Avogadro 2 (1.100.0) crashing when opening Orca output

Matthew_Graneri · January 22, 2025, 3:45pm

I try to use Avogadro on a MacBook Pro M1 Max, but I’m experiencing a bug which has been around for some time. If I try to open the output of an Orca calculation, Avogadro crashes immediately. This happens regardless of whether I use the ARM or Intel version of Avogadro.

I posted about this some time ago (Avogadro crashes when trying to open Orca output files), but I guess it has not yet been fixed…?

Also, in my previous report, it was suggested that the reason Avogadro was crashing was because I was using a customised basis set. In the output file I was testing today, this was not the case. I’ll attach the output file below.

Environment Information

Avogadro version: 1.100.0
Operating system and version: macOS Sequoia 15.2

Expected Behavior

Orca output file opens successfully

Actual Behavior

Avogadro crashes.

Steps to Reproduce

Attempt to open Orca output file

h2o-opt-freq-b3lyp-svpd.out (333.3 KB)

ghutchis · January 22, 2025, 3:55pm

I’ll take a look later today.

ghutchis · January 22, 2025, 5:29pm

Huh. This one’s weird - it’s crashing when calculating the density matrix. I found a variety of weird bugs on the way to 1.100 - probably the MO coefficients aren’t read correctly here.

Thanks.

Matthew_Graneri · September 26, 2025, 9:09am

Did you get a chance to look into this? I gave it another try with the latest version (1.101.0) and it still crashes when I try to open an Orca output.

ghutchis · September 27, 2025, 10:55pm

I had not - thanks for the reminder. I’ll see what I can do tomorrow (Sunday).

ghutchis · September 28, 2025, 4:45am

I think this should do it - seems to work read \ce{NO2^*} now & reminds me that I still need to work on the orbital table for open-shell systems…

github.com/OpenChemistry/avogadrolibs

Fix reading open-shell ORCA calculations

master ← ghutchis:fix-orca-openshell

opened 04:43AM - 28 Sep 25 UTC

ghutchis

+11 -5

Fixes #2039 Developer Certificate of Origin Version 1.1 Copyright (C) 200…4, 2006 The Linux Foundation and its contributors. 1 Letterman Drive Suite D4700 San Francisco, CA, 94129 Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Developer's Certificate of Origin 1.1 By making a contribution to this project, I certify that: (a) The contribution was created in whole or in part by me and I have the right to submit it under the open source license indicated in the file; or (b) The contribution is based upon previous work that, to the best of my knowledge, is covered under an appropriate open source license and I have the right under that license to submit that work with modifications, whether created in whole or in part by me, under the same open source license (unless I am permitted to submit under a different license), as indicated in the file; or (c) The contribution was provided directly to me by some other person who certified (a), (b) or (c) and I have not modified it. (d) I understand and agree that this project and the contribution are public and that a record of the contribution (including all personal information I submit with it, including my sign-off) is maintained indefinitely and may be redistributed consistent with this project or the open source license(s) involved.

Matthew_Graneri · September 29, 2025, 2:07pm

Thanks for that! How do I apply it to my copy of Avogadro?

ghutchis · September 29, 2025, 2:30pm

There should be a new nightly build tonight. Right now, both Mac builds need a bit of cleanup. (Intel is on a macOS release that randomly gives up when building the DMG and Apple Silicon needs some other updates.)

I can probably put together an Apple Silicon build from my laptop if it doesn’t pop up by tomorrow.

system · October 2, 2025, 10:50pm

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