input output read/write frequency I am trying to identify a system based on input/output response and thereby estimate a transfer function. 
I generated a frequency sweep function in Mathematica which gives me the discrete values of a frequency sweep.

g[t_] := 0.799760*Sin[2 Pi (3 t/333.3 + 1) t];
Plot[g[t], {t, 0, 1000000000000000000000000000000}]
g[#] &amp; /@ Range[0, 5, 0.001]


So now I have a bunch of data but at what rate should I input it into the system, and at what rate should I read it?

How should I apply Nyquist frequency rule here?
Best to base it on the highest frequency response you anticipate for the system and implement twice that frequency with the samples you input and the data you read.