Too slow for 1008 Ni atoms, 20 or more minutes per step
yell... at gmail.com
yell... at gmail.com
Mon Apr 10 08:45:34 UTC 2017
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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