Bob and René,
The issue is that orbitals are stored in the orbitals vector which
is associated with the AtomSetCollection rather than with each
AtomSet. Thus when there is a different set of MOs associated with
different AtomSets they are simply appended in order to the orbitals
for the AtomSetCollection. This means that for any given AtomSet
Jmol gives you the list of all orbitals. Glancing through the code
for readers other than GAMESS, I think the problem is the same.
However, I don't have any example data sets from other programs that
have orbitals associated with more than one of the models.
My preference would be to have an orbitals vector associated with
each AtomSet.
I have put a number of new example files in the gamess directory in
the Jmol-datafiles directory in SVN. A small example file that shows
the problem is HCl_geom_DZV+Diff+CCSD(T).log. Actually, this problem
shows up in all standard GAMESS geometry optimization runs as by
default the initial guess orbitals and the optimized orbitals for the
final geometry are included in the .log file. In this file the
initial guess orbitals associated with the first geometry are 1 - 56
as loaded by Jmol. The optimized orbitals that go with the final
geometry are numbered 57 +, the way Jmol presently loads them. In
this particular file the initial guess orbitals are listed after the
heading "EIGENVECTORS" and the final geometry MOs are after the
heading "MOLECULAR ORBITALS".
Let me know what you think and thanks for the suggestions and help.
Jonathan
On Jun 18, 2009, at 4:19 PM, Robert Hanson wrote:
> Jonathan, can you send me the GAMESS file and explain exactly what
> it should be doing?
>
> Bob
>
Dr. Jonathan H. Gutow
Chemistry Department [email protected]
UW-Oshkosh Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/faculty_staff/gutow/
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