def test_merge():
clusters = np.eye(5, dtype=np.int32)
groups = [(0, 1, 2), (3, 4)]
clusters_ = np.array([
[1, 1, 1, 0, 0],
[0, 0, 0, 1, 1],
[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0],
],
dtype=np.int32)
assert np.allclose(clusters_, Mapping.merge(clusters, groups))
def test_write_load(tmp_path):
harmonic, equivalencies = get_harmonic('uio66_ff')
mapping = Mapping(harmonic.atoms.get_masses(), equivalencies)
clusters = Mapping.merge(
mapping.clusters,
[(0, 1, 2, 5), (4, 8, 33, 6, 100)],
)
mapping.update_clusters(clusters)
mapping.update_identities(validate=True)
path_npz = tmp_path / 'mapping.npz'
mapping.write(path_npz)
loaded = Mapping.load(path_npz)
assert np.allclose(loaded.masses, mapping.masses)
for i in range(mapping.natoms):
assert loaded.atom_types[i] == mapping.atom_types[i]
assert np.allclose(loaded.clusters, mapping.clusters)