outside the box

[Steven Trohalaki]

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?

Thanks.

Steve T

[Axel]

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

[Steven Trohalaki]

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

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[Axel]

On Sunday, April 29, 2012 3:36:18 PM UTC-4, steve t wrote:

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?

what works well depends a lot on what file formats you use

and how proficient you are in using the corresponding viz tool.

i use VMD in combination with psf + dcd format files and 

wrapping coordinates is just one call to an bundled plugin.

however, it is often better to just enable periodic display

and get a better feel for how periodic boundaries would

affect the calculation, too.

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.

the way downhill may be shorter and steeper,

when going to the neighboring cell?

hard to tell with only a vague description.

axel.

 

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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