[lammps-users] Covalent Bonds

Hi all,

I never worked with covalent bonds in LAMMPS. I was just wondering how to make the atoms covalentely bonded ? For instance, I have a sphere (geometric shape) with Silicon atoms and I want all these atoms to be covalently bonded. If I can do this what are the properties which I need to input to LAMMPS or is it possible to do this in any software and then import into LAMMPS ?

Any suggestions would be greatly appreciated.


LAMMPS has several bond potentials. You define the
bond connectivity itself in the input data file. See the
doc page for the read_data command, or look at the data.peptide
file in examples/peptide.

Note that these are bonds with a fixed topology. There are potential
models for Si or SiO2 like that, e.g. an OPLS or CHARMM parameterization.
However if you want "bonds" to break/reform as Si atoms move around,
then that is really a pairwise potential from the LAMMPS perspective.
See the Stillinger-Weber or Tersoff potentials. These include 3-body
terms, but are computed as "pair" potentials in LAMMPS.