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This question has been lingering unanswered for some time. Answered with a comment, but technically still unanswered.

The multi-speed system in E+ is a heat pump. To properly model a multi-speed fan, a system that models a change in speed must be used. This was originally named a multi-speed heat pump. The heat pump uses a multi-speed cooling coil (Coil:Cooling:DX:MultiSpeed) with a multi-speed or multi-stage heating coil. Other heating coil types are allowed with this parent object but the point is that there are discrete speeds associated with the performance of this equipment type. The following example uses the input data dictionary (IDD) to show specific input syntax.

AirLoopHVAC:UnitaryHeatPump:AirToAir:MultiSpeed,
  N9, \field Number of Speeds for Heating
  N10, \field Number of Speeds for Cooling
  N11, \field Heating Speed 1 Supply Air Flow Rate
  N12, \field Heating Speed 2 Supply Air Flow Rate
  N13, \field Heating Speed 3 Supply Air Flow Rate
  N14, \field Heating Speed 4 Supply Air Flow Rate
  N15, \field Cooling Speed 1 Supply Air Flow Rate
  N16, \field Cooling Speed 2 Supply Air Flow Rate
  N17, \field Cooling Speed 3 Supply Air Flow Rate
  N18; \field Cooling Speed 4 Supply Air Flow Rate

This multi-speed heat pump must also use a multi-speed cooling coil, with inputs similar to those shown above, and choices for heating coil types, multi-speed or otherwise.

A new model, one which combines all coil types into a single parent object, can also model multi-speed coils. This is the AirloopHVAC:UnitarySystem. A field at the end of this object allows a user to specify a multi-speed performance object.

AirLoopHVAC:UnitarySystem,
  A26, \field Design Specification Multispeed Object Type
    \key UnitarySystemPerformance:Multispeed
  A27; \field Design Specification Multispeed Object Name

The multi-speed performance object looks identical to the inputs for the AirLoopHVAC:UnitaryHeatPump:AirToAir:MultiSpeed object except that flow ratios are used instead of actual flow rates.

UnitarySystemPerformance:Multispeed,
  A1 , \field Name
  N1 , \field Number of Speeds for Heating
  N2 , \field Number of Speeds for Cooling
  N3 , \field Heating Speed 1 Supply Air Flow Ratio
  N4 , \field Cooling Speed 1 Supply Air Flow Ratio
  N5 , \field Heating Speed 2 Supply Air Flow Ratio
  N6 , \field Cooling Speed 2 Supply Air Flow Ratio
  N7 , \field Heating Speed 3 Supply Air Flow Ratio
  N8 , \field Cooling Speed 3 Supply Air Flow Ratio
  N9 , \field Heating Speed 4 Supply Air Flow Ratio
  N10; \field Cooling Speed 4 Supply Air Flow Ratio

The difference between these two methods for modeling a multi-speed system is very subtle.

For the AirLoopHVAC:UnitaryHeatPump:AirToAir:MultiSpeed object, the speed inputs must be entered in two locations, the parent and the child object. If these inputs are autosized, the system performance is the same as that specified in the coil object. If the inputs are not autosized, the air flow rate is dictated by the parent object and the performance changes based on the parent object flow rates. See the Speed 1 Total Cooling Capacity Function of Flow Fraction Curve Name input field in the multi-speed cooling coil object for further description.

For the AirLoopHVAC:UnitarySystem object, the multi-speed performance object inputs need only be entered in the child (coil) object(s). Or, if the performance at the system level is different than that specified in the coil object, the UnitarySystemPerformance:Multispeed object can be used to enter non-design flow ratios. This option allows a multi-speed system to be operated (simulated) at flow rates different than design. For example, a system that has a dip switch that sets the flow rate to values other than those used for performance rating tests. As with the multi-speed heat pump described above, if all flows are autosized, the UnitarySystemPerformance:Multispeed object has no real impact.

To finish this discussion, the Fan:OnOff object inputs must include the performance curves needed to properly model a multi-speed system to correctly model the power and energy use.

Fan:OnOff,
  A5 , \field Fan Power Ratio Function of Speed Ratio Curve Name
  A6 , \field Fan Efficiency Ratio Function of Speed Ratio Curve Name

The PackagedTerminalHeatPump example file shows inputs related to the fan power and efficiency ratio performance curves.