mirror of https://github.com/phonopy/phono3py.git
Change of build system using cmake
Following issue#99, attempting changing build system. This commit includes the build system by combination with cmake.
This commit is contained in:
Atsushi Togo
parent
01742d44cb
commit
756ada6e07
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@ -9,36 +9,42 @@ on:
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jobs:
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build-linux:
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runs-on: ubuntu-latest
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defaults:
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run:
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shell: bash -l {0}
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strategy:
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matrix:
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python-version: [3.7, 3.8, 3.9]
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python-version: ["3.7", "3.8", "3.9", "3.10"]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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# Use conda-incubator/setup-miniconda for precise control of conda infrastructure
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- uses: conda-incubator/setup-miniconda@v2
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with:
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auto-update-conda: true
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channels: conda-forge
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channel-priority: strict
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python-version: ${{ matrix.python-version }}
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- name: Add conda to system path
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- name: Install dependent packages
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run: |
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# $CONDA is an environment variable pointing to the root of the miniconda directory
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echo $CONDA/bin >> $GITHUB_PATH
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- name: Install dependencies
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conda activate test
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conda install --yes python=${{ matrix.python-version }}
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#conda install --yes matplotlib-base pyyaml openblas h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler
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conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler
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- name: Install phonopy
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run: |
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conda install --yes -c conda-forge python=${{ matrix.python-version }}
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conda install --yes -c conda-forge matplotlib-base pyyaml openblas gcc_linux-64 h5py scipy pytest codecov pytest-cov spglib alm
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pip install https://github.com/phonopy/phonopy/archive/develop.zip --user
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- name: Set up phono3py
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conda activate test
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git clone --depth 1 https://github.com/phonopy/phonopy.git
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cd phonopy
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pip install -e . -vvv
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cd ..
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- name: Install phono3py
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run: |
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export CONDA_PREFIX=$CONDA
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echo "[phono3py]" > site.cfg
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echo "extra_compile_args = -fopenmp" >> site.cfg
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echo "extra_link_args = -lgomp" >> site.cfg
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python setup.py build
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pip install -e .
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- name: Test with pytest
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conda activate test
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pip install -e . -vvv
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- name: Run pytest
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run: |
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pytest --cov=./ --cov-report=xml
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pytest --cov=./ --cov-report=xml test
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v1
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with:
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@ -9,10 +9,10 @@ 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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# set(CMAKE_POSITION_INDEPENDENT_CODE ON)
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# Version numbers
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@ -24,19 +24,38 @@ set(phono3py_micro_version ${CMAKE_MATCH_3})
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set(serial "${phono3py_major_version}.${phono3py_minor_version}.${phono3py_micro_version}")
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set(soserial "1")
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if (USE_CONDA_PATH)
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message(STATUS "$ENV{CONDA_PREFIX}")
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set(CMAKE_MODULE_PATH $ENV{CONDA_PREFIX})
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set(MY_INCLUDES $ENV{CONDA_PREFIX}/include ${PROJECT_SOURCE_DIR}/c)
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link_directories($ENV{CONDA_PREFIX}/lib)
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else()
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set(MY_INCLUDES ${PROJECT_SOURCE_DIR}/c)
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endif()
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find_package(OpenMP)
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if (OpenMP_FOUND)
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set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
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message(STATUS "OpenMP lib ${OpenMP_C_LIBRARIES}")
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message(STATUS "OpenMP libs: ${OpenMP_C_LIBRARIES}")
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message(STATUS "OpenMP flags: ${OpenMP_C_FLAGS}")
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endif()
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# include_directories($ENV{CONDA_PREFIX}/include)
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# link_directories($ENV{CONDA_PREFIX}/lib)
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if (PHONO3PY OR PHONONMOD)
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find_package(BLAS REQUIRED) # set BLAS_LIBRARIES
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if (BLAS_FOUND)
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message(STATUS "BLAS libs: ${BLAS_LIBRARIES}")
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message(STATUS "BLAS flags: ${BLAS_LINKER_FLAGS}")
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endif()
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find_package(LAPACK REQUIRED) # set LAPACK_LIBRARIES
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if (LAPACK_FOUND)
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message(STATUS "LAPACK libs: ${LAPACK_LIBRARIES}")
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message(STATUS "LAPACK flags: ${LAPACK_LINKER_FLAGS}")
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endif()
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endif()
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if (PHONO3PY OR PHONONMOD)
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if (BLAS_LIBRARIES MATCHES "libmkl")
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message(STATUS "MKL library detected")
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add_compile_definitions(MKL_LAPACKE) # phono3py macro
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endif()
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endif()
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@ -46,7 +65,6 @@ endif()
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############
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if (PHONO3PY)
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# Source code
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include_directories("${PROJECT_SOURCE_DIR}/c")
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set(SOURCES_PHONO3PY
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${PROJECT_SOURCE_DIR}/c/bzgrid.c
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${PROJECT_SOURCE_DIR}/c/collision_matrix.c
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@ -69,18 +87,20 @@ if (PHONO3PY)
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${PROJECT_SOURCE_DIR}/c/triplet_grid.c
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${PROJECT_SOURCE_DIR}/c/triplet_iw.c)
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if (BUILD_SHARED_LIBRARIES)
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# Shared library
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add_library(ph3py SHARED ${SOURCES_PHONO3PY})
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if(NOT MSVC)
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target_link_libraries(ph3py m ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${OpenMP_C_LIBRARIES})
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endif()
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target_include_directories(ph3py PRIVATE ${MY_INCLUDES})
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set_property(TARGET ph3py PROPERTY VERSION ${serial})
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set_property(TARGET ph3py PROPERTY SOVERSION ${soserial})
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install(TARGETS ph3py LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
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endif()
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# Static link library
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add_library(ph3py_static STATIC ${SOURCES_PHONO3PY})
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target_link_libraries(ph3py_static m ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${OpenMP_C_LIBRARIES})
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target_include_directories(ph3py_static PRIVATE ${MY_INCLUDES})
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set_property(TARGET ph3py_static PROPERTY VERSION ${serial})
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set_property(TARGET ph3py_static PROPERTY SOVERSION ${soserial})
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set_property(TARGET ph3py_static PROPERTY OUTPUT_NAME ph3py)
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@ -101,18 +121,20 @@ if (PHONONMOD)
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${PROJECT_SOURCE_DIR}/c/phonon.c
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${PROJECT_SOURCE_DIR}/c/phononmod.c)
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if (BUILD_SHARED_LIBRARIES)
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# Shared library
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add_library(phmod SHARED ${SOURCES_PHONONMOD})
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if(NOT MSVC)
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target_link_libraries(phmod m ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${OpenMP_C_LIBRARIES})
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endif()
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target_include_directories(phmod PRIVATE ${MY_INCLUDES})
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set_property(TARGET phmod PROPERTY VERSION ${serial})
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set_property(TARGET phmod PROPERTY SOVERSION ${soserial})
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install(TARGETS phmod LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
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endif()
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# Static link library
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add_library(phmod_static STATIC ${SOURCES_PHONONMOD})
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target_link_libraries(phmod_static m ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${OpenMP_C_LIBRARIES})
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target_include_directories(phmod_static PRIVATE ${MY_INCLUDES})
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set_property(TARGET phmod_static PROPERTY VERSION ${serial})
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set_property(TARGET phmod_static PROPERTY SOVERSION ${soserial})
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set_property(TARGET phmod_static PROPERTY OUTPUT_NAME phmod)
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@ -139,18 +161,21 @@ if (GRIDSYS)
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${PROJECT_SOURCE_DIR}/c/triplet_grid.c
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${PROJECT_SOURCE_DIR}/c/triplet_iw.c)
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if (BUILD_SHARED_LIBRARIES)
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# Shared library
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add_library(gridsysmod SHARED ${SOURCES_GRIDSYSMOD})
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if(NOT MSVC)
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target_link_libraries(gridsysmod m ${OpenMP_C_LIBRARIES})
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endif()
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target_include_directories(gridsysmod PRIVATE ${MY_INCLUDES})
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set_property(TARGET gridsysmod PROPERTY VERSION ${serial})
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set_property(TARGET gridsysmod PROPERTY SOVERSION ${soserial})
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install(TARGETS gridsysmod LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
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endif()
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# Static link library
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add_library(gridsysmod_static STATIC ${SOURCES_GRIDSYSMOD})
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target_link_libraries(gridsysmod_static m ${OpenMP_C_LIBRARIES})
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target_include_directories(gridsysmod_static PRIVATE ${MY_INCLUDES})
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set_property(TARGET gridsysmod_static PROPERTY VERSION ${serial})
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set_property(TARGET gridsysmod_static PROPERTY SOVERSION ${soserial})
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set_property(TARGET gridsysmod_static PROPERTY OUTPUT_NAME gridsysmod)
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175
c/_lapackepy.c
175
c/_lapackepy.c
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@ -1,175 +0,0 @@
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/* Copyright (C) 2015 Atsushi Togo */
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/* All rights reserved. */
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/* This file is part of phonopy. */
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/* Redistribution and use in source and binary forms, with or without */
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/* modification, are permitted provided that the following conditions */
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/* are met: */
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/* * Redistributions of source code must retain the above copyright */
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/* notice, this list of conditions and the following disclaimer. */
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/* * Redistributions in binary form must reproduce the above copyright */
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/* notice, this list of conditions and the following disclaimer in */
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/* the documentation and/or other materials provided with the */
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/* distribution. */
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/* * Neither the name of the phonopy project nor the names of its */
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/* contributors may be used to endorse or promote products derived */
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/* from this software without specific prior written permission. */
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/* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS */
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/* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT */
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/* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS */
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/* FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE */
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/* COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, */
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/* INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, */
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/* BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; */
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/* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER */
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/* CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT */
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/* LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN */
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/* ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE */
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/* POSSIBILITY OF SUCH DAMAGE. */
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#include <Python.h>
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#include <assert.h>
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#include <numpy/arrayobject.h>
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#include <stdio.h>
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#include "lapack_wrapper.h"
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static PyObject *py_phonopy_pinv(PyObject *self, PyObject *args);
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static PyObject *py_phonopy_zheev(PyObject *self, PyObject *args);
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struct module_state {
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PyObject *error;
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};
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#if PY_MAJOR_VERSION >= 3
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#define GETSTATE(m) ((struct module_state *)PyModule_GetState(m))
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#else
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#define GETSTATE(m) (&_state)
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static struct module_state _state;
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#endif
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static PyObject *error_out(PyObject *m) {
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struct module_state *st = GETSTATE(m);
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PyErr_SetString(st->error, "something bad happened");
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return NULL;
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}
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static PyMethodDef _lapackepy_methods[] = {
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{"error_out", (PyCFunction)error_out, METH_NOARGS, NULL},
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{"pinv", py_phonopy_pinv, METH_VARARGS,
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"Pseudo-inverse using Lapack dgesvd"},
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{"zheev", py_phonopy_zheev, METH_VARARGS, "Lapack zheev wrapper"},
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{NULL, NULL, 0, NULL}};
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#if PY_MAJOR_VERSION >= 3
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static int _lapackepy_traverse(PyObject *m, visitproc visit, void *arg) {
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Py_VISIT(GETSTATE(m)->error);
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return 0;
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}
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static int _lapackepy_clear(PyObject *m) {
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Py_CLEAR(GETSTATE(m)->error);
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return 0;
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}
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static struct PyModuleDef moduledef = {
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PyModuleDef_HEAD_INIT, "_lapackepy", NULL,
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sizeof(struct module_state), _lapackepy_methods, NULL,
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_lapackepy_traverse, _lapackepy_clear, NULL};
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#define INITERROR return NULL
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PyObject *PyInit__lapackepy(void)
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#else
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#define INITERROR return
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void init_lapackepy(void)
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#endif
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{
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#if PY_MAJOR_VERSION >= 3
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PyObject *module = PyModule_Create(&moduledef);
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#else
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PyObject *module = Py_InitModule("_lapackepy", _lapackepy_methods);
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#endif
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struct module_state *st;
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if (module == NULL) INITERROR;
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st = GETSTATE(module);
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st->error = PyErr_NewException("_lapackepy.Error", NULL, NULL);
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if (st->error == NULL) {
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Py_DECREF(module);
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INITERROR;
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}
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#if PY_MAJOR_VERSION >= 3
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return module;
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#endif
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}
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static PyObject *py_phonopy_zheev(PyObject *self, PyObject *args) {
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PyArrayObject *dynamical_matrix;
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PyArrayObject *eigenvalues;
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int dimension;
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npy_cdouble *dynmat;
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double *eigvals;
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lapack_complex_double *a;
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int i, info;
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if (!PyArg_ParseTuple(args, "OO", &dynamical_matrix, &eigenvalues)) {
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return NULL;
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}
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dimension = (int)PyArray_DIMS(dynamical_matrix)[0];
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dynmat = (npy_cdouble *)PyArray_DATA(dynamical_matrix);
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eigvals = (double *)PyArray_DATA(eigenvalues);
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a = (lapack_complex_double *)malloc(sizeof(lapack_complex_double) *
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dimension * dimension);
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for (i = 0; i < dimension * dimension; i++) {
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a[i] = lapack_make_complex_double(dynmat[i].real, dynmat[i].imag);
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}
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info = phonopy_zheev(eigvals, a, dimension, 'L');
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for (i = 0; i < dimension * dimension; i++) {
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dynmat[i].real = lapack_complex_double_real(a[i]);
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dynmat[i].imag = lapack_complex_double_imag(a[i]);
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}
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free(a);
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return PyLong_FromLong((long)info);
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}
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static PyObject *py_phonopy_pinv(PyObject *self, PyObject *args) {
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PyArrayObject *data_in_py;
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PyArrayObject *data_out_py;
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double cutoff;
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int m;
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int n;
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double *data_in;
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double *data_out;
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int info;
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if (!PyArg_ParseTuple(args, "OOd", &data_out_py, &data_in_py, &cutoff)) {
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return NULL;
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}
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m = (int)PyArray_DIMS(data_in_py)[0];
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n = (int)PyArray_DIMS(data_in_py)[1];
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data_in = (double *)PyArray_DATA(data_in_py);
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data_out = (double *)PyArray_DATA(data_out_py);
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info = phonopy_pinv(data_out, data_in, m, n, cutoff);
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return PyLong_FromLong((long)info);
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}
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130
c/_phono3py.c
130
c/_phono3py.c
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@ -40,10 +40,15 @@
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#include <stdio.h>
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#include <stdlib.h>
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#include "lapack_wrapper.h"
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// #include "lapack_wrapper.h"
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#include "phono3py.h"
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#include "phonoc_array.h"
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typedef struct {
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double re;
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double im;
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} _lapack_complex_double;
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static PyObject *py_get_interaction(PyObject *self, PyObject *args);
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static PyObject *py_get_pp_collision(PyObject *self, PyObject *args);
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static PyObject *py_get_pp_collision_with_sigma(PyObject *self, PyObject *args);
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@ -92,10 +97,8 @@ static PyObject *py_diagonalize_collision_matrix(PyObject *self,
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PyObject *args);
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static PyObject *py_pinv_from_eigensolution(PyObject *self, PyObject *args);
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static PyObject *py_get_default_colmat_solver(PyObject *self, PyObject *args);
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static PyObject *py_lapacke_pinv(PyObject *self, PyObject *args);
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static void pinv_from_eigensolution(double *data, const double *eigvals,
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const long size, const double cutoff,
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const long pinv_method);
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static void show_colmat_info(const PyArrayObject *collision_matrix_py,
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const long i_sigma, const long i_temp,
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const long adrs_shift);
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@ -206,6 +209,8 @@ static PyMethodDef _phono3py_methods[] = {
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METH_VARARGS, "Pseudo-inverse from eigensolution"},
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{"default_colmat_solver", (PyCFunction)py_get_default_colmat_solver,
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METH_VARARGS, "Return default collison matrix solver by integer value"},
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{"lapacke_pinv", (PyCFunction)py_lapacke_pinv, METH_VARARGS,
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"Pseudo inversion using lapacke."},
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{NULL, NULL, 0, NULL}};
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|
||||
#if PY_MAJOR_VERSION >= 3
|
||||
|
|
@ -276,7 +281,7 @@ static PyObject *py_get_interaction(PyObject *self, PyObject *args) {
|
|||
|
||||
Darray *fc3_normal_squared;
|
||||
Darray *freqs;
|
||||
lapack_complex_double *eigvecs;
|
||||
_lapack_complex_double *eigvecs;
|
||||
long(*triplets)[3];
|
||||
long num_triplets;
|
||||
char *g_zero;
|
||||
|
|
@ -307,7 +312,7 @@ static PyObject *py_get_interaction(PyObject *self, PyObject *args) {
|
|||
freqs = convert_to_darray(py_frequencies);
|
||||
/* npy_cdouble and lapack_complex_double may not be compatible. */
|
||||
/* So eigenvectors should not be used in Python side */
|
||||
eigvecs = (lapack_complex_double *)PyArray_DATA(py_eigenvectors);
|
||||
eigvecs = (_lapack_complex_double *)PyArray_DATA(py_eigenvectors);
|
||||
triplets = (long(*)[3])PyArray_DATA(py_triplets);
|
||||
num_triplets = (long)PyArray_DIMS(py_triplets)[0];
|
||||
g_zero = (char *)PyArray_DATA(py_g_zero);
|
||||
|
|
@ -371,7 +376,7 @@ static PyObject *py_get_pp_collision(PyObject *self, PyObject *args) {
|
|||
double *gamma;
|
||||
long(*relative_grid_address)[4][3];
|
||||
double *frequencies;
|
||||
lapack_complex_double *eigenvectors;
|
||||
_lapack_complex_double *eigenvectors;
|
||||
long(*triplets)[3];
|
||||
long num_triplets;
|
||||
long *triplet_weights;
|
||||
|
|
@ -405,7 +410,7 @@ static PyObject *py_get_pp_collision(PyObject *self, PyObject *args) {
|
|||
relative_grid_address =
|
||||
(long(*)[4][3])PyArray_DATA(py_relative_grid_address);
|
||||
frequencies = (double *)PyArray_DATA(py_frequencies);
|
||||
eigenvectors = (lapack_complex_double *)PyArray_DATA(py_eigenvectors);
|
||||
eigenvectors = (_lapack_complex_double *)PyArray_DATA(py_eigenvectors);
|
||||
triplets = (long(*)[3])PyArray_DATA(py_triplets);
|
||||
num_triplets = (long)PyArray_DIMS(py_triplets)[0];
|
||||
triplet_weights = (long *)PyArray_DATA(py_triplet_weights);
|
||||
|
|
@ -471,7 +476,7 @@ static PyObject *py_get_pp_collision_with_sigma(PyObject *self,
|
|||
|
||||
double *gamma;
|
||||
double *frequencies;
|
||||
lapack_complex_double *eigenvectors;
|
||||
_lapack_complex_double *eigenvectors;
|
||||
long(*triplets)[3];
|
||||
long num_triplets;
|
||||
long *triplet_weights;
|
||||
|
|
@ -502,7 +507,7 @@ static PyObject *py_get_pp_collision_with_sigma(PyObject *self,
|
|||
|
||||
gamma = (double *)PyArray_DATA(py_gamma);
|
||||
frequencies = (double *)PyArray_DATA(py_frequencies);
|
||||
eigenvectors = (lapack_complex_double *)PyArray_DATA(py_eigenvectors);
|
||||
eigenvectors = (_lapack_complex_double *)PyArray_DATA(py_eigenvectors);
|
||||
triplets = (long(*)[3])PyArray_DATA(py_triplets);
|
||||
num_triplets = (long)PyArray_DIMS(py_triplets)[0];
|
||||
triplet_weights = (long *)PyArray_DATA(py_triplet_weights);
|
||||
|
|
@ -910,7 +915,7 @@ static PyObject *py_get_isotope_strength(PyObject *self, PyObject *args) {
|
|||
|
||||
double *gamma;
|
||||
double *frequencies;
|
||||
lapack_complex_double *eigenvectors;
|
||||
_lapack_complex_double *eigenvectors;
|
||||
long *band_indices;
|
||||
double *mass_variances;
|
||||
long num_band, num_band0;
|
||||
|
|
@ -924,7 +929,7 @@ static PyObject *py_get_isotope_strength(PyObject *self, PyObject *args) {
|
|||
|
||||
gamma = (double *)PyArray_DATA(py_gamma);
|
||||
frequencies = (double *)PyArray_DATA(py_frequencies);
|
||||
eigenvectors = (lapack_complex_double *)PyArray_DATA(py_eigenvectors);
|
||||
eigenvectors = (_lapack_complex_double *)PyArray_DATA(py_eigenvectors);
|
||||
band_indices = (long *)PyArray_DATA(py_band_indices);
|
||||
mass_variances = (double *)PyArray_DATA(py_mass_variances);
|
||||
num_band = (long)PyArray_DIMS(py_frequencies)[1];
|
||||
|
|
@ -954,7 +959,7 @@ static PyObject *py_get_thm_isotope_strength(PyObject *self, PyObject *args) {
|
|||
double *frequencies;
|
||||
long *ir_grid_points;
|
||||
long *weights;
|
||||
lapack_complex_double *eigenvectors;
|
||||
_lapack_complex_double *eigenvectors;
|
||||
long *band_indices;
|
||||
double *mass_variances;
|
||||
long num_band, num_band0, num_ir_grid_points;
|
||||
|
|
@ -971,7 +976,7 @@ static PyObject *py_get_thm_isotope_strength(PyObject *self, PyObject *args) {
|
|||
frequencies = (double *)PyArray_DATA(py_frequencies);
|
||||
ir_grid_points = (long *)PyArray_DATA(py_ir_grid_points);
|
||||
weights = (long *)PyArray_DATA(py_weights);
|
||||
eigenvectors = (lapack_complex_double *)PyArray_DATA(py_eigenvectors);
|
||||
eigenvectors = (_lapack_complex_double *)PyArray_DATA(py_eigenvectors);
|
||||
band_indices = (long *)PyArray_DATA(py_band_indices);
|
||||
mass_variances = (double *)PyArray_DATA(py_mass_variances);
|
||||
num_band = (long)PyArray_DIMS(py_frequencies)[1];
|
||||
|
|
@ -1763,92 +1768,29 @@ static PyObject *py_get_default_colmat_solver(PyObject *self, PyObject *args) {
|
|||
#endif
|
||||
}
|
||||
|
||||
static void pinv_from_eigensolution(double *data, const double *eigvals,
|
||||
const long size, const double cutoff,
|
||||
const long pinv_method) {
|
||||
long i, ib, j, k, max_l, i_s, j_s;
|
||||
double *tmp_data;
|
||||
double e, sum;
|
||||
long *l;
|
||||
static PyObject *py_lapacke_pinv(PyObject *self, PyObject *args) {
|
||||
PyArrayObject *data_in_py;
|
||||
PyArrayObject *data_out_py;
|
||||
double cutoff;
|
||||
|
||||
l = NULL;
|
||||
tmp_data = NULL;
|
||||
int m;
|
||||
int n;
|
||||
double *data_in;
|
||||
double *data_out;
|
||||
int info;
|
||||
|
||||
tmp_data = (double *)malloc(sizeof(double) * size * size);
|
||||
|
||||
#ifdef _OPENMP
|
||||
#pragma omp parallel for
|
||||
#endif
|
||||
for (i = 0; i < size * size; i++) {
|
||||
tmp_data[i] = data[i];
|
||||
if (!PyArg_ParseTuple(args, "OOd", &data_out_py, &data_in_py, &cutoff)) {
|
||||
return NULL;
|
||||
}
|
||||
|
||||
l = (long *)malloc(sizeof(long) * size);
|
||||
max_l = 0;
|
||||
for (i = 0; i < size; i++) {
|
||||
if (pinv_method == 0) {
|
||||
e = fabs(eigvals[i]);
|
||||
} else {
|
||||
e = eigvals[i];
|
||||
}
|
||||
if (e > cutoff) {
|
||||
l[max_l] = i;
|
||||
max_l++;
|
||||
}
|
||||
}
|
||||
m = (int)PyArray_DIMS(data_in_py)[0];
|
||||
n = (int)PyArray_DIMS(data_in_py)[1];
|
||||
data_in = (double *)PyArray_DATA(data_in_py);
|
||||
data_out = (double *)PyArray_DATA(data_out_py);
|
||||
|
||||
#ifdef _OPENMP
|
||||
#pragma omp parallel for private(ib, j, k, i_s, j_s, sum)
|
||||
#endif
|
||||
for (i = 0; i < size / 2; i++) {
|
||||
/* from front */
|
||||
i_s = i * size;
|
||||
for (j = i; j < size; j++) {
|
||||
j_s = j * size;
|
||||
sum = 0;
|
||||
for (k = 0; k < max_l; k++) {
|
||||
sum +=
|
||||
tmp_data[i_s + l[k]] * tmp_data[j_s + l[k]] / eigvals[l[k]];
|
||||
}
|
||||
data[i_s + j] = sum;
|
||||
data[j_s + i] = sum;
|
||||
}
|
||||
/* from back */
|
||||
ib = size - i - 1;
|
||||
i_s = ib * size;
|
||||
for (j = ib; j < size; j++) {
|
||||
j_s = j * size;
|
||||
sum = 0;
|
||||
for (k = 0; k < max_l; k++) {
|
||||
sum +=
|
||||
tmp_data[i_s + l[k]] * tmp_data[j_s + l[k]] / eigvals[l[k]];
|
||||
}
|
||||
data[i_s + j] = sum;
|
||||
data[j_s + ib] = sum;
|
||||
}
|
||||
}
|
||||
info = phonopy_pinv(data_out, data_in, m, n, cutoff);
|
||||
|
||||
/* when size is odd */
|
||||
if ((size % 2) == 1) {
|
||||
i = (size - 1) / 2;
|
||||
i_s = i * size;
|
||||
for (j = i; j < size; j++) {
|
||||
j_s = j * size;
|
||||
sum = 0;
|
||||
for (k = 0; k < max_l; k++) {
|
||||
sum +=
|
||||
tmp_data[i_s + l[k]] * tmp_data[j_s + l[k]] / eigvals[l[k]];
|
||||
}
|
||||
data[i_s + j] = sum;
|
||||
data[j_s + i] = sum;
|
||||
}
|
||||
}
|
||||
|
||||
free(l);
|
||||
l = NULL;
|
||||
|
||||
free(tmp_data);
|
||||
tmp_data = NULL;
|
||||
return PyLong_FromLong((long)info);
|
||||
}
|
||||
|
||||
static void show_colmat_info(const PyArrayObject *py_collision_matrix,
|
||||
|
|
|
|||
|
|
@ -35,9 +35,14 @@
|
|||
#include <Python.h>
|
||||
#include <numpy/arrayobject.h>
|
||||
|
||||
#include "lapack_wrapper.h"
|
||||
// #include "lapack_wrapper.h"
|
||||
#include "phononmod.h"
|
||||
|
||||
typedef struct {
|
||||
double re;
|
||||
double im;
|
||||
} _lapack_complex_double;
|
||||
|
||||
static PyObject *py_get_phonons_at_gridpoints(PyObject *self, PyObject *args);
|
||||
|
||||
struct module_state {
|
||||
|
|
@ -139,7 +144,7 @@ static PyObject *py_get_phonons_at_gridpoints(PyObject *self, PyObject *args) {
|
|||
double(*dielectric)[3];
|
||||
double *q_dir;
|
||||
double *freqs;
|
||||
lapack_complex_double *eigvecs;
|
||||
_lapack_complex_double *eigvecs;
|
||||
char *phonon_done;
|
||||
long *grid_points;
|
||||
long(*grid_address)[3];
|
||||
|
|
@ -168,7 +173,7 @@ static PyObject *py_get_phonons_at_gridpoints(PyObject *self, PyObject *args) {
|
|||
}
|
||||
|
||||
freqs = (double *)PyArray_DATA(py_frequencies);
|
||||
eigvecs = (lapack_complex_double *)PyArray_DATA(py_eigenvectors);
|
||||
eigvecs = (_lapack_complex_double *)PyArray_DATA(py_eigenvectors);
|
||||
phonon_done = (char *)PyArray_DATA(py_phonon_done);
|
||||
grid_points = (long *)PyArray_DATA(py_grid_points);
|
||||
grid_address = (long(*)[3])PyArray_DATA(py_grid_address);
|
||||
|
|
|
|||
|
|
@ -34,6 +34,8 @@
|
|||
|
||||
#include "lapack_wrapper.h"
|
||||
|
||||
#include <math.h>
|
||||
|
||||
#define min(a, b) ((a) > (b) ? (b) : (a))
|
||||
|
||||
#if defined(MKL_LAPACKE) || defined(SCIPY_MKL_H)
|
||||
|
|
@ -194,3 +196,91 @@ lapack_complex_double phonoc_complex_prod(const lapack_complex_double a,
|
|||
lapack_complex_double_real(a) * lapack_complex_double_imag(b));
|
||||
return c;
|
||||
}
|
||||
|
||||
void pinv_from_eigensolution(double *data, const double *eigvals,
|
||||
const long size, const double cutoff,
|
||||
const long pinv_method) {
|
||||
long i, ib, j, k, max_l, i_s, j_s;
|
||||
double *tmp_data;
|
||||
double e, sum;
|
||||
long *l;
|
||||
|
||||
l = NULL;
|
||||
tmp_data = NULL;
|
||||
|
||||
tmp_data = (double *)malloc(sizeof(double) * size * size);
|
||||
|
||||
#ifdef _OPENMP
|
||||
#pragma omp parallel for
|
||||
#endif
|
||||
for (i = 0; i < size * size; i++) {
|
||||
tmp_data[i] = data[i];
|
||||
}
|
||||
|
||||
l = (long *)malloc(sizeof(long) * size);
|
||||
max_l = 0;
|
||||
for (i = 0; i < size; i++) {
|
||||
if (pinv_method == 0) {
|
||||
e = fabs(eigvals[i]);
|
||||
} else {
|
||||
e = eigvals[i];
|
||||
}
|
||||
if (e > cutoff) {
|
||||
l[max_l] = i;
|
||||
max_l++;
|
||||
}
|
||||
}
|
||||
|
||||
#ifdef _OPENMP
|
||||
#pragma omp parallel for private(ib, j, k, i_s, j_s, sum)
|
||||
#endif
|
||||
for (i = 0; i < size / 2; i++) {
|
||||
/* from front */
|
||||
i_s = i * size;
|
||||
for (j = i; j < size; j++) {
|
||||
j_s = j * size;
|
||||
sum = 0;
|
||||
for (k = 0; k < max_l; k++) {
|
||||
sum +=
|
||||
tmp_data[i_s + l[k]] * tmp_data[j_s + l[k]] / eigvals[l[k]];
|
||||
}
|
||||
data[i_s + j] = sum;
|
||||
data[j_s + i] = sum;
|
||||
}
|
||||
/* from back */
|
||||
ib = size - i - 1;
|
||||
i_s = ib * size;
|
||||
for (j = ib; j < size; j++) {
|
||||
j_s = j * size;
|
||||
sum = 0;
|
||||
for (k = 0; k < max_l; k++) {
|
||||
sum +=
|
||||
tmp_data[i_s + l[k]] * tmp_data[j_s + l[k]] / eigvals[l[k]];
|
||||
}
|
||||
data[i_s + j] = sum;
|
||||
data[j_s + ib] = sum;
|
||||
}
|
||||
}
|
||||
|
||||
/* when size is odd */
|
||||
if ((size % 2) == 1) {
|
||||
i = (size - 1) / 2;
|
||||
i_s = i * size;
|
||||
for (j = i; j < size; j++) {
|
||||
j_s = j * size;
|
||||
sum = 0;
|
||||
for (k = 0; k < max_l; k++) {
|
||||
sum +=
|
||||
tmp_data[i_s + l[k]] * tmp_data[j_s + l[k]] / eigvals[l[k]];
|
||||
}
|
||||
data[i_s + j] = sum;
|
||||
data[j_s + i] = sum;
|
||||
}
|
||||
}
|
||||
|
||||
free(l);
|
||||
l = NULL;
|
||||
|
||||
free(tmp_data);
|
||||
tmp_data = NULL;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -59,4 +59,7 @@ int phonopy_dsyev(double *data, double *eigvals, const int size,
|
|||
lapack_complex_double phonoc_complex_prod(const lapack_complex_double a,
|
||||
const lapack_complex_double b);
|
||||
|
||||
void pinv_from_eigensolution(double *data, const double *eigvals,
|
||||
const long size, const double cutoff,
|
||||
const long pinv_method);
|
||||
#endif
|
||||
|
|
|
|||
|
|
@ -444,7 +444,7 @@ def _solve_fc3(
|
|||
solver = "numpy.linalg.pinv"
|
||||
else:
|
||||
try:
|
||||
import phono3py._lapackepy as lapackepy
|
||||
import phono3py._phono3py as phono3c
|
||||
|
||||
solver = "lapacke-dgesvd"
|
||||
except ImportError:
|
||||
|
|
@ -496,7 +496,7 @@ def _solve_fc3(
|
|||
inv_U = np.zeros(
|
||||
(rot_disps.shape[1], rot_disps.shape[0]), dtype="double", order="C"
|
||||
)
|
||||
lapackepy.pinv(inv_U, rot_disps, 1e-13)
|
||||
phono3c.lapacke_pinv(inv_U, rot_disps, 1e-13)
|
||||
|
||||
fc3 = np.zeros((num_atom, num_atom, 3, 3, 3), dtype="double", order="C")
|
||||
|
||||
|
|
|
|||
|
|
@ -1,5 +1,7 @@
|
|||
[build-system]
|
||||
requires = ["setuptools", "wheel", "numpy", "oldest-supported-numpy"]
|
||||
requires = ["setuptools", "wheel", "numpy"]
|
||||
#requires = ["setuptools", "wheel", "numpy", "oldest-supported-numpy"]
|
||||
#build-backend = "setuptools.build_meta"
|
||||
|
||||
[tool.flake8]
|
||||
max-line-length = 88
|
||||
|
|
|
|||
204
setup.py
204
setup.py
|
|
@ -1,135 +1,113 @@
|
|||
"""Phono3py setup.py."""
|
||||
"""Phono3py setup.py.
|
||||
|
||||
The build steps are as follows:
|
||||
|
||||
mkdir _build && cd _build
|
||||
cmake -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_EXPORT_COMPILE_COMMANDS=1 \
|
||||
-DPHONONMOD=on -DPHONO3PY=on -DCMAKE_INSTALL_PREFIX="" ..
|
||||
cmake --build . -v
|
||||
cd ..
|
||||
python setup.py build
|
||||
pip install -e .
|
||||
|
||||
"""
|
||||
import os
|
||||
import pathlib
|
||||
import shutil
|
||||
import subprocess
|
||||
|
||||
import numpy
|
||||
import setuptools
|
||||
|
||||
# Ensure that 'site.cfg' exists.
|
||||
if not os.path.exists("site.cfg"):
|
||||
msg_list = [
|
||||
'"site.cfg" file is needed to run setup.py.',
|
||||
"See about installation at https://phonopy.github.io/phono3py/install.html.",
|
||||
"A minimum setting of site.cfg to build with openmp support is:",
|
||||
"# ------------------------------",
|
||||
"[phono3py]",
|
||||
"extra_compile_args = -fopenmp",
|
||||
"# ------------------------------",
|
||||
"Please create an emply site.cfg (no-openmp support) to run setup.py",
|
||||
"unless any custom setting is needed, although this is considered unusual.",
|
||||
|
||||
def _run_cmake(build_dir):
|
||||
build_dir.mkdir()
|
||||
args = [
|
||||
"cmake",
|
||||
"-S",
|
||||
".",
|
||||
"-B",
|
||||
"_build",
|
||||
"-DPHONONMOD=on",
|
||||
"-DPHONO3PY=on",
|
||||
"-DCMAKE_INSTALL_PREFIX=.",
|
||||
]
|
||||
# if "CONDA_PREFIX" in os.environ:
|
||||
# args.append("-DUSE_CONDA_PATH=on")
|
||||
# if "CC" in os.environ:
|
||||
# args.append(f'-DCMAKE_C_COMPILER={os.environ["CC"]}')
|
||||
|
||||
raise FileNotFoundError("\n".join(msg_list))
|
||||
cmake_output = subprocess.check_output(args)
|
||||
print(cmake_output.decode("utf-8"))
|
||||
subprocess.check_call(["cmake", "--build", "_build", "-v"])
|
||||
return cmake_output
|
||||
|
||||
# Retrieve the default flags from the numpy installation
|
||||
# This also means one can override this with a site.cfg
|
||||
# configuration file
|
||||
from numpy.distutils.system_info import dict_append, get_info, system_info
|
||||
|
||||
def _clean_cmake(build_dir):
|
||||
shutil.rmtree(build_dir)
|
||||
|
||||
|
||||
build_dir = pathlib.Path.cwd() / "_build"
|
||||
found_extra_link_args = []
|
||||
found_extra_compile_args = []
|
||||
define_macros = []
|
||||
use_mkl_lapacke = False
|
||||
if build_dir.exists():
|
||||
pass
|
||||
else:
|
||||
cmake_output = _run_cmake(build_dir)
|
||||
found_flags = {}
|
||||
found_libs = {}
|
||||
for line in cmake_output.decode("utf-8").split("\n"):
|
||||
for key in ["BLAS", "LAPACK", "OpenMP"]:
|
||||
if f"{key} libs" in line and len(line.split()) > 3:
|
||||
found_libs[key] = line.split()[3].split(";")
|
||||
if f"{key} flags" in line and len(line.split()) > 3:
|
||||
found_flags[key] = line.split()[3].split(";")
|
||||
for key, value in found_libs.items():
|
||||
found_extra_link_args += value
|
||||
for element in value:
|
||||
if "libmkl" in element:
|
||||
use_mkl_lapacke = True
|
||||
for key, value in found_flags.items():
|
||||
found_extra_compile_args += value
|
||||
if use_mkl_lapacke:
|
||||
define_macros.append(("MKL_LAPACKE", None))
|
||||
print("=============================================")
|
||||
print(found_extra_compile_args)
|
||||
print(found_extra_link_args)
|
||||
print(define_macros)
|
||||
print("=============================================")
|
||||
|
||||
git_num = None
|
||||
|
||||
# use flags defined in numpy
|
||||
all_info_d = get_info("ALL")
|
||||
lapack_info_d = get_info("lapack_opt")
|
||||
|
||||
|
||||
class phono3py_info(system_info):
|
||||
"""See system_info in numpy."""
|
||||
|
||||
section = "phono3py"
|
||||
|
||||
def calc_info(self):
|
||||
"""Read in *all* options in the [phono3py] section of site.cfg."""
|
||||
info = self.calc_libraries_info()
|
||||
dict_append(info, **self.calc_extra_info())
|
||||
dict_append(info, include_dirs=self.get_include_dirs())
|
||||
self.set_info(**info)
|
||||
|
||||
|
||||
macros = []
|
||||
|
||||
# in numpy>=1.16.0, silence build warnings about deprecated API usage
|
||||
macros.append(("NPY_NO_DEPRECATED_API", "0"))
|
||||
|
||||
# Avoid divergence in tetrahedron method by ensuring denominator > 1e-10.
|
||||
# macros.append(("THM_EPSILON", "1e-10"))
|
||||
|
||||
with_threaded_blas = False
|
||||
with_mkl = False
|
||||
|
||||
# define options
|
||||
# these are the basic definitions for all extensions
|
||||
opts = lapack_info_d.copy()
|
||||
if "mkl" in opts.get("libraries", ""):
|
||||
with_mkl = True
|
||||
|
||||
if with_mkl:
|
||||
with_threaded_blas = True
|
||||
# generally this should not be needed since the numpy distutils
|
||||
# finding of MKL creates the SCIPY_MKL_H flag
|
||||
macros.append(("MKL_LAPACKE", None))
|
||||
|
||||
if with_threaded_blas:
|
||||
macros.append(("MULTITHREADED_BLAS", None))
|
||||
|
||||
# Create the dictionary for compiling the codes
|
||||
dict_append(opts, **all_info_d)
|
||||
dict_append(opts, include_dirs=["c"])
|
||||
dict_append(opts, define_macros=macros)
|
||||
# Add numpy's headers
|
||||
include_dirs = numpy.get_include()
|
||||
if include_dirs is not None:
|
||||
dict_append(opts, include_dirs=[include_dirs])
|
||||
|
||||
# Add any phono3py manual flags from here
|
||||
add_opts = phono3py_info().get_info()
|
||||
dict_append(opts, **add_opts)
|
||||
include_dirs = ["c", numpy.get_include()]
|
||||
# if "CONDA_PREFIX" in os.environ:
|
||||
# include_dirs.append(os.environ["CONDA_PREFIX"] + "/include")
|
||||
|
||||
# Different extensions
|
||||
extensions = []
|
||||
|
||||
# Define the modules
|
||||
sources_phono3py = [
|
||||
"c/_phono3py.c",
|
||||
"c/bzgrid.c",
|
||||
"c/collision_matrix.c",
|
||||
"c/fc3.c",
|
||||
"c/grgrid.c",
|
||||
"c/imag_self_energy_with_g.c",
|
||||
"c/interaction.c",
|
||||
"c/isotope.c",
|
||||
"c/lagrid.c",
|
||||
"c/lapack_wrapper.c",
|
||||
"c/phono3py.c",
|
||||
"c/phonoc_utils.c",
|
||||
"c/pp_collision.c",
|
||||
"c/real_self_energy.c",
|
||||
"c/real_to_reciprocal.c",
|
||||
"c/reciprocal_to_normal.c",
|
||||
"c/snf3x3.c",
|
||||
"c/tetrahedron_method.c",
|
||||
"c/triplet.c",
|
||||
"c/triplet_grid.c",
|
||||
"c/triplet_iw.c",
|
||||
]
|
||||
extensions.append(
|
||||
setuptools.Extension("phono3py._phono3py", sources=sources_phono3py, **opts)
|
||||
setuptools.Extension(
|
||||
"phono3py._phono3py",
|
||||
sources=["c/_phono3py.c"],
|
||||
extra_link_args=["_build/libph3py.a"] + found_extra_link_args,
|
||||
include_dirs=include_dirs,
|
||||
extra_compile_args=found_extra_compile_args,
|
||||
define_macros=define_macros,
|
||||
)
|
||||
)
|
||||
|
||||
|
||||
sources_phononmod = [
|
||||
"c/_phononmod.c",
|
||||
"c/dynmat.c",
|
||||
"c/lapack_wrapper.c",
|
||||
"c/phonon.c",
|
||||
"c/phononmod.c",
|
||||
]
|
||||
extensions.append(
|
||||
setuptools.Extension("phono3py._phononmod", sources=sources_phononmod, **opts)
|
||||
setuptools.Extension(
|
||||
"phono3py._phononmod",
|
||||
sources=["c/_phononmod.c"],
|
||||
extra_link_args=["_build/libphmod.a"] + found_extra_link_args,
|
||||
include_dirs=include_dirs,
|
||||
extra_compile_args=found_extra_compile_args,
|
||||
define_macros=define_macros,
|
||||
)
|
||||
|
||||
sources_lapackepy = ["c/_lapackepy.c", "c/lapack_wrapper.c"]
|
||||
extensions.append(
|
||||
setuptools.Extension("phono3py._lapackepy", sources=sources_lapackepy, **opts)
|
||||
)
|
||||
|
||||
packages_phono3py = [
|
||||
|
|
@ -204,3 +182,5 @@ if __name__ == "__main__":
|
|||
scripts=scripts_phono3py,
|
||||
ext_modules=extensions,
|
||||
)
|
||||
|
||||
_clean_cmake(build_dir)
|
||||
|
|
|
|||
Loading…
Reference in New Issue