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The calculations in G3.1.2.9 state to use CFM_s; which is the CFM of the supply. This CFM is auto-sized based on the flow rate needed in the Baseline building. This CFM will depend upon the space load sizing and is based on a 20F delta supply air temperature from setpoint per G3.1.2.8. So, per G3.1.2.9 one calculates the kW allowed per system Supply airflow rate only. This kW is allocated proportionally to the fans in the system (supply, return, exhaust, and relief). example: if the calculated Baseline Fan system is 10 kW of fan power and in the Proposed building the fan power is 50% supply, 30% return, and 20% exhaust; then this 10kW is split to 5kW supply, 3kW return, 2kW exhaust. I've also seen modelers who take this 10kW and split it based on the combined flow rate of the baseline's supply+exhaust+return+relief and apply this kW/CFM_bl_total to all fans in the baseline. The end result is probably highly similar for most cases since the Baseline fan system is still only 10kW. There is no allowance for return, exhaust, or relief flow. There are allowances for things like filtration or energy recovery, but not other fans in the system.

The directions in G3.1.2.8 will impact the system flow rates. So, while there's no power allowance for the return/relief fan, the presence of the return/relief fan should/will impact the calculated supply fan flow rate.

Note: All code references are to 90.1-2007 / LEEDv2009/3. 90.1-2010/LEEDv4 has same/similar requirements, but code section numbers are slightly different.