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

[Marcella Iannuzzi]

Dear Mostafa, 

The pbc tool of VMD allow to provide the information about the box per each 
frame.
As alternative, one can write a script to post process the cp2k output and 
apply the pbc as desired.

Regards
Marcella

On Wednesday, July 22, 2020 at 5:29:20 PM UTC+2 mos... at brown.edu wrote:

> 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 <ma... 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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