[CP2K-user] Bond sequences error

[Matt W]

Maybe check the names of atoms in the restart files. Perhaps H1 etc are 
only being called H in the restart or similar?

Matt

On Wednesday, June 3, 2020 at 4:27:11 PM UTC+1, Mayank Dodia wrote:
>
> 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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