Energyplus output : surface window net heat transfer rate

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The Surface Window Net Heat Transfer Rate output variable is the sum of many components (transmitted solar radiation, convective losses, etc.), and positive values indicate heat flow INTO the zone through the window. To understand how the west window's net heat transfer rate could be higher in winter, you should add output variables for these other components (transmitted solar radiation, convective losses, etc.). Seeing trends in these components should explain the net heat transfer rate results, such as your building is in the northern hemisphere and excess solar gains at lower altitude angles in the winter are greater than the conduction losses to colder outdoor air in winter.