diff --git a/emmet-builders/emmet/builders/materials/substrates.py b/emmet-builders/emmet/builders/materials/substrates.py new file mode 100644 index 0000000000..4e10da4431 --- /dev/null +++ b/emmet-builders/emmet/builders/materials/substrates.py @@ -0,0 +1,179 @@ +from typing import Optional, Dict, Iterable +from emmet.core.mpid import MPID +from maggma.core.store import Store +from maggma.core.builder import Builder +from pymatgen.core.structure import Structure +from pymatgen.analysis.elasticity.elastic import ElasticTensor +from pymatgen.symmetry.analyzer import SpacegroupAnalyzer + +from emmet.core.substrates import SubstratesDoc +from emmet.core.utils import jsanitize +from maggma.utils import grouper + + +class SubstratesBuilder(Builder): + def __init__( + self, + materials: Store, + substrates: Store, + elasticity: Optional[Store] = None, + query: Optional[Dict] = None, + **kwargs, + ): + """ + Calculates matching substrates + + Args: + materials (Store): Store of materials documents + diffraction (Store): Store of substrate matches + elasticity (Store): Store of elastic tensor documents + substrates_file (path): file of substrates to consider + query (dict): dictionary to limit materials to be analyzed + """ + self.materials = materials + self.substrates = substrates + self.elasticity = elasticity + self.query = query + self.kwargs = kwargs + + # Enforce that we key on material_id + self.materials.key = "material_id" + self.substrates.key = "material_id" + self.elasticity.key = "material_id" + + super().__init__( + sources=[materials, elasticity], + targets=[substrates], + **kwargs, + ) + + def prechunk(self, number_splits: int) -> Iterable[Dict]: + to_process_mat_ids = self._find_to_process() + + return [ + {"material_id": {"$in": list(chunk)}} + for chunk in grouper(to_process_mat_ids, number_splits) + ] + + def get_items(self): + """ + Gets all materials that need new substrates + + Returns: + generator of materials to calculate substrates + """ + + to_process_mat_ids = self._find_to_process() + + self.logger.info( + "Updating all substrate calculations for {} materials".format( + len(to_process_mat_ids) + ) + ) + + for mpid in to_process_mat_ids: + e_tensor = self.elasticity.query_one( + criteria={self.elasticity.key: mpid}, + properties=["elasticity", "last_updated"], + ) + e_tensor = ( + e_tensor.get("elasticity", {}).get("elastic_tensor", None) + if e_tensor + else None + ) + mat = self.materials.query_one( + criteria={self.materials.key: mpid}, + properties=["structure", "material_id", "last_updated"], + ) + + yield { + "structure": mat["structure"], + "material_id": mat[self.materials.key], + "elastic_tensor": e_tensor, + "last_updated": max( + mat.get("last_updated"), e_tensor.get("last_updated") + ), + } + + def process_item(self, item): + """ + Calculates substrate matches for all given substrates + + Args: + item (dict): a dict with a material_id and a structure + + Returns: + dict: a diffraction dict + """ + + mpid = MPID(item["material_id"]) + elastic_tensor = item.get("elastic_tensor", None) + elastic_tensor = ( + ElasticTensor.from_voigt(elastic_tensor) if elastic_tensor else None + ) + + self.logger.debug("Calculating substrates for {}".format(item["task_id"])) + + # Ensure we're using conventional standard to be consistent with IEEE elastic tensor setting + film = conventional_standard_structure(item) + + substrate_doc = SubstratesDoc.from_structure( + material_id=mpid, + structure=film, + elastic_tensor=elastic_tensor, + last_updated=item["last_updated"], + ) + + return jsanitize(substrate_doc.dict(), allow_bson=True) + + def update_targets(self, items): + """ + Inserts the new substrate matches into the substrates collection + + Args: + items ([[dict]]): a list of list of thermo dictionaries to update + """ + + items = list(filter(None, items)) + + if len(items) > 0: + self.logger.info("Updating {} substrate matches".format(len(items))) + self.substrates.update(docs=items) + else: + self.logger.info("No items to update") + + def ensure_indicies(self): + """ + Ensures indicies on the substrates, materials, and elastic collections + """ + # Search indicies for materials + self.materials.ensure_index(self.materials.key) + self.materials.ensure_index(self.materials.last_updated_field) + + # Search indicies for elasticity + self.elasticity.ensure_index(self.elasticity.key) + self.elasticity.ensure_index(self.elasticity.last_updated_field) + + # Search indicies for substrates + self.substrates.ensure_index(self.substrates.key) + self.substrates.ensure_index(self.substrates.last_updated_field) + + def _find_to_process(self): + self.logger.info("Substrate Builder Started") + + self.logger.info("Setting up indicies") + self.ensure_indicies() + + mat_keys = set(self.materials.distinct("material_id", criteria=self.query)) + updated_mats = self.materials.newer_in(self.substrates) + e_tensor_updated_mats = self.elasticity.newer_in(self.substrates) + + # To ensure all mats are within our scope + return set(e_tensor_updated_mats + updated_mats) & mat_keys + + +def conventional_standard_structure(doc): + """Get a conventional standard structure from doc["structure"].""" + s = Structure.from_dict(doc["structure"]) + spga = SpacegroupAnalyzer(s, symprec=0.1) + return spga.get_conventional_standard_structure() diff --git a/emmet-core/emmet/core/substrates/__init__.py b/emmet-core/emmet/core/substrates/__init__.py new file mode 100644 index 0000000000..f155fb8962 --- /dev/null +++ b/emmet-core/emmet/core/substrates/__init__.py @@ -0,0 +1 @@ +from emmet.core.substrates.substrates import SubstratesDoc diff --git a/emmet-core/emmet/core/substrates/structures.json b/emmet-core/emmet/core/substrates/structures.json new file mode 100644 index 0000000000..fb311dc712 --- /dev/null +++ b/emmet-core/emmet/core/substrates/structures.json @@ -0,0 +1,17143 @@ +[ + { + "name": "Aluminum", + "material_id": "mp-134", + "structure": { + "@module": "pymatgen.core.structure", + 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+ [ + 3.78741722, + 0.0, + 2.18666635 + ], + [ + 1.26247241, + 3.5708112, + 2.18666635 + ], + [ + 0.0, + 0.0, + 4.3733327 + ] + ], + "a": 4.373332702250636, + "b": 4.373332703817418, + "c": 4.3733327, + "alpha": 60.000000028874815, + "beta": 60.00000001702372, + "gamma": 59.99999997952967, + "volume": 59.14561543024554 + }, + "sites": [ + { + "species": [ + { + "element": "Zn", + "occu": 1 + } + ], + "abc": [ + 0.0, + 0.0, + 0.0 + ], + "xyz": [ + 0.0, + 0.0, + 0.0 + ], + "label": "Zn" + }, + { + "species": [ + { + "element": "Te", + "occu": 1 + } + ], + "abc": [ + 0.25, + 0.25, + 0.25 + ], + "xyz": [ + 1.2624724075, + 0.8927028, + 2.18666635 + ], + "label": "Te" + } + ] + } + } + ] diff --git a/emmet-core/emmet/core/substrates/substrates.py b/emmet-core/emmet/core/substrates/substrates.py new file mode 100644 index 0000000000..862769c697 --- /dev/null +++ b/emmet-core/emmet/core/substrates/substrates.py @@ -0,0 +1,129 @@ +import itertools +from operator import attrgetter +from pathlib import Path +from typing import Dict, List, Optional, Tuple + +from monty.serialization import loadfn +from pydantic import BaseModel, Field +from pymatgen.analysis.elasticity.elastic import ElasticTensor +from pymatgen.analysis.substrate_analyzer import SubstrateAnalyzer +from pymatgen.core.structure import Structure + +from emmet.core.material_property import PropertyDoc +from emmet.core.mpid import MPID + + +class Substrate(BaseModel): + name: str + material_id: MPID + structure: Structure + + +DEFAULT_SUBSTRATES = [ + Substrate(**d) for d in loadfn(Path(__file__).parent.joinpath("structures.json")) +] + + +class SubstrateMatch(BaseModel): + """A single substrate match""" + + substrate_id: MPID = Field(description="The MPID for the substrate") + substrate_orientation: Tuple[int, int, int] = Field( + description="The miller orientation of the substrate" + ) + substrate_formula: str = Field(description="The formula of the substrate") + film_orientation: Tuple[int, int, int] = Field( + description="The orientation of the material if grown as a film" + ) + matching_area: float = Field( + description="The minimal coinicidence matching area for this film orientation and substrate orientation" + ) + elastic_energy: float = Field(None, description="The elastic strain energy") + von_misess_strain: float = Field( + None, description="The Von mises strain for the film" + ) + + @classmethod + def from_structure( + cls, + film: Structure, + substrate: Structure, + substrate_id: MPID, + elastic_tensor: Optional[ElasticTensor] = None, + substrate_analyzer: SubstrateAnalyzer = SubstrateAnalyzer(), + ): + # Calculate lowest matches and group by substrate orientation + matches_by_orient = _groupby_itemkey( + substrate_analyzer.calculate( + film=film, + substrate=substrate, + elasticity_tensor=elastic_tensor, + lowest=True, + ), + item="match_area", + ) + + # Find the lowest area match for each substrate orientation + lowest_matches = [ + min(g, key=lambda x: x.match_area) for _, g in matches_by_orient + ] + + for match in lowest_matches: + yield SubstrateMatch( + substrate_id=substrate_id, + substrate_orientation=match.substrate_miller, + substrate_formula=substrate.composition.reduced_formula, + film_orientation=match.film_miller, + matching_area=match.match_area, + elastic_energy=match.elastic_energy, + strain=match.strain, + ) + + +class SubstratesDoc(PropertyDoc): + """Substrate matches computed for the material""" + + substrates: List[SubstrateMatch] = Field( + description="The list of matches for all given substrates" + ) + + @classmethod + def from_structure( # type: ignore[override] + cls, + material_id: MPID, + structure: Structure, + substrates: Optional[List[Substrate]] = None, + elastic_tensor: Optional[ElasticTensor] = None, + **kwargs + ): + substrates = substrates or DEFAULT_SUBSTRATES + all_matches = [] + for substrate in substrates: + all_matches.extend( + list( + SubstrateMatch.from_structure( + film=structure, + substrate=substrate.structure, + substrate_id=substrate.material_id, + elastic_tensor=elastic_tensor, + ) + ) + ) + # Sort based on energy if an elastic tensor is present otherwise the area + if elastic_tensor is not None: + all_matches = list(sorted(all_matches, key=lambda x: x.elastic_energy)) + else: + all_matches = list(sorted(all_matches, key=lambda x: x.matching_area)) + + return super().from_structure( + material_id=material_id, + structure=structure, + substrates=all_matches, + **kwargs + ) + + +def _groupby_itemkey(iterable, item): + """groupby keyed on (and pre-sorted by) attrgetter(item).""" + itemkey = attrgetter(item) + return itertools.groupby(sorted(iterable, key=itemkey), itemkey) diff --git a/emmet-core/requirements.txt b/emmet-core/requirements.txt index b07ffa005f..c3160dc819 100644 --- a/emmet-core/requirements.txt +++ b/emmet-core/requirements.txt @@ -1,4 +1,4 @@ -pymatgen==2022.0.10 +pymatgen==2022.0.11 monty==2021.7.8 pydantic==1.8.2 pybtex==0.24.0 diff --git a/emmet-core/setup.py b/emmet-core/setup.py index b0d01263d2..24cfd22ab9 100644 --- a/emmet-core/setup.py +++ b/emmet-core/setup.py @@ -10,7 +10,10 @@ author_email="feedback@materialsproject.org", url="https://github.com/materialsproject/emmet", packages=find_namespace_packages(include=["emmet.*"]), - package_data={"emmet.core.vasp.calc_types": ["*.yaml"]}, + package_data={ + "emmet.core.vasp.calc_types": ["*.yaml"], + "emmet.core.subtrates": ["*.json"], + }, include_package_data=True, install_requires=[ "pymatgen>=2021.3,<2023.0", diff --git a/tests/emmet-core/test_substrates.py b/tests/emmet-core/test_substrates.py new file mode 100644 index 0000000000..36981c9c27 --- /dev/null +++ b/tests/emmet-core/test_substrates.py @@ -0,0 +1,51 @@ +import pytest +from pymatgen.util.testing import PymatgenTest + +from emmet.core.substrates.substrates import ( + DEFAULT_SUBSTRATES, + SubstrateMatch, + SubstratesDoc, +) + +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", + ] +} + + +def test_substrate_match(): + doc = SubstrateMatch.from_structure( + film=DEFAULT_SUBSTRATES[0], + substrate=DEFAULT_SUBSTRATES[1], + substrate_id="mp-23", + ) + + assert doc is not None + + +@pytest.mark.parametrize("structure", test_structures.values()) +def test_substrate_doc(structure): + test_substrates = DEFAULT_SUBSTRATES[0:2] + doc = SubstratesDoc.from_structure( + material_id="mp-33", structure=structure, substrates=test_substrates + ) + assert doc is not None + assert doc.material_id == "mp-33" + assert len(doc.substrates) > 0