Hi Bob and Jonathan, many thanks for the prompt reply. It was actually me looking into the output file (by means of wxmacmolplt) when I spotted the problem. Unfortunately, looking into the log file directly is only feasable with small molecules (hence my water example) and not with larger ones.
Also, I spotted a second potential problem here: If the output file does contain a NBO5 calculation as well, the orbitals shown are those from the NBO calculation, at least I think so, and not 'normal' ones, if that does make sense. I post that here in case somebody else is running into the same problems. All the best from London and keep up the good work! Jörg > Message: 1 > Date: Tue, 15 Nov 2011 09:28:34 -0600 > From: Robert Hanson <[email protected]> > Subject: Re: [Jmol-users] MO HOMO problem with GAMESS output > To: [email protected] > Message-ID: > <CAF_YUvVKW1oiyy7k6Lsjx-XdXObbK8gUp4GM3XN=As7JtM=m...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Sure enough. We're just using orbital energies for assigning HOMO in this > case, and there was a bug there. Probably should be using the information > in the file, but we just aren't at this time. See > > http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip > > Bob > > On Tue, Nov 15, 2011 at 4:19 AM, J?rg Sa?mannshausen < > > [email protected]> wrote: > > Dear all, > > > > I am having a problem with a GAMESS output when I want to draw the > > HOMO/LUMO > > orbitals. I stumbled over it by chance when I was looking into the > > HOMO/LUMO > > of a large molecule and the problem can be repeated with a smaller > > molecule like water. > > I have attached the URL of the logfile from the GAMESS calculation > > <http://sassy-design.de/tmp/water-SP.log.gz> as well as the pictures > > of the HOMO, generated that way: > > frame 1.1; isosurface cutoff 0.05 mo homo fill translucent 0.5 > > <http://sassy-design.de/tmp/homo.png> > > and mo 5, generated that way: > > frame 1.1; isosurface cutoff 0.05 mo 5 fill translucent 0.5 > > http://sassy-design.de/tmp/mo5.png > > > > As the list does not really like email attachments (for good reasons), in > > brief: > > MO5 should be the HOMO and when you draw it that way: > > frame 1.1; isosurface cutoff 0.05 mo 5 fill translucent 0.5 > > you get the correct answer, i.e. that 'burger shaped' orbital with the > > two lobes being the bread and the molecule being the meat. :-) > > (see above link) > > > > However, using that command here: > > frame 1.1; isosurface cutoff 0.05 mo homo fill translucent 0.5 > > i.e. calling the HOMO directly, gives a different and wrong picture. It > > looks > > more like higher, unoccupied orbital to me. > > (see above link) > > > > I am using jmol-12.0.49. I also tried the version Bob suggested in his > > email > > from the 22 Jun 2011 with the same results. > > > > Anybody got any ideas? That seems to be a bug to me, at least with the > > GAMESS > > output. > > > > All the best from a foggy London > > > > J?rg > > > > -- > > ************************************************************* > > J?rg Sa?mannshausen > > University College London > > Department of Chemistry > > Gordon Street > > London > > WC1H 0AJ > > > > email: [email protected] > > web: http://sassy.formativ.net > > > > Please avoid sending me Word or PowerPoint attachments. > > See http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > ------------------------------------------------------------------------- > >----- RSA(R) Conference 2012 > > Save $700 by Nov 18 > > Register now > > http://p.sf.net/sfu/rsa-sfdev2dev1 > > _______________________________________________ > > Jmol-users mailing list > > [email protected] > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 2 > Date: Tue, 15 Nov 2011 09:42:39 -0600 > From: Jonathan Gutow <[email protected]> > Subject: Re: [Jmol-users] MO HOMO problem with GAMESS output > To: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain; charset=us-ascii > > Jorg, > > I'm pretty sure the problem is that we haven't included reading occupation > numbers into the GAMESS reader yet. I keep meaning to work on that, but it > hasn't been a high priority. GAMESS doesn't specify occupation numbers, > just the total number of electrons in most of its calculations, so we will > have to do a little counting... I always do that manually and want my > students to think about it, which is part of why I haven't pushed to get it > done. > > Jonathan -- ************************************************************* Jörg Saßmannshausen University College London Department of Chemistry Gordon Street London WC1H 0AJ email: [email protected] web: http://sassy.formativ.net Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. 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