[lammps-users] Installing LAMMPS

The generated dump file shows the atoms go outside the initialized box (by xlo xhi... in the data file) far >away from the perodic box and no atoms were re-generated.

What do you mean by this? The dump file you are generating has scaled coords,
so each atom coord should be between 0 and 1. They can be slighly out of
these bounds (see the dump doc page) due to when neighbor lists are regenerated.
But if they are far out of these bounds, then something is wrong with
your simulation,
e.g. atoms are moving too fast, and/or you are rebuilding neighbor
lists too infrequently.