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In order to reduce the influence on horizontal misalignment, which is caused by external velocity error under the external damping mode in Strapdown Inertial Navigation System (SINS for short), the technology of dual-system parallel processing is presented in the SINS calculation. Solution system 1 is the same as traditional solution model, in which log provides the external velocity; in solution system 2, external velocity is taken from solution system 1, and then the calculating in external damping mode continues after adjusting the damping parameters. Thus, the propagation path of external velocity error is changed, so that the influence on the accuracy of navigation information caused by this error is reduced. The simulation result shows that, the dual-system parallel processing technology can reduce the effect on horizontal misalignment effectively. And then, the experiment is operated by the FOG SINS which is made by our lab. The experiment results show the proposed method is valid.