We propose an atomistic model to describe the damage generation during ion irradiation in Si and its evolution upon anneal. We have included new features to the classical models used to describe damage in crystalline Si, that allow us to extend the atomistic approach to the modeling of continuous amorphous layers. The elementary units to describe the defective lattice are Si interstitials, vacancies and the bond defect, which is a local distortion of the lattice without any excess or deficit of atoms. More complex defect structures can be formed by the coalescence of these elementary units. The competition between the damage generation and its annihilation determines the damage accumulation that eventually may lead to amorphous layers. The same model is used for amorphizing and non-amorphizing implants, and the amorphization is the result of the simulation itself and not established as an input parameter.