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Adjust updating and resetting of react flags in execute #1432

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Merged
mjohnson541 merged 1 commit into from
Jul 23, 2018
Merged

Adjust updating and resetting of react flags in execute #1432

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104 changes: 47 additions & 57 deletions rmgpy/rmg/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -766,55 +766,51 @@ def execute(self, **kwargs):
for objectToEnlarge in objectsToEnlarge:
self.reactionModel.enlarge(objectToEnlarge)

if len(self.reactionModel.core.species) > numCoreSpecies or self.reactionModel.iterationNum == 1:
if modelSettings.filterReactions:
# Run a raw simulation to get updated reaction system threshold values
# Run with the same conditions as with pruning off
tempModelSettings = deepcopy(modelSettings)
tempModelSettings.fluxToleranceKeepInEdge = 0
# 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 modelSettings.filterReactions:
# Run a raw simulation to get updated reaction system threshold values
# Run with the same conditions as with pruning off
if not resurrected:
try:
reactionSystem.simulate(
coreSpecies = self.reactionModel.core.species,
coreReactions = self.reactionModel.core.reactions,
edgeSpecies = [],
edgeReactions = [],
surfaceSpecies = self.reactionModel.surface.species,
surfaceReactions = self.reactionModel.surface.reactions,
pdepNetworks = self.reactionModel.networkList,
modelSettings = tempModelSettings,
simulatorSettings = simulatorSettings,
conditions = self.rmg_memories[index].get_cond()
)
except:
self.updateReactionThresholdAndReactFlags(
rxnSysUnimolecularThreshold = reactionSystem.unimolecularThreshold,
rxnSysBimolecularThreshold = reactionSystem.bimolecularThreshold,
rxnSysTrimolecularThreshold = reactionSystem.trimolecularThreshold,
skipUpdate=True)
logging.warn('Reaction thresholds/flags for Reaction System {0} was not updated due to simulation failure'.format(index+1))
else:
self.updateReactionThresholdAndReactFlags(
rxnSysUnimolecularThreshold = reactionSystem.unimolecularThreshold,
rxnSysBimolecularThreshold = reactionSystem.bimolecularThreshold,
rxnSysTrimolecularThreshold = reactionSystem.trimolecularThreshold
)
else:
if not resurrected:
try:
reactionSystem.simulate(
coreSpecies = self.reactionModel.core.species,
coreReactions = self.reactionModel.core.reactions,
edgeSpecies = [],
edgeReactions = [],
surfaceSpecies = self.reactionModel.surface.species,
surfaceReactions = self.reactionModel.surface.reactions,
pdepNetworks = self.reactionModel.networkList,
modelSettings = tempModelSettings,
simulatorSettings = simulatorSettings,
conditions = self.rmg_memories[index].get_cond()
)
except:
self.updateReactionThresholdAndReactFlags(
rxnSysUnimolecularThreshold = reactionSystem.unimolecularThreshold,
rxnSysBimolecularThreshold = reactionSystem.bimolecularThreshold,
rxnSysTrimolecularThreshold = reactionSystem.trimolecularThreshold,
skipUpdate = True
skipUpdate=True)
logging.warn('Reaction thresholds/flags for Reaction System {0} was not updated due to simulation failure'.format(index+1))
else:
self.updateReactionThresholdAndReactFlags(
rxnSysUnimolecularThreshold = reactionSystem.unimolecularThreshold,
rxnSysBimolecularThreshold = reactionSystem.bimolecularThreshold,
rxnSysTrimolecularThreshold = reactionSystem.trimolecularThreshold
)
logging.warn('Reaction thresholds/flags for Reaction System {0} was not updated due to resurrection'.format(index+1))


logging.info('')
else:
self.updateReactionThresholdAndReactFlags()

self.updateReactionThresholdAndReactFlags(
rxnSysUnimolecularThreshold = reactionSystem.unimolecularThreshold,
rxnSysBimolecularThreshold = reactionSystem.bimolecularThreshold,
rxnSysTrimolecularThreshold = reactionSystem.trimolecularThreshold,
skipUpdate = True
)
logging.warn('Reaction thresholds/flags for Reaction System {0} was not updated due to resurrection'.format(index+1))

logging.info('')
else:
self.updateReactionThresholdAndReactFlags()

if not np.isinf(modelSettings.toleranceThermoKeepSpeciesInEdge):
self.reactionModel.setThermodynamicFilteringParameters(self.Tmax, toleranceThermoKeepSpeciesInEdge=modelSettings.toleranceThermoKeepSpeciesInEdge,
minCoreSizeForPrune=modelSettings.minCoreSizeForPrune,
Expand Down Expand Up @@ -1247,15 +1243,16 @@ def updateReactionThresholdAndReactFlags(self,
"""
numCoreSpecies = len(self.reactionModel.core.species)
prevNumCoreSpecies = len(self.unimolecularReact)
stale = True if numCoreSpecies > prevNumCoreSpecies else False


if self.filterReactions:
if stale:
# Reset and expand the react arrays if there were new core species added
self.unimolecularReact = np.zeros((numCoreSpecies), bool)
self.bimolecularReact = np.zeros((numCoreSpecies, numCoreSpecies), bool)
new_core_species = numCoreSpecies > prevNumCoreSpecies

# Always reset the react arrays from prior iterations
self.unimolecularReact = np.zeros((numCoreSpecies), bool)
self.bimolecularReact = np.zeros((numCoreSpecies, numCoreSpecies), bool)
if self.trimolecular:
self.trimolecularReact = np.zeros((numCoreSpecies, numCoreSpecies, numCoreSpecies), bool)

if self.filterReactions:
if new_core_species:
# Expand the threshold arrays if there were new core species added
unimolecularThreshold = np.zeros((numCoreSpecies), bool)
bimolecularThreshold = np.zeros((numCoreSpecies, numCoreSpecies), bool)
Expand All @@ -1267,7 +1264,6 @@ def updateReactionThresholdAndReactFlags(self,
self.bimolecularThreshold = bimolecularThreshold

if self.trimolecular:
self.trimolecularReact = np.zeros((numCoreSpecies, numCoreSpecies, numCoreSpecies), bool)
trimolecularThreshold = np.zeros((numCoreSpecies, numCoreSpecies, numCoreSpecies), bool)
trimolecularThreshold[:prevNumCoreSpecies,
:prevNumCoreSpecies,
Expand Down Expand Up @@ -1301,13 +1297,7 @@ def updateReactionThresholdAndReactFlags(self,
self.trimolecularThreshold[i,j,k] = True
else:
# We are not filtering reactions
if stale:
# Reset and expand the react arrays if there were new core species added
self.unimolecularReact = np.zeros((numCoreSpecies), bool)
self.bimolecularReact = np.zeros((numCoreSpecies, numCoreSpecies), bool)
if self.trimolecular:
self.trimolecularReact = np.zeros((numCoreSpecies, numCoreSpecies, numCoreSpecies), bool)

if new_core_species:
# React all the new core species unimolecularly
for i in xrange(prevNumCoreSpecies, numCoreSpecies):
self.unimolecularReact[i] = True
Expand Down