Poisson equation
This demo illustrates how to:
Solve a linear partial differential equation
Create and apply Dirichlet boundary conditions
Define Expressions
Define a FunctionSpace
Equation and problem definition
The Poisson equation is the canonical elliptic partial differential equation. For a domain \(\Omega \subset \mathbb{R}^n\) with boundary \(\partial \Omega = \Gamma_{D} \cup \Gamma_{N}\), the Poisson equation with particular boundary conditions reads:
Here, \(f\) and \(g\) are input data and \(n\) denotes the outward directed boundary normal. The most standard variational form of Poisson equation reads: find \(u \in V\) such that
where \(V\) is a suitable function space and
The expression \(a(u, v)\) is the bilinear form and \(L(v)\) is the linear form. It is assumed that all functions in \(V\) satisfy the Dirichlet boundary conditions (\(u = 0 \ {\rm on} \ \Gamma_{D}\)).
In this demo, we shall consider the following definitions of the input functions, the domain, and the boundaries:
\(\Omega = [0,1] \times [0,1]\) (a unit square)
\(\Gamma_{D} = \{(0, y) \cup (1, y) \subset \partial \Omega\}\) (Dirichlet boundary)
\(\Gamma_{N} = \{(x, 0) \cup (x, 1) \subset \partial \Omega\}\) (Neumann boundary)
\(g = \sin(5x)\) (normal derivative)
\(f = 10\exp(-((x - 0.5)^2 + (y - 0.5)^2) / 0.02)\) (source term)
Implementation
The implementation is split in two files: a file containing the definition of the variational forms expressed in UFL and a C++ file containing the actual solver.
Running this demo requires the files: demo_poisson/main.cpp,
demo_poisson/poisson.py and
demo_poisson/CMakeLists.txt.
UFL code
The UFL code is implemented in demo_poisson/poisson.py.
UFL code implemented in Python
The first step is to define the variational problem at hand. We define
the variational problem in UFL terms in a separate form file
demo_poisson/poisson.py. We begin by defining the finite
element:
from basix.ufl import element
from ufl import (
Coefficient,
Constant,
FunctionSpace,
Mesh,
TestFunction,
TrialFunction,
ds,
dx,
grad,
inner,
)
e = element("Lagrange", "triangle", 1)
The first argument to :py:class:FiniteElement is the finite element
family, the second argument specifies the domain, while the third
argument specifies the polynomial degree. Thus, in this case, our
element element consists of first-order, continuous Lagrange basis
functions on triangles (or in order words, continuous piecewise linear
polynomials on triangles).
Next, we use this element to initialize the trial and test functions (\(u\) and \(v\)) and the coefficient functions (\(f\) and \(g\)):
coord_element = element("Lagrange", "triangle", 1, shape=(2,))
mesh = Mesh(coord_element)
V = FunctionSpace(mesh, e)
u = TrialFunction(V)
v = TestFunction(V)
f = Coefficient(V)
g = Coefficient(V)
kappa = Constant(mesh)
Finally, we define the bilinear and linear forms according to the variational formulation of the equations:
a = kappa * inner(grad(u), grad(v)) * dx
L = inner(f, v) * dx + inner(g, v) * ds
C++ program
The main solver is implemented in the
demo_poisson/main.cpp file.
At the top we include the DOLFINx header file and the generated header file “Poisson.h” containing the variational forms for the Poisson equation. For convenience we also include the DOLFINx namespace.
#include "poisson.h"
#include <cmath>
#include <dolfinx.h>
#include <dolfinx/fem/Constant.h>
#include <dolfinx/fem/petsc.h>
#include <utility>
#include <vector>
using namespace dolfinx;
using T = PetscScalar;
using U = typename dolfinx::scalar_value_type_t<T>;
Then follows the definition of the coefficient functions (for \(f\) and
\(g\)), which are derived from the Expression class in
DOLFINx
Inside the main function, we begin by defining a mesh of the
domain. As the unit square is a very standard domain, we can use a
built-in mesh provided by the UnitSquareMesh factory. In
order to create a mesh consisting of 32 x 32 squares with each square
divided into two triangles, and the finite element space (specified
in the form file) defined relative to this mesh, we do as follows:
int main(int argc, char* argv[])
{
dolfinx::init_logging(argc, argv);
PetscInitialize(&argc, &argv, nullptr, nullptr);
{
// Create mesh and function space
auto part = mesh::create_cell_partitioner(mesh::GhostMode::shared_facet);
auto mesh = std::make_shared<mesh::Mesh<U>>(
mesh::create_rectangle<U>(MPI_COMM_WORLD, {{{0.0, 0.0}, {2.0, 1.0}}},
{32, 16}, mesh::CellType::triangle, part));
auto V = std::make_shared<fem::FunctionSpace<U>>(
fem::create_functionspace(functionspace_form_poisson_a, "u", mesh));
// Next, we define the variational formulation by initializing the
// bilinear and linear forms ($a$, $L$) using the previously
// defined {cpp:class}`FunctionSpace` `V`. Then we can create the
// source and boundary flux term ($f$, $g$) and attach these to the
// linear form.
// Prepare and set Constants for the bilinear form
auto kappa = std::make_shared<fem::Constant<T>>(2.0);
auto f = std::make_shared<fem::Function<T>>(V);
auto g = std::make_shared<fem::Function<T>>(V);
// Define variational forms
auto a = std::make_shared<fem::Form<T>>(fem::create_form<T>(
*form_poisson_a, {V, V}, {}, {{"kappa", kappa}}, {}));
auto L = std::make_shared<fem::Form<T>>(fem::create_form<T>(
*form_poisson_L, {V}, {{"f", f}, {"g", g}}, {}, {}));
// Now, the Dirichlet boundary condition ($u = 0$) can be created
// using the class {cpp:class}`DirichletBC`. A
// {cpp:class}`DirichletBC` takes two arguments: the value of the
// boundary condition, and the part of the boundary on which the
// condition applies. In our example, the value of the boundary
// condition (0.0) can represented using a {cpp:class}`Function`,
// and the Dirichlet boundary is defined by the indices of degrees
// of freedom to which the boundary condition applies. The
// definition of the Dirichlet boundary condition then looks as
// follows:
// Define boundary condition
auto facets = mesh::locate_entities_boundary(
*mesh, 1,
[](auto x)
{
using U = typename decltype(x)::value_type;
constexpr U eps = 1.0e-8;
std::vector<std::int8_t> marker(x.extent(1), false);
for (std::size_t p = 0; p < x.extent(1); ++p)
{
auto x0 = x(0, p);
if (std::abs(x0) < eps or std::abs(x0 - 2) < eps)
marker[p] = true;
}
return marker;
});
const auto bdofs = fem::locate_dofs_topological(
*V->mesh()->topology_mutable(), *V->dofmap(), 1, facets);
auto bc = std::make_shared<const fem::DirichletBC<T>>(0.0, bdofs, V);
f->interpolate(
[](auto x) -> std::pair<std::vector<T>, std::vector<std::size_t>>
{
std::vector<T> f;
for (std::size_t p = 0; p < x.extent(1); ++p)
{
auto dx = (x(0, p) - 0.5) * (x(0, p) - 0.5);
auto dy = (x(1, p) - 0.5) * (x(1, p) - 0.5);
f.push_back(10 * std::exp(-(dx + dy) / 0.02));
}
return {f, {f.size()}};
});
g->interpolate(
[](auto x) -> std::pair<std::vector<T>, std::vector<std::size_t>>
{
std::vector<T> f;
for (std::size_t p = 0; p < x.extent(1); ++p)
f.push_back(std::sin(5 * x(0, p)));
return {f, {f.size()}};
});
// Now, we have specified the variational forms and can consider
// the solution of the variational problem. First, we need to
// define a {cpp:class}`Function` `u` to store the solution. (Upon
// initialization, it is simply set to the zero function.) Next, we
// can call the `solve` function with the arguments `a == L`, `u`
// and `bc` as follows:
auto u = std::make_shared<fem::Function<T>>(V);
auto A = la::petsc::Matrix(fem::petsc::create_matrix(*a), false);
la::Vector<T> b(L->function_spaces()[0]->dofmap()->index_map,
L->function_spaces()[0]->dofmap()->index_map_bs());
MatZeroEntries(A.mat());
fem::assemble_matrix(la::petsc::Matrix::set_block_fn(A.mat(), ADD_VALUES),
*a, {bc});
MatAssemblyBegin(A.mat(), MAT_FLUSH_ASSEMBLY);
MatAssemblyEnd(A.mat(), MAT_FLUSH_ASSEMBLY);
fem::set_diagonal<T>(la::petsc::Matrix::set_fn(A.mat(), INSERT_VALUES), *V,
{bc});
MatAssemblyBegin(A.mat(), MAT_FINAL_ASSEMBLY);
MatAssemblyEnd(A.mat(), MAT_FINAL_ASSEMBLY);
b.set(0.0);
fem::assemble_vector(b.mutable_array(), *L);
fem::apply_lifting<T, U>(b.mutable_array(), {a}, {{bc}}, {}, T(1));
b.scatter_rev(std::plus<T>());
fem::set_bc<T, U>(b.mutable_array(), {bc});
la::petsc::KrylovSolver lu(MPI_COMM_WORLD);
la::petsc::options::set("ksp_type", "preonly");
la::petsc::options::set("pc_type", "lu");
lu.set_from_options();
lu.set_operator(A.mat());
la::petsc::Vector _u(la::petsc::create_vector_wrap(*u->x()), false);
la::petsc::Vector _b(la::petsc::create_vector_wrap(b), false);
lu.solve(_u.vec(), _b.vec());
// Update ghost values before output
u->x()->scatter_fwd();
// The function `u` will be modified during the call to solve. A
// {cpp:class}`Function` can be saved to a file. Here, we output
// the solution to a `VTK` file (specified using the suffix `.pvd`)
// for visualisation in an external program such as Paraview.
// Save solution in VTK format
io::VTKFile file(MPI_COMM_WORLD, "u.pvd", "w");
file.write<T>({*u}, 0.0);
#ifdef HAS_ADIOS2
// Save solution in VTX format
io::VTXWriter<U> vtx(MPI_COMM_WORLD, "u.bp", {u}, "bp4");
vtx.write(0);
#endif
}
PetscFinalize();
return 0;
}