Define the phase of transmission in Transfer matrix method?

You normally do not define the "phase" of transmission. Phase is a relative concept. A single electromagnetic mode only has "phase" of your are comparing it to another time-harmonic mode.

If you only have one source in your code, then changing the phase should have no effect.

But to answer your question, just multiply your source by a complex exponential to "add" phase to your source.

S1 = S1 * exp(i*phi);

This will add 'phi' phase to S1.

Hope this helps!

-tip