Hello, I'm new to the discussion board, and I've been trying to find a reason for a problem similar to what is discussed here:
http://www.mail-archive.com/meep-discuss@ab-initio.mit.edu/msg04994.html Namely, I am trying to read an input file for the dielectric function. The original data comes in contour format rather than pixel-dependent epsilon values, so currently I'm reading that file and using its contents to decide upon a pixel-dependent dielectric function. That process takes a long time, so I had the idea to load the resulting eps.h5 file that output_hdf5 creates for future runs. In short, the first run creates the dielectric grid and the eps.h5 file, and subsequent runs can just read that file. In practice, I've noticed that the values in the eps file, while qualitatively similar to the input data, don't match the values I'm returning from the eps function. The function basically checks the pixel value for three specific conditions and returns either 6, 4, or 1 accordingly (the values are fictitious, just for testing right now). However, in the eps file, I see a range of values from 1 to 2.25 (where the maximum value of 2.25 replaces epsilon at those places I attempted to return a 6.0). Suspecting that subpixel averaging was changing the actual values, I started checking the source code to make sure averaging is disabled. However, the structure() constructor sets use_anisotropic_averaging = false by default, and I'm doing nothing to change that (I never call set_epsilon after initializing the structure). As a test, using the same eps function, I set a simple check that returns the arbitrary value of 3.2 if p.x()<1. In the output eps.h5 file, I see some averaging near x=1, but the eps = 3.2 values are intact for x<1. So, some sort of manipulation of the dielectric function is still occurring. At the FAQ (http://ab-initio.mit.edu/wiki/index.php/Meep_FAQ<http://ab-initio.mit.edu/wiki/index.php/Meep_FAQ>), I read that "even though the internal ε values are indeed discontinuous when you disable subpixel averaging, the *output* file will still contain some "averaged" values at interfaces due to the interpolation from the Yee grid to the center-pixel grid." So, I suspect this interpolation is the cause, but I don't understand how values of 6.0 are being interpolated to 2.25. Admittedly, the 6.0 regions are rather narrow, so I broadened those regions considerably (by tens of pixels) to see if that would fix this "over-smoothing". However, doing this made no difference for the 6.0->2.25 replacement. At this stage, it seems to me that the easiest thing to do would be to create a separate script to read the contour file, process it, and output my own eps file to be read prior to subsequent simulations (taking subpixel averaging and the Yee grid out of the loop entirely). That way, I could guarantee reproducibility. However, I'm still concerned about why the values I"m returning from the epsilon dielectric function are being adjusted so considerably. Can anyone explain to me what I might be missing about how structures and their dielectric functions are established? Thanks for any help in advance, and have a good day! John Ball
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