VMD-L Mailing List

From: Joshua A. Anderson (joaander_at_umich.edu)
Date: Wed Apr 13 2011 - 11:34:52 CDT

Thanks for looking into this John, I don't think I would have found that latitude in the .js code!

Dropping that resolution down helps quite a bit, but a 4000 sphere test system still renders at less than 4fps. If switched to a point representation, (which vmd exports as a <pointset>) and went all the way to 64000 particles without dropping under 60fps (didn't even try higher). It would appear that there is a high overhead in javascript for processing the nodes in the scene graph. Too bad there isn't a <SphereSet> node. If I find some time to play next week, I might verify that an IndexedTriangleSet encoding of the spheres does indeed run faster than all the individual <sphere> nodes.
--------
Joshua A. Anderson, Ph.D.
Chemical Engineering Department, University of Michigan

On Apr 13, 2011, at 11:02 AM, John Stone wrote:

> 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
>
>