This Software Reference documents and summarizes all source code produced for a Ph.D. dissertation constructing an underwater virtual world for an Autonomous Underwater Vehicle (AUV). A critical bottleneck exists in Autonomous Underwater Vehicle design and development. It is tremendously difficult to observe, communicate with and test underwater robots, because they operate in a remote and hazardous environment where physical dynamics and sensing modalities are counterintuitive. An underwater virtual world can comprehensively model all salient functional characteristics of the real world in real time. This virtual world is designed from the perspective of the robot, enabling realistic AUV evaluation and testing in the laboratory. Three- dimensional real-time computer graphics are our window into that virtual world. Visualization of robot interactions within a virtual world permits sophisticated analyses of robot performance that are otherwise unavailable. Sonar visualization permits researchers to accurately look over the robot's shoulder or even see through the robot's eyes to intuitively understand sensor- environment interactions. Extending the theoretical derivation of a set of six degree-of-freedom hydrodynamics equations has provided a fully general physics- based model capable of producing highly nonlinear yet experimentally-verifiable response in real time.