celemental.exceptions.ValidationError: Following atoms are too close:


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.,

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

File “…/psi4conda/lib/python3.6/site-packages/qcelemental/molparse/from_string.py”, line 263, in from_string
File “…/psi4conda/lib/python3.6/site-packages/qcelemental/molparse/from_arrays.py”, line 123, in from_input_arrays
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

Please read our post for what needs to be in a help topic. In particular, “If Psi is not doing what you want: include your input file, version number, and relevant part of the output file”.

This strongly reminds me of a bug we already have fixed, in which case, all I can suggest is that you use a more recent version.

I’m struggling to understand your post. For example, when you say “I am working with a python code load psi4”, do you mean “I am working with a python code that imports Psi4”?

Thank you so much. I am very sorry for my carelessness. I have added the version and corrected load to imports. I am downloading the newest version of Psi4. After updated, log out, and re login, still the same problem :frowning: I think I got a fix! replace @ into #. The code would like to use @ as comment, sometimes it lead to problem. # seems to be fine :slight_smile:

I am not authorized to release the whole input (the python code imports psi4). I can only provide some sections. I am very sorry for this inconvenience.

Using @ for a comment is not accepted syntax in Psi4. Comments should instead be #.

The error message is telling you that having atoms that close to each other in space (~0.05 Angstroms) is unphysical.