Efficient electromagnetic solver based on rigorous coupled-wave analysis for 3D and 2D multi-layered structures with in-plane periodicity

Thank you for your transparent and usable Python port of S4.

To verify that the code works correctly, I attempted to reproduce the Fresnel equations using a simple two layer model -- the first layer with n=1, and the second with n=1.5. I have been unable to get this to work in Inkstone, but I did get it to work with an equivalent code for Phoebe-P S4 . Attached are the codes I used for both Inkstone, fresnel_inkstone_te.py (which doesn't work); and S4, Fresnel_S4_TE.py (working).

In inkstone, when I use angle = np.linspace(0, 90, 91) , I get the error: /inkstone/params.py:525: RuntimeWarning: Vacuum propagation constant 0 encountered. Possibly Wood's anomaly. warn("Vacuum propagation constant 0 encountered. Possibly Wood's anomaly.", RuntimeWarning)

When I use angle = np.linspace(1, 90, 90) , I get the error: Traceback (most recent call last): File "fresnel_inkstone_te.py", line 71, in glapf, glapb = s.GetPowerFlux('gla') File "/inkstone/simulator.py", line 1204, in GetPowerFlux self.solve() File "/inkstone/simulator.py", line 890, in solve self._calc_sm() File "/inkstone/simulator.py", line 704, in _calc_sm s = next(ll[-1] for ll in self.csms if ll[-1][1] == n_layers-2) StopIteration

If between the "air" air and "gla" glass layers, I add an intermediate layer: s.AddLayer(name='gla-int', thickness=1, material_background='glass')

and still keep angle = np.linspace(1, 90, 90) then I get the error

/.local/lib/python3.9/site-packages/inkstone/layer.py:545: RuntimeWarning: divide by zero encountered in divide vh = -1j * p @ v / w[:, None, :] /.local/lib/python3.9/site-packages/inkstone/layer.py:545: RuntimeWarning: invalid value encountered in divide vh = -1j * p @ v / w[:, None, :] Traceback (most recent call last): File "/inkstone/Fresnel_Inkstone/fresnel_inkstone_te.py", line 72, in glapf, glapb = s.GetPowerFlux('gla') File "/.local/lib/python3.9/site-packages/inkstone/simulator.py", line 1204, in GetPowerFlux self.solve() File "/.local/lib/python3.9/site-packages/inkstone/simulator.py", line 890, in solve self._calc_sm() File "/.local/lib/python3.9/site-packages/inkstone/simulator.py", line 682, in _calc_sm ll[ilm].solve() File "/.local/lib/python3.9/site-packages/inkstone/layer.py", line 702, in solve self._calc_im() File "/.local/lib/python3.9/site-packages/inkstone/layer.py", line 652, in _calc_im al0, bl0 = im(self.phil, self.psil, self.pr.phi0, self.pr.psi0, self._phil_is_idt) File "/.local/lib/python3.9/site-packages/inkstone/im.py", line 36, in im term2 = sla.solve(psi1, psi2) File "/.local/lib/python3.9/site-packages/scipy/linalg/_basic.py", line 140, in solve a1 = atleast_2d(_asarray_validated(a, check_finite=check_finite)) File "/.local/lib/python3.9/site-packages/scipy/_lib/_util.py", line 287, in _asarray_validated a = toarray(a) File "/.local/lib/python3.9/site-packages/numpy/lib/function_base.py", line 627, in asarray_chkfinite raise ValueError( ValueError: array must not contain infs or NaNs

Hi,

I'm trying to visualize the epsilon profile of the patterned layer named "slab" in the example file "phc_slab_circ_hole_spectrum.py", using ReconstructLayer (as defined on line 309 of simulator.py).

I'm not entirely sure about the correct usage of ReconstructLayer but I'm just doing: s.ReconstructLayer('slab', 100, 100) or s.ReconstructLayer('slab') (since nx and ny both seem to default to 101). In both cases, I get the error:

Traceback (most recent call last):
  File "phc_slab_circ_hole_spectrum.py", line 32, in <module>
    s.ReconstructLayer('slab')
  File "/home/sachin/miniconda3/lib/python3.7/site-packages/inkstone/simulator.py", line 337, in ReconstructLayer
    result = self.layers[name].reconstruct(nx, ny)
  File "/home/sachin/miniconda3/lib/python3.7/site-packages/inkstone/layer.py", line 395, in reconstruct
    for em in [fft.ifftshift(self.epsi_fs, axes=(0, 1)), fft.ifftshift(self.epsi_inv_fs, axes=(0, 1)), fft.ifftshift(self.mu_fs, axes=(0, 1)), fft.ifftshift(self.mu_inv_fs, axes=(0, 1))]]
  File "<__array_function__ internals>", line 6, in ifftshift
  File "/home/sachin/miniconda3/lib/python3.7/site-packages/numpy/fft/helper.py", line 121, in ifftshift
    shift = [-(x.shape[ax] // 2) for ax in axes]
  File "/home/sachin/miniconda3/lib/python3.7/site-packages/numpy/fft/helper.py", line 121, in <listcomp>
    shift = [-(x.shape[ax] // 2) for ax in axes]
IndexError: tuple index out of range

Could you please help me with this?

Thanks!