Create clusters

Hello dear all,
I already have a polycrystalline graphene sheet, i want to create Si, Sic and diamond clusters at 50 AA above the sheets. As I'm not expert in Lammps, could anyone help and guide me to how to create these clusters? For example, in case of Si cluster, i want a cluster with 16 atoms. And for Sic and diamond, i want almost same number of atoms on them.

Thank you and i really appreciate for your help in advance.

The most general way is to create a data file

that has the coords of all the atoms you want, including

the clusters. LAMMPS won’t do that for you,

that’s a pre-processing step (see the Pre/post page on

the web site).

If you have the sheets (substrate) and want to add

clusters dynamically during a simulation, then you

can use fix deposit with the molecule flag. And use

the molecule command to define the geometry of

a cluster in a molecule file. Again creating that

file (like a data file) is your job as a pre-processing

step. LAMMPS can’t do it for you. It doesn’t

know what you mean by a “cluster”.


One more idea. I think you could

also use the create_atoms single command

with the molecule option, to first read

a data file (substrate only) then position

N clusters (far apart from each other) at

specific points specified in the create_atoms

single command, above the substrate.

You’d still need to use the molecule command

and a mol file to create the template for one

cluster. Of course if a “cluster” is some simple

lattice of points (e.g. a fcc lattice in a small sphere),

then create_atoms with a region and a defined

lattice (orientation) could tile small clusters in
small spheres anywhere you

want to put them.