Consolidate gmsh plugin (#159)

* uz refactor
* ready for merge
* layerstack --> layer_stack
* finish migration to meshwell, remove legacy meshing code
* finish migration to meshwell, remove legacy meshing code
* fix docs
* remove removed functions
* fix init

docs/api_design.rst

@@ -12,14 +12,6 @@ Meshing
 .. autosummary::
    :toctree: _autosummary/
 
-    create_physical_mesh
-    mesh_from_polygons
-    MeshTracker
-    cleanup_component
-    fuse_polygons
-    round_coordinates
-    tile_shapes
-    to_polygons
     get_layer_overlaps_z
     get_layers_at_z
     list_unique_layer_stack_z

docs/notebooks/meshing_01_intro.py

@@ -53,8 +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
+from gplugins.gmsh.get_mesh import create_physical_mesh, get_mesh
 
 gf.config.rich_output()
 PDK = get_generic_pdk()

docs/notebooks/meshing_02_2D_xy_mesh.py

@@ -10,8 +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
+from gplugins.gmsh.get_mesh import create_physical_mesh, get_mesh
 
 gf.config.rich_output()
 PDK = get_generic_pdk()

docs/notebooks/meshing_03_2D_uz_mesh.py

@@ -10,8 +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
+from gplugins.gmsh.get_mesh import create_physical_mesh, get_mesh
 
 gf.config.rich_output()
 PDK = get_generic_pdk()

docs/notebooks/meshing_04_refinement.py

@@ -10,18 +10,15 @@
 # # %matplotlib widget
 
 # +
-from itertools import product
 
 import gdsfactory as gf
 import meshio
-import numpy as np
 from gdsfactory.generic_tech import get_generic_pdk
 from gdsfactory.pdk import get_layer_stack
 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
+from gplugins.gmsh.get_mesh import create_physical_mesh, get_mesh
 
 PDK = get_generic_pdk()
 PDK.activate()
@@ -99,7 +96,7 @@ def mesh_with_physicals(mesh, filename):
 #
 # An advantage of finite-volume and finite-element schemes is the ability for different nodes to have different characteristics lengths.
 #
-# This simply achieved to first order here by supplying a `resolutions` dict with keys referencing the `LayerStack` names, and for value a second dict with keys `resolution` and `distance` which control, respectively, the characteristic length within a region and the dropoff away from interfaces with this region.
+# This simply achieved to first order here by supplying a `resolutions` dict with keys referencing the `LayerStack` names, and for value a second dict with keys `resolution` and `DistMax / SizeMax` (see gmsh documentation) which control, respectively, the characteristic length within a region and the dropoff away from interfaces with this region.
 #
 # For example, to refine within the core only, one could use:
 
@@ -120,7 +117,7 @@ def mesh_with_physicals(mesh, filename):
 
 # Adding a dropoff at the interface:
 
-resolutions = {"core": {"resolution": 0.05, "distance": 5}}
+resolutions = {"core": {"resolution": 0.05, "DistMax": 1, "SizeMax": 0.2}}
 mesh = get_mesh(
     component=waveguide_trimmed,
     type="uz",
@@ -138,10 +135,10 @@ def mesh_with_physicals(mesh, filename):
 # Refining multiple elements simultaneously:
 
 resolutions = {
-    "core": {"resolution": 0.05, "distance": 1},
-    "slab90": {"resolution": 0.02, "distance": 1},
-    "via_contact": {"resolution": 0.2, "distance": 0},
-    "oxide": {"resolution": 1, "distance": 0},
+    "core": {"resolution": 0.05, "DistMax": 1, "SizeMax": 0.2},
+    "slab90": {"resolution": 0.02, "DistMax": 1, "SizeMax": 0.2},
+    "via_contact": {"resolution": 0.2},
+    "oxide": {"resolution": 1},
 }
 mesh = get_mesh(
     component=waveguide_trimmed,
@@ -156,46 +153,3 @@ def mesh_with_physicals(mesh, filename):
 mesh = mesh_with_physicals(mesh, filename)
 mesh = from_meshio(mesh)
 mesh.draw().show()
-
-# ## Fine mesh refinement
-#
-# You can fine mesh refine with the `global_meshsize_array` (default `None`) and `global_meshsize_interpolant_func` (default `scipy.interpolate.NearestNDInterpolator`) arguments, which define the characteristic length callback used by gmsh to select characteristic lengths at a local level.
-#
-# The `global_meshsize_array` has form [x,y,z,lc], with `x,y,z` in mesh units; here, `x` is `u` $\in$ [-2, 10] considering the y-coordinates of the xsection_bounds and the background padding, `y` $\in$ [-2,3], and `z` is always 0. These values could be estimated from the component bounding box.
-#
-# In practice, this array would most likely result from a physical simulation using the simulation domain coordinates, which would also yield a higher quality mesh by virtue of being smoother.
-#
-# For instance, if one wants to refine in a circle around the waveguide core, and have some asymmetry about the y-axis, a meshsize array like so could be defined:
-
-# +
-xs = np.linspace(-2, 10, 800)
-ys = np.linspace(-2, 3, 800)
-global_meshsize_array = []
-
-ls_large = 1
-ls_small = 0.05
-
-r = 0.75
-for x, y in product(xs, ys):
-    if (x - 4.0) ** 2 + (y) ** 2 <= r**2:
-        global_meshsize_array.append([x, y, 0, ls_small])
-    else:
-        global_meshsize_array.append([x, y, 0, ls_large])
-
-global_meshsize_array = np.array(global_meshsize_array)
-
-mesh = get_mesh(
-    component=waveguide_trimmed,
-    type="uz",
-    xsection_bounds=[(4, -4), (4, 4)],
-    layer_stack=filtered_layer_stack,
-    filename=f"{filename}.msh",
-    background_tag="oxide",
-    background_padding=(2.0, 2.0, 2.0, 2.0),
-    global_meshsize_array=global_meshsize_array,
-    default_resolution_min=ls_small,
-    default_resolution_max=ls_large,
-)
-mesh = mesh_with_physicals(mesh, filename)
-mesh = from_meshio(mesh)
-mesh.draw().show()

docs/notebooks/meshing_05_3D.py

@@ -13,8 +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
+from gplugins.gmsh.get_mesh import create_physical_mesh, get_mesh
 
 PDK = get_generic_pdk()
 PDK.activate()

gplugins/gmsh/__init__.py

@@ -7,16 +7,7 @@
     map_unique_layer_stack_z,
     order_layer_stack,
 )
-from gplugins.gmsh.get_mesh import get_mesh
-from gplugins.gmsh.mesh import create_physical_mesh, mesh_from_polygons
-from gplugins.gmsh.meshtracker import MeshTracker
-from gplugins.gmsh.parse_gds import (
-    cleanup_component,
-    fuse_polygons,
-    round_coordinates,
-    tile_shapes,
-    to_polygons,
-)
+from gplugins.gmsh.get_mesh import create_physical_mesh, get_mesh
 from gplugins.gmsh.uz_xsection_mesh import (
     get_u_bounds_layers,
     get_u_bounds_polygons,
@@ -26,10 +17,6 @@
 from gplugins.gmsh.xy_xsection_mesh import xy_xsection_mesh
 
 __all__ = [
-    "MeshTracker",
-    "cleanup_component",
-    "create_physical_mesh",
-    "fuse_polygons",
     "get_layer_overlaps_z",
     "get_layers_at_z",
     "get_u_bounds_layers",
@@ -38,12 +25,10 @@
     "get_mesh",
     "list_unique_layer_stack_z",
     "map_unique_layer_stack_z",
-    "mesh_from_polygons",
     "order_layer_stack",
     "round_coordinates",
-    "tile_shapes",
-    "to_polygons",
     "uz_xsection_mesh",
     "xy_xsection_mesh",
+    "create_physical_mesh",
 ]
 __version__ = "0.0.2"

gplugins/gmsh/define_polysurfaces.py

@@ -0,0 +1,39 @@
+from typing import Any
+
+from gdsfactory.technology import LayerStack
+from meshwell.polysurface import PolySurface
+from shapely.affinity import scale
+
+
+def define_polysurfaces(
+    polygons_dict: dict,
+    layer_stack: LayerStack,
+    model: Any,
+    resolutions: dict,
+    scale_factor: float = 1,
+):
+    """Define meshwell polysurfaces dimtags from gdsfactory information."""
+    polysurfaces_list = []
+
+    if resolutions is None:
+        resolutions = {}
+
+    for layername in polygons_dict.keys():
+        if polygons_dict[layername].is_empty:
+            continue
+
+        polysurfaces_list.append(
+            PolySurface(
+                polygons=scale(
+                    polygons_dict[layername],
+                    *(scale_factor,) * 2,
+                    origin=(0, 0, 0),
+                ),
+                model=model,
+                resolution=resolutions.get(layername, None),
+                mesh_order=layer_stack.layers.get(layername).mesh_order,
+                physical_name=layername,
+            )
+        )
+
+    return polysurfaces_list