[BUG] Mobile species defined in only one subdomain, but with a common interface for some other species

[jorgensd]

When defining a mobile species that lives only in a subdomain then festim tries to assign a concentration discontinuity interface condition on this species. Causing an error because that species doesn't exist on the other side.

In this case, an homogeneous neuman BC should be applied (no-flux). A simple way to do this is to just check for a given interface that the species lives in both subdomains. If not, then do nothing.

MWE

Run this code on fenicsx

my_model = F.HTransportProblemDiscontinuous()
my_model.mesh = F.Mesh1D(vertices=np.array([0.0, 1.0, 2.0, 3.0, 4.0]))
my_mat = F.Material(D_0=3, E_D=2, K_S_0=1, E_K_S=0, name="mat")

s0 = F.VolumeSubdomain1D(1, borders=[0.0, 2], material=my_mat)
s1 = F.VolumeSubdomain1D(2, borders=[2, 4], material=my_mat)
l0 = F.SurfaceSubdomain1D(1, x=0.0)
l1 = F.SurfaceSubdomain1D(2, x=4.0)
my_model.interfaces = [F.Interface(6, (s0, s1))]

my_model.temperature = 55
my_model.subdomains = [s0, s1, l0, l1]
my_model.surface_to_volume = {l0: s0, l1: s1}

my_model.species = [
    F.Species("H", subdomains=[s0]),
    F.Species("T", subdomains=[s0, s1], mobile=False),
]

filename = str(tmpdir.join("my_export.txt"))
my_export = F.VTXSpeciesExport(
    filename, field=my_model.species, subdomain=s0)
assert my_export.filename.suffix == ".bp"
my_model.exports = [my_export]
my_model.settings = F.Settings(atol=1, rtol=0.1)
my_model.settings.stepsize = F.Stepsize(initial_value=1)

my_model.initialise()