From: Robert H. <ha...@st...> - 2010-08-27 05:36:00
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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 <ha...@st...> wrote: > > > On Thu, Aug 26, 2010 at 8:21 AM, Pshemak Maslak <pm...@ch...> 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 |