def test_chemical_symbols(self):
basis = StructureFactory().ase_bulk('Fe', cubic=True)
basis[0] = 'Ni'
neigh = basis.get_neighbors(num_neighbors=1)
self.assertEqual(neigh.chemical_symbols[0, 0], 'Fe')
self.assertEqual(neigh.chemical_symbols[1, 0], 'Ni')
vacancy = StructureFactory().ase_bulk('Fe', cubic=True).repeat(4)
del vacancy[0]
neigh = vacancy.get_neighbors(num_neighbors=None, cutoff_radius=3)
self.assertEqual(neigh.chemical_symbols[0, -1], 'v')
def test_centrosymmetry(self):
structure = StructureFactory().ase_bulk('Fe').repeat(4)
cs = structure.get_neighbors(num_neighbors=8).centrosymmetry
self.assertAlmostEqual(cs.max(), 0)
self.assertAlmostEqual(cs.min(), 0)
structure.positions += 0.01 * (
2 * np.random.random(structure.positions.shape) - 1)
neigh = structure.get_neighbors(num_neighbors=8)
self.assertGreater(neigh.centrosymmetry.min(), 0)
self.assertTrue(
np.allclose(
neigh.centrosymmetry,
structure.analyse.pyscal_centro_symmetry(num_neighbors=8)))
def test_get_shells_flattened(self):
structure = StructureFactory().ase.bulk('Al', cubic=True).repeat(2)
del structure[0]
r = structure.cell[0, 0] * 0.49
neigh = structure.get_neighbors(cutoff_radius=r,
num_neighbors=None,
mode='flattened')
self.assertEqual(len(np.unique(neigh.shells)), 1)
self.assertEqual(len(neigh.shells), 360)
self.assertEqual(len(np.unique(neigh.get_local_shells())), 1)
self.assertEqual(len(neigh.get_local_shells()), 360)
self.assertEqual(len(np.unique(neigh.get_global_shells())), 1)
self.assertEqual(len(neigh.get_global_shells()), 360)
neigh = structure.get_neighbors(cutoff_radius=r, num_neighbors=None)
self.assertEqual(len(np.unique(neigh.flattened.shells)), 1)
self.assertEqual(len(neigh.flattened.shells), 360)
def test_numbers_of_neighbors(self):
basis = StructureFactory().ase.bulk('Al', cubic=True).repeat(2)
del basis[0]
neigh = basis.get_neighbors(num_neighbors=None,
cutoff_radius=0.45 * basis.cell[0, 0])
n, c = np.unique(neigh.numbers_of_neighbors, return_counts=True)
self.assertEqual(n.tolist(), [11, 12])
self.assertEqual(c.tolist(), [12, 19])
def test_atom_numbers(self):
structure = StructureFactory().ase.bulk('Al', cubic=True).repeat(2)
del structure[0]
r = structure.cell[0, 0] * 0.49
neigh = structure.get_neighbors(cutoff_radius=r,
num_neighbors=None,
mode='filled')
n = len(structure)
self.assertEqual(neigh.atom_numbers.sum(), int(n * (n - 1) / 2 * 12))
neigh = structure.get_neighbors(cutoff_radius=r,
num_neighbors=None,
mode='ragged')
for i, (a, d) in enumerate(zip(neigh.atom_numbers, neigh.distances)):
self.assertEqual(np.sum(a - len(d) * [i]), 0)
neigh = structure.get_neighbors(cutoff_radius=r,
num_neighbors=None,
mode='flattened')
labels, counts = np.unique(np.unique(neigh.atom_numbers,
return_counts=True)[1],
return_counts=True)
self.assertEqual(labels.tolist(), [11, 12])
self.assertEqual(counts.tolist(), [12, 19])
def test_get_distances_flattened(self):
structure = StructureFactory().ase.bulk('Al', cubic=True).repeat(2)
del structure[0]
r = structure.cell[0, 0] * 0.49
neigh = structure.get_neighbors(cutoff_radius=r,
num_neighbors=None,
mode='flattened')
self.assertAlmostEqual(np.std(neigh.distances), 0)
self.assertEqual(len(neigh.distances), 360)
self.assertEqual(neigh.vecs.shape, (
360,
3,
))
def test_get_all_pairs(self):
structure = StructureFactory().ase_bulk('Fe').repeat(4)
neigh = structure.get_neighbors(num_neighbors=8)
for n in [2, 4, 6]:
pairs = neigh._get_all_possible_pairs(n)
self.assertEqual(
(np.prod(np.arange(int(n / 2)) * 2 + 1), int(n / 2), 2),
pairs.shape)
for i in range(2**(n - 2)):
a = np.sort(np.random.choice(np.arange(n), 2, replace=False))
self.assertEqual(np.sum(np.all(a == pairs, axis=-1)),
np.prod(np.arange(int((n - 1) / 2)) * 2 + 1))
self.assertEqual(
np.ptp(
np.unique(neigh._get_all_possible_pairs(6),
return_counts=True)[1]), 0)
def test_modes(self):
basis = StructureFactory().ase.bulk('Al', cubic=True)
neigh = basis.get_neighbors()
self.assertTrue(neigh.mode == 'filled')
with self.assertRaises(KeyError):
neigh = basis.get_neighbors(mode='random_key')