def __init__(self, structure, oxi_states=None):
"""
Does initial Valence bond method to initialize oxidation states for user help
Overwridden by oxi_state specified by
Args: structure
pymatgen structure object to determine the oxidation states
min_max_oxi: any user specified min/max oxidation ranges for elements in structure
oxi_states: any user specified oxidation states of elements in structure
"""
oxi_states = oxi_states if oxi_states is not None else {}
struct_species = structure.types_of_specie
if (len(struct_species)
== 1) and struct_species[0].symbol not in oxi_states.keys():
oxi_states[struct_species[0].symbol] = 0
else:
vir = VIRE(structure)
for elt, oxi in vir.valences.items():
strip_key = ''.join([s for s in elt if s.isalpha()])
if strip_key not in oxi_states.keys():
oxi_states[strip_key] = oxi
self.oxi_states = oxi_states
print(
'\nThis is Full-User Charge Generation Mode.\n'
'Options are: (1) Range mode (input min and max of each each type of defect) '
'or (2) Individual mode (input each charge state you want for each defect)\n'
'\nWhen finished with specific defect, press ENTER to continue.')
rng_mod = raw_input('Please specify Range (R) or Individual (I) Mode:')
if 'R' == rng_mod.upper()[0]:
self.rangemode = True
else:
self.rangemode = False
def __init__(self, structure):
"""
Conservative defect charge generator based on the oxidation statess
determined by bond valence. Targetted materials are wideband
semiconductors and insulators. AxBy where A is cation and B is
anion will have charge assignments {A: [0:y], B:[-x:0]}. For these
systems, antisites typically have very high formation energies and
are ignored.
Args:
structure: pymatgen structure object
"""
struct_species = structure.types_of_specie
if len(struct_species) == 1:
oxi_states = {struct_species[0].symbol: 0}
else:
vir = VIRE(structure)
oxi_states = vir.valences
self.oxi_states = {}
for key, val in oxi_states.items():
strip_key = ''.join([s for s in key if s.isalpha()])
self.oxi_states[strip_key] = val
self.min_max_oxi = {}
for s in struct_species:
if isinstance(s, Specie):
el = s.element
elif isinstance(s, Element):
el = s
else:
continue
max_oxi = max(el.common_oxidation_states)
min_oxi = min(el.common_oxidation_states)
self.min_max_oxi[el.symbol] = (min_oxi, max_oxi)
def __init__(self, structure):
"""
Args:
structure: pymatgen structure object
"""
struct_species = structure.types_of_specie
if len(struct_species) == 1:
oxi_states = {struct_species[0].symbol: 0}
else:
vir = VIRE(structure)
oxi_states = vir.valences
self.oxi_states = {}
for key, val in oxi_states.items():
strip_key = ''.join([s for s in key if s.isalpha()])
self.oxi_states[strip_key] = val
def __init__(self, structure, min_max_oxi=None, oxi_states=None):
"""
Charge assignment based on the oxidation states referenced from
semiconductor database. Targetted materials are shallow and some
wideband semiconductors. For these systems, antisites are common and
their charge assignment for antisites follows vacancies
Args: structure
pymatgen structure object to determine the oxidation states
min_max_oxi: any user specified min/max oxidation ranges for elements in structure
oxi_states: any user specified oxidation states of elements in structure
"""
min_max_oxi = min_max_oxi if min_max_oxi is not None else {}
oxi_states = oxi_states if oxi_states is not None else {}
struct_species = structure.types_of_specie
if (len(struct_species)
== 1) and struct_species[0].symbol not in oxi_states.keys():
oxi_states[struct_species[0].symbol] = 0
else:
vir = VIRE(structure)
for elt, oxi in vir.valences.items():
strip_key = ''.join([s for s in elt if s.isalpha()])
if strip_key not in oxi_states.keys():
oxi_states[strip_key] = oxi
self.oxi_states = oxi_states
self.min_max_oxi_bulk = [0, 0]
for s in struct_species:
if isinstance(s, Specie):
el = s.element
elif isinstance(s, Element):
el = s
else:
continue
if el.symbol not in min_max_oxi.keys():
max_oxi = max(el.common_oxidation_states)
min_oxi = min(el.common_oxidation_states)
min_max_oxi[el.symbol] = [min_oxi, max_oxi]
if min_max_oxi[el.symbol][0] < self.min_max_oxi_bulk[0]:
self.min_max_oxi_bulk[0] = min_max_oxi[el.symbol][0]
if min_max_oxi[el.symbol][1] > self.min_max_oxi_bulk[1]:
self.min_max_oxi_bulk[1] = min_max_oxi[el.symbol][1]
self.min_max_oxi = min_max_oxi