On 8/26/2010 8:08 AM, Robert Hanson wrote:
Pshemak,
Jmol 12.0.9, just released, doesn't fix the problem with atomic
orbitals. Actually, it made it worse. Sorry about that! I forgot to
test it with radial functions that approach 0 from below at infinity.
The next release will fix that; I'll let you know when I finish it.
Tremendous thanks for the alerts and your constant work on that.
By the way, which version of 11.8 were you using?
I was using 11.8.24. Since I am new to it, I decided not to do
incremental updates until I understand Jmol better. I was using only
11.8.24 for about two months, and 12.08 since the last weekend
I did not find any difference between 12.0 and 11.8 regarding timing,
but I did notice that setting z_eff to 1.0 for an atomic orbital:
isosurface estrans2 cutoff 0.09 phase color darkred darkblue color
translucent atomicOrbital 2 0 0 1.0;
generates an unnecessarily VERY large grid, even for 11.8 and 11.6. In
this new version, that's limited to 40x40x40, which is fine for most
work; you can make it prettier (and slower) by adding RESOLUTION 6 or
something to that effect prior to the atomicOrbital parameter. This
speeds up the calculation immensely.
The point of my exercise was to illustrate relative sizes of hydrogen
orbitals. z-eff = 1 was set by design. These calculations worked very
well on 11.8 (I gave the relative times in the previous e-mail). 12.08
is slow in generating atomic orbitals to the point of not being usable
on the web (for simple atomic orbitals). I din not check other surfaces
yet with 12.0.8.
Also, contours: Yes, there are serious problems with contours in 12.0.
I'm looking into that.
About contours: I also got very confusing results with "set drawHover
true" that you recommended for reading the values of the contour lines.
Probably I am doing something wrong, but when I set it in my "applet"
all surfaces displayed in it (not just contours or projections) show
values when I hover about them (that part I could understand, it just
shows the plotted value), but the values makes no sense. The most
obvious one: an atomic orbital isosurface which by definition should
have all boundary values the same when hovered above shows a at least
two or three different values depending (in an way that I do not follow)
on where above the surface the cursor is. The values of some
cross-sections and contours make no sense either. For example, in one
case only one value shows (throughout all colors of the projection) that
seems to match the cutoff value of an isosurface (but from the previous
isosurface displayed). It was late last night so, I would like to
reproduce that behavior on a desktop (rather than through the server)
when I have more time.
4. 12.08 has difficulty in displaying jvxl file written by 11.8. It does
it very slowly (several minutes) and --after finally loading
-- the
model cannot be interacted with. I have encountered only one
example of
this difficulty, and the jvxl file re-written with 12.08 Jmol
works
fine. Could this have anything to do with the changes in the
spartan
file reader? (my jvxl files are based on smol spartan files)
send me one of these JVXL files so I can see it, along with the
model file. Best is if you
write toBob.jmol
and just send me that file.
I want first to confirm that behavior on my desktop. I do not want to
occupy your time with some random error. If I can confirm I will e-mail
you the details.
It looks like the last night was very confusing for me:
I have written an atomic surface (2p H orbital) jvxl file with 12.0.8.
(to go around the slowness issue for now). It loaded and displayed fine
on my webpage. It changed to translucent after I specified "isosurface
color translucent", but it would not change lobe colors with "isosurface
phase color darkred darkblue". The same works with 11.8-generated jvxl
files. Am I completely confused?
Thanks for all your help.
PM
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