Charge analysis and Gaussian CUBE file viewer

[egillsk]

Hi developers !

I have been able to run the new bader program on the cube files created in dacapo. I would like to do some analysis on my system wich is a dissolved proton in water and a metal slab. The perpose is to cheack out how much the hydrogen atom I initially placed in the water is dissolved and then we belive that the electron from the hydrogen is distributed in the metal slab, but we are not sure because we haven't done any analysis on that (but hopefully your bader program will solve that). What is the trick to see the charge on each atom? What should we look at? Wich output option should we use 1,2,3 or 4?

Have you any idea were it would be best for me to get Gaussian CUBE file viewer so that I can visulies what is going on in my system?

Best regards,

egillsk

[andri]

The official viewer for Gaussian is (I believe) GaussView (http://www.gaussian.com/gv_plat.htm) but I don't think it's free.

Another possibility is XCrysDen (http://www.xcrysden.org/). The people behind AtomEye might have some utilities for converting a CUBE file into a file format suitable for XCrysDen (http://164.107.79.177/Archive/Graphics/A/utils.html). They do at least have one for CHGCAR files. If they don't have one and a similar scripts can't script can't be found online then maybe somebody should look into writing such a file converter.

[graeme]

The amount of charge on each atom will be listed in the ACF.dat file, and in the output of the program if you choose option 4. In order to visualize the Bader volume around each atom, you can choose option 2, and specify which atom you are interested in. The BvAtxxxx.dat file has the same format as your initial charge density (cube file, for example), so that you can view it in a standard viewer. If you visualize the isosurface with a low value, you can see the outline of the Bader volume.

[Adrain]

Dear developers,

I always use molekel to view gaussian cube file. I try to produce a cube file from CHGCAR. Bit it only works fine for cubic cell. For hexagonal cell, I can not get the right charge plot.

Any comments are highly appreciated!

Best regards,
Adrain

[graeme]

Yeah, we have not implemented non-orthogonal cells yet. If enough people would find this valuable, this functionality could be added.

[crajesh]

hi all.
Is a proper program/script for converting CHGCAR to cube file developed for a general cell including the non-orthogonal cells..?
thanx in advance

rajesh