QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: lamkt on November 23, 2009, 05:48

Title: Visualization of VNL data
Post by: lamkt on November 23, 2009, 05:48

Dear all,

I would like to ask if anyone used other software to visualizing the data (e.g., Electron density) in the VNL files other than VNL?
While the graphics looks great using VNL, I can't seems to maneuver the figures to the correct position.  This is especially difficult when I want to compare the plots of different structures as I can't get to the same viewing angle.

Maybe I'm just a control freak but I would love to be able to control the rotation degrees of the figures.  Any tips on this will be great.

Cheers!

Title: Re: Visualization of VNL data
Post by: Anders Blom on November 23, 2009, 09:01

I agree that there are a couple of small details that can be improved in the camera handling in VNL, and this can be expected to appear in future versions.

Still, exporting to external visualizers is certainly relevant anyway, the main issue is just which file format to use.

The 2009.11 version of ATK/VNL has built-in support for exporting 3D grids into a CUBE file. I've tried to adapt that code to work with ATK 2008.10, the module is attached. Since I don't actually have any software at hand that can read cube files, I haven't had a chance to check that the export actually works, however... Hopefully someone in the community can assist with this task!

Here's an example of how to use it:

Code

from ATK.TwoProbe import *
from export_cube import *

scf = restoreSelfConsistentCalculation('lih2li-scf.nc')
electron_density = calculateElectronDensity (scf)

export_cube_file(electron_density,'file.cube')

Title: Re: Visualization of VNL data
Post by: lamkt on November 24, 2009, 08:37

Thank you! I'm assuming the CUBE file is for GaussView?

Title: Re: Visualization of VNL data
Post by: zh on November 24, 2009, 11:24

Beside GaussView, VESTA can also visualize the data in the CUBE format.