Does Lammps re-assign atom IDs when several atoms have been deleted during the simulation?

LAMMPS LAMMPS Mailing List Mirror
1

Dear everyone,
In my simulation, the atoms which left the free surface have been deleted on each step.
My problem is when I use OVITO to calculate the Displacement Vectors of the atoms, it seems very strange. The vectors indicate that, most of the atoms which are in the middle of the system have moved to the surface. The vectors are too large.
So I am wondering whether LAMMPS re-assign atom IDs when some of the atoms are deleted during the simulation.
Thanks very much!

Best Regards
Liu

2

So I am wondering whether LAMMPS re-assign atom IDs when some of the atoms >are deleted during the simulation.

Normally, not unless you tell it to.

E.g. the detele_atoms command has an option

to re-number the atom IDs.

Steve

3

Dear everyone,

In my simulation, the atoms which left the free surface have been deleted
on each step.

My problem is when I use OVITO to calculate the Displacement Vectors of
the atoms, it seems very strange. The vectors indicate that, most of the
atoms which are in the middle of the system have moved to the surface. The
vectors are too large.

So I am wondering whether LAMMPS re-assign atom IDs when some of the atoms
are deleted during the simulation.

it is ​more like​ly that this is an issue with the LAMMPS dump reader in
ovito. as the maintainer for the LAMMPS plugin for VMD, i can tell you,
that it is not at all easy to handle LAMMPS data consistently from
trajectories, especially when atoms are removed or added.

axel.