Windows (frame) in OS

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From the Input-Output Reference:

"The window vertices that you specify in the FenestrationSurface:Detailed object are those of the glazed part of the window, not the frame. EnergyPlus automatically subtracts the area of the frame—determined from the glazing dimensions and the frame width—from the area of the wall containing the window."

The assigned window dimensions retain their integrity, and frame thickness is removed from the parent wall.

There is also some information here regarding Frame vs. Glass Conductance that may be helpful to you. There are a few different ways of assigning these, mainly dependent upon the granularity of information you have.