Hi,
I am working with a python code imports psi4 (Psi4 1.3.2 release Git: Rev {HEAD} ecbda83)
The code created a string, e.g.,
Blockquote
H 0.0 0.0 0.7525902
O 0.0 0.0 -0.0474114
@H 0.0 0.0 1.5051804
@O 0.0 0.0 -0.0948229
@H 0.0 0.0 2.6340657
@O 0.0 0.0 -0.1659400
@H 0.0 0.0 3.7629510
@O 0.0 0.0 -0.2370572
then use psi4.geometry(the_above_string) to generate molecule, I got the following error message
Blockquote
File “…/psi4conda/lib/python3.6/site-packages/qcelemental/molparse/from_string.py”, line 263, in from_string
**molinit)
File “…/psi4conda/lib/python3.6/site-packages/qcelemental/molparse/from_arrays.py”, line 123, in from_input_arrays
verbose=1)
File “…/psi4conda/lib/python3.6/site-packages/qcelemental/molparse/from_arrays.py”, line 347, in from_arrays
tooclose=tooclose) # yapf: disable
File “…/psi4conda/lib/python3.6/site-packages/qcelemental/molparse/from_arrays.py”, line 586, in validate_and_fill_geometry
[(i, j, dm[i, j]) for i, j in zip(*tooclosem)]))
qcelemental.exceptions.ValidationError: Following atoms are too close: [(3, 1, 0.0474115), (5, 3, 0.0711171), (7, 5, 0.07111719999999999)]
Closing remaining open files:atomic_info.h5…done
it seems this type of message related to the length of directory name for other molecules. But I still unable to figure out possible reason for the above issue. Any insight would be helpful.
Thank you so much