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import string
from datetime import datetime
from monty.fractions import gcd
from optimade.models import Species, StructureResourceAttributes
from pymatgen.core.composition import Composition, formula_double_format
from pymatgen.core.structure import Structure
from emmet.core.base import EmmetBaseModel
from emmet.core.mpid import MPID
letters = "ABCDEFGHIJKLMNOPQRSTUVXYZ"
def optimade_form(comp: Composition):
symbols = sorted([str(e) for e in comp.keys()])
numbers = set([comp[s] for s in symbols if comp[s]])
reduced_form = []
for s in symbols:
reduced_form.append(s)
if comp[s] != 1 and len(numbers) > 1:
reduced_form.append(str(int(comp[s])))
return "".join(reduced_form)
def optimade_anonymous_form(comp: Composition):
reduced = comp.element_composition
if all(x == int(x) for x in comp.values()):
reduced /= gcd(*(int(i) for i in comp.values()))
anon = []
for e, amt in zip(string.ascii_uppercase, sorted(reduced.values(), reverse=True)):
if amt == 1:
amt_str = ""
elif abs(amt % 1) < 1e-8:
amt_str = str(int(amt))
else:
amt_str = str(amt)
anon.append(str(e))
anon.append(amt_str)
return "".join(anon)
def hill_formula(comp: Composition) -> str:
"""
:return: Hill formula. The Hill system (or Hill notation) is a system
of writing empirical chemical formulas, molecular chemical formulas and
components of a condensed formula such that the number of carbon atoms
in a molecule is indicated first, the number of hydrogen atoms next,
and then the number of all other chemical elements subsequently, in
alphabetical order of the chemical symbols. When the formula contains
no carbon, all the elements, including hydrogen, are listed
alphabetically.
"""
c = comp.element_composition
elements = sorted([el.symbol for el in c.keys()])
form_elements = []
if "C" in elements:
form_elements.append("C")
if "H" in elements:
form_elements.append("H")
form_elements.extend([el for el in elements if el != "C" and el != "H"])
else:
form_elements = elements
formula = [
f"{el}{formula_double_format(c[el]) if c[el] != 1 else ''}"
for el in form_elements
]
return "".join(formula)
class OptimadeMaterialsDoc(StructureResourceAttributes, EmmetBaseModel):
"""
Optimade Structure resource with a few extra MP specific fields for materials
Thermo calculations are stored as a nested dict, with keys corresponding to the functional
used to perform stability calc, i.e., R2SCAN, GGA_GGA+U_R2SCAN, or GGA_GGA+U
"""
material_id: MPID
chemical_system: str
stability: dict
@classmethod
def from_structure(
cls,
material_id: MPID,
structure: Structure,
last_updated_structure: datetime,
thermo_calcs: dict,
**kwargs,
) -> StructureResourceAttributes:
structure.remove_oxidation_states()
return OptimadeMaterialsDoc(
material_id=material_id,
chemical_system=structure.composition.chemical_system,
stability=thermo_calcs,
elements=sorted(set([e.symbol for e in structure.composition.elements])),
nelements=len(structure.composition.elements),
elements_ratios=list(structure.composition.fractional_composition.values()),
chemical_formula_descriptive=optimade_form(structure.composition),
chemical_formula_reduced=optimade_form(
structure.composition.get_reduced_composition_and_factor()[0]
),
chemical_formula_anonymous=optimade_anonymous_form(structure.composition),
chemical_formula_hill=hill_formula(structure.composition),
dimension_types=[1, 1, 1],
nperiodic_dimensions=3,
lattice_vectors=structure.lattice.matrix.tolist(),
cartesian_site_positions=[site.coords.tolist() for site in structure],
nsites=len(structure),
species=list(
{
site.species_string: Species(
chemical_symbols=[site.species_string],
concentration=[1.0],
name=site.species_string,
)
for site in structure
}.values()
),
species_at_sites=[site.species_string for site in structure],
last_modified=last_updated_structure,
structure_features=[],
**kwargs,
)
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