Add balanceSpecies feature

If a balance species is set mole fractions are generated thus:  the ranged mole fractions are varied within their ranges according to the algorithm while the others remain constant, then the balance species is adjusted so that all of the mole fractions sum to one.  This causes all mole fractions except the balanceSpecies to remain in their ranges

rmgpy/rmg/input.py

@@ -136,6 +136,7 @@ def simpleReactor(temperature,
                   nSimsTerm=6,
                   terminationConversion=None,
                   terminationTime=None,
+                  balanceSpecies=None,
                   sensitivity=None,
                   sensitivityThreshold=1e-3,
                   sensitivityTemperature=None,
@@ -209,7 +210,19 @@ def simpleReactor(temperature,
 
     system = SimpleReactor(T, P, initialMoleFractions, nSimsTerm, termination, sensitiveSpecies, sensitivityThreshold,sensConditions)
     rmg.reactionSystems.append(system)
-
+
+    rmg.balanceSpecies = balanceSpecies
+    if balanceSpecies: #check that the balanceSpecies can't be taken to zero
+        total = 0.0
+        for key,item in initialMoleFractions.iteritems():
+            if key == balanceSpecies:
+                assert not isinstance(item,list), 'balanceSpecies must not have a defined range'
+                xbspcs = item
+            if isinstance(item,list):
+                total += item[1]-item[0]
+
+        if total > xbspcs:
+            raise ValueError('The sum of the differences in the ranged mole fractions is greater than the mole fraction of the balance species, this would require the balanceSpecies mole fraction to be negative in some cases which is not allowed, either reduce the maximum mole fractions or dont use balanceSpecies')
 
 # Reaction systems
 def liquidReactor(temperature,

rmgpy/rmg/main.py

@@ -165,6 +165,7 @@ def clear(self):
 
         self.modelSettingsList = []
         self.simulatorSettingsList = []
+        self.balanceSpecies = None
 
         self.filterReactions=False
         self.unimolecularReact = None
@@ -560,7 +561,7 @@ def execute(self, **kwargs):
         if self.filterReactions:
             # Run the reaction system to update threshold and react flags
             for index, reactionSystem in enumerate(self.reactionSystems):
-                self.rmg_memories.append(RMG_Memory(reactionSystem))
+                self.rmg_memories.append(RMG_Memory(reactionSystem,self.balanceSpecies))
                 self.rmg_memories[index].generate_cond()
                 log_conditions(self.rmg_memories,index)
                 reactionSystem.initializeModel(
@@ -579,7 +580,7 @@ def execute(self, **kwargs):
                     rxnSysBimolecularThreshold=reactionSystem.bimolecularThreshold)
         else:
             for index, reactionSystem in enumerate(self.reactionSystems):
-                self.rmg_memories.append(RMG_Memory(reactionSystem))
+                self.rmg_memories.append(RMG_Memory(reactionSystem,self.balanceSpecies))
                 self.rmg_memories[index].generate_cond()
                 log_conditions(self.rmg_memories,index)
 
@@ -1560,15 +1561,19 @@ class RMG_Memory:
     class for remembering RMG simulations
     and determining what simulation to run next
     """
-    def __init__(self,reactionSystem):
+    def __init__(self,reactionSystem,bspc):
         self.Ranges = dict()
+
         if hasattr(reactionSystem,'Trange') and type(reactionSystem.Trange) == list:
             Trange = reactionSystem.Trange
             self.Ranges['T'] = [T.value_si for T in Trange]
         if hasattr(reactionSystem,'Prange') and type(reactionSystem.Prange) == list:
             Prange = reactionSystem.Prange
             self.Ranges['P'] = [np.log(P.value_si) for P in Prange]
         if hasattr(reactionSystem,'initialMoleFractions'):
+            if bspc:
+                self.initialMoleFractions = deepcopy(reactionSystem.initialMoleFractions)
+                self.balanceSpecies = [x for x in self.initialMoleFractions.keys() if x.label == bspc][0]  #find the balance species
             for key,value in reactionSystem.initialMoleFractions.iteritems():
                 assert key != 'T' and key != 'P', 'naming a species T or P is forbidden'
                 if type(value) == list:
@@ -1583,7 +1588,7 @@ def __init__(self,reactionSystem):
             if isinstance(term, TerminationTime):
                 self.tmax = term.time.value_si
 
-        self.normalize = hasattr(reactionSystem,'initialMoleFractions')
+        self.reactionSystem = reactionSystem
         self.conditionList = []
         self.scaledConditionList = []
         self.ts = []
@@ -1642,12 +1647,18 @@ def obj(y):
             if 'P' in newCond.keys():
                 newCond['P'] = np.exp(newCond['P'])
 
-            if self.normalize:
+            if hasattr(self,'initialMoleFractions'):
+                for key in self.initialMoleFractions.keys():
+                    if not isinstance(self.initialMoleFractions[key],list):
+                        newCond[key] = self.initialMoleFractions[key]
                 total = sum([val for key,val in newCond.iteritems() if key != 'T' and key != 'P'])
-                for key,val in newCond.iteritems():
-                    if key != 'T' and key != 'P':
-                        newCond[key] = val/total
-
+                if self.balanceSpecies is None:
+                    for key,val in newCond.iteritems():
+                        if key != 'T' and key != 'P':
+                            newCond[key] = val/total
+                else:
+                    newCond[self.balanceSpecies] = self.initialMoleFractions[self.balanceSpecies] + 1.0 - total
+
             self.conditionList.append(newCond)
             self.scaledConditionList.append(scaledNewCond)
         return