[lammps-users] Creating crystal islands on Si


I am trying to create islands of a material like Ge on Si. I have equilibrated both Ge and Si separately using the NPT fix. I have also put both lattices together such that each lattice extends to the edge of the simulation box to maintain periodicity. However, when I place a Ge island (a smaller 3D region) on top of Si, the Si atoms move in the empty regions of the simulation box. Also the Si lattice undergoes a lot of disorder to such an extent that it loses crystallinity.

Initially I thought this to be due to an incorrect interaction potential between the 2 materials. But I observe this even with Si islands on bulk Si and even if I place Si within a larger simulation box.

How do I create islands of one material over another? I would like to form a couple of islands and simulate rotation, translation, and coalescence of these islands.

I would really appreciate your help in how I should go about setting this up using LAMMPS.


If there is no lattice mis-match (e.g. Si on Si) and you
are just using a single potential (for Si), then you should
be able to create an island at lo temp. People do this
all the time in the literature, and there are likely several
papers in the LAMMPS pub list that do something like this.

For a mixed system you'd need to be sure you get
the relative lattices and cross-potential correct.