[CP2K-user] [CP2K:12421] Re: unwrapped ions during CELL_OPT

Pierre Cazade pierre.a... at gmail.com
Fri Oct 25 14:50:23 UTC 2019


Thank you for your suggestion. I will try to run again the cell_opt as 
you suggest. The question remains, why VASP leads to a different 
structure, expended yes but not to that extend. Both a and c reach about 
9.2 and b reaches 43.


On 25/10/2019 15:44, Travis wrote:
> Hi,
> Your input structure is very compressed. It should expand and your 
> final structure looks much more reasonable. The amount it is expanding 
> by, I would actually suggest redoing the CELL_OPT from the final 
> structure as your effective cutoff decreases when the cell volume 
> increases. Coordinates are unwrapped intentionally in all 
> calculations. You can impose PBC to wrap the coordinates using an 
> external program. I recommend Atomic Simulation Environment,
> Grab last image from foo-pos-1.xyz:
> https://github.com/pollardtp/asepylot/blob/master/general/pos2xyz.py
> Add cell parameters from command line args:
> https://github.com/pollardtp/asepylot/blob/master/general/xyz2vasp.py
> Generated structure is in POSCAR format, viewable with VESTA. Adapt to 
> your suiting.
> Delete this bit, it's specific to my setup.
> |
> fromrequireimportcheck_ase
> check_ase()
> |
> -T
> On Friday, October 25, 2019 at 5:46:21 AM UTC-3, Pierre-André Cazade 
> wrote:
>     Dear CP2K users,
>     I am running a CELL_OPT on a 280 atoms unit cell. It was poorly
>     resolved experimentally, yet I am surprised that some atoms wander
>     out of the unit cell and are not wrapped back in. It is quite
>     unexpected. According to the following topic:
>     https://groups.google.com/forum/#!topic/cp2k/rqOO2W04OPc
>     <https://groups.google.com/forum/#!topic/cp2k/rqOO2W04OPc> , CP2K
>     does not wrap atoms, at least in MD mode. This is very strange. Is
>     it intentional? Is it a bug? And does it affect in any kind of way
>     calculations?
>     I am bothered by the optimized structure which shows a
>     considerable increase of the "a" parameter. Again, I compared with
>     VASP and the final structure with the latter is much more
>     reasonable. I do not expect identical optimized structure but they
>     should not drift so much away from each other. Could this lack of
>     wrapping explain the divergence or it comes from inadequate SCF
>     parameters?
>     I attached the input file and the final restart file.
>     Regards,
>     Pierre
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Dr Pierre Cazade, PhD
AD3-023, Bernal Institute,
University of Limerick,
Plassey Park Road,
Castletroy, co. Limerick,

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