I have 2 problem.
1- I am going to model a “cluster deposition” by LAMMPS. However, I do not know how to make a circle of atoms as a cluster!!!
2- I am going to import some positions data to LAMMPS.but this thinks comes to my mind that: how can these positions find their equilibrium positions in LAMMPS. I have not done this before.
You dont state what you mean by a cluster. If you mean
those atoms have bonds between them, then the read_data
file defines the bonds. You can use the minimize command
to relax the initial config of the atoms. Or run dynamics
with fix viscous and a small timestep or use fix nve/limit.
You can also use zero velocity for all cluster atoms and the same translational one.