From: Vincent Ustach (vustach_at_outerbanks.umaryland.edu)
Date: Wed Jan 17 2018 - 15:40:12 CST

Thanks very much John. That was informative.

I typically use wireframe so I am not worried about shading at this point
but that is good to know.

Cheers,

Vinnie Ustach

On Wed, Jan 17, 2018 at 1:07 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> All of the conventional isosurface extraction schemes for scalar fields
> end up doing interpolation (trilinear, tricubic, ...) to find the points
> along the edges of cubes, tetrahedra, or other space filling shapes where
> the isosurface(s) pass through the space filling shape.
>
> The VMD "points" isosurface mode is different, it uses a very fast and
> simple
> scheme that skips the interpolation step (thereby saving massive numbers
> of slow memory accesses) and just compares values of voxels that are
> neighbors in the X-dimension, and draws a point when their values straddle
> the isovalue of interest. That makes the points isosurface scheme useful
> for interactive display of volumes that would otherwise present a massive
> rendering workload with the full-accuracy code path.
>
> The use of binary on/off voxel values in your volumes will work, but will
> give you somewhat poorly/oddly shaded surfaces due to the way surface
> normals
> are typically computed.
>
> Read here for details about what isosurfaces are and out they are computed
> on regularly spaced volumetric grids:
> https://en.wikipedia.org/wiki/Isosurface
>
> VMD uses Marching Cubes, which is described briefly here:
> https://en.wikipedia.org/wiki/Marching_cubes
>
> Best,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Wed, Jan 17, 2018 at 11:02:22AM -0500, Vincent Ustach wrote:
> > Dear VMD List,
> >
> > I have a field of 1s and 0s with isosurface representation in VMD
> (VMD for
> > LINUXAMD64, version 1.9.1 (February 1, 2012). I noticed that with Draw
> > Points, the Isovalue does not affect the isosurface. With Draw
> Wireframe
> > and Draw Solid Surface, an Isovalue of 1.0 gives the same surface as
> Draw
> > Points, but decreasing Isovalue towards 0.0 causes the isosurfaces to
> > expand.
> >
> > Since the grid has values of 0 and 1, I guess there is some
> interpolation
> > scheme that "finds" where the volume is equal to the Isovalue. Is that
> > true? Can someone please explain how it works?
> >
> > Best Regards,
> >
> > Vinnie Ustach
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>