Input file

[Vladimir Rybkin]

Dear Sushi,

looks fine, although your &GEO_OPT section is redundant since you are going 
to perform MD. Nevertheless, it will be ignored.

Yours,

Vladimir

вторник, 14 ноября 2017 г., 10:26:07 UTC+1 пользователь Sushi написал:
>
> Dear all,
>
> I try to run an Umbrella Sampling Simulation for the Cl- + H3C-Cl -> 
> Cl-CH3 + Cl- reaction to introduce myself to CP2K and I wanted to ask 
> whether my setup is okey or not. I am also very interested in possible 
> pitfalls and so on and things which can be improved. 
>
> Any help would be very appreciated
> Thanks in advanced
> Sushi
>
>
> &GLOBAL
>   PROJECT MD       
>   RUN_TYPE MD           
>   PRINT_LEVEL LOW            
> &END GLOBAL
>  
> &FORCE_EVAL
>   METHOD QuickStep
>   &DFT                       # Use density functional theory
>     BASIS_SET_FILE_NAME BASIS_MOLOPT
>     CHARGE -1
>     POTENTIAL_FILE_NAME POTENTIAL
>     &POISSON                    
>      PERIODIC NONE
>      PSOLVER  WAVELET          ! Type of solver
>     &END POISSON
>     &SCF                              
>       SCF_GUESS ATOMIC ! can be used to RESTART an interrupted calculation
>       MAX_SCF 30
>       EPS_SCF 1.0E-5 ! accuracy of the SCF procedure typically 1.0E-6 - 
> 1.0E-7
>       &OT
>         ! an accurate preconditioner suitable also for larger systems
>         PRECONDITIONER FULL_SINGLE_INVERSE
>         ! the most robust choice (DIIS might sometimes be faster, but not 
> as stable).
>         MINIMIZER DIIS
>       &END OT
>       &OUTER_SCF ! repeat the inner SCF cycle 10 times
>         MAX_SCF 10
>         EPS_SCF 1.0E-5 ! must match the above
>       &END
>       ! do not store the wfn during MD
>       &PRINT
>         &RESTART OFF
>         &END
>       &END
>     &END SCF
>     &MGRID
>       CUTOFF 400             # plane-wave cutoff for the charge density 
> [Rydbergs]
>     &END MGRID  
>     &XC                      # parameters for exchange-correlation 
> functional
>       &XC_FUNCTIONAL PBE
>       &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                    # box containing the molecule: 15x15x15 
> Angstroms
>       ABC [angstrom] 30 30 30
>       PERIODIC NONE
>     &END CELL
>     &COORD                   # coordinates of the atoms in the box 
> [Angstroms]
>       Cl  5.047   0.000   0.000 
>       C   1.244   0.000   0.000 
>       Cl -0.559   0.000   0.000  
>       H   1.608   0.000   1.028     
>       H   1.608  -0.890  -0.514 
>       H   1.608   0.890  -0.514 
>     &END COORD
>     &TOPOLOGY
>      &CENTER_COORDINATES T
>      &END
>     &END
>     &KIND H                  # basis sets and pseudo-potentials for atomic 
> species
>       ELEMENT H
>       BASIS_SET DZVP-MOLOPT-GTH
>       POTENTIAL GTH-PBE-q1
>     &END KIND
>     &KIND C
>       ELEMENT C
>       BASIS_SET DZVP-MOLOPT-GTH
>       POTENTIAL GTH-PBE-q4
>     &END KIND
>     &KIND Cl
>       ELEMENT Cl
>       BASIS_SET DZVP-MOLOPT-GTH
>       POTENTIAL GTH-PBE-q7
>     &END KIND
>
>     &COLVAR
>      &DISTANCE
>       ATOMS 1 2
>       AXIS X
>      &END
>      &PRINT
>       &PROGRAM_RUN_INFO ON
>        &EACH
>         MD 1
>        &END
>       &END PROGRAM_RUN_INFO
>      &END PRINT
>     &END
>   &END SUBSYS
> &END FORCE_EVAL
>
> &MOTION
>     &GEO_OPT
>         OPTIMIZER BFGS
>         MAX_ITER 100
>         MAX_DR [bohr] 0.003
>         &BFGS
>         &END
>     &END
>     &CONSTRAINT
>      &COLLECTIVE
>       COLVAR 1
>       MOLECULE 1
>       INTERMOLECULAR .TRUE.
>       TARGET [angstrom] 3.047
>       TARGET_GROWTH [angstrom] 0.1
>      &END
>     &END
> &MD
>     ENSEMBLE NVT
>     TEMPERATURE [K] 300
>     TIMESTEP [fs] 0.5
>     STEPS 4000
>     &THERMOSTAT
>      TYPE CSVR
>      &CSVR
>       TIMECON [fs] 20.
>      &END
>     &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
>     &END RESTART_HISTORY
>         &RESTART
>             BACKUP_COPIES 3
>             &EACH
>                 MD 1
>             &END
>         &END RESTART
>     &END PRINT
> &END
>
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