3. Implementing molecular dynamics

Simulation begins by defining the initial state, characterized by :

• the nature of the particles and the potential ;

• particle position ;

• boundary conditions ;

• the particle velocity field ;

• initial temperature.

To simplify the presentation, it is limited to a set of atoms of the same element with zero mean velocity (fixed center of gravity) and no rotational motion around the center of gravity. Only one interatomic potential is required, and the choice of potential is directly related to the nature of the atoms and the physical phenomena being studied.

In most cases, the initial position of the atoms is that which corresponds to the theoretical position...