[CP2K-user] Bond sequences error

[Mayank Dodia]

Hi Matt,

Thanks for your response. The restart file had the same atom names and the 
restart file matched with the previous input files. Unfortunately I didn't 
noticed earlier before that I had an energy convergence problem for the 
QM/MM system caused by distortion of the geometry of an QM-treated water 
molecule, which caused a problem in the plain MM MD run as well. 

Best Regards,
Mayank

On Wednesday, June 3, 2020 at 8:21:18 PM UTC+2, Matt W wrote:
>
> 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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