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About running TorsionDrive #340

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xiki-tempula opened this issue Jan 16, 2022 · 0 comments
Closed

About running TorsionDrive #340

xiki-tempula opened this issue Jan 16, 2022 · 0 comments

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@xiki-tempula
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xiki-tempula commented Jan 16, 2022

Describe the bug
I'm interested in running TorsionDrive following the interface of outlined by #305 (comment) but couldn't get the procedure to run.

To Reproduce

from geometric.molecule import Molecule
from qcengine.compute import compute_procedure
from qcelemental.models import DriverEnum
from qcelemental.models.procedures import TorsionDriveInput, \
    QCInputSpecification, OptimizationSpecification
from qcengine.procedures.torsiondrive import TorsionDriveProcedure
from qcelemental.models.common_models import Model
molecule = Molecule('test.xyz')
molecule.build_topology()

result = compute_procedure(
    input_data=TorsionDriveInput(
        keywords={
            "dihedrals": [(2, 0, 1, 5)],
            "grid_spacing": [15, ]
        },
        input_specification=QCInputSpecification(
            driver=DriverEnum.gradient,
            model=Model(method="UFF", basis=None)
        ),
        initial_molecule=molecule,
        optimization_spec=OptimizationSpecification(
            procedure="geomeTRIC",
            keywords={
                "coordsys": "dlc",
                "maxiter": 300,
                "program": "rdkit",
            }
        )
    ),
    procedure="torsiondrive"
)

print(result)

WIth test.xyz being

24
Coordinates from ORCA-job CN_H11C12N1_c5eace0d1ccbf515b6a0e1495ea48fe5~2_opt
  N   -0.14734773330158      0.36427415662708      0.27404221628527
  C   0.87642997276114     -0.47337558769163      0.71538193838427
  C   -1.47305098595612      0.03776706482306     -0.00995605239714
  H   0.09454863104194      1.33699089025511      0.17742506764776
  C   0.62900540834344     -1.66407989804081      1.41301505118399
  C   2.20550910176015     -0.07808479834656      0.50124124155727
  C   -1.85575540698289     -1.23922285446841     -0.44424080136003
  C   -2.44889434562448      1.04102614250225      0.08504023282233
  C   1.69108875493289     -2.44084190533860      1.85853563179447
  H   -0.39061227620670     -1.96322348199187      1.63021722109903
  C   3.25569101180997     -0.85596488191577      0.96764372725101
  H   2.40833739507763      0.84291902436477     -0.04053145738987
  C   -3.18556592017182     -1.49887595490090     -0.75002594484279
  H   -1.10838460416432     -2.01520625120065     -0.56987338441668
  C   -3.77044862428985      0.77132908819139     -0.24166887821415
  H   -2.16318775569790      2.03445854537413      0.42323208840750
  C   3.00941891995621     -2.05014493465937      1.64027773757711
  H   1.48020142447713     -3.35838091116040      2.40091373716700
  H   4.27692334307468     -0.52999713132821      0.79138794434983
  C   -4.15377101222979     -0.50322256690238     -0.65079747118207
  H   -3.46294583844032     -2.49328087055841     -1.08875440208402
  H   -4.50947357162152      1.56361848133573     -0.16216000040325
  H   3.83191130149393     -2.66302440850731      1.99456272492360
  H   -5.18962719004183     -0.71545695646225     -0.89490916816043

Expected behavior
I got the error.

Traceback (most recent call last):
  File "<input>", line 1, in <module>
  File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_umd.py", line 197, in runfile
    pydev_imports.execfile(filename, global_vars, local_vars)  # execute the script
  File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/_pydev_imps/_pydev_execfile.py", line 18, in execfile
    exec(compile(contents+"\n", file, 'exec'), glob, loc)
  File "test/run.py", line 12, in <module>
    input_data=TorsionDriveInput(
  File "pydantic/main.py", line 331, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for TorsionDriveInput
initial_molecule
  value is not a valid list (type=type_error.list)

Additional context
It is kind of hard to debug as there is no documentation for TorsionDriveInput.
Running the original workflow #305 (comment) will not work as well.

qcengine.version
'v0.21.0'
qcelemental.version
'v0.24.0'

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