Hello, thank you for your reply.
I understand that probably using the "internal S matrix" is not the right choice. I have therefore reset my code such that I use the "User S Matrix".

The simulation region now is the following

I have repeated the process that I described in the previous step. 

  • first I run EME Propagate for [(1,2)^1] and extract the User Matrix
  • second I run EME Propagate for [(1,2)^2] and extract User Matrix. As far as I understood, the User matrix should account for the periodicity
  • third I take the User Matrix of point 1 and calculate the S matrix of two cascaded systems. By right, this should be the same result as point 2. However, the two results differ again

I am not sure I fully understood the suggestion in the previous post. My goal is to get the S matrix of the single unit from EME such that I can use it in Python and cascade it N-times to access the modes field intensities in the middle of the structure. However, it seems that just cascading the S matrices extracted from EME does not give a result consistent with EME one