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# fmt: off
import numpy as np
from ase import Atoms
from ase.geometry import get_duplicate_atoms
def test_atoms_get_duplicates():
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
def test_no_duplicate_atoms():
"""test if it works if no duplicates are detected."""
at = Atoms('H3', positions=[[0., 0., 0.],
[1., 0., 0.],
[3, 2.2, 5.2]])
get_duplicate_atoms(at, delete=True)
dups = get_duplicate_atoms(at)
assert dups.size == 0
def test_pbc():
"""test if it works under PBCs."""
positions = [[0.0, 0.0, 0.0], [0.0, 0.0, 0.9]]
atoms = Atoms('H2', positions=positions, cell=np.eye(3), pbc=True)
dups = get_duplicate_atoms(atoms, cutoff=0.2)
np.testing.assert_array_equal(dups, [[0, 1]])
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