Describe the bug
I tried to run 2D torsion scan but failed.
To Reproduce
import numpy as np
from openff.toolkit import Molecule, ForceField
import qcengine
from qcelemental.models.procedures import TorsionDriveInput, TDKeywords, QCInputSpecification, OptimizationSpecification
# load the molecule
lig = Molecule.from_file('lig_ejm_55.sdf')
# load the combined bespokefit force field
ff = ForceField('combined.offxml')
# now make the scan job
torsion_task = TorsionDriveInput(
keywords=TDKeywords(
dihedrals=[(4, 10, 16, 12), (4, 7, 15, 11)],
grid_spacing=[15,15]
),
initial_molecule=[
lig.to_qcschema()
],
input_specification=QCInputSpecification(
model={'method': 'combined.offxml', 'basis': 'smirnoff'},
),
optimization_spec=OptimizationSpecification(
procedure='geometric',
keywords={
'program': 'openmm',
'coordsys': 'dlc',
'enforce': 0.1,
'reset': True,
'qccnv': True,
'epsilon': 0.0
}
)
)
result = qcengine.compute_procedure(torsion_task, 'torsiondrive', raise_error=True)
with open('combined_2D_scan.json', 'w') as output:
output.write(result.json())
Expected behavior
It runs.
Additional context
I got the error
Traceback (most recent call last):
File "/Users/zwu/mambaforge/envs/danny/lib/python3.11/site-packages/IPython/core/interactiveshell.py", line 3550, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "<ipython-input-2-3991d0bf5926>", line 1, in <module>
runfile('/Users/zwu/Desktop/Torsion/openff/run_torsion_drive.py', wdir='/Users/zwu/Desktop/Torsion/openff')
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 "/Users/zwu/Desktop/Torsion/openff/run_torsion_drive.py", line 41, in <module>
result = qcengine.compute_procedure(torsion_task, 'torsiondrive', raise_error=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zwu/mambaforge/envs/danny/lib/python3.11/site-packages/qcengine/compute.py", line 179, in compute_procedure
output_data = executor.compute(input_data, config)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zwu/mambaforge/envs/danny/lib/python3.11/site-packages/qcengine/procedures/torsiondrive.py", line 138, in compute
output_data = self._compute(input_model, config)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zwu/mambaforge/envs/danny/lib/python3.11/site-packages/qcengine/procedures/torsiondrive.py", line 70, in _compute
grid_point_results = self._spawn_optimizations(next_jobs=next_jobs, input_model=input_model, config=config)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zwu/mambaforge/envs/danny/lib/python3.11/site-packages/qcengine/procedures/torsiondrive.py", line 228, in _spawn_optimizations
grid_point_results = {
^
File "/Users/zwu/mambaforge/envs/danny/lib/python3.11/site-packages/qcengine/procedures/torsiondrive.py", line 229, in <dictcomp>
grid_point: [self._spawn_optimization(grid_point, job, input_model, config) for job in jobs]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zwu/mambaforge/envs/danny/lib/python3.11/site-packages/qcengine/procedures/torsiondrive.py", line 229, in <listcomp>
grid_point: [self._spawn_optimization(grid_point, job, input_model, config) for job in jobs]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zwu/mambaforge/envs/danny/lib/python3.11/site-packages/qcengine/procedures/torsiondrive.py", line 189, in _spawn_optimization
"set": [
^
File "/Users/zwu/mambaforge/envs/danny/lib/python3.11/site-packages/qcengine/procedures/torsiondrive.py", line 193, in <listcomp>
"value": int(angle),
^^^^^^^^^^
ValueError: invalid literal for int() with base 10: '15,180'
Describe the bug I tried to run 2D torsion scan but failed.
To Reproduce
Expected behavior It runs.
Additional context I got the error
I think one should change https://github.com/MolSSI/QCEngine/blob/master/qcengine/procedures/torsiondrive.py#L184 to
angles = grid_point.split(',')lig_ejm_55.sdf.zip