[CP2K-user] [CP2K:13657] Re: AIMD under PBC
Marcella Iannuzzi
marci... at gmail.com
Wed Jul 22 16:12:36 UTC 2020
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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>
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