Color by -> Segfault

[arugula_jones]

Three bugs that I grouped because they may be related. Tried on linux and mac.

Environment Information

Avogadro version: 1.98.1
Operating system and version: ubuntu jammy jellyfish, mac ventura 13.0.1

Expected Behavior

1. Create van der waals surface colored by electrostatic potential
2. Create electron density surface, colored by electrostatic potential.
3. Use “edit color opacity map”

Actual Behavior

Segmentation fault (core dumped)

Steps to Reproduce

open small molecule .fchk file from gaussian 16. try any of the above behavior. observe segfault.

Please upload files if appropriate here (or via file-sharing service like Dropbox or Pastebin)
./Avogadro2-x86_64_12.14.AppImage
Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use QT_QPA_PLATFORM=wayland to run on Wayland anyway.
Using locale: “en_US”
qt.network.ssl: QSslSocket: cannot resolve EVP_PKEY_base_id
qt.network.ssl: QSslSocket: cannot resolve SSL_get_peer_certificate
Extension plugins dynamically found… 47
“Checking for energy scripts in path /home/user/.local/share/OpenChemistry/Avogadro/energy”
“Checking for energy scripts in path /usr/share/ubuntu/OpenChemistry/Avogadro/energy”
“Checking for energy scripts in path /usr/local/share/OpenChemistry/Avogadro/energy”
“Checking for energy scripts in path /usr/share/OpenChemistry/Avogadro/energy”
“Checking for energy scripts in path /var/lib/snapd/desktop/OpenChemistry/Avogadro/energy”
“Checking for energy scripts in path /tmp/.mount_Avogadq0hfpa/usr/bin/…/lib/avogadro2/scripts/energy”
“Cannot load script /tmp/.mount_Avogadq0hfpa/usr/lib/avogadro2/scripts/energy/ani2x.py”
qt.network.ssl: QSslSocket: cannot call unresolved function SSL_get_peer_certificate
register GAFF
register GFN-FF
register GFN1
register GFN2
register MMFF94
register UFF
OBProcess::executeObabel: Running “/tmp/.mount_Avogadq0hfpa/usr/bin/obabel” “-L formats read”
OBProcess::executeObabel: Running “/tmp/.mount_Avogadq0hfpa/usr/bin/obabel” “-L formats write”
OBProcess::executeObabel: Running “/tmp/.mount_Avogadq0hfpa/usr/bin/obabel” “-L forcefields”
OBProcess::executeObabel: Running “/tmp/.mount_Avogadq0hfpa/usr/bin/obabel” “-L charges”
OBProcess::executeObabel: Running “/tmp/.mount_Avogadq0hfpa/usr/bin/obabel” “-V”
“/tmp/.mount_Avogadq0hfpa/usr/bin/obabel” found: “/tmp/.mount_Avogadq0hfpa/usr/bin/obabel: Open Babel 3.1.1 – Nov 2 2023 – 19:34:19”
“Checking for commands scripts in path /home/user/.local/share/OpenChemistry/Avogadro/commands”
“Checking for commands scripts in path /usr/share/ubuntu/OpenChemistry/Avogadro/commands”
“Checking for commands scripts in path /usr/local/share/OpenChemistry/Avogadro/commands”
“Checking for commands scripts in path /usr/share/OpenChemistry/Avogadro/commands”
“Checking for commands scripts in path /var/lib/snapd/desktop/OpenChemistry/Avogadro/commands”
“Checking for commands scripts in path /tmp/.mount_Avogadq0hfpa/usr/bin/…/lib/avogadro2/scripts/commands”
“Checking for inputGenerators scripts in path /home/user/.local/share/OpenChemistry/Avogadro/inputGenerators”
“Checking for inputGenerators scripts in path /usr/share/ubuntu/OpenChemistry/Avogadro/inputGenerators”
“Checking for inputGenerators scripts in path /usr/local/share/OpenChemistry/Avogadro/inputGenerators”
“Checking for inputGenerators scripts in path /usr/share/OpenChemistry/Avogadro/inputGenerators”
“Checking for inputGenerators scripts in path /var/lib/snapd/desktop/OpenChemistry/Avogadro/inputGenerators”
“Checking for inputGenerators scripts in path /tmp/.mount_Avogadq0hfpa/usr/bin/…/lib/avogadro2/scripts/inputGenerators”
“Checking for charges scripts in path /home/user/.local/share/OpenChemistry/Avogadro/charges”
“Checking for charges scripts in path /usr/share/ubuntu/OpenChemistry/Avogadro/charges”
“Checking for charges scripts in path /usr/local/share/OpenChemistry/Avogadro/charges”
“Checking for charges scripts in path /usr/share/OpenChemistry/Avogadro/charges”
“Checking for charges scripts in path /var/lib/snapd/desktop/OpenChemistry/Avogadro/charges”
“Checking for charges scripts in path /tmp/.mount_Avogadq0hfpa/usr/bin/…/lib/avogadro2/scripts/charges”
“Cannot load script /tmp/.mount_Avogadq0hfpa/usr/lib/avogadro2/scripts/charges/antechamber.py”
“Checking for formatScripts scripts in path /home/user/.local/share/OpenChemistry/Avogadro/formatScripts”
“Checking for formatScripts scripts in path /usr/share/ubuntu/OpenChemistry/Avogadro/formatScripts”
“Checking for formatScripts scripts in path /usr/local/share/OpenChemistry/Avogadro/formatScripts”
“Checking for formatScripts scripts in path /usr/share/OpenChemistry/Avogadro/formatScripts”
“Checking for formatScripts scripts in path /var/lib/snapd/desktop/OpenChemistry/Avogadro/formatScripts”
“Checking for formatScripts scripts in path /tmp/.mount_Avogadq0hfpa/usr/bin/…/lib/avogadro2/scripts/formatScripts”
Error starting RPC server: “QLocalServer::listen: Address in use”
Starting new server.
Open Babel formats ready: 146
Segmentation fault (core dumped)

[ghutchis]

@arugula_jones

Use “edit color opacity map”

Yeah, that’s the problem. That command is intended for VTK plots. This should fix it?
https://github.com/OpenChemistry/avogadrolibs/pull/1509

[arugula_jones]

Sorry, I think I was unclear. 1, 2, and 3 were three seperate errors, but not done in order. I grouped them (bad habit, I know) because I thought they were related. Does this change your response? See also that the fix Not finding forcefield saved in Avogadro.conf leads to segfault and failed launch - #2 by matterhorn103
seems to solve problem 1.

[ghutchis]

Can you check a nightly build?

For the electron density crash, are you using Molden or Orca files? I’m pretty sure I fixed that crash recently too.

[arugula_jones]

Ok, just tried the nightly. Looks like problem 1 and 3 were fixed but problem 2 was not. These are gaussian 16 .fchk files.

[ghutchis]

Since I’m about to leave the office, could you open a GitHub issue for problem 2? That would be helpful to remind me to fix it.

Thanks!

[ghutchis]

This fixes the crash - I found the underlying issue too.

Fix density color crash

[ghutchis]