Another thing that I don't understand is that when you specify the frequency of
a gaussian source, it actually as a different frequency. In the attached ctl
file, frequency is set to 0.15, but the transmitted flux in air shows 0.1636 !

Oh, never mind, I saw the attachment. I haven't had a chance to look at the output of your file, but I can guess what is happening.

You have a gaussian centered on 0.15 with a width of 0.3, which is pretty wide. When the pulse is this wide (in frequency), you can observe a computational detail: Meep's Gaussian pulse is not actually precisely a Guassian, it is the derivative of a Gaussian (this ensures that there is no net charge left in the computational cell after the pulse is gone, which prevents divergences in some cases with periodic boundaries). The difference between the two is small except for very broad Gaussians in frequency (short pulses in time).

Because the main reason to use a short pulse is to get a broad-spectrum response, and you have to normalize such a response by the input spectrum anyway as explained in the manual, the exact shape of the spectrum shouldn't actually matter.

Steven

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