What does S2，1 mean in CST MWS

Hi!
Can any one tell me what does S2,1 mean in CST Microwave Studio. Is it the power transmittance or modulus of amplitude coefficient?

Assuming you mean S21:
The circuit (port 1) is excited from a source with EMF = 2V and an output impedance equal to the reference impedance (characteristic impedance). This results in a forward voltage of 1V. The circuit output port (port 2) is terminated with its reference impedance (characteristic impedance). The output voltage across the termination is S21. In fact S21 is V2/V1forward when port 2 is terminated with the reference impedance (use complex calculus).
So S21 = -0.25 means that when you drive with a forward voltage of 1V (that is EMF = 2V) the output is -0.25V into the load (the load is the reference impedance).
When the reference impedance for port 1 differs from the reference impedance for port 2, you need a correction:
S21 = (V2/V1forward)*sqrt(Z1/Z2), to maintain good power relations.
So if you have a lossless transformer that converts 50 Ohms into 200 Ohms, S21 = 1 when Zref for port 1 is 50 Ohms and Zref for port 2 is 200 Ohms.
All power appears at the load (as there is perfect match). Note that the output voltage is twice the forward voltage.
S21 can be expressed in complex form (a + bj), modulus |S21| and argument (Arg(S21), and of course in dB ( 20*log(|S21|) ).
For a multiport system, all other ports are terminated with their reference impedances.

Thanks. In that case can I specify FWHM from |S21| plot or to specify FWHM I need |S21|^2?
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Thanks. In that case can I specify FWHM from |S21| plot or to specify FWHM I need

I can't tell you that as I don't know what is important for your application. If you are looking for half power (that is -3 dB below maximum), you need FWHM (Full Width of Half Maximum) of |S21|^2.