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There are a few relevant example files of methods packaged with v8.1. I am using one called AirflowNetwork_Multizone_HorizontalOpening.idf. I am currently applying this example on a project where I have stack flow through a 2 story atrium space. I have a lower level and upper level opening which I am modeling for natrual vent. Seems to be working out well.

Also, for anyone who doesn't know about the E+ sample files, check out the install directory \EnergyPlusV8-1-0\ExampleFiles\ . Also, there is a spreadsheet in that directory that summarizes each file and very handy for keyword searching.