def test_to_dict_and_from_dict(self):
file_name = os.path.join(test_dir, 'HEADER')
header = Header.from_file(file_name)
d = header.to_dict
header2 = Header.from_dict(d)
self.assertEqual(str(header), str(header2),
"Header 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)
d = header.as_dict()
header2 = Header.from_dict(d)
self.assertEqual(str(header), str(header2),
"Header failed to and from dict test")
def get_header(self, structure, source):
"""
Creates header string from structure object
Args:
structure:
pymatgen structure object
source:
string identifying source of structure
Returns:
HEADER string
"""
header = Header(structure)
Header.set_source(header, source)
return header.get_string()
def test_get_string(self):
cif_file = os.path.join(test_dir, 'CoO19128.cif')
h = Header.from_cif_file(cif_file)
head = str(h)
self.assertEqual(head.splitlines()[3].split()[-1],
HeaderTest.header_string.splitlines()[3].split()[-1],
"Failed to generate HEADER from structure")
def test_get_string(self):
cif_file = os.path.join(test_dir, 'CoO19128.cif')
h = Header.from_cif_file(cif_file)
head = str(h)
self.assertEqual(head.splitlines()[3].split()[-1],
HeaderTest.header_string.splitlines()[3].split()[-1],
"Failed to generate HEADER from structure")
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_init(self):
filepath = os.path.join(test_dir, 'HEADER')
header = Header.header_string_from_file(filepath)
h = header.splitlines()
hs = HeaderTest.header_string.splitlines()
for i, line in enumerate(h):
self.assertEqual(line, hs[i])
self.assertEqual(HeaderTest.header_string.splitlines(),
header.splitlines(), "Failed to read HEADER file")
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
pot = FeffPot(struct, 'O')
d = pot.as_dict()
pot2 = FeffPot.from_dict(d)
self.assertEqual(str(pot), str(pot2),
"FeffPot to and from dict does not match")
def test_to_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.to_dict
atoms2 = FeffAtoms.from_dict(d)
self.assertEqual(str(atoms), str(atoms2),
"FeffAtoms failed to and from dict test")
def test_init(self):
filepath = os.path.join(test_dir, 'HEADER')
header = Header.header_string_from_file(filepath)
h = header.splitlines()
hs = HeaderTest.header_string.splitlines()
for i, line in enumerate(h):
self.assertEqual(line, hs[i])
self.assertEqual(HeaderTest.header_string.splitlines(),
header.splitlines(), "Failed to read HEADER file")
def test_to_dict_and_from_dict(self):
file_name = os.path.join(test_dir, 'HEADER')
header = Header.from_file(file_name)
struct = header.struct
pot = FeffPot(struct, 'O')
d=pot.to_dict
pot2 = FeffPot.from_dict(d)
self.assertEqual(str(pot), str(pot2),
"FeffPot to and from dict does not match")
def get_header(self, structure, source='', comment=''):
"""
Creates header string from structure object
Args:
structure: A pymatgen structure object
source: Source identifier used to create structure, can be defined
however user wants to organize structures, calculations, etc.
example would be Materials Project material ID number.
comment: comment to include in header
Returns:
Header object to be used in feff.inp file from a pymatgen structure
"""
return Header(structure, source, comment)
def test_from_string(self):
header = Header.from_string(HeaderTest.header_string)
self.assertEqual(header.struct.composition.reduced_formula, "CoO",
"Failed to generate structure from HEADER string")
def test_from_string(self):
header = Header.from_string(HeaderTest.header_string)
self.assertEqual(header.struct.composition.reduced_formula, "CoO",
"Failed to generate structure from HEADER string")