1) Don't use (:,:,k) subscripting on Phi in your derivative function. ode45 only knows about Phi as a 36-element column vector.
2) Don't use Phi for multiple things! You are using it as the dummy variable in your anonymous function, and as the derivative function name, and as the input variable in your derivative function, and as the return variable from ode45. Use different names for these. Partly because some of these will cause errors, and partly for readability.
3) Make sure your derivative function reshapes the column vector input into a matrix, and then returns a column vector.
E.g.,
[t1, PhiResult] = ode45(@(t,Phi) PhiFun(A(:,:,k),Phi,t),tspan,Phi_0,opts);
:
function [ Phi_dot ] = PhiFun( A, Phi, t )
%UNTITLED2 Summary of this function goes here
% Detailed explanation goes here
Phi_dot = A*reshape(Phi,6,6);
Phi_dot = Phi_dot(:);
end
Then of course you will probably want to add some code to save the desired results from each iteration (the way it is now the results of each iteration overwrite the previous iteration).
