Tutorial:Visualization with VisIt

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The program VisIt is an open source data visualizer developed by Lawrence Livermore National Laborartory. It supports multiple platforms including Linux, OS X and Windows, most likely you can download a precompiled version for your platform here. For this tutorial we will assume that you have Visit installed and running.

We will use the following input file:

CalculationMode = gs
UnitsOutput = eV_Angstrom
Radius = 5*angstrom
Spacing = 0.15*angstrom

Output = density
OutputFormat = cube

XYZCoordinates = "benzene.xyz"

with the benzene.xyz file:

12
   Geometry of benzene (in Angstrom)
C  0.000  1.396  0.000
C  1.209  0.698  0.000
C  1.209 -0.698  0.000
C  0.000 -1.396  0.000
C -1.209 -0.698  0.000
C -1.209  0.698  0.000
H  0.000  2.479  0.000
H  2.147  1.240  0.000
H  2.147 -1.240  0.000
H  0.000 -2.479  0.000
H -2.147 -1.240  0.000
H -2.147  1.240  0.000

Note that we requested Octopus to output several quantities in cube format. This is a common format that can be read by several visualization and analysis programs. Each file includes a scalar field and the system geometry.


Now run Octopus, it will take a couple of minutes.

This will generate a file called density.cube under the static/. You can now run VisIt and open the file following the instructions given in this video:



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