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Hi there, Thanks for your interest in the DOE Prototype Models. EnergyPlus takes COPnf (no fan) inputs for the cooling coil objects and models fans in packaged systems as sperate objects. Therefore, the COP in the prototypes are COPnf. In the current models
COPnfcooling= (EER/3.413 + R) / (1-R) R is assumed to be 0.12
See PDF page 46. Thornton B.A., M.I. Rosenberg, E.E. Richman, W. Wang, Y. Xie, J. Zhang, and H. Cho, et al. 2011. Achieving the 30% Goal: Energy and Cost Savings Analysis of ASHRAE Standard 90.1-2010. PNNL-20405. Richland, WA: Pacific Northwest National Laboratory. http://www.pnl.gov/main/publications/external/technical_reports/PNNL-20405.pdf
ASHRAE Standard 90.1-2016 Appendix G has a new formula. See Section G3.1.2.1. Our prototype simulation team plan to adopt this new method in the future prototype updates.
For your second question, when a large thermal zone is expected to be served by more than one packaged single-zone systems, the autosized capacity of the large zone is used to determine the EER from the code table. Although it is reasonable to split the large capacity to multiple smaller units, our team has not used that approach to the published prototype models. In some special analysis projects, we have done the split using a rule of thumb approach.