[CP2K:3800] Re: outside the box
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
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.
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.
> Steve T
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