Dear lammps users
Recently, I ran a simulation with pppm method, and fortunately I tool good results.
But now, I assign “kspace_modify slab 3.0” to omit long coulomb intraction affect from periodic boxes in z direction. So, I changed boundaries to “p p f”.
Unfortunately, I get the following error in different circumstances.
{
ERROR on proc 1: Shake atoms 17521 17522 17523 missing on proc 1 at step
66079 (…/fix_shake.cpp:521)
MPI_ABORT was invoked on rank 1 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.
}
I tested different cutoff radius and neighbour, but the error occured again.
I will appreciate if you could help me.
Regards
Reza
changedinput.in
complete.data
Dear lammps users
Recently, I ran a simulation with pppm method, and fortunately I tool good
results.
But now, I assign "kspace_modify slab 3.0" to omit long coulomb intraction
affect from periodic boxes in z direction. So, I changed boundaries to "p p
f".
Unfortunately, I get the following error in different circumstances.
> {
> ERROR on proc 1: Shake atoms 17521 17522 17523 missing on proc 1 at step
> 66079 (../fix_shake.cpp:521)
> ------------------------------------------------------------
--------------
> MPI_ABORT was invoked on rank 1 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.
> }
I tested different cutoff radius and neighbour, but the error occured
again.
no big surprise here when looking at your system. if you run a simulation
of a droplet of a liquid in vacuum long enough, some molecule will
evaporate from the droplet and for a system with fixed boundaries, it will
eventually leave the box. have you visualized your trajectory? you should
see a molecule leaving the droplet before you receive the quoted error
message.
I will appreciate if you could help me.
you need to have some kind of mechanism to keep atoms from leaving the box
(in fact, for an accurate simulation, atoms should stay within the
original box confines, i.e. before the expansion through the PPPM kspace
slab solver). you can define walls with a (soft) harmonic potential, for
example.
axel.
Dear Axel
Thank you so much for your response.
Unfortunately, I got the previous error when I added another Graphene sheet to confine the simulation box. I tested different options of fix wall/reflect to do so,but the error emerged again.
I don’t know why this error occured for one molecule on two processor.
Error:
Dear Axel
Thank you so much for your response.
Unfortunately, I got the previous error when I added another Graphene
sheet to confine the simulation box. I tested different options of fix
wall/reflect to do so,but the error emerged again.
I don't know why this error occured for one molecule on two processor.
Error:
{
ERROR on proc 7: Shake atoms 17413 17414 17415 missing on proc 7 at step
373180 (../fix_shake.cpp:530)
ERROR on proc 3: Shake atoms 17413 17414 17415 missing on proc 3 at step
373180 (../fix_shake.cpp:530)
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 7 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.
}
I will appreciate if you could tell me the reason of this error.
http://lammps.sandia.gov/doc/Section_errors.html