Consitent layer stack name (#157)

-  update to latest tidy3d 2.4 and gdsfactory, unpin jax and jaxlib
- rename `layerstack` to `layer_stack` to be consistent with gdsfactory
- rename portnames to port_names  to be consistent with python convention

* fix docs and tests

docs/_config.yml

@@ -22,6 +22,7 @@ execute:
     - "*03_numerical_implantation*"
     - "*02_model_extraction*"
     - "*palace*"
+    - "*elmer_01_electrostatic*"
     - "*fdtdz*"
     # - "*sax_01_sax*"
     # - "*20_schematic_driven_layout*"

docs/api_design.rst

@@ -22,9 +22,9 @@ Meshing
     to_polygons
     get_layer_overlaps_z
     get_layers_at_z
-    list_unique_layerstack_z
-    map_unique_layerstack_z
-    order_layerstack
+    list_unique_layer_stack_z
+    map_unique_layer_stack_z
+    order_layer_stack
     get_u_bounds_layers
     get_u_bounds_polygons
     get_uz_bounds_layers

docs/notebooks/elmer_01_electrostatic.py

@@ -93,7 +93,8 @@
 c.add_ports(cap.ports)
 substrate = gf.components.bbox(bbox=simulation_box, layer=LAYER.WAFER)
 c << substrate
-c.flatten()
+c = c.flatten()
+c.plot()
 
 # %% [markdown]
 # ## Running the simulation
@@ -121,9 +122,8 @@
     mesh_parameters=dict(
         background_tag="vacuum",
         background_padding=(0,) * 5 + (700,),
-        portnames=c.ports,
+        port_names=c.ports.keys(),
         default_characteristic_length=200,
-        layer_portname_delimiter=(delimiter := "__"),
         resolutions={
             "bw": {
                 "resolution": 15,
@@ -135,7 +135,7 @@
                 "resolution": 40,
             },
             **{
-                f"bw{delimiter}{port}": {
+                f"bw{port}": {
                     "resolution": 20,
                     "DistMax": 30,
                     "DistMin": 10,

docs/notebooks/fdtdz_01.py

@@ -55,19 +55,19 @@
 )
 c.add_ports(gf.components.straight(length=length).get_ports_list())
 
-c.plot_matplotlib(show_ports=True)
+c.plot()
 # -
 
 # ### Define your LayerStack
 #
 # Here we load the generic LayerStack, but only keep the `core`, `clad`, and `box` layers:
 
-filtered_layerstack = LayerStack(
+filtered_layer_stack = LayerStack(
     layers={
         k: LAYER_STACK.layers[k] for k in ["clad", "box", "core", "slab90", "nitride"]
     }
 )
-filtered_layerstack
+filtered_layer_stack
 
 # We show how to inspect the resulting permittivity below to troubleshoot.
 
@@ -94,7 +94,7 @@
 
 out = get_sparameters_fdtdz(
     component=c,
-    layerstack=filtered_layerstack,
+    layer_stack=filtered_layer_stack,
     nm_per_pixel=20,
     extend_ports_length=0.0,
     zmin=-0.5,
@@ -119,7 +119,7 @@
 #
 # ### Permittivity distribution
 #
-# Pass the component, layerstack, and minz, and slice the simulation domain to inspect the permittivity.
+# Pass the component, layer_stack, and minz, and slice the simulation domain to inspect the permittivity.
 #
 # For xy-plane visualization, set `x = y = None` and choose a z-value:
 
@@ -130,7 +130,7 @@
 nm_per_pixel = 20
 
 epsilon = component_to_epsilon_pjz(
-    component=c, layerstack=filtered_layerstack, zmin=zmin
+    component=c, layer_stack=filtered_layer_stack, zmin=zmin
 )
 
 fig = plot_epsilon(

docs/notebooks/femwell_01_modes.py

@@ -32,7 +32,7 @@
 logging.basicConfig(level="WARNING", datefmt="[%X]", handlers=[RichHandler()])
 
 # +
-filtered_layerstack = LayerStack(
+filtered_layer_stack = LayerStack(
     layers={
         k: LAYER_STACK.layers[k]
         for k in (
@@ -44,13 +44,13 @@
     }
 )
 
-filtered_layerstack.layers[
+filtered_layer_stack.layers[
     "core"
-].thickness = 0.22  # Perturb the layerstack before simulating
+].thickness = 0.22  # Perturb the layer_stack before simulating
 
-filtered_layerstack.layers[
+filtered_layer_stack.layers[
     "slab90"
-].thickness = 0.09  # Perturb the layerstack before simulating
+].thickness = 0.09  # Perturb the layer_stack before simulating
 
 resolutions = {
     "core": {"resolution": 0.02, "distance": 2},
@@ -62,7 +62,7 @@
 
 modes = compute_cross_section_modes(
     cross_section=rib(width=0.6),
-    layerstack=filtered_layerstack,
+    layer_stack=filtered_layer_stack,
     wavelength=1.55,
     num_modes=4,
     resolutions=resolutions,
@@ -90,7 +90,7 @@
 for i, width in enumerate(tqdm(widths)):
     modes = compute_cross_section_modes(
         cross_section=gf.cross_section.strip(width=width),
-        layerstack=filtered_layerstack,
+        layer_stack=filtered_layer_stack,
         wavelength=1.55,
         num_modes=num_modes,
         resolutions=resolutions,

docs/notebooks/femwell_02_heater.py

@@ -28,7 +28,7 @@
 
 print(LAYER_STACK.layers.keys())
 
-filtered_layerstack = LayerStack(
+filtered_layer_stack = LayerStack(
     layers={
         k: gf.pdk.get_layer_stack().layers[k]
         for k in ("slab90", "core", "via_contact", "heater")
@@ -50,7 +50,7 @@ def mesh_with_physicals(mesh, filename):
     component=heater,
     type="uz",
     xsection_bounds=[(4, -4), (4, 4)],
-    layer_stack=filtered_layerstack,
+    layer_stack=filtered_layer_stack,
     filename=f"{filename}.msh",
 )
 mesh = mesh_with_physicals(mesh, filename)

docs/notebooks/meep_03_fields.py

@@ -44,7 +44,7 @@
     bottom=3.2,
 )
 
-component.plot_matplotlib()
+component.plot()
 # -
 
 # ## Define a continuous source simulation

docs/notebooks/meow_01.py

@@ -26,11 +26,11 @@
 # You also need to explicitly provide a LayerStack to define cross-sections, for instance the generic one:
 
 # +
-layerstack = LAYER_STACK
+layer_stack = LAYER_STACK
 
-filtered_layerstack = gf.technology.LayerStack(
+filtered_layer_stack = gf.technology.LayerStack(
     layers={
-        k: layerstack.layers[k]
+        k: layer_stack.layers[k]
         for k in (
             "slab90",
             "core",
@@ -45,7 +45,9 @@
 
 # The EME simulator can be instantiated with only these two elements, alongside parameters:
 
-eme = MEOW(component=c, layerstack=filtered_layerstack, wavelength=1.55, overwrite=True)
+eme = MEOW(
+    component=c, layer_stack=filtered_layer_stack, wavelength=1.55, overwrite=True
+)
 
 # Plotting functions allow you to check your simulation:
 
@@ -79,11 +81,11 @@
 # Lets sweep the length of the taper.
 
 # +
-layerstack = LAYER_STACK
+layer_stack = LAYER_STACK
 
-filtered_layerstack = gf.technology.LayerStack(
+filtered_layer_stack = gf.technology.LayerStack(
     layers={
-        k: layerstack.layers[k]
+        k: layer_stack.layers[k]
         for k in (
             "slab90",
             "core",
@@ -106,7 +108,7 @@
 for cell_length in cells_lengths:
     m = MEOW(
         component=c,
-        layerstack=filtered_layerstack,
+        layer_stack=filtered_layer_stack,
         wavelength=1.55,
         overwrite=True,
         spacing_y=-3,
@@ -124,7 +126,7 @@
 
 eme = MEOW(
     component=c,
-    layerstack=filtered_layerstack,
+    layer_stack=filtered_layer_stack,
     wavelength=1.55,
     overwrite=True,
     spacing_y=-3,
@@ -161,7 +163,7 @@
     c = gf.components.taper(width1=0.5, width2=2, length=length)
     eme = MEOW(
         component=c,
-        layerstack=filtered_layerstack,
+        layer_stack=filtered_layer_stack,
         wavelength=1.55,
         overwrite=True,
         spacing_y=-3,

docs/notebooks/meshing_01_intro.py

@@ -34,7 +34,7 @@
 #
 # While the latter method is much simpler for complex geometries, as of 2022 it does not preserve physical and mesh information, requiring manual "retagging" of the entities after the boolean operations, and driving its complexity back to bottom-up construction (especially for arbitrary geometries).
 #
-# As such, gdsfactory uses the first approach, where the mask layers and a layerstack are used as a guide to define the various physical entities, which are returned as tagged objects to the user.
+# As such, gdsfactory uses the first approach, where the mask layers and a layer_stack are used as a guide to define the various physical entities, which are returned as tagged objects to the user.
 #
 # ## Installation
 #
@@ -61,15 +61,15 @@
 PDK.activate()
 
 waveguide = gf.components.straight_pin(length=10, taper=None)
-waveguide
+waveguide.plot()
 # -
 
 # and a `LayerStack`. Here, we copy the example from `gdsfactory.generic_tech` for clarity).
 # The `info` dict contains miscellaneous information about the layers, including `mesh_order`, which determines which layer will appear in the mesh if layers overlap.
 
 # We can filter this stack to only focus on some layers:
 
-filtered_layerstack = LayerStack(
+filtered_layer_stack = LayerStack(
     layers={
         k: LAYER_STACK.layers[k]
         for k in (
@@ -91,7 +91,7 @@ def mesh_with_physicals(mesh, filename):
 
 # -
 
-scene = waveguide.to_3d(layer_stack=filtered_layerstack)
+scene = waveguide.to_3d(layer_stack=filtered_layer_stack)
 scene.show()
 
 # The various processing and meshing functions are located under `gplugins.gmsh` and can be called from there, but a shortcut is implemented to mesh directly from a component:
@@ -100,7 +100,7 @@ def mesh_with_physicals(mesh, filename):
     component=waveguide,
     type="xy",
     z=0.09,
-    layer_stack=filtered_layerstack,
+    layer_stack=filtered_layer_stack,
     filename="mesh.msh",
 )
 

docs/notebooks/meshing_02_2D_xy_mesh.py

@@ -18,10 +18,10 @@
 PDK.activate()
 
 waveguide = gf.components.straight_pin(length=10, taper=None)
-waveguide
+waveguide.plot()
 # -
 
-filtered_layerstack = LayerStack(
+filtered_layer_stack = LayerStack(
     layers={
         k: get_layer_stack().layers[k]
         for k in (
@@ -50,7 +50,7 @@ def mesh_with_physicals(mesh, filename):
     component=waveguide,
     type="xy",
     z=0.09,
-    layer_stack=filtered_layerstack,
+    layer_stack=filtered_layer_stack,
     filename=f"{filename}.msh",
 )
 mesh = mesh_with_physicals(mesh, filename)
@@ -63,7 +63,7 @@ def mesh_with_physicals(mesh, filename):
     component=waveguide,
     type="xy",
     z=0.0,
-    layer_stack=filtered_layerstack,
+    layer_stack=filtered_layer_stack,
     filename=f"{filename}.msh",
 )
 mesh = mesh_with_physicals(mesh, filename)
@@ -76,7 +76,7 @@ def mesh_with_physicals(mesh, filename):
     component=waveguide,
     type="xy",
     z=1.0,
-    layer_stack=filtered_layerstack,
+    layer_stack=filtered_layer_stack,
     filename=f"{filename}.msh",
 )
 mesh = mesh_with_physicals(mesh, filename)
@@ -96,14 +96,14 @@ def mesh_with_physicals(mesh, filename):
     )
 )
 
-waveguide_trimmed
+waveguide_trimmed.plot()
 # -
 
 mesh = get_mesh(
     component=waveguide_trimmed,
     type="xy",
     z=0.09,
-    layer_stack=filtered_layerstack,
+    layer_stack=filtered_layer_stack,
     filename=f"{filename}.msh",
 )
 mesh = mesh_with_physicals(mesh, filename)

docs/notebooks/meshing_03_2D_uz_mesh.py

@@ -26,10 +26,10 @@
     )
 )
 
-waveguide_trimmed
+waveguide_trimmed.plot()
 # -
 
-filtered_layerstack = LayerStack(
+filtered_layer_stack = LayerStack(
     layers={
         k: get_layer_stack().layers[k]
         for k in (
@@ -57,7 +57,7 @@ def mesh_with_physicals(mesh, filename):
     component=waveguide_trimmed,
     type="uz",
     xsection_bounds=[(4, -4), (4, 4)],
-    layer_stack=filtered_layerstack,
+    layer_stack=filtered_layer_stack,
     filename=f"{filename}.msh",
 )
 mesh = mesh_with_physicals(mesh, filename)
@@ -68,13 +68,13 @@ def mesh_with_physicals(mesh, filename):
 
 # ## Mesh background
 #
-# You can add a convenience argument to add a background mesh around the geometry (instead of defining a dummy polygon and layer in the layerstack with low mesh_order):
+# You can add a convenience argument to add a background mesh around the geometry (instead of defining a dummy polygon and layer in the layer_stack with low mesh_order):
 
 mesh = get_mesh(
     component=waveguide_trimmed,
     type="uz",
     xsection_bounds=[(4, -4), (4, 4)],
-    layer_stack=filtered_layerstack,
+    layer_stack=filtered_layer_stack,
     filename=f"{filename}.msh",
     background_tag="oxide",
     background_padding=(2.0, 2.0, 2.0, 2.0),