One word comes to mind ewww! Rectangular sections properties are not symetric like a nice round cyclinder.
Then you throw in localized buckling perhaps and more ewww....
If your FEA will give you a spring rate tha defines the localized krates of all 6DOF at the intersection between the pipe and the duct then you should define them in the beam element model at the intersection i.e., the pipe O.D. see the tech reference manual for nozzle flexibity modeling.... and good luck!
Remember you will end up with an approximation!
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Best Regards,
John C. Luf