On 8/30/2010 6:33 PM, Robert Hanson wrote:
Pshemak, thanks very much for that excellent list.
Run-times. I'm pretty sure this is isolated specifically to atomic
orbitals. It has to do with the size of the box used to create the
grid. Jmol 11.8.24 had a bug that sometimes truncated the box; Jmol
12.1.8 corrects that at the expense of time. Choose your resolution
and cutoff well. Resolution 7 for an orbital that is 20 angstroms wide
is just too high. You are creating a box 140 x 140 x 140 values, and
the created surface has 89,000 triangles. Well, yeah. 40 seconds!
It's way overkill. But, it is beautiful, and if that's what you want,
that's specifically what JVXL is for. Saving that 140x140x140 surface
as a JVXL file (only 136 Kb) loads in about 2 seconds on my computer.
Thanks for your extended explanation. I was exploring (learning) Jmol.
Since the calculations of that nature were fast in 11.8, it was a
surprise that they were so slow in 12.0.8 (improved since). Now I know,
how to minimize the calculation times. Unfortunately, information of
that nature is not readily available in the Jmol documentation.
JVXL file reading: eplot11.jvxl loads fine for me. Maybe that fix
didn't get in 12.0.8; try
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip (again)
please.
Yes, indeed 12.1 9 reads the "legacy" jvxl files. Thanks for fixing it.
contours: In this case there is still a bug, but there is a change as
well. Jmol 11.8 gave a circular outer contour because it was failing
to contour all the way through the data. That may have looked good in
some cases, but it was a bug. To get rid of the square you will now
use CONTOUR DISCRETE or CONTOUR INCREMENT to define your own contours.
The hole in the middle is correct. Filling that in is misleading,
because we don't have any data there.
Why is there a hole in the middle of 1s orbital wavefunction?
Thanks for all your help,
PM
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