Replace "Nothing" depletion targets with None

This change is more declarative and mitigates any changes
that there are errors if a target is Nothing, None, or their lower
cased varieties. This is helpful as the depletion chain gets
reduced down and we want to keep total removal rates for
isotopes that are present, but their products don't exist
in the new reduced chain.

Chain.form_matrix has been updated to handle targets that
are None for non-fission reactions and for decay reactions.
Documentation for ReactionTuple and DecayTuple have been
updated to indicate that the target attribute could be None.

openmc/deplete/chain.py

@@ -500,7 +500,7 @@ class Chain(object):
                 # Gain
                 for _, target, branching_ratio in nuc.decay_modes:
                     # Allow for total annihilation for debug purposes
-                    if target != 'Nothing':
+                    if target is not None:
                         branch_val = branching_ratio * decay_constant
 
                         if branch_val != 0.0:
@@ -525,17 +525,16 @@ class Chain(object):
                             matrix[i, i] -= path_rate
 
                     # Gain term; allow for total annihilation for debug purposes
-                    if target != 'Nothing':
-                        if r_type != 'fission':
-                            if path_rate != 0.0:
-                                k = self.nuclide_dict[target]
-                                matrix[k, i] += path_rate * br
-                        else:
-                            for product, y in fission_yields[nuc.name].items():
-                                yield_val = y * path_rate
-                                if yield_val != 0.0:
-                                    k = self.nuclide_dict[product]
-                                    matrix[k, i] += yield_val
+                    if r_type != 'fission':
+                        if target is not None and path_rate != 0.0:
+                            k = self.nuclide_dict[target]
+                            matrix[k, i] += path_rate * br
+                    else:
+                        for product, y in fission_yields[nuc.name].items():
+                            yield_val = y * path_rate
+                            if yield_val != 0.0:
+                                k = self.nuclide_dict[product]
+                                matrix[k, i] += yield_val
 
                 # Clear set of reactions
                 reactions.clear()

openmc/deplete/nuclide.py

@@ -30,8 +30,10 @@ Parameters
 ----------
 type : str
     Type of the decay mode, e.g., 'beta-'
-target : str
-    Nuclide resulting from decay
+target : str or None
+    Nuclide resulting from decay. A value of ``None`` implies the
+    target does not exist in the currently configured depletion
+    chain
 branching_ratio : float
     Branching ratio of the decay mode
 
@@ -53,8 +55,11 @@ Parameters
 ----------
 type : str
     Type of the reaction, e.g., 'fission'
-target : str
-    nuclide resulting from reaction
+target : str or None
+    Nuclide resulting from reaction. A value of ``None``
+    implies either no single target, e.g. from fission,
+    or that the target nuclide is not considered
+    in the current depletion chain
 Q : float
     Q value of the reaction in [eV]
 branching_ratio : float
@@ -179,6 +184,8 @@ class Nuclide(object):
         for decay_elem in element.iter('decay'):
             d_type = decay_elem.get('type')
             target = decay_elem.get('target')
+            if target is not None and target.lower() == "nothing":
+                target = None
             branching_ratio = float(decay_elem.get('branching_ratio'))
             nuc.decay_modes.append(DecayTuple(d_type, target, branching_ratio))
 
@@ -192,6 +199,8 @@ class Nuclide(object):
             # just set null values
             if r_type != 'fission':
                 target = reaction_elem.get('target')
+                if target is not None and target.lower() == "nothing":
+                    target = None
             else:
                 target = None
                 if fission_q is not None:
@@ -226,7 +235,7 @@ class Nuclide(object):
             for mode, daughter, br in self.decay_modes:
                 mode_elem = ET.SubElement(elem, 'decay')
                 mode_elem.set('type', mode)
-                mode_elem.set('target', daughter)
+                mode_elem.set('target', daughter or "Nothing")
                 mode_elem.set('branching_ratio', str(br))
 
         elem.set('reactions', str(len(self.reactions)))
@@ -234,7 +243,7 @@ class Nuclide(object):
             rx_elem = ET.SubElement(elem, 'reaction')
             rx_elem.set('type', rx)
             rx_elem.set('Q', str(Q))
-            if rx != 'fission':
+            if rx != 'fission' or daughter is not None:
                 rx_elem.set('target', daughter)
             if br != 1.0:
                 rx_elem.set('branching_ratio', str(br))
@@ -461,6 +470,7 @@ class FissionYieldDistribution(Mapping):
             data_elem.text = " ".join(map(str, yield_obj.yields))
 
 
+
 class FissionYield(Mapping):
     """Mapping for fission yields of a parent at a specific energy