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AvailabilityManager:NightCycle will control the AHU fans. The schedule in the fan object should be 1 during occupied hours and 0 during unoccupied. The same schedule is referenced in the AvailabilityManager:NightCycle object. If this is not working as expected, then compare your inputs with an example file (e.g. RefBldgMediumOfficeNew2004_Chicago.idf). If you cannot figure it out, then we need to see the idf (either here or at the helpdesk).

The chilled water system does not have an equivalent type of availability manager. If you set the chilled water pump control to Intermittent, then the chilled water loop will operate whenever any chilled water coil requests flow.