My pleasure. -- Jmol defaults to showing all orbitals, I believe. Just
like all atoms. :)
On Thu, Nov 17, 2011 at 8:41 AM, Jörg Saßmannshausen <
[email protected]> wrote:
> 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=
> [email protected]
> > > 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
>
>
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--
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
------------------------------------------------------------------------------
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
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