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 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")