How to fix: Index Exceeds Matrix Dimensions
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err: Index Exceeds Matrix Dimensions
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  Wan Ji
      
 am 29 Aug. 2021
        Hi, friend
ode45 function outputs a struct with size 1x1 when only one argument is for output data. If you want to output x solution as n*m double matrix use 
[t,x] = ode45(...);
Or use
[~,x] = ode45(...);   
instead of directly using
x = ode45.....
SO, I modified your code as
clc;
clear all;
t=linspace(0,1,10);
M=0.5;
beta=0.5;
p1=0.1;
p2=0.5;
f=@(t,x) [x(2);x(3);2*x(2).^2+2*(x(2)*x(5))-x(1)*x(3)-x(3)*x(4)+M.^2*x(2)/(1+1./beta);
            x(5);x(6);2*x(5).^2+2*(x(2)*x(5))-x(1)*x(6)-x(4)*x(6)+M.^2*x(5)/(1+1./beta)];
 err_threshold=1e-3;
 iterator =1;
 err=1; 
 while err > err_threshold
    if iterator == 1 
        [~,x]=ode45(f,[0 1],[0 1 p1 0 0.3 0],t);
       % ylim([0 5]);
     %plot(t,x(:,3),'--')
     m1=x(end,3);
     %.........................................
     [~,x]=ode45(f,[0 1],[0 1 p2 0 0.3 0],t);
     m2=x(end,3); 
     plot([p1 p2],[m1 m2]);
    else
        p2=(p2-p1)/(m2-m1)*(1.0-m1)+p1;
        [~,x]=ode45(f,[0 1],[0 1 p2 0 0.3 0],t);
     m2=x(end,3);
     plot([p2,m2]);
     err=abs(1-m2);
    end    
     iterator=iterator+1;
    end
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