Pshemak -- please try the version at
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
This should fix your isosurface problems. (Though those old atomic orbital
JVXL files that have huge grids will always load poorly.)
Bob
On Thu, Aug 26, 2010 at 11:34 PM, Robert Hanson <[email protected]> wrote:
>
>
> 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
>
--
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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