Add OPTIMADE adapter

pymatgen/io/optimade.py

@@ -0,0 +1,193 @@
+"""
+This module provides conversion between structure entries following the
+OPTIMADE (https://optimade.org) standard and pymatgen Structure objects.
+
+The code is adapted from the `optimade.adapters.structures.pymatgen` module in
+optimade-python-tools (https://github.com/Materials-Consortia/optimade-python-tools),
+and aims to work without requiring the explicit installation of the `optimade-python-tools`.
+
+"""
+
+from __future__ import annotations
+
+import itertools
+import json
+import math
+import re
+from functools import reduce
+from typing import TYPE_CHECKING
+
+from pymatgen.core.structure import Lattice, Structure
+
+if TYPE_CHECKING:
+    from collections.abc import Generator
+    from typing import Any
+
+
+__author__ = "Matthew Evans"
+
+
+def _pymatgen_species(
+    nsites: int,
+    species_at_sites: list[str],
+) -> list[dict[str, float]]:
+    """Create list of {"symbol": "concentration"} per site for constructing pymatgen Species objects.
+    Removes vacancies, if they are present.
+
+    This function is adapted from the `optimade.adapters.structures.pymatgen` module in `optimade-python-tools`,
+    with some of the generality removed (in terms of partial occupancy).
+
+    """
+    species = [{"name": _, "concentration": [1.0], "chemical_symbols": [_]} for _ in set(species_at_sites)]
+    species_dict = {_["name"]: _ for _ in species}
+
+    pymatgen_species = []
+    for site_number in range(nsites):
+        species_name = species_at_sites[site_number]
+        current_species = species_dict[species_name]
+
+        chemical_symbols = []
+        concentration = []
+        for index, symbol in enumerate(current_species["chemical_symbols"]):
+            if symbol == "vacancy":
+                # Skip. This is how pymatgen handles vacancies;
+                # to not include them, while keeping the concentration in a site less than 1.
+                continue
+            chemical_symbols.append(symbol)
+            concentration.append(current_species["concentration"][index])
+
+        pymatgen_species.append(dict(zip(chemical_symbols, concentration)))
+
+    return pymatgen_species
+
+
+def _optimade_anonymous_element_generator() -> Generator[str, None, None]:
+    """Generator that yields the next symbol in the A, B, Aa, ... Az OPTIMADE anonymous
+    element naming scheme.
+
+    """
+    from string import ascii_lowercase
+
+    for size in itertools.count(1):
+        for tuple_strings in itertools.product(ascii_lowercase, repeat=size):
+            list_strings = list(tuple_strings)
+            list_strings[0] = list_strings[0].upper()
+            yield "".join(list_strings)
+
+
+def _optimade_reduce_or_anonymize_formula(formula: str, alphabetize: bool = True, anonymize: bool = False) -> str:
+    """Takes an input formula, reduces it and either alphabetizes or anonymizes it
+    following the OPTIMADE standard.
+
+    """
+
+    numbers: list[int] = [int(n.strip() or 1) for n in re.split(r"[A-Z][a-z]*", formula)[1:]]
+    # Need to remove leading 1 from split and convert to ints
+
+    species: list[str] = re.findall("[A-Z][a-z]*", formula)
+
+    gcd = reduce(math.gcd, numbers)
+
+    if not len(species) == len(numbers):
+        raise ValueError(f"Something is wrong with the input formula: {formula}")
+
+    numbers = [n // gcd for n in numbers]
+
+    if anonymize:
+        numbers = sorted(numbers, reverse=True)
+        species = [s for _, s in zip(numbers, _optimade_anonymous_element_generator())]
+
+    elif alphabetize:
+        species, numbers = zip(*sorted(zip(species, numbers)))  # type: ignore[assignment]
+
+    return "".join(f"{s}{n if n != 1 else ''}" for n, s in zip(numbers, species))
+
+
+class OptimadeStructureAdapter:
+    """Adapter serves as a bridge between OPTIMADE structures and pymatgen objects."""
+
+    @staticmethod
+    def get_optimade_structure(structure: Structure, **kwargs) -> dict[str, str | dict[str, Any]]:
+        """Get a dictionary in the OPTIMADE Structure format from a pymatgen structure or molecule.
+
+        Args:
+            structure (Structure): pymatgen Structure
+            **kwargs: passed to the ASE Atoms constructor
+
+        Returns:
+            A dictionary serialization of the structure in the OPTIMADE format.
+
+        """
+        if not structure.is_ordered:
+            raise ValueError("OPTIMADE Adapter currently only supports ordered structures")
+
+        attributes: dict[str, Any] = {}
+        attributes["cartesian_site_positions"] = structure.lattice.get_cartesian_coords(structure.frac_coords).tolist()
+        attributes["lattice_vectors"] = structure.lattice.matrix.tolist()
+        attributes["species_at_sites"] = [_.symbol for _ in structure.species]
+        attributes["species"] = [
+            {"name": _.symbol, "chemical_symbols": [_.symbol], "concentration": [1]}
+            for _ in set(structure.composition.elements)
+        ]
+        attributes["dimension_types"] = [int(_) for _ in structure.lattice.pbc]
+        attributes["nperiodic_dimensions"] = sum(attributes["dimension_types"])
+        attributes["nelements"] = len(structure.composition.elements)
+        attributes["chemical_formula_anonymous"] = _optimade_reduce_or_anonymize_formula(
+            structure.composition.formula, anonymize=True
+        )
+        attributes["elements"] = sorted([_.symbol for _ in structure.composition.elements])
+        attributes["chemical_formula_reduced"] = _optimade_reduce_or_anonymize_formula(
+            structure.composition.formula, anonymize=False
+        )
+        attributes["chemical_formula_descriptive"] = structure.composition.formula
+        attributes["elements_ratios"] = [structure.composition.get_atomic_fraction(e) for e in attributes["elements"]]
+        attributes["nsites"] = len(attributes["species_at_sites"])
+
+        attributes["last_modified"] = None
+        attributes["immutable_id"] = None
+        attributes["structure_features"] = []
+
+        return {"attributes": attributes}
+
+    @staticmethod
+    def get_structure(resource: dict, embed_as_properties: bool = True) -> Structure:
+        """Get pymatgen structure from an OPTIMADE structure resource.
+
+        Args:
+            resource: OPTIMADE structure resource as a dictionary, JSON string, or the
+                corresponding attributes dictionary (i.e., `resource["attributes"]`).
+            embed_as_properties: Whether to embed the entire OPTIMADE resource dictionary
+                (which may include additional custom fields) as properties in the pymatgen Structure.
+
+        Returns:
+            Structure: Equivalent pymatgen Structure
+
+        """
+        if isinstance(resource, str):
+            try:
+                resource = json.loads(resource)
+            except json.JSONDecodeError as exc:
+                raise ValueError(f"Could not decode the input OPTIMADE resource as JSON: {exc}")
+
+        if "attributes" not in resource:
+            resource = {"attributes": resource}
+
+        id = resource.get("id", None)
+        attributes = resource["attributes"]
+        properties: dict[str, Any] = {"optimade_id": id}
+        if embed_as_properties:
+            properties["optimade_attributes"] = attributes
+
+        return Structure(
+            lattice=Lattice(
+                attributes["lattice_vectors"],
+                [bool(d) for d in attributes["dimension_types"]],  # type: ignore[arg-type]
+            ),
+            species=_pymatgen_species(
+                nsites=attributes["nsites"],
+                species_at_sites=attributes["species_at_sites"],
+            ),
+            coords=attributes["cartesian_site_positions"],
+            coords_are_cartesian=True,
+            properties=properties,
+        )

tests/io/test_optimade.py

@@ -0,0 +1,23 @@
+from __future__ import annotations
+
+import numpy as np
+
+from pymatgen.core import Structure
+from pymatgen.io.optimade import OptimadeStructureAdapter
+from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR
+
+STRUCTURE = Structure.from_file(f"{VASP_IN_DIR}/POSCAR")
+XYZ_STRUCTURE = f"{TEST_FILES_DIR}/io/xyz/acetylene.xyz"
+
+
+def test_get_optimade_from_structure():
+    optimade_structure = OptimadeStructureAdapter.get_optimade_structure(STRUCTURE)
+
+    assert optimade_structure["attributes"]["nsites"] == len(STRUCTURE)
+    assert optimade_structure["attributes"]["elements"] == ["Fe", "O", "P"]
+    assert optimade_structure["attributes"]["nelements"] == 3
+    assert optimade_structure["attributes"]["chemical_formula_reduced"] == "FeO4P"
+    assert optimade_structure["attributes"]["species_at_sites"] == 4 * ["Fe"] + 4 * ["P"] + 16 * ["O"]
+    np.testing.assert_array_almost_equal(
+        np.abs(optimade_structure["attributes"]["lattice_vectors"]), np.abs(STRUCTURE.lattice.matrix)
+    )