def test_cif_symmetry_operators(file):
"""Test that the non-translation part of the symmetry_operators is an invertible
matrix of determinant 1 | -1"""
with CIFParser(file) as p:
for sym_op in p.symmetry_operators():
t = sym_op[:3, :3]
assert round(abs(abs(np.linalg.det(t)) - 1), 7) == 0
def test_fractional_atoms(self):
""" Test the CIFParser returns fractional atomic coordinates. """
for name in self._cif_files():
with self.subTest(name.split("\\")[-1]):
with CIFParser(name) as p:
for atm in p.atoms():
self.assertLessEqual(atm.coords_fractional.max(), 1)
self.assertGreaterEqual(atm.coords_fractional.min(), 0)
def test_symmetry_operators(self):
""" Test that the non-translation part of the symmetry_operators is an invertible
matrix of determinant 1 | -1 """
for name in self._cif_files():
with self.subTest(name.split("\\")[-1]):
with CIFParser(name) as p:
for sym_op in p.symmetry_operators():
t = sym_op[:3, :3]
self.assertAlmostEqual(abs(np.linalg.det(t)), 1)
def test_cif_international_number(file):
"""Test that the international space group number found by
CIFParser is the same as spglib's"""
with CIFParser(file) as p:
from_parser = Hall2Number[p.hall_symbol()]
crystal = Crystal.from_cif(file)
from_spglib = crystal.international_number
assert from_parser == from_spglib
def test_site_occupancy(self):
""" Test that atom site occupancy is correctly parsed from CIF files. """
path = os.path.join("tests", "data", "SiC_partial_site_occ.cif")
with CIFParser(path) as parser:
atoms = list(parser.atoms())
for atm in filter(is_element("Si"), atoms):
self.assertEqual(atm.occupancy, 0.75)
for atm in filter(is_element("C"), atoms):
self.assertEqual(atm.occupancy, 0.85)
def test_cif_site_occupancy():
"""Test that atom site occupancy is correctly parsed from CIF files."""
path = Path(__file__).parent / "data" / "SiC_partial_site_occ.cif"
with CIFParser(path) as parser:
atoms = list(parser.atoms())
for atm in filter(is_element("Si"), atoms):
assert atm.occupancy == 0.75
for atm in filter(is_element("C"), atoms):
assert atm.occupancy == 0.85
def test_international_number(self):
""" Test that the international space group number found by
CIFParser is the same as spglib's """
for name in self._cif_files():
with self.subTest(name.split("\\")[-1]):
with CIFParser(name) as p:
from_parser = Hall2Number[p.hall_symbol()]
crystal = Crystal.from_cif(name)
from_spglib = crystal.international_number
self.assertEqual(from_parser, from_spglib)
def test_cif_fractional_atoms(file):
"""Test the CIFParser returns fractional atomic coordinates."""
with CIFParser(file) as p:
for atm in p.atoms():
assert atm.coords_fractional.max() <= 1
assert atm.coords_fractional.min() >= 0