[CP2K:8075] SCF, MD run-time verses atomic species.

Simiam Ghan simia... at gmail.com
Thu Aug 18 19:30:55 CEST 2016


Hi,
Thank you for the tips!  I am not using EXTRAPOLATION or PRECONDITIONER 
currently.   If I include them now will they affect the accuracy 
significantly?  I am in the middle of long MD trajectories of TiO2 crystal 
with water and KCl ions.  Also running the water box with ions.   My 
current setup is below (same for both systems).    The TiO2 system uses 
1-80 scf steps for each MD step. Would you recommend these changes for that 
system also?  Best regards.    


 &GLOBAL
   PRINT_LEVEL  MEDIUM
   PROJECT_NAME brookite
   RUN_TYPE  MD
 &END GLOBAL
 &MOTION
   &MD
     ENSEMBLE  NVT
     STEPS  250
     TIMESTEP     4.9999999999999989E-01
     STEP_START_VAL  3751
     TIME_START_VAL     4.3234999999995443E+03
     ECONS_START_VAL    -1.5206763646667368E+04
     TEMPERATURE     3.0000000000000000E+02
     &THERMOSTAT
       TYPE  NOSE
       REGION  GLOBAL
       &NOSE
         LENGTH  3
         TIMECON     1.9999999999999993E+01
         &COORD
               4.2157834584794962E-01   -3.8977051434234506E+00   
 3.0959934319656378E+02
         &END COORD
         &VELOCITY
               5.7927878733942134E-05    7.8527005854180164E-04   
 5.0048257140974906E-04
         &END VELOCITY
         &MASS
               1.4749962622867215E+06    6.4949196930282767E+02   
 6.4949196930282767E+02
         &END MASS
         &FORCE
               4.2152207720701857E-08    6.1579061284564603E-06   
-8.4610128141038230E-07
         &END FORCE
       &END NOSE
     &END THERMOSTAT
     &AVERAGES  T
       &RESTART_AVERAGES
         ITIMES_START  1
         AVECPU     9.1875550803485453E+01
         AVEHUGONIOT     0.0000000000000000E+00
         AVETEMP_BARO     0.0000000000000000E+00
         AVEPOT    -1.5208725197223592E+04
         AVEKIN     1.0826866556597368E+00
         AVETEMP     3.0108762437707566E+02
         AVEKIN_QM     0.0000000000000000E+00
         AVETEMP_QM     0.0000000000000000E+00
         AVEVOL     5.5116376409126919E+04
         AVECELL_A     2.7174261790895553E+01
         AVECELL_B     6.9659084710430690E+01
         AVECELL_C     2.9116900255502028E+01
         AVEALPHA     9.0000000000000071E+01
         AVEBETA     9.0000000000000071E+01
         AVEGAMMA     9.0000000000000071E+01
         AVE_ECONS     1.6039009887889247E+02
         AVE_PRESS     0.0000000000000000E+00
         AVE_PXX     0.0000000000000000E+00
       &END RESTART_AVERAGES
     &END AVERAGES
   &END MD
   &CONSTRAINT
     &FIXED_ATOMS
       COMPONENTS_TO_FIX  XYZ
       LIST  148 172 196 150 174 198 64 88 112 \
        259 270 281 221 234 247 149 173 197 289 \
        313 337 260 271 282 225 238 251 155 179 \
        203 163 187 211 164 188 212 290 314 338 \
        71 95 119 266 277 288 265 276 287
     &END FIXED_ATOMS
   &END CONSTRAINT
   &PRINT
     &TRAJECTORY  ON
       ADD_LAST  NUMERIC
       FILENAME trajectory
     &END TRAJECTORY
     &RESTART  SILENT
       ADD_LAST  NUMERIC
       &EACH
         MD  1
       &END EACH
     &END RESTART
   &END PRINT
 &END MOTION
 &FORCE_EVAL
   METHOD  QS
   &DFT
     BASIS_SET_FILE_NAME BASIS_MOLOPT
     POTENTIAL_FILE_NAME GTH_POTENTIALS
     &SCF
       MAX_SCF  300
       EPS_SCF     1.0000000000000001E-05
       SCF_GUESS  RESTART
       &OT  T
         PRECONDITIONER  NONE
       &END OT
       &PRINT
         &RESTART  ON
           ADD_LAST  NUMERIC
           BACKUP_COPIES  1
           &EACH
             MD  1
           &END EACH
         &END RESTART
       &END PRINT
     &END SCF
     &QS
       EPS_DEFAULT     1.0000000000000000E-10
       METHOD  GPW
     &END QS
     &MGRID
       NGRIDS  4
       CUTOFF     4.0000000000000000E+02
       REL_CUTOFF     4.0000000000000000E+01
     &END MGRID
     &XC
       DENSITY_CUTOFF     1.0000000000000000E-10
       GRADIENT_CUTOFF     1.0000000000000000E-10
       TAU_CUTOFF     1.0000000000000000E-10
       &XC_FUNCTIONAL  NO_SHORTCUT
         &PBE  T
           PARAMETRIZATION  ORIG
         &END PBE
       &END XC_FUNCTIONAL
       &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
     &END XC
     &POISSON
       PERIODIC  XYZ
     &END POISSON
     &PRINT
       &E_DENSITY_CUBE  SILENT
         ADD_LAST  NUMERIC
         STRIDE  1 1 1
         &EACH
           MD  99999999
         &END EACH
       &END E_DENSITY_CUBE
       &PDOS  SILENT
         ADD_LAST  NUMERIC
         FILENAME dosfile
         LOG_PRINT_KEY  T
         COMPONENTS  F
         NLUMO  -1
         &EACH
           MD  99999999
         &END EACH
       &END PDOS
     &END PRINT
   &END DFT


















On Thursday, August 18, 2016 at 3:05:57 PM UTC+3, jgh wrote:
>
> Hi 
>
> The PBE-D3 setup looks fine. 
>
> Yes, 10-20 SCF iterations during an MD are on the very high end for 
> such a well behaved system. I would try the following setup (in case you 
> don't use it already) 
>
> &QS 
>   .... 
>   EXTRAPOLATION ASPC 
>   EXTRAPOLATION_ORDER  4 
> &END QS 
>
> &OT 
>    PRECONDITIONER FULL_SINGLE_INVERSE 
>    MINIMIZER DIIS 
> &END OT 
>
> 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: 08/18/2016 01:08AM 
> Subject: Re: [CP2K:8075] SCF, MD run-time verses atomic species. 
>
> 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 
>
> Winterthurerstrasse 190 
>
> CH-8057 Zürich, Switzerland 
>
> --------------------------------------------------------------- 
>
>
>
> -----cp... at googlegroups.com wrote: -----To: cp2k <cp... at googlegroups.com> 
>
> From: Simiam Ghan 
>
> Sent by: cp... at googlegroups.com 
>
> 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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