What frame of reference should I use for my Simulink simulation of the F/A-18 Hornet? I want to simulate the Equations of Motions for F/A-18 Hornet (12 states &amp; 6 DOF) on MATLAB using Simulink.  I have the Aerodynamic model, from which I will get CL, CD, CY, Cl, Cn, Cm that are flight conditions dependent.

Now, the forces and moments calculated from these coefficients will be in Wind Axes because these coefficients are defined in that coordinate system only (correct me if I am wrong). For using these Aerodynamic Forces and Moments in Body Axes, do I need to convert them into body axes by multiplying a Direction Cosine Matrix, that converts vectors from Wind Axes to Body Axes? Or should I use the Wind Axes computation?

Assume, I took the first option and converted the forces and moments into Body Frame. But, there are terms like $p$, $q$, and $r$ in the computation of the coefficients mentioned above. These terms are defined in the body frame. So, should I use these values of $p$, $q$, $r$ that are in body axes and compute coefficients in wind axes? Or should I convert them also into wind axes before using them in the computation?



PS: Reference for the Aerodynamic Model of F/A-18 Hornet:


A. Chakraborty, P. Seiler, and G. J. Balas, Susceptibility of F/A-18 flight controllers to the falling-leaf mode: linear analysis, Journal of Guidance, Control, and Dynamics, Vol. 34, No. 1, pp. 57–72, 2011.
It's very prudent of you to be concerned about the axis frames in which different forces/motions are defined. It's a common mistake to ignore the fact that aerodynamic coefficients are normally defined in wind axes.

The standard approach is to calculate Equations of Motions in the body frame; this is how they are usually defined. For this, you'll indeed need a wind-to-body matrix (DCM). This is a simple matrix because it involves only two angles (beta and alpha), and these angles are normally small to be concerned about gimbal lock (the model is probably not defined where they are not small). Then you


Calculate the forces/moments that are defined in wind axes and rotate them to body.
Likewise, calculate forces and other things that are defined in the ground frame, such as gravity and wind per se, and rotate them to body. (It makes sense to use quaternions for that rather than DCM, but this is another matter).
Finally, you'll have forces that are defined directly in the body frame, such as thrust.


Now you can integrate EoM with all the data available in the body frame.

Regarding p, q, r (and such) used in calculation of the aerodynamic forces, these are usually body angular velocities that you can take directly from your EoM. However, you should double check if the aerodynamic model requires something else; this should be explicitly defined. Note that if you do need to rotate angular velocities, you can't use the same DCM but need to use the matrix that preserves the total angular momentum.