Abstract: Several parameters determine the performance of free electron lasers: the slice and the projected emittance, the slice energy spread, and the peak current are the most crucial ones. The peak current is essentially obtained by magnetic compression stages along the machine or occasionally assisted by velocity bunching at low energy. The minimum emittance and the alignment of the slices along the bunch are mainly determined in the low energy part of the accelerator (injector). Variations at the per-mille level of several parameters in this section of the machine strongly influence these quantities with highly nonlinear dynamic. We developed a numerical tool to perform the optimization of the injector. We applied this code to optimize the SwissFEL injector, assuming different gun designs, initial bunch lengths and intrinsic emittances. We obtained an emittance along the bunch of 0.14 mm mrad and around 0.08 mm mrad for the maximum and the minimum SwissFEL charges (200 and 10 pC, respectively). We applied the same tool to a running injector, where we automatized the optimization of the machine.
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