def get_integer_formula_and_factor(
self, max_denominator: int = 10000, iupac_ordering: bool = False
) -> Tuple[str, float]:
"""
Calculates an integer formula and factor.
Args:
max_denominator (int): all amounts in the el:amt dict are
first converted to a Fraction with this maximum denominator
iupac_ordering (bool, optional): Whether to order the
formula by the iupac "electronegativity" series, defined in
Table VI of "Nomenclature of Inorganic Chemistry (IUPAC
Recommendations 2005)". This ordering effectively follows
the groups and rows of the periodic table, except the
Lanthanides, Actinides and hydrogen. Note that polyanions
will still be determined based on the true electronegativity of
the elements.
Returns:
A pretty normalized formula and a multiplicative factor, i.e.,
Li0.5O0.25 returns (Li2O, 0.25). O0.25 returns (O2, 0.125)
"""
el_amt = self.get_el_amt_dict()
g = gcd_float(list(el_amt.values()), 1 / max_denominator)
d = {k: round(v / g) for k, v in el_amt.items()}
(formula, factor) = reduce_formula(d, iupac_ordering=iupac_ordering)
if formula in Composition.special_formulas:
formula = Composition.special_formulas[formula]
factor /= 2
return formula, factor * g
def get_ordered_integer_formula(el_amt, max_denominator=1000):
"""Converts a mapping of {element: stoichiometric value} to a alphabetically ordered string.
Given a dictionary of {element : stoichiometric value, ..}, returns a string with
elements ordered alphabetically and stoichiometric values normalized to smallest common
integer denominator.
Args:
el_amt: {element: stoichiometric value} mapping.
max_denominator: The maximum common denominator of stoichiometric values to use for
normalization. Smaller stoichiometric fractions will be converted to the same
integer stoichiometry.
Returns:
A material formula string with elements ordered alphabetically and the stoichiometry
normalized to the smallest integer fractions.
"""
g = gcd_float(list(el_amt.values()), 1 / max_denominator)
d = {k: round(v / g) for k, v in el_amt.items()}
formula = ""
for k in sorted(d):
if d[k] > 1:
formula += k + str(d[k])
elif d[k] != 0:
formula += k
return formula
def get_integer_formula_and_factor(self, max_denominator=10000,
iupac_ordering=False):
"""
Calculates an integer formula and factor.
Args:
max_denominator (int): all amounts in the el:amt dict are
first converted to a Fraction with this maximum denominator
iupac_ordering (bool, optional): Whether to order the
formula by the iupac "electronegativity" series, defined in
Table VI of "Nomenclature of Inorganic Chemistry (IUPAC
Recommendations 2005)". This ordering effectively follows
the groups and rows of the periodic table, except the
Lanthanides, Actanides and hydrogen. Note that polyanions
will still be determined based on the true electronegativity of
the elements.
Returns:
A pretty normalized formula and a multiplicative factor, i.e.,
Li0.5O0.25 returns (Li2O, 0.25). O0.25 returns (O2, 0.125)
"""
el_amt = self.get_el_amt_dict()
g = gcd_float(list(el_amt.values()), 1 / max_denominator)
d = {k: round(v / g) for k, v in el_amt.items()}
(formula, factor) = reduce_formula(
d, iupac_ordering=iupac_ordering)
if formula in Composition.special_formulas:
formula = Composition.special_formulas[formula]
factor /= 2
return formula, factor * g
def get_ordered_integer_formula(self, el_amt, max_denominator=1000):
# return alphabetically ordered formula with integer fractions
g = gcd_float(list(el_amt.values()), 1 / max_denominator)
d = {k: round(v / g) for k, v in el_amt.items()}
formula = ""
for k in sorted(d):
if d[k] > 1:
formula += k + str(d[k])
else:
formula += k
return formula
def _str_from_comp(cls, coeffs, compositions, reduce=False):
r_coeffs = np.zeros(len(coeffs))
r_formulas = []
for i, (amt, comp) in enumerate(zip(coeffs, compositions)):
formula, factor = comp.get_reduced_formula_and_factor()
r_coeffs[i] = amt * factor
r_formulas.append(formula)
if reduce:
factor = 1 / gcd_float(np.abs(r_coeffs))
r_coeffs *= factor
else:
factor = 1
return cls._str_from_formulas(r_coeffs, r_formulas), factor
def _str_from_comp(cls, coeffs, compositions, reduce=False):
r_coeffs = np.zeros(len(coeffs))
r_formulas = []
for i, (amt, comp) in enumerate(zip(coeffs, compositions)):
formula, factor = comp.get_reduced_formula_and_factor()
r_coeffs[i] = amt * factor
r_formulas.append(formula)
if reduce:
factor = 1 / gcd_float(np.abs(r_coeffs))
r_coeffs *= factor
else:
factor = 1
return cls._str_from_formulas(r_coeffs, r_formulas), factor
def get_ordered_integer_formula(el_amt, max_denominator=1000):
"""
Given a dictionary of {element : stoichiometric value, ..}, returns a string with
elements ordered alphabetically and stoichiometric values normalized to smallest common
ingeger denominator
:param el_amt:
:param max_denominator:
:return:
"""
# return alphabetically ordered formula with integer fractions
g = gcd_float(list(el_amt.values()), 1 / max_denominator)
d = {k: round(v / g) for k, v in el_amt.items()}
formula = ""
for k in sorted(d):
if d[k] > 1:
formula += k + str(d[k])
elif d[k] != 0:
formula += k
return formula
def get_integer_formula_and_factor(self, max_denominator=10000):
"""
Calculates an integer formula and factor.
Args:
max_denominator (int): all amounts in the el:amt dict are
first converted to a Fraction with this maximum denominator
Returns:
A pretty normalized formula and a multiplicative factor, i.e.,
Li0.5O0.25 returns (Li2O, 0.25). O0.25 returns (O2, 0.125)
"""
el_amt = self.get_el_amt_dict()
g = gcd_float(list(el_amt.values()), 1 / max_denominator)
d = {k: round(v / g) for k, v in el_amt.items()}
(formula, factor) = reduce_formula(d)
if formula in Composition.special_formulas:
formula = Composition.special_formulas[formula]
factor /= 2
return formula, factor * g
def get_integer_formula_and_factor(self, max_denominator=10000):
"""
Calculates an integer formula and factor.
Args:
max_denominator (int): all amounts in the el:amt dict are
first converted to a Fraction with this maximum denominator
Returns:
A pretty normalized formula and a multiplicative factor, i.e.,
Li0.5O0.25 returns (Li2O, 0.25). O0.25 returns (O2, 0.125)
"""
el_amt = self.get_el_amt_dict()
g = gcd_float(list(el_amt.values()), 1 / max_denominator)
d = {k: round(v / g) for k, v in el_amt.items()}
(formula, factor) = reduce_formula(d)
if formula in Composition.special_formulas:
formula = Composition.special_formulas[formula]
factor /= 2
return formula, factor * g
def test_gcd_float(self):
vs = [6.2, 12.4, 15.5 + 5e-9]
self.assertAlmostEqual(gcd_float(vs, 1e-8), 3.1)
def test_gcd_float(self):
vs = [6.2, 12.4, 15.5 + 5e-9]
self.assertAlmostEqual(gcd_float(vs, 1e-8), 3.1)
