1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
|
"""Tests of file_IO functions."""
from __future__ import annotations
import os
import pathlib
import tempfile
from typing import Literal
import h5py
import numpy as np
import pytest
import phonopy
from phonopy.file_IO import (
parse_BORN,
read_force_constants_hdf5,
write_force_constants_to_hdf5,
)
cwd = pathlib.Path(__file__).parent
cwd_called = pathlib.Path.cwd()
def test_parse_BORN():
"""Test of parse_BORN."""
ph = phonopy.load(cwd / "phonopy_disp_NaCl.yaml")
nac_params = parse_BORN(ph.primitive, filename=cwd / "BORN_NaCl")
z = np.eye(3) * 1.086875
epsilon = np.eye(3) * 2.43533967
np.testing.assert_allclose(nac_params["born"], [z, -z], atol=1e-5)
np.testing.assert_allclose(nac_params["dielectric"], epsilon, atol=1e-5)
assert pytest.approx(14.400) == nac_params["factor"]
@pytest.mark.parametrize("compression", ["gzip", "lzf", 1, 2, None])
def test_write_force_constants_to_hdf5(
compression: Literal["gzip", "lzf"] | int | None,
):
"""Test write_force_constants_to_hdf5."""
with tempfile.TemporaryDirectory() as temp_dir:
original_cwd = pathlib.Path.cwd()
os.chdir(temp_dir)
write_force_constants_to_hdf5(
np.zeros(1), physical_unit="eV/angstrom^2", compression=compression
)
with h5py.File("force_constants.hdf5", "r") as f:
fc = f["force_constants"]
if compression in ("gzip", "lzf"):
assert fc.compression == compression # type: ignore
elif isinstance(compression, int):
assert fc.compression == "gzip" # type: ignore
assert fc.compression_opts == compression # type: ignore
else:
assert fc.compression is None # type: ignore
for created_filename in ["force_constants.hdf5"]:
file_path = pathlib.Path(created_filename)
assert file_path.exists()
fc, physical_unit = read_force_constants_hdf5(
file_path, return_physical_unit=True
)
assert fc[0] == pytest.approx(0)
assert physical_unit == "eV/angstrom^2"
file_path.unlink()
_check_no_files()
os.chdir(original_cwd)
def _check_no_files():
assert not list(pathlib.Path(".").iterdir())
|
