From: SourceForge.net <no...@so...> - 2009-04-03 02:50:47
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Feature Requests item #2715807, was opened at 2009-03-26 19:26 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=2715807&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Priority: 5 Private: No Submitted By: Victor Rosas (vrosas) Assigned to: Nobody/Anonymous (nobody) Summary: Add NBO orbital visualization Initial Comment: Add ability to read and display the NBO orbitals produced by the GAMESS-US--NBO 5 combo. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-04-02 21:50 Message: See Jmol 11.7.32, http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.jar ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-04-02 20:28 Message: this is in place now. A very easy fix! Please let us know what you need to do in GAMESS to get this output. ---------------------------------------------------------------------- Comment By: Victor Rosas (vrosas) Date: 2009-04-02 17:57 Message: 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. ---------------------------------------------------------------------- Comment By: Nobody/Anonymous (nobody) Date: 2009-04-01 10:28 Message: I don't know -- send me the output, and I will see what I can do with it. Bob ---------------------------------------------------------------------- Comment By: Victor Rosas (vrosas) Date: 2009-04-01 09:32 Message: 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! ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-03-30 11:38 Message: 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. ---------------------------------------------------------------------- Comment By: Victor Rosas (vrosas) Date: 2009-03-30 11:30 Message: 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 ---------------------------------------------------------------------- Comment By: Jonathan Gutow (gutow) Date: 2009-03-27 12:02 Message: 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 ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-03-27 10:40 Message: also, it would be good to have the GAUSSIAN equivalent output. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-03-27 10:39 Message: 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. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=2715807&group_id=23629 |