On Wed, May 9, 2012 at 7:29 PM, Andrew Long <[email protected]>wrote:
> 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?)
>
just at the end, right? So you use vertexCount, not vertices.length
> 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)
>
It's the same. But it's repackaged for getProperty, and I suspect
vertexCount is being used to do that.
>
> 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?
>
>
Ho, ho. No easy answer to THAT question! htParams is a general mechanism
for passing supplemental information to and from the readers. I wouldn't
suggest creating a random AtomSetCollectionReader. Why do you need to do
that?
> 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.
>
>
It's not a texture. There are vertices, polygons, normals, and in most
cases vertexColixes.
> 3)what is a colix?
>
>
Color index. These are dynamically saved short values that stand in for
actual integer RGB color values and also encode translucency. g3d can
deliver color equivalents to colixes.
>
> 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. : )
>
>
>
Great.
> Cheers Andrew
>
>
> --
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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