how to fix this code in calling function

%% Call the transfer matrix R, T, A calculator function and build spectra
%%%may be need to % Convert angle to radians
[n1]=xlsread('SiO2_n_k.xlsx');
[n2]=xlsread('TiO2_n_k.xlsx');
L= 20;
i=1:L;
A = n1(i,2); %%%%% SiO2 refractive coefficient
B = n2(i,2);  %%%%% TiO2 refractive coefficient
l=n2(i,1);    %%%% wavelength
% Preallocate memory
R = zeros(1,L);
T = zeros(1,L);
A = zeros(1,L);
for m = 1:L
       % Reflection and transmission coefficients, r, t, not used, so
       % replace output with ~. Can add back in if needed. 
       % [r(m),t(m),R(m),T(m),A(m)]=jreftran_rt(wl(m),d,n(m,:),t0,polarization);
       % full form of jreftran_rt
    [r,t,R,T,A]=reftran_rt(l,[NaN,100,500,2000],[1,B,A,1.5],t0,polarization)
end

figure
plot(l,R);
figure
plot(l,A)    
 
%%%%%%%%%%%%%%%% the function 
function [r,t,R,T,A]=reftran_rt(l,d,n,t0,polarization)
%l = free space wavelength, nm
%d = layer thickness vector, nm
%n = layer complex refractive index vector
%t0= angle of incidence
%polarization should be 0 for TE (s-polarized), otherwise TM (p-polarized)

Z0=376.730313; %impedance of free space, Ohms

%the line below had mistakenly been a Z0/n instead of a n/Z0 in version 1!
Y=n./Z0; %admittance in terms of impedance of free space and refractive index, assuming non-magnetic media
g=1i*2*pi*n/l; %propagation constant in terms of free space wavelength and refractive index

%all of the calculations rely on cosine of the complex angle, but we can
%only find the sine of the complex angle from snells law. So we use the
%fact that cos(asin(x))=sqrt(1-x^2)
%t=asin(n(1)./n*sin(t0)), complex theta for each layer
ct=sqrt(1-(n(1)./n*sin(t0)).^2); %cosine theta

if polarization==0
    eta=Y.*ct; %tilted admittance, TE case
else
    eta=Y./ct; %tilted admittance, TM case
end

delta=1i*g.*d.*ct;

M=zeros(2,2,length(d));

for j=1:length(d)
    M(1,1,j)=cos(delta(j));
    M(1,2,j)=1i./eta(j).*sin(delta(j));
    M(2,1,j)=1i*eta(j).*sin(delta(j));
    M(2,2,j)=cos(delta(j));
end    

M_t=[1,0;0,1]; %M total
for j=2:(length(d)-1)
    M_t=M_t*M(:,:,j);
end

r=(eta(1)*(M_t(1,1)+M_t(1,2)*eta(end))-(M_t(2,1)+M_t(2,2)*eta(end)))/(eta(1)*(M_t(1,1)+M_t(1,2)*eta(end))+(M_t(2,1)+M_t(2,2)*eta(end)));
t=2*eta(1)/(eta(1)*(M_t(1,1)+M_t(1,2)*eta(end))+(M_t(2,1)+M_t(2,2)*eta(end)));

R=abs(r)^2;
T=real(eta(end)/eta(1))*abs(t)^2;
A=(4*eta(1)*real((M_t(1,1)+M_t(1,2)*eta(end))*conj(M_t(2,1)+M_t(2,2)*eta(end))-eta(end)))/abs(eta(1)*(M_t(1,1)+M_t(1,2)*eta(end))+(M_t(2,1)+M_t(2,2)*eta(end)))^2;
end

[Walter Roberson]

you did not post your data and you did not indicate which line the error is on.

[zina shadidi]

thank you Walter Roberson for your responce

My data was

n1= [400	3.2861	0
410	3.2248	0
420	3.1856	0
430	3.1624	0
440	3.1494	0
450	3.1405	0
460	3.1300	0
470	3.1041	0
480	3.0800	0
490	3.0538	0
500	3.0300	0
510	3.0138	0
520	3	0
530	2.9850	0
540	2.9700	0
550	2.9544	0
560	2.9400	0
570	2.9294	0
580	2.9200	0
590	2.9100	0
600	2.9000	0
610	2.8894	0
620	2.8800	0
630	2.8750	0
640	2.8700	0
650	2.8600	0
660	2.8500	0
670	2.8444	0
680	2.8400	0
690	2.8350	0
700	2.8300	0
710	2.8250	0
720	2.8200	0
730	2.8144	0
740	2.8100	0
750	2.8100	0
760	2.8100	0
770	2.8056	0];
n2 = [400	1.4701	0
410	1.4691	0
420	1.4681	0
430	1.4672	0
440	1.4663	0
450	1.4656	0
460	1.4648	0
470	1.4641	0
480	1.4635	0
490	1.4629	0
500	1.4623	0
510	1.4618	0
520	1.4613	0
530	1.4608	0
540	1.4603	0
550	1.4599	0
560	1.4595	0
570	1.4591	0
580	1.4587	0
590	1.4584	0
600	1.4580	0
610	1.4577	0
620	1.4574	0
630	1.4571	0
640	1.4568	0
650	1.4565	0
660	1.4563	0
670	1.4560	0
680	1.4558	0
690	1.4555	0
700	1.4553	0
710	1.4551	0
720	1.4549	0
730	1.4546	0
740	1.4544	0
750	1.4542	0]

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

and the error was

Error using horzcat

Dimensions of arrays being concatenated are not consistent.

Error in Untitled2 (line 22)

[r,t,R,T,A]=reftran_rt(l,[NaN,100,500,2000],[1,B,A,1.5],t0,polarization)

Answer 1

[Walter Roberson]

i=1:L;

That is a vector.

A = n1(i,2); %%%%% SiO2 refractive coefficient
B = n2(i,2);  %%%%% TiO2 refractive coefficient

You are indexing a 2D array with a vector of i values. The results in A and B is going to be a column vector of length L.

A = zeros(1,L);

You throw away everything you wrote into A, and replace it with a row vector of length L. not a column vector.

    [r,t,R,T,A]=reftran_rt(l,[NaN,100,500,2000],[1,B,A,1.5],t0,polarization)

In the sub-expression [1,B,A,1.5], the 1 is a scalar. In order for [] (horzcat) to work, everything after that 1 in the [] has to have one row. However, your B is a column vector of length L. Your A is a row vector of length L, so the A,1.5 part is okay, but the column B cannot go there.

If somehow B did fit, such as if you had transposed B into a row vector earlier, then the term would be a vector of length 1 + L + L + 1 = 2*L+2 . Are you sure that is appropriate?

I was going to say that you do the same calculation for every iteration of the for m loop, but then I noticed that you are updating A and it is the updated A that is going back into the next iteration, so potentially that is reasonable.

... But I can't help but think that what you really want is

    [r,t,R,T,A(m)]=reftran_rt(l,[NaN,100,500,2000],[1,B(m),A(m),1.5],t0,polarization);