Well, I don't know. This is going to be a challenge. I was able to read and visualize the XYZ file; reading is fastest with

set autoBond false

so as not to take the minute required to automatically bond all those atoms.

First thing I would suggest is to get those atom coordinates out of the JVXL file. Just add two "dummy" atoms -- one at each of the points across the diagonal. This will bring the file size down to about 1.5 Mb. For example:

-2  -387.05978  -387.05978   -43.12965
  819     0.94486     0.00000     0.00000
  819     0.00000     0.94486     0.00000
  141     0.00000     0.00000     0.94486
1 -387.0 -387.0 -43.13 //BOGUS H ATOM ADDED FOR JVXL FORMAT
2  387.0  387.0  43.13 //BOGUS He ATOM ADDED FOR JVXL FORMAT

But that's just a suggestion. The real problem is in the line that starts with

 1 698 1 11 1 828 1 10 1

This line identifies the critical edges for the Marching Cubes algorithm. It says, "1 voxel outside, 698 inside; 1 voxel outside, 11 inside...." It needs to sum to the total number of voxels, 94577301 (819 x 819 x 141), but it only sums to 11097130.

By the way, you can break the JVXL data up into as many lines as you like. Doesn't have to all be on one line like that.


That's a pretty big surface -- 94 million points. I'm pretty sure it will crash my installation of Java.

On Mon, Nov 29, 2010 at 10:19 AM, Gabriele Penazzi <g.penazzi@gmail.com> wrote:
Dear all,

I've a problem trying to plot a jvxl isosurface. My system is a 360
000 atoms quantum dot, and when I try to plot the isosurface nothing
appears, and the cutoff value is read as 0, despite it's never defined
as 0 in the file.

If I run the same with a smaller structure (~10 000 atoms), anything
is fine, so I think that probably the code I wrote to get the jvxl
file is correct. The file looks ok at a hand inspection as well.
Did anyone experienced such a problem, and did any of you ever tried
to use jvxl representation with hundred of thousand of atoms

You can find both the structure and the jvxl file here:


I'm working with jmol 12.0.22, Sun java 1.6.0_18, Linux 2.6.32-24 x86_64

Thanks in advance for any feedback.

Gabriele Penazzi

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