Merge pull request #565 from ReactionMechanismGenerator/anotherPdepFix

Fix pressure dependence convergence issue with filterReactions on

examples/rmg/heptane-filterReactions/input.py

@@ -0,0 +1,75 @@
+# Data sources
+database(
+    thermoLibraries = ['primaryThermoLibrary'],
+    reactionLibraries = [],
+    seedMechanisms = [],
+    kineticsDepositories = ['training'], 
+    kineticsFamilies = 'default',
+    kineticsEstimator = 'rate rules',
+)
+
+# Constraints on generated species
+generatedSpeciesConstraints(
+    maximumCarbonAtoms = 7,
+)
+
+# List of species
+species(
+    label='n-heptane',
+    structure=SMILES("CCCCCCC"),
+)
+
+species(
+    label='Ar',
+    reactive=False,
+    structure=SMILES("[Ar]"),
+)
+
+
+simpleReactor(
+    temperature=(1600,'K'),
+    pressure=(400,'Pa'),
+    initialMoleFractions={
+        "n-heptane": 0.02,
+        "Ar": 0.98,
+    },
+    terminationConversion={
+        'n-heptane': 0.99,
+    },
+    terminationTime=(1e6,'s'),
+)
+
+simpleReactor(
+    temperature=(2000,'K'),
+    pressure=(400,'Pa'),
+    initialMoleFractions={
+        "n-heptane": 0.02,
+        "Ar": 0.98,
+    },
+    terminationConversion={
+        'n-heptane': 0.99,
+    },
+    terminationTime=(1e6,'s'),
+)
+
+simulator(
+    atol=1e-16,
+    rtol=1e-8,
+)
+
+model(
+    toleranceMoveToCore=0.01,
+    toleranceInterruptSimulation=0.01,
+    filterReactions=True,
+)
+
+pressureDependence(
+    method='modified strong collision',
+    maximumGrainSize=(0.5,'kcal/mol'),
+    minimumNumberOfGrains=250,
+    temperatures=(300,3000,'K',8),
+    pressures=(0.001,100,'bar',5),
+    interpolation=('Chebyshev', 6, 4),
+)
+
+

rmgpy/rmg/main.py

@@ -609,35 +609,37 @@ def execute(self, inputFile, output_directory, **kwargs):
                 for objectToEnlarge in objectsToEnlarge:
                     self.reactionModel.enlarge(objectToEnlarge)
 
-                if self.filterReactions:
-                    # Run a raw simulation to get updated reaction system threshold values
-                    for index, reactionSystem in enumerate(self.reactionSystems):
-                        # Run with the same conditions as with pruning off
-                        reactionSystem.simulate(
-                            coreSpecies = self.reactionModel.core.species,
-                            coreReactions = self.reactionModel.core.reactions,
-                            edgeSpecies = [],
-                            edgeReactions = [],
-                            toleranceKeepInEdge = 0,
-                            toleranceMoveToCore = self.fluxToleranceMoveToCore,
-                            toleranceInterruptSimulation = self.fluxToleranceMoveToCore,
-                            pdepNetworks = self.reactionModel.networkList,
-                            absoluteTolerance = self.absoluteTolerance,
-                            relativeTolerance = self.relativeTolerance,
-                            filterReactions=True,
-                        )
-                        reactEdge = self.updateReactionThresholdAndReactFlags(
-                            rxnSysUnimolecularThreshold = reactionSystem.unimolecularThreshold,
-                            rxnSysBimolecularThreshold = reactionSystem.bimolecularThreshold)
-
-                    logging.info('')    
-                else:
-                    reactEdge = self.updateReactionThresholdAndReactFlags()
-
-                if reactEdge:
+                if len(self.reactionModel.core.species) > numCoreSpecies:
+                    # If there were core species added, then react the edge
+                    # If there were no new core species, it means the pdep network needs be updated through another enlarge core step
+                    if self.filterReactions:
+                        # Run a raw simulation to get updated reaction system threshold values
+                        for index, reactionSystem in enumerate(self.reactionSystems):
+                            # Run with the same conditions as with pruning off
+                            reactionSystem.simulate(
+                                coreSpecies = self.reactionModel.core.species,
+                                coreReactions = self.reactionModel.core.reactions,
+                                edgeSpecies = [],
+                                edgeReactions = [],
+                                toleranceKeepInEdge = 0,
+                                toleranceMoveToCore = self.fluxToleranceMoveToCore,
+                                toleranceInterruptSimulation = self.fluxToleranceMoveToCore,
+                                pdepNetworks = self.reactionModel.networkList,
+                                absoluteTolerance = self.absoluteTolerance,
+                                relativeTolerance = self.relativeTolerance,
+                                filterReactions=True,
+                            )
+                            self.updateReactionThresholdAndReactFlags(
+                                rxnSysUnimolecularThreshold = reactionSystem.unimolecularThreshold,
+                                rxnSysBimolecularThreshold = reactionSystem.bimolecularThreshold)
+
+                        logging.info('')    
+                    else:
+                        self.updateReactionThresholdAndReactFlags()
+
                     self.reactionModel.enlarge(reactEdge=True, 
-                        unimolecularReact=self.unimolecularReact, 
-                        bimolecularReact=self.bimolecularReact)
+                            unimolecularReact=self.unimolecularReact, 
+                            bimolecularReact=self.bimolecularReact)
 
             self.saveEverything()
 
@@ -715,7 +717,6 @@ def updateReactionThresholdAndReactFlags(self, rxnSysUnimolecularThreshold=None,
         prevNumCoreSpecies = len(self.unimolecularReact)
         stale = True if numCoreSpecies > prevNumCoreSpecies else False
 
-        reactEdge = True
 
         if self.filterReactions:
             if stale:
@@ -759,11 +760,7 @@ def updateReactionThresholdAndReactFlags(self, rxnSysUnimolecularThreshold=None,
                 for i in xrange(numCoreSpecies):
                     for j in xrange(prevNumCoreSpecies,numCoreSpecies):
                         self.bimolecularReact[i,j] = True
-            else:
-                # No reacting of edge because unimolecularReact and bimolecularReact will be False
-                reactEdge = False  
-
-        return reactEdge
+
 
     def saveEverything(self):
         """