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Database test #36

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merged 15 commits into from
May 20, 2014
Merged

Database test #36

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4ec1b16
Minor fixes to intra_H_migration family
nyee Apr 1, 2014
c3d4069
Fix bug with Leave one out test
nyee Apr 1, 2014
6243220
Minor corrections to in 1,2 Insertion family
nyee Apr 1, 2014
bffaac0
Added suggested solutions to name errors in checkWellFormed
nyee Apr 9, 2014
2bf5bb6
Fixes to R_Addition_MultipleBond family
nyee Apr 9, 2014
9440c56
Fixes to EvaluateKinetics.py database testing script.
rwest Apr 9, 2014
60c438d
More fixes to R_Addition Multiple Bond
nyee Apr 11, 2014
90768bc
Removed biradical singlets from R_MultipleBond Addition
nyee Apr 11, 2014
10ebf2d
Fixes to rule adj lists in Intra_R_Add_Endocyclic
nyee Apr 11, 2014
67b0376
Fixes to group definitions in Intra_R_Add_Endocylic
nyee Apr 14, 2014
bf66929
Fixes to Disproportionation family
nyee Apr 14, 2014
61f1ec9
Fixes to adjLists of 1,3_Insertion_RSR
nyee Apr 14, 2014
8355eda
Fixes to R_Addition_CSm using checkWellFormed
nyee May 9, 2014
935bdc1
Fix errors in 1,2_Insertion found with databaseTester
nyee May 9, 2014
82fe316
Fixes to H-Abstraction family: Part 1
nyee May 12, 2014
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31 changes: 19 additions & 12 deletions EvaluateKinetics.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -107,10 +107,10 @@ def getKineticsLeaveOneOut(family, missingGroups):

#returns the average temperature for the range given by the kinetic model
def getAverageTemp(kineticModel):
try:
return (kineticModel.Tmin.value + kineticModel.Tmax.value)/2
except AttributeError:
return 1000
# try:
# return (kineticModel.Tmin.value + kineticModel.Tmax.value)/2
# except AttributeError:
return 1000

#calculates the parity values for each
def calculateParity(exactKineticModel, approxKineticModel, T):
Expand All @@ -130,7 +130,7 @@ def analyzeForParity(exactKinetics, approxKinetics, T=None, cutoff=0):
exact=exactKinetics[key].getRateCoefficient(T)
approx=approxKinetics[key].getRateCoefficient(T)
dataPoint=[exact, approx]
if cutoff!=0 and math.log((float(exact)/float(approx)))**2 > cutoff**2:
if cutoff!=0 and math.log10((float(exact)/float(approx)))**2 > cutoff**2:
continue
parityData[key]=dataPoint

Expand All @@ -143,7 +143,7 @@ def analyzeForParity(exactKinetics, approxKinetics, T=None, cutoff=0):
def calculateQ(parityData):
Q=0
for key, value in parityData.iteritems():
Q+=(math.log(value[0]/value[1]))**2
Q+=(math.log10(value[0]/value[1]))**2
return (Q/len(parityData))**0.5

def createParityPlot(parityData):
Expand Down Expand Up @@ -435,9 +435,16 @@ def checkFamilies(FullDatabase):
if True in problemsExist:
outputFile.write(family + '\n')
if problemsExist[0]:
outputFile.write('\n' + 'These groups exist in rules.py but not groups.py:' + '\n')
for group in problems[0]:
outputFile.write(group + '\n')
outputFile.write('\n' + 'These groups exist in rules.py but not groups.py:' + '\n' + "A suggested match could be incorrect, but if 'No match' is written, it is true (and most unfortunate)" + '\n')
for group, matchedGroups in problems[0].iteritems():
outputFile.write(group + ', Suggested match from groups.py: ')
for matchedGroup in matchedGroups:
if matchedGroup==matchedGroups[-1]:
if len(matchedGroups)>1:
outputFile.write('and ')
outputFile.write(matchedGroup + '\n')
else:
outputFile.write(matchedGroup +', ' )
if problemsExist[1]:
outputFile.write('\n' + 'These groups do not match the definition in the rule' + '\n')
for rule, groups in problems[1].iteritems():
Expand Down Expand Up @@ -475,17 +482,17 @@ def checkFamilies(FullDatabase):
outputFile.write('\n\n')
if __name__ == '__main__':


databaseProjectRootPath = os.path.dirname( os.path.abspath( __file__ ))
#Thermo stuff
# ThermoDatabase=ThermoDatabase()
# ThermoDatabase.load(path)
# ThermoDatabase.save(r'C:\RMG-database\input\thermo_test')
# ThermoDatabase.save(path)
FullDatabase=RMGDatabase()
# path=r'C:\RMG-database\input\thermo'
path='C:\RMG-database\input'
path = os.path.join(databaseProjectRootPath, 'input')
# FullDatabase.load(thermoLibraries=)
FullDatabase.load(path)
FullDatabase.load(path, kineticsFamilies='all')
checkFamilies(FullDatabase)
# trialDir=r'C:\Users\User1\Dropbox\Research\RMG\kinetics\LeaveOneOut\test'
# trialDir=r'C:\RMG-database\input_test'
Expand Down
74 changes: 37 additions & 37 deletions input/kinetics/families/1,2_Insertion/groups.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -63,7 +63,7 @@
label = "carbene",
group =
"""
1 *1 C 2S {2,S} {3,S}
1 *1 Cs 2S {2,S} {3,S}
2 H 0 {1,S}
3 H 0 {1,S}
""",
Expand Down Expand Up @@ -194,7 +194,7 @@
label = "Cd_H",
group =
"""
1 *2 C 0 {2,D} {3,S} {4,S}
1 *2 Cd 0 {2,D} {3,S} {4,S}
2 C 0 {1,D}
3 *3 H 0 {1,S}
4 R 0 {1,S}
Expand All @@ -212,7 +212,7 @@
label = "Cd_pri",
group =
"""
1 *2 C 0 {2,D} {3,S} {4,S}
1 *2 Cd 0 {2,D} {3,S} {4,S}
2 C 0 {1,D}
3 *3 H 0 {1,S}
4 H 0 {1,S}
Expand All @@ -230,8 +230,8 @@
label = "ethene",
group =
"""
1 *2 C 0 {2,D} {3,S} {4,S}
2 C 0 {1,D} {5,S} {6,S}
1 *2 Cd 0 {2,D} {3,S} {4,S}
2 Cd 0 {1,D} {5,S} {6,S}
3 *3 H 0 {1,S}
4 H 0 {1,S}
5 H 0 {2,S}
Expand All @@ -250,7 +250,7 @@
label = "Cd_sec",
group =
"""
1 *2 C 0 {2,D} {3,S} {4,S}
1 *2 Cd 0 {2,D} {3,S} {4,S}
2 C 0 {1,D}
3 *3 H 0 {1,S}
4 R!H 0 {1,S}
Expand All @@ -268,7 +268,7 @@
label = "Cd/H/NonDeC",
group =
"""
1 *2 C 0 {2,D} {3,S} {4,S}
1 *2 Cd 0 {2,D} {3,S} {4,S}
2 C 0 {1,D}
3 *3 H 0 {1,S}
4 Cs 0 {1,S}
Expand All @@ -286,7 +286,7 @@
label = "Cd/H/NonDeO",
group =
"""
1 *2 C 0 {2,D} {3,S} {4,S}
1 *2 Cd 0 {2,D} {3,S} {4,S}
2 C 0 {1,D}
3 *3 H 0 {1,S}
4 O 0 {1,S}
Expand All @@ -304,7 +304,7 @@
label = "Cd/H/OneDe",
group =
"""
1 *2 C 0 {2,D} {3,S} {4,S}
1 *2 Cd 0 {2,D} {3,S} {4,S}
2 C 0 {1,D}
3 *3 H 0 {1,S}
4 {Cd,Ct,Cb,CO} 0 {1,S}
Expand Down Expand Up @@ -340,7 +340,7 @@
label = "Cs_H",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 R 0 {1,S}
4 R 0 {1,S}
Expand All @@ -359,7 +359,7 @@
label = "C_methane",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 H 0 {1,S}
4 H 0 {1,S}
Expand All @@ -378,7 +378,7 @@
label = "C_pri",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 H 0 {1,S}
4 H 0 {1,S}
Expand All @@ -397,7 +397,7 @@
label = "C_pri/NonDeC",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 H 0 {1,S}
4 H 0 {1,S}
Expand All @@ -416,7 +416,7 @@
label = "C_pri/NonDeO",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 H 0 {1,S}
4 H 0 {1,S}
Expand All @@ -435,7 +435,7 @@
label = "C_pri/De",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 H 0 {1,S}
4 H 0 {1,S}
Expand All @@ -454,7 +454,7 @@
label = "C_pri/Cd",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 H 0 {1,S}
4 H 0 {1,S}
Expand All @@ -473,7 +473,7 @@
label = "C_pri/Ct",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 H 0 {1,S}
4 H 0 {1,S}
Expand All @@ -492,7 +492,7 @@
label = "C_sec",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 H 0 {1,S}
4 R!H 0 {1,S}
Expand All @@ -511,7 +511,7 @@
label = "C/H2/NonDeC",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 H 0 {1,S}
4 Cs 0 {1,S}
Expand All @@ -530,7 +530,7 @@
label = "C/H2/NonDeO",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 H 0 {1,S}
4 O 0 {1,S}
Expand All @@ -549,7 +549,7 @@
label = "C/H2/CsO",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 H 0 {1,S}
4 O 0 {1,S}
Expand All @@ -568,7 +568,7 @@
label = "C/H2/O2",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 H 0 {1,S}
4 O 0 {1,S}
Expand All @@ -587,7 +587,7 @@
label = "C/H2/OneDe",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 H 0 {1,S}
4 {Cd,Ct,CO,Cb} 0 {1,S}
Expand All @@ -606,7 +606,7 @@
label = "C/H2/OneDeC",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 H 0 {1,S}
4 {Cd,Ct,CO,Cb} 0 {1,S}
Expand All @@ -625,7 +625,7 @@
label = "C/H2/OneDeO",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 H 0 {1,S}
4 {Cd,Ct,CO,Cb} 0 {1,S}
Expand All @@ -644,7 +644,7 @@
label = "C/H2/TwoDe",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 H 0 {1,S}
4 {Cd,Ct,CO,Cb} 0 {1,S}
Expand All @@ -663,7 +663,7 @@
label = "C_ter",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 R!H 0 {1,S}
4 R!H 0 {1,S}
Expand All @@ -682,7 +682,7 @@
label = "C/H/NonDeC",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 {Cs,O} 0 {1,S}
4 {Cs,O} 0 {1,S}
Expand All @@ -701,7 +701,7 @@
label = "C/H/Cs3",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 Cs 0 {1,S}
4 Cs 0 {1,S}
Expand All @@ -720,7 +720,7 @@
label = "C/H/NDMustO",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 O 0 {1,S}
4 {Cs,O} 0 {1,S}
Expand All @@ -739,7 +739,7 @@
label = "C/H/OneDe",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 {Cd,Ct,Cb,CO} 0 {1,S}
4 {Cs,O} 0 {1,S}
Expand All @@ -758,7 +758,7 @@
label = "C/H/Cs2",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 {Cd,Ct,Cb,CO} 0 {1,S}
4 Cs 0 {1,S}
Expand All @@ -777,7 +777,7 @@
label = "C/H/ODMustO",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 {Cd,Ct,Cb,CO} 0 {1,S}
4 O 0 {1,S}
Expand All @@ -796,7 +796,7 @@
label = "C/H/TwoDe",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 {Cd,Ct,Cb,CO} 0 {1,S}
4 {Cd,Ct,Cb,CO} 0 {1,S}
Expand All @@ -815,7 +815,7 @@
label = "C/H/Cs",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 {Cd,Ct,Cb,CO} 0 {1,S}
4 {Cd,Ct,Cb,CO} 0 {1,S}
Expand All @@ -834,7 +834,7 @@
label = "C/H/TDMustO",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 {Cd,Ct,Cb,CO} 0 {1,S}
4 {Cd,Ct,Cb,CO} 0 {1,S}
Expand All @@ -853,7 +853,7 @@
label = "C/H/ThreeDe",
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
1 *2 Cs 0 {2,S} {3,S} {4,S} {5,S}
2 *3 H 0 {1,S}
3 {Cd,Ct,Cb,CO} 0 {1,S}
4 {Cd,Ct,Cb,CO} 0 {1,S}
Expand Down
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