def test_get_layers(self):
a_0 = 4
struct = CrystalStructure('Al',
lattice_constants=a_0,
bravais_basis='fcc').repeat(10)
layers = struct.analyse.get_layers()
self.assertAlmostEqual(
np.linalg.norm(layers -
np.rint(2 * struct.positions / a_0).astype(int)), 0)
struct.append(Atoms(elements=['C'], positions=np.random.random(
(1, 3))))
self.assertEqual(
np.linalg.norm(layers - struct.analyse.get_layers(
id_list=struct.select_index('Al'))), 0)
self.assertEqual(
np.linalg.norm(layers - struct.analyse.get_layers(
id_list=struct.select_index('Al'), wrap_atoms=False)), 0)
with self.assertRaises(ValueError):
_ = struct.analyse.get_layers(distance_threshold=0)
with self.assertRaises(ValueError):
_ = struct.analyse.get_layers(id_list=[])
def test_get_layers(self):
a_0 = 4
struct = CrystalStructure('Al',
lattice_constants=a_0,
bravais_basis='fcc').repeat(10)
struct_pure = struct.copy()
layers = struct.analyse.get_layers()
self.assertAlmostEqual(
np.linalg.norm(layers -
np.rint(2 * struct.positions / a_0).astype(int)), 0)
struct.append(Atoms(elements=['C'], positions=np.random.random(
(1, 3))))
self.assertEqual(
np.linalg.norm(layers - struct.analyse.get_layers(
id_list=struct.select_index('Al'))), 0)
self.assertEqual(
np.linalg.norm(layers - struct.analyse.get_layers(
id_list=struct.select_index('Al'), wrap_atoms=False)), 0)
with self.assertRaises(ValueError):
_ = struct.analyse.get_layers(distance_threshold=0)
with self.assertRaises(ValueError):
_ = struct.analyse.get_layers(id_list=[])
self.assertTrue(
np.all(struct.analyse.get_layers() == struct.analyse.get_layers(
cluster_method=AgglomerativeClustering(
linkage='complete',
n_clusters=None,
distance_threshold=0.01))),
"Overriding cluster method with default parameters does not return the same results."
)
self.assertTrue(
np.all(struct_pure.analyse.get_layers() == struct_pure.analyse.
get_layers(cluster_method=DBSCAN(eps=0.01))),
"Overriding cluster method with DBSCAN does not return the same results for symmetric structure."
)