ORCA output file in avogadro to visualize orbitals

General Discussion Support
1

Dear all

I have been using ORCA to calculate orbitals, and using Avogadro 1.2.0 to visualize the orbitals.
Some times the Avogadro is not able to display the orbitals. So I lookes at the output file and I noticed that in each structure optimisation we have two times the energy and orbitals printed out in the file (I assume: the not optimized first and optimized later). When opening the output file in avogadro, the not optimices structure shows. But the energies wich are assinged to the HOMO and LUMO etc. are coresonding to the later print out. Now I was wondering whether the orbitals corespond to the optimized or not optimized structure. Is there a easy way to check this?

Thank you for clarifying.

Best Jakob

2

Hi. Are you using ORCA 5 now? The formatting of orca output files changed from v4 > v5, so they don’t get read properly with Avogadro 1 any more.

If you switch to using Avogadro 2 there is support for reading ORCA 5 output files.

3

The coordinate reading is a known bug, which has been fixed in Open Babel. But there’s no good way to fix Avogadro 1.2.

The orbitals read should indeed be the final orbitals, albeit on the final geometry.

My suggestion is to use one of the Avo2 betas: https://two.avogadro.cc/ which do have support for reading Orca 5 output.

4

Thank you for the fast answer, I was able to read in the ouput file from orca 5. But now I do not see the option to display the Orbitals, the option analysic/create surface/ does somehow not show any orbitals. Thank you
Best Jakob

5

In the Create Surfaces... menu there is a drop down list called “Surfaces”, and if you have MOs then “Molecular Orbital” should be an option in that. Is it not?

Then you can choose which MO and the resolution (I find automatic takes forever so medium is a good starting point, maybe high).

6

Thanks. yes there is but when I will press calculate avogadro is doing something, but it does not show me any orbitals. I will try later again, maybe I need to zoom out engough, but I thought I did. If it worked, I will let you know asap.

Best

7

I find that once the calculation is finished, the orbitals don’t display immediately, especially when the resolution was high/the calculation of the orbital took a long time.

Moving the molecule a bit/rotating/zooming/waiting tends to result in it appearing in the end though, in my experience.

8

Hey Matterhorn103

I m still not able to display the orbital: with the options shown in one of the scrennshot, after pressing the “calculating” bottom the screen shows the same as the seconde screenshot.

Best
Jakob
Screenshot_1
Screenshot_2

9

Unfortunately we can’t access those screenshots - they link to files on your computer. Can you use the upload button on the forum?

Thanks…

10

Sure thing, sorry aboute this, thank you for letting me know :slight_smile:

Screenshot_1
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Screenshot_2
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11

Turn on the “Meshes” display type.

12

I suppose ideally the calculation of a surface would automatically switch on meshes?

13

Yeah - I thought it already did. Working on the patch - there’s a signal to ask for a particular display type to turn on requestActiveDisplayTypes() … but the surface code wasn’t using it :thinking:

14

Okay, that fix is building now, along with a performance improvement for some kinds of meshes.

15

Sorry for the late answer, I was able to display the orbitals, with turning on the mesh, thank you.

16

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