Merge branch 'develop'

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
     exclude: ^example/AlN-LDA/
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.5.6
+  rev: v0.6.1
   hooks:
   - id: ruff
     args: [ "--fix", "--show-fixes" ]

doc/changelog.md

@@ -2,6 +2,10 @@
 
 # Change Log
 
+## Aug-23-2024: Version 3.4
+
+- Update for spglib v2.5 and for following the change in phonopy.
+
 ## Aug-8-2024: Version 3.3.4
 
 - Fix of command line user interface.

phono3py/cui/create_force_constants.py

@@ -347,7 +347,7 @@ def _read_phono3py_fc3(phono3py: Phono3py, symmetrize_fc3r, input_filename, log_
         filename = "fc3.hdf5"
     else:
         filename = "fc3." + input_filename + ".hdf5"
-    file_exists(filename, log_level)
+    file_exists(filename, log_level=log_level)
     if log_level:
         print('Reading fc3 from "%s".' % filename)
 
@@ -380,7 +380,7 @@ def _read_phono3py_fc2(phono3py, symmetrize_fc2, input_filename, log_level):
         filename = "fc2.hdf5"
     else:
         filename = "fc2." + input_filename + ".hdf5"
-    file_exists(filename, log_level)
+    file_exists(filename, log_level=log_level)
     if log_level:
         print('Reading fc2 from "%s".' % filename)
 
@@ -494,7 +494,7 @@ def _read_dataset_fc3(
         sys.exit(1)
     except FileNotFoundError as e:
         # from _get_type2_dataset
-        file_exists(e.filename, log_level)
+        file_exists(e.filename, log_level=log_level)
 
     if use_pypolymlp:
         phono3py.mlp_dataset = dataset
@@ -672,7 +672,7 @@ def _read_dataset_fc2(
             print_error()
         sys.exit(1)
     except FileNotFoundError as e:
-        file_exists(e.filename, log_level)
+        file_exists(e.filename, log_level=log_level)
 
     if phono3py.phonon_supercell_matrix is not None:
         phono3py.phonon_dataset = dataset

phono3py/cui/create_force_sets.py

@@ -77,7 +77,9 @@ def create_FORCES_FC3_and_FORCES_FC2(
     ]
     if cell_filename is not None:
         disp_filename_candidates.insert(0, cell_filename)
-    disp_filenames = files_exist(disp_filename_candidates, log_level, is_any=True)
+    disp_filenames = files_exist(
+        disp_filename_candidates, log_level=log_level, is_any=True
+    )
     disp_filename = disp_filenames[0]
     ph3py_yaml = Phono3pyYaml(settings={"force_sets": True})
     ph3py_yaml.read(disp_filename)
@@ -152,7 +154,7 @@ def create_FORCES_FC3_and_FORCES_FC2(
 def create_FORCES_FC2_from_FORCE_SETS(log_level):
     """Convert FORCE_SETS to FORCES_FC2."""
     filename = "FORCE_SETS"
-    file_exists(filename, log_level)
+    file_exists(filename, log_level=log_level)
     disp_dataset = parse_FORCE_SETS(filename=filename)
     write_FORCES_FC2(disp_dataset)
 
@@ -189,8 +191,8 @@ def create_FORCE_SETS_from_FORCES_FCx(
         len_first_line = get_length_of_first_line(f)
 
     if len_first_line == 3:
-        file_exists(disp_filename, log_level)
-        file_exists(forces_filename, log_level)
+        file_exists(disp_filename, log_level=log_level)
+        file_exists(forces_filename, log_level=log_level)
         ph3yml = Phono3pyYaml()
         ph3yml.read(disp_filename)
         if phonon_smat is None:
@@ -242,7 +244,7 @@ def _get_force_sets_fc2(
 
     force_filenames = settings.create_forces_fc2
     for filename in force_filenames:
-        file_exists(filename, log_level)
+        file_exists(filename, log_level=log_level)
 
     if log_level > 0:
         print(f"  Number of displacements: {num_disps}")
@@ -258,7 +260,7 @@ def _get_force_sets_fc2(
 
     if settings.subtract_forces:
         force_filename = settings.subtract_forces
-        file_exists(force_filename, log_level)
+        file_exists(force_filename, log_level=log_level)
         calc_dataset_zero = get_calc_dataset(
             interface_mode,
             num_atoms,
@@ -301,13 +303,13 @@ def _get_force_sets_fc3(
         raise RuntimeError("FC3 displacement dataset is broken.")
 
     if settings.create_forces_fc3_file:
-        file_exists(settings.create_forces_fc3_file, log_level)
+        file_exists(settings.create_forces_fc3_file, log_level=log_level)
         force_filenames = [x.strip() for x in open(settings.create_forces_fc3_file)]
     else:
         force_filenames = settings.create_forces_fc3
 
     for filename in force_filenames:
-        file_exists(filename, log_level)
+        file_exists(filename, log_level=log_level)
 
     if log_level > 0:
         print(f"  Number of displacements: {num_disps}")
@@ -326,7 +328,7 @@ def _get_force_sets_fc3(
 
     if settings.subtract_forces:
         force_filename = settings.subtract_forces
-        file_exists(force_filename, log_level)
+        file_exists(force_filename, log_level=log_level)
         calc_dataset = get_calc_dataset(
             interface_mode,
             num_atoms,

phono3py/cui/phono3py_script.py

@@ -114,7 +114,7 @@ def print_phono3py():
  | .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, |
  |_|                                |_|    |___/ """
     )
-    print_version(__version__)
+    print_version(__version__, package_name="phono3py")
     print_time()
 
 
@@ -244,7 +244,10 @@ def start_phono3py(**argparse_control) -> tuple[argparse.Namespace, int]:
         print("Python version %d.%d.%d" % sys.version_info[:3])
         import spglib
 
-        print("Spglib version %d.%d.%d" % spglib.get_version())
+        try:  # spglib.get_version() is deprecated.
+            print(f"Spglib version {spglib.spg_get_version()}")
+        except AttributeError:
+            print("Spglib version %d.%d.%d" % spglib.get_version())
 
         if deprecated:
             show_deprecated_option_warnings(deprecated)
@@ -264,7 +267,7 @@ def read_phono3py_settings(args, argparse_control, log_level):
     load_phono3py_yaml = argparse_control.get("load_phono3py_yaml", False)
 
     if len(args.filename) > 0:
-        file_exists(args.filename[0], log_level)
+        file_exists(args.filename[0], log_level=log_level)
         if load_phono3py_yaml:
             phono3py_conf_parser = Phono3pyConfParser(
                 filename=args.conf_filename,

phono3py/phonon/grid.py

@@ -38,6 +38,13 @@
 
 import warnings
 from collections.abc import Sequence
+
+try:
+    from spglib import SpglibDataset
+except ImportError:
+    from types import SimpleNamespace as SpglibDataset
+
+
 from typing import Optional, Union
 
 import numpy as np
@@ -137,7 +144,7 @@ def __init__(
         mesh: Union[int, float, Sequence, np.ndarray],
         reciprocal_lattice=None,
         lattice=None,
-        symmetry_dataset: Optional[dict] = None,
+        symmetry_dataset: Optional[Union[SpglibDataset]] = None,
         transformation_matrix: Optional[Union[Sequence, np.ndarray]] = None,
         is_shift: Optional[Union[list, np.ndarray]] = None,
         is_time_reversal: bool = True,
@@ -156,9 +163,10 @@ def __init__(
         lattice : array_like
             Direct primitive basis vectors given as row vectors shape=(3, 3),
             dtype='double', order='C'
-        symmetry_dataset : dict, optional
+        symmetry_dataset : SpglibDataset, optional
             Symmetry dataset (Symmetry.dataset) searched for the primitive cell
-            corresponding to ``reciprocal_lattice`` or ``lattice``.
+            corresponding to ``reciprocal_lattice`` or ``lattice``. For spglib <
+            v2.5, SimpleNamespace is used instead of SpglibDataset.
         transformation_matrix : array_like, optional
             Transformation matrix equivalent to ``transformation_matrix`` in
             spglib-dataset. This is only used when ``use_grg=True`` and
@@ -384,7 +392,7 @@ def reciprocal_operations(self):
         return self._reciprocal_operations
 
     @property
-    def symmetry_dataset(self):
+    def symmetry_dataset(self) -> SpglibDataset:
         """Return Symmetry.dataset."""
         return self._symmetry_dataset
 
@@ -472,7 +480,7 @@ def _set_rotations(self):
             direct_rotations = np.eye(3, dtype="int_", order="C").reshape(1, 3, 3)
         else:
             direct_rotations = np.array(
-                self._symmetry_dataset["rotations"], dtype="int_", order="C"
+                self._symmetry_dataset.rotations, dtype="int_", order="C"
             )
         rec_rotations = np.zeros((48, 3, 3), dtype="int_", order="C")
         num_rec_rot = recgrid.reciprocal_rotations(
@@ -530,7 +538,7 @@ def __init__(
         self,
         mesh: Union[int, float, Sequence, np.ndarray],
         lattice: Union[Sequence, np.ndarray],
-        symmetry_dataset: Optional[dict] = None,
+        symmetry_dataset: Optional[SpglibDataset] = None,
         transformation_matrix: Optional[Union[list, np.ndarray]] = None,
         use_grg: bool = True,
         force_SNF: bool = False,
@@ -547,9 +555,10 @@ def __init__(
         lattice : array_like
             Primitive basis vectors in direct space given as row vectors.
             shape=(3, 3), dtype='double', order='C'
-        symmetry_dataset : dict, optional
+        symmetry_dataset : SpglibDataset, optional
             Symmetry dataset of spglib (Symmetry.dataset) of primitive cell that
-            has `lattice`. Default is None.
+            has `lattice`. Default is None. For spglib <
+            v2.5, SimpleNamespace is used instead of SpglibDataset.
         transformation_matrix : array_like, optional
             Transformation matrix equivalent to ``transformation_matrix`` in
             spglib-dataset. This is only used when ``use_grg=True`` and
@@ -627,7 +636,7 @@ def _set_mesh_numbers(
         self,
         mesh: Union[int, float, Sequence, np.ndarray],
         use_grg: bool = False,
-        symmetry_dataset: Optional[dict] = None,
+        symmetry_dataset: Optional[SpglibDataset] = None,
         transformation_matrix: Optional[Union[list, np.ndarray]] = None,
         force_SNF=False,
         coordinates="reciprocal",
@@ -673,7 +682,7 @@ def _set_mesh_numbers(
                     self._D_diag = length2mesh(length, self._lattice)
                 else:
                     self._D_diag = length2mesh(
-                        length, self._lattice, rotations=symmetry_dataset["rotations"]
+                        length, self._lattice, rotations=symmetry_dataset.rotations
                     )
         if num_values == 9:
             self._run_grg(
@@ -703,7 +712,7 @@ def _run_grg(
             sym_dataset = symmetry_dataset
         else:  # transformation_matrix is not None
             sym_dataset = self._get_mock_symmetry_dataset(transformation_matrix)
-        if is_primitive_cell(sym_dataset["rotations"]):
+        if is_primitive_cell(sym_dataset.rotations):
             self._set_GRG_mesh(
                 sym_dataset,
                 length=length,
@@ -742,18 +751,23 @@ def _get_mock_symmetry_dataset(self, transformation_matrix) -> dict:
                 "be equal to or larger than 1."
             )
             raise RuntimeError(msg)
-        sym_dataset = {
-            "rotations": np.eye(3, dtype="intc", order="C").reshape(1, 3, 3),
-            "transformation_matrix": transformation_matrix,
-            "std_lattice": self._lattice,
-            "std_types": np.array([1], dtype="intc"),
-            "number": 1,
-        }
+
+        from types import SimpleNamespace
+
+        sym_dataset = SimpleNamespace(
+            **{
+                "rotations": np.eye(3, dtype="intc", order="C").reshape(1, 3, 3),
+                "transformation_matrix": transformation_matrix,
+                "std_lattice": self._lattice,
+                "std_types": np.array([1], dtype="intc"),
+                "number": 1,
+            }
+        )
         return sym_dataset
 
     def _set_GRG_mesh(
         self,
-        sym_dataset: dict,
+        sym_dataset: SpglibDataset,
         length: Optional[float] = None,
         grid_matrix=None,
         force_SNF=False,
@@ -807,22 +821,22 @@ def _get_grid_matrix(
             `reciprocal` (default) or `direct`.
 
         """
-        tmat = sym_dataset["transformation_matrix"]
+        tmat = sym_dataset.transformation_matrix
         conv_lat = np.dot(np.linalg.inv(tmat).T, self._lattice)
 
         # GRG is wanted to be generated with respect to std_lattice if possible.
         if _can_use_std_lattice(
             conv_lat,
             tmat,
-            sym_dataset["std_lattice"],
-            sym_dataset["rotations"],
+            sym_dataset.std_lattice,
+            sym_dataset.rotations,
         ):
-            conv_lat = sym_dataset["std_lattice"]
+            conv_lat = sym_dataset.std_lattice
             tmat = np.dot(self._lattice, np.linalg.inv(conv_lat)).T
 
         if coordinates == "direct":
             num_cells = int(np.prod(length2mesh(length, conv_lat)))
-            max_num_atoms = num_cells * len(sym_dataset["std_types"])
+            max_num_atoms = num_cells * len(sym_dataset.std_types)
             conv_mesh_numbers = estimate_supercell_matrix(
                 sym_dataset, max_num_atoms=max_num_atoms, max_iter=200
             )

phono3py/phonon3/interaction.py

@@ -772,8 +772,8 @@ def run_phonon_solver_with_eigvec_rotation(self):
         # perms.shape = (len(spg_ops), len(primitive)), dtype='intc'
         perms = compute_all_sg_permutations(
             self._primitive.scaled_positions,
-            self._bz_grid.symmetry_dataset["rotations"],
-            self._bz_grid.symmetry_dataset["translations"],
+            self._bz_grid.symmetry_dataset.rotations,
+            self._bz_grid.symmetry_dataset.translations,
             np.array(self._primitive.cell.T, dtype="double", order="C"),
             symprec=self._symprec,
         )
@@ -821,13 +821,13 @@ def _get_reciprocal_rotations_in_space_group_operations(self):
 
         """
         d2r_map = []
-        for r in self._bz_grid.symmetry_dataset["rotations"]:
+        for r in self._bz_grid.symmetry_dataset.rotations:
             for i, rec_r in enumerate(self._bz_grid.reciprocal_operations):
                 if (rec_r.T == r).all():
                     d2r_map.append(i)
                     break
 
-        assert len(d2r_map) == len(self._bz_grid.symmetry_dataset["rotations"])
+        assert len(d2r_map) == len(self._bz_grid.symmetry_dataset.rotations)
 
         return d2r_map
 
@@ -838,7 +838,7 @@ def _rotate_eigvecs(self, orig_gp, bzgp, r_cart, perm, t_i):
 
         """
         Rq = np.dot(self._bz_grid.QDinv, self._bz_grid.addresses[bzgp])
-        tau = self._bz_grid.symmetry_dataset["translations"][t_i]
+        tau = self._bz_grid.symmetry_dataset.translations[t_i]
         phase_factor = np.exp(-2j * np.pi * np.dot(Rq, tau))
         self._phonon_done[bzgp] = 1
         self._frequencies[bzgp, :] = self._frequencies[orig_gp, :]

phono3py/version.py

@@ -34,4 +34,4 @@
 # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
-__version__ = "3.3.4"
+__version__ = "3.4.0"

pyproject.toml

@@ -16,7 +16,7 @@ dependencies = [
     "matplotlib>=2.2.2",
     "h5py>=3.0",
     "spglib>=2.3",
-    "phonopy>=2.26,<2.27",
+    "phonopy>=2.27,<2.28",
 ]
 license = { file = "LICENSE" }