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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