#178 higher than d orbitals in MOs

closed
nobody
5
2010-09-01
2010-06-18
Rene Kanters
No

I was wondering whether it would be possible to have Jmol display MOs from quantum programs that are higher than the d orbitals.
I understand that currently Jmol ignores those oribitals so as long as an orbital one looks at doesn't have much f (g, h, i) contributions it should not affect the visual part much, but I wonder whether that is something that could be added without too much trouble...

Discussion

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  • Bob Hanson
    Bob Hanson
    2010-06-18

    Jmol handles up through F orbitals. Hard to believe there's a significant visual contribution from G,H,I. Examples?

     
  • Rene Kanters
    Rene Kanters
    2010-06-18

    Sorry about the mistake. I knew it does f's :-).

    Without being able to visualize the orbitals with and without the g (and higher) AO contributions it is hard to say whether the effect is large or not. You may be right indeed that it will not, but it would be nice to be able to see g orbitals even if they only contribute to virtual orbitals (like the Sn example I provided for the spherical/cartesian tests.

    I was wondering whether it may be (for you :-) and easy extension to what is already available. If it is then forget that I asked, if you would like to consider I think it would be a nice feature (that is why I posted it with feature requests).

    I'll talk to one of the students here who does some Sn calculations that involve g orbitals in the basis set to set up a calculation to get a g03 ouput file for that.

     
  • Bob Hanson
    Bob Hanson
    2010-06-18

    I think you just have to run the calculation with and without G orbitals to see what difference it makes. It's not a huge amount of code, but I don't know what the functions are, so it would definitely take some effort -- If you want to implement it, you certainly are welcome to. Good student project!

     
  • Rene Kanters
    Rene Kanters
    2010-06-18

    zipped tarbal of tm_sna.log

     
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  • Rene Kanters
    Rene Kanters
    2010-06-18

    zipped tarball of tm_snb.log

     
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  • Rene Kanters
    Rene Kanters
    2010-06-18

    I think I just lost my long message I was typing here.. Sigh... So here I go again.
    I just ran two calculations for Sn(CH3)4 (tm_sna.log with Sn as the first atom and tm_snb.log with Sn as the last atom) with NBO analysis.
    tm_sna.log has for NBO 82 a Rydberg state with 1.1239 AO contribution to the NBO. tm_snb.log has the same one as NBO 130 both for the last model in the structure). Loading these with filter "NBO" and doing a 'model last' then allows for
    tm_sna.log: MO 82 : see the Ry*(53)Sn, which looks like just an s orbital on a carbon, because no g-orbital contribution shown. That is misleading :-)
    tm_snb.log: MO 130 : shows no orbital whatsoever! Not even a label (I think that this is a bug?) MO 129 shows nicely the f-orbital, though.

     
  • Bob Hanson
    Bob Hanson
    2010-06-18

    ah, SO tricky... OK, so if you have two different sequences in the reader -- in this case Gaussian and NBO, then the sequence has to be tied to the orbital, not the collection of orbitals. Ah, so tricky!....

     
  • Bob Hanson
    Bob Hanson
    2010-06-18

    ok, that's taken care of. There was an additional bug in the NBO reader that was not checking for orbital type when the atom number was < 10. While this is tricky, I still contend it's way easier than having each reader re-organize it's MO coefficients on the fly. Especially for large numbers of orbitals like this. Just have to be careful! Please check it out, Rene.

     
  • Rene Kanters
    Rene Kanters
    2010-06-18

    I'll check it out.
    By the way, I wasn't disagreeing with you on your approach of not having each reader do the orbital reshuffling (which I may have started when I believe the qchem reader was the first one to have the orbital ordering different than gaussian). I was just having a hard time following all the intricacies of what you set up :-).

     
  • Rene Kanters
    Rene Kanters
    2010-06-18

    I just checked out the new version and am a bit surprised now that there are a bunch of NBOs that do not show anything, e.g., from tm_sna.tgz (filter "NBO" loaded) in the last model if you do MO 82 you won't see anything, all the way up to 99. At 100 it starts showing orbitals again. Is this because of the large g contributions? If so, maybe at least the mo label should show up with some kind of visual warning?

     
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