I am looking for accelerator codes/simulation packages which incorporate ion source as well as the accelerator components so that optimization studies can be performed for the full accelerator system.

Working with a 3MeV single ended pelletron.

Or are there any packages that are well connected: ion source --> extraction --> acceleration.

Space charge effects may only be significant in the ion source due to high current densities and relatively low velocities (30 KV extraction potential).

FEM methods are very computational intensive while matrix formalism programs generally do not consider space charge.

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