Dear Stuart,
The first task is to determine the required thickness of the elliptical nozzle. Next you must determine the required thickness of the rectangular vessel due to internal pressure. The method outlined in Appendix 13, is stressed based, so using Codecalc you will have to iterate to determine a value of tr.
Once you have the required thicknesses, you can use the nozzle program to determine the area of replacement. As you noted you model this as a flat type of geometry. In this case the flat head diameter becomes irrelevant because you will using the feature of enetering the required thickness of both the nozzle and vessel. In essence, you are giving the program answers that it would normally compute.
Also, the program will run when the nozzle diameter is greater than the shell diameter, but with a warning.
I hope this helps,
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Scott MayeuxCADWorx & Analysis Solutions
Intergraph Process, Power, & Marine