diff --git a/emmet-core/emmet/core/structure_group.py b/emmet-core/emmet/core/structure_group.py new file mode 100644 index 0000000000..bd035407a8 --- /dev/null +++ b/emmet-core/emmet/core/structure_group.py @@ -0,0 +1,222 @@ +import logging +import operator +from datetime import datetime +from itertools import groupby +from typing import List + +from monty.json import MontyDecoder +from pydantic import BaseModel, Field, validator +from pymatgen.analysis.structure_matcher import ElementComparator, StructureMatcher +from pymatgen.entries.computed_entries import ComputedStructureEntry + +from emmet.stubs import Composition, Structure + +logger = logging.getLogger(__name__) + + +def generic_groupby(list_in, comp=operator.eq): + """ + Group a list of unsortable objects + Args: + list_in: A list of generic objects + comp: (Default value = operator.eq) The comparator + Returns: + [int] list of labels for the input list + """ + list_out = [None] * len(list_in) + label_num = 0 + for i1, ls1 in enumerate(list_out): + if ls1 is not None: + continue + list_out[i1] = label_num + for i2, ls2 in list(enumerate(list_out))[i1 + 1 :]: + if comp(list_in[i1], list_in[i2]): + if list_out[i2] is None: + list_out[i2] = list_out[i1] + else: + list_out[i1] = list_out[i2] + label_num -= 1 + label_num += 1 + return list_out + + +def s_hash(el): + return el.data["comp_delith"] + + +class StructureGroupDoc(BaseModel): + """ + Group of structure + """ + + task_id: str = Field( + None, + description="The id of the group is represented by the lowest numerical valued id amoung this group.", + ) + + grouped_ids: list = Field( + None, + description="A list of materials ids for all of the materials that were grouped together.", + ) + + framework: str = Field( + None, + description="The chemical formula for the framwork (the materials system without working ion).", + ) + + ignored_species: list = Field(None, description="List of ignored atomic species.") + + chemsys: str = Field( + None, + description="The chemical system this group belongs to, if the atoms for the ignored species is present the chemsys will also include the ignored species.", + ) + + last_updated: datetime = Field( + None, + description="Timestamp when this document was built.", + ) + + # Make sure that the datetime field is properly formatted + @validator("last_updated", pre=True) + def last_updated_dict_ok(cls, v): + return MontyDecoder().process_decoded(v) + + @classmethod + def from_grouped_entries( + cls, entries: List[ComputedStructureEntry], ignored_species: List[str] + ) -> "StructureGroupDoc": + """ " + Assuming a list of entries are already grouped together, create a StructureGroupDoc + Args: + entries: A list of entries that is already grouped together. + """ + all_atoms = set() + for ient in entries: + all_atoms |= set(ient.composition.as_dict().keys()) + + common_atoms = all_atoms - set(ignored_species) + if len(common_atoms) == 0: + framework_str = "ignored" + else: + comp_d = {k: entries[0].composition.as_dict()[k] for k in common_atoms} + framework_comp = Composition.from_dict(comp_d) + framework_str = framework_comp.reduced_formula + ids = [ient.entry_id for ient in entries] + lowest_id = min(ids, key=_get_id_num) + + fields = { + "task_id": lowest_id, + "grouped_ids": ids, + "framework": framework_str, + "ignored_species": sorted(ignored_species), + "chemsys": "-".join(sorted(all_atoms)), + } + + return cls(**fields) + + @classmethod + def from_ungrouped_structure_entries( + cls, + entries: List[ComputedStructureEntry], + ignored_species: List[str], + ltol: float = 0.2, + stol: float = 0.3, + angle_tol: float = 5.0, + ) -> List["StructureGroupDoc"]: + """ + Create a list of StructureGroupDocs from a list of ungrouped entries. + + Args: + entries: The list of ComputedStructureEntries to process. + ignored_species: the list of ignored species for the structure matcher + ltol: length tolerance for the structure matcher + stol: site position tolerance for the structure matcher + angle_tol: angel tolerance for the structure matcher + """ + + results = [] + sm = StructureMatcher( + comparator=ElementComparator(), + primitive_cell=True, + ignored_species=ignored_species, + ltol=ltol, + stol=stol, + angle_tol=angle_tol, + ) + + # Add a framework field to each entry's data attribute + for ient in entries: + ient.data["framework"] = _get_framework( + ient.composition.reduced_formula, ignored_species + ) + + # split into groups for each framework, must sort before grouping + entries.sort(key=lambda x: x.data["framework"]) + framework_groups = groupby(entries, key=lambda x: x.data["framework"]) + + cnt_ = 0 + for framework, f_group in framework_groups: + # if you only have ignored atoms put them into one "ignored" groupd + f_group_l = list(f_group) + if framework == "ignored": + struct_group = cls.from_grouped_entries( + f_group_l, ignored_species=ignored_species + ) + cnt_ += len(struct_group.grouped_ids) + continue + + logger.debug( + f"Performing structure matching for {framework} with {len(f_group_l)} documents." + ) + for g in group_entries_with_structure_matcher(f_group_l, sm): + struct_group = cls.from_grouped_entries( + g, ignored_species=ignored_species + ) + cnt_ += len(struct_group.grouped_ids) + results.append(struct_group) + if cnt_ != len(entries): + raise RuntimeError( + "The number of entries in all groups the end does not match the number of supplied entries documents." + "Something is seriously wrong, please rebuild the entire database and see if the problem persists." + ) + return results + + +def group_entries_with_structure_matcher(g, struct_matcher): + """ + Group the entries together based on similarity of the primitive cells + Args: + g: a list of entries + Returns: + subgroups: subgroups that are grouped together based on structure similarity + """ + labs = generic_groupby( + g, + comp=lambda x, y: struct_matcher.fit(x.structure, y.structure, symmetric=True), + ) + for ilab in set(labs): + sub_g = [g[itr] for itr, jlab in enumerate(labs) if jlab == ilab] + yield [el for el in sub_g] + + +def _get_id_num(task_id): + if isinstance(task_id, int): + return task_id + if isinstance(task_id, str) and "-" in task_id: + return int(task_id.split("-")[-1]) + else: + raise ValueError("TaskID needs to be either a number or of the form xxx-#####") + + +def _get_framework(formula, ignored_species) -> str: + """ + Return the reduced formula of the entry without any of the ignored species + Return 'ignored' if the all the atoms are ignored + """ + dd_ = Composition(formula).as_dict() + if dd_.keys() == set(ignored_species): + return "ignored" + for ignored_sp in ignored_species: + if ignored_sp in dd_: + dd_.pop(ignored_sp) + return Composition.from_dict(dd_).reduced_formula diff --git a/tests/emmet-core/test_structure_group.py b/tests/emmet-core/test_structure_group.py new file mode 100644 index 0000000000..3862daf905 --- /dev/null +++ b/tests/emmet-core/test_structure_group.py @@ -0,0 +1,64 @@ +import pytest +from monty.serialization import loadfn +from pymatgen import Composition +from pymatgen.apps.battery.conversion_battery import ConversionElectrode +from pymatgen.apps.battery.insertion_battery import InsertionElectrode +from pymatgen.entries.computed_entries import ComputedEntry + +from emmet.core.electrode import ( + ConversionElectrodeDoc, + ConversionVoltagePairDoc, + InsertionElectrodeDoc, + InsertionVoltagePairDoc, +) +from emmet.core.structure_group import StructureGroupDoc + + +@pytest.fixture(scope="session") +def entries_lto(test_dir): + """ + Recycle the test cases from pymatgen + """ + entries = loadfn(test_dir / "LiTiO2_batt.json") + for itr, ient in enumerate(entries): + ient.entry_id = f"mp-{itr}" + return entries + + +@pytest.fixture(scope="session") +def entries_lfeo(test_dir): + """ + Recycle the test cases from pymatgen + """ + entries = loadfn(test_dir / "Li-Fe-O.json") + return entries + + +def test_StructureGroupDoc_from_grouped_entries(entries_lto): + sgroup_doc = StructureGroupDoc.from_grouped_entries( + entries_lto, ignored_species=["Li"] + ) + assert sgroup_doc.task_id == "mp-0" + assert sgroup_doc.grouped_ids == ["mp-0", "mp-1", "mp-2", "mp-3", "mp-4", "mp-5"] + assert sgroup_doc.framework == "TiO2" + assert sgroup_doc.ignored_species == ["Li"] + assert sgroup_doc.chemsys == "Li-O-Ti" + + +def test_StructureGroupDoc_from_ungrouped_entries(entries_lfeo): + entry_dict = {ient.entry_id: ient for ient in entries_lfeo} + sgroup_docs = StructureGroupDoc.from_ungrouped_structure_entries( + entries_lfeo, ignored_species=["Li"] + ) + + # Make sure that all the structure in each group has the same framework + for sgroup_doc in sgroup_docs: + framework_ref = sgroup_doc.framework + ignored = sgroup_doc.ignored_species + for entry_id in sgroup_doc.grouped_ids: + dd_ = entry_dict[entry_id].composition.as_dict() + for k in ignored: + if k in dd_: + dd_.pop(k) + framework = Composition.from_dict(dd_).reduced_formula + assert framework == framework_ref diff --git a/tests/test_files/Li-Fe-O.json b/tests/test_files/Li-Fe-O.json new file mode 100644 index 0000000000..ee8cda6603 --- /dev/null +++ b/tests/test_files/Li-Fe-O.json @@ -0,0 +1 @@ +[{"@module": "pymatgen.entries.computed_entries", "@class": "ComputedStructureEntry", "energy": -33.6601167, "composition": {"Fe": 4.0}, "energy_adjustments": [], "parameters": {"run_type": "GGA", "is_hubbard": false, "pseudo_potential": {"functional": "PBE", "labels": ["Fe_pv"], "pot_type": "paw"}, "hubbards": {}, "potcar_symbols": ["PBE Fe_pv"], "oxide_type": "None"}, "data": {"oxide_type": "None"}, "entry_id": "mp-1271693", "correction": 0.0, "structure": {"@module": "pymatgen.core.structure", "@class": "Structure", "charge": null, "lattice": {"matrix": [[2.328461, -0.193624, -0.710011], [1.145816, 1.98861, 3.247448], [0.349508, -3.784728, 2.192002]], "a": 2.441994369776065, "b": 3.9766043995675506, "c": 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