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In this paper a new algorithm for missile transfer alignment is supposed. The quaternion algorithm based on the specific force output and angular rate output of the master inertial navigation system and the slave inertial navigation system is deduced too. According to the motion relations between the master INS and the slave INS, the velocity relation and the acceleration relation are derived too. The computing simulation showed the performance of the new algorithm under the noise-disturbance. The new algorithm can be used prior to the more extractive alignment as it can provide smaller misalignment angle by which we can obtain the linear dynamic error model. As we know the linear dynamic error model is more simple for the transfer alignment, so the algorithm of this paper has engineering sense.