That is what I am doing. If I open a log file of a frequency only
calculation (i.e. no optimization then there is only one set of MOs and they
correspond to the MOs of the optimized structure.
Thanks again for all your help.
On Tue, Oct 5, 2010 at 3:35 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> 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
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Virtualization is moving to the mainstream and overtaking
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>>>>> easier or more difficult to achieve? Read this whitepaper to separate
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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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>>
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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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