emmet-builders 0.78.3__py3-none-any.whl → 0.86.0__py3-none-any.whl

emmet/builders/molecules/thermo.py

@@ -1,500 +0,0 @@
-from collections import defaultdict
-from datetime import datetime
-from itertools import chain
-from math import ceil
-from typing import Optional, Iterable, Iterator, List, Dict
-
-from pymatgen.core.structure import Molecule
-from pymatgen.analysis.molecule_matcher import MoleculeMatcher
-
-from maggma.builders import Builder
-from maggma.core import Store
-from maggma.utils import grouper
-
-from emmet.core.qchem.task import TaskDocument
-from emmet.core.qchem.molecule import MoleculeDoc, evaluate_lot
-from emmet.core.molecules.thermo import get_free_energy, MoleculeThermoDoc
-from emmet.core.qchem.calc_types import TaskType
-from emmet.core.utils import jsanitize
-from emmet.builders.settings import EmmetBuildSettings
-
-
-__author__ = "Evan Spotte-Smith"
-
-SETTINGS = EmmetBuildSettings()
-
-single_mol_thermo = {
-    "Zn1": {"enthalpy": 1.481, "entropy": 38.384},
-    "Xe1": {"enthalpy": 1.481, "entropy": 40.543},
-    "Tl1": {"enthalpy": 1.481, "entropy": 41.857},
-    "Ti1": {"enthalpy": 1.481, "entropy": 37.524},
-    "Te1": {"enthalpy": 1.481, "entropy": 40.498},
-    "Sr1": {"enthalpy": 1.481, "entropy": 39.334},
-    "Sn1": {"enthalpy": 1.481, "entropy": 40.229},
-    "Si1": {"enthalpy": 1.481, "entropy": 35.921},
-    "Sb1": {"enthalpy": 1.481, "entropy": 40.284},
-    "Se1": {"enthalpy": 1.481, "entropy": 39.05},
-    "S1": {"enthalpy": 1.481, "entropy": 36.319},
-    "Rn1": {"enthalpy": 1.481, "entropy": 42.095},
-    "Pt1": {"enthalpy": 1.481, "entropy": 41.708},
-    "Rb1": {"enthalpy": 1.481, "entropy": 39.23},
-    "Po1": {"enthalpy": 1.481, "entropy": 41.915},
-    "Pb1": {"enthalpy": 1.481, "entropy": 41.901},
-    "P1": {"enthalpy": 1.481, "entropy": 36.224},
-    "O1": {"enthalpy": 1.481, "entropy": 34.254},
-    "Ne1": {"enthalpy": 1.481, "entropy": 34.919},
-    "N1": {"enthalpy": 1.481, "entropy": 33.858},
-    "Na1": {"enthalpy": 1.481, "entropy": 35.336},
-    "Mg1": {"enthalpy": 1.481, "entropy": 35.462},
-    "Li1": {"enthalpy": 1.481, "entropy": 31.798},
-    "Kr1": {"enthalpy": 1.481, "entropy": 39.191},
-    "K1": {"enthalpy": 1.481, "entropy": 36.908},
-    "In1": {"enthalpy": 1.481, "entropy": 40.132},
-    "I1": {"enthalpy": 1.481, "entropy": 40.428},
-    "H1": {"enthalpy": 1.481, "entropy": 26.014},
-    "He1": {"enthalpy": 1.481, "entropy": 30.125},
-    "Ge1": {"enthalpy": 1.481, "entropy": 38.817},
-    "Ga1": {"enthalpy": 1.481, "entropy": 38.609},
-    "F1": {"enthalpy": 1.481, "entropy": 34.767},
-    "Cu1": {"enthalpy": 1.481, "entropy": 38.337},
-    "Cl1": {"enthalpy": 1.481, "entropy": 36.586},
-    "Ca1": {"enthalpy": 1.481, "entropy": 36.984},
-    "C1": {"enthalpy": 1.481, "entropy": 33.398},
-    "Br1": {"enthalpy": 1.481, "entropy": 39.012},
-    "Bi1": {"enthalpy": 1.481, "entropy": 41.915},
-    "Be1": {"enthalpy": 1.481, "entropy": 32.544},
-    "Ba1": {"enthalpy": 1.481, "entropy": 40.676},
-    "B1": {"enthalpy": 1.481, "entropy": 33.141},
-    "Au1": {"enthalpy": 1.481, "entropy": 41.738},
-    "At1": {"enthalpy": 1.481, "entropy": 41.929},
-    "As1": {"enthalpy": 1.481, "entropy": 38.857},
-    "Ar1": {"enthalpy": 1.481, "entropy": 36.983},
-    "Al1": {"enthalpy": 1.481, "entropy": 35.813},
-    "Ag1": {"enthalpy": 1.481, "entropy": 39.917},
-}
-
-
-class ThermoBuilder(Builder):
-    """
-    The ThermoBuilder extracts the highest-quality thermodynamic data from a
-    MoleculeDoc (lowest electronic energy, highest level of theory for each
-    solvent available).
-
-    This builder constructs MoleculeThermoDocs in two different ways: with and without
-    single-point energy corrections.
-
-    Before any documents are constructed, the following steps are taken:
-        1. Gather MoleculeDocs by formula
-        2. For each doc, identify tasks with thermodynamic information such as
-            zero-point energy, enthalpy, and entropy. Collect these "documents
-             including complete thermodynamics" (DICTs).
-        3. Separately, collect single-point energy calculations (SPECs).
-        4. Sort both sets of collected tasks (DICT and SPEC) by solvent
-
-    The first type of doc - those without corrections - can be constructed in
-    a straightforward fashion:
-        5. For each solvent, grab the best DICT (where "best" is defined as the
-            task generated using the highest level of theory with the lowest
-            electronic energy)
-        6. Convert this TaskDoc to MoleculeThermoDoc
-
-    The second type - those involving single-point energy corrections - are
-    generated differently and in a slightly more involved process:
-        7. For each of the "best" DICT docs identified in step 5 above:
-            7.1 For each solvent, grab the best SPEC
-            7.2 Try to match each best SPEC with a matching DICT (meaning that
-                the DICT and the SPEC have identical structure) where the DICT
-                is calculated at a lower or the same level of theory than the
-                SPEC
-            7.3 Convert each DICT-SPEC combination to create a MoleculeThermoDoc
-
-    In the case where there are multiple MoleculeThermoDocs made for a given solvent,
-    the different MoleculeThermoDocs will be ranked, first by level of theory (for
-    a doc made with an energy correction, the scores of the DICT and the SPEC
-    levels of theory will be averaged) and then by electronic energy.
-    """
-
-    def __init__(
-        self,
-        tasks: Store,
-        molecules: Store,
-        thermo: Store,
-        query: Optional[Dict] = None,
-        settings: Optional[EmmetBuildSettings] = None,
-        **kwargs,
-    ):
-        self.tasks = tasks
-        self.molecules = molecules
-        self.thermo = thermo
-        self.query = query if query else dict()
-        self.settings = EmmetBuildSettings.autoload(settings)
-        self.kwargs = kwargs
-
-        super().__init__(sources=[tasks, molecules], targets=[thermo], **kwargs)
-        # Uncomment in case of issue with mrun not connecting automatically to collections
-        # for i in [self.tasks, self.molecules, self.thermo]:
-        #     try:
-        #         i.connect()
-        #     except Exception as e:
-        #         print("Could not connect,", e)
-
-    def ensure_indexes(self):
-        """
-        Ensures indices on the collections needed for building
-        """
-
-        # Basic search index for tasks
-        self.tasks.ensure_index("task_id")
-        self.tasks.ensure_index("last_updated")
-        self.tasks.ensure_index("state")
-        self.tasks.ensure_index("formula_alphabetical")
-
-        # Search index for molecules
-        self.molecules.ensure_index("molecule_id")
-        self.molecules.ensure_index("last_updated")
-        self.molecules.ensure_index("task_ids")
-        self.molecules.ensure_index("formula_alphabetical")
-
-        # Search index for thermo
-        self.thermo.ensure_index("molecule_id")
-        self.thermo.ensure_index("task_id")
-        self.thermo.ensure_index("solvent")
-        self.thermo.ensure_index("lot_solvent")
-        self.thermo.ensure_index("property_id")
-        self.thermo.ensure_index("last_updated")
-        self.thermo.ensure_index("formula_alphabetical")
-
-    def prechunk(self, number_splits: int) -> Iterable[Dict]:  # pragma: no cover
-        """Prechunk the builder for distributed computation"""
-
-        temp_query = dict(self.query)
-        temp_query["deprecated"] = False
-
-        self.logger.info("Finding documents to process")
-        all_mols = list(
-            self.molecules.query(
-                temp_query, [self.molecules.key, "formula_alphabetical"]
-            )
-        )
-
-        processed_docs = set([e for e in self.thermo.distinct("molecule_id")])
-        to_process_docs = {d[self.molecules.key] for d in all_mols} - processed_docs
-        to_process_forms = {
-            d["formula_alphabetical"]
-            for d in all_mols
-            if d[self.molecules.key] in to_process_docs
-        }
-
-        N = ceil(len(to_process_forms) / number_splits)
-
-        for formula_chunk in grouper(to_process_forms, N):
-            yield {"query": {"formula_alphabetical": {"$in": list(formula_chunk)}}}
-
-    def get_items(self) -> Iterator[List[Dict]]:
-        """
-        Gets all items to process into thermo documents.
-        This does no datetime checking; relying on on whether
-        task_ids are included in the thermo Store
-
-        Returns:
-            generator or list relevant tasks and molecules to process into documents
-        """
-
-        self.logger.info("Thermo builder started")
-        self.logger.info("Setting indexes")
-        self.ensure_indexes()
-
-        # Save timestamp to mark buildtime
-        self.timestamp = datetime.utcnow()
-
-        # Get all processed molecules
-        temp_query = dict(self.query)
-        temp_query["deprecated"] = False
-
-        self.logger.info("Finding documents to process")
-        all_mols = list(
-            self.molecules.query(
-                temp_query, [self.molecules.key, "formula_alphabetical"]
-            )
-        )
-
-        processed_docs = set([e for e in self.thermo.distinct("molecule_id")])
-        to_process_docs = {d[self.molecules.key] for d in all_mols} - processed_docs
-        to_process_forms = {
-            d["formula_alphabetical"]
-            for d in all_mols
-            if d[self.molecules.key] in to_process_docs
-        }
-
-        self.logger.info(f"Found {len(to_process_docs)} unprocessed documents")
-        self.logger.info(f"Found {len(to_process_forms)} unprocessed formulas")
-
-        # Set total for builder bars to have a total
-        self.total = len(to_process_forms)
-
-        for formula in to_process_forms:
-            mol_query = dict(temp_query)
-            mol_query["formula_alphabetical"] = formula
-            molecules = list(self.molecules.query(criteria=mol_query))
-
-            yield molecules
-
-    def process_item(self, items: List[Dict]) -> List[Dict]:
-        """
-        Process the tasks into a MoleculeThermoDoc
-
-        Args:
-            items List[dict] : a list of MoleculeDocs in dict form
-
-        Returns:
-            [dict] : a list of new thermo docs
-        """
-
-        def _add_single_atom_enthalpy_entropy(
-            task: TaskDocument, doc: MoleculeThermoDoc
-        ):
-            initial_mol = task.output.initial_molecule
-            # If single atom, try to add enthalpy and entropy
-            if len(initial_mol) == 1:
-                if doc.total_enthalpy is None or doc.total_entropy is None:
-                    formula = initial_mol.composition.alphabetical_formula
-                    if formula in single_mol_thermo:
-                        vals = single_mol_thermo[formula]
-                        doc.total_enthalpy = vals["enthalpy"] * 0.043363
-                        doc.total_entropy = vals["entropy"] * 0.000043363
-                        doc.translational_enthalpy = vals["enthalpy"] * 0.043363
-                        doc.translational_entropy = vals["entropy"] * 0.000043363
-                        doc.free_energy = get_free_energy(
-                            doc.electronic_energy,
-                            vals["enthalpy"],
-                            vals["entropy"],
-                            convert_energy=False,
-                        )
-            return doc
-
-        mols = [MoleculeDoc(**item) for item in items]
-        formula = mols[0].formula_alphabetical
-        mol_ids = [m.molecule_id for m in mols]
-        self.logger.debug(f"Processing {formula} : {mol_ids}")
-
-        thermo_docs = list()
-
-        mm = MoleculeMatcher(tolerance=0.000001)
-
-        for mol in mols:
-            this_thermo_docs = list()
-            # Collect DICTs and SPECs
-            thermo_entries = [
-                e
-                for e in mol.entries
-                if e["output"]["enthalpy"] is not None
-                and e["output"]["entropy"] is not None
-                and e["charge"] == mol.charge
-                and e["spin_multiplicity"] == mol.spin_multiplicity
-            ]
-
-            sp_entries = list()
-            for entry in mol.entries:
-                if isinstance(entry["task_type"], TaskType):
-                    task_type = entry["task_type"].value
-                else:
-                    task_type = entry["task_type"]
-
-                if (
-                    task_type in ["Single Point", "Force"]
-                    and entry["charge"] == mol.charge
-                    and entry["spin_multiplicity"] == mol.spin_multiplicity
-                ):
-                    sp_entries.append(entry)
-
-            # Group both DICTs and SPECs by solvent environment
-            by_solvent_dict = defaultdict(list)
-            by_solvent_spec = defaultdict(list)
-            for entry in thermo_entries:
-                by_solvent_dict[entry["solvent"]].append(entry)
-            for entry in sp_entries:
-                by_solvent_spec[entry["solvent"]].append(entry)
-
-            if len(thermo_entries) == 0:
-                without_corrections = by_solvent_spec
-            else:
-                without_corrections = by_solvent_dict
-
-            # Construct without corrections
-            for solvent, entries in without_corrections.items():
-                best = sorted(
-                    entries,
-                    key=lambda x: (
-                        sum(evaluate_lot(x["level_of_theory"])),
-                        x["energy"],
-                    ),
-                )[0]
-                task = best["task_id"]
-
-                tdoc = self.tasks.query_one(
-                    {
-                        "task_id": task,
-                        "formula_alphabetical": formula,
-                        "orig": {"$exists": True},
-                    }
-                )
-
-                if tdoc is None:
-                    try:
-                        tdoc = self.tasks.query_one(
-                            {
-                                "task_id": int(task),
-                                "formula_alphabetical": formula,
-                                "orig": {"$exists": True},
-                            }
-                        )
-                    except ValueError:
-                        tdoc = None
-
-                if tdoc is None:
-                    continue
-
-                task_doc = TaskDocument(**tdoc)
-
-                if task_doc is None:
-                    continue
-
-                thermo_doc = MoleculeThermoDoc.from_task(
-                    task_doc, molecule_id=mol.molecule_id, deprecated=False
-                )
-                thermo_doc = _add_single_atom_enthalpy_entropy(task_doc, thermo_doc)
-                this_thermo_docs.append(thermo_doc)
-
-            # Construct with corrections
-            for solvent, entries in by_solvent_spec.items():
-                spec_sorted = sorted(
-                    entries,
-                    key=lambda x: (
-                        sum(evaluate_lot(x["level_of_theory"])),
-                        x["energy"],
-                    ),
-                )
-
-                for best_spec in spec_sorted:
-                    task_spec = best_spec["task_id"]
-
-                    matching_structures = list()
-                    for entry in thermo_entries:
-                        mol1 = Molecule.from_dict(entry["molecule"])
-                        mol2 = Molecule.from_dict(best_spec["molecule"])
-                        if (mm.fit(mol1, mol2) or mol1 == mol2) and (
-                            sum(evaluate_lot(best_spec["level_of_theory"]))
-                            < sum(evaluate_lot(entry["level_of_theory"]))
-                        ):
-                            matching_structures.append(entry)
-
-                    if len(matching_structures) == 0:
-                        continue
-
-                    best_dict = sorted(
-                        matching_structures,
-                        key=lambda x: (
-                            sum(evaluate_lot(x["level_of_theory"])),
-                            x["energy"],
-                        ),
-                    )[0]
-                    task_dict = best_dict["task_id"]
-
-                    tdict = self.tasks.query_one({"task_id": task_dict})
-                    if tdict is None:
-                        try:
-                            tdict = self.tasks.query_one({"task_id": int(task_dict)})
-                        except ValueError:
-                            tdict = None
-
-                    tspec = self.tasks.query_one({"task_id": task_spec})
-                    if tspec is None:
-                        try:
-                            tspec = self.tasks.query_one({"task_id": int(task_spec)})
-                        except ValueError:
-                            tspec = None
-
-                    if tdict is None or tspec is None:
-                        continue
-
-                    task_doc_dict = TaskDocument(**tdict)
-                    task_doc_spec = TaskDocument(**tspec)
-                    thermo_doc = MoleculeThermoDoc.from_task(
-                        task_doc_dict,
-                        correction_task=task_doc_spec,
-                        molecule_id=mol.molecule_id,
-                        deprecated=False,
-                    )
-                    thermo_doc = _add_single_atom_enthalpy_entropy(
-                        task_doc_dict, thermo_doc
-                    )
-                    this_thermo_docs.append(thermo_doc)
-                    break
-
-            docs_by_solvent = defaultdict(list)
-            for doc in this_thermo_docs:
-                if doc.correction_solvent is not None:
-                    docs_by_solvent[doc.correction_solvent].append(doc)
-                else:
-                    docs_by_solvent[doc.solvent].append(doc)
-
-            # If multiple documents exist for the same solvent, grab the best one
-            for _, collection in docs_by_solvent.items():
-                with_eval_e = list()
-                for member in collection:
-                    if member.correction_level_of_theory is None:
-                        with_eval_e.append(
-                            (
-                                member,
-                                sum(evaluate_lot(member.level_of_theory)),
-                                member.electronic_energy,
-                            )
-                        )
-                    else:
-                        dict_lot = sum(evaluate_lot(member.level_of_theory))
-                        spec_lot = sum(evaluate_lot(member.correction_level_of_theory))
-                        with_eval_e.append(
-                            (
-                                member,
-                                (dict_lot + spec_lot) / 2,
-                                member.electronic_energy,
-                            )
-                        )
-
-                thermo_docs.append(
-                    sorted(with_eval_e, key=lambda x: (x[1], x[2]))[0][0]
-                )
-
-        self.logger.debug(f"Produced {len(thermo_docs)} thermo docs for {formula}")
-
-        return jsanitize([doc.model_dump() for doc in thermo_docs], allow_bson=True)
-
-    def update_targets(self, items: List[List[Dict]]):
-        """
-        Inserts the new thermo docs into the thermo collection
-
-        Args:
-            items [[dict]]: A list of documents to update
-        """
-
-        docs = list(chain.from_iterable(items))  # type: ignore
-
-        # Add timestamp
-        for item in docs:
-            item.update(
-                {
-                    "_bt": self.timestamp,
-                }
-            )
-
-        molecule_ids = list({item["molecule_id"] for item in docs})
-
-        if len(items) > 0:
-            self.logger.info(f"Updating {len(docs)} thermo documents")
-            self.thermo.remove_docs({self.thermo.key: {"$in": molecule_ids}})
-            self.thermo.update(
-                docs=docs,
-                key=["molecule_id", "solvent"],
-            )
-        else:
-            self.logger.info("No items to update")