[CP2K:3623] Restart MD
Teodoro Laino
teodor... at gmail.com
Wed Nov 23 06:45:38 UTC 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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