The satellite clocks used in the BeiDou-2 satellite navigation System (BDS) are Chinese self-developed Rb atomic clocks, and their performances and stabilities are worse than GPS and Galileo satellite clocks. Due to special periodic noises and nonlinear system errors existing in the BDS clock offset series, the GPS ultra-rapid clock model, which uses a simple quadratic polynomial plus one periodic is not suitable for BDS. Therefore, an improved prediction model for BDS satellite clocks is proposed in order to enhance the precision of ultra-rapid predicted clock offsets. First, a basic quadratic polynomial model which is fit for the rubidium (Rb) clock is constructed for BDS. Second, the main cyclic terms are detected and identified by the Fast Fourier Transform (FFT) method according to every satellite clock offset series. The detected results show that most BDS clocks have special cyclic terms which are different from the orbit periods. Therefore, two main cyclic terms are added to absorb the periodic effects. Third, after the quadratic polynomial plus two periodic fitting, some evident nonlinear system errors also exist in the model residual, and the Back Propagation (BP) neural network model is chosen to compensate for these nonlinear system errors. The simulation results show that the performance and precision using the improved model are better than that of China iGMAS ultra-rapid prediction (ISU-P) products and the Deutsches GeoForschungsZentrum GFZ BDS ultra-rapid prediction (GBU-P) products. Comparing to ISU-P products, the average improvements using the proposed model in 3 h, 6 h, 12 h and 24 h are 23.1%, 21.3%, 20.2%, and 19.8%, respectively. Meanwhile the accuracy improvements of the proposed model are 9.9%, 13.9%, 17.3%, and 21.2% compared to GBU-P products. In addition, the kinematic Precise Point Positioning (PPP) example using 8 Multi-GNSS Experiment MGEX stations shows that the precision based on the proposed clock model has improved about 16%, 14%, and 38% in the North (N), East (E) and Height (H) components.
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