Meshing introduction#
gdsfactory has interfaces to external meshers (currently: gmsh).
Using a gdsfactory Component and a Layerstack reflecting the post-fabrication structure, you can automatically generate a 2D or 3D mesh suitable for physical simulation.
Within gdsfactory, this interface is currently used for:
finite-volume simulation through a DEVSIM plugin, for e.g. TCAD simulations
finite-element simulation through the femwell wrapper around scikit-fem, for e.g. mode solving and thermal simulations
Current features include:
GDS postprocessing – common interface for layout and simulation
A generic shapely <–> gmsh translator, which properly reuses gmsh objects, resulting in conformal handling of
lateral interfaces
vertical interfaces
polygon inclusions
polygon “holes”
2D meshing of in-plane cross-sections (e.g. x - y)
2D meshing of out-of-plane cross-sections (e.g. arbitrary xy line - z)
(In progress) 3D meshing
The mesh is returned tagged with LayerStack
labelfor each GDS layer according to a specificmesh_orderAll interfaces between layer entities are also tagged as
label1___label2to e.g. implement interfacial boundary conditionsDummy layers can be easily introduced in a component to provide extra lines and polygons with custom labels to e.g. implement boundary conditions, sources, etc.
Coarse resolution setting per label, and around interfaces
Fine resolution setting with callable
[x,y,z,mesh_size]functions (useful for simulation-driven refinement)
GMSH can be used one of two ways:
The traditional “bottom-up” way, where the user manually defines points, then line segments (from points), then lines (from segments), then closed curves (from lines), then surfaces (from curves), then closed shells (from surfaces), and finally volumes (from shells).
With CAD-type boolean operations (set operations on objects)
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 layer_stack are used as a guide to define the various physical entities, which are returned as tagged objects to the user.
Installation#
You can install the meshing plugins with pip install gplugins[gmsh].
Because PyVista does not work properly on headless systems we use Meshio.
Usage#
First, you can start with a gdsfactory Component
import gdsfactory as gf
import meshio
from gdsfactory.generic_tech import LAYER_STACK, get_generic_pdk
from gdsfactory.technology import LayerStack
from skfem.io import from_meshio
from gplugins.gmsh.get_mesh import create_physical_mesh, get_mesh
gf.config.rich_output()
PDK = get_generic_pdk()
PDK.activate()
waveguide = gf.components.straight_pin(length=10, taper=None)
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_layer_stack = LayerStack(
layers={
k: LAYER_STACK.layers[k]
for k in (
"slab90",
"core",
"via_contact",
)
}
)
filename = "mesh"
def mesh_with_physicals(mesh, filename):
mesh_from_file = meshio.read(f"{filename}.msh")
return create_physical_mesh(mesh_from_file, "triangle")
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:
mesh = get_mesh(
component=waveguide,
type="xy",
z=0.09,
layer_stack=filtered_layer_stack,
filename="mesh.msh",
)
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Info : Done meshing 1D (Wall 0.0118559s, CPU 0.029472s)
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Info : Done meshing 2D (Wall 0.0523746s, CPU 0.080349s)
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This returns a gmsh .msh mesh, also saved in filename if provided, which can be processed:
mesh.get_cells_type("triangle")
mesh = from_meshio(mesh)
mesh.draw().plot()
[]
The gmsh GUI can be used to load and inspect the .msh file:
meshio can also be used to convert the .msh to another arbitrary format, to observe for instance with Paraview. This is useful, for instance to preprocess the msh file using the create_mesh utility in order to consolidate entities with the same label:
mesh_from_file = meshio.read("mesh.msh")
triangle_mesh = create_physical_mesh(mesh_from_file, "triangle")
meshio.write("mesh.xdmf", triangle_mesh)
mesh = mesh_with_physicals(triangle_mesh, filename)
mesh = from_meshio(mesh)
mesh.draw().plot()
[]
You can opening the mesh.xdmf in paraview:
line_mesh = create_physical_mesh(mesh_from_file, "line")
meshio.write("facet_mesh.xdmf", line_mesh)
mesh = mesh_with_physicals(line_mesh, filename)
mesh = from_meshio(mesh)
mesh.draw().plot()
[]
Opening the facet_mesh.xdmf in paraview:
The xdmf files with consolidated physical groups can also be opened dynamically in a notebook with pyvista