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.