[lammps-users] Shake atoms missing

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1

Hi all

i am trying to study the properties of water. During the course of the simulation i have to delete water molecules from certain region in the simulation box. When i use the command
'delete_atoms region regwater compress no ’
i get the following error

application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
ERROR on proc 0: Shake atoms 1945 1946 1947 missing on proc 0 at step 500043
rank 0 in job 28 Maxwell_34072 caused collective abort of all ranks
exit status of rank 0: return code 1

i have attached the code and log file along with this mail.

can anyone suggest a remedy for this error?

in.waterbulk (1.75 KB)

log.lammps (3.63 KB)

2

Hi all

i am trying to study the properties of water. During the course of the
simulation i have to delete water molecules from certain region in the
simulation box. When i use the command
'delete_atoms region regwater compress no '
i get the following error

application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
ERROR on proc 0: Shake atoms 1945 1946 1947 missing on proc 0 at step 500043
rank 0 in job 28 Maxwell_34072 caused collective abort of all ranks
exit status of rank 0: return code 1

i have attached the code and log file along with this mail.

can anyone suggest a remedy for this error?

delete the bonds between those atoms that you are deleting?

axel.

3

thank you Axel for your valuable suggestion…but even after that i am getting an error like this

ERROR: Did not find fix shake partner info

i think some of molecules in the final system are broken due to the deletion of its partner atoms…i think ill have to go for some pre-processing steps…

4

thank you Axel for your valuable suggestion.....but even after that i am
getting an error like this

ERROR: Did not find fix shake partner info

have you tried unfixing shake before deleting the atoms/bonds/angles
and then recreating it after?

i think some of molecules in the final system are broken due to the deletion
of its partner atoms....i think ill have to go for some pre-processing
steps....

of course, you can only delete whole molecules when you have bonds as well.

axel.

5

It would be fatal to delete only some atoms
in a molecule with delete_atoms, But you can delete entire molecules
if you delete all the atoms in the molecule. If you
can't figure out how to do that (e.g. some atoms in
the molecule aren't inside your region), then you might
want to look at fix evaporate which has a molecule flag
which can account for that.

Steve