On Thu, Aug 26, 2010 at 8:21 AM, Pshemak Maslak <[email protected]> wrote:
> On 8/26/2010 8:08 AM, Robert Hanson wrote:
>
> Pshemak,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.
>
>
>
>
The speed is now much improved. The problem was that it was trying to do
very high resolution by default. Just set resolution to something small,
like 3, and it should be fine.
isosurface resolution....
I'm still surprised that 11.8 was any faster; my timings with 11.6 and 11.8
are virtually identical to 12.0.
>
> 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.
>
>
draw hover values are only significant for mapped isosurfaces, not simple
ones.
>
> 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?
>
>
I'll check. Make sure you indicate the colors before the file name:
isosurface color red green "t.jvxl"
should work. yes, I'm seeing atomic orbitals read back in in color. It's
possible there's a problem with orbitals written by 11.8 and read by 12.0...
OK, the very high resolution is slowing you down. Just save them from 12.0
and reload them from that --- after I update it!
Bob
--
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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