resolve propagator issues

[k-wolfinger]

Currently not getting good phase output of propagators + changes to mesh dimensions and extent.

[k-wolfinger]

To do

Improve padding:

• pad, smooth, propagate...
• use windowing
• 'automate' how many zero cells between edge and the first non-zero value?

Write a function that wraps the propagators and:

• Makes sure output is 2^n
• Truncates the wfr mesh if it is larger than a factor times the crystal radius
• Checkes dx and dy against a specified minimum (also not greater than ~0.1x crystal radius?)

[k-wolfinger]

Before closing:

• put in phase cut

[k-wolfinger]

@bruhwiler Two notes before creating the pull request:

1. Because of the windowing applied to the file-initialized fields, we now get fewer photons in file-init than in function-init (where previously they were the same)
2. We assume electric_field_y is zero in the file-init and other places. Should we change this?

[k-wolfinger]

New changes:

• Still pad 64x64, move windowing to the intensity file-data, try padding with a gaussian fit,
• Cut the mesh during propagation but don't touch phase
• Cut phase when plotting if needed

[bruhwiler]

Let's continue assuming E_y is zero for now.