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
|
# fmt: off
"""Tests for GEN format"""
import numpy as np
import pytest
from ase import Atoms
from ase.io import write
from ase.io.gen import read_gen
@pytest.mark.parametrize("fractional", [False, True])
@pytest.mark.parametrize("cell", [None, [[2.5, 0, 0], [2, 4, 0], [1, 2, 3]]])
@pytest.mark.parametrize("pbc", [False, [True, True, False], True])
@pytest.mark.parametrize("write_format", ["gen", "dftb"])
def test_gen(write_format: str, cell: list, pbc: bool, fractional: bool):
"""Test for `write_gen` and `read_gen`"""
if fractional and cell is None:
# fractional==True is invalid when cell is None.
return
positions = [[-0.1, 1.2, 0.3], [-0.1, 0.0, 0.2], [0.4, -0.9, 0.0]]
atoms = Atoms(symbols="OCO", pbc=pbc, cell=cell, positions=positions)
fname = "test.gen"
write(fname, atoms, format=write_format, fractional=fractional)
atoms_new = read_gen(fname)
assert np.all(atoms_new.numbers == atoms.numbers)
assert np.allclose(atoms_new.positions, atoms.positions)
if atoms.pbc.any() or fractional:
assert np.all(atoms_new.pbc)
assert np.allclose(atoms_new.cell, atoms.cell)
else:
assert np.all(~atoms_new.pbc)
assert np.allclose(atoms_new.cell, 0.0)
def test_gen_multiple():
"""Test multiple images (not supported by the format) that should fail"""
atoms = Atoms("H2")
with pytest.raises(ValueError):
write("test.gen", [atoms, atoms])
|
