We describe a mesh-free three-dimensional (3D) numerical scheme for solving the incompressible semi-geostrophic equations, based on semi-discrete optimal transport techniques. These results generalise previous two-dimensional (2D) implementations. The optimal transport methods we adopt are known for their structural preservation and energy conservation qualities and achieve an excellent level of efficiency and numerical energy-conservation. We use this scheme to generate numerical simulations of an important benchmark problem. To our knowledge, this is the first fully 3D simulation of this particular cyclone, evidencing the model's applicability to atmospheric and oceanic phenomena and offering a novel, robust tool for meteorological and oceanographic modelling.
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