docs

docs/_config.yml

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+# Book settings
+# Learn more at https://jupyterbook.org/customize/config.html
+
+title: My sample book
+author: The Jupyter Book Community
+logo: logo.png
+
+# Force re-execution of notebooks on each build.
+# See https://jupyterbook.org/content/execute.html
+execute:
+  execute_notebooks: force
+  exclude_patterns:
+    - 'gdsfactory_interface'
+
+# Define the name of the latex output file for PDF builds
+latex:
+  latex_documents:
+    targetname: book.tex
+
+# Add a bibtex file so that we can create citations
+bibtex_bibfiles:
+  - references.bib
+
+# Information about where the book exists on the web
+repository:
+  url: https://github.com/executablebooks/jupyter-book  # Online location of your book
+  path_to_book: docs  # Optional path to your book, relative to the repository root
+  branch: master  # Which branch of the repository should be used when creating links (optional)
+
+# Add GitHub buttons to your book
+# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository
+html:
+  use_issues_button: true
+  use_repository_button: true
+
+sphinx:
+  config:
+    html_js_files:
+    - https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js
+    mime_types:
+      application/vnd.plotly.v1+json: plotly

docs/_toc.yml

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+# Table of contents
+# Learn more at https://jupyterbook.org/customize/toc.html
+
+format: jb-book
+root: intro
+chapters:
+- file: intro_gmsh
+- file: polysurfaces
+- file: prisms
+- file: models
+- file: resolution
+- file: gdsfactory_interface

docs/gdsfactory_interface.py

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+# %% [markdown]
+# # GDSFactory integration
+# GDSFactory has an interface to meshwell (v1.0.7)
+
+# %% [markdown]
+# > **Warning**
+# > The GDSFactory plugin for meshwell/gmsh has not been updated since meshwell version 1.0.7! Some features may be missing, and some more bugs might be present.
+#
+# %%[markdown]
+# GDSFactory has the concept of a "LayerStack", which contains the information about the final fabricated layers:
+
+# %%
+import gmsh
+import gdsfactory as gf
+from gplugins.gmsh.get_mesh import get_mesh
+from gdsfactory.generic_tech.layer_stack import get_layer_stack
+
+PDK = gf.generic_tech.get_generic_pdk()
+PDK.bend_points_distance = 0.5
+
+LAYER_STACK = get_layer_stack()
+LAYER_STACK.pprint()
+
+
+# %%
+
+c = gf.components.spiral_heater.spiral_racetrack_heater_metal(num=3)
+c.plot()
+
+# %% [markdown]
+# In meshwell 1.0.7, only a ThresholdField as a distance from the surfaces/volumes was supported. From the GDSFactory plugin, this is entered as a dict for the LayerLevels:
+# %%
+resolutions = {}
+resolutions["core"] = {"resolution": 0.1, "distance": 5}
+resolutions["heater"] = {"resolution": 0.2, "distance": 10}
+# %% [markdown]
+# the "type" argument in get_mesh can be "xy", "uz", or "3D", depending on if a 2D in-plane, 2D out-of-plane cross-section, or 3D mesh si desired:
+
+# %%
+xbound = (c.dxmin + c.dxmax) / 2
+ymax = c.dymin
+ymin = (c.dymin + c.dymax) / 2
+
+mesh = get_mesh(
+    c,
+    type="uz",
+    xsection_bounds=[[xbound, ymin], [xbound, ymax]],
+    layer_stack=LAYER_STACK,
+    filename="heater_uz.msh",
+    resolutions=resolutions,
+    default_characteristic_length=10,
+    wafer_padding=50,
+    interface_delimiter="___",
+)
+
+# %%
+try:
+    gmsh.initialize()
+    gmsh.open("heater_uz.msh")
+    gmsh.fltk.run()
+except:  # noqa: E722
+    print("Skipping CAD GUI visualization - only available when running locally")
+
+# %%
+resolutions = {}
+resolutions["core"] = {"resolution": 0.5, "distance": 10}
+resolutions["heater"] = {"resolution": 5, "distance": 10}
+
+mesh = get_mesh(
+    c,
+    type="3D",
+    layer_stack=LAYER_STACK,
+    filename="heater_3D.msh",
+    resolutions=resolutions,
+    default_characteristic_length=20,
+    wafer_padding=50,
+    interface_delimiter="___",
+)
+
+# %%
+try:
+    gmsh.initialize()
+    gmsh.open("heater_3D.msh")
+    gmsh.fltk.run()
+except:  # noqa: E722
+    print("Skipping CAD GUI visualization - only available when running locally")
+# %%

docs/intro_gmsh.py

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+# %% [markdown]
+# # GMSH
+# Since meshwell is a wrapper around GMSH, we will first review GMSH  Python API. For a more thorough explanation of the below, see the GMSH documentation (https://gmsh.info/doc/texinfo/gmsh.html), tutorials (https://gitlab.onelab.info/gmsh/gmsh/-/tree/master/tutorials/python) and API (https://gitlab.onelab.info/gmsh/gmsh/-/blob/master/api/gmsh.py?ref_type=heads).
+
+# %%
+import gmsh
+import meshio
+from meshwell.visualization import plot2D
+
+# %% [markdown]
+# ## Bottom-up construction of CAD entities
+# The most general way to create CAD entities in GMSH is "bottom-up", going from points --> lines --> closed loops --> surfaces --> closed shells --> volumes
+
+# %%
+# Initialize GMSH
+gmsh.initialize()
+model = gmsh.model
+model.add("bottom_up")
+
+# Create points
+p1 = model.occ.addPoint(0, 0, 0)
+p2 = model.occ.addPoint(2, 0, 0)
+p3 = model.occ.addPoint(2, 1, 0)
+p4 = model.occ.addPoint(1, 1, 0)
+p5 = model.occ.addPoint(1, 2, 0)
+p6 = model.occ.addPoint(0, 2, 0)
+
+# Create lines
+l1 = model.occ.addLine(p1, p2)
+l2 = model.occ.addLine(p2, p3)
+l3 = model.occ.addLine(p3, p4)
+l4 = model.occ.addLine(p4, p5)
+l5 = model.occ.addLine(p5, p6)
+l6 = model.occ.addLine(p6, p1)
+
+# Create curve loop
+cl = model.occ.addCurveLoop([l1, l2, l3, l4, l5, l6])
+
+# Create surface
+s1 = model.occ.addPlaneSurface([cl])
+
+# Create the mesh
+model.occ.synchronize()
+model.mesh.generate(2)
+
+gmsh.write("bottom_up.xao")
+gmsh.write("bottom_up.msh")
+gmsh.finalize()
+
+# Read the mesh
+mesh = meshio.read("bottom_up.msh")
+
+# %%
+try:
+    gmsh.initialize()
+    gmsh.open("bottom_up.xao")
+    gmsh.fltk.run()
+except:  # noqa: E722
+    print("Skipping CAD GUI visualization - only available when running locally")
+
+# %%
+try:
+    gmsh.initialize()
+    gmsh.open("bottom_up.msh")
+    gmsh.fltk.run()
+except:  # noqa: E722
+    print("Skipping mesh GUI visualization - only available when running locally")
+
+# %%
+plot2D(mesh, wireframe=True)
+
+# %% [markdown]
+# ## Construction of CAD entities from primitives
+# A limited set of primitives (rectangles, circles, arcs, spheres, boxes, etc.) are also already implemented in GMSH:
+# %%
+gmsh.initialize()
+model = gmsh.model
+model.add("bottom_up")
+
+# Create rectangle
+box = model.occ.addRectangle(0, 0, 0, 1, 1)
+
+# Create circle
+circle = model.occ.addDisk(3, 0, 0, 0.5, 0.5)
+
+# Create the mesh
+model.occ.synchronize()
+model.mesh.generate(2)
+gmsh.write("primitives.msh")
+gmsh.finalize()
+
+# %%
+mesh = meshio.read("primitives.msh")
+plot2D(mesh, wireframe=True)
+
+# %% [markdown]
+# ## Constructive geometry operations
+# More complex elementary entities can also be created from constructive geometry operations (cut, fuse, intersect):
+
+# %%
+gmsh.initialize()
+model = gmsh.model
+model.add("bottom_up")
+
+# Create rectangle
+box = model.occ.addRectangle(-1, -1, 0, 2, 2)
+
+# Create circle
+circle = model.occ.addDisk(0, 0, 0, 0.5, 0.5)
+
+# Keep difference, delete originals
+difference = model.occ.cut(
+    [(2, box)], [(2, circle)], removeObject=True, removeTool=True
+)
+
+# Create the mesh
+model.occ.synchronize()
+model.mesh.generate(2)
+gmsh.write("booleans.msh")
+gmsh.finalize()
+
+# %%
+mesh = meshio.read("booleans.msh")
+plot2D(mesh, wireframe=True)
+
+# %% [markdown]
+# ## Physical entities
+# It is almost always extremely useful to be able to refer to all of the mesh nodes within a set of elementary entities. In GMSH, this is achieved by assigning a "physical" group to a set of elementary entities:
+
+# %%
+gmsh.initialize()
+model = gmsh.model
+model.add("physicals")
+
+# Create rectangle
+box1 = model.occ.addRectangle(0, 0, 0, 1, 1)
+box2 = model.occ.addRectangle(-2, -2, 0, 1, 1)
+
+# Create circle
+circle1 = model.occ.addDisk(3, 0, 0, 0.5, 0.5)
+circle2 = model.occ.addDisk(2, -2, 0, 0.5, 0.5)
+
+model.occ.synchronize()
+
+# Create physical groups
+model.addPhysicalGroup(2, [box1, box2], tag=1, name="boxes")
+model.addPhysicalGroup(2, [circle1, circle2], tag=2, name="circles")
+
+# Create the mesh
+model.occ.synchronize()
+model.mesh.generate(2)
+gmsh.write("physicals.msh")
+gmsh.finalize()
+
+# %%
+mesh = meshio.read("physicals.msh")
+plot2D(mesh)
+
+# %% [markdown]
+# ## The sharp bits
+#
+# ### Conflicting entities
+# When adding elementary entities, overlaps and interfaces are not "merged" by default: the entities will overlap and will be meshed separately. The resulting sub-meshes will not be connected.
+#
+#
+
+# %% [markdown]
+# ### Keeping track of integers
+# Whenever entities are created / transformed (e.g. when healing interfaces), there can be reassignment of the integer tags used to label them. In the official tutorials, entity tags are re-identified based on some characteristic like bounding extent to later assign to physical groups.