Merge pull request #617 from jhdark/multispecies_support

Multispecies support

festim/__init__.py

@@ -30,7 +30,7 @@
 
 from .settings import Settings
 
-from .species import Species, Trap, ImplicitSpecies
+from .species import Species, Trap, ImplicitSpecies, find_species_from_name
 
 from .subdomain.surface_subdomain import SurfaceSubdomain1D
 from .subdomain.volume_subdomain import VolumeSubdomain1D

festim/boundary_conditions/dirichlet_bc.py

@@ -69,6 +69,7 @@ def define_surface_subdomain_dofs(self, facet_meshtags, mesh, function_space):
         """
         bc_facets = facet_meshtags.find(self.subdomain.id)
         bc_dofs = fem.locate_dofs_topological(function_space, mesh.fdim, bc_facets)
+
         return bc_dofs
 
     def create_value(
@@ -98,7 +99,7 @@ def create_value(
             if "t" in arguments and "x" not in arguments and "T" not in arguments:
                 # only t is an argument
                 self.value_fenics = F.as_fenics_constant(
-                    mesh=mesh, value=self.value(t=t.value)
+                    mesh=mesh, value=self.value(t=float(t))
                 )
             else:
                 self.value_fenics = fem.Function(function_space)
@@ -118,25 +119,6 @@ def create_value(
                 )
                 self.value_fenics.interpolate(self.bc_expr)
 
-    def create_formulation(self, dofs, function_space):
-        """Applies the boundary condition
-        Args:
-            dofs (numpy.ndarray): the degrees of freedom of surface facets
-            function_space (dolfinx.fem.FunctionSpace): the function space
-        """
-        if isinstance(self.value_fenics, fem.Function):
-            form = fem.dirichletbc(
-                value=self.value_fenics,
-                dofs=dofs,
-            )
-        else:
-            form = fem.dirichletbc(
-                value=self.value_fenics,
-                dofs=dofs,
-                V=function_space,
-            )
-        return form
-
     def update(self, t):
         """Updates the boundary condition value
 

festim/exports/vtx.py

@@ -48,16 +48,16 @@ def field(self):
     @field.setter
     def field(self, value):
         # check that field is festim.Species or list of festim.Species
-        if not isinstance(value, F.Species) and not isinstance(value, list):
+        if not isinstance(value, (F.Species, str)) and not isinstance(value, list):
             raise TypeError(
-                "field must be of type festim.Species or list of festim.Species"
+                "field must be of type festim.Species or str or a list of festim.Species or str"
             )
         # check that all elements of list are festim.Species
         if isinstance(value, list):
             for element in value:
-                if not isinstance(element, F.Species):
+                if not isinstance(element, (F.Species, str)):
                     raise TypeError(
-                        "field must be of type festim.Species or list of festim.Species"
+                        "field must be of type festim.Species or str or a list of festim.Species or str"
                     )
         # if field is festim.Species, convert to list
         if not isinstance(value, list):
@@ -72,7 +72,10 @@ def define_writer(self, comm: mpi4py.MPI.Intracomm) -> None:
             comm (mpi4py.MPI.Intracomm): the MPI communicator
         """
         self.writer = VTXWriter(
-            comm, self.filename, [field.solution for field in self.field], "BP4"
+            comm,
+            self.filename,
+            [field.post_processing_solution for field in self.field],
+            "BP4",
         )
 
     def write(self, t: float):

festim/exports/xdmf.py

@@ -39,16 +39,16 @@ def field(self):
     @field.setter
     def field(self, value):
         # check that field is festim.Species or list of festim.Species
-        if not isinstance(value, F.Species) and not isinstance(value, list):
+        if not isinstance(value, (F.Species, str)) and not isinstance(value, list):
             raise TypeError(
-                "field must be of type festim.Species or list of festim.Species"
+                "field must be of type festim.Species or str or a list of festim.Species or str"
             )
         # check that all elements of list are festim.Species
         if isinstance(value, list):
             for element in value:
-                if not isinstance(element, F.Species):
+                if not isinstance(element, (F.Species, str)):
                     raise TypeError(
-                        "field must be of type festim.Species or list of festim.Species"
+                        "field must be of type festim.Species or str or a list of festim.Species or str"
                     )
         # if field is festim.Species, convert to list
         if not isinstance(value, list):
@@ -71,4 +71,4 @@ def write(self, t: float):
             t (float): the time of export
         """
         for field in self.field:
-            self.writer.write_function(field.solution, t)
+            self.writer.write_function(field.post_processing_solution, t)