def make_composition_energies_from_mp(
elements: List[str],
atom_energy_yaml: Optional[str] = None,
) -> CompositionEnergies:
"""Obtain the energies from Materials Project.
When the atom_energy_yaml is provided, the total energies are aligned
via atom energies.
"""
properties = ["task_id", "full_formula", "final_energy"]
query = MpQuery(elements, properties=properties)
comp_es = {}
if atom_energy_yaml:
energies = loadfn(atom_energy_yaml)
diff = {e: energies[e] - mp_energies[e] for e in elements}
else:
diff = {e: 0.0 for e in elements}
for m in query.materials:
key = Composition(m["full_formula"])
energy = m["final_energy"]
for k, v in key.as_dict().items():
energy += diff[k] * v
comp_es[key] = CompositionEnergy(energy, m["task_id"])
print(comp_es)
comp_es = remove_higher_energy_comp(comp_es)
print(comp_es)
return CompositionEnergies(comp_es)
def get_composition_from_string(comp_str):
"""validate and return composition from string `comp_str`."""
from pymatgen.core import Composition, Element
comp = Composition(comp_str)
for element in comp.elements:
Element(element)
formula = comp.get_integer_formula_and_factor()[0]
comp = Composition(formula)
return "".join(
[
"{}{}".format(key, int(value) if value > 1 else "")
for key, value in comp.as_dict().items()
]
)
