outside the box

[Axel]

On Wednesday, April 25, 2012 8:54:45 PM UTC-4, steve t wrote:
>
> Hey, I'm doing DFT optimization of a carbon nanotube and an aromatic   
> hydrocarbon that should adsorb on the CNT via pi-pi stacking. 
>
> The periodic cell has a=b=30 A, c=17 A; alpha=beta=90 deg, gamma=120   
> deg (the tube axis is along the z direction).  The optimization   
> completes but when I look at the final set of coordinates, the   
> aromatic hydrocarbon is in the cell adjacent to the parent cell.  I've   
> tried using @CENTER_COORDINATES but it doesn't help. 
>
> Does anyone have any suggestions as to how to keep both molecules in   
> the parent cell? 
>


why bother? they are identical due to PBC.
just wrap the coordinates back into the 
principal cell and you are done.

axel.

 

>
> Thanks. 
>
> Steve T 
>
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