Well, you have generator scripts installed in the commands directory. If you want to update the generators they should go into /home/rossi/.local/share/OpenChemistry/Avogadro/generators instead.
Hello,
I really apologize for talking so long to reply.
Here is what is in the current
/home/rossi/.local/share/OpenChemistry/Avogadro/generators directory
LICENSE dalton.py* gaussian.py* inputgeneratortest.py* mopac.py* orca.py* psi4.py* qchem.py*
README.md gamessuk.py* generators.cmake molpro.py* nwchem.py* plugin.json pyscf.py* terachem.py*
Do they have to be installed somehow? I obtained them from the avogenerators-master.zip
file which I downloaded. There really aren’t any clear instructions on what to do with the contents of this file one one downloads it.
Also the errors I am getting, and there are a lot of them for each plugin seems to be more than having them in the wrong directory.
Command: Unable to retrieve menu name for: “/home/rossi/.local/share/OpenChemistry/Avogadro/commands/other/dalton.py” . "Error running script ‘/usr/bin/python3 /home/rossi/.local/share/OpenChemistry/Avogadro/commands/other/dalton.py --menu-path --lang C’: Abnormal exit status 2 (Unknown error.: Unknown error)\n\nOutput:\nusage: Generate a DALTON input file. [-h] [–debug] [–print-options]\n [–generate-input] [–display-name]\n [–lang [LANG]]\nGenerate a DALTON input file.: error: unrecognized ar
The issue seems to be related to this post, i.e a python issue??
Can you please help with this? I am using Debian Linux.
The reason for my delay in responding is that I am giving a computational chemistry workshop for grad students and postdocs, and I wanted to show them Avogadro2.
It’s not a python issue. You have files in the “commands” directory, so it’s attempting to ask what menu they should install. Since they’re not commands, there’s an expected error and it will ignore them.
Once I get a bit of free time this week, I’m going to add an “install this script” feature and fix the download plugin feature.
If you have the generators in /home/rossi/.local/share/OpenChemistry/Avogadro/generators they will be used.
I am running Linux Mint and I just installed Avogaro2 from the software repository. I am not sure how to use the Avogenerators scripts.
Following your comments in this thread, I moved the scripts into .local/share/OpenChemistry/Avogadro/generators
Now what? Am I supposed to see a new menu item when I run Avogadro? There doesn’t seem to be anything that I can find in the menus. How do I run these scripts?
Yes. There would be new menu items - one for each program. In current versions, they would appear under Quantum => Input Generators. IIRC, there’s currently about 10.
(I say under current versions. Going forward with 1.94, there’s a new “Input” menu. Wording suggestions welcome.)
There seem to be some issues with the default packages. On Ubuntu at least, these features (which currently use Molequeue) aren’t enabled. There’s a new Flatpak, which has them turned on.
Nope. We use Python3, although they should be compatible with 2.7 for now.
I installed the flatpack version and I can see an Input Generators option under the Quantum menu, but it only lists CP2K and GAMESS, but none of the other options such as Mopac which is what I’m interested in using.
Which show that it is looking for plugins in these location.
Checking for “inputGenerators” scripts in “/app/share/OpenChemistry/Avogadro/inputGenerators”
Checking for “inputGenerators” scripts in “/usr/share/OpenChemistry/Avogadro/inputGenerators”
Checking for “inputGenerators” scripts in “/usr/share/runtime/share/OpenChemistry/Avogadro/inputGenerators”
Checking for “inputGenerators” scripts in “/run/host/share/OpenChemistry/Avogadro/inputGenerators”
Checking for “inputGenerators” scripts in “/app/bin/…/lib/avogadro2/scripts/inputGenerators”
I tried using the plugin downloader. It install the plugins in this location.
Which is not the same place it is looking for. So I recommend you to place the plugins in the directory I show above.
Downloading crystals.zip to /home/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro
Extracting /home/kev/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/crystals.zip to /home/kev/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/other/
Extraction successful
will still be create for system-wide installation as well.
Which I think is where it should be. So I think add “/home/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/other/” directory to plugin search path for Flatpak.
Not sure if it will work, will have to try it.
User can write to Flatpak, but if they install as system-wide, they will need root permission. It depends, but I encourage to install as user.
It is possible to install in external device like a USB storage. Using --installation flag. But I don’t think anyone really does it.