[CP2K:8085] SCF, MD run-time verses atomic species.

hut... at chem.uzh.ch hut... at chem.uzh.ch
Tue Aug 23 09:43:09 CEST 2016


Hi

REFERENCE_C9_TERM True

keeps the C6 terms used for the calculation of the C9 term constant.
This considerably simplifies the calculation of forces.

EPS_SCF in OT is MAXVAL(dE/dCai - lambda Sab*Cbi) [the 'gradient'] in
atomic units.

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: 08/21/2016 07:36PM
Subject: Re: [CP2K:8085] SCF, MD run-time verses atomic species.

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

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 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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