Hi I am having trouble accurately finding the refractive index of a structure I simulate in HFSS.

I have been using chapter 3 of optical metamaterials (Wenshan Cai Vladimir Shalaev) to aid me in creation of a script to define mu and epsilon from scatter parameters S11 and S21. Where Z and then the real and imaginary components of N are calculated and combined where

Epsilon = n/Z

and 

Mu = n*Z

My script.

clear all;

close all;

disp('test extraction routing');

%Known parameters d = thickness l = frequency k = wave number

%frequency adjusted to wavelength. d remains constant. For now using speed

%of light and freq to calculate wavelength

d=200e-9;

freqraw=load('freqs.csv');

freq=freqraw;

lambda=(2.99792458*10^8)./(freq*10^12);

k=(2.*pi)./lambda;

%Outputs S11 (r) and S21 (t) and phase variables

S11=load('magS11m2.csv');

S21=load('magS21m2.csv');

PhaseS11=load('phaseS11m2.csv');

PhaseS21=load('phaseS21m2.csv');

r = S11.*exp(j*PhaseS11);

t = S21.*exp(j*PhaseS21);

figure

hold on

plot(freq,abs(r),'r.')

plot(freq,abs(t),'b.')

title('reflection and transmission over frequency')

xlabel('freq')

ylabel('tranmission (red) and reflection (blue) over frequency')

for gh=1:length(freq);

% Impedance - Z - The route much be chosen which leads to the real

% component of Z being positive

q(gh)=1;

z(gh)=q(gh)*(sqrt(((1+r(gh)).^2-t(gh).^2)/((1-r(gh)).^2-t(gh).^2)));

if real(z(gh))