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This paper documents a successful methodology to model complex systems that require simultaneous system and board level thermal/fluid interactions. First, a CAD model integrating the board and system level geometry was created using Autodesk Inventor 4.0. This CAD model was then imported into a CFD Solver. The CFD solver used was CFDesign 4.1, a finite element fluid flow and heat transfer solver. CFDesign's ability to import geometry using any industry-standard format and quickly prepare it for simulation was the key to creating a CFD model that accurately predicts both system and board level thermal performance concurrently. By employing the above CAD and CFD tools in concert with experimentally validated assumptions, chip junction temperatures were accurately predicted as well as their sensitivities to system level characteristics.