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Hi Mariah,
If you are simulating a cube (as opposed to a continuous layer), try to have a distance of lambda/2 between the cube and the PML boundaries. In the current configuration, I believe that, what is being calculated is the amount of absorption in a small cubical volume. But the structure itself extends through the PML, which is the default if the structure touches the inner PML boundaries. In other words, you are calculating the absorption in a cubical portion of a layer thats extending semi-infinitely in two directions. Which will be different than the absorption in an isolated cube. So, if you are trying to calculate the absorption in an isolated cube, I believe this example: Calculating absorbed optical power – Higher accuracy method with multiple materials  will be very similar to your simulation.
Let me know if you have any questions.
Regards,
Amrita
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