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This EMS program looks correct. I suspect the program is working, however, the calling point is before the HVAC system simulates and, therefore, the TU is overwriting your flow rate. BeginTimestepBeforePredictor means on the next time step before the program predicts the zone loads.

Try changing the calling point to the next 2 choices, in that order, to see if changing the calling point helps.

The other options are:

EnergyManagementSystem:ProgramCallingManager,
 A2 , \field EnergyPlus Model Calling Point
   \type choice
   \key BeginNewEnvironment
   \key AfterNewEnvironmentWarmUpIsComplete
   \key BeginTimestepBeforePredictor
   \key AfterPredictorBeforeHVACManagers
   \key AfterPredictorAfterHVACManagers
   \key InsideHVACSystemIterationLoop
   \key EndOfZoneTimestepBeforeZoneReporting
   \key EndOfZoneTimestepAfterZoneReporting
   \key EndOfSystemTimestepBeforeHVACReporting
   \key EndOfSystemTimestepAfterHVACReporting
   \key EndOfZoneSizing
   \key EndOfSystemSizing
   \key AfterComponentInputReadIn
   \key UserDefinedComponentModel
   \key UnitarySystemSizing

This EMS program looks correct. I suspect the program is working, however, the calling point is before the HVAC system simulates and, therefore, the TU is overwriting your flow rate. BeginTimestepBeforePredictor means on the next time step before the program predicts the zone loads.

Try changing the calling point to the next 2 3 choices, in that order, to see if changing the calling point helps.

The other options are:

EnergyManagementSystem:ProgramCallingManager,
 A2 , \field EnergyPlus Model Calling Point
   \type choice
   \key BeginNewEnvironment
   \key AfterNewEnvironmentWarmUpIsComplete
   \key BeginTimestepBeforePredictor
   \key AfterPredictorBeforeHVACManagers
   \key AfterPredictorAfterHVACManagers
   \key InsideHVACSystemIterationLoop
   \key EndOfZoneTimestepBeforeZoneReporting
   \key EndOfZoneTimestepAfterZoneReporting
   \key EndOfSystemTimestepBeforeHVACReporting
   \key EndOfSystemTimestepAfterHVACReporting
   \key EndOfZoneSizing
   \key EndOfSystemSizing
   \key AfterComponentInputReadIn
   \key UserDefinedComponentModel
   \key UnitarySystemSizing