Attempt to manufacture photonics devices on silicon requires theoretical and numerical prediction. This essay presents Compound FDTD (C-FDTD) method for comprehensive simulation of silicon photonics devices. Although this method is comprehensive, it maintains conventional Yee algorithm. The method involves variation of refractive index due to nonlinear effects. With the help of this simulator, refractive index change due to free-carriers created through two photon absorption and Kerr effect in silicon waveguide is considered. Results indicate how to choose pump pulse shape to optimum operation of active photonics devices. Also conductivity variation of Si waveguide due to change in free-carrier density is studied. By considering variations in conductivity profile, we are able to design better schemes for sweep free carriers away with reverse bias or nonlinear photovoltaic effect for fast devices and Raman amplifiers