Cannot find common parent mesh in legacy FEniCS

General
1

Hello everyone,

When I run the following code of Stokes equations on a new machine:

from fenics import *

mesh = UnitSquareMesh(10, 10)
V = VectorFunctionSpace(mesh, "P", 2)
Q = FunctionSpace(mesh, "P", 1)
VQ = MixedFunctionSpace(V, Q)
(u, p) = TrialFunctions(VQ)
(v, q) = TestFunctions(VQ)
sol = Function(VQ)

mesh0 = Mesh(mesh)
V0 = VectorFunctionSpace(mesh0, "P", 2)
u0 = Function(V0)
u0.set_allow_extrapolation(True)

dx = Measure("dx", domain=mesh)
a = inner(grad(u), grad(v))*dx - p*div(v)*dx + q*div(u)*dx + Constant(0)*p*q*dx
L = dot(Constant((0, 1)), v)*dx + dot(u0, v)*dx
bc = DirichletBC(V, Constant((0, 0)), "on_boundary")

system = assemble_mixed_system(a == L, sol, bc)

I get the following error:

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
Cell In[7], line 21
     18 L = dot(Constant((0, 1)), v)*dx + dot(u0, v)*dx
     19 bc = DirichletBC(V, Constant((0, 0)), "on_boundary")
---> 21 system = assemble_mixed_system(a == L, sol, bc)

File /usr/lib/petsc/lib/python3/dist-packages/dolfin/fem/solving.py:478, in assemble_mixed_system(*args, **kwargs)
    476     # Create solver and call solve
    477     solver = MixedLinearVariationalSolver(problem)
--> 478     system = solver.assemble_system()
    479     return system
    480 else:

RuntimeError: Cannot find common parent mesh

After testing, I believe the error comes from the term dot(u0, v)*dx, as the functions u0 and u, v are considered unable to find a common parent mesh, even though their meshes are actually the same, and u0 has already been allowed to extrapolate. However, this error does not occur on my old machine.

Therefore, I suspect this might be related to the version of legacy FEniCS. The legacy FEniCS version for Ubuntu 24.04.1 LTS on my new machine is

fenics-dijitso:     2019.2.0.dev0
fenics-dolfin:      2019.2.0.64.dev0
fenics-ffc:         2019.2.0.dev0
fenics-fiat:        2019.2.0.dev0
fenics-ufl-legacy:  2022.3.0

while the legacy FEniCS version for Ubuntu 24.04.1 LTS on my old machine is

fenics-dijitso:     2019.2.0.dev0
fenics-dolfin:      2019.2.0.dev0
fenics-ffc:         2019.2.0.dev0
fenics-fiat:        2019.2.0.dev0
fenics-ufl-legacy:  2022.2.0

Is there any way to fix the error in the code above, or install a specific version of legacy FEniCS? I would appreciate any help.

2

Why are you using assemble_mixed_system, and not just assemble for this?

Why are you making a copy of the mesh?
Assemble_mixed_system was made to support MeshView, with mixed function spaces, not what you are trying to do above.

3

Thank you very much for your response.

Could you please explain this with some example code? Do you mean assembling the matrices and vectors of a == L separately and then combining them into a complete linear system? For example:

A11 = assemble(inner(grad(u), grad(v))*dx)
A12 = assemble(-p*div(v)*dx)
A21 = assemble(q*div(u)*dx)
A22 = assemble(Constant(0)*p*q*dx)
b1 = assemble(dot(Constant((0, 1)), v)*dx + dot(u0, v)*dx)

However, a warning message will also appear when assembling b1:

*** Warning: assemble() with forms involving integrands belonging to different meshes might be inappropriate.
 If you are using MeshView, please use assemble_mixed() instead

In the code, I intend to use u0 to represent any function from another mesh, which may appear in some iterations related to moving meshes. The mesh0 can also be any mesh, not necessarily a copy of mesh. The code above is a MWE of the issue I’m encountering. How should I modify my code to make it run successfully?

Even if I replace assemble_mixed_system(a == L, sol, bc) with solve(a == L, sol, bc), I still get an error message about

RuntimeError: Cannot find common parent mesh

I noticed that legacy DOLFIN seemed to have some major fixes last year, and the above code runs successfully in the version of fenics-dolfin: 2019.2.0.dev0 but throws an error in the version of fenics-dolfin: 2019.2.0.64.dev0. Could this issue be related to the latest updates in legacy FEniCS?