.out file - optimization - Avogadro2

General Discussion Support
1

I believe this to be a bug with Avogadro

Environment Information

Avogadro version: 2
Operating system and version: Windows 11 - Avogadro 2 - Version 1.97

Expected Behavior

Optimized geometry coordinates to be displayed

Actual Behavior

The input (initial) geometry coordinates is what is displayed

Steps to Reproduce

1- Open an optimization .out file (by GAMESS)
2- Try to generate a GAMESS input file from the .out file
3- If you are using Avogadro 1, it gives you the right (optimized) coordinates
4- If you are using Avogadro 2, it gives you the initial (unoptimized) coordinates

Hello!
I am running optimization jobs using GAMESS. I get the output in .out extension, which is very okay.
Well, there is a problem encountered in Avogadro2, not Avogadro1.

For Avogadro2, when I open the .out file, then press “input”, then choose “GAMESS”, I get the initial geometry coordinates.
This does not happen with Avogadro1, when I press “extensions”, then “GAMESS”, then “Input generator” where I get the right optimized coordinates.
I think I should report this as a bug in Avogadro2, unless I am not understanding it well.
Any help is highly appreciated, since I am moving from Avogadro to Avogadro2.
Thanks!

2

Definitely sounds like a bug. Can you please post the file? Thanks.

3

Thanks for your reply!
Here are an .out file (optimization job) and a screenshot showing the difference between how Avoagadro and Avogadro2 display the coordinates.

4

Oh. I understand. This is an ORCA file, not a GAMESS file.

Avogadro 1.2 had a “native” reader for ORCA files. Avogadro 1.9x relies on Open Babel, which had a bug in how ORCA files were read (i.e., only the first geometry … no idea why it survived since ORCA developers helped with the code.)

The bug is fixed in recent builds. I will work to integrate the “native” ORCA reader into 1.98 as well.

In the meantime, if you have Python installed on your Windows system, I suggest installing https://cclib.github.io/ in which case you can use the avogadro-cclib plugin (Download Extensions) to import the output:

Screenshot 2023-04-28 at 1.49.23 PM
Screenshot 2023-04-28 at 1.49.23 PM1180×544 77 KB

With the cclib import, you can actually access all coordinates through the optimization.

5

Thank you for your time.
The .out file is a GAMESS output from ChemCompute website (unless you mean it is formatted as ORCA output file).
But anyway I will try the mentioned plugin and inform you. I already have Python installed on my windows.
Thanks again.

6

My mistake. I was looking at files in my “Downloads” folder and picked the wrong output file. Sorry.

I’ll take a look at the internal GAMESS code. Clearly it should be picking the final step of a geometry optimization.

Thanks for the report!

This pull request should fix it for 1.98 (and eventually, I’ll put in support to read all the geometries):