first implementation of decay on mobile and traps

festim/__init__.py

@@ -90,6 +90,7 @@
 
 from .sources.source import Source
 from .sources.source_implantation_flux import ImplantationFlux
+from .sources.radioactive_decay import RadioactiveDecay
 
 from .materials.material import Material
 from .materials.materials import Materials

festim/concentration/mobile.py

@@ -1,4 +1,4 @@
-from festim import Concentration, FluxBC, k_B, R
+from festim import Concentration, FluxBC, k_B, R, RadioactiveDecay
 from fenics import *
 import sympy as sp
 
@@ -132,6 +132,9 @@ def create_source_form(self, dx):
                 volumes = source.volume
             else:
                 volumes = [source.volume]
+            if isinstance(source, RadioactiveDecay):
+                source.value = -source.form(self.mobile_concentration())
+
             for volume in volumes:
                 F_source += -source.value * self.test_function * dx(volume)
             if isinstance(source.value, (Expression, UserExpression)):

festim/concentration/traps/trap.py

@@ -1,4 +1,4 @@
-from festim import Concentration, k_B, Material, Theta
+from festim import Concentration, k_B, Material, Theta, RadioactiveDecay
 from fenics import *
 import sympy as sp
 import numpy as np
@@ -204,6 +204,8 @@ def create_source_form(self, dx):
             dx (fenics.Measure): the dx measure of the sim
         """
         for source in self.sources:
+            if isinstance(source, RadioactiveDecay):
+                source.value = -source.form(self.solution)
             self.F_source = -source.value * self.test_function * dx(source.volume)
             self.F += self.F_source
             self.sub_expressions.append(source.value)

festim/generic_simulation.py

@@ -188,7 +188,19 @@ def attribute_source_terms(self):
 
         # set sources
         for source in self.sources:
-            field_to_object[source.field].sources.append(source)
+            if isinstance(source, festim.RadioactiveDecay) and source.field == "all":
+                # this could be refactored if sources accept several fields
+                # (e.g. festim.Source(field=["0", "T"]))
+                # for field in source.field:
+                #    field_to_object[field].sources.append(source)
+
+                # create list of all unique festim.Concentration objects in field_to_object
+                # and assign source to each of them
+                for obj in set(field_to_object.values()):
+                    if isinstance(obj, festim.Concentration):
+                        obj.sources.append(source)
+            else:
+                field_to_object[source.field].sources.append(source)
 
     def attribute_boundary_conditions(self):
         """Assigns boundary_conditions to mobile and T"""

festim/sources/radioactive_decay.py

@@ -0,0 +1,10 @@
+from festim import Source
+
+
+class RadioactiveDecay(Source):
+    def __init__(self, decay_constant, volume, field="all") -> None:
+        self.decay_constant = decay_constant
+        super().__init__(value=None, volume=volume, field=field)
+
+    def form(self, concentration):
+        return self.decay_constant * concentration