parser.add_argument('-f', '--format', dest='format', type=str, nargs=1, choices=['cif', 'poscar'], default='poscar', help='Format of input file. Defaults to POSCAR')
parser.add_argument('-t', '--tolerance', dest='tolerance', type=float, nargs=1, help='Tolerance for symmetry determination')
args = parser.parse_args()
tolerance = float(args.tolerance[0]) if args.tolerance else 0.1
file_format = args.format
if args.input_file[0].lower().endswith(".cif"):
file_format = "cif"
elif args.input_file[0].upper().startswith("POSCAR"):
file_format = "poscar"
s = None
if file_format == 'poscar':
p = Poscar.from_file(args.input_file[0])
s = p.struct
else:
r = CifParser(args.input_file[0])
s = r.get_structures(False)[0]
if s:
finder = SymmetryFinder(s, tolerance)
dataset = finder.get_symmetry_dataset()
print "Spacegroup : {}".format(dataset['international'])
print "Int number : {}".format(dataset['number'])
print "Hall symbol : {}".format(dataset["hall"])
class SymmetryFinderTest(unittest.TestCase):
def setUp(self):
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR'))
self.structure = p.struct
self.sg = SymmetryFinder(self.structure, 0.001)
parser = CifParser(os.path.join(test_dir, 'Li10GeP2S12.cif'))
self.disordered_structure = parser.get_structures()[0]
self.disordered_sg = SymmetryFinder(self.disordered_structure, 0.001)
s = p.struct
editor = StructureEditor(p.struct)
site = s[0]
editor.delete_site(0)
editor.append_site(site.species_and_occu, site.frac_coords)
self.sg3 = SymmetryFinder(editor.modified_structure, 0.001)
def test_get_space_symbol(self):
self.assertEqual(self.sg.get_spacegroup_symbol(), "Pnma")
self.assertEqual(self.disordered_sg.get_spacegroup_symbol(), "P4_2/nmc")
self.assertEqual(self.sg3.get_spacegroup_symbol(), "Pnma")
def test_get_space_number(self):
self.assertEqual(self.sg.get_spacegroup_number(), 62)
self.assertEqual(self.disordered_sg.get_spacegroup_number(), 137)
def test_get_hall(self):
self.assertEqual(self.sg.get_hall(), '-P 2ac 2n')
self.assertEqual(self.disordered_sg.get_hall(), 'P 4n 2n -1n')
def test_get_pointgroup(self):
self.assertEqual(self.sg.get_pointgroup(), 'mmm')
self.assertEqual(self.disordered_sg.get_pointgroup(), '4/mmm')
def test_get_symmetry_dataset(self):
ds = self.sg.get_symmetry_dataset()
self.assertEqual(ds['international'], 'Pnma')
def test_get_crystal_system(self):
crystal_system = self.sg.get_crystal_system()
self.assertEqual('orthorhombic', crystal_system)
self.assertEqual('tetragonal', self.disordered_sg.get_crystal_system())
def test_get_symmetry_operations(self):
fracsymmops = self.sg.get_symmetry_operations()
symmops = self.sg.get_symmetry_operations(True)
self.assertEqual(len(symmops), 8)
latt = self.structure.lattice
for fop, op in zip(fracsymmops, symmops):
for site in self.structure:
newfrac = fop.operate(site.frac_coords)
newcart = op.operate(site.coords)
self.assertTrue(np.allclose(latt.get_fractional_coords(newcart), newfrac))
found = False
newsite = PeriodicSite(site.species_and_occu, newcart, latt, coords_are_cartesian=True)
for testsite in self.structure:
if newsite.is_periodic_image(testsite, 1e-3):
found = True
break
self.assertTrue(found)
def test_get_refined_structure(self):
for a in self.sg.get_refined_structure().lattice.angles:
self.assertEqual(a, 90)
refined = self.disordered_sg.get_refined_structure()
for a in refined.lattice.angles:
self.assertEqual(a, 90)
self.assertEqual(refined.lattice.a , refined.lattice.b)
def test_get_symmetrized_structure(self):
symm_struct = self.sg.get_symmetrized_structure()
for a in symm_struct.lattice.angles:
self.assertEqual(a, 90)
self.assertEqual(len(symm_struct.equivalent_sites), 5)
symm_struct = self.disordered_sg.get_symmetrized_structure()
self.assertEqual(len(symm_struct.equivalent_sites), 8)
def test_get_primitive(self):
"""
F m -3 m Li2O testing of converting to primitive cell
"""
self.assertIsNone(self.sg.find_primitive())
parser = CifParser(os.path.join(test_dir, 'Li2O.cif'))
structure = parser.get_structures(False)[0]
s = SymmetryFinder(structure)
primitive_structure = s.find_primitive()
self.assertEqual(primitive_structure.formula, "Li2 O1")
# This isn't what is expected. All the angles should be 60
self.assertAlmostEqual(primitive_structure.lattice.alpha, 120)
self.assertAlmostEqual(primitive_structure.lattice.beta, 60)
self.assertAlmostEqual(primitive_structure.lattice.gamma, 120)
self.assertAlmostEqual(primitive_structure.lattice.volume, structure.lattice.volume / 4.0)
