Thank you. As I repiled previously, plane wave cannot be combined with PML. Please refer the link I gave.
If this is a periodic structure, please use periodic BCs in the periodic axes, or Bloch BC in the plane of angled source.
If this is a non periodic structure, and you want to use plane wave, please use TFSF:
Total-Field Scattered-Field (TFSF) source - Simulation object
Understanding source normalization in the TFSF source
Tips and best practices when using the FDTD TFSF source
Usually TFSF is not used to calculate transmission and reflection. If you have questions please write a new post.
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