removed special class for species

Author: RemDelaporteMathurin

src/festim/__init__.py

@@ -51,7 +51,7 @@
 from .reaction import Reaction
 from .settings import Settings
 from .source import HeatSource, ParticleSource, SourceBase
-from .species import ImplicitSpecies, Species, find_species_from_name, SpeciesChangeVar
+from .species import ImplicitSpecies, Species, find_species_from_name
 from .stepsize import Stepsize
 from .subdomain.interface import Interface
 from .subdomain.surface_subdomain import SurfaceSubdomain, find_surface_from_id

src/festim/hydrogen_transport_problem.py

@@ -861,14 +861,17 @@ def initialise(self):
 
         self.create_implicit_species_value_fenics()
 
+        for species in self.species:
+            species.change_var = True
+
         self.define_temperature()
         self.define_boundary_conditions()
         self.create_source_values_fenics()
         self.create_flux_values_fenics()
         self.create_initial_conditions()
         self.create_formulation()
         self.create_solver()
-        self.override_post_processing_solution()  # NOTE this is the only difference with parent class
+        self.override_post_processing_solution()
         self.initialise_exports()
 
     def create_formulation(self):

src/festim/species.py

@@ -65,6 +65,7 @@ class Species:
     subdomain_to_post_processing_solution: dict
     subdomain_to_collapsed_function_space: dict
     subdomain_to_function_space: dict
+    change_var: bool = False
 
     def __init__(self, name: str = None, mobile=True, subdomains=None) -> None:
         self.name = name
@@ -92,7 +93,14 @@ def __str__(self) -> str:
 
     @property
     def concentration(self):
-        return self.solution
+        if self.change_var:
+            return self._concentration
+        else:
+            return self.solution
+
+    @concentration.setter
+    def concentration(self, value):
+        self._concentration = value
 
     @property
     def legacy(self) -> bool:
@@ -225,13 +233,3 @@ def find_species_from_name(name: str, species: list):
         if spe.name == name:
             return spe
     raise ValueError(f"Species {name} not found in list of species")
-
-
-class SpeciesChangeVar(Species):
-    @property
-    def concentration(self):
-        return self._concentration
-
-    @concentration.setter
-    def concentration(self, value):
-        self._concentration = value

test/system_tests/test_multi_material_change_of_var.py

@@ -103,8 +103,8 @@ def test_run():
         right_surface,
     ]
 
-    H = F.SpeciesChangeVar("H", mobile=True)
-    trapped_H = F.SpeciesChangeVar("H_trapped", mobile=False)
+    H = F.Species("H", mobile=True)
+    trapped_H = F.Species("H_trapped", mobile=False)
     empty_trap = F.ImplicitSpecies(n=0.5, others=[trapped_H])
 
     my_model.species = [H, trapped_H]
@@ -193,7 +193,7 @@ def c_exact_bot_np(x):
         bottom_surface,
     ]
 
-    H = F.SpeciesChangeVar("H", mobile=True)
+    H = F.Species("H", mobile=True)
 
     my_model.species = [H]