class DeformationTest(PymatgenTest):
def setUp(self):
self.norm_defo = Deformation.from_index_amount((0, 0), 0.02)
self.ind_defo = Deformation.from_index_amount((0, 1), 0.02)
self.non_ind_defo = Deformation([[1.0, 0.02, 0.02], [0.0, 1.0, 0.0],
[0.0, 0.0, 1.0]])
lattice = Lattice([[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]])
self.structure = Structure(lattice, ["Si", "Si"],
[[0, 0, 0], [0.75, 0.5, 0.75]])
def test_properties(self):
# green_lagrange_strain
self.assertArrayAlmostEqual(
self.ind_defo.green_lagrange_strain,
[[0., 0.01, 0.], [0.01, 0.0002, 0.], [0., 0., 0.]])
self.assertArrayAlmostEqual(
self.non_ind_defo.green_lagrange_strain,
[[0., 0.01, 0.01], [0.01, 0.0002, 0.0002], [0.01, 0.0002, 0.0002]])
def test_independence(self):
self.assertFalse(self.non_ind_defo.is_independent())
self.assertEqual(self.ind_defo.get_perturbed_indices()[0], (0, 1))
def test_apply_to_structure(self):
strained_norm = self.norm_defo.apply_to_structure(self.structure)
strained_ind = self.ind_defo.apply_to_structure(self.structure)
strained_non = self.non_ind_defo.apply_to_structure(self.structure)
# Check lattices
self.assertArrayAlmostEqual(
strained_norm.lattice.matrix,
[[3.9170018886, 0, 0], [1.958500946136, 3.32571019, 0],
[0, -2.21713849, 3.13550906]])
self.assertArrayAlmostEqual(
strained_ind.lattice.matrix,
[[3.84019793, 0, 0], [1.9866132, 3.32571019, 0],
[-0.04434277, -2.21713849, 3.13550906]])
self.assertArrayAlmostEqual(
strained_non.lattice.matrix,
[[3.84019793, 0, 0], [1.9866132, 3.3257102, 0],
[0.0183674, -2.21713849, 3.13550906]])
# Check coordinates
self.assertArrayAlmostEqual(strained_norm.sites[1].coords,
[3.91700189, 1.224e-06, 2.3516318])
self.assertArrayAlmostEqual(strained_ind.sites[1].coords,
[3.84019793, 1.224e-6, 2.3516318])
self.assertArrayAlmostEqual(strained_non.sites[1].coords,
[3.8872306, 1.224e-6, 2.3516318])
# Check convention for applying transformation
for vec, defo_vec in zip(self.structure.lattice.matrix,
strained_non.lattice.matrix):
new_vec = np.dot(self.non_ind_defo, np.transpose(vec))
self.assertArrayAlmostEqual(new_vec, defo_vec)
for coord, defo_coord in zip(self.structure.cart_coords,
strained_non.cart_coords):
new_coord = np.dot(self.non_ind_defo, np.transpose(coord))
self.assertArrayAlmostEqual(new_coord, defo_coord)
class DeformationTest(PymatgenTest):
def setUp(self):
self.norm_defo = Deformation.from_index_amount((0, 0), 0.02)
self.ind_defo = Deformation.from_index_amount((0, 1), 0.02)
self.non_ind_defo = Deformation([[1.0, 0.02, 0.02],
[0.0, 1.0, 0.0],
[0.0, 0.0, 1.0]])
lattice = Lattice([[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]])
self.structure = Structure(lattice, ["Si", "Si"], [[0, 0, 0],
[0.75, 0.5, 0.75]])
def test_properties(self):
# green_lagrange_strain
self.assertArrayAlmostEqual(self.ind_defo.green_lagrange_strain,
[[0., 0.01, 0.],
[0.01, 0.0002, 0.],
[0., 0., 0.]])
self.assertArrayAlmostEqual(self.non_ind_defo.green_lagrange_strain,
[[0., 0.01, 0.01],
[0.01, 0.0002, 0.0002],
[0.01, 0.0002, 0.0002]])
def test_independence(self):
self.assertFalse(self.non_ind_defo.is_independent())
self.assertEqual(self.ind_defo.get_perturbed_indices()[0], (0, 1))
def test_apply_to_structure(self):
strained_norm = self.norm_defo.apply_to_structure(self.structure)
strained_ind = self.ind_defo.apply_to_structure(self.structure)
strained_non = self.non_ind_defo.apply_to_structure(self.structure)
# Check lattices
self.assertArrayAlmostEqual(strained_norm.lattice.matrix,
[[3.9170018886, 0, 0],
[1.958500946136, 3.32571019, 0],
[0, -2.21713849, 3.13550906]])
self.assertArrayAlmostEqual(strained_ind.lattice.matrix,
[[3.84019793, 0.07680396, 0],
[1.92009897, 3.36411217, 0],
[0, -2.21713849, 3.13550906]])
self.assertArrayAlmostEqual(strained_non.lattice.matrix,
[[3.84019793, 0.07680396, 0.07680396],
[1.92009897, 3.36411217, 0.0384019794],
[0, -2.21713849, 3.13550906]])
# Check coordinates
self.assertArrayAlmostEqual(strained_norm.sites[1].coords,
[3.91700189, 1.224e-06, 2.3516318])
self.assertArrayAlmostEqual(strained_ind.sites[1].coords,
[3.84019793, 0.07680518, 2.3516318])
self.assertArrayAlmostEqual(strained_non.sites[1].coords,
[3.84019793, 0.07680518, 2.42843575])
class DeformationTest(PymatgenTest):
def setUp(self):
self.norm_defo = Deformation.from_index_amount((0, 0), 0.02)
self.ind_defo = Deformation.from_index_amount((0, 1), 0.02)
self.non_ind_defo = Deformation([[1.0, 0.02, 0.02], [0.0, 1.0, 0.0],
[0.0, 0.0, 1.0]])
lattice = Lattice([[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]])
self.structure = Structure(lattice, ["Si", "Si"],
[[0, 0, 0], [0.75, 0.5, 0.75]])
def test_properties(self):
# green_lagrange_strain
self.assertArrayAlmostEqual(
self.ind_defo.green_lagrange_strain,
[[0., 0.01, 0.], [0.01, 0.0002, 0.], [0., 0., 0.]])
self.assertArrayAlmostEqual(
self.non_ind_defo.green_lagrange_strain,
[[0., 0.01, 0.01], [0.01, 0.0002, 0.0002], [0.01, 0.0002, 0.0002]])
def test_independence(self):
self.assertFalse(self.non_ind_defo.is_independent())
self.assertEqual(self.ind_defo.get_perturbed_indices()[0], (0, 1))
def test_apply_to_structure(self):
strained_norm = self.norm_defo.apply_to_structure(self.structure)
strained_ind = self.ind_defo.apply_to_structure(self.structure)
strained_non = self.non_ind_defo.apply_to_structure(self.structure)
# Check lattices
self.assertArrayAlmostEqual(
strained_norm.lattice.matrix,
[[3.9170018886, 0, 0], [1.958500946136, 3.32571019, 0],
[0, -2.21713849, 3.13550906]])
self.assertArrayAlmostEqual(
strained_ind.lattice.matrix,
[[3.84019793, 0.07680396, 0], [1.92009897, 3.36411217, 0],
[0, -2.21713849, 3.13550906]])
self.assertArrayAlmostEqual(strained_non.lattice.matrix,
[[3.84019793, 0.07680396, 0.07680396],
[1.92009897, 3.36411217, 0.0384019794],
[0, -2.21713849, 3.13550906]])
# Check coordinates
self.assertArrayAlmostEqual(strained_norm.sites[1].coords,
[3.91700189, 1.224e-06, 2.3516318])
self.assertArrayAlmostEqual(strained_ind.sites[1].coords,
[3.84019793, 0.07680518, 2.3516318])
self.assertArrayAlmostEqual(strained_non.sites[1].coords,
[3.84019793, 0.07680518, 2.42843575])
class DeformationTest(PymatgenTest):
def setUp(self):
self.norm_defo = Deformation.from_index_amount((0, 0), 0.02)
self.ind_defo = Deformation.from_index_amount((0, 1), 0.02)
self.non_ind_defo = Deformation([[1.0, 0.02, 0.02],
[0.0, 1.0, 0.0],
[0.0, 0.0, 1.0]])
lattice = Lattice([[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]])
self.structure = Structure(lattice, ["Si", "Si"], [[0, 0, 0],
[0.75, 0.5, 0.75]])
def test_properties(self):
# green_lagrange_strain
self.assertArrayAlmostEqual(self.ind_defo.green_lagrange_strain,
[[0., 0.01, 0.],
[0.01, 0.0002, 0.],
[0., 0., 0.]])
self.assertArrayAlmostEqual(self.non_ind_defo.green_lagrange_strain,
[[0., 0.01, 0.01],
[0.01, 0.0002, 0.0002],
[0.01, 0.0002, 0.0002]])
def test_independence(self):
self.assertFalse(self.non_ind_defo.is_independent())
self.assertEqual(self.ind_defo.get_perturbed_indices()[0], (0, 1))
def test_apply_to_structure(self):
strained_norm = self.norm_defo.apply_to_structure(self.structure)
strained_ind = self.ind_defo.apply_to_structure(self.structure)
strained_non = self.non_ind_defo.apply_to_structure(self.structure)
# Check lattices
self.assertArrayAlmostEqual(strained_norm.lattice.matrix,
[[3.9170018886, 0, 0],
[1.958500946136, 3.32571019, 0],
[0, -2.21713849, 3.13550906]])
self.assertArrayAlmostEqual(strained_ind.lattice.matrix,
[[3.84019793, 0, 0],
[1.9866132, 3.32571019, 0],
[-0.04434277, -2.21713849, 3.13550906]])
self.assertArrayAlmostEqual(strained_non.lattice.matrix,
[[3.84019793, 0, 0],
[1.9866132, 3.3257102, 0],
[0.0183674, -2.21713849, 3.13550906]])
# Check coordinates
self.assertArrayAlmostEqual(strained_norm.sites[1].coords,
[3.91700189, 1.224e-06, 2.3516318])
self.assertArrayAlmostEqual(strained_ind.sites[1].coords,
[3.84019793, 1.224e-6, 2.3516318])
self.assertArrayAlmostEqual(strained_non.sites[1].coords,
[3.8872306, 1.224e-6, 2.3516318])
# Check convention for applying transformation
for vec, defo_vec in zip(self.structure.lattice.matrix,
strained_non.lattice.matrix):
new_vec = np.dot(self.non_ind_defo, np.transpose(vec))
self.assertArrayAlmostEqual(new_vec, defo_vec)
for coord, defo_coord in zip(self.structure.cart_coords, strained_non.cart_coords):
new_coord = np.dot(self.non_ind_defo, np.transpose(coord))
self.assertArrayAlmostEqual(new_coord, defo_coord)
