[CP2K-user] [CP2K:13657] Re: AIMD under PBC

[Abedi, Mostafa]

Dear Marcella,

Many thanks for your help. Now, I understand it. I've found a way to wrap
the coordinate into the box using VMD:
pbc set {xxx xxx xxx} -all  # the "xxx" is the length of the box
pbc box
pbc wrap -all

This works well for the NVE and NVT simulations that the length of the box
is fixed, but it is not a case for the NpT simulation box, where the volume
changes. Do you have any idea how that would be for the NpT one? I greatly
appreciate your help.

Thanks,
Mostafa

On Wed, Jul 22, 2020 at 10:25 AM Marcella Iannuzzi <marci... at gmail.com>
wrote:

> 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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