Are there any Workbench Simulation examples showing how to resolve initial interference and load a hyperelastic material followed by geometry file creation from the deformed element shapes?

Yes, please see the attached ANSYS Workbench Simulation 11.0 half-symmetry model of a rubber seal being held in place by two rigid bodies. The seal has significant initial interference. A rigid plunger then deforms the seal downward after the interference is resolved and the deformed geometry is used to create IGES geometry that can be used for subsequent FSI runs. The command objects, including a macro to create the IGES geometry, are fully commented.

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