class SpacegroupTest(unittest.TestCase):
def setUp(self):
p = Poscar.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))
self.structure = p.structure
self.sg1 = SpacegroupAnalyzer(self.structure, 0.001).get_space_group_operations()
def test_are_symmetrically_equivalent(self):
sites1 = [self.structure[i] for i in [0, 1]]
sites2 = [self.structure[i] for i in [2, 3]]
self.assertTrue(self.sg1.are_symmetrically_equivalent(sites1, sites2, 1e-3))
sites1 = [self.structure[i] for i in [0, 1]]
sites2 = [self.structure[i] for i in [0, 2]]
self.assertFalse(self.sg1.are_symmetrically_equivalent(sites1, sites2, 1e-3))
class SpacegroupTest(unittest.TestCase):
def setUp(self):
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR'))
self.structure = p.structure
self.sg1 = SpacegroupAnalyzer(self.structure, 0.001).get_spacegroup()
def test_are_symmetrically_equivalent(self):
sites1 = [self.structure[i] for i in [0, 1]]
sites2 = [self.structure[i] for i in [2, 3]]
self.assertTrue(
self.sg1.are_symmetrically_equivalent(sites1, sites2, 1e-3))
sites1 = [self.structure[i] for i in [0, 1]]
sites2 = [self.structure[i] for i in [0, 2]]
self.assertFalse(
self.sg1.are_symmetrically_equivalent(sites1, sites2, 1e-3))
class SpacegroupTest(unittest.TestCase):
def setUp(self):
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR'))
self.structure = p.structure
self.sg1 = SpacegroupAnalyzer(self.structure, 0.001).get_spacegroup()
def test_are_symmetrically_equivalent(self):
sites1 = [self.structure[i] for i in [0, 1]]
sites2 = [self.structure[i] for i in [2, 3]]
self.assertTrue(self.sg1.are_symmetrically_equivalent(sites1, sites2,
1e-3))
sites1 = [self.structure[i] for i in [0, 1]]
sites2 = [self.structure[i] for i in [0, 2]]
self.assertFalse(self.sg1.are_symmetrically_equivalent(sites1, sites2,
1e-3))
def find_noneq_cations(self, symm_prec=1e-3):
"""
Find a list of the site indices of all non-equivalent cations.
Returns:
(list): List of site indices
"""
symmops = SpacegroupAnalyzer(
self, symprec=symm_prec).get_space_group_operations()
cation_indices = [
index for index in range(len(self.sites))
if self.sites[index].species_string not in Cathode.standard_anions
]
# Start with adding the first cation
inequiv_cations = [cation_indices[0], ]
for index in cation_indices[1:]:
s1 = [self.sites[index], ]
# Check if the site is equivalent with one of the sites in the
# inequivalent list.
inequivalent = True
for inequive_index in inequiv_cations:
s2 = [self.sites[inequive_index], ]
if symmops.are_symmetrically_equivalent(
s1, s2, symm_prec=symm_prec):
inequivalent = False
if inequivalent:
inequiv_cations.append(index)
return inequiv_cations
