Autonomous underwater vehicles (AUVs) are an emerging technology with applications in very different fields, such as military, homeland defence, underwater surveys, environment monitoring, and oceanographic studies (Griffiths, 2003). Although the use of AUVs in some of these fields is already well established, there is still a great research effort in areas related to the design and operation of these vehicles. The Ocean Systems Group at FEUP (Faculty of Engineering at the University of Porto) and ISR - Porto (Institute for Systems and Robotics -Porto) conducts research activities in marine robotics and has accumulated expertise in the utilization of AUVs and in the development of particular subsystems. This chapter addresses the design of the navigation and control systems of the MARES AUV (Cruz & Matos, 2008), a state-of-the-art small size AUV developed by the authors and already demonstrated at sea operations in 2007. The implementation of these systems in the vehicle on-board software is also discussed.
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