Merge pull request #36 from nyee/databaseTest

Database test

Author: connie

EvaluateKinetics.py

@@ -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):
@@ -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
 
@@ -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):
@@ -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():
@@ -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'

input/kinetics/families/1,2_Insertion/groups.py

@@ -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}
 """,
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}
@@ -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}