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Presenting a satellite orbit dynamic equation with Earth-fixed coordinate, establishing an observation equation based on IGRF model, forming a navigation model for the magnetometer-based satellite navigation system. Building and simulating the magnetometer-based satellite orbit determination algorithm based on adaptive filter. Simulation results show that this model has simple structure, stronger capability of description. The algorithm is more reliable and has better astringency. It can be concluded that the algorithm solves the emanative problem of EKF.