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A control strategy for the guidance system of an autonomous underwater vehicle based on an integral variable structure controller was proposed. The system mathematical model was established, and was linearized over a specified operating point to suit for the controller design. An integral variable structure controller was designed based on variable structure control theory. The approach to reduce chatter was given. The simulation results show that the proposed controller is effective to eliminate the effects of modeling uncertainty, severe nonlinearity and external disturbances. The system presents good performances and the robustness of the system is good enough.