I've been wrapping my head around the guidance/flight control stuff a bunch lately as part of the modeling I've been doing for Gizmo & POGO. Turns out the general form of the control system that POGO uses (i.e. differential throttling with engine canting for roll control) has some interesting properties that I don't understand quite well enough yet to really write down. Much of this is because I am hard up against the limits of my understanding of linear algebra and rotation sequences. One thing that I have figured out is that canting the engines couples the control axes in ways that cannot readily be gotten rid of.
I just live with the cross-axis coupling, but you can rotate things a little and actually make the issue go away -- instead of thinking about throttling one engine up to pitch or yaw, throttle two adjacent engines up to rotate as if there was an engine exactly between them. The cants are opposite, so the rolls cancel out. I still leave my engines in line with my gyro axis for setup convenience, but if you make your vehicle axis between the engines like this, you can get pure torques.
John Carmack
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