Hi Bob, I am aware of the FILTER "xxx" facility but I (wrongly) assumed that if you don't use that keyword, jmol is reading out the 'normal' orbitals as opposed to the 'NBO' orbitals. So if you don't use the filter keyword you get the expected orbitals from the eigenvectors, that were my sentiments.
Thanks for shedding some light on it here! All the best from London Jörg On Thursday 17 November 2011 14:18:07 [email protected] wrote: > Message: 5 > Date: Thu, 17 Nov 2011 08:17:58 -0600 > From: Robert Hanson <[email protected]> > Subject: Re: [Jmol-users] MO HOMO problem with GAMESS output > To: [email protected] > Message-ID: > <CAF_YUvWRQNHOyzRh8O1M+Y=gpysgak4q6vo0-gbtyhwyhxv...@mail.gmail.com > > Content-Type: text/plain; charset="iso-8859-1" > > On Wed, Nov 16, 2011 at 3:43 PM, J?rg Sa?mannshausen < > > [email protected]> wrote: > > 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 feasible with > > small > > molecules (hence my water example) and not with larger ones. > > In what sense "looking" and in what sense "only feasible for small > molecules"? Is there something still to fix there? > > > 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. > > That's correct. If you include NBO orbitals, then Jmol presumes you want to > see them. From the documentation: > > GAMESS, GAUSSIAN, GenNBO, Jaguar, NWChem, PSI, and QCHEM > > *FILTER "xxx"* > > where "xxx" is a word on the line Jmol uses to identify a molecular > orbital. This allows selective loading of specific types of molecular > orbitals -- such as "alpha", "beta", or "NBO" -- for any of these file > types, "POPULATION" or "EDMISTON" or "PIPEK" for GAMESS. ("NBO" refers to > orbitals generated with the NBO 5.0 option *AONBO=P*; "EIGEN" or "!NBO" > will skip loading of these orbitals.) > > Bob > > -- > 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 -- ************************************************************* 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. And common sense. http://p.sf.net/sfu/splunk-novd2d _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
