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(OP)
n0 = 1;
n1 = 2.52;
n2 = 1.9;
n3 = 2.11;
n4 = 2.39;
n5 = 2.46;
lamda = 330*(10^-3);
pi = 3.14;
p = (n0)/(n2);
q = n0;
r = 1/(n2);
loop = 3;
tsap = 430;
taln = 900;
talgan1 = 107;
talgan2 = 128;
talgant = 583;
nrows = tsap + taln + (talgan1 + talgan2)*loop + talgant;

R = zeros(1,nrows);


for  t0 = 1:1:tsap;              % for saphhire
     Gr0 = 0;
     Ph0 = (2*(pi)*2*(n0)*(Gr0)*(t0))/lamda;
     X = [cos((Ph0)/2) (j/n0)*sin((Ph0)/2); (j*n0)*sin((Ph0)/2) cos((Ph0)/2)];
     Ro0 = ((p)*(X(1,1))+(q)*(X(1,2))-(r)*(X(2,1))-(X(2,2)));
     Ao0 = ((p)*(X(1,1))+(q)*(X(1,2))+(r)*(X(2,1))+(X(2,2)));
     Re0 = (Ro0)./(Ao0);
     Rc0 = conj(Re0);
     R(t0) = ((Re0).*(Rc0))*100;
     tl = t0;
end

     for t1 = 1:1:taln;        % for AlN
         
         Gr1 = 0.0003;
         t0 = tl + t1;
         Ph1 = (2*(pi)*2*(n3)*(Gr1)*(t1))/lamda;
         Y = [cos((Ph1)/2) (j/n3)*sin((Ph1)/2); (j*n3)*sin((Ph1)/2) cos((Ph1)/2)];
         Ro1 = ((p)*(Y(1,1))+(q)*(Y(1,2))-(r)*(Y(2,1))-(Y(2,2)));
         Ao1 = ((p)*(Y(1,1))+(q)*(Y(1,2))+(r)*(Y(2,1))+(Y(2,2)));
         Re1 = (Ro1)./(Ao1);
         Rc1 = conj(Re1);
         R(t0) = ((Re1).*(Rc1))*100;          
     end
tl = tl + t1;
    
    for k = 1:1:loop;
            for t2 = 1:1:talgan1;     % for 20% AlGaN
                t0 = tl + (k-1)*(talgan1 + talgan2)+t2;
                Gr2 = 0.0003;
                Ph2 = (2*(pi)*2*(n1)*(Gr2)*(t2))/lamda;
                Z = [cos((Ph2)/2) (j/n1)*sin((Ph2)/2); (j*n1)*sin((Ph2)/2) cos((Ph2)/2)];
                
                if k == 1                    
                    M = (Y)*(Z);
                 elseif  (k > 1 && k<= 20)
                    M = (M1)*(Z);
                end
            
                Ro2 = ((p)*(M(1,1))+(q)*(M(1,2))-(r)*(M(2,1))-(M(2,2)));
                Ao2 = ((p)*(M(1,1))+(q)*(M(1,2))+(r)*(M(2,1))+(M(2,2)));
                Re2 = (Ro2)./(Ao2);
                Rc2 = conj(Re2);
                R(t0) = ((Re2).*(Rc2))*100;    
            end

                for t3 = 1:1:talgan2;     % for 70% AlGaN
                    t0 = tl + k * talgan1 + (k-1) * talgan2 + t3;
                    Gr3 = 0.0003;
                    Ph3 = (2*(pi)*2*(n4)*(Gr3)*(t3))/lamda;
                    W = [cos((Ph3)/2) (j/n4)*sin((Ph3)/2); (j*n4)*sin((Ph3)/2) cos((Ph3)/2)];
            
                    M1 = (W)*(M);
                                                 
                    Ro3 = ((p)*(M1(1,1))+(q)*(M1(1,2))-(r)*(M1(2,1))-(M1(2,2)));
                    Ao3 = ((p)*(M1(1,1))+(q)*(M1(1,2))+(r)*(M1(2,1))+(M1(2,2)));
                    Re3 = (Ro3)./(Ao3);
                    Rc3 = conj(Re3);
                    R(t0) = ((Re3).*(Rc3))*100;    
                end
    end            
  tl = tl + loop * (talgan1 + talgan2);
  
                       for t4 = 1:1:talgant;     % for 15% AlGaN
                           t0 = tl + t4;
                           Gr4 = 0.0003;
                           Ph4 = (2*(pi)*2*(n5)*(Gr4)*(t4))/lamda;
                           V = [cos((Ph4)/2) (j/n5)*sin((Ph4)/2); (j*n5)*sin((Ph4)/2) cos((Ph4)/2)];
            
                           M2 = (V)*(M1);
            
                           Ro4 = ((p)*(M2(1,1))+(q)*(M2(1,2))-(r)*(M2(2,1))-(M2(2,2)));
                           Ao4 = ((p)*(M2(1,1))+(q)*(M2(1,2))+(r)*(M2(2,1))+(M2(2,2)));
                           Re4 = (Ro4)./(Ao4);
                           Rc4 = conj(Re4);
                           R(t0) = ((Re4).*(Rc4))*100;    
                        end  
                                            
plot(R);
grid on; xlabel('Time (s)'); ylabel('Reflectivity (%)');

I am trying to model a Bragg Reflector with Sapphire Substrate and AlGaN with varying Al molar fractions at growth temp and 330 nm wavelength.

Is the graph characteristics for the loop that includes the 20 iterations right

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