Introduce isort

.pre-commit-config.yaml

@@ -29,3 +29,9 @@ repos:
   rev: 6.1.1
   hooks:
   - id: pydocstyle
+
+- repo: https://github.com/pycqa/isort
+  rev: 5.8.0
+  hooks:
+    - id: isort
+      name: isort (python)

README.md

@@ -34,6 +34,13 @@ phono3py repository.
   "python.linting.pycodestyleEnabled": false,
   "python.linting.pydocstyleEnabled": true,
   "python.formatting.provider": "black",
+  "python.formatting.blackArgs": ["--line-length=88"],
+  "python.sortImports.args": ["--profile", "black"],
+  "[python]": {
+      "editor.codeActionsOnSave": {
+      "source.organizeImports": true
+    },
+  }
   ```
 
 - Use of pre-commit (https://pre-commit.com/) is encouraged.

example/Si-PBEsol/Si.py

@@ -1,8 +1,9 @@
 """Example to run thermal conductivity of Si."""
 import numpy as np
 from phonopy.interface.vasp import read_vasp
-from phono3py import Phono3py
+
 import phono3py
+from phono3py import Phono3py
 
 
 def run_thermal_conductivity():

example/zb-ZnTe-PBEsol/launch_phono3py_ZnTe_PBEsol_222.py

@@ -1,10 +1,10 @@
 """Launch script of ZnTe AiiDA calculation using aiida-phononpy."""
-from phonopy.interface.vasp import read_vasp_from_strings
-from aiida.manage.configuration import load_profile
-from aiida.orm import Float, Bool, Str
-from aiida.plugins import DataFactory, WorkflowFactory
 from aiida.engine import submit
+from aiida.manage.configuration import load_profile
+from aiida.orm import Bool, Float, Str
+from aiida.plugins import DataFactory, WorkflowFactory
 from aiida_phonopy.common.utils import phonopy_atoms_to_structure
+from phonopy.interface.vasp import read_vasp_from_strings
 
 load_profile()
 

phono3py/__init__.py

@@ -33,8 +33,8 @@
 # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
-from phono3py.version import __version__  # noqa F401
-from phono3py.api_phono3py import Phono3py  # noqa F401
-from phono3py.api_jointdos import Phono3pyJointDos  # noqa F401
 from phono3py.api_isotope import Phono3pyIsotope  # noqa F401
+from phono3py.api_jointdos import Phono3pyJointDos  # noqa F401
+from phono3py.api_phono3py import Phono3py  # noqa F401
 from phono3py.cui.load import load  # noqa F401
+from phono3py.version import __version__  # noqa F401

phono3py/api_isotope.py

@@ -35,6 +35,7 @@
 
 import numpy as np
 from phonopy.units import VaspToTHz
+
 from phono3py.other.isotope import Isotope
 
 

phono3py/api_jointdos.py

@@ -34,12 +34,12 @@
 # POSSIBILITY OF SUCH DAMAGE.
 
 import numpy as np
-from phonopy.units import VaspToTHz
 from phonopy.structure.symmetry import Symmetry
-from phono3py.phonon3.joint_dos import JointDos
+from phonopy.units import VaspToTHz
-from phono3py.phonon.grid import BZGrid
 
 from phono3py.file_IO import write_joint_dos
+from phono3py.phonon3.joint_dos import JointDos
+from phono3py.phonon.grid import BZGrid
 
 
 class Phono3pyJointDos:

phono3py/api_phono3py.py

@@ -34,59 +34,61 @@
 # POSSIBILITY OF SUCH DAMAGE.
 
 import warnings
+
 import numpy as np
-from phonopy.structure.symmetry import Symmetry
+from phonopy.harmonic.displacement import (
-from phonopy.structure.cells import (
+    directions_to_displacement_dataset,
-    get_supercell,
+    get_least_displacements,
-    get_primitive,
-    guess_primitive_matrix,
-    shape_supercell_matrix,
-    get_primitive_matrix,
-)
-from phonopy.structure.atoms import PhonopyAtoms
-from phonopy.structure.dataset import get_displacements_and_forces
-from phonopy.units import VaspToTHz
-from phonopy.harmonic.force_constants import (
-    symmetrize_force_constants,
-    symmetrize_compact_force_constants,
-    set_translational_invariance,
-    set_permutation_symmetry,
 )
 from phonopy.harmonic.force_constants import get_fc2 as get_phonopy_fc2
-from phonopy.interface.fc_calculator import get_fc2
+from phonopy.harmonic.force_constants import (
-from phonopy.harmonic.displacement import (
+    set_permutation_symmetry,
-    get_least_displacements,
+    set_translational_invariance,
-    directions_to_displacement_dataset,
+    symmetrize_compact_force_constants,
+    symmetrize_force_constants,
+)
+from phonopy.interface.fc_calculator import get_fc2
+from phonopy.structure.atoms import PhonopyAtoms
+from phonopy.structure.cells import (
+    get_primitive,
+    get_primitive_matrix,
+    get_supercell,
+    guess_primitive_matrix,
+    shape_supercell_matrix,
+)
+from phonopy.structure.dataset import get_displacements_and_forces
+from phonopy.structure.symmetry import Symmetry
+from phonopy.units import VaspToTHz
+
+from phono3py.interface.fc_calculator import get_fc3
+from phono3py.interface.phono3py_yaml import Phono3pyYaml
+from phono3py.phonon3.conductivity_LBTE import get_thermal_conductivity_LBTE
+from phono3py.phonon3.conductivity_RTA import get_thermal_conductivity_RTA
+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 (
+    set_permutation_symmetry_compact_fc3,
+    set_permutation_symmetry_fc3,
+    set_translational_invariance_compact_fc3,
+    set_translational_invariance_fc3,
 )
-from phono3py.version import __version__
 from phono3py.phonon3.imag_self_energy import (
     get_imag_self_energy,
     write_imag_self_energy,
 )
+from phono3py.phonon3.interaction import Interaction
 from phono3py.phonon3.real_self_energy import (
     get_real_self_energy,
     write_real_self_energy,
 )
 from phono3py.phonon3.spectral_function import run_spectral_function
-from phono3py.phonon3.interaction import Interaction
-from phono3py.phonon3.conductivity_RTA import get_thermal_conductivity_RTA
-from phono3py.phonon3.conductivity_LBTE import get_thermal_conductivity_LBTE
-from phono3py.phonon3.displacement_fc3 import (
-    get_third_order_displacements,
-    direction_to_displacement,
-)
-from phono3py.phonon3.fc3 import (
-    set_permutation_symmetry_fc3,
-    set_permutation_symmetry_compact_fc3,
-    set_translational_invariance_fc3,
-    set_translational_invariance_compact_fc3,
-    cutoff_fc3_by_zero,
-)
-from phono3py.phonon3.fc3 import get_fc3 as get_phono3py_fc3
 from phono3py.phonon.grid import BZGrid
-from phono3py.phonon3.dataset import get_displacements_and_forces_fc3
+from phono3py.version import __version__
-from phono3py.interface.phono3py_yaml import Phono3pyYaml
-from phono3py.interface.fc_calculator import get_fc3
 
 
 class Phono3py(object):

phono3py/cui/create_force_constants.py

@@ -35,33 +35,35 @@
 
 import os
 import sys
+
 import numpy as np
+from phonopy.cui.phonopy_script import file_exists, print_error
+from phonopy.file_IO import get_dataset_type2
 from phonopy.harmonic.force_constants import (
     show_drift_force_constants,
-    symmetrize_force_constants,
     symmetrize_compact_force_constants,
+    symmetrize_force_constants,
 )
-from phonopy.file_IO import get_dataset_type2
-from phonopy.cui.phonopy_script import print_error, file_exists
 from phonopy.interface.calculator import get_default_physical_units
-from phono3py.phonon3.fc3 import show_drift_fc3
+
+from phono3py.cui.show_log import show_phono3py_force_constants_settings
 from phono3py.file_IO import (
-    parse_disp_fc3_yaml,
+    get_length_of_first_line,
     parse_disp_fc2_yaml,
+    parse_disp_fc3_yaml,
     parse_FORCES_FC2,
     parse_FORCES_FC3,
-    read_fc3_from_hdf5,
     read_fc2_from_hdf5,
-    write_fc3_to_hdf5,
+    read_fc3_from_hdf5,
     write_fc2_to_hdf5,
-    get_length_of_first_line,
+    write_fc3_to_hdf5,
 )
-from phono3py.cui.show_log import show_phono3py_force_constants_settings
+from phono3py.interface.phono3py_yaml import Phono3pyYaml
 from phono3py.phonon3.fc3 import (
     set_permutation_symmetry_fc3,
     set_translational_invariance_fc3,
+    show_drift_fc3,
 )
-from phono3py.interface.phono3py_yaml import Phono3pyYaml
 
 
 def create_phono3py_force_constants(

phono3py/cui/create_supercells.py

@@ -33,14 +33,15 @@
 # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
+from phonopy.interface.calculator import write_supercells_with_displacements
+
 from phono3py import Phono3py
-from phono3py.file_IO import write_disp_fc3_yaml, write_disp_fc2_yaml
+from phono3py.file_IO import write_disp_fc2_yaml, write_disp_fc3_yaml
 from phono3py.interface.calculator import (
     get_additional_info_to_write_fc2_supercells,
     get_additional_info_to_write_supercells,
     get_default_displacement_distance,
 )
-from phonopy.interface.calculator import write_supercells_with_displacements
 
 
 def create_phono3py_supercells(

phono3py/cui/kaccum.py

@@ -1,16 +1,21 @@
 """Phono3py kaccum command line script."""
-import sys
 import argparse
-import numpy as np
+import sys
+
 import h5py
+import numpy as np
 from phonopy.cui.settings import fracval
-from phonopy.structure.cells import get_primitive
-from phonopy.structure.symmetry import Symmetry
 from phonopy.interface.calculator import read_crystal_structure
 from phonopy.phonon.dos import NormalDistribution
-from phonopy.structure.cells import get_primitive_matrix, guess_primitive_matrix
+from phonopy.structure.cells import (
-from phono3py.phonon.grid import BZGrid, get_ir_grid_points
+    get_primitive,
+    get_primitive_matrix,
+    guess_primitive_matrix,
+)
+from phonopy.structure.symmetry import Symmetry
+
 from phono3py.other.tetrahedron_method import get_integration_weights
+from phono3py.phonon.grid import BZGrid, get_ir_grid_points
 
 epsilon = 1.0e-8
 

phono3py/cui/load.py

@@ -35,15 +35,17 @@
 
 import os
 import typing
+
 import numpy as np
-from phono3py import Phono3py
+import phonopy.cui.load_helper as load_helper
-from phono3py.interface.phono3py_yaml import Phono3pyYaml
-from phono3py.cui.create_force_constants import parse_forces, forces_in_dataset
-from phono3py.file_IO import read_fc3_from_hdf5, read_fc2_from_hdf5
-from phono3py.phonon3.fc3 import show_drift_fc3
 from phonopy.harmonic.force_constants import show_drift_force_constants
 from phonopy.interface.calculator import get_default_physical_units
-import phonopy.cui.load_helper as load_helper
+
+from phono3py import Phono3py
+from phono3py.cui.create_force_constants import forces_in_dataset, parse_forces
+from phono3py.file_IO import read_fc2_from_hdf5, read_fc3_from_hdf5
+from phono3py.interface.phono3py_yaml import Phono3pyYaml
+from phono3py.phonon3.fc3 import show_drift_fc3
 
 
 def load(

phono3py/cui/phono3py_argparse.py

@@ -34,6 +34,7 @@
 # POSSIBILITY OF SUCH DAMAGE.
 
 import sys
+
 from phonopy.cui.phonopy_argparse import fix_deprecated_option_names
 
 
@@ -41,7 +42,9 @@ def get_parser(fc_symmetry=False, is_nac=False, load_phono3py_yaml=False):
     """Return ArgumentParser instance."""
     deprecated = fix_deprecated_option_names(sys.argv)
     import argparse
+
     from phonopy.interface.calculator import add_arguments_of_calculators
+
     from phono3py.interface.calculator import calculator_info
 
     parser = argparse.ArgumentParser(description="Phono3py command-line-tool")

phono3py/cui/phono3py_script.py

@@ -34,61 +34,62 @@
 # POSSIBILITY OF SUCH DAMAGE.
 
 import sys
+
 import numpy as np
-from phonopy.file_IO import write_FORCE_SETS, parse_FORCE_SETS, is_file_phonopy_yaml
-from phonopy.units import VaspToTHz, Bohr, Hartree
 from phonopy.cui.collect_cell_info import collect_cell_info
 from phonopy.cui.create_force_sets import check_number_of_force_files
-from phonopy.interface.calculator import (
-    get_force_sets,
-    get_default_physical_units,
-    get_interface_mode,
-)
 from phonopy.cui.phonopy_argparse import show_deprecated_option_warnings
-from phonopy.phonon.band_structure import get_band_qpoints
 from phonopy.cui.phonopy_script import (
-    store_nac_params,
+    file_exists,
+    files_exist,
+    get_fc_calculator_params,
     print_end,
     print_error,
     print_error_message,
     print_version,
-    file_exists,
+    store_nac_params,
-    files_exist,
-    get_fc_calculator_params,
 )
+from phonopy.file_IO import is_file_phonopy_yaml, parse_FORCE_SETS, write_FORCE_SETS
+from phonopy.interface.calculator import (
+    get_default_physical_units,
+    get_force_sets,
+    get_interface_mode,
+)
+from phonopy.phonon.band_structure import get_band_qpoints
 from phonopy.structure.cells import isclose as cells_isclose
-from phono3py.version import __version__
+from phonopy.units import Bohr, Hartree, VaspToTHz
-from phono3py.file_IO import (
+
-    parse_disp_fc2_yaml,
+from phono3py import Phono3py, Phono3pyIsotope, Phono3pyJointDos
-    parse_disp_fc3_yaml,
+from phono3py.cui.create_force_constants import create_phono3py_force_constants
-    read_phonon_from_hdf5,
+from phono3py.cui.create_supercells import create_phono3py_supercells
-    write_phonon_to_hdf5,
-    parse_FORCES_FC2,
-    write_FORCES_FC2,
-    write_FORCES_FC3,
-    get_length_of_first_line,
-    write_fc3_to_hdf5,
-    write_fc2_to_hdf5,
-)
-from phono3py.cui.settings import Phono3pyConfParser
 from phono3py.cui.load import set_dataset_and_force_constants
-from phono3py import Phono3py, Phono3pyJointDos, Phono3pyIsotope
-from phono3py.phonon3.gruneisen import run_gruneisen_parameters
-from phono3py.phonon.grid import get_grid_point_from_address
 from phono3py.cui.phono3py_argparse import get_parser
+from phono3py.cui.settings import Phono3pyConfParser
 from phono3py.cui.show_log import (
     show_general_settings,
-    show_phono3py_settings,
     show_phono3py_cells,
+    show_phono3py_settings,
+)
+from phono3py.cui.triplets_info import show_num_triplets, write_grid_points
+from phono3py.file_IO import (
+    get_length_of_first_line,
+    parse_disp_fc2_yaml,
+    parse_disp_fc3_yaml,
+    parse_FORCES_FC2,
+    read_phonon_from_hdf5,
+    write_fc2_to_hdf5,
+    write_fc3_to_hdf5,
+    write_FORCES_FC2,
+    write_FORCES_FC3,
+    write_phonon_to_hdf5,
 )
-from phono3py.cui.triplets_info import write_grid_points, show_num_triplets
-from phono3py.cui.create_supercells import create_phono3py_supercells
-from phono3py.cui.create_force_constants import create_phono3py_force_constants
 from phono3py.interface.phono3py_yaml import (
     Phono3pyYaml,
     displacements_yaml_lines_type1,
 )
-
+from phono3py.phonon3.gruneisen import run_gruneisen_parameters
+from phono3py.phonon.grid import get_grid_point_from_address
+from phono3py.version import __version__
 
 # import logging
 # logging.basicConfig()

phono3py/cui/settings.py

@@ -34,7 +34,7 @@
 # POSSIBILITY OF SUCH DAMAGE.
 
 import numpy as np
-from phonopy.cui.settings import Settings, ConfParser, fracval
+from phonopy.cui.settings import ConfParser, Settings, fracval
 
 
 class Phono3pySettings(Settings):

phono3py/cui/show_log.py

@@ -34,9 +34,12 @@
 # POSSIBILITY OF SUCH DAMAGE.
 
 import sys
+
 import numpy as np
 from phonopy.structure.cells import print_cell
 
+from phono3py.cui.settings import Phono3pySettings
+
 
 def show_general_settings(
     settings, run_mode, phono3py, cell_filename, input_filename, output_filename
@@ -106,12 +109,11 @@ def show_phono3py_cells(phono3py, settings):
     print("-" * 76)
 
 
-def show_phono3py_force_constants_settings(settings):
+def show_phono3py_force_constants_settings(settings: Phono3pySettings):
     """Show force constants settings."""
     read_fc3 = settings.read_fc3
     read_fc2 = settings.read_fc2
     symmetrize_fc3r = settings.is_symmetrize_fc3_r or settings.fc_symmetry
-    symmetrize_fc3q = settings.is_symmetrize_fc3_q
     symmetrize_fc2 = settings.is_symmetrize_fc2 or settings.fc_symmetry
 
     print("-" * 29 + " Force constants " + "-" * 30)
@@ -132,10 +134,6 @@ def show_phono3py_force_constants_settings(settings):
             "Imposing translational and index exchange symmetry to fc3: "
             "%s" % symmetrize_fc3r
         )
-        print(
-            ("Imposing symmetry of index exchange to fc3 in reciprocal " "space: %s")
-            % symmetrize_fc3q
-        )
 
     if settings.cutoff_fc3_distance is not None:
         print("FC3 cutoff distance: %s" % settings.cutoff_fc3_distance)

phono3py/cui/triplets_info.py

@@ -34,7 +34,8 @@
 # POSSIBILITY OF SUCH DAMAGE.
 
 import numpy as np
-from phono3py.file_IO import write_ir_grid_points, write_grid_address_to_hdf5
+
+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
 

phono3py/file_IO.py

@@ -35,13 +35,15 @@
 
 import os
 import warnings
-import numpy as np
+
 import h5py
+import numpy as np
+from phonopy.cui.load_helper import read_force_constants_from_hdf5
 
 # This import is deactivated for a while.
 # from phonopy.file_IO import write_force_constants_to_hdf5
 from phonopy.file_IO import check_force_constants_indices, get_cell_from_disp_yaml
-from phonopy.cui.load_helper import read_force_constants_from_hdf5
+
 from phono3py.version import __version__
 
 

phono3py/interface/phono3py_yaml.py

@@ -33,8 +33,8 @@
 # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
-from phonopy.interface.phonopy_yaml import PhonopyYaml
 import numpy as np
+from phonopy.interface.phonopy_yaml import PhonopyYaml
 
 
 class Phono3pyYaml(PhonopyYaml):

phono3py/other/isotope.py

@@ -34,20 +34,22 @@
 # POSSIBILITY OF SUCH DAMAGE.
 
 import warnings
+
 import numpy as np
 from phonopy.harmonic.dynamical_matrix import get_dynamical_matrix
+from phonopy.phonon.tetrahedron_mesh import get_tetrahedra_frequencies
+from phonopy.structure.atoms import isotope_data
 from phonopy.structure.symmetry import Symmetry
 from phonopy.structure.tetrahedron_method import TetrahedronMethod
-from phonopy.phonon.tetrahedron_mesh import get_tetrahedra_frequencies
 from phonopy.units import VaspToTHz
-from phonopy.structure.atoms import isotope_data
+
 from phono3py.other.tetrahedron_method import (
     get_integration_weights,
     get_unique_grid_points,
 )
-from phono3py.phonon.solver import run_phonon_solver_c, run_phonon_solver_py
-from phono3py.phonon.grid import BZGrid
 from phono3py.phonon.func import gaussian
+from phono3py.phonon.grid import BZGrid
+from phono3py.phonon.solver import run_phonon_solver_c, run_phonon_solver_py
 
 
 def get_mass_variances(primitive):

phono3py/phonon/func.py

@@ -34,7 +34,7 @@
 # POSSIBILITY OF SUCH DAMAGE.
 
 import numpy as np
-from phonopy.units import THzToEv, Kb, Hbar, EV, Angstrom, THz, AMU
+from phonopy.units import AMU, EV, Angstrom, Hbar, Kb, THz, THzToEv
 
 
 def gaussian(x, sigma):

phono3py/phonon/grid.py

@@ -36,11 +36,11 @@
 import numpy as np
 from phonopy.harmonic.force_constants import similarity_transformation
 from phonopy.structure.cells import (
-    get_primitive_matrix_by_centring,
     estimate_supercell_matrix,
+    get_primitive_matrix_by_centring,
     get_reduced_bases,
 )
-from phonopy.structure.grid_points import length2mesh, extract_ir_grid_points
+from phonopy.structure.grid_points import extract_ir_grid_points, length2mesh
 
 
 class BZGrid:

phono3py/phonon/solver.py

@@ -34,8 +34,8 @@
 # POSSIBILITY OF SUCH DAMAGE.
 
 import numpy as np
-from phonopy.units import VaspToTHz
 from phonopy.structure.cells import sparse_to_dense_svecs
+from phonopy.units import VaspToTHz
 
 
 def run_phonon_solver_c(

phono3py/phonon3/collision_matrix.py

@@ -34,7 +34,8 @@
 # POSSIBILITY OF SUCH DAMAGE.
 
 import numpy as np
-from phonopy.units import THzToEv, Kb
+from phonopy.units import Kb, THzToEv
+
 from phono3py.phonon3.imag_self_energy import ImagSelfEnergy
 from phono3py.phonon3.interaction import Interaction
 

phono3py/phonon3/conductivity.py

@@ -33,19 +33,21 @@
 # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
-import warnings
 import textwrap
-from typing import Optional, List
+import warnings
+from typing import List, Optional
+
 import numpy as np
-from phonopy.phonon.group_velocity import GroupVelocity
 from phonopy.harmonic.force_constants import similarity_transformation
+from phonopy.phonon.group_velocity import GroupVelocity
 from phonopy.phonon.thermal_properties import mode_cv as get_mode_cv
-from phonopy.units import THzToEv, EV, THz, Angstrom
+from phonopy.units import EV, Angstrom, THz, THzToEv
+
 from phono3py.file_IO import write_pp_to_hdf5
-from phono3py.phonon3.triplets import get_all_triplets
-from phono3py.phonon3.interaction import Interaction
 from phono3py.other.isotope import Isotope
-from phono3py.phonon.grid import get_ir_grid_points, get_grid_points_by_rotations
+from phono3py.phonon3.interaction import Interaction
+from phono3py.phonon3.triplets import get_all_triplets
+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)

phono3py/phonon3/conductivity_LBTE.py

@@ -37,23 +37,25 @@ import sys
 import time
 import warnings
 from typing import List
+
 import numpy as np
 from phonopy.phonon.degeneracy import degenerate_sets
 from phonopy.phonon.group_velocity import GroupVelocity
+from phonopy.units import Kb, THzToEv
+
+from phono3py.file_IO import (
+    read_collision_from_hdf5,
+    read_pp_from_hdf5,
+    write_collision_eigenvalues_to_hdf5,
+    write_collision_to_hdf5,
+    write_kappa_to_hdf5,
+    write_unitary_matrix_to_hdf5,
+)
+from phono3py.phonon3.collision_matrix import CollisionMatrix
 from phono3py.phonon3.conductivity import Conductivity, all_bands_exist, unit_to_WmK
 from phono3py.phonon3.conductivity import write_pp as _write_pp
 from phono3py.phonon3.interaction import Interaction
-from phono3py.phonon3.collision_matrix import CollisionMatrix
 from phono3py.phonon.grid import get_grid_points_by_rotations
-from phono3py.file_IO import (
-    write_kappa_to_hdf5,
-    write_collision_to_hdf5,
-    read_collision_from_hdf5,
-    write_collision_eigenvalues_to_hdf5,
-    write_unitary_matrix_to_hdf5,
-    read_pp_from_hdf5,
-)
-from phonopy.units import THzToEv, Kb
 
 
 class Conductivity_LBTE(Conductivity):

phono3py/phonon3/conductivity_RTA.py

@@ -34,19 +34,21 @@
 # POSSIBILITY OF SUCH DAMAGE.
 
 import sys
+
 import numpy as np
-from phonopy.structure.tetrahedron_method import TetrahedronMethod
 from phonopy.phonon.group_velocity import GroupVelocity
+from phonopy.structure.tetrahedron_method import TetrahedronMethod
+
 from phono3py.file_IO import (
-    write_kappa_to_hdf5,
     read_gamma_from_hdf5,
-    write_gamma_detail_to_hdf5,
     read_pp_from_hdf5,
+    write_gamma_detail_to_hdf5,
+    write_kappa_to_hdf5,
 )
 from phono3py.phonon3.conductivity import Conductivity, all_bands_exist, unit_to_WmK
 from phono3py.phonon3.conductivity import write_pp as _write_pp
-from phono3py.phonon3.interaction import Interaction
 from phono3py.phonon3.imag_self_energy import ImagSelfEnergy, average_by_degeneracy
+from phono3py.phonon3.interaction import Interaction
 from phono3py.phonon3.triplets import get_all_triplets
 from phono3py.phonon.grid import get_grid_points_by_rotations
 

phono3py/phonon3/displacement_fc3.py

@@ -35,14 +35,14 @@
 
 import numpy as np
 from phonopy.harmonic.displacement import (
-    get_least_displacements,
     directions_axis,
     get_displacement,
+    get_least_displacements,
     is_minus_displacement,
 )
 from phonopy.structure.atoms import PhonopyAtoms
-from phonopy.structure.symmetry import Symmetry
 from phonopy.structure.cells import get_smallest_vectors
+from phonopy.structure.symmetry import Symmetry
 
 
 def direction_to_displacement(

phono3py/phonon3/fc3.py

@@ -33,27 +33,29 @@
 # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
-import sys
 import logging
+import sys
+
 import numpy as np
 from phonopy.harmonic.force_constants import (
-    get_fc2,
-    similarity_transformation,
     distribute_force_constants,
-    solve_force_constants,
+    get_fc2,
-    get_rotated_displacement,
-    get_positions_sent_by_rot_inv,
     get_nsym_list_and_s2pp,
-)
+    get_positions_sent_by_rot_inv,
-from phono3py.phonon3.displacement_fc3 import (
+    get_rotated_displacement,
-    get_reduced_site_symmetry,
+    similarity_transformation,
-    get_bond_symmetry,
+    solve_force_constants,
-    get_smallest_vector_of_atom_pair,
 )
 from phonopy.structure.atoms import PhonopyAtoms
-from phonopy.structure.cells import compute_all_sg_permutations, Primitive
+from phonopy.structure.cells import Primitive, compute_all_sg_permutations
 from phonopy.structure.symmetry import Symmetry
 
+from phono3py.phonon3.displacement_fc3 import (
+    get_bond_symmetry,
+    get_reduced_site_symmetry,
+    get_smallest_vector_of_atom_pair,
+)
+
 logger = logging.getLogger(__name__)
 
 

phono3py/phonon3/gruneisen.py

@@ -34,11 +34,12 @@
 # POSSIBILITY OF SUCH DAMAGE.
 
 import sys
+
 import numpy as np
 from phonopy.harmonic.dynamical_matrix import get_dynamical_matrix
-from phonopy.units import VaspToTHz
-from phonopy.structure.grid_points import get_qpoints
 from phonopy.structure.cells import sparse_to_dense_svecs
+from phonopy.structure.grid_points import get_qpoints
+from phonopy.units import VaspToTHz
 
 
 def run_gruneisen_parameters(

phono3py/phonon3/imag_self_energy.py

@@ -35,16 +35,18 @@
 
 import sys
 from typing import List, Optional
+
 import numpy as np
-from phonopy.units import Hbar, EV, THz
 from phonopy.phonon.degeneracy import degenerate_sets
-from phono3py.phonon3.interaction import Interaction
+from phonopy.units import EV, Hbar, THz
-from phono3py.phonon3.triplets import get_triplets_integration_weights
+
-from phono3py.phonon.func import bose_einstein
 from phono3py.file_IO import (
     write_gamma_detail_to_hdf5,
     write_imag_self_energy_at_grid_point,
 )
+from phono3py.phonon3.interaction import Interaction
+from phono3py.phonon3.triplets import get_triplets_integration_weights
+from phono3py.phonon.func import bose_einstein
 
 
 def get_imag_self_energy(

phono3py/phonon3/interaction.py

@@ -34,21 +34,26 @@
 # POSSIBILITY OF SUCH DAMAGE.
 
 import warnings
+
 import numpy as np
 from phonopy.harmonic.dynamical_matrix import get_dynamical_matrix
-from phonopy.structure.cells import Primitive, sparse_to_dense_svecs
+from phonopy.structure.cells import (
-from phonopy.structure.symmetry import Symmetry
+    Primitive,
-from phonopy.units import VaspToTHz, Hbar, EV, Angstrom, THz, AMU
+    compute_all_sg_permutations,
-from phonopy.structure.cells import compute_all_sg_permutations
+    sparse_to_dense_svecs,
-from phono3py.phonon.grid import (
-    get_ir_grid_points,
-    get_grid_points_by_rotations,
-    BZGrid,
 )
-from phono3py.phonon.solver import run_phonon_solver_c, run_phonon_solver_py
+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_triplets_at_q, get_nosym_triplets_at_q
+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
 
 
 class Interaction:

phono3py/phonon3/joint_dos.py

@@ -33,24 +33,25 @@
 # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
-import warnings
 import sys
+import warnings
+
 import numpy as np
-from phonopy.units import VaspToTHz
+from phonopy.harmonic.dynamical_matrix import DynamicalMatrix, get_dynamical_matrix
 from phonopy.structure.cells import Primitive
-from phonopy.harmonic.dynamical_matrix import DynamicalMatrix
+from phonopy.structure.tetrahedron_method import TetrahedronMethod
+from phonopy.units import VaspToTHz
+
+from phono3py.phonon3.imag_self_energy import get_frequency_points
 from phono3py.phonon3.triplets import (
-    get_triplets_at_q,
     get_nosym_triplets_at_q,
     get_tetrahedra_vertices,
+    get_triplets_at_q,
     get_triplets_integration_weights,
 )
-from phono3py.phonon.solver import run_phonon_solver_c
 from phono3py.phonon.func import bose_einstein
 from phono3py.phonon.grid import BZGrid
-from phono3py.phonon3.imag_self_energy import get_frequency_points
+from phono3py.phonon.solver import run_phonon_solver_c
-from phonopy.harmonic.dynamical_matrix import get_dynamical_matrix
-from phonopy.structure.tetrahedron_method import TetrahedronMethod
 
 
 class JointDos(object):

phono3py/phonon3/real_self_energy.py

@@ -34,15 +34,17 @@
 # POSSIBILITY OF SUCH DAMAGE.
 
 import sys
+
 import numpy as np
-from phonopy.units import Hbar, EV, THz
 from phonopy.phonon.degeneracy import degenerate_sets
-from phono3py.phonon.func import bose_einstein
+from phonopy.units import EV, Hbar, THz
+
 from phono3py.file_IO import (
     write_real_self_energy_at_grid_point,
     write_real_self_energy_to_hdf5,
 )
 from phono3py.phonon3.imag_self_energy import get_frequency_points
+from phono3py.phonon.func import bose_einstein
 
 
 def get_real_self_energy(

phono3py/phonon3/spectral_function.py

@@ -34,17 +34,19 @@
 # POSSIBILITY OF SUCH DAMAGE.
 
 import sys
+
 import numpy as np
-from phono3py.phonon3.imag_self_energy import (
+
-    run_ise_at_frequency_points_batch,
-    get_frequency_points,
-    ImagSelfEnergy,
-)
-from phono3py.phonon3.real_self_energy import imag_to_real
 from phono3py.file_IO import (
     write_spectral_function_at_grid_point,
     write_spectral_function_to_hdf5,
 )
+from phono3py.phonon3.imag_self_energy import (
+    ImagSelfEnergy,
+    get_frequency_points,
+    run_ise_at_frequency_points_batch,
+)
+from phono3py.phonon3.real_self_energy import imag_to_real
 
 
 def run_spectral_function(

phono3py/phonon3/triplets.py

@@ -35,6 +35,7 @@
 
 import numpy as np
 from phonopy.structure.tetrahedron_method import TetrahedronMethod
+
 from phono3py.phonon.func import gaussian
 
 

phono3py/sscha/sscha.py

@@ -42,8 +42,9 @@ Formulae implemented are based on these papers:
 """
 
 import numpy as np
-from phonopy.units import VaspToTHz
 from phonopy.harmonic.dynmat_to_fc import DynmatToForceConstants
+from phonopy.units import VaspToTHz
+
 from phono3py.phonon.func import mode_length
 
 

pyproject.toml

@@ -7,3 +7,6 @@ extend-ignore = "E203,W503"
 
 [tool.black]
 line-length = 88
+
+[tool.isort]
+profile = "black"

scripts/phono3py-coleigplot

@@ -1,10 +1,11 @@
 #!/usr/bin/env python
 
+import argparse
 import os
 import sys
+
 import h5py
 import numpy as np
-import argparse
 
 epsilon = 1.0e-8
 

scripts/phono3py-kdeplot

@@ -1,11 +1,12 @@
 #!/usr/bin/env python
 
-import numpy as np
-import h5py
-import sys
-import os
-from scipy import stats
 import argparse
+import os
+import sys
+
+import h5py
+import numpy as np
+from scipy import stats
 
 epsilon = 1.0e-8
 

setup.py

@@ -1,17 +1,18 @@
 """Phono3py setup.py."""
 import os
-import sys
-import numpy
 import platform
+import sys
 import sysconfig
 
+import numpy
+
 try:
-    from setuptools import setup, Extension
+    from setuptools import Extension, setup
 
     use_setuptools = True
     print("setuptools is used.")
 except ImportError:
-    from distutils.core import setup, Extension
+    from distutils.core import Extension, setup
 
     use_setuptools = False
     print("distutils is used.")
@@ -114,10 +115,8 @@ elif os.path.isfile("libopenblas.py"):
     # Example of libopenblas.py
     # extra_link_args_lapacke += ['-lopenblas']
 
-    from libopenblas import (
+    from libopenblas import extra_link_args_lapacke as obl_extra_link_args_lapacke
-        extra_link_args_lapacke as obl_extra_link_args_lapacke,
+    from libopenblas import include_dirs_lapacke as obl_include_dirs_lapacke
-        include_dirs_lapacke as obl_include_dirs_lapacke,
-    )
 
     extra_link_args_lapacke = obl_extra_link_args_lapacke
     include_dirs_lapacke = obl_include_dirs_lapacke

test/conftest.py

@@ -1,10 +1,11 @@
 """Pytest conftest.py."""
 import os
-import pytest
+
 import phonopy
-import phono3py
+import pytest
 from phonopy.interface.phonopy_yaml import read_cell_yaml
 
+import phono3py
 
 current_dir = os.path.dirname(os.path.abspath(__file__))
 store_dense_gp_map = True

test/cui/test_kaccum.py

@@ -1,5 +1,6 @@
 """Test for kaccum.py."""
 import numpy as np
+
 from phono3py.cui.kaccum import KappaDOS, _get_mfp
 from phono3py.phonon.grid import get_ir_grid_points
 

test/other/test_isotope.py

@@ -1,5 +1,6 @@
 """Tests for isotope scatterings."""
 import numpy as np
+
 from phono3py import Phono3pyIsotope
 
 si_pbesol_iso = [

test/phonon/test_grid.py

@@ -1,13 +1,14 @@
 """Tests for grids."""
 import numpy as np
 from phonopy.structure.tetrahedron_method import TetrahedronMethod
+
 from phono3py.phonon.grid import (
-    get_grid_point_from_address,
-    get_grid_point_from_address_py,
     BZGrid,
-    _get_grid_points_by_rotations,
     _get_grid_points_by_bz_rotations_c,
     _get_grid_points_by_bz_rotations_py,
+    _get_grid_points_by_rotations,
+    get_grid_point_from_address,
+    get_grid_point_from_address_py,
 )
 
 

test/phonon3/test_displacements.py

@@ -1,8 +1,8 @@
 """Tests of displacements.py."""
-import phono3py
 import numpy as np
-from phono3py.phonon3.displacement_fc3 import get_smallest_vector_of_atom_pair
 
+import phono3py
+from phono3py.phonon3.displacement_fc3 import get_smallest_vector_of_atom_pair
 
 distances_NaCl = [
     0.0000000,

test/phonon3/test_fc3.py

@@ -1,5 +1,6 @@
 """Tests for fc3."""
 import numpy as np
+
 from phono3py.phonon3.fc3 import cutoff_fc3_by_zero
 
 

test/phonon3/test_interaction.py

@@ -1,6 +1,7 @@
 """Test Interaction class."""
-import pytest
 import numpy as np
+import pytest
+
 from phono3py.phonon3.interaction import Interaction
 
 itr_RTA_Si = [

test/phonon3/test_joint_dos.py

@@ -1,5 +1,6 @@
 """Tests for joint-density-of-states."""
 import numpy as np
+
 from phono3py.api_jointdos import Phono3pyJointDos
 
 si_freq_points = [

test/phonon3/test_real_self_energy.py

@@ -1,5 +1,6 @@
 """Test for real_self_energy.py."""
 import numpy as np
+
 from phono3py.phonon3.real_self_energy import ImagToReal
 
 si_pbesol_Delta = [

test/phonon3/test_spectral_function.py

@@ -1,5 +1,6 @@
 """Test spectral_function.py."""
 import numpy as np
+
 from phono3py.phonon3.spectral_function import SpectralFunction
 
 shifts = [

test/sscha/test_sscha.py

@@ -1,14 +1,15 @@
 """Tests for SSCHA routines."""
-import pytest
 import numpy as np
+import pytest
+from phonopy.phonon.qpoints import QpointsPhonon
+from phonopy.phonon.random_displacements import RandomDisplacements
+
 from phono3py.sscha.sscha import (
     DispCorrMatrix,
     DispCorrMatrixMesh,
     SupercellPhonon,
     ThirdOrderFC,
 )
-from phonopy.phonon.qpoints import QpointsPhonon
-from phonopy.phonon.random_displacements import RandomDisplacements
 
 try:
     ModuleNotFoundError