> On Jul 25, 2017, at 10:31 AM, Heligman, Daniel M. 
> <heligma...@buckeyemail.osu.edu> wrote:
> 
> The way I am subtracting it is by taking the raw field on the reflection side 
> of the computational cell and cutting out the portion of the signal that 
> contains the incident pulse.


This is easy to get wrong.  Generally, I recommend running two simulations — 
one with the scatterer and one without, and subtracting the latter fields from 
the former before Fourier transforming in order to get the scattered/reflected 
flux, similar to what is done in the Meep tutorial.

(Why not just use the built-in dft-flux feature for this, as in the Meep 
tutorial?)
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