fix tests

src/festim/boundary_conditions/__init__.py

@@ -1,4 +1,11 @@
 from .dirichlet_bc import FixedConcentrationBC, FixedTemperatureBC
 from .flux_bc import HeatFluxBC, ParticleFluxBC
+from .surface_reaction import SurfaceReactionBC
 
-__all__ = ["FixedConcentrationBC", "FixedTemperatureBC", "ParticleFluxBC", "HeatFluxBC"]
+__all__ = [
+    "FixedConcentrationBC",
+    "FixedTemperatureBC",
+    "ParticleFluxBC",
+    "SurfaceReactionBC",
+    "HeatFluxBC",
+]

src/festim/hydrogen_transport_problem.py

@@ -508,13 +508,26 @@ def assign_functions_to_species(self):
             spe.test_function = sub_test_functions[idx]
 
     def define_boundary_conditions(self):
+        # @jhdark this all_bcs could be a property
+        # I just don't want to modify self.boundary_conditions
+
+        # create all_bcs which includes all flux bcs from SurfaceReactionBC
+        all_bcs = self.boundary_conditions.copy()
         for bc in self.boundary_conditions:
-            if isinstance(bc, boundary_conditions.FixedConcentrationBC):
-                if isinstance(bc.species, str):
-                    # if name of species is given then replace with species object
-                    bc.species = _species.find_species_from_name(
-                        bc.species, self.species
-                    )
+            if isinstance(bc, boundary_conditions.SurfaceReactionBC):
+                all_bcs += bc.flux_bcs
+                all_bcs.remove(bc)
+
+        for bc in all_bcs:
+            if isinstance(bc.species, str):
+                # if name of species is given then replace with species object
+                bc.species = _species.find_species_from_name(bc.species, self.species)
+            if isinstance(bc, boundary_conditions.ParticleFluxBC):
+                bc.create_value_fenics(
+                    mesh=self.mesh.mesh,
+                    temperature=self.temperature_fenics,
+                    t=self.t,
+                )
 
         super().define_boundary_conditions()
 
@@ -684,6 +697,13 @@ def create_formulation(self):
                     * bc.species.test_function
                     * self.ds(bc.subdomain.id)
                 )
+            if isinstance(bc, boundary_conditions.SurfaceReactionBC):
+                for flux_bc in bc.flux_bcs:
+                    self.formulation -= (
+                        flux_bc.value_fenics
+                        * flux_bc.species.test_function
+                        * self.ds(flux_bc.subdomain.id)
+                    )
 
         # check if each species is defined in all volumes
         if not self.settings.transient:
@@ -717,8 +737,15 @@ def update_time_dependent_values(self):
             self.temperature_fenics.interpolate(self.temperature_expr)
 
         for bc in self.boundary_conditions:
-            if bc.temperature_dependent:
-                bc.update(t=t)
+            if isinstance(
+                bc,
+                (
+                    boundary_conditions.FixedConcentrationBC,
+                    boundary_conditions.ParticleFluxBC,
+                ),
+            ):
+                if bc.temperature_dependent:
+                    bc.update(t=t)
 
         for source in self.sources:
             if source.temperature_dependent:

test/system_tests/test_surface_reactions.py

@@ -331,6 +331,8 @@ def test_pressure_varies_in_time():
 
     expected_flux_after_pressure = -2 * k_d * pressure
     computed_flux_after_pressure = flux_as_array[time_as_array > t_pressure]
+    print(computed_flux_after_pressure)
+    print(expected_flux_after_pressure)
     assert np.allclose(
         computed_flux_after_pressure, expected_flux_after_pressure, rtol=1e-2
     )

test/test_h_transport_problem.py

@@ -1197,7 +1197,7 @@ def test_create_flux_values_fenics_multispecies():
     my_model.define_temperature()
 
     # RUN
-    my_model.define_boundary_conditions()
+    my_model.create_flux_values_fenics()
 
     # TEST
     assert np.isclose(my_model.boundary_conditions[0].value_fenics.value, 5)