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import pytest
import numpy as np
from ase.spacegroup import Spacegroup
from ase.lattice import FCC
from ase.spacegroup.spacegroup import parse_sitesym, parse_sitesym_single, parse_sitesym_element
def test_spacegroup_miscellaneous():
no = 225
sg = Spacegroup(no)
assert int(sg) == no == sg.no
assert sg.centrosymmetric
assert sg.symbol == 'F m -3 m'
assert sg.symbol in str(sg)
assert sg.lattice == 'F' # face-centered
assert sg.setting == 1
assert sg.scaled_primitive_cell == pytest.approx(FCC(1.0).tocell()[:])
assert sg.reciprocal_cell @ sg.scaled_primitive_cell == pytest.approx(
np.identity(3))
def test_spacegroup_parse_sitesym():
sitesyms = ["x,y,z", "0.25-y,x+1/4,-z", "x-1/4, y+3/4, 1/8-z", "x-y,-z+0.3-y,-1/2+x-y+z"]
expected_trans = np.array(
[
[+0.000, 0.000, 0.000], # x, y, z
[+0.250, 0.250, 0.000], # 0.25-y, x+1/4, -z
[-0.250, 0.750, 0.125], # x-1/4, y+3/4, 1/8-z
[+0.000, 0.300, -0.500] # x-y, -z+0.3-y, -1/2+x-y+z
],
dtype=float
)
expected_trans_bounded = expected_trans.copy()
expected_trans_bounded[2, 0] = 0.75
expected_trans_bounded[3, 2] = 0.50
expected_rot = np.array(
[
[[1, 0, 0], [0, 1, 0], [0, 0, 1]], # x, y, z
[[0, -1, 0], [1, 0, 0], [0, 0, -1]], # 0.25-y, x+1/4, -z
[[1, 0, 0], [0, 1, 0], [0, 0, -1]], # x-1/4, y+3/4, 1/8-z
[[1, -1, 0], [0, -1, -1], [1, -1, 1]] # # x-y, -z+0.3-y, -1/2+x-y+z
],
dtype=int
)
rot, trans = parse_sitesym(sitesyms)
rot_bounded, trans_bounded = parse_sitesym(sitesyms, force_positive_translation=True)
assert np.allclose(rot, expected_rot)
assert np.allclose(rot_bounded, expected_rot)
assert np.allclose(trans, expected_trans)
assert np.allclose(trans_bounded, expected_trans_bounded)
def test_spacegroup_parse_sitesym_single():
sitesym = "0.125-y,x-1/4,-z"
expected_rot = np.array([[0, -1, 0], [1, 0, 0], [0, 0, -1]], dtype=int)
expected_trans = np.array([0.125, -0.25, 0.0], dtype=float)
rot = np.arange(9, dtype=int).reshape(3, 3)
trans = np.zeros(3, dtype=float) + 2.0
parse_sitesym_single(sitesym, out_rot=rot, out_trans=trans)
assert np.allclose(rot, expected_rot)
assert np.allclose(trans, expected_trans)
def test_spacegroup_parse_sitesym_element():
element_list = ("x", "y", "z", "-x", "0.1+x", "-y-1/8", "+1/2-z", "x+z")
expected_rot_list = ([(0, 1)], [(1, 1)], [(2, 1)], [(0, -1)], [(0, 1)], [(1, -1)], [(2, -1)], [(0, 1), (2, 1)])
expected_trans_list = (0.0, 0.0, 0.0, 0.0, 0.1, -0.125, 0.5, 0.0)
for element, expected_rot, expected_trans in zip(element_list, expected_rot_list, expected_trans_list):
rot, trans = parse_sitesym_element(element)
assert rot == expected_rot
assert np.allclose(trans, expected_trans)
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