must be the MOs for the starting configuration. If you check, there might be
a way of turning those off, I don't know. Just ignore them.
On Tue, Oct 5, 2010 at 12:02 PM, Marco Zimmer-De Iuliis <marcoz...@gmail.com
> wrote:
> Hi Bob,
>
> I believe that the "molecular orbitals" it is reading in model 1.2 are
> actually the eigenvectors that the GAMESS program computes at the beginning
> of every geometry optimization.
>
> The molecular orbitals for the optimized structure are shown for the first
> model with any frequency information i.e. model 1.156 for example1.log and
> model 1.36 for example2.log.
>
> Thanks for the update - it is now very easy to see which model will give me
> the MOs.
>
> I hope this has not caused too much of a headache!
>
> Cheers,
>
> Marco
>
> On Mon, Oct 4, 2010 at 9:09 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>> actually there are two sets of orbitals in two different models in both of
>> your example files. You will see it when you do the load in the revised
>> version, where there is a new report when you load a model with molecular
>> orbitals:
>>
>> load example1.log
>> 263 models
>> 491 molecular orbitals in model 1.2
>> 150 molecular orbitals in model 1.156
>>
>> load example2.log
>> 119 models
>> 423 molecular orbitals in model 1.2
>> 136 molecular orbitals in model 1.36
>>
>>
>> Bob
>>
>>
>> On Mon, Oct 4, 2010 at 7:53 PM, Marco Zimmer-De Iuliis <
>> marcoz...@gmail.com> wrote:
>>
>>> Hi Bob,
>>>
>>> If I use ChemCraft (which is another output visualization program that
>>> we use in our lab), then it shows that the log file has a total of 150
>>> molecular orbitals. I realize this is a very large number of MOs, but it is
>>> a rather large molecule.
>>>
>>> I don't know if that helps, but I greatly appreciate your time on this.
>>>
>>> All the best,
>>> Marco
>>>
>>>
>>> On Mon, Oct 4, 2010 at 5:09 PM, Robert Hanson <hans...@stolaf.edu>wrote:
>>>
>>>> 491 molecular orbitals read in model 2
>>>> 150 molecular orbitals read in model 156
>>>>
>>>> Not sure what that's all about, but you probably do.
>>>> This is in the Java console. I'm thinking I should have it sent to the
>>>> standard console as well. People need to see this.
>>>>
>>>> Bob
>>>>
>>>>
>>>>
>>>> On Mon, Oct 4, 2010 at 12:19 PM, Marco Zimmer-De Iuliis <
>>>> marcoz...@gmail.com> wrote:
>>>>
>>>>> Hello all,
>>>>>
>>>>> As far as I understand it, Jmol should be able to display molecular
>>>>> orbitals from the output of a GAMESS(US) calculation (.log file).
>>>>>
>>>>> I have tried a number of different calculations (DFT geometry
>>>>> optimizations, energy caluclations, freuqency analysis) and when I open
>>>>> these files in Jmol, the "Molecular Orbitals" part of the menu is greyed
>>>>> out.
>>>>>
>>>>> I also took the examples from the Jmol wiki page and tried those and I
>>>>> get the same thing.
>>>>>
>>>>> How can I visualize molecular obritals? Why is this section greyed
>>>>> out? I am using Jmol 12.0.10.
>>>>>
>>>>> Thanks,
>>>>> Marco
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
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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
>>>>
>>>>
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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
>>
>>
>> ------------------------------------------------------------------------------
>> Beautiful is writing same markup. Internet Explorer 9 supports
>> standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3.
>> Spend less time writing and rewriting code and more time creating great
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>
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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
------------------------------------------------------------------------------
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Spend less time writing and rewriting code and more time creating great
experiences on the web. Be a part of the beta today.
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