So after some experimenting it seems like "isosurface resolution 1.5
molecular dots no fill" is the command to generate the perfect mesh. That
gives me 14606 vertices for azulene for a resolution of 1.5 and 5.8K
vertices if I use a resolution of 1.0. I think you're right, Using JMOL
inside a java function seems like it would be the most elegant way to do
all this plus it keeps all my code in mostly in one place. Is there a
recommended "api" or set of functions to use to interact with JMOL? so it
seems like the rough outline of input file generating function goes
something like this.
1)initiate JMOL
2)pass JMOL the command to load the base molecule
3)generate the isosurface using " isosurface resolution 1.5 molecular dots
no fill"
4)return the base molecule (is there an easy way to get JMOL to return a
neat array of the XYZ data? that's a point3f right? )
5)return the set of points on an iso surface(is there an easy way to get
JMOL to return a neat array of points ala step 4?)
6)generate the input files
7)?save the isosurface state?
Thanks again
Cheers Andrew
On Thu, May 3, 2012 at 3:16 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> Wow. No kidding!
>
> Yes, the resolution can easily be adjusted. That's a good idea.
>
> Don't worry about the coloring. That's just an array that can be filled
> easily; we'll find a simple way to do that. In the end you might want to
> write a Java app that embeds Jmol, and then we can expose that array for
> you.
>
> Bob
>
>
>
> On Wed, May 2, 2012 at 1:52 PM, Andrew Long <andrew.long.3...@gmail.com>wrote:
>
>
>
> --
> 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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