Dear Liu, 
I suppose you can consider the nonlinearity as 
a some addition intermediate step in FDTD algorithm. 
So the amplitude of signal does'n affect the epsilon tensor (or epsilon value), 
just when we compute D field from E field (maybe vice-versa, E from D, I don't 
know exactly), 
we use something like this D := n_0 + n_2 * E^2...
n_0 doesn't change! (n_0)^2 creates after output-epsilon...

You can See details for meep realization, e.g. here 
http://ab-initio.mit.edu/wiki/index.php/Units_and_nonlinearity_in_Meep

BR, 
Alexandr

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