Restart MD

Sandeep Kumar Reddy kuma... at gmail.com
Wed Nov 23 17:04:57 CET 2011


Hi,
     Since this system is big and takes to time to execute, i prepared two
water molecules system which will run very fast.

Please find the enclosed files.  One (run-20steps.tar.gz) is run for 20
steps.  And the other (run-10steps.tar.gz) is run for 10 steps intially,
and later, it is ran for 10 steps by making restart option active.

Comparing COLVAR files in both of them (run-20steps & run-10steps/restart)
show the differences from 11th step onwards.

Following is the differences between two files.

*run-20steps *

         0.0      5.66918      0.00000      0.00000      0.00000
0.00000
         0.5      5.66873      0.00000      0.00000      0.00000
0.00000
         1.0      5.67069      0.00000      0.00000      0.00000
0.00000
         1.5      5.67606      0.00000      0.00000      0.00000
0.00000
         2.0      5.68504      0.00000      0.00000      0.00000
0.00000
         2.5      5.69723      0.00000      0.00000      0.00000
0.00000
         3.0      5.71350      0.00000      0.00000      0.00000
0.00000
         3.5      5.73302      0.00000      0.00000      0.00000
0.00000
         4.0      5.75500      0.00000      0.00000      0.00000
0.00000
         4.5      5.78081      0.00000      0.00000      0.00000
0.00000
         5.0      5.80860      0.00000      0.00000      0.00000
0.00000
         5.5      5.83979      0.00000      0.00000      0.00000
0.00000
         6.0      5.87412      0.00000      0.00000      0.00000
0.00000
         6.5      5.91052      0.00000      0.00000      0.00000
0.00000
         7.0      5.95146      0.00000      0.00000      0.00000
0.00000
         7.5      5.99398      0.00000      0.00000      0.00000
0.00000
         8.0      6.03912      0.00000      0.00000      0.00000
0.00000
         8.5      6.08574      0.00000      0.00000      0.00000
0.00000
         9.0      6.13265      0.00000      0.00000      0.00000
0.00000
         9.5      6.18166      0.00000      0.00000      0.00000
0.00000
        10.0      6.23256      0.00000      0.00000      0.00000
0.00000

*run-10steps/restart :*


         0.0      5.66918      0.00000      0.00000      0.00000
0.00000
         0.5      5.66873      0.00000      0.00000      0.00000
0.00000
         1.0      5.67069      0.00000      0.00000      0.00000
0.00000
         1.5      5.67606      0.00000      0.00000      0.00000
0.00000
         2.0      5.68504      0.00000      0.00000      0.00000
0.00000
         2.5      5.69723      0.00000      0.00000      0.00000
0.00000
         3.0      5.71350      0.00000      0.00000      0.00000
0.00000
         3.5      5.73302      0.00000      0.00000      0.00000
0.00000
         4.0      5.75500      0.00000      0.00000      0.00000
0.00000
         4.5      5.78081      0.00000      0.00000      0.00000
0.00000
         5.0      5.80860      0.00000      0.00000      0.00000
0.00000
         5.0      5.80860      0.00000      0.00000      0.00000
0.00000
         5.5      5.83553      0.00000      0.00000      0.00000
0.00000
         6.0      5.86568      0.00000      0.00000      0.00000
0.00000
         6.5      5.89804      0.00000      0.00000      0.00000
0.00000
         7.0      5.93505      0.00000      0.00000      0.00000
0.00000
         7.5      5.97381      0.00000      0.00000      0.00000
0.00000
         8.0      6.01535      0.00000      0.00000      0.00000
0.00000
         8.5      6.05853      0.00000      0.00000      0.00000
0.00000
         9.0      6.10216      0.00000      0.00000      0.00000
0.00000
         9.5      6.14804      0.00000      0.00000      0.00000
0.00000
        10.0      6.19596      0.00000      0.00000      0.00000
0.00000


Regards,
Sandeep

On Nov 23, 11:45 am, Teodoro Laino <teodor... at gmail.com> wrote:
> provide an input file (+ all necessary files) that runs quickly (let's
say not more than 1 minute serial), that shows the problem, with detailed
info on how to do to reproduce the error you see.
> Teo
>
> On Nov 23, 2011, at 7:28 AM, Sandeep Kumar Reddy wrote:
>
>
>
>
>
>
>
> > Dear all,
> >             I am doing an MD run by restraining dihedral to some
value.  I have a problem with restarting this job.  When i used the
following options to restart this, the value of COLVAR 1  before and after
restart are not same.
>
> > Input file :
>
> > &FORCE_EVAL
> >   METHOD Quickstep
> >   &DFT
> >     BASIS_SET_FILE_NAME BASIS_MOLOPT
> >     POTENTIAL_FILE_NAME POTENTIAL
> >     CHARGE = 0
> >     &MGRID
> >       CUTOFF 280
> >       NGRIDS 5
> >       REL_CUTOFF 40
> >     &END MGRID
> >      &QS
> >        METHOD GPW
> >        EPS_DEFAULT 1.0E-10
> >      &END QS
> >      &SCF
> >        SCF_GUESS RESTART
> >        EPS_SCF 1.0E-6
> >        MAX_SCF 150
> > #       MIXING 0.3
> >        &OUTER_SCF
> >           EPS_SCF 1.0E-6
> >           MAX_SCF 50
> >        &END
> >     &OT
> >           MINIMIZER CG
> >           PRECONDITIONER FULL_ALL
> >           ENERGY_GAP 0.001
> >           STEPSIZE 0.05
> >        &END
>
> >     &END SCF
> >     &XC
> >      &XC_FUNCTIONAL BLYP
> >       &END XC_FUNCTIONAL
> >       &XC_GRID
> >         XC_SMOOTH_RHO NN50
> >         XC_DERIV SPLINE2
> >       &END
> >       &vdW_POTENTIAL
> >          DISPERSION_FUNCTIONAL PAIR_POTENTIAL
> >          &PAIR_POTENTIAL
> >             TYPE DFTD2
> >             REFERENCE_FUNCTIONAL BLYP
> >          &END PAIR_POTENTIAL
> >       &END vdW_POTENTIAL
>
> >    &END XC
> >   &END DFT
>
> >   &SUBSYS
> >     &CELL
> >       ABC 12.16174 12.16174 12.16174
> >     &END CELL
>
> >     &COORD
> >      @INCLUDE coor.xyz
> >     &END COORD
>
> >      &KIND O
> >       BASIS_SET TZV2P-MOLOPT-GTH-q6
> >       POTENTIAL GTH-BLYP-q6
> >     &END KIND
>
> >     &KIND C
> >       BASIS_SET TZV2P-MOLOPT-GTH-q4
> >       POTENTIAL GTH-BLYP-q4
> >     &END KIND
>
> >     &KIND H
> >       BASIS_SET TZV2P-MOLOPT-GTH-q1
> >       POTENTIAL GTH-BLYP-q1
> > #      MASS 2.016
> >     &END KIND
>
> >     &COLVAR
> >       &TORSION
> >         ATOMS  179 178 181 180
> >       &END
> >     &END
> >     &COLVAR
> >       &DISTANCE
> >         ATOMS  180 181
> >       &END
> >     &END
> >     &COLVAR
> >       &TORSION
> >          ATOMS  179 178 182 183
> >       &END
> >     &END
> >     &COLVAR
> >       &DISTANCE
> >         ATOMS  182 183
> >       &END
> >     &END
>
> >   &END SUBSYS
> > &END FORCE_EVAL
>
> > &GLOBAL
> >   PROJECT OUT-CA-AA-MD
> >   RUN_TYPE MD
> >   PRINT_LEVEL MEDIUM
> > &END GLOBAL
>
> > &MOTION
> >   &MD
> >     ENSEMBLE NVT
> >     STEPS 10000
> >     TIMESTEP 0.5
> >     &THERMOSTAT
> >       &NOSE
> >         LENGTH 3
> >         YOSHIDA 3
> >         TIMECON 100.0
> >         MTS 2
> >       &END NOSE
> >     &END THERMOSTAT
> >   TEMPERATURE 300.0
> >   &END MD
>
> >   &FREE_ENERGY
> >     &METADYN
> >       DO_HILLS .FALSE.
> >       &METAVAR
> >         COLVAR 1
> >         SCALE 1.
> >       &END
> >       &PRINT
> >         &COLVAR
> >            COMMON_ITERATION_LEVELS 3
> >            &EACH
> >              MD 1
> >            &END
> >         &END
> >       &END
> >       &METAVAR
> >         COLVAR 2
> >         SCALE 1.
> >       &END
> >       &PRINT
> >         &COLVAR
> >           COMMON_ITERATION_LEVELS 3
> >           &EACH
> >              MD 1
> >           &END
> >         &END
> >       &END
> >       &METAVAR
> >         COLVAR 2
> >         SCALE 1.
> >       &END
> >       &PRINT
> >         &COLVAR
> >           COMMON_ITERATION_LEVELS 3
> >           &EACH
> >              MD 1
> >           &END
> >         &END
> >       &END
> >       &METAVAR
> >         COLVAR 3
> >         SCALE 1.
> >       &END
> >       &PRINT
> >         &COLVAR
> >            COMMON_ITERATION_LEVELS 3
> >            &EACH
> >              MD 1
> >            &END
> >         &END
> >       &END
> >     &END
> >   &END
>
> >   &CONSTRAINT
> >     &CONSTRAINT_INFO
> >       &EACH
> >         MD 1
> >       &END
> >     &END
> >     &COLLECTIVE
> >       COLVAR 1
> >       INTERMOLECULAR 1
> >       TARGET 0.00
> >       TARGET_GROWTH  0.001
> >       TARGET_LIMIT   0.872647
> >       &RESTRAINT
> >         K [kcalmol]  20.0000
> >       &END
> >     &END
> >   &END
> >   &PRINT
> >     &VELOCITIES
> >       &EACH
> >         MD 1
> >       &END
> >     &END
> >     &FORCES
> >       &EACH
> >         MD 1
> >       &END
> >     &END
> >   &END
>
> > &END MOTION
>
> > &EXT_RESTART
> >     RESTART_FILE_NAME OUT-CA-AA-MD-1.restart
> >     RESTART_COUNTERS  T
> >     RESTART_POS  T
> >     RESTART_VEL  T
> >     RESTART_CONSTRAINT T
> >     RESTART_METADYNAMICS F
> > &END EXT_RESTART
>
> > --------------
>
> > Before restart, the  COLVAR file contains ..
>
> >   1470.0      0.70287      2.00213      2.00213     -0.23927
0.00000      0.00000      0.00000      0.00000      0.00000
0.00000      0.00000      0.00000      0.00000      0.00000
> >       1470.5      0.70864      1.98593      1.98593     -0.23249
0.00000      0.00000      0.00000      0.00000      0.00000
0.00000      0.00000      0.00000      0.00000      0.00000
> >       1471.0      0.71401      1.96755      1.96755     -0.22558
0.00000      0.00000      0.00000      0.00000      0.00000
0.00000      0.00000      0.00000      0.00000      0.00000
> >       1471.5      0.71885      1.94803      1.94803     -0.21857
0.00000      0.00000      0.00000      0.00000      0.00000
0.00000      0.00000      0.00000      0.00000      0.00000
> >       1472.0      0.72302      1.92860      1.92860     -0.21149
0.00000      0.00000      0.00000      0.00000      0.00000
0.00000      0.00000      0.00000      0.00000      0.00000
> >       1472.5      0.72638      1.91055      1.91055     -0.20437
0.00000      0.00000      0.00000      0.00000      0.00000
0.00000      0.00000      0.00000      0.00000      0.00000
> >       1473.0      0.72881      1.89520      1.89520     -0.19724
0.00000      0.00000      0.00000      0.00000      0.00000
0.00000      0.00000      0.00000      0.00000      0.00000
> >       1473.5      0.73017      1.88373      1.88373     -0.19014
0.00000      0.00000      0.00000      0.00000      0.00000
0.00000      0.00000      0.00000      0.00000      0.00000
> >       1474.0      0.73037      1.87703      1.87703     -0.18308
0.00000      0.00000      0.00000      0.00000      0.00000
0.00000      0.00000      0.00000      0.00000      0.00000
>
> > After restart,
>
> >       1470.5      0.70596      1.98584      1.98584     -0.23193
0.00000      0.00000      0.00000      0.00000      0.00000
0.00000      0.00000      0.00000      0.00000      0.00000
> >       1471.0      0.70867      1.96732      1.96732     -0.22446
0.00000      0.00000      0.00000      0.00000      0.00000
0.00000      0.00000      0.00000      0.00000      0.00000
> >       1471.5      0.71088      1.94763      1.94763     -0.21691
0.00000      0.00000      0.00000      0.00000      0.00000
0.00000      0.00000      0.00000      0.00000      0.00000
>
> > As can be seen, COLVAR1  value is not same at 1470.5, 1471.0 so on ..
th time step.   And also, ener file output is
>
> > Before restart,
>
> >      2941         1470.500000         0.264232649
305.633596492     -1071.124343277     -1070.837205951       110.006900000
> >       2942         1471.000000         0.262352431
303.458778818     -1071.122443287     -1070.837141220       126.382300000
> >       2943         1471.500000         0.258554740
299.066050830     -1071.118558109     -1070.837008858       109.594400000
> >       2944         1472.000000         0.254843481
294.773298732     -1071.114769705     -1070.836887261       108.996200000
> >       2945         1472.500000         0.253037023
292.683797430     -1071.112972727     -1070.836852718       109.157400000
> >       2946         1473.000000         0.253686059
293.434527505     -1071.113732934     -1070.836919998       125.062900000
> >       2947         1473.500000         0.255812040
295.893615199     -1071.116023855     -1070.837040816       108.843300000
> >       2948         1474.000000         0.257604549
297.966981110     -1071.117955614     -1070.837135519       125.324700000
>
> > after restart,
>
> >       2941         1470.500000         0.264119595
305.502828525     -1071.124357212     -1070.837332951       540.249300000
> >       2942         1471.000000         0.262260456
303.352392372     -1071.122478947     -1070.837268889       203.759400000
> >       2943         1471.500000         0.258489935
298.991092511     -1071.118620866     -1070.837136476       203.167400000
> >       2944         1472.000000         0.254807453
294.731625484     -1071.114861358     -1070.837015022       178.069300000
>
> > Can anybody help me out how to restart the job?
>
> > Thanks.
>
> > Regards,
> > Sandeep
>
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