import os
import urllib
import folium
import gmsh
import matplotlib.pyplot as plt
import numpy as np
import numpy.typing
import pyproj
import femlium
Auxiliary function to get a folium
Map
close to Lake Garda.
def get_garda_geo_map(boundary_icons: bool = False) -> folium.Map:
"""Get a map close to Lake Garda, and possibly add some boundary markers."""
# Add map close to Lake Garda
geo_map = folium.Map(location=[45.6389113, 10.7521368], zoom_start=10.3)
# Add markers
if boundary_icons:
location_markers = {
"Sarca": [45.87395405, 10.87087005],
"Mincio": [45.43259035, 10.7007715]
}
location_colors = {
"Sarca": "red",
"Mincio": "green"
}
for key in location_markers.keys():
folium.Marker(
location=location_markers[key],
tooltip=key,
icon=folium.Icon(color=location_colors[key])
).add_to(geo_map)
# Return folium map
return geo_map
get_garda_geo_map()
Read the file containing an approximation of the boundary of the lake from csv.
boundary_csv_filename = "garda.csv"
if not os.path.isfile(boundary_csv_filename):
os.makedirs("data", exist_ok=True)
boundary_csv_url = (
"https://raw.githubusercontent.com/FEMlium/FEMlium/main/"
"tutorials/01_introduction/data/garda.csv")
with urllib.request.urlopen(boundary_csv_url) as response, \
open(boundary_csv_filename, "wb") as boundary_csv_file:
boundary_csv_file.write(response.read())
points_and_markers = np.loadtxt("garda.csv", delimiter=",", skiprows=1)
points = points_and_markers[:, 0:2]
vertex_markers = points_and_markers[:, 2].astype(np.int64)
segment_markers = np.array(
[min(vertex_markers[v], vertex_markers[v + 1]) for v in range(points.shape[0] - 1)], dtype=np.int64)
Plot the domain boundary using matplotlib
.
fig = plt.figure(figsize=(12, 12))
fig.gca().plot(points[:, 0], points[:, 1])
fig.gca().axis("equal")
(616658.039149, 647061.960851, 5029877.225841, 5085382.774159)
Read a further file containing a curve that corresponds to approximately 1000 m from the shoreline.
interface_csv_filename = "garda_interface.csv"
if not os.path.isfile(interface_csv_filename):
os.makedirs("data", exist_ok=True)
interface_csv_url = (
"https://raw.githubusercontent.com/FEMlium/FEMlium/main/"
"tutorials/01_introduction/data/garda_interface.csv")
with urllib.request.urlopen(interface_csv_url) as response, \
open(interface_csv_filename, "wb") as interface_csv_file:
interface_csv_file.write(response.read())
points_inner = np.loadtxt("garda_interface.csv", delimiter=",", skiprows=1)
Plot the two curves with matplotlib
.
fig = plt.figure(figsize=(12, 12))
fig.gca().plot(points[:, 0], points[:, 1], "blue")
fig.gca().plot(points_inner[:, 0], points_inner[:, 1], "orange")
fig.gca().axis("equal")
(616658.039149, 647061.960851, 5029877.225841, 5085382.774159)
Define a pyproj
Transformer
to map between different reference systems, because the points read from file are stored a $(x, y)$ pairs in the EPSG32632 reference system, while the map produced by folium
is based on (latitude, longitude) pairs in the EPSG4326 reference system.
transformer = pyproj.Transformer.from_crs("epsg:32632", "epsg:4326", always_xy=True)
We define a domain plotter femlium.DomainPlotter
.
domain_plotter = femlium.DomainPlotter(transformer)
We use the domain_plotter
to draw the boundary of what will be the computational domain on top of the geographic map.
geo_map = get_garda_geo_map()
domain_plotter.add_domain_to(geo_map, points)
geo_map
We may change the color and the weight of the line.
geo_map = get_garda_geo_map()
domain_plotter.add_domain_to(geo_map, points, colors="blue", weights=3)
geo_map
Furthermore, we may set the colors and the weights of the boundary representation to depend on the markers associated to each segment. Such markers are typically used to set boundary labels for boundary conditions.
geo_map = get_garda_geo_map(boundary_icons=True)
colors = {
0: "blue",
1: "red",
2: "green"
}
weights = {
0: 2,
1: 5,
2: 5
}
domain_plotter.add_domain_to(geo_map, points, segment_markers, colors=colors, weights=weights)
geo_map
We may also plot two curves on the same map.
geo_map = get_garda_geo_map()
domain_plotter.add_domain_to(geo_map, points, colors="blue", weights=3)
domain_plotter.add_domain_to(geo_map, points_inner, colors="orange", weights=2)
geo_map
We then use gmsh
to generate a triangular mesh, and save it to file.
def generate_garda_mesh(
points: np.typing.NDArray[np.float64], segment_markers: np.typing.NDArray[np.int64],
points_inner: np.typing.NDArray[np.float64], h: float
) -> None:
"""Generate an unstructured mesh of the Lake."""
# Initialize gmsh
gmsh.initialize()
# Add model
gmsh.model.add("garda")
# Add points associated to outer boundary
num_points = points.shape[0] - 1 # exclude the last point, because it is a copy of the first one
for p in range(num_points):
gmsh.model.geo.addPoint(points[p, 0], points[p, 1], 0.0)
# Add points associted to inner interface
num_points_inner = points_inner.shape[0] - 1 # exclude the last point, because it is a copy of the first one
for p in range(num_points_inner):
gmsh.model.geo.addPoint(points_inner[p, 0], points_inner[p, 1], 0.0)
# Add segments associated to outer boundary
lines = list()
boundary_labels = {
1: list(), # shore
2: list(), # inflow
3: list() # outflow
}
for p in range(num_points):
point_p = p + 1
if point_p < num_points:
point_p_next = point_p + 1
else:
point_p_next = 1
segment = gmsh.model.geo.addLine(point_p, point_p_next)
lines.append(segment)
label = 1 + segment_markers[p]
label = int(round(label))
boundary_labels[label].append(segment)
# Add segments associated to inner interface
lines_inner = list()
for p in range(num_points_inner):
point_p = num_points + p + 1
if point_p < num_points + num_points_inner:
point_p_next = point_p + 1
else:
point_p_next = num_points + 1
segment = gmsh.model.geo.addLine(point_p, point_p_next)
lines_inner.append(segment)
# Add curve loops
boundary = gmsh.model.geo.addCurveLoop(lines)
interface = gmsh.model.geo.addCurveLoop(lines_inner)
# Add surfaces
near_shore = gmsh.model.geo.addPlaneSurface([boundary, interface])
far_from_shore = gmsh.model.geo.addPlaneSurface([interface])
# Synchronize
gmsh.model.geo.synchronize()
# Assign boundary labels
for (label, lines) in boundary_labels.items():
gmsh.model.addPhysicalGroup(1, lines, label)
# Assign subdomain labels
gmsh.model.addPhysicalGroup(2, [near_shore], 1)
gmsh.model.addPhysicalGroup(2, [far_from_shore], 2)
# We now define a Distance field, to measure the distance from the boundary
gmsh.model.mesh.field.add("Distance", 1)
gmsh.model.mesh.field.setNumbers(1, "PointsList", np.arange(1, num_points + 1))
gmsh.model.mesh.field.setNumbers(1, "CurvesList", lines)
gmsh.model.mesh.field.setNumber(1, "NumPointsPerCurve", 1)
# We then define a Threshold field, which uses the return value of the
# Distance field 1 in order to define a simple change in element size
# depending on the computed distances
#
# SizeMax - /------------------
# /
# /
# /
# SizeMin -o----------------/
# | | |
# Point DistMin DistMax
gmsh.model.mesh.field.add("Threshold", 2)
gmsh.model.mesh.field.setNumber(2, "InField", 1)
gmsh.model.mesh.field.setNumber(2, "SizeMin", h)
gmsh.model.mesh.field.setNumber(2, "SizeMax", 10 * h)
gmsh.model.mesh.field.setNumber(2, "DistMin", 600)
gmsh.model.mesh.field.setNumber(2, "DistMax", 6000)
# The mesh size should be derived from the second field, i.e. the Distance field
gmsh.model.mesh.field.setAsBackgroundMesh(2)
gmsh.option.setNumber("Mesh.MeshSizeExtendFromBoundary", 0)
gmsh.option.setNumber("Mesh.MeshSizeFromPoints", 0)
gmsh.option.setNumber("Mesh.MeshSizeFromCurvature", 0)
# Generate mesh
gmsh.model.mesh.generate(2)
# Write out the mesh in gmsh format
msh_path = "garda.msh"
if os.path.exists(msh_path):
os.remove(msh_path)
gmsh.write(msh_path)
# Finalize
gmsh.finalize()
generate_garda_mesh(points, segment_markers, points_inner, 300)
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Info : [ 0%] Meshing surface 1 (Plane, Frontal-Delaunay)
Info : [ 60%] Meshing surface 2 (Plane, Frontal-Delaunay) Info : Done meshing 2D (Wall 0.0820781s, CPU 0.083453s) Info : 3943 nodes 9647 elements Info : Writing 'garda.msh'... Info : Done writing 'garda.msh'
The mesh will be read in and displayed in one of the FEM backends available in femlium
. See the notebooks in the parent folder.