
|
|
|
|||
Loading…
Reference in New Issue