Too slow for 1008 Ni atoms, 20 or more minutes per step

[yell... at gmail.com]

Dear Marcella,

 

Thank you very much.

The smearing and mixing have been added according to your advice. Is 
BASIS_MOLOPT or BASIS_SET suitable for my system?

 

Best regards,

Huang

在 2017年4月11日星期二 UTC+8下午3:58:18，Marcella Iannuzzi写道：
>
> Dear  Huang,
>
> As already pointed out, you have to improve the computational settings and 
> provide enough computational resources.
> If the system is metallic, you need to use a standard diagonalization 
> as optimisation scheme, including the smearing of the occupation numbers 
> and a proper mixing. 
> The ELPA library for the diagonalisation, which replaces the corresponding 
> function of the ScaLapack, is to be preferred because of the significantly 
> better performance. 
> The orbital transformation method is not going to work for metallic 
> systems. In any case, when the SCF is not well converged, the electronic 
> structure and the forces are going to be wrong. What happens then is 
> totally out of control. 
> Kind regards
> Marcella
>
> On Monday, April 10, 2017 at 10:45:34 AM UTC+2, yel... at gmail.com wrote:
>>
>> Dear  cp2k  users and developers, 
>>
>> I am trying to run ab initio molecular dynamics on the system including 
>> 1008 Ni atoms with PBE functional. The 1*24 mpi task is too slow, around 80 
>> steps per day on average; the 3*24 mpi task is slower, 38 steps per day on 
>> average.
>>
>> Any help is highly appreciated.
>>
>>  
>>
>> Best regards,
>>
>>  Huang
>>
>>
>> CP2K version 4.1
>>
>>  SVN source code revision svn:17462
>>
>>  cp2kflags: fftw3 parallel mpi2 scalapack
>>
>> composer_xe_2015.2.164
>>
>> Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz Haswell
>>
>>
>> # Step Nr. Time[fs] Kin.[a.u.] Temp[K] Pot.[a.u.] Cons Qty[a.u.] 
>> UsedTime[s]
>>
>>  0 0.000000 9.566949152 2000.000000000 -170544.785566084 
>> -170535.208832257 0.000000000
>>
>>  1 1.000000 9.646234174 2016.574776405 -170554.174550500 
>> -170544.519479220 13708.945765018
>>
>>  2 2.000000 9.903391164 2070.334232377 -170556.710812560 
>> -170546.798982374 1826.637025118
>>
>>  3 3.000000 10.258759808 2144.625134870 -170557.585906167 
>> -170547.318873932 748.965154886
>>
>>  4 4.000000 10.622230399 2220.609774417 -170557.531726730 
>> -170546.901213604 856.725823164
>>
>>
>> &GLOBAL
>>
>>   ! limit the runs to 5min
>>
>>   ! WALLTIME 1000
>>
>>   ! reduce the amount of IO
>>
>>   IOLEVEL  LOW
>>
>>   ! the project name is made part of most output files... useful to keep 
>> order 
>>
>>   PROJECT Ni-1008-2k
>>
>>   ! various runtypes (energy, geo_opt, etc.) available.
>>
>>   RUN_TYPE MD             
>>
>> &END GLOBAL
>>
>>
>> &FORCE_EVAL
>>
>>   STRESS_TENSOR ANALYTICAL
>>
>>   ! the electronic structure part of CP2K is named Quickstep
>>
>>   METHOD Quickstep
>>
>>   &DFT
>>
>>     ! basis sets and pseudopotential files can be found in cp2k/data
>>
>>     BASIS_SET_FILE_NAME BASIS_SET
>>
>>     POTENTIAL_FILE_NAME GTH_POTENTIALS            
>>
>>
>>     ! Charge and multiplicity
>>
>>     CHARGE 0
>>
>>     MULTIPLICITY 1
>>
>>
>>     &MGRID
>>
>>        ! PW cutoff ... depends on the element (basis) too small cutoffs 
>> lead to the eggbox effect.
>>
>>        ! certain calculations (e.g. geometry optimization, vibrational 
>> frequencies,
>>
>>        ! NPT and cell optimizations, need higher cutoffs)
>>
>>        CUTOFF [Ry] 300 !500 
>>
>>     &END
>>
>>
>>     &QS
>>
>>        ! use the GPW method (i.e. pseudopotential based calculations with 
>> the Gaussian and Plane Waves scheme).
>>
>>        METHOD GPW 
>>
>>        ! default threshold for numerics ~ roughly numerical accuracy of 
>> the total energy per electron,
>>
>>        ! sets reasonable values for all other thresholds.
>>
>>        EPS_DEFAULT 1.0E-7 !10 
>>
>>        ! used for MD, the method used to generate the initial guess.
>>
>>        EXTRAPOLATION ASPC 
>>
>>     &END
>>
>>
>>     &POISSON
>>
>>        PERIODIC XYZ ! the default, gas phase systems should have 'NONE' 
>> and a wavelet solver
>>
>>     &END
>>
>>
>> !    &PRINT
>>
>> !       ! at the end of the SCF procedure generate cube files of the 
>> density
>>
>> !       &E_DENSITY_CUBE OFF
>>
>> !       &END E_DENSITY_CUBE
>>
>> !       ! compute eigenvalues and homo-lumo gap each 20nd MD step
>>
>> !       &MO_CUBES
>>
>> !          ! compute 4 unoccupied orbital energies
>>
>> !          NLUMO 4
>>
>> !          NHOMO 4
>>
>> !          ! but don't write the cube files
>>
>> !          WRITE_CUBE .FALSE.
>>
>> !          ! do this every 10th MD step.
>>
>> !          &EACH
>>
>> !            MD 20
>>
>> !          &END
>>
>> !       &END
>>
>> !    &END
>>
>>
>>     ! use the OT METHOD for robust and efficient SCF, suitable for all 
>> non-metallic systems.
>>
>>     &SCF                              
>>
>>       SCF_GUESS ATOMIC ! can be used to RESTART an interrupted calculation
>>
>>       MAX_SCF 50
>>
>>       EPS_SCF 1.0E-4 ! accuracy of the SCF procedure typically 1.0E-6 - 
>> 1.0E-7
>>
>>       ! do not store the wfn during MD
>>
>>       &PRINT
>>
>>         &RESTART OFF
>>
>>         &END
>>
>>       &END
>>
>>       
>>
>>       &OT
>>
>>         ! an accurate preconditioner suitable also for larger systems
>>
>>         PRECONDITIONER FULL_SINGLE_INVERSE
>>
>>         ! the most robust choice (DIIS might sometimes be faster, but not 
>> as stable).
>>
>>         MINIMIZER DIIS
>>
>>       &END OT
>>
>>       &OUTER_SCF ! repeat the inner SCF cycle 10 times
>>
>>         MAX_SCF 20
>>
>>         EPS_SCF 1.0E-4 ! must match the above
>>
>>       &END
>>
>>     &END SCF
>>
>>
>>     ! specify the exchange and correlation treatment
>>
>>     &XC
>>
>>       ! use a PBE functional 
>>
>>       &XC_FUNCTIONAL 
>>
>>          &PBE
>>
>>          &END
>>
>>       &END XC_FUNCTIONAL
>>
>>     &END XC
>>
>>   &END DFT
>>
>>  
>>
>>   ! description of the system
>>
>>   &SUBSYS
>>
>>     &CELL 
>>
>>       ! unit cells that are orthorhombic are more efficient with CP2K
>>
>>       ABC [angstrom] 21.98167992 21.98167992 25.64529419
>>
>>     &END CELL
>>
>>
>>     ! atom coordinates can be in the &COORD section,
>>
>>     ! or provided as an external file.
>>
>>     &TOPOLOGY
>>
>>       COORD_FILE_NAME Ni-1008-2k.xyz
>>
>>       COORD_FILE_FORMAT XYZ
>>
>>     &END
>>
>>
>>     ! MOLOPT basis sets are fairly costly,
>>
>>     ! but in the 'DZVP-MOLOPT-SR-GTH' available for all elements
>>
>>     ! their contracted nature makes them suitable
>>
>>     ! for condensed and gas phase systems alike.
>>
>>     &KIND Ni                              
>>
>>       BASIS_SET DZV-GTH-PADE        
>>
>>       POTENTIAL GTH-PBE-q18             
>>
>>     &END KIND
>>
>>   &END SUBSYS
>>
>> &END FORCE_EVAL
>>
>>
>> ! how to propagate the system, selection via RUN_TYPE in the &GLOBAL 
>> section
>>
>> &MOTION
>>
>> ! &GEO_OPT
>>
>> !   OPTIMIZER LBFGS ! Good choice for 'small' systems (use LBFGS for 
>> large systems)
>>
>> !   MAX_ITER  100
>>
>> !   MAX_DR    [bohr] 0.003 ! adjust target as needed
>>
>> !   &BFGS
>>
>> !   &END
>>
>> !  &END
>>
>>  &MD
>>
>>    ENSEMBLE NPT_I  ! sampling the canonical ensemble, accurate properties 
>> might need NVE
>>
>>    TEMPERATURE [K] 2000
>>
>>    TIMESTEP [fs] 1
>>
>>    STEPS 1000000
>>
>>    # GLE thermostat as generated at http://epfl-cosmo.github.io/gle4md 
>>
>>    # GLE provides an effective NVT sampling.
>>
>>    &BAROSTAT
>>
>>        PRESSURE 1.0
>>
>>    &END BAROSTAT
>>
>>    &THERMOSTAT
>>
>>       &NOSE
>>
>>       &END NOSE
>>
>>    &END THERMOSTAT
>>
>>  &END MD
>>
>>  &PRINT
>>
>>    &TRAJECTORY
>>
>>      &EACH
>>
>>        MD 100
>>
>>      &END EACH
>>
>>    &END TRAJECTORY
>>
>>    &VELOCITIES OFF
>>
>>    &END VELOCITIES
>>
>>    &FORCES OFF
>>
>>    &END FORCES
>>
>>    &RESTART_HISTORY
>>
>>      &EACH
>>
>>        MD 200
>>
>>      &END EACH
>>
>>    &END RESTART_HISTORY
>>
>>    &RESTART
>>
>>      BACKUP_COPIES 3
>>
>>      &EACH
>>
>>        MD 200
>>
>>      &END EACH
>>
>>    &END RESTART
>>
>>   &END PRINT
>>
>> &END
>>
>
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