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Fix problems with search for maxNetworkLeakRates during pruning #178

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Fix problems with search for maxNetworkLeakRates during pruning #178

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ad4c446
Removing lingering references to LenardJones class
shamelmerchant Dec 4, 2013
6427316
Fix to make standalone Cantherm work
shamelmerchant Dec 6, 2013
10b4d69
Add saturateH=True to fromAdjacencyList() in loadOldDictionary()
bbuesser Dec 20, 2013
8aec6aa
Merge remote-tracking branch 'GreenGroup/master'
bbuesser Jan 30, 2014
d3e08f1
Merge branch 'GreenGroup/master'
bbuesser Feb 2, 2014
46f5761
change loop length over PdepNetworks in search for maximum leak rates
bbuesser Feb 2, 2014
819b28a
Limit the search for electronic states to atoms involved in reaction
bbuesser Feb 4, 2014
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4 changes: 2 additions & 2 deletions rmgpy/data/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -371,9 +371,9 @@ def loadOldDictionary(self, path, pattern):
self.entries[label].item = makeLogicNode(' '.join(lines[1:]) )
# Otherwise convert adjacency list to molecule or pattern
elif pattern:
self.entries[label].item = Group().fromAdjacencyList(record)
self.entries[label].item = Group().fromAdjacencyList(record,saturateH=True)
else:
self.entries[label].item = Molecule().fromAdjacencyList(record)
self.entries[label].item = Molecule().fromAdjacencyList(record,saturateH=True)
except InvalidAdjacencyListError, e:
logging.error('Error while loading old-style dictionary "{0}"'.format(path))
logging.error('Error occurred while parsing adjacency list "{0}"'.format(label))
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4 changes: 2 additions & 2 deletions rmgpy/data/kinetics/family.py
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Expand Up @@ -1168,7 +1168,7 @@ def __generateProductStructures(self, reactantStructures, maps, forward, **optio
radical1 = atom1.radicalElectrons
spin1 = atom1.spinMultiplicity

if radical1 > 1 and radical1 < 4:
if atom1.label != '' and radical1 > 1 and radical1 < 4:

if radical1 == 2 and spin1 == 3:
atom1.setSpinMultiplicity(1)
Expand Down Expand Up @@ -1245,7 +1245,7 @@ def __generateProductStructures(self, reactantStructures, maps, forward, **optio
radical2 = atom2.radicalElectrons
spin2 = atom2.spinMultiplicity

if radical2 > 1 and radical2 < 4:
if atom2.label != '' and radical2 > 1 and radical2 < 4:

if radical2 == 2 and spin2 == 3:
atom2.setSpinMultiplicity(1)
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3 changes: 1 addition & 2 deletions rmgpy/rmg/model.py
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Expand Up @@ -1040,7 +1040,6 @@ def prune(self, reactionSystems, fluxToleranceKeepInEdge, maximumEdgeSpecies):

numCoreSpecies = len(self.core.species)
numEdgeSpecies = len(self.edge.species)
numPdepNetworks = self.networkCount

# All edge species that have not existed for more than two enlarge
# iterations are ineligible for pruning
Expand All @@ -1057,7 +1056,7 @@ def prune(self, reactionSystems, fluxToleranceKeepInEdge, maximumEdgeSpecies):
if maxEdgeSpeciesRates[i] < rate:
maxEdgeSpeciesRates[i] = rate

for i in range(numPdepNetworks):
for i in range(len(self.networkList)):
network = self.networkList[i]
rate = reactionSystem.maxNetworkLeakRates[i]
# Add the fraction of the network leak rate contributed by
Expand Down