[CP2K:7883] SCF, MD run-time verses atomic species.

Simiam Ghan simia... at gmail.com
Thu Aug 18 01:08:12 CEST 2016


Hello Juerg,
Thank you for your reply.  I added REFERENCE_C9_TERM .TRUE.  to the vdw 
section as you suggested and found that my MD simulation became twice (!) 
as fast.   That is, time per MD step went from ~60 sec to ~30 sec for box 
of water with 64 molecules and K,Cl ions.  I made a quick comparison of 
Energy_Force results with and without this flag and indeed forces and 
energies do not change significantly.   This is great news.  Why is this 
not a default?  What's the catch?   Also, would you say this is now a 
correct way to declare a PBE-D3 setup?


&VDW_POTENTIAL
         POTENTIAL_TYPE  PAIR_POTENTIAL
         &PAIR_POTENTIAL
           R_CUTOFF     1.5000000000000005E+01
           TYPE  DFTD3
           PARAMETER_FILE_NAME dftd3.dat
           REFERENCE_FUNCTIONAL PBE
           CALCULATE_C9_TERM  T
           REFERENCE_C9_TERM  T
         &END PAIR_POTENTIAL
       &END VDW_POTENTIAL

Finally, I mentioned earlier that 30 scf steps were needed to converge the 
same box of water with ions.   I was then using EPS_SCF = 1E-06.   Reducing 
this to EPS_SCF = 1E-05 brought the number down to 10-20 scf necessary. 
 Does that still sound high?   Is the definition of EPS_SCF documented 
somewhere, as it is apparently not just Energy convergence. 

Cheers,
Simiam Ghan




On Friday, July 1, 2016 at 3:10:52 PM UTC+3, jgh wrote:
>
> Hi 
>
> no this shouldn't be, but without more information I will have to guess. 
> You could also have a look at the timings at the end of the output to 
> see if some routines got slower or if all parts of the run were affected. 
>
> Two things to consider: 
>
> 1) Use REFERENCE_C9_TERM TRUE in order to reduce the time for vdW in MD. 
> 2) 30 SCF iterations in MD for such a simple system is pointing to a 
> problem 
>    with your setup. 
>
> regards 
>
> Juerg 
> -------------------------------------------------------------- 
> Juerg Hutter                         Phone : ++41 44 635 4491 
> Institut für Chemie C                FAX   : ++41 44 635 6838 
> Universität Zürich                   E-mail: hut... at chem.uzh.ch 
> <javascript:> 
> Winterthurerstrasse 190 
> CH-8057 Zürich, Switzerland 
> --------------------------------------------------------------- 
>
> -----cp... at googlegroups.com <javascript:> wrote: -----To: cp2k <
> cp... at googlegroups.com <javascript:>> 
> From: Simiam Ghan 
> Sent by: cp... at googlegroups.com <javascript:> 
> Date: 07/01/2016 01:38PM 
> Subject: [CP2K:7883] SCF, MD run-time verses atomic species. 
>
> Dear all,I am running NVT MD with Quickstep on a box of water with 64 
> molecules.   If I replace a water molecule with a KCl ion pair, i observe 
> that the MD and SCF step times more than double on my setup.  (MD from ~20 
> sec to ~46 sec). SCF iterations are converging (except the very first MD 
> step) in around 30 steps in both cases but each SCF now takes over twice as 
> long as before.   Is there an explanation of why such a 'small' change in 
> system could double the run time?  Is KCl really so heavy to calculate 
> compared to H2O?  The number of electrons in the system increases by 8, 
> from 512 to 520.  Below my KCl input file.  
> Greetings,Simiam 
>
>
> &GLOBAL 
>   PROJECT H2O_KCl  RUN_TYPE MD  PRINT_LEVEL MEDIUM 
> &END GLOBAL 
> &FORCE_EVAL 
>   METHOD Quickstep                                ! GPW method. 
>   &SUBSYS                                       ! A subsystem: 
> coordinates, topology, molecules and cell. 
>     &CELL                                       ! Supercell setup.      
> ABC [angstrom] 12.414 12.414 12.414        ! Using 64 H2O molecules, we 
> thus get a density of 1g/cm^3.      PERIODIC XYZ                           
>        ! Use PBC in all dimensions.    &END CELL 
>     &COORD    UNIT angstromH -0.567712 -0.469646 -0.645913H 0.626116 
> -0.687796 0.308193O 0 0 0(...)K 2.1035 2.1035 4.2735Cl 4.1035 4.1035 2.6035 
>                 ###H 3.73881 3.10388 5.46104 
> H 3.65742 2.89924 6.989O 3.1035 3.1035 6.207(...)    &END COORD 
>     &KIND O      BASIS_SET DZVP-MOLOPT-GTH-q6      POTENTIAL GTH-PBE-q6    
> &END KIND    &KIND H      BASIS_SET DZVP-MOLOPT-GTH-q1      POTENTIAL 
> GTH-PBE-q1    &END KIND     &KIND K      BASIS_SET DZVP-MOLOPT-SR-GTH-q9    
>   POTENTIAL GTH-PBE-q9    &END KIND    &KIND Cl      BASIS_SET 
> DZVP-MOLOPT-GTH-q7      POTENTIAL GTH-PBE-q7    &END KIND 
>
>
>
>
>   &END SUBSYS 
>  &DFT 
>     BASIS_SET_FILE_NAME  BASIS_MOLOPT    POTENTIAL_FILE_NAME 
>  GTH_POTENTIALS    !    SPIN_POLARIZED                ! Do spin-polarized 
> calculation 
>     &POISSON       PERIODIC XYZ    &END POISSON 
>     &QS      METHOD GPW      EPS_DEFAULT 1.0E-10   ! Set various epsilons 
> for QS to values that will lead                                    ! to 
> energy correct up to 1e-10.    &END QS 
>     &MGRID      CUTOFF 400    ! This is Ecut of eq. 39 in VandeVondele 
> (2005), i.e., plane-wave cutoff                               ! that 
> determines size of finest grid (see caption of Fig. 1). Cutoffs for         
>            ! the subsequent, coarser grid levels are given by eq. 39.      
> NGRIDS 4      ! This is N of eq. 39 in VandeVondele (2005), i.e., number of 
> grids used.      REL_CUTOFF 40 ! This controls the grid level onto which 
> Gaussians will be mapped.    &END MGRID 
>     &XC 
>       &XC_FUNCTIONAL        &PBE                           PARAMETRIZATION 
> ORIG        &END PBE      &END XC_FUNCTIONAL 
>       &VDW_POTENTIAL 
>          POTENTIAL_TYPE PAIR_POTENTIAL 
>          &PAIR_POTENTIAL            TYPE DFTD3            
> REFERENCE_FUNCTIONAL PBE            CALCULATE_C9_TERM .TRUE.            
> PARAMETER_FILE_NAME dftd3.dat            R_CUTOFF 15.0         &END 
> PAIR_POTENTIAL 
>       &END VDW_POTENTIAL 
>     &END XC 
>     &SCF 
>       SCF_GUESS RESTART                ! Use data from previous run as 
> initial guess for wavefunction.      EPS_SCF 1.0E-6                ! 
> Threshold for converged total energy.      MAX_SCF 300                ! 
> Maximum number of SCF iterations performed. 
>       &OT        PRECONDITIONER NONE        ! This should be stable with 
> respect to the "Cholesky errors"      &END OT 
>        &PRINT         &RESTART ON 
>                 BACKUP_COPIES 1 
>                        &EACH                        MD 1                  
>      &END EACH 
>                 ADD_LAST NUMERIC 
>          &END RESTART 
>        &END PRINT 
>     &END SCF 
>     &PRINT      &E_DENSITY_CUBE 
>         STRIDE 1 1 1 
>         &EACH                    MD 99999999        &END EACH 
>         ADD_LAST NUMERIC     &END E_DENSITY_CUBE 
>       &PDOS            COMPONENTS .FALSE.            NLUMO = -1            
> FILENAME dosfile            LOG_PRINT_KEY TRUE 
>             &EACH                MD 99999999            &END EACH 
>             ADD_LAST NUMERIC      &END PDOS 
>     &END PRINT 
>  &END DFT 
> &END FORCE_EVAL 
> &MOTION 
>         &MD                ENSEMBLE        NVT                STEPS       
>          10000                TEMPERATURE        300.0        ! K           
>      TIMESTEP        0.5        ! fs                               
>  &THERMOSTAT 
>                         REGION GLOBAL                        TYPE NOSE 
>                         &NOSE                                LENGTH 3     
>    ! Length of Nose-Hoover chain                                TIMECON 
> 20.0        ! Period of typical vibrational motion in system in fs         
>                &END NOSE                                                   
>              &END THERMOSTAT                        &END MD 
>         &PRINT 
>                 &RESTART 
>                         &EACH                              MD 1           
>              &END EACH 
>                         ADD_LAST NUMERIC 
>                 &END RESTART 
>                 &TRAJECTORY ON                           ADD_LAST NUMERIC  
>                          FILENAME trajectory                &END TRAJECTORY 
>         &END PRINT 
> &END MOTION 
>
>
>
>
>
> -- 
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