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I think there are different ways to calculate the nanopartical absorption:
1: calculate the loss of the waveguide from 1-R-T as a reference. Then simulate it with the np, and calculate the 1-R-T again. the difference is the absorption. To have better result, please use the same mesh. eg, if the np is small and you need to use override mesh to resolve it, keep this override mesh when simulating the bare waveguide.
2: use an analytical group to cover the np its self:
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Please note that the analysis group is rectangle shaped. In case the other materials surrounding the np also have losses, and the analysis group covers part of them, you will need to modify the script in the analysis group, eg, to create a filter that only picks up the fields inside np.
I hope this helps.