Merge pull request #195 from nikosavola/158-fix-elmer-and-palace-tests

Fix Elmer & Palace tests

docs/_config.yml

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

docs/notebooks/elmer_01_electrostatic.py

@@ -93,7 +93,6 @@
 c.add_ports(cap.ports)
 substrate = gf.components.bbox(bbox=simulation_box, layer=LAYER.WAFER)
 c << substrate
-c = c.flatten()
 c.plot()
 
 # %% [markdown]
@@ -135,7 +134,7 @@
                 "resolution": 40,
             },
             **{
-                f"bw{port}": {
+                f"bw__{port}": {  # `__` is used as the layer–port delimiter for Elmer
                     "resolution": 20,
                     "DistMax": 30,
                     "DistMin": 10,

docs/notebooks/palace_01_electrostatic.py

@@ -91,7 +91,7 @@
 c.add_ports(cap.ports)
 substrate = gf.components.bbox(bbox=simulation_box, layer=LAYER.WAFER)
 c << substrate
-c.flatten()
+c.plot()
 
 # %% [markdown]
 # ## Running the simulation
@@ -132,7 +132,7 @@
                 "resolution": 40,
             },
             **{
-                f"bw{port}": {
+                f"bw__{port}": {  # `__` is used as the layer–port delimiter for Palace
                     "resolution": 20,
                     "DistMax": 30,
                     "DistMin": 10,

docs/notebooks/palace_02_fullwave.py

@@ -129,7 +129,6 @@
 
 substrate = gf.components.bbox(bbox=simulation_box, layer=LAYER.WAFER)
 c << substrate
-c.flatten()
 c.show()
 
 # %% [markdown]

gplugins/elmer/get_capacitance.py

@@ -216,6 +216,7 @@ def run_capacitive_simulation_elmer(
     simulation_folder = Path(simulation_folder or temp_dir.name)
     simulation_folder.mkdir(exist_ok=True, parents=True)
 
+    port_delimiter = "__"  # won't cause trouble unlike #
     filename = component.name + ".msh"
     if mesh_file:
         shutil.copyfile(str(mesh_file), str(simulation_folder / filename))
@@ -225,7 +226,7 @@ def run_capacitive_simulation_elmer(
             type="3D",
             filename=simulation_folder / filename,
             layer_stack=layer_stack,
-            **(mesh_parameters or {}),
+            **((mesh_parameters or {}) | {"layer_port_delimiter": port_delimiter}),
         )
 
     # `interruptible` works on gmsh versions >= 4.11.2
@@ -248,9 +249,6 @@ def run_capacitive_simulation_elmer(
         next(k for k, v in layer_stack.layers.items() if v.layer == port.layer)
         for port in component.get_ports()
     }  # ports allowed only on metal
-    # TODO infer port delimiter from somewhere
-    # TODO raise error for port delimiters not supported by Elmer MATC or find how to escape
-    port_delimiter = "__"
     metal_surfaces = [
         e for e in mesh_surface_entities if any(ground in e for ground in ground_layers)
     ]

gplugins/elmer/tests/test_elmer.py

@@ -80,7 +80,6 @@ def get_reasonable_mesh_parameters(c: Component):
     )
 
 
-@pytest.mark.skip(reason="FIXME")
 def test_elmer_capacitance_simulation_runs(geometry) -> None:
     c = geometry
     run_capacitive_simulation_elmer(
@@ -91,8 +90,7 @@ def test_elmer_capacitance_simulation_runs(geometry) -> None:
     )
 
 
-@pytest.mark.skip(reason="FIXME")
-@pytest.mark.parametrize("n_processes", [(1), (2), (4)])
+@pytest.mark.parametrize("n_processes", [(1), (2)])
 def test_elmer_capacitance_simulation_n_processes(geometry, n_processes):
     c = geometry
     run_capacitive_simulation_elmer(
@@ -104,7 +102,6 @@ def test_elmer_capacitance_simulation_n_processes(geometry, n_processes):
     )
 
 
-@pytest.mark.skip(reason="FIXME")
 @pytest.mark.parametrize("element_order", [(1), (2), (3)])
 def test_elmer_capacitance_simulation_element_order(geometry, element_order) -> None:
     c = geometry

gplugins/gmsh/xy_xsection_mesh.py

@@ -73,6 +73,7 @@ def xy_xsection_mesh(
     n_threads: int = get_number_of_cores(),
     port_names: list[str] | None = None,
     gmsh_version: float | None = None,
+    layer_port_delimiter: str | None = None,
 ):
     """Mesh xy cross-section of component at height z.
 
@@ -93,6 +94,7 @@ def xy_xsection_mesh(
         round_tol: during gds --> mesh conversion cleanup, number of decimal points at which to round the gdsfactory/shapely points before introducing to gmsh
         simplify_tol: during gds --> mesh conversion cleanup, shapely "simplify" tolerance (make it so all points are at least separated by this amount)
         atol: tolerance used to establish equivalency between vertices
+        layer_port_delimiter: Delimiter to use for new layers generated for ports: "layer{delimiter}port_name".
     """
     if port_names:
         mesh_component = gf.Component()
@@ -102,6 +104,7 @@ def xy_xsection_mesh(
             component=mesh_component,
             port_names=port_names,
             layer_stack=layer_stack,
+            **(dict(delimiter=layer_port_delimiter) if layer_port_delimiter else {}),
         )
 
     # Fuse and cleanup polygons of same layer in case user overlapped them

gplugins/gmsh/xyz_mesh.py

@@ -151,6 +151,7 @@ def xyz_mesh(
     port_names: List[str] | None = None,
     edge_ports: List[str] | None = None,
     gmsh_version: float | None = None,
+    layer_port_delimiter: str | None = None,
 ) -> bool:
     """Full 3D mesh of component.
 
@@ -184,6 +185,7 @@ def xyz_mesh(
             }
         gmsh_version: Gmsh mesh format version. For example, Palace requires an older version of 2.2,
             see https://mfem.org/mesh-formats/#gmsh-mesh-formats.
+        layer_port_delimiter: Delimiter to use for new layers generated for ports: "layer{delimiter}port_name".
     """
     if port_names:
         mesh_component = gf.Component()
@@ -193,6 +195,7 @@ def xyz_mesh(
             component=mesh_component,
             port_names=port_names,
             layer_stack=layer_stack,
+            **(dict(delimiter=layer_port_delimiter) if layer_port_delimiter else {}),
         )
 
     # Fuse and cleanup polygons of same layer in case user overlapped them

gplugins/palace/get_capacitance.py

@@ -233,6 +233,7 @@ def run_capacitive_simulation_palace(
     simulation_folder = Path(simulation_folder or temp_dir.name)
     simulation_folder.mkdir(exist_ok=True, parents=True)
 
+    port_delimiter = "__"  # won't cause trouble unlike #
     filename = component.name + ".msh"
     if mesh_file:
         shutil.copyfile(str(mesh_file), str(simulation_folder / filename))
@@ -244,7 +245,7 @@ def run_capacitive_simulation_palace(
             layer_stack=layer_stack,
             n_threads=n_processes,
             gmsh_version=2.2,  # see https://mfem.org/mesh-formats/#gmsh-mesh-formats
-            **(mesh_parameters or {}),
+            **((mesh_parameters or {}) | {"layer_port_delimiter": port_delimiter}),
         )
 
     # re-read the mesh
@@ -267,8 +268,6 @@ def run_capacitive_simulation_palace(
         next(k for k, v in layer_stack.layers.items() if v.layer == port.layer)
         for port in component.get_ports()
     }  # ports allowed only on metal
-    # TODO infer port delimiter from somewhere
-    port_delimiter = "__"
     metal_surfaces = [
         e for e in mesh_surface_entities if any(ground in e for ground in ground_layers)
     ]