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import itertools
from ase import Atoms
from ase.geometry import get_distances
from ase.lattice.cubic import FaceCenteredCubic
def test_atoms_distance():
# Setup a chain of H,O,C
# H-O Dist = 2
# O-C Dist = 3
# C-H Dist = 5 with mic=False
# C-H Dist = 4 with mic=True
a = Atoms('HOC', positions=[(1, 1, 1), (3, 1, 1), (6, 1, 1)])
a.set_cell((9, 2, 2))
a.set_pbc((True, False, False))
# Calculate indiviually with mic=True
assert a.get_distance(0, 1, mic=True) == 2
assert a.get_distance(1, 2, mic=True) == 3
assert a.get_distance(0, 2, mic=True) == 4
# Calculate indiviually with mic=False
assert a.get_distance(0, 1, mic=False) == 2
assert a.get_distance(1, 2, mic=False) == 3
assert a.get_distance(0, 2, mic=False) == 5
# Calculate in groups with mic=True
assert (a.get_distances(0, [1, 2], mic=True) == [2, 4]).all()
# Calculate in groups with mic=False
assert (a.get_distances(0, [1, 2], mic=False) == [2, 5]).all()
# Calculate all with mic=True
assert (a.get_all_distances(mic=True) == [[0, 2, 4],
[2, 0, 3],
[4, 3, 0]]).all()
# Calculate all with mic=False
assert (a.get_all_distances(mic=False) == [[0, 2, 5],
[2, 0, 3],
[5, 3, 0]]).all()
# Scale Distance
old = a.get_distance(0, 1)
a.set_distance(0, 1, 0.9, add=True, factor=True)
new = a.get_distance(0, 1)
diff = new - 0.9 * old
assert abs(diff) < 10e-6
# Change Distance
old = a.get_distance(0, 1)
a.set_distance(0, 1, 0.9, add=True)
new = a.get_distance(0, 1)
diff = new - old - 0.9
assert abs(diff) < 10e-6
def test_antisymmetry():
size = 2
atoms = FaceCenteredCubic(size=[size, size, size],
symbol='Cu',
latticeconstant=2,
pbc=(1, 1, 1))
vmin, vlen = get_distances(atoms.get_positions(),
cell=atoms.cell,
pbc=True)
assert (vlen == vlen.T).all()
for i, j in itertools.combinations(range(len(atoms)), 2):
assert (vmin[i, j] == -vmin[j, i]).all()
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