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BEopt cannot currently model whole house fans. Using a mechanical ventilation system would be a poor workaround because those systems run 24/7, they will not operate only during periods/seasons with favorable outdoor temperatures.
If you are a more advanced user, one option with BEopt v3 is to run the simulation without the whole house fan, grab the HPXML file produced, modify it to include a whole house fan (example here), and then run it directly through OpenStudio-HPXML, which is the underlying simulation platform that BEopt uses to run EnergyPlus. But you'll be running the simulation entirely outside of BEopt at that point.
Or if you are an even more advanced user, you could modify the OpenStudio measure (Workflow/BEoptXMLtoHPXML/measure.rb
in your BEopt installation directory) to automatically add a whole house fan to the HPXML file that gets simulated. That would allow you to still perform simulations within BEopt.