[Pw_forum] Xcrysden 3D-charge plot for missing atoms-Reg

Tone Kokalj tone.kokalj at ijs.si
Tue Aug 5 09:35:26 CEST 2014

On Fri, 2014-07-25 at 15:09 +0530, Suresh A wrote:
> Respected experts/Dear Friends,
>                                                I have done
> optimisation for Cu doped tio2. Then I used postprocessing code for 3D
> charge density plot. It is known that atoms having negative sign in
> its coordinates will not be shown by XCRYSDEN. So i can not saw 3D
> charge plot for some  missing atoms in xcrysden.

This is not actually the case. First, the atoms which are shifted
"outside" the reference cell box (i.e., those having negative crystal
coordinate) are cropped only in the "nicely-cut unit cell" display mode,
but not in "translational asymmetric unit" mode (notice the two small
buttons right of the "Dihedral" button in the bottom toolbox). Second,
even if the atom is cropped, its charge density will still be shown
(actually, there are some specifics here of how the region for charge
density plot is selected). Thirdly, you can always "multiply" periodic
structure by showing more cells along periodic directions. The same can
be done with the charge density plot.

Please consider asking next time such question to xcrysden mailing list.


Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

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