Thanks for all the insight.  Your explanation makes sense to me.

I implemented your suggestions, in particular using a broad pulse (df = fcen/2), and using the stop-when-fields-decayed with run-sources+.

Unfortunately, I'm still getting screwy coefficients; excerpt:
wavelength: 604.651162790698,   T: 0.98135028867621     R: 3.20707950456041,    
loss: -3.18842979323663
wavelength: 595.419847328244,   T: 0.969381226910182    R: 2.60992271242882,    
loss: -2.579303939339
wavelength: 586.466165413534,   T: 0.804271397560674    R: 1.91364743999159,    
loss: -1.71791883755226
wavelength: 577.777777777778,   T: 0.623519685407492    R: 1.39742580647576,    
loss: -1.02094549188325
wavelength: 569.343065693431,   T: 0.49770368114167     R: 1.08833213798949,    
loss: -0.586035819131162
wavelength: 561.151079136691,   T: 0.413807765058018    R: 0.924171293043094,   
loss: -0.337979058101112
wavelength: 553.191489361702,   T: 0.372083557598435    R: 0.822500998525853,   
loss: -0.194584556124288
wavelength: 545.454545454546,   T: 0.36426804949468     R: 0.745516683229625,   
loss: -0.109784732724305

Obvious things to check, like increasing the resolution or PML
thickness or cell width and height didn't cause those numbers to
improve.  T seems to stay between 0 and 1.  R is all over the place.

I don't think it's a problem having to do with the way you recommend
to accumulate the Fourier transforms, because I was getting unreliable
coefficients when I tried calculating for single frequencies with a
gaussian source as well.

the source:
http://pastebin.us/19352

the command to run it:
touch asdf.hf && rm comput* *.png *.h5 && meep no-scatterer\?=true compute-flux\?=true 
test.ctl | tee lastrun.out && meep no-scatterer\?=false output-finalfield\?=true 
compute-flux\?=true test.ctl | tee -a lastrun.out


Best Regards,
Matt


On Wed, 28 Mar 2007, Steven G. Johnson wrote:

On Wed, 28 Mar 2007, Steven G. Johnson wrote:
 If you have a non-periodic structure in the x direction, or care about
 frequencies above the diffraction cutoff, then different input angles can
 scatter into the same output angle and there can be interference.  In this
 case, the power does not simply sum.

No, I take that back. My previous post was correct. The point is that the different angles correspond to different frequencies, so when you take a single Fourier component of the scattered field you really are looking at just a single angle.

 In that case, you really must put in a narrowband source (I think, unless
 there is some additional trick that is not occurring to me now). However,
 you

I take this back. Just put in a short pulse and you are fine, as I first said.

(Sorry, I've managed to confuse myself now.)

Steven

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