[CP2K:3623] Restart MD

Teodoro Laino teodor... at gmail.com
Wed Nov 23 07:45:38 CET 2011


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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