def test_new(self):
test_strain = Strain([[0., 0.01, 0.], [0.01, 0.0002, 0.], [0., 0.,
0.]])
self.assertArrayAlmostEqual(
test_strain,
test_strain.get_deformation_matrix().green_lagrange_strain)
self.assertRaises(ValueError, Strain,
[[0.1, 0.1, 0], [0, 0, 0], [0, 0, 0]])
def test_new(self):
test_strain = Strain([[0., 0.01, 0.],
[0.01, 0.0002, 0.],
[0., 0., 0.]])
self.assertArrayAlmostEqual(
test_strain,
test_strain.get_deformation_matrix().green_lagrange_strain)
self.assertRaises(ValueError, Strain, [[0.1, 0.1, 0],
[0, 0, 0],
[0, 0, 0]])
class StrainTest(PymatgenTest):
def setUp(self):
self.norm_str = Strain.from_deformation([[1.02, 0, 0], [0, 1, 0],
[0, 0, 1]])
self.ind_str = Strain.from_deformation([[1, 0.02, 0], [0, 1, 0],
[0, 0, 1]])
self.non_ind_str = Strain.from_deformation([[1, 0.02, 0.02], [0, 1, 0],
[0, 0, 1]])
with warnings.catch_warnings(record=True):
warnings.simplefilter("always")
self.no_dfm = Strain([[0., 0.01, 0.], [0.01, 0.0002, 0.],
[0., 0., 0.]])
def test_new(self):
test_strain = Strain([[0., 0.01, 0.], [0.01, 0.0002, 0.], [0., 0.,
0.]])
self.assertArrayAlmostEqual(
test_strain,
test_strain.get_deformation_matrix().green_lagrange_strain)
self.assertRaises(ValueError, Strain,
[[0.1, 0.1, 0], [0, 0, 0], [0, 0, 0]])
def test_from_deformation(self):
self.assertArrayAlmostEqual(self.norm_str,
[[0.0202, 0, 0], [0, 0, 0], [0, 0, 0]])
self.assertArrayAlmostEqual(
self.ind_str, [[0., 0.01, 0.], [0.01, 0.0002, 0.], [0., 0., 0.]])
self.assertArrayAlmostEqual(
self.non_ind_str,
[[0., 0.01, 0.01], [0.01, 0.0002, 0.0002], [0.01, 0.0002, 0.0002]])
def test_from_index_amount(self):
# From voigt index
test = Strain.from_index_amount(2, 0.01)
should_be = np.zeros((3, 3))
should_be[2, 2] = 0.01
self.assertArrayAlmostEqual(test, should_be)
# from full-tensor index
test = Strain.from_index_amount((1, 2), 0.01)
should_be = np.zeros((3, 3))
should_be[1, 2] = should_be[2, 1] = 0.01
self.assertArrayAlmostEqual(test, should_be)
def test_properties(self):
# deformation matrix
self.assertArrayAlmostEqual(self.ind_str.get_deformation_matrix(),
[[1, 0.02, 0], [0, 1, 0], [0, 0, 1]])
symm_dfm = Strain(
self.no_dfm).get_deformation_matrix(shape="symmetric")
self.assertArrayAlmostEqual(
symm_dfm,
[[0.99995, 0.0099995, 0], [0.0099995, 1.00015, 0], [0, 0, 1]])
self.assertArrayAlmostEqual(self.no_dfm.get_deformation_matrix(),
[[1, 0.02, 0], [0, 1, 0], [0, 0, 1]])
# voigt
self.assertArrayAlmostEqual(self.non_ind_str.voigt,
[0, 0.0002, 0.0002, 0.0004, 0.02, 0.02])
def test_convert_strain_to_deformation(self):
strain = Tensor(np.random.random((3, 3))).symmetrized
while not (np.linalg.eigvals(strain) > 0).all():
strain = Tensor(np.random.random((3, 3))).symmetrized
upper = convert_strain_to_deformation(strain, shape="upper")
symm = convert_strain_to_deformation(strain, shape="symmetric")
self.assertArrayAlmostEqual(np.triu(upper), upper)
self.assertTrue(Tensor(symm).is_symmetric())
for defo in upper, symm:
self.assertArrayAlmostEqual(defo.green_lagrange_strain, strain)
class StrainTest(PymatgenTest):
def setUp(self):
self.norm_str = Strain.from_deformation([[1.02, 0, 0],
[0, 1, 0],
[0, 0, 1]])
self.ind_str = Strain.from_deformation([[1, 0.02, 0],
[0, 1, 0],
[0, 0, 1]])
self.non_ind_str = Strain.from_deformation([[1, 0.02, 0.02],
[0, 1, 0],
[0, 0, 1]])
with warnings.catch_warnings(record=True):
warnings.simplefilter("always")
self.no_dfm = Strain([[0., 0.01, 0.],
[0.01, 0.0002, 0.],
[0., 0., 0.]])
def test_new(self):
test_strain = Strain([[0., 0.01, 0.],
[0.01, 0.0002, 0.],
[0., 0., 0.]])
self.assertArrayAlmostEqual(
test_strain,
test_strain.get_deformation_matrix().green_lagrange_strain)
self.assertRaises(ValueError, Strain, [[0.1, 0.1, 0],
[0, 0, 0],
[0, 0, 0]])
def test_from_deformation(self):
self.assertArrayAlmostEqual(self.norm_str,
[[0.0202, 0, 0],
[0, 0, 0],
[0, 0, 0]])
self.assertArrayAlmostEqual(self.ind_str,
[[0., 0.01, 0.],
[0.01, 0.0002, 0.],
[0., 0., 0.]])
self.assertArrayAlmostEqual(self.non_ind_str,
[[0., 0.01, 0.01],
[0.01, 0.0002, 0.0002],
[0.01, 0.0002, 0.0002]])
def test_from_index_amount(self):
# From voigt index
test = Strain.from_index_amount(2, 0.01)
should_be = np.zeros((3, 3))
should_be[2, 2] = 0.01
self.assertArrayAlmostEqual(test, should_be)
# from full-tensor index
test = Strain.from_index_amount((1, 2), 0.01)
should_be = np.zeros((3, 3))
should_be[1, 2] = should_be[2, 1] = 0.01
self.assertArrayAlmostEqual(test, should_be)
def test_properties(self):
# deformation matrix
self.assertArrayAlmostEqual(self.ind_str.get_deformation_matrix(),
[[1, 0.02, 0],
[0, 1, 0],
[0, 0, 1]])
symm_dfm = Strain(self.no_dfm).get_deformation_matrix(shape="symmetric")
self.assertArrayAlmostEqual(symm_dfm, [[0.99995,0.0099995, 0],
[0.0099995,1.00015, 0],
[0, 0, 1]])
self.assertArrayAlmostEqual(self.no_dfm.get_deformation_matrix(),
[[1, 0.02, 0],
[0, 1, 0],
[0, 0, 1]])
# voigt
self.assertArrayAlmostEqual(self.non_ind_str.voigt,
[0, 0.0002, 0.0002, 0.0004, 0.02, 0.02])
def test_convert_strain_to_deformation(self):
strain = Tensor(np.random.random((3, 3))).symmetrized
while not (np.linalg.eigvals(strain) > 0).all():
strain = Tensor(np.random.random((3, 3))).symmetrized
upper = convert_strain_to_deformation(strain, shape="upper")
symm = convert_strain_to_deformation(strain, shape="symmetric")
self.assertArrayAlmostEqual(np.triu(upper), upper)
self.assertTrue(Tensor(symm).is_symmetric())
for defo in upper, symm:
self.assertArrayAlmostEqual(defo.green_lagrange_strain, strain)
