[CP2K-user] [CP2K:19165] Re: regarding cp2k error CP2K requires molecules to be contiguous and we have detected a non contiguous one

[Matt Watkins]

Hello,
are you restarting the calculation? The message would tend to suggest that 
something has gone very wrong with the geometry of your system. Check it 
carefully.
In your input the obvious problem is EPS_DEFAULT is much too large. Stick 
with the default or better 1.0E-12 as you use a more demanding functional.
Matt

On Tuesday, 1 August 2023 at 09:04:17 UTC+1 Anmol wrote:

> Dear Cp2k community 
> i was running an NVT simulation for water after 3000 steps it is showing 
> me the error
> CP2K requires molecules to be contiguous and we have detected a non *
>  * [ABORT]    contiguous one!! In particular a molecule defined from index 
> (   *
>  *  \___/  4                   ) to (    41                   ) contains 
> other *
>  *    |     molecules, not connected! Too late at this stage everything 
> should *
>  *  O/|       be already ordered! If you have not yet employed the 
> REORDERING  *
>  * /| |            keyword, please do so.It may help to fix this issue.   
>      *
>  * / \                                           
>  topology_generate_util.F:326 *
>
>
> how to resolve this
>
> below i have attached input file 
> ##############
> !Specify Run Type and Print level
> &GLOBAL
>   PROJECT water
>   RUN_TYPE MD
>   PRINT_LEVEL MEDIUM
> &END GLOBAL
>
> !Force avail section
>
> &FORCE_EVAL
>   METHOD Quickstep
> !STRESS_TENSOR ANALYTICAL
>   &PRINT
>     &FORCES ON
>     &END FORCES
>   &END PRINT
>
>   &DFT
> BASIS_SET_FILE_NAME GTH_BASIS_SET
>     POTENTIAL_FILE_NAME POTENTIAL
> CHARGE 0
>     MULTIPLICITY 1
>  &XC
>       &XC_FUNCTIONAL
>         &MGGA_XC_B97M_V
>         &END MGGA_XC_B97M_V
>       &END XC_FUNCTIONAL
>       &VDW_POTENTIAL
>       &NON_LOCAL
>       TYPE RVV10
>       &END NON_LOCAL
>       &END VDW_POTENTIAL
>     &END XC
>     
> &QS
>       EPS_DEFAULT 1.0E-07
>     &END QS
>     &MGRID
>       CUTOFF 400
>       NGRIDS 4
>       REL_CUTOFF 70
>     &END MGRID
>
>     &SCF
>         SCF_GUESS ATOMIC
>         EPS_SCF 1.0E-07
>         MAX_SCF 20
>         &OT ON
>         MINIMIZER DIIS
>         PRECONDITIONER FULL_ALL
>         &END OT
>         &OUTER_SCF
>         MAX_SCF 100
>         &END OUTER_SCF
>     &END SCF
> &END
>
> &SUBSYS
>     &CELL 
>       ABC [angstrom] 10.00 10.00 10.00
>     &END CELL
>     &TOPOLOGY
>       COORD_FILE_NAME new_water.pdb
>       COORD_FILE_FORMAT PDB
>     &END
>
>     &KIND H                              
>       BASIS_SET TZV2P-GTH-q1
>       POTENTIAL GTH-BLYP-q1            
>     &END KIND
>     &KIND O
>       BASIS_SET TZV2P-GTH-q6
>       POTENTIAL GTH-PBE-q6
>     &END KIND
>   &END SUBSYS
> &END FORCE_EVAL
>
> &MOTION
> &GEO_OPT
>    OPTIMIZER LBFGS
>    MAX_ITER  100
>    MAX_FORCE 1.0E-03
>    RMS_DR    1.0E-03
>    RMS_FORCE 1.0E-03
>    MAX_DR    1.0E-03
>    &LBFGS
>    &END
>  &END
>
>  &MD
>    ENSEMBLE NVT 
>    TEMPERATURE [K] 300
>    TIMESTEP [fs] 0.5
>    STEPS 30000
>    &THERMOSTAT
>      REGION MASSIVE
>      TYPE GLE
>      &GLE
>        NDIM 5
>        A_SCALE [ps^-1] 1.00
>        A_LIST    1.859575861256e+2   2.726385349840e-1   1.152610045461e+1 
>  -3.641457826260e+1   2.317337581602e+2
>        A_LIST   -2.780952471206e-1   8.595159180871e-5   7.218904801765e-1 
>  -1.984453934386e-1   4.240925758342e-1
>        A_LIST   -1.482580813121e+1  -7.218904801765e-1   1.359090212128e+0 
>   5.149889628035e+0  -9.994926845099e+0
>        A_LIST   -1.037218912688e+1   1.984453934386e-1  -5.149889628035e+0 
>   2.666191089117e+1   1.150771549531e+1
>        A_LIST    2.180134636042e+2  -4.240925758342e-1   9.994926845099e+0 
>  -1.150771549531e+1   3.095839456559e+2
>      &END GLE
>    &END THERMOSTAT
>  &END
>
>  &PRINT
>     &TRAJECTORY
>       ADD_LAST NUMERIC
>       FORMAT XYZ
>       &EACH
>         MD 1
>       &END EACH
>     &END TRAJECTORY
>
>     &RESTART
>       ADD_LAST NUMERIC
>       &EACH
>         MD 1
>       &END EACH
>     &END RESTART
>     &RESTART_HISTORY ON
>     &END
>
>    &FORCES
>      FILENAME forces_nvt
>      &EACH
>      MD 1
>      &END EACH
>    &END FORCES
>
>   &STRESS
>      FILENAME stress_nvt
>      &EACH
>      MD 1
> &END EACH
>    &END STRESS
>
>  &END PRINT
>
>
> &END
> #####################
>
>
>
>

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