I have a 50nm thin Cu film. How do I calculate the deposition rate in Atoms/s instead of A/s. Do I just normalize the thickness by the atomic diameter?
It would depend on the crystal structure of the film. Copper is FCC in most cases so I would divide thickness by lattice constant/sqrt(2) to convert to number of atoms. Using atomic diameter over lattice parameters leaves more room for confusion since there are various definitions of the former depending on the nature of bonding in the material.
The approach be the crystal structure from Pralav Shetty is a good idea. You could simplify that even more: if it has the usual crystal structure, you could simply calculate the volume of the film, multiply that with the density and divide it by the molar mass of Cu.
in addition to what Jürgen Weippert said, additionally you have to multiply by the Avogadro number NA ~6,022*1023/mol to get the number of atoms. When calculating the volume times density divided by Cu atomic mass, you only get the number of moles in your sample. So please additionally multiply by NA to have the number of atoms.