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This paper describes a controller design method for inertially stabilized system of tracking radar. Its aim is to track a reference target trajectory while isolating any rigid body motion of a host ship. First, we treat the trajectory generation problem to make the control input for a target tracking on the moving base. Second, dynamic equation of motion is formulated by spring-mass-damper system to include rigid body dynamics as well as structural flexibility. The unknown parameters of the dynamic equation are estimated with experimental input output data by minimizing predicted error. Third, mixed sensitivity H∞ robust controller is designed to meet the conflict requirements of robustness and performance in the face of plant uncertainty. Finally, the proposed optimal controller is implemented and show the effectiveness of design methodology by experimental results.