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Please simulate a 2-port short uniform TLN. MODUA will be displaying the s-parameters after simulation. Please select PROCESS->FIND TRANSMISSION LINE PARAMETERS and provide the physical length. Then, you will have a table of the Ereff vs. Frequency.
The popular formula for effective permittivity calculation only takes the two-layer dielectric into account. You can find it in the transmission part of one microwave or microstrip patch antenna part of one antenna book. It's really complicated to calculate the effective permittivity of multi-layer dielectric.