[For what it's worth, the documentation at
http://chemapps.stolaf.edu/jmol/docs/misc/JVXL-format.pdf has been revised,
so the order there, in the document listed as "revised 4/21/2009" is correct
now. This statement refers to an earlier revision.]
On Thu, Apr 23, 2009 at 9:41 PM, William Cauchois <[email protected]>wrote:
> In case anyone is wondering, Robert Hanson helped me find the bug,
> which was due to an error in the JVXL spec. On page 7, they
> demonstrate the order in which to iterate over the voxels using three
> nested for loops. However, this order is reversed.
>
> Cheers,
> Bill
>
> On Thu, Apr 16, 2009 at 6:03 AM, Robert Hanson <[email protected]> wrote:
> > 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
> >>>
> >>>
> >>>
> ------------------------------------------------------------------------------
> >>> Stay on top of everything new and different, both inside and
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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
> >
> >
> ------------------------------------------------------------------------------
> > Stay on top of everything new and different, both inside and
> > around Java (TM) technology - register by April 22, and save
> > $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.
> > 300 plus technical and hands-on sessions. Register today.
> > Use priority code J9JMT32. http://p.sf.net/sfu/p
> > _______________________________________________
> > Jmol-users mailing list
> > [email protected]
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
> >
> >
>
>
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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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