Merge pull request #266 from phonopy/spglib-v2_5

Update to follow phonopy update for spglib v2.5

phono3py/cui/phono3py_script.py

@@ -244,6 +244,9 @@ def start_phono3py(**argparse_control) -> tuple[argparse.Namespace, int]:
         print("Python version %d.%d.%d" % sys.version_info[:3])
         import spglib
 
+        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:

phono3py/phonon/grid.py

@@ -38,6 +38,13 @@ from __future__ import annotations
 
 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 @@ class BZGrid:
         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 @@ class BZGrid:
         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 @@ class BZGrid:
         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 @@ class BZGrid:
             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 @@ class GridMatrix:
         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 @@ class GridMatrix:
         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 @@ class GridMatrix:
         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 @@ class GridMatrix:
                     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 @@ class GridMatrix:
             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 @@ class GridMatrix:
                 "be equal to or larger than 1."
             )
             raise RuntimeError(msg)
-        sym_dataset = {
+
+        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 @@ class GridMatrix:
             `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.std_lattice,
-            sym_dataset["rotations"],
+            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 @@ class Interaction:
         # 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.rotations,
-            self._bz_grid.symmetry_dataset["translations"],
+            self._bz_grid.symmetry_dataset.translations,
             np.array(self._primitive.cell.T, dtype="double", order="C"),
             symprec=self._symprec,
         )
@@ -821,13 +821,13 @@ class Interaction:
 
         """
         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 @@ class Interaction:
 
         """
         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, :]

test/phonon/test_grid.py

@@ -2425,7 +2425,7 @@ def test_GridMatrix_with_grid_matrix(ph_nacl: Phonopy):
     np.testing.assert_array_equal(gm.grid_matrix, mesh)
     np.testing.assert_array_equal(gm.D_diag, [9, 18, 18])
 
-    tmat = ph_nacl.primitive_symmetry.dataset["transformation_matrix"]
+    tmat = ph_nacl.primitive_symmetry.dataset.transformation_matrix
     gm = GridMatrix(mesh, ph_nacl.primitive.cell, transformation_matrix=tmat)
     np.testing.assert_array_equal(gm.grid_matrix, mesh)
     np.testing.assert_array_equal(gm.D_diag, [9, 18, 18])
@@ -2439,7 +2439,7 @@ def test_GridMatrix_with_transformation_matrix(ph_nacl: Phonopy):
 
     """
     mesh = 50.0
-    tmat = ph_nacl.primitive_symmetry.dataset["transformation_matrix"]
+    tmat = ph_nacl.primitive_symmetry.dataset.transformation_matrix
     gm = GridMatrix(
         mesh,
         ph_nacl.primitive.cell,