def _get_int_removals_helper(self, spec_amts_oxi, redox_el, redox_els,
numa):
"""
This is a helper method for get_removals_int_oxid!
Args:
spec_amts_oxi - a dict of species to their amounts in the structure
redox_el - the element to oxidize or reduce
redox_els - the full list of elements that might be oxidized or reduced
numa - a running set of numbers of A ion at integer oxidation steps
Returns:
a set of numbers A; steps for for oxidizing oxid_el first, then the other oxid_els in this list
"""
# If a given redox_el has multiple oxidation states present in the structure, we want
# to oxidize the lowest state or reduce the highest state
if self.working_ion_charge < 0:
oxid_old = max(spec.oxi_state for spec in spec_amts_oxi
if spec.symbol == redox_el.symbol)
oxid_new = math.ceil(oxid_old - 1)
lowest_oxid = defaultdict(lambda: 2, {"Cu": 1})
# if this is not a valid solution, break out of here and don't add anything to the list
if oxid_new < min(
os for os in Element(redox_el.symbol).oxidation_states
if os >= lowest_oxid[redox_el.symbol]):
return numa
else:
oxid_old = min(spec.oxi_state for spec in spec_amts_oxi
if spec.symbol == redox_el.symbol)
oxid_new = math.floor(oxid_old + 1)
# if this is not a valid solution, break out of here and don't add anything to the list
if oxid_new > redox_el.max_oxidation_state:
return numa
# update the spec_amts_oxi map to reflect that the redox took place
spec_old = Species(redox_el.symbol, oxid_old)
spec_new = Species(redox_el.symbol, oxid_new)
specamt = spec_amts_oxi[spec_old]
spec_amts_oxi = {
sp: amt
for sp, amt in spec_amts_oxi.items() if sp != spec_old
}
spec_amts_oxi[spec_new] = specamt
spec_amts_oxi = Composition(spec_amts_oxi)
# determine the amount of ion A in the structure needed for charge balance and add it to the list
oxi_noA = sum(spec.oxi_state * spec_amts_oxi[spec]
for spec in spec_amts_oxi
if spec.symbol not in self.working_ion.symbol)
a = max(0, -oxi_noA / self.working_ion_charge)
numa = numa.union({a})
# recursively try the other oxidation states
if a == 0:
return numa
for red in redox_els:
numa = numa.union(
self._get_int_removals_helper(spec_amts_oxi.copy(), red,
redox_els, numa))
return numa
def _get_int_removals_helper(self, spec_amts_oxi, oxid_el, oxid_els, numa):
"""
This is a helper method for get_removals_int_oxid!
Args:
spec_amts_oxi - a dict of species to their amounts in the structure
oxid_el - the element to oxidize
oxid_els - the full list of elements that might be oxidized
numa - a running set of numbers of A cation at integer oxidation steps
Returns:
a set of numbers A; steps for for oxidizing oxid_el first, then the other oxid_els in this list
"""
# If Mn is the oxid_el, we have a mixture of Mn2+, Mn3+, determine the minimum oxidation state for Mn
#this is the state we want to oxidize!
oxid_old = min([
spec.oxi_state for spec in spec_amts_oxi
if spec.symbol == oxid_el.symbol
])
oxid_new = math.floor(oxid_old + 1)
#if this is not a valid solution, break out of here and don't add anything to the list
if oxid_new > oxid_el.max_oxidation_state:
return numa
#update the spec_amts_oxi map to reflect that the oxidation took place
spec_old = Specie(oxid_el.symbol, oxid_old)
spec_new = Specie(oxid_el.symbol, oxid_new)
specamt = spec_amts_oxi[spec_old]
spec_amts_oxi = {
sp: amt
for sp, amt in spec_amts_oxi.items() if sp != spec_old
}
spec_amts_oxi[spec_new] = specamt
spec_amts_oxi = Composition(spec_amts_oxi)
#determine the amount of cation A in the structure needed for charge balance and add it to the list
oxi_noA = sum([
spec.oxi_state * spec_amts_oxi[spec] for spec in spec_amts_oxi
if spec.symbol not in self.cation.symbol
])
a = max(0, -oxi_noA / self.cation_charge)
numa = numa.union({a})
#recursively try the other oxidation states
if a == 0:
return numa
else:
for oxid_el in oxid_els:
numa = numa.union(
self._get_int_removals_helper(spec_amts_oxi.copy(),
oxid_el, oxid_els, numa))
return numa
def _get_int_removals_helper(self, spec_amts_oxi, oxid_el, oxid_els, numa):
"""
This is a helper method for get_removals_int_oxid!
Args:
spec_amts_oxi - a dict of species to their amounts in the structure
oxid_el - the element to oxidize
oxid_els - the full list of elements that might be oxidized
numa - a running set of numbers of A cation at integer oxidation steps
Returns:
a set of numbers A; steps for for oxidizing oxid_el first, then the other oxid_els in this list
"""
# If Mn is the oxid_el, we have a mixture of Mn2+, Mn3+, determine the minimum oxidation state for Mn
#this is the state we want to oxidize!
oxid_old = min([spec.oxi_state for spec in spec_amts_oxi if spec.symbol == oxid_el.symbol])
oxid_new = math.floor(oxid_old + 1)
#if this is not a valid solution, break out of here and don't add anything to the list
if oxid_new > oxid_el.max_oxidation_state:
return numa
#update the spec_amts_oxi map to reflect that the oxidation took place
spec_old = Specie(oxid_el.symbol, oxid_old)
spec_new = Specie(oxid_el.symbol, oxid_new)
specamt = spec_amts_oxi[spec_old]
spec_amts_oxi = {sp: amt for sp, amt in spec_amts_oxi.items() if sp != spec_old}
spec_amts_oxi[spec_new] = specamt
spec_amts_oxi = Composition(spec_amts_oxi)
#determine the amount of cation A in the structure needed for charge balance and add it to the list
oxi_noA = sum([spec.oxi_state * spec_amts_oxi[spec] for spec in spec_amts_oxi if
spec.symbol not in self.cation.symbol])
a = max(0, -oxi_noA / self.cation_charge)
numa = numa.union({a})
#recursively try the other oxidation states
if a == 0:
return numa
else:
for oxid_el in oxid_els:
numa = numa.union(
self._get_int_removals_helper(spec_amts_oxi.copy(), oxid_el, oxid_els, numa))
return numa
