[CP2K-user] [CP2K:17972] Re: Periodic and non-periodic box

Matt Watkins mattwatkinsuk at gmail.com
Tue Nov 1 14:39:36 UTC 2022

1) not that I am aware of. You can specify molecules and wrap them together 
somehow in VMD I seem to remember.
2) you need to make sure your molecules are connected in the non-periodic 
direction. You can use
to center the atoms in the cell. If the molecules are connected together 
then that should work once the cell is large enough.

On Sunday, 30 October 2022 at 08:11:09 UTC captai... at gmail.com wrote:

> Dear CP2K users and developer
>  I'm new in CP2K and my question are: 
> 1) Is there any way to print out the xyz file with the molecules ordered 
> inside the box because every time I run, it always print out in an 
> unordered way and to make it ordered I have to wrap it via VMD (see 
> input-1). 
> 2) I want to perform a non-periodic in Z direction, My first attempt is to 
> increase the unit cell (MULTIPLE_UNIT_CELL) by 2 or 3, but again as I 
> mention in the first question the output is unordered and when I use wrap 
> (VMD) it simply wrap it based on the value I seed for the pbc set. My 
> second attempt is to make only periodic in XY via POISSON and  CELL (see 
> input -2)  but I got an error stated that "* A non-periodic calculation 
> has been requested but the system size exceeds the cell size in at least 
> one of the non-periodic directions!*" any advice ?
> Thank you very much for your answer
> Kind regars

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