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: v0.8.2
+  rev: v0.8.3
   hooks:
   - id: ruff
     args: [ "--fix", "--show-fixes" ]

doc/changelog.md

@@ -2,6 +2,10 @@
 
 # Change Log
 
+## Dec-23-2024: Version 3.10.1
+
+- Replace `dtype="int_"` by `dtype="long"`.
+
 ## Dec-6-2024: Version 3.10.0
 
 - Update to follow the change of phonopy's internal functions

doc/conf.py

@@ -60,7 +60,7 @@
 # The short X.Y version.
 version = "3.10"
 # The full version, including alpha/beta/rc tags.
-release = "3.10.0"
+release = "3.10.1"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

phono3py/api_isotope.py

@@ -107,7 +107,7 @@ def run(self, grid_points, lang="C"):
             (len(self._sigmas), len(grid_points), len(self._iso.band_indices)),
             dtype="double",
         )
-        self._grid_points = np.array(grid_points, dtype="int_")
+        self._grid_points = np.array(grid_points, dtype="long")
 
         for j, gp in enumerate(grid_points):
             self._iso.set_grid_point(gp)

phono3py/api_phono3py.py

@@ -234,14 +234,14 @@ def __init__(
         # Create supercell and primitive cell
         self._unitcell = unitcell
         self._supercell_matrix = np.array(
-            shape_supercell_matrix(supercell_matrix), dtype="int_", order="C"
+            shape_supercell_matrix(supercell_matrix), dtype="long", order="C"
         )
         pmat = self._determine_primitive_matrix(primitive_matrix)
         self._primitive_matrix = pmat
         self._nac_params = None
         if phonon_supercell_matrix is not None:
             self._phonon_supercell_matrix = np.array(
-                shape_supercell_matrix(phonon_supercell_matrix), dtype="int_", order="C"
+                shape_supercell_matrix(phonon_supercell_matrix), dtype="long", order="C"
             )
         else:
             self._phonon_supercell_matrix = None
@@ -538,7 +538,7 @@ def supercell_matrix(self) -> np.ndarray:
 
         ndarray
             Supercell matrix with respect to unit cell.
-            shape=(3, 3), dtype='int_', order='C'
+            shape=(3, 3), dtype='long', order='C'
 
         """
         return self._supercell_matrix
@@ -549,7 +549,7 @@ def phonon_supercell_matrix(self) -> Optional[np.ndarray]:
 
         ndarray
             Supercell matrix with respect to unit cell.
-            shape=(3, 3), dtype='int_', order='C'
+            shape=(3, 3), dtype='long', order='C'
 
         """
         return self._phonon_supercell_matrix
@@ -743,10 +743,10 @@ def band_indices(self, band_indices):
     def _set_band_indices(self, band_indices=None):
         if band_indices is None:
             num_band = len(self._primitive) * 3
-            self._band_indices = [np.arange(num_band, dtype="int_")]
+            self._band_indices = [np.arange(num_band, dtype="long")]
         else:
-            self._band_indices = [np.array(bi, dtype="int_") for bi in band_indices]
-        self._band_indices_flatten = np.hstack(self._band_indices).astype("int_")
+            self._band_indices = [np.array(bi, dtype="long") for bi in band_indices]
+        self._band_indices_flatten = np.hstack(self._band_indices).astype("long")
 
     @property
     def masses(self) -> np.ndarray:
@@ -1948,7 +1948,7 @@ def run_thermal_conductivity(
             List of grid point indices where mode thermal conductivities are
             calculated. With None, all the grid points that are necessary
             for thermal conductivity are set internally.
-            shape(num_grid_points, ), dtype='int_'.
+            shape(num_grid_points, ), dtype='long'.
         boundary_mfp : float, optiona, default is None
             Mean free path in micrometre to calculate simple boundary
             scattering contribution to thermal conductivity.

phono3py/conductivity/base.py

@@ -281,7 +281,7 @@ def __init__(
         grid_points : array_like or None, optional
             Grid point indices in BZgrid. When None, ir-grid points are searched
             internally. Default is None.
-            shape=(grid_points, ), dtype='int_'.
+            shape=(grid_points, ), dtype='long'.
         temperatures : array_like, optional, default is None
             Temperatures at which thermal conductivity is calculated.
             shape=(temperature_points, ), dtype='double'.
@@ -676,15 +676,15 @@ def _get_point_operations(self) -> Tuple[np.ndarray, np.ndarray]:
         -------
         point_operations : ndarray
             Operations in reduced coordinates.
-            shape=(num_operations, 3, 3), dtype='int_'
+            shape=(num_operations, 3, 3), dtype='long'
         rotations_cartesian : ndarray
             Operations in Cartesian coordinates.
             shape=(num_operations, 3, 3), dtype='double'
 
         """
         if not self._is_kappa_star:
             point_operations = np.array(
-                [np.eye(3, dtype="int_")], dtype="int_", order="C"
+                [np.eye(3, dtype="long")], dtype="long", order="C"
             )
             rotations_cartesian = np.array(
                 [np.eye(3, dtype="double")], dtype="double", order="C"
@@ -702,24 +702,24 @@ def _get_grid_info(self, grid_points) -> Tuple[np.ndarray, np.ndarray, np.ndarra
         -------
         grid_points : ndarray
             Grid point indices in BZ-grid to be iterated over.
-            shape=(len(grid_points),), dtype='int_'
+            shape=(len(grid_points),), dtype='long'
         ir_grid_points : ndarray
             Irreducible grid points in BZ-grid on regular grid.
-            shape=(len(ir_grid_points),), dtype='int_'
+            shape=(len(ir_grid_points),), dtype='long'
         grid_weights : ndarray
             Grid weights of `grid_points`. If grid symmetry is not broken,
             these values are equivalent to numbers of k-star arms.
 
         """
         ir_grid_points, grid_weights = self._get_ir_grid_points(grid_points)
         if grid_points is not None:  # Specify grid points
-            _grid_points = np.array(grid_points, dtype="int_")
+            _grid_points = np.array(grid_points, dtype="long")
             _ir_grid_points = ir_grid_points
             _grid_weights = grid_weights
         elif not self._is_kappa_star:  # All grid points
             _grid_points = self._pp.bz_grid.grg2bzg
             _ir_grid_points = _grid_points
-            _grid_weights = np.ones(len(_grid_points), dtype="int_")
+            _grid_weights = np.ones(len(_grid_points), dtype="long")
         else:  # Automatic sampling
             _grid_points = ir_grid_points
             _ir_grid_points = ir_grid_points
@@ -777,7 +777,7 @@ def _get_ir_grid_points(self, grid_points):
             self._pp.bz_grid
         )
         ir_grid_points = np.array(
-            self._pp.bz_grid.grg2bzg[ir_grid_points], dtype="int_"
+            self._pp.bz_grid.grg2bzg[ir_grid_points], dtype="long"
         )
         if grid_points is None:
             grid_weights = ir_grid_weights
@@ -787,7 +787,7 @@ def _get_ir_grid_points(self, grid_points):
                 weights[gp] += 1
             grid_weights = np.array(
                 weights[ir_grid_map[self._pp.bz_grid.bzg2grg[grid_points]]],
-                dtype="int_",
+                dtype="long",
             )
 
         return ir_grid_points, grid_weights

phono3py/conductivity/direct_solution.py

@@ -287,7 +287,7 @@ def _set_kappa_reducible_colmat(self, kappa, mode_kappa, i_sigma, i_temp, weight
     def _get_rot_grid_points(self):
         num_ir_grid_points = len(self._ir_grid_points)
         rot_grid_points = np.zeros(
-            (num_ir_grid_points, len(self._point_operations)), dtype="int_"
+            (num_ir_grid_points, len(self._point_operations)), dtype="long"
         )
         if self._is_kappa_star:
             rotations = self._pp.bz_grid.rotations  # rotations of GR-grid
@@ -530,10 +530,10 @@ def _prepare_collision_matrix(self):
                 self._average_collision_matrix_by_degeneracy()
                 num_mesh_points = np.prod(self._pp.mesh_numbers)
                 num_rot = len(self._point_operations)
-                rot_grid_points = np.zeros((num_rot, num_mesh_points), dtype="int_")
+                rot_grid_points = np.zeros((num_rot, num_mesh_points), dtype="long")
                 # Ir-grid points and rot_grid_points in generalized regular grid
                 ir_gr_grid_points = np.array(
-                    self._pp.bz_grid.bzg2grg[self._ir_grid_points], dtype="int_"
+                    self._pp.bz_grid.bzg2grg[self._ir_grid_points], dtype="long"
                 )
                 for i in range(num_mesh_points):
                     rot_grid_points[:, i] = self._pp.bz_grid.bzg2grg[
@@ -544,7 +544,7 @@ def _prepare_collision_matrix(self):
                 self._expand_reducible_collisions(ir_gr_grid_points, rot_grid_points)
                 self._expand_local_values(ir_gr_grid_points, rot_grid_points)
             self._combine_reducible_collisions()
-            weights = np.ones(np.prod(self._pp.mesh_numbers), dtype="int_")
+            weights = np.ones(np.prod(self._pp.mesh_numbers), dtype="long")
             self._symmetrize_collision_matrix()
         else:
             self._combine_collisions()
@@ -647,7 +647,7 @@ def _get_weights(self):
         self._rot_grid_points : ndarray
             Grid points generated by applying point group to ir-grid-points
             in BZ-grid.
-            shape=(ir_grid_points, point_operations), dtype='int_'
+            shape=(ir_grid_points, point_operations), dtype='long'
 
         r_gps : grid points of arms of k-star with duplicates
             len(r_gps) == order of crystallographic point group

phono3py/conductivity/rta.py

@@ -372,7 +372,7 @@ class instance.
                     collisions,
                     np.array(
                         np.dot(tetrahedra, self._pp.bz_grid.P.T),
-                        dtype="int_",
+                        dtype="long",
                         order="C",
                     ),
                     self._frequencies,

phono3py/cui/kaccum_script.py

@@ -79,7 +79,7 @@ def _get_ir_grid_info(bz_grid: BZGrid, weights, qpoints=None, ir_grid_points=Non
     -------
     ir_grid_points : ndarray
         Ir-grid point indices in BZ-grid.
-        shape=(ir_grid_points, ), dtype='int_'
+        shape=(ir_grid_points, ), dtype='long'
     ir_grid_map : ndarray, optional, default=None
         Mapping table to ir-grid point indices in GR-grid.
 
@@ -289,9 +289,9 @@ def main():
         f_kappa = h5py.File(args.filenames[0], "r")
 
     if "grid_matrix" in f_kappa:
-        mesh = np.array(f_kappa["grid_matrix"][:], dtype="int_")
+        mesh = np.array(f_kappa["grid_matrix"][:], dtype="long")
     else:
-        mesh = np.array(f_kappa["mesh"][:], dtype="int_")
+        mesh = np.array(f_kappa["mesh"][:], dtype="long")
     if "temperature" in f_kappa:
         temperatures = f_kappa["temperature"][:]
     else:
@@ -308,7 +308,7 @@ def main():
         frequencies = np.array(f_kappa["frequency"][ir_grid_points_BZ], dtype="double")
     else:
         frequencies = f_kappa["frequency"][:]
-        ir_weights = np.ones(len(frequencies), dtype="int_")
+        ir_weights = np.ones(len(frequencies), dtype="long")
     primitive_symmetry = Symmetry(primitive)
     bz_grid = BZGrid(
         mesh,

phono3py/cui/phono3py_script.py

@@ -877,7 +877,7 @@ def init_phph_interaction(
     if settings.write_phonon:
         freqs, eigvecs, grid_address = phono3py.get_phonon_data()
         ir_grid_points, ir_grid_weights, _ = get_ir_grid_points(bz_grid)
-        ir_grid_points = np.array(bz_grid.grg2bzg[ir_grid_points], dtype="int_")
+        ir_grid_points = np.array(bz_grid.grg2bzg[ir_grid_points], dtype="long")
         filename = write_phonon_to_hdf5(
             freqs,
             eigvecs,

phono3py/cui/triplets_info.py

@@ -34,23 +34,27 @@
 # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
+from collections.abc import Sequence
+from typing import Optional, Union
+
 import numpy as np
+from phonopy.structure.atoms import PhonopyAtoms
 
 from phono3py.file_IO import write_grid_address_to_hdf5, write_ir_grid_points
-from phono3py.phonon.grid import get_ir_grid_points
+from phono3py.phonon.grid import BZGrid, get_ir_grid_points
 from phono3py.phonon3.triplets import get_triplets_at_q
 
 
 def write_grid_points(
-    primitive,
-    bz_grid,
-    band_indices=None,
-    sigmas=None,
-    temperatures=None,
-    is_kappa_star=True,
-    is_lbte=False,
-    compression="gzip",
-    filename=None,
+    primitive: PhonopyAtoms,
+    bz_grid: BZGrid,
+    band_indices: Optional[Union[Sequence, np.ndarray]] = None,
+    sigmas: Optional[Union[Sequence, np.ndarray]] = None,
+    temperatures: Optional[Union[Sequence, np.ndarray]] = None,
+    is_kappa_star: bool = True,
+    is_lbte: bool = False,
+    compression: Union[str, int] = "gzip",
+    filename: bool = None,
 ):
     """Write grid points into files."""
     ir_grid_points, ir_grid_weights = _get_ir_grid_points(
@@ -103,7 +107,11 @@ def write_grid_points(
 
 
 def show_num_triplets(
-    primitive, bz_grid, band_indices=None, grid_points=None, is_kappa_star=True
+    primitive: PhonopyAtoms,
+    bz_grid: BZGrid,
+    band_indices: Optional[Union[Sequence, np.ndarray]] = None,
+    grid_points: Optional[Union[Sequence, np.ndarray]] = None,
+    is_kappa_star: bool = True,
 ):
     """Show numbers of triplets at grid points."""
     tp_nums = _TripletsNumbers(bz_grid, is_kappa_star=is_kappa_star)
@@ -131,7 +139,7 @@ def show_num_triplets(
 
 
 class _TripletsNumbers:
-    def __init__(self, bz_grid, is_kappa_star=True):
+    def __init__(self, bz_grid: BZGrid, is_kappa_star: bool = True):
         self._bz_grid = bz_grid
         (
             self.ir_grid_points,
@@ -143,19 +151,19 @@ def get_number_of_triplets(self, gp):
         return num_triplets
 
 
-def _get_ir_grid_points(bz_grid, is_kappa_star=True):
+def _get_ir_grid_points(bz_grid: BZGrid, is_kappa_star: bool = True):
     if is_kappa_star:
         ir_grid_points, ir_grid_weights, _ = get_ir_grid_points(bz_grid)
-        ir_grid_points = np.array(bz_grid.grg2bzg[ir_grid_points], dtype="int_")
+        ir_grid_points = np.array(bz_grid.grg2bzg[ir_grid_points], dtype="long")
     else:
         ir_grid_points = np.array(
-            bz_grid.grg2bzg[: np.prod(bz_grid.D_diag)], dtype="int_", order="C"
+            bz_grid.grg2bzg[: np.prod(bz_grid.D_diag)], dtype="long", order="C"
         )
-        ir_grid_weights = np.ones(len(ir_grid_points), dtype="int_")
+        ir_grid_weights = np.ones(len(ir_grid_points), dtype="long")
 
     return ir_grid_points, ir_grid_weights
 
 
-def _get_number_of_triplets(bz_grid, grid_point, swappable=True):
+def _get_number_of_triplets(bz_grid: BZGrid, grid_point: int, swappable: bool = True):
     triplets_at_q = get_triplets_at_q(grid_point, bz_grid, swappable=swappable)[0]
     return len(triplets_at_q)

phono3py/file_IO.py

@@ -438,7 +438,7 @@ def write_grid_address_to_hdf5(
     mesh,
     grid_mapping_table,
     bz_grid=None,
-    compression="gzip",
+    compression: Union[str, int] = "gzip",
     filename=None,
 ):
     """Write grid addresses to grid_address.hdf5."""
@@ -714,7 +714,7 @@ def write_spectral_function_to_hdf5(
     if all_band_exist:
         _band_indices = None
     else:
-        _band_indices = np.hstack(band_indices).astype("int_")
+        _band_indices = np.hstack(band_indices).astype("long")
     suffix = _get_filename_suffix(
         mesh, grid_point=grid_point, band_indices=_band_indices, sigma=sigma
     )

phono3py/other/isotope.py

@@ -136,9 +136,9 @@ def __init__(
 
         num_band = len(self._primitive) * 3
         if band_indices is None:
-            self._band_indices = np.arange(num_band, dtype="int_")
+            self._band_indices = np.arange(num_band, dtype="long")
         else:
-            self._band_indices = np.array(band_indices, dtype="int_")
+            self._band_indices = np.array(band_indices, dtype="long")
 
         if self._bz_grid is None:
             primitive_symmetry = Symmetry(self._primitive, self._symprec)
@@ -153,7 +153,7 @@ def __init__(
     def set_grid_point(self, grid_point):
         """Initialize grid points."""
         self._grid_point = grid_point
-        self._grid_points = np.arange(len(self._bz_grid.addresses), dtype="int_")
+        self._grid_points = np.arange(len(self._bz_grid.addresses), dtype="long")
 
         if self._phonon_done is None:
             self._allocate_phonon()
@@ -319,7 +319,7 @@ def _set_integration_weights_py(self):
                 self._bz_grid.addresses,
                 np.array(
                     np.dot(thm.tetrahedra, self._bz_grid.P.T),
-                    dtype="int_",
+                    dtype="long",
                     order="C",
                 ),
                 self._bz_grid.grg2bzg,