Oh, wait, that's it. It's a bad JVXL file for sure. Please send me that. I
know this is very hard to debug.....
On Thu, Apr 16, 2009 at 8:01 AM, Robert Hanson <[email protected]> wrote:
> Bill, I can take a look at this, since I wrote much of the isosurface
> method code. Could very well be a bug there. What version of Jmol are you
> using? Please try swapping in the latest Jmol 11.7 jar file just to see if
> that makes any difference. It could be something that just didn't get fixed
> in the 11.6 code.
>
> Generally that result means there is an error in the writing of the JVXL
> file.
>
> Bob
>
>
>
> On Wed, Apr 15, 2009 at 6:26 PM, William Cauchois <[email protected]>wrote:
>
>> Hello,
>>
>> I am a developer working on the open-source mathematical software Sage
>> (<http://sagemath.org>). We use Jmol as one of our rendering backends
>> for plotting functions in 3D. I am currently helping to implement an
>> implicit 3D plotting feature, to graph contours of functions of the
>> form f(x,y,z)=c. You can view our progress at
>> <http://trac.sagemath.org/sage_trac/ticket/5249>. This type of plot is
>> an isosurface, so to communicate with the Jmol backend we chose to use
>> the JVXL format -- our software outputs a JVXL file describing the
>> plot which is then rendered by Jmol. However, many of the plots appear
>> very jagged when rendered by Jmol.
>>
>> Let me show you what I mean. Here are three pictures of the plot for
>> (x^3 + y^2 - z^2) = 0:
>> * This one is rendered at a low resolution (10x10x10) by Jmol:
>> <http://students.washington.edu/wcauchoi/misc/jmol_plot_lores.jpeg>.
>> The surface is not at all smooth.
>> * This one is rendered at a higher resolution (100x100x100) by Jmol:
>> <http://students.washington.edu/wcauchoi/misc/jmol_plot_hires.jpeg>.
>> The surface is covered in small bumps.
>> * For comparison, here it is rendered using Tachyon (our other
>> backend): <http://students.washington.edu/wcauchoi/misc/tachyon_plot.png
>> >.
>>
>> I've been trying to find bugs in our code, to no avail. Is there
>> anyone well-versed in the JVXL format who knows why this might be
>> happening?
>>
>> Thanks,
>> Bill Cauchois
>>
>>
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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
>
--
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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