Can i use Ems to change the area of a fenestration or a transmittance of a glazing material during the calculation process?

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I don't believe one can dynamically reset (during simulation via EMS) the geometry (i.e. vertices) of an EnergyPlus surface (including fenestrated subsurfaces). Look up the thermal envelope variables one is allowed to actuate. This includes material surface properties, like transmittances. An interesting UMH post on the topic. Best of luck.