I think you want to look at the contour functions. See the jmol
script documentation. You need to describe better what you want to do.
Slab controls how far forward and backward in the view window stuff is
drawn.
This is really a question for the users list. I have redirected this
discussion there.
Jonathan
On Dec 10, 2009, at 4:16 AM, Jan Brndiar wrote:
> Hi
> I'm using jmol to visualize some cross section throught the
> isosurface
> but the cross section looks very strange
>
> load "DENSITY.cube"
> slab plane {0,0,1,-11}
> slab on
> isosurface p1 plane {0,0,1,-10} file ""
>
>
> It's stratched and cutted... , but on the other side the isosurface
>
> isosurface s1 0.2 color red file "" translucent
>
> looks good up to rotation which doesn't matter. I'm using the latest
> version of jmol 11.9.10. Older versions produce the same result.
>
> DENSITY.cube is located on http://147.213.112.235:/fotky/jmol/
> DENSITY.cube
>
> this is copy of the console output. I think it's a bug when drawing or
> creating cross section or it can be solved without crackdown to the
> code.
>
> Jan Brndiar
>
> FileManager.getAtomSetCollectionFromFile(DENSITY.cube)
> FileManager opening /home/bxm/cpmd/jmol1/DENSITY.cube
> The Resolver thinks Cube
> openFile(DENSITY.cube): 115 ms
> ModelSet: haveSymmetry:false haveUnitcells:false
> haveFractionalCoord:false
> 1 model in this collection. Use getProperty "modelInfo" or getProperty
> "auxiliaryInfo" to inspect them.
> ModelSet: autobonding; use autobond=false to not generate bonds
> automatically
> isosurface p1 plane {0,0,1,-10} file "";
> FileManager opening /home/bxm/cpmd/jmol1/DENSITY.cube
> reading isosurface data from /home/bxm/cpmd/jmol1/DENSITY.cube
> data file type was determined to be Cube
> DENSITY: cube file created from cpmd Wannier file: DENSITY
> Total SCF Density
>
> voxel grid origin:(0.0, 0.0, 0.0)
> voxel grid count/vector:50 0.5619729 0.0 0.0
> voxel grid count/vector:50 0.28098598 0.48580202 0.0
> voxel grid count/vector:100 0.0 0.0 0.56691796
> JVXL read: 50 x 50 x 100 data points
> generateContours: 9 segments
> planar axes type 2 axis angle = 59.95507951548094 normal=(0.0, 0.0,
> 0.86563313)
> planar vectors / lengths:(0.29738325, 0.0, 0.0) / 0.29738325
> planar vectors / lengths:(0.14869137, 0.25707534, 0.0) / 0.29697955
> unit orthogonal plane vectors:(1.0, 0.0, 0.0)
> unit orthogonal plane vectors:(0.50067884, 0.86563313, 0.0)
> unit orthogonal plane vectors:(0.0, 0.0, 0.86563313)
> nSquares = 2401
> generateContourData min=0.021693513 max=0.28818858 nContours=9 (0
> specified) contourFromZero=true
> generateContours: 6117 vertices
> ColorManager: color scheme now "roygb" color value range: 0.0 to 0.0
> color "roygb" range 0.021693513 0.28818858
> p1 created with cutoff = 0.0 ; number of isosurfaces = 1
> isosurface s1 0.2 color red file "" translucent;
> FileManager opening /home/bxm/cpmd/jmol1/DENSITY.cube
> reading isosurface data from /home/bxm/cpmd/jmol1/DENSITY.cube
> data file type was determined to be Cube
> DENSITY: cube file created from cpmd Wannier file: DENSITY
> Total SCF Density
>
> voxel grid origin:(0.0, 0.0, 0.0)
> voxel grid count/vector:50 0.5619729 0.0 0.0
> voxel grid count/vector:50 0.28098598 0.48580202 0.0
> voxel grid count/vector:100 0.0 0.0 0.56691796
> JVXL read: 50 x 50 x 100 data points
> s1 created with cutoff = 0.2 ; number of isosurfaces = 2
>
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Dr. Jonathan H. Gutow
Chemistry Department [email protected]
UW-Oshkosh Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow
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