I was trying to do some very simple lattice dynamics calculations and so was trying to use LAMMPS’s harmomic bond-style. However, when I setup a small system it behaved very strangely.
The computational cell is the attached data.pos file, which consists of 5 atoms bonded. The first and last atoms (I thought) would be bonded accross the periodic boundary. This would then put them all in their equilibrium positions and have an energy of 0. Instead, they collide head-on as their bond is stretched across the center of the computational cell. This is my first time dealing with atom_style bond, but I had expected periodic boundaries to function. Does anyone know what I am missing to get this to work? Both OMP and and standard bond-style-harmonic act the same.
Thank you very much for your time. I am using the latest HEAD of lammps installed just now on March 13, 2013.
in.run (354 Bytes)
data.pos (215 Bytes)