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.InitialCondition(
        value=F.read_function_from_file(
            filename=filename, name="my_function", timestamp=0.2
        ),
        species=H,
    )
]
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 92.30769% with 3 lines in your changes missing coverage. Please review.

Project coverage is 96.08%. Comparing base (d061987) to head (67ae917).
Report is 248 commits behind head on fenicsx.

Files with missing lines	Patch %	Lines
src/festim/hydrogen_transport_problem.py	90.00%	2 Missing ⚠️
src/festim/initial_condition.py	92.85%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           fenicsx     #952      +/-   ##
===========================================
- Coverage    96.14%   96.08%   -0.07%     
===========================================
  Files           46       46              
  Lines         2567     2604      +37     
===========================================
+ Hits          2468     2502      +34     
- Misses          99      102       +3     

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[RemDelaporteMathurin]

@jhdark just updated the branch to pass with nightly, ready for review

[jhdark]

Looks like a great start, could do with some more docs.

But also is it worth making a base class InitialValueFromFile, then adding another class for reading a temperature field from a file? Doesn't look like it would be too difficult to add, but would obviously increase the size of the PR.

Plus, we could consider either some checks to make sure the mesh in the file is the same as the one defined in the problem, or could maybe add some functionality to interpolate between meshes?

[jhdark]

InitialCondition should support a fem.Function as value and then we can just bundle this in a one-liner. comm could also be an argument for full flexibility

import festim as F


def read_function_from_file(filename, name, timestamp, family="P", order=1):
    import dolfinx.fem as fem
    import mpi4py.MPI as MPI
    import adios4dolfinx

    mesh_in = adios4dolfinx.read_mesh(filename, MPI.COMM_WORLD)
    V_in = fem.functionspace(mesh_in, (family, order))
    u_in = fem.Function(V_in)
    adios4dolfinx.read_function(
        filename=filename,
        u=u_in,
        name=name,
        time=timestamp,
    )
    return u_in


my_model = F.HydrogenTransportProblem()

H = F.Species("H")
my_model.species = [H]

my_model.initial_conditions = [
    F.InitialCondition(
        value=read_function_from_file("filename.bp", "name in file", 100), species=H
    )
]

[RemDelaporteMathurin]

@jhdark I modified the PR according to our discussion and added some more documentation