dNis = Nis - Nth;
Ais = sqrt((AInj^2 - gammaN/gammaP*dNis)/(1 + g*dNis/gammaP));
dNis is negative.
That makes the numerator for the next line a value minus a negative value, which is positive, so the numerator is okay.
But with dNis being sufficiently negative, the denominator is negative, so overall you are taking square root of a negative value.
phi_Tr = zeros(size(A_Tr));
You do not assign any other value to phi_Tr, so phi_Tr is all zero at the time you semilogy(), which means you are trying to plot the log of 0.
