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Merged
merged 5 commits into from
Mar 31, 2014
Merged

Database test #33

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17082c2
Add wrapper for testing database
nyee Mar 17, 2014
fb48179
Add output for checking for unique groups
nyee Mar 28, 2014
6513a2d
fix AdjList in rules of Intra_R_Add_Exocyclic
nyee Mar 28, 2014
99b300c
Fix child relationships in R_Addition_Csm
nyee Mar 28, 2014
155821c
Fix errors in Disproportionation family
nyee Mar 30, 2014
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58 changes: 55 additions & 3 deletions EvaluateKinetics.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -421,6 +421,58 @@ def LeaveOneOut(FullDatabase, trialDir):
print 'These families had errors:', familiesWithErrors
return

def checkFamilies(FullDatabase):
familyStatus={}
for family in FullDatabase.kinetics.families:
print family
familyStatus[family]=FullDatabase.kinetics.families[family].checkWellFormed()

with open(r'DatabaseWellFormedSummary.txt', 'wb') as outputFile:
for family, problems in familyStatus.iteritems():
problemsExist=[]
for problem in problems:
problemsExist.append(not problem==[] and not problem=={})
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')
if problemsExist[1]:
outputFile.write('\n' + 'These groups do not match the definition in the rule' + '\n')
for rule, groups in problems[1].iteritems():
for group in groups:
if group==groups[-1]:
if len(groups)>1:
outputFile.write('and ')
outputFile.write(group + ' ')
else:
outputFile.write(group +', ' )
outputFile.write('in ' + rule + '\n')
if problemsExist[2]:
outputFile.write('\n' + 'These groups are not in the tree:' + '\n')
for group in problems[2]:
outputFile.write(group + '\n')
if problemsExist[3]:
outputFile.write('\n' + 'These groups are not unique' + '\n')
for key, groups in problems[3].iteritems():
outputFile.write(key + ' matches ')
for group in groups:
if group==groups[-1]:
if len(groups)>1:
outputFile.write('and ')
outputFile.write(group + '\n')
else:
outputFile.write(group +', ' )
if problemsExist[4]:
outputFile.write('\n' + 'These groups are not actually subgroups of their parent' + '\n')
for group, parent in problems[4].iteritems():
outputFile.write('Child: ' + group + ', Parent: ' + parent + '\n')
if problemsExist[5]:
outputFile.write('\n' + 'These groups are probably products, but you should check them anyway' + '\n')
for group in problems[5]:
outputFile.write(group + '\n')
outputFile.write('\n\n')
if __name__ == '__main__':


Expand All @@ -434,9 +486,9 @@ def LeaveOneOut(FullDatabase, trialDir):
path='C:\RMG-database\input'
# FullDatabase.load(thermoLibraries=)
FullDatabase.load(path)
checkFamilies(FullDatabase)
# trialDir=r'C:\Users\User1\Dropbox\Research\RMG\kinetics\LeaveOneOut\test'
trialDir=r'C:\RMG-database\input_test'
FullDatabase.save(trialDir)
# trialDir=r'C:\RMG-database\input_test'
# family=FullDatabase.kinetics.families['Disproportionation']
# entryKey='Y_1centerbirad;O_Cdrad'
#
Expand All @@ -447,6 +499,6 @@ def LeaveOneOut(FullDatabase, trialDir):

# NISTExact(FullDatabase, trialDir)
# countNodesAll(NISTDatabase, trialDir)
consistencyTest(FullDatabase)
# consistencyTest(FullDatabase)
# LeaveOneOut(FullDatabase, trialDir)

100 changes: 28 additions & 72 deletions input/kinetics/families/Disproportionation/groups.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@
entry(
index = 1,
label = "Y_rad_birad_trirad_quadrad",
group = "OR{Y_1centerquadrad, Y_1centertrirad, Y_2centerbirad, Y_1centerbirad, Y_rad}",
group = "OR{Y_1centerquadrad, Y_1centertrirad, Y_2centerbirad, Y_1centerbirad, Y_rad, H_rad}",
kinetics = None,
reference = None,
referenceType = "",
Expand All @@ -41,8 +41,8 @@
label = "XH_Rrad",
group =
"""
1 *2 R!H 0 {2,S} {3,S}
2 *3 R!H 1 {1,S}
1 *2 R!H 0 {2,{S,D}} {3,S}
2 *3 R!H 1 {1,{S,D}}
3 *4 H 0 {1,S}
""",
kinetics = None,
Expand Down Expand Up @@ -125,8 +125,7 @@
label = "Y_rad",
group =
"""
1 *1 R 1 {2,S}
2 R 0 {1,S}
1 *1 R 1
""",
kinetics = None,
reference = None,
Expand Down Expand Up @@ -166,8 +165,8 @@
label = "Ct_rad/Ct",
group =
"""
1 *1 C 1 {2,T}
2 C 0 {1,T}
1 *1 Ct 1 {2,T}
2 Ct 0 {1,T}
""",
kinetics = None,
reference = None,
Expand Down Expand Up @@ -1097,7 +1096,7 @@
1 *1 C 1 {2,S} {3,S} {4,S}
2 H 0 {1,S}
3 {Cd,Ct,Cb,CO} 0 {1,S}
4 {Cs,O,S} 0 {1,S}
4 {Cs,O,S,N} 0 {1,S}
""",
kinetics = None,
reference = None,
Expand Down Expand Up @@ -1440,7 +1439,7 @@
group =
"""
1 *2 Cd 0 {2,S} {3,S}
2 *3 {Cs,Cd,CO,O,S} 1 {1,S}
2 *3 {Cs,Cd,CO,O,S,N} 1 {1,S}
3 *4 H 0 {1,S}
""",
kinetics = None,
Expand Down Expand Up @@ -1550,7 +1549,7 @@
group =
"""
1 *2 CO 0 {2,S} {3,S}
2 *3 {Cs,Cd,CO,O,S} 1 {1,S}
2 *3 {Cs,Cd,CO,O,S,N} 1 {1,S}
3 *4 H 0 {1,S}
""",
kinetics = None,
Expand Down Expand Up @@ -1660,7 +1659,7 @@
group =
"""
1 *2 O 0 {2,S} {3,S}
2 *3 {Cs,Cd,CO,O,S} 1 {1,S}
2 *3 {Cs,Cd,CO,O,S,N} 1 {1,S}
3 *4 H 0 {1,S}
""",
kinetics = None,
Expand Down Expand Up @@ -1858,7 +1857,7 @@
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
2 *3 {Cs,Cd,CO,O,S} 1 {1,S}
2 *3 {Cs,Cd,CO,O,S,N} 1 {1,S}
3 *4 H 0 {1,S}
4 H 0 {1,S}
5 H 0 {1,S}
Expand Down Expand Up @@ -2002,7 +2001,7 @@
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
2 *3 {Cs,Cd,CO,O,S} 1 {1,S}
2 *3 {Cs,Cd,CO,O,S,N} 1 {1,S}
3 *4 H 0 {1,S}
4 H 0 {1,S}
5 R!H 0 {1,S}
Expand All @@ -2026,7 +2025,7 @@
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
2 *3 {Cs,Cd,CO,O,S} 1 {1,S}
2 *3 {Cs,Cd,CO,O,S,N} 1 {1,S}
3 *4 H 0 {1,S}
4 H 0 {1,S}
5 {Cs,O,S} 0 {1,S}
Expand Down Expand Up @@ -2146,7 +2145,7 @@
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
2 *3 {Cs,Cd,CO,O,S} 1 {1,S}
2 *3 {Cs,Cd,CO,O,S,N} 1 {1,S}
3 *4 H 0 {1,S}
4 H 0 {1,S}
5 {Cd,Ct,Cb,CO} 0 {1,S}
Expand Down Expand Up @@ -2266,7 +2265,7 @@
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
2 *3 {Cs,Cd,CO,O,S} 1 {1,S}
2 *3 {Cs,Cd,CO,O,S,N} 1 {1,S}
3 *4 H 0 {1,S}
4 R!H 0 {1,S}
5 R!H 0 {1,S}
Expand All @@ -2290,7 +2289,7 @@
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
2 *3 {Cs,Cd,CO,O,S} 1 {1,S}
2 *3 {Cs,Cd,CO,O,S,N} 1 {1,S}
3 *4 H 0 {1,S}
4 {Cs,O,S} 0 {1,S}
5 {Cs,O,S} 0 {1,S}
Expand Down Expand Up @@ -2410,7 +2409,7 @@
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
2 *3 {Cs,Cd,CO,O,S} 1 {1,S}
2 *3 {Cs,Cd,CO,O,S,N} 1 {1,S}
3 *4 H 0 {1,S}
4 {Cs,O,S} 0 {1,S}
5 {Cd,Ct,Cb,CO} 0 {1,S}
Expand Down Expand Up @@ -2530,7 +2529,7 @@
group =
"""
1 *2 C 0 {2,S} {3,S} {4,S} {5,S}
2 *3 {Cs,Cd,CO,O,S} 1 {1,S}
2 *3 {Cs,Cd,CO,O,S,N} 1 {1,S}
3 *4 H 0 {1,S}
4 {Cd,Ct,Cb,CO} 0 {1,S}
5 {Cd,Ct,Cb,CO} 0 {1,S}
Expand Down Expand Up @@ -2661,26 +2660,6 @@
],
)

entry(
index = 201,
label = "N3_atom_quartet",
group =
"""
1 *1 N3s 3
""",
kinetics = None,
reference = None,
referenceType = "",
shortDesc = u"""""",
longDesc =
u"""

""",
history = [
("Mon Nov 4 10:25:25 2013","Beat Buesser <[email protected]>","action","""Beat Buesser <[email protected]> created this value."""),
],
)

entry(
index = 202,
label = "CH_quartet",
Expand Down Expand Up @@ -3639,7 +3618,7 @@
group =
"""
1 *2 N 0 {2,S} {3,S}
2 *3 R 1 {1,S}
2 *3 R!H 1 {1,S}
3 *4 H 0 {1,S}
""",
kinetics = None,
Expand All @@ -3661,7 +3640,7 @@
group =
"""
1 *2 N3s 0 {2,S} {3,S}
2 *3 R 1 {1,S}
2 *3 R!H 1 {1,S}
3 *4 H 0 {1,S}
""",
kinetics = None,
Expand All @@ -3683,7 +3662,7 @@
group =
"""
1 *2 N3s 0 {2,S} {3,S} {4,S}
2 *3 R 1 {1,S}
2 *3 R!H 1 {1,S}
3 *4 H 0 {1,S}
4 H 0 {1,S}
""",
Expand Down Expand Up @@ -3821,7 +3800,7 @@
group =
"""
1 *2 N3s 0 {2,S} {3,S} {4,S}
2 *3 N 1 {1,S}
2 *3 R!H 1 {1,S}
3 *4 H 0 {1,S}
4 {Cs,N3s,Os} 0 {1,S}
""",
Expand All @@ -3844,7 +3823,7 @@
group =
"""
1 *2 N3s 0 {2,S} {3,S} {4,S}
2 *3 N 1 {1,S}
2 *3 R!H 1 {1,S}
3 *4 H 0 {1,S}
4 {Cd,Ct,Cb,CO} 0 {1,S}
""",
Expand All @@ -3867,7 +3846,7 @@
group =
"""
1 *2 {N5s,N5d} 0 {2,S} {3,S}
2 *3 R 1 {1,S}
2 *3 R!H 1 {1,S}
3 *4 H 0 {1,S}
""",
kinetics = None,
Expand Down Expand Up @@ -4276,7 +4255,7 @@
label = "N5d/H_d_Rrad",
group =
"""
1 *2 N3d 0 {2,D} {3,S}
1 *2 N5d 0 {2,D} {3,S}
2 *3 R!H 1 {1,D}
3 *4 H 0 {1,S}
""",
Expand All @@ -4292,29 +4271,7 @@
("Mon Nov 4 10:25:25 2013","Beat Buesser <[email protected]>","action","""Beat Buesser <[email protected]> created this value."""),
],
)

entry(
index = 275,
label = "N5dd/H_d_Rrad",
group =
"""
1 *2 N3d 0 {2,D} {3,S}
2 *3 R!H 1 {1,D}
3 *4 H 0 {1,S}
""",
kinetics = None,
reference = None,
referenceType = "",
shortDesc = u"""""",
longDesc =
u"""

""",
history = [
("Mon Nov 4 10:25:25 2013","Beat Buesser <[email protected]>","action","""Beat Buesser <[email protected]> created this value."""),
],
)


entry(
index = 276,
label = "XH_Rbirad",
Expand Down Expand Up @@ -4874,9 +4831,9 @@
L4: C_sec_rad
L5: C_rad/H/NonDeC
L5: C_rad/H/NonDeO
L5: C_rad/H/NonDeN
L6: C_rad/H/CsO
L6: C_rad/H/O2
L5: C_rad/H/NonDeN
L5: C_rad/H/NonDeS
L6: C_rad/H/CsS
L6: C_rad/H/S2
Expand Down Expand Up @@ -5007,8 +4964,7 @@
L5: N3d/H_d_Rrad
L6: N3d/H_d_Crad
L6: N3d/H_d_Nrad
L5: N5d/H_d_Rrad
L5: N5dd/H_d_Rrad
L5: N5d/H_d_Rrad
L2: XH_Rbirad
L3: XH_s_Rbirad
L4: CH_s_Rbirad
Expand Down
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