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The definition of Energy Related Costs, Annualized in the BEopt help file reads: "Annualized energy related costs, the default y-axis metric on the Cost/Energy Graph, are calculated by annualizing the energy related cash flows over the analysis period. The annualized cost is then subtracted from the reference for every cash flow but utility bills (i.e. the values displayed in the Cost/Energy graph are full annualized utility bills plus incremental annualized values for every other cash flow)."

The important fact here is that most costs are incremental relative to the reference building. So if you have a design that is also set as the reference, all incremental cash flows (including measure costs) are zero and only the annualized utility bill is displayed. When the design is compared to a different reference, then there are incremental cash flows (including measure costs) in addition to the annualized utility bill.

For this reason, you can't really compare Energy Related Costs, Annualized across different cases unless the same reference is used in all of them. If you do want to compare across cases with different references, you could use the Energy Related Costs, Life Cycle Cost metric instead.

The definition of Energy Related Costs, Annualized in the BEopt help file reads: "Annualized energy related costs, the default y-axis metric on the Cost/Energy Graph, are calculated by annualizing the energy related cash flows over the analysis period. The annualized cost is then subtracted from the reference for every cash flow but utility bills (i.e. the values displayed in the Cost/Energy graph are full annualized utility bills plus incremental annualized values for every other cash flow)."

The important fact here is that most costs are incremental relative to the reference building. So if you have a design that is also set as the reference, all incremental cash flows (including measure costs) are zero and only the annualized utility bill is displayed. When the design is compared to a different reference, then there are incremental cash flows (including measure costs) in addition to the annualized utility bill.

For this reason, you can't really compare Energy Related Costs, Annualized across different cases unless the same reference is used in all of them. If you do want to compare across cases with different references, you could use the Energy Related Costs, Life Cycle Cost metric instead. instead where all cash flows are absolute (not incremental).