def test_getter_and_ragged(self):
struct = CrystalStructure(elements='Al',
lattice_constants=4,
bravais_basis='fcc').repeat(2)
del struct[0]
neigh = struct.get_neighbors_by_distance(cutoff_radius=3)
vecs = neigh.get_vectors(allow_ragged=False)
distances = neigh.get_distances(allow_ragged=False)
indices = neigh.get_indices(allow_ragged=False)
neigh.allow_ragged = False
self.assertTrue(np.array_equal(neigh.distances, distances))
self.assertTrue(np.array_equal(neigh.indices, indices))
self.assertTrue(np.array_equal(neigh.vecs, vecs))
def test_getter_and_ragged(self):
struct = CrystalStructure(elements='Al',
lattice_constants=4,
bravais_basis='fcc').repeat(2)
del struct[0]
neigh = struct.get_neighbors_by_distance(cutoff_radius=3,
mode='filled')
vecs = neigh.filled.vecs
distances = neigh.filled.distances
indices = neigh.filled.indices
self.assertTrue(np.array_equal(neigh.distances, distances))
self.assertTrue(np.array_equal(neigh.indices, indices))
self.assertTrue(np.array_equal(neigh.vecs, vecs))
def test_allow_ragged(self):
struct = CrystalStructure(elements='Al',
lattice_constants=4,
bravais_basis='fcc').repeat(10)
del struct[0]
neigh = struct.get_neighbors_by_distance(cutoff_radius=3)
self.assertTrue(neigh.allow_ragged)
self.assertTrue(isinstance(neigh.indices, list))
indices = neigh.indices.copy()
with self.assertRaises(ValueError):
neigh.allow_ragged = 'yes'
neigh.allow_ragged = False
self.assertTrue(isinstance(neigh.indices, np.ndarray))
self.assertGreater(len(neigh.indices[0]), len(indices[0]))
with self.assertRaises(IndexError):
struct.positions[neigh.indices] = struct.positions[neigh.indices]
neigh.allow_ragged = True
self.assertTrue(np.array_equal(neigh.indices[0], indices[0]))
neigh = struct.get_neighbors(cutoff_radius=3, num_neighbors=None)
self.assertFalse(neigh.allow_ragged)
self.assertTrue(isinstance(neigh.indices, np.ndarray))