The accurate numerical simulation of wave disturbance within harbours requires consideration of both nonlinear and dispersive wave processes in order to capture such physical effects as wave refraction and diffraction, and nonlinear wave interactions such as the generation of harmonic waves. The Boussinesq equations are the simplest class of mathematical model that contain all these effects in a variable depth, shallow water environment. There are a variety of Boussinesq-type mathematical models and it is necessary to compare and contrast them both for their limitations with respect to the physical parameters of the problem and also for their ease of application as part of a suitable numerical model. It is decided here to consider a set of extended Boussinesq equations which provide an accurate model of the wave processes over a greater range of depths than the classical Boussinesq mathematical model.\ud \ud A method-of-lines numerical algorithm is proposed for these problems, combining a finite element spatial discretisation with existing, adaptive order, adaptive step size time integration software. Two simpler one-dimensional, nonlinear, dispersive wave models; the Korteweg-de Vries equation and Regularised Long Wave equation, are used in the initial development of the numerical methods. It is shown that within the shallow water framework a linear finite element method is sufficiently accurate for these problems.\ud \ud This numerical method is then applied to the one-dimensional extended Boussinesq equations. It is shown how the previously developed method can be directly used and that it is of similar accuracy to a previously published finite difference method. Initial conditions and boundary conditions are described in detail taking into account physical, mathematical and computational considerations. A new formulation of internal wave generation is developed which allows reflected waves to pass through the wave generation region. The performance of the numerical model is demonstrated by comparison against theoretical results, a previously published finite difference model and experimental results.\ud \ud The two-dimensional extended Boussinesq equation system is rewritten in a form suitable for the application of a linear triangular finite element spatial discretisation. The formulation of appropriate initial and boundary conditions in combination with the application of the time integration software to this equation system is considered in detail. The performance of the numerical method is tested by comparison with experimental data and the suitability of the model for harbour design is investigated by simulation of a realistic harbour geometry and wave conditions. \u
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