[CP2K-user] first principle MD in zeolite

[Vladimir Rybkin]

Dear Wu,

it would help if you sent you output, clarified the code version and the 
environment you used for you job. I does not look like a bug.

Yours,

Vladimir

среда, 17 июля 2019 г., 15:34:08 UTC+2 пользователь Peiyao Wu написал:
>
> I'm trying to run a first principle MD for a box with nitrogen and zeolite 
> (structure with xyz coordinate). The job started running with no error 
> message and terminate in about five minutes with "OT -----killed-----". 
> What are some things that might be wrong in my input file? 
>
>
> &GLOBAL
>
>   PROJECT MOF
>
>   RUN_TYPE MD
>
>   ! limit the runs to 5min
>
>   WALLTIME
>
>   ! reduce the amount of IO
>
>   IOLEVEL  LOW
>
> &END GLOBAL
>
>
> &FORCE_EVAL
>
>  METHOD QS
>
>  !STRESS_TENSOR DIAGONAL_NUMERICAL
>
>  &DFT
>
>   BASIS_SET_FILE_NAME ~/cp2k/data/BASIS_MOLOPT
>
>   POTENTIAL_FILE_NAME ~/cp2k/data/GTH_POTENTIALS
>
>   &MGRID
>
>    CUTOFF 300
>
>    NGRIDS 5
>
>   &END
>
>   &QS
>
>    METHOD GPW
>
>    EPS_DEFAULT 1.0E-10
>
>    EXTRAPOLATION ASPC
>
>   &END QS
>
>   &POISSON
>
>    PERIODIC XYZ
>
>   &END
>
>
>   &SCF
>
>    EPS_SCF 1.0E-6
>
>    SCF_GUESS ATOMIC
>
>    MAX_SCF 20
>
>    &OT
>
>     MINIMIZER DIIS
>
>     PRECONDITIONER FULL_KINETIC
>
>    &END OT
>
>    &OUTER_SCF
>
>     EPS_SCF 1.0E-6
>
>     MAX_SCF 10
>
>    &END OUTER_SCF
>
>   &END SCF
>
>   &XC
>
>    &XC_FUNCTIONAL PBE
>
>    &END
>
>    &VDW_POTENTIAL
>
>     POTENTIAL_TYPE PAIR_POTENTIAL
>
>     &PAIR_POTENTIAL
>
>      TYPE DFTD3
>
>      REFERENCE_C9_TERM .TRUE.
>
>      LONG_RANGE_CORRECTION .TRUE.
>
>      PARAMETER_FILE_NAME dftd3.dat
>
>      REFERENCE_FUNCTIONAL PBE
>
>      R_CUTOFF [angstrom] 10.0
>
>      EPS_CN 1.0E-6
>
>     &END PAIR_POTENTIAL
>
>    &END VDW_POTENTIAL
>
>   &END XC
>
>  &END DFT
>
>  &SUBSYS
>
>   &CELL
>
>    ABC 24.188 24.188 24.188
>
>    ALPHA_BETA_GAMMA 90.0 90.0 90.0
>
>   &END CELL
>
>   &COORD
>
>    @INCLUDE box1config.xyz
>
>   &END COORD
>
>   &KIND Si
>
>    BASIS_SET DZVP-MOLOPT-SR-GTH
>
>    POTENTIAL GTH-PBE-q4
>
>   &END KIND
>
>   &KIND Al
>
>    BASIS_SET DZVP-MOLOPT-SR-GTH
>
>    POTENTIAL GTH-PBE-q3
>
>   &END KIND
>
>   &KIND O
>
>    BASIS_SET DZVP-MOLOPT-SR-GTH
>
>    POTENTIAL GTH-PBE-q6
>
>    ELEMENT O
>
>   &END KIND
>
>   &KIND Ca
>
>    BASIS_SET DZVP-MOLOPT-SR-GTH
>
>    POTENTIAL GTH-PBE-q10
>
>   &END KIND
>
>   &KIND N
>
>    BASIS_SET DZVP-MOLOPT-SR-GTH
>
>    POTENTIAL GTH-PBE-q5
>
>   &END KIND
>
>  &END SUBSYS
>
> &END FORCE_EVAL
>
>
> &MOTION
>
>  &GEO_OPT
>
>    OPTIMIZER LBFGS ! Good choice for 'small' systems (use LBFGS for large 
> systems)
>
>    MAX_ITER  100
>
>    MAX_DR    [bohr] 0.003 ! adjust target as needed
>
>    &LBFGS
>
>    &END
>
>  &END
>
>  &MD
>
>    ENSEMBLE NVT  ! sampling the canonical ensemble, accurate properties 
> might need NVE
>
>    TEMPERATURE [K] 77.0
>
>    TIMESTEP [fs] 0.5
>
>    STEPS 100
>
>    # GLE thermostat as generated at http://epfl-cosmo.github.io/gle4md
>
>    # GLE provides an effective NVT sampling.
>
>    &THERMOSTAT
>
>      TYPE NOSE
>
>      REGION MASSIVE
>
>      &NOSE
>
>        LENGTH 3
>
>        YOSHIDA 3
>
>        TIMECON [wavenumber_t] 1000.0
>
>        MTS 2
>
>      &END NOSE
>
>     &END THERMOSTAT
>
>  &END
>
>   &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
>
> &END MOTION
>
>
>
>
>
>
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