Setup qcel.models.Molecule with non-contiguous fragments #298
Description
Trying the following example molecule from S22, I notice that there is something odd happening for molecules with fragment information:
import qcelemental as qcel
data = {
"symbols": [
"N", "N", "H", "H", "H", "H", "H", "H"
],
"geometry": [
-2.9833455085754399E+0, -8.8082052767279997E-2, 0.0000000000000000E+0,
2.9833455085754399E+0, 8.8082052767279997E-2, 0.0000000000000000E+0,
-4.0792036056518599E+0, 2.5775116682053001E-1, 1.5298565626144400E+0,
-1.6052680015564000E+0, 1.2438048124313399E+0, 0.0000000000000000E+0,
-4.0792036056518599E+0, 2.5775116682053001E-1, -1.5298565626144400E+0,
4.0792036056518599E+0, -2.5775116682053001E-1, -1.5298565626144400E+0,
1.6052680015564000E+0, -1.2438048124313399E+0, 0.0000000000000000E+0,
4.0792036056518599E+0, -2.5775116682053001E-1, 1.5298565626144400E+0
],
"fragments": [
[0, 2, 3, 4],
[1, 5, 6, 7],
],
}
for validate in (True, False):
try:
mol = qcel.models.Molecule(**data, validate=validate)
except qcel.exceptions.ValidationError as e:
print(f"Fails to setup with validate={validate}\n{str(e)}")Output from the run is an unexpected validation error when validating the input
Warning: QCElemental is reordering atoms to accommodate non-contiguous fragments
Fails to setup with validate=True
Error: QCElemental would need to reorder atoms to accommodate non-contiguous fragments
Why are non-contiguous fragments a validation error in qcel? The issue is probably that throw_reorder is always true at:
while the default is false at
but there seems to be no way to toggle throw_reorder other than skipping the validation step.