We develop a direct numerical method to study the general problem of nonlinear interactions of surface/interfacial waves with variable bottom topography in a two-layer density stratified fluid. We extend a powerful high-order spectral (HOS) method for nonlinear gravity wave dynamics in a homogeneous fluid to the case of a two-layer fluid over non-uniform bottom. The method is capable of capturing the nonlinear interactions among large number of surface/interfacial wave mode and bottom ripple components up to an arbitrary high order. The method preserves exponential convergence with respect to the number of modes of the original HOS and the (approximately) linear effort with respect to mode number and interaction order. The method is validated through systematic convergence tests and comparison to a semi-analytic solution we obtain for an exact nonlinear Stokes waves on a two-layer fluid (in uniform depth). We apply the numerical method to the three classes of generalized Bragg resonances studied in Alam, Liu & Yue (J. Fluid Mech., vol. 624, 2009, p. 225), and compare the perturbation predictions obtained there with the direct simulation results. An important finding is possibly the important effect of even higher-order nonlinear interactions not accounted for in the leading-order perturbation analyses. To illustrate the efficacy of the numerical method to the general problem, we consider a somewhat more complicated case involving two incident waves and three bottom ripple components with wavenumbers that lead to the possibility of multiple Bragg resonances. It is shown that the ensuing multiple (near) resonant interactions result in the generation of multiple new transmitted/reflected waves that fill a broad wavenumber band eventually leading to the loss of order and chaotic motion.
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