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from ase import Atoms
from ase.geometry import get_duplicate_atoms
at = Atoms('H5', positions=[[0., 0., 0.],
[1., 0., 0.],
[1.01, 0, 0],
[3, 2.2, 5.2],
[0.1, -0.01, 0.1]])
dups = get_duplicate_atoms(at)
assert all((dups == [[1, 2]]).tolist()) is True
dups = get_duplicate_atoms(at, cutoff=0.2)
assert all((dups == [[0, 4], [1, 2]]).tolist()) is True
get_duplicate_atoms(at, delete=True)
assert len(at) == 4
at = Atoms('H3', positions=[[0., 0., 0.],
[1., 0., 0.],
[3, 2.2, 5.2]])
# test if it works if no duplicates are detected.
get_duplicate_atoms(at, delete=True)
dups = get_duplicate_atoms(at)
assert dups.size == 0
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