We have developed an atomistic model to describe ion beam induced amorphization in silicon. The building block for the amorphous phase is the bond defect or IV pair, whose stability increases with the number of surrounding IV pairs. This feature explains the regrowth behaviour of different damage topologies and the kinetics of the crystalline to amorphous transition. Amorphous regions start their regrowth by the atoms in the interface, as they have less surrounding IV pairs. The model provides excellent quantitative agreement with experimental results. It captures the critical transition temperature as a function of the ion mass and dose rate. The superlinear increase of the accumulated damage with dose is also reproduced by the model.