[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

doc/conf.py

@@ -1,4 +1,5 @@
 """Sphinx phono3py configuration file."""
+
 #
 # phono3py documentation build configuration file, created by
 # sphinx-quickstart on Wed Jun 26 13:13:14 2013.

example/Si-PBEsol/Si.py

@@ -1,4 +1,5 @@
 """Example to run thermal conductivity of Si."""
+
 import numpy as np
 from phonopy.interface.vasp import read_vasp
 

example/zb-ZnTe-PBEsol/launch_phono3py_ZnTe_PBEsol_222.py

@@ -1,4 +1,5 @@
 """Launch script of ZnTe AiiDA calculation using aiida-phononpy."""
+
 from aiida.engine import submit
 from aiida.manage.configuration import load_profile
 from aiida.orm import Bool, Float, Str

phono3py/__init__.py

@@ -1,4 +1,5 @@
 """Shortcuts to important classes, methods, and variables."""
+
 # Copyright (C) 2019 Atsushi Togo
 # All rights reserved.
 #

phono3py/api_isotope.py

@@ -1,4 +1,5 @@
 """API for isotope scattering."""
+
 # Copyright (C) 2019 Atsushi Togo
 # All rights reserved.
 #

phono3py/api_jointdos.py

@@ -1,4 +1,5 @@
 """API for joint-density-of-states calculation."""
+
 # Copyright (C) 2019 Atsushi Togo
 # All rights reserved.
 #

phono3py/api_phono3py.py

@@ -1,4 +1,5 @@
 """Phono3py main class."""
+
 # Copyright (C) 2016 Atsushi Togo
 # All rights reserved.
 #

phono3py/conductivity/base.py

@@ -1,4 +1,5 @@
 """Thermal conductivity base class."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phono3py/conductivity/direct_solution.py

@@ -1,4 +1,5 @@
 """Calculate lattice thermal conductivity by direct solution."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #
@@ -517,9 +518,9 @@ 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."""

phono3py/conductivity/kubo.py

@@ -1,4 +1,5 @@
 """Kubo thermal conductivity base class."""
+
 # Copyright (C) 2022 Atsushi Togo
 # All rights reserved.
 #

phono3py/conductivity/rta.py

@@ -1,4 +1,5 @@
 """Lattice thermal conductivity calculation with RTA."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #
@@ -298,9 +299,9 @@ 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.

phono3py/conductivity/utils.py

@@ -1,4 +1,5 @@
 """Utilities for lattice thermal conductivity calculation."""
+
 # Copyright (C) 2022 Atsushi Togo
 # All rights reserved.
 #

phono3py/conductivity/wigner.py

@@ -1,4 +1,5 @@
 """Wigner thermal conductivity base class."""
+
 # Copyright (C) 2022 Michele Simoncelli
 # All rights reserved.
 #

phono3py/cui/create_force_constants.py

@@ -1,4 +1,5 @@
 """Force constants calculation utilities for command line user interface."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phono3py/cui/create_supercells.py

@@ -1,4 +1,5 @@
 """Utilities of main CUI script."""
+
 # Copyright (C) 2015 Atsushi Togo
 # All rights reserved.
 #

phono3py/cui/kaccum_script.py

@@ -1,4 +1,5 @@
 """Phono3py kaccum command line script."""
+
 import argparse
 import sys
 

phono3py/cui/load.py

@@ -1,4 +1,5 @@
 """Phono3py loader."""
+
 # Copyright (C) 2019 Atsushi Togo
 # All rights reserved.
 #

phono3py/cui/phono3py_argparse.py

@@ -1,4 +1,5 @@
 """Phono3py command option argument parser."""
+
 # Copyright (C) 2015 Atsushi Togo
 # All rights reserved.
 #

phono3py/cui/phono3py_script.py

@@ -1,4 +1,5 @@
 """Phono3py main command line script."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phono3py/cui/settings.py

@@ -1,4 +1,5 @@
 """Phono3py command option and conf file parser."""
+
 # Copyright (C) 2015 Atsushi Togo
 # All rights reserved.
 #

phono3py/cui/show_log.py

@@ -1,4 +1,5 @@
 """Utilities to show various logs for main CUI script."""
+
 # Copyright (C) 2015 Atsushi Togo
 # All rights reserved.
 #

phono3py/cui/triplets_info.py

@@ -1,4 +1,5 @@
 """Show and write triplets information."""
+
 # Copyright (C) 2015 Atsushi Togo
 # All rights reserved.
 #

phono3py/file_IO.py

@@ -1,4 +1,5 @@
 """File I/O methods."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phono3py/interface/alm.py

@@ -1,4 +1,5 @@
 """ALM interface for force constants calculation."""
+
 # Copyright (C) 2016 Atsushi Togo
 # All rights reserved.
 #

phono3py/interface/calculator.py

@@ -1,4 +1,5 @@
 """Utilities of calculator interfaces."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phono3py/interface/fc_calculator.py

@@ -1,4 +1,5 @@
 """Interfaces for force constants calculators."""
+
 # Copyright (C) 2019 Atsushi Togo
 # All rights reserved.
 #

phono3py/interface/phono3py_yaml.py

@@ -1,4 +1,5 @@
 """phono3py_yaml reader and writer."""
+
 # Copyright (C) 2016 Atsushi Togo
 # All rights reserved.
 #

phono3py/other/isotope.py

@@ -1,4 +1,5 @@
 """Isotope scattering calculation."""
+
 # Copyright (C) 2015 Atsushi Togo
 # All rights reserved.
 #

phono3py/other/kaccum.py

@@ -1,4 +1,5 @@
 """Calculated accumulated property with respect to other property."""
+
 from typing import Optional
 
 import numpy as np

phono3py/other/tetrahedron_method.py

@@ -1,4 +1,5 @@
 """Tetrahedron method python wrapper."""
+
 # Copyright (C) 2021 Atsushi Togo
 # All rights reserved.
 #

phono3py/phonon/func.py

@@ -1,4 +1,5 @@
 """Mathematical functions."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phono3py/phonon/grid.py

@@ -1,4 +1,5 @@
 """Regular grid tools."""
+
 # Copyright (C) 2021 Atsushi Togo
 # All rights reserved.
 #

phono3py/phonon/group_velocity_matrix.py

@@ -1,4 +1,5 @@
 """Calculate group velocity matrix."""
+
 # Copyright (C) 2021 Atsushi Togo
 # All rights reserved.
 #

phono3py/phonon/heat_capacity_matrix.py

@@ -1,4 +1,5 @@
 """Calculate group velocity matrix."""
+
 # Copyright (C) 2021 Atsushi Togo
 # All rights reserved.
 #

phono3py/phonon/solver.py

@@ -1,4 +1,5 @@
 """Create dynamical matrix and solve harmonic phonons on grid."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phono3py/phonon/velocity_operator.py

@@ -1,4 +1,5 @@
 """Velocity operator of Simoncelli, Marzari, and Mauri."""
+
 # Copyright (C) 2013 Atsushi Togo
 # All rights reserved.
 #

phono3py/phonon3/collision_matrix.py

@@ -1,4 +1,5 @@
 """Calculate collision matrix of direct solution of LBTE."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phono3py/phonon3/dataset.py

@@ -1,4 +1,5 @@
 """Parse displacement dataset."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phono3py/phonon3/displacement_fc3.py

@@ -1,4 +1,5 @@
 """Procedures to handle atomic displacements for fc3."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phono3py/phonon3/fc3.py

@@ -1,4 +1,5 @@
 """Calculate fc3."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phono3py/phonon3/gruneisen.py

@@ -1,4 +1,5 @@
 """Calculation of mode Grueneisen parameters from fc3."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phono3py/phonon3/imag_self_energy.py

@@ -1,4 +1,5 @@
 """Calculation of imaginary-part of self-energy of bubble diagram."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phono3py/phonon3/interaction.py

@@ -1,4 +1,5 @@
 """Calculate ph-ph interaction and phonons on grid."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phono3py/phonon3/joint_dos.py

@@ -1,4 +1,5 @@
 """Joint-density of states calculation."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phono3py/phonon3/real_self_energy.py

@@ -1,4 +1,5 @@
 """Calculate real-part of self-energy of bubble diagram."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phono3py/phonon3/real_to_reciprocal.py

@@ -1,4 +1,5 @@
 """Transform fc3 in real space to reciprocal space."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phono3py/phonon3/reciprocal_to_normal.py

@@ -1,4 +1,5 @@
 """Transform fc3 in reciprocal space to phonon space."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phono3py/phonon3/spectral_function.py

@@ -1,4 +1,5 @@
 """Calculate spectral function due to bubble diagram."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phono3py/phonon3/triplets.py

@@ -1,4 +1,5 @@
 """Utilities to handle q-point triplets."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phono3py/version.py

@@ -1,4 +1,5 @@
 """Define phono3py version."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

setup.py

@@ -7,6 +7,7 @@ To fully customize using site.cfg,
 set PHONO3PY_USE_CMAKE=false to avoid running cmake.
 
 """
+
 import os
 import pathlib
 import shutil

test/api/test_api_phono3py.py

@@ -1,4 +1,5 @@
 """Tests of Phono3py API."""
+
 from pathlib import Path
 
 from phono3py import Phono3py

test/conductivity/test_kappa_LBTE.py

@@ -1,4 +1,5 @@
 """Tests for direct solution of LBTE."""
+
 import numpy as np
 
 from phono3py.api_phono3py import Phono3py

test/conductivity/test_kappa_LBTE_Wigner.py

@@ -1,4 +1,5 @@
 """Tests for direct solution of LBTE."""
+
 import numpy as np
 import pytest
 

test/conductivity/test_kappa_RTA.py

@@ -1,4 +1,5 @@
 """Test for Conductivity_RTA.py."""
+
 import itertools
 
 import numpy as np

test/conductivity/test_kappa_RTA_Wigner.py

@@ -1,4 +1,5 @@
 """Test for Conductivity_RTA.py."""
+
 import itertools
 
 import numpy as np

test/conftest.py

@@ -1,4 +1,5 @@
 """Pytest conftest.py."""
+
 from pathlib import Path
 
 import numpy as np

test/cui/test_phono3py_load_script.py

@@ -1,4 +1,5 @@
 """Tests of Phono3py API."""
+
 from __future__ import annotations
 
 import os

test/interface/test_phono3py_yaml.py

@@ -1,4 +1,5 @@
 """Tests of PhonopyYaml."""
+
 from io import StringIO
 from pathlib import Path
 

test/other/test_isotope.py

@@ -1,4 +1,5 @@
 """Tests for isotope scatterings."""
+
 import numpy as np
 import pytest
 

test/other/test_kaccum.py

@@ -1,4 +1,5 @@
 """Test for kaccum.py."""
+
 import numpy as np
 
 from phono3py import Phono3py

test/phonon/test_grid.py

@@ -1,4 +1,5 @@
 """Tests for grids."""
+
 from __future__ import annotations
 
 import numpy as np

test/phonon/test_velocity_operator.py

@@ -1,4 +1,5 @@
 """Tests for velocity operator calculation."""
+
 import numpy as np
 from phonopy import Phonopy
 from phonopy.units import THzToCm, VaspToTHz

test/phonon3/test_displacements.py

@@ -1,4 +1,5 @@
 """Tests of displacements.py."""
+
 import numpy as np
 
 import phono3py

test/phonon3/test_fc3.py

@@ -1,4 +1,5 @@
 """Tests for fc3."""
+
 import numpy as np
 import pytest
 

test/phonon3/test_imag_self_energy.py

@@ -1,4 +1,5 @@
 """Test for imag_free_energy.py."""
+
 import numpy as np
 import pytest
 

test/phonon3/test_interaction.py

@@ -1,4 +1,5 @@
 """Test Interaction class."""
+
 from __future__ import annotations
 
 from collections.abc import Sequence

test/phonon3/test_joint_dos.py

@@ -1,4 +1,5 @@
 """Tests for joint-density-of-states."""
+
 import numpy as np
 import pytest
 

test/phonon3/test_real_self_energy.py

@@ -1,4 +1,5 @@
 """Test for real_self_energy.py."""
+
 import numpy as np
 
 from phono3py import Phono3py

test/phonon3/test_spectral_function.py

@@ -1,4 +1,5 @@
 """Test spectral_function.py."""
+
 import numpy as np
 import pytest
 

test/phonon3/test_triplets.py

@@ -1,4 +1,5 @@
 """Test for triplets.py."""
+
 import numpy as np
 import pytest
 from phonopy import Phonopy

test/sscha/test_sscha.py

@@ -1,4 +1,5 @@
 """Tests for SSCHA routines."""
+
 import numpy as np
 import pytest
 from phonopy.phonon.qpoints import QpointsPhonon