René,
Thanks, I'll take a look at that data file. I thought the two code
examples were doing the same thing, but maybe it is the issue of
zeroing out the moData. I'll look at it.
Jonathan
On Jun 19, 2009, at 10:54 AM, René Kanters wrote:
> Hi Jonathan,
>
> The way I understand it (and it has been a little while since I messed
> with this), is that the setMOData function associates the moData
> hashtable argument (that contains the basis set and orbital
> information) with an atomset. I have been looking at qchem data with
> multiple models each with their own orbitals without a problem. The
> thing to remember is to make sure to create a new moData hashtable
> whenever a new model needs one (as I did in the qchem reader whenever
> I encounter the definition of the basis to be used. (To be sure, I
> null the moData the moment a new structure is encountered).
>
> I just added a qchem output file to the Jmol-datafiles that has
> orbitals for each of the optimization steps for optimizing water.
>
> I hope this helps.
> René
>
> On Jun 19, 2009, at 9:12 AM, Jonathan Gutow wrote:
>
>> 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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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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