use index of refraction to calculate transfer matrices in crystal slices

[nickgoldring]

Use n0 and n2 from FEniCS thermal simulation to construct Gaussian duct transfer matrices slice-by-slice for wavefront propagation. Initial notebook for this work can be found here: https://github.com/radiasoft/rslaser/blob/master/examples/thermal/rslaser_fenics_gsnduct01.ipynb