Avogadro 1.2 macos and Orca outputs

General Discussion Support
1

Hi,
First of all, thanks a lot for developing and distributing such a great program for computational chemists.

I am experiencing a few problems with Avogadro on Mac and Orca/Gaussian outputs.

Environment Information

Avogadro version: 1.2.0 Git: c1fcc5b
Operating system and version: macOS 0.14.6

I am experiencing two issues:

  1. when making a geometry optimization with Orca and opening the corresponding output file, Avogadro reads the initial geometry only and not the final optimized one. As a test I ran the same calculation with gaussian and opened the output with Avogadro. In that case, Avogadro successfully reads the final optimized geometry in that case.

  2. When plotting MOs coming either from Orca or Gaussian, the coloring method for the surfaces turns automatically to black for both phases of the orbital. I need to manually change the coloring method in the Surface representation, but then when I quit, this setting is not saved.

Something that might help debugging it, although what I am about to describe is also weird to me.
I can fix the problem temporary as follows:
i) delete all Avogadro related files in /Users/user_name/Library
ii) open the output file (e.g., that of Orca)
-> the orbitals are still colored in black
iii) close Avogadro and reopen the output file
-> the orbitals are depicted as expected in bleu/red
iv) close Avogadro and reopen the output file
-> the orbitals are again colored in black

I would suggest to try opening/closing several times in order to reproduce the bug.

You can find outputs for a simple geometry optimization of N2 using Orca and Gaussian here:

Thanks in advance for your help.

All the best,
Antoine

2

Hi,

Another issue: while reading a frequency calculation output from Orca, Avogadro won’t show imaginary frequencies and corresponding modes if any.

Here is an example output for an aniline molecule with planer amino croup (instead of pyramidal). In the output there is an imaginary mode that corresponds to the motion of the improper angle of the amino group. But In Avogadro (macOS), this mode is skipped in the vibrations window.

Thanks again.

Best,
Antoine

3

Hello Antoine, I do not have problem 1 unless the calculation has not been successful/has not finished. In that case Avogadro shows the original geometry. Best wishes, p.