Question-and-Answer Resource for the Building Energy Modeling Community
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In addition to what Julien suggested, you can also use the ParametricPreprocessor that comes with EnergyPlus to modify the coordinates on the windows to achieve the sensitivity to Window to Wall Ratio. See the documentation at:
http://bigladdersoftware.com/epx/docs/8-4/input-output-reference/group-parametrics.html#group-parametrics
and the example files:
The first does some vertex manipulation so it is probably the place to start.
