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geoffhutchison.net
Geoff Hutchison
@geoffhutchison.net
2.7K followers 1.1K following 440 posts
Chemist, Scientist, Husband, Dad, Runner, Teacher. I develop Avogadro + OpenBabel to find new materials for energy applications @Pitt_Chemistry he/him
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geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · Nov 15
Welcome to all the newcomers to #ChemSky 🧪

I don't post much, but you'll get a dose of #compchem and materials discovery, a bit of #machinelearning (with skepticism) and some sprinkling of #Pittsburgh (including @pitt.bsky.social and @pittchem.bsky.social)

Enjoy some recent @avogadro.cc renders
Image of an endofullerene - a translucent sodium atom encased in a C60 buckminsterfullerene molecule, rendered by Avogadro Image of a zirconium metal complex with a translucent green sphere representing the Zr metal ion interacting, labeled by Zr characters, bonded to two cyclopentadienyl rings, a methyl group and a hydrogen
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geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · 17h
More MOF awards 🎉
pittchemistry.bsky.social
Pitt Chemistry @pittchemistry.bsky.social · 17h
Professor Nathaniel Rosi has received the Pittsburgh Award from the Pittsburgh Section of the American Chemical Society, which recognizes distinguished service to the field of chemistry. Read about him and his work here: zurl.co/PDITj
Professor Rosi received Pittsburgh Award from Pittsburgh ACS! | Department of Chemistry
Professor Nathaniel Rosi has received the Pittsburgh Award from the Pittsburgh Section of the American Chemical Society, which recognizes distinguished service to the field of chemistry. Rosi is being recognized for his contributions to the design and development of chiral nanomaterials as well as new classes of biomolecule-based multicomponent and multidomain metal-organic frameworks (MOFs) having  applications ranging from carbon capture to contaminant separation. 
zurl.co
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Reposted by Geoff Hutchison
avogadro.cc
Avogadro Project @avogadro.cc · 23h
Do you use Windows? We're now on the Windows app store:

We will now offer signed MSIX packages with releases, in addition to the traditional installer.

apps.microsoft.com/detail/9n21v...

Let us know how it works at discuss.avogadro.cc
Avogadro2 - Free download and install on Windows | Microsoft Store
Avogadro is a molecular editor and visualization tool, designed for students and researchers alike. Used in computational chemistry, molecular modeling, chemistry education, bioinformatics, materials ...
apps.microsoft.com
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geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · 3d
#compchem
cenmag.bsky.social
C&EN (Chemical & Engineering News) @cenmag.bsky.social · 3d
Monica Olvera de la Cruz brings chemical simulations into the real world

This computational chemist unites theoretical and experimental science using physics, biology, and chemistry. #HispanicHeritageMonth

cen.acs.org/materials/po...
Monica Olvera de la Cruz brings chemical simulations into the real world
This researcher unites theoretical and experimental science using physics, biology, and chemistry
cen.acs.org
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geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · 3d
I'm definitely using this one in my class this spring.
dailycorrelation.bsky.social
Daily Spurious Correlation 🤖 @dailycorrelation.bsky.social · 3d
The distance between Saturn and the moon correlates with Bachelor's degrees awarded in Physical sciences (r=0.987)
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geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · 7d
Yes, it already has distance, angle, torsion constraints. At the moment, we don't have "generate a set of geometries," (i.e., bond length or torsion scan) but it's a reasonable ask. Probably not until after this Oct. 23rd release though.
geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · 7d
Avogadro v1 had this feature - it’s taken a while to build up the pieces in Avo2, and I’m sure there are still bugs. The optimize geometry is still there, but interactive optimization is useful for some tasks like teaching or steering towards a particular confirmation.
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geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · 7d
Pixi is great because it works with uv as well as conda. Since a bunch of chemistry-related packages are on conda-forge (e.g., xtb, crest, psi4…) it's convenient to have both. Really fast too.
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geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · 7d
You can already do that. That's how I wrote the adapter scripts. 😉

The problem is that a lot of end users don't have Python and don't know how to set things up. @olexandr.bsky.social is right - it's possible to compile models, but in the meantime, we'll use pixi to create environments if needed
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geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · 8d
Contributions always welcome. If you can get someone to get initial code working, I’m happy to help.
geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · 8d
And to be complete, I have a whole pile of scripts for ML potentials, XTB .. calculating charges with antechamber (AM1BCC, etc.) as well as using pymatgen, ASE, etc.

Avogadro2 is really easy to extend with Python
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geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · 8d
I have scripts for ANI and AIMNET2 already. The main holdup is that they assume you have all the Python packages installed, setup, etc.

Coming soon is a feature that uses pixi to install anything you need when adding Avogadro2 plugins.

BTW - is there syntax for AIMNET with unit cells?
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geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · 8d
Well, the framework can use any method now. You can write Python adapters to ML, GFN-FF, DFTB or tblite, etc. Just needs energies and gradients.

For small molecules, MMFF94 or GAFF work fairly well.

Several MOF / materials folks did ask for UFF with periodic boundaries though. 🤷‍♂️
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geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · 8d
Sure. I could use some suggestions in terms of thermostats, since I've never implemented them. Berendsen is fairly easy, but seems like a bad idea?

I guess Bussi-Donadio-Parrinello?
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geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · 8d
Oh, it's wonderful for teaching, as well as pushing and pulling into a particular conformation.

Just required building up piece-by-piece since people want to use ML methods, GFN2, etc.
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geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · 8d
Tested out some water clusters during lunch.
- MMFF94 has point charges and hydrogen bonds
- UFF does not (so water molecules push apart)

At some point I'll add some simple dynamics…

#compchem #compchemsky
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geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · 8d
That's really useful - including the example with the chelating ligand.
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geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · 8d
I know this has been one of the most widely requested features. Should be in the release on 10/23

#chemsky #compchemsky #opensource
avogadro.cc
Avogadro Project @avogadro.cc · 8d
If you've been wondering about the status of the AutoOptimize interactive optimization in Avogadro2 - coming later this month 👀
Screenshot of Avogadro2 using the interactive AutoOptimize tool to minimize a molecule (n-pentane) using the UFF force field. Text reads UFF ΔE = -229.80 kcal/mol
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geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · 11d
"Pittsburgh’s universities and hospitals are the big employers that economically and socially are actually really analogous to what the mills were 80 years ago"

www.bloomberg.com/news/feature...
Trump Is Targeting an Economic Revival Story
Pittsburgh shows how universities and hospitals can fuel renewal — and why Trump’s manufacturing push and cuts to higher education could undermine it.
www.bloomberg.com
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geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · 14d
I guess I'm happy that we installed #solar at our house in 2020, but this seems like it deserves more reporting...
moreperfectunion.bsky.social
More Perfect Union @moreperfectunion.bsky.social · 14d
Electricity now costs up to 267% more than it did five years ago in areas near data centers.

www.bloomberg.com/graphics/202...
AI Data Centers Are Sending Power Bills Soaring
Wholesale electricity costs as much as 267% more than it did five years ago in areas near data centers. That’s being passed on to customers.
www.bloomberg.com
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geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · 16d
That particular image is 1536 x 604, or roughly 5" x 2" at 300 dpi. (I have a high-res screen.)

PDF is something of a "container" format. You can store bitmap images, text, vector graphics.. a lot of different things. The best are resolution-independent (e.g, draw a line from x to y points)
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geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · 17d
Probably depends a bit on the resolution - the PDF is actually surprisingly small (65 Kb for this one) because it's all vectors.

But yes, GIF can get excellent compression when there's limited colors like line plots.
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geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · 17d
#compchemsky

Now offers tools to save computed spectra as PNG, PDF, SVG .. or the underlying data.

Found a really nice #opensource #openscience plotting library
avogadro.cc
Avogadro Project @avogadro.cc · 17d
👀

Coming soon...
Dialog titled "Vibrational Spectra" showing the computed infrared spectra of caffeine with two plots, one in black labeled "smoothed" and one in red labeled "raw"
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geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · 18d
BTW, lots of great collaborations between @pittchemistry.bsky.social and the School of Pharmacy
velvetjournigan.bsky.social
Velvet Journigan @velvetjournigan.bsky.social · 20d
Come to our Graduate Program Open House at the University of Pittsburgh School of Pharmacy, October 22nd ! 🔬💊🌠
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geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · 18d
#chemsky
royalsociety.org
The Royal Society @royalsociety.org · 20d
Our Career Development Fellowships are now for applications. This scheme provides talented early career scientists from underrepresented backgrounds in STEM with research funding and training opportunities to build a successful research career: #RSGrants royalsociety.org/grants/caree...
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geoffhutchison.net
Geoff Hutchison @geoffhutchison.net · 19d
aka "my AI model has no idea the relationship between a mile and a kilometer" or "my AI model can't do math" - not sure which is worse!
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