Software for simulating atom interaction

  • #1
I´m looking for a software that would allow me to test atom interaction acurretly in 3D, with public variables (i.e. customizable parameters) like the pressure and the temperature. I´m looking for something that takes into account S, P, D orbits with their real shape and the real numbers of electrons with their respective charges. Something that can portrait hybridization well, that can show bonding of every kind.
I´d like something that´s freeware, but if you know about a good paid app it would be useful to know that too.
I´m really hoping this kind of program exists.

Answers and Replies

  • #2
The one I hear most often about: (or directly go to their site at

Long list:

But somehow I have a gut feeling you will be not able to use neither of these packages, as they all require an extensive knowledge about the quantum chemistry/physics and quite a lot of math (both calculus and linear algebra). The way you worded your question seems to be suggesting you have only superficial knowledge - that won't be enough.
  • #3
Well, you´re right in part: I´m no expert, I´am a visual artist. BUT I need very precise representations. For what I see in youtube, the program that you suggested doesn´t meet the requirements: it doesn´t show the sub-orbitals at all instead it shows this poor representation of atoms that flood the internet that have this "balls". The movements are also extremely simpified and not simulated at all. So, you´re right in that I´m looking for something that is easy to work with (if possible), but at the same time, the 3D simulation should be way more accurate than this and the atom images more precise. Obviously some simplification is always needed but not this much. For what I need this is almost kid stuff. I´m sure it´s great for doing calculations that I haven´t even dream of, but visually (or structuraly if you want) it´s not good.
PS: Perhaps it has some option to do a more serious representation that isn´t usually used?
  • #4
I am afraid what you look for doesn't make much sense in terms of results of quantum calculations. Orbitals that you see in books are just a simplified models, calculated using some assumptions. They are not "real" nor "precise" nor "serious". Thus it is hard to guess what you really look for - most likely some kind of a visualization that you imagined, but which is not related to a real thing. I think the only way of rendering what you think of is to use CGI modeling, not quantum models.
  • #5
So would you say that I shouldn´t use this type of orbit:
What would you recommend instead?

You confuse me a moment when you said "CGI modeling": the display that you see in this app (Gauss) is CGI, and it has been of course rendered. If the program does indeed calculate the position of the particles in 3D space, and can aproximate the path of the electron cloud and the nucleus you just need to take the data and, yes, render it. That way you can build a proper 3D real-time simulation. So, you´re sure this doesn´t exist?
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  • #6
lennon, physical electrons do not work the way you think. The electronic motion can be computed (using quantum chemistry software, e.g., the program listed by Borek), but the wave functions these programs calculate cannot be visualized easily (for a start: they are not three-dimensional, but 3.5*N dimensional where N is the number of electrons and I included the discrete spin dimension as 0.5...). Now, orbitals *can* be visualized, but they are neither unique nor are they physical wave functions. Computed molecular orbitals would look nowhere like what you imagine them to look like, and they would not be easy to compute and visualize in any case (and certainly not for the complex environments you mentioned in your first post). Atomic orbitals are an even more difficult beast: Strictly speaking they have physical meaning only in ATOMS, not in molecules, and even in atoms they are not the real wave functions... (except for hydrogen)

I understand that this may sound very confusing. So I would like to stress that all these objects and their relationships are well understood in science, but it requires knowledge of advanced quantum mechanics to make any sense of it (high school level won't do, and even undergrad level in chemistry or physics might not be enough). Without this, even if you COULD make a proper visualization, the observer would have no idea how to interpret what he/she is seeing.
  • #7
Well, thanks for pointing all this out, seems that there´s much more than I can chew. I´m just often not confortable with all that "trust me I´m a scientist" thing, (I´m sure you know the feeling).
I thought the spin didn´t affected the overall shape, that it only meant the particle needed to made 2 cycles to come to it´s original state (being half of the time in that 0.5 dimension you talked about), and since there are 2 electrons in each orbit you´d have the same overal orbital shape in our 3D space, since in most cases there´s at least one electron existing in this plane.
Even if you were to have ten dimensions I don´t really understand why this should be a problem since you could calculate every dimension and only render the ones that exist in the 3D world, you just need the xyz coordinates.
You say the orbitals are different in moelcules and I was expecting that since the interaction is different if the electron is being shared. I have seen how hybridization distrot things, so, I could imagine that this shearing could generate an effect. What I guess I didn´t see comming was that they´re not physical wave functions. I don´t get it very well (what type of wave functions are they? can´t waves always be translated in geometrical space?)
Well, as said, I don´t like to be taken away of things just because I wouldn´t understand them, but ok, I guess I don´t have much of an option other than to keep studying this subject. Thanks for taking the time to explain why it´s so difficult. Still I´d like to ask one question. First let me say that I´m not that worry at the moment with wether if the viewer or observer can interpret what she/he is seeing. My question is if it is impossible to do or if it´s just something out of the reach of current computation.
I also would like to say that I just find it pitiful that after almost a century of quantum physics still the only representation availabale is one ball per atom.
I have tried to come up with periodic tables with suborbitals as the ones previously mentioned, and they´re much more clear, you can understand better for example why elements with D orbitals are good conductors and things like that. It´s quite a pitty that the visual representation can´t advance any further.

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