def test_degeneracy(self):
sym_perm = self.cell.get_symmetry_permutation()
self.assertEqual(self.cell.get_degeneracy(sym_perm), 1)
### more complex test
arr_lat = np.array([[3.0, 0, 0], [0, 2.0, 0.0], [0, 0, 1.0]])
positions = [[0.00000, 0.00000, 0.00000], [0.00000, 0.50000, 0.00000],
[0.33333, 0.00000, 0.00000], [0.33333, 0.50000, 0.00000],
[0.66666, 0.00000, 0.00000], [0.66666, 0.50000, 0.00000],
[0.16666, 0.25000, 0.50000], [0.16666, 0.75000, 0.50000],
[0.50000, 0.25000, 0.50000], [0.50000, 0.75000, 0.50000],
[0.83333, 0.25000, 0.50000], [0.83333, 0.75000, 0.50000]]
arr_positions = np.array(positions)
arr_numbers = np.array([5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6])
gcell = GeneralCell(arr_lat, arr_positions, arr_numbers)
self.assertEqual(gcell.get_degeneracy(sym_perm), 12)
arr_numbers = np.array([5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6])
gcell = GeneralCell(arr_lat, arr_positions, arr_numbers)
self.assertEqual(gcell.get_degeneracy(sym_perm), 6)
class testGeneralCell(unittest.TestCase):
def setUp(self):
arr_lat = np.array([[3.0, 0, 0], [0, 2.0, 0.0], [0, 0, 1.0]])
positions = [[0.00000, 0.00000, 0.00000], [0.00000, 0.50000, 0.00000],
[0.33333, 0.00000, 0.00000], [0.33333, 0.50000, 0.00000],
[0.66666, 0.00000, 0.00000], [0.66666, 0.50000, 0.00000],
[0.16666, 0.25000, 0.50000], [0.16666, 0.75000, 0.50000],
[0.50000, 0.25000, 0.50000], [0.50000, 0.75000, 0.50000],
[0.83333, 0.25000, 0.50000], [0.83333, 0.75000, 0.50000]]
arr_positions = np.array(positions)
arr_numbers = np.array([6] * 12)
self.cell = GeneralCell(arr_lat, arr_positions, arr_numbers)
# def test_eq(self):
# arr_lat = np.array([[3.0, 0, 0], [0, 2.0, 0.0], [0, 0, 1.0]])
# positions = [
# [0.00000, 0.00000, 0.00000],
# [0.00000, 0.50000, 0.00000],
# [0.33333, 0.00000, 0.00000],
# [0.33333, 0.50000, 0.00000],
# [0.66666, 0.00000, 0.00000],
# [0.66666, 0.50000, 0.00000],
# [0.16666, 0.25000, 0.50000],
# [0.16666, 0.75000, 0.50000],
# [0.50000, 0.25000, 0.50000],
# [0.50000, 0.75000, 0.50000],
# [0.83333, 0.25000, 0.50000],
# [0.83333, 0.75000, 0.50000]
# ]
# arr_positions = np.array(positions)
# arr_numbers = np.array([6]*12)
# cell = GeneralCell(arr_lat, arr_positions, arr_numbers)
# self.assertEqual(cell, self.cell)
#
# arr_lat = np.array([[3.0, 0, 0], [0, 2.0, 0.0], [0, 0, 1.0]])
# positions = [
# [0.00000, 0.00000, 0.00000],
# [0.00000, 0.50000, 0.00000],
# [0.33333, 0.00000, 0.00000],
# [0.66666, 0.50000, 0.00000],
# [0.16666, 0.25000, 0.50000],
# [0.16666, 0.75000, 0.50000],
# [0.33333, 0.50000, 0.00000],
# [0.66666, 0.00000, 0.00000],
# [0.50000, 0.25000, 0.50000],
# [0.50000, 0.75000, 0.50000],
# [0.83333, 0.25000, 0.50000],
# [0.83333, 0.75000, 0.50000]
# ]
# arr_positions = np.array(positions)
# arr_numbers = np.array([6]*12)
# cell = GeneralCell(arr_lat, arr_positions, arr_numbers)
# self.assertEqual(cell, self.cell)
#
# arr_lat = np.array([[3.0, 0, 0], [0, 2.0, 0.0], [0, 0, 1.0]])
# positions = [
# [0.00000, 0.00000, 0.00000],
# [0.00000, 0.50000, 0.00000],
# [0.33333, 0.00000, 0.00000],
# [0.33333, 0.50000, 0.00000],
# [0.66666, 0.00000, 0.00000],
# [0.66666, 0.50000, 0.00000],
# [0.16666, 0.25000, 0.50000],
# [0.16666, 0.75000, 0.50000],
# [0.50000, 0.25000, 0.50000],
# [0.50000, 0.75000, 0.50000],
# [0.83333, 0.25000, 0.50000],
# [0.83333, 0.75000, 0.50000]
# ]
# arr_positions = np.array(positions)
# arr_numbers = np.array([4]*12)
# cell = GeneralCell(arr_lat, arr_positions, arr_numbers)
# self.assertNotEqual(cell, self.cell)
#
# arr_lat = np.array([[2.0, 0, 0], [0, 2.0, 0.0], [0, 0, 1.0]])
# positions = [
# [0.00000, 0.00000, 0.00000],
# [0.00000, 0.50000, 0.00000],
# [0.33333, 0.00000, 0.00000],
# [0.33333, 0.50000, 0.00000],
# [0.66666, 0.00000, 0.00000],
# [0.66666, 0.50000, 0.00000],
# [0.16666, 0.25000, 0.50000],
# [0.16666, 0.75000, 0.50000],
# [0.50000, 0.25000, 0.50000],
# [0.50000, 0.75000, 0.50000],
# [0.83333, 0.25000, 0.50000],
# [0.83333, 0.75000, 0.50000]
# ]
# arr_positions = np.array(positions)
# arr_numbers = np.array([6]*12)
# cell = GeneralCell(arr_lat, arr_positions, arr_numbers)
# self.assertNotEqual(cell, self.cell)
def test_get_speckle_num(self):
self.assertEqual(self.cell.get_speckle_num(Specie("B")), 0)
self.assertEqual(self.cell.get_speckle_num(Specie("C")), 12)
def test_property(self):
np.testing.assert_equal(self.cell.numbers, np.array([6] * 12))
self.assertEqual(self.cell.comment, 'C12')
def test_get_symmetry(self):
sym = self.cell.get_spacegroup()
self.assertEqual(sym, 'Im-3m (229)')
def test_get_symmetry_permutation(self):
sym_num = len(self.cell.get_symmetry_permutation())
self.assertEqual(sym_num, 96)
def test_is_primitive(self):
self.assertFalse(self.cell.is_primitive())
def test_degeneracy(self):
sym_perm = self.cell.get_symmetry_permutation()
self.assertEqual(self.cell.get_degeneracy(sym_perm), 1)
### more complex test
arr_lat = np.array([[3.0, 0, 0], [0, 2.0, 0.0], [0, 0, 1.0]])
positions = [[0.00000, 0.00000, 0.00000], [0.00000, 0.50000, 0.00000],
[0.33333, 0.00000, 0.00000], [0.33333, 0.50000, 0.00000],
[0.66666, 0.00000, 0.00000], [0.66666, 0.50000, 0.00000],
[0.16666, 0.25000, 0.50000], [0.16666, 0.75000, 0.50000],
[0.50000, 0.25000, 0.50000], [0.50000, 0.75000, 0.50000],
[0.83333, 0.25000, 0.50000], [0.83333, 0.75000, 0.50000]]
arr_positions = np.array(positions)
arr_numbers = np.array([5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6])
gcell = GeneralCell(arr_lat, arr_positions, arr_numbers)
self.assertEqual(gcell.get_degeneracy(sym_perm), 12)
arr_numbers = np.array([5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6])
gcell = GeneralCell(arr_lat, arr_positions, arr_numbers)
self.assertEqual(gcell.get_degeneracy(sym_perm), 6)
def test_get_cartesian(self):
arr_lat = np.array([[3.0, 0, 0], [0, 2.0, 0.0], [0, 0, 1.0]])
positions = [[0.00000, 0.00000, 0.00000], [0.00000, 0.50000, 0.00000],
[0.33333, 0.00000, 0.00000], [0.33333, 0.50000, 0.00000],
[0.66666, 0.00000, 0.00000], [0.66666, 0.50000, 0.00000],
[0.16666, 0.25000, 0.50000], [0.16666, 0.75000, 0.50000],
[0.50000, 0.25000, 0.50000], [0.50000, 0.75000, 0.50000],
[0.83333, 0.25000, 0.50000], [0.83333, 0.75000, 0.50000]]
arr_positions = np.array(positions)
arr_numbers = np.array([6] * 12)
cell = GeneralCell(arr_lat, arr_positions, arr_numbers)
cart_coor = cell.get_cartesian()
cart_ans = np.array([[0., 0., 0.], [0., 1., 0.], [0.49998, 0.5, 0.5],
[0.49998, 1.5, 0.5], [0.99999, 0., 0.],
[0.99999, 1., 0.], [1.5, 0.5, 0.5],
[1.5, 1.5, 0.5], [1.99998, 0., 0.],
[1.99998, 1., 0.], [2.49999, 0.5, 0.5],
[2.49999, 1.5, 0.5]])
self.assertTrue(np.allclose(cart_coor, cart_ans))
arr_numbers = np.array([6, 6, 6, 5, 6, 5, 6, 6, 6, 6, 6, 6])
cell = GeneralCell(arr_lat, arr_positions, arr_numbers)
cart_coor = cell.get_cartesian(Specie('B'))
cart_ans = np.array([[0.49998, 1.5, 0.5], [0.99999, 1., 0.]])
def test_supercell(self):
scale_mat = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 2]])
scell = self.cell.supercell(scale_mat)
arr_lat = np.array([[3.0, 0, 0], [0, 2.0, 0.0], [0, 0, 2.0]])
positions = [[0., 0., 0.], [0., 0., 0.5], [0., 0.5,
0.], [0., 0.5, 0.5],
[0.16666, 0.25, 0.25], [0.16666, 0.25, 0.75],
[0.16666, 0.75, 0.25], [0.16666, 0.75, 0.75],
[0.33333, 0., 0.], [0.33333, 0., 0.5], [0.33333, 0.5, 0.],
[0.33333, 0.5, 0.5], [0.5, 0.25, 0.25], [0.5, 0.25, 0.75],
[0.5, 0.75, 0.25], [0.5, 0.75, 0.75], [0.66666, 0., 0.],
[0.66666, 0., 0.5], [0.66666, 0.5, 0.],
[0.66666, 0.5, 0.5], [0.83333, 0.25, 0.25],
[0.83333, 0.25, 0.75], [0.83333, 0.75, 0.25],
[0.83333, 0.75, 0.75]]
arr_positions = np.array(positions)
arr_numbers = np.array([6] * 24)
ans_scell = GeneralCell(arr_lat, arr_positions, arr_numbers)
self.assertTrue(np.allclose(scell.positions, arr_positions))