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 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 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
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_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
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 from_file(xmu_dat_file="xmu.dat", feff_inp_file="feff.inp"):
"""
Get Xmu from file.
Args:
xmu_dat_file (str): filename and path for xmu.dat
feff_inp_file (str): filename and path of feff.inp input file
Returns:
Xmu object
"""
data = np.loadtxt(xmu_dat_file)
header = Header.from_file(feff_inp_file)
parameters = Tags.from_file(feff_inp_file)
pots = Potential.pot_string_from_file(feff_inp_file)
absorbing_atom = pots.splitlines()[1].split()[2]
return Xmu(header, parameters, absorbing_atom, data)
def from_file(xmu_dat_file="xmu.dat", feff_inp_file="feff.inp"):
"""
Get Xmu from file.
Args:
xmu_dat_file (str): filename and path for xmu.dat
feff_inp_file (str): filename and path of feff.inp input file
Returns:
Xmu object
"""
data = np.loadtxt(xmu_dat_file)
header = Header.from_file(feff_inp_file)
parameters = Tags.from_file(feff_inp_file)
pots = Potential.pot_string_from_file(feff_inp_file)
absorbing_atom = pots.splitlines()[1].split()[2]
return Xmu(header, parameters, absorbing_atom, data)
def from_file(filename="xmu.dat", input_filename="feff.inp"):
"""
Get Xmu from file.
Args:
filename: filename and path for xmu.dat
input_filename: filename and path of feff.inp input file
Returns:
Xmu object
"""
data = np.loadtxt(filename)
header = Header.from_file(input_filename)
parameters = Tags.from_file(input_filename)
pots = Potential.pot_string_from_file(input_filename)
central_atom = pots.splitlines()[1].split()[2]
return Xmu(header, parameters, central_atom, data)
def from_file(xmu_dat_file="xmu.dat", feff_inp_file="feff.inp"):
"""
Get Xmu from file.
Args:
xmu_dat_file (str): filename and path for xmu.dat
feff_inp_file (str): filename and path of feff.inp input file
Returns:
Xmu object
"""
data = np.loadtxt(xmu_dat_file)
header = Header.from_file(feff_inp_file)
parameters = Tags.from_file(feff_inp_file)
pots = Potential.pot_string_from_file(feff_inp_file)
# site index (Note: in feff it starts from 1)
if "RECIPROCAL" in parameters:
absorbing_atom = parameters["TARGET"]
# species symbol
else:
absorbing_atom = pots.splitlines()[1].split()[2]
return Xmu(header, parameters, absorbing_atom, data)
def from_file(xmu_dat_file="xmu.dat", feff_inp_file="feff.inp"):
"""
Get Xmu from file.
Args:
xmu_dat_file (str): filename and path for xmu.dat
feff_inp_file (str): filename and path of feff.inp input file
Returns:
Xmu object
"""
data = np.loadtxt(xmu_dat_file)
header = Header.from_file(feff_inp_file)
parameters = Tags.from_file(feff_inp_file)
pots = Potential.pot_string_from_file(feff_inp_file)
# site index (Note: in feff it starts from 1)
if "RECIPROCAL" in parameters:
absorbing_atom = parameters["TARGET"]
# species symbol
else:
absorbing_atom = pots.splitlines()[3].split()[2]
return Xmu(header, parameters, absorbing_atom, data)