#151 Add NBO orbital visualization

closed
Bob Hanson
None
5
2009-04-09
2009-03-27
Victor Rosas
No

Add ability to read and display the NBO orbitals produced by the GAMESS-US--NBO 5 combo.

Discussion

  • Victor Rosas
    Victor Rosas
    2009-03-27

    NBO output for several molecules

     
    Attachments
  • Bob Hanson
    Bob Hanson
    2009-03-27

    Shouldn't be a problem. I need more files:

    1) images of specific NBOs for a variety of compounds
    2) more sophisticated calculations involving D orbitals, diffuse functions, etc.

     
  • Bob Hanson
    Bob Hanson
    2009-03-27

    also, it would be good to have the GAUSSIAN equivalent output.

     
  • Jonathan Gutow
    Jonathan Gutow
    2009-03-27

    I have a bunch of calculations of small molecules at higher levels and could generate more. Should I send them to you or is there someplace we are keeping them?

    I cannot provide you with the NBO stuff. That will have to come from Victor Rosas.

    Also while your doing this could you pick up the partial charges out of the file? That's probably better than me working on that feature in little bits.

    Jonathan

     
  • Victor Rosas
    Victor Rosas
    2009-03-30

    Hey Jonathan, can you suggest a list of small molecules and levels of theory? That way I can do the NBO calcs so we end up with a consistent set.

    BTW,
    Bob, I can provide the NBO calcs, as for images, I cannot produce any, thus the Feature Request. I'll look up in the literature, to find some images that may be of help.

    Thanx

    Victor

     
  • Bob Hanson
    Bob Hanson
    2009-03-30

    the key is that we get GAMESS output having the NBO option with more advanced calculations involving D orbitals, for instance.

    There is also the possibility that this is already done for us and there is nothing to do at all in Jmol. Please check with GAMESS documentation first about possible output of NBO MO coefficients.

     
  • Victor Rosas
    Victor Rosas
    2009-04-01

    Hello Bob,

    Reading the NBO manual, I found that there is a keyword to print the AO-->NBO transformation matrix. Is this what we need?

    Have a nice day!

     
  • I don't know -- send me the output, and I will see what I can do with it.

    Bob

     
  • Victor Rosas
    Victor Rosas
    2009-04-02

    Ok. Here are two output files in a tarred file (hoac.tar.gz). One (hoac.out) is the normal gamess-produced output file, and it includes the AO-->NBO transformation matrix produced by NBO. The coefficients have few decimal places.

    The other, hoac.37, is the same matrix but with many more decimal places. In a single run NBO produces either one, but not both.

    These are from a single point calc on acetic acid, HF/6-31G* level.

     
  • Victor Rosas
    Victor Rosas
    2009-04-02

    HOAc ao2nbo transformation matrix

     
    Attachments
  • Bob Hanson
    Bob Hanson
    2009-04-03

    this is in place now. A very easy fix! Please let us know what you need to do in GAMESS to get this output.

     
  • Victor Rosas
    Victor Rosas
    2009-04-03

    Bob, let me tell you...

    you are the greatest! Thank you *very* much.
    To generate this output, the user needs to specify the following card:

    $NBO AONBO=P $END

    in the GAMESS input file. This is for GAMESS-US compiled with NBO5.G

    Thanx again. Have a nice day!
    Victor

     
  • Bob Hanson
    Bob Hanson
    2009-04-09

    • assigned_to: nobody --> hansonr
    • status: open --> closed