Merge pull request #62 from qpv-research-group/inkstone_integration

Inkstone integration

.github/workflows/testing.yml

@@ -16,10 +16,10 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.9', '3.10']
-        exclude:
-          - os: windows-latest
-            python-version: '3.9'
+        python-version: ['3.9', '3.10', '3.11']
+#        exclude:
+#          - os: windows-latest
+#            python-version: '3.9'
 
     steps:
     - uses: actions/checkout@v1
@@ -41,8 +41,8 @@ jobs:
 
     - name: Install python dependencies
       run: |
-        python -m pip install --upgrade setuptools wheel pip twine numba
-        pip install -e .[dev]
+        python -m pip install --upgrade setuptools wheel pip 
+        pip install .
 
     - name: Install S4 in Linux
       if: matrix.os == 'ubuntu-latest'
@@ -64,19 +64,18 @@ jobs:
 
     - name: Install on Linux and MacOS
       if: matrix.os != 'windows-latest'
-      run: pip install -e .
+      run: pip install .
 
     - name: Install on Windows
       if: matrix.os == 'windows-latest'
       run: |
-        pip install -e .
+        pip install .
       shell: powershell
 
     - name: Test with pytest
       run: |
         pip install pytest-cov pytest-rerunfailures
-        pytest --cov-report= --cov=rayflare tests/ --reruns 3
-
+        pytest --cov-report= --cov=rayflare tests/ --reruns 5
 
     - name: Codecov
       if: matrix.os == 'ubuntu-latest'

docs/Installation/installation.rst

@@ -97,7 +97,7 @@ To do a normal installation from PyPI (using :literal:`pip`):
     pip install setuptools wheel numba
     pip install rayflare
 
-This will install install the most recent version uploaded to PyPI (currently 1.2.0), which is not necessarily the most
+This will install install the most recent version uploaded to PyPI (currently 1.2.1), which is not necessarily the most
 up to date version.
 
 To install RayFlare from source (GitHub):

docs/Options/user_options.rst

@@ -9,7 +9,7 @@ rule, values with units of distance (wavelength, depth spacing) are in m while a
 General options/options for matrix framework
 ---------------------------------------------
 
-- **wavelengths**: wavelengths at which to carry out calculations (in m)
+- **wavelength**: wavelengths at which to carry out calculations (in m)
 - **theta_in**: polar angle of incident light (in radians)
 - **phi_in**: azimuthal angle of incident light (in radians). If you are using the angular redistribution matrix framework,
   you can also set this to 'all' to spread the incident light evenly over all the azimuthal bins
@@ -34,9 +34,12 @@ Options used only by RCWA (S4)
 ---------------------------------------------
 
 - **A_per_order**: whether or not to calculate absorption per diffraction order (Boolean)
-- **S4_options**: options which are passed to S4. See S4 documentation for details
+- **S4_options**: options which are passed to S4. See S4 documentation for details. Note that these are
+  not used by Inkstone.
 - **orders**: the number of Fourier orders to retain. The actual number of orders used may be different, depending on
   the lattice truncation rule used.
+- **RCWA_method**: 'Inkstone' or 'S4'. If 'Inkstone', the Inkstone RCWA implementation is used. If 'S4', the S4 RCWA implementation is used.
+  The default is S4. Note that this is not case-sensitive.
 
 
 Options used only by the ray-tracer

docs/news.rst

@@ -8,6 +8,18 @@ To update to the latest version of RayFlare, run the following command in your t
 
    pip install rayflare --upgrade
 
+Version 1.2.1 released (2023-11-19)
+------------------------------------
+**Highlights:**
+
+- New RCWA method ([Inkstone](https://github.com/alexysong/inkstone) now intergrated with RayFlare.
+  This is an all-Python program which is therefore easy to install (unlike S4). This means all core u
+  functionality of RayFlare is now available without the need to compile anything on your computer.
+  Users can toggle between S4 and Inkstone by setting the ``RCWA_method`` option.
+- Calculations with unpolarized light using RCWA should be faster now.
+- The ``wavelengths`` user options is now called ``wavelength``, for compatibility with Solcore.
+  ``wavelengths`` still works, but will be deprecated in future.
+
 Version 1.2.0 released (2023-03-21)
 ------------------------------------
 

docs/requirements.txt

@@ -7,4 +7,5 @@ joblib==1.1.0
 matplotlib==3.5.1
 scipy==1.7.3
 solcore==5.7.5
-nbsphinx==0.8.8
+nbsphinx==0.8.8
+inkstone==0.3.12

examples/GaAs_GaAs_Si_spacer_tmm_rt.py

@@ -49,14 +49,12 @@
 options.n_rays = 2000
 options.randomize_surface = True
 options.project_name = "GaAs_GaAs_Si_spacer_tmm_rt"
-options.wavelengths = wavelengths
+options.wavelength = wavelengths
 
 # Set up materials
 # from solcore.absorption_calculator import download_db
 # download_db() # uncomment to download the database if you haven't already
-epoxy_result = search_db("NOA-61")[
-    0
-]  # Norland optical adhesive 61. n = 1.5, typical for materials used in this way
+epoxy_result = search_db("NOA-61")[0]  # Norland optical adhesive 61. n = 1.5, typical for materials used in this way
 
 MgF2_pageid = str(search_db(os.path.join("MgF2", "Rodriguez-de Marcos"))[0][0])
 Ta2O5_pageid = str(search_db(os.path.join("Ta2O5", "Rodriguez-de Marcos"))[0][0])
@@ -94,10 +92,10 @@
 aSi_n = material("aSi_n")()
 
 plt.figure()
-plt.plot(wavelengths*1e9, GaAs.n(wavelengths), label='GaAs')
-plt.plot(wavelengths*1e9, GaInP.n(wavelengths), label='GaInP')
-plt.plot(wavelengths*1e9, NOA.n(wavelengths), label='epoxy')
-plt.plot(wavelengths*1e9, Si.n(wavelengths), label='Si')
+plt.plot(wavelengths * 1e9, GaAs.n(wavelengths), label="GaAs")
+plt.plot(wavelengths * 1e9, GaInP.n(wavelengths), label="GaInP")
+plt.plot(wavelengths * 1e9, NOA.n(wavelengths), label="epoxy")
+plt.plot(wavelengths * 1e9, Si.n(wavelengths), label="Si")
 plt.show()
 
 # x = np.linspace(0, 1, 6)
@@ -140,9 +138,7 @@
 
 Si_back_labels = ["a-Si i", "a-Si n", "ITO (back)"]
 
-front_surface = planar_surface(
-    interface_layers=front_layers, prof_layers=cell_layer_ind
-)
+front_surface = planar_surface(interface_layers=front_layers, prof_layers=cell_layer_ind)
 Si_surface = regular_pyramids(upright=True, interface_layers=Si_front_layers)
 back_surface = regular_pyramids(upright=False, interface_layers=Si_back_layers)
 
@@ -183,29 +179,19 @@
         Si_back_plot_labels.append(Si_back_labels[j1])
 
 plt.figure(figsize=(8, 4))
-plt.plot(options.wavelengths * 1e9, result["T"], label="T (Al)")
-plt.plot(options.wavelengths * 1e9, result["R"], '--', label="R")
+plt.plot(options.wavelength * 1e9, result["T"], label="T (Al)")
+plt.plot(options.wavelength * 1e9, result["R"], "--", label="R")
 
 if len(front_plot_res) > 0:
-    plt.plot(
-        options.wavelengths * 1e9, np.array(front_plot_res).T, label=front_plot_labels
-    )
+    plt.plot(options.wavelength * 1e9, np.array(front_plot_res).T, label=front_plot_labels)
 
 if len(Si_front_plot_res) > 0:
-    plt.plot(
-        options.wavelengths * 1e9,
-        np.array(Si_front_plot_res).T,
-        label=Si_front_plot_labels,
-    )
+    plt.plot(options.wavelength * 1e9, np.array(Si_front_plot_res).T, label=Si_front_plot_labels)
 
-plt.plot(options.wavelengths * 1e9, result["A_per_layer"][:, 1], label="Si")
+plt.plot(options.wavelength * 1e9, result["A_per_layer"][:, 1], label="Si")
 
 if len(Si_back_plot_res) > 0:
-    plt.plot(
-        options.wavelengths * 1e9,
-        np.array(Si_back_plot_res).T,
-        label=Si_back_plot_labels,
-    )
+    plt.plot(options.wavelength * 1e9, np.array(Si_back_plot_res).T, label=Si_back_plot_labels)
 
 plt.legend(bbox_to_anchor=(1.05, 1))
 plt.xlabel("Wavelength (nm)")
@@ -215,31 +201,12 @@
 
 # limiting currents:
 
-light_source = LightSource(
-    source_type="standard",
-    version="AM1.5g",
-    x=wavelengths,
-    output_units="photon_flux_per_m",
-)
+light_source = LightSource(source_type="standard", version="AM1.5g", x=wavelengths, output_units="photon_flux_per_m")
 
 photon_flux = light_source.spectrum(wavelengths)[1]
 
-J_GaAs_1 = (
-    q
-    * np.trapz(
-        result["A_per_interface"][0][:, cell_layer_ind[0] - 1] * photon_flux,
-        wavelengths,
-    )
-    / 10
-)
-J_GaAs_2 = (
-    q
-    * np.trapz(
-        result["A_per_interface"][0][:, cell_layer_ind[1] - 1] * photon_flux,
-        wavelengths,
-    )
-    / 10
-)
+J_GaAs_1 = q * np.trapz(result["A_per_interface"][0][:, cell_layer_ind[0] - 1] * photon_flux, wavelengths) / 10
+J_GaAs_2 = q * np.trapz(result["A_per_interface"][0][:, cell_layer_ind[1] - 1] * photon_flux, wavelengths) / 10
 J_Si = q * np.trapz(result["A_per_layer"][:, 1] * photon_flux, wavelengths) / 10
 
-print(J_GaAs_1, J_GaAs_2, J_Si)
+print(J_GaAs_1, J_GaAs_2, J_Si)

examples/HIT_emissivity.ipynb

@@ -53,7 +53,7 @@
     "wavelengths = np.round(np.floor(np.exp(wavelengths)) * 1e-9, 12)\n",
     "\n",
     "options = default_options()\n",
-    "options.wavelengths = wavelengths\n",
+    "options.wavelength = wavelengths\n",
     "options.project_name = \"HIT_notebook\"\n",
     "options.n_rays = 5000\n",
     "options.n_theta_bins = 20\n",

examples/HIT_emissivity.py

@@ -36,15 +36,13 @@
 wavelengths = np.round(np.floor(np.exp(wavelengths)) * 1e-9, 12)
 
 options = default_options()
-options.wavelengths = wavelengths
+options.wavelength = wavelengths
 options.project_name = "HIT_notebook"
 options.n_rays = 5000
 options.n_theta_bins = 20
 options.nx = 5
 options.ny = 5
-_, _, angle_vector = make_angle_vector(
-    options["n_theta_bins"], options["phi_symmetry"], options["c_azimuth"]
-)
+_, _, angle_vector = make_angle_vector(options["n_theta_bins"], options["phi_symmetry"], options["c_azimuth"])
 options.bulk_profile = True
 options.phi_symmetry = np.pi / 2
 
@@ -70,12 +68,8 @@
 surf = regular_pyramids(elevation_angle=55, upright=True)
 surf_back = regular_pyramids(elevation_angle=55, upright=False)
 
-front_surf = Interface(
-    "RT_TMM", texture=surf, layers=front_materials, name="HIT_front", coherent=True
-)
-back_surf = Interface(
-    "RT_TMM", texture=surf_back, layers=back_materials, name="HIT_back", coherent=True
-)
+front_surf = Interface("RT_TMM", texture=surf, layers=front_materials, name="HIT_front", coherent=True)
+back_surf = Interface("RT_TMM", texture=surf_back, layers=back_materials, name="HIT_back", coherent=True)
 
 
 bulk_Si = BulkLayer(170e-6, Si, name="Si_bulk")  # bulk thickness in m
@@ -117,11 +111,7 @@
 # calculated photogenerated current (Jsc with 100% EQE)
 
 spectr_flux = LightSource(
-    source_type="standard",
-    version="AM1.5g",
-    x=wavelengths,
-    output_units="photon_flux_per_m",
-    concentration=1,
+    source_type="standard", version="AM1.5g", x=wavelengths, output_units="photon_flux_per_m", concentration=1
 ).spectrum(wavelengths)[1]
 
 Jph_Si = q * np.trapz(RAT["A_bulk"][0] * spectr_flux, wavelengths) / 10  # mA/cm2
@@ -155,16 +145,16 @@
 # plot total R, A, T
 fig = plt.figure(figsize=(5, 4))
 ax = plt.subplot(111)
-ax.semilogx(options["wavelengths"] * 1e6, R_escape + R_0, "--k", label=r"$R_{total}$")
-ax.semilogx(options["wavelengths"] * 1e6, R_0, "-.k", label=r"$R_0$")
+ax.semilogx(options["wavelength"] * 1e6, R_escape + R_0, "--k", label=r"$R_{total}$")
+ax.semilogx(options["wavelength"] * 1e6, R_0, "-.k", label=r"$R_0$")
 ax.stackplot(
-    options["wavelengths"] * 1e6,
+    options["wavelength"] * 1e6,
     allres,
     labels=["Ag", "Back ITO", "a-Si (back)", "Bulk Si", "a-Si (front)", "Front ITO"],
 )
 ax.semilogx(emissivity[:, 0], emissivity[:, 1], "-k")
 ax.set_xlabel(r"Wavelength ($\mu$m)")
 ax.set_ylabel("Absorption/Emissivity")
-ax.set_xlim(min(options["wavelengths"] * 1e6), max(options["wavelengths"] * 1e6))
+ax.set_xlim(min(options["wavelength"] * 1e6), max(options["wavelength"] * 1e6))
 ax.set_ylim(0, 1)
 plt.show()