A1: with "Gn" it means grating order. Without it it means the total transmission or reflection.
A2: there are several reason why (abs^2(S21_ Gn)) larger than one:
1) it used the fields instead of the actual s parameters. so in theory the transmitted field intensity can be larger than the incident intensity. Please refer Fresnel coefficient t. It seems you have material in the transmission side (cover cladding or superstrate)?
2) if the simulation is not run long enough, or the autoshut off min is not small enough, the Fourier transform is not accurate.
3) PML may have strong interaction.
Most likely it is #1.
- "angle(S21_Gn)" via the GUI "S->visualize"
- By using the script "fdtd_unit_cell_plot_phase_T" after running the height and radius sweep.
the two methods give different results. "
Phase is a subtle quantity. When the frequency is involved, internally it begins with low frequency as a reference point. If you do the loop otherwise, it will create different reference point. I would suggest to use the exmaple file instead of using your own so to create issues.