actually, what you're describing about mopeks (I didn't really make out what you intended it to do)
sounds a lot like Eureqa of which a demonstration program was released in 2009 and usable versions for other scientists have been available for a few years. (even better, it's absolutely free).

You feed it datapoints, and it finds the equation(s) that fit the data.

It sounds similar to what your mopeks appears to want to do, but it's incredibly fast. It finds a solution for a double pendulum in a matter of hours. (this is several orders of magnitude more complex than a square root).

It is a feat in itself to make a proper simulator for this, then think about reversing the output of the simulator back into it's input of pendulum lengths and mass and gravity.