QC-program keywords (#239)

* helper function to get program specific keywords * lint * Add test for XTB verbosity (#244) --------- Co-authored-by: Josh A. Mitchell <[email protected]>
openforcefield · Mar 23, 2023 · 6b57aa6 · 6b57aa6
1 parent ac5dd88
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diff --git a/openff/bespokefit/executor/services/qcgenerator/worker.py b/openff/bespokefit/executor/services/qcgenerator/worker.py
@@ -62,6 +62,24 @@ def _select_atom(atoms: List[Atom]) -> int:
     return candidate.molecule_atom_index
 
 
+def _get_program_keywords(program: str) -> Dict[str, str]:
+    """
+    Generate a set of pre-defined keywords for the calculation based on the program.
+    These are based on experience.
+
+    Args:
+        program: The name of the program which will run the calculation
+
+    Returns:
+         A dictionary of program specific keywords
+    """
+    keywords = {}
+    if program.lower() == "xtb":
+        # <https://github.com/openforcefield/openff-bespokefit/issues/238>
+        keywords["verbosity"] = "muted"
+    return keywords
+
+
 @celery_app.task(acks_late=True)
 def compute_torsion_drive(task_json: str) -> TorsionDriveResult:
     """Runs a torsion drive using QCEngine."""
@@ -118,6 +136,7 @@ def compute_torsion_drive(task_json: str) -> TorsionDriveResult:
         input_specification=QCInputSpecification(
             model=task.model,
             driver=DriverEnum.gradient,
+            keywords=_get_program_keywords(task.program),
         ),
         optimization_spec=OptimizationSpecification(
             procedure=task.optimization_spec.program,
@@ -171,6 +190,7 @@ def compute_optimization(
             input_specification=QCInputSpecification(
                 model=task.model,
                 driver=DriverEnum.gradient,
+                keywords=_get_program_keywords(task.program),
             ),
             initial_molecule=molecule.to_qcschema(conformer=i),
         )

diff --git a/openff/bespokefit/tests/executor/services/qcgenerator/test_worker.py b/openff/bespokefit/tests/executor/services/qcgenerator/test_worker.py
@@ -41,6 +41,40 @@ def test_compute_torsion_drive():
     assert all([atom.atomic_number != 1 for atom in atoms])
 
 
+def test_compute_torsion_drive_xtb():
+    task = Torsion1DTask(
+        smiles="[F][CH2:1][CH2:2][F]",
+        central_bond=(1, 2),
+        grid_spacing=180,
+        scan_range=(-180, 180),
+        program="xtb",
+        model=Model(method="gfn2xtb", basis=None),
+    )
+
+    result_json = worker.compute_torsion_drive(task.json())
+    assert isinstance(result_json, str)
+
+    result_dict = json.loads(result_json)
+    assert isinstance(result_dict, dict)
+
+    result = TorsionDriveResult.parse_obj(result_dict)
+    assert result.success
+
+    cmiles = result.final_molecules["180"].extras[
+        "canonical_isomeric_explicit_hydrogen_mapped_smiles"
+    ]
+
+    # Make sure a molecule can be created from CMILES
+    final_molecule = Molecule.from_mapped_smiles(cmiles)
+    assert Molecule.are_isomorphic(final_molecule, Molecule.from_smiles("FCCF"))[0]
+    dihedral = result.keywords.dihedrals[0]
+    # make sure heavy atoms are targeted
+    atoms = [final_molecule.atoms[i] for i in dihedral]
+    assert all([atom.atomic_number != 1 for atom in atoms])
+    # Make sure the "muted" verbosity was used
+    assert result_dict["input_specification"]["keywords"]["verbosity"] == "muted"
+
+
 def test_compute_optimization():
     task = OptimizationTask(
         smiles="CCCCC",