Point sources in DOLFINx

Author: Jørgen S. Dokken

SPDX-License-Identifier: MIT

In this example, we will illustrate how to apply a point source to a Poisson problem.

\[\begin{split} \begin{align} -\nabla^2 u &= f \quad \text{in } \Omega, \\ f &= \gamma \delta(x - p) \quad \text{in } \Omega, \end{align} \end{split}\]

with homogeneous Dirichlet boundary conditions.

Using integration by parts, we obtain the variational problem:

Find \(u_h\in V_0\) such that

\[ \begin{align} \int_\Omega \nabla u_h \cdot \nabla v \mathrm{d}x &= \int_\Omega \gamma\delta(x-p) v \mathrm{d}x = \gamma v(p) \quad \forall v \in V_0, \end{align} \]

from mpi4py import MPI
from petsc4py import PETSc

import dolfinx
import ufl
import numpy as np
import scifem

We start by creating the mesh and function space. To illustrate the usage the point source function, we will consider a vector space with to components, and we will only apply the point source to the second component of our problem.

N = 40
domain = dolfinx.mesh.create_unit_square(MPI.COMM_WORLD, N, N)
domain.name = "mesh"
tdim = domain.topology.dim
domain.topology.create_connectivity(tdim-1, tdim)

Create the two-component vector space. The solution in the first component will be 0.

value_shape = (2,)
V = dolfinx.fem.functionspace(domain, ("Lagrange", 2, value_shape))

Create standard variational form

u = ufl.TrialFunction(V)
v = ufl.TestFunction(V)
a = ufl.inner(ufl.grad(u), ufl.grad(v)) * ufl.dx

Create Dirichlet boundary conditions

boundary_facets = dolfinx.mesh.exterior_facet_indices(domain.topology)
dofs = dolfinx.fem.locate_dofs_topological(V, 1, boundary_facets)
u_bc = dolfinx.fem.Function(V)
u_bc.x.array[:] = 0
bc = dolfinx.fem.dirichletbc(u_bc, dofs)

We are now ready to apply the point source. First, we create the right hand side vector for the problem, and initialize it as zero.

b = dolfinx.fem.Function(V)
b.x.array[:] = 0

Secondly we define the point sources we want to apply.

Warning

Note that if running in parallel, we only supply the points on a single process. The other process gets an empty array.

geom_dtype = domain.geometry.x.dtype
if domain.comm.rank == 0:
    points = np.array([[0.68, 0.362, 0],
                       [0.14, 0.213, 0]], dtype=geom_dtype)
else:
    points = np.zeros((0, 3), dtype=geom_dtype)

Next, we create the point source object and apply it to the right hand side vector.

gamma = 1.
point_source = scifem.PointSource(V.sub(1), points, magnitude=gamma)
point_source.apply_to_vector(b)

We can continue to solve our variational problem as usual

a_compiled = dolfinx.fem.form(a)
dolfinx.fem.petsc.apply_lifting(b.x.petsc_vec, [a_compiled], [[bc]])
b.x.scatter_reverse(dolfinx.la.InsertMode.add)
dolfinx.fem.petsc.set_bc(b.x.petsc_vec, [bc])
b.x.scatter_forward()

A = dolfinx.fem.petsc.assemble_matrix(a_compiled, bcs=[bc])
A.assemble()

Set up a direct solver an solve the linear system

ksp = PETSc.KSP().create(domain.comm)
ksp.setOperators(A)
ksp.setType(PETSc.KSP.Type.PREONLY)
ksp.getPC().setType(PETSc.PC.Type.LU)
ksp.getPC().setFactorSolverType("mumps")

uh = dolfinx.fem.Function(V)
ksp.solve(b.x.petsc_vec, uh.x.petsc_vec)
uh.x.scatter_forward()

We can now plot the solution

import pyvista

pyvista.start_xvfb()
topology, cell_types, geometry = dolfinx.plot.vtk_mesh(V)
values = np.zeros((geometry.shape[0], 3), dtype=np.float64)
values[:, :len(uh)] = uh.x.array.real.reshape((geometry.shape[0], len(uh)))

Create a point cloud of glyphs

function_grid = pyvista.UnstructuredGrid(topology, cell_types, geometry)
function_grid["u"] = values
glyphs = function_grid.glyph(orient="u", factor=0.2)

Create a pyvista-grid for the mesh

domain.topology.create_connectivity(domain.topology.dim, domain.topology.dim)
grid = pyvista.UnstructuredGrid(*dolfinx.plot.vtk_mesh(domain, domain.topology.dim))

Create plotter

plotter = pyvista.Plotter()
plotter.add_mesh(grid, style="wireframe", color="k")
plotter.add_mesh(glyphs)
plotter.view_xy()
if not pyvista.OFF_SCREEN:
    plotter.show()

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