Merge branch 'rc'

phonopy · Jun 19, 2024 · 781c96c · 781c96c
2 parents 10b04a0 + 080ba03
commit 781c96c
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diff --git a/.github/workflows/phono3py-pytest-conda-mkl-phphmtblas.yml b/.github/workflows/phono3py-pytest-conda-mkl-phphmtblas.yml
@@ -15,9 +15,9 @@ jobs:
         python-version: ["3.12"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     # Use conda-incubator/setup-miniconda for precise control of conda infrastructure
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         miniforge-version: latest
     - name: Install dependent packages
@@ -26,6 +26,13 @@ jobs:
         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
         conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler
+    - name: Install symfc develop branch
+      run: |
+        conda activate test
+        git clone --depth 1 https://github.com/symfc/symfc.git
+        cd symfc
+        pip install -e . -vvv
+        cd ..
     - name: Install phonopy develop branch
       run: |
         conda activate test

diff --git a/.github/workflows/phono3py-pytest-conda-mkl-v2.yml b/.github/workflows/phono3py-pytest-conda-mkl-v2.yml
@@ -15,9 +15,9 @@ jobs:
         python-version: ["3.12"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     # Use conda-incubator/setup-miniconda for precise control of conda infrastructure
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         miniforge-version: latest
     - name: Install dependent packages
@@ -26,6 +26,13 @@ jobs:
         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
         conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler
+    - name: Install symfc develop branch
+      run: |
+        conda activate test
+        git clone --depth 1 https://github.com/symfc/symfc.git
+        cd symfc
+        pip install -e . -vvv
+        cd ..
     - name: Install phonopy develop branch
       run: |
         conda activate test

diff --git a/.github/workflows/phono3py-pytest-conda-mkl.yml b/.github/workflows/phono3py-pytest-conda-mkl.yml
@@ -15,9 +15,9 @@ jobs:
         python-version: ["3.12"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     # Use conda-incubator/setup-miniconda for precise control of conda infrastructure
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         miniforge-version: latest
     - name: Install dependent packages
@@ -26,6 +26,13 @@ jobs:
         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
         conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler
+    - name: Install symfc develop branch
+      run: |
+        conda activate test
+        git clone --depth 1 https://github.com/symfc/symfc.git
+        cd symfc
+        pip install -e . -vvv
+        cd ..
     - name: Install phonopy develop branch
       run: |
         conda activate test

diff --git a/.github/workflows/phono3py-pytest-conda-numpy2.yml b/.github/workflows/phono3py-pytest-conda-numpy2.yml
@@ -0,0 +1,59 @@
+name: Pytest with openblas and numpy 2.0
+
+on:
+  pull_request:
+    branches: [ develop ]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+    # Use conda-incubator/setup-miniconda for precise control of conda infrastructure
+    - uses: conda-incubator/setup-miniconda@v3
+      with:
+        miniforge-version: latest
+    - name: Install dependent packages
+      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
+    - name: Install spglib develop branch
+      run: |
+        conda activate test
+        git clone --depth 1 https://github.com/spglib/spglib.git
+        cd spglib
+        pip install -e . -vvv
+        cd ..
+    - name: Install symfc develop branch
+      run: |
+        conda activate test
+        git clone --depth 1 https://github.com/symfc/symfc.git
+        cd symfc
+        pip install -e . -vvv
+        cd ..
+    - name: Install phonopy develop branch
+      run: |
+        conda activate test
+        git clone --depth 1 https://github.com/phonopy/phonopy.git
+        cd phonopy
+        PHONOPY_USE_OPENMP=true pip install -e . -vvv
+        cd ..
+    - name: Install phono3py
+      run: |
+        conda activate test
+        pip install -e . -vvv
+    - name: Run pytest
+      run: |
+        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
@@ -15,9 +15,9 @@ jobs:
         python-version: ["3.12"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     # Use conda-incubator/setup-miniconda for precise control of conda infrastructure
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         miniforge-version: latest
     - name: Install dependent packages
@@ -26,6 +26,13 @@ jobs:
         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
         #conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler
+    - name: Install symfc develop branch
+      run: |
+        conda activate test
+        git clone --depth 1 https://github.com/symfc/symfc.git
+        cd symfc
+        pip install -e . -vvv
+        cd ..
     - name: Install phonopy develop branch
       run: |
         conda activate test

diff --git a/.github/workflows/phono3py-pytest-conda.yml b/.github/workflows/phono3py-pytest-conda.yml
@@ -15,9 +15,9 @@ jobs:
         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     # Use conda-incubator/setup-miniconda for precise control of conda infrastructure
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         miniforge-version: latest
     - name: Install dependent packages

diff --git a/.github/workflows/publish-gh-pages.yml b/.github/workflows/publish-gh-pages.yml
@@ -15,8 +15,8 @@ jobs:
         python-version: ["3.11"]
 
     steps:
-    - uses: actions/checkout@v2
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: actions/checkout@v4
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         auto-update-conda: true
         channels: conda-forge

diff --git a/.github/workflows/publish-to-test-pypi.yml b/.github/workflows/publish-to-test-pypi.yml
@@ -17,9 +17,9 @@ jobs:
         python-version: ["3.10", ]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     # Use conda-incubator/setup-miniconda for precise control of conda infrastructure
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         auto-update-conda: true
         channels: conda-forge

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/pycqa/flake8
-  rev: 7.0.0
+  rev: 7.1.0
   hooks:
   - id: flake8
     args:

diff --git a/doc/changelog.md b/doc/changelog.md
@@ -2,6 +2,11 @@
 
 # Change Log
 
+## Jun-19-2024: Version 3.1.2
+
+- Treatment of numpy 2.0.
+- Experimental support of symfc.
+
 ## Jun-7-2024: Version 3.1.1
 
 - Minor fix related to typehint for python-3.8.

diff --git a/doc/conf.py b/doc/conf.py
@@ -60,7 +60,7 @@
 # The short X.Y version.
 version = "3.1"
 # The full version, including alpha/beta/rc tags.
-release = "3.1.1"
+release = "3.1.2"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/phono3py/api_phono3py.py b/phono3py/api_phono3py.py
@@ -1329,6 +1329,7 @@ def produce_fc3(
                 fc_calculator=fc3_calculator,
                 fc_calculator_options=fc3_calculator_options,
                 is_compact_fc=is_compact_fc,
+                symmetry=self._symmetry,
                 log_level=self._log_level,
             )
         else:
@@ -1425,6 +1426,8 @@ def produce_fc2(
                 fc_calculator=fc2_calculator,
                 fc_calculator_options=fc2_calculator_options,
                 atom_list=p2s_map,
+                symmetry=self._phonon_supercell_symmetry,
+                symprec=self._symprec,
                 log_level=self._log_level,
             )
         else:

diff --git a/phono3py/cui/phono3py_argparse.py b/phono3py/cui/phono3py_argparse.py
@@ -713,6 +713,13 @@ def get_parser(fc_symmetry=False, is_nac=False, load_phono3py_yaml=False):
         default=None,
         help="Cutoff width of smearing function (ratio to sigma value)",
     )
+    parser.add_argument(
+        "--symfc",
+        dest="use_symfc",
+        action="store_true",
+        default=None,
+        help="Use symfc for generating force constants",
+    )
     parser.add_argument(
         "--spf",
         dest="is_spectral_function",

diff --git a/phono3py/file_IO.py b/phono3py/file_IO.py
@@ -280,7 +280,7 @@ def write_fc3_to_hdf5(fc3, filename="fc3.hdf5", p2s_map=None, compression="gzip"
 
     """
     with h5py.File(filename, "w") as w:
-        w.create_dataset("version", data=np.string_(__version__))
+        w.create_dataset("version", data=np.bytes_(__version__))
         w.create_dataset("fc3", data=fc3, compression=compression)
         if p2s_map is not None:
             w.create_dataset("p2s_map", data=p2s_map)
@@ -352,9 +352,9 @@ def write_force_constants_to_hdf5(
                 dset = w.create_dataset(
                     "physical_unit", (1,), dtype="S%d" % len(physical_unit)
                 )
-                dset[0] = np.string_(physical_unit)
+                dset[0] = np.bytes_(physical_unit)
             if version is not None:
-                w.create_dataset("version", data=np.string_(version))
+                w.create_dataset("version", data=np.bytes_(version))
 
     write_force_constants_to_hdf5(
         force_constants,
@@ -385,7 +385,7 @@ def write_grid_address_to_hdf5(
     suffix = _get_filename_suffix(mesh, filename=filename)
     full_filename = "grid_address" + suffix + ".hdf5"
     with h5py.File(full_filename, "w") as w:
-        w.create_dataset("version", data=np.string_(__version__))
+        w.create_dataset("version", data=np.bytes_(__version__))
         w.create_dataset("mesh", data=mesh)
         if bz_grid is not None and bz_grid.grid_matrix is not None:
             w.create_dataset("grid_matrix", data=bz_grid.grid_matrix)
@@ -577,7 +577,7 @@ def write_real_self_energy_to_hdf5(
     full_filename += ".hdf5"
 
     with h5py.File(full_filename, "w") as w:
-        w.create_dataset("version", data=np.string_(__version__))
+        w.create_dataset("version", data=np.bytes_(__version__))
         w.create_dataset("grid_point", data=grid_point)
         w.create_dataset("mesh", data=mesh)
         if bz_grid is not None and bz_grid.grid_matrix is not None:
@@ -666,7 +666,7 @@ def write_spectral_function_to_hdf5(
     full_filename += ".hdf5"
 
     with h5py.File(full_filename, "w") as w:
-        w.create_dataset("version", data=np.string_(__version__))
+        w.create_dataset("version", data=np.bytes_(__version__))
         w.create_dataset("grid_point", data=grid_point)
         w.create_dataset("mesh", data=mesh)
         if bz_grid is not None and bz_grid.grid_matrix is not None:
@@ -713,7 +713,7 @@ def write_collision_to_hdf5(
     )
     full_filename = "collision" + suffix + ".hdf5"
     with h5py.File(full_filename, "w") as w:
-        w.create_dataset("version", data=np.string_(__version__))
+        w.create_dataset("version", data=np.bytes_(__version__))
         w.create_dataset("temperature", data=temperature)
         if gamma is not None:
             w.create_dataset("gamma", data=gamma)
@@ -751,7 +751,7 @@ def write_collision_to_hdf5(
 def write_full_collision_matrix(collision_matrix, filename="fcm.hdf5"):
     """Write full (non-symmetrized) collision matrix to collision-*.hdf5."""
     with h5py.File(filename, "w") as w:
-        w.create_dataset("version", data=np.string_(__version__))
+        w.create_dataset("version", data=np.bytes_(__version__))
         w.create_dataset("collision_matrix", data=collision_matrix)
 
 
@@ -776,7 +776,7 @@ def write_unitary_matrix_to_hdf5(
     )
     hdf5_filename = "unitary" + suffix + ".hdf5"
     with h5py.File(hdf5_filename, "w") as w:
-        w.create_dataset("version", data=np.string_(__version__))
+        w.create_dataset("version", data=np.bytes_(__version__))
         w.create_dataset("temperature", data=temperature)
         if unitary_matrix is not None:
             w.create_dataset("unitary_matrix", data=unitary_matrix)
@@ -816,7 +816,7 @@ def write_collision_eigenvalues_to_hdf5(
         mesh, sigma=sigma, sigma_cutoff=sigma_cutoff, filename=filename
     )
     with h5py.File("coleigs" + suffix + ".hdf5", "w") as w:
-        w.create_dataset("version", data=np.string_(__version__))
+        w.create_dataset("version", data=np.bytes_(__version__))
         w.create_dataset("temperature", data=temperatures)
         w.create_dataset("collision_eigenvalues", data=collision_eigenvalues)
         w.close()
@@ -885,7 +885,7 @@ def write_kappa_to_hdf5(
     )
     full_filename = "kappa" + suffix + ".hdf5"
     with h5py.File(full_filename, "w") as w:
-        w.create_dataset("version", data=np.string_(__version__))
+        w.create_dataset("version", data=np.bytes_(__version__))
         w.create_dataset("temperature", data=temperature)
         w.create_dataset("mesh", data=mesh)
         if bz_grid is not None and bz_grid.grid_matrix is not None:
@@ -1159,7 +1159,7 @@ def write_pp_to_hdf5(
     full_filename = "pp" + suffix + ".hdf5"
 
     with h5py.File(full_filename, "w") as w:
-        w.create_dataset("version", data=np.string_(__version__))
+        w.create_dataset("version", data=np.bytes_(__version__))
         if pp is not None:
             if g_zero is None:
                 w.create_dataset("pp", data=pp, compression=compression)
@@ -1323,7 +1323,7 @@ def write_gamma_detail_to_hdf5(
     full_filename = "gamma_detail" + suffix + ".hdf5"
 
     with h5py.File(full_filename, "w") as w:
-        w.create_dataset("version", data=np.string_(__version__))
+        w.create_dataset("version", data=np.bytes_(__version__))
         w.create_dataset("temperature", data=temperature)
         w.create_dataset("mesh", data=mesh)
         if bz_grid is not None and bz_grid.grid_matrix is not None:
@@ -1397,7 +1397,7 @@ def write_phonon_to_hdf5(
     full_filename = "phonon" + suffix + ".hdf5"
 
     with h5py.File(full_filename, "w") as w:
-        w.create_dataset("version", data=np.string_(__version__))
+        w.create_dataset("version", data=np.bytes_(__version__))
         w.create_dataset("mesh", data=mesh)
         if bz_grid is not None and bz_grid.grid_matrix is not None:
             w.create_dataset("grid_matrix", data=bz_grid.grid_matrix)