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You can always create a construction equivalent to that of your door, and assign this to a surface (= a wall) that is sized like the door, in order to get the envelope losses.

By default a door like a window are always closed in EnergyPlus. That is unless you use the advanced AirflowNetwork objects. Alternatively, you can more simply model the infiltration using a schedule in the ZoneInfiltration:DesignFlowRate. You could say for example that you have a pretty high ACH during your loading times (=bay is open), and a regular ACH otherwise (=bay is closed)