[CP2K-user] Bond sequences error

[Mayank Dodia]

Hi,

Sorry for reposting, but can someone help me understand what exactly the 
error is and how should I resolve it?

On Monday, June 1, 2020 at 7:01:17 AM UTC+2, Mayank Dodia wrote:
>
> Hi,
>
> Has anyone experienced this sort of error?
>
>
>  *******************************************************************************
>  *   ___                                                                  
>      *
>  *  /   \                                                                  
>     *
>  * [ABORT] different sequence of bonds for same molecule kind molecule 
> type  = *
>  *  \___/       1 molecule number=    634 NOT FOUND! Check the 
> connectivity of *
>  *    |                                your system.                        
>     *
>  *  O/|                                                                    
>     *
>  * /| |                                                                    
>     *
>  * / \                                                    
> topology_util.F:1117 *
>
>  *******************************************************************************
>
>
>  ===== Routine Calling Stack =====
>
>             4 topology_molecules_check
>             3 connectivity_control
>             2 topology_control
>             1 CP2K
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
> :
> system msg for write_line failure : Bad file descriptor
>
> I was running a QMMM file and this failure occurred after a restarted 
> calculation which ran without any issues before. I tried rerunning the 
> calculation by simplifying it to plain MM input with just solvent water 
> molecules, without success, and I am not really sure where the error is. 
> Can someone help me understand what exactly the error is and how should I 
> resolve it?
>
> Best Regards,
> MayankDodia
>
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