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import pytest
import numpy as np
from ase.build import bulk
from ase.spacegroup import crystal, Spacegroup
from ase.spacegroup.spacegroup import SpacegroupValueError
from ase.spacegroup import utils
@pytest.fixture(params=[
# Use lambda's to not crash during collection if there's an error
lambda: {
'atoms': bulk('NaCl', crystalstructure='rocksalt', a=4.1),
'spacegroup': 225,
'expected': [[0, 0, 0], [0.5, 0.5, 0.5]]
},
# diamond
lambda: {
'atoms':
crystal('C', [(0, 0, 0)],
spacegroup=227,
cellpar=[4, 4, 4, 90, 90, 90],
primitive_cell=True),
'spacegroup':
227,
'expected': [[0, 0, 0]]
},
lambda: {
'atoms':
crystal('Mg', [(1 / 3, 2 / 3, 3 / 4)],
spacegroup=194,
cellpar=[3.21, 3.21, 5.21, 90, 90, 120]),
'spacegroup':
194,
'expected': [(1 / 3, 2 / 3, 3 / 4)]
},
lambda: {
'atoms':
crystal(['Ti', 'O'],
basis=[(0, 0, 0), (0.3, 0.3, 0.0)],
spacegroup=136,
cellpar=[4, 4, 6, 90, 90, 90]),
'spacegroup':
Spacegroup(136),
'expected': [(0, 0, 0), (0.3, 0.3, 0.0)]
},
])
def basis_tests(request):
"""Fixture which returns a dictionary with some test inputs and expected values
for testing the `get_basis` function."""
return request.param()
def test_get_basis(basis_tests):
"""Test explicitly passing spacegroup and getting basis"""
atoms = basis_tests['atoms']
expected = basis_tests['expected']
spacegroup = basis_tests['spacegroup']
basis = utils.get_basis(atoms, spacegroup=spacegroup)
assert np.allclose(basis, expected)
def test_get_basis_infer_sg(basis_tests):
"""Test inferring spacegroup, which uses 'get_basis_spglib' under the hood"""
pytest.importorskip('spglib')
atoms = basis_tests['atoms']
expected = basis_tests['expected']
basis = utils.get_basis(atoms)
assert np.allclose(basis, expected)
def test_get_basis_spglib(basis_tests):
"""Test getting the basis using spglib"""
pytest.importorskip('spglib')
atoms = basis_tests['atoms']
expected = basis_tests['expected']
basis = utils._get_basis_spglib(atoms)
assert np.allclose(basis, expected)
def test_get_basis_ase(basis_tests):
atoms = basis_tests['atoms']
spacegroup = basis_tests['spacegroup']
expected = basis_tests['expected']
basis = utils._get_basis_ase(atoms, spacegroup)
assert np.allclose(basis, expected)
@pytest.mark.parametrize('spacegroup', [251.5, [1, 2, 3], np.array([255])])
def test_get_basis_wrong_type(basis_tests, spacegroup):
atoms = basis_tests['atoms']
with pytest.raises(SpacegroupValueError):
utils._get_basis_ase(atoms, spacegroup)
with pytest.raises(SpacegroupValueError):
utils.get_basis(atoms, spacegroup=spacegroup)
@pytest.mark.parametrize('method', [None, 12, 'nonsense', True, False])
def test_get_basis_wrong_method(basis_tests, method):
"""Test passing in un-supported methods"""
atoms = basis_tests['atoms']
with pytest.raises(ValueError):
utils.get_basis(atoms, method=method)
def test_get_basis_group_1(basis_tests):
"""Always use spacegroup 1, nothing should be symmetrically equivalent"""
atoms = basis_tests['atoms']
scaled = atoms.get_scaled_positions()
spacegroup = 1
basis = utils.get_basis(atoms, spacegroup)
# Basis should now be the same as the scaled positions
assert np.allclose(basis, scaled)
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