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Merge pull request #312 from phonopy/int_-to-long 

Change dtype=int_ to long
This commit is contained in:
Atsushi Togo 2024-12-18 13:32:04 +09:00 committed by GitHub
parent b96d130359 4341f8c6c6
commit 88418e2543
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GPG Key ID: B5690EEEBB952194
20 changed files with 230 additions and 221 deletions
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2
phono3py/api_isotope.py
View File

@ -107,7 +107,7 @@ class Phono3pyIsotope:
(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)

16
phono3py/api_phono3py.py
View File

@ -234,14 +234,14 @@ class Phono3py:
# 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 @@ class Phono3py:
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 @@ class Phono3py:
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 @@ class Phono3py:
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 @@ class Phono3py:
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.

18
phono3py/conductivity/base.py
View File

@ -281,7 +281,7 @@ class ConductivityBase(ABC):
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'.
@ -676,7 +676,7 @@ class ConductivityBase(ABC):
-------
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'
@ -684,7 +684,7 @@ class ConductivityBase(ABC):
"""
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"
@ -702,10 +702,10 @@ class ConductivityBase(ABC):
-------
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.
@ -713,13 +713,13 @@ class ConductivityBase(ABC):
"""
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 @@ class ConductivityBase(ABC):
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 @@ class ConductivityBase(ABC):
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

10
phono3py/conductivity/direct_solution.py
View File

@ -287,7 +287,7 @@ class ConductivityLBTEBase(ConductivityBase):
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 @@ class ConductivityLBTEBase(ConductivityBase):
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 @@ class ConductivityLBTEBase(ConductivityBase):
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 @@ class ConductivityLBTEBase(ConductivityBase):
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

2
phono3py/conductivity/rta.py
View File

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

8
phono3py/cui/kaccum_script.py
View File

@ -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,

2
phono3py/cui/phono3py_script.py
View File

@ -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,

42
phono3py/cui/triplets_info.py
View File

@ -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 @@ class _TripletsNumbers:
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)

4
phono3py/file_IO.py
View File

@ -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
)

8
phono3py/other/isotope.py
View File

@ -136,9 +136,9 @@ class Isotope:
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 @@ class Isotope:
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 @@ class Isotope:
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,

18
phono3py/other/kaccum.py
View File

@ -76,17 +76,17 @@ class KappaDOSTHM:
ir_grid_points : ndarray
Irreducible grid point indices in GR-grid (as obtained by
get_ir_grid_points).
shape=(num_ir_grid_points, ), dtype='int_'
shape=(num_ir_grid_points, ), dtype='long'
ir_grid_weights : ndarray
Weights of irreducible grid points. Its sum is the number of grid
points in GR-grid (prod(D_diag)) (as obtained by
get_ir_grid_points).
shape=(num_ir_grid_points, ), dtype='int_'
shape=(num_ir_grid_points, ), dtype='long'
ir_grid_map : ndarray
Index mapping table to irreducible grid points from all grid points
in GR-grid such as, [0, 0, 2, 3, 3, ...]. (as obtained by
get_ir_grid_points).
shape=(prod(D_diag), ), dtype='int_'
shape=(prod(D_diag), ), dtype='long'
frequency_points : array_like, optional, default=None
This is used as the frequency points. When None, frequency points
are created from `num_sampling_points`.
@ -120,7 +120,7 @@ class KappaDOSTHM:
bz_grid.bzg2grg, _ir_grid_map, _ir_grid_points
)
if ir_grid_weights is None:
grid_weights = np.ones(mode_kappa.shape[1], dtype="int_")
grid_weights = np.ones(mode_kappa.shape[1], dtype="long")
else:
grid_weights = ir_grid_weights
for j, function in enumerate(("J", "I")):
@ -164,13 +164,13 @@ class KappaDOSTHM:
----------
bzg2grg : ndarray
Mapping table from BZ-grid to GR-grid.
shape=(len(all-BZ-grid-points), ), dtype='int_'
shape=(len(all-BZ-grid-points), ), dtype='long'
ir_grid_map : ndarray
Mapping table from all grid points to ir-grid points in GR-grid.
shape=(np.prod(D_diag), ), dtype='int_'
shape=(np.prod(D_diag), ), dtype='long'
ir_grid_points : ndarray
Irreducible grid points in GR-grid. shape=(num_ir_grid_points, ),
dtype='int_'
dtype='long'
Returns
-------
@ -184,7 +184,7 @@ class KappaDOSTHM:
# ir-grid points in GR-grid to the index of unique grid points.
gp_map = {j: i for i, j in enumerate(unique_gps)}
bzgp2irgp_map = np.array(
[gp_map[ir_grid_map[grgp]] for grgp in bzg2grg], dtype="int_"
[gp_map[ir_grid_map[grgp]] for grgp in bzg2grg], dtype="long"
)
return bzgp2irgp_map
@ -210,7 +210,7 @@ class GammaDOSsmearing:
shape=(ir_grid_points, num_band), dtype='double'
ir_grid_weights : ndarray
Grid point weights at ir-grid points.
shape=(ir_grid_points, ), dtype='int_'
shape=(ir_grid_points, ), dtype='long'
sigma : float
Smearing width.
num_sampling_points : int, optional, default=100

28
phono3py/other/tetrahedron_method.py
View File

@ -57,23 +57,23 @@ def get_unique_grid_points(grid_points, bz_grid: BZGrid):
-------
ndarray
Unique grid points on tetrahedron vertices around input grid points.
shape=(unique_grid_points, ), dtype='int_'.
shape=(unique_grid_points, ), dtype='long'.
"""
import phono3py._phono3py as phono3c
if _check_ndarray_state(grid_points, "int_"):
if _check_ndarray_state(grid_points, "long"):
_grid_points = grid_points
else:
_grid_points = np.array(grid_points, dtype="int_")
_grid_points = np.array(grid_points, dtype="long")
thm = TetrahedronMethod(bz_grid.microzone_lattice)
unique_vertices = np.array(
np.dot(thm.get_unique_tetrahedra_vertices(), bz_grid.P.T),
dtype="int_",
dtype="long",
order="C",
)
neighboring_grid_points = np.zeros(
len(unique_vertices) * len(_grid_points), dtype="int_"
len(unique_vertices) * len(_grid_points), dtype="long"
)
phono3c.neighboring_grid_points(
neighboring_grid_points,
@ -84,7 +84,7 @@ def get_unique_grid_points(grid_points, bz_grid: BZGrid):
bz_grid.gp_map,
bz_grid.store_dense_gp_map * 1 + 1,
)
unique_grid_points = np.array(np.unique(neighboring_grid_points), dtype="int_")
unique_grid_points = np.array(np.unique(neighboring_grid_points), dtype="long")
return unique_grid_points
@ -111,7 +111,7 @@ def get_integration_weights(
Grid information in reciprocal space.
grid_points : array_like, optional, default=None
Grid point indices in BZ-grid. If None, all regular grid points in
BZ-grid. shape=(grid_points, ), dtype='int_'
BZ-grid. shape=(grid_points, ), dtype='long'
bzgp2irgp_map : array_like, optional, default=None
Grid point index mapping from bz_grid to index of the first dimension of
`grid_values` array, i.e., usually irreducible grid point count.
@ -131,15 +131,15 @@ def get_integration_weights(
np.dot(
get_tetrahedra_relative_grid_address(bz_grid.microzone_lattice), bz_grid.P.T
),
dtype="int_",
dtype="long",
order="C",
)
if grid_points is None:
_grid_points = bz_grid.grg2bzg
elif _check_ndarray_state(grid_points, "int_"):
elif _check_ndarray_state(grid_points, "long"):
_grid_points = grid_points
else:
_grid_points = np.array(grid_points, dtype="int_")
_grid_points = np.array(grid_points, dtype="long")
if _check_ndarray_state(grid_values, "double"):
_grid_values = grid_values
else:
@ -149,11 +149,11 @@ def get_integration_weights(
else:
_sampling_points = np.array(sampling_points, dtype="double")
if bzgp2irgp_map is None:
_bzgp2irgp_map = np.arange(len(grid_values), dtype="int_")
elif _check_ndarray_state(bzgp2irgp_map, "int_"):
_bzgp2irgp_map = np.arange(len(grid_values), dtype="long")
elif _check_ndarray_state(bzgp2irgp_map, "long"):
_bzgp2irgp_map = bzgp2irgp_map
else:
_bzgp2irgp_map = np.array(bzgp2irgp_map, dtype="int_")
_bzgp2irgp_map = np.array(bzgp2irgp_map, dtype="long")
num_grid_points = len(_grid_points)
num_band = _grid_values.shape[1]
@ -188,7 +188,7 @@ def get_tetrahedra_relative_grid_address(microzone_lattice):
"""
import phono3py._phono3py as phono3c
relative_grid_address = np.zeros((24, 4, 3), dtype="int_", order="C")
relative_grid_address = np.zeros((24, 4, 3), dtype="long", order="C")
phono3c.tetrahedra_relative_grid_address(
relative_grid_address, np.array(microzone_lattice, dtype="double", order="C")
)

150
phono3py/phonon/grid.py
View File

@ -156,7 +156,7 @@ class BZGrid:
"""Init method.
mesh : array_like or float
Mesh numbers or length. shape=(3,), dtype='int_'
Mesh numbers or length. shape=(3,), dtype='long'
reciprocal_lattice : array_like
Reciprocal primitive basis vectors given as column vectors shape=(3,
3), dtype='double', order='C'
@ -174,7 +174,7 @@ class BZGrid:
is_shift : array_like or None, optional
[0, 0, 0] (or [False, False, False]) gives Gamma center mesh and
value 1 (or True) gives half mesh shift along the basis vectors.
Default is None. dtype='int_', shape=(3,)
Default is None. dtype='long', shape=(3,)
is_time_reveral : bool, optional
Inversion symmetry is included in reciprocal point group. Default is
True.
@ -205,9 +205,9 @@ class BZGrid:
self._addresses = None
self._gp_map = None
self._grid_matrix = None
self._D_diag = np.ones(3, dtype="int_")
self._Q = np.eye(3, dtype="int_", order="C")
self._P = np.eye(3, dtype="int_", order="C")
self._D_diag = np.ones(3, dtype="long")
self._Q = np.eye(3, dtype="long", order="C")
self._P = np.eye(3, dtype="long", order="C")
self._QDinv = None
self._microzone_lattice = None
self._rotations = None
@ -237,7 +237,7 @@ class BZGrid:
This corresponds to the mesh numbers in transformed reciprocal
basis vectors.
shape=(3,), dtype='int_'
shape=(3,), dtype='long'
"""
return self._D_diag
@ -247,7 +247,7 @@ class BZGrid:
"""Left unimodular matrix after SNF: D=PAQ.
Left unimodular matrix after SNF: D=PAQ.
shape=(3, 3), dtype='int_', order='C'.
shape=(3, 3), dtype='long', order='C'.
"""
return self._P
@ -257,7 +257,7 @@ class BZGrid:
"""Right unimodular matrix after SNF: D=PAQ.
Right unimodular matrix after SNF: D=PAQ.
shape=(3, 3), dtype='int_', order='C'.
shape=(3, 3), dtype='long', order='C'.
"""
return self._Q
@ -276,9 +276,9 @@ class BZGrid:
def PS(self):
"""Integer shift vectors of GRGrid."""
if self._is_shift is None:
return np.zeros(3, dtype="int_")
return np.zeros(3, dtype="long")
else:
return np.array(np.dot(self.P, self._is_shift), dtype="int_")
return np.array(np.dot(self.P, self._is_shift), dtype="long")
@property
def grid_matrix(self):
@ -286,7 +286,7 @@ class BZGrid:
Grid generating matrix used for SNF.
When SNF is used, ndarray, otherwise None.
shape=(3, 3), dtype='int_', order='C'.
shape=(3, 3), dtype='long', order='C'.
"""
return self._grid_matrix
@ -298,7 +298,7 @@ class BZGrid:
Integer grid address of the points in Brillouin zone including
surface. There are two types of address order by either
`store_dense_gp_map` is True or False.
shape=(np.prod(D_diag) + some on surface, 3), dtype='int_', order='C'.
shape=(np.prod(D_diag) + some on surface, 3), dtype='long', order='C'.
"""
return self._addresses
@ -324,7 +324,7 @@ class BZGrid:
"""Transform grid point indices from BZG to GRG.
Grid index mapping table from BZGrid to GRgrid.
shape=(len(addresses), ), dtype='int_'.
shape=(len(addresses), ), dtype='long'.
Equivalent to
get_grid_point_from_address(
@ -339,7 +339,7 @@ class BZGrid:
Grid index mapping table from GRgrid to BZGrid. Unique one
of translationally equivalent grid points in BZGrid is chosen.
shape=(prod(D_diag), ), dtype='int_'.
shape=(prod(D_diag), ), dtype='long'.
"""
return self._grg2bzg
@ -370,7 +370,7 @@ class BZGrid:
Rotation matrices for GR-grid addresses (g) defined as g'=Rg. This can
be different from ``reciprocal_operations`` when GR-grid is used because
grid addresses are defined on an oblique lattice.
shape=(rotations, 3, 3), dtype='int_', order='C'.
shape=(rotations, 3, 3), dtype='long', order='C'.
"""
return self._rotations
@ -386,7 +386,7 @@ class BZGrid:
Reciprocal space rotation matrices in fractional coordinates defined as
q'=Rq.
shape=(rotations, 3, 3), dtype='int_', order='C'.
shape=(rotations, 3, 3), dtype='long', order='C'.
"""
return self._reciprocal_operations
@ -411,7 +411,7 @@ class BZGrid:
Grid point indices corresponding to the grid addresses. Each
returned grid point index is one of those of the
translationally equivalent grid points.
shape=(n, ), dtype='int_' when multiple addresses are given.
shape=(n, ), dtype='long' when multiple addresses are given.
Otherwise one integer value is returned.
"""
@ -423,7 +423,7 @@ class BZGrid:
)
gps = [get_grid_point_from_address(adrs, self._D_diag) for adrs in addresses]
return np.array(self._grg2bzg[gps], dtype="int_")
return np.array(self._grg2bzg[gps], dtype="long")
def _generate_grid(
self, mesh, use_grg=False, force_SNF=False, SNF_coordinates="reciprocal"
@ -454,9 +454,9 @@ class BZGrid:
store_dense_gp_map=self._store_dense_gp_map,
)
if self._store_dense_gp_map:
self._grg2bzg = np.array(self._gp_map[:-1], dtype="int_")
self._grg2bzg = np.array(self._gp_map[:-1], dtype="long")
else:
self._grg2bzg = np.arange(np.prod(self._D_diag), dtype="int_")
self._grg2bzg = np.arange(np.prod(self._D_diag), dtype="long")
self._QDinv = np.array(
self.Q * (1 / self.D_diag.astype("double")), dtype="double", order="C"
@ -477,17 +477,17 @@ class BZGrid:
import phono3py._recgrid as recgrid
if self._symmetry_dataset is None:
direct_rotations = np.eye(3, dtype="int_", order="C").reshape(1, 3, 3)
direct_rotations = np.eye(3, dtype="long", order="C").reshape(1, 3, 3)
else:
direct_rotations = np.array(
self._symmetry_dataset.rotations, dtype="int_", order="C"
self._symmetry_dataset.rotations, dtype="long", order="C"
)
rec_rotations = np.zeros((48, 3, 3), dtype="int_", order="C")
rec_rotations = np.zeros((48, 3, 3), dtype="long", order="C")
num_rec_rot = recgrid.reciprocal_rotations(
rec_rotations, direct_rotations, self._is_time_reversal
)
self._reciprocal_operations = np.array(
rec_rotations[:num_rec_rot], dtype="int_", order="C"
rec_rotations[:num_rec_rot], dtype="long", order="C"
)
self._rotations_cartesian = np.array(
[
@ -498,7 +498,7 @@ class BZGrid:
order="C",
)
self._rotations = np.zeros(
self._reciprocal_operations.shape, dtype="int_", order="C"
self._reciprocal_operations.shape, dtype="long", order="C"
)
if not recgrid.transform_rotations(
self._rotations, self._reciprocal_operations, self._D_diag, self._Q
@ -550,8 +550,8 @@ class GridMatrix:
Mesh numbers or length. With float number, either conventional or
generalized regular grid is computed depending on the given flags
(`use_grg`, `force_SNF`). Given ndarry with
shape=(3,), dtype='int_': conventional regular grid shape=(3,
3), dtype='int_': generalized regular grid
shape=(3,), dtype='long': conventional regular grid shape=(3,
3), dtype='long': generalized regular grid
lattice : array_like
Primitive basis vectors in direct space given as row vectors.
shape=(3, 3), dtype='double', order='C'
@ -577,9 +577,9 @@ class GridMatrix:
self._mesh = mesh
self._lattice = lattice
self._grid_matrix = None
self._D_diag = np.ones(3, dtype="int_")
self._Q = np.eye(3, dtype="int_", order="C")
self._P = np.eye(3, dtype="int_", order="C")
self._D_diag = np.ones(3, dtype="long")
self._Q = np.eye(3, dtype="long", order="C")
self._P = np.eye(3, dtype="long", order="C")
self._set_mesh_numbers(
mesh,
@ -596,7 +596,7 @@ class GridMatrix:
Grid generating matrix used for SNF.
When SNF is used, ndarray, otherwise None.
shape=(3, 3), dtype='int_', order='C'.
shape=(3, 3), dtype='long', order='C'.
"""
return self._grid_matrix
@ -607,7 +607,7 @@ class GridMatrix:
This corresponds to the mesh numbers in transformed reciprocal
basis vectors.
shape=(3,), dtype='int_'
shape=(3,), dtype='long'
"""
return self._D_diag
@ -617,7 +617,7 @@ class GridMatrix:
"""Left unimodular matrix after SNF: D=PAQ.
Left unimodular matrix after SNF: D=PAQ.
shape=(3, 3), dtype='int_', order='C'.
shape=(3, 3), dtype='long', order='C'.
"""
return self._P
@ -627,7 +627,7 @@ class GridMatrix:
"""Right unimodular matrix after SNF: D=PAQ.
Right unimodular matrix after SNF: D=PAQ.
shape=(3, 3), dtype='int_', order='C'.
shape=(3, 3), dtype='long', order='C'.
"""
return self._Q
@ -694,7 +694,7 @@ class GridMatrix:
coordinates,
)
if num_values == 3:
self._D_diag = np.array(mesh, dtype="int_")
self._D_diag = np.array(mesh, dtype="long")
def _run_grg(
self,
@ -785,12 +785,12 @@ class GridMatrix:
sym_dataset, length, coordinates=coordinates
)
elif grid_matrix is not None:
_grid_matrix = np.array(grid_matrix, dtype="int_", order="C")
_grid_matrix = np.array(grid_matrix, dtype="long", order="C")
# If grid_matrix is a diagonal matrix, use it as D matrix.
gm_diag = np.diagonal(_grid_matrix)
if (np.diag(gm_diag) == _grid_matrix).all() and not force_SNF:
self._D_diag = np.array(gm_diag, dtype="int_")
self._D_diag = np.array(gm_diag, dtype="long")
else:
import phono3py._recgrid as recgrid
@ -849,7 +849,7 @@ class GridMatrix:
inv_tmat_int = np.rint(inv_tmat).astype(int)
assert (np.abs(inv_tmat - inv_tmat_int) < 1e-5).all()
grid_matrix = np.array(
(inv_tmat_int * conv_mesh_numbers).T, dtype="int_", order="C"
(inv_tmat_int * conv_mesh_numbers).T, dtype="long", order="C"
)
return grid_matrix
@ -875,12 +875,12 @@ def get_grid_point_from_address(address, D_diag):
----------
address : array_like
Grid address.
shape=(3, ) or (n, 3), dtype='int_'
shape=(3, ) or (n, 3), dtype='long'
D_diag : array_like
This corresponds to mesh numbers. More precisely, this gives
diagonal elements of diagonal matrix of Smith normal form of
grid generating matrix. See the detail in the docstring of BZGrid.
shape=(3,), dtype='int_'
shape=(3,), dtype='long'
Returns
-------
@ -890,18 +890,18 @@ def get_grid_point_from_address(address, D_diag):
ndarray
GR-grid point indices.
shape=(n, ), dtype='int_'
shape=(n, ), dtype='long'
"""
import phono3py._recgrid as recgrid
adrs_array = np.array(address, dtype="int_", order="C")
mesh_array = np.array(D_diag, dtype="int_")
adrs_array = np.array(address, dtype="long", order="C")
mesh_array = np.array(D_diag, dtype="long")
if adrs_array.ndim == 1:
return recgrid.grid_index_from_address(adrs_array, mesh_array)
gps = np.zeros(adrs_array.shape[0], dtype="int_")
gps = np.zeros(adrs_array.shape[0], dtype="long")
for i, adrs in enumerate(adrs_array):
gps[i] = recgrid.grid_index_from_address(adrs, mesh_array)
return gps
@ -917,15 +917,15 @@ def get_ir_grid_points(bz_grid: BZGrid):
-------
ir_grid_points : ndarray
Irreducible grid point indices in GR-grid.
shape=(num_ir_grid_points, ), dtype='int_'
shape=(num_ir_grid_points, ), dtype='long'
ir_grid_weights : ndarray
Weights of irreducible grid points. Its sum is the number of
grid points in GR-grid (prod(D_diag)).
shape=(num_ir_grid_points, ), dtype='int_'
shape=(num_ir_grid_points, ), dtype='long'
ir_grid_map : ndarray
Index mapping table to irreducible grid points from all grid points
such as, [0, 0, 2, 3, 3, ...].
shape=(prod(D_diag), ), dtype='int_'
shape=(prod(D_diag), ), dtype='long'
"""
ir_grid_map = _get_ir_grid_map(bz_grid.D_diag, bz_grid.rotations, PS=bz_grid.PS)
@ -949,7 +949,7 @@ def get_grid_points_by_rotations(
Rotation matrices {R} with respect to basis vectors of GR-grid.
Defined by g'=Rg, where g is the grid point address represented by
three integers in BZ-grid.
dtype='int_', shape=(rotations, 3, 3)
dtype='long', shape=(rotations, 3, 3)
with_surface : Bool, optional
This parameter affects to how to treat grid points on BZ surface.
When False, rotated BZ surface points are moved to representative
@ -961,7 +961,7 @@ def get_grid_points_by_rotations(
-------
rot_grid_indices : ndarray
BZ-grid point indices obtained after rotating a grid point index.
dtype='int_', shape=(rotations,)
dtype='long', shape=(rotations,)
"""
if reciprocal_rotations is not None:
@ -993,7 +993,7 @@ def _get_grid_points_by_bz_rotations(bz_gp, bz_grid: BZGrid, rotations, lang="C"
def _get_grid_points_by_bz_rotations_c(bz_gp, bz_grid: BZGrid, rotations):
import phono3py._recgrid as recgrid
bzgps = np.zeros(len(rotations), dtype="int_")
bzgps = np.zeros(len(rotations), dtype="long")
for i, r in enumerate(rotations):
bzgps[i] = recgrid.rotate_bz_grid_index(
bz_gp,
@ -1017,7 +1017,7 @@ def _get_grid_points_by_bz_rotations_py(bz_gp, bz_grid: BZGrid, rotations):
"""
rot_adrs = np.dot(rotations, bz_grid.addresses[bz_gp])
grgps = get_grid_point_from_address(rot_adrs, bz_grid.D_diag)
bzgps = np.zeros(len(grgps), dtype="int_")
bzgps = np.zeros(len(grgps), dtype="long")
if bz_grid.store_dense_gp_map:
for i, (gp, adrs) in enumerate(zip(grgps, rot_adrs)):
indices = np.where(
@ -1057,20 +1057,20 @@ def _get_grid_address(D_diag):
----------
D_diag : array_like
Three integers that represent the generalized regular grid.
shape=(3, ), dtype='int_'
shape=(3, ), dtype='long'
Returns
-------
gr_grid_addresses : ndarray
Integer triplets that represents grid point addresses in
generalized regular grid.
shape=(prod(D_diag), 3), dtype='int_'
shape=(prod(D_diag), 3), dtype='long'
"""
import phono3py._recgrid as recgrid
gr_grid_addresses = np.zeros((np.prod(D_diag), 3), dtype="int_")
recgrid.gr_grid_addresses(gr_grid_addresses, np.array(D_diag, dtype="int_"))
gr_grid_addresses = np.zeros((np.prod(D_diag), 3), dtype="long")
recgrid.gr_grid_addresses(gr_grid_addresses, np.array(D_diag, dtype="long"))
return gr_grid_addresses
@ -1139,37 +1139,37 @@ def _relocate_BZ_grid_address(
import phono3py._recgrid as recgrid
if PS is None:
_PS = np.zeros(3, dtype="int_")
_PS = np.zeros(3, dtype="long")
else:
_PS = np.array(PS, dtype="int_")
bz_grid_addresses = np.zeros((np.prod(D_diag) * 8, 3), dtype="int_", order="C")
bzg2grg = np.zeros(len(bz_grid_addresses), dtype="int_")
_PS = np.array(PS, dtype="long")
bz_grid_addresses = np.zeros((np.prod(D_diag) * 8, 3), dtype="long", order="C")
bzg2grg = np.zeros(len(bz_grid_addresses), dtype="long")
if store_dense_gp_map:
bz_map = np.zeros(np.prod(D_diag) + 1, dtype="int_")
bz_map = np.zeros(np.prod(D_diag) + 1, dtype="long")
else:
bz_map = np.zeros(np.prod(D_diag) * 9 + 1, dtype="int_")
bz_map = np.zeros(np.prod(D_diag) * 9 + 1, dtype="long")
# Mpr^-1 = Lr^-1 Lp
reclat_T = np.array(np.transpose(reciprocal_lattice), dtype="double", order="C")
reduced_basis = get_reduced_bases(reclat_T)
tmat_inv = np.dot(np.linalg.inv(reduced_basis.T), reclat_T.T)
tmat_inv_int = np.rint(tmat_inv).astype("int_")
tmat_inv_int = np.rint(tmat_inv).astype("long")
assert (np.abs(tmat_inv - tmat_inv_int) < 1e-5).all()
num_gp = recgrid.bz_grid_addresses(
bz_grid_addresses,
bz_map,
bzg2grg,
np.array(D_diag, dtype="int_"),
np.array(np.dot(tmat_inv_int, Q), dtype="int_", order="C"),
np.array(D_diag, dtype="long"),
np.array(np.dot(tmat_inv_int, Q), dtype="long", order="C"),
_PS,
np.array(reduced_basis.T, dtype="double", order="C"),
store_dense_gp_map * 1 + 1,
)
bz_grid_addresses = np.array(bz_grid_addresses[:num_gp], dtype="int_", order="C")
bzg2grg = np.array(bzg2grg[:num_gp], dtype="int_")
bz_grid_addresses = np.array(bz_grid_addresses[:num_gp], dtype="long", order="C")
bzg2grg = np.array(bzg2grg[:num_gp], dtype="long")
return bz_grid_addresses, bz_map, bzg2grg
@ -1182,34 +1182,34 @@ def _get_ir_grid_map(D_diag, grg_rotations, PS=None):
This corresponds to mesh numbers. More precisely, this gives
diagonal elements of diagonal matrix of Smith normal form of
grid generating matrix. See the detail in the docstring of BZGrid.
shape=(3,), dtype='int_'
shape=(3,), dtype='long'
grg_rotations : array_like
GR-grid rotation matrices.
dtype='int_', shape=(grg_rotations, 3)
dtype='long', shape=(grg_rotations, 3)
PS : array_like
GR-grid shift defined.
dtype='int_', shape=(3,)
dtype='long', shape=(3,)
Returns
-------
ir_grid_map : ndarray
Grid point mapping from all indices to ir-gird-point indices in GR-grid.
dtype='int_', shape=(prod(mesh),)
dtype='long', shape=(prod(mesh),)
"""
import phono3py._recgrid as recgrid
ir_grid_map = np.zeros(np.prod(D_diag), dtype="int_")
ir_grid_map = np.zeros(np.prod(D_diag), dtype="long")
if PS is None:
_PS = np.zeros(3, dtype="int_")
_PS = np.zeros(3, dtype="long")
else:
_PS = np.array(PS, dtype="int_")
_PS = np.array(PS, dtype="long")
num_ir = recgrid.ir_grid_map(
ir_grid_map,
np.array(D_diag, dtype="int_"),
np.array(D_diag, dtype="long"),
_PS,
np.array(grg_rotations, dtype="int_", order="C"),
np.array(grg_rotations, dtype="long", order="C"),
)
if num_ir > 0:

6
phono3py/phonon/solver.py
View File

@ -67,7 +67,7 @@ def run_phonon_solver_c(
See Interaction.get_phonons().
grid_points : ndarray
Grid point indices.
shape=(grid_points, ), dtype='int_'
shape=(grid_points, ), dtype='long'
grid_address : ndarray
See BZGrid.addresses.
QDinv : ndarray
@ -127,7 +127,7 @@ def run_phonon_solver_c(
is_nac_q_zero = True
_nac_q_direction = np.array(nac_q_direction, dtype="double")
assert grid_points.dtype == np.dtype("int_")
assert grid_points.dtype == np.dtype("long")
assert grid_points.flags.c_contiguous
assert QDinv.dtype == np.dtype("double")
assert QDinv.flags.c_contiguous
@ -256,4 +256,4 @@ def _get_fc_elements_mapping(dm, fc):
fc_p2s = np.arange(len(p2s_map), dtype="intc")
fc_s2p = s2pp_map
return np.array(fc_p2s, dtype="int_"), np.array(fc_s2p, dtype="int_")
return np.array(fc_p2s, dtype="long"), np.array(fc_s2p, dtype="long")

6
phono3py/phonon3/collision_matrix.py
View File

@ -91,7 +91,7 @@ class CollisionMatrix(ImagSelfEnergy):
if not self._is_reducible_collision_matrix:
self._num_ir_grid_points = num_ir_grid_points
self._rot_grid_points = np.array(
self._pp.bz_grid.bzg2grg[rot_grid_points], dtype="int_", order="C"
self._pp.bz_grid.bzg2grg[rot_grid_points], dtype="long", order="C"
)
self._rotations_cartesian = rotations_cartesian
@ -269,8 +269,8 @@ class CollisionMatrix(ImagSelfEnergy):
"""
map_triplets = self._triplets_map_at_q
map_q = self._ir_map_at_q
gp2tp = -np.ones(len(map_triplets), dtype="int_")
tp2s = -np.ones(len(map_triplets), dtype="int_")
gp2tp = -np.ones(len(map_triplets), dtype="long")
tp2s = -np.ones(len(map_triplets), dtype="long")
swapped = np.zeros(len(map_triplets), dtype="bytes")
num_tps = 0

32
phono3py/phonon3/fc3.py
View File

@ -110,13 +110,13 @@ def get_fc3(
if is_compact_fc and "cutoff_distance" not in disp_dataset:
s2p_map = primitive.s2p_map
p2p_map = primitive.p2p_map
s2compact = np.array([p2p_map[i] for i in s2p_map], dtype="int_")
s2compact = np.array([p2p_map[i] for i in s2p_map], dtype="long")
target_atoms = [i for i in p2s_map if i not in first_disp_atoms]
else:
# distribute_fc3 prefers pure translation operations in distributing
# fc3. Below, fc3 already computed are distributed to the first index
# atoms in primitive cell, and then distribute to all the other atoms.
s2compact = np.arange(len(supercell), dtype="int_")
s2compact = np.arange(len(supercell), dtype="long")
target_atoms = [i for i in p2s_map if i not in first_disp_atoms]
distribute_fc3(
fc3,
@ -211,7 +211,7 @@ def distribute_fc3(
if rot_i in pure_trans_indices:
rot_index = rot_i
break
atom_mapping = np.array(permutations[rot_index], dtype="int_")
atom_mapping = np.array(permutations[rot_index], dtype="long")
rot = rotations[rot_index]
rot_cart_inv = np.array(
similarity_transformation(lattice, rot).T, dtype="double", order="C"
@ -271,10 +271,10 @@ def set_permutation_symmetry_compact_fc3(fc3, primitive):
s2pp_map, nsym_list = get_nsym_list_and_s2pp(s2p_map, p2p_map, permutations)
phono3c.permutation_symmetry_compact_fc3(
fc3,
np.array(permutations, dtype="int_", order="C"),
np.array(s2pp_map, dtype="int_"),
np.array(p2s_map, dtype="int_"),
np.array(nsym_list, dtype="int_"),
np.array(permutations, dtype="long", order="C"),
np.array(s2pp_map, dtype="long"),
np.array(p2s_map, dtype="long"),
np.array(nsym_list, dtype="long"),
)
except ImportError as exc:
text = (
@ -325,10 +325,10 @@ def set_translational_invariance_compact_fc3(fc3, primitive: Primitive):
permutations = primitive.atomic_permutations
s2pp_map, nsym_list = get_nsym_list_and_s2pp(s2p_map, p2p_map, permutations)
permutations = np.array(permutations, dtype="int_", order="C")
s2pp_map = np.array(s2pp_map, dtype="int_")
p2s_map = np.array(p2s_map, dtype="int_")
nsym_list = np.array(nsym_list, dtype="int_")
permutations = np.array(permutations, dtype="long", order="C")
s2pp_map = np.array(s2pp_map, dtype="long")
p2s_map = np.array(p2s_map, dtype="long")
nsym_list = np.array(nsym_list, dtype="long")
phono3c.transpose_compact_fc3(
fc3, permutations, s2pp_map, p2s_map, nsym_list, 0
) # dim[0] <--> dim[1]
@ -492,7 +492,7 @@ def _solve_fc3(
rot_map_syms = get_positions_sent_by_rot_inv(
lattice, positions, site_symmetry, symprec
)
rot_map_syms = np.array(rot_map_syms, dtype="int_", order="C")
rot_map_syms = np.array(rot_map_syms, dtype="long", order="C")
rot_disps = get_rotated_displacement(displacements_first, site_sym_cart)
logger.debug("pinv")
@ -599,10 +599,10 @@ def show_drift_fc3(fc3, primitive=None, name="fc3"):
p2p_map = primitive.p2p_map
permutations = primitive.atomic_permutations
s2pp_map, nsym_list = get_nsym_list_and_s2pp(s2p_map, p2p_map, permutations)
permutations = np.array(permutations, dtype="int_", order="C")
s2pp_map = np.array(s2pp_map, dtype="int_")
p2s_map = np.array(p2s_map, dtype="int_")
nsym_list = np.array(nsym_list, dtype="int_")
permutations = np.array(permutations, dtype="long", order="C")
s2pp_map = np.array(s2pp_map, dtype="long")
p2s_map = np.array(p2s_map, dtype="long")
nsym_list = np.array(nsym_list, dtype="long")
num_patom = fc3.shape[0]
num_satom = fc3.shape[1]
maxval1 = 0

22
phono3py/phonon3/interaction.py
View File

@ -170,8 +170,8 @@ class Interaction:
self._svecs, self._multi = self._primitive.get_smallest_vectors()
self._masses = np.array(self._primitive.masses, dtype="double")
self._p2s = np.array(self._primitive.p2s_map, dtype="int_")
self._s2p = np.array(self._primitive.s2p_map, dtype="int_")
self._p2s = np.array(self._primitive.p2s_map, dtype="long")
self._s2p = np.array(self._primitive.s2p_map, dtype="long")
n_satom, n_patom, _ = self._multi.shape
self._all_shortest = np.zeros(
(n_patom, n_satom, n_satom), dtype="byte", order="C"
@ -233,7 +233,7 @@ class Interaction:
Returns
-------
ndarray
shape=(3, ), dtype='int_'
shape=(3, ), dtype='long'
"""
return self._bz_grid.D_diag
@ -332,7 +332,7 @@ class Interaction:
Returns
-------
ndarray
shape=(num_specified_bands, ), dtype='int_'
shape=(num_specified_bands, ), dtype='long'
"""
return self._band_indices
@ -715,7 +715,7 @@ class Interaction:
self.run_phonon_solver_with_eigvec_rotation()
else:
self._run_phonon_solver_c(
np.arange(len(self._bz_grid.addresses), dtype="int_")
np.arange(len(self._bz_grid.addresses), dtype="long")
)
else:
self._run_phonon_solver_c(grid_points)
@ -743,12 +743,12 @@ class Interaction:
self._phonon_done[self._bz_grid.gp_Gamma] = 0
if is_nac:
self._done_nac_at_gamma = True
self.run_phonon_solver(np.array([self._bz_grid.gp_Gamma], dtype="int_"))
self.run_phonon_solver(np.array([self._bz_grid.gp_Gamma], dtype="long"))
else:
self._done_nac_at_gamma = False
_nac_q_direction = self._nac_q_direction
self._nac_q_direction = None
self.run_phonon_solver(np.array([self._bz_grid.gp_Gamma], dtype="int_"))
self.run_phonon_solver(np.array([self._bz_grid.gp_Gamma], dtype="long"))
self._nac_q_direction = _nac_q_direction
def run_phonon_solver_with_eigvec_rotation(self):
@ -860,7 +860,7 @@ class Interaction:
in this method.
"""
r_inv = -np.eye(3, dtype="int_")
r_inv = -np.eye(3, dtype="long")
bz_grid_points_solved = []
for bzgp, done in enumerate(self._phonon_done):
if done:
@ -882,7 +882,7 @@ class Interaction:
[
bzgp_mq,
],
dtype="int_",
dtype="long",
)
)
bz_grid_points_solved.append(bzgp_mq)
@ -925,9 +925,9 @@ class Interaction:
def _set_band_indices(self, band_indices):
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")
def _run_c(self, g_zero):
import phono3py._phono3py as phono3c

8
phono3py/phonon3/joint_dos.py
View File

@ -263,7 +263,7 @@ class JointDos:
)
raise RuntimeError(msg)
self.run_phonon_solver(np.array([gamma_gp, grid_point], dtype="int_"))
self.run_phonon_solver(np.array([gamma_gp, grid_point], dtype="long"))
def run_phonon_solver(self, grid_points=None):
"""Calculate phonons at grid_points.
@ -273,7 +273,7 @@ class JointDos:
"""
if grid_points is None:
_grid_points = np.arange(len(self._bz_grid.addresses), dtype="int_")
_grid_points = np.arange(len(self._bz_grid.addresses), dtype="long")
else:
_grid_points = grid_points
@ -306,11 +306,11 @@ class JointDos:
"""
self._phonon_done[self._bz_grid.gp_Gamma] = 0
if is_nac:
self.run_phonon_solver(np.array([self._bz_grid.gp_Gamma], dtype="int_"))
self.run_phonon_solver(np.array([self._bz_grid.gp_Gamma], dtype="long"))
else:
_nac_q_direction = self._nac_q_direction
self._nac_q_direction = None
self.run_phonon_solver(np.array([self._bz_grid.gp_Gamma], dtype="int_"))
self.run_phonon_solver(np.array([self._bz_grid.gp_Gamma], dtype="long"))
self._nac_q_direction = _nac_q_direction
def run(self):

67
phono3py/phonon3/triplets.py
View File

@ -34,7 +34,8 @@
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
from typing import TYPE_CHECKING, Union
from collections.abc import Sequence
from typing import TYPE_CHECKING, Optional, Union
import numpy as np
from phonopy.structure.tetrahedron_method import TetrahedronMethod
@ -49,11 +50,11 @@ if TYPE_CHECKING:
def get_triplets_at_q(
grid_point,
grid_point: int,
bz_grid: BZGrid,
reciprocal_rotations=None,
is_time_reversal=True,
swappable=True,
reciprocal_rotations: Optional[Union[Sequence, np.ndarray]] = None,
is_time_reversal: bool = True,
swappable: bool = True,
):
"""Generate q-point triplets.
@ -66,7 +67,7 @@ def get_triplets_at_q(
reciprocal_rotations : array_like or None, optional
Rotation matrices {R} with respect to reciprocal basis vectors.
Defined by q'=Rq.
dtype='int_', shape=(rotations, 3, 3)
dtype='long', shape=(rotations, 3, 3)
is_time_reversal : bool, optional
Inversion symemtry is added if it doesn't exist. Default is True.
swappable : bool, optional
@ -77,10 +78,10 @@ def get_triplets_at_q(
triplets_at_q : ndarray
Symmetry reduced number of triplets are stored as grid point
integer numbers in BZGrid system.
shape=(n_triplets, 3), dtype='int_'
shape=(n_triplets, 3), dtype='long'
weights : ndarray
Weights of triplets in Brillouin zone
shape=(n_triplets,), dtype='int_'
shape=(n_triplets,), dtype='long'
map_triplets : ndarray or None
Mapping table of all triplets to symmetrically independent
tripelts in generalized regular grid system. More precisely,
@ -88,11 +89,11 @@ def get_triplets_at_q(
independent q' of q+q'+q''=G. Considering q' is enough because
q is fixed and q''=G-q-q' where G is automatically determined
to choose smallest |G|.
shape=(prod(mesh),), dtype='int_'
shape=(prod(mesh),), dtype='long'
map_q : ndarray
Irreducible q-points stabilized by q-point of specified grid_point
in generalized regular grid system.
shape=(prod(mesh),), dtype='int_'
shape=(prod(mesh),), dtype='long'
"""
if reciprocal_rotations is None:
@ -117,7 +118,7 @@ def get_triplets_at_q(
return triplets_at_q, weights, map_triplets, map_q
def get_all_triplets(grid_point, bz_grid):
def get_all_triplets(grid_point: int, bz_grid: BZGrid):
"""Return all triplets of a grid point.
Almost equivalent to ``get_nosym_triplets_at_q``.
@ -125,20 +126,20 @@ def get_all_triplets(grid_point, bz_grid):
"""
triplets_at_q, _ = _get_BZ_triplets_at_q(
grid_point, bz_grid, np.arange(np.prod(bz_grid.D_diag), dtype="int_")
grid_point, bz_grid, np.arange(np.prod(bz_grid.D_diag), dtype="long")
)
return triplets_at_q
def get_nosym_triplets_at_q(grid_point, bz_grid: BZGrid):
def get_nosym_triplets_at_q(grid_point: int, bz_grid: BZGrid):
"""Return triplets information without imposing mesh symmetry.
See the docstring of get_triplets_at_q.
"""
map_triplets = np.arange(np.prod(bz_grid.D_diag), dtype="int_")
map_q = np.arange(np.prod(bz_grid.D_diag), dtype="int_")
map_triplets = np.arange(np.prod(bz_grid.D_diag), dtype="long")
map_q = np.arange(np.prod(bz_grid.D_diag), dtype="long")
triplets_at_q, weights = _get_BZ_triplets_at_q(grid_point, bz_grid, map_triplets)
return triplets_at_q, weights, map_triplets, map_q
@ -238,11 +239,11 @@ def _get_triplets_reciprocal_mesh_at_q(
fixed_grid_number : int
Grid point of q0
D_diag : array_like
Diagonal part of the diagonal matrix by SNF. shape=(3,), dtype='int_'
Diagonal part of the diagonal matrix by SNF. shape=(3,), dtype='long'
rec_rotations : array_like
Rotation matrices in reciprocal space, where the rotation matrix R is
defined like q'=Rq. Time reversal symmetry is taken care of by
is_time_reversal. shape=(n_rot, 3, 3), dtype='int_'
is_time_reversal. shape=(n_rot, 3, 3), dtype='long'
is_time_reversal : bool
Inversion symemtry is added if it doesn't exist.
swappable : bool
@ -256,24 +257,24 @@ def _get_triplets_reciprocal_mesh_at_q(
independent q' of q+q'+q''=G. Considering q' is enough because q is
fixed and q''=G-q-q' where G is automatically determined to choose
smallest |G| without considering BZ surface (see docstring of
_get_BZ_triplets_at_q.) shape=(prod(mesh),), dtype='int_'
_get_BZ_triplets_at_q.) shape=(prod(mesh),), dtype='long'
map_q : ndarray
Irreducible q-points stabilized by q-point of specified grid_point.
shape=(prod(mesh),), dtype='int_'
shape=(prod(mesh),), dtype='long'
"""
import phono3py._phono3py as phono3c
map_triplets = np.zeros(np.prod(D_diag), dtype="int_")
map_q = np.zeros(np.prod(D_diag), dtype="int_")
map_triplets = np.zeros(np.prod(D_diag), dtype="long")
map_q = np.zeros(np.prod(D_diag), dtype="long")
num_triplets = phono3c.triplets_reciprocal_mesh_at_q(
map_triplets,
map_q,
fixed_grid_number,
np.array(D_diag, dtype="int_"),
np.array(D_diag, dtype="long"),
is_time_reversal * 1,
np.array(rec_rotations, dtype="int_", order="C"),
np.array(rec_rotations, dtype="long", order="C"),
swappable * 1,
)
assert num_triplets == len(np.unique(map_triplets))
@ -306,40 +307,40 @@ def _get_BZ_triplets_at_q(bz_grid_index, bz_grid: BZGrid, map_triplets):
q''=G-q-q' where G is automatically determined to choose
smallest |G| without considering BZ surface (see docstring of
_get_BZ_triplets_at_q.)
shape=(prod(mesh),), dtype='int_'
shape=(prod(mesh),), dtype='long'
Returns
-------
triplets : ndarray
Symmetry reduced number of triplets are stored as grid point
integer numbers.
shape=(n_triplets, 3), dtype='int_'
shape=(n_triplets, 3), dtype='long'
ir_weights : ndarray
Weights of triplets at a fixed q0.
shape=(n_triplets,), dtype='int_'
shape=(n_triplets,), dtype='long'
"""
import phono3py._phono3py as phono3c
weights = np.zeros(len(map_triplets), dtype="int_")
weights = np.zeros(len(map_triplets), dtype="long")
for g in map_triplets:
weights[g] += 1
ir_weights = np.extract(weights > 0, weights)
triplets = -np.ones((len(ir_weights), 3), dtype="int_")
triplets = -np.ones((len(ir_weights), 3), dtype="long")
num_ir_ret = phono3c.BZ_triplets_at_q(
triplets,
bz_grid_index,
bz_grid.addresses,
bz_grid.gp_map,
map_triplets,
np.array(bz_grid.D_diag, dtype="int_"),
np.array(bz_grid.D_diag, dtype="long"),
bz_grid.Q,
bz_grid.store_dense_gp_map * 1 + 1,
)
assert num_ir_ret == len(ir_weights)
return triplets, np.array(ir_weights, dtype="int_")
return triplets, np.array(ir_weights, dtype="long")
def _set_triplets_integration_weights_c(
@ -357,7 +358,7 @@ def _set_triplets_integration_weights_c(
g,
g_zero,
frequency_points, # f0
np.array(np.dot(tetrahedra, pp.bz_grid.P.T), dtype="int_", order="C"),
np.array(np.dot(tetrahedra, pp.bz_grid.P.T), dtype="long", order="C"),
pp.bz_grid.D_diag,
triplets_at_q,
frequencies, # f1
@ -380,7 +381,7 @@ def _set_triplets_integration_weights_py(
thm = TetrahedronMethod(pp.bz_grid.microzone_lattice)
triplets_at_q = pp.get_triplets_at_q()[0]
tetrahedra_vertices = _get_tetrahedra_vertices(
np.array(np.dot(thm.tetrahedra, pp.bz_grid.P.T), dtype="int_", order="C"),
np.array(np.dot(thm.tetrahedra, pp.bz_grid.P.T), dtype="long", order="C"),
triplets_at_q,
pp.bz_grid,
)
@ -414,7 +415,7 @@ def _get_tetrahedra_vertices(relative_address, triplets_at_q, bz_grid: BZGrid):
"""
num_triplets = len(triplets_at_q)
vertices = np.zeros((num_triplets, 2, 24, 4), dtype="int_")
vertices = np.zeros((num_triplets, 2, 24, 4), dtype="long")
for i, tp in enumerate(triplets_at_q):
for j, adrs_shift in enumerate((relative_address, -relative_address)):
adrs = bz_grid.addresses[tp[j + 1]] + adrs_shift

2
test/phonon/test_grid.py
View File

@ -1446,7 +1446,7 @@ def test_agno2_BZGrid_with_shift(agno2_cell: PhonopyAtoms):
def test_relocate_BZ_grid_address_FCC():
"""Test of _relocate_BZ_grid_address by FCC."""
D_diag = [4, 4, 4]
Q = np.eye(3, dtype="int_")
Q = np.eye(3, dtype="long")
reciprocal_lattice = np.array([[-1, 1, 1], [1, -1, 1], [1, 1, -1]], dtype="double")
bz_grid_addresses, bz_map, bzg2grg = _relocate_BZ_grid_address(
D_diag,