def check(structure, center, tolerance=1e-8):
from numpy import abs, sqrt, all
from pylada.crystal import coordination_shells
# check we get the coordination_shells of zinc-blende.
neighs = coordination_shells(structure, 5, center, tolerance)
assert len(neighs) == 5
assert len(neighs[0]) == 4
for atom, diff, dist in neighs[0]:
assert abs(dist - sqrt(3.0) * 0.25) < tolerance
assert all(abs(abs(diff) - 0.25) < tolerance)
assert len(neighs[1]) == 12
for atom, diff, dist in neighs[1]:
assert abs(dist - sqrt(2.0) * 0.5) < tolerance
assert len([0 for u in diff if abs(u) < tolerance]) == 1
assert len([0 for u in diff if abs(abs(u) - 0.5) < tolerance]) == 2
assert len(neighs[2]) == 12
for atom, diff, dist in neighs[2]:
assert abs(dist - sqrt(0.75 * 0.75 + 2. * 0.25 * 0.25)) < tolerance
assert len([0 for u in diff if abs(abs(u) - 0.25) < tolerance]) == 2
assert len([0 for u in diff if abs(abs(u) - 0.75) < tolerance]) == 1
assert len(neighs[3]) == 6
for atom, diff, dist in neighs[3]:
assert abs(dist - 1.) < tolerance
assert len([0 for u in diff if abs(u) < tolerance]) == 2
assert len([0 for u in diff if abs(abs(u) - 1.) < tolerance]) == 1
assert len(neighs[4]) == 12
for atom, diff, dist in neighs[4]:
assert abs(dist - sqrt(2 * 0.75 * 0.75 + 0.25 * 0.25)) < tolerance
assert len([0 for u in diff if abs(abs(u) - 0.75) < tolerance]) == 2
assert len([0 for u in diff if abs(abs(u) - 0.25) < tolerance]) == 1
def check_against_neighbors(structure, tolerance=1e-8):
from bisect import bisect_right
from pylada.crystal import coordination_shells, neighbors
distances = [u[-1] for u in neighbors(structure, 150, [0, 0, 0], tolerance)]
shells = coordination_shells(structure, 10, [0, 0, 0], tolerance)
for j in range(8):
i = bisect_right(distances, max([u[-1] for u in shells[j]]))
assert i == sum([len(shell) for shell in shells[:j + 1]])
