SCF, MD run-time verses atomic species.

Simiam Ghan simia... at gmail.com
Fri Jul 1 11:38:47 UTC 2016


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 angstrom
H -0.567712 -0.469646 -0.645913
H 0.626116 -0.687796 0.308193
O 0 0 0
(...)
K 2.1035 2.1035 4.2735
Cl 4.1035 4.1035 2.6035                 ###
H 3.73881 3.10388 5.46104
H 3.65742 2.89924 6.989
O 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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