The longitudinal modulation to the electron beam by a coherent seed laser pulse is widely used for generating fully coherent,short wavelength radiation in various harmonic generation free electron laser (FEL) schemes.After introducing the density modulation,microstructures down to attosecond scale are produced over the distance of one seed laser wavelength.In order to take into account the microstructures in the theoretical and numerical analysis,in the frame of undulator period averaged approach,a modified model for harmonic generation FEL is developed in this paper.With the modified model,three harmonic generation FEL examples are investigated by employing Shanghai soft X-ray FEL (SXFEL) parameters.In FEL schemes with ultra-high harmonic generation and ultra-short pulse,the modified model presents some interesting aspects which are helpful for understanding of radiation pulse evolution,bunching efficiency and noise propagation issues.
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