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Migrate to ruff

This commit is contained in:
Atsushi Togo 2024-06-21 13:49:24 +09:00
parent 28bfc2cc75
commit 7a83fdfb32
35 changed files with 207 additions and 162 deletions
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29
.pre-commit-config.yaml
View File

@ -10,31 +10,12 @@ repos:
exclude: ^conda/
- id: check-added-large-files
- repo: https://github.com/pycqa/flake8
rev: 7.1.0
- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.1.13
hooks:
- id: flake8
args:
- "--max-line-length=88"
- "--ignore=E203,W503"
- repo: https://github.com/psf/black
rev: 24.4.2
hooks:
- id: black
args:
- --line-length=88
- repo: https://github.com/pycqa/pydocstyle
rev: 6.3.0
hooks:
- id: pydocstyle
- repo: https://github.com/pycqa/isort
rev: 5.13.2
hooks:
- id: isort
name: isort (python)
- id: ruff
args: [ "--fix", "--show-fixes" ]
- id: ruff-format
- repo: https://github.com/Takishima/cmake-pre-commit-hooks
rev: v1.9.6

2
phono3py/api_jointdos.py
View File

@ -40,12 +40,12 @@ from phonopy.structure.symmetry import Symmetry
from phonopy.units import VaspToTHz
from phono3py.file_IO import write_joint_dos
from phono3py.phonon.grid import BZGrid
from phono3py.phonon3.imag_self_energy import (
get_freq_points_batches,
get_frequency_points,
)
from phono3py.phonon3.joint_dos import JointDos
from phono3py.phonon.grid import BZGrid
class Phono3pyJointDos:

6
phono3py/api_phono3py.py
View File

@ -72,19 +72,20 @@ from phono3py.conductivity.direct_solution import get_thermal_conductivity_LBTE
from phono3py.conductivity.rta import get_thermal_conductivity_RTA
from phono3py.interface.fc_calculator import get_fc3
from phono3py.interface.phono3py_yaml import Phono3pyYaml
from phono3py.phonon.grid import BZGrid
from phono3py.phonon3.dataset import get_displacements_and_forces_fc3
from phono3py.phonon3.displacement_fc3 import (
direction_to_displacement,
get_third_order_displacements,
)
from phono3py.phonon3.fc3 import cutoff_fc3_by_zero
from phono3py.phonon3.fc3 import get_fc3 as get_phono3py_fc3
from phono3py.phonon3.fc3 import (
cutoff_fc3_by_zero,
set_permutation_symmetry_compact_fc3,
set_permutation_symmetry_fc3,
set_translational_invariance_compact_fc3,
set_translational_invariance_fc3,
)
from phono3py.phonon3.fc3 import get_fc3 as get_phono3py_fc3
from phono3py.phonon3.imag_self_energy import (
get_imag_self_energy,
write_imag_self_energy,
@ -95,7 +96,6 @@ from phono3py.phonon3.real_self_energy import (
write_real_self_energy,
)
from phono3py.phonon3.spectral_function import run_spectral_function
from phono3py.phonon.grid import BZGrid
from phono3py.version import __version__

22
phono3py/conductivity/base.py
View File

@ -45,10 +45,10 @@ from phonopy.phonon.thermal_properties import mode_cv
from phonopy.units import EV, Angstrom, Kb, THz, THzToEv
from phono3py.other.isotope import Isotope
from phono3py.phonon.grid import get_grid_points_by_rotations, get_ir_grid_points
from phono3py.phonon3.collision_matrix import CollisionMatrix
from phono3py.phonon3.imag_self_energy import ImagSelfEnergy
from phono3py.phonon3.interaction import Interaction
from phono3py.phonon.grid import get_grid_points_by_rotations, get_ir_grid_points
unit_to_WmK = (
(THz * Angstrom) ** 2 / (Angstrom**3) * EV / THz / (2 * np.pi)
@ -81,6 +81,7 @@ class HeatCapacityMixIn:
"Use attribute, Conductivity.mode_heat_capacities "
"instead of Conductivity.get_mode_heat_capacities().",
DeprecationWarning,
stacklevel=2,
)
return self.mode_heat_capacities
@ -129,6 +130,7 @@ class ConductivityMixIn(HeatCapacityMixIn):
warnings.warn(
"Use attribute, Conductivity.kappa " "instead of Conductivity.get_kappa().",
DeprecationWarning,
stacklevel=2,
)
return self.kappa
@ -143,6 +145,7 @@ class ConductivityMixIn(HeatCapacityMixIn):
"Use attribute, Conductivity.mode_kappa "
"instead of Conductivity.get_mode_kappa().",
DeprecationWarning,
stacklevel=2,
)
return self.mode_kappa
@ -165,6 +168,7 @@ class ConductivityMixIn(HeatCapacityMixIn):
"Use attribute, Conductivity.group_velocities "
"instead of Conductivity.get_group_velocities().",
DeprecationWarning,
stacklevel=2,
)
return self.group_velocities
@ -179,6 +183,7 @@ class ConductivityMixIn(HeatCapacityMixIn):
"Use attribute, Conductivity.gv_by_gv "
"instead of Conductivity.get_gv_by_gv().",
DeprecationWarning,
stacklevel=2,
)
return self.gv_by_gv
@ -413,6 +418,7 @@ class ConductivityBase(ABC):
"Use attribute, Conductivity.mesh_numbers "
"instead of Conductivity.get_mesh_numbers().",
DeprecationWarning,
stacklevel=2,
)
return self.mesh_numbers
@ -440,6 +446,7 @@ class ConductivityBase(ABC):
"Use attribute, Conductivity.frequencies "
"instead of Conductivity.get_frequencies().",
DeprecationWarning,
stacklevel=2,
)
return self.frequencies
@ -458,6 +465,7 @@ class ConductivityBase(ABC):
"Use attribute, Conductivity.qpoints "
"instead of Conductivity.get_qpoints().",
DeprecationWarning,
stacklevel=2,
)
return self.qpoints
@ -480,6 +488,7 @@ class ConductivityBase(ABC):
"Use attribute, Conductivity.grid_points "
"instead of Conductivity.get_grid_points().",
DeprecationWarning,
stacklevel=2,
)
return self.grid_points
@ -494,6 +503,7 @@ class ConductivityBase(ABC):
"Use attribute, Conductivity.grid_weights "
"instead of Conductivity.get_grid_weights().",
DeprecationWarning,
stacklevel=2,
)
return self.grid_weights
@ -513,6 +523,7 @@ class ConductivityBase(ABC):
"Use attribute, Conductivity.temperatures "
"instead of Conductivity.get_temperatures().",
DeprecationWarning,
stacklevel=2,
)
return self.temperatures
@ -522,6 +533,7 @@ class ConductivityBase(ABC):
"Use attribute, Conductivity.temperatures "
"instead of Conductivity.set_temperatures().",
DeprecationWarning,
stacklevel=2,
)
self.temperatures = temperatures
@ -540,6 +552,7 @@ class ConductivityBase(ABC):
warnings.warn(
"Use attribute, Conductivity.gamma " "instead of Conductivity.get_gamma().",
DeprecationWarning,
stacklevel=2,
)
return self.gamma
@ -548,6 +561,7 @@ class ConductivityBase(ABC):
warnings.warn(
"Use attribute, Conductivity.gamma " "instead of Conductivity.set_gamma().",
DeprecationWarning,
stacklevel=2,
)
self.gamma = gamma
@ -567,6 +581,7 @@ class ConductivityBase(ABC):
"Use attribute, Conductivity.gamma_isotope "
"instead of Conductivity.get_gamma_isotope().",
DeprecationWarning,
stacklevel=2,
)
return self.gamma_isotope
@ -576,6 +591,7 @@ class ConductivityBase(ABC):
"Use attribute, Conductivity.gamma_isotope "
"instead of Conductivity.set_gamma_isotope().",
DeprecationWarning,
stacklevel=2,
)
self.gamma_isotope = gamma_iso
@ -590,6 +606,7 @@ class ConductivityBase(ABC):
"Use attribute, Conductivity.sigmas "
"instead of Conductivity.get_sigmas().",
DeprecationWarning,
stacklevel=2,
)
return self.sigmas
@ -604,6 +621,7 @@ class ConductivityBase(ABC):
"Use attribute, Conductivity.sigma_cutoff_width "
"instead of Conductivity.get_sigma_cutoff_width().",
DeprecationWarning,
stacklevel=2,
)
return self.sigma_cutoff_width
@ -618,6 +636,7 @@ class ConductivityBase(ABC):
"Use attribute, Conductivity.grid_point_count "
"instead of Conductivity.get_grid_point_count().",
DeprecationWarning,
stacklevel=2,
)
return self.grid_point_count
@ -632,6 +651,7 @@ class ConductivityBase(ABC):
"Use attribute, Conductivity.averaged_pp_interaction "
"instead of Conductivity.get_averaged_pp_interaction().",
DeprecationWarning,
stacklevel=2,
)
return self.averaged_pp_interaction

12
phono3py/conductivity/direct_solution.py
View File

@ -56,9 +56,9 @@ from phono3py.conductivity.wigner import (
get_conversion_factor_WTE,
)
from phono3py.file_IO import read_pp_from_hdf5
from phono3py.phonon.grid import get_grid_points_by_rotations
from phono3py.phonon3.collision_matrix import CollisionMatrix
from phono3py.phonon3.interaction import Interaction, all_bands_exist
from phono3py.phonon.grid import get_grid_points_by_rotations
class ConductivityLBTEBase(ConductivityBase):
@ -163,6 +163,7 @@ class ConductivityLBTEBase(ConductivityBase):
"Use attribute, Conductivity_LBTE.collision_matrix "
"instead of Conductivity_LBTE.get_collision_matrix().",
DeprecationWarning,
stacklevel=2,
)
return self.collision_matrix
@ -172,6 +173,7 @@ class ConductivityLBTEBase(ConductivityBase):
"Use attribute, Conductivity_LBTE.collision_matrix "
"instead of Conductivity_LBTE.set_collision_matrix().",
DeprecationWarning,
stacklevel=2,
)
self.collision_matrix = collision_matrix
@ -517,9 +519,9 @@ class ConductivityLBTEBase(ConductivityBase):
else:
i_data = 0
self._gamma[j, k, i_data] = self._collision.imag_self_energy
self._collision_matrix[j, k, i_data] = (
self._collision.get_collision_matrix()
)
self._collision_matrix[
j, k, i_data
] = self._collision.get_collision_matrix()
def _prepare_collision_matrix(self):
"""Collect pieces and construct collision matrix."""
@ -1271,6 +1273,7 @@ class ConductivityLBTE(ConductivityMixIn, ConductivityLBTEBase):
"Use attribute, Conductivity_LBTE.kappa_RTA "
"instead of Conductivity_LBTE.get_kappa_RTA().",
DeprecationWarning,
stacklevel=2,
)
return self.kappa_RTA
@ -1285,6 +1288,7 @@ class ConductivityLBTE(ConductivityMixIn, ConductivityLBTEBase):
"Use attribute, Conductivity_LBTE.mode_kappa_RTA "
"instead of Conductivity_LBTE.get_mode_kappa_RTA().",
DeprecationWarning,
stacklevel=2,
)
return self.mode_kappa_RTA

10
phono3py/conductivity/rta.py
View File

@ -54,9 +54,9 @@ from phono3py.conductivity.wigner import (
)
from phono3py.file_IO import read_pp_from_hdf5
from phono3py.other.tetrahedron_method import get_tetrahedra_relative_grid_address
from phono3py.phonon.grid import get_grid_points_by_rotations
from phono3py.phonon3.imag_self_energy import ImagSelfEnergy, average_by_degeneracy
from phono3py.phonon3.interaction import Interaction, all_bands_exist
from phono3py.phonon.grid import get_grid_points_by_rotations
class ConductivityRTABase(ConductivityBase):
@ -298,9 +298,9 @@ class ConductivityRTABase(ConductivityBase):
self._gamma_N[j, k, i] = g_N
self._gamma_U[j, k, i] = g_U
if self._is_gamma_detail:
self._gamma_detail_at_q[k] = (
self._collision.get_detailed_imag_self_energy()
)
self._gamma_detail_at_q[
k
] = self._collision.get_detailed_imag_self_energy()
def _set_gamma_at_sigmas_lowmem(self, i):
"""Calculate gamma without storing ph-ph interaction strength.
@ -921,7 +921,7 @@ class ConductivityKuboRTA(ConductivityKuboMixIn, ConductivityRTABase):
return
g = g_sum[i_band] + g_sum[j_band]
for i_pair, (a, b) in enumerate(
for i_pair, _ in enumerate(
([0, 0], [1, 1], [2, 2], [1, 2], [0, 2], [0, 1])
):
old_settings = np.seterr(all="raise")

13
phono3py/conductivity/utils.py
View File

@ -34,7 +34,6 @@
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
import sys
from typing import TYPE_CHECKING, Optional, Union
@ -367,7 +366,7 @@ class ConductivityRTAWriter:
all_triplets = get_all_triplets(gp, interaction.bz_grid)
if all_bands_exist(interaction):
for j, sigma in enumerate(sigmas):
for sigma in sigmas:
write_gamma_detail_to_hdf5(
temperatures,
mesh,
@ -384,7 +383,7 @@ class ConductivityRTAWriter:
verbose=verbose,
)
else:
for j, sigma in enumerate(sigmas):
for sigma in sigmas:
for k, bi in enumerate(interaction.get_band_indices()):
write_gamma_detail_to_hdf5(
temperatures,
@ -871,7 +870,7 @@ class ShowCalcProgress:
("#%6s " + " %-10s" * 6)
% ("T(K)", "xx", "yy", "zz", "yz", "xz", "xy")
)
for j, (t, k) in enumerate(zip(temperatures, kappa[i])):
for t, k in zip(temperatures, kappa[i]):
print(("%7.1f " + " %10.3f" * 6) % ((t,) + tuple(k)))
print("")
@ -936,13 +935,13 @@ class ShowCalcProgress:
% (" \t T(K)", "xx", "yy", "zz", "yz", "xz", "xy")
)
if kappa_P_RTA is not None:
for j, (t, k) in enumerate(zip(temperatures, kappa_P_RTA[i])):
for t, k in zip(temperatures, kappa_P_RTA[i]):
print("K_P\t" + ("%7.1f " + " %10.3f" * 6) % ((t,) + tuple(k)))
print(" ")
for j, (t, k) in enumerate(zip(temperatures, kappa_C[i])):
for t, k in zip(temperatures, kappa_C[i]):
print("K_C\t" + ("%7.1f " + " %10.3f" * 6) % ((t,) + tuple(k)))
print(" ")
for j, (t, k) in enumerate(zip(temperatures, kappa_TOT_RTA[i])):
for t, k in zip(temperatures, kappa_TOT_RTA[i]):
print("K_T\t" + ("%7.1f " + " %10.3f" * 6) % ((t,) + tuple(k)))
print("")

2
phono3py/cui/phono3py_argparse.py
View File

@ -516,7 +516,7 @@ def get_parser(fc_symmetry=False, is_nac=False, load_phono3py_yaml=False):
action="store_true",
default=False,
help="Deactivate summation of partial kappa at q-stars",
),
)
parser.add_argument(
"--nomeshsym",
dest="is_nomeshsym",

2
phono3py/cui/phono3py_script.py
View File

@ -89,9 +89,9 @@ from phono3py.file_IO import (
write_phonon_to_hdf5,
)
from phono3py.interface.phono3py_yaml import Phono3pyYaml
from phono3py.phonon.grid import get_grid_point_from_address, get_ir_grid_points
from phono3py.phonon3.fc3 import show_drift_fc3
from phono3py.phonon3.gruneisen import run_gruneisen_parameters
from phono3py.phonon.grid import get_grid_point_from_address, get_ir_grid_points
from phono3py.version import __version__
# import logging

2
phono3py/cui/settings.py
View File

@ -709,7 +709,7 @@ class Phono3pyConfParser(ConfParser):
# specials
if conf_key in ("create_forces_fc2", "create_forces_fc3"):
if type(confs[conf_key]) is str:
if isinstance(confs[conf_key], str):
fnames = confs[conf_key].split()
else:
fnames = confs[conf_key]

3
phono3py/cui/show_log.py
View File

@ -48,7 +48,8 @@ def show_general_settings(
):
"""Show general setting information."""
is_primitive_axes_auto = (
type(phono3py.primitive_matrix) is str and phono3py.primitive_matrix == "auto"
isinstance(phono3py.primitive_matrix, str)
and phono3py.primitive_matrix == "auto"
)
primitive_matrix = phono3py.primitive_matrix
supercell_matrix = phono3py.supercell_matrix

2
phono3py/cui/triplets_info.py
View File

@ -37,8 +37,8 @@
import numpy as np
from phono3py.file_IO import write_grid_address_to_hdf5, write_ir_grid_points
from phono3py.phonon3.triplets import get_triplets_at_q
from phono3py.phonon.grid import get_ir_grid_points
from phono3py.phonon3.triplets import get_triplets_at_q
def write_grid_points(

28
phono3py/file_IO.py
View File

@ -57,7 +57,9 @@ def write_disp_fc3_yaml(dataset, supercell, filename="disp_fc3.yaml"):
This function should not be called from phono3py script from version 3.
"""
warnings.warn("write_disp_fc3_yaml() is deprecated.", DeprecationWarning)
warnings.warn(
"write_disp_fc3_yaml() is deprecated.", DeprecationWarning, stacklevel=2
)
w = open(filename, "w")
w.write("natom: %d\n" % dataset["natom"])
@ -155,7 +157,9 @@ def write_disp_fc2_yaml(dataset, supercell, filename="disp_fc2.yaml"):
This function should not be called from phono3py script from version 3.
"""
warnings.warn("write_disp_fc2_yaml() is deprecated.", DeprecationWarning)
warnings.warn(
"write_disp_fc2_yaml() is deprecated.", DeprecationWarning, stacklevel=2
)
w = open(filename, "w")
w.write("natom: %d\n" % dataset["natom"])
@ -251,7 +255,7 @@ def write_FORCES_FC3(disp_dataset, forces_fc3=None, fp=None, filename="FORCES_FC
else:
# for forces in forces_fc3[i]:
# w.write("%15.10f %15.10f %15.10f\n" % (tuple(forces)))
for j in range(natom):
for _ in range(natom):
w.write("%15.10f %15.10f %15.10f\n" % (0, 0, 0))
count += 1
@ -339,8 +343,8 @@ def write_fc2_to_hdf5(
):
try:
import h5py
except ImportError:
raise ModuleNotFoundError("You need to install python-h5py.")
except ImportError as exc:
raise ModuleNotFoundError("You need to install python-h5py.") from exc
with h5py.File(filename, "w") as w:
w.create_dataset(
@ -1480,7 +1484,9 @@ def parse_disp_fc2_yaml(filename="disp_fc2.yaml", return_cell=False):
This function should not be called from phono3py script from version 3.
"""
warnings.warn("parse_disp_fc2_yaml() is deprecated.", DeprecationWarning)
warnings.warn(
"parse_disp_fc2_yaml() is deprecated.", DeprecationWarning, stacklevel=2
)
dataset = _parse_yaml(filename)
natom = dataset["natom"]
@ -1507,7 +1513,9 @@ def parse_disp_fc3_yaml(filename="disp_fc3.yaml", return_cell=False):
This function should not be called from phono3py script from version 3.
"""
warnings.warn("parse_disp_fc3_yaml() is deprecated.", DeprecationWarning)
warnings.warn(
"parse_disp_fc3_yaml() is deprecated.", DeprecationWarning, stacklevel=2
)
dataset = _parse_yaml(filename)
natom = dataset["natom"]
@ -1547,7 +1555,7 @@ def parse_FORCES_FC2(disp_dataset, filename="FORCES_FC2", unit_conversion_factor
num_disp = len(disp_dataset["first_atoms"])
forces_fc2 = []
with open(filename, "r") as f2:
for i in range(num_disp):
for _ in range(num_disp):
forces = _parse_force_lines(f2, num_atom)
if forces is None:
return []
@ -1681,7 +1689,7 @@ def _parse_yaml(file_yaml):
So this is obsolete at v2 and later versions.
"""
warnings.warn("_parse_yaml() is deprecated.", DeprecationWarning)
warnings.warn("_parse_yaml() is deprecated.", DeprecationWarning, stacklevel=2)
import yaml
@ -1720,7 +1728,7 @@ def _write_cell_yaml(w, supercell):
These methods are also deprecated.
"""
warnings.warn("write_cell_yaml() is deprecated.", DeprecationWarning)
warnings.warn("write_cell_yaml() is deprecated.", DeprecationWarning, stacklevel=2)
w.write("lattice:\n")
for axis in supercell.get_cell():

10
phono3py/interface/phono3py_yaml.py
View File

@ -152,9 +152,9 @@ class Phono3pyYamlLoader(PhonopyYamlLoaderBase):
dataset = None
if "displacement_pairs" in self._yaml:
disp = self._yaml["displacement_pairs"][0]
if type(disp) is dict: # type1
if isinstance(disp, dict): # type1
dataset = self._parse_fc3_dataset_type1(len(self._data.supercell))
elif type(disp) is list: # type2
elif isinstance(disp, list): # type2
if "displacement" in disp[0]:
dataset = self._parse_force_sets_type2()
if "displacement_pair_info" in self._yaml:
@ -507,7 +507,7 @@ def _displacements_yaml_lines_type1_info(dataset):
if "duplicates" in dataset and dataset["duplicates"]:
lines.append(" duplicated_supercell_ids: " "# 0 means perfect supercell")
# Backward compatibility for dict type
if type(dataset["duplicates"]) is dict:
if isinstance(dataset["duplicates"], dict):
for disp1_id, j in dataset["duplicates"].items():
lines.append(" - [ %d, %d ]" % (int(disp1_id), j))
else:
@ -580,7 +580,7 @@ def read_phono3py_yaml(
) -> Phono3pyYamlData:
"""Read phono3py.yaml like file."""
yaml_data = load_yaml(filename)
if type(yaml_data) is str:
if isinstance(yaml_data, str):
msg = f'Could not load "{filename}" properly.'
raise TypeError(msg)
return load_phono3py_yaml(
@ -597,7 +597,7 @@ def load_phono3py_yaml(
"""Return Phono3pyYamlData instance loading yaml data.
Parameters
-----------
----------
yaml_data : dict
"""

1
phono3py/phonon/grid.py
View File

@ -716,6 +716,7 @@ class GridMatrix:
warnings.warn(
"Non primitive cell input. Unable to use GR-grid.",
RuntimeWarning,
stacklevel=2,
)
return False

14
phono3py/phonon3/displacement_fc3.py
View File

@ -350,13 +350,11 @@ def _find_duplicates(direction_dataset):
duplucates = []
done = []
for i, direction1 in enumerate(direction_dataset):
for direction1 in direction_dataset:
n1 = direction1["number"]
for directions2 in direction1["second_atoms"]:
n2 = directions2["number"]
if (
n2 > n1 and (n2, n1) not in done and (n2, n1) in direction_sets
): # noqa E129
if n2 > n1 and (n2, n1) not in done and (n2, n1) in direction_sets: # noqa E129
done.append((n2, n1))
duplucates += _compare(
n1,
@ -368,14 +366,14 @@ def _find_duplicates(direction_dataset):
)
done = []
for i, direction1 in enumerate(direction_dataset):
for direction1 in direction_dataset:
n1 = direction1["number"]
for directions2 in direction1["second_atoms"]:
n2 = directions2["number"]
if n1 == n2 and n1 not in done:
done.append(n1)
duplucates += _compare_opposite(
n1, direction_sets[(n1, n1)], pair_idx[(n1, n1)]
direction_sets[(n1, n1)], pair_idx[(n1, n1)]
)
return duplucates
@ -393,10 +391,10 @@ def _compare(n1, n2, dset1, dset2, pidx1, pidx2):
return [[i, j] for (i, j) in duplucates if i > j]
def _compare_opposite(n1, dset1, pidx1):
def _compare_opposite(dset1, pidx1):
flip_sets = np.array(dset1)[:, [3, 4, 5, 0, 1, 2]]
duplucates = []
for i, d1 in enumerate(dset1):
for d1 in dset1:
eq_indices = np.where(np.abs(flip_sets + d1).sum(axis=1) == 0)[0]
if len(eq_indices) > 0:
duplucates += [[pidx1[j], 0] for j in eq_indices]

58
phono3py/phonon3/fc3.py
View File

@ -276,12 +276,12 @@ def set_permutation_symmetry_compact_fc3(fc3, primitive):
np.array(p2s_map, dtype="int_"),
np.array(nsym_list, dtype="int_"),
)
except ImportError:
except ImportError as exc:
text = (
"Import error at phono3c.permutation_symmetry_compact_fc3. "
"Corresponding python code is not implemented."
)
raise RuntimeError(text)
raise RuntimeError(text) from exc
def _copy_permutation_symmetry_fc3_elem(fc3, fc3_elem, a, b, c):
@ -339,29 +339,29 @@ def set_translational_invariance_compact_fc3(fc3, primitive: Primitive):
_set_translational_invariance_fc3_per_index(fc3, index=1)
_set_translational_invariance_fc3_per_index(fc3, index=2)
except ImportError:
except ImportError as exc:
text = (
"Import error at phono3c.tranpose_compact_fc3. "
"Corresponding python code is not implemented."
)
raise RuntimeError(text)
raise RuntimeError(text) from exc
def _set_translational_invariance_fc3_per_index(fc3, index=0):
for i in range(fc3.shape[(1 + index) % 3]):
for j in range(fc3.shape[(2 + index) % 3]):
for k, l, m in list(np.ndindex(3, 3, 3)):
for k, ll, m in list(np.ndindex(3, 3, 3)):
if index == 0:
fc3[:, i, j, k, l, m] -= (
np.sum(fc3[:, i, j, k, l, m]) / fc3.shape[0]
fc3[:, i, j, k, ll, m] -= (
np.sum(fc3[:, i, j, k, ll, m]) / fc3.shape[0]
)
elif index == 1:
fc3[j, :, i, k, l, m] -= (
np.sum(fc3[j, :, i, k, l, m]) / fc3.shape[1]
fc3[j, :, i, k, ll, m] -= (
np.sum(fc3[j, :, i, k, ll, m]) / fc3.shape[1]
)
elif index == 2:
fc3[i, j, :, k, l, m] -= (
np.sum(fc3[i, j, :, k, l, m]) / fc3.shape[2]
fc3[i, j, :, k, ll, m] -= (
np.sum(fc3[i, j, :, k, ll, m]) / fc3.shape[2]
)
@ -465,7 +465,7 @@ def _solve_fc3(
print("Displacements (in Angstrom):")
else:
print("One displacement (in Angstrom):")
for i, v in enumerate(displacements_first):
for v in displacements_first:
print(" [%7.4f %7.4f %7.4f]" % tuple(v))
sys.stdout.flush()
if verbose > 2:
@ -577,19 +577,19 @@ def show_drift_fc3(fc3, primitive=None, name="fc3"):
klm1 = [0, 0, 0]
klm2 = [0, 0, 0]
klm3 = [0, 0, 0]
for i, j, k, l, m in list(np.ndindex((num_atom, num_atom, 3, 3, 3))):
val1 = fc3[:, i, j, k, l, m].sum()
val2 = fc3[i, :, j, k, l, m].sum()
val3 = fc3[i, j, :, k, l, m].sum()
for i, j, k, ll, m in list(np.ndindex((num_atom, num_atom, 3, 3, 3))):
val1 = fc3[:, i, j, k, ll, m].sum()
val2 = fc3[i, :, j, k, ll, m].sum()
val3 = fc3[i, j, :, k, ll, m].sum()
if abs(val1) > abs(maxval1):
maxval1 = val1
klm1 = [k, l, m]
klm1 = [k, ll, m]
if abs(val2) > abs(maxval2):
maxval2 = val2
klm2 = [k, l, m]
klm2 = [k, ll, m]
if abs(val3) > abs(maxval3):
maxval3 = val3
klm3 = [k, l, m]
klm3 = [k, ll, m]
else:
try:
import phono3py._phono3py as phono3c
@ -614,29 +614,29 @@ def show_drift_fc3(fc3, primitive=None, name="fc3"):
phono3c.transpose_compact_fc3(
fc3, permutations, s2pp_map, p2s_map, nsym_list, 0
) # dim[0] <--> dim[1]
for i, j, k, l, m in np.ndindex((num_patom, num_satom, 3, 3, 3)):
val1 = fc3[i, :, j, k, l, m].sum()
for i, j, k, ll, m in np.ndindex((num_patom, num_satom, 3, 3, 3)):
val1 = fc3[i, :, j, k, ll, m].sum()
if abs(val1) > abs(maxval1):
maxval1 = val1
klm1 = [k, l, m]
klm1 = [k, ll, m]
phono3c.transpose_compact_fc3(
fc3, permutations, s2pp_map, p2s_map, nsym_list, 0
) # dim[0] <--> dim[1]
for i, j, k, l, m in np.ndindex((num_patom, num_satom, 3, 3, 3)):
val2 = fc3[i, :, j, k, l, m].sum()
val3 = fc3[i, j, :, k, l, m].sum()
for i, j, k, ll, m in np.ndindex((num_patom, num_satom, 3, 3, 3)):
val2 = fc3[i, :, j, k, ll, m].sum()
val3 = fc3[i, j, :, k, ll, m].sum()
if abs(val2) > abs(maxval2):
maxval2 = val2
klm2 = [k, l, m]
klm2 = [k, ll, m]
if abs(val3) > abs(maxval3):
maxval3 = val3
klm3 = [k, l, m]
except ImportError:
klm3 = [k, ll, m]
except ImportError as exc:
text = (
"Import error at phono3c.tranpose_compact_fc3. "
"Corresponding python code is not implemented."
)
raise RuntimeError(text)
raise RuntimeError(text) from exc
text = "Max drift of %s: " % name
text += "%f (%s%s%s) " % (maxval1, "xyz"[klm1[0]], "xyz"[klm1[1]], "xyz"[klm1[2]])

6
phono3py/phonon3/gruneisen.py
View File

@ -270,9 +270,7 @@ class Gruneisen:
):
f.write("- nqpoint: %d\n" % len(path))
f.write(" phonon:\n")
for i, (q, d, g_at_q, freqs_at_q) in enumerate(
zip(path, distances, gs, fs)
): # noqa E125
for q, d, g_at_q, freqs_at_q in zip(path, distances, gs, fs):
f.write(" - q-position: [ %10.7f, %10.7f, %10.7f ]\n" % tuple(q))
f.write(" distance: %10.7f\n" % d)
f.write(" band:\n")
@ -415,7 +413,7 @@ class Gruneisen:
for j in range(3):
for k in range(3):
for ll in range(3):
for m in range(3):
for _ in range(3):
dPhidu[nu, pi, i, j, k, ll] = (
fc3[p2s[nu], pi, :, i, j, :] * Y[:, :, k, ll]
).sum()

7
phono3py/phonon3/imag_self_energy.py
View File

@ -46,9 +46,9 @@ from phono3py.file_IO import (
write_gamma_detail_to_hdf5,
write_imag_self_energy_at_grid_point,
)
from phono3py.phonon.func import bose_einstein
from phono3py.phonon3.interaction import Interaction
from phono3py.phonon3.triplets import get_triplets_integration_weights
from phono3py.phonon.func import bose_einstein
class ImagSelfEnergy:
@ -170,6 +170,7 @@ class ImagSelfEnergy:
"Use attribute, ImagSelfEnergy.imag_self_energy "
"instead of ImagSelfEnergy.get_imag_self_energy().",
DeprecationWarning,
stacklevel=2,
)
return self.imag_self_energy
@ -200,6 +201,7 @@ class ImagSelfEnergy:
"Use attribute, ImagSelfEnergy.detailed_imag_self_energy "
"instead of ImagSelfEnergy.get_detailed_imag_self_energy().",
DeprecationWarning,
stacklevel=2,
)
return self.detailed_imag_self_energy
@ -222,6 +224,7 @@ class ImagSelfEnergy:
"Use attribute, ImagSelfEnergy.unit_conversion_factor "
"instead of ImagSelfEnergy.get_unit_conversion_factor().",
DeprecationWarning,
stacklevel=2,
)
return self.unit_conversion_factor
@ -268,6 +271,7 @@ class ImagSelfEnergy:
"Use attribute, ImagSelfEnergy.frequency_points "
"instead of ImagSelfEnergy.set_frequency_points().",
DeprecationWarning,
stacklevel=2,
)
self.frequency_points = frequency_points
@ -289,6 +293,7 @@ class ImagSelfEnergy:
"Use attribute, ImagSelfEnergy.temperature "
"instead of ImagSelfEnergy.set_temperature().",
DeprecationWarning,
stacklevel=2,
)
self.temperature = temperature

21
phono3py/phonon3/interaction.py
View File

@ -45,15 +45,15 @@ from phonopy.structure.cells import Primitive, compute_all_sg_permutations
from phonopy.structure.symmetry import Symmetry
from phonopy.units import AMU, EV, Angstrom, Hbar, THz, VaspToTHz
from phono3py.phonon3.real_to_reciprocal import RealToReciprocal
from phono3py.phonon3.reciprocal_to_normal import ReciprocalToNormal
from phono3py.phonon3.triplets import get_nosym_triplets_at_q, get_triplets_at_q
from phono3py.phonon.grid import (
BZGrid,
get_grid_points_by_rotations,
get_ir_grid_points,
)
from phono3py.phonon.solver import run_phonon_solver_c, run_phonon_solver_py
from phono3py.phonon3.real_to_reciprocal import RealToReciprocal
from phono3py.phonon3.reciprocal_to_normal import ReciprocalToNormal
from phono3py.phonon3.triplets import get_nosym_triplets_at_q, get_triplets_at_q
class Interaction:
@ -222,6 +222,7 @@ class Interaction:
"Use attribute, Interaction.interaction_strength "
"instead of Interaction.get_interaction_strength().",
DeprecationWarning,
stacklevel=2,
)
return self.interaction_strength
@ -243,6 +244,7 @@ class Interaction:
"Use attribute, Interaction.mesh_numbers "
"instead of Interaction.get_mesh_numbers().",
DeprecationWarning,
stacklevel=2,
)
return self.mesh_numbers
@ -261,6 +263,7 @@ class Interaction:
warnings.warn(
"Use attribute, Interaction.fc3 " "instead of Interaction.get_fc3().",
DeprecationWarning,
stacklevel=2,
)
return self.fc3
@ -275,6 +278,7 @@ class Interaction:
"Use attribute, Interaction.dynamical_matrix "
"instead of Interaction.get_dynamical_matrix().",
DeprecationWarning,
stacklevel=2,
)
return self.dynamical_matrix
@ -289,6 +293,7 @@ class Interaction:
"Use attribute, Interaction.primitive "
"instead of Interaction.get_primitive().",
DeprecationWarning,
stacklevel=2,
)
return self.primitive
@ -338,6 +343,7 @@ class Interaction:
"Use attribute, Interaction.band_indices "
"instead of Interaction.get_band_indices().",
DeprecationWarning,
stacklevel=2,
)
return self.band_indices
@ -373,6 +379,7 @@ class Interaction:
"Use attribute, Interaction.nac_q_direction "
"instead of Interaction.get_nac_q_direction().",
DeprecationWarning,
stacklevel=2,
)
return self.nac_q_direction
@ -382,6 +389,7 @@ class Interaction:
"Use attribute, Interaction.nac_q_direction "
"instead of Interaction.set_nac_q_direction().",
DeprecationWarning,
stacklevel=2,
)
self.nac_q_direction = nac_q_direction
@ -402,6 +410,7 @@ class Interaction:
"Use attribute, Interaction.zero_value_positions "
"instead of Interaction.get_zero_value_positions().",
DeprecationWarning,
stacklevel=2,
)
return self.zero_value_positions
@ -436,6 +445,7 @@ class Interaction:
"Use attribute, Interaction.frequency_factor_to_THz ",
"instead of Interaction.get_frequency_factor_to_THz().",
DeprecationWarning,
stacklevel=2,
)
return self.frequency_factor_to_THz
@ -450,6 +460,7 @@ class Interaction:
"Use attribute, Interaction.lapack_zheev_uplo "
"instead of Interaction.get_lapack_zheev_uplo().",
DeprecationWarning,
stacklevel=2,
)
return self.lapack_zheev_uplo
@ -464,6 +475,7 @@ class Interaction:
"Use attribute, Interaction.cutoff_frequency "
"instead of Interaction.get_cutoff_frequency().",
DeprecationWarning,
stacklevel=2,
)
return self.cutoff_frequency
@ -520,6 +532,7 @@ class Interaction:
"Use attribute, Interaction.averaged_interaction "
"instead of Interaction.get_averaged_interaction().",
DeprecationWarning,
stacklevel=2,
)
return self.averaged_interaction
@ -540,6 +553,7 @@ class Interaction:
"Use attribute, Interaction.unit_conversion_factor "
"instead of Interaction.get_unit_conversion_factor().",
DeprecationWarning,
stacklevel=2,
)
return self.unit_conversion_factor
@ -554,6 +568,7 @@ class Interaction:
"Use attribute, Interaction.constant_averaged_interaction "
"instead of Interaction.get_constant_averaged_interaction().",
DeprecationWarning,
stacklevel=2,
)
return self.constant_averaged_interaction

31
phono3py/phonon3/joint_dos.py
View File

@ -42,14 +42,14 @@ from phonopy.harmonic.dynamical_matrix import DynamicalMatrix, get_dynamical_mat
from phonopy.structure.cells import Primitive, Supercell
from phonopy.units import VaspToTHz
from phono3py.phonon.func import bose_einstein
from phono3py.phonon.grid import BZGrid, get_grid_point_from_address
from phono3py.phonon.solver import run_phonon_solver_c
from phono3py.phonon3.triplets import (
get_nosym_triplets_at_q,
get_triplets_at_q,
get_triplets_integration_weights,
)
from phono3py.phonon.func import bose_einstein
from phono3py.phonon.grid import BZGrid, get_grid_point_from_address
from phono3py.phonon.solver import run_phonon_solver_c
class JointDos:
@ -129,7 +129,7 @@ class JointDos:
def get_joint_dos(self):
"""Return joint-density-of-states."""
warnings.warn("Use attribute, joint_dos", DeprecationWarning)
warnings.warn("Use attribute, joint_dos", DeprecationWarning, stacklevel=2)
return self.joint_dos
@property
@ -143,7 +143,9 @@ class JointDos:
def get_frequency_points(self):
"""Return frequency points."""
warnings.warn("Use attribute, frequency_points", DeprecationWarning)
warnings.warn(
"Use attribute, frequency_points", DeprecationWarning, stacklevel=2
)
return self.frequency_points
def get_phonons(self):
@ -157,7 +159,7 @@ class JointDos:
def get_primitive(self):
"""Return primitive cell."""
warnings.warn("Use attribute, primitive", DeprecationWarning)
warnings.warn("Use attribute, primitive", DeprecationWarning, stacklevel=2)
return self.primitive
@property
@ -172,7 +174,7 @@ class JointDos:
def get_mesh_numbers(self):
"""Return mesh numbers by three integer values."""
warnings.warn("Use attribute, mesh_numbers", DeprecationWarning)
warnings.warn("Use attribute, mesh_numbers", DeprecationWarning, stacklevel=2)
return self.mesh
@property
@ -189,7 +191,9 @@ class JointDos:
def set_nac_q_direction(self, nac_q_direction=None):
"""Set q-direction for NAC."""
warnings.warn("Use attribute, nac_q_direction", DeprecationWarning)
warnings.warn(
"Use attribute, nac_q_direction", DeprecationWarning, stacklevel=2
)
self.nac_q_direction = nac_q_direction
@property
@ -209,6 +213,7 @@ class JointDos:
warnings.warn(
"Use attribute, JointDOS.sigma instead of JointDOS.set_sigma()",
DeprecationWarning,
stacklevel=2,
)
self.sigma = sigma
@ -401,14 +406,16 @@ class JointDos:
def _run_py_with_g_at_temperature(self, jdos, i):
g = self._g
n = self._occupations
for k, l in list(np.ndindex(g.shape[3:])):
for k, ll in list(np.ndindex(g.shape[3:])):
weights = np.where(
np.logical_or(n[:, 0, k] < 0, n[:, 1, l] < 0), 0, self._weights_at_q
np.logical_or(n[:, 0, k] < 0, n[:, 1, ll] < 0), 0, self._weights_at_q
)
jdos[i, 1] += np.dot(
(n[:, 0, k] + n[:, 1, l] + 1) * g[0, :, i, k, l], weights
(n[:, 0, k] + n[:, 1, ll] + 1) * g[0, :, i, k, ll], weights
)
jdos[i, 0] += np.dot(
(n[:, 0, k] - n[:, 1, ll]) * g[1, :, i, k, ll], weights
)
jdos[i, 0] += np.dot((n[:, 0, k] - n[:, 1, l]) * g[1, :, i, k, l], weights)
def _init_dynamical_matrix(self):
self._dm = get_dynamical_matrix(

14
phono3py/phonon3/real_self_energy.py
View File

@ -44,9 +44,9 @@ from phono3py.file_IO import (
write_real_self_energy_at_grid_point,
write_real_self_energy_to_hdf5,
)
from phono3py.phonon.func import bose_einstein
from phono3py.phonon3.imag_self_energy import get_frequency_points
from phono3py.phonon3.interaction import Interaction
from phono3py.phonon.func import bose_einstein
class RealSelfEnergy:
@ -247,8 +247,8 @@ class RealSelfEnergy:
)
def _run_py_with_band_indices(self):
for i, (triplet, w, interaction) in enumerate(
zip(self._triplets_at_q, self._weights_at_q, self._pp_strength)
for triplet, w, interaction in zip(
self._triplets_at_q, self._weights_at_q, self._pp_strength
):
freqs = self._frequencies[triplet]
for j, bi in enumerate(self._band_indices):
@ -286,11 +286,11 @@ class RealSelfEnergy:
def _run_py_with_frequency_points(self):
for k, fpoint in enumerate(self._frequency_points):
for i, (triplet, w, interaction) in enumerate(
zip(self._triplets_at_q, self._weights_at_q, self._pp_strength)
for triplet, w, interaction in zip(
self._triplets_at_q, self._weights_at_q, self._pp_strength
):
freqs = self._frequencies[triplet]
for j, bi in enumerate(self._band_indices):
for j, _ in enumerate(self._band_indices):
if self._temperature > 0:
self._real_self_energies[
k, j
@ -442,7 +442,7 @@ class ImagToReal:
fpoints = []
coef = self._df / np.pi
i_zero = (len(self._im_part) - 1) // 2
for i, im_part_at_i in enumerate(self._im_part):
for i, _ in enumerate(self._im_part):
if i < i_zero:
continue
fpoint = self._all_frequency_points[i] + self._df / 2

4
phono3py/phonon3/spectral_function.py
View File

@ -214,7 +214,7 @@ class SpectralFunction:
def run(self):
"""Calculate spectral function over grid points."""
for gp_index in self:
for _ in self:
pass
def __iter__(self):
@ -354,7 +354,7 @@ class SpectralFunction:
if self._log_level:
print("* Spectral function")
frequencies = self._pp.get_phonons()[0]
for j, temp in enumerate(self._temperatures):
for j, _ in enumerate(self._temperatures):
for k, bi in enumerate(self._pp.band_indices):
freq = frequencies[grid_point, bi]
gammas = self._gammas[sigma_i, j, i, k]

7
phono3py/phonon3/triplets.py
View File

@ -109,9 +109,10 @@ def get_triplets_at_q(
)
triplets_at_q, weights = _get_BZ_triplets_at_q(grid_point, bz_grid, map_triplets)
assert (
np.prod(bz_grid.D_diag) == weights.sum()
), "Num grid points %d, sum of weight %d" % (np.prod(bz_grid.D_diag), weights.sum())
assert np.prod(bz_grid.D_diag) == weights.sum(), (
"Num grid points %d, sum of weight %d"
% (np.prod(bz_grid.D_diag), weights.sum())
)
return triplets_at_q, weights, map_triplets, map_q

23
pyproject.toml
View File

@ -1,14 +1,19 @@
[build-system]
requires = ["setuptools", "wheel", "numpy"]
#requires = ["setuptools", "wheel", "numpy", "oldest-supported-numpy"]
#build-backend = "setuptools.build_meta"
[tool.flake8]
max-line-length = 88
extend-ignore = "E203,W503"
[tool.black]
[tool.ruff]
line-length = 88
select = [
"F", # Flake8
"B", # Black
"I", # isort
"E", # pycodestyle-errors
"D", # pydocstyle
]
extend-ignore = [
"D417",
"D100",
]
[tool.isort]
profile = "black"
[tool.ruff.lint.pydocstyle]
convention = "numpy"

10
scripts/phono3py-coleigplot
View File

@ -11,7 +11,7 @@ epsilon = 1.0e-8
def get_options():
# Arg-parser
"""Parse command line options."""
parser = argparse.ArgumentParser(description="Plot collision matrix eigenvalues")
parser.add_argument(
"--temperature",
@ -33,6 +33,7 @@ def get_options():
def get_t_index(temperatures, args):
"""Return temperature index."""
if len(temperatures) > 29:
t_index = 30
else:
@ -45,6 +46,7 @@ def get_t_index(temperatures, args):
def plot_one(ax, coleigs, temperatures, args):
"""Plot collision matrix eigenvalues at one temperature."""
t_index = get_t_index(temperatures, args)
coleigs_p = coleigs[t_index].copy()
coleigs_n = coleigs[t_index].copy()
@ -56,6 +58,7 @@ def plot_one(ax, coleigs, temperatures, args):
def plot_one_file(ax, args):
"""Plot collision matrix eigenvalues at one temperature from file."""
filename = args.filenames[0]
if os.path.isfile(filename):
with h5py.File(filename, "r") as f:
@ -68,6 +71,7 @@ def plot_one_file(ax, args):
def plot_more(ax, coleigs, temperatures, args):
"""Update plot by collision matrix eigenvalues from one file."""
t_index = get_t_index(temperatures[0], args)
y = [np.abs(v[t_index]) for v in coleigs]
ax.semilogy(np.transpose(y), ".", markersize=5)
@ -75,6 +79,7 @@ def plot_more(ax, coleigs, temperatures, args):
def plot_more_files(ax, args):
"""Plot collision matrix eigenvalues from multiple files."""
temperatures = []
coleigs = []
for filename in args.filenames:
@ -89,6 +94,7 @@ def plot_more_files(ax, args):
def plot(args: argparse.Namespace):
"""Plot collision matrix eigenvalues."""
import matplotlib.pyplot as plt
_, ax = plt.subplots()
@ -108,6 +114,7 @@ def plot(args: argparse.Namespace):
def write_dat(args: argparse.Namespace):
"""Write collision matrix eigenvalues to a file in gnuplot style."""
with open("coleigs.dat", "w") as w:
for filename in args.filenames:
with h5py.File(filename) as f:
@ -125,6 +132,7 @@ def write_dat(args: argparse.Namespace):
def main(args: argparse.Namespace):
"""Run phono3py-coleigplot."""
if args.savetxt:
write_dat(args)
else:

13
scripts/phono3py-kdeplot
View File

@ -12,6 +12,7 @@ epsilon = 1.0e-8
def collect_data(gamma, weights, frequencies, cutoff, max_freq):
"""Collect data for making input of Gaussian-KDE."""
freqs = []
mode_prop = []
for w, freq, g in zip(weights, frequencies, gamma):
@ -37,8 +38,7 @@ def collect_data(gamma, weights, frequencies, cutoff, max_freq):
def run_KDE(x, y, nbins, x_max=None, y_max=None, density_ratio=0.1):
"""Running Gaussian-KDE by scipy"""
"""Run Gaussian-KDE by scipy."""
x_min = 0
if x_max is None:
_x_max = np.rint(x.max() * 1.1)
@ -95,6 +95,7 @@ def plot(
point_size=5,
title=None,
):
"""Plot lifetime distribution."""
xmax = np.max(x)
ymax = np.max(y)
x_cut = []
@ -159,7 +160,7 @@ def plot(
def get_options():
# Arg-parser
"""Parse command-line arguments."""
parser = argparse.ArgumentParser(
description="Plot property density with gaussian KDE"
)
@ -206,7 +207,7 @@ def get_options():
"Number of bins in which data are assigned, "
"i.e., determining resolution of plot"
),
),
)
parser.add_argument(
"--no-points", dest="no_points", action="store_true", help="Do not show points"
)
@ -246,9 +247,7 @@ def get_options():
def main(args):
#
# Matplotlib setting
#
"""Run phono3py-kdeplot."""
import matplotlib
matplotlib.use("Agg")

4
setup.py
View File

@ -188,12 +188,12 @@ def _get_extensions(build_dir):
found_libs[key] = line.split()[3].split(";")
if f"{key} flags" in line and len(line.split()) > 3:
found_flags[key] = line.split()[3].split(";")
for key, value in found_libs.items():
for _, value in found_libs.items():
found_extra_link_args += value
for element in value:
if "libmkl" in element:
use_mkl_lapacke = True
for key, value in found_flags.items():
for _, value in found_flags.items():
found_extra_compile_args += value
if use_mkl_lapacke:
params["define_macros"].append(("MKL_LAPACKE", None))

1
test/conductivity/test_kappa_RTA.py
View File

@ -111,7 +111,6 @@ def test_kappa_RTA_si_nosym(si_pbesol: Phono3py, si_pbesol_nosym: Phono3py):
def test_kappa_RTA_si_nomeshsym(si_pbesol: Phono3py, si_pbesol_nomeshsym: Phono3py):
"""Test RTA without considering mesh symmetry by Si."""
if si_pbesol_nomeshsym._make_r0_average:
ref_kappa_RTA_si_nomeshsym = [81.147, 81.147, 81.147, 0.000, 0.000, 0.000]
else:

1
test/conductivity/test_kappa_RTA_Wigner.py
View File

@ -92,7 +92,6 @@ def test_kappa_RTA_si_with_sigma_iso(si_pbesol: Phono3py):
def test_kappa_RTA_si_nosym(si_pbesol: Phono3py, si_pbesol_nosym: Phono3py):
"""Test RTA without considering symmetry by Si."""
if si_pbesol_nosym._make_r0_average:
ref_kappa_P_RTA_si_nosym = [39.396, 39.222, 39.368, -0.096, -0.022, 0.026]
ref_kappa_C_si_nosym = [0.009, 0.009, 0.009, 0.000, 0.000, 0.000]

1
test/cui/test_phono3py_load_script.py
View File

@ -45,6 +45,7 @@ class MockArgs:
return (getattr(self, field.name) for field in fields(self))
def __contains__(self, item):
"""Implement in operator."""
return item in (field.name for field in fields(self))

1
test/other/test_kaccum.py
View File

@ -298,6 +298,7 @@ def test_GammaDOSsmearing(nacl_pbe: Phono3py):
def test_run_prop_dos(si_pbesol: Phono3py):
"""Test of run_prop_dos."""
ph3 = si_pbesol
ph3.mesh_numbers = [7, 7, 7]
ph3.init_phph_interaction()

2
test/phonon3/test_joint_dos.py
View File

@ -5,8 +5,8 @@ import pytest
from phono3py import Phono3py
from phono3py.api_jointdos import Phono3pyJointDos
from phono3py.phonon3.joint_dos import JointDos
from phono3py.phonon.grid import BZGrid
from phono3py.phonon3.joint_dos import JointDos
si_freq_points = [
0.0000000,

2
test/phonon3/test_triplets.py
View File

@ -7,12 +7,12 @@ from phonopy.structure.atoms import PhonopyAtoms
from phonopy.structure.symmetry import Symmetry
from phono3py import Phono3py
from phono3py.phonon.grid import BZGrid, get_grid_point_from_address
from phono3py.phonon3.triplets import (
_get_BZ_triplets_at_q,
_get_triplets_reciprocal_mesh_at_q,
get_triplets_at_q,
)
from phono3py.phonon.grid import BZGrid, get_grid_point_from_address
def test_get_triplets_at_q_type1(si_pbesol_111):

5
test/sscha/test_sscha.py
View File

@ -13,11 +13,6 @@ from phono3py.sscha.sscha import (
get_sscha_matrices,
)
try:
ModuleNotFoundError
except NameError:
ModuleNotFoundError = ImportError
si_pbesol_upsilon0_0 = [[3.849187e02, 0, 0], [0, 3.849187e02, 0], [0, 0, 3.849187e02]]
si_pbesol_upsilon1_34 = [
[1.886404, -1.549705, -1.126055],