import os
import urllib
import dolfinx.io
import dolfinx.mesh
import mpi4py.MPI
import numpy as np
import numpy.typing
import viskex
Read in and plot mesh
msh_filename = "data/garda.msh"
if not os.path.isfile(msh_filename):
os.makedirs("data", exist_ok=True)
msh_url = (
"https://raw.githubusercontent.com/FEMlium/FEMlium/main/"
"tutorials/01_introduction/data/garda.msh")
with urllib.request.urlopen(msh_url) as response, open(msh_filename, "wb") as msh_file:
msh_file.write(response.read())
mesh, subdomains, boundaries = dolfinx.io.gmshio.read_from_msh(
"data/garda.msh", comm=mpi4py.MPI.COMM_WORLD, rank=0, gdim=2)
Info : Reading 'data/garda.msh'... Info : 2390 entities Info : 3937 nodes Info : 7872 elements Info : Done reading 'data/garda.msh'
viskex.dolfinx.plot_mesh(mesh)
error: XDG_RUNTIME_DIR is invalid or not set in the environment. MESA: error: ZINK: failed to choose pdev glx: failed to create drisw screen
viskex.dolfinx.plot_mesh(mesh, dim=2)
error: XDG_RUNTIME_DIR is invalid or not set in the environment.
MESA: error: ZINK: failed to choose pdev glx: failed to create drisw screen
viskex.dolfinx.plot_mesh(mesh, dim=1)
error: XDG_RUNTIME_DIR is invalid or not set in the environment.
MESA: error: ZINK: failed to choose pdev glx: failed to create drisw screen
viskex.dolfinx.plot_mesh(mesh, dim=0)
error: XDG_RUNTIME_DIR is invalid or not set in the environment. MESA: error: ZINK: failed to choose pdev glx: failed to create drisw screen
Plot subdomains
viskex.dolfinx.plot_mesh_tags(mesh, subdomains, "subdomains")
error: XDG_RUNTIME_DIR is invalid or not set in the environment. MESA: error: ZINK: failed to choose pdev glx: failed to create drisw screen
Plot boundaries
viskex.dolfinx.plot_mesh_tags(mesh, boundaries, "boundaries")
error: XDG_RUNTIME_DIR is invalid or not set in the environment. MESA: error: ZINK: failed to choose pdev glx: failed to create drisw screen
Plot a scalar field
scalar_function_space = dolfinx.fem.functionspace(mesh, ("CG", 2))
centroid = np.array([631544.0, 5054515.0])
def scalar_field_eval(x: np.typing.NDArray[np.float64]) -> np.typing.NDArray[np.float64]:
"""Evaluate the scalar field."""
rho = np.sqrt((x[0] - centroid[0])**2 + (x[1] - centroid[1])**2)
theta = np.arctan2(x[1] - centroid[1], x[0] - centroid[0])
return rho / np.sqrt(1 - 0.5 * np.cos(theta)**2) # type: ignore[no-any-return]
scalar_field = dolfinx.fem.Function(scalar_function_space)
scalar_field.interpolate(scalar_field_eval)
viskex.dolfinx.plot_scalar_field(scalar_field, "scalar")
error: XDG_RUNTIME_DIR is invalid or not set in the environment. MESA: error: ZINK: failed to choose pdev glx: failed to create drisw screen
Plot a vector field
vector_function_space = dolfinx.fem.functionspace(mesh, ("CG", 2, (mesh.geometry.dim, )))
def vector_field_eval(x: np.typing.NDArray[np.float64]) -> np.typing.NDArray[np.float64]:
"""Evaluate the vector field."""
rho = np.sqrt((x[0] - centroid[0])**2 + (x[1] - centroid[1])**2)
theta = np.arctan2(x[1] - centroid[1], x[0] - centroid[0])
values = np.zeros((2, x.shape[1]))
values[0] = - rho * np.sin(theta)
values[1] = rho * np.cos(theta)
return values
vector_field = dolfinx.fem.Function(vector_function_space)
vector_field.interpolate(vector_field_eval)
viskex.dolfinx.plot_vector_field(vector_field, "vector")
error: XDG_RUNTIME_DIR is invalid or not set in the environment. MESA: error: ZINK: failed to choose pdev glx: failed to create drisw screen
viskex.dolfinx.plot_vector_field(vector_field, "vector", glyph_factor=0.1)
error: XDG_RUNTIME_DIR is invalid or not set in the environment. MESA: error: ZINK: failed to choose pdev glx: failed to create drisw screen