Molecular dynamics is applied to systems containing usually a few thousands atoms. Surface effects, i.e. interactions of atoms with the container wall or effects of the free surface, are dominant in such small systems. In simulations of the crystal bulk those surface effects are not of interest and may be eliminated by means of periodic boundary conditions. In order to implement the periodic boundary conditions for atoms in a volume , we imagine that the volume is only a small part of the bulk material. The volume is called the computational (or primary) cell, it represents the bulk material to extent that the bulk is assumed to be composed of the primary cell surrounded by exact replicas of itself. These replicas are called image cells. The image cells are the same size and shape. Thus, the primary cell is periodically replicated in all directions to form a macroscopic sample (See Fig. 3.1).
In order to simulate the surface the periodic boundary conditions have to be altered. We use periodic boundary conditions only in the and directions, which are parallel to the surface. The system is represented as a slab of layers oriented perpendicular to the direction. Each layer contains atoms arranged in a bcc pattern. The bottom layers are fixed to mimic the effects of an infinite bulk of the solid.