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Thank you, all three of your questions are very good questions. I see I need to improve on the documentation.
1) Only "...painted" (dielectric_dielectric) or dielectric_metal surfaces can reflect photons. The exampleN06 does not define such a surface; but the code example: "Example 5.8. Dielectric-dielectric surface properties defined via the G4OpticalSurface" in the Application Developers Guide does. If the reflectivity is not specified the program defaults to 1.
2) For the UNIFIED model, sigma_alpha defaults to 0. For the GLISUR model polish defaults to 1 (even if you specify the finish as 'ground').
The constructor of the G4OpticalSurface has this form:
G4OpticalSurface(const G4String& name, G4OpticalSurfaceModel model = glisur, G4OpticalSurfaceFinish finish = polished, G4SurfaceType type = dielectric_dielectric, G4double value = 1.0);
where the 'value' corresponds to 'polish' for model=glisur and 'sigma_alpha' for model=unified. See:
You can also set sigma_alpha once you have the pointer to the G4OpticalSurface (in the unified model case):
3) The optical properties of surfaces and material should bracket the full emission spectrum you have specified. No use to produce optical photons through scintillation in an energy regime where you don't know/specify the index of refraction of your scintillator, for example. And while the emission spectrum may be complicated and requires many points to describe it accurately, the index of refraction may not change at all over the range. In that case, all you have to do is specify the two extremes of the emission spectrum. (the exampleN06 has a bit of an inconsistency 2.038*eV should read 2.034*eV or less.)
Another optical photon simulation example you might want to look at is: /examples/extended/optical/LXe
Hope this answers your questions, Peter