Optimade Materials Doc

emmet-builders/emmet/builders/materials/optimade.py

@@ -0,0 +1,48 @@
+from maggma.builders.map_builder import MapBuilder
+from maggma.core import Store
+from pymatgen.core.structure import Structure
+
+from emmet.core.optimade import OptimadeMaterialsDoc
+from emmet.core.utils import jsanitize
+
+
+class OptimadeMaterialsBuilder(MapBuilder):
+    def __init__(
+        self,
+        materials: Store,
+        optimade: Store,
+        **kwargs,
+    ):
+        """
+        Creates Optimade compatible structure docs for the materials
+
+        Args:
+            materials: Store of materials docs
+            optimade: Store to update with optimade document
+            query : query on materials to limit search
+        """
+        self.materials = materials
+        self.optimade = optimade
+        self.kwargs = kwargs
+
+        # Enforce that we key on material_id
+        self.materials.key = "material_id"
+        self.optimade.key = "material_id"
+        super().__init__(
+            source=materials,
+            target=optimade,
+            projection=["structure"],
+            **kwargs,
+        )
+
+    def unary_function(self, item):
+        structure = Structure.from_dict(item["structure"])
+        mpid = item["material_id"]
+        last_updated = item["last_updated"]
+
+        optimade_doc = OptimadeMaterialsDoc.from_structure(
+            structure=structure, material_id=mpid, last_updated=last_updated
+        )
+        doc = jsanitize(optimade_doc.dict(), allow_bson=True)
+
+        return doc

emmet-core/emmet/core/optimade.py

@@ -0,0 +1,121 @@
+import string
+from datetime import datetime
+from typing import Dict
+
+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.mpid import MPID
+
+letters = "ABCDEFGHIJKLMNOPQRSTUVXYZ"
+
+
+def optimade_form(comp: Composition):
+
+    symbols = sorted([str(e) for e in comp.keys()])
+    reduced_form = []
+    for s in symbols:
+        reduced_form.append(s)
+        if comp[s] != 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 = [
+        "%s%s" % (el, formula_double_format(c[el]) if c[el] != 1 else "")
+        for el in form_elements
+    ]
+    return "".join(formula)
+
+
+class OptimadeMaterialsDoc(StructureResourceAttributes):
+    """Optimade Structure resource with a few extra MP specific fields for materials"""
+
+    material_id: MPID
+    _mp_chemical_system: str
+
+    @classmethod
+    def from_structure(
+        cls, structure: Structure, material_id: MPID, last_updated: datetime, **kwargs
+    ) -> StructureResourceAttributes:
+
+        structure.remove_oxidation_states()
+        return OptimadeMaterialsDoc(
+            material_id=material_id,
+            _mp_chemical_system=structure.composition.chemical_system,
+            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_features=[],
+            **kwargs
+        )

emmet-core/requirements.txt

@@ -7,3 +7,4 @@ seekpath==2.0.1
 setuptools-scm==6.0.1
 robocrys==0.2.7
 matminer==0.7.3
+optimade==0.16.1

tests/emmet-core/test_optimade.py

@@ -0,0 +1,40 @@
+from datetime import datetime
+
+import pytest
+from pymatgen.core.structure import Structure
+from pymatgen.util.testing import PymatgenTest
+
+from emmet.core.optimade import OptimadeMaterialsDoc
+from emmet.core.oxidation_states import OxidationStateDoc
+
+test_structures = {
+    name: struc.get_reduced_structure()
+    for name, struc in PymatgenTest.TEST_STRUCTURES.items()
+    if name
+    in [
+        "SiO2",
+        "Li2O",
+        "LiFePO4",
+        "TlBiSe2",
+        "K2O2",
+        "Li3V2(PO4)3",
+        "CsCl",
+        "Li2O2",
+        "NaFePO4",
+        "Pb2TiZrO6",
+        "SrTiO3",
+        "TiO2",
+        "BaNiO3",
+        "VO2",
+    ]
+}
+
+
+@pytest.mark.parametrize("structure", test_structures.values())
+def test_oxidation_state(structure: Structure):
+    """Very simple test to make sure this actually works"""
+    print(f"Should work : {structure.composition}")
+    doc = OptimadeMaterialsDoc.from_structure(
+        structure, material_id=33, last_updated=datetime.utcnow()
+    )
+    assert doc is not None