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The ship course / roll system is a nonlinear and strongly coupled system. Based on the parameter uncertainty of the ship course / roll coupled model, a decentralized variable structure control algorithm is adopted. The interconnection matrices are regarded as the parameter matrix of the nominal system under the known condition of the interconnection terms. The global asymptotic stability of the decentralized variable structure control algorithm is achieved. The simulation results show that, the proposed control method can control the ship yaw and roll very efficiently with high accuracy, conciseness and would be easy to be realized.