Regarding Wind Energy, I would recommend OpenWind for flat terrain conditions. On complex terrain conditions it is advisable to run a more sophisticated CFD tool - such as WindSim, Meteodyn or some OpenSource implementation.
Greenius Simulation software for the technical and economical calculations as they are needed for planning and installation of renewable power projects such as:
Solar thermal parabolic trough power plants, Photovoltaic systems, Wind parks and Dish/Stirling systems.
The below mentioned review cites several references on mathematical modelling of biomass pyrolysis , which produce biofuels; a type of renewable energy. Happy new year.
do your simulations with MATLAB. A software usually does not consider some aspects and linearizes many formulas. So use your own code and write a fitness function code in MATLAB M-file and finally enjoy a wide range of optimization algorithms.