[CP2K-user] AIMD under PBC

[Marcella Iannuzzi]

Dear Mostafa

CP2K does not wrap the coordinates into the primary box, but works with the 
absolute coordinates.
The PBC are anyway internally applied by calculating energy and forces, 
hence the interaction field in which your molecules move is correct. 
To verify the actual situation within the simulation box just apply PBC 
when using the visualisation tool of your choice.

Regards
Marcella


On Wednesday, July 22, 2020 at 3:47:52 PM UTC+2 mos... at brown.edu wrote:

> Hi Everyone,
> I am trying to perform AIMD for a periodic system containing 8 CH4 
> molecules. Everything goes well, but after a few hundred steps, methane 
> molecules start to leave the box. This is really strange behavior because 
> the simulation is running under PBC and if one molecule leaves the box, one 
> of its images must enter through the opposite face with exactly the same 
> way and direction. But this is not happening in my simulations. So, it 
> seems PBC is not working. I believe something is wrong in my input file, 
> but I can not figure out what it is. I greatly appreciate it if someone 
> could help me to fix this issue. Many thanks.      
>
> &GLOBAL
>   PROJECT methane
>   RUN_TYPE MD   
>   WALLTIME 1000000
>   PRINT_LEVEL  MEDIUM
> &END GLOBAL
>
> &FORCE_EVAL
>   METHOD Quickstep
>   &DFT
>     BASIS_SET_FILE_NAME BASIS_MOLOPT
>     POTENTIAL_FILE_NAME GTH_POTENTIALS             
>     CHARGE 0
>     MULTIPLICITY 1
>     &MGRID
>        CUTOFF [Ry] 400 
>     &END
>     &QS
>        METHOD GPW 
>        EPS_DEFAULT 1.0E-10 
>        EXTRAPOLATION ASPC 
>     &END
>     &POISSON
>        PERIODIC XYZ 
>        POISSON_SOLVER PERIODIC
>     &END
>     &SCF
>       &PRINT
>         &RESTART OFF
>         &END
>       &END                 
>       SCF_GUESS ATOMIC 
>       MAX_SCF 30
>       EPS_SCF 1.0E-6 
>       &OT
>         PRECONDITIONER FULL_SINGLE_INVERSE
>         MINIMIZER CG
>       &END OT
>       &OUTER_SCF 
>         MAX_SCF 10
>         EPS_SCF 1.0E-6 
>       &END
>     &END SCF
>     &XC
>       &XC_FUNCTIONAL
>        &PBE
>        &END
>       &END XC_FUNCTIONAL
>       &VDW_POTENTIAL
>          POTENTIAL_TYPE PAIR_POTENTIAL 
>          &PAIR_POTENTIAL
>             PARAMETER_FILE_NAME dftd3.dat
>             TYPE DFTD3
>             REFERENCE_FUNCTIONAL PBE
>             R_CUTOFF [angstrom] 16
>          &END
>       &END VDW_POTENTIAL
>     &END XC
>   &END DFT
>    &SUBSYS
>     &CELL 
>       ABC [angstrom] 9.2 9.2 9.2
>       PERIODIC XYZ
>     &END CELL
>     &TOPOLOGY
>       COORD_FILE_NAME methane.xyz
>       COORD_FILE_FORMAT XYZ
>     &END
>     &KIND H
>       ELEMENT H
>       BASIS_SET SZV-MOLOPT-GTH
>       POTENTIAL GTH-PBE-q1
>     &END KIND
>     &KIND C
>       ELEMENT C
>       BASIS_SET SZV-MOLOPT-GTH
>       POTENTIAL GTH-PBE-q4
>     &END KIND
>   &END SUBSYS
>   &PRINT
>     &FORCES ON
>      FILENAME forces 
>     &END
>   &END
> &END FORCE_EVAL
>
> &MOTION
>  &GEO_OPT
>    OPTIMIZER BFGS 
>    MAX_ITER  1000
>    MAX_DR    [bohr] 0.003 
>    &BFGS
>    &END
>  &END
>   &MD
>    ENSEMBLE NVE
>    STEPS 10000
>    TIMESTEP 0.5
>    TEMPERATURE 500
>  &END MD
>  &PRINT
>    &CELL
>     FILENAME cell 
>    &END
>  &END
> &END MOTION
>
>
> Best,
> Mostafa
>
>
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