[CP2K:3800] Re: outside the box

Axel akoh... at gmail.com
Sun Apr 29 22:05:01 CEST 2012



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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