VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 13 2011 - 10:02:38 CDT

Joshua,
  Just a quick addendum:
It looks like the X3DOM team has added a new runtime API for
controlling things like the rendering stats display and other
attributes that are separate from the X3D scene itself:
  http://x3dom.org/x3dom/example/x3dom_runtime.html
  http://x3dom.org/x3dom/doc/api/files/x3dmain-js.html

I'm going to ask them to add new APIs to set the triangulated
mesh resolution of the various higher level geometric primitives
by this same mechanism, as I think that it's a close match to
what they are already doing with that API. In the mean time,
one can use this to shut off the statistics display and other
stuff, which is a nice little improvement. I'll grab their
new code and give it a spin soon.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Apr 13, 2011 at 09:49:34AM -0500, John Stone wrote:
> Hi Joshua,
> I think that the sphere resolution is something that X3D leaves
> as a decision that is entirely up to the viewer program and is not
> specified by the X3D scene itself.
>
> I suppose the idea behind the approach taken by X3D is that the
> viewer could implement the sphere primitive with GLSL shaders
> like I do in VMD and not draw a triangulated sphere at all.
>
> Here's the X3D spec for the sphere geometry node:
> http://www.web3d.org/x3d/specifications/OLD/ISO-IEC-19775-X3DAbstractSpecification/Part01/components/geometry3D.html#Sphere
>
> In this case the X3DOM viewer itself is picking the sphere resolution.
>
> I just spent a couple of minutes digging into the x3dom.js source code
> and on or about line 721 of the code (search for the string
> "latitudeBands"), you can see this:
>
> var latNumber,longNumber;var latitudeBands=24;var longitudeBands=24;var theta,sinTheta,cosTheta;var phi,sinPhi,cosPhi;var x,y,z,u,v;for(latNumbe r=0;latNumber<=latitudeBands;latNumber++)
> [...]
>
>
> Human-readable version (line 721 of my 3 month old copy of x3dom.js):
> var latNumber,longNumber;
> var latitudeBands=24;
> var longitudeBands=24;
> var theta,sinTheta,cosTheta;
> var phi,sinPhi,cosPhi;
> var x,y,z,u,v;
> for(latNumber=0; latNumber<=latitudeBands; latNumber++)
> [...]
>
> I would suggest changing "latitudeBands" and "longitudeBands"
> values to 6 (very coarse), 8, or maybe 12. Any of those
> should give you a very big boost in sphere rendering speed in X3DOM
> vs. what you see when the loops are set to 24.
> Just use values that match the VdW sphere "resolution" parameter
> you prefer in VMD, and that should give you the same general appearance.
>
> You can see similar for loops for Cylinders, Torii, and other shapes, so
> any geometry you want to fiddle with you can just edit the x3dom.js
> source code to get what you want in the short-term.
>
> I'll contact the authors of X3DOM and suggest that they add some
> special tags to let the user override these default resolution
> parameters without having to modify the code... :-)
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Apr 13, 2011 at 08:09:37AM -0400, Joshua A. Anderson wrote:
> > Hi list,
> >
> > I'm trying out the new X3DOM export (its pretty cool). Has anyone else run into performance issues with exporting VDW representations? Have you found a solution?
> >
> > VMD sensibly emits a <Sphere> node for each sphere in the representation. But the rendering ( at least in Firefox 4 ) uses a ridiculous number of triangles for each sphere and display performance suffers. The little x3dom status display reports over 2 million triangles in a tiny 1800 particle test model I exported.
> > --------
> > Joshua A. Anderson, Ph.D.
> > Chemical Engineering Department, University of Michigan
> >
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078