[CP2K:8079] SCF, MD run-time verses atomic species.
Simiam Ghan
simia... at gmail.com
Sun Aug 21 17:36:13 UTC 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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