We should be able to get that going. D and F functions are in for Gaussian,
but this format may be slightly different from what we've seen. Please send
me (directly) a sample file and a few snapshots from GaussView, and I'll
see what's wrong there.
Version of Jmol?
Bob Hanson
On Thu, Jul 19, 2012 at 3:06 PM, Maxime Guillaume
<[email protected]>wrote:
> Dear JMol users,
>
> I am presently trying to use JMol to plot the molecular orbitals that are
> printed in a gaussian09 log file, using the pop=full keyword.
> Nevertheless it seems that JMol has some problem to read the log file,
> which is a basic Ru complex (the N3 complex), in the reading routine of the
> molecular orbitals. It seems in particular that JMol has problems reading
> the format of the MO of gaussian if it contains D functions. Indeed, the
> MO input looks like
>
> Eigenvalues -- -88.79541 -88.79533 -19.20017 -19.20001 -19.19976
> 1 1 Ru 1S -0.00003 -0.00004 0.00016 0.00016 0.00018
> 2 2S 0.00008 0.00008 0.00007 0.00006 0.00006
> 3 3S -0.00154 -0.00152 0.00016 0.00036 0.00023
> 4 4PX 0.00005 -0.00005 -0.00003 0.00002 0.00003
> 5 4PY -0.00006 0.00006 0.00002 -0.00004 0.00001
> 6 4PZ 0.00008 0.00008 0.00002 0.00003 0.00001
> 7 5PX 0.00106 -0.00109 -0.00043 -0.00014 -0.00051
> 8 5PY -0.00069 0.00076 -0.00046 0.00004 -0.00059
> 9 5PZ 0.00095 0.00088 -0.00044 -0.00017 0.00040
> 10 6PX -0.00008 0.00008 0.00003 0.00030 0.00025
> 11 6PY 0.00041 -0.00044 0.00022 0.00001 0.00019
> 12 6PZ -0.00039 -0.00035 0.00017 0.00010 -0.00009
> 13 7D 0 -0.00001 -0.00001 -0.00001 0.00000 -0.00002
>
> and the console message:
>
> Error reading Gaussian file Molecular Orbitals at line: 13 7D
> 0 -0.00001 -0.00001 -0.00001 0.00000 -0.00002
>
> And the reading bugs on all the "D 0" lines. Replacing the white space
> with a + makes JMol to run ok, so this looks like a bug of reading that
> will happen as soon as we will have D functions ? Did anyone already
> encountered this problem, and would have any idea whether I'm facing some
> localized bug, or if it is something common in the present version of JMol ?
> Another problem comes afterwards, if I replace these white space by "+", I
> can read the MOs, but when I plot them using the command console (with mo=1
> for instance), nothing is displayed, only the molecular structure, but no
> MOs at all, and at that moment the error console does not print any error
> message...
>
> I know that it is possible to circumvene this problem by reading MO
> directly through cube files, but so far, I am just able to read cubes
> containing one MO only. So if I want to plot several MOs (to describe an
> electronic excitation for instance) I need one cube file per MO, while one
> cube file could contain all the needed MOs in theory. I was hoping to find
> a more flexible way to plot MOs through the log file, as it is supposed to
> be used finally inside a wiki page.
>
> If anybody has a suggestion on the best and easiest way to generate my MOs
> plots with JMol, I would greatly appreciate any help !
>
> Thanks a lot in advance for any suggestion or help
>
> Regards
>
> M. Guillaume
>
>
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>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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
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