When simulating periodic patterning of a structure, such as a photonic crystal cavity, we often want the patterning to extend into the PML region like in the following image:
Otherwise, there can be an impedance mismatch between the patterned region and the PML which can lead to reflections from the PML.
By default, the “extend structure through pml” option which is set in the simulation region’s “Boundary conditions” tab is selected, which means that any structures contained within in the PML region won’t be simulated. You can de-select this option to allow the pattering within the PML region to be simulated:
More information about extending the structure through the PML can be found on the following KB page: