emmet-builders 0.84.2rc7__py3-none-any.whl → 0.84.2rc9__py3-none-any.whl

emmet/builders/qchem/molecules.py

@@ -138,7 +138,6 @@ class MoleculesAssociationBuilder(Builder):
         self.tasks.ensure_index("formula_alphabetical")
         self.tasks.ensure_index("smiles")
         self.tasks.ensure_index("species_hash")
-        self.tasks.ensure_index("coord_hash")
 
         # Search index for molecules
         self.assoc.ensure_index("molecule_id")
@@ -166,9 +165,7 @@ class MoleculesAssociationBuilder(Builder):
         N = ceil(len(to_process_hashes) / number_splits)
 
         for hash_chunk in grouper(to_process_hashes, N):
-            query = dict(temp_query)
-            query["species_hash"] = {"$in": list(hash_chunk)}
-            yield {"query": query}
+            yield {"query": {"species_hash": {"$in": list(hash_chunk)}}}
 
     def get_items(self) -> Iterator[List[TaskDocument]]:
         """
@@ -393,7 +390,6 @@ class MoleculesBuilder(Builder):
         self.assoc.ensure_index("last_updated")
         self.assoc.ensure_index("task_ids")
         self.assoc.ensure_index("formula_alphabetical")
-        self.assoc.ensure_index("species_hash")
 
         # Search index for molecules
         self.molecules.ensure_index("molecule_id")
@@ -437,18 +433,16 @@ class MoleculesBuilder(Builder):
             xyz_species_id_map[d[self.assoc.key]] = this_id
         to_process_docs = assoc_ids - processed_docs
 
-        to_process_hashes = {
-            d["species_hash"]
+        to_process_forms = {
+            d["formula_alphabetical"]
             for d in all_assoc
             if xyz_species_id_map[d[self.assoc.key]] in to_process_docs
         }
 
-        N = ceil(len(to_process_hashes) / number_splits)
+        N = ceil(len(to_process_forms) / number_splits)
 
-        for hash_chunk in grouper(to_process_hashes, N):
-            query = dict(temp_query)
-            query["species_hash"] = {"$in": list(hash_chunk)}
-            yield {"query": query}
+        for formula_chunk in grouper(to_process_forms, N):
+            yield {"query": {"formula_alphabetical": {"$in": list(formula_chunk)}}}
 
     def get_items(self) -> Iterator[List[Dict]]:
         """
@@ -501,21 +495,21 @@ class MoleculesBuilder(Builder):
             xyz_species_id_map[d[self.assoc.key]] = this_id
         to_process_docs = assoc_ids - processed_docs
 
-        to_process_hashes = {
-            d["species_hash"]
+        to_process_forms = {
+            d["formula_alphabetical"]
             for d in all_assoc
             if xyz_species_id_map[d[self.assoc.key]] in to_process_docs
         }
 
         self.logger.info(f"Found {len(to_process_docs)} unprocessed documents")
-        self.logger.info(f"Found {len(to_process_hashes)} unprocessed hashes")
+        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_hashes)
+        self.total = len(to_process_forms)
 
-        for shash in to_process_hashes:
+        for formula in to_process_forms:
             assoc_query = dict(temp_query)
-            assoc_query["species_hash"] = shash
+            assoc_query["formula_alphabetical"] = formula
             assoc = list(self.assoc.query(criteria=assoc_query))
 
             yield assoc
@@ -532,9 +526,9 @@ class MoleculesBuilder(Builder):
         """
 
         assoc = [MoleculeDoc(**item) for item in items]
-        shash = assoc[0].species_hash
+        formula = assoc[0].formula_alphabetical
         mol_ids = [a.molecule_id for a in assoc]
-        self.logger.debug(f"Processing {shash} : {mol_ids}")
+        self.logger.debug(f"Processing {formula} : {mol_ids}")
 
         complete_mol_docs = list()
 
@@ -652,7 +646,7 @@ class MoleculesBuilder(Builder):
 
                 complete_mol_docs.append(base_doc)
 
-        self.logger.debug(f"Produced {len(complete_mol_docs)} molecules for {shash}")
+        self.logger.debug(f"Produced {len(complete_mol_docs)} molecules for {formula}")
 
         return jsanitize(
             [mol.model_dump() for mol in complete_mol_docs], allow_bson=True

{emmet_builders-0.84.2rc7.dist-info → emmet_builders-0.84.2rc9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: emmet-builders
-Version: 0.84.2rc7
+Version: 0.84.2rc9
 Summary: Builders for the Emmet Library
 Home-page: https://github.com/materialsproject/emmet
 Author: The Materials Project

{emmet_builders-0.84.2rc7.dist-info → emmet_builders-0.84.2rc9.dist-info}/RECORD

@@ -32,23 +32,21 @@ emmet/builders/matscholar/missing_compositions.py,sha256=RGQOEhfmJ6YMbjD4osLWqs7
 emmet/builders/mobility/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 emmet/builders/mobility/migration_graph.py,sha256=WEXtPSn0UE5Q8mnvJ-T19FB3_LrZ3ojvNyRBs1PXWRg,3923
 emmet/builders/molecules/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-emmet/builders/molecules/atomic.py,sha256=DBG_FScwT7YU1GgI69yRrR3_wUoWBwiP1uBvbL7xP3Y,20839
-emmet/builders/molecules/bonds.py,sha256=aHp9U_LX3sZvdTIaZj2T8PG_wTFYqw6nOcYC-4MiI0E,12103
-emmet/builders/molecules/electric.py,sha256=ldoLSfIAjue6YQlyXkgJRXLcfh178goiarjI_f_EtH4,10065
-emmet/builders/molecules/metal_binding.py,sha256=kimYsmQWdmukRRX2_GgVywCNRhNHz_-fp2oMYJTVMrg,23308
-emmet/builders/molecules/orbitals.py,sha256=nIsmx0m6Zi402opHE6OoEljGgQ2714p1Gig8Py1IXrU,10060
-emmet/builders/molecules/redox.py,sha256=52er0zK_IVQ0UYUh7svml-zwlvOtbptz1D8ZYCglfI0,18448
-emmet/builders/molecules/summary.py,sha256=7KHsnc9PBstps6s-hK4mYrWOBHt26_PTPKsCSFw3018,13848
-emmet/builders/molecules/thermo.py,sha256=MutvuYJsU0Hj5Qaa_Z7qnikM6mkPSBPNE4RG8JK4qes,19874
-emmet/builders/molecules/trajectory.py,sha256=oKrmWtKJ6mC0d1uJRE7g72X97kkS7JQ7nMhupVOUEUU,18163
-emmet/builders/molecules/vibration.py,sha256=_FA-tRixghsJdlls6oO9U2abxCHWqWv5SucbxpP5mVQ,9520
+emmet/builders/molecules/atomic.py,sha256=X590oMDIPaHJMk0Xuy_r4hATm1TEj0hKfJD6ofi1asg,20823
+emmet/builders/molecules/bonds.py,sha256=5orXkCBgBBOqz1iGoacDUb5iGMsOPVmdmghtQLud9ZU,12086
+emmet/builders/molecules/metal_binding.py,sha256=gyL5Nu1pmu0ZJq4HgTxwLh8_1696pJiMnrFggFESnjo,23317
+emmet/builders/molecules/orbitals.py,sha256=W_7_3zz9bFfHQZgAMdp3PSSt4PDH4DVZVervHPrv1Pk,10041
+emmet/builders/molecules/redox.py,sha256=HHmj-nFMTEV7qq3g3GM2lB5RdLUMBE-xOIZogIgmORc,18427
+emmet/builders/molecules/summary.py,sha256=I9-4-oKoUSg5sxvr-CHYVIuCyD48mpV9rsMno4pbbOk,13198
+emmet/builders/molecules/thermo.py,sha256=DizVM9rLXo7AhHW3cq0Bo6vO1OI6YtK4PeIVixmt47g,19855
+emmet/builders/molecules/vibration.py,sha256=9LNeKh8BHck-ooW4XzAZAFeio2u6bDwdsUV1aA5XVb4,9501
 emmet/builders/qchem/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-emmet/builders/qchem/molecules.py,sha256=qI8WFOJ69FMPu9hxGzoFR4V3y4qO7UhtzVZwG9AWPpw,26382
+emmet/builders/qchem/molecules.py,sha256=CZyVQzjfb-_gAS997BFbd9xkKwvwPWrquNH0Aoy6oY8,26217
 emmet/builders/vasp/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 emmet/builders/vasp/materials.py,sha256=5bjP-W5-gmSjDzmcHdF7bviwgk4ywUceCL4FcF9Ya9c,12700
-emmet/builders/vasp/mp_potcar_stats.json.gz,sha256=RD6gbZEmmmKQYRKpFtEKHzncGO1WsLYMPjn3wvONrIc,291869
+emmet/builders/vasp/mp_potcar_stats.json.gz,sha256=x3bn4gSMj1U_3bR2qKIaBtbJlYT-EJgoUIMFTA9bvaU,338957
 emmet/builders/vasp/task_validator.py,sha256=bmRTDiOWof4rpHVg3ksoxocN9xxieYu7IE-ylMjYOVs,2922
-emmet_builders-0.84.2rc7.dist-info/METADATA,sha256=QqGWpUDogkBmmZbyiHsduf3OWrUR3lfjmlBZigf8Kzk,2162
-emmet_builders-0.84.2rc7.dist-info/WHEEL,sha256=eOLhNAGa2EW3wWl_TU484h7q1UNgy0JXjjoqKoxAAQc,92
-emmet_builders-0.84.2rc7.dist-info/top_level.txt,sha256=6GcpbmWPeFhNCTfDFilb8GQ4T1UQu4z9c5jpobjwE-Q,6
-emmet_builders-0.84.2rc7.dist-info/RECORD,,
+emmet_builders-0.84.2rc9.dist-info/METADATA,sha256=KApWsvZ71L5eRNIbqjPK3TE1eP5Sb5uYVU-3bQ5AJBM,2162
+emmet_builders-0.84.2rc9.dist-info/WHEEL,sha256=eOLhNAGa2EW3wWl_TU484h7q1UNgy0JXjjoqKoxAAQc,92
+emmet_builders-0.84.2rc9.dist-info/top_level.txt,sha256=6GcpbmWPeFhNCTfDFilb8GQ4T1UQu4z9c5jpobjwE-Q,6
+emmet_builders-0.84.2rc9.dist-info/RECORD,,

emmet/builders/molecules/electric.py

@@ -1,282 +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 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.electric import ElectricMultipoleDoc
-from emmet.core.utils import jsanitize
-from emmet.builders.settings import EmmetBuildSettings
-
-
-__author__ = "Evan Spotte-Smith"
-
-SETTINGS = EmmetBuildSettings()
-
-
-class ElectricMultipoleBuilder(Builder):
-    """
-    The ElectricMultipoleBuilder defines the electric multipole properties of a MoleculeDoc.
-
-    This builder will attempt to build documents for each molecule, in each solvent.
-    For each molecule-solvent combination, the highest-quality
-    data available (based on level of theory and electronic energy) will be used.
-
-    The process is as follows:
-        1. Gather MoleculeDocs by species hash
-        2. For each molecule, group all tasks by solvent.
-        3. For each solvent, grab the best TaskDoc (doc with elecrtric dipole/multipole information
-        that has the highest level of theory with the lowest electronic energy) for the molecule
-        4. Convert TaskDoc to ElectricMultipoleDoc
-    """
-
-    def __init__(
-        self,
-        tasks: Store,
-        molecules: Store,
-        multipoles: Store,
-        query: Optional[Dict] = None,
-        settings: Optional[EmmetBuildSettings] = None,
-        **kwargs,
-    ):
-        self.tasks = tasks
-        self.molecules = molecules
-        self.multipoles = multipoles
-        self.query = query if query else dict()
-        self.settings = EmmetBuildSettings.autoload(settings)
-        self.kwargs = kwargs
-
-        super().__init__(sources=[tasks, molecules], targets=[multipoles], **kwargs)
-        # Uncomment in case of issue with mrun not connecting automatically to collections
-        # for i in [self.tasks, self.molecules, self.multipoles]:
-        #     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")
-        self.tasks.ensure_index("species_hash")
-
-        # 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")
-        self.molecules.ensure_index("species_hash")
-
-        # Search index for electric
-        self.multipoles.ensure_index("method")
-        self.multipoles.ensure_index("molecule_id")
-        self.multipoles.ensure_index("task_id")
-        self.multipoles.ensure_index("solvent")
-        self.multipoles.ensure_index("lot_solvent")
-        self.multipoles.ensure_index("property_id")
-        self.multipoles.ensure_index("last_updated")
-        self.multipoles.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, "species_hash"])
-        )
-
-        processed_docs = set([e for e in self.multipoles.distinct("molecule_id")])
-        to_process_docs = {d[self.molecules.key] for d in all_mols} - processed_docs
-        to_process_hashes = {
-            d["species_hash"]
-            for d in all_mols
-            if d[self.molecules.key] in to_process_docs
-        }
-
-        N = ceil(len(to_process_hashes) / number_splits)
-
-        for hash_chunk in grouper(to_process_hashes, N):
-            query = dict(temp_query)
-            query["species_hash"] = {"$in": list(hash_chunk)}
-            yield {"query": query}
-
-    def get_items(self) -> Iterator[List[Dict]]:
-        """
-        Gets all items to process into multipole documents.
-        This does no datetime checking; relying on on whether
-        task_ids are included in the multipoles Store
-
-        Returns:
-            generator or list relevant tasks and molecules to process into documents
-        """
-
-        self.logger.info("Electric multipoles 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, "species_hash"])
-        )
-
-        processed_docs = set([e for e in self.multipoles.distinct("molecule_id")])
-        to_process_docs = {d[self.molecules.key] for d in all_mols} - processed_docs
-        to_process_hashes = {
-            d["species_hash"]
-            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_hashes)} unprocessed hashes")
-
-        # Set total for builder bars to have a total
-        self.total = len(to_process_hashes)
-
-        for shash in to_process_hashes:
-            mol_query = dict(temp_query)
-            mol_query["species_hash"] = shash
-            molecules = list(self.molecules.query(criteria=mol_query))
-
-            yield molecules
-
-    def process_item(self, items: List[Dict]) -> List[Dict]:
-        """
-        Process the tasks into ElectricMultipoleDocs
-
-        Args:
-            tasks List[Dict] : a list of MoleculeDocs in dict form
-
-        Returns:
-            [dict] : a list of new electric multipole docs
-        """
-
-        mols = [MoleculeDoc(**item) for item in items]
-        shash = mols[0].species_hash
-        mol_ids = [m.molecule_id for m in mols]
-        self.logger.debug(f"Processing {shash} : {mol_ids}")
-
-        multipole_docs = list()
-
-        for mol in mols:
-            # Relevant tasks are those with the correct charge and spin
-            # for which there are AT LEAST electric dipoles present
-            # (ideally, multipole information would also be present)
-            multip_entries = [
-                e
-                for e in mol.entries
-                if e["charge"] == mol.charge
-                and e["spin_multiplicity"] == mol.spin_multiplicity
-                and (e["output"].get("dipoles") is not None)
-            ]
-
-            # Organize by solvent environment
-            by_solvent = defaultdict(list)
-            for entry in multip_entries:
-                by_solvent[entry["solvent"]].append(entry)
-
-            for solvent, entries in by_solvent.items():
-                # No documents with enthalpy and entropy
-                if len(entries) == 0:
-                    continue
-                else:
-                    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,
-                        "species_hash": shash,
-                        "orig": {"$exists": True},
-                    }
-                )
-
-                if tdoc is None:
-                    try:
-                        tdoc = self.tasks.query_one(
-                            {
-                                "task_id": int(task),
-                                "species_hash": shash,
-                                "orig": {"$exists": True},
-                            }
-                        )
-                    except ValueError:
-                        tdoc = None
-
-                if tdoc is None:
-                    continue
-
-                task_doc = TaskDocument(**tdoc)
-
-                if task_doc is None:
-                    continue
-
-                multipole_doc = ElectricMultipoleDoc.from_task(
-                    task_doc, molecule_id=mol.molecule_id, deprecated=False
-                )
-                multipole_docs.append(multipole_doc)
-
-        self.logger.debug(
-            f"Produced {len(multipole_docs)} electric multipole docs for {shash}"
-        )
-
-        return jsanitize([doc.model_dump() for doc in multipole_docs], allow_bson=True)
-
-    def update_targets(self, items: List[List[Dict]]):
-        """
-        Inserts the new documents into the multipoles collection
-
-        Args:
-            items [[dict]]: A list of documents to update
-        """
-
-        docs = list(chain.from_iterable(items))  # type: ignore
-
-        # Add timestamp
-        for item in docs:
-            item.update(
-                {
-                    "_bt": self.timestamp,
-                }
-            )
-
-        molecule_ids = list({item["molecule_id"] for item in docs})
-
-        if len(items) > 0:
-            self.logger.info(f"Updating {len(docs)} electric multipole documents")
-            self.multipoles.remove_docs({self.multipoles.key: {"$in": molecule_ids}})
-            # Neither molecule_id nor method need to be unique, but the combination must be
-            self.multipoles.update(
-                docs=docs,
-                key=["molecule_id", "solvent"],
-            )
-        else:
-            self.logger.info("No items to update")