scatter_sim_0_gen_single_spect.m

% This generates the data for a single spectrum of a particle composed of alternating shells of silica and TiO2. The r list gives the list of thicknesses in order from the center outward. The orders have been estimated based on how much loss was percieved as you go to higher orders. 
% Note that this is only for a silica and tio2 geometry. For
% JAggregates/more geometries, other files must be used. 
% Ensure that spherical_T_matrix and spherical_T_matrix/bessel are loaded. 
% varagin is UP TO 3 variables:
%      lambda_limit, eps, order
%   lambda limit specifies the range. Eps the materials, Order the order to compute to. 

function spectrum = scatter_0_generate_spectrum(r,varargin)
lamLimit = 400;
orderLimit = 0;
epsIn = [];
if (nargin ==4)
	lamLimit = varargin{1};
	epsIn = varargin{2};
	orderLimit = varargin{3};
end
if (nargin ==3)
	lamLimit = varargin{1};
	epsIn = varargin{2};
end
if (nargin ==2)
	lamLimit = varargin{1};
end


lambda = linspace(lamLimit, 800, (800-lamLimit)+1)';
omega = 2*pi./lambda;
data = load('data.mat');
eps_silver = interp1(data.omega_silver,data.epsilon_silver,omega);
%eps_gold   = interp1(data.omega_gold,data.epsilon_gold,omega);

eps_silica = 2.04*ones(length(omega), 1);
my_lam = lambda./1000;
eps_tio2 = 5.913+(.2441)*1./(my_lam.*my_lam-.0803);
eps_water  = 1.77*ones(length(omega), 1);
% load data on epsilon

eps = [];
for i = 1:length(r)
    if mod(i,2) == 1
        %eps = [eps eps_gold];
        eps = [eps eps_silica];
        %eps = [eps eps_silver];
    else
    	%eps = [eps eps_silver];
        eps = [eps eps_tio2];
        %eps = [eps eps_silica];
	end
end
eps = [eps eps_water];
if length(epsIn) > 0
	disp('Overriding eps...')
	eps = epsIn;
end

order = 25;
if length(r) ==2 || length(r) == 3
	order = 4;
end
if length(r)  == 4 || length(r) == 5
	order = 9;
end
if length(r) == 6 || length(r) == 7
	order = 12;
end
if length(r) == 8 || length(r) == 9
	order = 15;
end
if length(r) == 10 || length(r) == 11
    order = 18;
end
if orderLimit > 0
	disp('Orderring order limit')
	order = orderLimit;
end

spectrum = total_cs(r,omega,eps,order)/(pi*sum(r)^2);