We have carried out a classical molecular dynamics study to quantify the conditions under which damage is generated by ion implantation in silicon at energies below the displacement threshold. The obtained results have been used to construct a general framework for damage generation which captures the transition from ballistic (high above the displacement threshold) to thermal (around and below the displacement threshold) regime. The model, implemented in a binary collision code, has been successfully used to simulate monatomic and especially molecular implantations, where nonlinear effects occur. It reproduces the amount and morphology of generated damage at atomic level in good agreement with classical molecular dynamics simulations but with a computational gain factor of ∼103 to ∼104. The incorporation of this damage model to process simulators will improve the prediction of amorphization conditions and provide a convenient tool for simulating molecular implants not available to date. Although this work has been focused on silicon, the model can be applied with appropriate calibration to other materials where the thermal regime of damage generation plays an important role.