A builder for classical md workflows

.github/workflows/testing.yml

@@ -30,7 +30,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
           channels: anaconda, conda-forge
 
-      - name: Install OpenBabel
+      - name: Install all conda requirements
         shell: bash -l {0}
         run: |
           conda install openbabel openff-toolkit>=0.14.0 openff-interchange>=0.3.22 sqlite -y

emmet-builders/emmet/builders/openmm/__init__.py

@@ -0,0 +1 @@
+from emmet.builders.openmm.core import ElectrolyteBuilder

emmet-builders/emmet/builders/openmm/core.py

@@ -0,0 +1,361 @@
+from typing import Optional, List, Union
+from pathlib import Path
+
+import numpy as np
+
+from maggma.core import Builder, Store
+from maggma.stores import MemoryStore
+from emmet.builders.openmm.utils import (
+    create_solute,
+    identify_solute,
+    identify_networking_solvents,
+)
+from emmet.core.openff.solvation import SolvationDoc
+from emmet.core.openff.benchmarking import SolventBenchmarkingDoc
+from emmet.core.openmm import OpenMMTaskDocument
+from emmet.core.openmm.calculations import CalculationsDoc
+from emmet.core.utils import jsanitize
+
+from emmet.builders.openmm.openmm_utils import (
+    insert_blobs,
+    instantiate_universe,
+    resolve_traj_path,
+    task_doc_to_universe,
+)
+
+
+class ElectrolyteBuilder(Builder):
+    """
+    Builder to create solvation and calculations documents from OpenMM task documents.
+
+    This class processes molecular dynamics (MD) simulations and generates
+    comprehensive reports including solvation properties and calculation results.
+    It leverages the OpenFF toolkit and MDAnalysis for molecular topology and trajectory
+    handling, respectively.
+    """
+
+    def __init__(
+        self,
+        md_docs: Store,
+        blobs: Store,
+        solute: Optional[Store] = None,
+        calculations: Optional[Store] = None,
+        query: Optional[dict] = None,
+        solute_analysis_classes: Union[List[str], str] = "all",
+        solvation_fallback_radius: float = 3,
+        chunk_size: int = 10,
+    ):
+        self.md_docs = md_docs
+        self.blobs = blobs
+        self.solute = solute or MemoryStore()
+        self.calculations = calculations or MemoryStore()
+        self.query = query or {}
+        self.solute_analysis_classes = solute_analysis_classes
+        self.solvation_fallback_radius = solvation_fallback_radius
+
+        self.md_docs.key = "uuid"
+        self.blobs.key = "blob_uuid"
+        if self.solute:
+            self.solute.key = "job_uuid"
+        if self.calculations:
+            self.calculations.key = "job_uuid"
+
+        super().__init__(
+            sources=[md_docs, blobs],
+            targets=[self.solute, self.calculations],
+            chunk_size=chunk_size,
+        )
+
+    # def prechunk(self, number_splits: int):  # pragma: no cover
+    #     """
+    #     Prechunk method to perform chunking by the key field
+    #     """
+    #     q = dict(self.query)
+    #     keys = self.electronic_structure.newer_in(
+    #         self.materials, criteria=q, exhaustive=True
+    #     )
+    #     N = ceil(len(keys) / number_splits)
+    #     for split in grouper(keys, N):
+    #         yield {"query": {self.materials.key: {"$in": list(split)}}}
+
+    def get_items(self, local_trajectories=False):
+        self.logger.info("Electrolyte builder started.")
+
+        hosts = self.md_docs.query(self.query, ["hosts"])
+        flow_ids = {doc["hosts"][-1] for doc in hosts}  # top level flows
+
+        job_groups = []
+        for flow_id in flow_ids:
+            # the last item in hosts should be the top level workflow
+            host_match = {"$expr": {"$eq": [{"$arrayElemAt": ["$hosts", -1]}, flow_id]}}
+            job_groups.append(list(self.md_docs.query(criteria=host_match)))
+
+        items = []
+        for jobs in job_groups:
+            # find the job with the most calcs in the flow, presumably the last
+            len_calcs = [len(job["output"]["calcs_reversed"] or []) for job in jobs]
+            last_job = jobs[np.argmax(len_calcs)]
+
+            insert_blobs(
+                self.blobs, last_job["output"], include_traj=not local_trajectories
+            )
+
+            items.append(last_job)
+
+        return items
+
+    def get_items_from_directories(self):
+        # query will be ignored
+        return
+
+    def process_items(
+        self,
+        items: List,
+        local_trajectories: bool = False,
+        rebase_traj_path: Optional[tuple[Path, Path]] = None,
+    ):
+        """
+
+        Parameters
+        ----------
+        items: the items from get_items
+        local_trajectories: whether to look for files locally in lieu of downloading
+        rebase_traj_path: useful if the launch directory has moved
+
+        Returns
+        -------
+
+        """
+        self.logger.info(f"Processing {len(items)} materials for electrolyte builder.")
+
+        processed_items = []
+        for item in items:
+            # create task_doc
+            task_doc = OpenMMTaskDocument.parse_obj(item["output"])
+
+            # _ is needed bc traj_path may be a tmpfile and a reference must be in scope
+            traj_path, _ = resolve_traj_path(
+                task_doc, local_trajectories, rebase_traj_path
+            )
+
+            u = task_doc_to_universe(task_doc, traj_path)
+
+            # create solute_doc
+            solute = create_solute(
+                u,
+                solute_name=identify_solute(u),
+                networking_solvents=identify_networking_solvents(u),
+                fallback_radius=self.solvation_fallback_radius,
+                analysis_classes=self.solute_analysis_classes,
+            )
+            solute.run()
+            solvation_doc = SolvationDoc.from_solute(
+                solute, job_uuid=item["uuid"], flow_uuid=item["hosts"][-1]
+            )
+            calculations_doc = CalculationsDoc.from_calcs_reversed(
+                task_doc.calcs_reversed,
+                job_uuid=item["uuid"],
+                flow_uuid=item["hosts"][-1],
+            )
+
+            # create docs
+            # TODO: what cleanup do I need?
+            docs = {
+                "solute": jsanitize(solvation_doc.model_dump()),
+                "calculations": jsanitize(calculations_doc.model_dump()),
+            }
+
+            processed_items.append(docs)
+
+        return processed_items
+
+    def update_targets(self, items: List):
+        if len(items) > 0:
+            self.logger.info(f"Found {len(items)} electrolyte docs to update.")
+
+            solutes = [item["solute"] for item in items]
+            self.solute.update(solutes)
+
+            calculations = [item["calculations"] for item in items]
+            self.calculations.update(calculations)
+
+        else:
+            self.logger.info("No items to update.")
+
+    def instantiate_universe(
+        self,
+        job_uuid: str,
+        traj_directory: Union[str, Path] = ".",
+        overwrite_local_traj: bool = True,
+    ):
+        """
+        Instantiate a MDAnalysis universe from a task document.
+
+        This is useful if you want to analyze a small number of systems
+        without running the whole build pipeline.
+
+        To get a solute, call create_solute using the universe. See
+        the body of process_items for the appropriate syntax.
+
+        Args:
+            job_uuid: str
+                The UUID of the job.
+            traj_directory: str
+                Name of the DCD file to write.
+            overwrite_local_traj: bool
+                Whether to overwrite the local trajectory if it exists.
+        """
+        return instantiate_universe(
+            self.md_docs, self.blobs, job_uuid, traj_directory, overwrite_local_traj
+        )
+
+
+class BenchmarkingBuilder(Builder):
+    """
+    Builder to create solvation and calculations documents from OpenMM task documents.
+
+    This class processes molecular dynamics (MD) simulations and generates
+    comprehensive reports including solvation properties and calculation results.
+    It leverages the OpenFF toolkit and MDAnalysis for molecular topology and trajectory
+    handling, respectively.
+    """
+
+    def __init__(
+        self,
+        md_docs: Store,
+        blobs: Store,
+        benchmarking: Optional[Store] = None,
+        query: Optional[dict] = None,
+        chunk_size: int = 10,
+    ):
+        self.md_docs = md_docs
+        self.blobs = blobs
+        self.benchmarking = benchmarking or MemoryStore()
+        self.query = query or {}
+
+        self.md_docs.key = "uuid"
+        self.blobs.key = "blob_uuid"
+        self.benchmarking.key = "job_uuid"
+
+        super().__init__(
+            sources=[md_docs, blobs],
+            targets=[self.benchmarking],
+            chunk_size=chunk_size,
+        )
+
+    # def prechunk(self, number_splits: int):  # pragma: no cover
+    #     """
+    #     Prechunk method to perform chunking by the key field
+    #     """
+    #     q = dict(self.query)
+    #     keys = self.electronic_structure.newer_in(
+    #         self.materials, criteria=q, exhaustive=True
+    #     )
+    #     N = ceil(len(keys) / number_splits)
+    #     for split in grouper(keys, N):
+    #         yield {"query": {self.materials.key: {"$in": list(split)}}}
+
+    def get_items(self, local_trajectories=False):
+        self.logger.info("Electrolyte builder started.")
+
+        hosts = self.md_docs.query(self.query, ["hosts"])
+        flow_ids = {doc["hosts"][-1] for doc in hosts}  # top level flows
+
+        job_groups = []
+        for flow_id in flow_ids:
+            # the last item in hosts should be the top level workflow
+            host_match = {"$expr": {"$eq": [{"$arrayElemAt": ["$hosts", -1]}, flow_id]}}
+            job_groups.append(list(self.md_docs.query(criteria=host_match)))
+
+        items = []
+        for jobs in job_groups:
+            # find the job with the most calcs in the flow, presumably the last
+            len_calcs = [len(job["output"]["calcs_reversed"] or []) for job in jobs]
+            last_job = jobs[np.argmax(len_calcs)]
+
+            insert_blobs(
+                self.blobs, last_job["output"], include_traj=not local_trajectories
+            )
+
+            items.append(last_job)
+
+        return items
+
+    def get_items_from_directories(self):
+        # query will be ignored
+        return
+
+    def process_items(
+        self,
+        items,
+        local_trajectories: bool = False,
+        rebase_traj_path: Optional[tuple[Path, Path]] = None,
+        **benchmarking_kwargs,
+    ):
+        self.logger.info(f"Processing {len(items)} materials for electrolyte builder.")
+
+        processed_items = []
+        for item in items:
+            # create task_doc
+            task_doc = OpenMMTaskDocument.parse_obj(item["output"])
+
+            # _ is needed bc traj_path may be a tmpfile and a reference must be in scope
+            traj_path, _ = resolve_traj_path(
+                task_doc, local_trajectories, rebase_traj_path
+            )
+
+            u = task_doc_to_universe(task_doc, traj_path)
+
+            benchmarking_doc = SolventBenchmarkingDoc.from_universe(
+                u,
+                temperature=task_doc.calcs_reversed[0].input.temperature,
+                density=task_doc.calcs_reversed[0].output.density[-1],
+                job_uuid=item["uuid"],
+                flow_uuid=item["hosts"][-1],
+                tags=task_doc.tags,
+                **benchmarking_kwargs,
+            )
+
+            del u
+
+            docs = {
+                "benchmarking": jsanitize(benchmarking_doc.model_dump()),
+            }
+
+            processed_items.append(docs)
+
+        return processed_items
+
+    def update_targets(self, items: List):
+        if len(items) > 0:
+            self.logger.info(f"Found {len(items)} electrolyte docs to update.")
+
+            calculations = [item["benchmarking"] for item in items]
+            self.benchmarking.update(calculations)
+
+        else:
+            self.logger.info("No items to update.")
+
+    def instantiate_universe(
+        self,
+        job_uuid: str,
+        traj_directory: Union[str, Path] = ".",
+        overwrite_local_traj: bool = True,
+    ):
+        """
+        Instantiate a MDAnalysis universe from a task document.
+
+        This is useful if you want to analyze a small number of systems
+        without running the whole build pipeline.
+
+        Args:
+            job_uuid: str
+                The UUID of the job.
+            traj_directory: str
+                Name of the DCD file to write.
+            overwrite_local_traj: bool
+                Whether to overwrite the local trajectory if it exists.
+        """
+        return instantiate_universe(
+            self.md_docs, self.blobs, job_uuid, traj_directory, overwrite_local_traj
+        )