Our primary tools continue to be opensource R&D codes, so we have picked OpenFOAM and ElmerFEM. The benefit of picking these codes is that we have access to the underlying numerical methods, and can adapt code to suit our purposes. They are also really well supported, and have small communities of scientists extending their applications all the time.
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The OpenFOAM® (Open Field Operation and Manipulation) CFD Toolbox is a free, open source CFD software package which has a large user base across most areas of engineering and science, from both commercial and academic organisations. For more information visit OpenFOAM's website
Elmer is an open source multiphysical simulation software. Elmer includes physical models of fluid dynamics, structural mechanics, electromagnetics, heat transfer and acoustics, for example. These are described by partial differential equations which Elmer solves by the Finite Element Method (FEM). For more information visit ElmerFEM's website