to_gmsh --> get_mesh (#150)

Co-authored-by: Joaquin Matres <4514346+joamatab@users.noreply.github.com>

docs/notebooks/femwell_02_heater.py

@@ -11,7 +11,7 @@
 from gdsfactory.technology import LayerStack
 from skfem.io import from_meshio
 
-from gplugins.gmsh.mesh import create_physical_mesh
+from gplugins.gmsh.mesh import create_physical_mesh, get_mesh
 
 gf.config.rich_output()
 PDK = get_generic_pdk()
@@ -46,7 +46,8 @@ def mesh_with_physicals(mesh, filename):
 
 # -
 
-mesh = heater.to_gmsh(
+mesh = get_mesh(
+    component=heater,
     type="uz",
     xsection_bounds=[(4, -4), (4, 4)],
     layer_stack=filtered_layerstack,

docs/notebooks/meshing_01_intro.py

@@ -53,6 +53,7 @@
 from gdsfactory.technology import LayerStack
 from skfem.io import from_meshio
 
+from gplugins.gmsh.get_mesh import get_mesh
 from gplugins.gmsh.mesh import create_physical_mesh
 
 gf.config.rich_output()
@@ -95,8 +96,12 @@ def mesh_with_physicals(mesh, filename):
 
 # 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:
 
-mesh = waveguide.to_gmsh(
-    type="xy", z=0.09, layer_stack=filtered_layerstack, filename="mesh.msh"
+mesh = get_mesh(
+    component=waveguide,
+    type="xy",
+    z=0.09,
+    layer_stack=filtered_layerstack,
+    filename="mesh.msh",
 )
 
 # This returns a gmsh `.msh` mesh, also saved in `filename` if provided, which can be processed:

docs/notebooks/meshing_02_2D_xy_mesh.py

@@ -10,6 +10,7 @@
 from gdsfactory.technology import LayerStack
 from skfem.io import from_meshio
 
+from gplugins.gmsh.get_mesh import get_mesh
 from gplugins.gmsh.mesh import create_physical_mesh
 
 gf.config.rich_output()
@@ -45,26 +46,38 @@ def mesh_with_physicals(mesh, filename):
 # At `z=0.09` um, according to the layer stack above we should see polygons from all three layers:
 
 filename = "mesh"
-mesh = waveguide.to_gmsh(
-    type="xy", z=0.09, layer_stack=filtered_layerstack, filename=f"{filename}.msh"
+mesh = get_mesh(
+    component=waveguide,
+    type="xy",
+    z=0.09,
+    layer_stack=filtered_layerstack,
+    filename=f"{filename}.msh",
 )
 mesh = mesh_with_physicals(mesh, filename)
 mesh = from_meshio(mesh)
 mesh.draw().plot()
 
 # At `z=0`, you can see only the core and slab:
 
-mesh = waveguide.to_gmsh(
-    type="xy", z=0.0, layer_stack=filtered_layerstack, filename=f"{filename}.msh"
+mesh = get_mesh(
+    component=waveguide,
+    type="xy",
+    z=0.0,
+    layer_stack=filtered_layerstack,
+    filename=f"{filename}.msh",
 )
 mesh = mesh_with_physicals(mesh, filename)
 mesh = from_meshio(mesh)
 mesh.draw().plot()
 
 # At `z=1.0`, you can only see the vias appear:
 
-mesh = waveguide.to_gmsh(
-    type="xy", z=1.0, layer_stack=filtered_layerstack, filename=f"{filename}.msh"
+mesh = get_mesh(
+    component=waveguide,
+    type="xy",
+    z=1.0,
+    layer_stack=filtered_layerstack,
+    filename=f"{filename}.msh",
 )
 mesh = mesh_with_physicals(mesh, filename)
 mesh = from_meshio(mesh)
@@ -86,8 +99,12 @@ def mesh_with_physicals(mesh, filename):
 waveguide_trimmed
 # -
 
-mesh = waveguide_trimmed.to_gmsh(
-    type="xy", z=0.09, layer_stack=filtered_layerstack, filename=f"{filename}.msh"
+mesh = get_mesh(
+    component=waveguide_trimmed,
+    type="xy",
+    z=0.09,
+    layer_stack=filtered_layerstack,
+    filename=f"{filename}.msh",
 )
 mesh = mesh_with_physicals(mesh, filename)
 mesh = from_meshio(mesh)

docs/notebooks/meshing_03_2D_uz_mesh.py

@@ -10,6 +10,7 @@
 from gdsfactory.technology import LayerStack
 from skfem.io import from_meshio
 
+from gplugins.gmsh.get_mesh import get_mesh
 from gplugins.gmsh.mesh import create_physical_mesh
 
 gf.config.rich_output()
@@ -52,7 +53,8 @@ def mesh_with_physicals(mesh, filename):
 
 # Choosing the line going from `y=-4` to `y=4` at `x=4`, which crosses slab, via, and core:
 
-mesh = waveguide_trimmed.to_gmsh(
+mesh = get_mesh(
+    component=waveguide_trimmed,
     type="uz",
     xsection_bounds=[(4, -4), (4, 4)],
     layer_stack=filtered_layerstack,
@@ -68,7 +70,8 @@ def mesh_with_physicals(mesh, filename):
 #
 # 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):
 
-mesh = waveguide_trimmed.to_gmsh(
+mesh = get_mesh(
+    component=waveguide_trimmed,
     type="uz",
     xsection_bounds=[(4, -4), (4, 4)],
     layer_stack=filtered_layerstack,

docs/notebooks/meshing_04_refinement.py

@@ -20,6 +20,7 @@
 from gdsfactory.technology import LayerStack
 from skfem.io import from_meshio
 
+from gplugins.gmsh.get_mesh import get_mesh
 from gplugins.gmsh.mesh import create_physical_mesh
 
 PDK = get_generic_pdk()
@@ -60,7 +61,8 @@ def mesh_with_physicals(mesh, filename):
 # With `default_resolution_max` set to 1 um and `default_resolution_min` set to 100 nm:
 
 # +
-mesh = waveguide_trimmed.to_gmsh(
+mesh = get_mesh(
+    component=waveguide_trimmed,
     type="uz",
     xsection_bounds=[(4, -4), (4, 4)],
     layer_stack=filtered_layerstack,
@@ -78,7 +80,8 @@ def mesh_with_physicals(mesh, filename):
 
 # With `default_resolution_max` set to 300 nm and `default_resolution_max` set to 50 nm:
 
-mesh = waveguide_trimmed.to_gmsh(
+mesh = get_mesh(
+    component=waveguide_trimmed,
     type="uz",
     xsection_bounds=[(4, -4), (4, 4)],
     layer_stack=filtered_layerstack,
@@ -101,7 +104,8 @@ def mesh_with_physicals(mesh, filename):
 # For example, to refine within the core only, one could use:
 
 resolutions = {"core": {"resolution": 0.05, "distance": 0}}
-mesh = waveguide_trimmed.to_gmsh(
+mesh = get_mesh(
+    component=waveguide_trimmed,
     type="uz",
     xsection_bounds=[(4, -4), (4, 4)],
     layer_stack=filtered_layerstack,
@@ -117,7 +121,8 @@ def mesh_with_physicals(mesh, filename):
 # Adding a dropoff at the interface:
 
 resolutions = {"core": {"resolution": 0.05, "distance": 5}}
-mesh = waveguide_trimmed.to_gmsh(
+mesh = get_mesh(
+    component=waveguide_trimmed,
     type="uz",
     xsection_bounds=[(4, -4), (4, 4)],
     layer_stack=filtered_layerstack,
@@ -138,7 +143,8 @@ def mesh_with_physicals(mesh, filename):
     "via_contact": {"resolution": 0.2, "distance": 0},
     "oxide": {"resolution": 1, "distance": 0},
 }
-mesh = waveguide_trimmed.to_gmsh(
+mesh = get_mesh(
+    component=waveguide_trimmed,
     type="uz",
     xsection_bounds=[(4, -4), (4, 4)],
     layer_stack=filtered_layerstack,
@@ -178,7 +184,8 @@ def mesh_with_physicals(mesh, filename):
 
 global_meshsize_array = np.array(global_meshsize_array)
 
-mesh = waveguide_trimmed.to_gmsh(
+mesh = get_mesh(
+    component=waveguide_trimmed,
     type="uz",
     xsection_bounds=[(4, -4), (4, 4)],
     layer_stack=filtered_layerstack,

docs/notebooks/meshing_05_3D.py

@@ -13,6 +13,7 @@
 from gdsfactory.technology import LayerStack
 from skfem.io import from_meshio
 
+from gplugins.gmsh.get_mesh import get_mesh
 from gplugins.gmsh.mesh import create_physical_mesh
 
 PDK = get_generic_pdk()
@@ -49,7 +50,8 @@ def mesh_with_physicals(mesh, filename):
 
 # -
 
-mesh = waveguide.to_gmsh(
+mesh = get_mesh(
+    component=waveguide,
     type="3D",
     layer_stack=filtered_layerstack,
     filename=f"{filename}.msh",
@@ -80,7 +82,8 @@ def mesh_with_physicals(mesh, filename):
 print(waveguide.ports["top_e1"])
 print(waveguide.ports["bot_e1"])
 
-mesh = waveguide.to_gmsh(
+mesh = get_mesh(
+    component=waveguide,
     type="3D",
     layer_stack=filtered_layerstack,
     filename=f"{filename}.msh",

gplugins/elmer/get_capacitance.py

@@ -17,6 +17,7 @@
 from numpy import isfinite
 from pandas import read_csv
 
+
 from gplugins.common.base_models.simulation import ElectrostaticResults
 from gplugins.common.types import RFMaterialSpec
 from gplugins.common.utils.async_helpers import (
@@ -190,7 +191,7 @@ def run_capacitive_simulation_elmer(
             Default is a temporary directory.
         simulator_params: Elmer-specific parameters. See template file for more details.
         mesh_parameters:
-            Keyword arguments to provide to :func:`~Component.to_gmsh`.
+            Keyword arguments to provide to :func:`get_mesh`.
         mesh_file: Path to a ready mesh to use. Useful for reusing one mesh file.
             By default a mesh is generated according to ``mesh_parameters``.
 
@@ -223,7 +224,8 @@ def run_capacitive_simulation_elmer(
     if mesh_file:
         shutil.copyfile(str(mesh_file), str(simulation_folder / filename))
     else:
-        component.to_gmsh(
+        get_mesh(
+            component=component,
             type="3D",
             filename=simulation_folder / filename,
             layer_stack=layer_stack,

gplugins/femwell/mode_solver.py

@@ -14,6 +14,8 @@
     Mesh,
 )
 
+from gplugins.gmsh.get_mesh import get_mesh
+
 mesh_filename = "mesh.msh"
 
 
@@ -127,7 +129,8 @@ def compute_component_slice_modes(
     """
 
     # Mesh
-    mesh = component.to_gmsh(
+    mesh = get_mesh(
+        component=component,
         type="uz",
         xsection_bounds=xsection_bounds,
         layer_stack=layerstack,

gplugins/femwell/solve_thermal.py

@@ -68,6 +68,8 @@ def get_thermal_conductivities(basis):
     from gdsfactory.generic_tech import LAYER_STACK
     from skfem import Mesh
 
+    from gplugins.gmsh.get_mesh import get_mesh
+
     LAYER_STACK.layers["heater"].thickness = 0.13
     LAYER_STACK.layers["heater"].zmin = 2.2
     heater_len = 1  # 1 um, so normalized
@@ -83,7 +85,9 @@ def get_thermal_conductivities(basis):
 
     # ====== MESH =====
     filtered_layerstack = LAYER_STACK
-    filtered_layerstack.get_component_with_derived_layers(heater).to_gmsh(
+    heater_derived = filtered_layerstack.get_component_with_derived_layers(heater)
+    get_mesh(
+        component=heater_derived,
         type="uz",
         xsection_bounds=[(3, c.bbox[0, 1]), (3, c.bbox[1, 1])],
         # xsection_bounds=[(3, -4), (3, 4)],

gplugins/gmsh/get_mesh.py

@@ -0,0 +1,78 @@
+import importlib.util
+
+from gdsfactory import Component
+from gdsfactory.typings import ComponentSpec, Layer, LayerStack
+
+from gplugins.gmsh.uz_xsection_mesh import uz_xsection_mesh
+from gplugins.gmsh.xy_xsection_mesh import xy_xsection_mesh
+from gplugins.gmsh.xyz_mesh import xyz_mesh
+
+
+def get_mesh(
+    component: ComponentSpec,
+    type: str,
+    layer_stack: LayerStack,
+    z: float | None = None,
+    xsection_bounds=None,
+    wafer_padding: float = 0.0,
+    wafer_layer: Layer = (99999, 0),
+    **kwargs,
+):
+    """Returns a gmsh mesh of the component for finite element simulation.
+
+    Arguments:
+        component: component
+        type: one of "xy", "uz", or "3D". Determines the type of mesh to return.
+        layer_stack: LayerStack object containing layer information.
+        z: used to define z-slice for xy meshing.
+        xsection_bounds: used to define in-plane line for uz meshing.
+        wafer_padding: padding beyond bbox to add to WAFER layers.
+        wafer_layer: layer to use for WAFER padding.
+
+    Keyword Args:
+        Arguments for the target meshing function in gplugins.gmsh
+
+
+    TODO! make compatible with new unified plugins interface
+    """
+
+    # Add WAFER layer:
+    padded_component = Component()
+    padded_component << component
+    (xmin, ymin), (xmax, ymax) = component.bbox
+    points = [
+        [xmin - wafer_padding, ymin - wafer_padding],
+        [xmax + wafer_padding, ymin - wafer_padding],
+        [xmax + wafer_padding, ymax + wafer_padding],
+        [xmin - wafer_padding, ymax + wafer_padding],
+    ]
+    padded_component.add_polygon(points, layer=wafer_layer)
+    padded_component.add_ports(component.get_ports_list())
+
+    if type == "xy":
+        if z is None:
+            raise ValueError(
+                'For xy-meshing, a z-value must be provided via the float argument "z".'
+            )
+
+        return xy_xsection_mesh(padded_component, z, layer_stack, **kwargs)
+    elif type == "uz":
+        if xsection_bounds is None:
+            raise ValueError(
+                "For uz-meshing, you must provide a line in the xy-plane "
+                "via the Tuple argument [[x1,y1], [x2,y2]] xsection_bounds."
+            )
+
+        return uz_xsection_mesh(
+            padded_component, xsection_bounds, layer_stack, **kwargs
+        )
+    elif type == "3D":
+        spec = importlib.util.find_spec("meshwell")
+        if spec is None:
+            print(
+                "3D meshing requires meshwell, see https://github.com/simbilod/meshwell or run pip install meshwell."
+            )
+
+        return xyz_mesh(padded_component, layer_stack, **kwargs)
+    else:
+        raise ValueError('Required argument "type" must be one of "xy", "uz", or "3D".')

gplugins/gmsh/parse_gds.py

@@ -114,6 +114,8 @@ def tile_shapes(shapes_dict):
 if __name__ == "__main__":
     from gdsfactory.generic_tech import LAYER_STACK
 
+    from gplugins.gmsh.get_mesh import get_mesh
+
     c = gf.components.straight_heater_doped_rib()
-    c.to_gmsh(type="xy", layer_stack=LAYER_STACK, z=0)
-    c.to_gmsh(type="xy", layer_stack=LAYER_STACK, z=0)
+    get_mesh(component=c, type="xy", layer_stack=LAYER_STACK, z=0)
+    get_mesh(component=c, type="xy", layer_stack=LAYER_STACK, z=0)