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from __future__ import annotations
import pathlib
from typing import TYPE_CHECKING
import numpy as np
from spglib import (
MagneticSpaceGroupType,
find_primitive,
get_magnetic_spacegroup_type,
get_magnetic_symmetry_from_database,
get_pointgroup,
get_spacegroup,
get_spacegroup_type,
get_symmetry_dataset,
standardize_cell,
)
if TYPE_CHECKING:
from conftest import CrystalData
# fmt: off
spg_to_hall = [
1, 2, 3, 6, 9, 18, 21, 30, 39, 57, # noqa: E241
60, 63, 72, 81, 90, 108, 109, 112, 115, 116, # noqa: E241
119, 122, 123, 124, 125, 128, 134, 137, 143, 149,
155, 161, 164, 170, 173, 176, 182, 185, 191, 197,
203, 209, 212, 215, 218, 221, 227, 228, 230, 233,
239, 245, 251, 257, 263, 266, 269, 275, 278, 284,
290, 292, 298, 304, 310, 313, 316, 322, 334, 335,
337, 338, 341, 343, 349, 350, 351, 352, 353, 354,
355, 356, 357, 358, 359, 361, 363, 364, 366, 367,
368, 369, 370, 371, 372, 373, 374, 375, 376, 377,
378, 379, 380, 381, 382, 383, 384, 385, 386, 387,
388, 389, 390, 391, 392, 393, 394, 395, 396, 397,
398, 399, 400, 401, 402, 404, 406, 407, 408, 410,
412, 413, 414, 416, 418, 419, 420, 422, 424, 425,
426, 428, 430, 431, 432, 433, 435, 436, 438, 439,
440, 441, 442, 443, 444, 446, 447, 448, 449, 450,
452, 454, 455, 456, 457, 458, 460, 462, 463, 464,
465, 466, 467, 468, 469, 470, 471, 472, 473, 474,
475, 476, 477, 478, 479, 480, 481, 482, 483, 484,
485, 486, 487, 488, 489, 490, 491, 492, 493, 494,
495, 497, 498, 500, 501, 502, 503, 504, 505, 506,
507, 508, 509, 510, 511, 512, 513, 514, 515, 516,
517, 518, 520, 521, 523, 524, 525, 527, 529, 530, 531]
# fmt: on
def get_spgnum(name: str) -> int:
"""Get number reference from filename."""
file_name = pathlib.Path(name).stem
spgnum = int(file_name.split("_")[1])
return spgnum
def test_get_symmetry_dataset(crystal_data: CrystalData):
symprec = 1e-5
dataset = get_symmetry_dataset(crystal_data.cell, symprec=symprec)
spgnum = get_spgnum(crystal_data.name)
assert dataset.number == spgnum
for i in range(spg_to_hall[spgnum - 1], spg_to_hall[spgnum]):
dataset_with_hall_number = get_symmetry_dataset(
crystal_data.cell, hall_number=i, symprec=symprec
)
assert dataset_with_hall_number.hall_number == i
spg_type = get_spacegroup_type(dataset_with_hall_number.hall_number)
assert dataset_with_hall_number.international == spg_type.international_short
assert dataset_with_hall_number.hall == spg_type.hall_symbol
assert dataset_with_hall_number.choice == spg_type.choice
assert dataset_with_hall_number.pointgroup == spg_type.pointgroup_international
wyckoffs = dataset.wyckoffs
assert wyckoffs == crystal_data.ref["wyckoffs"]
def test_standardize_cell_and_pointgroup(crystal_data: CrystalData):
spgnum = get_spgnum(crystal_data.name)
symprec = 1e-5
std_cell = standardize_cell(
crystal_data.cell,
to_primitive=False,
no_idealize=True,
symprec=symprec,
)
dataset = get_symmetry_dataset(std_cell, symprec=symprec)
assert dataset.number == spgnum
# The test for point group has to be done after standardization.
ptg_symbol, _, _ = get_pointgroup(dataset.rotations)
assert dataset.pointgroup == ptg_symbol
def test_standardize_cell_from_primitive(crystal_data: CrystalData):
spgnum = get_spgnum(crystal_data.name)
symprec = 1e-5
prim_cell = standardize_cell(
crystal_data.cell,
to_primitive=True,
no_idealize=True,
symprec=symprec,
)
std_cell = standardize_cell(
prim_cell,
to_primitive=False,
no_idealize=True,
symprec=symprec,
)
dataset = get_symmetry_dataset(std_cell, symprec=symprec)
assert dataset.number == spgnum
def test_standardize_cell_to_primitive(crystal_data: CrystalData):
spgnum = get_spgnum(crystal_data.name)
symprec = 1e-5
prim_cell = standardize_cell(
crystal_data.cell,
to_primitive=True,
no_idealize=True,
symprec=symprec,
)
dataset = get_symmetry_dataset(prim_cell, symprec=symprec)
assert dataset.number == spgnum
def test_refine_cell(crystal_data_dataset):
crystal_data = crystal_data_dataset["crystal_data"]
dataset_0 = crystal_data_dataset["dataset"]
symprec = crystal_data_dataset["symprec"]
spgnum = get_spgnum(crystal_data.name)
ref_cell_0 = (
dataset_0.std_lattice,
dataset_0.std_positions,
dataset_0.std_types,
)
dataset_1 = get_symmetry_dataset(ref_cell_0, symprec=symprec)
# Check the same space group type is found.
assert dataset_1.number == spgnum
# Check if the same structure is obtained when applying
# standardization again, i.e., examining non cycling behaviour.
# Currently only for orthorhombic.
ref_cell_1 = (
dataset_1.std_lattice,
dataset_1.std_positions,
dataset_1.std_types,
)
dataset_2 = get_symmetry_dataset(ref_cell_1, symprec=symprec)
np.testing.assert_equal(
dataset_1.std_types,
dataset_2.std_types,
)
np.testing.assert_allclose(
dataset_1.std_lattice,
dataset_2.std_lattice,
atol=symprec,
)
diff = dataset_1.std_positions - dataset_2.std_positions
diff -= np.rint(diff)
np.testing.assert_allclose(diff, 0, atol=symprec)
def test_get_spacegroup():
cell = (
[
[1.0, 0.0, 0.0],
[0.0, 1.0, 0.0],
[0.0, 0.0, 1.0],
],
[
[0.0, 0.0, 0.0],
[0.0, 0.5, 0.5],
[0.5, 0.0, 0.5],
[0.5, 0.5, 0.0],
],
[0, 0, 0, 0],
)
assert get_spacegroup(cell) == "Fm-3m (225)"
assert get_spacegroup(cell, symbol_type=1) == "Oh^5 (225)"
def test_find_primitive(crystal_data_dataset):
crystal_data = crystal_data_dataset["crystal_data"]
dataset = crystal_data_dataset["dataset"]
symprec = crystal_data_dataset["symprec"]
primitive = find_primitive(crystal_data.cell, symprec=symprec)
spg_type = get_spacegroup_type(dataset.hall_number)
c = spg_type.international_short[0]
if c in ["A", "B", "C", "I"]:
multiplicity = 2
elif c == "F":
multiplicity = 4
elif c == "R":
assert spg_type.choice == "H"
if spg_type.choice == "H":
multiplicity = 3
else: # spg_type['choice'] == 'R'
multiplicity = 1
else:
multiplicity = 1
assert len(dataset.std_types) == len(primitive[2]) * multiplicity
def test_magnetic_spacegroup_type():
# P 3 -2"
actual1 = get_magnetic_spacegroup_type(1279)
expect1 = MagneticSpaceGroupType(
uni_number=1279,
litvin_number=1279,
bns_number="156.49",
og_number="156.1.1279",
number=156,
type=1,
)
assert actual1 == expect1
# -P 2 2ab 1'
actual2 = get_magnetic_spacegroup_type(452)
expect2 = MagneticSpaceGroupType(
uni_number=452,
litvin_number=442,
bns_number="55.354",
og_number="55.2.442",
number=55,
type=2,
)
assert actual2 == expect2
# P 31 2 1c' (0 0 1)
actual3 = get_magnetic_spacegroup_type(1262)
expect3 = MagneticSpaceGroupType(
uni_number=1262,
litvin_number=1270,
bns_number="151.32",
og_number="153.4.1270",
number=151,
type=4,
)
assert actual3 == expect3
def test_magnetic_symmetry_database():
# UNI: R31'_c[R3] (1242), BNS: R_I3 (146.12)
# Hexagonal axes: hall_number: 433
data_h_actual = get_magnetic_symmetry_from_database(1242)
for key in ["rotations", "translations", "time_reversals"]:
assert len(data_h_actual[key]) == 18
# Rhombohedral axes: hall_number: 434
data_r_actual = get_magnetic_symmetry_from_database(1242, hall_number=434)
data_r_expect = {
"rotations": np.array(
[
# x,y,z
[
[1, 0, 0],
[0, 1, 0],
[0, 0, 1],
],
# y,z,x
[
[0, 0, 1],
[1, 0, 0],
[0, 1, 0],
],
# y+1/2,z+1/2,x+1/2'
[
[0, 0, 1],
[1, 0, 0],
[0, 1, 0],
],
# z,x,y
[
[0, 1, 0],
[0, 0, 1],
[1, 0, 0],
],
# x+1/2,y+1/2,z+1/2'
[
[1, 0, 0],
[0, 1, 0],
[0, 0, 1],
],
# z+1/2,x+1/2,y+1/2'
[
[0, 1, 0],
[0, 0, 1],
[1, 0, 0],
],
],
dtype=np.int32,
),
"translations": np.array(
[
[0, 0, 0],
[0, 0, 0],
[0.5, 0.5, 0.5],
[0, 0, 0],
[0.5, 0.5, 0.5],
[0.5, 0.5, 0.5],
],
),
"time_reversals": np.array(
[
[0, 0, 1, 0, 1, 1],
],
),
}
for key in ["rotations", "translations", "time_reversals"]:
assert np.allclose(data_r_actual[key], data_r_expect[key])
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