I am just following the code in the threads. This is the actual transmission reflection (blue: reflection, green : transmission) of my structure.

Now I am doing the s-parameter analysis to verify. Later I will check for RCP /LCP conversion for different structures. The transmission as I have followed is coming using the code:

The transmission is more or less ok. The amplitudes are different because I am using (abs)^2. The transmission:

I have modified it for reflection mode dividing n2/n1 since the amplitude was coming to 4,4.2 (>1). The dips are not matching with the normal source and monitor reflection. This is the reflection:

can you help me in sorting out this?