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OK This is a summary from Jason DeGraw's answer. The regular AFN model is based on pressure and temperature difference in different zones (see Engineering Reference in E+), and so it cannot be used to calculate temperature stratification in one thermal zone,(the restriction mentioned in I/O reference), because the theories of temperature stratification in one zone are more complex then the assumption of pressure model in AFN. For example, when dividing a large space into some subzones, you actually make a wrong assumption that the large space has a temperature stratification with the same pattern of the subzones you defined. And of course, that is incorrect. No one knows the real airflow pattern in a large zone without more advanced simulations or measurements.

If you want to know the true flow pattern in one single zone, it needs CFD or measurement, and then calibrate your Roomairmodel in the Energyplus. When you cannot use CFD or other methods, how to define the Roomair model is based on your engineering judgement. (be careful)

Thanks for Jason DeGraw's patient explanation.