def test_all_OK(self):
atom = Atom(coordinates=[0, 0.5, 0.989], species='Mn345')
self.assertAlmostEqual(atom.x, 0.)
self.assertAlmostEqual(atom.y, 0.5)
self.assertAlmostEqual(atom.z, 0.989)
self.assertEqual(atom.species, 'Mn345')
self.assertEqual(atom.element, 'Mn345')
def test_add_atom(self):
# non-`Atom` instance
with self.assertRaises(StructureError):
self.structure.add_atom('Si')
# correct usage
self.structure.add_atom(Atom([0, 0, 0], 'Si12'))
self.assertEqual(len(self.structure.atoms), 1)
self.assertListEqual(self.structure.list_of_species, ['Si12'])
def test_all_OK(self):
self.structure.comment = 'bcc-CsCl'
self.structure.lattice_vectors = [[3.42, 0, 0], [0, 3.42, 0], [0, 0, 3.42]]
self.structure.coordinate_system = 'direct'
self.structure.add_atom(Atom([0, 0, 0], 'Cs'))
self.structure.add_atom(Atom([0.5, 0.5, 0.5], 'Cl'))
# composition_dict
self.assertDictEqual(self.structure.composition_dict, {'Cs': 1, 'Cl': 1})
# list_of_species
self.assertListEqual(self.structure.list_of_species, ['Cl', 'Cs'])
poscar = """bcc-CsCl
1.00000000000000
3.42000000000000 0.00000000000000 0.00000000000000
0.00000000000000 3.42000000000000 0.00000000000000
0.00000000000000 0.00000000000000 3.42000000000000
Cl Cs
1 1
Direct
0.50000000000000 0.50000000000000 0.50000000000000
0.00000000000000 0.00000000000000 0.00000000000000"""
self.assertEqual(self.structure.POSCAR, poscar)
def read_poscar(poscar_file='POSCAR'):
"""
:param poscar_file: Location of the VASP POSCAR (version 5) file
NOTE: Names of all species (line 6) need to begin with the symbol of a real element.
:return: `kelpie.structure.Structure` object
"""
if not os.path.isfile(poscar_file):
error_message = 'Specified POSCAR file {} not found'.format(
poscar_file)
raise FileNotFoundError(error_message)
with open(poscar_file, 'r') as fr:
poscar_lines = [line.strip() for line in fr.readlines()]
if not _consistent_number_of_atoms(poscar_lines):
error_message = 'Mismatch between the number of atoms (Line 7) and the number of atomic coordinates (Lines 9-)'
raise KelpieIOError(error_message)
poscar_blocks = [
'system_title', 'scaling_constant', 'lattice_vectors',
'list_of_species', 'list_of_number_of_atoms',
'repeating_list_of_species', 'coordinate_system',
'list_of_atomic_coordinates'
]
poscar_as_dict = {}
for block in poscar_blocks:
poscar_as_dict[block] = globals()['_{}'.format(block)](poscar_lines)
s = Structure()
s.comment = poscar_as_dict['system_title']
s.scaling_constant = poscar_as_dict['scaling_constant']
s.lattice_vectors = poscar_as_dict['lattice_vectors']
s.coordinate_system = poscar_as_dict['coordinate_system']
for ac, sp in zip(poscar_as_dict['list_of_atomic_coordinates'],
poscar_as_dict['repeating_list_of_species']):
atom = Atom(coordinates=ac, species=sp)
s.add_atom(atom)
return s
def test_no_coordinate(self):
with self.assertRaises(AtomError):
Atom(species='Al')
def test_non_string_species(self):
with self.assertRaises(AtomError):
Atom(coordinates=[0, 0, 0], species='1Al')
def test_species_starts_with_unknown_element_symbol(self):
with self.assertRaises(AtomError):
Atom(coordinates=[0, 0, 0], species='Af')
def test_no_species(self):
with self.assertRaises(AtomError):
Atom(coordinates=[0, 0, 0])
def test_coordinates_shape(self):
with self.assertRaises(AtomError):
Atom(coordinates=[], species='Al')
with self.assertRaises(AtomError):
Atom(coordinates=[0, 1, 2, 3], species='Al')
def test_non_float_coordinates(self):
with self.assertRaises(AtomError):
Atom(coordinates=[0., 'A', 0.], species='Al')