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Add single point jobs to the end of torsiondrives #167

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Add single point jobs to the end of torsiondrives #167

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e70beb1
add torsiondrive single point spec and job
jthorton Apr 27, 2022
af2612b
fix tests and cli, update sp spec name to be more general
jthorton Apr 29, 2022
5c60118
remove parallel code and update tests
jthorton Apr 29, 2022
b7999db
Split torsion drive single-points into separate tasks (#176)
SimonBoothroyd May 20, 2022
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2 changes: 2 additions & 0 deletions openff/bespokefit/cli/executor/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@ def _run_cli(
force_field_path: Optional[str],
target_torsion_smirks: Tuple[str],
default_qc_spec: Optional[Tuple[str, str, str]],
evaluation_qc_spec: Optional[Tuple[str, str, str]],
Comment on lines 24 to +25
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It might be good to swap this to

Suggested change
default_qc_spec: Optional[Tuple[str, str, str]],
evaluation_qc_spec: Optional[Tuple[str, str, str]],
default_qc_spec: Optional[Tuple[str, str, str]],
optimization_qc_spec: Optional[Tuple[str, str, str]],

as the optimization spec is likely the optional thing users will want to tweak, rather than the final level of theory?

workflow_name: Optional[str],
workflow_file_name: Optional[str],
directory: Optional[str],
Expand Down Expand Up @@ -85,6 +86,7 @@ def _run_cli(
force_field_path=force_field_path,
target_torsion_smirks=target_torsion_smirks,
default_qc_spec=default_qc_spec,
evaluation_qc_spec=evaluation_qc_spec,
workflow_name=workflow_name,
workflow_file_name=workflow_file_name,
allow_multiple_molecules=False,
Expand Down
47 changes: 33 additions & 14 deletions openff/bespokefit/cli/executor/submit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -88,6 +88,13 @@ def submit_options(allow_multiple_molecules: bool = False):
"then 'none' should be specified.",
required=False,
),
optgroup.option(
"--evaluation-qc-spec",
type=(str, str, str),
help="The program, method and basis used to refine the default specification. In the case of a torsion drive"
"this is the specification used to evaluate the PES on the geometries from the default spec.",
required=False,
),
]


Expand All @@ -97,6 +104,7 @@ def _to_input_schema(
force_field_path: Optional[str],
target_torsion_smirks: Tuple[str],
default_qc_spec: Optional[Tuple[str, str, str]],
evaluation_qc_spec: Optional[Tuple[str, str, str]],
workflow_name: Optional[str],
workflow_file_name: Optional[str],
) -> "BespokeOptimizationSchema":
Expand Down Expand Up @@ -135,21 +143,28 @@ def _to_input_schema(
workflow_factory.initial_force_field = force_field_path
if len(target_torsion_smirks) > 0:
workflow_factory.target_torsion_smirks = [*target_torsion_smirks]
if default_qc_spec is not None:

program, method, basis = default_qc_spec

if basis.lower() == "none":
basis = None

workflow_factory.default_qc_specs = [
QCSpec(
program=program,
method=method,
basis=basis,
spec_description="CLI provided spec",
for spec, name in [
(default_qc_spec, "default_qc_spec"),
(evaluation_qc_spec, "evaluation_qc_spec"),
]:
if spec is not None:

program, method, basis = spec

if basis.lower() == "none":
basis = None

setattr(
workflow_factory,
name,
QCSpec(
program=program,
method=method,
basis=basis,
spec_name=name,
spec_description=f"CLI provided spec {name}",
),
)
]

except FileNotFoundError:

Expand Down Expand Up @@ -201,6 +216,7 @@ def _submit(
force_field_path: Optional[str],
target_torsion_smirks: Tuple[str],
default_qc_spec: Optional[Tuple[str, str, str]],
evaluation_qc_spec: Optional[Tuple[str, str, str]],
workflow_name: Optional[str],
workflow_file_name: Optional[str],
allow_multiple_molecules: bool,
Expand Down Expand Up @@ -269,6 +285,7 @@ def _submit(
force_field_path,
target_torsion_smirks,
default_qc_spec,
evaluation_qc_spec,
workflow_name,
workflow_file_name,
)
Expand Down Expand Up @@ -330,6 +347,7 @@ def _submit_cli(
force_field_path: Optional[List[str]],
target_torsion_smirks: Tuple[str],
default_qc_spec: Optional[Tuple[str, str, str]],
evaluation_qc_spec: Optional[Tuple[str, str, str]],
workflow_name: Optional[str],
workflow_file_name: Optional[str],
save_submission: bool,
Expand All @@ -350,6 +368,7 @@ def _submit_cli(
force_field_path=force_field_path,
target_torsion_smirks=target_torsion_smirks,
default_qc_spec=default_qc_spec,
evaluation_qc_spec=evaluation_qc_spec,
workflow_name=workflow_name,
workflow_file_name=workflow_file_name,
allow_multiple_molecules=True,
Expand Down
7 changes: 3 additions & 4 deletions openff/bespokefit/data/schemas/debug.json
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Original file line number Diff line number Diff line change
Expand Up @@ -80,8 +80,7 @@
"heuristic": "path_length",
"keep_non_rotor_ring_substituents": false
},
"default_qc_specs": [
{
"default_qc_spec": {
"method": "uff",
"basis": null,
"program": "rdkit",
Expand All @@ -97,6 +96,6 @@
"mayer_indices"
],
"keywords": null
}
]
},
"evaluation_qc_spec": null
}
7 changes: 3 additions & 4 deletions openff/bespokefit/data/schemas/default.json
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Original file line number Diff line number Diff line change
Expand Up @@ -81,8 +81,7 @@
"heuristic": "path_length",
"keep_non_rotor_ring_substituents": false
},
"default_qc_specs": [
{
"default_qc_spec": {
"method": "B3LYP-D3BJ",
"basis": "DZVP",
"program": "psi4",
Expand All @@ -98,6 +97,6 @@
"mayer_indices"
],
"keywords": null
}
]
},
"evaluation_qc_spec": null
}
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