[CP2K:3800] Re: outside the box

Steven Trohalaki steven.t... at mac.com
Sun Apr 29 21:36:18 CEST 2012


yes, i understand that i can wrap everything into one cell but it  
would just be easier to check intermediate and final geometries if  
there were a way to have CP2K output geometries of both molecules in  
the same cell.  or, is there a visualization package that works well  
with CP2K?

BTW, everything stays in the parent cell when alpha=beta=gamma=90 deg,  
so i wonder why it's different when alpha=beta=90 deg, gamma=120 deg.

steve t


On Apr 25, 2012, at 9:18 PM, Axel wrote:

>
>
> 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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