call bounding_box_tree() in initialise()

[RemDelaporteMathurin]

Proposed changes

This fixes #498 by calling mesh.bounding_box_tree() in Simulation.initialise()

This was suggested by the FEniCS community to solve the processes communication issues.

I tested the fix with this MWE:

import festim as F
import fenics as f

my_model = F.Simulation(log_level=20)
mesh_size = 20
mesh = f.UnitSquareMesh(mesh_size, mesh_size)
material_tag = 1
volume_markers = f.MeshFunction("size_t", mesh, mesh.topology().dim(), material_tag)
surface_markers = f.MeshFunction("size_t", mesh, 1, 0)

boundary_left = f.CompiledSubDomain("on_boundary && near(x[0], L, tol)", tol=1e-14, L=0)
boundary_left.mark(surface_markers, 1)
my_model.mesh = F.Mesh(
    mesh=mesh, volume_markers=volume_markers, surface_markers=surface_markers
)
my_model.materials = F.Materials(
    [
        F.Material(
            id=material_tag,
            D_0=1,
            E_D=1,
            S_0=1,
            E_S=1,
        ),
    ]
)
my_model.T = F.Temperature(value=300)
my_model.boundary_conditions = [
    F.DirichletBC(surfaces=1, value=1e20, field=0),
]
my_model.settings = F.Settings(
    transient=False,
    absolute_tolerance=1e12,
    relative_tolerance=1e-08,
    chemical_pot=True,
)
my_model.initialise()
my_model.run()

mpirun -np 2 python3 test.py

Before the fix the solver would just hang.

Now the problem is solved correctly:

Process 0: Computed global bounding box tree with 3 boxes.
Process 1: Computed global bounding box tree with 3 boxes.
Process 0: No Jacobian form specified for nonlinear variational problem.
Process 0: Differentiating residual form F to obtain Jacobian J = F'.
Process 1: No Jacobian form specified for nonlinear variational problem.
Process 1: Differentiating residual form F to obtain Jacobian J = F'.
Process 0: Solving nonlinear variational problem.
Process 1: Solving nonlinear variational problem.
  Process 0: Newton iteration 0: r (abs) = 0.000e+00 (tol = 1.000e-10) r (rel) = -nan (tol = 1.000e-09)
  Process 0: Newton solver finished in 0 iterations and 0 linear solver iterations.
Process 0: No Jacobian form specified for nonlinear variational problem.
Process 0: Differentiating residual form F to obtain Jacobian J = F'.
Process 1: No Jacobian form specified for nonlinear variational problem.
Process 1: Differentiating residual form F to obtain Jacobian J = F'.
Process 0: Solving nonlinear variational problem.
Process 1: Solving nonlinear variational problem.
  Process 0: Newton iteration 0: r (abs) = 3.536e-02 (tol = 1.000e-10) r (rel) = 1.000e+00 (tol = 1.000e-09)
  Process 0: Newton iteration 1: r (abs) = 1.482e-18 (tol = 1.000e-10) r (rel) = 4.191e-17 (tol = 1.000e-09)
  Process 0: Newton solver finished in 1 iterations and 1 linear solver iterations.
Process 0: No Jacobian form specified for nonlinear variational problem.
Process 0: Differentiating residual form F to obtain Jacobian J = F'.
Process 1: No Jacobian form specified for nonlinear variational problem.
Process 1: Differentiating residual form F to obtain Jacobian J = F'.
Process 0: Solving nonlinear variational problem.
Process 1: Solving nonlinear variational problem.
  Process 0: Newton iteration 0: r (abs) = 3.241e-19 (tol = 1.000e-10) r (rel) = 1.000e+00 (tol = 1.000e-09)
  Process 0: Newton solver finished in 0 iterations and 0 linear solver iterations.
Process 0: Solving nonlinear variational problem.
Process 1: Solving nonlinear variational problem.
  Process 0: Newton iteration 0: r (abs) = 8.356e+37 (tol = 1.000e+12) r (rel) = 1.000e+00 (tol = 1.000e-08)
  Process 0: Newton iteration 1: r (abs) = 1.562e+22 (tol = 1.000e+12) r (rel) = 1.869e-16 (tol = 1.000e-08)
  Process 0: Newton solver finished in 1 iterations and 1 linear solver iterations.
Process 0: Solving nonlinear variational problem.
Process 1: Solving nonlinear variational problem.
  Process 0: Newton iteration 0: r (abs) = 0.000e+00 (tol = 1.000e-10) r (rel) = -nan (tol = 1.000e-10)
  Process 0: Newton solver finished in 0 iterations and 0 linear solver iterations.
Defining initial values
Defining variational problem
Defining source terms
Defining boundary conditions
Solving steady state problem...
Solved problem in 0.00 s
Defining initial values
Defining variational problem
Defining source terms
Defining boundary conditions
Solving steady state problem...
Solved problem in 0.00 s

Types of changes

What types of changes does your code introduce to FESTIM?

• Bugfix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Code refactoring
• Documentation Update (if none of the other choices apply)
• New tests

Checklist

• Black formatted
• Unit tests pass locally with my changes
• I have added tests that prove my fix is effective or that my feature works
• I have added necessary documentation (if appropriate)

[codecov]

Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (5e71059) 98.84% compared to head (65c6119) 98.84%.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #571   +/-   ##
=======================================
  Coverage   98.84%   98.84%           
=======================================
  Files          56       56           
  Lines        2072     2073    +1     
=======================================
+ Hits         2048     2049    +1     
  Misses         24       24           

Files Changed	Coverage Δ
festim/generic_simulation.py	100.00% <100.00%> (ø)

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[RemDelaporteMathurin]

@jhdark @ehodille have been testing this fix locally and it seems to work well enough.
We can merge this!