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from __future__ import annotations
import numpy as np
from spglib import get_symmetry_from_database
def test_change_of_basis(crystal_data_dataset):
crystal_data = crystal_data_dataset["crystal_data"]
dataset = crystal_data_dataset["dataset"]
symprec = crystal_data_dataset["symprec"]
std_pos = dataset.std_positions
tmat = dataset.transformation_matrix
orig_shift = dataset.origin_shift
lat = np.dot(crystal_data.cell[0].T, np.linalg.inv(tmat))
pos = np.dot(crystal_data.cell[1], tmat.T) + orig_shift
for p in pos:
diff = std_pos - p
diff -= np.rint(diff)
diff = np.dot(diff, lat.T)
delta = np.sqrt((diff**2).sum(axis=1))
indices = np.where(delta < symprec)[0]
assert len(indices) == 1
def test_std_symmetry(crystal_data_dataset):
dataset = crystal_data_dataset["dataset"]
symmetry = get_symmetry_from_database(dataset.hall_number)
std_pos = dataset.std_positions
# for r, t in zip(symmetry['rotations'], symmetry['translations']):
# for rp in (np.dot(std_pos, r.T) + t):
# diff = std_pos - rp
# diff -= np.rint(diff)
# num_match = len(np.where(abs(diff).sum(axis=1) < 1e-3)[0])
# self.assertEqual(num_match, 1, msg="%s" % fname)
# Equivalent above by numpy hack
# 15 sec on macOS 2.3 GHz Intel Core i5 (4times faster than above)
rot = symmetry["rotations"]
trans = symmetry["translations"]
# (n_sym, 3, n_atom)
rot_pos = np.dot(rot, std_pos.T) + trans[:, :, None]
for p in std_pos:
diff = rot_pos - p[None, :, None]
diff -= np.rint(diff)
num_match = (abs(diff).sum(axis=1) < 1e-3).sum(axis=1)
assert all(num_match == 1)
def test_std_rotation(crystal_data_dataset):
crystal_data = crystal_data_dataset["crystal_data"]
dataset = crystal_data_dataset["dataset"]
symprec = crystal_data_dataset["symprec"]
std_lat = dataset.std_lattice
tmat = dataset.transformation_matrix
lat = np.dot(crystal_data.cell[0].T, np.linalg.inv(tmat))
lat_rot = np.dot(dataset.std_rotation_matrix, lat)
np.testing.assert_allclose(
std_lat,
lat_rot.T,
atol=symprec,
)
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