Primal single-domain formulation

Primal single-domain formulation#

In this example, we consider the formulation from Chapter 5.2.1 of [KMR21].

Find \(u_i\in V_i=V(\Omega_i)\) and \(u_e\in V_e=V(\Omega_e)\) such that

\[\begin{split} \int_{\Omega_e} \sigma_e \nabla u_e \cdot \nabla v_e~\mathrm{d}x + \int_\Gamma \frac{C_m}{\Delta t} (u_e - u_i) v_e ~\mathrm{d}s &= \int_{\Omega_e} f_e v_e ~\mathrm{d}x - \frac{C_m}{\Delta t} \int_\Gamma f v_e ~\mathrm{d}s \\ \int_{\Omega_i} \sigma_i \nabla u_i \cdot \nabla v_i~\mathrm{d}x + \int_\Gamma \frac{C_m}{\Delta t} (u_i - u_e) v_i ~\mathrm{d}s &= \int_{\Omega_i} f_i v_i ~\mathrm{d}x + \frac{C_m}{\Delta t} \int_\Gamma f v_i ~\mathrm{d}s \end{split}\]

for all \(v_e\in V_e\) and \(v_i\in V_i\).

We start by importing the necessary libraries

from mpi4py import MPI
from petsc4py import PETSc
import dolfinx
from ufl import (
    inner,
    grad,
    TestFunctions,
    TrialFunctions,
    FacetNormal,
    MixedFunctionSpace,
    sin,
    pi,
    extract_blocks,
    Measure,
    SpatialCoordinate,
    cos,
    div,
)
import numpy as np
import scifem

Next, we define the intracellular and extracellular domain. In the following examples, we will use \(\Omega_e = [x_L, x_U]\times[y_L, y_U]\) and \(\Omega_i = [0,1]^2\setminus\Omega_e\). We define the bounds and make a set of convenience functions to marker the domains.

x_L = 0.25
x_U = 0.75
y_L = 0.25
y_U = 0.75


def lower_bound(x, i, bound, tol=1e-12):
    return x[i] >= bound - tol


def upper_bound(x, i, bound, tol=1e-12):
    return x[i] <= bound + tol


def omega_interior_marker(x, tol=1e-12):
    return (
        lower_bound(x, 0, x_L, tol=tol)
        & lower_bound(x, 1, y_L, tol=tol)
        & upper_bound(x, 0, x_U, tol=tol)
        & upper_bound(x, 1, y_U, tol=tol)
    )

With the convenience functions we can set up \(\Omega\)

M = 400
omega = dolfinx.mesh.create_unit_square(
    MPI.COMM_WORLD, M, M, ghost_mode=dolfinx.mesh.GhostMode.shared_facet
)

We create a MeshTags objects that marks the interior cells with interior_marker, and the remaining (exterior) cells with exterior_marker.

interior_cells = dolfinx.mesh.locate_entities(
    omega, omega.topology.dim, omega_interior_marker
)
interior_marker = 2
exterior_marker = 3
cell_map = omega.topology.index_map(omega.topology.dim)
num_cells_local = cell_map.size_local + cell_map.num_ghosts
cell_marker = np.full(num_cells_local, exterior_marker, dtype=np.int32)
cell_marker[interior_cells] = interior_marker
ct = dolfinx.mesh.meshtags(
    omega, omega.topology.dim, np.arange(num_cells_local, dtype=np.int32), cell_marker
)

Next, we create a Mesh for \(\Omega_i\) and \(\Omega_e\) using scifem.extract_submesh():

omega_i, interior_to_parent, _, _, _ = scifem.extract_submesh(
    omega, ct, interior_marker
)
omega_e, exterior_to_parent, e_vertex_to_parent, _, _ = scifem.extract_submesh(
    omega, ct, exterior_marker
)

We identity the facets on the interface \(\Gamma\) using scifem.find_interface().

gamma_facets = scifem.find_interface(ct, interior_marker, exterior_marker)

We create a MeshTags object that marks the facets on \(\Gamma\) with interface_marker and additionally marks all exterior facets with boundary_marker. Any facet not on \(\Gamma\) or \(\partial\Omega\) is excluded from the MeshTags object.

omega.topology.create_connectivity(omega.topology.dim - 1, omega.topology.dim)
exterior_facets = dolfinx.mesh.exterior_facet_indices(omega.topology)
facet_map = omega.topology.index_map(omega.topology.dim - 1)
num_facets_local = facet_map.size_local + facet_map.num_ghosts
facets = np.arange(num_facets_local, dtype=np.int32)
interface_marker = 4
boundary_marker = 5
marker = np.full_like(facets, -1, dtype=np.int32)
marker[gamma_facets] = interface_marker
marker[exterior_facets] = boundary_marker
marker_filter = np.flatnonzero(marker != -1).astype(np.int32)
ft = dolfinx.mesh.meshtags(
    omega, omega.topology.dim - 1, marker_filter, marker[marker_filter]
)
ft.name = "interface_marker"

For the volume integrals, we create an integration measure that integrates over \(\Omega\). However, we create a restriction of the integration measure to \(\Omega_i\) and \(\Omega_e\) using the py calling the measure with the appropriate marker. Note that this would result in a zero integration measure if we had not passed ct into the initializer of dx.

dx = Measure("dx", domain=omega, subdomain_data=ct)
dxI = dx(interior_marker)
dxE = dx(exterior_marker)

Setting up the mixed function space and variational form#

We create each of the spaces, and make them a mixed function space, which we can extract test and trial functions from.

element = ("Lagrange", 1)
Vi = dolfinx.fem.functionspace(omega_i, element)
Ve = dolfinx.fem.functionspace(omega_e, element)
W = MixedFunctionSpace(Vi, Ve)
vi, ve = TestFunctions(W)
ui, ue = TrialFunctions(W)

Consistent restrictions#

Next, for the interface integrals, we want to create a measure that integrates over \(\Gamma\). However, as \(\Gamma\) connects to two cells, one from \(\Omega_i\) and one from \(\Omega_e\), we need to define the appropriate restrictions of \(u_e\), \(u_i\), \(v_e\), and \(v_i\) to the interface. This is done by calling scifem.compute_interface_data(), which returns the integration data order such that the “+” side of the restriction corresponds to the smallest cell tag of interior_marker and exterior_marker. We pass in the ordered integration data to the initializer of a measure.

i_res = "+" if interior_marker < exterior_marker else "-"
e_res = "-" if interior_marker < exterior_marker else "+"
ordered_integration_data = scifem.compute_interface_data(ct, ft.find(interface_marker))
interface_tag = 2
dGamma = Measure(
    "dS",
    domain=omega,
    subdomain_data=[(interface_tag, ordered_integration_data.flatten())],
    subdomain_id=interface_tag,
)

Next, we define the trace operators on the interface for each of the functions.

tr_ui = ui(i_res)
tr_ue = ue(e_res)
tr_vi = vi(i_res)
tr_ve = ve(e_res)

Variational formulation#

We define the problem parameters as Constant objects. This is to make the code efficient, enven if we change the parameter values later.

sigma_e = dolfinx.fem.Constant(omega_e, 2.0)
sigma_i = dolfinx.fem.Constant(omega_i, 1.0)
Cm = dolfinx.fem.Constant(omega, 1.0)
dt = dolfinx.fem.Constant(omega, 1.0e-2)

# Next, we define the exact solution of each of the potentials
x, y = SpatialCoordinate(omega)
ue_exact = sin(pi * (x + y))
ui_exact = sigma_e / sigma_i * ue_exact + cos(pi * (x - x_L) * (x - x_U)) * cos(
    pi * (y - y_L) * (y - y_U)
)

Method of manufactured solutions#

We also define corresponding right hand side source terms \(f\), \(f_i\), \(f_e\) that fulfills the strong form of the equations, given the exact solutions above. This is called the method of manufactured solutions.

n = FacetNormal(omega)
n_e = n(e_res)
Im = sigma_e * inner(grad(ue_exact), n_e)
T = Cm / dt
f = ui_exact - ue_exact - 1 / T * Im
f_e = -div(sigma_e * grad(ue_exact))
f_i = -div(sigma_i * grad(ui_exact))

We can then define the variational formulation with the bilinear form a and linear form L

a = sigma_e * inner(grad(ue), grad(ve)) * dxE
a += sigma_i * inner(grad(ui), grad(vi)) * dxI
a += T * (tr_ue - tr_ui) * tr_ve * dGamma
a += T * (tr_ui - tr_ue) * tr_vi * dGamma
L = T * inner(f, (tr_vi - tr_ve)) * dGamma
L += f_e * ve * dxE
L += f_i * vi * dxI

We impose a Dirichlet boundary condition on the outer boundary of \(\Omega_e\). To do this, we transfer the facet tags (ft) from the parent mesh to the submesh (omega_e) by calling scifem.transfer_meshtags_to_submesh().

sub_tag, _ = scifem.transfer_meshtags_to_submesh(
    ft, omega_e, e_vertex_to_parent, exterior_to_parent
)

With the tags transferred onto the submesh, we can locate the degree of freedom (dofs) that we want to constrain with dolfinx.fem.locate_dofs_topological()

omega_e.topology.create_connectivity(omega_e.topology.dim - 1, omega_e.topology.dim)
bc_dofs = dolfinx.fem.locate_dofs_topological(
    Ve, omega_e.topology.dim - 1, sub_tag.find(boundary_marker)
)

We interpolate the exact solution into the appropriate function space and create a DirichletBC object using the dolfinx.fem.dirichletbc() constructor.

u_bc = dolfinx.fem.Function(Ve)
u_bc.interpolate(lambda x: np.sin(np.pi * (x[0] + x[1])))
bc = dolfinx.fem.dirichletbc(u_bc, bc_dofs)

Preconditioning of the system#

[KM21] suggests using the following preconditioner for the system:

\[\begin{split} P &= \begin{pmatrix} \int_{\Omega_i} \sigma_i \nabla u_i \cdot \nabla v_i + u_i v_i ~\mathrm{d}x & 0 \\ 0 & \int_{\Omega_e} \sigma_e \nabla u_e \cdot \nabla v_e ~\mathrm{d}x \end{pmatrix} \end{split}\]
P = sigma_e * inner(grad(ue), grad(ve)) * dxE
P += sigma_i * inner(grad(ui), grad(vi)) * dxI
P += inner(ui, vi) * dxI

Solving the system#

We use the LinearProblem class to set up a solver for the linear system. We use extract_blocks to extract the block structure of the bilinear form, linear form, and preconditioner. We pass in a list of EntityMaps for each of the meshes used in the formulation to ensure that the assembly is done correctly.

ui = dolfinx.fem.Function(Vi, name="ui")
ue = dolfinx.fem.Function(Ve, name="ue")
entity_maps = [interior_to_parent, exterior_to_parent]
petsc_options = {
    "ksp_type": "cg",
    "pc_type": "lu",
    "pc_factor_mat_solver_type": "mumps",
    "ksp_rtol": 1e-12,
    "ksp_atol": 1e-12,
    "ksp_monitor": None,
    "ksp_norm_type": "preconditioned",
    "ksp_error_if_not_converged": True,
}
problem = dolfinx.fem.petsc.LinearProblem(
    extract_blocks(a),
    extract_blocks(L),
    P=extract_blocks(P),
    u=[ui, ue],
    bcs=[bc],
    petsc_options=petsc_options,
    petsc_options_prefix="primal_single_",
    entity_maps=entity_maps,
)
problem.solve()

  Residual norms for primal_single_ solve.
  0 KSP Residual norm 1.592227017093e+05
  1 KSP Residual norm 7.435763569040e+03
  2 KSP Residual norm 2.023889546503e+03
  3 KSP Residual norm 1.766440952677e+03
  4 KSP Residual norm 4.203523357980e+01
  5 KSP Residual norm 6.847686080957e+00
  6 KSP Residual norm 3.471341487743e+00
  7 KSP Residual norm 2.080799337254e+02

  8 KSP Residual norm 2.561256131308e+00
  9 KSP Residual norm 7.932329557990e-01
 10 KSP Residual norm 1.314658484807e+00
 11 KSP Residual norm 2.915677170831e-01
 12 KSP Residual norm 4.949324111105e-02
 13 KSP Residual norm 7.326576293014e-02
 14 KSP Residual norm 2.986177663666e+00
 15 KSP Residual norm 4.572708045739e-03
 16 KSP Residual norm 2.040019934651e-02
 17 KSP Residual norm 4.753682989523e-03
 18 KSP Residual norm 3.062511820069e-04
 19 KSP Residual norm 1.337504687829e-04
 20 KSP Residual norm 3.258062998908e-03
 21 KSP Residual norm 3.390152963977e-03
 22 KSP Residual norm 7.260942657918e-05

 23 KSP Residual norm 3.017473176204e-04
 24 KSP Residual norm 2.842095506277e-05
 25 KSP Residual norm 4.730294179567e-05
 26 KSP Residual norm 8.774456313607e-06
 27 KSP Residual norm 5.430877719674e-05
 28 KSP Residual norm 1.671179422325e-04
 29 KSP Residual norm 9.321400947663e-06
 30 KSP Residual norm 1.781718522863e-06
 31 KSP Residual norm 1.095768730535e-06
 32 KSP Residual norm 6.044301942507e-07
 33 KSP Residual norm 1.226214628043e-07

[Coefficient(FunctionSpace(Mesh(blocked element (Basix element (P, triangle, 1, gll_warped, unset, False, float64, []), (2,)), 1), Basix element (P, triangle, 1, gll_warped, unset, False, float64, [])), 1),
 Coefficient(FunctionSpace(Mesh(blocked element (Basix element (P, triangle, 1, gll_warped, unset, False, float64, []), (2,)), 2), Basix element (P, triangle, 1, gll_warped, unset, False, float64, [])), 2)]

We check the numbers of iterations and the reason for convergence

num_iterations = problem.solver.getIterationNumber()
converged_reason = problem.solver.getConvergedReason()
PETSc.Sys.Print(f"Solver converged in: {num_iterations} with reason {converged_reason}")

Solver converged in: 33 with reason 2

If we have adios2.Adios installed, we can save the solution to a file that can be visualized in Paraview

if dolfinx.has_adios2:
    with dolfinx.io.VTXWriter(omega_i.comm, "uh_i.bp", [ui], engine="BP5") as bp:
        bp.write(0.0)
    with dolfinx.io.VTXWriter(omega_i.comm, "uh_e.bp", [ue], engine="BP5") as bp:
        bp.write(0.0)

Finally, we compute the \(L^2\) error of each of the potentials

error_ui = dolfinx.fem.form(
    inner(ui - ui_exact, ui - ui_exact) * dxI, entity_maps=entity_maps
)
error_ue = dolfinx.fem.form(
    inner(ue - ue_exact, ue - ue_exact) * dxE, entity_maps=entity_maps
)
L2_ui = np.sqrt(scifem.assemble_scalar(error_ui, entity_maps=entity_maps))
L2_ue = np.sqrt(scifem.assemble_scalar(error_ue, entity_maps=entity_maps))

PETSc.Sys.Print(f"L2(ui): {L2_ui:.2e}\nL2(ue): {L2_ue:.2e}")

L2(ui): 1.01e-05
L2(ue): 1.31e-05
[KM21]

Miroslav Kuchta and Kent-André Mardal. Iterative Solvers for EMI Models, pages 70–86. Springer International Publishing, Cham, 2021. doi:10.1007/978-3-030-61157-6_6.

[KMR21]

Miroslav Kuchta, Kent-André Mardal, and Marie E. Rognes. Solving the EMI Equations using Finite Element Methods, pages 56–69. Springer International Publishing, Cham, 2021. doi:10.1007/978-3-030-61157-6_5.

Contents