codacy changes

docs/Examples/examples.rst

@@ -46,6 +46,15 @@ Full list of GitHub examples
 These examples are available in the `GitHub repository <https://github.com/qpv-research-group/rayflare/tree/devel/examples>`_; a list
 is provided here to give an overview of what is covered in each example.
 
+TMM
+#####
 
+1.
+
+Ray-tracing
+#############
+
+RCWA
+######
 
 .. _solcore-education: https://qpv-research-group.github.io/solcore-education/solcore-workshop-2/schedule.html

examples/analytical_rt_comparison.py

@@ -5,7 +5,6 @@
 from rayflare.textures import regular_pyramids, planar_surface
 from rayflare.ray_tracing import rt_structure
 from solcore import material
-import seaborn as sns
 from rayflare.options import default_options
 from solcore.structure import Layer
 from time import time

examples/phong_scattering_2.py

@@ -22,9 +22,6 @@
 d = 100e-6
 # setting up Solcore materials
 Air = material("Air")()
-
-from solcore.absorption_calculator import download_db, search_db
-
 Si = material("Si")()
 SiN = material("Si3N4")()
 

examples/rt_pyramids.py

@@ -1,3 +1,13 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+# # Ray-tracing with regular pyramids
+# 
+# This example shows how to define a structure, and the form of the calculation outputs, for a silicon wafer with pyramid texturing on the front surface and a planar rear surface, and compares the results with those of a well-known wafer ray-tracer (PVLighthouse). The absorption profile is also calculated automatically.
+
+# In[25]:
+
+
 import numpy as np
 
 from rayflare.ray_tracing import rt_structure
@@ -11,15 +21,23 @@
 import matplotlib.pyplot as plt
 import seaborn as sns
 
+
+# We define the relevant materials. In this case, we are going to compare the results at the end with ray-tracing results from PVLighthouse's wafer ray tracer, so we want to make sure we are using exactly the same optical constant data. For this, we will use Solcore's ability to download and pull materials from the refractiveindex.info database. First we download the database (if you've already done this previously you will be prompted to ask if you would like to re-download it) and then we search it for the Green 2008 silicon optical constant data. We then define a Solcore material by referencing this search result (for this version of the database, it is the entry with page id 566). We then set some options: the number of rays to trace at each wavelengths, how many x/y points to scan across, the wavelengths, and that the computation should be done in parallel (by default this will use all the available cores).
+
+# In[26]:
+
+
 # setting up some colours for plotting
 pal = sns.color_palette("husl", 4)
 
 
 # setting up Solcore materials
 Air = material("Air")()
 
-from solcore.absorption_calculator import download_db, search_db
+from solcore.absorption_calculator import search_db
 
+# download refractiveindex.info database if necessary
+# from solcore.absorption_calculator import download_db
 # download_db()
 Si_Green2008 = search_db("Green-2008")[0][0]
 Si = material(str(Si_Green2008), nk_db=True)()
@@ -36,46 +54,130 @@
 options.depth_spacing_bulk = si("0.1um")
 options.parallel = True
 
+
+# Define the structure: the front is made of inverted regular triangles (upright=False) with an opening angle of 55 degrees and a size of 2 microns. The back surface is planar. The rt_structure class takes a list of textures and a list of materials; there must always be one more entry in the list of textures than the number of materials (the incidence and transmission media are specified separately). We then calculate the reflection, transmission, and absorption per layer. The absorption profile will also be calculated because for ray-tracing this requires essentially no additional work, since it only uses Beer-Lambert like absorption.
+
+# In[27]:
+
+
 flat_surf = planar_surface(size=2)  # pyramid size in microns
-triangle_surf = regular_pyramids(55, upright=False, size=2,
-                                 analytical=True, phong=False,
-                                 phong_options=[25, True])
+triangle_surf = regular_pyramids(55, upright=False, size=2)
 
 # set up ray-tracing options
 rtstr = rt_structure(
     textures=[triangle_surf, flat_surf],
     materials=[Si],
-    widths=[si("100um")],
+    widths=[si("300um")],
     incidence=Air,
     transmission=Air,
 )
 
 result = rtstr.calculate(options)
 
-plt.figure()
-plt.plot(options.wavelength*1e9, result['R'], label='R')
-plt.plot(options.wavelength*1e9, result['A_per_layer'], label='A_bulk')
-plt.plot(options.wavelength*1e9, result['T'], label='T')
+
+# Plot results, and compare them with PVLighthouse ray-tracing results for the same structure.
+
+# In[28]:
+
+
+PVlighthouse = np.loadtxt("data/RAT_data_300um_2um_55.csv", delimiter=",", skiprows=1)
+
+fig = plt.figure(figsize=(9, 3.7))
+plt.subplot(1, 2, 1)
+plt.plot(
+    options.wavelength * 1e9,
+    result["R"],
+    "-o",
+    color=pal[0],
+    label=r"R$_{total}$",
+    fillstyle="none",
+)
+plt.plot(
+    options.wavelength * 1e9,
+    result["R0"],
+    "-o",
+    color=pal[1],
+    label=r"R$_0$",
+    fillstyle="none",
+)
+plt.plot(
+    options.wavelength * 1e9,
+    result["T"],
+    "-o",
+    color=pal[2],
+    label=r"T",
+    fillstyle="none",
+)
+plt.plot(
+    options.wavelength * 1e9,
+    result["A_per_layer"][:, 0],
+    "-o",
+    color=pal[3],
+    label=r"A",
+    fillstyle="none",
+)
+plt.plot(PVlighthouse[:, 0], PVlighthouse[:, 2], "--", color=pal[0])
+plt.plot(PVlighthouse[:, 0], PVlighthouse[:, 9], "--", color=pal[2])
+plt.plot(PVlighthouse[:, 0], PVlighthouse[:, 3], "--", color=pal[1])
+plt.plot(PVlighthouse[:, 0], PVlighthouse[:, 5], "--", color=pal[3])
+plt.title("a)", loc="left")
+plt.plot(-1, -1, "-ok", label="RayFlare")
+plt.plot(-1, -1, "--k", label="PVLighthouse")
+plt.xlabel("Wavelength (nm)")
+plt.ylabel("R / A / T")
+plt.ylim(0, 1)
+plt.xlim(300, 1200)
+
 plt.legend()
+
+A_single_pass = 1 - np.exp(-200e-6 * Si.alpha(options.wavelength))
+A_single_pass_PVL = 1 - np.exp(-200e-6 * Si.alpha(PVlighthouse[:, 0] / 1e9))
+lambertian = 4 * Si.n(options.wavelength) ** 2
+
+plt.subplot(1, 2, 2)
+plt.plot(
+    options.wavelength * 1e9,
+    result["A_per_layer"][:, 0] / A_single_pass,
+    "-k",
+    label="RayFlare raytracer",
+)
+plt.plot(
+    PVlighthouse[:, 0],
+    PVlighthouse[:, 5] / A_single_pass_PVL,
+    "--b",
+    label="PVLighthouse",
+)
+plt.legend(loc="upper left")
+plt.xlabel("Wavelength (nm)")
+plt.ylabel("Path length enhancement")
+plt.xlim(300, 1200)
+plt.title("b)", loc="left")
 plt.show()
 
-# make histogram of theta for transmitted rays only
 
-transmitted_indices = [result['thetas'][i] > np.pi/2 for i in range(len(result))]
+# Plotting the absorption profile at wavelengths bigger than about 1000 nm:
 
-angle_bins = np.linspace(0, np.pi, 41)
+# In[29]:
 
-theta_dist = np.array([np.histogram(result['thetas'][i1],
-                                    bins=40, range=(0, np.pi), density=True)[0]
-    for i1 in range(len(options.wavelength))])
 
-theta_dist = theta_dist[options.wavelength*1e9 > 900]
-theta_dist  = theta_dist[:, theta_dist.shape[1]//2:]
+min_wl = 1000
+ind = np.argmin(np.abs(options.wavelength * 1e9 - min_wl))
+
+z_pos = np.arange(0, 300, options.depth_spacing_bulk * 1e6)
 
 plt.figure()
-plt.imshow(theta_dist, aspect='auto', cmap='viridis', extent=(np.pi/2, np.pi, 900, options.wavelength[-1]*1e9))
-plt.xlabel('Theta (rad)')
-plt.ylabel('Wavelength (nm)')
-plt.colorbar()
-plt.title('Theta distribution of transmitted rays')
-plt.show()
+pcm = plt.pcolormesh(
+    z_pos, options.wavelength[ind:] * 1e9, result["profile"][ind:, :], shading="auto"
+)
+plt.colorbar(pcm)
+plt.gca().invert_yaxis()
+plt.xlabel(r"Depth ($\mu$m)")
+plt.ylabel("Wavelength (nm)")
+plt.show()
+
+
+# In[29]:
+
+
+
+

rayflare/ray_tracing/analytical_rt.py

@@ -198,11 +198,6 @@ def analytical_start(nks,
 
     while single_direction:
 
-        normals = surfaces[surf_index].N
-
-        n0 = nks[mat_i]
-        n1 = nks[next_mat]
-
         I_rem_data = I_remaining.data[0]
 
         R_data, A_data, T_data, R_pol, T_pol, A_int_detail = analytical_per_face(surfaces[surf_index],

rayflare/ray_tracing/rt_structure.py

@@ -14,10 +14,9 @@
 from joblib import Parallel, delayed
 from copy import deepcopy
 from solcore.state import State
-from scipy.spatial.transform import Rotation
 from numba import jit
 
-from rayflare.utilities import get_savepath, get_wavelength, process_pol
+from rayflare.utilities import get_savepath, get_wavelength
 from rayflare.transfer_matrix_method.lookup_table import make_TMM_lookuptable
 from rayflare import logger
 from .analytical_rt import analytical_start, dummy_prop_rays

tests/test_analytical_rt.py

@@ -57,7 +57,6 @@ def test_total_RAT_TMM():
     from rayflare.options import default_options
     from solcore.structure import Layer
     import numpy as np
-    from pytest import approx
 
     Si = material("Si")()
     Air = material("Air")()
@@ -88,7 +87,6 @@ def test_total_RAT_TMM():
         widths=[50e-6, 100e-6],
         incidence=Air, transmission=Air,
         use_TMM=True, options=options,
-        save_location="current",
         overwrite=True,
     )
 
@@ -261,7 +259,7 @@ def test_phong_scattering():
     # to do two surfaces to check.
 
     from rayflare.ray_tracing import rt_structure
-    from rayflare.textures import regular_pyramids, planar_surface
+    from rayflare.textures import planar_surface
     from solcore import material
     from rayflare.options import default_options
 
@@ -278,8 +276,6 @@ def test_phong_scattering():
     max_angle = np.arccos((5e-3)**(1/alpha))
 
     x = np.linspace(0, max_angle, 6)
-    # analytical power law:
-    power_law = np.cos(x)**alpha
 
     options.nx = 10
     options.ny = 10