[CP2K-user] [CP2K:13671] Re: AIMD under PBC

Abedi, Mostafa mostaf... at brown.edu
Tue Jul 28 17:07:48 UTC 2020
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Dear Matthias,
Many thanks for your great suggestion. That is exactly what I need.

Best,
Mostafa

On Mon, Jul 27, 2020 at 10:39 AM Krack Matthias (PSI) <matthi... at psi.ch>
wrote:

> Hi Mostafa
>
>
>
> You can also try the (stand-alone) program xyz2dcd (
> https://github.com/cp2k/cp2k/blob/master/src/motion/xyz2dcd.F) from the
> current cp2k trunk which dumps the frames from a CP2K xyz trajectory file
> in dcd format optionally with wrapped coordinates (flags –pbc and –pbc0)
> using either fixed cell parameters (flags –abc and –cell) or the actual
> cell information for each frame from the corresponding CP2K cell file of
> the same NpT run, e.g. by running
>
>
>
> xyz2dcd –pbc –cell_file project-1.cell project-pos-1.xyz
> >project-pos-1_wrapped.dcd
>
>
>
> The generated binary file project-pos-1.dcd in DCD format with wrapped
> coordinates and the corresponding cell information for each frame can be
> loaded into VMD or converted again back to xyz (XMOL) format using
>
>
>
> dumpdcd -xyz project-pos-1.xyz –of XMOL –o project-pos-1_wrapped.xyz
> project-pos-1_wrapped.dcd
>
>
>
> xyz2dcd and dumpdcd are compiled automatically with the current CP2K trunk
> version and can be found then in folder cp2k/exe/<arch>/, but they can also
> be compiled independently, e.g. using
>
>
>
> gfortran –ffree-form –o xyz2dcd xyz2dcd.F
>
>
>
> The flag –h provides further usage info.
>
>
>
> HTH
>
>
>
> Matthias
>
>
>
> *From:* cp... at googlegroups.com <cp... at googlegroups.com> *On Behalf Of *Abedi,
> Mostafa
> *Sent:* Mittwoch, 22. Juli 2020 17:29
> *To:* cp... at googlegroups.com
> *Subject:* Re: [CP2K:13657] Re: AIMD under PBC
>
>
>
> 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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