[CP2K:8079] SCF, MD run-time verses atomic species.

Simiam Ghan simia... at gmail.com
Sun Aug 21 19:36:13 CEST 2016


Greetings Juerg, 
I attached a picture showing the effect of REFERENCE_C9_TERM and 
EXTRAPOLATION and PRECONDITIONER on my MD simulation.  Together they have 
reduced time per MD step from 75-200sec to 36sec and SCF count from 1-80 to 
6.    Now, as this seems too good to be true I did an ENERGY_FORCE 
calculation on a snapshot of the system with and without REFERENCE_C9_TERM: 
the difference in total energy is  0.02meV/atom.  With/without the 
EXTRAPOLATION and PRECONDITIONER which you gave me the total energy 
difference is 1meV/atom.  This difference is reduced if i tighten EPS_SCF 
from 1E-5 to 1E-6. I have not checked if these small changes translate to 
better/worse accuracy. 

Could you elaborate on what REFERENCE_C9_TERM does: how does it double 
speed while maintaining accuracy? Why is it not a default? 
Also , could you explain the definition of EPS_SCF, for example what are 
its units?

Many thanks,
Simiam

P.S.  EXTRAPOLATION and PRECONDITIONER also put a stop to drifting in the 
Cons.Quantity of the .ener file, thank you. 




On Friday, August 19, 2016 at 10:11:48 AM UTC+3, jgh wrote:
>
> Hi 
>
> Setting an apropriate preconditioner and the DIIS minimizer will 
> speed up convergence and will not affect accuracy. 
> The ASPC order=4 setting gives you better initial wavefunctions 
> (=faster convergence) and better energy conservation (=stability of MD). 
> Again accuracy will be the same or better. 
>
> 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 07:31PM 
> Subject: Re: [CP2K:8079] SCF, MD run-time verses atomic species. 
>
> 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 
>
> 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: 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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