def test_supercell_info_distances(supercell_info):
assert supercell_info.coords("H1") == Coordination(
{
"H": [3.91],
"He": [2.5, 3.0, 3.5]
}, 4.25, {1, 4, 5, 6})
assert supercell_info.coords("He1") == Coordination(
{
"H": [2.5, 3.0, 3.5],
"He": [3.91]
}, 4.25, {0, 2, 3, 7})
def test_coord_distances(mocker, ortho_conventional):
mock = mocker.patch("pydefect.util.structure_tools.defaults")
mock.cutoff_distance_factor = 3.9051248 / 2.5 + 1e-5 # = 1.562
distances = Distances(ortho_conventional, center_coord=[0.5, 0.5, 0.5])
actual = distances.coordination(include_on_site=True)
expected = Coordination({"H": [2.5, 3.0, 3.5], "He": [0.0, 3.91]},
3.905,
neighboring_atom_indices=[1, 2, 3, 4, 7])
assert actual == expected
actual = distances.coordination()
expected = Coordination({"H": [2.5, 3.0, 3.5], "He": [3.91]},
3.905,
neighboring_atom_indices=[1, 2, 3, 4])
assert actual == expected
def test_find_inequivalent_coords(simple_cubic):
df = DataFrame(
[[0.1, 0.0, 0.0, 1.0], [0.0, 0.1, 0.0, 1.0], [0.0, 0.0, 0.1, 1.0],
[0.9, 0.0, 0.0, 1.0], [0.0, 0.9, 0.0, 1.0], [0.0, 0.0, 0.9, 1.0]],
columns=["a", "b", "c", "value"])
actual = find_inequivalent_coords(simple_cubic, df)
expected = CoordInfo(site_symmetry="4mm",
coordination=Coordination({"H": [0.1]}, 0.13, [0]),
frac_coords=[(0.1, 0.0, 0.0), (0.0, 0.1, 0.0),
(0.0, 0.0, 0.1), (0.9, 0.0, 0.0),
(0.0, 0.9, 0.0), (0.0, 0.0, 0.9)],
quantities=[1.0] * 6)
assert actual[0] == expected
def local_extrema(simple_cubic, vol_params):
coordination = Coordination({"Mn": [1.0, 2.0]},
cutoff=4.0,
neighboring_atom_indices=[1, 2])
local_extremum = CoordInfo(site_symmetry="3m",
coordination=coordination,
frac_coords=[(0.1, 0.1, 0.1)],
quantities=[1.234])
coordination = Coordination({"Mn": [1.0, 2.0]},
cutoff=4.0,
neighboring_atom_indices=[1, 2])
local_extremum2 = CoordInfo(site_symmetry="4mm",
coordination=coordination,
frac_coords=[(0.1, 0.0, 0.0)],
quantities=[2.101])
return VolumetricDataLocalExtrema(
unit_cell=simple_cubic,
is_min=True,
extrema_points=[local_extremum, local_extremum2],
info="test",
params=vol_params)
def test_supercell_info_interstitials_distances(supercell_info):
assert supercell_info.interstitial_coords(0) == Coordination(
{
'H': [2.62, 2.62, 2.62, 2.62],
'He': [2.62, 2.62, 2.62, 2.62]
}, 4.457, {0, 1, 2, 3, 4, 5, 6, 7})
def test_coordination_msonable(tmpdir):
assert_msonable(Coordination({"H": [2.5, 3.0, 3.5]}, 3.905, [1]))