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def test_distance():
import itertools
import numpy as np
from ase import Atoms, Atom
from ase.geometry import distance
# artificial structure
org = Atoms('COPNS',
[[-1.75072, 0.62689, 0.00000],
[0.58357, 2.71652, 0.00000],
[-5.18268, 1.36522, 0.00000],
[-1.86663, -0.77867, 2.18917],
[-1.80586, 0.20783, -2.79331]])
maxdist = 3.0e-13
# translate
for dx in range(3, 10, 2):
new = org.copy()
new.translate([dx / np.sqrt(2), -dx / np.sqrt(2), 0])
dist = distance(org, new, True)
dist2 = distance(org, new, False)
print('translation', dx, '-> distance', dist)
assert dist < maxdist
assert dist == dist2
# rotate
for axis in ['x', '-y', 'z', np.array([1, 1, 1] / np.sqrt(3))]:
for rot in [20, 200]:
new = org.copy()
new.translate(-new.get_center_of_mass())
new.rotate(rot, axis)
dist = distance(org, new, True)
dist2 = distance(org, new, False)
print('rotation', axis, ', angle', rot, '-> distance', dist)
assert dist < maxdist
assert dist == dist2
if 0:
# reflect
new = Atoms()
cm = org.get_center_of_mass()
for a in org:
new.append(Atom(a.symbol, -(a.position - cm)))
dist = distance(org, new)
print('reflected -> distance', dist)
# permute
for i, a in enumerate(org):
if i < 3:
a.symbol = 'H'
for indxs in itertools.permutations(range(3)):
new = org.copy()
for c in range(3):
new[c].position = org[indxs[c]].position
dist = distance(org, new)
print('permutation', indxs, '-> distance', dist)
assert dist < maxdist
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