VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Feb 21 2007 - 09:44:21 CST

On Wed, 21 Feb 2007, Avell Diroll wrote:

JS> > check just slightly differently to allow you to get your surface even though
JS> > this specific case is definitely marginal at best. Try rendering the
JS> > isosurface for isovalues 0, 0.0001, and 0.000001 and you'll see how
JS> > small the volume gradient is at the outer edges of your box.

how about adding a 'cutoff' threshold that will set all gridpoints to
zero for the purpose of isosurface rendering if the absolute value of
the grid point is below that threashold?

we're doing something similar in the gradient corrected functionals in
the density functional theory codes. below a certain density the data
is too 'noisy' and you can get huge gradients due to that noise. since
the density is _very_ low, it is error from ignoring that contribution
(can be checked with much larger basis sets) is very small than the
one introduced from the spuriously high gradients.

axel. 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.