Do you think of something like that?

@PH13: I was just thinking of Mathematica! And no. The first few images, again, look like blurred fireworks. I'm looking for visually rigid, 3D structures.

Also, I want to visualize a complete atom. I am well aware of the current orbital visualization techniques.

@VatsalManot I am not sure I completely understand what you are looking for? Are you looking for a way to visualize all the orbitals of an atom at once in a single 3D model?

What do you think of, when you say "complete atom"? I don't get that. Atoms are protons and neutrons surrounded by electrons. You can visualize the orbitals and you can visualize properties that relie on those orbitals as e.g. the electron density, the electrostatic potential, etc.

@PH13: I can't quite visualize how these orbitals are layered in shells.

@Philipp: Exactly. I can see this working on a computer, where one can just 'zoom' into the atom going deeper and deeper into the layers.

@PH13: A complete atom is one that contains shells in layers.

Putting all orbitals one over another will give you a sphere.

@PH13: Then you mean to say that atoms look like clumped snowballs?

@VatsalManot I can only speculate that such a thing is achievable in Mathematica by combining all the orbitals into one picture but I can guarantee you it would be a mess. A big problem would be that higher orbitals themselves already have a layered structure, e.g. the isosurface of a 1s orbital is a simple sphere with, say, radius 1, and the isosurface of a 2s orbital consists of 2 spheres, one at radius 2 and one at radius 0.9 or something, so you will have a very hard time telling all those orbitals apart.

I thought about writing a reply, but it so boring that I will just say one phrase: "There is no orbitals."

@Wildcat Spoken like a real DFT guru :)

@Wildcat: I am aware of that. But I'd still like a theoretical visualization.

@VatsalManot, what do you want to visualize then? Which physical quantity?

@VatsalManot, theoretically no such visualization is possible.

@Wildcat: We have visualizations for orbitals, don't we?

@VatsalManot, yes we do. But you have to understand five things: 1) We visualize orbitals by drawing their isosurfaces, thus, orbitals and their visualizations are different things. 2) An orbitals are not real anyway. 3) Yes, I mean that. Orbitals are not real. 4) Did I already said that orbitals are not real? 5) Just in case if I did not: orbitals are not real.

@Wildcat: Just as we have visualizations for these non-real orbitals (I stated that I am aware of the fact that they are not real), why cannot we have visualizations for layers of these non-real orbitals?

@VatsalManot, you surely can have such picture: as Philipp suggested in principle you can superimpose isosurfaces for all orbitals of an atom (though, I'm not sure about "all"). But! The resulting picture would not have the meaning you are looking for: it will be just a picture of superimposed isosurfaces of orbitals of an atom, but it won't be a picture of an atom. Do you feel the difference?

I think I'm starting to understand. Thanks for your answer anyway.

I think some of the issue is the idea of "visualizing an entire ANYTHING" is not doable. Visualizations always start with a list of traits of the object that they wish to view, and then attempt to find a image or video which effectively conveys those traits. You might be more successful identifying exactly what traits you want to see, rather than saying "I want to see everything, including the layers." We may be able to better guide you to a visualization that meets your needs.

@Wildcat This comment should have a frame ;)

@VatsalManot This is your room now, I'd like to ask you to direct anyone that has an interest in the topic to discuss it here :D

@Martin-マーチン: Hey, thanks!

Absolutely no problem :D

Not really related, but I couldn't help notice that a button didn't automatically appear for comment to chat migration.

It got a little bit messy below the post, so the system informed us...

Like when I'm on StackOverflow, or Physics StackExchange, there's a button that appears automatically.

Which allows me to migrate the comments to a chatroom.

You were replying to various people and not having a discussion with only one person.

In the latter case only the string of comments with that one person would be moved to chat, not the other ones.

Oh, that makes sense.

In cases with 20+ comments, the mods get a prompt, so that they can migrate every comment

And I thought this discussion might be worth keeping.

Me too. I feel that my question should a help a lot of students understand what they're really looking for. Things like visualization are usually skimmed in schools, and we're left ignorant and confused.

I mean, we just started orbital geometry, and to my great surprise not a single one of my classmates thought about visualizing a whole atom. The answer by @Wildcat was helpful, and I eventually realized that no such picture is really possible.

also: cond-mat.de/sims/multiplet/computation.html

room topic changed to How do I visualize an atom? (by Vatsal Manot) Discussion: Imported from a comment discussion on chemistry.stackexchange.com/questions/33971/… [atoms] [orbitals]