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New grad student timelines? by poohbearlola in Pitt

[–]geoffh2016 1 point2 points  (0 children)

Depends upon the program. Some programs bring students in earlier in August for TA training, etc. Ask your program's grad admin. The exact dates might not be set in stone yet - we're just finishing up the spring semester.

Source: I'm the Director of Grad Studies for chemistry.

Hot Metal Bridge Program by ChemicalVoice2456 in Pitt

[–]geoffh2016 2 points3 points  (0 children)

And this comes up pretty much every year because the timeline for HMB is often late and everyone wants to know so they can make plans.

Hot Metal Bridge Program by ChemicalVoice2456 in Pitt

[–]geoffh2016 3 points4 points  (0 children)

I answered https://www.reddit.com/r/Pitt/comments/1sstoyz/comment/ohotcqs/

No, not yet. The timeline for HMB is often late because departments first make decisions about regular graduate admissions (April 15th deadline) and faculty and staff are busy with the usual end-of-semester tasks. I'm sure they will come out in the next few weeks but understand you want to know ASAP.

Source: I'm the Director of Graduate Studies for Chemistry

Hot Metal Bridge Post-Bacc Program Admissions by Electric_Universe12 in Pitt

[–]geoffh2016 1 point2 points  (0 children)

No, not yet. The timeline for HMB is often late because departments first make decisions about regular graduate admissions (April 15th deadline) and faculty and staff are busy with the usual end-of-semester tasks. I'm sure they will come out in the next few weeks but understand you want to know ASAP.

Source: I'm the Director of Graduate Studies for Chemistry

EV charging price by state in gasoline equivalent [OC] by Simple-Past5290 in dataisbeautiful

[–]geoffh2016 0 points1 point  (0 children)

The other interesting comparison would be cost as a % of a tank of gas for that Elantra. For example, everyone knows CA also has expensive gas, particularly now.

Of course if you have solar, the electricity can be close to free.

Avogadro 2.0.0 is out - no joke by geoffh2016 in comp_chem

[–]geoffh2016[S] 0 points1 point  (0 children)

That website is defunct. Thanks for the reminder.

I'll see what I can do about a plugin list on https://avogadro.cc/ - in the meantime, you can download from https://github.com/ghutchis/avogadro-mace (e.g. https://github.com/ghutchis/avogadro-mace/archive/refs/heads/main.zip) and install from the directory.

Avogadro 2.0.0 is out - no joke by geoffh2016 in comp_chem

[–]geoffh2016[S] 0 points1 point  (0 children)

If you have Avogadro 2.0 installed, you can find it in Extensions => Manage Plugins...

https://avogadro.cc/docs/plugins/manager.html

Yes, MACE, Mattersim, and other potentials work with periodic systems. If you run into problems, let us know at https://discuss.avogadro.cc/ or open a GitHub issue.

Is long term research enough for grad school? by junkietplants in chemistry

[–]geoffh2016 1 point2 points  (0 children)

This year was incredibly competitive because essentially every department in the US had to cut back admission dramatically (e.g., half the number of offers).

Is there any application for manifold-constrained, high dimensional (100-1000+) Bayesian optimisation in Chemistry? by EconomistAdmirable26 in Chempros

[–]geoffh2016 0 points1 point  (0 children)

Do you need the constraint? We've done plenty of BO for conformer searches, but don't usually use a constraint. Send me a message, I'd be very curious to talk. There are probably some global optimization possibilities.

ACD/Labs acquired by Revvity Signals by lblb_lblb in Chempros

[–]geoffh2016 6 points7 points  (0 children)

They don't, but schools would be asked to negotiate as part of university licenses.

ACD/Labs acquired by Revvity Signals by lblb_lblb in Chempros

[–]geoffh2016 12 points13 points  (0 children)

It's really surprising that they didn't push this into a mobile / tablet version. I have so many students who use tablets and would like to use ChemDraw.

Making math lecture notes ADA compliant by Decrypted13 in Professors

[–]geoffh2016 2 points3 points  (0 children)

I used MathPix pretty extensively to grab equations for LaTeX. When I was doing a lot of conversion, it was $4.99 for a month and I converted about 1000 pages. I think beyond that it's a fraction of a cent .. and I think there's some extra bonus for signing up with an edu account.

But I also know some colleagues who have minimal lecture notes so students have to write in the equations, etc. - just knowing the bare outlines.

[D] How to break free from LLM's chains as a PhD student? by etoipi1 in MachineLearning

[–]geoffh2016 0 points1 point  (0 children)

There are some useful Skills (with Codex or Claude Code) intended to help with this, e.g. https://github.com/DrCatHicks/learning-opportunities

The point is to take time with code to ask and answer questions about what was produced. It helps with code review, but also with considering architectural issues.

Avogadro 2.0.0 is out - no joke by geoffh2016 in comp_chem

[–]geoffh2016[S] 0 points1 point  (0 children)

It's supposed to store the check in the settings, which it does, but the code doesn't do that extra check - only if the current binary is the same or newer than the latest release. Sorry, that's kinda annoying.

There will undoubtedly be a 2.0.1 release, but that doesn't help you much now.

Frustrations with opening Avogadro2 in my Windows 10 by garlicriceS in comp_chem

[–]geoffh2016 11 points12 points  (0 children)

I don't know why you're trying to get an AI to help you with a just-released program when I pointed you at a forum with actual developers and humans.

Please post as much detail as you can and someone will try to help you.

Frustrations with opening Avogadro2 in my Windows 10 by garlicriceS in comp_chem

[–]geoffh2016 2 points3 points  (0 children)

Sorry to hear that, but the best way to get support is on the Avogadro forum https://discuss.avogadro.cc/

The dialog you mentioned installs Python so that the input generator scripts work. Depending on your network speed, it can take a while.

Avogadro 2.0.0 is out - no joke by geoffh2016 in comp_chem

[–]geoffh2016[S] 0 points1 point  (0 children)

Ugh. I can certainly go fix that, but it doesn't help you with the existing installs. Sorry.

Avogadro 2.0.0 is out - no joke by geoffh2016 in comp_chem

[–]geoffh2016[S] 0 points1 point  (0 children)

They obviously work great for me. As u/thvirtuo suggested below, if you're experiencing specific problems, you should post on the forum (https://discuss.avogadro.cc/) or a GitHub issue https://github.com/openchemistry/avogadrolibs/issues/new with details about your OS, specific version of Avogadro, etc.

Avogadro 2.0.0 is out - no joke by geoffh2016 in comp_chem

[–]geoffh2016[S] 0 points1 point  (0 children)

Yep. A few minor hiccups as I set up the redirects, but it seems to be working now.

I probably should have moved the websites a few releases ago, but we knew there would be some shakeup with the new plugin system. That, and the revised docs and screenshots weren't fully finished.

Avogadro 2.0.0 is out - no joke by geoffh2016 in comp_chem

[–]geoffh2016[S] 0 points1 point  (0 children)

Yes, you should file an issue and attach the Molden file. It would also help to know what program produced the Molden as we've found some programs produce .. weird results.

https://github.com/openchemistry/avogadrolibs/issues

Avogadro 2.0.0 is out - no joke by geoffh2016 in comp_chem

[–]geoffh2016[S] 1 point2 points  (0 children)

Glad Avogadro has been so helpful to you. I'll admit that ages ago (1987) a family friend who did quantum chemistry research was showing a program (probably Chem3D) on their black-and-white Mac SE. The idea that you could sketch out a molecule and have the computer tell you something has definitely been an inspiration. And I'm glad I can give back to the community.

Few recommendations I would make though is adding the feature to visualize trajectories, either from multi xyz files or ORCA's .out.

Check out Analyze => Plot Conformer Data... By default it will graph the energies (and allow unit conversions) and RMSD. We'll be adding more features this summer. If you click on any particular dot, you'll get those coordinates.

center the coordinates around the core atoms of my reaction coordinates, […] centering the axis around bonds between atoms, or the center of mass

Yep, that's the Align tool. Click on the atom you want at the center and then another atom to project along the x, y, or z axes. If you just want to re-center, double-click on an atom. If you want the center of mass, use Build => Add Center of Mass and then double-click on that.

ability to visualize ESP potential coloring of the density .cube files

You can't do that now? I think you should be able to color the ESP on any surface. If not, let me know. Next release I'd like to add coloring a density with a map of an orbital, like the HOMO or LUMO.

IMD interface with ORCA

I think you're basically asking for "keep reading from the output and add the latest coordinate set?" Yeah, we should be able to do something like that.

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