def test_get_string(self):
header = Header.from_string(HeaderTest.header_string)
struc = header.struct
central_atom = 'O'
a = FeffAtoms(struc, central_atom)
atoms = a.get_string()
self.assertEqual(atoms.splitlines()[3].split()[4], central_atom,
"failed to create ATOMS string")
def test_get_string(self):
header = Header.from_string(HeaderTest.header_string)
struc = header.struct
central_atom = 'O'
a = FeffAtoms(struc, central_atom)
atoms = a.get_string()
self.assertEqual(atoms.splitlines()[3].split()[4], central_atom,
"failed to create ATOMS string")
def test_as_dict_and_from_dict(self):
file_name = os.path.join(test_dir, 'HEADER')
header = Header.from_file(file_name)
struct = header.struct
atoms = FeffAtoms(struct, 'O')
d = atoms.as_dict()
atoms2 = FeffAtoms.from_dict(d)
self.assertEqual(str(atoms), str(atoms2),
"FeffAtoms failed to and from dict test")
def test_as_dict_and_from_dict(self):
file_name = os.path.join(test_dir, 'HEADER')
header = Header.from_file(file_name)
struct = header.struct
atoms = FeffAtoms(struct, 'O')
d = atoms.as_dict()
atoms2 = FeffAtoms.from_dict(d)
self.assertEqual(str(atoms), str(atoms2),
"FeffAtoms failed to and from dict test")
def get_feff_atoms(self, structure, central_atom):
"""
Creates string representation of atomic shell coordinates using in
ATOMS file and feff.inp.
Args:
structure:
structure object
central_atom:
symbol for absorbing atom
Returns:
String representation of atoms file.
"""
atoms = FeffAtoms(structure, central_atom)
return atoms.get_string()
def get_feff_atoms(self, structure, central_atom):
"""
Creates string representation of atomic shell coordinates using in
ATOMS file and feff.inp.
Args:
structure: pymatgen structure object
central_atom: atom symbol string for absorbing atom
Returns:
FeffAtoms object
"""
return FeffAtoms(structure, central_atom)
def test_init(self):
filepath = os.path.join(test_dir, 'ATOMS')
atoms = FeffAtoms.atoms_string_from_file(filepath)
self.assertEqual(atoms.splitlines()[3].split()[4], 'O',
"failed to read ATOMS file")
def test_init(self):
filepath = os.path.join(test_dir, 'ATOMS')
atoms = FeffAtoms.atoms_string_from_file(filepath)
self.assertEqual(atoms.splitlines()[3].split()[4], 'O',
"failed to read ATOMS file")
