Geophysical flows support the propagation of stable nonlinear internal waves (internal solitary waves or ISWs) with complex generation mechanisms. At least two regimes of ISWs generation in the pycnocline, both involving the interaction between a tidal flow and the bottom topography, are known in the ocean. They can either be directly induced above topographies (primary generation) or by a topographic internal wave beam impinging on the pycnocline. This " secondary generation " process is the subject-matter of the present study. The present work relies on direct numerical simulations of an academic configuration inspired by oceanic observations. It aims at describing the different steps involved in the secondary generation process. To mimic the oceanic case, the internal wave beam is emitted from the topography at the bottom of the flow. First, the linear scattering of the internal wave beam at the pycnocline is studied in a linear configuration. Increasing the forcing amplitude leads to the generation of steep isopycnal troughs in the pycnocline, at the locations of the internal wave beam impacts. The dynamics of these troughs is studied in details, which permits to associate them with propagating ISW2s that emerge from the second normal mode. Finally, the evolution of the structure of normal modes 2 and 3 with respect to the pycnocline strength, as well as the role played by the topography , is analyzed. This study is a step to complete and unify previous independent analytical studies of the secondary generation process.