[lammps-users] Imposing a gap between two layers

Steve, LAMMPS users,
I am trying to explore the impact of gap between two silicon layers on thermal transport.
After I impose an initial gap (say 1 nm between two layers), and perform a NVT simulation, I notice from visualizing the dump files that the atoms fill up the gap. After the NVT simulation, I plan to do a NVE simulation in conjunction with fix/thermal conductivity.

Is there a way to impose the gap in a physically defendable way?


I don't know the physical reason for the gap. But you could
impose additional force constraints on atoms near the
gap to keep them apart, you could insert fictitious inert
atoms in the gap to keep others out, you could use
some sort of wall potential to repel atoms from the
plane of the gap, etc.