tds_example

tds_example.py

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+import festim as F
+import numpy as np
+
+L = 3e-06
+vertices = np.linspace(0, L, num=1000)
+
+my_mesh = F.Mesh1D(vertices)
+
+my_model = F.HydrogenTransportProblem()
+my_model.mesh = my_mesh
+
+my_mat = F.Material(D_0=1.9e-7, E_D=0.2, name="my_mat")
+my_subdomain = F.VolumeSubdomain1D(id=1, borders=[0, L], material=my_mat)
+left_surface = F.SurfaceSubdomain1D(id=1, x=0)
+right_surface = F.SurfaceSubdomain1D(id=2, x=L)
+my_model.subdomains = [
+    my_subdomain,
+    left_surface,
+    right_surface,
+]
+
+mobile_H = F.Species("H")
+trapped_H = F.Species("trapped_H", mobile=False)
+empty_trap = F.ImplicitSpecies(n=1e-3 * 6.3e28, others=[trapped_H], name="empty_trap")
+my_model.species = [mobile_H, trapped_H]
+
+my_model.reactions = [
+    F.Reaction(
+        p_0=1e13,
+        E_p=0.87,
+        k_0=3.8e-17,
+        E_k=0.2,
+        reactant1=mobile_H,
+        reactant2=empty_trap,
+        product=trapped_H,
+    )
+]
+
+from ufl import conditional, lt
+
+implantation_time = 100
+implantation_temp = 300
+temperature_ramp = 8  # K/s
+
+
+def temp_function(t):
+    ramping_temperature = implantation_temp + temperature_ramp * (t - implantation_time)
+    return conditional(lt(t, implantation_time), implantation_temp, ramping_temperature)
+
+
+my_model.temperature = temp_function
+
+my_model.boundary_conditions = [
+    F.DirichletBC(subdomain=right_surface, value=0, species="H"),
+    F.DirichletBC(subdomain=left_surface, value=1e12, species=mobile_H),
+]
+my_model.exports = [
+    F.VTXExport("mobile_concentration_h.bp", field=mobile_H),  # produces 0 in file
+    F.VTXExport("trapped_concentration_h.bp", field=trapped_H),  # produces 0 in file
+    F.XDMFExport("mobile_concentration_h.xdmf", field=mobile_H),
+    F.XDMFExport("trapped_concentration_h.xdmf", field=trapped_H),
+]
+
+my_model.settings = F.Settings(
+    atol=1e10,
+    rtol=1e-10,
+    max_iterations=30,
+    final_time=200,
+)
+
+my_model.settings.stepsize = F.Stepsize(initial_value=1 / 20)
+
+my_model.initialise()
+
+from petsc4py import PETSc
+
+my_model.solver.convergence_criterion = "incremental"
+ksp = my_model.solver.krylov_solver
+opts = PETSc.Options()
+option_prefix = ksp.getOptionsPrefix()
+opts[f"{option_prefix}ksp_type"] = "cg"
+opts[f"{option_prefix}pc_type"] = "gamg"
+opts[f"{option_prefix}pc_factor_mat_solver_type"] = "mumps"
+ksp.setFromOptions()
+
+times, flux_values = my_model.run()