Alright after a week of coding I've got it the first half working.
success!! Thanks again for the help.
http://i.imgur.com/wa01S.jpg
A couple of things I've found out along the way.
1)JMOL sets the generic java console to a console that's accessable via the
help menu.
2)the Point3f[] vertices array inside meshsurface will contain null
values. (possible bug that the rest of the program can ignore?)
3) the totally number of vertices returned by the vertices array is vastly
different from print getProperty("isosurfaceInfo.
vertices").length . (I imagine this is because its being counted
differently? maybe total corners of triangles rather than just vertices)
So at this point I need to read in all of the Gaussian out files, shade the
surface and then display. So now I have some questions.
1)how exactly does the
GaussianReader<=MOReader<=BassisFunctionReader<=AtomSetCollectionReader
work exactly? and what is a htParams exactly? does it need to be
initialized before I create a random AtomSetCollectionReader?
2)How exactly is the texture data for the isosurfaces stored? (or is it
even a texture?) I'm guessing public Map<String, BitSet> vertexColorMap;
has something todo with it but I haven't spent enough time sifting through
it to figure out how it works.
3)what is a colix?
Thanks again for your help. with luck I'll have this finished in time to
get this into a paper we're trying to publish in JACS. knock on wood. : )
Cheers Andrew
On Mon, May 7, 2012 at 7:30 PM, Robert Hanson <[email protected]> wrote:
> thank you!
>
>
> On Mon, May 7, 2012 at 3:44 AM, Angel Herráez <[email protected]>wrote:
>
>> > write test.vrl
>>
>> That should be
>>
>> write test.wrl
>> or
>> write test.vrml
>> or
>> write vrml test.whatever
>>
>> (not sure if both will work; the 3rd is safest)
>>
>>
>>
>>
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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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threat landscape has changed and how IT managers can respond. Discussions
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