mirror of https://github.com/phonopy/phono3py.git
147 lines
5.2 KiB
Python
147 lines
5.2 KiB
Python
"""Utilities of main CUI script."""
|
|
# Copyright (C) 2015 Atsushi Togo
|
|
# All rights reserved.
|
|
#
|
|
# This file is part of phono3py.
|
|
#
|
|
# Redistribution and use in source and binary forms, with or without
|
|
# modification, are permitted provided that the following conditions
|
|
# are met:
|
|
#
|
|
# * Redistributions of source code must retain the above copyright
|
|
# notice, this list of conditions and the following disclaimer.
|
|
#
|
|
# * Redistributions in binary form must reproduce the above copyright
|
|
# notice, this list of conditions and the following disclaimer in
|
|
# the documentation and/or other materials provided with the
|
|
# distribution.
|
|
#
|
|
# * Neither the name of the phonopy project nor the names of its
|
|
# contributors may be used to endorse or promote products derived
|
|
# from this software without specific prior written permission.
|
|
#
|
|
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
|
|
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
|
|
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
|
|
# FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
|
|
# COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
|
|
# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
|
|
# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
|
|
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
|
|
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
|
|
# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
|
|
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
|
|
# POSSIBILITY OF SUCH DAMAGE.
|
|
|
|
from phono3py import Phono3py
|
|
from phono3py.file_IO import write_disp_fc3_yaml, write_disp_fc2_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(
|
|
cell_info,
|
|
settings,
|
|
symprec,
|
|
output_filename=None,
|
|
interface_mode="vasp",
|
|
log_level=1,
|
|
):
|
|
"""Create displacements and supercells.
|
|
|
|
Distance unit used is that for the calculator interface.
|
|
The default unit is Angstron.
|
|
|
|
"""
|
|
optional_structure_info = cell_info["optional_structure_info"]
|
|
|
|
if settings.displacement_distance is None:
|
|
distance = get_default_displacement_distance(interface_mode)
|
|
else:
|
|
distance = settings.displacement_distance
|
|
phono3py = Phono3py(
|
|
cell_info["unitcell"],
|
|
cell_info["supercell_matrix"],
|
|
primitive_matrix=cell_info["primitive_matrix"],
|
|
phonon_supercell_matrix=cell_info["phonon_supercell_matrix"],
|
|
is_symmetry=settings.is_symmetry,
|
|
symprec=symprec,
|
|
calculator=interface_mode,
|
|
)
|
|
phono3py.generate_displacements(
|
|
distance=distance,
|
|
cutoff_pair_distance=settings.cutoff_pair_distance,
|
|
is_plusminus=settings.is_plusminus_displacement,
|
|
is_diagonal=settings.is_diagonal_displacement,
|
|
)
|
|
|
|
if log_level:
|
|
print("")
|
|
print('Unit cell was read from "%s".' % optional_structure_info[0])
|
|
print("Displacement distance: %s" % distance)
|
|
|
|
if output_filename is None:
|
|
filename = "disp_fc3.yaml"
|
|
else:
|
|
filename = "disp_fc3." + output_filename + ".yaml"
|
|
num_disps, num_disp_files = write_disp_fc3_yaml(
|
|
phono3py.dataset, phono3py.supercell, filename=filename
|
|
)
|
|
ids = []
|
|
disp_cells = []
|
|
for i, cell in enumerate(phono3py.supercells_with_displacements):
|
|
if cell is not None:
|
|
ids.append(i + 1)
|
|
disp_cells.append(cell)
|
|
|
|
additional_info = get_additional_info_to_write_supercells(
|
|
interface_mode, phono3py.supercell_matrix
|
|
)
|
|
write_supercells_with_displacements(
|
|
interface_mode,
|
|
phono3py.supercell,
|
|
disp_cells,
|
|
optional_structure_info,
|
|
displacement_ids=ids,
|
|
zfill_width=5,
|
|
additional_info=additional_info,
|
|
)
|
|
|
|
if log_level:
|
|
print("Number of displacements: %d" % num_disps)
|
|
if settings.cutoff_pair_distance is not None:
|
|
print(
|
|
"Cutoff distance for displacements: %s" % settings.cutoff_pair_distance
|
|
)
|
|
print("Number of displacement supercell files created: %d" % num_disp_files)
|
|
|
|
if phono3py.phonon_supercell_matrix is not None:
|
|
if output_filename is None:
|
|
filename = "disp_fc2.yaml"
|
|
else:
|
|
filename = "disp_fc2." + output_filename + ".yaml"
|
|
|
|
num_disps = write_disp_fc2_yaml(
|
|
phono3py.phonon_dataset, phono3py.phonon_supercell, filename=filename
|
|
)
|
|
additional_info = get_additional_info_to_write_fc2_supercells(
|
|
interface_mode, phono3py.phonon_supercell_matrix
|
|
)
|
|
write_supercells_with_displacements(
|
|
interface_mode,
|
|
phono3py.supercell,
|
|
phono3py.phonon_supercells_with_displacements,
|
|
optional_structure_info,
|
|
zfill_width=5,
|
|
additional_info=additional_info,
|
|
)
|
|
|
|
if log_level:
|
|
print("Number of displacements for special fc2: %d" % num_disps)
|
|
|
|
return phono3py
|