Question: FFT for system of ODEs

I have a system of nonlinear ODE and I solved them numerically using rkf45. the solution is in time domain and the variables are x, y and z.

I want to convert this solution from time domain to frequency domain. I know that I should do FFT, but I do not know how to do this. 

I tried to do this, but I found that I have to get the solution of x, y and z in the form of vector with respect to time. I am not sure if I understant this problem corectly.

Thanks in advance.

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