festim-dev/FESTIM

Describe the bug Running a transient sim with an OutflowBC raises an AttributeError 'OutflowBC' object has no attribute 'time_dependent'. To Reproduce import numpy as np from dolfinx import fem, mesh as dmesh from mpi4py import MPI import festim as F m = dmesh.create_unit_interval(MPI.COMM_WORLD, 20) left = F.SurfaceSubdomain1D(id=1, x=0.0) right = F.SurfaceSubdomain1D(id=2, x=1.0) vol = F.VolumeSubdomain1D( id=1, borders=[0.0, 1.0], material=F.Material(D_0=1.0, E_D=0.0) ) H = F.Species("H") W = fem.functionspace(m, ("DG", 0, (1,))) v = fem.Function(W) v.x.array[:] = 1.0 model = F.HydrogenTransportProblem( mesh=F.Mesh(m), subdomains=[vol, left, right], species=[H], temperature=500.0, boundary_conditions=[ F.FixedConcentrationBC(subdomain=left, value=1.0, species=H), F.OutflowBC(subdomain=right, species=H), ], drift_terms=[F.AdvectionTerm(velocity=v, subdomain=vol, species=H)], settings=F.Settings( atol=1e-10, rtol=1e-10, tra

(generated by Claude because I didn't have time, will go back to it later) Summary Flagging a convention issue rather than a bug: SurfaceReactionBC has no way to express the statistical degeneracy of a mixed isotopologue channel, and the natural way to write H + D <-> HD is silently inconsistent with detailed balance. Same root cause as the InterfaceReaction discussion in #1222: the rate is the plain product of reactant concentrations, and stoichiometry is expressed only by repeating a species in reactant. The physics For recombination, the forward step carries a degeneracy that the reverse step does not: there are two ways to pick an (H, D) pair to recombine, but an HD molecule dissociates only one way. Writing the homonuclear channel as k_r c_H^2 absorbs the one-half that avoids double counting identical pairs, so consistency requires k_r(HD) = 2 k_r(HH) with equal k_d. This is what reproduces the classical P_HD^2 / (P_H2 P_D2) = 4, i.e. H2 : HD : D2 = 1 : 2 : 1 at equal H and D. No

After this is released: FEniCS/dolfinx#4172 we will be able to move the import of transfer_meshtags_to_submesh from scifem to dolfinx

For very large simulations, even with a rtol=1e-5 the export will be exported very far from the desired export time. Consider the following: import numpy as np import festim as F model = F.HydrogenTransportProblem() model.mesh = F.Mesh1D(np.linspace(0, 1, 10)) mat = F.Material(D_0=1.0, E_D=0.0) vol = F.VolumeSubdomain1D(id=1, material=mat, borders=[0, 1]) model.subdomains = [vol] H = F.Species("H") model.species = [H] model.temperature = 300 model.settings = F.Settings(atol=1e-12, rtol=1e-12, final_time=0.9e8 + 20) model.settings.stepsize = F.Stepsize(1, milestones=[0.9e8]) model.exports = [ F.Profile1DExport(H, subdomain=vol, times=[0.9e8]), ] model.initialise() model.t.value = 0.9e8 - 10 model.run() assert abs(model.exports[0].t[0] - 0.9e8) < 1e-12, ( "time of export is far from the expected" ) proposed solution expose rtol and atol in is_it_time_to_export as an argument of F.Settings that will be used for all exports Tagging @AdriaLlealS