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Visualize Guassian cube files
Date: 2005/01/20 22:36
Name: zhufeng

Dear openmx users:

When I use gOpenMol(latest version) to visualize the Guassian cube files generated by openmx, some errors are reported by gOpenMol:
* Convert a 'cube' output from Gaussian94/98 into the *
* plot format known by gOpenMol (or SCARECROW). *
* *
* Leif Laaksonen (CSC) 2003 *
* Email: *
* Version: 23/09/03 *

The CUBE file is from a Gaussian98 calculation
The CUBE file contains the gradient!
The CUBE file contains the Laplacian!
Gradient norm is calculated from the CUBE file gradient!

Input file: '/home/houzf/openmx1.6/nanotube/ctube.lumo0_0_0_r.cube'
Output file (plot file): '/home/houzf/openmx1.6/nanotube/ctube.lumo0_0_0_r.plt'
Coordinate file (in CHARMM 'crd' format): '/home/houzf/openmx1.crd'

Title in file (job title):
Number of atoms: 36, x-, y-, z-origin (in Anstrom): -2.099102,-1.211837,0.065991
Number of points: 100, in direction (x,y,z) 0.132033 -0.076230 0.000000
$ERROR - first input has to be pure x-axis (y: -0.076230 , z: 0.000000)
What I calculated is the (9,0) carbon nanotube. When I use the example file (C60.dat) to calculate the C60, and then use gOpenMol to visualize the cube files, similar errors also occur. I visualize the cube files according to the steps shown in the manuals of gOpenMol.
Because these errors, the *.plt files can't be generated by gOpenMol. Finally I can't get the coutour pictures.

I would appreciate if someone can tell me how to solve it.

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Re: Visualize Guassian cube files ( No.1 )
Date: 2005/01/21 15:52
Name: T. Ozaki

Dear Dr. zhufeng,

The error you met comes from the orthorhombic unit cell.
gOpenMol does not support a cube file of orthorhombic cell,
while XCrysDen supports any cube file of both orthogonal and
orthorhombic cells. So, you will be able to use XCrysDen
to visualize your system with any orthorhombic cell.

Best regards,

Taisuke Ozaki

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