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Phase calculation related error due to incorrect boundary conditions?

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I am trying to simulate a metal insulator metal fishnet structure which in infinite in the yz plane and the TE polarized wave propagates in the z direction. I have applied PEC on the planes (xy planes) perpendicular to the electric field (Ez) and perfect magnetic conductor (PMC) on the planes perpendicular (xz planes) to magnetic field (Hy) . I then calculate the transmission and reflection away from the structure as shown in the attached image.
I am able to get the correct, transmission T= |t|^2 and reflection R= |r|^2, however, my extracted phase for the transmission (t) and reflection (r) are incorrect.

I tried the following

1. I used port boundary condition to excite and terminate the wave and PEC and PMC as described above to ensure the infinite periodicity in the yz plane. Why is the phase extracted from the S- parameter is not correct ?

2. I tried using scattering boundary to excite and terminate the wave with PEC and PMC as described. In this case, I could correct T but incorrect phase for the transmission. Reflection |R| was greater than 1, which is incorrect.

Can anyone tell me the correct boundary conditions and the means of exciting the wave?
Any help will be appreciated.
Thank you.

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