Merge pull request #330 from phonopy/pre-commit-ci-update-config

[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -35,7 +35,7 @@ repos:
     - "--ignore=E203,W503,E501"
 
 - repo: https://github.com/psf/black
-  rev: 23.12.1
+  rev: 24.1.1
   hooks:
   - id: black
     args:

doc/conf.py

@@ -1,4 +1,5 @@
 """Sphinx configuration of phonopy documentation."""
+
 # -*- coding: utf-8 -*-
 #
 # phonopy documentation build configuration file, created by

example/Al-QHA/Al-QHA.py

@@ -1,4 +1,5 @@
 """Example of QHA calculation by Al."""
+
 import numpy as np
 import yaml
 from yaml import CLoader as Loader

example/Al2O3/Al2O3.py

@@ -1,4 +1,5 @@
 """Example by corundum Al2O3."""
+
 import numpy as np
 
 import phonopy

example/MgB2/MgB2.py

@@ -1,4 +1,5 @@
 """Example of calculation of irreps of MgB2."""
+
 import numpy as np
 
 import phonopy

example/NaCl/NaCl-band-gv.py

@@ -1,4 +1,5 @@
 """Example of band structure and group velocity calculation by NaCl."""
+
 from typing import List
 
 import numpy as np

example/NaCl/NaCl-band.py

@@ -1,4 +1,5 @@
 """NaCl band structure calculation example."""
+
 import phonopy
 from phonopy.phonon.band_structure import get_band_qpoints
 

example/NaCl/NaCl-gv.py

@@ -1,4 +1,5 @@
 """Group velocity example by NaCl."""
+
 import matplotlib.pyplot as plt
 import numpy as np
 

example/NaCl/NaCl-read_write_fc.py

@@ -1,4 +1,5 @@
 """Example to read and write FORCE_CONSTANTS file."""
+
 import phonopy
 from phonopy.file_IO import parse_FORCE_CONSTANTS, write_FORCE_CONSTANTS
 

example/NaCl/NaCl-yaml.py

@@ -1,4 +1,5 @@
 """Example to obtain PhonopyYaml instance."""
+
 import phonopy
 from phonopy.interface.phonopy_yaml import PhonopyYaml
 

example/NaCl/NaCl.py

@@ -1,4 +1,5 @@
 """Example of NaCl calculation."""
+
 from typing import List
 
 import numpy as np

example/Si-QHA/Si.py

@@ -1,4 +1,5 @@
 """QHA example of Si."""
+
 import tarfile
 
 import matplotlib.pyplot as plt

example/Si-gruneisen/Si-gruneisen.py

@@ -1,4 +1,5 @@
 """Example to calculate mode Grueneisen parameters."""
+
 from typing import List
 
 import numpy as np

example/Si-lammps/generate_displacements.py

@@ -1,4 +1,5 @@
 """A script to generate supercells with displacements for LAMMPS."""
+
 import phonopy
 from phonopy.interface.calculator import write_supercells_with_displacements
 from phonopy.interface.phonopy_yaml import read_cell_yaml

phonopy/__init__.py

@@ -1,4 +1,5 @@
 """Phonon calculation code: Phonopy."""
+
 # Copyright (C) 2015 Atsushi Togo
 # All rights reserved.
 #

phonopy/api_gruneisen.py

@@ -1,4 +1,5 @@
 """API of mode Grueneisen parameter calculation."""
+
 # Copyright (C) 2015 Atsushi Togo
 # All rights reserved.
 #

phonopy/api_phonopy.py

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

phonopy/api_qha.py

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

phonopy/cui/__init__.py

@@ -1,4 +1,5 @@
 """Routines for command user interface."""
+
 # Copyright (C) 2021 Atsushi Togo
 # All rights reserved.
 #

phonopy/cui/collect_cell_info.py

@@ -1,4 +1,5 @@
 """Routines to collect crystal structure information."""
+
 # Copyright (C) 2018 Atsushi Togo
 # All rights reserved.
 #

phonopy/cui/create_force_sets.py

@@ -1,4 +1,5 @@
 """Utilities to create force sets for main CUI script."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phonopy/cui/load.py

@@ -1,4 +1,5 @@
 """Phonopy loader."""
+
 # Copyright (C) 2018 Atsushi Togo
 # All rights reserved.
 #

phonopy/cui/load_helper.py

@@ -1,4 +1,5 @@
 """Helper methods of phonopy loader."""
+
 # Copyright (C) 2018 Atsushi Togo
 # All rights reserved.
 #

phonopy/cui/phonopy_argparse.py

@@ -1,4 +1,5 @@
 """Phonopy command line argument parser."""
+
 # Copyright (C) 2016 Atsushi Togo
 # All rights reserved.
 #

phonopy/cui/phonopy_script.py

@@ -1,4 +1,5 @@
 """Phonopy command user interface."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phonopy/cui/settings.py

@@ -1,4 +1,5 @@
 """Phonopy input and command option tools."""
+
 # Copyright (C) 2011 Atsushi Togo
 # All rights reserved.
 #
@@ -1639,9 +1640,9 @@ class PhonopyConfParser(ConfParser):
 
         if "rd_temperature" in arg_list:
             if self._args.rd_temperature is not None:
-                self._confs[
-                    "random_displacement_temperature"
-                ] = self._args.rd_temperature
+                self._confs["random_displacement_temperature"] = (
+                    self._args.rd_temperature
+                )
 
         if "temperature" in arg_list:
             if self._args.temperature is not None:
@@ -1660,11 +1661,7 @@ class PhonopyConfParser(ConfParser):
         if "random_seed" in arg_list:
             if self._args.random_seed:
                 seed = self._args.random_seed
-                if (
-                    np.issubdtype(type(seed), np.integer)
-                    and seed >= 0
-                    and seed < 2**32
-                ):
+                if np.issubdtype(type(seed), np.integer) and seed >= 0 and seed < 2**32:
                     self._confs["random_seed"] = seed
 
         if "include_fc" in arg_list:

phonopy/cui/show_symmetry.py

@@ -1,4 +1,5 @@
 """Show symmetry information invoked by --symmetry command option."""
+
 # Copyright (C) 2011 Atsushi Togo
 # All rights reserved.
 #

phonopy/exception.py

@@ -1,4 +1,5 @@
 """Phonopy exceptions."""
+
 # Copyright (C) 2022 Atsushi Togo
 # All rights reserved.
 #

phonopy/file_IO.py

@@ -1,4 +1,5 @@
 """File I/O related routines."""
+
 # Copyright (C) 2011 Atsushi Togo
 # All rights reserved.
 #

phonopy/gruneisen/__init__.py

@@ -1,4 +1,5 @@
 """Mode Grueneisen paramater calculation."""
+
 # Copyright (C) 2017 Atsushi Togo
 # All rights reserved.
 #

phonopy/gruneisen/band_structure.py

@@ -1,4 +1,5 @@
 """Mode Grueneisen parameter band structure calculation."""
+
 # Copyright (C) 2012 Atsushi Togo
 # All rights reserved.
 #

phonopy/gruneisen/core.py

@@ -1,4 +1,5 @@
 """Mode Grueneisen parameter calculation."""
+
 # Copyright (C) 2012 Atsushi Togo
 # All rights reserved.
 #

phonopy/gruneisen/mesh.py

@@ -1,4 +1,5 @@
 """Mode Grueneisen parameters calculation on sampling mesh."""
+
 # Copyright (C) 2012 Atsushi Togo
 # All rights reserved.
 #

phonopy/harmonic/__init__.py

@@ -1,4 +1,5 @@
 """Routines of pre-phonon calculations."""
+
 # Copyright (C) 2021 Atsushi Togo
 # All rights reserved.
 #

phonopy/harmonic/derivative_dynmat.py

@@ -1,4 +1,5 @@
 """Calculation of derivative of dynamical matrix with respect to q."""
+
 # Copyright (C) 2013 Atsushi Togo
 # All rights reserved.
 #

phonopy/harmonic/displacement.py

@@ -1,4 +1,5 @@
 """Routines to handle displacements in supercells."""
+
 # Copyright (C) 2011 Atsushi Togo
 # All rights reserved.
 #

phonopy/harmonic/dynmat_to_fc.py

@@ -1,4 +1,5 @@
 """Transform dynamical matrix to force constants."""
+
 # Copyright (C) 2014 Atsushi Togo
 # All rights reserved.
 #

phonopy/harmonic/force_constants.py

@@ -1,4 +1,5 @@
 """Force constants calculation."""
+
 # Copyright (C) 2011 Atsushi Togo
 # All rights reserved.
 #

phonopy/interface/__init__.py

@@ -1,4 +1,5 @@
 """Routines for user and calculator interfaces to phonopy."""
+
 # Copyright (C) 2019 Atsushi Togo
 # All rights reserved.
 #

phonopy/interface/abacus.py

@@ -1,4 +1,5 @@
 """ABACUS calculator interface."""
+
 # Copyright (C) 2022 Yuyang Ji
 # All rights reserved.
 #

phonopy/interface/abinit.py

@@ -1,4 +1,5 @@
 """Abinit calculator interface."""
+
 # Copyright (C) 2014 Atsushi Togo
 # All rights reserved.
 #

phonopy/interface/aims.py

@@ -1,4 +1,5 @@
 """FHIaims calculator interface."""
+
 # FHIaims.py - IO routines for phonopy-FHI-aims
 # methods compatible with the corresponding ones from ase.io.aims
 # only minimal subset of functionality required within phonopy context is implemented

phonopy/interface/alm.py

@@ -1,4 +1,5 @@
 """ALM force constants interface."""
+
 # Copyright (C) 2018 Atsushi Togo
 # All rights reserved.
 #

phonopy/interface/calculator.py

@@ -1,4 +1,5 @@
 """Routines to handle various calculator interfaces."""
+
 # Copyright (C) 2014 Atsushi Togo
 # All rights reserved.
 #

phonopy/interface/castep.py

@@ -1,4 +1,5 @@
 """CASTEP calculator interface."""
+
 # Copyright (C) 2014 Atsushi Togo
 # All rights reserved.
 #

phonopy/interface/cif.py

@@ -1,4 +1,5 @@
 """Tests for CIF tools."""
+
 # Copyright (C) 2016 Atsushi Togo
 # All rights reserved.
 #

phonopy/interface/cp2k.py

@@ -1,4 +1,5 @@
 """CP2K calculator interface."""
+
 # vim: set fileencoding=utf-8 :
 # Copyright (C) 2017-2019 Tiziano Müller
 # All rights reserved.

phonopy/interface/crystal.py

@@ -1,4 +1,5 @@
 """CRYSTAL calculator interface."""
+
 # Copyright (C) 2016 Antti J. Karttunen (antti.j.karttunen@iki.fi)
 # All rights reserved.
 #

phonopy/interface/dftbp.py

@@ -1,4 +1,5 @@
 """DFTB+ calculator interface."""
+
 # Copyright (C) 2015 Atsushi Togo
 # All rights reserved.
 #

phonopy/interface/elk.py

@@ -1,4 +1,5 @@
 """Elk calculator interface."""
+
 # Copyright (C) 2015 Atsushi Togo
 # All rights reserved.
 #

phonopy/interface/fc_calculator.py

@@ -1,4 +1,5 @@
 """Force constants calculator interface."""
+
 # Copyright (C) 2019 Atsushi Togo
 # All rights reserved.
 #

phonopy/interface/fleur.py

@@ -1,4 +1,5 @@
 """Fleur calculator interface."""
+
 # Copyright (C) 2021 Alexander Neukirchen
 # All rights reserved.
 #

phonopy/interface/hiphive_interface.py

@@ -1,4 +1,5 @@
 """hiPhive force constants calculator interface."""
+
 # Copyright (C) 2018 Atsushi Togo
 # All rights reserved.
 #

phonopy/interface/lammps.py

@@ -1,4 +1,5 @@
 """LAMMPS calculator interface."""
+
 # Copyright (C) 2023 Atsushi Togo
 # All rights reserved.
 #

phonopy/interface/phonopy_yaml.py

@@ -1,4 +1,5 @@
 """phonopy.yaml reader and writer."""
+
 # Copyright (C) 2018 Atsushi Togo
 # All rights reserved.
 #

phonopy/interface/qe.py

@@ -1,4 +1,5 @@
 """QE calculator interface."""
+
 # Copyright (C) 2014 Atsushi Togo
 # All rights reserved.
 #

phonopy/interface/siesta.py

@@ -1,4 +1,5 @@
 """SIESTA calculator interface."""
+
 # Copyright (C) 2015 Henrique Pereira Coutada Miranda
 # All rights reserved.
 #

phonopy/interface/turbomole.py

@@ -1,4 +1,5 @@
 """CRYSTAL calculator interface."""
+
 # Copyright (C) 2019 Antti J. Karttunen (antti.j.karttunen@iki.fi)
 # All rights reserved.
 #

phonopy/interface/vasp.py

@@ -1,4 +1,5 @@
 """VASP calculator interface."""
+
 # Copyright (C) 2011 Atsushi Togo
 # All rights reserved.
 #

phonopy/interface/wien2k.py

@@ -1,4 +1,5 @@
 """Wien2k calculator interface."""
+
 # Copyright (C) 2011 Atsushi Togo
 # All rights reserved.
 #

phonopy/phonon/__init__.py

@@ -1,4 +1,5 @@
 """Routines of phonon and post-phonon calculations."""
+
 # Copyright (C) 2021 Atsushi Togo
 # All rights reserved.
 #

phonopy/phonon/animation.py

@@ -1,4 +1,5 @@
 """Convert phonon results to animation formats."""
+
 # Copyright (C) 2011 Atsushi Togo
 # All rights reserved.
 #

phonopy/phonon/character_table.py

@@ -1,4 +1,5 @@
 """Character table datasets of point groups."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phonopy/phonon/degeneracy.py

@@ -1,4 +1,5 @@
 """Utility routines to handle degeneracy."""
+
 # Copyright (C) 2014 Atsushi Togo
 # All rights reserved.
 #

phonopy/phonon/dos.py

@@ -1,4 +1,5 @@
 """Calculation of density of states."""
+
 # Copyright (C) 2011 Atsushi Togo
 # All rights reserved.
 #

phonopy/phonon/group_velocity.py

@@ -1,4 +1,5 @@
 """Group velocity calculation."""
+
 # Copyright (C) 2013 Atsushi Togo
 # All rights reserved.
 #

phonopy/phonon/irreps.py

@@ -1,4 +1,5 @@
 """Calculate irreducible representation from eigenvectors."""
+
 # Copyright (C) 2011 Atsushi Togo
 # All rights reserved.
 #

phonopy/phonon/mesh.py

@@ -1,4 +1,5 @@
 """Phonon calculation on sampling mesh."""
+
 # Copyright (C) 2011 Atsushi Togo
 # All rights reserved.
 #

phonopy/phonon/modulation.py

@@ -1,4 +1,5 @@
 """Create atomic displacements."""
+
 # Copyright (C) 2011 Atsushi Togo
 # All rights reserved.
 #

phonopy/phonon/moment.py

@@ -1,4 +1,5 @@
 """Calculate phonon state moments."""
+
 # Copyright (C) 2016 Atsushi Togo
 # All rights reserved.
 #

phonopy/phonon/qpoints.py

@@ -1,4 +1,5 @@
 """Phonon calculation at specific q-points."""
+
 # Copyright (C) 2011 Atsushi Togo
 # All rights reserved.
 #

phonopy/phonon/random_displacements.py

@@ -1,4 +1,5 @@
 """Calculate random displacements from phonons at finite temperatures."""
+
 # Copyright (C) 2018 Atsushi Togo
 # All rights reserved.
 #

phonopy/phonon/tetrahedron_mesh.py

@@ -1,4 +1,5 @@
 """Linear tetrahedron method on regular grid."""
+
 # copyright (C) 2013 Atsushi Togo
 # All rights reserved.
 #

phonopy/phonon/thermal_displacement.py

@@ -1,4 +1,5 @@
 """Calculations of thermal displacements."""
+
 # Copyright (C) 2011 Atsushi Togo
 # All rights reserved.
 #

phonopy/phonon/thermal_properties.py

@@ -1,4 +1,5 @@
 """Phonon thermal properties at constant volume."""
+
 # Copyright (C) 2011 Atsushi Togo
 # All rights reserved.
 #

phonopy/qha/__init__.py

@@ -1,4 +1,5 @@
 """Quasi harmonic approximation."""
+
 # Copyright (C) 2012 Atsushi Togo
 # All rights reserved.
 #

phonopy/qha/core.py

@@ -1,4 +1,5 @@
 """Core routines for QHA."""
+
 # Copyright (C) 2012 Atsushi Togo
 # All rights reserved.
 #
@@ -1123,9 +1124,7 @@ class QHA:
                     msg += ["At least 5 volume points are needed for the fitting."]
                 raise RuntimeError("\n".join(msg))
 
-            dsdv_t = np.dot(
-                parameters[:4], np.array([4 * x**3, 3 * x**2, 2 * x, 1])
-            )
+            dsdv_t = np.dot(parameters[:4], np.array([4 * x**3, 3 * x**2, 2 * x, 1]))
             self._volume_entropy_parameters.append(parameters)
 
             try:

phonopy/qha/electron.py

@@ -1,4 +1,5 @@
 """Calculation of free energy of one-electronic states."""
+
 # Copyright (C) 2018 Atsushi Togo
 # All rights reserved.
 #

phonopy/qha/eos.py

@@ -1,4 +1,5 @@
 """Equation of states and fitting routine."""
+
 # Copyright (C) 2012 Atsushi Togo
 # All rights reserved.
 #
@@ -80,11 +81,7 @@ def get_eos(eos):
         x = (v / p[3]) ** (1.0 / 3)
         xi = 3.0 / 2 * (p[2] - 1)
         return p[0] + (
-            9
-            * p[1]
-            * p[3]
-            / (xi**2)
-            * (1 + (xi * (1 - x) - 1) * np.exp(xi * (1 - x)))
+            9 * p[1] * p[3] / (xi**2) * (1 + (xi * (1 - x) - 1) * np.exp(xi * (1 - x)))
         )
 
     if eos == "murnaghan":

phonopy/spectrum/__init__.py

@@ -1,4 +1,5 @@
 """Routines to calculate power spectrum from MD data."""
+
 # Copyright (C) 2021 Atsushi Togo
 # All rights reserved.
 #

phonopy/spectrum/dynamic_structure_factor.py

@@ -1,4 +1,5 @@
 """Calculate dynamic structure factor at harmonic level."""
+
 # Copyright (C) 2016 Atsushi Togo
 # All rights reserved.
 #

phonopy/spectrum/velocity.py

@@ -1,4 +1,5 @@
 """Routines to analyze MD velocity data."""
+
 # Copyright (C) 2016 Atsushi Togo
 # All rights reserved.
 #

phonopy/structure/__init__.py

@@ -1,4 +1,5 @@
 """Crystal structure routines in direct and reciprocal spaces."""
+
 # Copyright (C) 2021 Atsushi Togo
 # All rights reserved.
 #

phonopy/structure/atoms.py

@@ -1,4 +1,5 @@
 """PhonopyAtoms class and routines related to atoms."""
+
 # Copyright (C) 2011 Atsushi Togo
 # All rights reserved.
 #

phonopy/structure/brillouin_zone.py

@@ -1,4 +1,5 @@
 """Use first Brillouin zone (Wigner–Seitz cell) to locate q-points."""
+
 # Copyright (C) 2013 Atsushi Togo
 # All rights reserved.
 #

phonopy/structure/cells.py

@@ -1,4 +1,5 @@
 """Primitive cell and supercell, and related utilities."""
+
 # Copyright (C) 2011 Atsushi Togo
 # All rights reserved.
 #

phonopy/structure/dataset.py

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

phonopy/structure/snf.py

@@ -1,4 +1,5 @@
 """Calculation of Smith normal form of 3x3 matrix."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phonopy/structure/symmetry.py

@@ -1,4 +1,5 @@
 """Crystal symmetry routines."""
+
 # Copyright (C) 2011 Atsushi Togo
 # All rights reserved.
 #

phonopy/structure/tetrahedron_method.py

@@ -1,4 +1,5 @@
 """Core routine of linear tetrahedon method on regular grid."""
+
 # Copyright (C) 2013 Atsushi Togo
 # All rights reserved.
 #

phonopy/unfolding/__init__.py

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

phonopy/unfolding/core.py

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

phonopy/units.py

@@ -1,4 +1,5 @@
 """Collection of physical units."""
+
 # Copyright (C) 2011 Atsushi Togo
 # All rights reserved.
 #

phonopy/utils.py

@@ -1,4 +1,5 @@
 """Utility functions."""
+
 # Copyright (C) 2022 Atsushi Togo
 # All rights reserved.
 #

phonopy/version.py

@@ -1,4 +1,5 @@
 """Phonopy version number only."""
+
 # Copyright (C) 2013 Atsushi Togo
 # All rights reserved.
 #

setup.py

@@ -7,6 +7,7 @@ Custom parameter setting can be written in site.cfg.
 Examples are written at _get_params_from_site_cfg().
 
 """
+
 import os
 import pathlib
 import shutil

test/conftest.py

@@ -1,4 +1,5 @@
 """Pytest configuration."""
+
 from __future__ import annotations
 
 from collections.abc import Callable

test/gruneisen/test_gruneisen.py

@@ -1,4 +1,5 @@
 """Tests for mode Grueneisen parameter calculations."""
+
 import numpy as np
 
 from phonopy.api_gruneisen import PhonopyGruneisen

test/harmonic/test_derivative_dynmat.py

@@ -1,4 +1,5 @@
 """Tests for routines in derivative_dynmat.py."""
+
 import numpy as np
 
 from phonopy import Phonopy

test/harmonic/test_displacements.py

@@ -1,4 +1,5 @@
 """Tests for displacements."""
+
 import itertools
 from copy import deepcopy
 from typing import Optional