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Re: [lammps-users] (no subject)


From: Vanessa Oklejas <voklejas@...24...>
Date: Thu, 07 Sep 2017 16:35:46 +0000

It's hard to diagnose what the problem could be here. Did you look at the dump file? That usually helps. 

I would look at the bond, angle, dihedral coefficients that you've specified. I'm not sure what potential you are using, but it seems odd (to me) that there are no bond, angle or dihedral coefficients defined for Si-O interactions. 

Also, the temperature of the system is far below that of what you specified it to be, which is an indication that something is wrong well before the run ended. I usually encounter this kind of error when the system is far from equilibrium and atoms are flying out of the simulation box.  

On Thu, Sep 7, 2017 at 9:09 AM neda Sanchuli via lammps-users <lammps-users@lists.sourceforge.net> wrote:
Dear all,

I want to simulate water on SiO2 surface. I attach log  file. After 2800000 steps I got this error:


ERROR on proc 3: Bond atoms 38902 38903 missing on proc 3 at step 2813793

MPI_ABORT was invoked on rank 3 in communicator MPI_COMM_WORLD with errorcode 1.
NOTE: invoking MPI_ABORT causes open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on exactly when open MPI kills them.


Please help me in this regard.



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