def get_chemical_formula(
self,
mode: str = 'hill',
empirical: bool = False,
) -> str:
"""Get chemical formula.
See documentation of ase.atoms.Atoms.get_chemical_formula()."""
# XXX Delegate the work to the Formula object!
if mode in ('reduce', 'all') and empirical:
warnings.warn("Empirical chemical formula not available "
"for mode '{}'".format(mode))
if len(self) == 0:
return ''
numbers = self.numbers
if mode == 'reduce':
n = len(numbers)
changes = np.concatenate(
([0], np.arange(1, n)[numbers[1:] != numbers[:-1]]))
symbols = [chemical_symbols[e] for e in numbers[changes]]
counts = np.append(changes[1:], n) - changes
tokens = []
for s, c in zip(symbols, counts):
tokens.append(s)
if c > 1:
tokens.append(str(c))
formula = ''.join(tokens)
elif mode == 'all':
formula = ''.join([chemical_symbols[n] for n in numbers])
else:
symbols = [chemical_symbols[Z] for Z in numbers]
f = Formula('', _tree=[(symbols, 1)])
if empirical:
f, _ = f.reduce()
if mode in {'hill', 'metal'}:
formula = f.format(mode)
else:
raise ValueError(
"Use mode = 'all', 'reduce', 'hill' or 'metal'.")
return formula
def get_latex_symbol(self):
"""Returns latex-formatted symbol string."""
s = self.symbol
s = Formula(s)
return s.format("latex")
