Nightly build and disappearing vibrational modes

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1

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I believe this to be a bug with Avogadro:
(Please describe your bug or issue)

Environment Information

Avogadro version: 2.0 nightly build
Operating system and version: MacOS 15.7.3

Expected Behavior

Opening .qcout (QChem output generated by Spartan) file with vibrational modes should open the Vibrational Modes window with the Analyze-> Vibrational Modes menu active. Should be able to select various modes and start/stop the normal mode animation.

Actual Behavior

Opening QChem (via Spartan) .qcout files with normal modes in nightly builds opens the Vibrational Modes window. As soon as a mode is animated (Start Animation) the list of modes disappears and the window content is blank. The animation does start and it can be stopped (Stop Animation) but no other mode can be selected. Also the Analyze → Vibrational Modes… menu is greyed out. Only way to restore is to close and reopen file. This doesn’t always work as sometimes the Vibrational Modes window does not appear. Have to try multiple times.

With Avogadro 2.0 current build it is even stranger. If I open the .qcout files there are no vibrational modes available. If I try to open a .out file that should have vibrational modes I get an error reading the file but the (empty) Vibrational Mode window appears. I can then open or select (if already open in Avogadro) the .qcout file and there are the Vibrational Modes as expected. I can then animate any one of them and the window contents do not disappear.

Bit confusing. I have done my best to describe.

Steps to Reproduce

voutput.out (44.6 KB)

Please upload files if appropriate here (or via file-sharing service like Dropbox or Pastebin)

2

One of the changes after 2.0 invalidates vibrational modes, spectra, orbitals, etc. when the molecule changes. It’s likely that animating the vibrational mode is triggering a “molecule has changed, invalidate everything” signal.

I’ll take a look.

What you’re saying is that if you open a file with .qcout you see no vibrational modes, but if you rename the extension to .out you get some? Do you have the cclib plugin installed? Otherwise, I’m not sure how this would differ, but I’m mainly going to figure out what’s happening with the current development code.

3

I did not rename. These are two separate files (one .out that gives a file read error and a .qcout file). I have cclib installed. But, full disclosure, I can’t replicate this behavior just now. I get the file read error on the .out file in the current build. The .qcout file opens in the current build but no vibrational modes. In the nightly build, it is hit or miss whether the vibrational modes window even opens. It did once just now but subsequent attempts (after quitting and relaunching) are not opening the vibrational modes window. Avo 1.0 still reliably opens the Vibrations pane (and nothing disappears).

Since I have the nightly and current builds installed, I assume they are sharing settings files, etc. That might be an issue.

4

It would help to have both files if these are different.

This has to do with code and parsing - there’s no issue with sharing settings between the 2.0 release and nightly.

5

voutput_bifurcated.out (44.3 KB)

I was unable to upload this with the .qcout extension so I changed it to .out for the purposes of uploading it here. Thanks.