Most likely you'll want to treat this as an exceptional calculation measure. Energyplus has better capability for modeling natural ventilation than most other 90.1 approved simulation tools. If using another program, modelers will typically model this by treating it as scheduled infiltration. The schedule would be developed using a spreadsheet and hourly weather data.
If you use the economizer function in your modeling program, you'll be hit with a penalty for fan energy use that doesn't really occur with natural ventilation. Another approach is to still use the economizer function and manually subtract out fan energy.
I encourage others on this forum to comment on their approaches. Please also try the BLDG-SIM forum for additional feedback.