Transmission spectrum for optical waveguide

Hello,

I am currently trying to extract a transmission spectrum from a Si waveguide on top of SiO2 substrate. There are some gold particles on top of the Si (this configuration is taken from an article in which they simulate it with FDTD). I tried several things to extract the transmission spectrum:

1) S21 parameter in dB
2) ratio of the Poynting flux at the input and output (tried both with fields Ex,Ey,Ez, emw.Hx, emw.Hy and emw.Hz and with fields from the Boundary mode electric/magnetic field)

I am however not able to get the right profile (for some wavelenghts I even get quit high gains which is unphysical).

It seems that also reflections are taken into account, but in an experiment you will only take the ratio of the actual input power (which is forward propagating) and the forward propagating output power.

Does anybody know how to extract a sensible transmission spectrum (which you would obtain in experiments).

Thanks in advance.

F. Peyskens