def test_FCC_primitive(self):
# Create the simulation cell.
structure = Cell()
structure.set_basis(lengths=[0.70710678118655, 0.70710678118655,
1.0], angles=[45, 90, 60])
structure.add_atom(Atom([0, 0, 0], 0))
# Run tessellation.
result = VoronoiTessellationCalculator.compute(structure,
radical=False)
# Test results.
self.assertEqual(structure.n_atoms(), len(result))
self.assertTrue(result[0].geometry_is_valid())
self.assertEqual(12, len(result[0].get_faces()))
poly_index = result[0].get_polyhedron_shape()
self.assertEqual(12, poly_index[4])
poly_index = result[0].get_coordination_shell_shape(result)
self.assertEqual(12, poly_index[4])
def test_FCC(self):
# Create the simulation cell.
structure = Cell()
structure.add_atom(Atom([0, 0, 0], 0))
structure.add_atom(Atom([0.5, 0.5, 0], 0))
structure.add_atom(Atom([0.5, 0, 0.5], 0))
structure.add_atom(Atom([0, 0.5, 0.5], 0))
# Run tessellation.
result = VoronoiTessellationCalculator.compute(structure,
radical=False)
# Test results.
self.assertEqual(structure.n_atoms(), len(result))
for cell in result:
self.assertTrue(cell.geometry_is_valid())
self.assertEqual(12, len(cell.get_faces()))
self.assertAlmostEqual(0.25, cell.get_volume(), delta=1e-6)
poly_index = cell.get_polyhedron_shape()
self.assertEqual(12, poly_index[4])
poly_index = result[0].get_coordination_shell_shape(result)
self.assertEqual(12, poly_index[4])
def test_simple_cubic(self):
# Create the simulation cell.
structure = Cell()
atom = Atom([0, 0, 0], 0)
structure.add_atom(atom)
# Run tessellation.
result = VoronoiTessellationCalculator.compute(structure,
radical=False)
# Test results.
self.assertEqual(structure.n_atoms(), len(result))
self.assertEqual(6, len(result[0].get_faces()))
self.assertAlmostEqual(structure.volume(), result[0].get_volume(),
delta=1e-6)
poly_index = result[0].get_polyhedron_shape()
self.assertEqual(6, poly_index[4])
poly_index = result[0].get_coordination_shell_shape(result)
self.assertEqual(6, poly_index[0])
# Test out the nearest neighbor shells.
# 1st NN shell.
nns = result[0].get_neighbor_shell(result, 1)
self.assertEqual(6, len(nns))
# 2nd NN shell.
nns = result[0].get_neighbor_shell(result, 2)
self.assertEqual(18, len(nns))
# 3rd - 5th NN shell.
for s in range(3, 6):
nns = result[0].get_neighbor_shell(result, s)
for image in nns:
cell = image.get_supercell()
self.assertAlmostEqual(s, sum([abs(cell[i]) for i in range(
3)]), delta=1e-6)
# Test path NNs.
# 0th NN.
paths = result[0].get_neighbors_by_walks(result, 0)
self.assertEqual(1, len(paths))
total_weight = sum(list(paths.values()))
self.assertAlmostEqual(1.0, total_weight, delta=1e-6)
# 1st NN.
paths = result[0].get_neighbors_by_walks(result, 1)
self.assertEqual(6, len(paths))
total_weight = sum(list(paths.values()))
np_tst.assert_array_almost_equal([1/6.0]*6, list(paths.values()))
self.assertAlmostEqual(1.0, total_weight, delta=1e-6)
# 2nd NN.
paths = result[0].get_neighbors_by_walks(result, 2)
self.assertEqual(18, len(paths))
total_weight = sum(list(paths.values()))
for (k,v) in iteritems(paths):
if 2 in k.get_supercell() or -2 in k.get_supercell():
self.assertAlmostEqual(1 / 30.0, v, delta=1e-6)
else:
self.assertAlmostEqual(2 / 30.0, v, delta=1e-6)
self.assertAlmostEqual(1.0, total_weight, delta=1e-6)