Handling mezzanine in OpenStudio Geometry

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Surfaces and zones being non-convex isn't really a problem, and indeed is perfectly normal - it's hard to avoid unless you have very simple geometry. The main thing it affects is that you cannot set the solar distribution to FullInteriorAndExteriorWithReflections and that's fine. FullExteriorWithReflections typically leads to very similar results with the simpler internal solar radiation distribution assumptions, and if you have a situation where interior solar distribution is really important you can always try out the PixelCounting shadow calculation algorithm instead which is more flexible.

The bigger thing to be aware of is that EnergyPlus assumes that all air in a zone is evenly mixed, and really has trouble capturing the kinds of temperature differences you can get on mezzanine floors from heat rising etc.