Checkpointing

[RemDelaporteMathurin]

Proposed changes

Contributes to #946 for the mono-material case. Checkpointing (ie. reading a function from a file) is implemented by leveraging adios4dolfinx (thanks @jorgensd for this!).

As it doesn't support submeshes for now, this only works for the non-mixed domain approach in the HydrogenTransportProblem class

Usage:

import festim as F

import dolfinx
import adios4dolfinx
import mpi4py.MPI as MPI

# build initial condition
mesh = dolfinx.mesh.create_unit_square(
    MPI.COMM_WORLD, nx=10, ny=10, cell_type=dolfinx.cpp.mesh.CellType.quadrilateral
)
el = "P"
degree = 1
V = dolfinx.fem.functionspace(mesh, (el, degree))


def f(x):
    return x[1] ** 2 + 2 * x[0] ** 2


u_ref = dolfinx.fem.Function(V)
u_ref.interpolate(f)
filename = "initial_condition.bp"

adios4dolfinx.write_mesh(filename, mesh)
adios4dolfinx.write_function(filename, u_ref, name="my_function", time=0.2)

# create problem
my_problem = F.HydrogenTransportProblem()
H = F.Species("H")
my_problem.species = [H]
my_problem.mesh = F.Mesh(mesh)
my_problem.initial_conditions = [
    F.InitialConcentrationFromFile(
        filename=filename, species=H, name="my_function", timestamp=0.2
    )
]
mat = F.Material(D_0=1, E_D=0.1, name="dummy_mat")
my_problem.subdomains = [F.VolumeSubdomain(id=0, material=mat)]

my_problem.temperature = 300

my_problem.exports = [
    F.VTXSpeciesExport(
        filename="H.bp",
        field=H,
        subdomain=my_problem.subdomains[0],
        checkpoint=False,
    ),
    F.VTXSpeciesExport(
        filename="H_for_checkpoint.bp",
        field=H,
        subdomain=my_problem.subdomains[0],
        checkpoint=True,
    )
]

my_problem.settings = F.Settings(atol=1e-10, rtol=1e-10, final_time=100)
my_problem.settings.stepsize = F.Stepsize(1)
my_problem.initialise()
my_problem.run()

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

Attention: Patch coverage is 96.07843% with 2 lines in your changes missing coverage. Please review.

Project coverage is 96.00%. Comparing base (96d62ff) to head (bf6be2a).

Files with missing lines	Patch %	Lines
src/festim/hydrogen_transport_problem.py	93.10%	2 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           fenicsx     #952      +/-   ##
===========================================
- Coverage    96.02%   96.00%   -0.02%     
===========================================
  Files           45       45              
  Lines         2439     2478      +39     
===========================================
+ Hits          2342     2379      +37     
- Misses          97       99       +2     

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