[CP2K-user] [CP2K:13074] NPT simulation of 64 water molecules

Thomas Kühne tku... at gmail.com
Tue Apr 7 16:23:27 UTC 2020


Dear Anna, 

looks mostly fine to me. However, is SCALE_C 0.0 intentionally and correct? 
If so, can you please provide a similar density plot than in the paper or at least 
quantify the drop in particle density?

Cheers, 
Thomas

> Am 07.04.2020 um 12:56 schrieb ANNA VARGHESE <annav... at gmail.com>:
> 
> 
> Dear All,
> I am trying to run NPT simulation of 64 water molecules following https://aip.scitation.org/doi/am-pdf/10.1063/1.4986284 <https://aip.scitation.org/doi/am-pdf/10.1063/1.4986284> .  I observe a drop in density at the end of density. Can anyone look at this input file and tell me where am I going wrong? 
> 
> Thanks in advance,
> 
> 
> &GLOBAL
>   ! the project name is made part of most output files... useful to keep order
>   PROJECT WATER
>   ! various runtypes (energy, geo_opt, etc.) available.
>   RUN_TYPE MD
>   ! reduce the amount of IO
>   IOLEVEL  LOW
> &END GLOBAL
> 
> &FORCE_EVAL
>   ! the electronic structure part of CP2K is named Quickstep
>   METHOD Quickstep
> STRESS_TENSOR ANALYTICAL
>   &DFT
>     ! basis sets and pseudopotential files can be found in cp2k/data
>     BASIS_SET_FILE_NAME GTH_BASIS_SETS
>     POTENTIAL_FILE_NAME GTH_POTENTIALS            
> 
> 
>     ! Charge and multiplicity
>     CHARGE 0
>     MULTIPLICITY 1
> 
>     &MGRID
>        ! PW cutoff ... depends on the element (basis) too small cutoffs lead to the eggbox effect.
>        ! certain calculations (e.g. geometry optimization, vibrational frequencies,
>        ! NPT and cell optimizations, need higher cutoffs)
>        CUTOFF [Ry] 800 
>     &END
> 
>     &QS
>        ! use the GPW method (i.e. pseudopotential based calculations with the Gaussian and Plane Waves scheme).
>        METHOD GPW 
>        ! default threshold for numerics ~ roughly numerical accuracy of the total energy per electron,
>        ! sets reasonable values for all other thresholds.
>        EPS_DEFAULT 1.0E-10 
>        ! used for MD, the method used to generate the initial guess.
>        EXTRAPOLATION ASPC 
>     &END
> 
>     &POISSON
>        PERIODIC XYZ ! the default, gas phase systems should have 'NONE' and a wavelet solver
>     &END
> 
>     &PRINT
>        ! at the end of the SCF procedure generate cube files of the density
>        &E_DENSITY_CUBE OFF
>        &END E_DENSITY_CUBE
>        ! compute eigenvalues and homo-lumo gap each 10nd MD step
>        &MO_CUBES
>           NLUMO 4
>           NHOMO 4
>           WRITE_CUBE .FALSE.
>           &EACH
>             MD 10
>           &END
>        &END
>     &END
> 
> 
>  ! use the OT METHOD for robust and efficient SCF, suitable for all non-metallic systems.
>     &SCF                              
>       SCF_GUESS ATOMIC ! can be used to RESTART an interrupted calculation
>       MAX_SCF 30
>       EPS_SCF 1.0E-6 ! 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-6 ! must match the above
>       &END
>       ! do not store the wfn during MD
>       &PRINT
>         &RESTART OFF
>         &END
>       &END
>     &END SCF
> 
>     ! specify the exchange and correlation treatment
>     &XC
>       ! use a PBE functional 
>       &XC_FUNCTIONAL 
>          &PBE
>           PARAMETRIZATION revPBE
>           SCALE_C 0.0
>          &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
>  
>   ! description of the system
>   &SUBSYS
>     &CELL 
>       ! unit cells that are orthorhombic are more efficient with CP2K
>       ABC [angstrom] 14.77 14.77 14.77
>     &END CELL
> 
>     ! atom coordinates can be in the &COORD section,
>     ! or provided as an external file.
>     &TOPOLOGY
>       COORD_FILE_NAME water.xyz
>       COORD_FILE_FORMAT XYZ
>     &END
> 
>     &KIND H
>       BASIS_SET TZV2P-GTH
>       POTENTIAL GTH-PBE-q1
>     &END KIND
>     &KIND O
>       BASIS_SET TZV2P-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
>  &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 NPT_I  ! sampling the canonical ensemble, accurate properties might need NVE
>    TEMPERATURE [K] 300
>    TIMESTEP [fs] 0.5
>    STEPS 10000
>   &BAROSTAT
>     PRESSURE 1.03                 # PRESSURE, unit[bar]
>     TIMECON 300
>   &END BAROSTAT
> 
> &THERMOSTAT
>     REGION MASSIVE
>     &NOSE                    #Uses the Nose-Hoover thermostat
>       TIMECON 11.12           #timeconstant of the thermostat chain, how often does thermostat adjust your system
>     &END NOSE
>   &END
> 
>  &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
> 
> 
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> <water.inp>



==============================
Thomas D. Kühne
Dynamics of Condensed Matter
Chair of Theoretical Chemistry
University of Paderborn
Warburger Str. 100
D-33098 Paderborn
Germany
tdku... at mail.upb.de
+49/(0)5251/60-5726

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