diff --git a/emmet-builders/emmet/builders/materials/electrodes.py b/emmet-builders/emmet/builders/materials/electrodes.py new file mode 100644 index 0000000000..d4b9e22033 --- /dev/null +++ b/emmet-builders/emmet/builders/materials/electrodes.py @@ -0,0 +1,410 @@ +import operator +import math +from collections import namedtuple +from datetime import datetime +from functools import lru_cache +from itertools import groupby, chain +from pprint import pprint +from typing import Iterable, Dict, List, Any + +from emmet.core.electrode import InsertionElectrodeDoc +from emmet.core.structure_group import StructureGroupDoc +from emmet.core.utils import jsanitize +from maggma.builders import Builder, MapBuilder +from maggma.stores import MongoStore +from monty.json import MontyEncoder +from numpy import unique +from pymatgen import Composition +from pymatgen.analysis.structure_matcher import StructureMatcher, ElementComparator +from pymatgen.apps.battery.insertion_battery import InsertionElectrode +from pymatgen.core import Structure +from pymatgen.entries.computed_entries import ComputedStructureEntry + +__author__ = "Jimmy Shen" +__email__ = "jmmshn@lbl.gov" + +from pymatgen.entries.computed_entries import ComputedEntry + + +def s_hash(el): + return el.data["comp_delith"] + + +# MatDoc = namedtuple("MatDoc", ["task_id", "structure", "formula_pretty", "framework"]) + +REDOX_ELEMENTS = [ + "Ti", + "V", + "Cr", + "Mn", + "Fe", + "Co", + "Ni", + "Cu", + "Nb", + "Mo", + "Sn", + "Sb", + "W", + "Re", + "Bi", + "C", + "Hf", +] + +# WORKING_IONS = ["Li", "Be", "Na", "Mg", "K", "Ca", "Rb", "Sr", "Cs", "Ba"] + +MAT_PROPS = [ + "structure", + "task_id", + "formula_pretty", +] + +sg_fields = ["number", "hall_number", "international", "hall", "choice"] + + +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 + + +class StructureGroupBuilder(Builder): + def __init__( + self, + materials: MongoStore, + sgroups: MongoStore, + working_ion: str, + query: dict = None, + ltol: float = 0.2, + stol: float = 0.3, + angle_tol: float = 5.0, + check_newer: bool = True, + **kwargs, + ): + """ + Aggregate materials entries into sgroups that are topotactically similar to each other. + This is an incremental builder that makes ensures that each materials id belongs to one StructureGroupDoc document + Args: + materials (Store): Store of materials documents that contains the structures + sgroups (Store): Store of grouped material ids + query (dict): dictionary to limit materials to be analyzed --- + only applied to the materials when we need to group structures + the phase diagram is still constructed with the entire set + """ + self.materials = materials + self.sgroups = sgroups + self.working_ion = working_ion + self.query = query if query else {} + self.ltol = ltol + self.stol = stol + self.angle_tol = angle_tol + self.check_newer = check_newer + super().__init__(sources=[materials], targets=[sgroups], **kwargs) + + def prechunk(self, number_splits: int) -> Iterable[Dict]: + """ + TODO can implement this for distributed runs by adding filters + """ + pass + + def get_items(self): + """ + Summary of the steps: + - query the materials database for different chemical systems that satisfies the base query + "contains redox element and working ion" + - Get the full chemsys list of interest + - The main loop is over all these chemsys. within the main loop: + - get newest timestamp for the material documents (max_mat_time) + - get the oldest timestamp for the target documents (min_target_time) + - if min_target_time is < max_mat_time then nuke all the target documents + """ + + # All potentially interesting chemsys must contain the working ion + base_query = { + "$and": [ + {"elements": {"$in": REDOX_ELEMENTS + [self.working_ion]}}, + self.query.copy(), + ] + } + self.logger.debug(f"Initial Chemsys QUERY: {base_query}") + + # get a chemsys that only contains the working ion since the working ion + # must be present for there to be voltage steps + all_chemsys = self.materials.distinct("chemsys", criteria=base_query) + # Contains the working ion but not ONLY the working ion + all_chemsys = [ + *filter( + lambda x: self.working_ion in x and len(x) > 1, + [chemsys_.split("-") for chemsys_ in all_chemsys], + ) + ] + + self.logger.debug( + f"Performing initial checks on {len(all_chemsys)} chemical systems containing redox elements with or without the Working Ion." + ) + self.total = len(all_chemsys) + + for chemsys_l in all_chemsys: + chemsys = "-".join(sorted(chemsys_l)) + chemsys_wo = "-".join(sorted(set(chemsys_l) - {self.working_ion})) + chemsys_query = { + "$and": [ + {"chemsys": {"$in": [chemsys_wo, chemsys]}}, + {"_sbxn": {"$in": ["core"]}}, + self.query.copy(), + ] + } + self.logger.debug(f"QUERY: {chemsys_query}") + + all_mats_in_chemsys = list( + self.materials.query( + criteria=chemsys_query, + properties=MAT_PROPS + [self.materials.last_updated_field], + ) + ) + self.logger.debug( + f"Found {len(all_mats_in_chemsys)} materials in {chemsys_wo}" + ) + if self.check_newer: + all_target_docs = list( + self.sgroups.query( + criteria={"chemsys": chemsys}, + properties=[ + "task_id", + self.sgroups.last_updated_field, + "grouped_ids", + ], + ) + ) + self.logger.debug( + f"Found {len(all_target_docs)} Grouped documents in {chemsys_wo}" + ) + + mat_times = [ + mat_doc[self.materials.last_updated_field] + for mat_doc in all_mats_in_chemsys + ] + max_mat_time = max(mat_times, default=datetime.min) + self.logger.debug( + f"The newest material doc was generated at {max_mat_time}." + ) + + target_times = [ + g_doc[self.materials.last_updated_field] + for g_doc in all_target_docs + ] + min_target_time = min(target_times, default=datetime.max) + self.logger.debug( + f"The newest GROUP doc was generated at {min_target_time}." + ) + + mat_ids = set([mat_doc["task_id"] for mat_doc in all_mats_in_chemsys]) + + # If any material id is missing or if any material id has been updated + target_mat_ids = set() + for g_doc in all_target_docs: + target_mat_ids |= set(g_doc["grouped_ids"]) + + self.logger.debug( + f"There are {len(mat_ids)} material ids in the source database vs {len(target_mat_ids)} in the target database." + ) + if mat_ids == target_mat_ids and max_mat_time < min_target_time: + continue + else: + self.logger.info( + f"Nuking all {len(target_mat_ids)} documents in chemsys {chemsys} in the target database." + ) + self._remove_targets(list(target_mat_ids)) + + yield {"chemsys": chemsys, "materials": all_mats_in_chemsys} + + def update_targets(self, items: List): + items = list(filter(None, chain.from_iterable(items))) + if len(items) > 0: + self.logger.info("Updating {} sgroups documents".format(len(items))) + for struct_group_dict in items: + struct_group_dict[self.sgroups.last_updated_field] = datetime.utcnow() + self.sgroups.update(docs=items, key=["task_id"]) + else: + self.logger.info("No items to update") + + def _entry_from_mat_doc(self, mdoc): + # Note since we are just structure grouping we don't need to be careful with energy or correction + # All of the energy analysis is left to other builders + d_ = { + "entry_id": mdoc["task_id"], + "structure": mdoc["structure"], + "energy": -math.inf, + "correction": -math.inf, + } + return ComputedStructureEntry.from_dict(d_) + + def process_item(self, item: Any) -> Any: + entries = [*map(self._entry_from_mat_doc, item["materials"])] + s_groups = StructureGroupDoc.from_ungrouped_structure_entries( + entries=entries, + ignored_species=[self.working_ion], + ltol=self.ltol, + stol=self.stol, + angle_tol=self.angle_tol, + ) + # append the working_ion to the group ids + for sg in s_groups: + sg.task_id = f"{sg.task_id}_{self.working_ion}" + return [sg.dict() for sg in s_groups] + + def _remove_targets(self, rm_ids): + self.sgroups.remove_docs({"task_id": {"$in": rm_ids}}) + + +class InsertionElectrodeBuilder(MapBuilder): + def __init__( + self, + grouped_materials: MongoStore, + insertion_electrode: MongoStore, + thermo: MongoStore, + material: MongoStore, + query: dict = None, + **kwargs, + ): + self.grouped_materials = grouped_materials + self.insertion_electrode = insertion_electrode + self.thermo = thermo + self.material = material + qq_ = {} if query is None else query + qq_.update({"structure_matched": True, "has_distinct_compositions": True}) + super().__init__( + source=self.grouped_materials, + target=self.insertion_electrode, + query=qq_, + **kwargs, + ) + + def get_items(self): + """""" + + @lru_cache(None) + def get_working_ion_entry(working_ion): + with self.thermo as store: + working_ion_docs = [*store.query({"chemsys": working_ion})] + best_wion = min( + working_ion_docs, key=lambda x: x["thermo"]["energy_per_atom"] + ) + return best_wion + + def modify_item(item): + self.logger.debug( + f"Looking for {len(item['grouped_ids'])} task_ids in the Thermo DB." + ) + with self.thermo as store: + thermo_docs = [ + *store.query( + { + "$and": [ + {"task_id": {"$in": item["grouped_ids"]}}, + {"_sbxn": {"$in": ["core"]}}, + ] + }, + properties=["task_id", "_sbxn", "thermo"], + ) + ] + + with self.material as store: + material_docs = [ + *store.query( + { + "$and": [ + {"task_id": {"$in": item["grouped_ids"]}}, + {"_sbxn": {"$in": ["core"]}}, + ] + }, + properties=["task_id", "structure"], + ) + ] + + self.logger.debug(f"Found for {len(thermo_docs)} Thermo Documents.") + if len(item["ignored_species"]) != 1: + raise ValueError( + "Insertion electrode can only be defined for one working ion species" + ) + working_ion_doc = get_working_ion_entry(item["ignored_species"][0]) + return { + "task_id": item["task_id"], + "working_ion_doc": working_ion_doc, + "working_ion": item["ignored_species"][0], + "thermo_docs": thermo_docs, + "material_docs": material_docs, + } + + yield from map(modify_item, super().get_items()) + + def unary_function(self, item): + """ + - Add volume information to each entry to create the insertion electrode document + - Add the host structure + """ + entries = [tdoc_["thermo"]["entry"] for tdoc_ in item["thermo_docs"]] + entries = list(map(ComputedEntry.from_dict, entries)) + working_ion_entry = ComputedEntry.from_dict( + item["working_ion_doc"]["thermo"]["entry"] + ) + working_ion = working_ion_entry.composition.reduced_formula + decomp_energies = { + d_["task_id"]: d_["thermo"]["e_above_hull"] for d_ in item["thermo_docs"] + } + mat_structures = { + mat_d_["task_id"]: Structure.from_dict(mat_d_["structure"]) + for mat_d_ in item["material_docs"] + } + + least_wion_ent = min( + entries, key=lambda x: x.composition.get_atomic_fraction(working_ion) + ) + mdoc_ = next( + filter( + lambda x: x["task_id"] == least_wion_ent.entry_id, + item["material_docs"], + ) + ) + host_structure = Structure.from_dict(mdoc_["structure"]) + host_structure.remove_species([item["working_ion"]]) + + for ient in entries: + if mat_structures[ient.entry_id].composition != ient.composition: + raise RuntimeError( + f"In {item['task_id']}: the compositions for task {ient.entry_id} are matched " + "between the StructureGroup DB and the Thermo DB " + ) + ient.data["volume"] = mat_structures[ient.entry_id].volume + ient.data["decomposition_energy"] = decomp_energies[ient.entry_id] + + ie = InsertionElectrodeDoc.from_entries( + grouped_entries=entries, + working_ion_entry=working_ion_entry, + task_id=item["task_id"], + host_structure=host_structure, + ) + if ie is None: + return {"failed_reason": "unable to create InsertionElectrode document"} + return jsanitize(ie.dict()) diff --git a/emmet-core/emmet/core/electrode.py b/emmet-core/emmet/core/electrode.py index 47f03a6945..50dbe76b44 100644 --- a/emmet-core/emmet/core/electrode.py +++ b/emmet-core/emmet/core/electrode.py @@ -1,5 +1,5 @@ from datetime import datetime -from typing import Dict, List +from typing import Dict, List, Union from monty.json import MontyDecoder from pydantic import BaseModel, Field, validator @@ -9,6 +9,7 @@ from pymatgen.core.periodic_table import Element from pymatgen.entries.computed_entries import ComputedEntry +from emmet.core.utils import jsanitize from emmet.stubs import Composition, Structure @@ -127,10 +128,13 @@ def from_entries( working_ion_entry: ComputedEntry, task_id: str, host_structure: Structure, - ): - ie = InsertionElectrode.from_entries( - entries=grouped_entries, working_ion_entry=working_ion_entry - ) + ) -> Union["InsertionElectrodeDoc", None]: + try: + ie = InsertionElectrode.from_entries( + entries=grouped_entries, working_ion_entry=working_ion_entry + ) + except IndexError: + return None d = ie.get_summary_dict() d["num_steps"] = d.pop("nsteps", None) d["last_updated"] = datetime.utcnow() @@ -203,58 +207,3 @@ def from_composition_and_entries( d["num_steps"] = d.pop("nsteps", None) d["last_updated"] = datetime.utcnow() return cls(task_id=task_id, framework=Composition(d["framework_formula"]), **d) - - -class StructureGroupDoc(BaseModel): - """ - Document model for the intermediate structure matching database used to build the insertion electrode documents. - """ - - task_id: str = Field( - None, - description="The combined task_id of the grouped document is given by the numerically smallest task id " - "followed by '_Li' or whichever working atom is considered the working ion during grouping.", - ) - - structure_matched: bool = Field( - None, - description="True if the structures in this group has been matched to each other. This is False for groups " - "that contain all the left over structures with the same framework.", - ) - - has_distinct_compositions: bool = Field( - None, - description="True if multiple working ion fractions are available in the group, which means a voltage " - "step exits.", - ) - - grouped_task_ids: List[str] = Field( - None, - description="The ids of the materials that have been grouped by the structure matcher.", - ) - - entry_data: Dict = Field( - None, - description="Dictionary keyed by the task_id, contains the 'composition' and 'volume' of each material.", - ) - - framework_formula: str = Field( - None, description="The formula of the host framework." - ) - - working_ion: Element = Field(None, description="The working ion") - - chemsys: str = Field( - None, - description="The chemsys this group belongs to. Always includes the working ion", - ) - - last_updated: datetime = Field( - None, - description="Timestamp for the most recent calculation for this Material document", - ) - - # 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) diff --git a/emmet-core/emmet/core/polar.py b/emmet-core/emmet/core/polar.py index ab45a9aa13..295ee3a5bd 100644 --- a/emmet-core/emmet/core/polar.py +++ b/emmet-core/emmet/core/polar.py @@ -44,7 +44,7 @@ class Dielectric(PropertyDoc): @classmethod def from_ionic_and_electronic(cls, ionic: Matrix3D, electronic: Matrix3D): - total = np.sum(ionic, electronic).tolist() + total = np.sum(ionic, electronic).tolist() # type: ignore return cls( **{ @@ -81,7 +81,7 @@ class Piezoelectric(PropertyDoc): @classmethod def from_ionic_and_electronic(cls, ionic: Matrix3D, electronic: Matrix3D): - total = BasePiezoTensor.from_voigt(np.sum(ionic, electronic)) + total = BasePiezoTensor.from_voigt(np.sum(ionic, electronic)) # type: ignore directions, charges, strains = np.linalg.svd(total, full_matrices=False) max_index = np.argmax(np.abs(charges)) diff --git a/emmet-core/emmet/core/structure_group.py b/emmet-core/emmet/core/structure_group.py new file mode 100644 index 0000000000..a4c10812ff --- /dev/null +++ b/emmet-core/emmet/core/structure_group.py @@ -0,0 +1,243 @@ +import logging +import operator +from datetime import datetime +from itertools import groupby +from typing import Iterable, List, Union + +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 ComputedEntry, ComputedStructureEntry + +from emmet.stubs import Composition, Structure + +logger = logging.getLogger(__name__) + + +def generic_groupby(list_in, comp=operator.eq) -> List[int]: + """ + 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 = [-1] * len(list_in) + label_num = 0 + for i1, ls1 in enumerate(list_out): + if ls1 != -1: + 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 combined task_id of the grouped document is given by the numerically smallest task id ", + ) + + structure_matched: bool = Field( + None, + description="True if the structure matching was performed to group theses entries together." + "This is False for groups that contain all the left over entries like the ones that only " + "contain the ignored species.", + ) + + has_distinct_compositions: bool = Field( + None, description="True if multiple compositions are present in the group." + ) + + grouped_ids: list = Field( + None, + description="A list of materials ids for all of the materials that were grouped together.", + ) + + framework_formula: str = Field( + None, + description="The chemical formula for the framework (the materials system without the ignored species).", + ) + + 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[Union[ComputedEntry, ComputedStructureEntry]], + ignored_species: List[str], + structure_matched: bool, + ) -> "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() + all_comps = set() + for ient in entries: + all_atoms |= set(ient.composition.as_dict().keys()) + all_comps.add(ient.composition.reduced_formula) + + 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, + "structure_matched": structure_matched, + "framework_formula": framework_str, + "ignored_species": sorted(ignored_species), + "chemsys": "-".join(sorted(all_atoms | set(ignored_species))), + "has_distinct_compositions": len(all_comps) > 1, + } + + return cls(**fields) + + @classmethod + def from_ungrouped_structure_entries( + cls, + entries: List[Union[ComputedEntry, 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, structure_matched=False + ) + 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, structure_matched=True + ) + 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 +) -> Iterable[List[Union[ComputedStructureEntry]]]: + """ + 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) -> Union[int, str]: + 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/setup.cfg b/setup.cfg index 7a1155a830..75e9591afa 100644 --- a/setup.cfg +++ b/setup.cfg @@ -3,7 +3,7 @@ addopts = --durations=30 [pycodestyle] count = True -ignore = E121,E123,E126,E133,E226,E241,E242,E704,W503,W504,W505,E741,W605,W293 +ignore = E121,E123,E126,E133,E226,E241,E242,E704,W503,W504,W505,E741,W605,W293,E203 max-line-length = 120 statistics = True diff --git a/tests/emmet-core/test_electrodes.py b/tests/emmet-core/test_electrodes.py index 675224c2de..7001b8367e 100644 --- a/tests/emmet-core/test_electrodes.py +++ b/tests/emmet-core/test_electrodes.py @@ -73,6 +73,7 @@ def test_InsertionDocs(insertion_elec): for sub_elec in elec.get_sub_electrodes(adjacent_only=True): vp = InsertionVoltagePairDoc.from_sub_electrode(sub_electrode=sub_elec) assert vp.average_voltage == sub_elec.get_average_voltage() + # assert type(ie.dict()["host_structure"]) == dict # This might be a requirement in the future def test_ConversionDocs_from_entries(conversion_elec): diff --git a/tests/emmet-core/test_structure_group.py b/tests/emmet-core/test_structure_group.py new file mode 100644 index 0000000000..ad554eb1a1 --- /dev/null +++ b/tests/emmet-core/test_structure_group.py @@ -0,0 +1,65 @@ +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"], structure_matched=True + ) + 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_formula == "TiO2" + assert sgroup_doc.ignored_species == ["Li"] + assert sgroup_doc.chemsys == "Li-O-Ti" + assert sgroup_doc.has_distinct_compositions is True + + +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_formula + 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..3723aae0e3 --- /dev/null +++ b/tests/test_files/Li-Fe-O.json @@ -0,0 +1,246332 @@ +[ + { + "@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": 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