Periodic and non-periodic box

[captain mus]

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
MUS

[Matt Watkins]

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

&TOPOLOGY

      CENTER_COORDINATES

to center the atoms in the cell. If the molecules are connected together then that should work once the cell is large enough.

Matt

[captain mus]

Hi Matt

Thank you for your response, I will try it. btw I actually follow the instruction from your youtube channel. thank you for making a great video.

Best Regards
MuS