I can’t get the Avogenerators, or any other plugin, to show up in Avogadro. I can see the plugin in /Users/me/Library/Application Support/OpenChemistry. I am not sure of the correct path to set for python but believe it to be /usr/bin/. I wonder if the issue is that I am still on Mojave with python 2.7?
Avogadro version: 1.95.1
Operating system and version:
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You need to install a more modern Python, yes.
I’d generally suggest mamba-forge - it’s conda but faster. This installs Python 3.9.
Thanks for this. I am a linux poser so I am not familiar with mamba-forge. I looked at the linked file and I gather this is a bash script to install mamba (a package manager I think). Then I would use that to install python3 and maybe cclib as well? Sorry for the basic questions. Thanks.
The script would install a minimal Python install (e.g.,
numpy etc.) +
mamba which, yes, is a package manager. You can then either use
pip3 to install cclib.
mamba install cclib or
pip3 install cclib
What do I do if I don’t see “Download Plugins” option in the “Extensions” menu?
What version are you running? That’s in the Extensions menu … certainly in 1.94 or 1.95.
I installed mamba (with updated Python) and then installed cclib. All good and I was able to open the Gaussian output file.
However, the python path settings don’t seem to reliably stick. If I double click on a file in MacOS that launches Avo2, the extensions are not loaded. If I launch Avo2 directly (e.g. using Spotlight), the extensions are loaded.
Huh. That’s interesting. I’ll check it out. Might be a few days since grades are due tomorrow, but that’s an odd one.
Glad to hear it works otherwise!
Another bit of information. Accessing Analysis → Vibrational Modes crashes Avo2 every time. I don’t know if it as an issue with cclib but I see the same thing with Open Babel. FYI.
Can you please post or send me an example file? Thanks.
May I email an example to you? I don’t see a way to message you a file on this forum. Thanks for your time.
Whatever is easiest. You can also open an issue and upload Issues · OpenChemistry/avogadrolibs · GitHub