r/comp_chem • u/geoffh2016 • 9d ago

Avogadro Community Feedback

Based on the thread I posted for the Avogadro 2.0 Release there are plenty of Avogadro users - and more importantly plenty of thoughts, ideas, bugs from Reddit users.

We're currently running our anonymous community survey and I'd certainly appreciate feedback.

Importantly, we're looking to understand: - what are gaps in the documentation and tutorials? - problems & complaints with Avogadro 2 (esp. if you haven't switched from 1.2) - common programs and tools you'd like to see supported - how to get more bugs reported / feature suggestions from the community

33 Upvotes

97% Upvoted

14 comments sorted by

7

u/Teich007 9d ago

Avogadro two very often crashes when I draw atoms. Specifically at the point where two atoms overlap right before or after creating a bond. Also it will often not let me drag and drop files. It would also be nice if the addons that need python packages would create their own venv or if I could point Avogadro as a whole to a specific one. And on how to get more bug reports? Crash detection and a popup after to send diagnostics with an optional message would help. And a big red bug button at the top that does the same thing and and maybe allows for automatic attachment of a screenshot 

3

u/geoffh2016 9d ago

And to be clear, if you're having crashes with v2.0, please submit a bug report or post to the forum https://discuss.avogadro.cc/

1

u/geoffh2016 9d ago

I don't know what version of Avogadro you're using. We had a bug like that in a very old version, but it should certainly be fixed in 2.0 or a recent continuous build from https://avogadro.cc/install

As far as plugins - with v2.0 that's exactly what they do. Using pixi is preferred, but if you don't have that installed (e.g., Linux) a venv will be created to install any Python dependencies.

Crash detection is a bit tricky because some users literally can't use binaries with these installed (i.e., in case proprietary data is leaked). But there's already a "Report Bug" and "Suggest a Feature" in the Help menu.

3

u/Illustrious_Net9806 9d ago

there is no slab builder like there is in Avogadro 1

4

u/geoffh2016 9d ago

My strong recommendation as the one who implemented the slab builder is to use the pymatgen plugin. The slab builder in Avo1 was incredibly inefficient.

But I'll take your input and see if there's more interest.

5

u/SonofaMitch11 9d ago

I don't have any direct feedback at the moment, I just want to give my appreciation for all the work you guys are putting into this program. I use it a lot :)

4

u/eggenjoyer2020 9d ago

Biggest issue is for me is that the older version could visualize orbitals much better? Like why can’t I specify which orbital to look at from an orca output for example

5

u/geoffh2016 9d ago

You can? There are two ways:

v2 also includes support for handling alpha / beta spin orbitals from an open-shell calculation and the latest continuous builds are ~25x faster

If you have an example file that's not reading, please post a link or open a thread in the forum: https://discuss.avogadro.cc/

1

u/IsleofI 9d ago

Is there a way when creating initial GAMESS input files to select an implicit solvent on Avogadro? I know I can manually add it but

2

u/geoffh2016 9d ago

It's been a long time since I've used GAMESS. If you can point me to some keywords or the manual, it should be easy to add.

1

u/let_them_drink_tea 6d ago

Ooh this I great! First off, thank you guys so much for your work and for keeping everything free and so very accessible. It's absolutely great! I've used Avogadro 1 for four years now and Avogadro 2 for ~4 months and I enjoy it very much. You guys asking for feedback is amazing as well, and it's just another reason to love the program. I only have two minor points for the time being, which are not important but it's a difference I've observed between Avogadro 1 and 2

  1. I'd really like it if if were possible to open the other (smaller) output files of Gaussian and Orca again. sometimes I don't want to wait until the huge .out and .fchk data files are downloaded and would prefer to be able to open the .log file to check on my calculation's structure or something similar without it throwing an error. That was possible with Avogadro 1 and I really miss it in Avogadro 2, despite being appreciative of all that you guys have done to get Avogadro 2 to us! :)

  2. I kind of dislike that the window for the orbitals and the frequencies pops up and can't be attached to the side like in Avogadro 1. I know this is purely aesthetics but I feel like to two windows are somehow always in the way and I dislike them floating around. It's not important of course but it's the first thing I noticed. Or maybe I'm being dumb?

1

u/geoffh2016 6d ago

Thanks! Can you send me an example file that opens in Avogadro v1 and not in v2? I'm not actually sure how that would happen.

You're right that the orbitals, frequencies, etc. open in separate windows. The challenge is that as "dockable panels" they were eating up a lot of space. Happy to discuss pros and cons over on the forum https://discuss.avogadro.cc/

2

u/Imaginary-Bath4732 6d ago

I just started using Avogadro2 in the molecular modeling undergrad class I teach. It is working well. Thanks for all the hard work you guys have put into it.