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EnergyPlus treats outdoor air entering a zone similarly whether it is from infiltration or natural ventilation.

However, infiltration values are typically far lower than what is needed to meet the ventilation requirement, so you'll need to add more natural ventilation. You can check this by reporting the infiltration air flow rate versus the ventilation requirement from your design specification outdoor air object.

The Add Wind and Stack Open Area OpenStudio measure on BCL approximates natural ventilation assuming you don't have significant inter-zone air transfer.

If you do have significant inter-zone air transfer you'll need to use the Airflow Network in EnergyPlus, and an EMS program if you have some sophisticated logic to turn the natural ventilation on/off.