Morii
July 3, 2023, 3:26am
1
I’m a beginner with Avogadro, using it for molecular orbital calculations. As discussed in a few forums, Avogadro version 1.2 is no longer operational, leading me to try using Avogadro 1.97.
I have an issue with Avogadro 1.2.0 drawing on one of my computers
Environment Information
Avogadro version: 1.2.0
Operating system and version: Windows 10
Expected Behavior
Proper Drawing
Actual Behavior
Every time I try to use the drawing tool, I cannot build off of another atom. For example, I want to draw propane. I can get no further than ethane, I cannot add another atom. I can no longer click on atoms and substitute them with different atoms. Additionally, other tools are starting …
However, I’ve noticed that, unlike version 1.2, Avogadro 1.97 doesn’t appear to include tools such as Abinit, Gaussian, Q-Chem, etc. After spending several hours trying to find these tools, I’m wondering if it’s just me missing something or if these tools are simply not supported in this version.
Yes, they do, although many features in Avogadro 1.9x require Python. Do you have Python installed?
Morii
July 3, 2023, 5:32am
3
Thanks for your reply. I’ve just installed Python. I anticipate that I’ll be primarily using ORCA. Is there a guide on how to add an ORCA tab? Thank you!
@Morii Maybe your instance of Avogadro’s GUI does not (yet) offer an entry Input → Orca to open a widget like the one depicted below
If so, the installation of the Avogadro generators (via Extensions → Download Plugins) can help:
Morii
July 3, 2023, 7:49am
5
@Thomas Thank you for your suggestion. However, nothing shows up in the plugin download section of my Avogadro
What OS are you running? How did you install Avogadro?
As far as Python, if you go to Extensions => Set Python Path… you can set the location of your Python command
Morii
July 3, 2023, 3:38pm
7
I’ve downloaded Avogadro2 from the link below, and I’m currently using it on Windows 11.
https://two.avogadro.cc/
If you can set the path to your Python install and restart Avogadro, you should have access to the Orca (and other) interface.
Morii
July 3, 2023, 9:56pm
9
I’m inexperienced in languages like Python, so I find this confusing. I’ve set the Python path as you instructed, but what’s the next step? Should I place the libraries in the path where Avogadro2 is installed?
I apologize for the naive question.
I don’t think it’s a naive question. Let me make sure:
you’ve set the Python path
you’ve re-started Avogadro
And “Orca” (among others) doesn’t appear in the Input menu?
If that’s the case, it would help to see the directories inside Program Files / Avogadro 2
(or wherever you installed it).
There should be a directory labeled “scripts” which has:
charges
formatScripts
inputGenerators
The last of these should have a bunch of Python scripts, e.g.
Morii
July 4, 2023, 12:05am
11
Thank you. The input file list has been generated! However, an error seems to be occurring. I suspect there may be a flaw within the orca.py code.
Error running script ‘C:/Users/morii/AppData/Local/Programs/Python/Python311/python.exe C:/Program Files/Avogadro2/lib/avogadro2/scripts/inputGenerators/orca.py --generate-input --lang en_US’: Abnormal exit status 1 (Unknown error.: Unknown error)
Output:
Traceback (most recent call last):
File “C:\Program Files\Avogadro2\lib\avogadro2\scripts\inputGenerators\orca.py”, line 320, in
print(json.dumps(generateInput()))
^^^^^^^^^^^^^^^
File “C:\Program Files\Avogadro2\lib\avogadro2\scripts\inputGenerators\orca.py”, line 284, in generateInput
inp = generateInputFile(opts[‘options’])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “C:\Program Files\Avogadro2\lib\avogadro2\scripts\inputGenerators\orca.py”, line 159, in generateInputFile
theory = opts[‘Theory’]
~~~~^^^^^^^^^^
KeyError: ‘Theory’
Morii
July 4, 2023, 1:03am
12
Also, there’s a typo, “defaut,” in the orca.py file