Merge branch 'develop' into publish-gh-pages

phonopy · Jul 27, 2024 · 8ca39c5 · 8ca39c5
2 parents c292c20 + 10d6641
commit 8ca39c5
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diff --git a/.github/workflows/phono3py-pytest-conda-mkl-phphmtblas.yml b/.github/workflows/phono3py-pytest-conda-mkl-phphmtblas.yml
@@ -24,7 +24,7 @@ jobs:
       run: |
         conda activate test
         conda install --yes python=${{ matrix.python-version }}
-        conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler cxx-compiler
+        conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest spglib alm cmake c-compiler cxx-compiler
     - name: Install symfc develop branch
       run: |
         conda activate test
@@ -45,8 +45,5 @@ jobs:
         PHPHCALC_USE_MTBLAS=ON pip install -e . -vvv
     - name: Run pytest
       run: |
-        pytest -v --cov=./ --cov-report=xml test
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
-      with:
-        verbose: true
+        conda activate test
+        pytest -v test
diff --git a/.github/workflows/phono3py-pytest-conda-mkl-v2.yml b/.github/workflows/phono3py-pytest-conda-mkl-v2.yml
@@ -24,7 +24,7 @@ jobs:
       run: |
         conda activate test
         conda install --yes python=${{ matrix.python-version }}
-        conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler cxx-compiler
+        conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest spglib alm cmake c-compiler cxx-compiler
     - name: Install symfc develop branch
       run: |
         conda activate test
@@ -45,8 +45,5 @@ jobs:
         pip install -e . -vvv
     - name: Run pytest
       run: |
-        pytest --v2 -v --cov=./ --cov-report=xml test
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
-      with:
-        verbose: true
+        conda activate test
+        pytest --v2 -v test
diff --git a/.github/workflows/phono3py-pytest-conda-mkl.yml b/.github/workflows/phono3py-pytest-conda-mkl.yml
@@ -45,6 +45,7 @@ jobs:
         pip install -e . -vvv
     - name: Run pytest
       run: |
+        conda activate test
         pytest -v --cov=./ --cov-report=xml test
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v3

diff --git a/.github/workflows/phono3py-pytest-conda-numpy2.yml b/.github/workflows/phono3py-pytest-conda-numpy2.yml
@@ -24,7 +24,7 @@ jobs:
       run: |
         conda activate test
         conda install --yes python=${{ matrix.python-version }}
-        conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py "numpy=2" scipy pytest codecov pytest-cov cmake c-compiler cxx-compiler
+        conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py "numpy=2" scipy pytest cmake c-compiler cxx-compiler
     - name: Install spglib develop branch
       run: |
         conda activate test
@@ -52,8 +52,5 @@ jobs:
         pip install -e . -vvv
     - name: Run pytest
       run: |
+        conda activate test
         pytest -v test
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
-      with:
-        verbose: true
diff --git a/.github/workflows/phono3py-pytest-conda-phphmtblas.yml b/.github/workflows/phono3py-pytest-conda-phphmtblas.yml
@@ -24,7 +24,7 @@ jobs:
       run: |
         conda activate test
         conda install --yes python=${{ matrix.python-version }}
-        conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler cxx-compiler
+        conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py scipy pytest spglib alm cmake c-compiler cxx-compiler
     - name: Install symfc develop branch
       run: |
         conda activate test
@@ -45,8 +45,5 @@ jobs:
         PHPHCALC_USE_MTBLAS=ON pip install -e . -vvv
     - name: Run pytest
       run: |
-        pytest -v --cov=./ --cov-report=xml test
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
-      with:
-        verbose: true
+        conda activate test
+        pytest -v test
diff --git a/.github/workflows/phono3py-pytest-conda.yml b/.github/workflows/phono3py-pytest-conda.yml
@@ -12,7 +12,7 @@ jobs:
         shell: bash -l {0}
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v4
@@ -24,7 +24,7 @@ jobs:
       run: |
         conda activate test
         conda install --yes python=${{ matrix.python-version }}
-        conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler cxx-compiler
+        conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py scipy pytest spglib alm cmake c-compiler cxx-compiler
     - name: Install phonopy develop branch
       run: |
         conda activate test
@@ -38,8 +38,5 @@ jobs:
         pip install -e . -vvv
     - name: Run pytest
       run: |
-        pytest -v --cov=./ --cov-report=xml test
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
-      with:
-        verbose: true
+        conda activate test
+        pytest -v test
diff --git a/.github/workflows/publish-to-test-pypi.yml b/.github/workflows/publish-to-test-pypi.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.12, ]
+        python-version: ["3.12"]
 
     steps:
     - uses: actions/checkout@v4

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -11,7 +11,7 @@ repos:
   - id: check-added-large-files
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.5.1
+  rev: v0.5.4
   hooks:
   - id: ruff
     args: [ "--fix", "--show-fixes" ]

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -2,6 +2,7 @@ cmake_minimum_required(VERSION 3.20)
 
 option(BUILD_PHPHCALC_LIB "Option to build phph calculation module" OFF)
 option(BUILD_PHONONCALC_LIB "Option to build phonon calculation module" OFF)
+option(BUILD_RECGRID_LIB "Option to build reciprocal space grid module" OFF)
 option(BUILD_GRIDSYS_LIB "Option to build gridsys module" OFF)
 option(PHONO3PY_WITH_Fortran "enable fortran interface" OFF)
 option(PHONO3PY_USE_OMP "Option to search OpenMP library" ON)
@@ -125,27 +126,61 @@ if(BUILD_PHPHCALC_LIB
 endif()
 
 # ###################################################################################
-# Build phphcalc module #
+# Reciprocal space grid library #
+# ###################################################################################
+if(BUILD_RECGRID_LIB
+   OR BUILD_PHPHCALC_LIB
+   OR BUILD_NANOBIND_MODULE)
+    # Source code
+    set(SOURCES_PHPHCALC
+        ${PROJECT_SOURCE_DIR}/c/bzgrid.c ${PROJECT_SOURCE_DIR}/c/grgrid.c
+        ${PROJECT_SOURCE_DIR}/c/lagrid.c ${PROJECT_SOURCE_DIR}/c/snf3x3.c
+        ${PROJECT_SOURCE_DIR}/c/recgrid.c)
+
+    if(BUILD_SHARED_LIBS)
+        # Shared library
+        add_library(recgrid_lib SHARED ${SOURCES_PHPHCALC})
+    else()
+        # Static link library
+        add_library(recgrid_lib STATIC ${SOURCES_PHPHCALC})
+    endif()
+
+    if(NOT BUILD_NANOBIND_MODULE)
+        if(BUILD_SHARED_LIBS)
+            set_property(TARGET recgrid_lib PROPERTY VERSION ${SERIAL})
+            set_property(TARGET recgrid_lib PROPERTY SOVERSION ${SOSERIAL})
+            install(TARGETS recgrid_lib LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
+        else()
+            set_property(TARGET recgrid_lib PROPERTY VERSION ${SERIAL})
+            set_property(TARGET recgrid_lib PROPERTY SOVERSION ${SOSERIAL})
+            set_property(TARGET recgrid_lib PROPERTY OUTPUT_NAME recgrid_lib)
+            install(TARGETS recgrid_lib ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+        endif()
+
+        # Header file
+        install(FILES ${PROJECT_SOURCE_DIR}/c/recgrid.h
+                DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+    endif()
+endif()
+
+# ###################################################################################
+# Ph-ph calculation library #
 # ###################################################################################
 if(BUILD_PHPHCALC_LIB OR BUILD_NANOBIND_MODULE)
     # Source code
     set(SOURCES_PHPHCALC
-        ${PROJECT_SOURCE_DIR}/c/bzgrid.c
         ${PROJECT_SOURCE_DIR}/c/collision_matrix.c
         ${PROJECT_SOURCE_DIR}/c/fc3.c
-        ${PROJECT_SOURCE_DIR}/c/grgrid.c
         ${PROJECT_SOURCE_DIR}/c/imag_self_energy_with_g.c
         ${PROJECT_SOURCE_DIR}/c/interaction.c
         ${PROJECT_SOURCE_DIR}/c/isotope.c
-        ${PROJECT_SOURCE_DIR}/c/lagrid.c
         ${PROJECT_SOURCE_DIR}/c/lapack_wrapper.c
         ${PROJECT_SOURCE_DIR}/c/phono3py.c
-        ${PROJECT_SOURCE_DIR}/c/phonoc_utils.c
+        ${PROJECT_SOURCE_DIR}/c/funcs.c
         ${PROJECT_SOURCE_DIR}/c/pp_collision.c
         ${PROJECT_SOURCE_DIR}/c/real_self_energy.c
         ${PROJECT_SOURCE_DIR}/c/real_to_reciprocal.c
         ${PROJECT_SOURCE_DIR}/c/reciprocal_to_normal.c
-        ${PROJECT_SOURCE_DIR}/c/snf3x3.c
         ${PROJECT_SOURCE_DIR}/c/tetrahedron_method.c
         ${PROJECT_SOURCE_DIR}/c/triplet.c
         ${PROJECT_SOURCE_DIR}/c/triplet_grid.c
@@ -156,10 +191,12 @@ if(BUILD_PHPHCALC_LIB OR BUILD_NANOBIND_MODULE)
         add_library(phphcalc_lib SHARED ${SOURCES_PHPHCALC})
 
         if(OpenMP_FOUND)
-            target_link_libraries(phphcalc_lib PRIVATE BLAS::BLAS LAPACK::LAPACK
-                                                       OpenMP::OpenMP_C)
+            target_link_libraries(
+                phphcalc_lib PRIVATE recgrid_lib BLAS::BLAS LAPACK::LAPACK
+                                     OpenMP::OpenMP_C)
         else()
-            target_link_libraries(phphcalc_lib PRIVATE BLAS::BLAS LAPACK::LAPACK)
+            target_link_libraries(phphcalc_lib PRIVATE recgrid_lib BLAS::BLAS
+                                                       LAPACK::LAPACK)
         endif()
 
         target_include_directories(phphcalc_lib PRIVATE ${MY_INCLUDES})
@@ -188,10 +225,10 @@ if(BUILD_PHPHCALC_LIB OR BUILD_NANOBIND_MODULE)
         add_library(phphcalc_lib STATIC ${SOURCES_PHPHCALC})
 
         if(OpenMP_FOUND)
-            target_link_libraries(phphcalc_lib BLAS::BLAS LAPACK::LAPACK
+            target_link_libraries(phphcalc_lib recgrid_lib BLAS::BLAS LAPACK::LAPACK
                                   OpenMP::OpenMP_C)
         else()
-            target_link_libraries(phphcalc_lib BLAS::BLAS LAPACK::LAPACK)
+            target_link_libraries(phphcalc_lib recgrid_lib BLAS::BLAS LAPACK::LAPACK)
         endif()
 
         target_include_directories(phphcalc_lib PRIVATE ${MY_INCLUDES})
@@ -236,7 +273,7 @@ if(BUILD_PHPHCALC_LIB OR BUILD_NANOBIND_MODULE)
 endif()
 
 # ###################################################################################
-# phononcalc #
+# Phonon calculation library #
 # ###################################################################################
 if(BUILD_PHONONCALC_LIB OR BUILD_NANOBIND_MODULE)
     # Source code
@@ -311,7 +348,7 @@ if(BUILD_PHONONCALC_LIB OR BUILD_NANOBIND_MODULE)
 endif()
 
 # ###################################################################################
-# grid #
+# gridsys #
 # ###################################################################################
 if(BUILD_GRIDSYS_LIB)
     # Source code
@@ -321,7 +358,7 @@ if(BUILD_GRIDSYS_LIB)
         ${PROJECT_SOURCE_DIR}/c/gridsys.c
         ${PROJECT_SOURCE_DIR}/c/lagrid.c
         ${PROJECT_SOURCE_DIR}/c/niggli.c
-        ${PROJECT_SOURCE_DIR}/c/phonoc_utils.c
+        ${PROJECT_SOURCE_DIR}/c/funcs.c
         ${PROJECT_SOURCE_DIR}/c/snf3x3.c
         ${PROJECT_SOURCE_DIR}/c/tetrahedron_method.c
         ${PROJECT_SOURCE_DIR}/c/triplet.c
@@ -388,11 +425,15 @@ if(BUILD_NANOBIND_MODULE)
                         ${PROJECT_SOURCE_DIR}/c/_phono3py.cpp)
     nanobind_add_module(_phononcalc STABLE_ABI ${PROJECT_SOURCE_DIR}/c/phononcalc.h
                         ${PROJECT_SOURCE_DIR}/c/_phononcalc.cpp)
+    nanobind_add_module(_recgrid STABLE_ABI ${PROJECT_SOURCE_DIR}/c/recgrid.h
+                        ${PROJECT_SOURCE_DIR}/c/_recgrid.cpp)
 
     target_link_libraries(_phono3py PRIVATE phphcalc_lib)
     target_link_libraries(_phononcalc PRIVATE phononcalc_lib)
+    target_link_libraries(_recgrid PRIVATE recgrid_lib)
 
     target_compile_definitions(_phono3py PRIVATE THM_EPSILON=1e-10)
     install(TARGETS _phono3py LIBRARY DESTINATION ${SKBUILD_PROJECT_NAME})
     install(TARGETS _phononcalc LIBRARY DESTINATION ${SKBUILD_PROJECT_NAME})
+    install(TARGETS _recgrid LIBRARY DESTINATION ${SKBUILD_PROJECT_NAME})
 endif()
diff --git a/c/_phono3py.cpp b/c/_phono3py.cpp
@@ -1179,14 +1179,6 @@ NB_MODULE(_phono3py, m) {
     m.def("triplets_integration_weights", &py_get_triplets_integration_weights);
     m.def("triplets_integration_weights_with_sigma",
           &py_get_triplets_integration_weights_with_sigma);
-    m.def("grid_index_from_address", &py_get_grid_index_from_address);
-    m.def("ir_grid_map", &py_get_ir_grid_map);
-    m.def("gr_grid_addresses", &py_get_gr_grid_addresses);
-    m.def("reciprocal_rotations", &py_get_reciprocal_rotations);
-    m.def("transform_rotations", &py_transform_rotations);
-    m.def("snf3x3", &py_get_snf3x3);
-    m.def("bz_grid_addresses", &py_get_bz_grid_addresses);
-    m.def("rotate_bz_grid_index", &py_rotate_bz_grid_addresses);
     m.def("diagonalize_collision_matrix", &py_diagonalize_collision_matrix);
     m.def("pinv_from_eigensolution", &py_pinv_from_eigensolution);
     m.def("default_colmat_solver", &py_get_default_colmat_solver);