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 <[email protected]> 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 <
> [email protected]> 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 <[email protected]> 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 <
>>> [email protected]> 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
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Virtualization is moving to the mainstream and overtaking
>>>> non-virtualized
>>>> environment for deploying applications. Does it make network security
>>>> easier or more difficult to achieve? Read this whitepaper to separate
>>>> the
>>>> two and get a better understanding.
>>>> http://p.sf.net/sfu/hp-phase2-d2d
>>>> _______________________________________________
>>>> Jmol-users mailing list
>>>> [email protected]
>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>>
>>>>
>>>
>>>
>>> --
>>> 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 non-virtualized
>>> environment for deploying applications. Does it make network security
>>> easier or more difficult to achieve? Read this whitepaper to separate the
>>> two and get a better understanding.
>>> http://p.sf.net/sfu/hp-phase2-d2d
>>> _______________________________________________
>>> Jmol-users mailing list
>>> [email protected]
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> 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
>> experiences on the web. Be a part of the beta today.
>> http://p.sf.net/sfu/beautyoftheweb
>>
>> _______________________________________________
>> Jmol-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> 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
> experiences on the web. Be a part of the beta today.
> http://p.sf.net/sfu/beautyoftheweb
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
------------------------------------------------------------------------------
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
experiences on the web. Be a part of the beta today.
http://p.sf.net/sfu/beautyoftheweb
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
