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|
"""Tests of Phonopy --symmetry."""
from __future__ import annotations
import os
import pathlib
import tempfile
import numpy as np
import pytest
import yaml
import phonopy
from phonopy.cui.phonopy_argparse import PhonopyMockArgs
from phonopy.cui.phonopy_script import main
from phonopy.structure.atoms import PhonopyAtoms
from phonopy.structure.cells import Primitive
cwd = pathlib.Path(__file__).parent
@pytest.mark.parametrize("is_ncl", [False, True])
def test_phonopy_disp_Cr(is_ncl: bool):
"""Test phonopy -d option."""
with tempfile.TemporaryDirectory() as temp_dir:
original_cwd = pathlib.Path.cwd()
os.chdir(temp_dir)
try:
cell_filename = cwd / "POSCAR-unitcell_Cr"
if is_ncl:
magmoms = "0 0 1 0 0 -1"
else:
magmoms = "1 -1"
argparse_control = _get_phonopy_args(
cell_filename=cell_filename,
supercell_dimension="2 2 2",
is_displacement=True,
magmoms=magmoms,
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
magmom_file_path = pathlib.Path("MAGMOM")
assert magmom_file_path.exists()
with open(magmom_file_path) as f:
vals = [float(v) for v in f.readline().split()[2:]]
if is_ncl:
np.testing.assert_allclose(
vals,
np.ravel([[0, 0, 1]] * 8 + [[0, 0, -1]] * 8), # type: ignore
)
else:
np.testing.assert_allclose(vals, [1.0] * 8 + [-1.0] * 8)
for created_filename in [
"MAGMOM",
"POSCAR-001",
"SPOSCAR",
"phonopy_disp.yaml",
]:
file_path = pathlib.Path(created_filename)
assert file_path.exists()
file_path.unlink()
_check_no_files()
finally:
os.chdir(original_cwd)
def test_create_force_sets():
"""Test phonopy --create-force-sets command."""
with tempfile.TemporaryDirectory() as temp_dir:
original_cwd = pathlib.Path.cwd()
os.chdir(temp_dir)
try:
argparse_control = _get_phonopy_args(
cell_filename=cwd / "NaCl" / "phonopy_disp.yaml.xz",
create_force_sets=[
cwd / "NaCl" / "vasprun.xml-001.xz",
cwd / "NaCl" / "vasprun.xml-002.xz",
],
load_phonopy_yaml=False,
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
for created_filename in ("FORCE_SETS",):
file_path = pathlib.Path(created_filename)
assert file_path.exists()
file_path.unlink()
argparse_control = _get_phonopy_args(
cell_filename=cwd / "NaCl" / "phonopy_disp.yaml.xz",
create_force_sets=[
cwd / "NaCl" / "vasprun.xml-002.xz",
cwd / "NaCl" / "vasprun.xml-001.xz",
],
)
with pytest.raises(RuntimeError) as excinfo:
main(**argparse_control)
_check_no_files()
finally:
os.chdir(original_cwd)
@pytest.mark.parametrize("load_phonopy_yaml", [False, True])
def test_phonopy_load(load_phonopy_yaml: bool):
"""Test phonopy/phonopy-load command."""
pytest.importorskip("symfc")
with tempfile.TemporaryDirectory() as temp_dir:
original_cwd = pathlib.Path.cwd()
os.chdir(temp_dir)
try:
# Check sys.exit(0)
argparse_control = _get_phonopy_args(
filename=cwd / ".." / ".." / "phonopy_params_NaCl-1.00.yaml.xz",
load_phonopy_yaml=load_phonopy_yaml,
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
# Clean files created by phonopy-load script.
for created_filename in ("phonopy.yaml",):
file_path = pathlib.Path(created_filename)
assert file_path.exists()
file_path.unlink()
_check_no_files()
finally:
os.chdir(original_cwd)
@pytest.mark.parametrize("load_phonopy_yaml", [False, True])
def test_unit_conversion_factor(load_phonopy_yaml: bool):
"""Test unit_conversion_factor using phonopy/phonopy-load command."""
with tempfile.TemporaryDirectory() as temp_dir:
original_cwd = pathlib.Path.cwd()
os.chdir(temp_dir)
try:
# Check sys.exit(0)
argparse_control = _get_phonopy_args(
filename=cwd / ".." / ".." / "phonopy_params_NaCl-fd.yaml.xz",
band_paths="0 0 0 0 0 1/2",
frequency_conversion_factor=100,
load_phonopy_yaml=load_phonopy_yaml,
)
with pytest.warns(DeprecationWarning):
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
if load_phonopy_yaml:
ref_freq = 47.3113552091
else:
ref_freq = 29.5294946098
with open("band.yaml") as f:
band = yaml.safe_load(f)
assert band["phonon"][0]["band"][5]["frequency"] == pytest.approx(
ref_freq
)
# Clean files created by phonopy-load script.
for created_filename in ("phonopy.yaml", "band.yaml"):
file_path = pathlib.Path(created_filename)
assert file_path.exists()
file_path.unlink()
_check_no_files()
finally:
os.chdir(original_cwd)
@pytest.mark.parametrize("load_phonopy_yaml", [False, True])
def test_unit_conversion_factor_QE(load_phonopy_yaml: bool):
"""Test unit_conversion_factor for QE using phonopy/phonopy-load command."""
pytest.importorskip("symfc")
with tempfile.TemporaryDirectory() as temp_dir:
original_cwd = pathlib.Path.cwd()
os.chdir(temp_dir)
try:
# Check sys.exit(0)
argparse_control = _get_phonopy_args(
filename=cwd / ".." / ".." / "phonopy_params_NaCl-QE.yaml.xz",
band_paths="0 0 0 0 0 1/2",
load_phonopy_yaml=load_phonopy_yaml,
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
if load_phonopy_yaml:
ref_freq = 7.3823649712
else:
ref_freq = 4.5259552147
with open("band.yaml") as f:
band = yaml.safe_load(f)
assert band["phonon"][0]["band"][5]["frequency"] == pytest.approx(
ref_freq
)
# Clean files created by phonopy-load script.
for created_filename in ("phonopy.yaml", "band.yaml"):
file_path = pathlib.Path(created_filename)
assert file_path.exists()
file_path.unlink()
_check_no_files()
finally:
os.chdir(original_cwd)
def test_phonopy_is_check_symmetry():
"""Test phonopy --symmetry command with phonopy.yaml input structure."""
with tempfile.TemporaryDirectory() as temp_dir:
original_cwd = pathlib.Path.cwd()
os.chdir(temp_dir)
try:
# Check sys.exit(0)
argparse_control = _get_phonopy_args(
filename=cwd / ".." / ".." / "phonopy_params_NaCl-1.00.yaml.xz",
load_phonopy_yaml=False,
is_check_symmetry=True,
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
# Clean files created by phonopy --symmetry command.
file_path = pathlib.Path("phonopy_symcells.yaml")
assert file_path.exists()
ph = phonopy.load(file_path)
assert type(ph.unitcell) is PhonopyAtoms
assert type(ph.primitive) is Primitive
file_path.unlink()
_check_no_files()
finally:
os.chdir(original_cwd)
def test_conf_file():
"""Test phonopy CONFILE."""
with tempfile.TemporaryDirectory() as temp_dir:
original_cwd = pathlib.Path.cwd()
os.chdir(temp_dir)
try:
argparse_control = _get_phonopy_args(
filename=cwd / "dim.conf",
cell_filename=cwd / "POSCAR-unitcell_Cr",
load_phonopy_yaml=False,
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
for created_filename in ("POSCAR-001", "SPOSCAR", "phonopy_disp.yaml"):
file_path = pathlib.Path(created_filename)
assert file_path.exists()
file_path.unlink()
_check_no_files()
finally:
os.chdir(original_cwd)
def test_config_option():
"""Test phonopy-yaml --config."""
pytest.importorskip("symfc")
with tempfile.TemporaryDirectory() as temp_dir:
original_cwd = pathlib.Path.cwd()
os.chdir(temp_dir)
try:
argparse_control = _get_phonopy_args(
filename=cwd / ".." / ".." / "phonopy_params_NaCl-1.00.yaml.xz",
conf_filename=cwd / "mesh.conf",
load_phonopy_yaml=True,
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
# Clean files created by phonopy-load script.
for created_filename in ("phonopy.yaml", "mesh.yaml"):
file_path = pathlib.Path(created_filename)
assert file_path.exists()
file_path.unlink()
_check_no_files()
finally:
os.chdir(original_cwd)
def test_anime():
"""Test phonopy/phonopy-load command."""
with tempfile.TemporaryDirectory() as temp_dir:
original_cwd = pathlib.Path.cwd()
os.chdir(temp_dir)
try:
# Check sys.exit(0)
argparse_control = _get_phonopy_args(
filename=cwd / ".." / ".." / "phonopy_params_NaCl-1.00.yaml.xz",
anime="0 0 0",
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
_ls()
# Clean files created by phonopy-load script.
for created_filename in ("phonopy.yaml", "anime.ascii"):
file_path = pathlib.Path(created_filename)
assert file_path.exists()
file_path.unlink()
_check_no_files()
finally:
os.chdir(original_cwd)
def test_tdm_cif():
"""Test phonopy command with thermal displacement matrices cif output."""
pytest.importorskip("symfc")
with tempfile.TemporaryDirectory() as temp_dir:
original_cwd = pathlib.Path.cwd()
os.chdir(temp_dir)
try:
# Check sys.exit(0)
argparse_control = _get_phonopy_args(
filename=cwd / ".." / ".." / "phonopy_params_NaCl-1.00.yaml.xz",
thermal_displacement_matrices_cif=1000,
mesh_numbers="5 5 5",
load_phonopy_yaml=True,
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
# Clean files created by phonopy-load script.
for created_filename in (
"phonopy.yaml",
"tdispmat.cif",
"thermal_displacement_matrices.yaml",
):
file_path = pathlib.Path(created_filename)
assert file_path.exists()
file_path.unlink()
_check_no_files()
finally:
os.chdir(original_cwd)
pass
def _ls():
current_dir = pathlib.Path(".")
for file in current_dir.iterdir():
print(file.name)
def _check_no_files():
assert not list(pathlib.Path(".").iterdir())
def _get_phonopy_args(
anime: str | None = None,
band_paths: str | None = None,
cell_filename: str | os.PathLike | None = None,
conf_filename: str | os.PathLike | None = None,
create_force_sets: list[str | os.PathLike] | None = None,
filename: str | os.PathLike | None = None,
frequency_conversion_factor: float | None = None,
is_displacement: bool | None = None,
is_check_symmetry: bool = False,
load_phonopy_yaml: bool = False,
magmoms: str | None = None,
mesh_numbers: str | None = None,
supercell_dimension: str | None = None,
thermal_displacement_matrices_cif: float | None = None,
use_pypolymlp: bool = False,
):
if filename is None:
_filename = []
else:
_filename = [filename]
mockargs = PhonopyMockArgs(
anime=anime,
band_paths=band_paths,
cell_filename=cell_filename,
conf_filename=conf_filename,
create_force_sets=create_force_sets,
filename=_filename,
frequency_conversion_factor=frequency_conversion_factor,
is_displacement=is_displacement,
is_check_symmetry=is_check_symmetry,
log_level=1,
magmoms=magmoms,
mesh_numbers=mesh_numbers,
thermal_displacement_matrices_cif=thermal_displacement_matrices_cif,
supercell_dimension=supercell_dimension,
use_pypolymlp=use_pypolymlp,
)
if load_phonopy_yaml:
argparse_control = {
"load_phonopy_yaml": True,
"args": mockargs,
}
else:
argparse_control = {
"load_phonopy_yaml": False,
"args": mockargs,
}
return argparse_control
|
