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 from_dict(cls, xdict):
"""
Returns Xmu object from dictionary
"""
header = Header.from_dict(xdict['HEADER'])
return cls(header, xdict['TAGS'], xdict['c_atom'],
np.array(xdict['xmu']))
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_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
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 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_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 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 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)
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()[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)
def from_file(feff_inp_file='feff.inp', ldos_file='ldos'):
""""
Creates LDos object from raw Feff ldos files by
by assuming they are numbered consecutively, i.e. ldos01.dat
ldos02.dat...
Args:
feff_inp_file (str): input file of run to obtain structure
ldos_file (str): output ldos file of run to obtain dos info, etc.
"""
header_str = Header.header_string_from_file(feff_inp_file)
header = Header.from_string(header_str)
structure = header.struct
nsites = structure.num_sites
pot_string = Potential.pot_string_from_file(feff_inp_file)
dicts = Potential.pot_dict_from_string(pot_string)
pot_dict = dicts[0]
with zopen(ldos_file + "00.dat", "r") as fobject:
f = fobject.readlines()
efermi = float(f[0].split()[4])
dos_energies = []
ldos = {}
for i in range(1, len(pot_dict) + 1):
if len(str(i)) == 1:
ldos[i] = np.loadtxt("{}0{}.dat".format(ldos_file, i))
else:
ldos[i] = np.loadtxt("{}{}.dat".format(ldos_file, i))
for i in range(0, len(ldos[1])):
dos_energies.append(ldos[1][i][0])
all_pdos = []
vorb = {"s": Orbital.s, "p": Orbital.py, "d": Orbital.dxy,
"f": Orbital.f0}
forb = {"s": 0, "p": 1, "d": 2, "f": 3}
dlength = len(ldos[1])
for i in range(nsites):
pot_index = pot_dict[structure.species[i].symbol]
all_pdos.append(defaultdict(dict))
for k, v in vorb.items():
density = [ldos[pot_index][j][forb[k] + 1]
for j in range(dlength)]
updos = density
downdos = None
if downdos:
all_pdos[-1][v] = {Spin.up: updos, Spin.down: downdos}
else:
all_pdos[-1][v] = {Spin.up: updos}
pdos = all_pdos
vorb2 = {0: Orbital.s, 1: Orbital.py, 2: Orbital.dxy, 3: Orbital.f0}
pdoss = {structure[i]: {v: pdos[i][v]
for v in vorb2.values()}
for i in range(len(pdos))}
forb = {"s": 0, "p": 1, "d": 2, "f": 3}
tdos = [0] * dlength
for i in range(nsites):
pot_index = pot_dict[structure.species[i].symbol]
for v in forb.values():
density = [ldos[pot_index][j][v + 1] for j in range(dlength)]
for j in range(dlength):
tdos[j] = tdos[j] + density[j]
tdos = {Spin.up: tdos}
dos = Dos(efermi, dos_energies, tdos)
complete_dos = CompleteDos(structure, dos, pdoss)
charge_transfer = LDos.charge_transfer_from_file(feff_inp_file,
ldos_file)
return LDos(complete_dos, charge_transfer)
def from_file(feff_inp_file="feff.inp", ldos_file="ldos"):
"""
Creates LDos object from raw Feff ldos files by
by assuming they are numbered consecutively, i.e. ldos01.dat
ldos02.dat...
Args:
feff_inp_file (str): input file of run to obtain structure
ldos_file (str): output ldos file of run to obtain dos info, etc.
"""
header_str = Header.header_string_from_file(feff_inp_file)
header = Header.from_string(header_str)
structure = header.struct
nsites = structure.num_sites
parameters = Tags.from_file(feff_inp_file)
if "RECIPROCAL" in parameters:
pot_dict = {}
pot_readstart = re.compile(".*iz.*lmaxsc.*xnatph.*xion.*folp.*")
pot_readend = re.compile(".*ExternalPot.*switch.*")
pot_inp = re.sub(r"feff.inp", r"pot.inp", feff_inp_file)
dos_index = 1
begin = 0
with zopen(pot_inp, "r") as potfile:
for line in potfile:
if len(pot_readend.findall(line)) > 0:
break
if begin == 1:
begin += 1
continue
if begin == 2:
z_number = int(line.strip().split()[0])
ele_name = Element.from_Z(z_number).name
if ele_name not in pot_dict:
pot_dict[ele_name] = dos_index
else:
pot_dict[ele_name] = min(dos_index,
pot_dict[ele_name])
dos_index += 1
if len(pot_readstart.findall(line)) > 0:
begin = 1
else:
pot_string = Potential.pot_string_from_file(feff_inp_file)
dicts = Potential.pot_dict_from_string(pot_string)
pot_dict = dicts[0]
with zopen(ldos_file + "00.dat", "r") as fobject:
f = fobject.readlines()
efermi = float(f[0].split()[4])
dos_energies = []
ldos = {}
for i in range(1, len(pot_dict) + 1):
if len(str(i)) == 1:
ldos[i] = np.loadtxt(f"{ldos_file}0{i}.dat")
else:
ldos[i] = np.loadtxt(f"{ldos_file}{i}.dat")
for i in range(0, len(ldos[1])):
dos_energies.append(ldos[1][i][0])
all_pdos = []
vorb = {
"s": Orbital.s,
"p": Orbital.py,
"d": Orbital.dxy,
"f": Orbital.f0
}
forb = {"s": 0, "p": 1, "d": 2, "f": 3}
dlength = len(ldos[1])
for i in range(nsites):
pot_index = pot_dict[structure.species[i].symbol]
all_pdos.append(defaultdict(dict))
for k, v in vorb.items():
density = [
ldos[pot_index][j][forb[k] + 1] for j in range(dlength)
]
updos = density
downdos = None
if downdos:
all_pdos[-1][v] = {Spin.up: updos, Spin.down: downdos}
else:
all_pdos[-1][v] = {Spin.up: updos}
pdos = all_pdos
vorb2 = {0: Orbital.s, 1: Orbital.py, 2: Orbital.dxy, 3: Orbital.f0}
pdoss = {
structure[i]: {v: pdos[i][v]
for v in vorb2.values()}
for i in range(len(pdos))
}
forb = {"s": 0, "p": 1, "d": 2, "f": 3}
tdos = [0] * dlength
for i in range(nsites):
pot_index = pot_dict[structure.species[i].symbol]
for v in forb.values():
density = [ldos[pot_index][j][v + 1] for j in range(dlength)]
for j in range(dlength):
tdos[j] = tdos[j] + density[j]
tdos = {Spin.up: tdos}
dos = Dos(efermi, dos_energies, tdos)
complete_dos = CompleteDos(structure, dos, pdoss)
charge_transfer = LDos.charge_transfer_from_file(
feff_inp_file, ldos_file)
return LDos(complete_dos, charge_transfer)
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 from_file(feff_inp_file='feff.inp', ldos_file='ldos'):
""""
Creates LDos object from raw Feff ldos files by
by assuming they are numbered consecutively, i.e. ldos01.dat
ldos02.dat...
Args:
feff_inp_file (str): input file of run to obtain structure
ldos_file (str): output ldos file of run to obtain dos info, etc.
"""
header_str = Header.header_string_from_file(feff_inp_file)
header = Header.from_string(header_str)
structure = header.struct
nsites = structure.num_sites
pot_string = Potential.pot_string_from_file(feff_inp_file)
dicts = Potential.pot_dict_from_string(pot_string)
pot_dict = dicts[0]
with zopen(ldos_file + "00.dat", "r") as fobject:
f = fobject.readlines()
efermi = float(f[0].split()[4])
dos_energies = []
ldos = {}
for i in range(1, len(pot_dict) + 1):
if len(str(i)) == 1:
ldos[i] = np.loadtxt("{}0{}.dat".format(ldos_file, i))
else:
ldos[i] = np.loadtxt("{}{}.dat".format(ldos_file, i))
for i in range(0, len(ldos[1])):
dos_energies.append(ldos[1][i][0])
all_pdos = []
vorb = {
"s": Orbital.s,
"p": Orbital.py,
"d": Orbital.dxy,
"f": Orbital.f0
}
forb = {"s": 0, "p": 1, "d": 2, "f": 3}
dlength = len(ldos[1])
for i in range(nsites):
pot_index = pot_dict[structure.species[i].symbol]
all_pdos.append(defaultdict(dict))
for k, v in vorb.items():
density = [
ldos[pot_index][j][forb[k] + 1] for j in range(dlength)
]
updos = density
downdos = None
if downdos:
all_pdos[-1][v] = {Spin.up: updos, Spin.down: downdos}
else:
all_pdos[-1][v] = {Spin.up: updos}
pdos = all_pdos
vorb2 = {0: Orbital.s, 1: Orbital.py, 2: Orbital.dxy, 3: Orbital.f0}
pdoss = {
structure[i]: {v: pdos[i][v]
for v in vorb2.values()}
for i in range(len(pdos))
}
forb = {"s": 0, "p": 1, "d": 2, "f": 3}
tdos = [0] * dlength
for i in range(nsites):
pot_index = pot_dict[structure.species[i].symbol]
for v in forb.values():
density = [ldos[pot_index][j][v + 1] for j in range(dlength)]
for j in range(dlength):
tdos[j] = tdos[j] + density[j]
tdos = {Spin.up: tdos}
dos = Dos(efermi, dos_energies, tdos)
complete_dos = CompleteDos(structure, dos, pdoss)
charge_transfer = LDos.charge_transfer_from_file(
feff_inp_file, ldos_file)
return LDos(complete_dos, charge_transfer)
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")