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I have looked over your design and while I do have a couple of points to improve your results, I am not able to help much further without you specifying what exactly is your problem with the results.
1. Your simulation domain is defined in the y direction from 0 to 0.25um. This was done by setting your substrate to 0. There is nothing wrong with this except that you specified your source to be at a y position of 0 which is running right along the PBC. I am assuming you want your source in the center of the XY plane, set your y position to 0.125um.
2. Your spheres are made of a Lorentz-Drude material, I recommend running smaller time steps than required by the auto setting to ensure that you have a stable simulation. Your setting was fine but it is something to keep in mind.
3. When creating the spectrum you want to make sure you are plotting the full (Pz) component and not just Pz-x or Pz-y. See attached figure.
4. What version of the software are you using?Scott
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