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One must be careful not to double-count ventilation loads. ZoneVentilation:DesignFlowRate was originally intended to model non-HVAC system ventilation - such as exhaust fans in a gymnasium or open windows. For ventilation provided by the HVAC system, DesignSpecification:OutdoorAir is used to autosize the OA flow rates if the HVAC system has an outdoor air mixer.

DesignSpecification:OutdoorAir can also be used in ZoneHVAC:IdealLoadsAirSystem to include ventilation requirements. This was not an option with the original ideal load system, and so (if I remember correctly) OpenStudio adds a ZoneVentilation:DesingFlowRate object to account for ventilation loads when running with Ideal Air Loads. I believe OpenStudio still works this way.

So, adding ZoneVentilation:DesignFlowRate objects back into the reference building idf is double-counting the ventilation loads. It's fine for comparing the design zone loads back to the OpenStudio Ideal Loads simulation, but it's not what you want when using a full HVAC system.

One must be careful not to double-count ventilation loads. ZoneVentilation:DesignFlowRate was originally intended to model non-HVAC system ventilation - such as exhaust fans in a gymnasium or open windows. For ventilation provided by the HVAC system, DesignSpecification:OutdoorAir is used to autosize the OA flow rates if the HVAC system has an outdoor air mixer.

DesignSpecification:OutdoorAir can also be used in ZoneHVAC:IdealLoadsAirSystem to include ventilation requirements. This was not an option with the original ideal load system, and so (if I remember correctly) OpenStudio adds a ZoneVentilation:DesingFlowRate ZoneVentilation:DesignFlowRate object to account for ventilation loads when running with Ideal Air Loads. I believe OpenStudio still works this way.

So, adding ZoneVentilation:DesignFlowRate objects back into the reference building idf is double-counting the ventilation loads. It's fine for comparing the design zone loads back to the OpenStudio Ideal Loads simulation, but it's not what you want when using a full HVAC system.