Re: [Jmol-users] Sage and JVXL

[Robert H. <ha...@st...>]

Jason,

ho, ho! Now there's a challenge...

I am totally excited to hear that the Sage community (
http://www.sagemath.org/) has embraced Jmol. What a cool thing. This is what
open source is all about.

The JVXL file format is described in
http://chemapps.stolaf.edu/jmol/docs/misc/JVXL-format.pdf Take a look there
and see what you think. I'm not sure that is going to do the trick for you.
But we can certainly work together to get something that does. I think it
explains the basic idea. That we start with a 3D grid of values and aim to
create an isosurface based on a given cutoff value. We use the marching cube
algorithm, so we are basically creating a serial list of edges. It is this
list of edges that is being registered on the line with the numbers you
refer to below. There are lots of options.

What exactly does a 3d contourplot look like? If you show me one, I might
have some ideas.

Bob

On Tue, Feb 3, 2009 at 10:15 AM, <jas...@cr...> wrote:

> Hello all,
>
> First, thanks again for the fantastic job on jmol.  We absolutely love
> it over here in the Sage community.
>
> I'd like to work on implementing a 3d contourplot function to plot level
> surfaces of a function with three variables.  It seems that the best way
> to approach this is to have Sage generate a JVXL file and sent that to
> jmol.  I spend some time last night trying to understand the file
> format, but I'm getting confused.  I also tried to find the relevant
> file in the jmol codebase that took a function or data set for a grid of
> points and generated a jvxl file.  However, I don't think I found the
> right file (I found the file that does the marching cubes algorithm in
> the jvxl directory).
>
> Is there any simple example of a simple surface and a step-by-step
> walkthrough of creating a jvxl file?  Which jmol source file would have
> similar code?  One thing I'm confused about is the statement in the pdf
> file of the format that "We simply list the number of voxels found
> sequentially on each side: 115922 outside, 2 inside, 6333 outside, 4
> inside..."  How exactly did you get the number 115922?
>
> Thanks,
>
> Jason
>
>
>
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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