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.
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.
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.
Also,
isosurface escontour plane xy contour 30 atomicOrbital 1 0 0 1.0
implements too many contours for the resolution. I'll look into that.
...and there is still a bug with the contour colors themselves.....
Draw hover -- right, there was a bug there that was killing the hover
watcher. That's fixed for 12.1.9 and 12.0.11.
Bob
On Mon, Aug 30, 2010 at 7:36 AM, Pshemak Maslak <[email protected]> wrote:
> I am afraid that some things did not get resolved in the new versions.
> Below is the list.
>
>
> set drawHover true; isosurface escontour plane xy contour 30
> atomicOrbital 1 0 0 1.0
>
> in.11.8.24 contour lines draw; can be read without set drawhover true
> [square bracket indicate that the script was run with and without that
> command]
> in 12.0.8 works fine; contours can be read with set drawHover true (the
> values are slightly higher than those in 11.8.24)
> in 12.0.10 and 12.1.8 three extra long triangles displayed and
> unfinished contour corners; contour values not shown with or without set
> drawHover true; contour in the center have different color than in the
> 11.8.24 and 12.0.8
>
> __________________________________________________________________
>
> [st drawHover true]; isosurface escross color absolute -0.01 0.9 plane
> xy resolution 6 atomicOrbital 1 0 0 1.0
>
> in 11.8.24, circular color-filled contours produced with values read on
> color boundaries without set drawHover true
> in 12.0.8 circular color contours produced with values read on contour
> boundaries only with set drawHover true; values slightly higher than
> those in 11.8.24
> in 12.0.10 and 12.1.8 the largest contour is square, an there is a
> "hole" in the middle, the surface looks different, the values do not
> show with set drawHover
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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