Re: [Jmol-users] radial plots

[John K. <jwk...@al...>]

Hi Bob,
This exchange reminded me about Jmol's excellent "isosurface atomicorbital"
command. It works fine. However, I am attempting to automate this using the
command-line options shown on the stolaf docs page, but the "-o" option
seems to have no effect. In win 11 (or several Linux versions) the command
"Jmol.jar -ios c:/docs/4px.scr -g300x400" gives a nice 4px orbital, but the
console is still showing. What is the actual purpose of the "-o" option?
John Keller
P.S. The 4px.scr is as follows:
background white; axes on; axes scale 1.0;
set antialiasdisplay off;
isosurface id atom sphere 0.15;
isosurface id px4 sign phase resolution 5.0 atomicorbital 4 1 1 4 mesh
nofill;
rotate x -90;   zoom 120;


On Thu, Dec 11, 2025 at 7:48 PM Robert Hanson via Jmol-users <
jmo...@li...> wrote:

> Mark, if you are just examining the radial nodes in many-electron *atoms*
> instead of looking at textbook hydrogen-like orbitals. We can illustrate
> that. Jmol does not need MO programs to display atomic orbitals. It can
> calculate them itself using the Schroedinger equation.  Thus the
>
> isosurface ATOMICORBITAL n l m Zeff
>
> option.
>
> [image: image.png]
>
> The Zeff is what you are looking for. This is the effective nuclear
> charge. The idea is that each orbital shell - 1s 2s 2p 3s 3p 3d .... when
> fully occupied is a spherical electron density. And for any atom with more
> than one electron, we can approximate the effect of more than one electron
> by positing an "effective" nuclear charge (Z_eff) that roughly accounts for
> shielding the positive charge in the nucleus in atoms from the outermost
> electrons. The shielding is not perfect of course. But there are tables of
> these Z_eff for the elements. See [
> https://chem.libretexts.org/Courses/Saint_Marys_College_Notre_Dame_IN/CHEM_342%3A_Bio-inorganic_Chemistry/Readings/Week_1%3A_Analysis_of_Periodic_Trends/1.1%3A_Concepts_and_principles_that_explain_periodic_trends/1.1.2%3A_Effective_Nuclear_Charge#:~:text=simple%20rules
> ]
>
> for example. So you can change that parameter at will and at least
> visualize how, for example, the 1s core electrons are very close to the
> nucleus, on average, compared to the 3s orbital electron in sodium.
>
> Since the shielding is not perfect (3s orbital still has some electron
> density near the nucleus, just not much), 3s orbitals for Na are larger
> than the 3s orbital for H,. In contrast, the 1s core orbital electron
> density is way closer to the nucleus in Na than in H (Z_eff 10.63 vs Z_eff
> 1). But going across the periodic table, Z_eff, just as Z, is increasing
> even for the valence orbitals, so we see this effective atomic radius
> trending smaller and smaller as we go from left to right along a period.
>
>
> As for the function that could be plotted as radial electron density, I
> think you can probably find those somewhere.
>
>
>  (Zeff = 6)
>   (Zeff = 8)
>
> [image: image.png]  [image: image.png]
>
> That said, I think the documentation is misleading there. The Zeff=6 "for
> carbon" is only true for the 1s core orbital there. The Zeff for an element
> is different for different orbitals with, for example, 2p having higher
> Zeff than 2s, because 2p orbitals don't have the radial node that 2s
> orbitals have and so are effectively closer to the nucleus, on average.
> Jmol does not maintain this table, though it certainly could.
>
> Bob
>
>
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