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.
Thanks,
Peri.
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.
Steve