# Navier-Stokes with a Lorentz force term

Hi fenics experts!

I’m trying to model the stationary Navier-stokes equations with a Lorentz force term. I was wondering if I have the correct variational formulation here and if you have any advice for running the simulation more efficiently as it is currently very computationally intensive.

Governing equations:

\rho(\mathbf{u}\cdot \nabla\mathbf{u}) = -\nabla p + \mu\nabla^{2}\mathbf{u} + \mathbf{J} \times \mathbf{B}

\nabla \cdot \mathbf{u} = 0

Where:
\mathbf{J} = \sigma(-\nabla \Phi + \mathbf{u} \times \mathbf{B})

I think I can expand the Lorentz force term as:
\begin{align*} \mathbf{J} \times \mathbf{B} &= -\mathbf{B} \times \sigma (-\nabla \Phi + \mathbf{u} \times \mathbf{B})\\ &= \sigma[(-\mathbf{B} \times -\nabla \Phi) + (-\mathbf{B} \times (\mathbf{u} \times \mathbf{B})]\\ &= \sigma[(\mathbf{B} \times \nabla \Phi) -(\mathbf{B} \cdot \mathbf{B})\mathbf{u} + (\mathbf{B} \cdot \mathbf{u})\mathbf{B}] \end{align*}

Additionally, assuming the fluid is electrically neutral thus, \nabla \cdot \mathbf{J} = 0. This leads to an equation for the electric potential \Phi:

\nabla^{2}\Phi = \nabla \cdot (\mathbf{u} \times \mathbf{B})

Assuming Dirichlet BC’s on all walls of the domain for the velocity and pressure, and assuming electrically insulated walls (\partial \phi / \partial n=0). I think the weak formulation is as follows for the momentum:

\int_{\Omega} \rho (\mathbf{u}\cdot \nabla\mathbf{u}) \cdot \mathbf{v} - \int_{\Omega} p\nabla\cdot\mathbf{v} + \int_{\Omega} \mu\nabla\mathbf{u}\cdot\nabla\mathbf{v} - \\ \ \sigma \left(\int_{\Omega} (\mathbf{B} \times \nabla \Phi) \cdot \mathbf{v} + \int_{\Omega} (\mathbf{B} \cdot \mathbf{B})\mathbf{u} \cdot \mathbf{v} - \int_{\Omega} (\mathbf{B} \cdot \mathbf{u})\mathbf{B} \cdot \mathbf{v} \right) = 0 \ \ \ \forall \mathbf{v} \in V

for continuity:

\int_{\Omega} q (\nabla \cdot \mathbf{u}) = 0 \ \ \ \forall \mathbf{q} \in Q

and for the electrical potential:

\int_{\Omega} \nabla\mathbf{\phi} \cdot \nabla \mathbf{q2} - \int_{\Omega} ((\nabla \times \mathbf{u}) \cdot \mathbf{B}) \cdot \mathbf{q2} + \int_{\Omega} ((\nabla \times \mathbf{B}) \cdot \mathbf{u}) \cdot \mathbf{q2} = 0 \ \ \ \forall \mathbf{q2} \in Q2

I have implemented it in the following example:

Would love to have your feedback and apologies for the length of the post

from fenics import *

N = 15
mesh = UnitCubeMesh(N, N, N)
V_ele = VectorElement("CG", mesh.ufl_cell(), 3)
Q_ele = FiniteElement("CG", mesh.ufl_cell(), 1)
W = FunctionSpace(mesh, MixedElement([V_ele, Q_ele, Q_ele]))

fixed_wall_locations = "near(x[1], 0.) | near(x[1], 1.) | near(x[2], 0.) | near(x[2], 1.)"
inlet = "near(x[0], 0.)"
outlet = "near(x[0], 1.)"
velocity_inlet = DirichletBC(W.sub(0), Constant((10, 0, 0)), inlet)
pressure_outlet = DirichletBC(W.sub(1), Constant(0), outlet)
noslip = DirichletBC(W.sub(0), (0, 0, 0), fixed_wall_locations)
bcu = [velocity_inlet, pressure_outlet, noslip]

func = Function(W)
u, p, phi = split(func)
v, q, q_2 = TestFunctions(W)
B = Constant((0, -1, 0))
sigma = Constant(1)

# Momentum
F = (
- inner(p, div(v)) * dx
+ sigma * (inner(cross(B, grad(phi)), v) * dx
+ inner(u * dot(B, B), v) * dx
- inner(B * dot(B, u), v) * dx)
)

# CFD continuity
F += - inner(q, div(u)) * dx

# electric continuity
- inner(dot(B, curl(u)) + dot(u, curl(B)), q_2) * dx
)

solve(F == 0, func, bcu, solver_parameters={'newton_solver': {'linear_solver': 'mumps'}})

Is this a typo? Your element pair for velocity-pressure doesn’t appear stable.

Regarding computational expense, large 3D problems typically benefit from iterative solvers. Mumps will not scale optimally. There’s a vast literature on the topic of preconditioning the Navier-Stokes system. Preconditioning your Poisson type problem for the electric potential should be trivial. I highly recommend dolfinx for block assembly facilitating preconditioning the individual blocks and tying them together with whichever clever method you like. See for example the Stokes demo.

Thanks so much for getting back nate!

Is there a more optimal element-pair that would be better to use?

Yeah, I have read a lot about preconditioning, but I’m not sure how to implement it. I actually haven’t used fenicsx either yet, perhaps this would be a good example to get started.

I would have expected the standard Taylor-Hood pair, e.g.

V_ele = VectorElement("CG", mesh.ufl_cell(), 2)
Q_ele = FiniteElement("CG", mesh.ufl_cell(), 1)


If you can’t solve with this pair there’s clearly something I’m missing from trying to understand your code.

Hi Nate!

Yes, the standard Taylor-Hood pair works much better, although I have to increase the relative tolerance rather high (1e-02) for the model to converge in all cases. Not sure how normal this is.

I have also started adapting the stokes demo, first converting it to Navier-Stokes before trying to implement the MHD effects too however I’m having some issues.

I have the variational form as

a = form([[inner(grad(u), grad(v)) * dx, inner(dot(grad(u), u), v) * dx, inner(p, div(v)) * dx],
[inner(div(u), q) * dx, None]])


However, I think I have the form wrong as I’m getting errors.

Heres the code used and error message:

import numpy as np

import ufl
from dolfinx import cpp as _cpp
from dolfinx import fem
from dolfinx.fem import (Constant, Function, FunctionSpace, dirichletbc,
extract_function_spaces, form,
locate_dofs_geometrical, locate_dofs_topological)
from dolfinx.io import XDMFFile
from dolfinx.mesh import (CellType, GhostMode, create_rectangle,
locate_entities_boundary)

from mpi4py import MPI
from petsc4py import PETSc

# Create mesh
msh = create_rectangle(MPI.COMM_WORLD,
[np.array([0, 0]), np.array([1, 1])],
[100, 100],
CellType.triangle, GhostMode.none)

def noslip_boundary(x):
return np.logical_or(np.logical_or(np.isclose(x[0], 0.0),
np.isclose(x[0], 1.0)),
np.isclose(x[1], 0.0))

def lid(x):
return np.isclose(x[1], 1.0)

def lid_velocity_expression(x):
return np.stack((np.ones(x.shape[1]), np.zeros(x.shape[1])))

P2 = ufl.VectorElement("Lagrange", msh.ufl_cell(), 2)
P1 = ufl.FiniteElement("Lagrange", msh.ufl_cell(), 1)
V, Q = FunctionSpace(msh, P2), FunctionSpace(msh, P1)

# boundary conditions:
noslip = np.zeros(msh.geometry.dim, dtype=PETSc.ScalarType)
facets = locate_entities_boundary(msh, 1, noslip_boundary)
bc0 = dirichletbc(noslip, locate_dofs_topological(V, 1, facets), V)

lid_velocity = Function(V)
lid_velocity.interpolate(lid_velocity_expression)
facets = locate_entities_boundary(msh, 1, lid)
bc1 = dirichletbc(lid_velocity, locate_dofs_topological(V, 1, facets))

bcs = [bc0, bc1]

# Define variational problem
(u, p) = ufl.TrialFunction(V), ufl.TrialFunction(Q)
(v, q) = ufl.TestFunction(V), ufl.TestFunction(Q)
f = Constant(msh, (PETSc.ScalarType(0), PETSc.ScalarType(0)))

[inner(div(u), q) * dx, None]])

L = form([inner(f, v) * dx, inner(Constant(msh, PETSc.ScalarType(0)), q) * dx])

# block-diagonal preconditioner:
a_p11 = form(inner(p, q) * dx)
a_p = [[a[0][0], None],
[None, a_p11]]

# ### Monolithic block iterative solver
A = fem.petsc.assemble_matrix_block(a, bcs=bcs)
A.assemble()

P = fem.petsc.assemble_matrix_block(a_p, bcs=bcs)
P.assemble()
b = fem.petsc.assemble_vector_block(L, a, bcs=bcs)

# Set near nullspace for pressure
null_vec = A.createVecLeft()
offset = V.dofmap.index_map.size_local * V.dofmap.index_map_bs
null_vec.array[offset:] = 1.0
null_vec.normalize()
nsp = PETSc.NullSpace().create(vectors=[null_vec])
assert nsp.test(A)
A.setNullSpace(nsp)

# Build IndexSets for each field (global dof indices for each field)
V_map = V.dofmap.index_map
Q_map = Q.dofmap.index_map
offset_u = V_map.local_range[0] * V.dofmap.index_map_bs + Q_map.local_range[0]
offset_p = offset_u + V_map.size_local * V.dofmap.index_map_bs
is_u = PETSc.IS().createStride(V_map.size_local * V.dofmap.index_map_bs, offset_u, 1, comm=PETSc.COMM_SELF)
is_p = PETSc.IS().createStride(Q_map.size_local, offset_p, 1, comm=PETSc.COMM_SELF)

# Create Krylov solver
ksp = PETSc.KSP().create(msh.comm)
ksp.setOperators(A, P)
ksp.setTolerances(rtol=1e-9)
ksp.setType("minres")
ksp.getPC().setType("fieldsplit")
ksp.getPC().setFieldSplitIS(
("u", is_u),
("p", is_p))

# Configure velocity and pressure sub KSPs
ksp_u, ksp_p = ksp.getPC().getFieldSplitSubKSP()
ksp_u.setType("preonly")
ksp_u.getPC().setType("gamg")
ksp_p.setType("preonly")
ksp_p.getPC().setType("jacobi")

# Monitor the convergence of the KSP
opts = PETSc.Options()
opts["ksp_monitor"] = None
opts["ksp_view"] = None
ksp.setFromOptions()

# Compute solution
x = A.createVecRight()
ksp.solve(b, x)


and error:

Traceback (most recent call last):
File "/home/fenics/shared/test.py", line 59, in <module>
File "/usr/local/dolfinx-real/lib/python3.10/dist-packages/dolfinx/fem/forms.py", line 166, in form
return _create_form(form)
File "/usr/local/dolfinx-real/lib/python3.10/dist-packages/dolfinx/fem/forms.py", line 163, in _create_form
return list(map(lambda sub_form: _create_form(sub_form), form))
File "/usr/local/dolfinx-real/lib/python3.10/dist-packages/dolfinx/fem/forms.py", line 163, in <lambda>
return list(map(lambda sub_form: _create_form(sub_form), form))
File "/usr/local/dolfinx-real/lib/python3.10/dist-packages/dolfinx/fem/forms.py", line 163, in _create_form
return list(map(lambda sub_form: _create_form(sub_form), form))
File "/usr/local/dolfinx-real/lib/python3.10/dist-packages/dolfinx/fem/forms.py", line 163, in <lambda>
return list(map(lambda sub_form: _create_form(sub_form), form))
File "/usr/local/dolfinx-real/lib/python3.10/dist-packages/dolfinx/fem/forms.py", line 161, in _create_form
return _form(form)
File "/usr/local/dolfinx-real/lib/python3.10/dist-packages/dolfinx/fem/forms.py", line 135, in _form
ufcx_form, module, code = jit.ffcx_jit(mesh.comm, form,
File "/usr/local/dolfinx-real/lib/python3.10/dist-packages/dolfinx/jit.py", line 56, in mpi_jit
return local_jit(*args, **kwargs)
File "/usr/local/dolfinx-real/lib/python3.10/dist-packages/dolfinx/jit.py", line 204, in ffcx_jit
r = ffcx.codegeneration.jit.compile_forms([ufl_object], parameters=p_ffcx, **p_jit)
File "/usr/local/lib/python3.10/dist-packages/ffcx/codegeneration/jit.py", line 168, in compile_forms
impl = _compile_objects(decl, forms, form_names, module_name, p, cache_dir,
File "/usr/local/lib/python3.10/dist-packages/ffcx/codegeneration/jit.py", line 232, in _compile_objects
_, code_body = ffcx.compiler.compile_ufl_objects(ufl_objects, prefix=module_name, parameters=parameters)
File "/usr/local/lib/python3.10/dist-packages/ffcx/compiler.py", line 97, in compile_ufl_objects
analysis = analyze_ufl_objects(ufl_objects, parameters)
File "/usr/local/lib/python3.10/dist-packages/ffcx/analysis.py", line 85, in analyze_ufl_objects
form_data = tuple(_analyze_form(form, parameters) for form in forms)
File "/usr/local/lib/python3.10/dist-packages/ffcx/analysis.py", line 85, in <genexpr>
form_data = tuple(_analyze_form(form, parameters) for form in forms)
File "/usr/local/lib/python3.10/dist-packages/ffcx/analysis.py", line 168, in _analyze_form
form_data = ufl.algorithms.compute_form_data(
File "/usr/local/lib/python3.10/dist-packages/ufl/algorithms/compute_form_data.py", line 407, in compute_form_data
check_form_arity(preprocessed_form, self.original_form.arguments(), complex_mode)  # Currently testing how fast this is
File "/usr/local/lib/python3.10/dist-packages/ufl/algorithms/check_arities.py", line 177, in check_form_arity
check_integrand_arity(itg.integrand(), arguments, complex_mode)
File "/usr/local/lib/python3.10/dist-packages/ufl/algorithms/check_arities.py", line 159, in check_integrand_arity
arg_tuples = map_expr_dag(rules, expr, compress=False)
File "/usr/local/lib/python3.10/dist-packages/ufl/corealg/map_dag.py", line 36, in map_expr_dag
result, = map_expr_dags(function, [expression], compress=compress,
File "/usr/local/lib/python3.10/dist-packages/ufl/corealg/map_dag.py", line 99, in map_expr_dags
r = handlers[v._ufl_typecode_](v, *[vcache[u] for u in v.ufl_operands])
File "/usr/local/lib/python3.10/dist-packages/ufl/algorithms/check_arities.py", line 63, in product
raise ArityMismatch("Multiplying expressions with overlapping form argument number {0}, argument is {1}.".format(x[0].number(), _afmt(x)))
File "/usr/local/lib/python3.10/dist-packages/ufl/algorithms/check_arities.py", line 19, in _afmt
return tuple("conj({0})".format(arg) if conj else str(arg)
File "/usr/local/lib/python3.10/dist-packages/ufl/algorithms/check_arities.py", line 20, in <genexpr>
for arg, conj in atuple)
TypeError: cannot unpack non-iterable bool object


If you truly mean relative tolerance, this would not be acceptable for me. I would not consider the solver to have converged and assume that I have not found a suitable approximation of the true solution. See for example Default absolute tolerance and relative tolerance - #4 by nate.

You’ve not written the block formulation correctly. The first row has three columns and the second row has two.

Yeah I thought the relative tolerance was too high, the solver gets stuck after a few iterations otherwise, I will experiment with alternate initial guesses and relaxation parameters and such.

regarding the variation form for a, should it be like this then:

a = form([[inner(dot(grad(u), u), v) * dx, inner(grad(u), grad(v)) * dx, inner(p, div(v)) * dx],
[inner(div(u), q) * dx, None, None]])


Perhaps familiarise yourself with what the block matrix representation of the discrete FEM discretisation of the weak formulation should look like. As a starting point perhaps you could take a look at Preconditioned iterative methods for Stokes flow problems arising in computational geodynamics - ScienceDirect. There may be better introductions which are less technical; however, this paper comes to mind.

Is it possible to solve this problem in transient using a backward difference approximation?

I’ve tried to adapt the tutorial example, but not sure how to integrate the poison-type problem into the solving process? I have this so far:

from mpi4py import MPI
from petsc4py import PETSc
import numpy as np
import tqdm.autonotebook

from dolfinx.fem import (
Constant,
Function,
FunctionSpace,
dirichletbc,
form,
locate_dofs_geometrical,
)
from dolfinx.fem.petsc import (
assemble_matrix,
assemble_vector,
apply_lifting,
create_vector,
set_bc,
create_matrix,
)
from dolfinx.io import XDMFFile, VTXWriter
from dolfinx.mesh import create_box, create_rectangle, create_unit_cube
from ufl import (
FiniteElement,
TestFunction,
TrialFunction,
VectorElement,
div,
dot,
dx,
inner,
lhs,
rhs,
cross,
curl,
)

mesh = create_box(
MPI.COMM_WORLD, [np.array([0, 0, 0]), np.array([1, 1, 1])], [10, 10, 10]
)
t = 0
T = 1
dt = 1 / 100  # Time step size
num_steps = int(T / dt)
k = Constant(mesh, PETSc.ScalarType(dt))
mu = Constant(mesh, PETSc.ScalarType(1))  # Dynamic viscosity
rho = Constant(mesh, PETSc.ScalarType(1))  # Density

v_cg2 = VectorElement("CG", mesh.ufl_cell(), 2)
s_cg1 = FiniteElement("CG", mesh.ufl_cell(), 1)
s2_cg1 = FiniteElement("CG", mesh.ufl_cell(), 1)
V = FunctionSpace(mesh, v_cg2)
Q = FunctionSpace(mesh, s_cg1)
Q2 = FunctionSpace(mesh, s2_cg1)

def walls(x):
walls_1 = np.logical_or(np.isclose(x[1], 0), np.isclose(x[1], 1))
walls_2 = np.logical_or(np.isclose(x[2], 0), np.isclose(x[2], 1))
return np.logical_or(walls_1, walls_2)

def hartmann_walls(x):
return np.logical_or(np.isclose(x[1], 0), np.isclose(x[1], 1))

def inlet(x):
return np.isclose(x[0], 0)

def outlet(x):
return np.isclose(x[0], 1)

def inlet_velocity(x):
values = np.zeros((mesh.geometry.dim, x.shape[1]), dtype=PETSc.ScalarType)
values[0] = 1

return values

u_noslip = np.array((0,) * mesh.geometry.dim, dtype=PETSc.ScalarType)
bc_noslip = dirichletbc(u_noslip, locate_dofs_geometrical(V, walls), V)

u_inlet = Function(V)
u_inlet.interpolate(inlet_velocity)
bc_inflow = dirichletbc(u_inlet, locate_dofs_geometrical(V, inlet))
bc_outflow = dirichletbc(PETSc.ScalarType(0), locate_dofs_geometrical(Q, outlet), Q)

bc_fully_conductive = dirichletbc(
PETSc.ScalarType(0), locate_dofs_geometrical(Q2, hartmann_walls), Q2
)

bcu = [bc_noslip, bc_inflow]
bcp = [bc_outflow]
bcphi = [bc_fully_conductive]

u = TrialFunction(V)
v = TestFunction(V)
u_ = Function(V)
u_.name = "u"
u_s = Function(V)
u_s2 = Function(V)
u_n = Function(V)
u_n1 = Function(V)
p = TrialFunction(Q)
q = TestFunction(Q)
p_ = Function(Q)
p_.name = "p"
p_n = Function(Q)
phi = TrialFunction(Q2)
q2 = TestFunction(Q2)
phi_ = Function(Q2)
phi_.name = "phi"
phi_n = Function(Q2)

B = Constant(mesh, PETSc.ScalarType((0, -1, 0)))
Ha = Constant(mesh, (PETSc.ScalarType(10)))
N = Ha**2

f = N * (
+ inner(u_s * dot(B, B), v) * dx
- inner(B * dot(B, u_s), v) * dx
)

F1 = rho / k * dot(u - u_n, v) * dx
F1 += inner(dot(1.5 * u_n - 0.5 * u_n1, 0.5 * nabla_grad(u + u_n)), v) * dx
F1 += 0.5 * mu * inner(grad(u + u_n), grad(v)) * dx - dot(p_, div(v)) * dx
a1 = form(lhs(F1))
L1 = form(rhs(F1))
A1 = create_matrix(a1)
b1 = create_vector(L1)

L2 = form(-rho / k * dot(div(u_s), q) * dx)
A2 = assemble_matrix(a2, bcs=bcp)
A2.assemble()
b2 = create_vector(L2)

F2 = (
- inner(dot(B, curl(u_s)) + dot(u_s, curl(B)), q2) * dx
)
a3 = form(lhs(F2))
L3 = form(rhs(F2))
A3 = create_matrix(a3)
b3 = create_vector(L3)

a4 = form(rho * dot(u, v) * dx)
L4 = form(rho * dot(u_s, v) * dx - k * dot(nabla_grad(p_n), v) * dx + f)
A4 = assemble_matrix(a4)
A4.assemble()
b4 = create_vector(L4)

# Solver for step 1
solver1 = PETSc.KSP().create(mesh.comm)
solver1.setOperators(A1)
solver1.setType(PETSc.KSP.Type.BCGS)
pc1 = solver1.getPC()
pc1.setType(PETSc.PC.Type.JACOBI)

# Solver for step 2
solver2 = PETSc.KSP().create(mesh.comm)
solver2.setOperators(A2)
solver2.setType(PETSc.KSP.Type.MINRES)
pc2 = solver2.getPC()
pc2.setType(PETSc.PC.Type.HYPRE)
pc2.setHYPREType("boomeramg")

# Solver for step 3
solver3 = PETSc.KSP().create(mesh.comm)
solver3.setOperators(A2)
solver3.setType(PETSc.KSP.Type.MINRES)
pc3 = solver3.getPC()
pc3.setType(PETSc.PC.Type.HYPRE)
pc3.setHYPREType("boomeramg")

# Solver for step 4
solver4 = PETSc.KSP().create(mesh.comm)
solver4.setOperators(A4)
solver4.setType(PETSc.KSP.Type.CG)
pc4 = solver4.getPC()
pc4.setType(PETSc.PC.Type.SOR)

results_folder = "Results/MHD_testing/"
u_xdmf = XDMFFile(mesh.comm, results_folder + "u.xdmf", "w")
u_xdmf.write_mesh(mesh)
u_xdmf.write_function(u_, t)
p_xdmf = XDMFFile(mesh.comm, results_folder + "p.xdmf", "w")
p_xdmf.write_mesh(mesh)
p_xdmf.write_function(p_, t)
phi_xdmf = XDMFFile(mesh.comm, results_folder + "phi.xdmf", "w")
phi_xdmf.write_mesh(mesh)
phi_xdmf.write_function(phi_, t)

progress = tqdm.autonotebook.tqdm(desc="Solving Navier-Stokes", total=num_steps)
for i in range(num_steps):
progress.update(1)
# Update current time step
t += dt

# Step 1: Tentative velocity step
A1.zeroEntries()
assemble_matrix(A1, a1, bcs=bcu)
A1.assemble()
with b1.localForm() as loc:
loc.set(0)
assemble_vector(b1, L1)
apply_lifting(b1, [a1], [bcu])
set_bc(b1, bcu)
solver1.solve(b1, u_s.vector)
u_s.x.scatter_forward()

# Step 2: Pressure corrrection step
with b2.localForm() as loc:
loc.set(0)
assemble_vector(b2, L2)
apply_lifting(b2, [a2], [bcp])
set_bc(b2, bcp)
solver2.solve(b2, p_n.vector)
p_n.x.scatter_forward()

p_.vector.axpy(1, p_n.vector)
p_.x.scatter_forward()

# Step 4: Phi correction step
with b3.localForm() as loc:
loc.set(0)
assemble_vector(b3, L3)
apply_lifting(b3, [a3], [bcphi])
set_bc(b3, bcphi)
solver3.solve(b3, phi_n.vector)
phi_n.x.scatter_forward()

phi_.vector.axpy(1, phi_n.vector)
phi_.x.scatter_forward()

# Step 3: Velocity correction step
with b4.localForm() as loc:
loc.set(0)
assemble_vector(b4, L4)
solver4.solve(b4, u_.vector)
u_.x.scatter_forward()

# Write solutions to file
u_xdmf.write_function(u_, t)
p_xdmf.write_function(p_, t)
phi_xdmf.write_function(phi_, t)

# Update variable with solution from this time step
with u_.vector.localForm() as loc_, u_n.vector.localForm() as loc_n, u_n1.vector.localForm() as loc_n1:
loc_n.copy(loc_n1)
loc_.copy(loc_n)

u_xdmf.close()
p_xdmf.close()
phi_xdmf.close()

`