This tutorial is part of multiphenicsx.

Tutorial 02: Navier-Stokes problem

In this tutorial we compare the formulation of a Navier-Stokes problem using standard assembly with mixed function spaces and block assembly. This tutorial serves as a reminder on how to solve a nonlinear problem in dolfinx interfacing to SNES (part of PETSc), and shows a further usage of multiphenicsx.fem.petsc.BlockVecSubVectorWrapper.

import typing

import basix.ufl
import dolfinx.fem
import dolfinx.fem.petsc
import dolfinx.io
import gmsh
import mpi4py.MPI
import numpy as np
import numpy.typing
import petsc4py.PETSc
import ufl
import viskex

import multiphenicsx.fem
import multiphenicsx.fem.petsc

Constitutive parameters

nu = 0.01


def u_in_eval(x: np.typing.NDArray[np.float64]) -> np.typing.NDArray[  # type: ignore[no-any-unimported]
        petsc4py.PETSc.ScalarType]:
    """Return the flat velocity profile at the inlet."""
    values = np.zeros((2, x.shape[1]))
    values[0, :] = 1.0
    return values


def u_wall_eval(x: np.typing.NDArray[np.float64]) -> np.typing.NDArray[  # type: ignore[no-any-unimported]
        petsc4py.PETSc.ScalarType]:
    """Return the zero velocity at the wall."""
    return np.zeros((2, x.shape[1]))

Geometrical parameters

pre_step_length = 4.
after_step_length = 14.
pre_step_height = 3.
after_step_height = 5.
mesh_size = 1. / 5.

Mesh

gmsh.initialize()
gmsh.model.add("mesh")

p0 = gmsh.model.geo.addPoint(0.0, after_step_height - pre_step_height, 0.0, mesh_size)
p1 = gmsh.model.geo.addPoint(pre_step_length, after_step_height - pre_step_height, 0.0, mesh_size)
p2 = gmsh.model.geo.addPoint(pre_step_length, 0.0, 0.0, mesh_size)
p3 = gmsh.model.geo.addPoint(pre_step_length + after_step_length, 0.0, 0.0, mesh_size)
p4 = gmsh.model.geo.addPoint(pre_step_length + after_step_length, after_step_height, 0.0, mesh_size)
p5 = gmsh.model.geo.addPoint(0.0, after_step_height, 0.0, mesh_size)
l0 = gmsh.model.geo.addLine(p0, p1)
l1 = gmsh.model.geo.addLine(p1, p2)
l2 = gmsh.model.geo.addLine(p2, p3)
l3 = gmsh.model.geo.addLine(p3, p4)
l4 = gmsh.model.geo.addLine(p4, p5)
l5 = gmsh.model.geo.addLine(p5, p0)
line_loop = gmsh.model.geo.addCurveLoop([l0, l1, l2, l3, l4, l5])
domain = gmsh.model.geo.addPlaneSurface([line_loop])

gmsh.model.geo.synchronize()
gmsh.model.addPhysicalGroup(1, [l5], 1)
gmsh.model.addPhysicalGroup(1, [l0, l1, l2, l4], 2)
gmsh.model.addPhysicalGroup(2, [domain], 0)
gmsh.model.mesh.generate(2)

Info    : Meshing 1D...
Info    : [  0%] Meshing curve 1 (Line)
Info    : [ 20%] Meshing curve 2 (Line)
Info    : [ 40%] Meshing curve 3 (Line)
Info    : [ 60%] Meshing curve 4 (Line)
Info    : [ 70%] Meshing curve 5 (Line)
Info    : [ 90%] Meshing curve 6 (Line)
Info    : Done meshing 1D (Wall 0.000541273s, CPU 0s)
Info    : Meshing 2D...
Info    : Meshing surface 1 (Plane, Frontal-Delaunay)
Info    : Done meshing 2D (Wall 0.0522577s, CPU 0.046807s)
Info    : 2520 nodes 5044 elements

mesh, subdomains, boundaries = dolfinx.io.gmshio.model_to_mesh(
    gmsh.model, comm=mpi4py.MPI.COMM_WORLD, rank=0, gdim=2)
gmsh.finalize()

# Create connectivities required by the rest of the code
mesh.topology.create_connectivity(mesh.topology.dim - 1, mesh.topology.dim)

boundaries_1 = boundaries.indices[boundaries.values == 1]
boundaries_2 = boundaries.indices[boundaries.values == 2]

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_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

Function spaces

V_element = basix.ufl.element("Lagrange", mesh.basix_cell(), 2, shape=(mesh.geometry.dim, ))
Q_element = basix.ufl.element("Lagrange", mesh.basix_cell(), 1)

Standard formulation using a mixed function space

def run_monolithic() -> dolfinx.fem.Function:
    """Run standard formulation using a mixed function space."""
    # Function spaces
    W_element = basix.ufl.mixed_element([V_element, Q_element])
    W = dolfinx.fem.functionspace(mesh, W_element)

    # Test and trial functions: monolithic
    vq = ufl.TestFunction(W)
    (v, q) = ufl.split(vq)
    dup = ufl.TrialFunction(W)
    up = dolfinx.fem.Function(W)
    (u, p) = ufl.split(up)

    # Variational forms
    F = (nu * ufl.inner(ufl.grad(u), ufl.grad(v)) * ufl.dx
         + ufl.inner(ufl.grad(u) * u, v) * ufl.dx
         - ufl.inner(p, ufl.div(v)) * ufl.dx
         + ufl.inner(ufl.div(u), q) * ufl.dx)
    J = ufl.derivative(F, up, dup)

    # Boundary conditions
    W0 = W.sub(0)
    V, _ = W0.collapse()
    u_in = dolfinx.fem.Function(V)
    u_in.interpolate(u_in_eval)
    u_wall = dolfinx.fem.Function(V)
    u_wall.interpolate(u_wall_eval)
    bdofs_V_1 = dolfinx.fem.locate_dofs_topological((W0, V), mesh.topology.dim - 1, boundaries_1)
    bdofs_V_2 = dolfinx.fem.locate_dofs_topological((W0, V), mesh.topology.dim - 1, boundaries_2)
    inlet_bc = dolfinx.fem.dirichletbc(u_in, bdofs_V_1, W0)
    wall_bc = dolfinx.fem.dirichletbc(u_wall, bdofs_V_2, W0)
    bc = [inlet_bc, wall_bc]

    # Class for interfacing with SNES
    class NavierStokesProblem:
        """Define a nonlinear problem, interfacing with SNES."""

        def __init__(  # type: ignore[no-any-unimported]
            self, F: ufl.Form, J: ufl.Form, solution: dolfinx.fem.Function,
            bcs: list[dolfinx.fem.DirichletBC], P: typing.Optional[ufl.Form] = None
        ) -> None:
            self._F = dolfinx.fem.form(F)
            self._J = dolfinx.fem.form(J)
            self._obj_vec = dolfinx.fem.petsc.create_vector(self._F)
            self._solution = solution
            self._bcs = bcs
            self._P = P

        def create_snes_solution(self) -> petsc4py.PETSc.Vec:  # type: ignore[no-any-unimported]
            """
            Create a petsc4py.PETSc.Vec to be passed to petsc4py.PETSc.SNES.solve.

            The returned vector will be initialized with the initial guess provided in `self._solution`.
            """
            x = self._solution.x.petsc_vec.copy()
            with x.localForm() as _x, self._solution.x.petsc_vec.localForm() as _solution:
                _x[:] = _solution
            return x

        def update_solution(self, x: petsc4py.PETSc.Vec) -> None:  # type: ignore[no-any-unimported]
            """Update `self._solution` with data in `x`."""
            x.ghostUpdate(addv=petsc4py.PETSc.InsertMode.INSERT, mode=petsc4py.PETSc.ScatterMode.FORWARD)
            with x.localForm() as _x, self._solution.x.petsc_vec.localForm() as _solution:
                _solution[:] = _x

        def obj(  # type: ignore[no-any-unimported]
            self, snes: petsc4py.PETSc.SNES, x: petsc4py.PETSc.Vec
        ) -> np.float64:
            """Compute the norm of the residual."""
            self.F(snes, x, self._obj_vec)
            return self._obj_vec.norm()  # type: ignore[no-any-return]

        def F(  # type: ignore[no-any-unimported]
            self, snes: petsc4py.PETSc.SNES, x: petsc4py.PETSc.Vec, F_vec: petsc4py.PETSc.Vec
        ) -> None:
            """Assemble the residual."""
            self.update_solution(x)
            with F_vec.localForm() as F_vec_local:
                F_vec_local.set(0.0)
            dolfinx.fem.petsc.assemble_vector(F_vec, self._F)
            dolfinx.fem.petsc.apply_lifting(F_vec, [self._J], [self._bcs], x0=[x], alpha=-1.0)
            F_vec.ghostUpdate(addv=petsc4py.PETSc.InsertMode.ADD, mode=petsc4py.PETSc.ScatterMode.REVERSE)
            dolfinx.fem.petsc.set_bc(F_vec, self._bcs, x, -1.0)

        def J(  # type: ignore[no-any-unimported]
            self, snes: petsc4py.PETSc.SNES, x: petsc4py.PETSc.Vec, J_mat: petsc4py.PETSc.Mat,
            P_mat: petsc4py.PETSc.Mat
        ) -> None:
            """Assemble the jacobian."""
            J_mat.zeroEntries()
            dolfinx.fem.petsc.assemble_matrix(  # type: ignore[misc]
                J_mat, self._J, self._bcs, diagonal=1.0)  # type: ignore[arg-type]
            J_mat.assemble()
            if self._P is not None:
                P_mat.zeroEntries()
                dolfinx.fem.petsc.assemble_matrix(  # type: ignore[misc]
                    P_mat, self._P, self._bcs, diagonal=1.0)  # type: ignore[arg-type]
                P_mat.assemble()

    # Create problem
    problem = NavierStokesProblem(F, J, up, bc)
    F_vec = dolfinx.fem.petsc.create_vector(problem._F)
    J_mat = dolfinx.fem.petsc.create_matrix(problem._J)

    # Solve
    snes = petsc4py.PETSc.SNES().create(mesh.comm)
    snes.setTolerances(max_it=20)
    snes.getKSP().setType("preonly")
    snes.getKSP().getPC().setType("lu")
    snes.getKSP().getPC().setFactorSolverType("mumps")
    snes.setObjective(problem.obj)
    snes.setFunction(problem.F, F_vec)
    snes.setJacobian(problem.J, J=J_mat, P=None)
    snes.setMonitor(lambda _, it, residual: print(it, residual))
    up_copy = problem.create_snes_solution()
    snes.solve(None, up_copy)
    problem.update_solution(up_copy)  # TODO can this be safely removed?
    up_copy.destroy()
    snes.destroy()
    return up

up_m = run_monolithic()
(u_m, p_m) = (up_m.sub(0).collapse(), up_m.sub(1).collapse())

Create element

0 5.423530856245577
1 0.12945659318075836

2 0.04875205308048853
3 0.01245509718119217
4 0.01045448218377124
5 0.0008411904377641378
6 4.2733147396818654e-05

7 5.832046606872697e-08
8 2.8938906872571975e-13

viskex.dolfinx.plot_vector_field(u_m, "u")

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(u_m, "u", glyph_factor=1.0)

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

viskex.dolfinx.plot_scalar_field(p_m, "p")

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

Block formulation using two independent function spaces

def run_block() -> tuple[dolfinx.fem.Function, dolfinx.fem.Function]:
    """Run block formulation using two independent function spaces."""
    # Function spaces
    V = dolfinx.fem.functionspace(mesh, V_element)
    Q = dolfinx.fem.functionspace(mesh, Q_element)

    # Test and trial functions
    (v, q) = (ufl.TestFunction(V), ufl.TestFunction(Q))
    (du, dp) = (ufl.TrialFunction(V), ufl.TrialFunction(Q))
    (u, p) = (dolfinx.fem.Function(V), dolfinx.fem.Function(Q))

    # Variational forms
    F = [(nu * ufl.inner(ufl.grad(u), ufl.grad(v)) * ufl.dx + ufl.inner(ufl.grad(u) * u, v) * ufl.dx
          - ufl.inner(p, ufl.div(v)) * ufl.dx),
         ufl.inner(ufl.div(u), q) * ufl.dx]
    J = [[ufl.derivative(F[0], u, du), ufl.derivative(F[0], p, dp)],
         [ufl.derivative(F[1], u, du), ufl.derivative(F[1], p, dp)]]

    # Boundary conditions
    u_in = dolfinx.fem.Function(V)
    u_in.interpolate(u_in_eval)
    u_wall = dolfinx.fem.Function(V)
    u_wall.interpolate(u_wall_eval)
    bdofs_V_1 = dolfinx.fem.locate_dofs_topological(V, mesh.topology.dim - 1, boundaries_1)
    bdofs_V_2 = dolfinx.fem.locate_dofs_topological(V, mesh.topology.dim - 1, boundaries_2)
    inlet_bc = dolfinx.fem.dirichletbc(u_in, bdofs_V_1)
    wall_bc = dolfinx.fem.dirichletbc(u_wall, bdofs_V_2)
    bc = [inlet_bc, wall_bc]

    # Class for interfacing with SNES
    class NavierStokesProblem:
        """Define a nonlinear problem, interfacing with SNES."""

        def __init__(  # type: ignore[no-any-unimported]
            self, F: list[ufl.Form], J: list[list[ufl.Form]],
            solutions: tuple[dolfinx.fem.Function, dolfinx.fem.Function],
            bcs: list[dolfinx.fem.DirichletBC],
            P: typing.Optional[list[list[ufl.Form]]] = None
        ) -> None:
            self._F = dolfinx.fem.form(F)
            self._J = dolfinx.fem.form(J)
            self._obj_vec = dolfinx.fem.petsc.create_vector_block(self._F)
            self._solutions = solutions
            self._bcs = bcs
            self._P = P

        def create_snes_solution(self) -> petsc4py.PETSc.Vec:  # type: ignore[no-any-unimported]
            """
            Create a petsc4py.PETSc.Vec to be passed to petsc4py.PETSc.SNES.solve.

            The returned vector will be initialized with the initial guesses provided in `self._solutions`,
            properly stacked together in a single block vector.
            """
            x = dolfinx.fem.petsc.create_vector_block(self._F)
            with multiphenicsx.fem.petsc.BlockVecSubVectorWrapper(x, [V.dofmap, Q.dofmap]) as x_wrapper:
                for x_wrapper_local, sub_solution in zip(x_wrapper, self._solutions):
                    with sub_solution.x.petsc_vec.localForm() as sub_solution_local:
                        x_wrapper_local[:] = sub_solution_local
            return x

        def update_solutions(self, x: petsc4py.PETSc.Vec) -> None:  # type: ignore[no-any-unimported]
            """Update `self._solutions` with data in `x`."""
            x.ghostUpdate(addv=petsc4py.PETSc.InsertMode.INSERT, mode=petsc4py.PETSc.ScatterMode.FORWARD)
            with multiphenicsx.fem.petsc.BlockVecSubVectorWrapper(x, [V.dofmap, Q.dofmap]) as x_wrapper:
                for x_wrapper_local, sub_solution in zip(x_wrapper, self._solutions):
                    with sub_solution.x.petsc_vec.localForm() as sub_solution_local:
                        sub_solution_local[:] = x_wrapper_local

        def obj(  # type: ignore[no-any-unimported]
            self, snes: petsc4py.PETSc.SNES, x: petsc4py.PETSc.Vec
        ) -> np.float64:
            """Compute the norm of the residual."""
            self.F(snes, x, self._obj_vec)
            return self._obj_vec.norm()  # type: ignore[no-any-return]

        def F(  # type: ignore[no-any-unimported]
            self, snes: petsc4py.PETSc.SNES, x: petsc4py.PETSc.Vec, F_vec: petsc4py.PETSc.Vec
        ) -> None:
            """Assemble the residual."""
            self.update_solutions(x)
            with F_vec.localForm() as F_vec_local:
                F_vec_local.set(0.0)
            dolfinx.fem.petsc.assemble_vector_block(  # type: ignore[misc]
                F_vec, self._F, self._J, self._bcs, x0=x, alpha=-1.0)

        def J(  # type: ignore[no-any-unimported]
            self, snes: petsc4py.PETSc.SNES, x: petsc4py.PETSc.Vec, J_mat: petsc4py.PETSc.Mat,
            P_mat: petsc4py.PETSc.Mat
        ) -> None:
            """Assemble the jacobian."""
            J_mat.zeroEntries()
            dolfinx.fem.petsc.assemble_matrix_block(  # type: ignore[misc]
                J_mat, self._J, self._bcs, diagonal=1.0)  # type: ignore[arg-type]
            J_mat.assemble()
            if self._P is not None:
                P_mat.zeroEntries()
                dolfinx.fem.petsc.assemble_matrix_block(  # type: ignore[misc]
                    P_mat, self._P, self._bcs, diagonal=1.0)  # type: ignore[arg-type]
                P_mat.assemble()

    # Create problem
    problem = NavierStokesProblem(F, J, (u, p), bc)
    F_vec = dolfinx.fem.petsc.create_vector_block(problem._F)
    J_mat = dolfinx.fem.petsc.create_matrix_block(problem._J)

    # Solve
    snes = petsc4py.PETSc.SNES().create(mesh.comm)
    snes.setTolerances(max_it=20)
    snes.getKSP().setType("preonly")
    snes.getKSP().getPC().setType("lu")
    snes.getKSP().getPC().setFactorSolverType("mumps")
    snes.setObjective(problem.obj)
    snes.setFunction(problem.F, F_vec)
    snes.setJacobian(problem.J, J=J_mat, P=None)
    snes.setMonitor(lambda _, it, residual: print(it, residual))
    solution = problem.create_snes_solution()
    snes.solve(None, solution)
    problem.update_solutions(solution)  # TODO can this be safely removed?
    solution.destroy()
    snes.destroy()
    return (u, p)

(u_b, p_b) = run_block()

Create element
Create element

0 5.423530856245578
1 0.1294565931807582

2 0.048752053080488224
3 0.012455097181192405
4 0.010454482183771556

5 0.0008411904377641823
6 4.273314739682205e-05
7 5.8320466065962444e-08

8 2.8938586036790035e-13

viskex.dolfinx.plot_vector_field(u_b, "u", glyph_factor=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_scalar_field(p_b, "p")

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

Error computation between mixed and block cases

def run_error(
    u_m: dolfinx.fem.Function, p_m: dolfinx.fem.Function, u_b: dolfinx.fem.Function, p_b: dolfinx.fem.Function
) -> None:
    """Compute errors between the mixed and block cases."""
    u_m_norm = np.sqrt(mesh.comm.allreduce(
        dolfinx.fem.assemble_scalar(dolfinx.fem.form(ufl.inner(ufl.grad(u_m), ufl.grad(u_m)) * ufl.dx)),
        op=mpi4py.MPI.SUM))
    err_u_norm = np.sqrt(mesh.comm.allreduce(
        dolfinx.fem.assemble_scalar(
            dolfinx.fem.form(ufl.inner(ufl.grad(u_b - u_m), ufl.grad(u_b - u_m)) * ufl.dx)),
        op=mpi4py.MPI.SUM))
    p_m_norm = np.sqrt(mesh.comm.allreduce(
        dolfinx.fem.assemble_scalar(dolfinx.fem.form(ufl.inner(p_m, p_m) * ufl.dx)), op=mpi4py.MPI.SUM))
    err_p_norm = np.sqrt(mesh.comm.allreduce(
        dolfinx.fem.assemble_scalar(dolfinx.fem.form(ufl.inner(p_b - p_m, p_b - p_m) * ufl.dx)),
        op=mpi4py.MPI.SUM))
    print("Relative error for velocity component is equal to", err_u_norm / u_m_norm)
    print("Relative error for pressure component is equal to", err_p_norm / p_m_norm)
    assert np.isclose(err_u_norm / u_m_norm, 0., atol=1.e-10)
    assert np.isclose(err_p_norm / p_m_norm, 0., atol=1.e-10)

run_error(u_m, p_m, u_b, p_b)

Relative error for velocity component is equal to 6.165562228179097e-15
Relative error for pressure component is equal to 4.9063246456190605e-15