def test_conversion(self):
# Make an FCC cell.
cell = Cell()
cell.set_basis(lengths=[3.5, 3.6, 3.4], angles=[89, 90, 91])
cell.add_atom(Atom([0, 0, 0], 0))
cell.add_atom(Atom([0.5, 0.5, 0], 1))
cell.add_atom(Atom([0.5, 0, 0.5], 1))
cell.add_atom(Atom([0, 0.5, 0.5], 1))
cell.set_type_name(0, "Al")
cell.set_type_name(1, "Ni")
# Convert it to string.
vio = VASP5IO()
temp = vio.convert_structure_to_string(cell)
# Convert it back.
new_cell = vio.parse_file(list_of_lines=temp)
# Check to make sure everything is good.
self.assertAlmostEqual(cell.volume(), new_cell.volume(), delta=1e-4)
self.assertEqual(cell.n_types(), new_cell.n_types())
np_tst.assert_array_almost_equal(cell.get_lattice_vectors()[1],
new_cell.get_lattice_vectors()[1],
decimal=4)
new_temp = vio.convert_structure_to_string(new_cell)
np_tst.assert_equal(temp, new_temp)
def test_parse_from_file(self):
vio = VASP5IO()
# this_file_path = os.path.dirname(__file__)
# abs_path = os.path.join(this_file_path, "../../test-files/")
abs_path = pkg_resources.resource_filename('chemml', os.path.join('datasets', 'data', 'magpie_python_test'))
cell = vio.parse_file(file_name=os.path.join(abs_path, "393-Ta1.vasp"))
self.assertAlmostEqual(556.549, cell.volume(), delta=1e-2)
self.assertAlmostEqual(10.218, cell.get_lattice_vectors()[0][0],
delta=1e-2)
self.assertEqual(30, cell.n_atoms())
np_tst.assert_array_almost_equal([0.681, 0.818, 0.998],
cell.get_atom(29).get_position(),
decimal=2)
def test_layered_compound(self):
structure = VASP5IO.parse_file(file_name=os.path.join(self.abs_path, "16234-O2Si1.vasp"))
# Run tessellation.
result = VoronoiTessellationCalculator.compute(structure,
radical=False)
# Test results.
total_vol = 0.0
for cell in result:
total_vol += cell.get_volume()
self.assertTrue(cell.geometry_is_valid())
vol_error = (total_vol - structure.volume()) / structure.volume()
self.assertAlmostEqual(0.0, vol_error, delta=1e-2)
def test_B(self):
structure = VASP5IO.parse_file(file_name=os.path.join(self.abs_path, "673-B1.vasp"))
# Run tessellation.
result = VoronoiTessellationCalculator.compute(structure,
radical=False)
# Test results.
total_vol = 0.0
for cell in result:
total_vol += cell.get_volume()
self.assertTrue(cell.geometry_is_valid())
self.assertAlmostEqual(structure.volume(), total_vol,
delta=total_vol * 0.01)
def test_ICSD_examples(self):
example = ["3315-Ge2Os2Th1", "1001-N1Y1", "11375-C2N1",
"12012-Ge2Ru2Tb1", "3778-Sr1Zn2", "4746-Cd1Cu4Er1"]
for e in example:
structure = VASP5IO.parse_file(file_name=os.path.join(self.abs_path, e +".vasp"))
# Run tessellation.
result = VoronoiTessellationCalculator.compute(structure,
radical=False)
# Test results.
total_vol = 0.0
for cell in result:
total_vol += cell.get_volume()
self.assertTrue(cell.geometry_is_valid())
vol_error = (total_vol - structure.volume()) / structure.volume()
self.assertAlmostEqual(0.0, vol_error, delta=1e-2)