Merge remote-tracking branch 'origin/main' into DorisReiter-patch-1

.github/workflows/build.yml

@@ -21,10 +21,10 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: "3.12"
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@v2
         with:
-          version: '1.9.2'
-      - uses: julia-actions/cache@v1
+          version: '1.10.2'
+      - uses: julia-actions/cache@v2
       - name: Install JuliaFormatter and format
         run: |
           julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter"))'

.github/workflows/docs.yml

@@ -37,7 +37,7 @@ jobs:
           installer-parallel: true
       - name: Install dependencies
         run: |
-          sudo apt-get install -y libglu1-mesa
+          sudo apt-get install -y libglu1-mesa xvfb
           poetry install --no-interaction
           pip install --upgrade scipy
           mamba install slepc4py=*=complex* -y
@@ -47,18 +47,22 @@ jobs:
           pip install gdsfactory gplugins
           pip list
       
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@v2
         with:
-          version: '1.9.3'
-      - uses: julia-actions/cache@v1
+          version: '1.10.3'
+      - uses: julia-actions/cache@v2
         with:
           cache-name: ${{ runner.os }}-${{ steps.get-date.outputs.date }}
           cache-compiled: "true"
       - uses: julia-actions/julia-buildpkg@v1
-      - name: Install dependencies
+      - name: Install julia dependencies
         run: |
           pip install juliacall
           julia -e 'using Pkg; Pkg.add("PythonCall")'
+      - name: Precompile julia dependencies
+        continue-on-error: true
+        run: |
+          julia --project=~/work/femwell/femwell -e 'using Pkg; Pkg.precompile()'
       - uses: actions/cache@v4
         with:
           path: |

docs/_toc.yml

@@ -9,26 +9,31 @@ parts:
       - file: install
   - caption: Derivation of the equations
     chapters:
-      - file: math/maxwell
-        sections:
-        - file: math/waveguide_port
-        - file: math/overlap_integrals
-      - file: math/thermal
-      - file: math/dispersion
-      - file: math/coupled_mode_theory
-      - file: math/schroedinger
+    - file: math/maxwell
+      sections:
+      - file: math/maxwell_quantities
+      - file: math/waveguide_port
+      - file: math/overlap_integrals
+    - file: math/thermal
+    - file: math/dispersion
+    - file: math/coupled_mode_theory
+    - file: math/schroedinger
 
   - caption: Examples
     chapters:
     - file: photonics/examples/waveguide_modes.py
-    #- file: photonics/examples/leaky_waveguide.py
-    #- file: photonics/examples/bent_waveguide.py
-    - file: photonics/examples/vary_width.py
-    - file: photonics/examples/vary_wavelength.py
-    - file: photonics/examples/selecting_modes.py
-    - file: photonics/examples/calculate_GVD.py
-    - file: photonics/examples/fiber_overlap.py
-    - file: photonics/examples/crosstalk.py
+      sections:
+      #- file: photonics/examples/leaky_waveguide.py
+      #- file: photonics/examples/bent_waveguide.py
+      - file: photonics/examples/vary_width.py
+      - file: photonics/examples/vary_wavelength.py
+      - file: photonics/examples/selecting_modes.py
+      - file: photonics/examples/calculate_GVD.py
+      - file: photonics/examples/fiber_overlap.py
+      - file: photonics/examples/crosstalk.py
+      - file: photonics/examples/propagation_loss.py
+      - file: photonics/examples/effective_area.py
+      - file: photonics/examples/crosstalk_reduction/crosstalk_reduction.py
     - file: photonics/examples/metal_heater_phase_shifter.py
     - file: photonics/examples/metal_heater_phase_shifter_transient.py
     - file: photonics/examples/si_heater_phase_shifter.py
@@ -38,9 +43,7 @@ parts:
     - file: photonics/examples/grating_coupler.py
     - file: photonics/examples/coupled_mode_theory.py
     - file: photonics/examples/depletion_waveguide.py
-    - file: photonics/examples/effective_area.py
     - file: photonics/examples/refinement.py
-    - file: photonics/examples/propagation_loss.py
     - file: electronics/examples/capacitor.py
     - file: electronics/examples/coax_cable.py
     - file: electronics/examples/coplanar_waveguide_vary_width.py

docs/benchmarks/mode_solver.py

@@ -1,26 +1,28 @@
 # ---
 # jupyter:
 #   jupytext:
-#     formats: py:light,md:myst
+#     formats: py:percent,md:myst
 #     text_representation:
 #       extension: .py
-#       format_name: light
-#       format_version: '1.5'
-#       jupytext_version: 1.14.4
+#       format_name: percent
+#       format_version: '1.3'
+#       jupytext_version: 1.16.1
 #   kernelspec:
 #     display_name: Python 3
 #     name: python3
 # ---
 
+# %% [markdown]
 # # Benchmark of the mode solver 2
 
+# %% [markdown]
 # Reproducing {cite}`Hadley2002`, where the modes of a strip and
 # several rib waveguide were calculated and presented with an error value.
 # The error for all modes is calculated to be smaller than $\pm 3 \cdot 10^{-6}$,
 # thus this should be the maximum derivation for our simulations.
 # The results are presented here:
 
-# + tags=["remove-stderr", "hide-input", "hide-output"]
+# %% tags=["remove-stderr", "hide-input", "hide-output"]
 from collections import OrderedDict
 
 import numpy as np
@@ -135,7 +137,7 @@
     neff_values_femwell_scipy.append(np.real(modes[0].n_eff))
 
 
-# + tags=["remove-stderr", "hide-input"]
+# %% tags=["remove-stderr", "hide-input"]
 pd.DataFrame(
     {
         "slab_thickness": slab_thicknesses,
@@ -160,8 +162,8 @@
     ],
     subset=["difference scipy", "difference julia"],  # "difference slepc",
 )
-# -
 
+# %% [markdown]
 # ## Bibliography
 #
 # ```{bibliography}

docs/benchmarks/mode_solver_rectangle.py

@@ -1,26 +1,28 @@
 # ---
 # jupyter:
 #   jupytext:
-#     formats: py:light,md:myst
+#     formats: py:percent,md:myst
 #     text_representation:
 #       extension: .py
-#       format_name: light
-#       format_version: '1.5'
-#       jupytext_version: 1.14.4
+#       format_name: percent
+#       format_version: '1.3'
+#       jupytext_version: 1.15.0
 #   kernelspec:
 #     display_name: Python 3
 #     name: python3
 # ---
 
+# %% [markdown]
 # # Benchmark of the mode solver 1
 
+# %% [markdown]
 # Reproducing {cite}`Hadley2002`, where the modes of a analytically solvable geometry are calculated.
 # The error for all modes is calculated to be smaller than $\pm 1 \cdot 10^{-8}$.
 # We'll show that we get pretty close, but will stop at a resonable resolution to keep the runtime sensible.
 # Getting even higher accurancy will be left open for adaptive refinement.
 # The results are presented here:
 
-# + tags=["remove-stderr", "hide-input"]
+# %% tags=["remove-stderr", "hide-input"]
 from collections import OrderedDict
 
 import numpy as np
@@ -87,16 +89,16 @@
 
 pd.DataFrame(
     {
-        "epsilons": [
+        "Epsilons": [
             f"{epsilons['core']:.2f} / {epsilons['clad']:.2f}" for epsilons in epsilons_paper
         ],
-        "reference value": (f"{n:.8f}" for n in neff_values_paper),
-        "calculated value slepc": (f"{n:.8f}" for n in neff_values_femwell_slepc),
-        "difference slepc": (
+        "Reference value": (f"{n:.8f}" for n in neff_values_paper),
+        "Calculated value slepc": (f"{n:.8f}" for n in neff_values_femwell_slepc),
+        "Difference slepc": (
             f"{n1-n2:.8f}" for n1, n2 in zip(neff_values_paper, neff_values_femwell_slepc)
         ),
-        "calculated value scipy": (f"{n:.8f}" for n in neff_values_femwell_scipy),
-        "difference scipy": (
+        "Calculated value scipy": (f"{n:.8f}" for n in neff_values_femwell_scipy),
+        "Difference scipy": (
             f"{n1-n2:.8f}" for n1, n2 in zip(neff_values_paper, neff_values_femwell_scipy)
         ),
     }
@@ -105,10 +107,10 @@
         "background-color: green" if abs(float(difference)) < 5e-6 else "background-color: red"
         for difference in differences
     ],
-    subset=["difference slepc", "difference scipy"],
+    subset=["Difference slepc", "Difference scipy"],
 )
-# -
 
+# %% [markdown]
 # ## Bibliography
 #
 # ```{bibliography}

docs/julia/heater_3d.jl

@@ -11,7 +11,7 @@
 #   kernelspec:
 #     display_name: base
 #     language: julia
-#     name: julia-1.9
+#     name: julia-1.10
 # ---
 
 # %% [markdown]
@@ -101,9 +101,9 @@ thermal_diffisitivities =
 # The next step is to define the boundary conditions, this can be done simply via julia-dicts:
 
 # %% tags=["remove-stderr", "hide-output"]
-boundary_potentials = Dict(["metal3#e1___None" => 0.4, "metal3#e2___None" => 0.0])
+boundary_potentials = Dict(["metal3#e1___clad" => 0.4, "metal3#e2___clad" => 0.0])
 boundary_temperatures =
-    Dict("metal3#e1___None" => 0.4, "metal3#e2___None" => 0.0, "box___None" => 0.0)
+    Dict("metal3#e1___None" => 0.0, "metal3#e2___None" => 0.0, "box___None" => 0.0)
 
 # %% [markdown]
 # Now we're ready to do the simulations! First we simulate the electrical potential,
@@ -136,9 +136,10 @@ println(
 )
 
 # %% [markdown]
-# And we write the fields to a file for visualisation using paraview:
+# And we write the fields to a vtu-file for visualisation using paraview:
 
 # %% tags=["remove-stderr", "hide-output"]
+Base.zero(::Type{String}) = ""
 writevtk(
     Ω,
     "results",
@@ -148,6 +149,7 @@ writevtk(
         "temperature" => temperature(T0),
         "heat flux" => heat_flux(T0),
         "tags" => τ,
+        "tag_name" => (tag -> get_tag_name(labels, tag)) ∘ τ,
     ],
 )
 

docs/julia/heater_3d_mesh.py

@@ -8,7 +8,7 @@
 
 # Choose some component
 c = gf.component.Component()
-waveguide = c << gf.get_component(gf.components.straight_heater_metal(length=40))
+waveguide = c << gf.get_component(gf.components.straight_heater_metal(length=80))
 e1 = c << gf.components.straight(1, cross_section="xs_m3")
 e1.connect(e1["e1"], waveguide["l_e1"])
 e2 = c << gf.components.straight(1, cross_section="xs_m3")

docs/julia/lithium_niobate_phase_shifter.jl

@@ -11,7 +11,7 @@
 #   kernelspec:
 #     display_name: base
 #     language: julia
-#     name: julia-1.9
+#     name: julia-1.10
 # ---
 
 # %% [markdown]

docs/julia/microstrip.jl

@@ -11,7 +11,7 @@
 #   kernelspec:
 #     display_name: base
 #     language: julia
-#     name: julia-1.9
+#     name: julia-1.10
 # ---
 
 # %% [markdown]

docs/julia/thermal_fill.jl

@@ -11,7 +11,7 @@
 #   kernelspec:
 #     display_name: base
 #     language: julia
-#     name: julia-1.9
+#     name: julia-1.10
 # ---
 
 # %% [markdown]

docs/julia/thermal_simple.jl

@@ -11,7 +11,7 @@
 #   kernelspec:
 #     display_name: base
 #     language: julia
-#     name: julia-1.9
+#     name: julia-1.10
 # ---
 
 # %% [markdown]

docs/julia/waveguide.jl

@@ -11,7 +11,7 @@
 #   kernelspec:
 #     display_name: base
 #     language: julia
-#     name: julia-1.9
+#     name: julia-1.10
 # ---
 
 # %% [markdown]

docs/julia/waveguide_anisotropic.jl

@@ -11,7 +11,7 @@
 #   kernelspec:
 #     display_name: base
 #     language: julia
-#     name: julia-1.9
+#     name: julia-1.10
 # ---
 
 # %% [markdown]

docs/julia/waveguide_bent.jl

@@ -11,7 +11,7 @@
 #   kernelspec:
 #     display_name: base
 #     language: julia
-#     name: julia-1.9
+#     name: julia-1.10
 # ---
 
 # %% [markdown]

docs/julia/waveguide_bent_coupling.jl

@@ -11,7 +11,7 @@
 #   kernelspec:
 #     display_name: base
 #     language: julia
-#     name: julia-1.9
+#     name: julia-1.10
 # ---
 
 # %% [markdown]

docs/julia/waveguide_overlap_integral.jl

@@ -11,7 +11,7 @@
 #   kernelspec:
 #     display_name: base
 #     language: julia
-#     name: julia-1.9
+#     name: julia-1.10
 # ---
 
 # %% [markdown]