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Reporting above outputs at detailed frequency as opposed to hourly would show better comparison. Available capacity is calculated by multiplying reference capacity reported in eio or html output files to ChillerCapFT as mentioned in Engineering reference link above. Note that RefBldgLargeOfficeNew2004_Chicago.idf does HVAC sizing simulation for sizing periods, so for the data snippet posted above Initial Design Size Reference Capacity should be used as opposed to Nominal Capacity. v7 idf shows perfect comparison between manually calculated versus E+ outputs (v7 hourly output, detailed output). Internally, E+ doesn't calculate hourly COP or EIR values.