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import ase
import numpy as np
tol = 1e-9
cell = np.array([[1., 0., 0.],
[0.5, np.sqrt(3) / 2, 0.],
[0., 0., 1.]]) * 10
pos = np.dot(np.array([[0.0, 0.0, 0.0],
[0.5, 0.5, 0.5],
[0.2, 0.2, 0.2],
[0.25, 0.5, 0.0]]), cell)
a = ase.Atoms('C4', pos, cell=cell, pbc=True)
rpos = a.get_scaled_positions()
# non-mic distance between atom 0 and 1
d01F = np.linalg.norm(np.dot(rpos[1], cell))
# mic distance between atom 0 (image [0,1,0]) and 1
d01T = np.linalg.norm(np.dot(rpos[1] - np.array([0, 1, 0]), cell))
d02F = np.linalg.norm(np.dot(rpos[2], cell))
d02T = d02F
# non-mic distance between atom 0 and 3
d03F = np.linalg.norm(np.dot(rpos[3], cell))
# mic distance between atom 0 (image [0,1,0]) and 3
d03T = np.linalg.norm(np.dot(rpos[3] - np.array([0, 1, 0]), cell))
# get_distance(mic=False)
assert abs(a.get_distance(0, 1, mic=False) - d01F) < tol
assert abs(a.get_distance(0, 2, mic=False) - d02F) < tol
assert abs(a.get_distance(0, 3, mic=False) - d03F) < tol
# get_distance(mic=True)
assert abs(a.get_distance(0, 1, mic=True) - d01T) < tol
assert abs(a.get_distance(0, 2, mic=True) - d02T) < tol
assert abs(a.get_distance(0, 3, mic=True) - d03T) < tol
# get_distance(mic=False, vector=True)
assert all(abs(a.get_distance(0, 1, mic=False, vector=True)
- np.array([7.5, np.sqrt(18.75), 5.0])) < tol)
assert all(abs(a.get_distance(0, 2, mic=False, vector=True)
- np.array([3., np.sqrt(3.), 2.0])) < tol)
# get_distance(mic=True, vector=True)
assert np.all(abs(a.get_distance(0, 1, mic=True, vector=True)
- np.array([-2.5, np.sqrt(18.75), -5.0])) < tol)
assert np.all(abs(a.get_distance(0, 2, mic=True, vector=True)
- np.array([3., np.sqrt(3.), 2.0])) < tol)
# get_all_distances(mic=False)
all_dist = a.get_all_distances(mic=False)
assert abs(all_dist[0, 1] - d01F) < tol
assert abs(all_dist[0, 2] - d02F) < tol
assert abs(all_dist[0, 3] - d03F) < tol
assert all(abs(np.diagonal(all_dist)) < tol)
# get_all_distances(mic=True)
all_dist_mic = a.get_all_distances(mic=True)
assert abs(all_dist_mic[0, 1] - d01T) < tol
assert abs(all_dist_mic[0, 2] - d02T) < tol
assert abs(all_dist_mic[0, 3] - d03T) < tol
assert all(abs(np.diagonal(all_dist)) < tol)
# get_distances(mic=False)
for i in range(4):
assert all(abs(a.get_distances(i, [0, 1, 2, 3], mic=False) -
all_dist[i]) < tol)
# get_distances(mic=True)
assert all(abs(a.get_distances(0, [0, 1, 2, 3], mic=True)
- all_dist_mic[0]) < tol)
assert all(abs(a.get_distances(1, [0, 1, 2, 3], mic=True)
- all_dist_mic[1]) < tol)
assert all(abs(a.get_distances(2, [0, 1, 2, 3], mic=True)
- all_dist_mic[2]) < tol)
assert all(abs(a.get_distances(3, [0, 1, 2, 3], mic=True)
- all_dist_mic[3]) < tol)
# get_distances(mic=False, vec=True)
assert np.all(abs(a.get_distances(0, [0, 1, 2, 3], mic=False, vector=True)
- np.array([a.get_distance(0, i, vector=True)
for i in [0, 1, 2, 3]])) < tol)
assert np.all(abs(a.get_distances(1, [0, 1, 2, 3], mic=False, vector=True)
- np.array([a.get_distance(1, i, vector=True)
for i in [0, 1, 2, 3]])) < tol)
assert np.all(abs(a.get_distances(2, [0, 1, 2, 3], mic=False, vector=True)
- np.array([a.get_distance(2, i, vector=True)
for i in [0, 1, 2, 3]])) < tol)
assert np.all(abs(a.get_distances(3, [0, 1, 2, 3], mic=False, vector=True)
- np.array([a.get_distance(3, i, vector=True)
for i in [0, 1, 2, 3]])) < tol)
# get_distances(mic=True, vec=True)
assert np.all(abs(a.get_distances(0, [0, 1, 2, 3], mic=True, vector=True)
- np.array([a.get_distance(0, i, mic=True, vector=True)
for i in [0, 1, 2, 3]])) < tol)
assert np.all(abs(a.get_distances(1, [0, 1, 2, 3], mic=True, vector=True)
- np.array([a.get_distance(1, i, mic=True, vector=True)
for i in [0, 1, 2, 3]])) < tol)
assert np.all(abs(a.get_distances(2, [0, 1, 2, 3], mic=True, vector=True)
- np.array([a.get_distance(2, i, mic=True, vector=True)
for i in [0, 1, 2, 3]])) < tol)
assert np.all(abs(a.get_distances(3, [0, 1, 2, 3], mic=True, vector=True)
- np.array([a.get_distance(3, i, mic=True, vector=True)
for i in [0, 1, 2, 3]])) < tol)
# set_distance
a.set_distance(0, 1, 11., mic=False)
assert abs(a.get_distance(0, 1, mic=False) - 11.) < tol
assert abs(a.get_distance(0, 1, mic=True) - np.sqrt(46)) < tol
# set_distance(mic=True)
a.set_distance(0, 1, 3., mic=True)
assert abs(a.get_distance(0, 1, mic=True) - 3.) < tol
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