Why i should Assign Bondary Condition ，where i've already Feeded in CST MWS

I'm simulating One of the IEEE paper , but i've got some problem , i used two ports( X dimension) for feeding through Waveguide port , but when i want to assign Boundary condition to another Dimension , i have to assign to feeding port.

please chech my file : http://www.fileswap.com/dl/AXLWrQRLuh/

original shape : ../imgqa/eboard/Antenna/rf-vonjzdodjjk.gif

also according to the article : in our simulations all the outer
boundaries except input and output ports have been chosen as
perfectly matched layer (PML). Since, wave propagation takes
place through dielectric medium, most appropriate definition
of characteristic impedance is based upon power and voltage
i.e. Z PV = V·V/P . An impedance line is defined on the ports
to integrate electric field and thereby to calculate voltage,
while power P has been calculated from the surface integral
of (  E × H ) over the surface of the port.

thanks for the attention

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