[CP2K-user] [CP2K:17038] Simulating liquid DMSO

DMITRII Drugov dresearcher1991 at gmail.com
Thu May 26 00:09:58 UTC 2022
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Hi,

Please have a look at the setting for ab initio MD.
https://brehm-research.de/files/spec_tutorial_2018.pdf

If you want to increase the time step to 1 fs you can use deuterium mass
for hydrogen atoms.

Best,
Dmitrii


On Thu, May 26, 2022 at 5:16 AM Thomas Kühne <tkuehne at gmail.com> wrote:

> Dear Henrique Junior,
>
> if these are subsequent step separated by 0.5fs than this looks all very
> reasonable to me.
> The atoms don’t move a hell a lot within half a femtosecond.
>
> Best,
> Thomas Kühne
>
> Am 27.04.2022 um 21:22 schrieb Henrique Junior <henriquecsj at gmail.com>:
>
> Hi everyone, I hope you are all doing fine.
>
> CP2K is completely new for me, and it is proving to be a challenge. I am
> attempting to simulate liquid DMSO (a simple molecule with 10 atoms) just
> as a test. So far, I have tried to build my input based on tutorials
> simulating liquid water and tweaking it for DMSO.
>
> The calculation is running fine and converging quite smoothly but looking
> at the DMSO-pos-1.xyz file that’s being generated I can see that the
> atoms are barely shaking. I’m attaching (and showing below) my input and
> the xyz file. Any help would be much appreciated.
>
> Thanks in advance.
>
> Vvvvvvvvvvvvvvvvvvvvvvvvvv INPUT vvvvvvvvvvvvvvvvvvvvvvvvvv
>
> &GLOBAL
>   PROJECT DMSO
>   RUN_TYPE MD
> &END GLOBAL
>
> &FORCE_EVAL
>   METHOD Quickstep
>   &DFT
>     BASIS_SET_FILE_NAME GTH_BASIS_SETS
>     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 ! the default, gas phase systems should have 'NONE'
> and a wavelet solver
>     &END
>
>     &PRINT
>        &E_DENSITY_CUBE OFF
>        &END E_DENSITY_CUBE
>        &MO_CUBES
>           NLUMO 4
>           NHOMO 4
>           WRITE_CUBE .FALSE.
>           &EACH
>             MD 10
>           &END
>        &END
>     &END
>
>     &SCF
>       SCF_GUESS ATOMIC
>       MAX_SCF 500
>       EPS_SCF 1.0E-6
>       &OT
>         PRECONDITIONER FULL_SINGLE_INVERSE
>         MINIMIZER DIIS
>       &END OT
>       &OUTER_SCF ! repeat the inner SCF cycle 10 times
>         MAX_SCF 10
>         EPS_SCF 1.0E-6
>       &END
>       &PRINT
>         &RESTART OFF
>       &END
>       &END
>     &END SCF
>
>     &XC
>       &XC_FUNCTIONAL
>          &PBE
>          &END
>       &END XC_FUNCTIONAL
>       ! adding Grimme's D3 correction (by default without C9 terms)
>       &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] 9.0 9.0 9.0
>     &END CELL
>
>     &TOPOLOGY
>       COORD_FILE_NAME DMSOcaixa.xyz
>       COORD_FILE_FORMAT XYZ
>     &END
>
>     &KIND H
>       BASIS_SET DZVP-MOLOPT-SR-GTH
>       POTENTIAL GTH-PBE-q1
>     &END KIND
>     &KIND C
>       BASIS_SET DZVP-MOLOPT-SR-GTH
>       POTENTIAL GTH-PBE-q4
>     &END KIND
>     &KIND O
>       BASIS_SET DZVP-MOLOPT-SR-GTH
>       POTENTIAL GTH-PBE-q6
>     &END KIND
>     &KIND S
>       BASIS_SET DZVP-MOLOPT-SR-GTH
>       POTENTIAL GTH-PBE-q6
>     &END KIND
>   &END SUBSYS
> &END FORCE_EVAL
>
> ! how to propagate the system, selection via RUN_TYPE in the &GLOBAL
> section
> &MOTION
>   &PRINT
>     &TRAJECTORY
>       &EACH
>         MD 1
>       &END EACH
>     &END TRAJECTORY
>     &VELOCITIES OFF
>     &END VELOCITIES
>     &FORCES OFF
>     &END FORCES
>     &RESTART_HISTORY
>       &EACH
>         MD 500
>       &END EACH
>     &END RESTART_HISTORY
>     &RESTART
>       BACKUP_COPIES 3
>       &EACH
>         MD 1
>       &END EACH
>     &END RESTART
>   &END PRINT
>  &GEO_OPT
>    OPTIMIZER BFGS ! Good choice for 'small' systems (use LBFGS for large
> systems)
>    MAX_ITER  100
>    MAX_DR    [bohr] 0.003 ! adjust target as needed
>    &BFGS
>    &END
>  &END
>  &MD
>    ENSEMBLE NVT  ! sampling the canonical ensemble, accurate properties
> might need NVE
>    TEMPERATURE [K] 300
>    TIMESTEP [fs] 0.5
>    STEPS 1000
>    # GLE thermostat as generated at http://epfl-cosmo.github.io/gle4md
>    # GLE provides an effective NVT sampling.
>    &THERMOSTAT
>      REGION MASSIVE
>      TYPE GLE
>      &GLE
>        NDIM 5
>        A_SCALE [ps^-1] 1.00
>        A_LIST    1.859575861256e+2   2.726385349840e-1   1.152610045461e+1
>  -3.641457826260e+1   2.317337581602e+2
>        A_LIST   -2.780952471206e-1   8.595159180871e-5   7.218904801765e-1
>  -1.984453934386e-1   4.240925758342e-1
>        A_LIST   -1.482580813121e+1  -7.218904801765e-1   1.359090212128e+0
>   5.149889628035e+0  -9.994926845099e+0
>        A_LIST   -1.037218912688e+1   1.984453934386e-1  -5.149889628035e+0
>   2.666191089117e+1   1.150771549531e+1
>        A_LIST    2.180134636042e+2  -4.240925758342e-1   9.994926845099e+0
>  -1.150771549531e+1   3.095839456559e+2
>      &END GLE
>    &END THERMOSTAT
>  &END
> &END
>
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> .
> <DMSO.inp><DMSO-pos-1.xyz>
>
>
>
>
> ==============================
> Thomas D. Kühne
> Dynamics of Condensed Matter
> Chair of Theoretical Chemistry
> University of Paderborn
> Warburger Str. 100
> D-33098 Paderborn
> Germany
> thomas.kuehne at upb.de
> +49/(0)5251/60-5726
>
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> .
>

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